diff --git a/CMake/BuildConfigurations/PhenotypingRelease.cmake b/CMake/BuildConfigurations/PhenotypingRelease.cmake new file mode 100644 index 0000000000..15c1467ec2 --- /dev/null +++ b/CMake/BuildConfigurations/PhenotypingRelease.cmake @@ -0,0 +1,15 @@ +include(${CMAKE_CURRENT_LIST_DIR}/WorkbenchRelease.cmake) + +list(APPEND MITK_CONFIG_PACKAGES + Vigra +) + +list(APPEND MITK_CONFIG_PLUGINS + org.mitk.gui.qt.basicimageprocessing + org.mitk.gui.qt.radiomics +) + +if(NOT MITK_USE_SUPERBUILD) + set(BUILD_BasicImageProcessingMiniApps ON CACHE BOOL "" FORCE) + set(BUILD_ClassificationMiniApps ON CACHE BOOL "" FORCE) +endif() diff --git a/CMake/BuildConfigurations/WorkbenchRelease.cmake b/CMake/BuildConfigurations/WorkbenchRelease.cmake index e4b4da592b..694b4b9e35 100644 --- a/CMake/BuildConfigurations/WorkbenchRelease.cmake +++ b/CMake/BuildConfigurations/WorkbenchRelease.cmake @@ -1,24 +1,28 @@ include(${CMAKE_CURRENT_LIST_DIR}/Default.cmake) set(MITK_CONFIG_PACKAGES ${MITK_CONFIG_PACKAGES} MatchPoint ) set(MITK_CONFIG_PLUGINS ${MITK_CONFIG_PLUGINS} org.mitk.gui.qt.multilabelsegmentation org.mitk.matchpoint.core.helper org.mitk.gui.qt.matchpoint.algorithm.browser org.mitk.gui.qt.matchpoint.algorithm.control org.mitk.gui.qt.matchpoint.mapper org.mitk.gui.qt.matchpoint.framereg org.mitk.gui.qt.matchpoint.visualizer org.mitk.gui.qt.matchpoint.evaluator org.mitk.gui.qt.matchpoint.manipulator ) +if(NOT MITK_USE_SUPERBUILD) + set(BUILD_CoreCmdApps ON CACHE BOOL "" FORCE) +endif() + set(MITK_VTK_DEBUG_LEAKS OFF CACHE BOOL "Enable VTK Debug Leaks" FORCE) find_package(Doxygen REQUIRED) # Ensure that the in-application help can be build set(BLUEBERRY_QT_HELP_REQUIRED ON CACHE BOOL "Required Qt help documentation in plug-ins" FORCE) diff --git a/CMake/FindDCMTK.cmake b/CMake/FindDCMTK.cmake deleted file mode 100644 index aec7baacfe..0000000000 --- a/CMake/FindDCMTK.cmake +++ /dev/null @@ -1,342 +0,0 @@ -#.rst: -# FindDCMTK -# --------- -# -# Find DCMTK libraries and applications -# -# The module defines the following variables:: -# -# DCMTK_INCLUDE_DIRS - Directories to include to use DCMTK -# DCMTK_LIBRARIES - Files to link against to use DCMTK -# DCMTK_FOUND - If false, don't try to use DCMTK -# DCMTK_DIR - (optional) Source directory for DCMTK -# -# Compatibility -# ^^^^^^^^^^^^^ -# -# This module is able to find a version of DCMTK that does or does not export -# a *DCMTKConfig.cmake* file. It applies a two step process: -# -# * Step 1: Attempt to find DCMTK version providing a *DCMTKConfig.cmake* file. -# * Step 2: If step 1 failed, rely on *FindDCMTK.cmake* to set `DCMTK_*` variables details below. -# -# -# `Recent DCMTK -# `_ -# provides a *DCMTKConfig.cmake* :manual:`package configuration file -# `. To exclusively use the package configuration file -# (recommended when possible), pass the `NO_MODULE` option to -# :command:`find_package`. For example, `find_package(DCMTK NO_MODULE)`. -# This requires official DCMTK snapshot *3.6.1_20140617* or newer. -# -# -# Until all clients update to the more recent DCMTK, build systems will need -# to support different versions of DCMTK. -# -# On any given system, the following combinations of DCMTK versions could be -# considered: -# -# +--------+---------------------+-----------------------+-------------------+ -# | | SYSTEM DCMTK | LOCAL DCMTK | Supported ? | -# +--------+---------------------+-----------------------+-------------------+ -# | Case A | NA | [ ] DCMTKConfig | YES | -# +--------+---------------------+-----------------------+-------------------+ -# | Case B | NA | [X] DCMTKConfig | YES | -# +--------+---------------------+-----------------------+-------------------+ -# | Case C | [ ] DCMTKConfig | NA | YES | -# +--------+---------------------+-----------------------+-------------------+ -# | Case D | [X] DCMTKConfig | NA | YES | -# +--------+---------------------+-----------------------+-------------------+ -# | Case E | [ ] DCMTKConfig | [ ] DCMTKConfig | YES (*) | -# +--------+---------------------+-----------------------+-------------------+ -# | Case F | [X] DCMTKConfig | [ ] DCMTKConfig | NO | -# +--------+---------------------+-----------------------+-------------------+ -# | Case G | [ ] DCMTKConfig | [X] DCMTKConfig | YES | -# +--------+---------------------+-----------------------+-------------------+ -# | Case H | [X] DCMTKConfig | [X] DCMTKConfig | YES | -# +--------+---------------------+-----------------------+-------------------+ -# -# (*) See Troubleshooting section. -# -# Legend: -# -# NA ...............: Means that no System or Local DCMTK is available -# -# [ ] DCMTKConfig ..: Means that the version of DCMTK does NOT export a DCMTKConfig.cmake file. -# -# [X] DCMTKConfig ..: Means that the version of DCMTK exports a DCMTKConfig.cmake file. -# -# -# Troubleshooting -# ^^^^^^^^^^^^^^^ -# -# What to do if my project finds a different version of DCMTK? -# -# Remove DCMTK entry from the CMake cache per :command:`find_package` -# documentation. - -#============================================================================= -# Copyright 2004-2009 Kitware, Inc. -# Copyright 2009-2010 Mathieu Malaterre -# Copyright 2010 Thomas Sondergaard -# -# Distributed under the OSI-approved BSD License (the "License"); -# see accompanying file Copyright.txt for details. -# -# This software is distributed WITHOUT ANY WARRANTY; without even the -# implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -# See the License for more information. -#============================================================================= -# (To distribute this file outside of CMake, substitute the full -# License text for the above reference.) - -# -# Written for VXL by Amitha Perera. -# Upgraded for GDCM by Mathieu Malaterre. -# Modified for EasyViz by Thomas Sondergaard. -# - -set(_dcmtk_dir_description "The directory of DCMTK build or install tree.") - -# Ensure that DCMTK_DIR is set to a reasonable default value -# so that DCMTK libraries can be found on a standard Unix distribution. -# It also overwrite the value of DCMTK_DIR after this one has been -# set by a successful discovery of DCMTK by the unpatched FindDCMTK.cmake module -# distributed with CMake (as of 0167cea) -if(NOT DCMTK_DIR OR DCMTK_DIR STREQUAL "/usr/include/dcmtk") - set(DCMTK_DIR "/usr" CACHE PATH ${_dcmtk_dir_description} FORCE) -endif() - -set(_SAVED_DCMTK_DIR ${DCMTK_DIR}) - -# -# Step1: Attempt to find a version of DCMTK providing a DCMTKConfig.cmake file. -# -if(NOT DCMTK_FIND_QUIETLY) - message(STATUS "Trying to find DCMTK expecting DCMTKConfig.cmake") -endif() -find_package(DCMTK QUIET NO_MODULE) -if(DCMTK_FOUND - AND NOT "x" STREQUAL "x${DCMTK_LIBRARIES}" - AND NOT "x" STREQUAL "x${DCMTK_INCLUDE_DIRS}") - - if(NOT DCMTK_FIND_QUIETLY) - message(STATUS "Trying to find DCMTK expecting DCMTKConfig.cmake - ok") - endif() - return() -else() - if(NOT DCMTK_FIND_QUIETLY) - message(STATUS "Trying to find DCMTK expecting DCMTKConfig.cmake - failed") - endif() -endif() - -if(NOT DCMTK_FIND_QUIETLY) - message(STATUS "Trying to find DCMTK relying on FindDCMTK.cmake") -endif() - -# Restore the value reset by the previous call to 'find_package(DCMTK QUIET NO_MODULE)' -set(DCMTK_DIR ${_SAVED_DCMTK_DIR} CACHE PATH ${_dcmtk_dir_description} FORCE) - - -# -# Step2: Attempt to find a version of DCMTK that does NOT provide a DCMTKConfig.cmake file. -# - -# prefer DCMTK_DIR over default system paths like /usr/lib -if(DCMTK_DIR) - set(CMAKE_PREFIX_PATH ${DCMTK_DIR}/lib ${CMAKE_PREFIX_PATH}) # this is given to FIND_LIBRARY or FIND_PATH -endif() - -# Find all libraries, store debug and release separately -foreach(lib - dcmpstat - dcmsr - dcmsign - dcmtls - dcmqrdb - dcmnet - dcmjpeg - dcmimage - dcmimgle - dcmdata - dcmpmap - oflog - ofstd - ijg12 - ijg16 - ijg8 - ) - - # Find Release libraries - find_library(DCMTK_${lib}_LIBRARY_RELEASE - ${lib} - PATHS - ${DCMTK_DIR}/${lib}/libsrc - ${DCMTK_DIR}/${lib}/libsrc/Release - ${DCMTK_DIR}/${lib}/Release - ${DCMTK_DIR}/lib - ${DCMTK_DIR}/lib/Release - ${DCMTK_DIR}/dcmjpeg/lib${lib}/Release - NO_DEFAULT_PATH - ) - - # Find Debug libraries - find_library(DCMTK_${lib}_LIBRARY_DEBUG - ${lib}${DCMTK_CMAKE_DEBUG_POSTFIX} - PATHS - ${DCMTK_DIR}/${lib}/libsrc - ${DCMTK_DIR}/${lib}/libsrc/Debug - ${DCMTK_DIR}/${lib}/Debug - ${DCMTK_DIR}/lib - ${DCMTK_DIR}/lib/Debug - ${DCMTK_DIR}/dcmjpeg/lib${lib}/Debug - NO_DEFAULT_PATH - ) - - mark_as_advanced(DCMTK_${lib}_LIBRARY_RELEASE) - mark_as_advanced(DCMTK_${lib}_LIBRARY_DEBUG) - - # Add libraries to variable according to build type - if(DCMTK_${lib}_LIBRARY_RELEASE) - list(APPEND DCMTK_LIBRARIES optimized ${DCMTK_${lib}_LIBRARY_RELEASE}) - endif() - - if(DCMTK_${lib}_LIBRARY_DEBUG) - list(APPEND DCMTK_LIBRARIES debug ${DCMTK_${lib}_LIBRARY_DEBUG}) - endif() - -endforeach() - -set(CMAKE_THREAD_LIBS_INIT) -if(DCMTK_oflog_LIBRARY_RELEASE OR DCMTK_oflog_LIBRARY_DEBUG) - # Hack - Not having a DCMTKConfig.cmake file to read the settings from, we will attempt to - # find the library in all cases. - # Ideally, pthread library should be discovered only if DCMTK_WITH_THREADS is enabled. - set(CMAKE_THREAD_PREFER_PTHREAD TRUE) - find_package(Threads) -endif() - -if(CMAKE_THREAD_LIBS_INIT) - list(APPEND DCMTK_LIBRARIES ${CMAKE_THREAD_LIBS_INIT}) -endif() - -# -# SPECIFIC CASE FOR DCMTK BUILD DIR as DCMTK_DIR -# (as opposed to a DCMTK install dir) -# Have to find the source directory. -if(EXISTS ${DCMTK_DIR}/CMakeCache.txt) - load_cache(${DCMTK_DIR} READ_WITH_PREFIX "EXT" - DCMTK_SOURCE_DIR) - if(NOT EXISTS ${EXTDCMTK_SOURCE_DIR}) - message(FATAL_ERROR - "DCMTK build directory references -nonexistant DCMTK source directory ${EXTDCMTK_SOURCE_DIR}") - endif() -endif() - -set(DCMTK_config_TEST_HEADER osconfig.h) -set(DCMTK_dcmdata_TEST_HEADER dctypes.h) -set(DCMTK_dcmimage_TEST_HEADER dicoimg.h) -set(DCMTK_dcmimgle_TEST_HEADER dcmimage.h) -set(DCMTK_dcmjpeg_TEST_HEADER djdecode.h) -set(DCMTK_dcmnet_TEST_HEADER assoc.h) -set(DCMTK_dcmpstat_TEST_HEADER dcmpstat.h) -set(DCMTK_dcmqrdb_TEST_HEADER dcmqrdba.h) -set(DCMTK_dcmsign_TEST_HEADER sicert.h) -set(DCMTK_dcmsr_TEST_HEADER dsrtree.h) -set(DCMTK_dcmtls_TEST_HEADER tlslayer.h) -set(DCMTK_ofstd_TEST_HEADER ofstdinc.h) -set(DCMTK_oflog_TEST_HEADER oflog.h) -set(DCMTK_dcmjpls_TEST_HEADER djlsutil.h) - -set(DCMTK_INCLUDE_DIR_NAMES) -message("Using default CMAKE FindDCMTK") -foreach(dir - config - dcmdata - dcmimage - dcmimgle - dcmjpeg - dcmjpls - dcmnet - dcmpstat - dcmqrdb - dcmsign - dcmsr - dcmtls - dcmpmap - ofstd - oflog) - if(EXTDCMTK_SOURCE_DIR) - set(SOURCE_DIR_PATH - ${EXTDCMTK_SOURCE_DIR}/${dir}/include/dcmtk/${dir}) - endif() - find_path(DCMTK_${dir}_INCLUDE_DIR - ${DCMTK_${dir}_TEST_HEADER} - PATHS - ${DCMTK_DIR}/${dir}/include - ${DCMTK_DIR}/${dir} - ${DCMTK_DIR}/include/dcmtk/${dir} - ${DCMTK_DIR}/${dir}/include/dcmtk/${dir} - ${DCMTK_DIR}/include/${dir} - ${SOURCE_DIR_PATH} - ) - mark_as_advanced(DCMTK_${dir}_INCLUDE_DIR) - list(APPEND DCMTK_INCLUDE_DIR_NAMES DCMTK_${dir}_INCLUDE_DIR) - - if(DCMTK_${dir}_INCLUDE_DIR) - # add the 'include' path so eg - #include "dcmtk/dcmimgle/dcmimage.h" - # works - get_filename_component(_include ${DCMTK_${dir}_INCLUDE_DIR} PATH) - get_filename_component(_include ${_include} PATH) - list(APPEND - DCMTK_INCLUDE_DIRS - ${DCMTK_${dir}_INCLUDE_DIR} - ${_include}) - endif() -endforeach() - -list(APPEND DCMTK_INCLUDE_DIRS ${DCMTK_DIR}/include) - -if(WIN32) - list(APPEND DCMTK_LIBRARIES netapi32 wsock32) -endif() - -if(DCMTK_ofstd_INCLUDE_DIR) - get_filename_component(DCMTK_dcmtk_INCLUDE_DIR - ${DCMTK_ofstd_INCLUDE_DIR} - PATH - CACHE) - list(APPEND DCMTK_INCLUDE_DIRS ${DCMTK_dcmtk_INCLUDE_DIR}) - mark_as_advanced(DCMTK_dcmtk_INCLUDE_DIR) -endif() - -# Compatibility: This variable is deprecated -set(DCMTK_INCLUDE_DIR ${DCMTK_INCLUDE_DIRS}) - -include(FindPackageHandleStandardArgs) -find_package_handle_standard_args(DCMTK - REQUIRED_VARS ${DCMTK_INCLUDE_DIR_NAMES} DCMTK_LIBRARIES - FAIL_MESSAGE "Please set DCMTK_DIR and re-run configure") - -# Workaround bug in packaging of DCMTK 3.6.0 on Debian. -# See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=637687 -if(DCMTK_FOUND AND UNIX AND NOT APPLE) - include(CheckCXXSourceCompiles) - set(CMAKE_REQUIRED_FLAGS ) - set(CMAKE_REQUIRED_DEFINITIONS ) - set(CMAKE_REQUIRED_INCLUDES ${DCMTK_INCLUDE_DIRS}) - set(CMAKE_REQUIRED_LIBRARIES ${DCMTK_LIBRARIES}) - set(CMAKE_REQUIRED_QUIET ${DCMTK_FIND_QUIETLY}) - check_cxx_source_compiles("#include \n#include \nint main(int,char*[]){return 0;}" - DCMTK_HAVE_CONFIG_H_OPTIONAL - ) - if(NOT DCMTK_HAVE_CONFIG_H_OPTIONAL) - set(DCMTK_DEFINITIONS "HAVE_CONFIG_H") - endif() -endif() - -if(NOT DCMTK_FIND_QUIETLY) - message(STATUS "Trying to find DCMTK relying on FindDCMTK.cmake - ok") -endif() diff --git a/CMake/MITKDashboardScript.download.cmake b/CMake/MITKDashboardScript.download.cmake index a6f9daa5b3..55111521d7 100644 --- a/CMake/MITKDashboardScript.download.cmake +++ b/CMake/MITKDashboardScript.download.cmake @@ -1,698 +1,702 @@ #[============================================================================[ Helper functions ]============================================================================] function(get_macos_codename) set(macos_codename "") set(software_license_file "\ /System/Library/CoreServices/Setup Assistant.app\ /Contents/Resources/en.lproj/OSXSoftwareLicense.rtf") if(EXISTS "${software_license_file}") file(READ "${software_license_file}" software_license) if(software_license MATCHES "SOFTWARE LICENSE AGREEMENT FOR macOS ([^\n]+)") set(macos_codename "${CMAKE_MATCH_1}") endif() endif() set(${ARGV0} ${macos_codename} PARENT_SCOPE) endfunction() function(get_macos_name) set(macos_name "macOS") get_macos_codename(macos_codename) if(macos_codename) set(macos_name "${macos_name} ${macos_codename}") endif() execute_process( RESULT_VARIABLE error_code OUTPUT_VARIABLE version OUTPUT_STRIP_TRAILING_WHITESPACE COMMAND "sw_vers" "-productVersion") if(0 EQUAL error_code AND version) set(macos_name "${macos_name} ${version}") endif() set(${ARGV0} ${macos_name} PARENT_SCOPE) endfunction() function(get_linux_name) set(linux_name "Linux") set(os_release_file "/etc/os-release") if(EXISTS "${os_release_file}") file(STRINGS "${os_release_file}" os_release) set(name "") set(version_id "") foreach(line ${os_release}) if(NOT name AND line MATCHES "^NAME=[\"]?([^\"]+)") set(name "${CMAKE_MATCH_1}") continue() endif() if(NOT version_id AND line MATCHES "^VERSION_ID=\"?([^\"]+)") set(version_id "${CMAKE_MATCH_1}") continue() endif() if(name AND version_id) break() endif() endforeach() if(name) set(linux_name "${name}") endif() if(version_id) set(linux_name "${linux_name} ${version_id}") endif() endif() set(${ARGV0} ${linux_name} PARENT_SCOPE) endfunction() function(get_windows_name) set(windows_name "Windows") execute_process( RESULT_VARIABLE error_code OUTPUT_VARIABLE version OUTPUT_STRIP_TRAILING_WHITESPACE COMMAND "wmic" "os" "get" "Version" "-value") if(0 EQUAL error_code AND version) if(version MATCHES "Version=([0-9]+)\\.([0-9]+)") set(windows_name "${windows_name} ${CMAKE_MATCH_1}") if(NOT 0 EQUAL CMAKE_MATCH_2) set(windows_name "${windows_name}.${CMAKE_MATCH_2}") endif() endif() endif() set(${ARGV0} ${windows_name} PARENT_SCOPE) endfunction() function(get_os_name) set(os_name "") if(APPLE) get_macos_name(os_name) elseif(UNIX) get_linux_name(os_name) elseif(WIN32) get_windows_name(os_name) endif() set(${ARGV0} ${os_name} PARENT_SCOPE) endfunction() function(download_string) cmake_parse_arguments(PARSE_ARGV 0 ARG "" "URL;OUTPUT_VARIABLE" "") get_temp_directory(temp_dir) string(RANDOM random_filename) while(EXISTS "${temp_dir}/${random_filename}") string(RANDOM random_filename) endwhile() set(temp_output_file "${temp_dir}/${random_filename}") download_file( URL ${ARG_URL} OUTPUT_FILE ${temp_output_file} ERROR_CODE error_code) set(output "") if(EXISTS "${temp_output_file}") file(READ "${temp_output_file}" output) file(REMOVE "${temp_output_file}") endif() set(${ARG_OUTPUT_VARIABLE} ${output} PARENT_SCOPE) endfunction() function(find_vswhere) get_temp_directory(temp_dir) set(latest_vswhere "${temp_dir}/vswhere.exe") set(vswhere "vswhere.exe-NOTFOUND") if(EXISTS "${latest_vswhere}") set(vswhere "${latest_vswhere}") else() set(program_files_x86 "PROGRAMFILES(X86)") set(program_files_x86 "$ENV{${program_files_x86}}") set(system_vswhere "${program_files_x86}/Microsoft Visual Studio/Installer/vswhere.exe") if(EXISTS "${system_vswhere}") set(vswhere "${system_vswhere}") else() download_string( URL "https://api.github.com/repos/microsoft/vswhere/releases/latest" OUTPUT_VARIABLE latest_vswhere_json) if(latest_vswhere_json MATCHES "\"browser_download_url\": *\"([^\"]*)\"") download_file( URL "${CMAKE_MATCH_1}" OUTPUT_FILE "${latest_vswhere}" ERROR_CODE error_code) if (0 EQUAL error_code) set(vswhere "${latest_vswhere}") endif() endif() endif() endif() set(${ARGV0} "${vswhere}" PARENT_SCOPE) endfunction() function(vswhere) cmake_parse_arguments(PARSE_ARGV 0 ARG "" "PROPERTY;OUTPUT_VARIABLE" "") set(property_value "") if(CTEST_CMAKE_GENERATOR MATCHES "^Visual Studio ([0-9]+)") set(major_version "${CMAKE_MATCH_1}") math(EXPR next_major_version "${major_version} + 1") find_vswhere(vswhere) if (vswhere) execute_process( OUTPUT_VARIABLE property_value OUTPUT_STRIP_TRAILING_WHITESPACE COMMAND ${vswhere} "-requires" "Microsoft.VisualStudio.Workload.NativeDesktop" "-version" "[${major_version},${next_major_version})" "-property" "${ARG_PROPERTY}" "-format" "value") endif() endif() set(${ARG_OUTPUT_VARIABLE} ${property_value} PARENT_SCOPE) endfunction() function(get_visual_studio_name) set(visual_studio_name "Visual Studio") if(CTEST_CMAKE_GENERATOR MATCHES "^Visual Studio [0-9]+ ([0-9]+)") set(product_line_version "${CMAKE_MATCH_1}") set(visual_studio_name "${visual_studio_name} ${product_line_version}") vswhere(PROPERTY "catalog_productDisplayVersion" OUTPUT_VARIABLE product_display_version) if(product_display_version) set(visual_studio_name "${visual_studio_name} ${product_display_version}") endif() endif() set(${ARGV0} ${visual_studio_name} PARENT_SCOPE) endfunction() function(get_compiler_name) set(compiler_name "") if(CTEST_CMAKE_GENERATOR MATCHES "^Visual Studio") get_visual_studio_name(compiler_name) else() get_temp_directory(temp_dir) file(WRITE "${temp_dir}/src/CMakeLists.txt" "\ project(probe C) message(STATUS \"CMAKE_C_COMPILER_ID=\\\"\${CMAKE_C_COMPILER_ID}\\\"\") message(STATUS \"CMAKE_C_COMPILER_VERSION=\\\"\${CMAKE_C_COMPILER_VERSION}\\\"\")") file(REMOVE_RECURSE "${temp_dir}/build") unset(options) foreach(option ${MITK_SUPERBUILD_OPTIONS}) list(APPEND options "-D" "${option}") endforeach() execute_process( RESULT_VARIABLE error_code OUTPUT_VARIABLE compiler ERROR_QUIET COMMAND ${CMAKE_COMMAND} "-S" "${temp_dir}/src" "-B" "${temp_dir}/build" "-G" "${CTEST_CMAKE_GENERATOR}" ${options}) if(0 EQUAL error_code) if(compiler MATCHES "CMAKE_C_COMPILER_ID=\"([^\"]*)\"") set(compiler_name "${CMAKE_MATCH_1}") if(compiler MATCHES "CMAKE_C_COMPILER_VERSION=\"([^\"]*)\"") set(version "${CMAKE_MATCH_1}") if(version MATCHES "^([0-9]+\\.[0-9]+\\.[0-9]+)") set(version "${CMAKE_MATCH_1}") endif() string(REGEX REPLACE "\\.0$" "" version "${version}") set(compiler_name "${compiler_name} ${version}") endif() endif() endif() endif() set(${ARGV0} ${compiler_name} PARENT_SCOPE) endfunction() function(get_default_build_name) get_os_name(default_build_name) get_compiler_name(compiler_name) if(compiler_name) set(default_build_name "${default_build_name} ${compiler_name}") endif() set(default_build_name "${default_build_name} ${CTEST_BUILD_CONFIGURATION}") if(MITK_BUILD_CONFIGURATION) set(default_build_name "${default_build_name} ${MITK_BUILD_CONFIGURATION}") endif() if(MITK_BUILD_NAME_SUFFIX) set(default_build_name "${default_build_name} ${MITK_BUILD_NAME_SUFFIX}") endif() set(${ARGV0} ${default_build_name} PARENT_SCOPE) endfunction() function(git) cmake_parse_arguments(PARSE_ARGV 0 ARG "" "WORKING_DIRECTORY;OUTPUT_VARIABLE;RESULT_VARIABLE" "") if(NOT ARG_WORKING_DIRECTORY) set(ARG_WORKING_DIRECTORY "${CTEST_SOURCE_DIRECTORY}") endif() get_filename_component(ARG_WORKING_DIRECTORY "${ARG_WORKING_DIRECTORY}" ABSOLUTE) execute_process( WORKING_DIRECTORY "${ARG_WORKING_DIRECTORY}" RESULT_VARIABLE error_code OUTPUT_VARIABLE output OUTPUT_STRIP_TRAILING_WHITESPACE COMMAND "${CTEST_GIT_COMMAND}" ${ARG_UNPARSED_ARGUMENTS}) if(ARG_OUTPUT_VARIABLE) set(${ARG_OUTPUT_VARIABLE} ${output} PARENT_SCOPE) endif() if(ARG_RESULT_VARIABLE) set(${ARG_RESULT_VARIABLE} ${error_code} PARENT_SCOPE) endif() endfunction() function(git_log) cmake_parse_arguments(PARSE_ARGV 0 ARG "" "WORKING_DIRECTORY;COMMIT_HASH;COMMITTER;SUBJECT" "") if(NOT ARG_WORKING_DIRECTORY) set(ARG_WORKING_DIRECTORY "${CTEST_SOURCE_DIRECTORY}") endif() get_filename_component(ARG_WORKING_DIRECTORY "${ARG_WORKING_DIRECTORY}" ABSOLUTE) set(args WORKING_DIRECTORY "${ARG_WORKING_DIRECTORY}" "log" "-1") if(ARG_COMMIT_HASH) unset(commit_hash) git(OUTPUT_VARIABLE commit_hash ${args} "--pretty=%h" ) if(commit_hash) set(${ARG_COMMIT_HASH} ${commit_hash} PARENT_SCOPE) endif() endif() if(ARG_COMMITTER) unset(committer) git(OUTPUT_VARIABLE committer ${args} "--pretty=%cn" ) if(committer) set(${ARG_COMMITTER} ${committer} PARENT_SCOPE) endif() endif() if(ARG_SUBJECT) unset(subject) git(OUTPUT_VARIABLE subject ${args} "--pretty=%s" ) if(subject) set(${ARG_SUBJECT} ${subject} PARENT_SCOPE) endif() endif() endfunction() function(rm) execute_process(COMMAND ${CMAKE_COMMAND} "-E" "rm" "-rf" ${ARGN}) endfunction() function(submit) cmake_parse_arguments(PARSE_ARGV 0 ARG "" "" "PARTS") if(MITK_SUBMIT_URL) set(submit_url "SUBMIT_URL" "${MITK_SUBMIT_URL}") else() unset(submit_url) endif() if(MITK_AUTH_TOKEN) set(http_header HTTPHEADER "Authorization: Bearer ${MITK_AUTH_TOKEN}") else() unset(http_header) endif() ctest_submit(${submit_url} ${http_header} RETRY_COUNT 3 RETRY_DELAY 5 PARTS ${ARG_PARTS}) endfunction() #[============================================================================[ Actual script ]============================================================================] cmake_minimum_required(VERSION 3.18 FATAL_ERROR) find_program(CTEST_GIT_COMMAND git) if(NOT CTEST_GIT_COMMAND) message(FATAL_ERROR "Git not found") endif() if(NOT CTEST_CMAKE_GENERATOR MATCHES "^Visual Studio") unset(CTEST_CMAKE_GENERATOR_PLATFORM) endif() if(CTEST_CMAKE_GENERATOR MATCHES "^(Unix Makefiles|Ninja)$") set(CTEST_USE_LAUNCHERS ON) endif() if(NOT CTEST_SITE) unset(CTEST_SITE) site_name(CTEST_SITE) endif() if(NOT CTEST_BUILD_NAME) get_default_build_name(CTEST_BUILD_NAME) endif() set(CTEST_SOURCE_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/src/MITK") set(CTEST_BINARY_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}/build") set(indent " ") message("CTest settings") if(MITK_SUBMIT_URL) message("${indent}Submit URL: ${MITK_SUBMIT_URL}") endif() message("\ ${indent}Dashboard model: ${CTEST_DASHBOARD_MODEL} ${indent}Build name: ${CTEST_BUILD_NAME} ${indent}Site: ${CTEST_SITE}") if(MITK_CLEAN_SOURCE_DIR OR MITK_CLEAN_BINARY_DIR) message("Clean") if(MITK_CLEAN_SOURCE_DIR) set(clean_dir "${CMAKE_CURRENT_SOURCE_DIR}/src") message("${indent}Source directory: ${clean_dir}") rm("${clean_dir}") endif() if(MITK_CLEAN_BINARY_DIR) set(clean_dir "${CMAKE_CURRENT_SOURCE_DIR}/build") message("${indent}Binary directory: ${clean_dir}") rm("${clean_dir}") endif() endif() message("MITK repository") if(NOT EXISTS "${CTEST_SOURCE_DIRECTORY}") message("\ ${indent}Clone repository: ${MITK_REPOSITORY} ${indent}Branch: ${MITK_BRANCH}") set(CTEST_CHECKOUT_COMMAND "\"${CTEST_GIT_COMMAND}\" clone --branch=${MITK_BRANCH} -- ${MITK_REPOSITORY} MITK") ctest_start(${CTEST_DASHBOARD_MODEL}) else() git_log(COMMIT_HASH old_revision COMMITTER committer SUBJECT subject) message("\ ${indent}Update repository: ${CTEST_SOURCE_DIRECTORY} ${indent}Branch: ${MITK_BRANCH} ${indent}Old revision: ${old_revision} (committed by ${committer}) ${indent}${indent}${subject}") ctest_start(${CTEST_DASHBOARD_MODEL}) set(CTEST_UPDATE_OPTIONS "--tags origin ${MITK_BRANCH}") ctest_update(RETURN_VALUE return_value) if(-1 EQUAL return_value) return() endif() git_log(COMMIT_HASH new_revision) if(new_revision STREQUAL old_revision) message("${indent}New revision: up-to-date") else() git_log(COMMITTER committer SUBJECT subject) message("\ ${indent}New revision: ${new_revision} (committed by ${committer}) ${indent}${indent}${subject}") endif() endif() unset(extension_dirs) if(MITK_EXTENSIONS) list(LENGTH MITK_EXTENSIONS mitk_extensions_size) math(EXPR max_index "${mitk_extensions_size} - 1") foreach(name_index RANGE 0 ${max_index} 3) list(GET MITK_EXTENSIONS ${name_index} name) math(EXPR url_index "${name_index} + 1") list(GET MITK_EXTENSIONS ${url_index} url) math(EXPR branch_index "${name_index} + 2") list(GET MITK_EXTENSIONS ${branch_index} branch) message("${name} repository") set(extension_dir "${CMAKE_CURRENT_SOURCE_DIR}/src/${name}") list(APPEND extension_dirs "${extension_dir}") if(NOT EXISTS "${extension_dir}") message("\ ${indent}Clone repository: ${url} ${indent}Branch: ${branch}") git("clone" "--quiet" "--branch=${branch}" "${url}" "${name}" WORKING_DIRECTORY "${extension_dir}/..") else() git_log(COMMIT_HASH old_revision COMMITTER committer SUBJECT subject WORKING_DIRECTORY "${extension_dir}") message("\ ${indent}Update repository: ${extension_dir} ${indent}Branch: ${branch} ${indent}Old revision: ${old_revision} (committed by ${committer}) ${indent}${indent}${subject}") git("fetch" "--quiet" "--tags" "origin" "${branch}" WORKING_DIRECTORY "${extension_dir}") git("diff" "--quiet" "HEAD" "FETCH_HEAD" WORKING_DIRECTORY "${extension_dir}" RESULT_VARIABLE error_code) if(NOT error_code EQUAL 0) git("reset" "--quiet" "--hard" "FETCH_HEAD" WORKING_DIRECTORY "${extension_dir}") endif() git_log(COMMIT_HASH new_revision WORKING_DIRECTORY "${extension_dir}") if(new_revision STREQUAL old_revision) message("${indent}New revision: up-to-date") else() git_log(COMMITTER committer SUBJECT subject WORKING_DIRECTORY "${extension_dir}") message("\ ${indent}New revision: ${new_revision} (committed by ${committer}) ${indent}${indent}${subject}") endif() endif() endforeach() endif() submit(PARTS Update) set(options "-D" "MITK_CTEST_SCRIPT_MODE:STRING=${CTEST_DASHBOARD_MODEL}" # "-D" "SUPERBUILD_EXCLUDE_MITKBUILD_TARGET:BOOL=TRUE" ) +if(NOT WIN32) + list(APPEND options "-D" "CMAKE_BUILD_TYPE:STRING=${CTEST_BUILD_CONFIGURATION}") +endif() + if(extension_dirs) string (REPLACE ";" "\\\;" extension_dirs "${extension_dirs}") list(APPEND options "-D" "MITK_EXTENSION_DIRS:STRING=${extension_dirs}") endif() if(MITK_BUILD_CONFIGURATION) list(APPEND options "-D" "MITK_BUILD_CONFIGURATION:STRING=${MITK_BUILD_CONFIGURATION}") endif() if(MITK_BUILD_OPTIONS) get_temp_directory(temp_dir) set(mitk_initial_cache_file "${temp_dir}/MITKInitialCache.cmake") file(WRITE "${mitk_initial_cache_file}" "") foreach(mitk_option ${MITK_BUILD_OPTIONS}) if(mitk_option MATCHES "^([^:]+):([^=]+)=(.*)") set(var "${CMAKE_MATCH_1}") set(type "${CMAKE_MATCH_2}") set(value "${CMAKE_MATCH_3}") file(APPEND "${mitk_initial_cache_file}" "set(${var} \"${value}\" CACHE ${type} \"\" FORCE)\n") endif() endforeach() list(APPEND options "-D" "MITK_INITIAL_CACHE_FILE:FILEPATH=${mitk_initial_cache_file}") endif() foreach(option ${MITK_SUPERBUILD_OPTIONS}) list(APPEND options "-D" "${option}") endforeach() ctest_configure(OPTIONS "${options}" RETURN_VALUE return_value) submit(PARTS Configure) if(NOT 0 EQUAL return_value) submit(PARTS Done) return() endif() include("${CTEST_BINARY_DIRECTORY}/SuperBuildTargets.cmake") if(NOT SUPERBUILD_TARGETS) submit(PARTS Done) message(FATAL_ERROR "SUPERBUILD_TARGETS variable not set in SuperBuildTargets.cmake") else() set(mitk_targets MITK-Data MITK-Utilities MITK-Configure MITK-build ) list(LENGTH SUPERBUILD_TARGETS n) list(LENGTH mitk_targets num_mitk_targets) math(EXPR n "${n} + ${num_mitk_targets}") set(i 1) unset(append) foreach(target ${SUPERBUILD_TARGETS} ${mitk_targets}) message("MITK superbuild - [${i}/${n}] Build ${target}") if(NOT target IN_LIST mitk_targets) list(APPEND CTEST_CUSTOM_WARNING_EXCEPTION ".*") set(pop_warning_exception TRUE) else() set(pop_warning_exception FALSE) endif() ctest_build(TARGET ${target} NUMBER_ERRORS num_build_errors NUMBER_WARNINGS num_build_warnings RETURN_VALUE return_value ${append}) if(pop_warning_exception) list(POP_BACK CTEST_CUSTOM_WARNING_EXCEPTION) endif() submit(PARTS Build) if(0 LESS num_build_warnings) message("${indent}${num_build_warnings} warning(s)") endif() if(NOT (0 EQUAL return_value AND 0 EQUAL num_build_errors)) submit(PARTS Done) message("${indent}${num_build_errors} error(s)") return() else() message("${indent}${target} was built successfully") endif() if(NOT append) set(append APPEND) endif() math(EXPR i "${i} + 1") endforeach() endif() if(MITK_BUILD_DOCUMENTATION) message("MITK build - Build documentation") list(APPEND CTEST_CUSTOM_WARNING_EXCEPTION ".*") ctest_build(TARGET doc BUILD "${CTEST_BINARY_DIRECTORY}/MITK-build" NUMBER_ERRORS num_doc_errors NUMBER_WARNINGS num_doc_warnings RETURN_VALUE return_value APPEND ) list(POP_BACK CTEST_CUSTOM_WARNING_EXCEPTION) submit(PARTS Build) if(0 LESS num_doc_warnings) message("${indent}${num_doc_warnings} warning(s)") endif() if(NOT (0 EQUAL return_value AND 0 EQUAL num_doc_errors)) submit(PARTS Done) message("${indent}${num_doc_errors} error(s)") return() else() message("${indent}Documentation was built successfully") endif() endif() message("Run unit tests...") set(CTEST_CONFIGURATION_TYPE "${CTEST_BUILD_CONFIGURATION}") ctest_test( BUILD "${CTEST_BINARY_DIRECTORY}/MITK-build" PARALLEL_LEVEL 4) submit(PARTS Test Done) message("Done") diff --git a/CMake/PackageDepends/MITK_DCMTK_Config.cmake b/CMake/PackageDepends/MITK_DCMTK_Config.cmake index 155a9ab47b..c331c55e9a 100644 --- a/CMake/PackageDepends/MITK_DCMTK_Config.cmake +++ b/CMake/PackageDepends/MITK_DCMTK_Config.cmake @@ -1,10 +1,10 @@ -if( NOT WIN32 AND NOT APPLE ) +if(NOT WIN32 AND NOT APPLE) set(MISSING_LIBS_REQUIRED_BY_DCMTK tiff z) -endif( NOT WIN32 AND NOT APPLE ) +endif() -set(QT_USE_QTSQL 1) - -find_package(DCMTK) +if(NOT DCMTK_FOUND) + find_package(DCMTK REQUIRED) +endif() list(APPEND ALL_INCLUDE_DIRECTORIES ${DCMTK_INCLUDE_DIRS}) list(APPEND ALL_LIBRARIES ${DCMTK_LIBRARIES} ${MISSING_LIBS_REQUIRED_BY_DCMTK}) diff --git a/CMake/RunInstalledApp.bat b/CMake/RunInstalledApp.bat index 8ca0361f5c..cc4426bab3 100644 --- a/CMake/RunInstalledApp.bat +++ b/CMake/RunInstalledApp.bat @@ -1 +1 @@ -start "" /B /D bin bin/%~n0.exe %* +"%~dp0bin\%~n0.exe" %* diff --git a/CMake/RunInstalledWin32App.bat b/CMake/RunInstalledWin32App.bat new file mode 100644 index 0000000000..9fc52a8f4b --- /dev/null +++ b/CMake/RunInstalledWin32App.bat @@ -0,0 +1 @@ +start "" /B "%~dp0bin\%~n0.exe" %* diff --git a/CMake/mitkFunctionCreateBlueBerryApplication.cmake b/CMake/mitkFunctionCreateBlueBerryApplication.cmake index 8869470500..f31bdfb29d 100644 --- a/CMake/mitkFunctionCreateBlueBerryApplication.cmake +++ b/CMake/mitkFunctionCreateBlueBerryApplication.cmake @@ -1,231 +1,231 @@ #! #! Create a BlueBerry application. #! #! \brief This function will create a BlueBerry application together with all #! necessary provisioning and configuration data and install support. #! #! \param NAME (required) The name of the executable. #! \param DESCRIPTION (optional) A human-readable description of your application. #! The usage depends on the CPack generator (on Windows, this is a descriptive #! text for the created shortcuts). #! \param SOURCES (optional) A list of source files to compile into your executable. Defaults #! to .cpp. #! \param PLUGINS (optional) A list of required plug-ins. Defaults to all known plug-ins. #! \param EXCLUDE_PLUGINS (optional) A list of plug-ins which should not be used. Mainly #! useful if PLUGINS was not used. #! \param LINK_LIBRARIES A list of libraries to be linked with the executable. #! \param LIBRARY_DIRS A list of directories to pass through to MITK_INSTALL_TARGETS #! \param NO_PROVISIONING (option) Do not create provisioning files. #! \param NO_INSTALL (option) Do not install this executable #! #! Assuming that there exists a file called MyApp.cpp, an example call looks like: #! \code #! mitkFunctionCreateBlueBerryApplication( #! NAME MyApp #! DESCRIPTION "MyApp - New ways to explore medical data" #! EXCLUDE_PLUGINS org.mitk.gui.qt.extapplication #! ) #! \endcode #! function(mitkFunctionCreateBlueBerryApplication) cmake_parse_arguments(_APP "NO_PROVISIONING;NO_INSTALL" "NAME;DESCRIPTION" "SOURCES;PLUGINS;EXCLUDE_PLUGINS;LINK_LIBRARIES;LIBRARY_DIRS" ${ARGN}) if(NOT _APP_NAME) message(FATAL_ERROR "NAME argument cannot be empty.") endif() if(NOT _APP_SOURCES) set(_APP_SOURCES ${_APP_NAME}.cpp) endif() if(NOT _APP_PLUGINS) ctkFunctionGetAllPluginTargets(_APP_PLUGINS) else() set(_plugins ${_APP_PLUGINS}) set(_APP_PLUGINS) foreach(_plugin ${_plugins}) string(REPLACE "." "_" _plugin_target ${_plugin}) list(APPEND _APP_PLUGINS ${_plugin_target}) endforeach() # get all plug-in dependencies ctkFunctionGetPluginDependencies(_plugin_deps PLUGINS ${_APP_PLUGINS} ALL) # add the dependencies to the list of application plug-ins list(APPEND _APP_PLUGINS ${_plugin_deps}) endif() # ----------------------------------------------------------------------- # Set up include and link dirs for the executable # ----------------------------------------------------------------------- include_directories( ${org_blueberry_core_runtime_INCLUDE_DIRS} ) # ----------------------------------------------------------------------- # Add executable icon (Windows) # ----------------------------------------------------------------------- set(WINDOWS_ICON_RESOURCE_FILE "") if(WIN32) if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/icons/${_APP_NAME}.rc") set(WINDOWS_ICON_RESOURCE_FILE "${CMAKE_CURRENT_SOURCE_DIR}/icons/${_APP_NAME}.rc") endif() endif() # ----------------------------------------------------------------------- # Create the executable and link libraries # ----------------------------------------------------------------------- set(_app_compile_flags ) if(WIN32) set(_app_compile_flags "${_app_compile_flags} -DPOCO_NO_UNWINDOWS -DWIN32_LEAN_AND_MEAN") endif() if(MITK_SHOW_CONSOLE_WINDOW) add_executable(${_APP_NAME} MACOSX_BUNDLE ${_APP_SOURCES} ${WINDOWS_ICON_RESOURCE_FILE}) else() add_executable(${_APP_NAME} MACOSX_BUNDLE WIN32 ${_APP_SOURCES} ${WINDOWS_ICON_RESOURCE_FILE}) endif() -if(NOT CMAKE_CURRENT_SOURCE_DIR MATCHES "^${CMAKE_SOURCE_DIR}.*") +if(NOT CMAKE_CURRENT_SOURCE_DIR MATCHES "^${CMAKE_SOURCE_DIR}/.*") foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) - if(CMAKE_CURRENT_SOURCE_DIR MATCHES "^${MITK_EXTENSION_DIR}.*") + if("${CMAKE_CURRENT_SOURCE_DIR}/" MATCHES "^${MITK_EXTENSION_DIR}/.*") get_filename_component(MITK_EXTENSION_ROOT_FOLDER "${MITK_EXTENSION_DIR}" NAME) set_property(TARGET ${_APP_NAME} PROPERTY FOLDER "${MITK_EXTENSION_ROOT_FOLDER}/Applications") break() endif() endforeach() else() set_property(TARGET ${_APP_NAME} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Applications") endif() mitk_use_modules(TARGET ${_APP_NAME} MODULES MitkAppUtil) set_target_properties(${_APP_NAME} PROPERTIES COMPILE_FLAGS "${_app_compile_flags}") target_link_libraries(${_APP_NAME} PRIVATE org_blueberry_core_runtime ${_APP_LINK_LIBRARIES}) if(WIN32) target_link_libraries(${_APP_NAME} PRIVATE ${QT_QTMAIN_LIBRARY}) endif() # ----------------------------------------------------------------------- # Add executable icon and bundle name (Mac) # ----------------------------------------------------------------------- if(APPLE) if( _APP_DESCRIPTION) set_target_properties(${_APP_NAME} PROPERTIES MACOSX_BUNDLE_NAME "${_APP_DESCRIPTION}") else() set_target_properties(${_APP_NAME} PROPERTIES MACOSX_BUNDLE_NAME "${_APP_NAME}") endif() set(icon_name "icon.icns") set(icon_full_path "${CMAKE_CURRENT_SOURCE_DIR}/icons/${icon_name}") if(EXISTS "${icon_full_path}") set_target_properties(${_APP_NAME} PROPERTIES MACOSX_BUNDLE_ICON_FILE "${icon_name}") file(COPY ${icon_full_path} DESTINATION "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${_APP_NAME}.app/Contents/Resources/") INSTALL (FILES ${icon_full_path} DESTINATION "${_APP_NAME}.app/Contents/Resources/") endif() endif() # ----------------------------------------------------------------------- # Set build time dependencies # ----------------------------------------------------------------------- # This ensures that all enabled plug-ins are up-to-date when the # executable is build. if(_APP_PLUGINS) ctkMacroGetAllProjectTargetLibraries("${_APP_PLUGINS}" _project_plugins) if(_APP_EXCLUDE_PLUGINS AND _project_plugins) set(_exclude_targets) foreach(_exclude_plugin ${_APP_EXCLUDE_PLUGINS}) string(REPLACE "." "_" _exclude_target ${_exclude_plugin}) list(APPEND _exclude_targets ${_exclude_target}) endforeach() list(REMOVE_ITEM _project_plugins ${_exclude_targets}) endif() if(_project_plugins) add_dependencies(${_APP_NAME} ${_project_plugins}) endif() endif() # ----------------------------------------------------------------------- # Additional files needed for the executable # ----------------------------------------------------------------------- if(NOT _APP_NO_PROVISIONING) # Create a provisioning file, listing all plug-ins set(_prov_file "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${_APP_NAME}.provisioning") mitkFunctionCreateProvisioningFile(FILE ${_prov_file} PLUGINS ${_APP_PLUGINS} EXCLUDE_PLUGINS ${_APP_EXCLUDE_PLUGINS} ) endif() # Create a .ini file for initial parameters if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${_APP_NAME}.ini") configure_file(${_APP_NAME}.ini ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${_APP_NAME}.ini) endif() # Create batch and VS user files for Windows platforms include(mitkFunctionCreateWindowsBatchScript) if(WIN32) set(template_name "start${_APP_NAME}.bat.in") if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/${template_name}") foreach(BUILD_TYPE debug release) mitkFunctionCreateWindowsBatchScript(${template_name} ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/start${_APP_NAME}_${BUILD_TYPE}.bat ${BUILD_TYPE}) endforeach() endif() mitkFunctionConfigureVisualStudioUserProjectFile( NAME ${_APP_NAME} ) endif(WIN32) # ----------------------------------------------------------------------- # Install support # ----------------------------------------------------------------------- if(NOT _APP_NO_INSTALL) # This installs all third-party CTK plug-ins mitkFunctionInstallThirdPartyCTKPlugins(${_APP_PLUGINS} EXCLUDE ${_APP_EXCLUDE_PLUGINS}) if(COMMAND BlueBerryApplicationInstallHook) set(_real_app_plugins ${_APP_PLUGINS}) if(_APP_EXCLUDE_PLUGINS) list(REMOVE_ITEM _real_app_plugins ${_APP_EXCLUDE_PLUGINS}) endif() BlueBerryApplicationInstallHook(APP_NAME ${_APP_NAME} PLUGINS ${_real_app_plugins}) endif() # Install the executable MITK_INSTALL_TARGETS(EXECUTABLES ${_APP_NAME} LIBRARY_DIRS ${_APP_LIBRARY_DIRS} GLOB_PLUGINS ) if(NOT _APP_NO_PROVISIONING) # Install the provisioning file mitkFunctionInstallProvisioningFiles(${_prov_file}) endif() # On Linux, create a shell script to start a relocatable application if(UNIX AND NOT APPLE) install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME "${_APP_NAME}.sh") elseif(WIN32) - install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.bat" DESTINATION "." RENAME "${_APP_NAME}.bat") + install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledWin32App.bat" DESTINATION "." RENAME "${_APP_NAME}.bat") endif() # Tell cpack the executables that you want in the start menu as links set(MITK_CPACK_PACKAGE_EXECUTABLES ${MITK_CPACK_PACKAGE_EXECUTABLES} "${_APP_NAME};${_APP_DESCRIPTION}" CACHE INTERNAL "Collecting windows shortcuts to executables") endif() endfunction() function(FunctionCreateBlueBerryApplication) message(SEND_ERROR "The function FunctionCreateBlueBerryApplication was renamed to mitkFunctionCreateBlueBerryApplication in MITK 2015.05") endfunction() diff --git a/CMake/mitkFunctionCreateMatchPointDeployedAlgorithm.cmake b/CMake/mitkFunctionCreateMatchPointDeployedAlgorithm.cmake index 7478718143..688e4afc38 100644 --- a/CMake/mitkFunctionCreateMatchPointDeployedAlgorithm.cmake +++ b/CMake/mitkFunctionCreateMatchPointDeployedAlgorithm.cmake @@ -1,114 +1,111 @@ #! #! Create a Command Line App. #! #! \brief This function will create a command line executable and the scripts required to run it #! #! \param NAME (required) Name of the algorithm / cmake target #! \param DEPENDS (optional) Required MITK modules beyond MitkCommandLine #! \param PACKAGE_DEPENDS (optional) list of "packages" this command line app depends on (e.g. ITK, VTK, etc.) #! \param TARGET_DEPENDS (optional) list of additional CMake targets this command line app depends on #! \param CPP_FILES (optional) list of cpp files, if it is not given NAME.cpp is assumed #! \param INCLUDE_DIRS (optional): All directories that should be added as include dirs to the project #! \param PROFILE (optional): The profile file that should be used for the algorithm. If not set it is "./.profile". #! \param NO_PROFILE_GEN (optional): Flag. If set no profile resource will be generated. #! \param ADDITIONAL_LIBS (optional) List of additional private libraries linked to this module. #! The folder containing the library will be added to the global list of library search paths. #! \param H_FILES (optional) List of public header files for this module. #! Assuming that there exists a file called MyApp.cpp, an example call looks like: #! \code #! mitkFunctionCreateCommandLineApp( #! NAME MyApp #! DEPENDS MitkCore MitkPlanarFigure #! PACKAGE_DEPENDS ITK VTK #! ) #! \endcode #! function(mitkFunctionCreateMatchPointDeployedAlgorithm) set(_function_params NAME # Name of the algorithm/target PROFILE # Profile of the algorithm that should be used ) set(_function_multiparams DEPENDS # list of modules this command line app depends on PACKAGE_DEPENDS # list of "packages" this command line app depends on (e.g. ITK, VTK, etc.) TARGET_DEPENDS # list of CMake targets this command line app depends on CPP_FILES # (optional) list of cpp files, if it is not given NAME.cpp is assumed INCLUDE_DIRS # include directories: [PUBLIC|PRIVATE|INTERFACE] ADDITIONAL_LIBS # list of addidtional private libraries linked to this module. H_FILES # list of header files: [PUBLIC|PRIVATE] ) set(_function_options NO_PROFILE_GEN #Flag that indicates that no profile resource should be generated. ) cmake_parse_arguments(ALG "${_function_options}" "${_function_params}" "${_function_multiparams}" ${ARGN}) if( NOT (DEFINED MITK_USE_MatchPoint) OR NOT (${MITK_USE_MatchPoint})) message(FATAL_ERROR "Need package Matchpoint to deploy MatchPoint Algorithms.") endif() if(NOT ALG_NAME) message(FATAL_ERROR "NAME argument cannot be empty.") endif() - SET(ALG_TARGET "MDRA_${ALG_NAME}") + set(ALG_TARGET "MDRA_${ALG_NAME}") if(NOT ALG_CPP_FILES) set(ALG_CPP_FILES "${ALG_NAME}.cpp") endif() - IF(NOT ALG_PROFILE) + if(NOT ALG_PROFILE) set(ALG_PROFILE "${ALG_NAME}.profile") - ENDIF(NOT ALG_PROFILE) - - IF(NOT ALG_NO_PROFILE_GEN) - MESSAGE(STATUS "... generate MDRA profile for ${ALG_NAME} (from ${ALG_PROFILE})...") - - include(${MatchPoint_SOURCE_DIR}/CMake/mapFunctionCreateAlgorithmProfile.cmake) - CREATE_ALGORITHM_PROFILE(${ALG_NAME} ${ALG_PROFILE}) + endif() - MESSAGE(STATUS "... algorithm UID: ${ALGORITHM_PROFILE_UID}") - ENDIF(NOT ALG_NO_PROFILE_GEN) + if(NOT ALG_NO_PROFILE_GEN) + message(STATUS "Generate MDRA profile for ${ALG_NAME} (from ${ALG_PROFILE})") + include(${MatchPoint_SOURCE_DIR}/CMake/mapFunctionCreateAlgorithmProfile.cmake) + CREATE_ALGORITHM_PROFILE(${ALG_NAME} ${ALG_PROFILE}) + endif() - MESSAGE(STATUS "... deploy MDRA algorithm ${ALG_NAME}...") + message(STATUS "Deploy MDRA algorithm ${ALG_NAME}") ADD_LIBRARY(${ALG_TARGET} SHARED ${ALG_CPP_FILES} ${ALGORITHM_PROFILE_FILE}) - SET_TARGET_PROPERTIES(${ALG_TARGET} PROPERTIES + set_target_properties(${ALG_TARGET} PROPERTIES OUTPUT_NAME "mdra-${MatchPoint_VERSION_MAJOR}-${MatchPoint_VERSION_MINOR}_${ALG_NAME}" OUTPUT_NAME_DEBUG "mdra-D-${MatchPoint_VERSION_MAJOR}-${MatchPoint_VERSION_MINOR}_${ALG_NAME}" PREFIX "" FOLDER "${MITK_ROOT_FOLDER}/Modules/MatchPointAlgorithms") mitk_use_modules(TARGET ${ALG_TARGET} MODULES ${ALG_DEPENDS} PACKAGES PRIVATE MatchPoint ${ALG_PACKAGE_DEPENDS} ) if(ALG_TARGET_DEPENDS) target_link_libraries(${ALG_TARGET} ${ALG_TARGET_DEPENDS}) endif() target_include_directories(${ALG_TARGET} PRIVATE ${ALG_INCLUDE_DIRS} ${CMAKE_CURRENT_BINARY_DIR}) if(ALG_ADDITIONAL_LIBS) target_link_libraries(${ALG_TARGET} PRIVATE ${ALG_ADDITIONAL_LIBS}) get_property(_mitk_additional_library_search_paths GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS) foreach(_lib_filepath ${ALG_ADDITIONAL_LIBS}) get_filename_component(_search_path "${_lib_filepath}" PATH) if(_search_path) list(APPEND _mitk_additional_library_search_paths "${_search_path}") endif() endforeach() if(_mitk_additional_library_search_paths) list(REMOVE_DUPLICATES _mitk_additional_library_search_paths) set_property(GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS ${_mitk_additional_library_search_paths}) endif() endif() MITK_INSTALL(TARGETS ${ALG_TARGET}) endfunction() diff --git a/CMake/mitkFunctionCreatePlugin.cmake b/CMake/mitkFunctionCreatePlugin.cmake index d0da785c81..b2d27259d5 100644 --- a/CMake/mitkFunctionCreatePlugin.cmake +++ b/CMake/mitkFunctionCreatePlugin.cmake @@ -1,356 +1,357 @@ #! \brief Creates a MITK CTK plugin. #! #! This function should be called from the plugins CMakeLists.txt file. #! The target name is available after the macro call as ${PLUGIN_TARGET} #! to add additional libraries in your CMakeLists.txt. Include paths and link #! libraries are set depending on the value of the Required-Plugins header #! in your manifest_headers.cmake file. #! #! This function internally calls ctkMacroBuildPlugin() and adds support #! for Qt Help files and installers. #! #! Options: #! \param TEST_PLUGIN Mark this plug-in as a testing plug-in. #! \param NO_INSTALL Don't install this plug-in. #! #! Parameters: #! #! \param EXPORT_DIRECTIVE (required) The export directive to use in the generated #! _Exports.h file. #! #! Multi-value parameters (all optional): #! #! \param EXPORTED_INCLUDE_SUFFIXES A list of sub-directories which should #! be added to the current source directory. The resulting directories #! will be available in the set of include directories of depending plug-ins. #! \param MODULE_DEPENDS (optional) A list of Modules this plug-in depends on. #! \param PACKAGE_DEPENDS (optional) A list of external packages this plug-in depends on. #! \param TARGET_DEPENDS (optional) A list of CMake targets this plug-in depends on. #! \param DOXYGEN_TAGFILES (optional) Which external tag files should be available for the plugin documentation #! \param MOC_OPTIONS (optional) Additional options to pass to the Qt MOC compiler #! \param WARNINGS_NO_ERRORS (optional) Do not handle compiler warnings as errors function(mitk_create_plugin) # options set(arg_options TEST_PLUGIN # Mark this plug-in as a testing plug-in NO_INSTALL # Don't install this plug-in NO_QHP_TRANSFORM WARNINGS_NO_ERRORS ) # single value arguments set(arg_single EXPORT_DIRECTIVE # (required) TODO: could be generated via CMake as it is done for MITK modules already ) # multiple value arguments set(arg_multiple EXPORTED_INCLUDE_SUFFIXES # (optional) additional public include directories MODULE_DEPENDS # (optional) PACKAGE_DEPENDS TARGET_DEPENDS DOXYGEN_TAGFILES MOC_OPTIONS SUBPROJECTS # deprecated ) cmake_parse_arguments(_PLUGIN "${arg_options}" "${arg_single}" "${arg_multiple}" ${ARGN}) if(_PLUGIN_TEST_PLUGIN) set(_PLUGIN_NO_INSTALL 1) set(is_test_plugin "TEST_PLUGIN") else() set(is_test_plugin) endif() set(_PLUGIN_MOC_OPTIONS "-DBOOST_NO_TEMPLATE_PARTIAL_SPECIALIZATION -DBOOST_TT_HAS_OPERATOR_HPP_INCLUDED ${_PLUGIN_MOC_OPTIONS}") set(PLUGIN_TARGET ${PROJECT_NAME}) mitk_check_module_dependencies(MODULES ${_PLUGIN_MODULE_DEPENDS} PACKAGES ${_PLUGIN_PACKAGE_DEPENDS} MISSING_DEPENDENCIES_VAR _missing_deps MODULE_DEPENDENCIES_VAR _module_deps PACKAGE_DEPENDENCIES_VAR _package_deps) if(_missing_deps) if(NOT MITK_BUILD_ALL_PLUGINS) message(SEND_ERROR "${PROJECT_NAME} is missing requirements and won't be built. Missing: ${_missing_deps}") else() message(STATUS "${PROJECT_NAME} is missing requirements and won't be built. Missing: ${_missing_deps}") endif() return() endif() foreach(_module_dep ${_PLUGIN_MODULE_DEPENDS}) if(TARGET ${_module_dep}) get_target_property(AUTLOAD_DEP ${_module_dep} MITK_AUTOLOAD_DIRECTORY) if (AUTLOAD_DEP) message(SEND_ERROR "Plugin \"${PROJECT_NAME}\" has an invalid dependency on autoload module \"${_module_dep}\". Check MITK_CREATE_PLUGIN usage for \"${PROJECT_NAME}\".") endif() endif() endforeach() # -------------- All dependencies are resolved ------------------ message(STATUS "Creating CTK plugin ${PROJECT_NAME}") include(files.cmake) set(_PLUGIN_CPP_FILES ${CPP_FILES}) set(_PLUGIN_MOC_H_FILES ${MOC_H_FILES}) set(_PLUGIN_UI_FILES ${UI_FILES}) set(_PLUGIN_CACHED_RESOURCE_FILES ${CACHED_RESOURCE_FILES}) set(_PLUGIN_TRANSLATION_FILES ${TRANSLATION_FILES}) set(_PLUGIN_QRC_FILES ${QRC_FILES}) set(_PLUGIN_H_FILES ${H_FILES}) set(_PLUGIN_TXX_FILES ${TXX_FILES}) set(_PLUGIN_DOX_FILES ${DOX_FILES}) set(_PLUGIN_CMAKE_FILES ${CMAKE_FILES} files.cmake) set(_PLUGIN_FILE_DEPENDENCIES ${FILE_DEPENDENCIES}) if(CTK_PLUGINS_OUTPUT_DIR) set(_output_dir "${CTK_PLUGINS_OUTPUT_DIR}") else() set(_output_dir "") endif() # Compute the plugin dependencies ctkFunctionGetTargetLibraries(_PLUGIN_target_libraries "") #------------------------------------------------------------# #------------------ Qt Help support -------------------------# set(PLUGIN_GENERATED_QCH_FILES ) if(BLUEBERRY_USE_QT_HELP AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/documentation/UserManual") set(PLUGIN_DOXYGEN_INPUT_DIR "${CMAKE_CURRENT_SOURCE_DIR}/documentation/UserManual") set(PLUGIN_DOXYGEN_OUTPUT_DIR "${CMAKE_CURRENT_BINARY_DIR}/documentation/UserManual") # Create a list of Doxygen tag files from the plug-in dependencies set(PLUGIN_DOXYGEN_TAGFILES) foreach(_dep_target ${_PLUGIN_target_libraries}) string(REPLACE _ . _dep ${_dep_target}) get_target_property(_is_imported ${_dep_target} IMPORTED) if(_is_imported) get_target_property(_import_loc_debug ${_dep_target} IMPORTED_LOCATION_DEBUG) get_target_property(_import_loc_release ${_dep_target} IMPORTED_LOCATION_RELEASE) # There is not necessarily a debug and release build if(_import_loc_release) set(_import_loc ${_import_loc_release}) else() set(_import_loc ${_import_loc_debug}) endif() get_filename_component(_target_filename "${_import_loc}" NAME) # on windows there might be a Debug or Release subdirectory string(REGEX REPLACE "/bin/plugins/(Debug/|Release/)?${_target_filename}" "/Plugins/${_dep}/documentation/UserManual" plugin_tag_dir "${_import_loc}" ) else() set(plugin_tag_dir "${CMAKE_BINARY_DIR}/Plugins/${_dep}/documentation/UserManual") endif() set(_tag_file "${plugin_tag_dir}/${_dep_target}.tag") if(EXISTS ${_tag_file}) set(PLUGIN_DOXYGEN_TAGFILES "${PLUGIN_DOXYGEN_TAGFILES} \"${_tag_file}=qthelp://${_dep}/bundle/\"") endif() endforeach() if(_PLUGIN_DOXYGEN_TAGFILES) set(PLUGIN_DOXYGEN_TAGFILES "${PLUGIN_DOXYGEN_TAGFILES} ${_PLUGIN_DOXYGEN_TAGFILES}") endif() #message("PLUGIN_DOXYGEN_TAGFILES: ${PLUGIN_DOXYGEN_TAGFILES}") if(_PLUGIN_NO_QHP_TRANSFORM) set(_use_qhp_xsl 0) else() set(_use_qhp_xsl 1) endif() _FUNCTION_CREATE_CTK_QT_COMPRESSED_HELP(PLUGIN_GENERATED_QCH_FILES ${_use_qhp_xsl}) list(APPEND _PLUGIN_CACHED_RESOURCE_FILES ${PLUGIN_GENERATED_QCH_FILES}) endif() #------------------------------------------------------------# #------------------ Create Plug-in --------------------------# mitkFunctionOrganizeSources( SOURCE ${_PLUGIN_CPP_FILES} HEADER ${_PLUGIN_H_FILES} TXX ${_PLUGIN_TXX_FILES} DOC ${_PLUGIN_DOX_FILES} UI ${_PLUGIN_UI_FILES} QRC ${_PLUGIN_QRC_FILES} ${_PLUGIN_CACHED_RESOURCE_FILES} META ${_PLUGIN_META_FILES} MOC ${MY_MOC_CPP} GEN_UI ${MY_UI_CPP} GEN_QRC ${MY_QRC_SRCS} ) ctkMacroBuildPlugin( NAME ${PLUGIN_TARGET} EXPORT_DIRECTIVE ${_PLUGIN_EXPORT_DIRECTIVE} SRCS ${_PLUGIN_CPP_FILES} ${_PLUGIN_H_FILES} ${CORRESPONDING__H_FILES} ${GLOBBED__H_FILES} MOC_SRCS ${_PLUGIN_MOC_H_FILES} MOC_OPTIONS ${_PLUGIN_MOC_OPTIONS} UI_FORMS ${_PLUGIN_UI_FILES} EXPORTED_INCLUDE_SUFFIXES ${_PLUGIN_EXPORTED_INCLUDE_SUFFIXES} RESOURCES ${_PLUGIN_QRC_FILES} TARGET_LIBRARIES ${_PLUGIN_target_libraries} CACHED_RESOURCEFILES ${_PLUGIN_CACHED_RESOURCE_FILES} TRANSLATIONS ${_PLUGIN_TRANSLATION_FILES} OUTPUT_DIR ${_output_dir} NO_INSTALL # we install the plug-in ourselves ${is_test_plugin} ) mitk_use_modules(TARGET ${PLUGIN_TARGET} MODULES ${_PLUGIN_MODULE_DEPENDS} PACKAGES ${_PLUGIN_PACKAGE_DEPENDS} ) if(_PLUGIN_TARGET_DEPENDS) target_link_libraries(${PLUGIN_TARGET} ${_PLUGIN_TARGET_DEPENDS}) endif() set_property(TARGET ${PLUGIN_TARGET} APPEND PROPERTY COMPILE_DEFINITIONS US_MODULE_NAME=${PLUGIN_TARGET}) set_property(TARGET ${PLUGIN_TARGET} PROPERTY US_MODULE_NAME ${PLUGIN_TARGET}) - if(NOT CMAKE_CURRENT_SOURCE_DIR MATCHES "^${CMAKE_SOURCE_DIR}.*") + if(NOT CMAKE_CURRENT_SOURCE_DIR MATCHES "^${CMAKE_SOURCE_DIR}/.*") foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) - if(CMAKE_CURRENT_SOURCE_DIR MATCHES "^${MITK_EXTENSION_DIR}.*") + if("${CMAKE_CURRENT_SOURCE_DIR}/" MATCHES "^${MITK_EXTENSION_DIR}/.*") get_filename_component(MITK_EXTENSION_ROOT_FOLDER "${MITK_EXTENSION_DIR}" NAME) set_property(TARGET ${PLUGIN_TARGET} PROPERTY FOLDER "${MITK_EXTENSION_ROOT_FOLDER}/Plugins") break() endif() endforeach() else() set_property(TARGET ${PLUGIN_TARGET} PROPERTY FOLDER "${MITK_ROOT_FOLDER}/Plugins") endif() set(plugin_c_flags) set(plugin_cxx_flags) if(NOT _PLUGIN_WARNINGS_NO_ERRORS) if(MSVC_VERSION) mitkFunctionCheckCAndCXXCompilerFlags("/WX" plugin_c_flags plugin_cxx_flags) else() mitkFunctionCheckCAndCXXCompilerFlags(-Werror plugin_c_flags plugin_cxx_flags) mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=c++0x-static-nonintegral-init" plugin_c_flags plugin_cxx_flags) mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=static-member-init" plugin_c_flags plugin_cxx_flags) mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=unknown-warning" plugin_c_flags plugin_cxx_flags) mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=gnu" plugin_c_flags plugin_cxx_flags) mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=cast-function-type" plugin_c_flags plugin_cxx_flags) mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=inconsistent-missing-override" plugin_c_flags plugin_cxx_flags) + mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated-declarations" plugin_c_flags plugin_cxx_flags) endif() endif() if(plugin_c_flags) string(REPLACE " " ";" plugin_c_flags "${plugin_c_flags}") target_compile_options(${PLUGIN_TARGET} PRIVATE ${plugin_c_flags}) endif() if(plugin_cxx_flags) string(REPLACE " " ";" plugin_cxx_flags "${plugin_cxx_flags}") target_compile_options(${PLUGIN_TARGET} PRIVATE ${plugin_cxx_flags}) endif() if(_PLUGIN_TEST_PLUGIN) find_package(CppUnit REQUIRED) target_include_directories(${PLUGIN_TARGET} PRIVATE ${CppUnit_INCLUDE_DIRS}) target_link_libraries(${PLUGIN_TARGET} PRIVATE ${CppUnit_LIBRARIES}) endif() if(mbilog_FOUND) target_link_libraries(${PLUGIN_TARGET} PRIVATE mbilog) endif() set(_PLUGIN_META_FILES "${CMAKE_CURRENT_SOURCE_DIR}/manifest_headers.cmake") if(EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/plugin.xml") list(APPEND _PLUGIN_META_FILES "${CMAKE_CURRENT_SOURCE_DIR}/plugin.xml") endif() set(PLUGIN_TARGET ${PLUGIN_TARGET} PARENT_SCOPE) #------------------------------------------------------------# #------------------ Installer support -----------------------# if(NOT _PLUGIN_NO_INSTALL) set(install_directories "") if(NOT MACOSX_BUNDLE_NAMES) set(install_directories bin/plugins) else(NOT MACOSX_BUNDLE_NAMES) foreach(bundle_name ${MACOSX_BUNDLE_NAMES}) list(APPEND install_directories ${bundle_name}.app/Contents/MacOS/plugins) endforeach(bundle_name) endif(NOT MACOSX_BUNDLE_NAMES) foreach(install_subdir ${install_directories}) mitkFunctionInstallCTKPlugin(TARGETS ${PLUGIN_TARGET} DESTINATION ${install_subdir}) endforeach() set(_autoload_targets ) foreach(_dependency ${_module_deps}) get_target_property(_dep_autoloads ${_dependency} MITK_AUTOLOAD_TARGETS) if (_dep_autoloads) list(APPEND _autoload_targets ${_dep_autoloads}) endif() endforeach() # The MITK_AUTOLOAD_TARGETS property is used in the mitkFunctionInstallAutoLoadModules # macro which expects a list of plug-in targets. if (_autoload_targets) list(REMOVE_DUPLICATES _autoload_targets) set_target_properties(${PLUGIN_TARGET} PROPERTIES MITK_AUTOLOAD_TARGETS "${_autoload_targets}") endif() endif() endfunction() function(_FUNCTION_CREATE_CTK_QT_COMPRESSED_HELP qch_file use_xsl) set(_manifest_path "${CMAKE_CURRENT_SOURCE_DIR}/manifest_headers.cmake") if(NOT EXISTS ${_manifest_path}) message(FATAL_ERROR "${_manifest_path} not found") endif() include(${_manifest_path}) string(REPLACE "_" "." Plugin-SymbolicName "${PLUGIN_TARGET}") configure_file(${MITK_SOURCE_DIR}/Documentation/doxygen_plugin_manual.conf.in ${PLUGIN_DOXYGEN_OUTPUT_DIR}/doxygen.conf ) set(_qhp_xsl_file "${MITK_SOURCE_DIR}/Documentation/qhp_toc.xsl") set(_generated_qhp_file "${PLUGIN_DOXYGEN_OUTPUT_DIR}/html/index.qhp") set(_transformed_qhp_file "${PLUGIN_DOXYGEN_OUTPUT_DIR}/html/${PLUGIN_TARGET}.qhp") set(${qch_file} "${CMAKE_CURRENT_BINARY_DIR}/resources/${PLUGIN_TARGET}.qch") set(_xsl_command ) if(use_xsl) set(_xsl_command COMMAND ${QT_XMLPATTERNS_EXECUTABLE} ${_qhp_xsl_file} ${_generated_qhp_file} -output ${_transformed_qhp_file}) endif() file(GLOB _file_dependencies "${PLUGIN_DOXYGEN_INPUT_DIR}/*") add_custom_command(OUTPUT ${${qch_file}} # Generate a Qt help project (index.qhp) with doxygen COMMAND ${DOXYGEN_EXECUTABLE} ${PLUGIN_DOXYGEN_OUTPUT_DIR}/doxygen.conf # Use a XSL transformation to get rid of the top-level entry ${_xsl_command} # Generate the final Qt compressed help file (.qch) COMMAND ${QT_HELPGENERATOR_EXECUTABLE} ${_transformed_qhp_file} -o ${${qch_file}} DEPENDS ${PLUGIN_DOXYGEN_OUTPUT_DIR}/doxygen.conf ${_file_dependencies} ) #set_source_files_properties(${qch_file} PROPERTIES GENERATED 1) set(${qch_file} ${${qch_file}} PARENT_SCOPE) endfunction() function(MACRO_CREATE_MITK_CTK_PLUGIN) message(SEND_ERROR "The function MACRO_CREATE_MITK_CTK_PLUGIN was renamed to mitk_create_plugin in MITK 2015.05.") endfunction() diff --git a/CMake/mitkFunctionUseModules.cmake b/CMake/mitkFunctionUseModules.cmake index 173e0a5a95..c1bec4eae5 100644 --- a/CMake/mitkFunctionUseModules.cmake +++ b/CMake/mitkFunctionUseModules.cmake @@ -1,163 +1,169 @@ function(_mitk_parse_package_args) set(package_list ${ARGN}) set(PUBLIC_PACKAGE_NAMES ) set(PRIVATE_PACKAGE_NAMES ) set(INTERFACE_PACKAGE_NAMES ) set(_package_visibility PRIVATE) foreach(_package ${package_list}) if(_package STREQUAL "PUBLIC" OR _package STREQUAL "PRIVATE" OR _package STREQUAL "INTERFACE") set(_package_visibility ${_package}) else() list(APPEND packages ${_package}) set(_package_name ) set(_package_components_list ) string(REPLACE "|" ";" _package_list ${_package}) if("${_package_list}" STREQUAL "${_package}") set(_package_name ${_package}) else() list(GET _package_list 0 _package_name) list(GET _package_list 1 _package_components) string(REPLACE "+" ";" _package_components_list "${_package_components}") if(NOT _package_name OR NOT _package_components) message(SEND_ERROR "PACKAGE argument syntax wrong. ${_package} is not of the form PACKAGE[|COMPONENT1[+COMPONENT2]...]") endif() endif() list(APPEND ${_package_visibility}_PACKAGE_NAMES ${_package_name}) list(APPEND ${_package_visibility}_${_package_name}_REQUIRED_COMPONENTS ${_package_components_list}) endif() endforeach() # remove duplicates and set package components in parent scope foreach(_package_visibility PUBLIC PRIVATE INTERFACE) foreach(_package_name ${${_package_visibility}_PACKAGE_NAMES}) if(${_package_visibility}_${_package_name}_REQUIRED_COMPONENTS) list(REMOVE_DUPLICATES ${_package_visibility}_${_package_name}_REQUIRED_COMPONENTS) endif() set(${_package_visibility}_${_package_name}_REQUIRED_COMPONENTS ${${_package_visibility}_${_package_name}_REQUIRED_COMPONENTS} PARENT_SCOPE) endforeach() endforeach() set(PUBLIC_PACKAGE_NAMES ${PUBLIC_PACKAGE_NAMES} PARENT_SCOPE) set(PRIVATE_PACKAGE_NAMES ${PRIVATE_PACKAGE_NAMES} PARENT_SCOPE) set(INTERFACE_PACKAGE_NAMES ${INTERFACE_PACKAGE_NAMES} PARENT_SCOPE) set(PACKAGE_NAMES ${PUBLIC_PACKAGE_NAMES} ${PRIVATE_PACKAGE_NAMES} ${INTERFACE_PACKAGE_NAMES} PARENT_SCOPE) endfunction() function(_include_package_config pkg_config_file) # wrap the inclusion of the MITK__Config.cmake file in a # function to create a scope for its variables; this allows # multiple inclusions of the file in the parent scope include(${pkg_config_file}) set(ALL_INCLUDE_DIRECTORIES ${ALL_INCLUDE_DIRECTORIES} PARENT_SCOPE) + set(ALL_LINK_DIRECTORIES ${ALL_LINK_DIRECTORIES} PARENT_SCOPE) set(ALL_LIBRARIES ${ALL_LIBRARIES} PARENT_SCOPE) set(ALL_COMPILE_DEFINITIONS ${ALL_COMPILE_DEFINITIONS} PARENT_SCOPE) set(ALL_COMPILE_OPTIONS ${ALL_COMPILE_OPTIONS} PARENT_SCOPE) endfunction() #! This CMake function sets up the necessary include directories, #! linker dependencies, and compile flags for a given target which #! depends on a set of MITK modules or packages. #! #! A package argument is of the form #! #! [PUBLIC|PRIVATE|INTERFACE] PACKAGE[|COMPONENT1[+COMPONENT2]...] #! #! where PACKAGE is the package name (e.g. VTK) and components are #! the names of required package components or libraries. #! #! If a dependency is not available, an error is thrown. function(mitk_use_modules) set(_macro_params TARGET # The target name (required) ) set(_macro_multiparams MODULES # MITK modules which the given TARGET uses PACKAGES # MITK packages which the given TARGET uses ) set(_macro_options ) cmake_parse_arguments(USE "${_macro_options}" "${_macro_params}" "${_macro_multiparams}" ${ARGN}) # Sanity checks if(NOT USE_TARGET) message(SEND_ERROR "Required TARGET argument missing.") elseif(NOT TARGET ${USE_TARGET}) message(SEND_ERROR "The given TARGET argument ${USE_TARGET} is not a valid target") endif() set(depends ${USE_MODULES}) set(package_depends ${USE_PACKAGES}) if(depends) # Iterate over all module dependencies foreach(dependency ${depends}) if(TARGET ${dependency} AND NOT MODULE_IS_DEPRECATED) get_target_property(_is_interface_lib ${dependency} TYPE) if(NOT _is_interface_lib) get_target_property(_dependency_deprecated_since ${dependency} MITK_MODULE_DEPRECATED_SINCE) if(_dependency_deprecated_since) message(WARNING "Module ${dependency} is deprecated since ${_dependency_deprecated_since}") endif() endif() endif() endforeach() target_link_libraries(${USE_TARGET} PUBLIC ${depends}) endif() # Parse package dependencies if(package_depends) _mitk_parse_package_args(${package_depends}) # Some package config files like MITK_Qt5_Config.cmake rely on a # properly set "MODULE_NAME" variable for the current target. set(MODULE_NAME ${USE_TARGET}) # Read all package information foreach(_package_visibility INTERFACE PUBLIC PRIVATE) foreach(_package ${${_package_visibility}_PACKAGE_NAMES}) set(ALL_INCLUDE_DIRECTORIES) + set(ALL_LINK_DIRECTORIES) set(ALL_LIBRARIES) set(ALL_COMPILE_DEFINITIONS) set(ALL_COMPILE_OPTIONS) set(${_package}_REQUIRED_COMPONENTS_BY_MODULE ${${_package_visibility}_${_package}_REQUIRED_COMPONENTS}) set(_package_found 0) foreach(dir ${MODULES_PACKAGE_DEPENDS_DIRS}) if((NOT DEFINED MITK_USE_${_package} OR MITK_USE_${_package}) AND EXISTS "${dir}/MITK_${_package}_Config.cmake") _include_package_config("${dir}/MITK_${_package}_Config.cmake") set(_package_found 1) break() endif() endforeach() if(_package_found) if(ALL_INCLUDE_DIRECTORIES) list(REMOVE_DUPLICATES ALL_INCLUDE_DIRECTORIES) target_include_directories(${USE_TARGET} SYSTEM ${_package_visibility} ${ALL_INCLUDE_DIRECTORIES}) endif() + if(ALL_LINK_DIRECTORIES) + list(REMOVE_DUPLICATES ALL_LINK_DIRECTORIES) + target_link_directories(${USE_TARGET} ${_package_visibility} ${ALL_LINK_DIRECTORIES}) + endif() if(ALL_LIBRARIES) # Don't remove "duplicats" because ALL_LIBRARIES may be of the form: # "general;bla;debug;blad;general;foo;debug;food" target_link_libraries(${USE_TARGET} ${_package_visibility} ${ALL_LIBRARIES}) endif() if(ALL_COMPILE_DEFINITIONS) list(REMOVE_DUPLICATES ALL_COMPILE_DEFINITIONS) # Compile definitions are always added "PRIVATE" to avoid multiple definitions # on the command line due to transitive and direct dependencies adding the # same definitions. target_compile_definitions(${USE_TARGET} PRIVATE ${ALL_COMPILE_DEFINITIONS}) endif() if(ALL_COMPILE_OPTIONS) list(REMOVE_DUPLICATES ALL_COMPILE_OPTIONS) target_compile_options(${USE_TARGET} ${_package_visibility} ${ALL_COMPILE_OPTIONS}) endif() else() message(SEND_ERROR "Missing package: ${_package}") endif() endforeach() endforeach() endif() endfunction() diff --git a/CMake/mitkInstallRules.cmake b/CMake/mitkInstallRules.cmake index c9ae3f0b51..062879f3ff 100644 --- a/CMake/mitkInstallRules.cmake +++ b/CMake/mitkInstallRules.cmake @@ -1,172 +1,177 @@ # Install MITK icon and logo MITK_INSTALL(FILES "${MITK_SOURCE_DIR}/mitk.ico" "${MITK_SOURCE_DIR}/mitk.bmp") # Helper vars if(WIN32) set(_prefix "") set(_ext ".dll") elseif(UNIX) set(_prefix "lib") if(APPLE) set(_ext ".dylib") else() set(_ext ".so") endif() endif() # Install MITK executables including auto-load modules get_property(_mitk_executable_targets GLOBAL PROPERTY MITK_EXECUTABLE_TARGETS) if(_mitk_executable_targets) get_property(_mitk_module_targets GLOBAL PROPERTY MITK_MODULE_TARGETS) foreach(_mitk_module_target ${_mitk_module_targets}) if(TARGET ${_mitk_module_target}) get_target_property(_mitk_autoload_targets ${_mitk_module_target} MITK_AUTOLOAD_TARGETS) if (_mitk_autoload_targets) foreach(_mitk_autoload_target ${_mitk_autoload_targets}) get_target_property(_mitk_autoload_directory ${_mitk_autoload_target} MITK_AUTOLOAD_DIRECTORY) if (_mitk_autoload_directory) if(WIN32) get_target_property(_target_location ${_mitk_autoload_target} RUNTIME_OUTPUT_DIRECTORY) else() get_target_property(_target_location ${_mitk_autoload_target} LIBRARY_OUTPUT_DIRECTORY) endif() if(NOT CMAKE_CFG_INTDIR STREQUAL ".") set(_target_location "${_target_location}/Release") endif() set(_mitk_autoload_target_filename "${_prefix}${_mitk_autoload_target}${_ext}") set(_mitk_autoload_target_filepath "${_target_location}/${_mitk_autoload_target_filename}") set(_install_DESTINATION "${_mitk_autoload_directory}") MITK_INSTALL(FILES ${_mitk_autoload_target_filepath}) if(UNIX AND NOT APPLE) install(CODE "file(RPATH_REMOVE FILE \"\${CMAKE_INSTALL_PREFIX}/bin/${_mitk_autoload_directory}/${_mitk_autoload_target_filename}\")") endif() endif() endforeach() endif() endif() endforeach() set(_install_DESTINATION "") foreach(_mitk_executable_target ${_mitk_executable_targets}) get_target_property(_no_install ${_mitk_executable_target} NO_INSTALL) if(_no_install) continue() endif() MITK_INSTALL_TARGETS(EXECUTABLES ${_mitk_executable_target} GLOB_PLUGINS) if(UNIX AND NOT APPLE) install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.sh" DESTINATION "." RENAME "${_mitk_executable_target}.sh") elseif(WIN32) - install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.bat" DESTINATION "." RENAME "${_mitk_executable_target}.bat") + get_target_property(_win32_exec ${_mitk_executable_target} WIN32_EXECUTABLE) + if(_win32_exec) + install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledWin32App.bat" DESTINATION "." RENAME "${_mitk_executable_target}.bat") + else() + install(PROGRAMS "${MITK_SOURCE_DIR}/CMake/RunInstalledApp.bat" DESTINATION "." RENAME "${_mitk_executable_target}.bat") + endif() endif() endforeach() endif() # Install PythonQt if(MITK_USE_Python3 AND PythonQt_DIR) set(_python_qt_lib "${PythonQt_DIR}/") if(WIN32) set(_python_qt_lib "${_python_qt_lib}bin") else() set(_python_qt_lib "${_python_qt_lib}lib") endif() set(_python_qt_lib "${_python_qt_lib}/${_prefix}PythonQt${_ext}") MITK_INSTALL(FILES ${_python_qt_lib}) endif() # Install Qt plugins if(MITK_USE_Qt5) get_property(_qmake_location TARGET ${Qt5Core_QMAKE_EXECUTABLE} PROPERTY IMPORT_LOCATION) get_filename_component(_qmake_path ${_qmake_location} DIRECTORY) set(_install_DESTINATION "plugins/sqldrivers") MITK_INSTALL(FILES "${_qmake_path}/../plugins/sqldrivers/${_prefix}qsqlite${_ext}") set(_install_DESTINATION "plugins/imageformats") MITK_INSTALL(FILES "${_qmake_path}/../plugins/imageformats/${_prefix}qsvg${_ext}") set(_install_DESTINATION "plugins/iconengines") MITK_INSTALL(FILES "${_qmake_path}/../plugins/iconengines/${_prefix}qsvgicon${_ext}") # Install platform-specific Qt plugins set(_install_DESTINATION "plugins/platforms") if(WIN32) MITK_INSTALL(FILES "${_qmake_path}/../plugins/platforms/qwindows.dll") elseif(APPLE) MITK_INSTALL(FILES "${_qmake_path}/../plugins/platforms/libqcocoa.dylib") elseif(UNIX) MITK_INSTALL(FILES "${_qmake_path}/../plugins/platforms/libqxcb.so") set(_install_DESTINATION "plugins/xcbglintegrations") MITK_INSTALL(FILES "${_qmake_path}/../plugins/xcbglintegrations/libqxcb-glx-integration.so") endif() # Install platform-specific Qt styles set(_install_DESTINATION "plugins/styles") if(WIN32) MITK_INSTALL(FILES "${_qmake_path}/../plugins/styles/qwindowsvistastyle.dll") elseif(APPLE) MITK_INSTALL(FILES "${_qmake_path}/../plugins/styles/libqmacstyle.dylib") endif() # Install Qt WebEngine if(APPLE) set(_install_DESTINATION "../Frameworks/QtWebEngineCore.framework") get_filename_component(_real_path "${_qmake_path}/../lib/QtWebEngineCore.framework/Helpers" REALPATH) MITK_INSTALL(DIRECTORY ${_real_path} USE_SOURCE_PERMISSIONS) # Translations are included in the Resources directory of # QtWebEngineCore.framework and are installed by default. else() set(_install_DESTINATION "") if(WIN32) MITK_INSTALL(PROGRAMS "${_qmake_path}/QtWebEngineProcess.exe") elseif(UNIX) MITK_INSTALL(PROGRAMS "${_qmake_path}/../libexec/QtWebEngineProcess") endif() # make sure resources and translations exist and try system location as well if(EXISTS "${_qmake_path}/../resources") MITK_INSTALL(DIRECTORY "${_qmake_path}/../resources") elseif(EXISTS "/usr/share/qt5/resources") MITK_INSTALL(DIRECTORY "/usr/share/qt5/resources") else() message(WARNING "No webengine resources found!") endif() set(_install_DESTINATION "translations") if(EXISTS "${_qmake_path}/../translations/qtwebengine_locales") MITK_INSTALL(DIRECTORY "${_qmake_path}/../translations/qtwebengine_locales") elseif(EXISTS "/usr/share/qt5/translations/qtwebengine_locales") MITK_INSTALL(DIRECTORY "/usr/share/qt5/translations/qtwebengine_locales") else() message(WARNING "No webengine translations found!") endif() endif() endif() set(_install_DESTINATION "") # Install MatchPoint binaries that are not auto-detected if(MITK_USE_MatchPoint) MITK_INSTALL(DIRECTORY "${MITK_EXTERNAL_PROJECT_PREFIX}/bin/" FILES_MATCHING PATTERN "MapUtilities*") MITK_INSTALL(DIRECTORY "${MITK_EXTERNAL_PROJECT_PREFIX}/bin/" FILES_MATCHING PATTERN "MapAlgorithms*") endif() # IMPORTANT: Restore default install destination! Do not edit this file beyond this line! set(_install_DESTINATION "") diff --git a/CMakeExternals/DCMQI.cmake b/CMakeExternals/DCMQI.cmake index f0cbb3ee51..dc0e078434 100644 --- a/CMakeExternals/DCMQI.cmake +++ b/CMakeExternals/DCMQI.cmake @@ -1,65 +1,65 @@ #----------------------------------------------------------------------------- # DCMQI #----------------------------------------------------------------------------- if(MITK_USE_DCMQI) # Sanity checks if(DEFINED DCMQI_DIR AND NOT EXISTS ${DCMQI_DIR}) message(FATAL_ERROR "DCMQI_DIR variable is defined but corresponds to non-existing directory") endif() set(proj DCMQI) set(proj_DEPENDENCIES DCMTK ITK) set(DCMQI_DEPENDS ${proj}) if(NOT DEFINED DCMQI_DIR) set(additional_cmake_args) if(CTEST_USE_LAUNCHERS) list(APPEND additional_cmake_args "-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake" ) endif() mitk_query_custom_ep_vars() ExternalProject_Add(${proj} LIST_SEPARATOR ${sep} - GIT_REPOSITORY https://github.com/qiicr/dcmqi.git - GIT_TAG 99192b76 + GIT_REPOSITORY https://github.com/QIICR/dcmqi.git + GIT_TAG 83f498e9 UPDATE_COMMAND "" INSTALL_COMMAND "" CMAKE_GENERATOR ${gen} CMAKE_GENERATOR_PLATFORM ${gen_platform} CMAKE_ARGS ${ep_common_args} ${additional_cmake_args} #-DCMAKE_INSTALL_PREFIX:PATH= -DBUILD_SHARED_LIBS:BOOL=ON -DDCMQI_BUILD_APPS:BOOL=OFF -DDCMTK_DIR:PATH=${DCMTK_DIR} -DITK_DIR:PATH=${ITK_DIR} -DITK_NO_IO_FACTORY_REGISTER_MANAGER:BOOL=ON -DDCMQI_SUPERBUILD:BOOL=OFF -DDCMQI_CMAKE_CXX_STANDARD:STRING=14 ${${proj}_CUSTOM_CMAKE_ARGS} CMAKE_CACHE_ARGS ${ep_common_cache_args} ${${proj}_CUSTOM_CMAKE_CACHE_ARGS} CMAKE_CACHE_DEFAULT_ARGS ${ep_common_cache_default_args} ${${proj}_CUSTOM_CMAKE_CACHE_DEFAULT_ARGS} DEPENDS ${proj_DEPENDENCIES} ) ExternalProject_Get_Property(${proj} binary_dir) set(DCMQI_DIR ${binary_dir}) #set(${proj}_DIR ${ep_prefix}) #message(${proj}_DIR: ${${proj}_DIR}) #mitkFunctionInstallExternalCMakeProject(${proj}) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif() endif() diff --git a/CMakeExternals/Poco.cmake b/CMakeExternals/Poco.cmake index dea7ce375c..dd5d7bcd72 100644 --- a/CMakeExternals/Poco.cmake +++ b/CMakeExternals/Poco.cmake @@ -1,75 +1,93 @@ #----------------------------------------------------------------------------- # Poco #----------------------------------------------------------------------------- if(MITK_USE_Poco) # Sanity checks if(DEFINED Poco_DIR AND NOT EXISTS ${Poco_DIR}) message(FATAL_ERROR "Poco_DIR variable is defined but corresponds to non-existing directory") endif() set(proj Poco) set(proj_DEPENDENCIES ) set(${proj}_DEPENDS ${proj}) if(NOT DEFINED ${proj}_DIR) set(additional_cmake_args ) if(CTEST_USE_LAUNCHERS) list(APPEND additional_cmake_args "-DCMAKE_PROJECT_${proj}_INCLUDE:FILEPATH=${CMAKE_ROOT}/Modules/CTestUseLaunchers.cmake" ) endif() mitk_query_custom_ep_vars() + set(ssl_args + -DENABLE_CRYPTO:BOOL=OFF + -DENABLE_NETSSL:BOOL=OFF + -DENABLE_NETSSL_WIN:BOOL=OFF + ) + + if(OpenSSL_FOUND) + set(ssl_args + -DENABLE_CRYPTO:BOOL=ON + -DENABLE_NETSSL:BOOL=ON + -DFORCE_OPENSSL:BOOL=ON + ) + + if(OPENSSL_ROOT_DIR) + list(APPEND ssl_args + "-DOPENSSL_ROOT_DIR:PATH=${OPENSSL_ROOT_DIR}" + ) + endif() + endif() + ExternalProject_Add(${proj} LIST_SEPARATOR ${sep} URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/poco-1.9.0.tar.gz URL_MD5 1011839033f72de138f0c523c2caa121 CMAKE_GENERATOR ${gen} CMAKE_GENERATOR_PLATFORM ${gen_platform} CMAKE_ARGS ${ep_common_args} ${additional_cmake_args} + ${ssl_args} -DENABLE_XML:BOOL=ON -DENABLE_JSON:BOOL=ON -DENABLE_MONGODB:BOOL=OFF -DENABLE_PDF:BOOL=OFF -DENABLE_UTIL:BOOL=ON -DENABLE_NET:BOOL=ON - -DENABLE_NETSSL:BOOL=OFF - -DENABLE_NETSSL_WIN:BOOL=OFF - -DENABLE_CRYPTO:BOOL=OFF -DENABLE_DATA:BOOL=OFF -DENABLE_DATA_SQLITE:BOOL=OFF -DENABLE_DATA_MYSQL:BOOL=OFF -DENABLE_DATA_ODBC:BOOL=OFF -DENABLE_SEVENZIP:BOOL=OFF -DENABLE_ZIP:BOOL=ON -DENABLE_APACHECONNECTOR:BOOL=OFF -DENABLE_CPPPARSER:BOOL=OFF -DENABLE_POCODOC:BOOL=OFF -DENABLE_PAGECOMPILER:BOOL=OFF -DENABLE_PAGECOMPILER_FILE2PAGE:BOOL=OFF ${${proj}_CUSTOM_CMAKE_ARGS} CMAKE_CACHE_ARGS ${ep_common_cache_args} ${${proj}_CUSTOM_CMAKE_CACHE_ARGS} CMAKE_CACHE_DEFAULT_ARGS ${ep_common_cache_default_args} ${${proj}_CUSTOM_CMAKE_CACHE_DEFAULT_ARGS} DEPENDS ${proj_DEPENDENCIES} ) set(${proj}_DIR ${ep_prefix}) mitkFunctionInstallExternalCMakeProject(${proj}) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif() endif() diff --git a/CMakeLists.txt b/CMakeLists.txt index e3b390abe2..3516d75dbd 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,1438 +1,1455 @@ 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) #----------------------------------------------------------------------------- # Superbuild Option - Enabled by default #----------------------------------------------------------------------------- option(MITK_USE_SUPERBUILD "Build MITK and the projects it depends on via SuperBuild.cmake." ON) if(MITK_USE_SUPERBUILD) project(MITK-superbuild) set(MITK_SOURCE_DIR ${PROJECT_SOURCE_DIR}) set(MITK_BINARY_DIR ${PROJECT_BINARY_DIR}) else() - project(MITK VERSION 2018.04.99) + project(MITK VERSION 2021.02.00) include_directories(SYSTEM ${MITK_SUPERBUILD_BINARY_DIR}) endif() #----------------------------------------------------------------------------- # MITK Extension Feature #----------------------------------------------------------------------------- set(MITK_EXTENSION_DIRS "" CACHE STRING "") unset(MITK_ABSOLUTE_EXTENSION_DIRS) foreach(MITK_EXTENSION_DIR ${MITK_EXTENSION_DIRS}) get_filename_component(MITK_ABSOLUTE_EXTENSION_DIR "${MITK_EXTENSION_DIR}" ABSOLUTE) list(APPEND MITK_ABSOLUTE_EXTENSION_DIRS "${MITK_ABSOLUTE_EXTENSION_DIR}") endforeach() set(MITK_DIR_PLUS_EXTENSION_DIRS "${MITK_SOURCE_DIR}" ${MITK_ABSOLUTE_EXTENSION_DIRS}) #----------------------------------------------------------------------------- # Update CMake module path #----------------------------------------------------------------------------- set(MITK_CMAKE_DIR ${MITK_SOURCE_DIR}/CMake) set(CMAKE_MODULE_PATH ${MITK_CMAKE_DIR}) foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) set(MITK_CMAKE_EXTENSION_DIR "${MITK_EXTENSION_DIR}/CMake") if(EXISTS "${MITK_CMAKE_EXTENSION_DIR}") list(APPEND CMAKE_MODULE_PATH "${MITK_CMAKE_EXTENSION_DIR}") endif() endforeach() #----------------------------------------------------------------------------- # CMake function(s) and macro(s) #----------------------------------------------------------------------------- # Standard CMake macros include(FeatureSummary) include(CTest) include(CMakeParseArguments) include(FindPackageHandleStandardArgs) # MITK macros include(mitkFunctionGetGccVersion) include(mitkFunctionCheckCompilerFlags) include(mitkFunctionSuppressWarnings) # includes several functions include(mitkMacroEmptyExternalProject) include(mitkFunctionEnableBuildConfiguration) include(mitkFunctionWhitelists) include(mitkFunctionAddExternalProject) include(mitkFunctionAddLibrarySearchPaths) SUPPRESS_VC_DEPRECATED_WARNINGS() #----------------------------------------------------------------------------- # Set a default build type if none was specified #----------------------------------------------------------------------------- if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES) message(STATUS "Setting build type to 'Debug' as none was specified.") set(CMAKE_BUILD_TYPE Debug CACHE STRING "Choose the type of build." FORCE) # Set the possible values of build type for cmake-gui set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo") endif() #----------------------------------------------------------------------------- # Check miminum macOS version #----------------------------------------------------------------------------- -# The minimum supported macOS version is 10.13. If you use a version less than 10.13, there is no guarantee that the build still works. +# The minimum supported macOS version is 10.14. If you use a version less than +# 10.14, there is no guarantee that the build still works. if(APPLE) exec_program(sw_vers ARGS -productVersion OUTPUT_VARIABLE macos_version) - if (macos_version VERSION_LESS "10.13") - message(WARNING "Detected macOS version \"${macos_version}\" is not supported anymore. Minimum required macOS version is at least 10.13.") + if (macos_version VERSION_LESS "10.14") + message(WARNING "Detected macOS version \"${macos_version}\" is not supported anymore. Minimum required macOS version is at least 10.14.") endif() - if (CMAKE_OSX_DEPLOYMENT_TARGET AND CMAKE_OSX_DEPLOYMENT_TARGET VERSION_LESS 10.13) - message(WARNING "Detected macOS deployment target \"${CMAKE_OSX_DEPLOYMENT_TARGET}\" is not supported anymore. Minimum required macOS version is at least 10.13.") + if (CMAKE_OSX_DEPLOYMENT_TARGET AND CMAKE_OSX_DEPLOYMENT_TARGET VERSION_LESS 10.14) + message(WARNING "Detected macOS deployment target \"${CMAKE_OSX_DEPLOYMENT_TARGET}\" is not supported anymore. Minimum required macOS version is at least 10.14.") endif() endif() #----------------------------------------------------------------------------- # Check miminum compiler versions #----------------------------------------------------------------------------- if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU") # require at least gcc 4.9 as provided by ppa:ubuntu-toolchain-r/test for Ubuntu 14.04 if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.9) message(FATAL_ERROR "GCC version must be at least 4.9 If you are using Ubuntu 14.04, you can easily install gcc and g++ 4.9 (or any later version available) in addition to your version ${CMAKE_CXX_COMPILER_VERSION}: sudo add-apt-repository ppa:ubuntu-toolchain-r/test sudo apt-get update sudo apt-get install gcc-4.9 g++-4.9 Make sure to explicitly specify these compilers when configuring MITK: CMAKE_C_COMPILER:FILEPATH=/usr/bin/gcc-4.9 CMAKE_CXX_COMPILER:FILEPATH=/usr/bin/g++-4.9 For more information on the proposed PPA see the Toolchain Updates section of https://wiki.ubuntu.com/ToolChain.") endif() elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang") # require at least clang 3.4 if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 3.4) message(FATAL_ERROR "Clang version must be at least 3.4") endif() elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "AppleClang") # require at least clang 5.0 if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0) message(FATAL_ERROR "Apple Clang version must be at least 5.0") endif() elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC") # require at least Visual Studio 2017 if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 19.10) message(FATAL_ERROR "Microsoft Visual Studio 2017 or newer required") endif() else() message(WARNING "You are using an unsupported compiler! Compilation has only been tested with Clang (Linux or Apple), GCC and MSVC.") endif() if(CMAKE_COMPILER_IS_GNUCXX) mitkFunctionGetGccVersion(${CMAKE_CXX_COMPILER} GCC_VERSION) else() set(GCC_VERSION 0) endif() set(MITK_CXX_STANDARD 14) set(CMAKE_CXX_EXTENSIONS 0) set(CMAKE_CXX_STANDARD ${MITK_CXX_STANDARD}) set(CMAKE_CXX_STANDARD_REQUIRED 1) # This is necessary to avoid problems with compile feature checks. # CMAKE_CXX_STANDARD seems to only set the -std=c++14 flag for targets. # However, compile flag checks also need to be done with -std=c++14. # The MITK_CXX14_FLAG variable is also used for external projects # build during the MITK super-build. mitkFunctionCheckCompilerFlags("-std=c++14" MITK_CXX14_FLAG) #----------------------------------------------------------------------------- # Warn if source or build path is too long #----------------------------------------------------------------------------- if(WIN32) set(_src_dir_length_max 50) set(_bin_dir_length_max 50) if(MITK_USE_SUPERBUILD) set(_src_dir_length_max 34) # _src_dir_length_max - strlen(ep/src/ITK-build) set(_bin_dir_length_max 40) # _bin_dir_length_max - strlen(MITK-build) endif() string(LENGTH "${MITK_SOURCE_DIR}" _src_n) string(LENGTH "${MITK_BINARY_DIR}" _bin_n) # The warnings should be converted to errors if(_src_n GREATER _src_dir_length_max) message(WARNING "MITK source code directory path length is too long (${_src_n} > ${_src_dir_length_max})." "Please move the MITK source code directory to a directory with a shorter path." ) endif() if(_bin_n GREATER _bin_dir_length_max) message(WARNING "MITK build directory path length is too long (${_bin_n} > ${_bin_dir_length_max})." "Please move the MITK build directory to a directory with a shorter path." ) endif() endif() #----------------------------------------------------------------------------- # Additional MITK Options (also shown during superbuild) #----------------------------------------------------------------------------- # ----------------------------------------- # General build options option(BUILD_SHARED_LIBS "Build MITK with shared libraries" ON) option(WITH_COVERAGE "Enable/Disable coverage" OFF) option(BUILD_TESTING "Test the project" ON) option(MITK_FAST_TESTING "Disable long-running tests like packaging" OFF) option(MITK_XVFB_TESTING "Execute test drivers through xvfb-run" OFF) option(MITK_BUILD_ALL_APPS "Build all MITK applications" OFF) option(MITK_BUILD_EXAMPLES "Build the MITK Examples" OFF) option(MITK_ENABLE_PIC_READER "Enable support for reading the DKFZ pic file format." ON) mark_as_advanced( MITK_XVFB_TESTING MITK_FAST_TESTING MITK_BUILD_ALL_APPS MITK_ENABLE_PIC_READER ) #----------------------------------------------------------------------------- # Set UI testing flags #----------------------------------------------------------------------------- if(MITK_XVFB_TESTING) set(MITK_XVFB_TESTING_COMMAND "xvfb-run" "--auto-servernum" CACHE STRING "Command and options to test through Xvfb") mark_as_advanced(MITK_XVFB_TESTING_COMMAND) endif(MITK_XVFB_TESTING) # ----------------------------------------- # Other options set(MITK_CUSTOM_REVISION_DESC "" CACHE STRING "Override MITK revision description") mark_as_advanced(MITK_CUSTOM_REVISION_DESC) set_property(GLOBAL PROPERTY MITK_EXTERNAL_PROJECTS "") include(CMakeExternals/ExternalProjectList.cmake) foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) set(MITK_CMAKE_EXTERNALS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/CMakeExternals") if(EXISTS "${MITK_CMAKE_EXTERNALS_EXTENSION_DIR}/ExternalProjectList.cmake") include("${MITK_CMAKE_EXTERNALS_EXTENSION_DIR}/ExternalProjectList.cmake") endif() endforeach() # ----------------------------------------- # Other MITK_USE_* options not related to # external projects build via the # MITK superbuild option(MITK_USE_BLUEBERRY "Build the BlueBerry platform" ON) option(MITK_USE_OpenCL "Use OpenCL GPU-Computing library" OFF) option(MITK_USE_OpenMP "Use OpenMP" OFF) option(MITK_USE_Python3 "Use Python 3" OFF) #----------------------------------------------------------------------------- # Build configurations #----------------------------------------------------------------------------- set(_buildConfigs "Custom") file(GLOB _buildConfigFiles CMake/BuildConfigurations/*.cmake) foreach(_buildConfigFile ${_buildConfigFiles}) get_filename_component(_buildConfigFile ${_buildConfigFile} NAME_WE) list(APPEND _buildConfigs ${_buildConfigFile}) endforeach() foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) file(GLOB _extBuildConfigFiles "${MITK_EXTENSION_DIR}/CMake/BuildConfigurations/*.cmake") foreach(_extBuildConfigFile ${_extBuildConfigFiles}) get_filename_component(_extBuildConfigFile "${_extBuildConfigFile}" NAME_WE) list(APPEND _buildConfigs "${_extBuildConfigFile}") endforeach() list(REMOVE_DUPLICATES _buildConfigs) endforeach() set(MITK_BUILD_CONFIGURATION "Custom" CACHE STRING "Use pre-defined MITK configurations") set_property(CACHE MITK_BUILD_CONFIGURATION PROPERTY STRINGS ${_buildConfigs}) mitkFunctionEnableBuildConfiguration() mitkFunctionCreateWhitelistPaths(MITK) mitkFunctionFindWhitelists(MITK) # ----------------------------------------- # Qt version related variables option(MITK_USE_Qt5 "Use Qt 5 library" ON) if(MITK_USE_Qt5) if(WIN32) set(MITK_QT5_MINIMUM_VERSION 5.12.9) else() set(MITK_QT5_MINIMUM_VERSION 5.12) endif() set(MITK_QT5_COMPONENTS Concurrent OpenGL PrintSupport Script Sql Svg Widgets Xml XmlPatterns WebEngineWidgets UiTools Help LinguistTools) if(APPLE) list(APPEND MITK_QT5_COMPONENTS DBus) elseif(UNIX) list(APPEND MITK_QT5_COMPONENTS X11Extras) endif() # Hint at default install locations of Qt if(NOT Qt5_DIR) if(MSVC) set(_dir_candidates "C:/Qt") if(CMAKE_GENERATOR MATCHES "^Visual Studio [0-9]+ ([0-9]+)") set(_compilers "msvc${CMAKE_MATCH_1}") elseif(CMAKE_GENERATOR MATCHES "Ninja") include(mitkFunctionGetMSVCVersion) mitkFunctionGetMSVCVersion() if(VISUAL_STUDIO_PRODUCT_NAME MATCHES "^Visual Studio ([0-9]+)") set(_compilers "msvc${CMAKE_MATCH_1}") endif() endif() if(_compilers MATCHES "[0-9]+") if (CMAKE_MATCH_0 EQUAL 2019) list(APPEND _compilers "msvc2017") # Binary compatible to 2019 endif() endif() else() set(_dir_candidates ~/Qt) if(APPLE) set(_compilers clang) else() list(APPEND _dir_candidates /opt/Qt) set(_compilers gcc) endif() endif() if(CMAKE_SIZEOF_VOID_P EQUAL 8) foreach(_compiler ${_compilers}) list(APPEND _compilers64 "${_compiler}_64") endforeach() set(_compilers ${_compilers64}) endif() foreach(_dir_candidate ${_dir_candidates}) get_filename_component(_dir_candidate ${_dir_candidate} REALPATH) foreach(_compiler ${_compilers}) set(_glob_expression "${_dir_candidate}/5.*/${_compiler}") file(GLOB _hints ${_glob_expression}) list(SORT _hints) list(APPEND MITK_QT5_HINTS ${_hints}) endforeach() endforeach() endif() find_package(Qt5 ${MITK_QT5_MINIMUM_VERSION} COMPONENTS ${MITK_QT5_COMPONENTS} REQUIRED HINTS ${MITK_QT5_HINTS}) endif() # ----------------------------------------- # Custom dependency logic +if(WIN32 AND Qt5_DIR) + set(_dir_candidate "${Qt5_DIR}/../../../../../Tools/OpenSSL/Win_x64") + get_filename_component(_dir_candidate ${_dir_candidate} ABSOLUTE) + if(EXISTS "${_dir_candidate}") + set(OPENSSL_ROOT_DIR "${_dir_candidate}") + endif() +endif() + +find_package(OpenSSL) + option(MITK_USE_SYSTEM_Boost "Use the system Boost" OFF) set(MITK_USE_Boost_LIBRARIES "" CACHE STRING "A semi-colon separated list of required Boost libraries") if(MITK_USE_cpprestsdk) - if(WIN32 AND Qt5_DIR) - set(_dir_candidate "${Qt5_DIR}/../../../../../Tools/OpenSSL/Win_x64") - get_filename_component(_dir_candidate ${_dir_candidate} ABSOLUTE) - if(EXISTS "${_dir_candidate}") - set(OPENSSL_ROOT_DIR "${_dir_candidate}") - endif() - endif() - find_package(OpenSSL QUIET) if(NOT OpenSSL_FOUND) set(openssl_message "Could not find OpenSSL (dependency of C++ REST SDK).\n") if(UNIX) if(APPLE) set(openssl_message "${openssl_message}Please install it using your favorite package management " "system (i.e. Homebrew or MacPorts).\n") else() set(openssl_message "${openssl_message}Please install the dev package of OpenSSL (i.e. libssl-dev).\n") endif() else() set(openssl_message "${openssl_message}Please either install Win32 OpenSSL:\n" " https://slproweb.com/products/Win32OpenSSL.html\n" "Or use the Qt Maintenance tool to install:\n" " Developer and Designer Tools > OpenSSL Toolkit > OpenSSL 64-bit binaries\n") endif() set(openssl_message "${openssl_message}If it still cannot be found, you can hint CMake to find OpenSSL by " "adding/setting the OPENSSL_ROOT_DIR variable to the root directory of an " "OpenSSL installation. Make sure to clear variables of partly found " "versions of OpenSSL before, or they will be mixed up.") message(FATAL_ERROR ${openssl_message}) endif() list(APPEND MITK_USE_Boost_LIBRARIES date_time regex system) if(UNIX) list(APPEND MITK_USE_Boost_LIBRARIES atomic chrono filesystem random thread) endif() list(REMOVE_DUPLICATES MITK_USE_Boost_LIBRARIES) set(MITK_USE_Boost_LIBRARIES ${MITK_USE_Boost_LIBRARIES} CACHE STRING "A semi-colon separated list of required Boost libraries" FORCE) endif() if(MITK_USE_Python3) set(MITK_USE_ZLIB ON CACHE BOOL "" FORCE) if(APPLE AND CMAKE_FRAMEWORK_PATH AND CMAKE_FRAMEWORK_PATH MATCHES "python3\\.?([0-9]+)") find_package(Python3 3.${CMAKE_MATCH_1} EXACT REQUIRED COMPONENTS Interpreter Development NumPy) else() find_package(Python3 REQUIRED COMPONENTS Interpreter Development NumPy) endif() if(WIN32) string(REPLACE "\\" "/" Python3_STDARCH "${Python3_STDARCH}") string(REPLACE "\\" "/" Python3_STDLIB "${Python3_STDLIB}") string(REPLACE "\\" "/" Python3_SITELIB "${Python3_SITELIB}") endif() link_directories(${Python3_LIBRARY_DIRS}) 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, itk::RGBAPixel" 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, itk::RGBAPixel" CACHE STRING "List of composite pixel types used in AccessByItk and InstantiateAccessFunction macros" FORCE) endif() if(NOT MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES) string(REPLACE "," ";" _integral_types ${MITK_ACCESSBYITK_INTEGRAL_PIXEL_TYPES}) string(REPLACE "," ";" _floating_types ${MITK_ACCESSBYITK_FLOATING_PIXEL_TYPES}) foreach(_scalar_type ${_integral_types} ${_floating_types}) set(MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES "${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}itk::VariableLengthVector<${_scalar_type}>,") endforeach() string(LENGTH "${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}" _length) math(EXPR _length "${_length} - 1") string(SUBSTRING "${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES}" 0 ${_length} MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES) set(MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES ${MITK_ACCESSBYITK_VECTOR_PIXEL_TYPES} CACHE STRING "List of vector pixel types used in AccessByItk and InstantiateAccessFunction macros for itk::VectorImage types" FORCE) endif() if(NOT MITK_ACCESSBYITK_DIMENSIONS) set(MITK_ACCESSBYITK_DIMENSIONS "2,3" CACHE STRING "List of dimensions used in AccessByItk and InstantiateAccessFunction macros") endif() find_package(Git REQUIRED) #----------------------------------------------------------------------------- # Superbuild script #----------------------------------------------------------------------------- if(MITK_USE_SUPERBUILD) include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake") # Print configuration summary message("\n\n") feature_summary( DESCRIPTION "------- FEATURE SUMMARY FOR ${PROJECT_NAME} -------" WHAT ALL) return() endif() #***************************************************************************** #**************************** END OF SUPERBUILD **************************** #***************************************************************************** #----------------------------------------------------------------------------- # Organize MITK targets in folders #----------------------------------------------------------------------------- set_property(GLOBAL PROPERTY USE_FOLDERS ON) set(MITK_ROOT_FOLDER "MITK" CACHE STRING "") mark_as_advanced(MITK_ROOT_FOLDER) #----------------------------------------------------------------------------- # CMake function(s) and macro(s) #----------------------------------------------------------------------------- include(WriteBasicConfigVersionFile) include(CheckCXXSourceCompiles) include(GenerateExportHeader) include(mitkFunctionAddCustomModuleTest) include(mitkFunctionCheckModuleDependencies) include(mitkFunctionCompileSnippets) include(mitkFunctionConfigureVisualStudioUserProjectFile) include(mitkFunctionCreateBlueBerryApplication) include(mitkFunctionCreateCommandLineApp) include(mitkFunctionCreateModule) include(mitkFunctionCreatePlugin) include(mitkFunctionCreateProvisioningFile) include(mitkFunctionGetLibrarySearchPaths) include(mitkFunctionGetVersion) include(mitkFunctionGetVersionDescription) include(mitkFunctionInstallAutoLoadModules) include(mitkFunctionInstallCTKPlugin) include(mitkFunctionInstallProvisioningFiles) include(mitkFunctionInstallThirdPartyCTKPlugins) include(mitkFunctionOrganizeSources) include(mitkFunctionUseModules) if( ${MITK_USE_MatchPoint} ) include(mitkFunctionCreateMatchPointDeployedAlgorithm) endif() include(mitkMacroConfigureItkPixelTypes) include(mitkMacroCreateExecutable) include(mitkMacroCreateModuleTests) include(mitkMacroGenerateToolsLibrary) include(mitkMacroGetLinuxDistribution) include(mitkMacroGetPMDPlatformString) include(mitkMacroInstall) include(mitkMacroInstallHelperApp) include(mitkMacroInstallTargets) include(mitkMacroMultiplexPicType) # Deprecated include(mitkMacroCreateCTKPlugin) #----------------------------------------------------------------------------- # Global CMake variables #----------------------------------------------------------------------------- # Required and enabled C++14 features for all MITK code. # These are added as PUBLIC compile features to all MITK modules. set(MITK_CXX_FEATURES cxx_auto_type cxx_decltype cxx_enum_forward_declarations cxx_extended_friend_declarations cxx_extern_templates cxx_final cxx_lambdas cxx_local_type_template_args cxx_long_long_type cxx_nullptr cxx_override cxx_range_for cxx_right_angle_brackets cxx_rvalue_references cxx_static_assert cxx_strong_enums cxx_template_template_parameters cxx_trailing_return_types cxx_variadic_macros ) if(NOT DEFINED CMAKE_DEBUG_POSTFIX) # We can't do this yet because the CTK Plugin Framework # cannot cope with a postfix yet. #set(CMAKE_DEBUG_POSTFIX d) endif() #----------------------------------------------------------------------------- # Output directories. #----------------------------------------------------------------------------- set(_default_LIBRARY_output_dir lib) set(_default_RUNTIME_output_dir bin) set(_default_ARCHIVE_output_dir lib) foreach(type LIBRARY RUNTIME ARCHIVE) # Make sure the directory exists if(MITK_CMAKE_${type}_OUTPUT_DIRECTORY AND NOT EXISTS ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}) message("Creating directory MITK_CMAKE_${type}_OUTPUT_DIRECTORY: ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}") file(MAKE_DIRECTORY "${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}") endif() if(MITK_CMAKE_${type}_OUTPUT_DIRECTORY) set(CMAKE_${type}_OUTPUT_DIRECTORY ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}) else() set(CMAKE_${type}_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${_default_${type}_output_dir}) set(MITK_CMAKE_${type}_OUTPUT_DIRECTORY ${CMAKE_${type}_OUTPUT_DIRECTORY}) endif() set(CMAKE_${type}_OUTPUT_DIRECTORY ${CMAKE_${type}_OUTPUT_DIRECTORY} CACHE INTERNAL "Output directory for ${type} files.") mark_as_advanced(CMAKE_${type}_OUTPUT_DIRECTORY) endforeach() #----------------------------------------------------------------------------- # Set MITK specific options and variables (NOT available during superbuild) #----------------------------------------------------------------------------- +if(OpenSSL_FOUND AND WIN32) + set(MITK_OPENSSL_SSL_DLL "" CACHE FILEPATH "") + set(MITK_OPENSSL_CRYPTO_DLL "" CACHE FILEPATH "") + + 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} ${MITK_CXX14_FLAG}") set(MITK_CXX_FLAGS_DEBUG ) set(MITK_CXX_FLAGS_RELEASE ) set(MITK_EXE_LINKER_FLAGS ) set(MITK_SHARED_LINKER_FLAGS ) if(WIN32) set(MITK_CXX_FLAGS "${MITK_CXX_FLAGS} -DPOCO_NO_UNWINDOWS -DWIN32_LEAN_AND_MEAN -DNOMINMAX") mitkFunctionCheckCompilerFlags("/wd4005" MITK_CXX_FLAGS) # warning C4005: macro redefinition mitkFunctionCheckCompilerFlags("/wd4231" MITK_CXX_FLAGS) # warning C4231: nonstandard extension used : 'extern' before template explicit instantiation # the following line should be removed after fixing bug 17637 mitkFunctionCheckCompilerFlags("/wd4316" MITK_CXX_FLAGS) # warning C4316: object alignment on heap mitkFunctionCheckCompilerFlags("/wd4180" MITK_CXX_FLAGS) # warning C4180: qualifier applied to function type has no meaning mitkFunctionCheckCompilerFlags("/wd4251" MITK_CXX_FLAGS) # warning C4251: 'identifier' : class 'type' needs to have dll-interface to be used by clients of class 'type2' endif() if(APPLE) set(MITK_CXX_FLAGS "${MITK_CXX_FLAGS} -DGL_SILENCE_DEPRECATION") # Apple deprecated OpenGL in macOS 10.14 endif() if(NOT MSVC_VERSION) foreach(_flag -Wall -Wextra -Wpointer-arith -Winvalid-pch -Wcast-align -Wwrite-strings -Wno-error=gnu -Wno-error=unknown-pragmas # The strict-overflow warning is generated by ITK template code -Wno-error=strict-overflow -Woverloaded-virtual -Wstrict-null-sentinel #-Wold-style-cast #-Wsign-promo -Wno-error=deprecated-copy -Wno-array-bounds -fdiagnostics-show-option ) mitkFunctionCheckCAndCXXCompilerFlags(${_flag} MITK_C_FLAGS MITK_CXX_FLAGS) endforeach() endif() if(CMAKE_COMPILER_IS_GNUCXX AND NOT APPLE) mitkFunctionCheckCompilerFlags("-Wl,--no-undefined" MITK_SHARED_LINKER_FLAGS) mitkFunctionCheckCompilerFlags("-Wl,--as-needed" MITK_SHARED_LINKER_FLAGS) endif() if(CMAKE_COMPILER_IS_GNUCXX) mitkFunctionCheckCAndCXXCompilerFlags("-fstack-protector-all" MITK_C_FLAGS MITK_CXX_FLAGS) set(MITK_CXX_FLAGS_RELEASE "-U_FORTIFY_SOURCES -D_FORTIFY_SOURCE=2 ${MITK_CXX_FLAGS_RELEASE}") endif() set(MITK_MODULE_LINKER_FLAGS ${MITK_SHARED_LINKER_FLAGS}) set(MITK_EXE_LINKER_FLAGS ${MITK_SHARED_LINKER_FLAGS}) #----------------------------------------------------------------------------- # MITK Packages #----------------------------------------------------------------------------- set(MITK_MODULES_PACKAGE_DEPENDS_DIR ${MITK_SOURCE_DIR}/CMake/PackageDepends) set(MODULES_PACKAGE_DEPENDS_DIRS ${MITK_MODULES_PACKAGE_DEPENDS_DIR}) foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) set(MITK_PACKAGE_DEPENDS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/CMake/PackageDepends") if(EXISTS "${MITK_PACKAGE_DEPENDS_EXTENSION_DIR}") list(APPEND MODULES_PACKAGE_DEPENDS_DIRS "${MITK_PACKAGE_DEPENDS_EXTENSION_DIR}") endif() endforeach() if(NOT MITK_USE_SYSTEM_Boost) set(Boost_NO_SYSTEM_PATHS 1) endif() set(Boost_USE_MULTITHREADED 1) set(Boost_USE_STATIC_LIBS 0) set(Boost_USE_STATIC_RUNTIME 0) set(Boost_ADDITIONAL_VERSIONS 1.74 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 # Config.cmake files pointed at by _DIR variables. # Otherwise, existing Find.cmake files could fail. if(DEFINED ${_package}_DIR) #we store the information because it will be overwritten by find_package #and would get lost for all EPs that use on Find.cmake instead of config #files. set(_temp_EP_${_package}_dir ${${_package}_DIR}) endif(DEFINED ${_package}_DIR) find_package(${_package} QUIET CONFIG) string(TOUPPER "${_package}" _package_uc) if(NOT (${_package}_FOUND OR ${_package_uc}_FOUND)) if(DEFINED _temp_EP_${_package}_dir) set(${_package}_DIR ${_temp_EP_${_package}_dir} CACHE PATH "externaly set dir of the package ${_package}" FORCE) endif(DEFINED _temp_EP_${_package}_dir) find_package(${_package} REQUIRED) endif() endif() endif() endforeach() # Ensure that the MITK CMake module path comes first set(CMAKE_MODULE_PATH ${MITK_CMAKE_DIR} ${CMAKE_MODULE_PATH} ) if(MITK_USE_DCMTK) - # Due to the preferred CONFIG mode in find_package calls above, - # the DCMTKConfig.cmake file is read, which does not provide useful - # package information. We explictly need MODULE mode to find DCMTK. if(${_dcmtk_dir_orig} MATCHES "${MITK_EXTERNAL_PROJECT_PREFIX}.*") # Help our FindDCMTK.cmake script find our super-build DCMTK set(DCMTK_DIR ${MITK_EXTERNAL_PROJECT_PREFIX}) else() # Use the original value set(DCMTK_DIR ${_dcmtk_dir_orig}) endif() - find_package(DCMTK REQUIRED MODULE) endif() if(MITK_USE_DCMQI) # Due to the preferred CONFIG mode in find_package calls above, # the DCMQIConfig.cmake file is read, which does not provide useful # package information. We explictly need MODULE mode to find DCMQI. # Help our FindDCMQI.cmake script find our super-build DCMQI set(DCMQI_DIR ${MITK_EXTERNAL_PROJECT_PREFIX}) find_package(DCMQI REQUIRED) endif() if(MITK_USE_OpenIGTLink) link_directories(${OpenIGTLink_LIBRARY_DIRS}) endif() if(MITK_USE_OpenCL) find_package(OpenCL REQUIRED) endif() if(MITK_USE_OpenMP) find_package(OpenMP REQUIRED COMPONENTS CXX) else() find_package(OpenMP QUIET COMPONENTS CXX) if(OpenMP_FOUND) set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE) elseif(APPLE AND OpenMP_libomp_LIBRARY AND NOT OpenMP_CXX_LIB_NAMES) set(OpenMP_CXX_LIB_NAMES libomp CACHE STRING "" FORCE) get_filename_component(openmp_lib_dir "${OpenMP_libomp_LIBRARY}" DIRECTORY) set(openmp_include_dir "${openmp_lib_dir}/../include") if(EXISTS "${openmp_include_dir}") get_filename_component(openmp_include_dir "${openmp_include_dir}" REALPATH) set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I${openmp_include_dir}" CACHE STRING "" FORCE) find_package(OpenMP QUIET COMPONENTS CXX) if(OpenMP_FOUND) set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE) endif() endif() endif() endif() # Qt support if(MITK_USE_Qt5) find_package(Qt5Core ${MITK_QT5_MINIMUM_VERSION} REQUIRED) # at least Core required get_target_property(_qmake_exec Qt5::qmake LOCATION) execute_process(COMMAND ${_qmake_exec} -query QT_INSTALL_BINS RESULT_VARIABLE _result OUTPUT_VARIABLE QT_BINARY_DIR ERROR_VARIABLE _error ) string(STRIP "${QT_BINARY_DIR}" QT_BINARY_DIR) if(_result OR NOT EXISTS "${QT_BINARY_DIR}") message(FATAL_ERROR "Could not determine Qt binary directory: ${_result} ${QT_BINARY_DIR} ${_error}") endif() find_program(QT_HELPGENERATOR_EXECUTABLE NAMES qhelpgenerator qhelpgenerator-qt5 qhelpgenerator5 PATHS ${QT_BINARY_DIR} NO_DEFAULT_PATH ) find_program(QT_COLLECTIONGENERATOR_EXECUTABLE NAMES qcollectiongenerator qcollectiongenerator-qt5 qcollectiongenerator5 PATHS ${QT_BINARY_DIR} NO_DEFAULT_PATH ) find_program(QT_ASSISTANT_EXECUTABLE NAMES assistant assistant-qt5 assistant5 PATHS ${QT_BINARY_DIR} NO_DEFAULT_PATH ) find_program(QT_XMLPATTERNS_EXECUTABLE NAMES xmlpatterns PATHS ${QT_BINARY_DIR} NO_DEFAULT_PATH ) mark_as_advanced(QT_HELPGENERATOR_EXECUTABLE QT_COLLECTIONGENERATOR_EXECUTABLE QT_ASSISTANT_EXECUTABLE QT_XMLPATTERNS_EXECUTABLE ) if(MITK_USE_BLUEBERRY) option(BLUEBERRY_USE_QT_HELP "Enable support for integrating plugin documentation into Qt Help" ${DOXYGEN_FOUND}) mark_as_advanced(BLUEBERRY_USE_QT_HELP) # Sanity checks for in-application BlueBerry plug-in help generation if(BLUEBERRY_USE_QT_HELP) set(_force_blueberry_use_qt_help_to_off 0) if(NOT DOXYGEN_FOUND) message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because Doxygen was not found.") set(_force_blueberry_use_qt_help_to_off 1) endif() if(DOXYGEN_FOUND AND DOXYGEN_VERSION VERSION_LESS 1.8.7) message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because Doxygen version 1.8.7 or newer not found.") set(_force_blueberry_use_qt_help_to_off 1) endif() if(NOT QT_HELPGENERATOR_EXECUTABLE) message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because QT_HELPGENERATOR_EXECUTABLE is empty.") set(_force_blueberry_use_qt_help_to_off 1) endif() if(NOT MITK_USE_Qt5) message("> Forcing BLUEBERRY_USE_QT_HELP to OFF because MITK_USE_Qt5 is OFF.") set(_force_blueberry_use_qt_help_to_off 1) endif() if(NOT QT_XMLPATTERNS_EXECUTABLE) message("You have enabled Qt Help support, but QT_XMLPATTERNS_EXECUTABLE is empty") set(_force_blueberry_use_qt_help_to_off 1) endif() if(_force_blueberry_use_qt_help_to_off) set(BLUEBERRY_USE_QT_HELP OFF CACHE BOOL "Enable support for integrating plugin documentation into Qt Help" FORCE) endif() endif() if(BLUEBERRY_QT_HELP_REQUIRED AND NOT BLUEBERRY_USE_QT_HELP) message(FATAL_ERROR "BLUEBERRY_USE_QT_HELP is required to be set to ON") endif() endif() endif() #----------------------------------------------------------------------------- # Testing #----------------------------------------------------------------------------- if(BUILD_TESTING) #[[ See T27701 # Initial cache for ProjectTemplate and PluginGenerator tests configure_file( CMake/mitkTestInitialCache.txt.in ${MITK_BINARY_DIR}/mitkTestInitialCache.txt @ONLY )]] # Configuration for the CMake-generated test driver set(CMAKE_TESTDRIVER_EXTRA_INCLUDES "#include ") set(CMAKE_TESTDRIVER_BEFORE_TESTMAIN " try {") set(CMAKE_TESTDRIVER_AFTER_TESTMAIN " } catch (const std::exception& e) { fprintf(stderr, \"%s\\n\", e.what()); return EXIT_FAILURE; } catch (...) { printf(\"Exception caught in the test driver\\n\"); return EXIT_FAILURE; }") set(MITK_TEST_OUTPUT_DIR "${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} ${MITK_MODULE_LINKER_FLAGS}") #----------------------------------------------------------------------------- # Add subdirectories #----------------------------------------------------------------------------- add_subdirectory(Utilities) set(MITK_WRAP_PYTHON_ENABLED OFF) if(MITK_USE_SWIG AND MITK_USE_Python3) find_package(SWIG 4.0.2 COMPONENTS python) if(SWIG_FOUND) option(MITK_WRAP_PYTHON "" ON) if(MITK_WRAP_PYTHON) set(MITK_WRAP_PYTHON_ENABLED ON) endif() else() message(SEND_ERROR "SWIG not found!") endif() endif() add_subdirectory(Modules) include("${CMAKE_CURRENT_SOURCE_DIR}/Modules/ModuleList.cmake") mitkFunctionWhitelistModules(MITK MITK_MODULES) set(MITK_ROOT_FOLDER_BACKUP "${MITK_ROOT_FOLDER}") foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) get_filename_component(MITK_ROOT_FOLDER "${MITK_EXTENSION_DIR}" NAME) set(MITK_MODULES_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Modules") if(EXISTS "${MITK_MODULES_EXTENSION_DIR}/ModuleList.cmake") set(MITK_MODULES "") include("${MITK_MODULES_EXTENSION_DIR}/ModuleList.cmake") foreach(mitk_module ${MITK_MODULES}) add_subdirectory("${MITK_MODULES_EXTENSION_DIR}/${mitk_module}" "Modules/${mitk_module}") endforeach() endif() set(MITK_MODULE_NAME_PREFIX ${MITK_DEFAULT_MODULE_NAME_PREFIX}) endforeach() set(MITK_ROOT_FOLDER "${MITK_ROOT_FOLDER_BACKUP}") add_subdirectory(Wrapping) set(MITK_DOXYGEN_OUTPUT_DIR "${PROJECT_BINARY_DIR}/Documentation/Doxygen" CACHE PATH "Output directory for doxygen generated documentation.") if(MITK_USE_BLUEBERRY) include("${CMAKE_CURRENT_SOURCE_DIR}/Plugins/PluginList.cmake") mitkFunctionWhitelistPlugins(MITK MITK_PLUGINS) set(mitk_plugins_fullpath "") foreach(mitk_plugin ${MITK_PLUGINS}) list(APPEND mitk_plugins_fullpath Plugins/${mitk_plugin}) endforeach() set(MITK_PLUGIN_REGEX_LIST "") foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) set(MITK_PLUGINS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Plugins") if(EXISTS "${MITK_PLUGINS_EXTENSION_DIR}/PluginList.cmake") set(MITK_PLUGINS "") include("${MITK_PLUGINS_EXTENSION_DIR}/PluginList.cmake") foreach(mitk_plugin ${MITK_PLUGINS}) list(APPEND mitk_plugins_fullpath "${MITK_PLUGINS_EXTENSION_DIR}/${mitk_plugin}") endforeach() endif() endforeach() if(EXISTS ${MITK_PRIVATE_MODULES}/PluginList.cmake) include(${MITK_PRIVATE_MODULES}/PluginList.cmake) foreach(mitk_plugin ${MITK_PRIVATE_PLUGINS}) list(APPEND mitk_plugins_fullpath ${MITK_PRIVATE_MODULES}/${mitk_plugin}) endforeach() endif() if(MITK_BUILD_EXAMPLES) include("${CMAKE_CURRENT_SOURCE_DIR}/Examples/Plugins/PluginList.cmake") set(mitk_example_plugins_fullpath ) foreach(mitk_example_plugin ${MITK_EXAMPLE_PLUGINS}) list(APPEND mitk_example_plugins_fullpath Examples/Plugins/${mitk_example_plugin}) list(APPEND mitk_plugins_fullpath Examples/Plugins/${mitk_example_plugin}) endforeach() endif() # Specify which plug-ins belong to this project macro(GetMyTargetLibraries all_target_libraries varname) set(re_ctkplugin_mitk "^org_mitk_[a-zA-Z0-9_]+$") set(re_ctkplugin_bb "^org_blueberry_[a-zA-Z0-9_]+$") set(_tmp_list) list(APPEND _tmp_list ${all_target_libraries}) ctkMacroListFilter(_tmp_list re_ctkplugin_mitk re_ctkplugin_bb MITK_PLUGIN_REGEX_LIST OUTPUT_VARIABLE ${varname}) endmacro() # Get infos about application directories and build options set(mitk_apps_fullpath "") foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS}) set(MITK_APPLICATIONS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Applications") if(EXISTS "${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake") set(MITK_APPS "") include("${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake") foreach(mitk_app ${MITK_APPS}) # extract option_name string(REPLACE "^^" "\\;" target_info ${mitk_app}) set(target_info_list ${target_info}) list(GET target_info_list 0 directory_name) list(GET target_info_list 1 option_name) if(${option_name}) list(APPEND mitk_apps_fullpath "${MITK_APPLICATIONS_EXTENSION_DIR}/${directory_name}^^${option_name}") endif() endforeach() endif() endforeach() if (mitk_plugins_fullpath) ctkMacroSetupPlugins(${mitk_plugins_fullpath} BUILD_OPTION_PREFIX MITK_BUILD_ APPS ${mitk_apps_fullpath} BUILD_ALL ${MITK_BUILD_ALL_PLUGINS} COMPACT_OPTIONS) endif() set(MITK_PLUGIN_USE_FILE "${MITK_BINARY_DIR}/MitkPluginUseFile.cmake") if(${PROJECT_NAME}_PLUGIN_LIBRARIES) ctkFunctionGeneratePluginUseFile(${MITK_PLUGIN_USE_FILE}) else() file(REMOVE ${MITK_PLUGIN_USE_FILE}) set(MITK_PLUGIN_USE_FILE ) endif() endif() #----------------------------------------------------------------------------- # Documentation #----------------------------------------------------------------------------- if(DOXYGEN_FOUND) add_subdirectory(Documentation) endif() #----------------------------------------------------------------------------- # Installation #----------------------------------------------------------------------------- # set MITK cpack variables # These are the default variables, which can be overwritten ( see below ) include(mitkSetupCPack) set(use_default_config ON) set(ALL_MITK_APPS "") set(activated_apps_no 0) foreach(MITK_EXTENSION_DIR ${MITK_DIR_PLUS_EXTENSION_DIRS}) set(MITK_APPLICATIONS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Applications") if(EXISTS "${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake") set(MITK_APPS "") include("${MITK_APPLICATIONS_EXTENSION_DIR}/AppList.cmake") foreach(mitk_app ${MITK_APPS}) string(REPLACE "^^" "\\;" target_info ${mitk_app}) set(target_info_list ${target_info}) list(GET target_info_list 0 directory_name) list(GET target_info_list 1 option_name) list(GET target_info_list 2 executable_name) list(APPEND ALL_MITK_APPS "${MITK_EXTENSION_DIR}/Applications/${directory_name}^^${option_name}^^${executable_name}") if(${option_name} OR MITK_BUILD_ALL_APPS) MATH(EXPR activated_apps_no "${activated_apps_no} + 1") endif() endforeach() endif() endforeach() list(LENGTH ALL_MITK_APPS app_count) if(app_count EQUAL 1 AND (activated_apps_no EQUAL 1 OR MITK_BUILD_ALL_APPS)) # Corner case if there is only one app in total set(use_project_cpack ON) elseif(activated_apps_no EQUAL 1 AND NOT MITK_BUILD_ALL_APPS) # Only one app is enabled (no "build all" flag set) set(use_project_cpack ON) else() # Less or more then one app is enabled set(use_project_cpack OFF) endif() foreach(mitk_app ${ALL_MITK_APPS}) # extract target_dir and option_name string(REPLACE "^^" "\\;" target_info ${mitk_app}) set(target_info_list ${target_info}) list(GET target_info_list 0 target_dir) list(GET target_info_list 1 option_name) list(GET target_info_list 2 executable_name) # check if the application is enabled if(${option_name} OR MITK_BUILD_ALL_APPS) # check whether application specific configuration files will be used if(use_project_cpack) # use files if they exist if(EXISTS "${target_dir}/CPackOptions.cmake") include("${target_dir}/CPackOptions.cmake") endif() if(EXISTS "${target_dir}/CPackConfig.cmake.in") set(CPACK_PROJECT_CONFIG_FILE "${target_dir}/CPackConfig.cmake") configure_file(${target_dir}/CPackConfig.cmake.in ${CPACK_PROJECT_CONFIG_FILE} @ONLY) set(use_default_config OFF) endif() endif() # add link to the list list(APPEND CPACK_CREATE_DESKTOP_LINKS "${executable_name}") endif() endforeach() # if no application specific configuration file was used, use default if(use_default_config) configure_file(${MITK_SOURCE_DIR}/MITKCPackOptions.cmake.in ${MITK_BINARY_DIR}/MITKCPackOptions.cmake @ONLY) set(CPACK_PROJECT_CONFIG_FILE "${MITK_BINARY_DIR}/MITKCPackOptions.cmake") endif() # include CPack model once all variables are set include(CPack) # Additional installation rules include(mitkInstallRules) #----------------------------------------------------------------------------- # Last configuration steps #----------------------------------------------------------------------------- # ---------------- Export targets ----------------- set(MITK_EXPORTS_FILE "${MITK_BINARY_DIR}/MitkExports.cmake") file(REMOVE ${MITK_EXPORTS_FILE}) set(targets_to_export) get_property(module_targets GLOBAL PROPERTY MITK_MODULE_TARGETS) if(module_targets) list(APPEND targets_to_export ${module_targets}) endif() if(MITK_USE_BLUEBERRY) if(MITK_PLUGIN_LIBRARIES) list(APPEND targets_to_export ${MITK_PLUGIN_LIBRARIES}) endif() endif() export(TARGETS ${targets_to_export} APPEND FILE ${MITK_EXPORTS_FILE}) set(MITK_EXPORTED_TARGET_PROPERTIES ) foreach(target_to_export ${targets_to_export}) get_target_property(autoload_targets ${target_to_export} MITK_AUTOLOAD_TARGETS) if(autoload_targets) set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES} set_target_properties(${target_to_export} PROPERTIES MITK_AUTOLOAD_TARGETS \"${autoload_targets}\")") endif() get_target_property(autoload_dir ${target_to_export} MITK_AUTOLOAD_DIRECTORY) if(autoload_dir) set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES} set_target_properties(${target_to_export} PROPERTIES MITK_AUTOLOAD_DIRECTORY \"${autoload_dir}\")") endif() get_target_property(deprecated_module ${target_to_export} MITK_MODULE_DEPRECATED_SINCE) if(deprecated_module) set(MITK_EXPORTED_TARGET_PROPERTIES "${MITK_EXPORTED_TARGET_PROPERTIES} set_target_properties(${target_to_export} PROPERTIES MITK_MODULE_DEPRECATED_SINCE \"${deprecated_module}\")") endif() endforeach() # ---------------- External projects ----------------- get_property(MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS_CONFIG GLOBAL PROPERTY MITK_ADDITIONAL_LIBRARY_SEARCH_PATHS) set(MITK_CONFIG_EXTERNAL_PROJECTS ) #string(REPLACE "^^" ";" _mitk_external_projects ${MITK_EXTERNAL_PROJECTS}) foreach(ep ${MITK_EXTERNAL_PROJECTS}) get_property(_components GLOBAL PROPERTY MITK_${ep}_COMPONENTS) set(MITK_CONFIG_EXTERNAL_PROJECTS "${MITK_CONFIG_EXTERNAL_PROJECTS} set(MITK_USE_${ep} ${MITK_USE_${ep}}) set(MITK_${ep}_DIR \"${${ep}_DIR}\") set(MITK_${ep}_COMPONENTS ${_components}) ") endforeach() foreach(ep ${MITK_EXTERNAL_PROJECTS}) get_property(_package GLOBAL PROPERTY MITK_${ep}_PACKAGE) get_property(_components GLOBAL PROPERTY MITK_${ep}_COMPONENTS) if(_components) set(_components_arg COMPONENTS \${_components}) else() set(_components_arg) endif() if(_package) set(MITK_CONFIG_EXTERNAL_PROJECTS "${MITK_CONFIG_EXTERNAL_PROJECTS} if(MITK_USE_${ep}) set(${ep}_DIR \${MITK_${ep}_DIR}) if(MITK_${ep}_COMPONENTS) mitkMacroFindDependency(${_package} COMPONENTS \${MITK_${ep}_COMPONENTS}) else() mitkMacroFindDependency(${_package}) endif() endif()") endif() endforeach() # ---------------- Tools ----------------- configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactory.cpp.in ${MITK_BINARY_DIR}/ToolExtensionITKFactory.cpp.in COPYONLY) configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactoryLoader.cpp.in ${MITK_BINARY_DIR}/ToolExtensionITKFactoryLoader.cpp.in COPYONLY) configure_file(${MITK_SOURCE_DIR}/CMake/ToolGUIExtensionITKFactory.cpp.in ${MITK_BINARY_DIR}/ToolGUIExtensionITKFactory.cpp.in COPYONLY) # ---------------- Configure files ----------------- configure_file(mitkVersion.h.in ${MITK_BINARY_DIR}/mitkVersion.h) configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h) set(IPFUNC_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/ipFunc) set(UTILITIES_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities) configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h) configure_file(MITKConfig.cmake.in ${MITK_BINARY_DIR}/MITKConfig.cmake @ONLY) write_basic_config_version_file(${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake VERSION ${MITK_VERSION_STRING} COMPATIBILITY AnyNewerVersion) #----------------------------------------------------------------------------- # MITK Applications #----------------------------------------------------------------------------- # This must come after MITKConfig.h was generated, since applications # might do a find_package(MITK REQUIRED). add_subdirectory(Applications) if(MSVC AND TARGET MitkWorkbench) set_directory_properties(PROPERTIES VS_STARTUP_PROJECT MitkWorkbench) endif() foreach(MITK_EXTENSION_DIR ${MITK_ABSOLUTE_EXTENSION_DIRS}) set(MITK_APPLICATIONS_EXTENSION_DIR "${MITK_EXTENSION_DIR}/Applications") if(EXISTS "${MITK_APPLICATIONS_EXTENSION_DIR}/CMakeLists.txt") add_subdirectory("${MITK_APPLICATIONS_EXTENSION_DIR}" "Applications") endif() endforeach() #----------------------------------------------------------------------------- # MITK Examples #----------------------------------------------------------------------------- if(MITK_BUILD_EXAMPLES) # This must come after MITKConfig.h was generated, since applications # might do a find_package(MITK REQUIRED). add_subdirectory(Examples) endif() #----------------------------------------------------------------------------- # Print configuration summary #----------------------------------------------------------------------------- message("\n\n") feature_summary( DESCRIPTION "------- FEATURE SUMMARY FOR ${PROJECT_NAME} -------" WHAT ALL ) diff --git a/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox b/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox index 26f23d216f..2b948a8ba5 100644 --- a/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox +++ b/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/BuildInstructions.dox @@ -1,214 +1,236 @@ /** \page BuildInstructionsPage Build Instructions \tableofcontents \section BuildInstructions_Introduction Introduction The CMake-based build system of MITK supports a "superbuild" process, meaning that it will download, configure, and build all required third-party libraries (except Qt) automatically. These instructions will show you how to use the MITK superbuild. \note This page explains explicitly how to build MITK itself. If you want to create your own project based on MITK, the process described below is completely automated. Please see \ref HowToNewProject. For more advanced users, the last sections explains how to inject custom build libraries into the superbuild process. \section BuildInstructions_Prerequisites Prerequisites You need: -# Git (there are also numerous third-party graphical clients available). We recommend using Git, but see below for a way how to get the current source code without using it. -# CMake (version \minimumCMakeVersion or higher) -# Qt \minimumQt5Version if you plan to develop Qt-based applications -# If you are using macOS you need an XCode installation and the Command Line Tools as it provides the neccessary compilers and SDKs +To build MITK on Linux, install the following packages, e. g. with APT: + +\code{.unparsed} +sudo apt install build-essential doxygen git graphviz libfreetype6-dev libglu1-mesa-dev libssl-dev libtiff5-dev libwrap0-dev libxcomposite1 libxcursor1 libxi-dev libxkbcommon-x11-0 libxt-dev mesa-common-dev +\endcode + +For the optional and experimental (!) Python integration, install NumPy and SimpleITK v1.x, e. g.: + +\code{.unparsed} +sudo apt install python3-numpy python3-pip +pip3 install SimpleITK==1.* +\endcode + \section BuildInstructions_Qt A note about Qt As we do not provide Qt in the MITK superbuild you need to install Qt manually. The Qt Company provides online installers for all supported platforms. +We highly recommend to install Qt to the default location of the installer as it will allow MITK to automatically find Qt without any further action needed. + +Make sure to also select the following required components: + - QtWebEngine + - QtScript + +On Windows, the Qt installer offers a welcome and straight forward way to install OpenSSL. +You find it under the Tools node. + \section BuildInstructions_Get_Source Get a source tree Since MITK is under active development we recommend to use Git to check out the latest stable release from the homepage. If you decide to use the most current nightly release, make sure to get a stable tree: Check the MITK dashboard before checking out. If the build tree is not clean, you can specify an older revision for the checkout or get a stable tar ball from www.mitk.org. To clone MITK's current Git repository do: \code git clone https://phabricator.mitk.org/source/mitk.git MITK \endcode \section BuildInstructions_Build_With_CMake Build MITK with CMake Create a new directory for the superbuild binary tree, change to it and call CMake: In the shell (assuming your current directory is the same as the one where you issued the git clone command): \code mkdir MITK-superbuild cd MITK-superbuild ccmake ../MITK \endcode If you use Windows or prefer to use the CMake GUI, start the CMake GUI and enter the location of the source tree and binary tree, choose a suitable generator and configure the project. CMake will present you a couple of options, these are the most important ones: - CMAKE_PREFIX_PATH The path to your Qt installation, e.g., C:/Qt/5.12.9/msvc2017_64 or /home/user/Qt/5.12.9/gcc_64 - MITK_USE_BLUEBERRY Build the BlueBerry application framework - MITK_USE_Boost_LIBRARIES If you need binary Boost libraries, specify them here. - MITK_USE_OpenCV Build MITK code which depends on OpenCV (this will download and build OpenCV 2.4) - MITK_USE_Python3 Enables Python wrapping in MITK. This will also configure ITK, VTK, and OpenCV (if enabled) to build Python wrappers. - MITK_USE_Qt5 Build MITK code which depends on Qt 5 If you are satisfied with the configuration of your MITK superbuild, generate the project files with CMake by pressing "Generate". Linux and macOS users usually just enter "make" (optionally supplying the number threads to be used for a parallel build): \code make -j6 \endcode Windows users using Visual Studio can open the generated MITK-superbuild.sln solution file in the MITK-superbuild directory and start the build by building the BUILD_ALL project. \section BuildInstructions_Customize Customize your MITK superbuild The MITK superbuild configures MITK as well as all external libraries. The build directories of these libraries, and of MITK itself are located inside the MITK-superbuild directory. For example, the directory layout may look like: \code MITK-superbuild |- ep "external projects" |-bin |-lib |-include |-src |- MITK-build \endcode To change the configuration of the MITK build itself, choose the MITK-build directory as the binary directory in the CMake GUI (not the MITK-superbuild directory). After generating the project files, build the MITK project by either issuing "make" in the MITK-build directory (Linux, macOS), or by opening MITK-build/MITK.sln (Windows). You may also change the configuration of any project configured via the superbuild process. Make sure to also build the changed project and also the projects which depend on it. \section BuildInstructions_Running Running Applications On Linux, just execute the application you want to run. MITK executables are located in MITK-superbuild/MITK-build/bin On Windows, the PATH environment variable must contain the directories containing the third-party libraries. This is automatically done from Visual Studio. For running the applications directly use the generated batch files in the MITK-superbuild/MITK-build/bin. \section BuildInstructions_Documentation Documentation If you have the Doxygen documentation tool installed, you get a new project (Visual Studio) or "make" target named "doc". You can build this to generate the HTML documentation of MITK in the Documentation/Doxygen directory of your MITK-build binary tree or in the MITK_DOXYGEN_OUTPUT_DIR CMake variable (if specified). \section BuildInstructions_Extending Extend MITK on your own (using the application framework BlueBerry) Please see \ref NewPluginPage \section BuildInstructions_As_Toolkit Use MITK in your own project (as a toolkit) To use MITK in your external project, add the CMake command find_package(MITK REQUIRED) to your CMakeLists.txt and make use of the CMake macros mitk_create_module() and mitk_create_executable() provided by MITK. Here is a very basic example CMakeLists.txt including MITK as a project: \code cmake_minimum_required(VERSION 3.10 FATAL_ERROR) project(MyProject) -find_package(MITK 2018.04.02 REQUIRED) +find_package(MITK 2021.02 REQUIRED) add_executable(MyApp main.cpp) target_link_libraries(MyApp MitkCore) \endcode with the main.ccp being \code #include #include int main() { MITK_INFO << "Hello world!"; return 0; } \endcode \section BuildInstructions_Advanced_Customization Superbuild customization You can inject pre-build third-party libraries into the MITK superbuild by setting certain CMake variables before the first configure step. MITK will then use these third-party libraries instead of downloading and building them by itself. Note that you must take care of configuring those libraries with all options MITK requires. The variables listed below are provided for injecting third-party libraries. Their occurrence in the CMake GUI or in ccmake may depend on specific MITK_USE_* options set to ON. You may also use the variable names below without the EXTERNAL_ prefix, for example when providing their values on a command line call to CMake. - EXTERNAL_BOOST_ROOT Set this variable to your custom Boost installation - EXTERNAL_CTK_DIR Set this variable to your CTK binary tree (the directory containing the CTKConfig.cmake file) - EXTERNAL_CableSwig_DIR Set this variable to your CableSwig binary tree for Python wrapping (the directory containing the CableSwigConfig.cmake file) - EXTERNAL_DCMTK_DIR Set this variable to your DCMTK binary tree (the directory containing the DCMTKConfig.cmake file) - EXTERNAL_GDCM_DIR Set this variable to your GDCM binary tree (the directory containing the GDCMConfig.cmake file) - EXTERNAL_ITK_DIR Set this variable to your ITK binary tree (the directory containing the ITKConfig.cmake file) - EXTERNAL_OpenCV_DIR Set this variable to your OpenCV binary tree (the directory containing the OpenCVConfig.cmake file) - EXTERNAL_VTK_DIR Set this variable to your VTK binary tree (the directory containing the VTKConfig.cmake file) To set CMake options before the first configure step is invoked, supply them on the command line, i.e. \code ccmake -DITK_DIR:PATH=/opt/ITK-release ../MITK \endcode */ diff --git a/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/SupportedPlatforms.md b/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/SupportedPlatforms.md index 84e8914622..596dadc9b5 100644 --- a/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/SupportedPlatforms.md +++ b/Documentation/Doxygen/3-DeveloperManual/Starting/SettingUpMITK/SupportedPlatforms.md @@ -1,48 +1,49 @@ Supported Platforms {#SupportedPlatformsPage} =================== MITK is a cross-platform framework that is available for the following platforms: - Windows - Linux - macOS Supported Platforms Details --------------------------- The MITK team provides support for the most frequently used platforms and continuously runs testing procedures to ensure compatibility. Due to the large amount of possible combinations of operating systems and compiler versions, we divide platform support into two test categories: Tier 1 and Tier 2. Although MITK may be built on a broader range of platform-compiler combinations, only a subset of these are actively supported by the MITK development team. Tier 1 Platforms ---------------- All Tier 1 platforms are continuously tested by our unit test suite and other internal testing procedures. Errors or bugs discovered in these platforms are prioritized and corrected as soon as possible. | Platform | Compilers | ----------------------------------- | -------------------------------------------------- | Microsoft Windows 10 (x64) | Visual Studio 2019 (latest update) | Linux Ubuntu 20.04 (x64) | Default GCC version | Linux Ubuntu 18.04 (x64) | Default GCC version +| Apple macOS 10.14 "Mojave" | Default Apple Clang version Tier 2 Platforms ---------------- Tier 2 platforms may or may not be tested on a regular basis. Some Tier 2 platforms are used by individual members of the MITK development team on a daily basis and some only receive occasional testing. While we strive to support these platforms, MITK users should note that errors may be present in released versions as well as in the current master branch. | Platform | Compilers | ----------------------------------- | -------------------------------------------------- | Microsoft Windows 10 (x64) | Visual Studio 2017 (latest update) | Apple macOS 10.15 "Catalina" | Default Apple Clang version -| Apple macOS 10.14 "Mojave" | Default Apple Clang version +| Apple macOS 11.1 "Big Sur" (x64) | Default Apple Clang version All platforms not listed above are not officially supported by the MITK team. However, we will happily accept contributions to improve support for other platforms. diff --git a/Documentation/Doxygen/4-API/Pages.dox b/Documentation/Doxygen/4-API/Pages.dox index dae4e22610..3cb9ec9d13 100644 --- a/Documentation/Doxygen/4-API/Pages.dox +++ b/Documentation/Doxygen/4-API/Pages.dox @@ -1,36 +1,39 @@ /** \defgroup MITKDeprecatedAPI Deprecated \page deprecatedSince2012_09 Deprecated as of 2012.09 \ingroup MITKDeprecatedAPI \page deprecatedSince2013_03 Deprecated as of 2013.03 \ingroup MITKDeprecatedAPI \page deprecatedSince2013_06 Deprecated as of 2013.06 \ingroup MITKDeprecatedAPI \page deprecatedSince2013_09 Deprecated as of 2013.09 \ingroup MITKDeprecatedAPI \page deprecatedSince2014_03 Deprecated as of 2014.03 \ingroup MITKDeprecatedAPI \page deprecatedSince2014_10 Deprecated as of 2014.10 \ingroup MITKDeprecatedAPI \page deprecatedSince2015_05 Deprecated as of 2015.05 \ingroup MITKDeprecatedAPI \page deprecatedSince2016_03 Deprecated as of 2016.03 \ingroup MITKDeprecatedAPI \page deprecatedSince2016_11 Deprecated as of 2016.11 \ingroup MITKDeprecatedAPI \page deprecatedSince2018_04 Deprecated as of 2018.04 \ingroup MITKDeprecatedAPI +\page deprecatedSince2021_02 Deprecated as of 2021.02 +\ingroup MITKDeprecatedAPI + */ diff --git a/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExample.cpp b/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExample.cpp index de72b6f722..f1f35e83a3 100644 --- a/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExample.cpp +++ b/Examples/Plugins/org.mitk.example.gui.pcaexample/src/internal/PCAExample.cpp @@ -1,167 +1,167 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include // Qmitk #include "PCAExample.h" // Qt #include // mitk image #include const std::string PCAExample::VIEW_ID = "org.mitk.views.pcaexample"; void PCAExample::SetFocus() { m_Controls.buttonPerformImageProcessing->setFocus(); } void PCAExample::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(BtnPerfomPCAClicked())); //initialize point set widget and point set node mitk::DataNode::Pointer PointSetNode = mitk::DataNode::New(); PointSetNode->SetName("PCA Example Pointset"); mitk::PointSet::Pointer newPtSet = mitk::PointSet::New(); PointSetNode->SetData(newPtSet); m_Controls.m_pointSetWidget->SetPointSetNode(PointSetNode); this->GetDataStorage()->Add(PointSetNode); } PCAExample::PCAExample() { } PCAExample::~PCAExample() { //clean up mitk::DataNode::Pointer ptSetNode = m_Controls.m_pointSetWidget->GetPointSetNode(); m_Controls.m_pointSetWidget->SetPointSetNode(nullptr); this->GetDataStorage()->Remove(ptSetNode); this->GetDataStorage()->Remove(m_Axis1Node); this->GetDataStorage()->Remove(m_Axis2Node); this->GetDataStorage()->Remove(m_Axis3Node); } void PCAExample::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList &nodes) { // iterate all selected objects, adjust warning visibility foreach (mitk::DataNode::Pointer node, nodes) { if (node.IsNotNull() && dynamic_cast(node->GetData())) { m_Controls.buttonPerformImageProcessing->setEnabled(true); return; } } } void PCAExample::BtnPerfomPCAClicked() { std::vector eigenVectors; std::vector eigenValues; mitk::Vector3D mean; bool success = comutePCA(m_Controls.m_pointSetWidget->GetPointSet(), eigenVectors, eigenValues, mean); this->showEigenvectors(eigenVectors, eigenValues, mean); MITK_INFO << "PCA: " << success; } bool PCAExample::comutePCA(mitk::PointSet::Pointer input, std::vector &eigenVectors, std::vector &eigenValues, mitk::Vector3D &pointsMean) { //Step 1: Construct data matrix vnl_matrix dataMatrix(3, input->GetSize(), 0.0); int size = input->GetSize(); for (int i=0; iGetPoint(i)[0]; dataMatrix[1][i] = input->GetPoint(i)[1]; dataMatrix[2][i] = input->GetPoint(i)[2]; } //Step 2: Remove average for each row (Mittelwertbefreiung) mitk::Vector3D mean; for (int i = 0; i < size; i++) { mean += mitk::Vector3D(dataMatrix.get_column(i)); } mean /= size; for (int i = 0; i covMatrix = (1.0 / (size - 1.0)) * dataMatrix * dataMatrix.transpose(); //Step 4: Singular value composition vnl_svd svd(covMatrix); //Store results and print them to the console MITK_INFO << "DataMatrix: " << "\n" << dataMatrix; MITK_INFO << "CovMatrix: " << "\n" << covMatrix; for (int i = 0; i < 3; i++) { eigenVectors.push_back(svd.U().get_column(i)); eigenValues.push_back(sqrt(svd.W(i))); MITK_INFO << "Eigenvector " << i << ": " << eigenVectors.at(i); MITK_INFO << "Eigenvalue " << i << ": " << eigenValues.at(i); } //Compute center of points for (int i = 0; i < size; i++) { pointsMean += input->GetPoint(i).GetVectorFromOrigin(); } pointsMean /= size; return true; } void PCAExample::showEigenvectors(std::vector eigenVectors, std::vector eigenValues, mitk::Vector3D center) { m_Axis1Node = mitk::DataNode::New(); m_Axis1Node->SetName("Eigenvector 1"); mitk::PointSet::Pointer axis1 = mitk::PointSet::New(); - axis1->InsertPoint(0, center); - axis1->InsertPoint(1, (center + eigenVectors.at(0)*eigenValues.at(0))); + axis1->InsertPoint(0, mitk::Point3D(center)); + axis1->InsertPoint(1, mitk::Point3D(center + eigenVectors.at(0)*eigenValues.at(0))); m_Axis1Node->SetData(axis1); m_Axis1Node->SetBoolProperty("show contour", true); m_Axis1Node->SetColor(1, 0, 0); this->GetDataStorage()->Add(m_Axis1Node); m_Axis2Node = mitk::DataNode::New(); m_Axis2Node->SetName("Eigenvector 2"); mitk::PointSet::Pointer axis2 = mitk::PointSet::New(); - axis2->InsertPoint(0, center); - axis2->InsertPoint(1, (center + eigenVectors.at(1)*eigenValues.at(1))); + axis2->InsertPoint(0, mitk::Point3D(center)); + axis2->InsertPoint(1, mitk::Point3D(center + eigenVectors.at(1)*eigenValues.at(1))); m_Axis2Node->SetData(axis2); m_Axis2Node->SetBoolProperty("show contour", true); m_Axis2Node->SetColor(1, 0, 0); this->GetDataStorage()->Add(m_Axis2Node); m_Axis3Node = mitk::DataNode::New(); m_Axis3Node->SetName("Eigenvector 3"); mitk::PointSet::Pointer axis3 = mitk::PointSet::New(); - axis3->InsertPoint(0, center); - axis3->InsertPoint(1, (center + eigenVectors.at(2)*eigenValues.at(2))); + axis3->InsertPoint(0, mitk::Point3D(center)); + axis3->InsertPoint(1, mitk::Point3D(center + eigenVectors.at(2)*eigenValues.at(2))); m_Axis3Node->SetData(axis3); m_Axis3Node->SetBoolProperty("show contour", true); m_Axis3Node->SetColor(1, 0, 0); this->GetDataStorage()->Add(m_Axis3Node); } diff --git a/LICENSE b/LICENSE index d68700c4ab..4cd2f3576a 100644 --- a/LICENSE +++ b/LICENSE @@ -1,29 +1,29 @@ BSD 3-Clause License -Copyright (c) 2003-2019, German Cancer Research Center (DKFZ) +Copyright (c) 2003-2021, German Cancer Research Center (DKFZ) All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/Modules/AlgorithmsExt/src/mitkCropTimestepsImageFilter.cpp b/Modules/AlgorithmsExt/src/mitkCropTimestepsImageFilter.cpp index a4caf11eff..d1c2edf31d 100644 --- a/Modules/AlgorithmsExt/src/mitkCropTimestepsImageFilter.cpp +++ b/Modules/AlgorithmsExt/src/mitkCropTimestepsImageFilter.cpp @@ -1,147 +1,158 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkCropTimestepsImageFilter.h" #include #include #include #include void mitk::CropTimestepsImageFilter::VerifyInputImage(const mitk::Image* inputImage) const { if (!inputImage->IsInitialized()) mitkThrow() << "Input image is not initialized."; if (!inputImage->IsVolumeSet()) mitkThrow() << "Input image volume is not set."; auto geometry = inputImage->GetGeometry(); if (nullptr == geometry || !geometry->IsValid()) mitkThrow() << "Input image has invalid geometry."; if (inputImage->GetDimension() != 4) { mitkThrow() << "CropTimestepsImageFilter only works with 2D+t and 3D+t images."; } if (inputImage->GetTimeSteps() ==1) { mitkThrow() << "Input image has only one timestep."; } if (!geometry->GetImageGeometry()) mitkThrow() << "Geometry of input image is not an image geometry."; } void mitk::CropTimestepsImageFilter::GenerateOutputInformation() { Image::ConstPointer input = this->GetInput(); Image::Pointer output = this->GetOutput(); if (m_LowerBoundaryTimestep > m_UpperBoundaryTimestep) { mitkThrow() << "lower timestep is larger than upper timestep."; } if (m_UpperBoundaryTimestep == std::numeric_limits::max()) { m_UpperBoundaryTimestep = input->GetTimeSteps(); } else if (m_UpperBoundaryTimestep > input->GetTimeSteps()) { m_UpperBoundaryTimestep = input->GetTimeSteps(); MITK_WARN << "upper boundary timestep set to " << m_UpperBoundaryTimestep; } m_DesiredRegion = ComputeDesiredRegion(); unsigned int dimension = input->GetDimension(); auto dimensions = new unsigned int[dimension]; itk2vtk(m_DesiredRegion.GetSize(), dimensions); if (dimension > 3) memcpy(dimensions + 3, input->GetDimensions() + 3, (dimension - 3) * sizeof(unsigned int)); dimensions[3] = m_UpperBoundaryTimestep - m_LowerBoundaryTimestep; // create basic slicedGeometry that will be initialized below output->Initialize(mitk::PixelType(input->GetPixelType()), dimension, dimensions); delete[] dimensions; auto newTimeGeometry = AdaptTimeGeometry(input->GetTimeGeometry(), m_LowerBoundaryTimestep, m_UpperBoundaryTimestep); output->SetTimeGeometry(newTimeGeometry); output->SetPropertyList(input->GetPropertyList()); } mitk::SlicedData::RegionType mitk::CropTimestepsImageFilter::ComputeDesiredRegion() const { auto desiredRegion = this->GetInput()->GetLargestPossibleRegion(); auto index = desiredRegion.GetIndex(); auto size = desiredRegion.GetSize(); unsigned int timeDimension = 3; index[timeDimension] = m_LowerBoundaryTimestep; size[timeDimension] = m_UpperBoundaryTimestep - m_LowerBoundaryTimestep; desiredRegion.SetIndex(index); desiredRegion.SetSize(size); return desiredRegion; } mitk::TimeGeometry::Pointer mitk::CropTimestepsImageFilter::AdaptTimeGeometry(mitk::TimeGeometry::ConstPointer sourceGeometry, unsigned int startTimestep, unsigned int endTimestep) const { auto newTimeGeometry = mitk::ArbitraryTimeGeometry::New(); newTimeGeometry->ClearAllGeometries(); - for (unsigned int timestep = startTimestep; timestep < endTimestep; timestep++) { + for (unsigned int timestep = startTimestep; timestep < endTimestep; timestep++) + { auto geometryForTimePoint = sourceGeometry->GetGeometryForTimeStep(timestep); - newTimeGeometry->AppendNewTimeStep(geometryForTimePoint, - sourceGeometry->GetMinimumTimePoint(timestep), - sourceGeometry->GetMaximumTimePoint(timestep)); + auto minTP = sourceGeometry->GetMinimumTimePoint(timestep); + auto maxTP = sourceGeometry->GetMaximumTimePoint(timestep); + /////////////////////////////////////// + // Workarround T27883. See https://phabricator.mitk.org/T27883#219473 for more details. + // This workarround should be removed as soon as T28262 is solved! + if (timestep + 1 == sourceGeometry->CountTimeSteps() && minTP == maxTP) + { + maxTP = minTP + 1.; + } + // End of workarround for T27883 + ////////////////////////////////////// + + newTimeGeometry->AppendNewTimeStepClone(geometryForTimePoint, minTP, maxTP); } return newTimeGeometry.GetPointer(); } void mitk::CropTimestepsImageFilter::GenerateData() { const auto* inputImage = this->GetInput(); mitk::Image::Pointer output = this->GetOutput(); if ((output->IsInitialized() == false)) return; auto timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(inputImage); unsigned int timeStart = m_DesiredRegion.GetIndex(3); unsigned int timeEnd = timeStart + m_DesiredRegion.GetSize(3); for (unsigned int timestep = timeStart; timestep < timeEnd; ++timestep) { timeSelector->SetTimeNr(timestep); timeSelector->UpdateLargestPossibleRegion(); mitk::ImageReadAccessor imageAccessorWithOneTimestep(timeSelector->GetOutput()); output->SetVolume(imageAccessorWithOneTimestep.GetData(), timestep-timeStart); } } void mitk::CropTimestepsImageFilter::SetInput(const InputImageType* image) { if (this->GetInput() == image) return; Superclass::SetInput(image); } void mitk::CropTimestepsImageFilter::SetInput(unsigned int index, const InputImageType* image) { if (0 != index) mitkThrow() << "Input index " << index << " is invalid."; this->SetInput(image); } void mitk::CropTimestepsImageFilter::VerifyInputInformation() { Superclass::VerifyInputInformation(); VerifyInputImage(this->GetInput()); } diff --git a/Modules/AppUtil/src/mitkBaseApplication.cpp b/Modules/AppUtil/src/mitkBaseApplication.cpp index 273c1c2521..e41a40fe79 100644 --- a/Modules/AppUtil/src/mitkBaseApplication.cpp +++ b/Modules/AppUtil/src/mitkBaseApplication.cpp @@ -1,875 +1,875 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace { void outputQtMessage(QtMsgType type, const QMessageLogContext&, const QString& msg) { auto message = msg.toStdString(); switch (type) { case QtDebugMsg: MITK_DEBUG << message; break; case QtInfoMsg: MITK_INFO << message; break; case QtWarningMsg: MITK_WARN << message; break; case QtCriticalMsg: MITK_ERROR << message; break; case QtFatalMsg: MITK_ERROR << message; abort(); default: MITK_INFO << message; break; } } } namespace mitk { const QString BaseApplication::ARG_APPLICATION = "BlueBerry.application"; const QString BaseApplication::ARG_CLEAN = "BlueBerry.clean"; const QString BaseApplication::ARG_CONSOLELOG = "BlueBerry.consoleLog"; const QString BaseApplication::ARG_DEBUG = "BlueBerry.debug"; const QString BaseApplication::ARG_FORCE_PLUGIN_INSTALL = "BlueBerry.forcePlugins"; const QString BaseApplication::ARG_HOME = "BlueBerry.home"; const QString BaseApplication::ARG_NEWINSTANCE = "BlueBerry.newInstance"; const QString BaseApplication::ARG_NO_LAZY_REGISTRY_CACHE_LOADING = "BlueBerry.noLazyRegistryCacheLoading"; const QString BaseApplication::ARG_NO_REGISTRY_CACHE = "BlueBerry.noRegistryCache"; const QString BaseApplication::ARG_PLUGIN_CACHE = "BlueBerry.plugin_cache_dir"; const QString BaseApplication::ARG_PLUGIN_DIRS = "BlueBerry.plugin_dirs"; const QString BaseApplication::ARG_PRELOAD_LIBRARY = "BlueBerry.preloadLibrary"; const QString BaseApplication::ARG_PRODUCT = "BlueBerry.product"; const QString BaseApplication::ARG_PROVISIONING = "BlueBerry.provisioning"; const QString BaseApplication::ARG_REGISTRY_MULTI_LANGUAGE = "BlueBerry.registryMultiLanguage"; const QString BaseApplication::ARG_SPLASH_IMAGE = "BlueBerry.splashscreen"; const QString BaseApplication::ARG_STORAGE_DIR = "BlueBerry.storageDir"; const QString BaseApplication::ARG_XARGS = "xargs"; const QString BaseApplication::ARG_LOG_QT_MESSAGES = "Qt.logMessages"; const QString BaseApplication::PROP_APPLICATION = "blueberry.application"; const QString BaseApplication::PROP_FORCE_PLUGIN_INSTALL = BaseApplication::ARG_FORCE_PLUGIN_INSTALL; const QString BaseApplication::PROP_NEWINSTANCE = BaseApplication::ARG_NEWINSTANCE; const QString BaseApplication::PROP_NO_LAZY_REGISTRY_CACHE_LOADING = BaseApplication::ARG_NO_LAZY_REGISTRY_CACHE_LOADING; const QString BaseApplication::PROP_NO_REGISTRY_CACHE = BaseApplication::ARG_NO_REGISTRY_CACHE; const QString BaseApplication::PROP_PRODUCT = "blueberry.product"; const QString BaseApplication::PROP_REGISTRY_MULTI_LANGUAGE = BaseApplication::ARG_REGISTRY_MULTI_LANGUAGE; class SplashCloserCallback : public QRunnable { public: SplashCloserCallback(QSplashScreen* splashscreen) : m_Splashscreen(splashscreen) { } void run() override { this->m_Splashscreen->close(); } private: QSplashScreen *m_Splashscreen; // Owned by BaseApplication::Impl }; struct BaseApplication::Impl { ctkProperties m_FWProps; QCoreApplication *m_QApp; int m_Argc; char **m_Argv; #ifdef Q_OS_MAC std::vector m_Argv_macOS; #endif QString m_AppName; QString m_OrgaName; QString m_OrgaDomain; bool m_SingleMode; bool m_SafeMode; QSplashScreen *m_Splashscreen; SplashCloserCallback *m_SplashscreenClosingCallback; bool m_LogQtMessages; QStringList m_PreloadLibs; QString m_ProvFile; Impl(int argc, char **argv) : m_Argc(argc), m_Argv(argv), #ifdef Q_OS_MAC m_Argv_macOS(), #endif m_SingleMode(false), m_SafeMode(true), m_Splashscreen(nullptr), m_SplashscreenClosingCallback(nullptr), m_LogQtMessages(false) { #ifdef Q_OS_MAC /* On macOS the process serial number is passed as an command line argument (-psn_) in certain circumstances. This option causes a Poco exception. We remove it, if present. */ m_Argv_macOS.reserve(argc + 1); const char psn[] = "-psn"; for (int i = 0; i < argc; ++i) { if (0 == strncmp(argv[i], psn, sizeof(psn) - 1)) continue; m_Argv_macOS.push_back(argv[i]); } m_Argv_macOS.push_back(nullptr); m_Argc = static_cast(m_Argv_macOS.size() - 1); m_Argv = m_Argv_macOS.data(); #endif } ~Impl() { delete m_SplashscreenClosingCallback; delete m_Splashscreen; delete m_QApp; } QVariant getProperty(const QString &property) const { auto iter = m_FWProps.find(property); return m_FWProps.end() != iter ? iter.value() : QVariant(); } void handleBooleanOption(const std::string &name, const std::string &) { if (ARG_LOG_QT_MESSAGES.toStdString() == name) { m_LogQtMessages = true; return; } auto fwKey = QString::fromStdString(name); // Translate some keys to proper framework properties if (ARG_CONSOLELOG == fwKey) fwKey = ctkPluginFrameworkLauncher::PROP_CONSOLE_LOG; // For all other options we use the command line option name as the // framework property key. m_FWProps[fwKey] = true; } void handlePreloadLibraryOption(const std::string &, const std::string &value) { m_PreloadLibs.push_back(QString::fromStdString(value)); } void handleClean(const std::string &, const std::string &) { m_FWProps[ctkPluginConstants::FRAMEWORK_STORAGE_CLEAN] = ctkPluginConstants::FRAMEWORK_STORAGE_CLEAN_ONFIRSTINIT; } void initializeCTKPluginFrameworkProperties(Poco::Util::LayeredConfiguration &configuration) { // Add all configuration key/value pairs as framework properties Poco::Util::LayeredConfiguration::Keys keys; Poco::Util::LayeredConfiguration::Keys keyStack; configuration.keys(keyStack); std::vector keyChain; while (!keyStack.empty()) { const auto currSubKey = keyStack.back(); if (!keyChain.empty() && keyChain.back() == currSubKey) { keyChain.pop_back(); keyStack.pop_back(); continue; } Poco::Util::LayeredConfiguration::Keys subKeys; configuration.keys(currSubKey, subKeys); if (subKeys.empty()) { std::string finalKey; keyStack.pop_back(); for (const auto& key : keyChain) finalKey += key + '.'; finalKey += currSubKey; keys.push_back(finalKey); } else { keyChain.push_back(currSubKey); for (const auto& key : subKeys) keyStack.push_back(key); } } for (const auto& key : keys) { if (configuration.hasProperty(key)) { // .ini and command line options overwrite already inserted keys auto qKey = QString::fromStdString(key); m_FWProps[qKey] = QString::fromStdString(configuration.getString(key)); } } } void parseProvisioningFile(const QString &filePath) { // Skip parsing if the file path is empty if (filePath.isEmpty()) return; auto consoleLog = this->getProperty(ctkPluginFrameworkLauncher::PROP_CONSOLE_LOG).toBool(); // Read initial plugins from a provisioning file QFileInfo provFile(filePath); QStringList pluginsToStart; if (provFile.exists()) { MITK_INFO(consoleLog) << "Using provisioning file: " << qPrintable(provFile.absoluteFilePath()); ProvisioningInfo provInfo(provFile.absoluteFilePath()); // It can still happen that the encoding is not compatible with the fromUtf8 function (i.e. when // manipulating the LANG variable). The QStringList in provInfo is empty then. if (provInfo.getPluginDirs().empty()) { MITK_ERROR << "Cannot search for provisioning file, the retrieved directory list is empty.\n" << "This can happen if there are some special non-ASCII characters in the install path."; } else { for(const auto& pluginPath : provInfo.getPluginDirs()) ctkPluginFrameworkLauncher::addSearchPath(pluginPath); auto pluginUrlsToStart = provInfo.getPluginsToStart(); - for (const auto& url : pluginUrlsToStart) + for (const auto& url : qAsConst(pluginUrlsToStart)) pluginsToStart.push_back(url.toString()); } } else { MITK_INFO(consoleLog) << "Provisionig file does not exist."; } if (!pluginsToStart.isEmpty()) { m_FWProps[ctkPluginFrameworkLauncher::PROP_PLUGINS] = pluginsToStart; // Use transient start with declared activation policy (this helps when the provisioning file // changes and some plug-ins should not be installed in the application any more). ctkPlugin::StartOptions startOptions(ctkPlugin::START_TRANSIENT | ctkPlugin::START_ACTIVATION_POLICY); m_FWProps[ctkPluginFrameworkLauncher::PROP_PLUGINS_START_OPTIONS] = static_cast(startOptions); } } }; BaseApplication::BaseApplication(int argc, char **argv) : Application(), d(new Impl(argc, argv)) { } BaseApplication::~BaseApplication() { delete d; } void BaseApplication::printHelp(const std::string &, const std::string &) { Poco::Util::HelpFormatter help(this->options()); help.setAutoIndent(); help.setCommand(this->commandName()); help.format(std::cout); exit(EXIT_OK); } void BaseApplication::setApplicationName(const QString &name) { if (nullptr != qApp) qApp->setApplicationName(name); d->m_AppName = name; } QString BaseApplication::getApplicationName() const { return nullptr != qApp ? qApp->applicationName() : d->m_AppName; } void BaseApplication::setOrganizationName(const QString &name) { if (nullptr != qApp) qApp->setOrganizationName(name); d->m_OrgaName = name; } QString BaseApplication::getOrganizationName() const { return nullptr != qApp ? qApp->organizationName() : d->m_OrgaName; } void BaseApplication::setOrganizationDomain(const QString &domain) { if (nullptr != qApp) qApp->setOrganizationDomain(domain); d->m_OrgaDomain = domain; } QString BaseApplication::getOrganizationDomain() const { return nullptr != qApp ? qApp->organizationDomain() : d->m_OrgaDomain; } void BaseApplication::setSingleMode(bool singleMode) { if (nullptr != qApp) return; d->m_SingleMode = singleMode; } bool BaseApplication::getSingleMode() const { return d->m_SingleMode; } void BaseApplication::setSafeMode(bool safeMode) { if (nullptr != qApp && nullptr == d->m_QApp) return; d->m_SafeMode = safeMode; nullptr == d->m_QApp && getSingleMode() ? static_cast(d->m_QApp)->setSafeMode(safeMode) : static_cast(d->m_QApp)->setSafeMode(safeMode); } bool BaseApplication::getSafeMode() const { return d->m_SafeMode; } void BaseApplication::setPreloadLibraries(const QStringList &libraryBaseNames) { d->m_PreloadLibs = libraryBaseNames; } QStringList BaseApplication::getPreloadLibraries() const { return d->m_PreloadLibs; } void BaseApplication::setProvisioningFilePath(const QString &filePath) { d->m_ProvFile = filePath; } QString BaseApplication::getProvisioningFilePath() const { auto provFilePath = d->m_ProvFile; // A null QString means look up a default provisioning file if (provFilePath.isNull() && nullptr != qApp) { QFileInfo appFilePath(QCoreApplication::applicationFilePath()); QDir basePath(QCoreApplication::applicationDirPath()); auto provFileName = appFilePath.baseName() + ".provisioning"; QFileInfo provFile(basePath.absoluteFilePath(provFileName)); #ifdef Q_OS_MAC /* * On macOS, if started from the build directory, the .provisioning file is located at: * * The executable path is: * * In this case we have to cdUp threetimes. * * During packaging the MitkWorkbench.provisioning file is placed at the same * level like the executable. Nothing has to be done. */ if (!provFile.exists()) { basePath.cdUp(); basePath.cdUp(); basePath.cdUp(); provFile = basePath.absoluteFilePath(provFileName); } #endif if (provFile.exists()) { provFilePath = provFile.absoluteFilePath(); } #ifdef CMAKE_INTDIR else { basePath.cdUp(); provFile.setFile(basePath.absoluteFilePath(provFileName)); if (provFile.exists()) provFilePath = provFile.absoluteFilePath(); } #endif } return provFilePath; } void BaseApplication::initializeQt() { if (nullptr != qApp) return; // If parameters have been set before, we have to store them to hand them // through to the application auto appName = this->getApplicationName(); auto orgName = this->getOrganizationName(); auto orgDomain = this->getOrganizationDomain(); // Create a QCoreApplication instance this->getQApplication(); // Provide parameters to QCoreApplication this->setApplicationName(appName); this->setOrganizationName(orgName); this->setOrganizationDomain(orgDomain); if (d->m_LogQtMessages) qInstallMessageHandler(outputQtMessage); QWebEngineUrlScheme qtHelpScheme("qthelp"); qtHelpScheme.setFlags(QWebEngineUrlScheme::LocalScheme | QWebEngineUrlScheme::LocalAccessAllowed); QWebEngineUrlScheme::registerScheme(qtHelpScheme); } void BaseApplication::initialize(Poco::Util::Application &self) { // 1. Call the super-class method Poco::Util::Application::initialize(self); // 2. Initialize the Qt framework (by creating a QCoreApplication) this->initializeQt(); // 3. Seed the random number generator, once at startup. QTime time = QTime::currentTime(); qsrand((uint)time.msec()); // 4. Load the "default" configuration, which involves parsing // an optional .ini file and parsing any // command line arguments this->loadConfiguration(); // 5. Add configuration data from the command line and the // optional .ini file as CTK plugin // framework properties. d->initializeCTKPluginFrameworkProperties(this->config()); // 6. Initialize splash screen if an image path is provided // in the .ini file this->initializeSplashScreen(qApp); // 7. Set the custom CTK Plugin Framework storage directory QString storageDir = this->getCTKFrameworkStorageDir(); if (!storageDir.isEmpty()) d->m_FWProps[ctkPluginConstants::FRAMEWORK_STORAGE] = storageDir; // 8. Set the library search paths and the pre-load library property this->initializeLibraryPaths(); auto preloadLibs = this->getPreloadLibraries(); if (!preloadLibs.isEmpty()) d->m_FWProps[ctkPluginConstants::FRAMEWORK_PRELOAD_LIBRARIES] = preloadLibs; // 9. Initialize the CppMicroServices library. // The initializeCppMicroServices() method reuses the // FRAMEWORK_STORAGE property, so we call it after the // getCTKFrameworkStorageDir method. this->initializeCppMicroServices(); // 10. Parse the (optional) provisioning file and set the // correct framework properties. d->parseProvisioningFile(this->getProvisioningFilePath()); // 11. Set the CTK Plugin Framework properties ctkPluginFrameworkLauncher::setFrameworkProperties(d->m_FWProps); } void BaseApplication::uninitialize() { auto pfw = this->getFramework(); if (pfw) { pfw->stop(); // Wait for up to 10 seconds for the CTK plugin framework to stop pfw->waitForStop(10000); } Poco::Util::Application::uninitialize(); } int BaseApplication::getArgc() const { return d->m_Argc; } char **BaseApplication::getArgv() const { return d->m_Argv; } QString BaseApplication::getCTKFrameworkStorageDir() const { QString storageDir; if (this->getSingleMode()) { // This function checks if an instance is already running and either sends a message to // it containing the command line arguments or checks if a new instance was forced by // providing the BlueBerry.newInstance command line argument. In the latter case, a path // to a temporary directory for the new application's storage directory is returned. storageDir = handleNewAppInstance(static_cast(d->m_QApp), d->m_Argc, d->m_Argv, ARG_NEWINSTANCE); } if (storageDir.isEmpty()) { // This is a new instance and no other instance is already running. We specify the // storage directory here (this is the same code as in berryInternalPlatform.cpp) // so that we can re-use the location for the persistent data location of the // the CppMicroServices library. // Append a hash value of the absolute path of the executable to the data location. // This allows to start the same application from different build or install trees. storageDir = QStandardPaths::writableLocation(QStandardPaths::GenericDataLocation) + "/" + this->getOrganizationName() + "/" + this->getApplicationName() + '_'; storageDir += QString::number(qHash(QCoreApplication::applicationDirPath())) + "/"; } return storageDir; } void BaseApplication::initializeCppMicroServices() { auto storageDir = this->getProperty(ctkPluginConstants::FRAMEWORK_STORAGE).toString(); if (!storageDir.isEmpty()) us::ModuleSettings::SetStoragePath((storageDir + "us" + QDir::separator()).toStdString()); } QCoreApplication *BaseApplication::getQApplication() const { if (nullptr == qApp) { vtkOpenGLRenderWindow::SetGlobalMaximumNumberOfMultiSamples(0); auto defaultFormat = QVTKOpenGLNativeWidget::defaultFormat(); defaultFormat.setSamples(0); QSurfaceFormat::setDefaultFormat(defaultFormat); #ifdef Q_OS_OSX QCoreApplication::setAttribute(Qt::AA_DontCreateNativeWidgetSiblings); #endif QCoreApplication::setAttribute(Qt::AA_ShareOpenGLContexts); d->m_QApp = this->getSingleMode() ? static_cast(new QmitkSingleApplication(d->m_Argc, d->m_Argv, this->getSafeMode())) : static_cast(new QmitkSafeApplication(d->m_Argc, d->m_Argv, this->getSafeMode())); } return qApp; } void BaseApplication::initializeLibraryPaths() { QStringList suffixes; suffixes << "plugins"; #ifdef Q_OS_WINDOWS suffixes << "bin/plugins"; #ifdef CMAKE_INTDIR suffixes << "bin/" CMAKE_INTDIR "/plugins"; #endif #else suffixes << "lib/plugins"; #ifdef CMAKE_INTDIR suffixes << "lib/" CMAKE_INTDIR "/plugins"; #endif #endif #ifdef Q_OS_MAC suffixes << "../../plugins"; #endif // We add a couple of standard library search paths for plug-ins QDir appDir(QCoreApplication::applicationDirPath()); // Walk one directory up and add bin and lib sub-dirs; this might be redundant appDir.cdUp(); - for (const auto& suffix : suffixes) + for (const auto& suffix : qAsConst(suffixes)) ctkPluginFrameworkLauncher::addSearchPath(appDir.absoluteFilePath(suffix)); } int BaseApplication::main(const std::vector &args) { // Start the plugin framework and all installed plug-ins according to their auto-start setting QStringList arguments; for (auto const &arg : args) arguments.push_back(QString::fromStdString(arg)); if (nullptr != d->m_Splashscreen) { // A splash screen is displayed. Create the closing callback. d->m_SplashscreenClosingCallback = new SplashCloserCallback(d->m_Splashscreen); } return ctkPluginFrameworkLauncher::run(d->m_SplashscreenClosingCallback, QVariant::fromValue(arguments)).toInt(); } void BaseApplication::defineOptions(Poco::Util::OptionSet &options) { Poco::Util::Option helpOption("help", "h", "print this help text"); helpOption.callback(Poco::Util::OptionCallback(this, &BaseApplication::printHelp)); options.addOption(helpOption); Poco::Util::Option newInstanceOption(ARG_NEWINSTANCE.toStdString(), "", "forces a new instance of this application"); newInstanceOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(newInstanceOption); Poco::Util::Option cleanOption(ARG_CLEAN.toStdString(), "", "cleans the plugin cache"); cleanOption.callback(Poco::Util::OptionCallback(d, &Impl::handleClean)); options.addOption(cleanOption); Poco::Util::Option productOption(ARG_PRODUCT.toStdString(), "", "the id of the product to be launched"); productOption.argument("").binding(PROP_PRODUCT.toStdString()); options.addOption(productOption); Poco::Util::Option appOption(ARG_APPLICATION.toStdString(), "", "the id of the application extension to be executed"); appOption.argument("").binding(PROP_APPLICATION.toStdString()); options.addOption(appOption); Poco::Util::Option provOption(ARG_PROVISIONING.toStdString(), "", "the location of a provisioning file"); provOption.argument("").binding(ARG_PROVISIONING.toStdString()); options.addOption(provOption); Poco::Util::Option storageDirOption(ARG_STORAGE_DIR.toStdString(), "", "the location for storing persistent application data"); storageDirOption.argument("").binding(ctkPluginConstants::FRAMEWORK_STORAGE.toStdString()); options.addOption(storageDirOption); Poco::Util::Option consoleLogOption(ARG_CONSOLELOG.toStdString(), "", "log messages to the console"); consoleLogOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(consoleLogOption); Poco::Util::Option debugOption(ARG_DEBUG.toStdString(), "", "enable debug mode"); debugOption.argument("", false).binding(ctkPluginFrameworkLauncher::PROP_DEBUG.toStdString()); options.addOption(debugOption); Poco::Util::Option forcePluginOption(ARG_FORCE_PLUGIN_INSTALL.toStdString(), "", "force installing plug-ins with same symbolic name"); forcePluginOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(forcePluginOption); Poco::Util::Option preloadLibsOption(ARG_PRELOAD_LIBRARY.toStdString(), "", "preload a library"); preloadLibsOption.argument("") .repeatable(true) .callback(Poco::Util::OptionCallback(d, &Impl::handlePreloadLibraryOption)); options.addOption(preloadLibsOption); Poco::Util::Option noRegistryCacheOption(ARG_NO_REGISTRY_CACHE.toStdString(), "", "do not use a cache for the registry"); noRegistryCacheOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(noRegistryCacheOption); Poco::Util::Option noLazyRegistryCacheLoadingOption(ARG_NO_LAZY_REGISTRY_CACHE_LOADING.toStdString(), "", "do not use lazy cache loading for the registry"); noLazyRegistryCacheLoadingOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(noLazyRegistryCacheLoadingOption); Poco::Util::Option registryMultiLanguageOption(ARG_REGISTRY_MULTI_LANGUAGE.toStdString(), "", "enable multi-language support for the registry"); registryMultiLanguageOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(registryMultiLanguageOption); Poco::Util::Option splashScreenOption(ARG_SPLASH_IMAGE.toStdString(), "", "optional picture to use as a splash screen"); splashScreenOption.argument("").binding(ARG_SPLASH_IMAGE.toStdString()); options.addOption(splashScreenOption); Poco::Util::Option xargsOption(ARG_XARGS.toStdString(), "", "Extended argument list"); xargsOption.argument("").binding(ARG_XARGS.toStdString()); options.addOption(xargsOption); Poco::Util::Option logQtMessagesOption(ARG_LOG_QT_MESSAGES.toStdString(), "", "log Qt messages"); logQtMessagesOption.callback(Poco::Util::OptionCallback(d, &Impl::handleBooleanOption)); options.addOption(logQtMessagesOption); Poco::Util::Application::defineOptions(options); } QSharedPointer BaseApplication::getFramework() const { return ctkPluginFrameworkLauncher::getPluginFramework(); } ctkPluginContext *BaseApplication::getFrameworkContext() const { auto framework = getFramework(); return framework ? framework->getPluginContext() : nullptr; } void BaseApplication::initializeSplashScreen(QCoreApplication * application) const { auto pixmapFileNameProp = d->getProperty(ARG_SPLASH_IMAGE); if (!pixmapFileNameProp.isNull()) { auto pixmapFileName = pixmapFileNameProp.toString(); QFileInfo checkFile(pixmapFileName); if (checkFile.exists() && checkFile.isFile()) { QPixmap pixmap(checkFile.absoluteFilePath()); d->m_Splashscreen = new QSplashScreen(pixmap, Qt::WindowStaysOnTopHint); d->m_Splashscreen->show(); application->processEvents(); } } } QHash BaseApplication::getFrameworkProperties() const { return d->m_FWProps; } int BaseApplication::run() { this->init(d->m_Argc, d->m_Argv); return Application::run(); } void BaseApplication::setProperty(const QString &property, const QVariant &value) { d->m_FWProps[property] = value; } QVariant BaseApplication::getProperty(const QString &property) const { return d->getProperty(property); } void BaseApplication::installTranslator(QTranslator* translator) { this->getQApplication()->installTranslator(translator); } bool BaseApplication::isRunning() { auto app = dynamic_cast(this->getQApplication()); if (nullptr != app) app->isRunning(); mitkThrow() << "Method not implemented."; } void BaseApplication::sendMessage(const QByteArray msg) { auto app = dynamic_cast(this->getQApplication()); if (nullptr != app) app->sendMessage(msg); mitkThrow() << "Method not implemented."; } } diff --git a/Modules/BoundingShape/src/Interactions/mitkBoundingShapeInteractor.cpp b/Modules/BoundingShape/src/Interactions/mitkBoundingShapeInteractor.cpp index 51bd761e0a..3b7b0340bf 100644 --- a/Modules/BoundingShape/src/Interactions/mitkBoundingShapeInteractor.cpp +++ b/Modules/BoundingShape/src/Interactions/mitkBoundingShapeInteractor.cpp @@ -1,609 +1,609 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "../DataManagement/mitkBoundingShapeUtil.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include "usGetModuleContext.h" #include "usModuleRegistry.h" // Properties to allow the user to interact with the base data const char *selectedColorPropertyName = "Bounding Shape.Selected Color"; const char *deselectedColorPropertyName = "Bounding Shape.Deselected Color"; const char *activeHandleIdPropertyName = "Bounding Shape.Active Handle ID"; const char *boundingShapePropertyName = "Bounding Shape"; namespace mitk { class BoundingShapeInteractor::Impl { public: Impl() : ScrollEnabled(false), RotationEnabled(false) { Point3D initialPoint; initialPoint.Fill(0.0); for (int i = 0; i < 6; ++i) Handles.push_back(Handle(initialPoint, i, GetHandleIndices(i))); } ~Impl() {} bool ScrollEnabled; Point3D InitialPickedWorldPoint; Point3D LastPickedWorldPoint; Point2D InitialPickedDisplayPoint; std::vector Handles; Handle ActiveHandle; Geometry3D::Pointer OriginalGeometry; bool RotationEnabled; std::map DisplayInteractorConfigs; }; } mitk::BoundingShapeInteractor::BoundingShapeInteractor() : m_Impl(new Impl) { } mitk::BoundingShapeInteractor::~BoundingShapeInteractor() { this->RestoreNodeProperties(); delete m_Impl; } void mitk::BoundingShapeInteractor::ConnectActionsAndFunctions() { // **Conditions** that can be used in the state machine, to ensure that certain conditions are met, before actually // executing an action CONNECT_CONDITION("isHoveringOverObject", CheckOverObject); CONNECT_CONDITION("isHoveringOverHandles", CheckOverHandles); // **Function** in the statemachine patterns also referred to as **Actions** CONNECT_FUNCTION("selectObject", SelectObject); CONNECT_FUNCTION("deselectObject", DeselectObject); CONNECT_FUNCTION("deselectHandles", DeselectHandles); CONNECT_FUNCTION("initInteraction", InitInteraction); CONNECT_FUNCTION("translateObject", TranslateObject); CONNECT_FUNCTION("selectHandle", SelectHandle); CONNECT_FUNCTION("scaleObject", ScaleObject); // CONNECT_FUNCTION("rotateObject",RotateObject); } // RotateObject(StateMachineAction*, InteractionEvent* interactionEvent) // void mitk::BoundingShapeInteractor::RotateGeometry(mitk::ScalarType angle, int rotationaxis, mitk::BaseGeometry* // geometry) //{ // mitk::Vector3D rotationAxis = geometry->GetAxisVector(rotationaxis); // float pointX = 0.0f; // float pointY = 0.0f; // float pointZ = 0.0f; // mitk::Point3D pointOfRotation; // pointOfRotation.Fill(0.0); // this->GetDataNode()->GetFloatProperty(anchorPointX, pointX); // this->GetDataNode()->GetFloatProperty(anchorPointY, pointY); // this->GetDataNode()->GetFloatProperty(anchorPointZ, pointZ); // pointOfRotation[0] = pointX; // pointOfRotation[1] = pointY; // pointOfRotation[2] = pointZ; // // mitk::RotationOperation* doOp = new mitk::RotationOperation(OpROTATE, pointOfRotation, rotationAxis, angle); // // geometry->ExecuteOperation(doOp); // delete doOp; //} void mitk::BoundingShapeInteractor::SetRotationEnabled(bool rotationEnabled) { m_Impl->RotationEnabled = rotationEnabled; } void mitk::BoundingShapeInteractor::DataNodeChanged() { mitk::DataNode::Pointer newInputNode = this->GetDataNode(); if (newInputNode == nullptr) return; // add color properties mitk::ColorProperty::Pointer selectedColor = dynamic_cast(newInputNode->GetProperty(selectedColorPropertyName)); mitk::ColorProperty::Pointer deselectedColor = dynamic_cast(newInputNode->GetProperty(deselectedColorPropertyName)); if (selectedColor.IsNull()) newInputNode->AddProperty(selectedColorPropertyName, mitk::ColorProperty::New(0.0, 1.0, 0.0)); if (deselectedColor.IsNull()) newInputNode->AddProperty(deselectedColorPropertyName, mitk::ColorProperty::New(1.0, 1.0, 1.0)); newInputNode->SetProperty(boundingShapePropertyName, mitk::BoolProperty::New(true)); newInputNode->AddProperty(activeHandleIdPropertyName, mitk::IntProperty::New(-1)); newInputNode->SetProperty("layer", mitk::IntProperty::New(101)); newInputNode->SetBoolProperty("fixedLayer", mitk::BoolProperty::New(true)); newInputNode->SetBoolProperty("pickable", true); mitk::ColorProperty::Pointer initialColor = dynamic_cast(newInputNode->GetProperty(deselectedColorPropertyName)); if (initialColor.IsNotNull()) { newInputNode->SetColor(initialColor->GetColor()); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::BoundingShapeInteractor::HandlePositionChanged(const InteractionEvent *interactionEvent, Point3D ¢er) { GeometryData::Pointer geometryData = dynamic_cast(this->GetDataNode()->GetData()); int timeStep = interactionEvent->GetSender()->GetTimeStep(this->GetDataNode()->GetData()); mitk::BaseGeometry::Pointer geometry = geometryData->GetGeometry(timeStep); std::vector cornerPoints = GetCornerPoints(geometry, true); if (m_Impl->Handles.size() == 6) { // set handle positions Point3D pointLeft = CalcAvgPoint(cornerPoints[5], cornerPoints[6]); Point3D pointRight = CalcAvgPoint(cornerPoints[1], cornerPoints[2]); Point3D pointTop = CalcAvgPoint(cornerPoints[0], cornerPoints[6]); Point3D pointBottom = CalcAvgPoint(cornerPoints[7], cornerPoints[1]); Point3D pointFront = CalcAvgPoint(cornerPoints[2], cornerPoints[7]); Point3D pointBack = CalcAvgPoint(cornerPoints[4], cornerPoints[1]); m_Impl->Handles[0].SetPosition(pointLeft); m_Impl->Handles[1].SetPosition(pointRight); m_Impl->Handles[2].SetPosition(pointTop); m_Impl->Handles[3].SetPosition(pointBottom); m_Impl->Handles[4].SetPosition(pointFront); m_Impl->Handles[5].SetPosition(pointBack); // calculate center based on half way of the distance between two opposing cornerpoints center = CalcAvgPoint(cornerPoints[7], cornerPoints[0]); } } void mitk::BoundingShapeInteractor::SetDataNode(DataNode *node) { this->RestoreNodeProperties(); // if there is another node set, restore it's color if (node == nullptr) return; DataInteractor::SetDataNode(node); // calls DataNodeChanged internally this->DataNodeChanged(); } bool mitk::BoundingShapeInteractor::CheckOverObject(const InteractionEvent *interactionEvent) { const auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) return false; GeometryData::Pointer geometryData = dynamic_cast(this->GetDataNode()->GetData()); int timeStep = interactionEvent->GetSender()->GetTimeStep(this->GetDataNode()->GetData()); BaseGeometry::Pointer geometry = geometryData->GetGeometry(timeStep); // calculates translation based on offset+extent not on the transformation matrix (because the cube is located in the // center not in the origin) vtkSmartPointer imageTransform = geometry->GetVtkTransform()->GetMatrix(); Point3D center = geometry->GetCenter(); auto translation = vtkSmartPointer::New(); auto transform = vtkSmartPointer::New(); translation->Translate(center[0] - imageTransform->GetElement(0, 3), center[1] - imageTransform->GetElement(1, 3), center[2] - imageTransform->GetElement(2, 3)); transform->SetMatrix(imageTransform); transform->PostMultiply(); transform->Concatenate(translation); transform->Update(); mitk::Vector3D extent; for (unsigned int i = 0; i < 3; ++i) extent[i] = (geometry->GetExtent(i)); Point3D currentWorldPosition; Point2D currentDisplayPosition = positionEvent->GetPointerPositionOnScreen(); interactionEvent->GetSender()->DisplayToWorld(currentDisplayPosition, currentWorldPosition); ScalarType transformedPosition[4]; transformedPosition[0] = currentWorldPosition[0]; transformedPosition[1] = currentWorldPosition[1]; transformedPosition[2] = currentWorldPosition[2]; transformedPosition[3] = 1; // transform point from world to object coordinates transform->GetInverse()->TransformPoint(transformedPosition, transformedPosition); // check if the world point is within bounds bool isInside = (transformedPosition[0] >= (-extent[0] / 2.0)) && (transformedPosition[0] <= (extent[0] / 2.0)) && (transformedPosition[1] >= (-extent[1] / 2.0)) && (transformedPosition[1] <= (extent[1] / 2.0)) && (transformedPosition[2] >= (-extent[2] / 2.0)) && (transformedPosition[2] <= (extent[2] / 2.0)); return isInside; } bool mitk::BoundingShapeInteractor::CheckOverHandles(const InteractionEvent *interactionEvent) { Point3D boundingBoxCenter; HandlePositionChanged(interactionEvent, boundingBoxCenter); const auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) return false; Point2D displayCenterPoint; // to do: change to actual time step (currently not necessary because geometry remains the same for each timestep int timeStep = 0; GeometryData::Pointer geometryData = dynamic_cast(this->GetDataNode()->GetData()); BaseGeometry::Pointer geometry = geometryData->GetUpdatedTimeGeometry()->GetGeometryForTimeStep(timeStep); std::vector cornerPoints = GetCornerPoints(geometry, true); interactionEvent->GetSender()->WorldToDisplay(boundingBoxCenter, displayCenterPoint); double scale = interactionEvent->GetSender()->GetScaleFactorMMPerDisplayUnit(); // GetDisplaySizeInMM mitk::DoubleProperty::Pointer handleSizeProperty = dynamic_cast(this->GetDataNode()->GetProperty("Bounding Shape.Handle Size Factor")); ScalarType initialHandleSize; if (handleSizeProperty != nullptr) initialHandleSize = handleSizeProperty->GetValue(); else initialHandleSize = 1.0 / 40.0; mitk::Point2D displaysize = interactionEvent->GetSender()->GetDisplaySizeInMM(); ScalarType handlesize = ((displaysize[0] + displaysize[1]) / 2.0) * initialHandleSize; unsigned int handleNum = 0; for (auto &handle : m_Impl->Handles) { Point2D centerpoint; interactionEvent->GetSender()->WorldToDisplay(handle.GetPosition(), centerpoint); Point2D currentDisplayPosition = positionEvent->GetPointerPositionOnScreen(); if ((currentDisplayPosition.EuclideanDistanceTo(centerpoint) < (handlesize / scale)) && (currentDisplayPosition.EuclideanDistanceTo(displayCenterPoint) > (handlesize / scale))) // check if mouse is hovering over center point { handle.SetActive(true); m_Impl->ActiveHandle = handle; this->GetDataNode()->GetPropertyList()->SetProperty(activeHandleIdPropertyName, mitk::IntProperty::New(handleNum++)); this->GetDataNode()->GetData()->Modified(); RenderingManager::GetInstance()->RequestUpdateAll(); return true; } else { handleNum++; handle.SetActive(false); } this->GetDataNode()->GetPropertyList()->SetProperty(activeHandleIdPropertyName, mitk::IntProperty::New(-1)); } return false; } void mitk::BoundingShapeInteractor::SelectHandle(StateMachineAction *, InteractionEvent *) { this->DisableCrosshairNavigation(); DataNode::Pointer node = this->GetDataNode(); if (node.IsNull()) return; mitk::ColorProperty::Pointer selectedColor = dynamic_cast(node->GetProperty(deselectedColorPropertyName)); if (selectedColor.IsNotNull()) { this->GetDataNode()->GetPropertyList()->SetProperty("color", selectedColor); } this->GetDataNode()->GetData()->UpdateOutputInformation(); // Geometry is up-to-date this->GetDataNode()->GetData()->Modified(); RenderingManager::GetInstance()->RequestUpdateAll(); return; } void mitk::BoundingShapeInteractor::DeselectHandles(StateMachineAction *, InteractionEvent *) { this->DisableCrosshairNavigation(); DataNode::Pointer node = this->GetDataNode(); if (node.IsNull()) return; this->GetDataNode()->GetPropertyList()->SetProperty(activeHandleIdPropertyName, mitk::IntProperty::New(-1)); this->GetDataNode()->GetData()->UpdateOutputInformation(); // Geometry is up-to-date this->GetDataNode()->GetData()->Modified(); RenderingManager::GetInstance()->RequestUpdateAll(); return; } void mitk::BoundingShapeInteractor::SelectObject(StateMachineAction *, InteractionEvent *) { this->DisableCrosshairNavigation(); // disable crosshair interaction and scolling if user is hovering over the object DataNode::Pointer node = this->GetDataNode(); if (node.IsNull()) return; mitk::ColorProperty::Pointer selectedColor = dynamic_cast(node->GetProperty(selectedColorPropertyName)); if (selectedColor.IsNotNull()) { node->GetPropertyList()->SetProperty("color", selectedColor); } this->GetDataNode()->GetData()->UpdateOutputInformation(); // Geometry is up-to-date this->GetDataNode()->GetData()->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); return; } void mitk::BoundingShapeInteractor::DeselectObject(StateMachineAction *, InteractionEvent *) { this->EnableCrosshairNavigation(); // enable crosshair interaction and scolling if user is hovering over the object DataNode::Pointer node = this->GetDataNode(); if (node.IsNull()) return; mitk::ColorProperty::Pointer deselectedColor = dynamic_cast(node->GetProperty(deselectedColorPropertyName)); if (deselectedColor.IsNotNull()) { node->GetPropertyList()->SetProperty("color", deselectedColor); } this->GetDataNode()->GetData()->UpdateOutputInformation(); // Geometry is up-to-date this->GetDataNode()->GetData()->Modified(); RenderingManager::GetInstance()->RequestUpdateAll(); return; } void mitk::BoundingShapeInteractor::InitInteraction(StateMachineAction *, InteractionEvent *interactionEvent) { InitMembers(interactionEvent); } bool mitk::BoundingShapeInteractor::InitMembers(InteractionEvent *interactionEvent) { auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) return false; // get initial position coordinates m_Impl->InitialPickedDisplayPoint = positionEvent->GetPointerPositionOnScreen(); m_Impl->InitialPickedWorldPoint = positionEvent->GetPositionInWorld(); m_Impl->LastPickedWorldPoint = positionEvent->GetPositionInWorld(); return true; } void mitk::BoundingShapeInteractor::TranslateObject(StateMachineAction *, InteractionEvent *interactionEvent) { auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) return; int timeStep = interactionEvent->GetSender()->GetTimeStep(this->GetDataNode()->GetData()); mitk::BaseGeometry::Pointer geometry = this->GetDataNode()->GetData()->GetUpdatedTimeGeometry()->GetGeometryForTimeStep(timeStep); Vector3D spacing = geometry->GetSpacing(); Point3D currentPickedPoint; interactionEvent->GetSender()->DisplayToWorld(positionEvent->GetPointerPositionOnScreen(), currentPickedPoint); Vector3D interactionMove; // pixel aligned shifting of the bounding box interactionMove[0] = std::round((currentPickedPoint[0] - m_Impl->LastPickedWorldPoint[0]) / spacing[0]) * spacing[0]; interactionMove[1] = std::round((currentPickedPoint[1] - m_Impl->LastPickedWorldPoint[1]) / spacing[1]) * spacing[1]; interactionMove[2] = std::round((currentPickedPoint[2] - m_Impl->LastPickedWorldPoint[2]) / spacing[2]) * spacing[2]; if ((interactionMove[0] + interactionMove[1] + interactionMove[2]) != 0.0) // only update current position if a movement occured { m_Impl->LastPickedWorldPoint = currentPickedPoint; geometry->SetOrigin(geometry->GetOrigin() + interactionMove); this->GetDataNode()->GetData()->UpdateOutputInformation(); // Geometry is up-to-date this->GetDataNode()->GetData()->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } return; } void mitk::BoundingShapeInteractor::ScaleObject(StateMachineAction *, InteractionEvent *interactionEvent) { auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) return; GeometryData::Pointer geometryData = dynamic_cast(this->GetDataNode()->GetData()); Point3D handlePickedPoint = m_Impl->ActiveHandle.GetPosition(); Point3D currentPickedPoint; interactionEvent->GetSender()->DisplayToWorld(positionEvent->GetPointerPositionOnScreen(), currentPickedPoint); int timeStep = interactionEvent->GetSender()->GetTimeStep(this->GetDataNode()->GetData()); mitk::BaseGeometry::Pointer geometry = geometryData->GetGeometry(timeStep); Vector3D spacing = geometry->GetSpacing(); // pixel aligned bounding box Vector3D interactionMove; interactionMove[0] = (currentPickedPoint[0] - m_Impl->LastPickedWorldPoint[0]); interactionMove[1] = (currentPickedPoint[1] - m_Impl->LastPickedWorldPoint[1]); interactionMove[2] = (currentPickedPoint[2] - m_Impl->LastPickedWorldPoint[2]); std::vector faces = m_Impl->ActiveHandle.GetFaceIndices(); auto pointscontainer = mitk::BoundingBox::PointsContainer::New(); // calculate cornerpoints from geometry plus visualization offset std::vector cornerPoints = GetCornerPoints(geometry, true); unsigned int num = 0; - for (auto point : cornerPoints) + for (const auto &point : cornerPoints) { pointscontainer->InsertElement(num++, point); } // calculate center based on half way of the distance between two opposing cornerpoints mitk::Point3D center = CalcAvgPoint(cornerPoints[7], cornerPoints[0]); Vector3D faceNormal; faceNormal[0] = handlePickedPoint[0] - center[0]; faceNormal[1] = handlePickedPoint[1] - center[1]; faceNormal[2] = handlePickedPoint[2] - center[2]; Vector3D faceShift = ((faceNormal * interactionMove) / (faceNormal.GetNorm() * faceNormal.GetNorm())) * faceNormal; // calculate cornerpoints from geometry without visualization offset to update actual geometry cornerPoints = GetCornerPoints(geometry, false); num = 0; - for (auto point : cornerPoints) + for (const auto &point : cornerPoints) { pointscontainer->InsertElement(num++, point); } bool positionChangeThreshold = true; for (int numFaces = 0; numFaces < 8; numFaces++) // estimate the corresponding face and shift its assigned points { if ((numFaces != faces[0]) && (numFaces != faces[1]) && (numFaces != faces[2]) && (numFaces != faces[3])) { Point3D point = pointscontainer->GetElement(numFaces); if (m_Impl->RotationEnabled) // apply if geometry is rotated at a pixel aligned shift is not possible { point[0] += faceShift[0]; point[1] += faceShift[1]; point[2] += faceShift[2]; } else // shift pixelwise { point[0] += std::round(faceShift[0] / spacing[0]) * spacing[0]; point[1] += std::round(faceShift[1] / spacing[1]) * spacing[1]; point[2] += std::round(faceShift[2] / spacing[2]) * spacing[2]; } if (point == pointscontainer->GetElement(numFaces)) positionChangeThreshold = false; else m_Impl->LastPickedWorldPoint = point; pointscontainer->InsertElement(numFaces, point); } } if (positionChangeThreshold) // update only if bounding box is shifted at least by one pixel { auto inverse = mitk::AffineTransform3D::New(); geometry->GetIndexToWorldTransform()->GetInverse(inverse); for (unsigned int pointid = 0; pointid < 8; pointid++) { pointscontainer->InsertElement(pointid, inverse->TransformPoint(pointscontainer->GetElement(pointid))); } auto bbox = mitk::BoundingBox::New(); bbox->SetPoints(pointscontainer); bbox->ComputeBoundingBox(); mitk::Point3D BBmin = bbox->GetMinimum(); mitk::Point3D BBmax = bbox->GetMaximum(); if (std::abs(BBmin[0] - BBmax[0]) > 0.01 && std::abs(BBmin[1] - BBmax[1]) > 0.01 && std::abs(BBmin[2] - BBmax[2]) > 0.01) // TODO: check if the extent is greater than zero { geometry->SetBounds(bbox->GetBounds()); geometry->Modified(); this->GetDataNode()->GetData()->UpdateOutputInformation(); // Geometry is up-to-date this->GetDataNode()->GetData()->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } return; } void mitk::BoundingShapeInteractor::RestoreNodeProperties() { mitk::DataNode::Pointer inputNode = this->GetDataNode(); if (inputNode.IsNull()) return; mitk::ColorProperty::Pointer color = (mitk::ColorProperty::New(1.0, 1.0, 1.0)); if (color.IsNotNull()) { inputNode->GetPropertyList()->SetProperty("color", color); } inputNode->SetProperty("layer", mitk::IntProperty::New(99)); inputNode->SetProperty(boundingShapePropertyName, mitk::BoolProperty::New(false)); inputNode->GetPropertyList()->DeleteProperty(activeHandleIdPropertyName); EnableCrosshairNavigation(); // update rendering mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::BoundingShapeInteractor::EnableCrosshairNavigation() { // enable the crosshair navigation // Re-enabling InteractionEventObservers that have been previously disabled for legacy handling of Tools // in new interaction framework for (auto it = m_Impl->DisplayInteractorConfigs.begin(); it != m_Impl->DisplayInteractorConfigs.end(); ++it) { if (it->first) { mitk::DisplayInteractor *displayInteractor = static_cast( us::GetModuleContext()->GetService(it->first)); if (displayInteractor != nullptr) { // here the regular configuration is loaded again displayInteractor->SetEventConfig(it->second); // MITK_INFO << "restore config"; } } } m_Impl->DisplayInteractorConfigs.clear(); m_Impl->ScrollEnabled = true; } void mitk::BoundingShapeInteractor::DisableCrosshairNavigation() { // dont deactivate twice, else we will clutter the config list ... if (m_Impl->ScrollEnabled == false) return; // As a legacy solution the display interaction of the new interaction framework is disabled here to avoid conflicts // with tools // Note: this only affects InteractionEventObservers (formerly known as Listeners) all DataNode specific interaction // will still be enabled m_Impl->DisplayInteractorConfigs.clear(); std::vector> listEventObserver = us::GetModuleContext()->GetServiceReferences(); for (auto it = listEventObserver.begin(); it != listEventObserver.end(); ++it) { auto *displayInteractor = dynamic_cast(us::GetModuleContext()->GetService(*it)); if (displayInteractor != nullptr) { // remember the original configuration m_Impl->DisplayInteractorConfigs.insert(std::make_pair(*it, displayInteractor->GetEventConfig())); // here the alternative configuration is loaded displayInteractor->SetEventConfig("DisplayConfigMITKNoCrosshair.xml"); // MITK_INFO << "change config"; } } m_Impl->ScrollEnabled = false; } diff --git a/Modules/CEST/src/mitkCustomTagParser.cpp b/Modules/CEST/src/mitkCustomTagParser.cpp index d9d082671b..fbfee566c0 100644 --- a/Modules/CEST/src/mitkCustomTagParser.cpp +++ b/Modules/CEST/src/mitkCustomTagParser.cpp @@ -1,846 +1,846 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkCustomTagParser.h" #include #include #include "mitkCESTPropertyHelper.h" #include "mitkIPropertyPersistence.h" #include "usGetModuleContext.h" #include "usModule.h" #include "usModuleContext.h" #include "usModuleResource.h" #include "usModuleResourceStream.h" #include #include #include #include #include #include #include #include #include #include #include namespace { mitk::IPropertyPersistence *GetPersistenceService() { mitk::IPropertyPersistence *result = nullptr; std::vector> persRegisters = us::GetModuleContext()->GetServiceReferences(); if (!persRegisters.empty()) { if (persRegisters.size() > 1) { MITK_WARN << "Multiple property description services found. Using just one."; } result = us::GetModuleContext()->GetService(persRegisters.front()); } return result; }; } const std::string mitk::CustomTagParser::m_CESTPropertyPrefix = "CEST."; const std::string mitk::CustomTagParser::m_RevisionPropertyName = m_CESTPropertyPrefix + "Revision"; const std::string mitk::CustomTagParser::m_JSONRevisionPropertyName = m_CESTPropertyPrefix + "revision_json"; const std::string mitk::CustomTagParser::m_RevisionIndependentMapping = "\n" " \"sProtConsistencyInfo.tSystemType\" : \"SysType\",\n" " \"sProtConsistencyInfo.flNominalB0\" : \"NominalB0\",\n" " \"sTXSPEC.asNucleusInfo[0].lFrequency\" : \"FREQ\",\n" " \"sTXSPEC.asNucleusInfo[0].flReferenceAmplitude\" : \"RefAmp\",\n" " \"alTR[0]\" : \"TR\",\n" " \"alTE[0]\" : \"TE\",\n" " \"lAverages\" : \"averages\",\n" " \"lRepetitions\" : \"repetitions\",\n" " \"adFlipAngleDegree[0]\" : \"ImageFlipAngle\",\n" " \"lTotalScanTimeSec\" : \"TotalScanTime\","; const std::string mitk::CustomTagParser::m_DefaultJsonString = "{\n" " \"default mapping, corresponds to revision 1416\" : \"revision_json\",\n" " \"sWiPMemBlock.alFree[1]\" : \"AdvancedMode\",\n" " \"sWiPMemBlock.alFree[2]\" : \"RecoveryMode\",\n" " \"sWiPMemBlock.alFree[3]\" : \"DoubleIrrMode\",\n" " \"sWiPMemBlock.alFree[4]\" : \"BinomMode\",\n" " \"sWiPMemBlock.alFree[5]\" : \"MtMode\",\n" " \"sWiPMemBlock.alFree[6]\" : \"PreparationType\",\n" " \"sWiPMemBlock.alFree[7]\" : \"PulseType\",\n" " \"sWiPMemBlock.alFree[8]\" : \"SamplingType\",\n" " \"sWiPMemBlock.alFree[9]\" : \"SpoilingType\",\n" " \"sWiPMemBlock.alFree[10]\" : \"measurements\",\n" " \"sWiPMemBlock.alFree[11]\" : \"NumberOfPulses\",\n" " \"sWiPMemBlock.alFree[12]\" : \"NumberOfLockingPulses\",\n" " \"sWiPMemBlock.alFree[13]\" : \"PulseDuration\",\n" " \"sWiPMemBlock.alFree[14]\" : \"DutyCycle\",\n" " \"sWiPMemBlock.alFree[15]\" : \"RecoveryTime\",\n" " \"sWiPMemBlock.alFree[16]\" : \"RecoveryTimeM0\",\n" " \"sWiPMemBlock.alFree[17]\" : \"ReadoutDelay\",\n" " \"sWiPMemBlock.alFree[18]\" : \"BinomDuration\",\n" " \"sWiPMemBlock.alFree[19]\" : \"BinomDistance\",\n" " \"sWiPMemBlock.alFree[20]\" : \"BinomNumberofPulses\",\n" " \"sWiPMemBlock.alFree[21]\" : \"BinomPreRepetions\",\n" " \"sWiPMemBlock.alFree[22]\" : \"BinomType\",\n" " \"sWiPMemBlock.adFree[1]\" : \"Offset\",\n" " \"sWiPMemBlock.adFree[2]\" : \"B1Amplitude\",\n" " \"sWiPMemBlock.adFree[3]\" : \"AdiabaticPulseMu\",\n" " \"sWiPMemBlock.adFree[4]\" : \"AdiabaticPulseBW\",\n" " \"sWiPMemBlock.adFree[5]\" : \"AdiabaticPulseLength\",\n" " \"sWiPMemBlock.adFree[6]\" : \"AdiabaticPulseAmp\",\n" " \"sWiPMemBlock.adFree[7]\" : \"FermiSlope\",\n" " \"sWiPMemBlock.adFree[8]\" : \"FermiFWHM\",\n" " \"sWiPMemBlock.adFree[9]\" : \"DoubleIrrDuration\",\n" " \"sWiPMemBlock.adFree[10]\" : \"DoubleIrrAmplitude\",\n" " \"sWiPMemBlock.adFree[11]\" : \"DoubleIrrRepetitions\",\n" " \"sWiPMemBlock.adFree[12]\" : \"DoubleIrrPreRepetitions\"\n" "}"; mitk::CustomTagParser::CustomTagParser(std::string relevantFile) : m_ClosestInternalRevision(""), m_ClosestExternalRevision("") { std::string pathToDirectory; std::string fileName; itksys::SystemTools::SplitProgramPath(relevantFile, pathToDirectory, fileName); m_DicomDataPath = pathToDirectory; m_ParseStrategy = "Automatic"; m_RevisionMappingStrategy = "Fuzzy"; } std::string mitk::CustomTagParser::ExtractRevision(std::string sequenceFileName) { //all rules are case insesitive. Thus we convert everything to lower case //in order to check everything only once. std::string cestPrefix = "cest"; std::string cestPrefix2 = "_cest"; std::string cestPrefix3 = "\\cest"; //this version covers the fact that the strings extracted //from the SIEMENS tag has an additional prefix that is seperated by backslash. std::string revisionPrefix = "_rev"; std::transform(sequenceFileName.begin(), sequenceFileName.end(), sequenceFileName.begin(), ::tolower); bool isCEST = sequenceFileName.compare(0, cestPrefix.length(), cestPrefix) == 0; std::size_t foundPosition = 0; if (!isCEST) { foundPosition = sequenceFileName.find(cestPrefix2); isCEST = foundPosition != std::string::npos; } if (!isCEST) { foundPosition = sequenceFileName.find(cestPrefix3); isCEST = foundPosition != std::string::npos; } if (!isCEST) { mitkThrow() << "Invalid CEST sequence file name. No CEST prefix found. Could not extract revision."; } foundPosition = sequenceFileName.find(revisionPrefix, foundPosition); if (foundPosition == std::string::npos) { mitkThrow() << "Invalid CEST sequence file name. No revision prefix was found in CEST sequence file name. Could not extract revision."; } std::string revisionString = sequenceFileName.substr(foundPosition + revisionPrefix.length(), std::string::npos); std::size_t firstNoneNumber = revisionString.find_first_not_of("0123456789"); if (firstNoneNumber != std::string::npos) { revisionString.erase(firstNoneNumber, std::string::npos); } return revisionString; } bool mitk::CustomTagParser::IsT1Sequence(std::string preparationType, std::string recoveryMode, std::string spoilingType, std::string revisionString) { bool isT1 = false; // if a forced parse strategy is set, use that one if ("T1" == m_ParseStrategy) { return true; } if ("CEST/WASABI" == m_ParseStrategy) { return false; } if (("T1Recovery" == preparationType) || ("T1Inversion" == preparationType)) { isT1 = true; } // How to interpret the recoveryMode depends on the age of the sequence // older sequences use 0 = false and 1 = true, newer ones 1 = false and 2 = true. // A rough rule of thumb is to assume that if the SpoilingType is 0, then the first // convention is chosen, if it is 1, then the second applies. Otherwise // we assume revision 1485 and newer to follow the new convention. // This unfortunate heuristic is due to somewhat arbitrary CEST sequence implementations. if (!isT1) { std::string thisIsTrue = "1"; std::string thisIsFalse = "0"; if ("0" == spoilingType) { thisIsFalse = "0"; thisIsTrue = "1"; } else if ("1" == spoilingType) { thisIsFalse = "1"; thisIsTrue = "2"; } else { int revisionNrWeAssumeToBeDifferenciating = 1485; if (std::stoi(revisionString) - revisionNrWeAssumeToBeDifferenciating < 0) { thisIsFalse = "0"; thisIsTrue = "1"; } else { thisIsFalse = "1"; thisIsTrue = "2"; } } if (thisIsFalse == recoveryMode) { isT1 = false; } else if (thisIsTrue == recoveryMode) { isT1 = true; } } return isT1; } mitk::PropertyList::Pointer mitk::CustomTagParser::ParseDicomPropertyString(std::string dicomPropertyString) { auto results = mitk::PropertyList::New(); if ("" == dicomPropertyString) { //MITK_ERROR << "Could not parse empty custom dicom string"; return results; } std::map privateParameters; // The Siemens private tag contains information like "43\52\23\34". // We jump over each "\" and convert the number; std::string bytes; { const std::size_t SUBSTR_LENGTH = 2; const std::size_t INPUT_LENGTH = dicomPropertyString.length(); if (INPUT_LENGTH < SUBSTR_LENGTH) return results; const std::size_t MAX_INPUT_OFFSET = INPUT_LENGTH - SUBSTR_LENGTH; bytes.reserve(INPUT_LENGTH / 3 + 1); try { for (std::size_t i = 0; i <= MAX_INPUT_OFFSET; i += 3) { std::string byte_string = dicomPropertyString.substr(i, SUBSTR_LENGTH); int byte = static_cast(std::stoi(byte_string.c_str(), nullptr, 16)); bytes.push_back(byte); } } catch (const std::invalid_argument&) // std::stoi() could not perform conversion { return results; } } // extract parameter list std::string parameterListString; { const std::string ASCCONV_BEGIN = "### ASCCONV BEGIN ###"; const std::string ASCCONV_END = "### ASCCONV END ###"; auto offset = bytes.find(ASCCONV_BEGIN); if (std::string::npos == offset) return results; offset += ASCCONV_BEGIN.length(); auto count = bytes.find(ASCCONV_END, offset); if (std::string::npos == count) return results; count -= offset; parameterListString = bytes.substr(offset, count); } boost::replace_all(parameterListString, "\r\n", "\n"); boost::char_separator newlineSeparator("\n"); boost::tokenizer> parameters(parameterListString, newlineSeparator); for (const auto ¶meter : parameters) { std::vector parts; boost::split(parts, parameter, boost::is_any_of("=")); if (parts.size() == 2) { parts[0].erase(std::remove(parts[0].begin(), parts[0].end(), ' '), parts[0].end()); parts[1].erase(parts[1].begin(), parts[1].begin() + 1); // first character is a space privateParameters[parts[0]] = parts[1]; } } std::string revisionString = ""; try { revisionString = ExtractRevision(privateParameters["tSequenceFileName"]); } catch (const std::exception &e) { MITK_ERROR << "Cannot deduce revision information. Reason: "<< e.what(); return results; } results->SetProperty(m_RevisionPropertyName, mitk::StringProperty::New(revisionString)); std::string jsonString = GetRevisionAppropriateJSONString(revisionString); boost::property_tree::ptree root; std::istringstream jsonStream(jsonString); try { boost::property_tree::read_json(jsonStream, root); } catch (const boost::property_tree::json_parser_error &e) { mitkThrow() << "Could not parse json file. Error was:\n" << e.what(); } - for (auto it : root) + for (const auto &it : root) { if (it.second.empty()) { std::string propertyName = m_CESTPropertyPrefix + it.second.data(); if (m_JSONRevisionPropertyName == propertyName) { results->SetProperty(propertyName, mitk::StringProperty::New(it.first)); } else { results->SetProperty(propertyName, mitk::StringProperty::New(privateParameters[it.first])); } } else { MITK_ERROR << "Currently no support for nested dicom tag descriptors in json file."; } } std::string offset = ""; std::string measurements = ""; results->GetStringProperty("CEST.Offset", offset); results->GetStringProperty("CEST.measurements", measurements); if (measurements.empty()) { std::string stringRepetitions = ""; results->GetStringProperty("CEST.repetitions", stringRepetitions); std::string stringAverages = ""; results->GetStringProperty("CEST.averages", stringAverages); const auto ERROR_STRING = "Could not find measurements, fallback assumption of repetitions + averages could not be determined either."; if (!stringRepetitions.empty() && !stringAverages.empty()) { std::stringstream measurementStream; try { measurementStream << std::stoi(stringRepetitions) + std::stoi(stringAverages); measurements = measurementStream.str(); MITK_INFO << "Could not find measurements, assuming repetitions + averages. That is: " << measurements; } catch (const std::invalid_argument&) { MITK_ERROR << ERROR_STRING; } } else { MITK_WARN << ERROR_STRING; } } std::string preparationType = ""; std::string recoveryMode = ""; std::string spoilingType = ""; results->GetStringProperty(CEST_PROPERTY_NAME_PREPERATIONTYPE().c_str(), preparationType); results->GetStringProperty(CEST_PROPERTY_NAME_RECOVERYMODE().c_str(), recoveryMode); results->GetStringProperty(CEST_PROPERTY_NAME_SPOILINGTYPE().c_str(), spoilingType); if (this->IsT1Sequence(preparationType, recoveryMode, spoilingType, revisionString)) { MITK_INFO << "Parsed as T1 image"; std::stringstream trecStream; std::string trecPath = m_DicomDataPath + "/TREC.txt"; auto trec = ReadListFromFile(trecPath); if(trec.empty()) { MITK_WARN << "Assumed T1, but could not load TREC at " << trecPath; } results->SetStringProperty(CEST_PROPERTY_NAME_TREC().c_str(), trec.c_str()); } else { MITK_INFO << "Parsed as CEST or WASABI image"; std::string sampling = ""; bool hasSamplingInformation = results->GetStringProperty("CEST.SamplingType", sampling); if (hasSamplingInformation) { std::string offsets = GetOffsetString(sampling, offset, measurements); results->SetStringProperty(CEST_PROPERTY_NAME_OFFSETS().c_str(), offsets.c_str()); } else { MITK_WARN << "Could not determine sampling type."; } } //persist all properties mitk::IPropertyPersistence *persSrv = GetPersistenceService(); if (persSrv) { auto propertyMap = results->GetMap(); for (auto const &prop : *propertyMap) { PropertyPersistenceInfo::Pointer info = PropertyPersistenceInfo::New(); std::string key = prop.first; std::replace(key.begin(), key.end(), '.', '_'); info->SetNameAndKey(prop.first, key); persSrv->AddInfo(info); } } return results; } std::string mitk::CustomTagParser::ReadListFromFile(const std::string& filePath) { std::stringstream listStream; std::ifstream list(filePath.c_str()); list.imbue(std::locale("C")); if (list.good()) { std::string currentValue; while (std::getline(list, currentValue)) { listStream << currentValue << " "; } } return listStream.str(); } mitk::PropertyList::Pointer mitk::CustomTagParser::ParseDicomProperty(mitk::TemporoSpatialStringProperty *dicomProperty) { if (!dicomProperty) { MITK_ERROR << "DICOM property empty"; } auto results = mitk::PropertyList::New(); if (dicomProperty) { results = ParseDicomPropertyString(dicomProperty->GetValue()); } return results; } std::vector mitk::CustomTagParser::GetInternalRevisions() { const std::vector configs = us::GetModuleContext()->GetModule()->FindResources("/", "*.json", false); std::vector availableRevisionsVector; for (const auto& resource : configs) { availableRevisionsVector.push_back(std::stoi(resource.GetBaseName())); } return availableRevisionsVector; } std::vector mitk::CustomTagParser::GetExternalRevisions() { std::string stringToJSONDirectory = GetExternalJSONDirectory(); std::string prospectiveJsonsPath = stringToJSONDirectory + "/*.json"; std::set JsonFiles; Poco::Glob::glob(prospectiveJsonsPath, JsonFiles, Poco::Glob::GLOB_CASELESS); std::vector availableRevisionsVector; for (const auto& jsonpath : JsonFiles) { std::string jsonDir; std::string jsonName; itksys::SystemTools::SplitProgramPath(jsonpath, jsonDir, jsonName); std::string revision = itksys::SystemTools::GetFilenameWithoutExtension(jsonName); // disregard jsons which contain letters in their name bool onlyNumbers = (revision.find_first_not_of("0123456789") == std::string::npos); if(onlyNumbers) { availableRevisionsVector.push_back(std::stoi(revision)); } } return availableRevisionsVector; } std::string mitk::CustomTagParser::GetClosestLowerRevision(std::string revisionString, std::vector availableRevisionsVector) { // descending order std::sort(availableRevisionsVector.begin(), availableRevisionsVector.end(), std::greater<>()); int revision = std::stoi(revisionString); int index = 0; int numberOfRevisions = availableRevisionsVector.size(); while (index < numberOfRevisions) { // current mapping still has a higher revision number if ((availableRevisionsVector[index] - revision) > 0) { ++index; } else { break; } } if (index < numberOfRevisions) { std::stringstream foundRevisionStream; foundRevisionStream << availableRevisionsVector[index]; return foundRevisionStream.str(); } return ""; } void mitk::CustomTagParser::GetClosestLowerRevision(std::string revisionString) { m_ClosestInternalRevision = GetClosestLowerRevision(revisionString, GetInternalRevisions()); m_ClosestExternalRevision = GetClosestLowerRevision(revisionString, GetExternalRevisions()); if ("Strict" == m_RevisionMappingStrategy && !((0 == m_ClosestInternalRevision.compare(revisionString)) || (0 == m_ClosestExternalRevision.compare(revisionString)))) { // strict revision mapping and neither revision does match the dicom meta data std::stringstream errorMessageStream; errorMessageStream << "\nCould not parse dicom data in strict mode, data revision " << revisionString << " has no known matching parameter mapping. To use the closest known older parameter mapping select the " << "\"Fuzzy\" revision mapping option when loading the data.\n" << "\nCurrently known revision mappings are:\n Precompiled:"; for (const auto revision : GetInternalRevisions()) { errorMessageStream << " " << revision; } errorMessageStream << "\n External:"; for (const auto revision : GetExternalRevisions()) { errorMessageStream << " " << revision; } errorMessageStream << "\n\nExternal revision mapping descriptions should be located at\n\n"; std::string stringToJSONDirectory = GetExternalJSONDirectory(); errorMessageStream << stringToJSONDirectory; errorMessageStream << "\n\nTo provide an external mapping for this revision create a " << revisionString << ".json there. You might need to create the directory first."; mitkThrow() << errorMessageStream.str(); } } std::string mitk::CustomTagParser::GetRevisionAppropriateJSONString(std::string revisionString) { std::string returnValue = ""; if ("" == revisionString) { MITK_WARN << "Could not extract revision"; } else { GetClosestLowerRevision(revisionString); bool useExternal = false; bool useInternal = false; if ("" != m_ClosestExternalRevision) { useExternal = true; } if ("" != m_ClosestInternalRevision) { useInternal = true; } if (useExternal && useInternal) { if (std::stoi(m_ClosestInternalRevision) > std::stoi(m_ClosestExternalRevision)) { useExternal = false; } } if (useExternal) { std::string stringToJSONDirectory = GetExternalJSONDirectory(); std::string prospectiveJsonPath = stringToJSONDirectory + "/" + m_ClosestExternalRevision + ".json"; std::ifstream externalJSON(prospectiveJsonPath.c_str()); if (externalJSON.good()) { MITK_INFO << "Found external json for CEST parameters at " << prospectiveJsonPath; std::stringstream buffer; buffer << externalJSON.rdbuf(); returnValue = buffer.str(); useInternal = false; } } if (useInternal) { std::string filename = m_ClosestInternalRevision + ".json"; us::ModuleResource jsonResource = us::GetModuleContext()->GetModule()->GetResource(filename); if (jsonResource.IsValid() && jsonResource.IsFile()) { MITK_INFO << "Found no external json for CEST parameters. Closest internal mapping is for revision " << m_ClosestInternalRevision; us::ModuleResourceStream jsonStream(jsonResource); std::stringstream buffer; buffer << jsonStream.rdbuf(); returnValue = buffer.str(); } } } if ("" == returnValue) { MITK_WARN << "Could not identify parameter mapping for the given revision " << revisionString << ", using default mapping."; returnValue = m_DefaultJsonString; } // inject the revision independent mapping before the first newline { returnValue.insert(returnValue.find("\n"), m_RevisionIndependentMapping); } return returnValue; } std::string mitk::CustomTagParser::GetOffsetString(std::string samplingType, std::string offset, std::string measurements) { std::stringstream results; results.imbue(std::locale("C")); std::string normalizationIndicatingOffset = "-300"; double offsetDouble = 0.0; int measurementsInt = 0; bool validOffset = false; bool validMeasurements = false; if ("" != offset) { validOffset = true; offsetDouble = std::stod(offset); } if ("" != measurements) { validMeasurements = true; measurementsInt = std::stoi(measurements); } std::vector offsetVector; if (validOffset && validMeasurements) { for (int step = 0; step < measurementsInt -1; ++step) { double currentOffset = -offsetDouble + 2 * step * offsetDouble / (measurementsInt - 2.0); offsetVector.push_back(currentOffset); } } else { MITK_WARN << "Invalid offset or measurements, offset calculation will only work for list sampling type."; } if (samplingType == "1" || samplingType == "Regular") { if (validOffset && validMeasurements) { results << normalizationIndicatingOffset << " "; for (const auto& entry : offsetVector) { results << entry << " "; } } } else if (samplingType == "2" || samplingType == "Alternating") { if (validOffset && validMeasurements) { results << normalizationIndicatingOffset << " "; for (auto& entry : offsetVector) { entry = std::abs(entry); } std::sort(offsetVector.begin(), offsetVector.end(), std::greater<>()); for (unsigned int index = 0; index < offsetVector.size(); ++index) { offsetVector[index] = std::pow(-1, index) * offsetVector[index]; } for (auto& entry : offsetVector) { results << entry << " "; } } } else if (samplingType == "3" || samplingType == "List") { std::string listPath = m_DicomDataPath + "/LIST.txt"; auto values = ReadListFromFile(listPath); if (!values.empty()) { results << values; } else { MITK_ERROR << "Could not load list at " << listPath; } } else if (samplingType == "4" || samplingType == "SingleOffset") { if (validOffset && validMeasurements) { results << normalizationIndicatingOffset << " "; for (int step = 0; step < measurementsInt - 1; ++step) { results << offsetDouble << " "; } } } else { MITK_WARN << "Encountered unknown sampling type."; } std::string resultString = results.str(); // replace multiple spaces by a single space std::string::iterator newEnditerator = std::unique(resultString.begin(), resultString.end(), [=](char lhs, char rhs) { return (lhs == rhs) && (lhs == ' '); } ); resultString.erase(newEnditerator, resultString.end()); if ((resultString.length() > 0) && (resultString.at(resultString.length() - 1) == ' ')) { resultString.erase(resultString.end() - 1, resultString.end()); } if ((resultString.length() > 0) && (resultString.at(0) == ' ')) { resultString.erase(resultString.begin(), ++(resultString.begin())); } return resultString; } void mitk::CustomTagParser::SetParseStrategy(std::string parseStrategy) { m_ParseStrategy = parseStrategy; } void mitk::CustomTagParser::SetRevisionMappingStrategy(std::string revisionMappingStrategy) { m_RevisionMappingStrategy = revisionMappingStrategy; } std::string mitk::CustomTagParser::GetExternalJSONDirectory() { std::string moduleLocation = us::GetModuleContext()->GetModule()->GetLocation(); std::string stringToModule; std::string libraryName; itksys::SystemTools::SplitProgramPath(moduleLocation, stringToModule, libraryName); std::stringstream jsonDirectory; jsonDirectory << stringToModule << "/CESTRevisionMapping"; return jsonDirectory.str(); } diff --git a/Modules/Chart/include/QmitkChartWidget.h b/Modules/Chart/include/QmitkChartWidget.h index a4276f1d2a..5e84e3fe45 100644 --- a/Modules/Chart/include/QmitkChartWidget.h +++ b/Modules/Chart/include/QmitkChartWidget.h @@ -1,358 +1,358 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 QmitkC3jsWidget_h #define QmitkC3jsWidget_h #include #include #include #include class QmitkChartxyData; /*! \brief QmitkChartWidget is a widget to display various charts based on the javascript chart library plotly. * \details Data is added via AddData1D() or AddData2D().\n * There can be multiple charts (of different types with different properties) created by calling AddData1D or AddData2D multiple times.\n\n * The following chart types are supported: * * line chart * * bar chart * * spline chart * * pie chart * * scatter chart * * area chart * * area spline chart. * * Technical details: The javascript code is embedded in a QWebEngineView. The actual js code is implemented in resource\Chart.js. * \sa https://plot.ly/javascript/ for further information about the used javaScript library. * \ingroup Modules/Chart */ class MITKCHART_EXPORT QmitkChartWidget : public QWidget { Q_OBJECT public: /*! * \brief enum of diagram types. */ enum class ChartType { bar, /*!< bar chart, see https://plot.ly/javascript/bar-charts/ */ line, /*!< line chart, see https://plot.ly/javascript/line-charts/ */ spline, /*!< spline chart (smoothed line chart), see https://plot.ly/~jduelfer/23/spline/#/ */ pie, /*!< pie chart, see https://plot.ly/javascript/pie-charts/ */ area, /*!< area chart, see https://plot.ly/javascript/filled-area-plots/ */ area_spline, /*!< area-spline chart, similar to https://plot.ly/~jduelfer/23/spline/#/ */ scatter /*!< scatter chart, see https://plot.ly/javascript/line-and-scatter/ */ }; /*! * \brief enum of chart style (modifies background and line color). */ enum class ColorTheme { darkstyle, /*!< background color: dark gray, foreground color: white*/ lightstyle /*!< background color: white, foreground color: black */ }; enum class LineStyle { solid, dashed }; enum class MarkerSymbol { circle, diamond, cross, square, pentagon, star, x, diamond_tall, star_diamond, star_triangle_up, star_triangle_down, asterisk, cross_thin, x_thin }; enum class ChartColor { red, orange, yellow, green, blue, purple, brown, magenta, tan, cyan, olive, maroon, navy, aquamarine, turqouise, silver, lime, teal, indigo, violet, pink, black, white, grey }; enum class AxisScale { linear, log }; /*! * \brief enum of legend position. * See https://plot.ly/javascript/legend/ */ enum class LegendPosition { bottomMiddle, bottomRight, topRight, topLeft, middleRight }; explicit QmitkChartWidget(QWidget* parent = nullptr); //for UnitTests explicit QmitkChartWidget(QWidget *parent, bool unitTest); ~QmitkChartWidget() override; /*! * \brief Adds 1D data to the widget * \details internally, the list is converted to a map with increasing integers keys starting at 0. * \param data1D * \param label the name of the data that is also used as identifier. * \param chartType the chart type that should be used for this data entry * \note the data can be cleared with ClearDiagram() * \note If the label name already exists, the name is replaced with a unique one by concatenating numbers to it. * \warning Pie chart is significantly different than the other chart types. Here, the data given by AddData1D is summed. Each entry represents a different category. */ void AddData1D(const std::vector& data1D, const std::string& label, ChartType chartType = ChartType::bar); /*! * \brief Updates data of an existing label * \param data1D the 1D data , \sa AddData1D * \param label the (existing) label * \note if the label does not exist, nothing happens */ void UpdateData1D(const std::vector &data1D, const std::string &label); /*! * \sa UpdateData1D * \sa AddData2D */ void UpdateData2D(const std::vector< std::pair > &data2D, const std::string &label); void UpdateChartExampleData(const std::vector< std::pair >& data2D, const std::string& label, const std::string& type, const std::string& color, const std::string& lineStyle, const std::string& pieLabelsData = 0); /*! * \brief Adds 2D data to the widget. Call repeatedly for displaying multiple charts. * \details each entry represents a data point: key: value --> x-value: y-value. * \param data2D * \param label the name of the data that is also used as identifier. * \param chartType the chart type that should be used for this data entry * \note the data can be cleared with ClearDiagram() * \note If the label name already exists, the name is replaced with a unique one by concatenating numbers to it. * \warning Pie chart is significantly different than the other chart types. Here, the data given by AddData1D is summed. Each entry represents a different category. */ void AddData2D(const std::vector< std::pair > &data2D, const std::string &label, ChartType chartType = ChartType::bar); //Add Function for the ChartExample void AddChartExampleData(const std::vector< std::pair >& data2D, const std::string& label, const std::string& type, const std::string& color, const std::string& style, const std::string& pieLabelsData = 0); /*! * \brief Removes data from the widget, works for 1D and 2D Data * \param label the name of the data that is also used as identifier. - * \note All data can be cleared with ClearDiagram() + * \note All data can be cleared with Clear() * \throws Invalid Argument Exception when the label cannot be found */ void RemoveData(const std::string& label); void UpdateLabel(const std::string& existingLabel, const std::string& newLabel); QmitkChartxyData *GetDataElementByLabel(const std::string& label) const; /*! * \brief Sets the color of one data entry (identifier is previously assigned label) * \details the color name can be "red" or a hex number (\c \#FF0000 ). * \warning Either define all data entries with a color or no data entry. If a mixed approach is used, * plotly choses the color of the data entry (that could be the same as a user defined color). * \note If an unknown label is given, nothing happens. * \sa https://www.w3schools.com/cssref/css_colors.asp */ void SetColor(const std::string& label, const std::string& colorName); /*! * \brief Sets the line style of one data entry (identifier is previously assigned label) * \details two line styles are possible: LineStyle::solid and LineStyle::dashed. * The default line style is solid. * \note If an unknown label is given, nothing happens. * \warning only sets the line style if the current chart type is ChartType::line. * However, the line style remains also if the chart changes (e.g. new chart type) */ void SetLineStyle(const std::string& label, LineStyle style); /*! * \brief Sets the marker style of one data entry (identifier is previously assigned label) * \note If an unknown label is given, nothing happens. */ void SetMarkerSymbol(const std::string &label, MarkerSymbol symbol); /*! * \brief Sets the axis scale to either linear (default) or logarithmic. * \sa https://plot.ly/javascript/log-plot/ */ void SetYAxisScale(AxisScale scale); void SetXAxisLabel(const std::string& label); void SetYAxisLabel(const std::string& label); /*! * \brief Sets labels for pie chart data. * \note in AddData1D, the label still has to be given that acts as a unique id. However, the label is omitted then. */ void SetPieLabels(const std::vector &pieLabels, const std::string &label); /*! * \brief Sets a title for the chart. */ void SetTitle(const std::string &title); /*! * \brief Sets the chart type for a data entry * \details for available types, see ChartType * \note If an unknown label is given, nothing happens. * \warning Pie chart is significantly different than the other chart types. Here, the data given by AddData1D is summed. Each entry represents a different category. * \sa DiagramType for available types */ void SetChartType(const std::string& label, ChartType type); /*! * \brief Sets error bars for data in x direction * \note If only error plus is provided, the error bars are symmetrical * \param label the name of the data that is also used as identifier. * \param errorPlus the error in positive direction * \param errorMinus the error in negative direction. Same as error plus if omitted */ void SetXErrorBars(const std::string &label, const std::vector &errorPlus, const std::vector& errorMinus = std::vector()); /*! * \brief Sets error bars for data in y direction * \details for parameters, see SetXErrorBars * \note If only error plus is provided, the error bars are symmetrical */ void SetYErrorBars(const std::string &label, const std::vector &errorPlus, const std::vector &errorMinus = std::vector()); /*! * \brief Sets the legend position. * \details Default position is bottom. * \sa LegendPosition for available types */ void SetLegendPosition(LegendPosition position); void SetShowLegend(bool show); void SetStackedData(bool stacked); /*! * \brief Displays the chart in the widget * \param showSubChart if a subchart is displayed inside the widget or not. * \note if no data has been provided, (\sa AddData1D AddData2D), an empty chart is displayed. */ void Show(bool showSubChart=false); /*! * \brief Either displays the dataPoints or not * \param showDataPoints if dataPoints are displayed inside the widget or not. * \details: example for not showing points: https://plot.ly/javascript/line-charts/#styling-line-plot * example for showing the points: https://plot.ly/javascript/pointcloud/ */ void SetShowDataPoints(bool showDataPoints); /*! * \brief Clears all data inside and resets the widget. */ void Clear(); /*! * \brief Sets the theme of the widget. * \details default is dark theme as in MITK. * \warning has to be called before Show() or Reload() to work */ void SetTheme(ColorTheme themeEnabled); /*! * \brief Sets whether the subchart shall be shown. * \details Changes the state of the current chart object. * \note Needs to be reloaded with Reload() to display changes. */ void SetShowSubchart(bool showSubChart); /*! * \brief Sets whether the error bars shall be shown. * \details Changes the state of the current chart object. * \note Needs to be reloaded with Reload() to display changes. * \param showErrorBars if error bars are displayed or not. */ void SetShowErrorBars(bool showErrorBars); /*! * \brief Sets the min and max x values of the chart * \details Zooms in to view the values between minValue and maxValue in x direction */ void SetMinMaxValueXView(double minValueX,double maxValueX); /*! * \brief Sets the min and max y values of the chart * \details Zooms in to view the values between minValue and maxValue in y direction */ void SetMinMaxValueYView(double minValueY, double maxValueY); /*! * \brief Reloads the chart in the widget * \details reloading may be needed to display added data in an existing chart */ void Reload(); QSize sizeHint() const override; void SavePlotAsImage(); public slots: void OnLoadFinished(bool isLoadSuccessful); void OnPageSuccessfullyLoaded(); signals: void PageSuccessfullyLoaded(); private: /*! source: https://stackoverflow.com/questions/29383/converting-bool-to-text-in-c*/ std::string convertBooleanValue(bool value) const; class Impl; std::unique_ptr m_Impl; }; #endif diff --git a/Modules/Chart/src/QmitkChartWidget.cpp b/Modules/Chart/src/QmitkChartWidget.cpp index 68be33632a..dff85d5543 100644 --- a/Modules/Chart/src/QmitkChartWidget.cpp +++ b/Modules/Chart/src/QmitkChartWidget.cpp @@ -1,936 +1,940 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include #include #include #include #include "mitkExceptionMacro.h" #include #include class CustomPage : public QWebEnginePage { public: CustomPage(QObject *parent = nullptr) : QWebEnginePage(parent) {} virtual void javaScriptConsoleMessage(JavaScriptConsoleMessageLevel /*level*/, const QString &message, int lineNumber, const QString & /*sourceID*/) override { MITK_INFO << "JS > " << lineNumber << ": " << message.toStdString(); } }; class QmitkChartWidget::Impl final { public: explicit Impl(QWidget *parent); ~Impl(); Impl(const Impl &) = delete; Impl &operator=(const Impl &) = delete; void AddData1D(const std::vector &data1D, const std::string &label, QmitkChartWidget::ChartType chartType); void AddData2D(const std::vector< std::pair > &data2D, const std::string &label, QmitkChartWidget::ChartType chartType); void AddChartExampleData(const std::vector< std::pair >& data2D, const std::string& label, const std::string& type, const std::string& color, const std::string& style, const std::string& pieLabelsData = 0); void UpdateData1D(const std::vector &data1D, const std::string &label); void UpdateData2D(const std::vector< std::pair > &data2D, const std::string &label); void UpdateChartExampleData(const std::vector< std::pair >& data2D, const std::string& label, const std::string& type, const std::string& color, const std::string& lineStyle, const std::string& pieLabelsData = 0); void RemoveData(const std::string &label); void UpdateLabel(const std::string &existingLabel, const std::string &newLabel); QmitkChartxyData* GetDataElementByLabel(const std::string& label) const; void ClearData(); void SetColor(const std::string &label, const std::string &colorName); void SetLineStyle(const std::string &label, LineStyle style); void SetMarkerSymbol(const std::string &label, MarkerSymbol symbol); void SetYAxisScale(AxisScale scale); void SetXAxisLabel(const std::string &label); void SetYAxisLabel(const std::string &label); void SetPieLabels(const std::vector &pieLabels, const std::string &label); void SetTitle(const std::string &title); void SetXErrorBars(const std::string &label, const std::vector &errorPlus, const std::vector &errorMinus = std::vector()); void SetYErrorBars(const std::string &label, const std::vector &errorPlus, const std::vector &errorMinus = std::vector()); std::string GetThemeName() const; void SetThemeName(ColorTheme style); void SetLegendPosition(LegendPosition position); void Show(bool showSubChart); void SetShowLegend(bool show); void SetShowErrorBars(bool show); void SetStackedData(bool stacked); void SetShowDataPoints(bool showDataPoints = false); void SetShowSubchart(bool showSubChart); void SetChartType(const std::string &label, QmitkChartWidget::ChartType chartType); void SetMinMaxValueXView(double minValueX, double maxValueX); void SetMinMaxValueYView(double minValueY, double maxValueY); QList ConvertErrorVectorToQList(const std::vector &error); QList ConvertVectorToQList(const std::vector &vec); std::string ConvertChartTypeToString(QmitkChartWidget::ChartType chartType) const; void ClearJavaScriptChart(); void InitializeJavaScriptChart(); void CallJavaScriptFuntion(const QString &command); QSize sizeHint() const; void GetImageUrl(); private: using ChartxyDataVector = std::vector>; std::string GetUniqueLabelName(const QList &labelList, const std::string &label) const; QList GetDataLabels(const ChartxyDataVector &c3xyData) const; QWebChannel *m_WebChannel; QWebEngineView *m_WebEngineView; QmitkChartData m_C3Data; ChartxyDataVector m_C3xyData; std::map m_ChartTypeToName; std::map m_ChartColorToName; std::map m_ColorThemeToName; std::map m_LegendPositionToName; std::map m_LineStyleToName; std::map m_MarkerSymbolToName; std::map m_AxisScaleToName; }; QmitkChartWidget::Impl::Impl(QWidget *parent) : m_WebChannel(new QWebChannel(parent)), m_WebEngineView(new QWebEngineView(parent)) { // disable context menu for QWebEngineView m_WebEngineView->setContextMenuPolicy(Qt::NoContextMenu); m_WebEngineView->setPage(new CustomPage()); // Set the webengineview to an initial empty page. The actual chart will be loaded once the data is calculated. m_WebEngineView->load(QUrl(QStringLiteral("qrc:///Chart/empty.html"))); m_WebEngineView->page()->setWebChannel(m_WebChannel); m_WebEngineView->settings()->setAttribute(QWebEngineSettings::FocusOnNavigationEnabled, false); + //This is added as a workarround for T28252 (https://phabricator.mitk.org/T28252) + //can be removed if task is properly fixed. + m_WebEngineView->settings()->setAttribute(QWebEngineSettings::ShowScrollBars, false); + connect(m_WebEngineView, SIGNAL(loadFinished(bool)), parent, SLOT(OnLoadFinished(bool))); auto layout = new QGridLayout(parent); layout->setMargin(0); layout->addWidget(m_WebEngineView); m_ChartTypeToName.emplace(ChartType::bar, "bar"); m_ChartTypeToName.emplace(ChartType::line, "line"); m_ChartTypeToName.emplace(ChartType::spline, "spline"); m_ChartTypeToName.emplace(ChartType::pie, "pie"); m_ChartTypeToName.emplace(ChartType::area, "area"); m_ChartTypeToName.emplace(ChartType::area_spline, "area-spline"); m_ChartTypeToName.emplace(ChartType::scatter, "scatter"); m_ChartColorToName.emplace(ChartColor::red, "red"); m_ChartColorToName.emplace(ChartColor::orange, "orange"); m_ChartColorToName.emplace(ChartColor::yellow, "yellow"); m_ChartColorToName.emplace(ChartColor::green, "green"); m_ChartColorToName.emplace(ChartColor::blue, "blue"); m_ChartColorToName.emplace(ChartColor::purple, "purple"); m_ChartColorToName.emplace(ChartColor::brown, "brown"); m_ChartColorToName.emplace(ChartColor::magenta, "magenta"); m_ChartColorToName.emplace(ChartColor::tan, "tan"); m_ChartColorToName.emplace(ChartColor::cyan, "cyan"); m_ChartColorToName.emplace(ChartColor::olive, "olive"); m_ChartColorToName.emplace(ChartColor::maroon, "maroon"); m_ChartColorToName.emplace(ChartColor::navy, "navy"); m_ChartColorToName.emplace(ChartColor::aquamarine, "aquamarine"); m_ChartColorToName.emplace(ChartColor::turqouise, "turqouise"); m_ChartColorToName.emplace(ChartColor::silver, "silver"); m_ChartColorToName.emplace(ChartColor::lime, "lime"); m_ChartColorToName.emplace(ChartColor::teal, "teal"); m_ChartColorToName.emplace(ChartColor::indigo, "indigo"); m_ChartColorToName.emplace(ChartColor::violet, "violet"); m_ChartColorToName.emplace(ChartColor::pink, "pink"); m_ChartColorToName.emplace(ChartColor::black, "black"); m_ChartColorToName.emplace(ChartColor::white, "white"); m_ChartColorToName.emplace(ChartColor::grey, "grey"); m_LegendPositionToName.emplace(LegendPosition::bottomMiddle, "bottomMiddle"); m_LegendPositionToName.emplace(LegendPosition::bottomRight, "bottomRight"); m_LegendPositionToName.emplace(LegendPosition::topRight, "topRight"); m_LegendPositionToName.emplace(LegendPosition::topLeft, "topLeft"); m_LegendPositionToName.emplace(LegendPosition::middleRight, "middleRight"); m_LineStyleToName.emplace(LineStyle::solid, "solid"); m_LineStyleToName.emplace(LineStyle::dashed, "dashed"); m_MarkerSymbolToName.emplace(MarkerSymbol::circle, "circle"); m_MarkerSymbolToName.emplace(MarkerSymbol::cross, "cross"); m_MarkerSymbolToName.emplace(MarkerSymbol::diamond, "diamond"); m_MarkerSymbolToName.emplace(MarkerSymbol::pentagon, "pentagon"); m_MarkerSymbolToName.emplace(MarkerSymbol::square, "square"); m_MarkerSymbolToName.emplace(MarkerSymbol::star, "star"); m_MarkerSymbolToName.emplace(MarkerSymbol::x, "x"); m_MarkerSymbolToName.emplace(MarkerSymbol::diamond_tall, "diamond-tall"); m_MarkerSymbolToName.emplace(MarkerSymbol::star_diamond, "star-diamond"); m_MarkerSymbolToName.emplace(MarkerSymbol::star_triangle_up, "star-triangle-up"); m_MarkerSymbolToName.emplace(MarkerSymbol::star_triangle_down, "star-triangle-down"); m_MarkerSymbolToName.emplace(MarkerSymbol::asterisk, "asterisk"); m_MarkerSymbolToName.emplace(MarkerSymbol::cross_thin, "cross-thin"); m_MarkerSymbolToName.emplace(MarkerSymbol::x_thin, "x-thin"); m_AxisScaleToName.emplace(AxisScale::linear, ""); m_AxisScaleToName.emplace(AxisScale::log, "log"); m_ColorThemeToName.emplace(ColorTheme::lightstyle, "light"); m_ColorThemeToName.emplace(ColorTheme::darkstyle, "dark"); } QmitkChartWidget::Impl::~Impl() {} std::string QmitkChartWidget::Impl::GetThemeName() const { return m_C3Data.GetThemeName().toString().toStdString(); } std::string CheckForCorrectHex(const std::string &colorName) { std::regex rgx("([A-Fa-f0-9]{6}|[A-Fa-f0-9]{3})"); std::smatch match; if (!colorName.empty() && colorName.at(0) != '#' && std::regex_search(colorName.begin(), colorName.end(), match, rgx)) { return "#" + colorName; } else { return colorName; } } void QmitkChartWidget::Impl::GetImageUrl() { m_C3Data.EmitSignalImageUrl(); } void QmitkChartWidget::Impl::AddData1D(const std::vector &data1D, const std::string &label, QmitkChartWidget::ChartType type) { std::vector< std::pair > transformedData2D; unsigned int count = 0; // transform the 1D data to 2D data for (const auto &ele : data1D) { transformedData2D.emplace_back(count, ele); count++; } AddData2D(transformedData2D, label, type); } void QmitkChartWidget::Impl::AddData2D(const std::vector< std::pair > &data2D, const std::string &label, QmitkChartWidget::ChartType type) { const std::string chartTypeName(m_ChartTypeToName.at(type)); auto definedLabels = GetDataLabels(m_C3xyData); auto uniqueLabel = GetUniqueLabelName(definedLabels, label); unsigned int sizeOfC3xyData = static_cast(m_C3xyData.size()); m_C3xyData.push_back(std::make_unique(data2D, QVariant(QString::fromStdString(uniqueLabel)), QVariant(QString::fromStdString(chartTypeName)), QVariant(sizeOfC3xyData))); } void QmitkChartWidget::Impl::AddChartExampleData(const std::vector< std::pair >& data2D, const std::string& label, const std::string& type, const std::string& color, const std::string& lineStyle, const std::string& pieLabelsData) { auto definedLabels = GetDataLabels(m_C3xyData); auto uniqueLabel = GetUniqueLabelName(definedLabels, label); if (type == "scatter") { SetShowDataPoints(true); MITK_INFO << "Enabling data points for all because of scatter plot"; } unsigned int sizeOfC3xyData = static_cast(m_C3xyData.size()); std::unique_ptr chartData = std::make_unique( data2D, QVariant(QString::fromStdString(uniqueLabel)), QVariant(QString::fromStdString(type)), QVariant(sizeOfC3xyData)); chartData->SetColor(QVariant(QString::fromStdString(color))); chartData->SetLineStyle(QVariant(QString::fromStdString(lineStyle))); if (pieLabelsData != "") { std::string pieLabelsDataWorkingString = pieLabelsData; QList pieLabelsDataList; while (pieLabelsDataWorkingString.size() != 0) { QVariant oneElement = QString::fromStdString(pieLabelsDataWorkingString.substr(0, pieLabelsDataWorkingString.find(";"))); pieLabelsDataList.push_back(oneElement); if (pieLabelsDataWorkingString.find(";") != std::string::npos) { pieLabelsDataWorkingString.erase(0, pieLabelsDataWorkingString.find(";") + 1); } else { pieLabelsDataWorkingString.erase(pieLabelsDataWorkingString.begin(), pieLabelsDataWorkingString.end()); } } chartData->SetPieLabels(pieLabelsDataList); } m_C3xyData.push_back(std::move(chartData)); } void QmitkChartWidget::Impl::UpdateData1D(const std::vector &data1D, const std::string &label) { std::vector< std::pair > transformedData2D; unsigned int count = 0; // transform the 1D data to 2D data for (const auto &ele : data1D) { transformedData2D.emplace_back( count, ele ); count++; } UpdateData2D(transformedData2D, label); } void QmitkChartWidget::Impl::UpdateData2D(const std::vector< std::pair > &data2D, const std::string &label) { auto element = GetDataElementByLabel(label); if (element) element->SetData(data2D); } void QmitkChartWidget::Impl::UpdateChartExampleData(const std::vector< std::pair >& data2D, const std::string& label, const std::string& type, const std::string& color, const std::string& lineStyle, const std::string& pieLabelsData) { UpdateData2D(data2D, label); auto element = GetDataElementByLabel(label); if (element) { element->SetChartType(QString::fromStdString(type)); element->SetColor(QString::fromStdString(color)); element->SetLineStyle(QString::fromStdString(lineStyle)); if (pieLabelsData != "") { std::string pieLabelsDataWorkingString = pieLabelsData; QList pieLabelsDataList; while (pieLabelsDataWorkingString.size() != 0) { QVariant oneElement = QString::fromStdString(pieLabelsDataWorkingString.substr(0, pieLabelsDataWorkingString.find(";"))); pieLabelsDataList.push_back(oneElement); if (pieLabelsDataWorkingString.find(";") != std::string::npos) { pieLabelsDataWorkingString.erase(0, pieLabelsDataWorkingString.find(";") + 1); } else { pieLabelsDataWorkingString.erase(pieLabelsDataWorkingString.begin(), pieLabelsDataWorkingString.end()); } } element->SetPieLabels(pieLabelsDataList); } } } void QmitkChartWidget::Impl::RemoveData(const std::string &label) { for (ChartxyDataVector::iterator iter = m_C3xyData.begin(); iter != m_C3xyData.end(); ++iter) { if ((*iter)->GetLabel().toString().toStdString() == label) { m_C3xyData.erase(iter); return; } } throw std::invalid_argument("Cannot Remove Data because the label does not exist."); } void QmitkChartWidget::Impl::ClearData() { for (auto &xyData : m_C3xyData) { m_WebChannel->deregisterObject(xyData.get()); } m_C3xyData.clear(); } void QmitkChartWidget::Impl::UpdateLabel(const std::string &existingLabel, const std::string &newLabel) { auto element = GetDataElementByLabel(existingLabel); if (element) { auto definedLabels = GetDataLabels(m_C3xyData); auto uniqueLabel = GetUniqueLabelName(definedLabels, newLabel); element->SetLabel(QString::fromStdString(uniqueLabel)); } } void QmitkChartWidget::Impl::SetColor(const std::string &label, const std::string &colorName) { auto element = GetDataElementByLabel(label); if (element) { auto colorChecked = CheckForCorrectHex(colorName); element->SetColor(QVariant(QString::fromStdString(colorChecked))); } } void QmitkChartWidget::Impl::SetLineStyle(const std::string &label, LineStyle style) { auto element = GetDataElementByLabel(label); const std::string lineStyleName(m_LineStyleToName.at(style)); element->SetLineStyle(QVariant(QString::fromStdString(lineStyleName))); } void QmitkChartWidget::Impl::SetMarkerSymbol(const std::string &label, MarkerSymbol symbol) { auto element = GetDataElementByLabel(label); const std::string markerSymbolName(m_MarkerSymbolToName.at(symbol)); element->SetMarkerSymbol(QVariant(QString::fromStdString(markerSymbolName))); } void QmitkChartWidget::Impl::SetYAxisScale(AxisScale scale) { const std::string axisScaleName(m_AxisScaleToName.at(scale)); m_C3Data.SetYAxisScale(QString::fromStdString(axisScaleName)); } QmitkChartxyData *QmitkChartWidget::Impl::GetDataElementByLabel(const std::string &label) const { for (const auto &qmitkChartxyData : m_C3xyData) { if (qmitkChartxyData->GetLabel().toString() == label.c_str()) { return qmitkChartxyData.get(); } } return nullptr; } QList QmitkChartWidget::Impl::GetDataLabels(const ChartxyDataVector &c3xyData) const { QList dataLabels; for (auto element = c3xyData.begin(); element != c3xyData.end(); ++element) { dataLabels.push_back((*element)->GetLabel()); } return dataLabels; } void QmitkChartWidget::Impl::SetXAxisLabel(const std::string &label) { m_C3Data.SetXAxisLabel(QString::fromStdString(label)); } void QmitkChartWidget::Impl::SetYAxisLabel(const std::string &label) { m_C3Data.SetYAxisLabel(QString::fromStdString(label)); } void QmitkChartWidget::Impl::SetPieLabels(const std::vector &pieLabels, const std::string &label) { auto element = GetDataElementByLabel(label); if (element) { if (element->GetChartType() == QVariant("pie")) { auto dataY = element->GetYData(); element->SetPieLabels(ConvertVectorToQList(pieLabels)); if (static_cast(dataY.size()) != pieLabels.size()) { MITK_INFO << "data has " << dataY.size() << " entries whereas pie labels have " << pieLabels.size() << " entries. Unnamed pie labels automatically get a numerical label."; } } else { MITK_INFO << "label" << label << "has chart type " << element->GetChartType().toString().toStdString() << ", but pie is required"; } } } void QmitkChartWidget::Impl::SetTitle(const std::string &title) { m_C3Data.SetTitle(QString::fromStdString(title)); } void QmitkChartWidget::Impl::SetThemeName(QmitkChartWidget::ColorTheme style) { const std::string themeName(m_ColorThemeToName.at(style)); m_C3Data.SetThemeName(QString::fromStdString(themeName)); } void QmitkChartWidget::Impl::SetLegendPosition(QmitkChartWidget::LegendPosition legendPosition) { const std::string legendPositionName(m_LegendPositionToName.at(legendPosition)); m_C3Data.SetLegendPosition(QString::fromStdString(legendPositionName)); } void QmitkChartWidget::Impl::Show(bool showSubChart) { if (m_C3xyData.empty()) { MITK_WARN << "no data available for display in chart"; } else { m_C3Data.SetAppearance(showSubChart, m_C3xyData.front()->GetChartType() == QVariant("pie")); } InitializeJavaScriptChart(); } void QmitkChartWidget::Impl::SetShowLegend(bool show) { m_C3Data.SetShowLegend(show); } void QmitkChartWidget::Impl::SetStackedData(bool stacked) { m_C3Data.SetStackedData(stacked); } void QmitkChartWidget::Impl::SetShowErrorBars(bool show) { m_C3Data.SetShowErrorBars(show); } void QmitkChartWidget::Impl::SetShowDataPoints(bool showDataPoints) { if (showDataPoints == true) { m_C3Data.SetDataPointSize(6.5); } else { m_C3Data.SetDataPointSize(0); } } void QmitkChartWidget::Impl::SetShowSubchart(bool showSubChart) { m_C3Data.SetShowSubchart(showSubChart); } void QmitkChartWidget::Impl::SetChartType(const std::string &label, QmitkChartWidget::ChartType chartType) { auto element = GetDataElementByLabel(label); if (element) { if (chartType == ChartType::scatter) { SetShowDataPoints(true); MITK_INFO << "Enabling data points for all because of scatter plot"; } const std::string chartTypeName(m_ChartTypeToName.at(chartType)); element->SetChartType(QVariant(QString::fromStdString(chartTypeName))); } } void QmitkChartWidget::Impl::SetMinMaxValueXView(double minValueX, double maxValueX) { m_C3Data.SetMinValueXView(minValueX); m_C3Data.SetMaxValueXView(maxValueX); } void QmitkChartWidget::Impl::SetMinMaxValueYView(double minValueY, double maxValueY) { m_C3Data.SetMinValueYView(minValueY); m_C3Data.SetMaxValueYView(maxValueY); } QList QmitkChartWidget::Impl::ConvertErrorVectorToQList(const std::vector &error) { QList errorConverted; for (const auto &aValue : error) { errorConverted.append(aValue); } return errorConverted; } QList QmitkChartWidget::Impl::ConvertVectorToQList(const std::vector &vec) { QList vecConverted; for (const auto &aValue : vec) { vecConverted.append(QString::fromStdString(aValue)); } return vecConverted; } void QmitkChartWidget::Impl::SetXErrorBars(const std::string &label, const std::vector &errorPlus, const std::vector &errorMinus) { auto element = GetDataElementByLabel(label); if (element) { auto errorConvertedPlus = ConvertErrorVectorToQList(errorPlus); auto errorConvertedMinus = ConvertErrorVectorToQList(errorMinus); element->SetXErrorDataPlus(errorConvertedPlus); element->SetXErrorDataMinus(errorConvertedMinus); } } void QmitkChartWidget::Impl::SetYErrorBars(const std::string &label, const std::vector &errorPlus, const std::vector &errorMinus) { auto element = GetDataElementByLabel(label); if (element) { auto errorConvertedPlus = ConvertErrorVectorToQList(errorPlus); auto errorConvertedMinus = ConvertErrorVectorToQList(errorMinus); element->SetYErrorDataPlus(errorConvertedPlus); element->SetYErrorDataMinus(errorConvertedMinus); } } std::string QmitkChartWidget::Impl::ConvertChartTypeToString(QmitkChartWidget::ChartType chartType) const { return m_ChartTypeToName.at(chartType); } QSize QmitkChartWidget::Impl::sizeHint() const { return QSize(400, 300); } void QmitkChartWidget::Impl::CallJavaScriptFuntion(const QString &command) { m_WebEngineView->page()->runJavaScript(command); } void QmitkChartWidget::Impl::ClearJavaScriptChart() { m_WebEngineView->load(QUrl(QStringLiteral("qrc:///Chart/empty.html"))); } void QmitkChartWidget::Impl::InitializeJavaScriptChart() { auto alreadyRegisteredObjects = m_WebChannel->registeredObjects(); auto alreadyRegisteredObjectsValues = alreadyRegisteredObjects.values(); // only register objects that have not been registered yet if (alreadyRegisteredObjectsValues.indexOf(&m_C3Data) == -1) { m_WebChannel->registerObject(QStringLiteral("chartData"), &m_C3Data); } unsigned count = 0; for (auto &xyData : m_C3xyData) { // only register objects that have not been registered yet if (alreadyRegisteredObjectsValues.indexOf(xyData.get()) == -1) { QString variableName = "xyData" + QString::number(count); m_WebChannel->registerObject(variableName, xyData.get()); } count++; } m_WebEngineView->load(QUrl(QStringLiteral("qrc:///Chart/QmitkChartWidget.html"))); } std::string QmitkChartWidget::Impl::GetUniqueLabelName(const QList &labelList, const std::string &label) const { QString currentLabel = QString::fromStdString(label); int counter = 0; while (labelList.contains(currentLabel)) { currentLabel = QString::fromStdString(label + std::to_string(counter)); counter++; } return currentLabel.toStdString(); } QmitkChartWidget::QmitkChartWidget(QWidget *parent) : QWidget(parent), m_Impl(new Impl(this)) { connect(this, &QmitkChartWidget::PageSuccessfullyLoaded, this, &QmitkChartWidget::OnPageSuccessfullyLoaded); } QmitkChartWidget::~QmitkChartWidget() {} void QmitkChartWidget::SetColor(const std::string &label, const std::string &colorName) { m_Impl->SetColor(label, colorName); } void QmitkChartWidget::SetLineStyle(const std::string &label, LineStyle style) { m_Impl->SetLineStyle(label, style); } void QmitkChartWidget::SetMarkerSymbol(const std::string &label, MarkerSymbol symbol) { m_Impl->SetMarkerSymbol(label, symbol); } void QmitkChartWidget::SetYAxisScale(AxisScale scale) { m_Impl->SetYAxisScale(scale); } void QmitkChartWidget::AddData1D(const std::vector &data1D, const std::string &label, ChartType type) { m_Impl->AddData1D(data1D, label, type); } void QmitkChartWidget::AddData2D(const std::vector< std::pair >& data2D, const std::string& label, ChartType type) { m_Impl->AddData2D(data2D, label, type); } void QmitkChartWidget::AddChartExampleData(const std::vector< std::pair >& data2D, const std::string& label, const std::string& type, const std::string& color, const std::string& lineStyle, const std::string& pieLabelsData) { m_Impl->AddChartExampleData(data2D, label, type, color, lineStyle, pieLabelsData); } void QmitkChartWidget::UpdateData1D(const std::vector &data1D, const std::string &label) { m_Impl->UpdateData1D(data1D, label); } void QmitkChartWidget::UpdateData2D(const std::vector< std::pair > &data2D, const std::string &label) { m_Impl->UpdateData2D(data2D, label); } void QmitkChartWidget::UpdateChartExampleData(const std::vector< std::pair >& data2D, const std::string& label, const std::string& type, const std::string& color, const std::string& lineStyle, const std::string& pieLabelsData) { m_Impl->UpdateChartExampleData(data2D, label, type, color, lineStyle, pieLabelsData); } void QmitkChartWidget::RemoveData(const std::string &label) { m_Impl->RemoveData(label); } void QmitkChartWidget::UpdateLabel(const std::string &existingLabel, const std::string &newLabel) { m_Impl->UpdateLabel(existingLabel, newLabel); } QmitkChartxyData* QmitkChartWidget::GetDataElementByLabel(const std::string& label) const { return m_Impl->GetDataElementByLabel(label); } void QmitkChartWidget::SetXAxisLabel(const std::string &label) { m_Impl->SetXAxisLabel(label); } void QmitkChartWidget::SetYAxisLabel(const std::string &label) { m_Impl->SetYAxisLabel(label); } void QmitkChartWidget::SetPieLabels(const std::vector &pieLabels, const std::string &label) { m_Impl->SetPieLabels(pieLabels, label); } void QmitkChartWidget::SetTitle(const std::string &title) { m_Impl->SetTitle(title); } void QmitkChartWidget::SetShowDataPoints(bool showDataPoints) { m_Impl->SetShowDataPoints(showDataPoints); } void QmitkChartWidget::SetChartType(const std::string &label, ChartType type) { m_Impl->SetChartType(label, type); } void QmitkChartWidget::SetXErrorBars(const std::string &label, const std::vector &errorPlus, const std::vector &errorMinus) { m_Impl->SetXErrorBars(label, errorPlus, errorMinus); } void QmitkChartWidget::SetYErrorBars(const std::string &label, const std::vector &errorPlus, const std::vector &errorMinus) { m_Impl->SetYErrorBars(label, errorPlus, errorMinus); } void QmitkChartWidget::SetLegendPosition(LegendPosition position) { m_Impl->SetLegendPosition(position); } void QmitkChartWidget::SetShowLegend(bool show) { m_Impl->SetShowLegend(show); } void QmitkChartWidget::SetStackedData(bool stacked) { m_Impl->SetStackedData(stacked); } void QmitkChartWidget::Show(bool showSubChart) { m_Impl->Show(showSubChart); } void QmitkChartWidget::Clear() { m_Impl->ClearData(); m_Impl->ClearJavaScriptChart(); } void QmitkChartWidget::OnLoadFinished(bool isLoadSuccessful) { if (isLoadSuccessful) { emit PageSuccessfullyLoaded(); } } void QmitkChartWidget::OnPageSuccessfullyLoaded() { auto themeName = m_Impl->GetThemeName(); QString command; if (themeName == "dark") { command = QString("changeTheme('dark')"); } else { command = QString("changeTheme('light')"); } m_Impl->CallJavaScriptFuntion(command); } void QmitkChartWidget::SetTheme(ColorTheme themeEnabled) { m_Impl->SetThemeName(themeEnabled); } void QmitkChartWidget::SetShowSubchart(bool showSubChart) { m_Impl->SetShowSubchart(showSubChart); } void QmitkChartWidget::SetShowErrorBars(bool showErrorBars) { m_Impl->SetShowErrorBars(showErrorBars); } void QmitkChartWidget::SetMinMaxValueXView(double minValueX, double maxValueX) { m_Impl->SetMinMaxValueXView(minValueX, maxValueX); } void QmitkChartWidget::SetMinMaxValueYView(double minValueY, double maxValueY) { m_Impl->SetMinMaxValueYView(minValueY, maxValueY); } void QmitkChartWidget::Reload() { const QString command = QString("Reload()"); m_Impl->CallJavaScriptFuntion(command); } QSize QmitkChartWidget::sizeHint() const { return m_Impl->sizeHint(); } void QmitkChartWidget::SavePlotAsImage() { m_Impl->GetImageUrl(); } diff --git a/Modules/Classification/CLCore/include/mitkAbstractGlobalImageFeature.h b/Modules/Classification/CLCore/include/mitkAbstractGlobalImageFeature.h index b72e15a9f5..c28967a9e4 100644 --- a/Modules/Classification/CLCore/include/mitkAbstractGlobalImageFeature.h +++ b/Modules/Classification/CLCore/include/mitkAbstractGlobalImageFeature.h @@ -1,342 +1,342 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkAbstractGlobalImageFeature_h #define mitkAbstractGlobalImageFeature_h #include #include #include #include #include // STD Includes // Eigen #include // MITK includes #include namespace mitk { /**Used as ID for features calculated by feature classes*/ struct MITKCLCORE_EXPORT FeatureID { /**Name of the feature*/ std::string name; /**Name of the feature class*/ std::string featureClass; /**ID for the setting that is represented by parameters and is specified by the feature class while calculating the features. It must be as unique as the parameters themself.*/ std::string settingID; /**Alternative name that containes the legacy naming of the feature that encodes the parametersetting directly in the string.*/ std::string legacyName; /**Version of the feature definition*/ std::string version = "1"; using ParametersType = std::map; ParametersType parameters; bool operator < (const FeatureID& rh) const; bool operator ==(const FeatureID& rh) const; }; /**Helper that takes a pass templateID clones it and populates it with the also passed informations befor returning it. * @param templateID reference ID that should be cloned. * @param name Name of the feature.*/ MITKCLCORE_EXPORT FeatureID CreateFeatureID(FeatureID templateID, std::string name); /** * * * ## Histogram Configuration ## * Most Feature Generation Classes that use histograms use the same parameters and * initialization logic. In general, all information can be passed either by the corresponding * Setter (which does not differenciate between global setting and feature specific setting) and * a parameter object which can be obtained from the command line arguments, for example. * * If the image values are used for the initializiation of the histogram, it can be defined * whether the whole image is used or only the masked areas to find minima and maxima. This is * done by the option SetIgnoreMask or the corrsponding options - * -NAME::ignore-mask-for-histogram and -ignore-mask-for-histogram. If these are + * -%NAME::ignore-mask-for-histogram and -ignore-mask-for-histogram. If these are * true, the whole image is used for the calculation. * * Depending on the passed arguments, different initialization methods are used. The initialization * is in the following order: * - If Minimum Intensity, Maximum Intensity, and Binsize: The histogram is * initialized between the minimum and maximum intensity. the number of bins is determined by the * binsize. If the distance between minimum and maximum is not a multiple of the binsize, the maximum * is increase so that it is. * - Minimum Intensity, Bins, and Binsize: The histogram is initialized with the * given binsize, and the intensity range from the minimum to \f$maximum = minimum + binsize*bins\f$. * - Minimum Intensity, Maximum Intensity, and Bins: The histogram is initialized * between the given minimum and maximum intensity. The binsize is calculated so that the number * of bins is equal to the given number of bins. * - Binsize, and Minimum Intensity: The maximum is set to the maximum that * occur in the given image. Depending if the mask is considered or not, either only masked voxels or * the whole image is used for the calculation. The initialization is then equal as if the minimum * and maximum would have been given right from the beginning. * - Binsize, and Maximum Intensity: The minimum intensity is set to the minimum that * occur in the given image. Depending if the mask is considered or not, either only masked voxels or * the whole image is used for the calculation. The initialization is then equal as if the minimum * and maximum would have been given right from the beginning. * - Binsize: The maximum and the minimum intensity is set to the minimum and maximum that * occur in the given image. Depending if the mask is considered or not, either only masked voxels or * the whole image is used for the calculation. The initialization is then equal as if the minimum * and maximum would have been given right from the beginning. * - Bins, and Minimum Intensity: The maximum is calculated from the image. Depending * if the mask is considered or not, either only masked voxels or the whole image is used for the calculation. The histogram is * then initialized as if these values would have been given as minimum and maximum intensity. * - Bins, and Maximum Intensity: The minimum is calculated from the image. Depending * if the mask is considered or not, either only masked voxels or the whole image is used for the calculation. The histogram is * then initialized as if these values would have been given as minimum and maximum intensity. * - Bins: The minimum and the maximum is calculated from the image. Depending * if the mask is considered or not, either only masked voxels or * the whole image is used for the calculation. The histogram is * then initialized as if these values would have been given as minimum and maximum intensity. * - No Parameter given:The minimum and maximum intensity from the whole image or masked image is calculated and * the histogram then initialized to this with a standard number of bins (Is set by each filter on its own.) * * ### Remark about command line parameter#### * There are generally two options to set a parameter via the command line. A global one that works for * all filters that use histograms and a local one that set this parameter specific for this filter. The * local parameters start with the filter name (Indiciated by NAME) followed by two colons, for example * vol::min to set the minimum intensity for the volume filter. The global parameter is overwritten * by the local parameter, if it is specified. Otherwise, it is still valid. If this prevents the specification * of an histogram initialization method (for example, because the binsize is globally specified but the histogram * should be initialized using a fixed numbe of bins), the parameter NAME::ignore-global-histogram can be passed. * Then, all global histogram parameters are ignored and only local ones are used. * * The maximum intensity can be set by different command line parameters: global for all filters that use histograms * by -minimum-intensity and -minimum. Alternative it can be set only for this filter by - * -NAME::minimum and -NAME::min. + * -%NAME::minimum and -%NAME::min. * * The minimum intensity can be set by different command line parameters: global for all filters that use histograms * by -maximum-intensity and -maximum. Alternative it can be set only for this filter by - * -NAME::maximum and -NAME::max. + * -%NAME::maximum and -%NAME::max. * * The binsize can be set by different command line parameters: global for all filters that use histograms * by -binsize. Alternative it can be set only for this filter by - * -NAME::binsize. + * -%NAME::binsize. * * The number of bins can be set by different command line parameters: global for all filters that use histograms * by -bins. Alternative it can be set only for this filter by - * -NAME::bins. + * -%NAME::bins. * ### Note to the developers ### * All features are supposed to work the same way if a histogram is used somewhere in * the code. For this, each derived class that makes use of a histogram should use * the Quantifier object. In order to use this object correctly, the AddArguments-Function should * contain the line AddQuantifierArguments(parser);, the CalculateFeaturesUsingParameters function * should contain the line InitializeQuantifierFromParameters(feature, mask); and the CalculateFeatures function * sould contain the line InitializeQuantifier(image, mask);. These function * calls ensure that the necessary options are given to the configuration file, and that the initialization * of the quantifier is done correctly. This ensures an consistend behavior over all FeatureGeneration Classes. * */ class MITKCLCORE_EXPORT AbstractGlobalImageFeature : public BaseData { public: mitkClassMacro(AbstractGlobalImageFeature, BaseData); typedef std::vector< std::pair > FeatureListType; using ParametersType = FeatureID::ParametersType; /** * \brief Calculates the feature of this abstact interface. Does not necessarily considers the parameter settings. */ FeatureListType CalculateFeatures(const Image* image, const Image* mask); virtual FeatureListType CalculateFeatures(const Image* image, const Image* mask, const Image* maskNoNAN) = 0; /** * \brief Calculates the given feature Slice-wise. Might not be availble for an individual filter! */ FeatureListType CalculateFeaturesSlicewise(const Image::Pointer & image, const Image::Pointer &mask, int sliceID); /** * \brief Calculates the feature of this abstact interface. Does not necessarily considers the parameter settings. */ virtual void CalculateAndAppendFeaturesSliceWise(const Image::Pointer & image, const Image::Pointer &mask, int sliceID, FeatureListType &featureList, bool checkParameterActivation = true); /** * \brief Calculates the feature of this abstact interface. Does not necessarily considers the parameter settings. * @param image * @param mask * @param maskNoNaN * @param featureList * @param checkParameterActivation Indicates if the features should only be calculated and added if the FeatureClass is activated in the parameters. * True: only append if activated in the parametes. False: always and append it. */ void CalculateAndAppendFeatures(const Image* image, const Image* mask, const Image* maskNoNaN, FeatureListType &featureList, bool checkParameterActivation = true); itkSetMacro(Prefix, std::string); itkSetMacro(ShortName, std::string); itkSetMacro(LongName, std::string); itkSetMacro(FeatureClassName, std::string); itkSetMacro(Direction, int); void SetParameters(ParametersType param) { m_Parameters = param; this->ConfigureQuantifierSettingsByParameters(); this->ConfigureSettingsByParameters(param); this->Modified(); }; itkGetConstMacro(Prefix, std::string); itkGetConstMacro(ShortName, std::string); itkGetConstMacro(LongName, std::string); itkGetConstMacro(FeatureClassName, std::string); itkGetConstMacro(Parameters, ParametersType); itkGetMacro(Quantifier, IntensityQuantifier::Pointer); itkGetConstMacro(Direction, int); itkSetMacro(MinimumIntensity, double); itkSetMacro(UseMinimumIntensity, bool); itkSetMacro(MaximumIntensity, double); itkSetMacro(UseMaximumIntensity, bool); itkGetConstMacro(MinimumIntensity, double); itkGetConstMacro(UseMinimumIntensity, bool); itkGetConstMacro(MaximumIntensity, double); itkGetConstMacro(UseMaximumIntensity, bool); itkSetMacro(Binsize, double); itkSetMacro(UseBinsize, bool); itkGetConstMacro(Binsize, double); itkGetConstMacro(UseBinsize, bool); itkSetMacro(MorphMask, mitk::Image::Pointer); itkGetConstMacro(MorphMask, mitk::Image::Pointer); itkSetMacro(Bins, int); itkSetMacro(UseBins, bool); itkGetConstMacro(UseBins, bool); itkGetConstMacro(Bins, int); itkSetMacro(IgnoreMask, bool); itkGetConstMacro(IgnoreMask, bool); itkSetMacro(EncodeParametersInFeaturePrefix, bool); itkGetConstMacro(EncodeParametersInFeaturePrefix, bool); itkBooleanMacro(EncodeParametersInFeaturePrefix); std::string GetOptionPrefix() const { if (!m_Prefix.empty()) return m_Prefix + "::" + m_ShortName; return m_ShortName; } /** Can be called to add all relevant argument for configuring the feature instance to the passed parser instance. Must be implemented be derived classes. For adding the quantifier arguments use AddQuantifierArguments(...) as helper function.*/ virtual void AddArguments(mitkCommandLineParser &parser) const = 0; /** Helper function that generates the legacy feature name without encoding of parameters; as it is used e.g. in the unit tests.*/ static std::string GenerateLegacyFeatureNameWOEncoding(const FeatureID& id); protected: std::vector SplitDouble(std::string str, char delimiter); virtual FeatureListType DoCalculateFeatures(const Image* image, const Image* mask) = 0; void AddQuantifierArguments(mitkCommandLineParser& parser) const; /** Ensures that all quantifier relevant variables of the instance are set correctly given the information in m_Parameters.*/ void ConfigureQuantifierSettingsByParameters(); /** Ensures that the instance is configured according to the information given in the passed parameters. * This method will be called by SetParameters(...) after ConfigureQuantifierSettingsByParameters() was called.*/ virtual void ConfigureSettingsByParameters(const ParametersType& parameters); /**Initializes the quantifier gigen the quantifier relevant variables and the passed arguments.*/ void InitializeQuantifier(const Image* image, const Image* mask, unsigned int defaultBins = 256); /** Helper that encodes the quantifier parameters in a string (e.g. used for the legacy feature name)*/ std::string QuantifierParameterString() const; /* Creates a template feature id. * it will set the featureClass, the settingID (assuming that it is the featureClass with the passed suffix * and all parameters that are global or have the option prefix of the instance.*/ FeatureID CreateTemplateFeatureID(std::string settingsSuffix = "", FeatureID::ParametersType additionalParams = {}); /** Helper that generates the legacy feature names for a passed FeatureID. * Format of the legacy feature name is: \::[\::]\ * Overwrite GenerateLegacyFeatureNamePart and GenerateLegacyFeatureEncoding to change behavior in * derived classes. */ virtual std::string GenerateLegacyFeatureName(const FeatureID& id) const; virtual std::string GenerateLegacyFeatureNamePart(const FeatureID& id) const; virtual std::string GenerateLegacyFeatureEncoding(const FeatureID& id) const; public: //#ifndef DOXYGEN_SKIP void SetRequestedRegionToLargestPossibleRegion() override {}; bool RequestedRegionIsOutsideOfTheBufferedRegion() override { return true; }; bool VerifyRequestedRegion() override { return false; }; void SetRequestedRegion (const itk::DataObject * /*data*/) override {}; // Override bool IsEmpty() const override { if(IsInitialized() == false) return true; const TimeGeometry* timeGeometry = const_cast(this)->GetUpdatedTimeGeometry(); if(timeGeometry == nullptr) return true; return false; } private: std::string m_Prefix; // Prefix before all input parameters std::string m_ShortName; // Name of all variables std::string m_LongName; // Long version of the name (For turning on) std::string m_FeatureClassName; ParametersType m_Parameters; // Parameter setting mitk::Image::Pointer m_MorphMask = nullptr; IntensityQuantifier::Pointer m_Quantifier; //Quantifier relevant variables double m_MinimumIntensity = 0; bool m_UseMinimumIntensity = false; double m_MaximumIntensity = 100; bool m_UseMaximumIntensity = false; bool m_EncodeParametersInFeaturePrefix = false; double m_Binsize = 1; bool m_UseBinsize = false; int m_Bins = 256; bool m_UseBins = true; int m_Direction = 0; bool m_IgnoreMask = false; //#endif // Skip Doxygen }; } #endif //mitkAbstractGlobalImageFeature_h diff --git a/Modules/Classification/CLMiniApps/CLGlobalImageFeatures.cpp b/Modules/Classification/CLMiniApps/CLGlobalImageFeatures.cpp index 76b347d77a..80ba5e8016 100644 --- a/Modules/Classification/CLMiniApps/CLGlobalImageFeatures.cpp +++ b/Modules/Classification/CLMiniApps/CLGlobalImageFeatures.cpp @@ -1,789 +1,786 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkCLPolyToNrrd_cpp #define mitkCLPolyToNrrd_cpp #include "time.h" #include #include #include #include "mitkCommandLineParser.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "itkNearestNeighborInterpolateImageFunction.h" #include "itkResampleImageFilter.h" #include #include #include "QmitkRegisterClasses.h" #include "QmitkRenderWindow.h" #include "vtkRenderLargeImage.h" #include "vtkPNGWriter.h" typedef itk::Image< double, 3 > FloatImageType; typedef itk::Image< unsigned short, 3 > MaskImageType; template class punct_facet : public std::numpunct { public: punct_facet(charT sep) : m_Sep(sep) { } protected: charT do_decimal_point() const override { return m_Sep; } private: charT m_Sep; }; template void ResampleImage(itk::Image* itkImage, float resolution, mitk::Image::Pointer& newImage) { typedef itk::Image ImageType; typedef itk::ResampleImageFilter ResampleFilterType; typename ResampleFilterType::Pointer resampler = ResampleFilterType::New(); auto spacing = itkImage->GetSpacing(); auto size = itkImage->GetLargestPossibleRegion().GetSize(); for (unsigned int i = 0; i < VImageDimension; ++i) { size[i] = size[i] / (1.0*resolution)*(1.0*spacing[i])+1.0; } spacing.Fill(resolution); resampler->SetInput(itkImage); resampler->SetSize(size); resampler->SetOutputSpacing(spacing); resampler->SetOutputOrigin(itkImage->GetOrigin()); resampler->SetOutputDirection(itkImage->GetDirection()); resampler->Update(); newImage->InitializeByItk(resampler->GetOutput()); mitk::GrabItkImageMemory(resampler->GetOutput(), newImage); } template static void CreateNoNaNMask(itk::Image* itkValue, mitk::Image::Pointer mask, mitk::Image::Pointer& newMask) { typedef itk::Image< TPixel, VImageDimension> LFloatImageType; typedef itk::Image< unsigned short, VImageDimension> LMaskImageType; typename LMaskImageType::Pointer itkMask = LMaskImageType::New(); mitk::CastToItkImage(mask, itkMask); typedef itk::ImageDuplicator< LMaskImageType > DuplicatorType; typename DuplicatorType::Pointer duplicator = DuplicatorType::New(); duplicator->SetInputImage(itkMask); duplicator->Update(); auto tmpMask = duplicator->GetOutput(); itk::ImageRegionIterator mask1Iter(itkMask, itkMask->GetLargestPossibleRegion()); itk::ImageRegionIterator mask2Iter(tmpMask, tmpMask->GetLargestPossibleRegion()); itk::ImageRegionIterator imageIter(itkValue, itkValue->GetLargestPossibleRegion()); while (!mask1Iter.IsAtEnd()) { mask2Iter.Set(0); if (mask1Iter.Value() > 0) { // Is not NaN if (imageIter.Value() == imageIter.Value()) { mask2Iter.Set(1); } } ++mask1Iter; ++mask2Iter; ++imageIter; } newMask->InitializeByItk(tmpMask); mitk::GrabItkImageMemory(tmpMask, newMask); } template static void ResampleMask(itk::Image* itkMoving, mitk::Image::Pointer ref, mitk::Image::Pointer& newMask) { typedef itk::Image< TPixel, VImageDimension> LMaskImageType; typedef itk::NearestNeighborInterpolateImageFunction< LMaskImageType> NearestNeighborInterpolateImageFunctionType; typedef itk::ResampleImageFilter ResampleFilterType; typename NearestNeighborInterpolateImageFunctionType::Pointer nn_interpolator = NearestNeighborInterpolateImageFunctionType::New(); typename LMaskImageType::Pointer itkRef = LMaskImageType::New(); mitk::CastToItkImage(ref, itkRef); typename ResampleFilterType::Pointer resampler = ResampleFilterType::New(); resampler->SetInput(itkMoving); resampler->SetReferenceImage(itkRef); resampler->UseReferenceImageOn(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); newMask->InitializeByItk(resampler->GetOutput()); mitk::GrabItkImageMemory(resampler->GetOutput(), newMask); } static void ExtractSlicesFromImages(mitk::Image::Pointer image, mitk::Image::Pointer mask, mitk::Image::Pointer maskNoNaN, mitk::Image::Pointer morphMask, int direction, std::vector &imageVector, std::vector &maskVector, std::vector &maskNoNaNVector, std::vector &morphMaskVector) { typedef itk::Image< double, 2 > FloatImage2DType; typedef itk::Image< unsigned short, 2 > MaskImage2DType; FloatImageType::Pointer itkFloat = FloatImageType::New(); MaskImageType::Pointer itkMask = MaskImageType::New(); MaskImageType::Pointer itkMaskNoNaN = MaskImageType::New(); MaskImageType::Pointer itkMorphMask = MaskImageType::New(); mitk::CastToItkImage(mask, itkMask); mitk::CastToItkImage(maskNoNaN, itkMaskNoNaN); mitk::CastToItkImage(image, itkFloat); mitk::CastToItkImage(morphMask, itkMorphMask); int idxA, idxB, idxC; switch (direction) { case 0: idxA = 1; idxB = 2; idxC = 0; break; case 1: idxA = 0; idxB = 2; idxC = 1; break; case 2: idxA = 0; idxB = 1; idxC = 2; break; default: idxA = 1; idxB = 2; idxC = 0; break; } auto imageSize = image->GetLargestPossibleRegion().GetSize(); FloatImageType::IndexType index3D; FloatImage2DType::IndexType index2D; FloatImage2DType::SpacingType spacing2D; spacing2D[0] = itkFloat->GetSpacing()[idxA]; spacing2D[1] = itkFloat->GetSpacing()[idxB]; for (unsigned int i = 0; i < imageSize[idxC]; ++i) { FloatImage2DType::RegionType region; FloatImage2DType::IndexType start; FloatImage2DType::SizeType size; start[0] = 0; start[1] = 0; size[0] = imageSize[idxA]; size[1] = imageSize[idxB]; region.SetIndex(start); region.SetSize(size); FloatImage2DType::Pointer image2D = FloatImage2DType::New(); image2D->SetRegions(region); image2D->Allocate(); MaskImage2DType::Pointer mask2D = MaskImage2DType::New(); mask2D->SetRegions(region); mask2D->Allocate(); MaskImage2DType::Pointer masnNoNaN2D = MaskImage2DType::New(); masnNoNaN2D->SetRegions(region); masnNoNaN2D->Allocate(); MaskImage2DType::Pointer morph2D = MaskImage2DType::New(); morph2D->SetRegions(region); morph2D->Allocate(); unsigned long voxelsInMask = 0; for (unsigned int a = 0; a < imageSize[idxA]; ++a) { for (unsigned int b = 0; b < imageSize[idxB]; ++b) { index3D[idxA] = a; index3D[idxB] = b; index3D[idxC] = i; index2D[0] = a; index2D[1] = b; image2D->SetPixel(index2D, itkFloat->GetPixel(index3D)); mask2D->SetPixel(index2D, itkMask->GetPixel(index3D)); masnNoNaN2D->SetPixel(index2D, itkMaskNoNaN->GetPixel(index3D)); morph2D->SetPixel(index2D, itkMorphMask->GetPixel(index3D)); voxelsInMask += (itkMask->GetPixel(index3D) > 0) ? 1 : 0; } } image2D->SetSpacing(spacing2D); mask2D->SetSpacing(spacing2D); masnNoNaN2D->SetSpacing(spacing2D); morph2D->SetSpacing(spacing2D); mitk::Image::Pointer tmpFloatImage = mitk::Image::New(); tmpFloatImage->InitializeByItk(image2D.GetPointer()); mitk::GrabItkImageMemory(image2D, tmpFloatImage); mitk::Image::Pointer tmpMaskImage = mitk::Image::New(); tmpMaskImage->InitializeByItk(mask2D.GetPointer()); mitk::GrabItkImageMemory(mask2D, tmpMaskImage); mitk::Image::Pointer tmpMaskNoNaNImage = mitk::Image::New(); tmpMaskNoNaNImage->InitializeByItk(masnNoNaN2D.GetPointer()); mitk::GrabItkImageMemory(masnNoNaN2D, tmpMaskNoNaNImage); mitk::Image::Pointer tmpMorphMaskImage = mitk::Image::New(); tmpMorphMaskImage->InitializeByItk(morph2D.GetPointer()); mitk::GrabItkImageMemory(morph2D, tmpMorphMaskImage); if (voxelsInMask > 0) { imageVector.push_back(tmpFloatImage); maskVector.push_back(tmpMaskImage); maskNoNaNVector.push_back(tmpMaskNoNaNImage); morphMaskVector.push_back(tmpMorphMaskImage); } } } static void SaveSliceOrImageAsPNG(mitk::Image::Pointer image, mitk::Image::Pointer mask, std::string path, int index) { // Create a Standalone Datastorage for the single purpose of saving screenshots.. mitk::StandaloneDataStorage::Pointer ds = mitk::StandaloneDataStorage::New(); QmitkRenderWindow renderWindow; renderWindow.GetRenderer()->SetDataStorage(ds); auto nodeI = mitk::DataNode::New(); nodeI->SetData(image); auto nodeM = mitk::DataNode::New(); nodeM->SetData(mask); ds->Add(nodeI); ds->Add(nodeM); auto geo = ds->ComputeBoundingGeometry3D(ds->GetAll()); mitk::RenderingManager::GetInstance()->InitializeViews(geo); mitk::SliceNavigationController::Pointer sliceNaviController = renderWindow.GetSliceNavigationController(); unsigned int numberOfSteps = 1; if (sliceNaviController) { numberOfSteps = sliceNaviController->GetSlice()->GetSteps(); sliceNaviController->GetSlice()->SetPos(0); } renderWindow.show(); renderWindow.resize(256, 256); for (unsigned int currentStep = 0; currentStep < numberOfSteps; ++currentStep) { if (sliceNaviController) { sliceNaviController->GetSlice()->SetPos(currentStep); } renderWindow.GetRenderer()->PrepareRender(); vtkRenderWindow* renderWindow2 = renderWindow.GetVtkRenderWindow(); mitk::BaseRenderer* baserenderer = mitk::BaseRenderer::GetInstance(renderWindow2); auto vtkRender = baserenderer->GetVtkRenderer(); vtkRender->GetRenderWindow()->WaitForCompletion(); vtkRenderLargeImage* magnifier = vtkRenderLargeImage::New(); magnifier->SetInput(vtkRender); magnifier->SetMagnification(3.0); std::stringstream ss; ss << path << "_Idx-" << index << "_Step-"<> tmpImageName; auto fileWriter = vtkPNGWriter::New(); fileWriter->SetInputConnection(magnifier->GetOutputPort()); fileWriter->SetFileName(tmpImageName.c_str()); fileWriter->Write(); fileWriter->Delete(); } } int main(int argc, char* argv[]) { // Commented : Updated to a common interface, include, if possible, mask is type unsigned short, uses Quantification, Comments // Name follows standard scheme with Class Name::Feature Name // Commented 2: Updated to use automatic inclusion of list of parameters if required. mitk::GIFImageDescriptionFeatures::Pointer ipCalculator = mitk::GIFImageDescriptionFeatures::New(); // Commented 2, Tested mitk::GIFFirstOrderStatistics::Pointer firstOrderCalculator = mitk::GIFFirstOrderStatistics::New(); //Commented 2 mitk::GIFFirstOrderHistogramStatistics::Pointer firstOrderHistoCalculator = mitk::GIFFirstOrderHistogramStatistics::New(); // Commented 2, Tested mitk::GIFFirstOrderNumericStatistics::Pointer firstOrderNumericCalculator = mitk::GIFFirstOrderNumericStatistics::New(); // Commented 2, Tested mitk::GIFVolumetricStatistics::Pointer volCalculator = mitk::GIFVolumetricStatistics::New(); // Commented 2, Tested mitk::GIFVolumetricDensityStatistics::Pointer voldenCalculator = mitk::GIFVolumetricDensityStatistics::New(); // Commented 2, Tested mitk::GIFCooccurenceMatrix::Pointer coocCalculator = mitk::GIFCooccurenceMatrix::New(); // Commented 2, Will not be tested mitk::GIFCooccurenceMatrix2::Pointer cooc2Calculator = mitk::GIFCooccurenceMatrix2::New(); //Commented 2 mitk::GIFNeighbouringGreyLevelDependenceFeature::Pointer ngldCalculator = mitk::GIFNeighbouringGreyLevelDependenceFeature::New(); //Commented 2, Tested mitk::GIFGreyLevelRunLength::Pointer rlCalculator = mitk::GIFGreyLevelRunLength::New(); // Commented 2 mitk::GIFGreyLevelSizeZone::Pointer glszCalculator = mitk::GIFGreyLevelSizeZone::New(); // Commented 2, Tested mitk::GIFGreyLevelDistanceZone::Pointer gldzCalculator = mitk::GIFGreyLevelDistanceZone::New(); //Commented 2, Tested mitk::GIFLocalIntensity::Pointer lociCalculator = mitk::GIFLocalIntensity::New(); //Commented 2, Tested mitk::GIFIntensityVolumeHistogramFeatures::Pointer ivohCalculator = mitk::GIFIntensityVolumeHistogramFeatures::New(); // Commented 2 mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::Pointer ngtdCalculator = mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::New(); //Commented 2, Tested mitk::GIFCurvatureStatistic::Pointer curvCalculator = mitk::GIFCurvatureStatistic::New(); //Commented 2, Tested std::vector features; features.push_back(volCalculator.GetPointer()); features.push_back(voldenCalculator.GetPointer()); features.push_back(curvCalculator.GetPointer()); features.push_back(firstOrderCalculator.GetPointer()); features.push_back(firstOrderNumericCalculator.GetPointer()); features.push_back(firstOrderHistoCalculator.GetPointer()); features.push_back(ivohCalculator.GetPointer()); features.push_back(lociCalculator.GetPointer()); features.push_back(coocCalculator.GetPointer()); features.push_back(cooc2Calculator.GetPointer()); features.push_back(ngldCalculator.GetPointer()); features.push_back(rlCalculator.GetPointer()); features.push_back(glszCalculator.GetPointer()); features.push_back(gldzCalculator.GetPointer()); features.push_back(ipCalculator.GetPointer()); features.push_back(ngtdCalculator.GetPointer()); mitkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); mitk::cl::GlobalImageFeaturesParameter param; param.AddParameter(parser); parser.addArgument("--","-", mitkCommandLineParser::String, "---", "---", us::Any(),true); for (auto cFeature : features) { cFeature->AddArguments(parser); } parser.addArgument("--", "-", mitkCommandLineParser::String, "---", "---", us::Any(), true); parser.addArgument("description","d",mitkCommandLineParser::String,"Text","Description that is added to the output",us::Any()); parser.addArgument("direction", "dir", mitkCommandLineParser::String, "Int", "Allows to specify the direction for Cooc and RL. 0: All directions, 1: Only single direction (Test purpose), 2,3,4... Without dimension 0,1,2... ", us::Any()); parser.addArgument("slice-wise", "slice", mitkCommandLineParser::String, "Int", "Allows to specify if the image is processed slice-wise (number giving direction) ", us::Any()); parser.addArgument("output-mode", "omode", mitkCommandLineParser::Int, "Int", "Defines the format of the output. 0: (Default) results of an image / slice are written in a single row;" " 1: results of an image / slice are written in a single column; 2: store the result of on image as structured radiomocs report (XML)."); // Miniapp Infos parser.setCategory("Classification Tools"); parser.setTitle("Global Image Feature calculator"); parser.setDescription("Calculates different global statistics for a given segmentation / image combination"); parser.setContributor("German Cancer Research Center (DKFZ)"); std::map parsedArgs = parser.parseArguments(argc, argv); param.ParseParameter(parsedArgs); if (parsedArgs.size()==0) { return EXIT_FAILURE; } if ( parsedArgs.count("help") || parsedArgs.count("h")) { return EXIT_SUCCESS; } - //bool savePNGofSlices = true; - //std::string folderForPNGOfSlices = "E:\\tmp\\bonekamp\\fig\\"; - std::string version = "Version: 1.23"; MITK_INFO << version; std::ofstream log; if (param.useLogfile) { log.open(param.logfilePath, std::ios::app); log << std::endl; log << version; log << "Image: " << param.imagePath; log << "Mask: " << param.maskPath; } if (param.useDecimalPoint) { std::cout.imbue(std::locale(std::cout.getloc(), new punct_facet(param.decimalPoint))); } //representing the original loaded image data without any prepropcessing that might come. mitk::Image::Pointer loadedImage = mitk::IOUtil::Load(param.imagePath); //representing the original loaded mask data without any prepropcessing that might come. mitk::Image::Pointer loadedMask = mitk::IOUtil::Load(param.maskPath); mitk::Image::Pointer image = loadedImage; mitk::Image::Pointer mask = loadedMask; mitk::Image::Pointer tmpImage = loadedImage; mitk::Image::Pointer tmpMask = loadedMask; mitk::Image::Pointer morphMask = mask; if (param.useMorphMask) { morphMask = mitk::IOUtil::Load(param.morphPath); } log << " Check for Dimensions -"; if ((image->GetDimension() != mask->GetDimension())) { MITK_INFO << "Dimension of image does not match. "; MITK_INFO << "Correct one image, may affect the result"; if (image->GetDimension() == 2) { mitk::Convert2Dto3DImageFilter::Pointer multiFilter2 = mitk::Convert2Dto3DImageFilter::New(); multiFilter2->SetInput(tmpImage); multiFilter2->Update(); image = multiFilter2->GetOutput(); } if (mask->GetDimension() == 2) { mitk::Convert2Dto3DImageFilter::Pointer multiFilter3 = mitk::Convert2Dto3DImageFilter::New(); multiFilter3->SetInput(tmpMask); multiFilter3->Update(); mask = multiFilter3->GetOutput(); } } int writeDirection = 0; if (parsedArgs.count("output-mode")) { writeDirection = us::any_cast(parsedArgs["output-mode"]); } log << " Check for Resolution -"; if (param.resampleToFixIsotropic) { mitk::Image::Pointer newImage = mitk::Image::New(); AccessByItk_2(image, ResampleImage, param.resampleResolution, newImage); image = newImage; } log << " Resample if required -"; if (param.resampleMask) { mitk::Image::Pointer newMaskImage = mitk::Image::New(); AccessByItk_2(mask, ResampleMask, image, newMaskImage); mask = newMaskImage; } if ( ! mitk::Equal(mask->GetGeometry(0)->GetOrigin(), image->GetGeometry(0)->GetOrigin())) { MITK_INFO << "Not equal Origins"; if (param.ensureSameSpace) { MITK_INFO << "Warning!"; MITK_INFO << "The origin of the input image and the mask do not match. They are"; MITK_INFO << "now corrected. Please check to make sure that the images still match"; image->GetGeometry(0)->SetOrigin(mask->GetGeometry(0)->GetOrigin()); } else { return -1; } } log << " Check for Equality -"; if ( ! mitk::Equal(mask->GetGeometry(0)->GetSpacing(), image->GetGeometry(0)->GetSpacing())) { MITK_INFO << "Not equal Spacing"; if (param.ensureSameSpace) { MITK_INFO << "Warning!"; MITK_INFO << "The spacing of the mask was set to match the spacing of the input image."; MITK_INFO << "This might cause unintended spacing of the mask image"; image->GetGeometry(0)->SetSpacing(mask->GetGeometry(0)->GetSpacing()); } else { MITK_INFO << "The spacing of the mask and the input images is not equal."; MITK_INFO << "Terminating the programm. You may use the '-fi' option"; return -1; } } int direction = 0; if (parsedArgs.count("direction")) { direction = mitk::cl::splitDouble(parsedArgs["direction"].ToString(), ';')[0]; } MITK_INFO << "Start creating Mask without NaN"; mitk::Image::Pointer maskNoNaN = mitk::Image::New(); AccessByItk_2(image, CreateNoNaNMask, mask, maskNoNaN); //CreateNoNaNMask(mask, image, maskNoNaN); bool sliceWise = false; int sliceDirection = 0; unsigned int currentSlice = 0; bool imageToProcess = true; std::vector floatVector; std::vector maskVector; std::vector maskNoNaNVector; std::vector morphMaskVector; if ((parsedArgs.count("slice-wise")) && image->GetDimension() > 2) { MITK_INFO << "Enabled slice-wise"; sliceWise = true; sliceDirection = mitk::cl::splitDouble(parsedArgs["slice-wise"].ToString(), ';')[0]; MITK_INFO << sliceDirection; ExtractSlicesFromImages(image, mask, maskNoNaN, morphMask, sliceDirection, floatVector, maskVector, maskNoNaNVector, morphMaskVector); MITK_INFO << "Slice"; } log << " Configure features -"; for (auto cFeature : features) { if (param.defineGlobalMinimumIntensity) { cFeature->SetMinimumIntensity(param.globalMinimumIntensity); cFeature->SetUseMinimumIntensity(true); } if (param.defineGlobalMaximumIntensity) { cFeature->SetMaximumIntensity(param.globalMaximumIntensity); cFeature->SetUseMaximumIntensity(true); } if (param.defineGlobalNumberOfBins) { cFeature->SetBins(param.globalNumberOfBins); MITK_INFO << param.globalNumberOfBins; } cFeature->SetParameters(parsedArgs); cFeature->SetDirection(direction); cFeature->SetEncodeParametersInFeaturePrefix(param.encodeParameter); } bool addDescription = parsedArgs.count("description"); mitk::cl::FeatureResultWriter writer(param.outputPath, writeDirection); if (param.useDecimalPoint) { writer.SetDecimalPoint(param.decimalPoint); } std::string description = ""; if (addDescription) { description = parsedArgs["description"].ToString(); } mitk::Image::Pointer cImage = image; mitk::Image::Pointer cMask = mask; mitk::Image::Pointer cMaskNoNaN = maskNoNaN; mitk::Image::Pointer cMorphMask = morphMask; if (param.useHeader) { writer.AddColumn("SoftwareVersion"); writer.AddColumn("Patient"); writer.AddColumn("Image"); writer.AddColumn("Segmentation"); } // Create a QTApplication and a Datastorage // This is necessary in order to save screenshots of // each image / slice. QApplication qtapplication(argc, argv); QmitkRegisterClasses(); std::vector allStats; log << " Begin Processing -"; while (imageToProcess) { if (sliceWise) { cImage = floatVector[currentSlice]; cMask = maskVector[currentSlice]; cMaskNoNaN = maskNoNaNVector[currentSlice]; cMorphMask = morphMaskVector[currentSlice]; imageToProcess = (floatVector.size()-1 > (currentSlice)) ? true : false ; } else { imageToProcess = false; } if (param.writePNGScreenshots) { SaveSliceOrImageAsPNG(cImage, cMask, param.pngScreenshotsPath, currentSlice); } if (param.writeAnalysisImage) { mitk::IOUtil::Save(cImage, param.anaylsisImagePath); } if (param.writeAnalysisMask) { mitk::IOUtil::Save(cMask, param.analysisMaskPath); } mitk::AbstractGlobalImageFeature::FeatureListType stats; for (auto cFeature : features) { log << " Calculating " << cFeature->GetFeatureClassName() << " -"; cFeature->SetMorphMask(cMorphMask); cFeature->CalculateAndAppendFeatures(cImage, cMask, cMaskNoNaN, stats, !param.calculateAllFeatures); } for (std::size_t i = 0; i < stats.size(); ++i) { std::cout << stats[i].first.legacyName << " - " << stats[i].second << std::endl; } writer.AddHeader(description, currentSlice, stats, param.useHeader, addDescription); if (true) { writer.AddSubjectInformation(MITK_REVISION); writer.AddSubjectInformation(param.imageFolder); writer.AddSubjectInformation(param.imageName); writer.AddSubjectInformation(param.maskName); } writer.AddResult(description, currentSlice, stats, param.useHeader, addDescription); allStats.push_back(stats); ++currentSlice; } log << " Process Slicewise -"; if (sliceWise) { mitk::AbstractGlobalImageFeature::FeatureListType statMean, statStd; for (std::size_t i = 0; i < allStats[0].size(); ++i) { auto cElement1 = allStats[0][i]; cElement1.first.legacyName = "SliceWise Mean " + cElement1.first.legacyName; cElement1.second = 0.0; auto cElement2 = allStats[0][i]; cElement2.first.legacyName = "SliceWise Var. " + cElement2.first.legacyName; cElement2.second = 0.0; statMean.push_back(cElement1); statStd.push_back(cElement2); } for (auto cStat : allStats) { for (std::size_t i = 0; i < cStat.size(); ++i) { statMean[i].second += cStat[i].second / (1.0*allStats.size()); } } for (auto cStat : allStats) { for (std::size_t i = 0; i < cStat.size(); ++i) { statStd[i].second += (cStat[i].second - statMean[i].second)*(cStat[i].second - statMean[i].second) / (1.0*allStats.size()); } } for (std::size_t i = 0; i < statMean.size(); ++i) { std::cout << statMean[i].first.legacyName << " - " << statMean[i].second << std::endl; std::cout << statStd[i].first.legacyName << " - " << statStd[i].second << std::endl; } if (true) { writer.AddSubjectInformation(MITK_REVISION); writer.AddSubjectInformation(param.imageFolder); writer.AddSubjectInformation(param.imageName); writer.AddSubjectInformation(param.maskName + " - Mean"); } writer.AddResult(description, currentSlice, statMean, param.useHeader, addDescription); if (true) { writer.AddSubjectInformation(MITK_REVISION); writer.AddSubjectInformation(param.imageFolder); writer.AddSubjectInformation(param.imageName); writer.AddSubjectInformation(param.maskName + " - Var."); } writer.AddResult(description, currentSlice, statStd, param.useHeader, addDescription); } int returnCode = EXIT_SUCCESS; if (!param.outputXMLPath.empty()) { if (sliceWise) { MITK_ERROR << "Xml output is not supported in slicewise mode"; returnCode = EXIT_FAILURE; } else { mitk::cl::CLResultXMLWriter xmlWriter; xmlWriter.SetCLIArgs(parsedArgs); xmlWriter.SetFeatures(allStats.front()); xmlWriter.SetImage(loadedImage); xmlWriter.SetMask(loadedMask); xmlWriter.SetMethodName("CLGlobalImageFeatures"); xmlWriter.SetMethodVersion(version + "(mitk: " MITK_VERSION_STRING+")"); xmlWriter.SetOrganisation("German Cancer Research Center (DKFZ)"); xmlWriter.SetPipelineUID(param.pipelineUID); xmlWriter.write(param.outputXMLPath); } } if (param.useLogfile) { log << "Finished calculation" << std::endl; log.close(); } return returnCode; } #endif diff --git a/Modules/Classification/CLMiniApps/CLResampleImageToReference.cpp b/Modules/Classification/CLMiniApps/CLResampleImageToReference.cpp index 5f6be21168..4bae1ca503 100644 --- a/Modules/Classification/CLMiniApps/CLResampleImageToReference.cpp +++ b/Modules/Classification/CLMiniApps/CLResampleImageToReference.cpp @@ -1,112 +1,134 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkCLResampleImageToReference_cpp #define mitkCLResampleImageToReference_cpp #include "mitkCommandLineParser.h" #include #include #include #include #include #include // ITK #include "itkLinearInterpolateImageFunction.h" #include "itkWindowedSincInterpolateImageFunction.h" #include "itkNearestNeighborInterpolateImageFunction.h" #include "itkIdentityTransform.h" #include "itkResampleImageFilter.h" template void -ResampleImageToReferenceFunction(itk::Image* itkReference, mitk::Image::Pointer moving, std::string ergPath) +ResampleImageToReferenceFunction(itk::Image* itkReference, mitk::Image::Pointer moving, std::string ergPath, int interp=0) { typedef itk::Image InputImageType; // Identify Transform typedef itk::IdentityTransform T_Transform; typename T_Transform::Pointer _pTransform = T_Transform::New(); _pTransform->SetIdentity(); typedef itk::WindowedSincInterpolateImageFunction< InputImageType, VImageDimension> WindowedSincInterpolatorType; typename WindowedSincInterpolatorType::Pointer sinc_interpolator = WindowedSincInterpolatorType::New(); typedef itk::LinearInterpolateImageFunction< InputImageType> LinearInterpolateImageFunctionType; typename LinearInterpolateImageFunctionType::Pointer lin_interpolator = LinearInterpolateImageFunctionType::New(); typedef itk::NearestNeighborInterpolateImageFunction< InputImageType> NearestNeighborInterpolateImageFunctionType; typename NearestNeighborInterpolateImageFunctionType::Pointer nn_interpolator = NearestNeighborInterpolateImageFunctionType::New(); typename InputImageType::Pointer itkMoving = InputImageType::New(); mitk::CastToItkImage(moving,itkMoving); typedef itk::ResampleImageFilter ResampleFilterType; typename ResampleFilterType::Pointer resampler = ResampleFilterType::New(); resampler->SetInput(itkMoving); resampler->SetReferenceImage( itkReference ); resampler->UseReferenceImageOn(); resampler->SetTransform(_pTransform); - //if ( sincInterpol) - // resampler->SetInterpolator(sinc_interpolator); - //else + + switch(interp) + { + case 0: + { + resampler->SetInterpolator(lin_interpolator); + break; + } + case 1: + { + resampler->SetInterpolator(nn_interpolator); + break; + } + case 2: + { + resampler->SetInterpolator(sinc_interpolator); + break; + } + default: resampler->SetInterpolator(lin_interpolator); + } resampler->Update(); // Convert back to mitk mitk::Image::Pointer result = mitk::Image::New(); result->InitializeByItk(resampler->GetOutput()); GrabItkImageMemory(resampler->GetOutput(), result); MITK_INFO << "writing result to: " << ergPath; mitk::IOUtil::Save(result, ergPath); //return result; } int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); // required params - parser.addArgument("fix", "f", mitkCommandLineParser::Image, "Input Image", "Path to the input VTK polydata", us::Any(), false, false, false, mitkCommandLineParser::Input); - parser.addArgument("moving", "m", mitkCommandLineParser::File, "Output text file", "Target file. The output statistic is appended to this file.", us::Any(), false, false, false, mitkCommandLineParser::Output); - parser.addArgument("output", "o", mitkCommandLineParser::File, "Extension", "File extension. Default is .nii.gz", us::Any(), false, false, false, mitkCommandLineParser::Output); + parser.addArgument("fix", "f", mitkCommandLineParser::Image, "Fixed Image", "fixed image file", us::Any(), false, false, false, mitkCommandLineParser::Input); + parser.addArgument("moving", "m", mitkCommandLineParser::File, "Moving Image", "moving image file", us::Any(), false, false, false, mitkCommandLineParser::Output); + parser.addArgument("output", "o", mitkCommandLineParser::File, "Output Image", "output image", us::Any(), false, false, false, mitkCommandLineParser::Output); + parser.addArgument("interpolator", "", mitkCommandLineParser::Int, "Interpolator:", "interpolator type: 0=linear (default), 1=nearest neighbor, 2=sinc", 0); // Miniapp Infos parser.setCategory("Classification Tools"); parser.setTitle("Resample Image To Reference"); parser.setDescription("Resamples an image (moving) to an given image (fix) without additional registration."); parser.setContributor("German Cancer Research Center (DKFZ)"); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size() == 0) { return EXIT_FAILURE; } if (parsedArgs.count("help") || parsedArgs.count("h")) { return EXIT_SUCCESS; } mitk::Image::Pointer fix = mitk::IOUtil::Load(parsedArgs["fix"].ToString()); mitk::Image::Pointer moving = mitk::IOUtil::Load(parsedArgs["moving"].ToString()); mitk::Image::Pointer erg = mitk::Image::New(); - - AccessByItk_2(fix, ResampleImageToReferenceFunction, moving, parsedArgs["output"].ToString()); + + int interpolator = 0; + if (parsedArgs.count("interpolator")) + interpolator = us::any_cast(parsedArgs["interpolator"]); + + AccessByItk_3(fix, ResampleImageToReferenceFunction, moving, parsedArgs["output"].ToString(), interpolator); } #endif diff --git a/Modules/Classification/CLUtilities/test/mitkGIFCooc2Test.cpp b/Modules/Classification/CLUtilities/test/mitkGIFCooc2Test.cpp index 5ea6e310af..feb9e30118 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFCooc2Test.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFCooc2Test.cpp @@ -1,247 +1,247 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include "mitkIOUtil.h" #include #include class mitkGIFCooc2TestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFCooc2TestSuite); MITK_TEST(ImageDescription_PhantomTest_3D); MITK_TEST(ImageDescription_PhantomTest_2D); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest_3D() { mitk::GIFCooccurenceMatrix2::Pointer featureCalculator = mitk::GIFCooccurenceMatrix2::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[valuePair.first.featureClass + "::" + valuePair.first.name] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 18 features.", std::size_t(93), featureList.size()); // These values are obtained with IBSI (3D Comb) // Standard accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Joint Maximum with Large IBSI Phantom Image", 0.509, results["Co-occurenced Based Features::Overall Joint Maximum"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Joint Average with Large IBSI Phantom Image", 2.149, results["Co-occurenced Based Features::Overall Joint Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Joint Variance with Large IBSI Phantom Image", 3.132, results["Co-occurenced Based Features::Overall Joint Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Joint Entropy with Large IBSI Phantom Image", 2.574, results["Co-occurenced Based Features::Overall Joint Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Difference Average with Large IBSI Phantom Image", 1.379, results["Co-occurenced Based Features::Overall Difference Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Difference Variance with Large IBSI Phantom Image", 3.215, results["Co-occurenced Based Features::Overall Difference Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Difference Entropy with Large IBSI Phantom Image", 1.641, results["Co-occurenced Based Features::Overall Difference Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Sum Average with Large IBSI Phantom Image", 4.298, results["Co-occurenced Based Features::Overall Sum Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Sum Variance with Large IBSI Phantom Image", 7.412, results["Co-occurenced Based Features::Overall Sum Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Sum Entropy with Large IBSI Phantom Image", 2.110, results["Co-occurenced Based Features::Overall Sum Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Angular Second Moment with Large IBSI Phantom Image", 0.291, results["Co-occurenced Based Features::Overall Angular Second Moment"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Contrast with Large IBSI Phantom Image", 5.118, results["Co-occurenced Based Features::Overall Contrast"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Dissimilarity with Large IBSI Phantom Image", 1.380, results["Co-occurenced Based Features::Overall Dissimilarity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Inverse Difference with Large IBSI Phantom Image", 0.688, results["Co-occurenced Based Features::Overall Inverse Difference"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Inverse Difference Normalized with Large IBSI Phantom Image", 0.856, results["Co-occurenced Based Features::Overall Inverse Difference Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Inverse Difference Moment with Large IBSI Phantom Image", 0.631, results["Co-occurenced Based Features::Overall Inverse Difference Moment"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Inverse Difference Moment Normalized with Large IBSI Phantom Image", 0.902, results["Co-occurenced Based Features::Overall Inverse Difference Moment Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Inverse Variance with Large IBSI Phantom Image", 0.057, results["Co-occurenced Based Features::Overall Inverse Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Correlation with Large IBSI Phantom Image", 0.183, results["Co-occurenced Based Features::Overall Correlation"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Autocorrelation with Large IBSI Phantom Image", 5.192, results["Co-occurenced Based Features::Overall Autocorrelation"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Cluster Tendency with Large IBSI Phantom Image", 7.412, results["Co-occurenced Based Features::Overall Cluster Tendency"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Cluster Shade with Large IBSI Phantom Image", 17.419, results["Co-occurenced Based Features::Overall Cluster Shade"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Cluster Prominence with Large IBSI Phantom Image", 147.464, results["Co-occurenced Based Features::Overall Cluster Prominence"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall First Measure of Information Correlation with Large IBSI Phantom Image", -0.0288, results["Co-occurenced Based Features::Overall First Measure of Information Correlation"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Second Measure of Information Correlation with Large IBSI Phantom Image", 0.269, results["Co-occurenced Based Features::Overall Second Measure of Information Correlation"], 0.001); // These values are obtained by manually running the tool // Values might be wrong. CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Row Maximum with Large IBSI Phantom Image", 0.679, results["Co-occurenced Based Features::Overall Row Maximum"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Row Average with Large IBSI Phantom Image", 2.149, results["Co-occurenced Based Features::Overall Row Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Row Variance with Large IBSI Phantom Image", 3.132, results["Co-occurenced Based Features::Overall Row Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Row Entropy with Large IBSI Phantom Image", 1.306, results["Co-occurenced Based Features::Overall Row Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall First Row-Column Entropy with Large IBSI Phantom Image", 2.611, results["Co-occurenced Based Features::Overall First Row-Column Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Overall Second Row-Column Entropy with Large IBSI Phantom Image", 2.611, results["Co-occurenced Based Features::Overall Second Row-Column Entropy"], 0.001); // These values are obtained with IBSI (3D Avg) // Standard accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Joint Maximum with Large IBSI Phantom Image", 0.503, results["Co-occurenced Based Features::Mean Joint Maximum"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Joint Average with Large IBSI Phantom Image", 2.143, results["Co-occurenced Based Features::Mean Joint Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Joint Variance with Large IBSI Phantom Image", 3.099, results["Co-occurenced Based Features::Mean Joint Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Joint Entropy with Large IBSI Phantom Image", 2.399, results["Co-occurenced Based Features::Mean Joint Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Difference Average with Large IBSI Phantom Image", 1.431, results["Co-occurenced Based Features::Mean Difference Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Difference Variance with Large IBSI Phantom Image", 3.056, results["Co-occurenced Based Features::Mean Difference Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Difference Entropy with Large IBSI Phantom Image", 1.563, results["Co-occurenced Based Features::Mean Difference Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Sum Average with Large IBSI Phantom Image", 4.2859, results["Co-occurenced Based Features::Mean Sum Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Sum Variance with Large IBSI Phantom Image", 7.072, results["Co-occurenced Based Features::Mean Sum Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Sum Entropy with Large IBSI Phantom Image", 1.9226, results["Co-occurenced Based Features::Mean Sum Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Angular Second Moment with Large IBSI Phantom Image", 0.303, results["Co-occurenced Based Features::Mean Angular Second Moment"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Contrast with Large IBSI Phantom Image", 5.3245, results["Co-occurenced Based Features::Mean Contrast"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Dissimilarity with Large IBSI Phantom Image", 1.431, results["Co-occurenced Based Features::Mean Dissimilarity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Inverse Difference with Large IBSI Phantom Image", 0.6766, results["Co-occurenced Based Features::Mean Inverse Difference"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Inverse Difference Normalized with Large IBSI Phantom Image", 0.8506, results["Co-occurenced Based Features::Mean Inverse Difference Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Inverse Difference Moment with Large IBSI Phantom Image", 0.6177, results["Co-occurenced Based Features::Mean Inverse Difference Moment"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Inverse Difference Moment Normalized with Large IBSI Phantom Image", 0.8984, results["Co-occurenced Based Features::Mean Inverse Difference Moment Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Inverse Variance with Large IBSI Phantom Image", 0.0604, results["Co-occurenced Based Features::Mean Inverse Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Correlation with Large IBSI Phantom Image", 0.157, results["Co-occurenced Based Features::Mean Correlation"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Autocorrelation with Large IBSI Phantom Image", 5.05544, results["Co-occurenced Based Features::Mean Autocorrelation"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Cluster Tendency with Large IBSI Phantom Image", 7.0728, results["Co-occurenced Based Features::Mean Cluster Tendency"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Cluster Shade with Large IBSI Phantom Image", 16.6441, results["Co-occurenced Based Features::Mean Cluster Shade"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Cluster Prominence with Large IBSI Phantom Image", 144.703, results["Co-occurenced Based Features::Mean Cluster Prominence"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean First Measure of Information Correlation with Large IBSI Phantom Image", -0.15684, results["Co-occurenced Based Features::Mean First Measure of Information Correlation"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Second Measure of Information Correlation with Large IBSI Phantom Image", 0.519588, results["Co-occurenced Based Features::Mean Second Measure of Information Correlation"], 0.001); // These values are obtained by manually running the tool // Values might be wrong. CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Row Maximum with Large IBSI Phantom Image", 0.6808, results["Co-occurenced Based Features::Mean Row Maximum"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Row Average with Large IBSI Phantom Image", 2.143, results["Co-occurenced Based Features::Mean Row Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Row Variance with Large IBSI Phantom Image", 3.0993, results["Co-occurenced Based Features::Mean Row Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Row Entropy with Large IBSI Phantom Image", 1.29699, results["Co-occurenced Based Features::Mean Row Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean First Row-Column Entropy with Large IBSI Phantom Image", 2.5939, results["Co-occurenced Based Features::Mean First Row-Column Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Co-occurenced Based Features::Mean Second Row-Column Entropy with Large IBSI Phantom Image", 2.5939, results["Co-occurenced Based Features::Mean Second Row-Column Entropy"], 0.001); } void ImageDescription_PhantomTest_2D() { mitk::GIFCooccurenceMatrix2::Pointer featureCalculator = mitk::GIFCooccurenceMatrix2::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeaturesSlicewise(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large, 2); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 558 features.", std::size_t(558), featureList.size()); // These values are obtained with IBSI // Standard accuracy is 0.01 // These values are obtained with IBSI (2D Comb) // Standard accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Joint Maximum with Large IBSI Phantom Image", 0.512, results["SliceWise Mean Co-occurenced Based Features::Overall Joint Maximum"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Joint Average with Large IBSI Phantom Image", 2.143, results["SliceWise Mean Co-occurenced Based Features::Overall Joint Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Joint Variance with Large IBSI Phantom Image", 2.7115, results["SliceWise Mean Co-occurenced Based Features::Overall Joint Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Joint Entropy with Large IBSI Phantom Image", 2.2383, results["SliceWise Mean Co-occurenced Based Features::Overall Joint Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Difference Average with Large IBSI Phantom Image", 1.3990, results["SliceWise Mean Co-occurenced Based Features::Overall Difference Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Difference Variance with Large IBSI Phantom Image", 3.06426, results["SliceWise Mean Co-occurenced Based Features::Overall Difference Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Difference Entropy with Large IBSI Phantom Image", 1.49262, results["SliceWise Mean Co-occurenced Based Features::Overall Difference Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Sum Average with Large IBSI Phantom Image", 4.28686, results["SliceWise Mean Co-occurenced Based Features::Overall Sum Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Sum Variance with Large IBSI Phantom Image", 5.65615, results["SliceWise Mean Co-occurenced Based Features::Overall Sum Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Sum Entropy with Large IBSI Phantom Image", 1.79494, results["SliceWise Mean Co-occurenced Based Features::Overall Sum Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Angular Second Moment with Large IBSI Phantom Image", 0.351678, results["SliceWise Mean Co-occurenced Based Features::Overall Angular Second Moment"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Contrast with Large IBSI Phantom Image", 5.19019, results["SliceWise Mean Co-occurenced Based Features::Overall Contrast"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Dissimilarity with Large IBSI Phantom Image", 1.3990, results["SliceWise Mean Co-occurenced Based Features::Overall Dissimilarity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Inverse Difference with Large IBSI Phantom Image", 0.683294, results["SliceWise Mean Co-occurenced Based Features::Overall Inverse Difference"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Inverse Difference Normalized with Large IBSI Phantom Image", 0.8538, results["SliceWise Mean Co-occurenced Based Features::Overall Inverse Difference Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Inverse Difference Moment with Large IBSI Phantom Image", 0.625003, results["SliceWise Mean Co-occurenced Based Features::Overall Inverse Difference Moment"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Inverse Difference Moment Normalized with Large IBSI Phantom Image", 0.90088, results["SliceWise Mean Co-occurenced Based Features::Overall Inverse Difference Moment Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Inverse Variance with Large IBSI Phantom Image", 0.055286, results["SliceWise Mean Co-occurenced Based Features::Overall Inverse Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Correlation with Large IBSI Phantom Image", 0.0173072, results["SliceWise Mean Co-occurenced Based Features::Overall Correlation"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Autocorrelation with Large IBSI Phantom Image", 5.13953, results["SliceWise Mean Co-occurenced Based Features::Overall Autocorrelation"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Cluster Tendency with Large IBSI Phantom Image", 5.6561, results["SliceWise Mean Co-occurenced Based Features::Overall Cluster Tendency"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Cluster Shade with Large IBSI Phantom Image", 6.97661, results["SliceWise Mean Co-occurenced Based Features::Overall Cluster Shade"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Cluster Prominence with Large IBSI Phantom Image", 80.3855, results["SliceWise Mean Co-occurenced Based Features::Overall Cluster Prominence"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall First Measure of Information Correlation with Large IBSI Phantom Image", -0.0340891, results["SliceWise Mean Co-occurenced Based Features::Overall First Measure of Information Correlation"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Second Measure of Information Correlation with Large IBSI Phantom Image", 0.2625, results["SliceWise Mean Co-occurenced Based Features::Overall Second Measure of Information Correlation"], 0.001); // These values are obtained by manually running the tool // Values might be wrong. CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Row Maximum with Large IBSI Phantom Image", 0.682689, results["SliceWise Mean Co-occurenced Based Features::Overall Row Maximum"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Row Average with Large IBSI Phantom Image", 2.14343, results["SliceWise Mean Co-occurenced Based Features::Overall Row Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Row Variance with Large IBSI Phantom Image", 2.71158, results["SliceWise Mean Co-occurenced Based Features::Overall Row Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Row Entropy with Large IBSI Phantom Image", 1.13773, results["SliceWise Mean Co-occurenced Based Features::Overall Row Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall First Row-Column Entropy with Large IBSI Phantom Image", 2.27545, results["SliceWise Mean Co-occurenced Based Features::Overall First Row-Column Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Overall Second Row-Column Entropy with Large IBSI Phantom Image", 2.27545, results["SliceWise Mean Co-occurenced Based Features::Overall Second Row-Column Entropy"], 0.001); // These values are obtained with IBSI (2D Avg) // Standard accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Joint Maximum with Large IBSI Phantom Image", 0.5188, results["SliceWise Mean Co-occurenced Based Features::Mean Joint Maximum"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Joint Average with Large IBSI Phantom Image", 2.14242, results["SliceWise Mean Co-occurenced Based Features::Mean Joint Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Joint Variance with Large IBSI Phantom Image", 2.6877, results["SliceWise Mean Co-occurenced Based Features::Mean Joint Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Joint Entropy with Large IBSI Phantom Image", 2.04966, results["SliceWise Mean Co-occurenced Based Features::Mean Joint Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Difference Average with Large IBSI Phantom Image", 1.42247, results["SliceWise Mean Co-occurenced Based Features::Mean Difference Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Difference Variance with Large IBSI Phantom Image", 2.90159, results["SliceWise Mean Co-occurenced Based Features::Mean Difference Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Difference Entropy with Large IBSI Phantom Image", 1.39615, results["SliceWise Mean Co-occurenced Based Features::Mean Difference Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Sum Average with Large IBSI Phantom Image", 4.28484, results["SliceWise Mean Co-occurenced Based Features::Mean Sum Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Sum Variance with Large IBSI Phantom Image", 5.47293, results["SliceWise Mean Co-occurenced Based Features::Mean Sum Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Sum Entropy with Large IBSI Phantom Image", 1.60319, results["SliceWise Mean Co-occurenced Based Features::Mean Sum Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Angular Second Moment with Large IBSI Phantom Image", 0.367529, results["SliceWise Mean Co-occurenced Based Features::Mean Angular Second Moment"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Contrast with Large IBSI Phantom Image", 5.27785, results["SliceWise Mean Co-occurenced Based Features::Mean Contrast"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Dissimilarity with Large IBSI Phantom Image", 1.42247, results["SliceWise Mean Co-occurenced Based Features::Mean Dissimilarity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Inverse Difference with Large IBSI Phantom Image", 0.677949, results["SliceWise Mean Co-occurenced Based Features::Mean Inverse Difference"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Inverse Difference Normalized with Large IBSI Phantom Image", 0.851399, results["SliceWise Mean Co-occurenced Based Features::Mean Inverse Difference Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Inverse Difference Moment with Large IBSI Phantom Image", 0.618737, results["SliceWise Mean Co-occurenced Based Features::Mean Inverse Difference Moment"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Inverse Difference Moment Normalized with Large IBSI Phantom Image", 0.899219, results["SliceWise Mean Co-occurenced Based Features::Mean Inverse Difference Moment Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Inverse Variance with Large IBSI Phantom Image", 0.0566983, results["SliceWise Mean Co-occurenced Based Features::Mean Inverse Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Correlation with Large IBSI Phantom Image", -.012107, results["SliceWise Mean Co-occurenced Based Features::Mean Correlation"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Autocorrelation with Large IBSI Phantom Image", 5.09437, results["SliceWise Mean Co-occurenced Based Features::Mean Autocorrelation"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Cluster Tendency with Large IBSI Phantom Image", 5.47293, results["SliceWise Mean Co-occurenced Based Features::Mean Cluster Tendency"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Cluster Shade with Large IBSI Phantom Image", 6.99782, results["SliceWise Mean Co-occurenced Based Features::Mean Cluster Shade"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Cluster Prominence with Large IBSI Phantom Image", 79.1126, results["SliceWise Mean Co-occurenced Based Features::Mean Cluster Prominence"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean First Measure of Information Correlation with Large IBSI Phantom Image", -0.15512, results["SliceWise Mean Co-occurenced Based Features::Mean First Measure of Information Correlation"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Second Measure of Information Correlation with Large IBSI Phantom Image", 0.487457, results["SliceWise Mean Co-occurenced Based Features::Mean Second Measure of Information Correlation"], 0.001); // These values are obtained by manually running the tool // Values might be wrong. CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Row Maximum with Large IBSI Phantom Image", 0.689717, results["SliceWise Mean Co-occurenced Based Features::Mean Row Maximum"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Row Average with Large IBSI Phantom Image", 2.14242, results["SliceWise Mean Co-occurenced Based Features::Mean Row Average"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Row Variance with Large IBSI Phantom Image", 2.6877, results["SliceWise Mean Co-occurenced Based Features::Mean Row Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Row Entropy with Large IBSI Phantom Image", 1.1238, results["SliceWise Mean Co-occurenced Based Features::Mean Row Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean First Row-Column Entropy with Large IBSI Phantom Image", 2.24761, results["SliceWise Mean Co-occurenced Based Features::Mean First Row-Column Entropy"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Co-occurenced Based Features::Mean Second Row-Column Entropy with Large IBSI Phantom Image", 2.24761, results["SliceWise Mean Co-occurenced Based Features::Mean Second Row-Column Entropy"], 0.001); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFCooc2 ) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFCurvatureStatisticTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFCurvatureStatisticTest.cpp index 77591dcee2..d56d087a0d 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFCurvatureStatisticTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFCurvatureStatisticTest.cpp @@ -1,118 +1,118 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include "mitkIOUtil.h" #include #include class mitkGIFCurvatureStatisticTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFCurvatureStatisticTestSuite); MITK_TEST(ImageDescription_PhantomTest); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest() { mitk::GIFCurvatureStatistic::Pointer featureCalculator = mitk::GIFCurvatureStatistic::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 44 features.", std::size_t(44), featureList.size()); // These values are obtained by a run of the filter. // The might be wrong! CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Minimum Mean Curvature with Large IBSI Phantom Image", -1.51, results["Curvature Feature::Minimum Mean Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Maximum Mean Curvature with Large IBSI Phantom Image", 0.51, results["Curvature Feature::Maximum Mean Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Mean Mean Curvature with Large IBSI Phantom Image", 0.095, results["Curvature Feature::Mean Mean Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Standard Deviation Mean Curvature with Large IBSI Phantom Image", 0.45, results["Curvature Feature::Standard Deviation Mean Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Skewness Mean Curvature with Large IBSI Phantom Image", -2.55, results["Curvature Feature::Skewness Mean Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Mean Positive Mean Curvature with Large IBSI Phantom Image", 0.30, results["Curvature Feature::Mean Positive Mean Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Standard Deviation Positive Mean Curvature with Large IBSI Phantom Image", 0.12, results["Curvature Feature::Standard Deviation Positive Mean Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Skewness Positive Mean Curvature with Large IBSI Phantom Image", 0.60, results["Curvature Feature::Skewness Positive Mean Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Mean Negative Mean Curvature with Large IBSI Phantom Image", -0.955, results["Curvature Feature::Mean Negative Mean Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Standard Deviation Negative Mean Curvature with Large IBSI Phantom Image", 0.56, results["Curvature Feature::Standard Deviation Negative Mean Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Skewness Negative Mean Curvature with Large IBSI Phantom Image", 0.09, results["Curvature Feature::Skewness Negative Mean Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Minimum Gaussian Curvature with Large IBSI Phantom Image", -0.211, results["Curvature Feature::Minimum Gaussian Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Maximum Gaussian Curvature with Large IBSI Phantom Image", 1.81, results["Curvature Feature::Maximum Gaussian Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Mean Gaussian Curvature with Large IBSI Phantom Image", 0.14, results["Curvature Feature::Mean Gaussian Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Standard Deviation Gaussian Curvature with Large IBSI Phantom Image", 0.42, results["Curvature Feature::Standard Deviation Gaussian Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Skewness Gaussian Curvature with Large IBSI Phantom Image", 3.51, results["Curvature Feature::Skewness Gaussian Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Mean Positive Gaussian Curvature with Large IBSI Phantom Image", 0.26, results["Curvature Feature::Mean Positive Gaussian Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Standard Deviation Positive Gaussian Curvature with Large IBSI Phantom Image", 0.53, results["Curvature Feature::Standard Deviation Positive Gaussian Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Skewness Positive Gaussian Curvature with Large IBSI Phantom Image", 2.52, results["Curvature Feature::Skewness Positive Gaussian Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Mean Negative Gaussian Curvature with Large IBSI Phantom Image", -0.03, results["Curvature Feature::Mean Negative Gaussian Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Standard Deviation Negative Gaussian Curvature with Large IBSI Phantom Image", 0.055, results["Curvature Feature::Standard Deviation Negative Gaussian Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Skewness Negative Gaussian Curvature with Large IBSI Phantom Image", -1.92, results["Curvature Feature::Skewness Negative Gaussian Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Minimum Minimum Curvature with Large IBSI Phantom Image", -2.19, results["Curvature Feature::Minimum Minimum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Maximum Minimum Curvature with Large IBSI Phantom Image", 0.35, results["Curvature Feature::Maximum Minimum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Mean Minimum Curvature with Large IBSI Phantom Image", -0.11, results["Curvature Feature::Mean Minimum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Standard Deviation Minimum Curvature with Large IBSI Phantom Image", 0.573, results["Curvature Feature::Standard Deviation Minimum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Skewness Minimum Curvature with Large IBSI Phantom Image", -2.742, results["Curvature Feature::Skewness Minimum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Mean Positive Minimum Curvature with Large IBSI Phantom Image", 0.161, results["Curvature Feature::Mean Positive Minimum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Standard Deviation Positive Minimum Curvature with Large IBSI Phantom Image", 0.165, results["Curvature Feature::Standard Deviation Positive Minimum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Skewness Positive Minimum Curvature with Large IBSI Phantom Image", 0.108, results["Curvature Feature::Skewness Positive Minimum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Mean Negative Minimum Curvature with Large IBSI Phantom Image", -0.42, results["Curvature Feature::Mean Negative Minimum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Standard Deviation Negative Minimum Curvature with Large IBSI Phantom Image", 0.733, results["Curvature Feature::Standard Deviation Negative Minimum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Skewness Negative Minimum Curvature with Large IBSI Phantom Image", -1.73, results["Curvature Feature::Skewness Negative Minimum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Minimum Maximum Curvature with Large IBSI Phantom Image", -0.83, results["Curvature Feature::Minimum Maximum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Maximum Maximum Curvature with Large IBSI Phantom Image", 0.79, results["Curvature Feature::Maximum Maximum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Mean Maximum Curvature with Large IBSI Phantom Image", 0.30, results["Curvature Feature::Mean Maximum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Standard Deviation Maximum Curvature with Large IBSI Phantom Image", 0.369, results["Curvature Feature::Standard Deviation Maximum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Skewness Maximum Curvature with Large IBSI Phantom Image", -1.617, results["Curvature Feature::Skewness Maximum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Mean Positive Maximum Curvature with Large IBSI Phantom Image", 0.419, results["Curvature Feature::Mean Positive Maximum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Standard Deviation Positive Maximum Curvature with Large IBSI Phantom Image", 0.217, results["Curvature Feature::Standard Deviation Positive Maximum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Skewness Positive Maximum Curvature with Large IBSI Phantom Image", -0.958, results["Curvature Feature::Skewness Positive Maximum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Mean Negative Maximum Curvature with Large IBSI Phantom Image", -0.44, results["Curvature Feature::Mean Negative Maximum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Standard Deviation Negative Maximum Curvature with Large IBSI Phantom Image", 0.399, results["Curvature Feature::Standard Deviation Negative Maximum Curvature"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Curvature Feature::Skewness Negative Maximum Curvature with Large IBSI Phantom Image", 0.109, results["Curvature Feature::Skewness Negative Maximum Curvature"], 0.01); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFCurvatureStatistic ) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFFirstOrderHistogramStatisticsTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFFirstOrderHistogramStatisticsTest.cpp index 92a79b47c9..33ff00e6cb 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFFirstOrderHistogramStatisticsTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFFirstOrderHistogramStatisticsTest.cpp @@ -1,123 +1,123 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include "mitkIOUtil.h" #include #include class mitkGIFFirstOrderHistogramStatisticsTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFFirstOrderHistogramStatisticsTestSuite); MITK_TEST(ImageDescription_PhantomTest); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest() { mitk::GIFFirstOrderHistogramStatistics::Pointer featureCalculator = mitk::GIFFirstOrderHistogramStatistics::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 46 features.", std::size_t(46), featureList.size()); // These values are obtained by a run of the filter. // The might be wrong! CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Mean Value should be 2.15 with Large IBSI Phantom Image", 2.15, results["First Order Histogram::Mean Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Variance Value should be 3.05 with Large IBSI Phantom Image", 3.05, results["First Order Histogram::Variance Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Skewness Value should be 1.08 with Large IBSI Phantom Image", 1.08, results["First Order Histogram::Skewness Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Excess Kurtosis Value should be -0.355 with Large IBSI Phantom Image", -0.355, results["First Order Histogram::Excess Kurtosis Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Median Value should be 1 with Large IBSI Phantom Image", 1.0, results["First Order Histogram::Median Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Minimum Value should be 1 with Large IBSI Phantom Image", 1, results["First Order Histogram::Minimum Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Percentile 10 Value should be 0.648 with Large IBSI Phantom Image", 0.648, results["First Order Histogram::Percentile 10 Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Percentile 90 Value should be 4.475 with Large IBSI Phantom Image", 4.475, results["First Order Histogram::Percentile 90 Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Maximum Value should be 6 with Large IBSI Phantom Image", 6, results["First Order Histogram::Maximum Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Mode Value should be 1 with Large IBSI Phantom Image", 1, results["First Order Histogram::Mode Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Interquantile Range Value should be 2.9 with Large IBSI Phantom Image", 2.911, results["First Order Histogram::Interquantile Range Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Range Value should be 5 with Large IBSI Phantom Image", 5, results["First Order Histogram::Range Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Mean Absolute Deviation Value should be 1.55 with Large IBSI Phantom Image", 1.55, results["First Order Histogram::Mean Absolute Deviation Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Robust Mean Absolute Deviation Value should be 1.11 with Large IBSI Phantom Image", 1.11, results["First Order Histogram::Robust Mean Absolute Deviation Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Median Absolute Deviation Value should be 1.14 with Large IBSI Phantom Image", 1.14, results["First Order Histogram::Median Absolute Deviation Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Coefficient of Variation Value should be 0.812 with Large IBSI Phantom Image", 0.812, results["First Order Histogram::Coefficient of Variation Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Quantile coefficient of Dispersion Value should be 0.626 with Large IBSI Phantom Image", 0.626, results["First Order Histogram::Quantile coefficient of Dispersion Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Entropy Value should be 1.27 with Large IBSI Phantom Image", 1.27, results["First Order Histogram::Entropy Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Uniformity Value should be 0.512 with Large IBSI Phantom Image", 0.512, results["First Order Histogram::Uniformity Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Robust Mean Index should be 0.746 with Large IBSI Phantom Image", 0.746, results["First Order Histogram::Robust Mean Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Robust Mean Value should be 1.746 with Large IBSI Phantom Image", 1.746, results["First Order Histogram::Robust Mean Value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Number of Bins should be 6", 6, results["First Order Histogram::Number of Bins"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Bin Size should be 1", 1, results["First Order Histogram::Bin Size"], 0.01); // These values are taken from the IBSI Initiative to ensure compatibility // The values are given with an accuracy of 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Mean Index should be 2.15 with Large IBSI Phantom Image", 2.15, results["First Order Histogram::Mean Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Variance Index should be 3.05 with Large IBSI Phantom Image", 3.05, results["First Order Histogram::Variance Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Skewness Index should be 1.08 with Large IBSI Phantom Image", 1.08, results["First Order Histogram::Skewness Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Excess Kurtosis Index should be -0.355 with Large IBSI Phantom Image", -0.355, results["First Order Histogram::Excess Kurtosis Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Median Index should be 1 with Large IBSI Phantom Image", 1.0, results["First Order Histogram::Median Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Minimum Index should be 1 with Large IBSI Phantom Image", 1, results["First Order Histogram::Minimum Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Percentile 10 Index should be 1 with Large IBSI Phantom Image", 1, results["First Order Histogram::Percentile 10 Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Percentile 90 Index should be 2.15 with Large IBSI Phantom Image", 4, results["First Order Histogram::Percentile 90 Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Maximum Index should be 6 with Large IBSI Phantom Image", 6, results["First Order Histogram::Maximum Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Mode Index should be 1 with Large IBSI Phantom Image", 1, results["First Order Histogram::Mode Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Interquantile Range Index should be 3 with Large IBSI Phantom Image", 3, results["First Order Histogram::Interquantile Range Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Range Index should be 5 with Large IBSI Phantom Image", 5, results["First Order Histogram::Range Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Mean Absolute Deviation Index should be 3 with Large IBSI Phantom Image", 1.55, results["First Order Histogram::Mean Absolute Deviation Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Robust Mean Absolute Deviation Index should be 1.11 with Large IBSI Phantom Image", 1.11, results["First Order Histogram::Robust Mean Absolute Deviation Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Median Absolute Deviation Index should be 1.14 with Large IBSI Phantom Image", 1.14, results["First Order Histogram::Median Absolute Deviation Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Coefficient of Variation Index should be 0.812 with Large IBSI Phantom Image", 0.812, results["First Order Histogram::Coefficient of Variation Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Quantile coefficient of Dispersion Index should be 0.6 with Large IBSI Phantom Image", 0.6, results["First Order Histogram::Quantile coefficient of Dispersion Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Entropy Index should be 1.27 with Large IBSI Phantom Image", 1.27, results["First Order Histogram::Entropy Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Uniformity Index should be 0.512 with Large IBSI Phantom Image", 0.512, results["First Order Histogram::Uniformity Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Maximum Gradient should be 8 with Large IBSI Phantom Image", 8, results["First Order Histogram::Maximum Gradient"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Maximum Gradient Index should be 3 with Large IBSI Phantom Image", 3, results["First Order Histogram::Maximum Gradient Index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Minimum Gradient should be -50 with Large IBSI Phantom Image", -50, results["First Order Histogram::Minimum Gradient"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Histogram::Minimum Gradient Index should be 3 with Large IBSI Phantom Image", 1, results["First Order Histogram::Minimum Gradient Index"], 0.01); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFFirstOrderHistogramStatistics ) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFFirstOrderNumericStatisticsTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFFirstOrderNumericStatisticsTest.cpp index b6c31c2ee1..6a6f51ef36 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFFirstOrderNumericStatisticsTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFFirstOrderNumericStatisticsTest.cpp @@ -1,109 +1,109 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include "mitkIOUtil.h" #include #include class mitkGIFFirstOrderNumericStatisticsTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFFirstOrderNumericStatisticsTestSuite); MITK_TEST(ImageDescription_PhantomTest); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest() { mitk::GIFFirstOrderNumericStatistics::Pointer featureCalculator = mitk::GIFFirstOrderNumericStatistics::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 50 features.", std::size_t(50), featureList.size()); // These values are obtained by a run of the filter. // The might be wrong! CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Mean with Large IBSI Phantom Image", 2.15, results["First Order Numeric::Mean"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Variance with Large IBSI Phantom Image", 3.05, results["First Order Numeric::Variance"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Skewness with Large IBSI Phantom Image", 1.08, results["First Order Numeric::Skewness"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Excess kurtosis with Large IBSI Phantom Image", -0.355, results["First Order Numeric::Excess kurtosis"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Median with Large IBSI Phantom Image", 1, results["First Order Numeric::Median"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Minimum with Large IBSI Phantom Image", 1, results["First Order Numeric::Minimum"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::10th Percentile with Large IBSI Phantom Image", 1, results["First Order Numeric::10th Percentile"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::90th Percentile with Large IBSI Phantom Image", 4, results["First Order Numeric::90th Percentile"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Maximum with Large IBSI Phantom Image", 6, results["First Order Numeric::Maximum"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Interquantile range with Large IBSI Phantom Image", 3, results["First Order Numeric::Interquantile range"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Range with Large IBSI Phantom Image", 5, results["First Order Numeric::Range"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Mean absolute deviation with Large IBSI Phantom Image", 1.55, results["First Order Numeric::Mean absolute deviation"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Robust mean absolute deviation with Large IBSI Phantom Image", 1.11, results["First Order Numeric::Robust mean absolute deviation"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Median absolute deviation with Large IBSI Phantom Image", 1.15, results["First Order Numeric::Median absolute deviation"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Coefficient of variation with Large IBSI Phantom Image", 0.812, results["First Order Numeric::Coefficient of variation"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Quantile coefficient of dispersion with Large IBSI Phantom Image", 0.6, results["First Order Numeric::Quantile coefficient of dispersion"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Energy with Large IBSI Phantom Image", 567, results["First Order Numeric::Energy"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Root mean square with Large IBSI Phantom Image", 2.77, results["First Order Numeric::Root mean square"], 0.01); // These values are taken from the IBSI Initiative to ensure compatibility // The values are given with an accuracy of 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Standard Deviation with Large IBSI Phantom Image", 1.74513, results["First Order Numeric::Standard Deviation"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Kurtosis with Large IBSI Phantom Image", 2.64538, results["First Order Numeric::Kurtosis"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Robust mean with Large IBSI Phantom Image", 1.74627, results["First Order Numeric::Robust mean"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Robust variance with Large IBSI Phantom Image", 1.65204, results["First Order Numeric::Robust variance"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Covered image intensity range with Large IBSI Phantom Image", 0.83333, results["First Order Numeric::Covered image intensity range"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Mode index with Large IBSI Phantom Image",0 , results["First Order Numeric::Mode index"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Mode value with Large IBSI Phantom Image", 1, results["First Order Numeric::Mode value"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Mode probability with Large IBSI Phantom Image", 0.675676, results["First Order Numeric::Mode probability"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Entropy with Large IBSI Phantom Image", -1.26561, results["First Order Numeric::Entropy"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Uniformtiy with Large IBSI Phantom Image", 0.512418, results["First Order Numeric::Uniformtiy"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Number of voxels with Large IBSI Phantom Image", 74 , results["First Order Numeric::Number of voxels"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Sum of voxels with Large IBSI Phantom Image", 159, results["First Order Numeric::Sum of voxels"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Voxel space with Large IBSI Phantom Image", 8, results["First Order Numeric::Voxel space"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Voxel volume with Large IBSI Phantom Image", 8, results["First Order Numeric::Voxel volume"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order Numeric::Image Dimension with Large IBSI Phantom Image", 3, results["First Order Numeric::Image Dimension"], 0.01); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFFirstOrderNumericStatistics ) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFFirstOrderStatisticsTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFFirstOrderStatisticsTest.cpp index c6683a7255..af41a4c4cd 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFFirstOrderStatisticsTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFFirstOrderStatisticsTest.cpp @@ -1,108 +1,108 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include "mitkIOUtil.h" #include #include class mitkGIFFirstOrderStatisticsTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFFirstOrderStatisticsTestSuite); MITK_TEST(ImageDescription_PhantomTest); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest() { mitk::GIFFirstOrderStatistics::Pointer featureCalculator = mitk::GIFFirstOrderStatistics::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 50 features.", std::size_t(50), featureList.size()); // These values are obtained by a run of the filter. // The might be wrong! // These values are taken from the IBSI Initiative to ensure compatibility // The values are given with an accuracy of 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Mean with Large IBSI Phantom Image", 2.15, results["First Order::Mean"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Unbiased Variance with Large IBSI Phantom Image", 3.09, results["First Order::Unbiased Variance"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Biased Variance with Large IBSI Phantom Image", 3.05, results["First Order::Biased Variance"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Skewness with Large IBSI Phantom Image", 1.08, results["First Order::Skewness"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Kurtosis with Large IBSI Phantom Image", 2.65, results["First Order::Kurtosis"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Median with Large IBSI Phantom Image", 1, results["First Order::Median"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Minimum with Large IBSI Phantom Image", 1, results["First Order::Minimum"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Maximum with Large IBSI Phantom Image", 6, results["First Order::Maximum"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Range with Large IBSI Phantom Image", 5, results["First Order::Range"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Mean Absolute Deviation with Large IBSI Phantom Image", 1.55, results["First Order::Mean Absolute Deviation"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Robust Mean Absolute Deviation with Large IBSI Phantom Image", 1.11, results["First Order::Robust Mean Absolute Deviation"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Median Absolute Deviation with Large IBSI Phantom Image", 1.15, results["First Order::Median Absolute Deviation"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Coefficient of variation with Large IBSI Phantom Image", 0.812, results["First Order::Coefficient Of Variation"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Quantile coefficient of dispersion with Large IBSI Phantom Image", 0.625, results["First Order::Quantile Coefficient Of Dispersion"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Energy with Large IBSI Phantom Image", 567, results["First Order::Energy"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Root mean square with Large IBSI Phantom Image", 2.77, results["First Order::Root Mean Square"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Entropy with Large IBSI Phantom Image", 1.26561, results["First Order::Entropy"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Excess Kurtosis with Large IBSI Phantom Image", -0.35462, results["First Order::Excess Kurtosis"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Covered image intensity range with Large IBSI Phantom Image", 0.5555555, results["First Order::Covered Image Intensity Range"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Sum of voxels with Large IBSI Phantom Image", 159, results["First Order::Sum"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Mode with Large IBSI Phantom Image", 1, results["First Order::Mode"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Mode Probability with Large IBSI Phantom Image", 50, results["First Order::Mode Probability"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Unbiased Standard deviation with Large IBSI Phantom Image", 1.757, results["First Order::Unbiased Standard deviation"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Biased Standard deviation with Large IBSI Phantom Image", 1.74627, results["First Order::Biased Standard deviation"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Robust mean with Large IBSI Phantom Image", 1.74627, results["First Order::Robust Mean"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Number Of Voxels with Large IBSI Phantom Image", 74, results["First Order::Number Of Voxels"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::10th Percentile with Large IBSI Phantom Image", 0.648, results["First Order::10th Percentile"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::90th Percentile with Large IBSI Phantom Image", 4.475, results["First Order::90th Percentile"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Interquantile Range with Large IBSI Phantom Image", 2.91125, results["First Order::Interquartile Range"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Voxel Space with Large IBSI Phantom Image", 8, results["First Order::Voxel Space"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Voxel Volume with Large IBSI Phantom Image", 8, results["First Order::Voxel Volume"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("First Order::Image Dimension with Large IBSI Phantom Image", 3, results["First Order::Image Dimension"], 0.01); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFFirstOrderStatistics ) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFGreyLevelDistanceZoneTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFGreyLevelDistanceZoneTest.cpp index b197e1405f..3a9e7c9361 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFGreyLevelDistanceZoneTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFGreyLevelDistanceZoneTest.cpp @@ -1,143 +1,143 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include "mitkIOUtil.h" #include #include class mitkGIFGreyLevelDistanceZoneTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFGreyLevelDistanceZoneTestSuite ); MITK_TEST(ImageDescription_PhantomTest_3D); MITK_TEST(ImageDescription_PhantomTest_2D); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest_3D() { mitk::GIFGreyLevelDistanceZone::Pointer featureCalculator = mitk::GIFGreyLevelDistanceZone::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[valuePair.first.featureClass+"::"+valuePair.first.name] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 19 features.", std::size_t(19), featureList.size()); // These values are obtained with IBSI // Standard accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Small Distance Emphasis with Large IBSI Phantom Image", 1, results["Grey Level Distance Zone::Small Distance Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Large Distance Emphasis with Large IBSI Phantom Image", 1, results["Grey Level Distance Zone::Large Distance Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Low Grey Level Emphasis with Large IBSI Phantom Image", 0.253, results["Grey Level Distance Zone::Low Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::High Grey Level Emphasis with Large IBSI Phantom Image", 15.6, results["Grey Level Distance Zone::High Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Small Distance Low Grey Level Emphasis with Large IBSI Phantom Image", 0.253, results["Grey Level Distance Zone::Small Distance Low Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Small Distance High Grey Level Emphasis with Large IBSI Phantom Image", 15.6, results["Grey Level Distance Zone::Small Distance High Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Large Distance Low Grey Level Emphasis with Large IBSI Phantom Image", 0.253, results["Grey Level Distance Zone::Large Distance Low Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Large Distance High Grey Level Emphasis with Large IBSI Phantom Image", 15.6, results["Grey Level Distance Zone::Large Distance High Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Grey Level Non-Uniformity with Large IBSI Phantom Image", 1.4, results["Grey Level Distance Zone::Grey Level Non-Uniformity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Grey Level Non-Uniformity Normalized with Large IBSI Phantom Image", 0.28, results["Grey Level Distance Zone::Grey Level Non-Uniformity Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Distance Size Non-Uniformity with Large IBSI Phantom Image", 5, results["Grey Level Distance Zone::Distance Size Non-Uniformity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Distance Size Non-Uniformity Normalized with Large IBSI Phantom Image", 1, results["Grey Level Distance Zone::Distance Size Non-Uniformity Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Zone Percentage with Large IBSI Phantom Image", 0.0676, results["Grey Level Distance Zone::Zone Percentage"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Grey Level Variance with Large IBSI Phantom Image", 2.64, results["Grey Level Distance Zone::Grey Level Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Zone Distance Variance with Large IBSI Phantom Image", 0, results["Grey Level Distance Zone::Zone Distance Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Zone Distance Entropy with Large IBSI Phantom Image", 1.92, results["Grey Level Distance Zone::Zone Distance Entropy"], 0.01); //CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone:: with Large IBSI Phantom Image", 0.045, results["Grey Level Distance Zone::"], 0.001); // These values are obtained by manually running the tool // Values might be wrong. CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Grey Level Mean with Large IBSI Phantom Image", 3.6, results["Grey Level Distance Zone::Grey Level Mean"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Zone Distance Mean with Large IBSI Phantom Image", 1, results["Grey Level Distance Zone::Zone Distance Mean"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone::Grey Level Entropy with Large IBSI Phantom Image", 1.92, results["Grey Level Distance Zone::Grey Level Entropy"], 0.01); } void ImageDescription_PhantomTest_2D() { mitk::GIFGreyLevelDistanceZone::Pointer featureCalculator = mitk::GIFGreyLevelDistanceZone::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeaturesSlicewise(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large, 2); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 114 features.", std::size_t(114), featureList.size()); // These values are obtained with IBSI // Standard accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Small Distance Emphasis with Large IBSI Phantom Image", 0.946, results["SliceWise Mean Grey Level Distance Zone::Small Distance Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Large Distance Emphasis with Large IBSI Phantom Image", 1.21, results["SliceWise Mean Grey Level Distance Zone::Large Distance Emphasis"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Low Grey Level Emphasis with Large IBSI Phantom Image", 0.371, results["SliceWise Mean Grey Level Distance Zone::Low Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::High Grey Level Emphasis with Large IBSI Phantom Image", 16.4, results["SliceWise Mean Grey Level Distance Zone::High Grey Level Emphasis"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Small Distance Low Grey Level Emphasis with Large IBSI Phantom Image", 0.367, results["SliceWise Mean Grey Level Distance Zone::Small Distance Low Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Small Distance High Grey Level Emphasis with Large IBSI Phantom Image", 15.2, results["SliceWise Mean Grey Level Distance Zone::Small Distance High Grey Level Emphasis"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Large Distance Low Grey Level Emphasis with Large IBSI Phantom Image", 0.386, results["SliceWise Mean Grey Level Distance Zone::Large Distance Low Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Large Distance High Grey Level Emphasis with Large IBSI Phantom Image", 21.3, results["SliceWise Mean Grey Level Distance Zone::Large Distance High Grey Level Emphasis"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Grey Level Non-Uniformity with Large IBSI Phantom Image", 1.41, results["SliceWise Mean Grey Level Distance Zone::Grey Level Non-Uniformity"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Grey Level Non-Uniformity Normalized with Large IBSI Phantom Image", 0.323, results["SliceWise Mean Grey Level Distance Zone::Grey Level Non-Uniformity Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Distance Size Non-Uniformity with Large IBSI Phantom Image", 3.79, results["SliceWise Mean Grey Level Distance Zone::Distance Size Non-Uniformity"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Distance Size Non-Uniformity Normalized with Large IBSI Phantom Image", 0.898, results["SliceWise Mean Grey Level Distance Zone::Distance Size Non-Uniformity Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Zone Percentage with Large IBSI Phantom Image", 0.24, results["SliceWise Mean Grey Level Distance Zone::Zone Percentage"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Grey Level Variance with Large IBSI Phantom Image", 3.97, results["SliceWise Mean Grey Level Distance Zone::Grey Level Variance"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Zone Distance Variance with Large IBSI Phantom Image", 0.051, results["SliceWise Mean Grey Level Distance Zone::Zone Distance Variance"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Zone Distance Entropy with Large IBSI Phantom Image", 1.73, results["SliceWise Mean Grey Level Distance Zone::Zone Distance Entropy"], 0.01); //CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Distance Zone:: with Large IBSI Phantom Image", 0.045, results["Grey Level Distance Zone::"], 0.001); // These values are obtained by manually running the tool // Values might be wrong. CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Grey Level Mean with Large IBSI Phantom Image", 3.526, results["SliceWise Mean Grey Level Distance Zone::Grey Level Mean"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Zone Distance Mean with Large IBSI Phantom Image", 1.071, results["SliceWise Mean Grey Level Distance Zone::Zone Distance Mean"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Distance Zone::Grey Level Entropy with Large IBSI Phantom Image", 1.732, results["SliceWise Mean Grey Level Distance Zone::Grey Level Entropy"], 0.01); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFGreyLevelDistanceZone ) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFGreyLevelSizeZoneTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFGreyLevelSizeZoneTest.cpp index 46adb4a03b..d101342762 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFGreyLevelSizeZoneTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFGreyLevelSizeZoneTest.cpp @@ -1,141 +1,141 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include "mitkIOUtil.h" #include #include class mitkGIFGreyLevelSizeZoneTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFGreyLevelSizeZoneTestSuite ); MITK_TEST(ImageDescription_PhantomTest_3D); MITK_TEST(ImageDescription_PhantomTest_2D); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest_3D() { mitk::GIFGreyLevelSizeZone::Pointer featureCalculator = mitk::GIFGreyLevelSizeZone::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 18 features.", std::size_t(18), featureList.size()); // These values are obtained with IBSI // Standard accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Small Zone Emphasis with Large IBSI Phantom Image", 0.255, results["Grey Level Size Zone::Small Zone Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Large Zone Emphasis with Large IBSI Phantom Image", 550, results["Grey Level Size Zone::Large Zone Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Low Grey Level Emphasis with Large IBSI Phantom Image", 0.253, results["Grey Level Size Zone::Low Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::High Grey Level Emphasis with Large IBSI Phantom Image", 15.6, results["Grey Level Size Zone::High Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Small Zone Low Grey Level Emphasis with Large IBSI Phantom Image", 0.0256, results["Grey Level Size Zone::Small Zone Low Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Small Zone High Grey Level Emphasis with Large IBSI Phantom Image", 2.76, results["Grey Level Size Zone::Small Zone High Grey Level Emphasis"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Large Zone Low Grey Level Emphasis with Large IBSI Phantom Image", 503, results["Grey Level Size Zone::Large Zone Low Grey Level Emphasis"], 1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Large Zone High Grey Level Emphasis with Large IBSI Phantom Image", 1495, results["Grey Level Size Zone::Large Zone High Grey Level Emphasis"], 1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Grey Level Non-Uniformity with Large IBSI Phantom Image", 1.4, results["Grey Level Size Zone::Grey Level Non-Uniformity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Grey Level Non-Uniformity Normalized with Large IBSI Phantom Image", 0.28, results["Grey Level Size Zone::Grey Level Non-Uniformity Normalized"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Zone Size Non-Uniformity with Large IBSI Phantom Image", 1, results["Grey Level Size Zone::Zone Size Non-Uniformity"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Zone Size Non-Uniformity Normalized with Large IBSI Phantom Image", 0.2, results["Grey Level Size Zone::Zone Size Non-Uniformity Normalized"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Zone Percentage with Large IBSI Phantom Image", 0.0676, results["Grey Level Size Zone::Zone Percentage"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Grey Level Variance with Large IBSI Phantom Image", 2.64, results["Grey Level Size Zone::Grey Level Variance"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Zone Size Variance with Large IBSI Phantom Image", 331, results["Grey Level Size Zone::Zone Size Variance"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Zone Size Entropy with Large IBSI Phantom Image", 2.32, results["Grey Level Size Zone::Zone Size Entropy"], 0.01); //CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone:: with Large IBSI Phantom Image", 0.045, results["Grey Level Size Zone::"], 0.001); // These values are obtained by manually running the tool // Values might be wrong. CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Grey Level Mean with Large IBSI Phantom Image", 3.6, results["Grey Level Size Zone::Grey Level Mean"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Grey Level Size Zone::Zone Size Mean with Large IBSI Phantom Image", 14.8, results["Grey Level Size Zone::Zone Size Mean"], 0.001); } void ImageDescription_PhantomTest_2D() { mitk::GIFGreyLevelSizeZone::Pointer featureCalculator = mitk::GIFGreyLevelSizeZone::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeaturesSlicewise(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large, 2); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 108 features.", std::size_t(108), featureList.size()); // These values are obtained with IBSI // Standard accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Small Zone Emphasis with Large IBSI Phantom Image", 0.363, results["SliceWise Mean Grey Level Size Zone::Small Zone Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Large Zone Emphasis with Large IBSI Phantom Image", 43.9, results["SliceWise Mean Grey Level Size Zone::Large Zone Emphasis"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Low Grey Level Emphasis with Large IBSI Phantom Image", 0.371, results["SliceWise Mean Grey Level Size Zone::Low Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::High Grey Level Emphasis with Large IBSI Phantom Image", 16.4, results["SliceWise Mean Grey Level Size Zone::High Grey Level Emphasis"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Small Zone Low Grey Level Emphasis with Large IBSI Phantom Image", 0.0259, results["SliceWise Mean Grey Level Size Zone::Small Zone Low Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Small Zone High Grey Level Emphasis with Large IBSI Phantom Image", 10.3, results["SliceWise Mean Grey Level Size Zone::Small Zone High Grey Level Emphasis"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Large Zone Low Grey Level Emphasis with Large IBSI Phantom Image", 40.4, results["SliceWise Mean Grey Level Size Zone::Large Zone Low Grey Level Emphasis"], 1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Large Zone High Grey Level Emphasis with Large IBSI Phantom Image", 113, results["SliceWise Mean Grey Level Size Zone::Large Zone High Grey Level Emphasis"], 1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Grey Level Non-Uniformity with Large IBSI Phantom Image", 1.41, results["SliceWise Mean Grey Level Size Zone::Grey Level Non-Uniformity"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Grey Level Non-Uniformity Normalized with Large IBSI Phantom Image", 0.323, results["SliceWise Mean Grey Level Size Zone::Grey Level Non-Uniformity Normalized"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Zone Size Non-Uniformity with Large IBSI Phantom Image", 1.49, results["SliceWise Mean Grey Level Size Zone::Zone Size Non-Uniformity"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Zone Size Non-Uniformity Normalized with Large IBSI Phantom Image", 0.333, results["SliceWise Mean Grey Level Size Zone::Zone Size Non-Uniformity Normalized"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Zone Percentage with Large IBSI Phantom Image", 0.24, results["SliceWise Mean Grey Level Size Zone::Zone Percentage"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Grey Level Variance with Large IBSI Phantom Image", 3.97, results["SliceWise Mean Grey Level Size Zone::Grey Level Variance"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Zone Size Variance with Large IBSI Phantom Image", 21, results["SliceWise Mean Grey Level Size Zone::Zone Size Variance"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Zone Size Entropy with Large IBSI Phantom Image", 1.93, results["SliceWise Mean Grey Level Size Zone::Zone Size Entropy"], 0.01); //CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone:: with Large IBSI Phantom Image", 0.045, results["SliceWise Mean Grey Level Size Zone::"], 0.001); // These values are obtained by manually running the tool // Values might be wrong. CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Grey Level Mean with Large IBSI Phantom Image", 3.526, results["SliceWise Mean Grey Level Size Zone::Grey Level Mean"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Grey Level Size Zone::Zone Size Mean with Large IBSI Phantom Image", 4.59524, results["SliceWise Mean Grey Level Size Zone::Zone Size Mean"], 0.001); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFGreyLevelSizeZone ) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFImageDescriptionFeaturesTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFImageDescriptionFeaturesTest.cpp index 74aa3d40c5..2c0851bd79 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFImageDescriptionFeaturesTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFImageDescriptionFeaturesTest.cpp @@ -1,91 +1,91 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include "mitkIOUtil.h" #include #include class mitkGIFImageDescriptionFeaturesTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFImageDescriptionFeaturesTestSuite ); MITK_TEST(ImageDescription_PhantomTest); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest() { mitk::GIFImageDescriptionFeatures::Pointer featureCalculator = mitk::GIFImageDescriptionFeatures::New(); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 22 features.", std::size_t(22), featureList.size()); // These values are calculated obtained by using this filter. Changes, especially with mean values could happen. CPPUNIT_ASSERT_EQUAL_MESSAGE("Diagnostic::Image Dimension X should be 7 with Large IBSI Phantom Image", int(7), int(results["Diagnostic::Image Dimension X"])); CPPUNIT_ASSERT_EQUAL_MESSAGE("Diagnostic::Image Dimension Y should be 6 with Large IBSI Phantom Image", int(6), int(results["Diagnostic::Image Dimension Y"])); CPPUNIT_ASSERT_EQUAL_MESSAGE("Diagnostic::Image Dimension Z should be 6 with Large IBSI Phantom Image", int(6), int(results["Diagnostic::Image Dimension Z"])); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Diagnostic::Image Spacing X should be 2 with Large IBSI Phantom Image", 2.0, results["Diagnostic::Image Spacing X"], 0.0001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Diagnostic::Image Spacing Y should be 2 with Large IBSI Phantom Image", 2.0, results["Diagnostic::Image Spacing Y"], 0.0001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Diagnostic::Image Spacing Z should be 2 with Large IBSI Phantom Image", 2.0, results["Diagnostic::Image Spacing Z"], 0.0001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Diagnostic::Image Mean intensity should be 0.6865 with Large IBSI Phantom Image", 0.686508, results["Diagnostic::Image Mean intensity"], 0.0001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Diagnostic::Image Minimum intensity should be 0 with Large IBSI Phantom Image", 0, results["Diagnostic::Image Minimum intensity"], 0.0001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Diagnostic::Image Maximum intensity should be 9 with Large IBSI Phantom Image", 9, results["Diagnostic::Image Maximum intensity"], 0.0001); CPPUNIT_ASSERT_EQUAL_MESSAGE("Diagnostic::Mask Dimension X should be 7 with Large IBSI Phantom Image", int(7), int(results["Diagnostic::Mask Dimension X"])); CPPUNIT_ASSERT_EQUAL_MESSAGE("Diagnostic::Mask Dimension Y should be 6 with Large IBSI Phantom Image", int(6), int(results["Diagnostic::Mask Dimension Y"])); CPPUNIT_ASSERT_EQUAL_MESSAGE("Diagnostic::Mask Dimension Z should be 6 with Large IBSI Phantom Image", int(6), int(results["Diagnostic::Mask Dimension Z"])); CPPUNIT_ASSERT_EQUAL_MESSAGE("Diagnostic::Mask bounding box X should be 5 with Large IBSI Phantom Image", int(5), int(results["Diagnostic::Mask bounding box X"])); CPPUNIT_ASSERT_EQUAL_MESSAGE("Diagnostic::Mask bounding box Y should be 4 with Large IBSI Phantom Image", int(4), int(results["Diagnostic::Mask bounding box Y"])); CPPUNIT_ASSERT_EQUAL_MESSAGE("Diagnostic::Mask bounding box Z should be 4 with Large IBSI Phantom Image", int(4), int(results["Diagnostic::Mask bounding box Z"])); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Diagnostic::Mask Spacing X should be 2 with Large IBSI Phantom Image", 2.0, results["Diagnostic::Mask Spacing X"], 0.0001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Diagnostic::Mask Spacing Y should be 2 with Large IBSI Phantom Image", 2.0, results["Diagnostic::Mask Spacing Y"], 0.0001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Diagnostic::Mask Spacing Z should be 2 with Large IBSI Phantom Image", 2.0, results["Diagnostic::Mask Spacing Z"], 0.0001); CPPUNIT_ASSERT_EQUAL_MESSAGE("Diagnostic::Mask Voxel Count should be 74 with Large IBSI Phantom Image", int(74), int(results["Diagnostic::Mask Voxel Count"])); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Diagnostic::Mask Mean intensity should be 2.14865 with Large IBSI Phantom Image", 2.14865, results["Diagnostic::Mask Mean intensity"], 0.0001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Diagnostic::Mask Minimum intensity should be 1 with Large IBSI Phantom Image", 1, results["Diagnostic::Mask Minimum intensity"], 0.0001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Diagnostic::Mask Maximum intensity should be 6 with Large IBSI Phantom Image", 6, results["Diagnostic::Mask Maximum intensity"], 0.0001); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFImageDescriptionFeatures ) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFIntensityVolumeHistogramTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFIntensityVolumeHistogramTest.cpp index d8c238b798..533d4859df 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFIntensityVolumeHistogramTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFIntensityVolumeHistogramTest.cpp @@ -1,155 +1,155 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include "mitkIOUtil.h" #include #include class mitkGIFIntensityVolumeHistogramTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE( mitkGIFIntensityVolumeHistogramTestSuite); MITK_TEST(ImageDescription_PhantomTest_Large); MITK_TEST(ImageDescription_PhantomTest_Small); MITK_TEST(ImageDescription_PhantomTest_2D); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest_Large() { mitk::GIFIntensityVolumeHistogramFeatures::Pointer featureCalculator = mitk::GIFIntensityVolumeHistogramFeatures::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 7 features.", std::size_t(7), featureList.size()); // These values are obtained in cooperation with IBSI // Reported with an accuracy of 0.1 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Volume fraction at 0.10 intensity with Large IBSI Phantom Image", 0.3243, results["Intensity Volume Histogram::Volume fraction at 0.10 intensity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Volume fraction at 0.90 intensity with Large IBSI Phantom Image", 0.09459, results["Intensity Volume Histogram::Volume fraction at 0.90 intensity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Intensity at 0.10 volume with Large IBSI Phantom Image", 5, results["Intensity Volume Histogram::Intensity at 0.10 volume"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Intensity at 0.90 volume with Large IBSI Phantom Image", 2, results["Intensity Volume Histogram::Intensity at 0.90 volume"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Difference volume fraction at 0.10 and 0.90 intensity with Large IBSI Phantom Image", 0.22973, results["Intensity Volume Histogram::Difference volume fraction at 0.10 and 0.90 intensity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Difference intensity at 0.10 and 0.90 volume with Large IBSI Phantom Image", 3, results["Intensity Volume Histogram::Difference intensity at 0.10 and 0.90 volume"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Area under IVH curve with Large IBSI Phantom Image", 0.32027, results["Intensity Volume Histogram::Area under IVH curve"], 0.001); } void ImageDescription_PhantomTest_Small() { mitk::GIFIntensityVolumeHistogramFeatures::Pointer featureCalculator = mitk::GIFIntensityVolumeHistogramFeatures::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Small, m_IBSI_Phantom_Mask_Small); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 7 features.", std::size_t(7), featureList.size()); // These values are obtained in cooperation with IBSI // Reported with an accuracy of 0.1 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Volume fraction at 0.10 intensity with Large IBSI Phantom Image", 0.3243, results["Intensity Volume Histogram::Volume fraction at 0.10 intensity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Volume fraction at 0.90 intensity with Large IBSI Phantom Image", 0.09459, results["Intensity Volume Histogram::Volume fraction at 0.90 intensity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Intensity at 0.10 volume with Large IBSI Phantom Image", 5, results["Intensity Volume Histogram::Intensity at 0.10 volume"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Intensity at 0.90 volume with Large IBSI Phantom Image", 2, results["Intensity Volume Histogram::Intensity at 0.90 volume"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Difference volume fraction at 0.10 and 0.90 intensity with Large IBSI Phantom Image", 0.22973, results["Intensity Volume Histogram::Difference volume fraction at 0.10 and 0.90 intensity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Difference intensity at 0.10 and 0.90 volume with Large IBSI Phantom Image", 3, results["Intensity Volume Histogram::Difference intensity at 0.10 and 0.90 volume"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Intensity Volume Histogram::Area under IVH curve with Large IBSI Phantom Image", 0.32027, results["Intensity Volume Histogram::Area under IVH curve"], 0.001); } void ImageDescription_PhantomTest_2D() { mitk::GIFIntensityVolumeHistogramFeatures::Pointer featureCalculator = mitk::GIFIntensityVolumeHistogramFeatures::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeaturesSlicewise(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large, 2); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 42 features.", std::size_t(42), featureList.size()); // These values are obtained by calculating on the features // Could be wrong! CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Intensity Volume Histogram::Volume fraction at 0.10 intensity with Large IBSI Phantom Image", 0.31539, results["SliceWise Mean Intensity Volume Histogram::Volume fraction at 0.10 intensity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Intensity Volume Histogram::Volume fraction at 0.90 intensity with Large IBSI Phantom Image", 0.0924106, results["SliceWise Mean Intensity Volume Histogram::Volume fraction at 0.90 intensity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Intensity Volume Histogram::Intensity at 0.10 volume with Large IBSI Phantom Image", 6, results["SliceWise Mean Intensity Volume Histogram::Intensity at 0.10 volume"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Intensity Volume Histogram::Intensity at 0.90 volume with Large IBSI Phantom Image", 2, results["SliceWise Mean Intensity Volume Histogram::Intensity at 0.90 volume"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Intensity Volume Histogram::Difference volume fraction at 0.10 and 0.90 intensity with Large IBSI Phantom Image", 0.222979, results["SliceWise Mean Intensity Volume Histogram::Difference volume fraction at 0.10 and 0.90 intensity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Intensity Volume Histogram::Difference intensity at 0.10 and 0.90 volume with Large IBSI Phantom Image", 4, results["SliceWise Mean Intensity Volume Histogram::Difference intensity at 0.10 and 0.90 volume"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Intensity Volume Histogram::Area under IVH curve with Large IBSI Phantom Image", 0.314325, results["SliceWise Mean Intensity Volume Histogram::Area under IVH curve"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Var. Intensity Volume Histogram::Volume fraction at 0.10 intensity with Large IBSI Phantom Image", 0.0248178, results["SliceWise Var. Intensity Volume Histogram::Volume fraction at 0.10 intensity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Var. Intensity Volume Histogram::Volume fraction at 0.90 intensity with Large IBSI Phantom Image", 0.00149203, results["SliceWise Var. Intensity Volume Histogram::Volume fraction at 0.90 intensity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Var. Intensity Volume Histogram::Intensity at 0.10 volume with Large IBSI Phantom Image", 1, results["SliceWise Var. Intensity Volume Histogram::Intensity at 0.10 volume"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Var. Intensity Volume Histogram::Intensity at 0.90 volume with Large IBSI Phantom Image", 0, results["SliceWise Var. Intensity Volume Histogram::Intensity at 0.90 volume"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Var. Intensity Volume Histogram::Difference volume fraction at 0.10 and 0.90 intensity with Large IBSI Phantom Image", 0.01414, results["SliceWise Var. Intensity Volume Histogram::Difference volume fraction at 0.10 and 0.90 intensity"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Var. Intensity Volume Histogram::Difference intensity at 0.10 and 0.90 volume with Large IBSI Phantom Image", 1, results["SliceWise Var. Intensity Volume Histogram::Difference intensity at 0.10 and 0.90 volume"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Var. Intensity Volume Histogram::Area under IVH curve with Large IBSI Phantom Image", 0.0110923, results["SliceWise Var. Intensity Volume Histogram::Area under IVH curve"], 0.001); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFIntensityVolumeHistogram) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFLocalIntensityTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFLocalIntensityTest.cpp index 25df1f8a28..a6af3c6327 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFLocalIntensityTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFLocalIntensityTest.cpp @@ -1,110 +1,110 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include "mitkIOUtil.h" #include #include class mitkGIFLocalIntensityTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFLocalIntensityTestSuite); MITK_TEST(ImageDescription_PhantomTest_Small); MITK_TEST(ImageDescription_PhantomTest_Large); MITK_TEST(ImageDescription_PhantomTest_Large_RangeChanged); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest_Small() { mitk::GIFLocalIntensity::Pointer featureCalculator = mitk::GIFLocalIntensity::New(); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Small, m_IBSI_Phantom_Mask_Small); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 2 features.", std::size_t(2), featureList.size()); // These values are obtained in cooperation with IBSI // Reported with an accuracy of 0.1 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Local Intensity::Local Intensity Peak with Large IBSI Phantom Image", 2.6, results["Local Intensity::2. Local Intensity Peak"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Local Intensity::Global Intensity Peak with Large IBSI Phantom Image", 3.1, results["Local Intensity::2. Global Intensity Peak"], 0.1); } void ImageDescription_PhantomTest_Large() { mitk::GIFLocalIntensity::Pointer featureCalculator = mitk::GIFLocalIntensity::New(); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 2 features.", std::size_t(2), featureList.size()); // These values are obtained by running the tool // They might be wrong CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Local Intensity::Local Intensity Peak with Large IBSI Phantom Image", 1.43, results["Local Intensity::2. Local Intensity Peak"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Local Intensity::Global Intensity Peak with Large IBSI Phantom Image", 1.43, results["Local Intensity::2. Global Intensity Peak"], 0.01); } void ImageDescription_PhantomTest_Large_RangeChanged() { mitk::GIFLocalIntensity::Pointer featureCalculator = mitk::GIFLocalIntensity::New(); featureCalculator->SetRange(1); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 2 features.", std::size_t(2), featureList.size()); // These values are obtained by running the tool // They might be wrong CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Local Intensity::Local Intensity Peak with Large IBSI Phantom Image", 6, results["Local Intensity::2. Local Intensity Peak"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Local Intensity::Global Intensity Peak with Large IBSI Phantom Image", 6, results["Local Intensity::2. Global Intensity Peak"], 0.01); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFLocalIntensity ) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFNeighbourhoodGreyToneDifferenceFeaturesTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFNeighbourhoodGreyToneDifferenceFeaturesTest.cpp index ff0c33fce9..d87d6aa325 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFNeighbourhoodGreyToneDifferenceFeaturesTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFNeighbourhoodGreyToneDifferenceFeaturesTest.cpp @@ -1,107 +1,107 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include "mitkIOUtil.h" #include #include class mitkGIFNeighbourhoodGreyToneDifferenceFeaturesTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFNeighbourhoodGreyToneDifferenceFeaturesTestSuite); MITK_TEST(ImageDescription_PhantomTest_3D); MITK_TEST(ImageDescription_PhantomTest_2D); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest_3D() { mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::Pointer featureCalculator = mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 5 features.", std::size_t(5), featureList.size()); // These values are obtained with IBSI // Standard accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbourhood Grey Tone Difference::Coarsness with Large IBSI Phantom Image", 0.0296, results["Neighbourhood Grey Tone Difference::Coarsness"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbourhood Grey Tone Difference::Contrast with Large IBSI Phantom Image", 0.584, results["Neighbourhood Grey Tone Difference::Contrast"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbourhood Grey Tone Difference::Busyness with Large IBSI Phantom Image", 6.54, results["Neighbourhood Grey Tone Difference::Busyness"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbourhood Grey Tone Difference::Complexity with Large IBSI Phantom Image", 13.5, results["Neighbourhood Grey Tone Difference::Complexity"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbourhood Grey Tone Difference::Strength with Large IBSI Phantom Image", 0.763, results["Neighbourhood Grey Tone Difference::Strength"], 0.01); } void ImageDescription_PhantomTest_2D() { mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::Pointer featureCalculator = mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeaturesSlicewise(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large, 2); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 30 features.", std::size_t(30), featureList.size()); // These values are obtained with IBSI // Standard accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbourhood Grey Tone Difference::Coarsness with Large IBSI Phantom Image", 0.121, results["SliceWise Mean Neighbourhood Grey Tone Difference::Coarsness"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbourhood Grey Tone Difference::Contrast with Large IBSI Phantom Image", 0.925, results["SliceWise Mean Neighbourhood Grey Tone Difference::Contrast"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbourhood Grey Tone Difference::Busyness with Large IBSI Phantom Image", 2.99, results["SliceWise Mean Neighbourhood Grey Tone Difference::Busyness"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbourhood Grey Tone Difference::Complexity with Large IBSI Phantom Image", 10.4, results["SliceWise Mean Neighbourhood Grey Tone Difference::Complexity"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbourhood Grey Tone Difference::Strength with Large IBSI Phantom Image", 2.88, results["SliceWise Mean Neighbourhood Grey Tone Difference::Strength"], 0.01); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFNeighbourhoodGreyToneDifferenceFeatures ) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFNeighbouringGreyLevelDependenceFeatureTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFNeighbouringGreyLevelDependenceFeatureTest.cpp index 989fb21ca4..a12cdc4289 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFNeighbouringGreyLevelDependenceFeatureTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFNeighbouringGreyLevelDependenceFeatureTest.cpp @@ -1,151 +1,151 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include "mitkIOUtil.h" #include #include class mitkGIFNeighbouringGreyLevelDependenceFeatureTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFNeighbouringGreyLevelDependenceFeatureTestSuite ); MITK_TEST(ImageDescription_PhantomTest_3D); MITK_TEST(ImageDescription_PhantomTest_2D); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest_3D() { mitk::GIFNeighbouringGreyLevelDependenceFeature::Pointer featureCalculator = mitk::GIFNeighbouringGreyLevelDependenceFeature::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 24 features.", std::size_t(24), featureList.size()); // These values are obtained with IBSI // Standard accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Low Dependence Emphasis with Large IBSI Phantom Image", 0.045, results["Neighbouring Grey Level Dependence::Low Dependence Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::High Dependence Emphasis with Large IBSI Phantom Image", 109, results["Neighbouring Grey Level Dependence::High Dependence Emphasis"], 1.0); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Low Grey Level Count Emphasis with Large IBSI Phantom Image", 0.693, results["Neighbouring Grey Level Dependence::Low Grey Level Count Emphasis"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::High Grey Level Count Emphasis with Large IBSI Phantom Image", 7.66, results["Neighbouring Grey Level Dependence::High Grey Level Count Emphasis"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Low Dependence Low Grey Level Emphasis with Large IBSI Phantom Image", 0.00963, results["Neighbouring Grey Level Dependence::Low Dependence Low Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Low Dependence High Grey Level Emphasis with Large IBSI Phantom Image", 0.736, results["Neighbouring Grey Level Dependence::Low Dependence High Grey Level Emphasis"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::High Dependence Low Grey Level Emphasis with Large IBSI Phantom Image", 102, results["Neighbouring Grey Level Dependence::High Dependence Low Grey Level Emphasis"], 1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::High Dependence High Grey Level Emphasis with Large IBSI Phantom Image", 235, results["Neighbouring Grey Level Dependence::High Dependence High Grey Level Emphasis"], 1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Grey Level Non-Uniformity with Large IBSI Phantom Image", 37.9, results["Neighbouring Grey Level Dependence::Grey Level Non-Uniformity"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Grey Level Non-Uniformity Normalised with Large IBSI Phantom Image", 0.512, results["Neighbouring Grey Level Dependence::Grey Level Non-Uniformity Normalised"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Dependence Count Non-Uniformity with Large IBSI Phantom Image", 4.86, results["Neighbouring Grey Level Dependence::Dependence Count Non-Uniformity"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Dependence Count Non-Uniformity Normalised with Large IBSI Phantom Image", 0.0657, results["Neighbouring Grey Level Dependence::Dependence Count Non-Uniformity Normalised"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Dependence Count Percentage with Large IBSI Phantom Image", 1, results["Neighbouring Grey Level Dependence::Dependence Count Percentage"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Grey Level Variance with Large IBSI Phantom Image", 3.05, results["Neighbouring Grey Level Dependence::Grey Level Variance"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Dependence Count Variance with Large IBSI Phantom Image", 22.1, results["Neighbouring Grey Level Dependence::Dependence Count Variance"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Dependence Count Entropy with Large IBSI Phantom Image", 4.4, results["Neighbouring Grey Level Dependence::Dependence Count Entropy"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Dependence Count Energy with Large IBSI Phantom Image", 0.0533, results["Neighbouring Grey Level Dependence::Dependence Count Energy"], 0.01); // These values are obtained by manually running the tool // Values might be wrong. CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Grey Level Mean with Large IBSI Phantom Image", 2.15, results["Neighbouring Grey Level Dependence::Grey Level Mean"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Dependence Count Mean with Large IBSI Phantom Image", 9.32, results["Neighbouring Grey Level Dependence::Dependence Count Mean"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Expected Neighbourhood Size with Large IBSI Phantom Image", 26, results["Neighbouring Grey Level Dependence::Expected Neighbourhood Size"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Average Neighbourhood Size with Large IBSI Phantom Image", 14.24, results["Neighbouring Grey Level Dependence::Average Neighbourhood Size"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Average Incomplete Neighbourhood Size with Large IBSI Phantom Image", 14.24, results["Neighbouring Grey Level Dependence::Average Incomplete Neighbourhood Size"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Percentage of complete Neighbourhoods with Large IBSI Phantom Image", 0, results["Neighbouring Grey Level Dependence::Percentage of complete Neighbourhoods"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Neighbouring Grey Level Dependence::Percentage of Dependence Neighbour Voxels with Large IBSI Phantom Image", 0.584, results["Neighbouring Grey Level Dependence::Percentage of Dependence Neighbour Voxels"], 0.01); } void ImageDescription_PhantomTest_2D() { mitk::GIFNeighbouringGreyLevelDependenceFeature::Pointer featureCalculator = mitk::GIFNeighbouringGreyLevelDependenceFeature::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeaturesSlicewise(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large, 2); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 144 features.", std::size_t(144), featureList.size()); // These values are obtained with IBSI // Standard accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Low Dependence Emphasis with Large IBSI Phantom Image", 0.158, results["SliceWise Mean Neighbouring Grey Level Dependence::Low Dependence Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::High Dependence Emphasis with Large IBSI Phantom Image", 19.2, results["SliceWise Mean Neighbouring Grey Level Dependence::High Dependence Emphasis"], 1.0); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Low Grey Level Count Emphasis with Large IBSI Phantom Image", 0.702, results["SliceWise Mean Neighbouring Grey Level Dependence::Low Grey Level Count Emphasis"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::High Grey Level Count Emphasis with Large IBSI Phantom Image", 7.49, results["SliceWise Mean Neighbouring Grey Level Dependence::High Grey Level Count Emphasis"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Low Dependence Low Grey Level Emphasis with Large IBSI Phantom Image", 0.0473, results["SliceWise Mean Neighbouring Grey Level Dependence::Low Dependence Low Grey Level Emphasis"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Low Dependence High Grey Level Emphasis with Large IBSI Phantom Image", 3.06, results["SliceWise Mean Neighbouring Grey Level Dependence::Low Dependence High Grey Level Emphasis"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::High Dependence Low Grey Level Emphasis with Large IBSI Phantom Image", 17.6, results["SliceWise Mean Neighbouring Grey Level Dependence::High Dependence Low Grey Level Emphasis"], 1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::High Dependence High Grey Level Emphasis with Large IBSI Phantom Image", 49.5, results["SliceWise Mean Neighbouring Grey Level Dependence::High Dependence High Grey Level Emphasis"], 1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Grey Level Non-Uniformity with Large IBSI Phantom Image", 10.2, results["SliceWise Mean Neighbouring Grey Level Dependence::Grey Level Non-Uniformity"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Grey Level Non-Uniformity Normalised with Large IBSI Phantom Image", 0.562, results["SliceWise Mean Neighbouring Grey Level Dependence::Grey Level Non-Uniformity Normalised"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Non-Uniformity with Large IBSI Phantom Image", 3.96, results["SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Non-Uniformity"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Non-Uniformity Normalised with Large IBSI Phantom Image", 0.212, results["SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Non-Uniformity Normalised"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Percentage with Large IBSI Phantom Image", 1, results["SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Percentage"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Grey Level Variance with Large IBSI Phantom Image", 2.7, results["SliceWise Mean Neighbouring Grey Level Dependence::Grey Level Variance"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Variance with Large IBSI Phantom Image", 2.73, results["SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Variance"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Entropy with Large IBSI Phantom Image", 2.71, results["SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Entropy"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Energy with Large IBSI Phantom Image", 0.17, results["SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Energy"], 0.01); // These values are obtained by manually running the tool // Values might be wrong. CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Grey Level Mean with Large IBSI Phantom Image", 2.12, results["SliceWise Mean Neighbouring Grey Level Dependence::Grey Level Mean"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Mean with Large IBSI Phantom Image", 3.98, results["SliceWise Mean Neighbouring Grey Level Dependence::Dependence Count Mean"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Expected Neighbourhood Size with Large IBSI Phantom Image", 8, results["SliceWise Mean Neighbouring Grey Level Dependence::Expected Neighbourhood Size"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Average Neighbourhood Size with Large IBSI Phantom Image", 5.20, results["SliceWise Mean Neighbouring Grey Level Dependence::Average Neighbourhood Size"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Average Incomplete Neighbourhood Size with Large IBSI Phantom Image", 4.5598, results["SliceWise Mean Neighbouring Grey Level Dependence::Average Incomplete Neighbourhood Size"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Percentage of complete Neighbourhoods with Large IBSI Phantom Image", 0.1831, results["SliceWise Mean Neighbouring Grey Level Dependence::Percentage of complete Neighbourhoods"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("SliceWise Mean Neighbouring Grey Level Dependence::Percentage of Dependence Neighbour Voxels with Large IBSI Phantom Image", 0.579, results["SliceWise Mean Neighbouring Grey Level Dependence::Percentage of Dependence Neighbour Voxels"], 0.01); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFNeighbouringGreyLevelDependenceFeature ) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFVolumetricDensityStatisticsTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFVolumetricDensityStatisticsTest.cpp index c1de6520b6..f3aed016f3 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFVolumetricDensityStatisticsTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFVolumetricDensityStatisticsTest.cpp @@ -1,88 +1,88 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include "mitkIOUtil.h" #include #include class mitkGIFVolumetricDensityStatisticsTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFVolumetricDensityStatisticsTestSuite); MITK_TEST(ImageDescription_PhantomTest); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest() { mitk::GIFVolumetricDensityStatistics::Pointer featureCalculator = mitk::GIFVolumetricDensityStatistics::New(); featureCalculator->SetUseBinsize(true); featureCalculator->SetBinsize(1.0); featureCalculator->SetUseMinimumIntensity(true); featureCalculator->SetUseMaximumIntensity(true); featureCalculator->SetMinimumIntensity(0.5); featureCalculator->SetMaximumIntensity(6.5); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Image Diagnostics should calculate 13 features.", std::size_t(13), featureList.size()); // These values are obtained by a run of the filter. // The might be wrong! // These values are obtained in collaboration with IBSI. // They are usually reported with an accuracy of 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Volume integrated intensity with Large IBSI Phantom Image", 1195, results["Morphological Density::Volume integrated intensity"], 1.0); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Volume Moran's I index with Large IBSI Phantom Image", 0.0397, results["Morphological Density::Volume Moran's I index"], 0.0001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Volume Geary's C measure with Large IBSI Phantom Image", 0.974, results["Morphological Density::Volume Geary's C measure"], 0.001); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Volume Volume density axis-aligned bounding box with Large IBSI Phantom Image", 0.87, results["Morphological Density::Volume density axis-aligned bounding box"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Surface Volume density axis-aligned bounding box with Large IBSI Phantom Image", 0.87, results["Morphological Density::Surface density axis-aligned bounding box"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Volume Volume oriented minimum bounding box with Large IBSI Phantom Image", 0.87, results["Morphological Density::Volume density oriented minimum bounding box"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Surface Volume oriented minimum bounding box with Large IBSI Phantom Image", 0.86, results["Morphological Density::Surface density oriented minimum bounding box"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Volume Volume approx. enclosing ellipsoid with Large IBSI Phantom Image", 1.17, results["Morphological Density::Volume density approx. enclosing ellipsoid"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Surface Volume approx. enclosing ellipsoid with Large IBSI Phantom Image", 1.34, results["Morphological Density::Surface density approx. enclosing ellipsoid"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Volume Volume minimum volume enclosing ellipsoid with Large IBSI Phantom Image", 0.24, results["Morphological Density::Volume density approx. minimum volume enclosing ellipsoid"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Surface Volume minimum volume enclosing ellipsoid with Large IBSI Phantom Image", 0.49, results["Morphological Density::Surface density approx. minimum volume enclosing ellipsoid"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Volume Volume convex hull with Large IBSI Phantom Image", 0.96, results["Morphological Density::Volume density convex hull"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Morphological Density::Surface Volume convex hull with Large IBSI Phantom Image", 1.03, results["Morphological Density::Surface density convex hull"], 0.01); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFVolumetricDensityStatistics ) diff --git a/Modules/Classification/CLUtilities/test/mitkGIFVolumetricStatisticsTest.cpp b/Modules/Classification/CLUtilities/test/mitkGIFVolumetricStatisticsTest.cpp index c23fb3317f..2b8d874e9c 100644 --- a/Modules/Classification/CLUtilities/test/mitkGIFVolumetricStatisticsTest.cpp +++ b/Modules/Classification/CLUtilities/test/mitkGIFVolumetricStatisticsTest.cpp @@ -1,106 +1,106 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include "mitkIOUtil.h" #include #include class mitkGIFVolumetricStatisticsTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkGIFVolumetricStatisticsTestSuite); MITK_TEST(ImageDescription_PhantomTest); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::Pointer m_IBSI_Phantom_Image_Small; mitk::Image::Pointer m_IBSI_Phantom_Image_Large; mitk::Image::Pointer m_IBSI_Phantom_Mask_Small; mitk::Image::Pointer m_IBSI_Phantom_Mask_Large; public: void setUp(void) override { m_IBSI_Phantom_Image_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Small.nrrd")); m_IBSI_Phantom_Image_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Image_Large.nrrd")); m_IBSI_Phantom_Mask_Small = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Small.nrrd")); m_IBSI_Phantom_Mask_Large = mitk::IOUtil::Load(GetTestDataFilePath("Radiomics/IBSI_Phantom_Mask_Large.nrrd")); } void ImageDescription_PhantomTest() { mitk::GIFVolumetricStatistics::Pointer featureCalculator = mitk::GIFVolumetricStatistics::New(); auto featureList = featureCalculator->CalculateFeatures(m_IBSI_Phantom_Image_Large, m_IBSI_Phantom_Mask_Large); std::map results; - for (auto valuePair : featureList) + for (const auto &valuePair : featureList) { MITK_INFO << mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first) << " : " << valuePair.second; results[mitk::AbstractGlobalImageFeature::GenerateLegacyFeatureNameWOEncoding(valuePair.first)] = valuePair.second; } CPPUNIT_ASSERT_EQUAL_MESSAGE("Volume Statistic should calculate 33 features.", std::size_t(38), featureList.size()); // These values are obtained in cooperation with IBSI // Default accuracy is 0.01 CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Volume (mesh based) with Large IBSI Phantom Image", 556, results["Volumetric Features::Volume (mesh based)"], 1.0); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Volume (voxel based) with Large IBSI Phantom Image", 592, results["Volumetric Features::Volume (voxel based)"], 1.0); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Surface (mesh based) with Large IBSI Phantom Image", 388, results["Volumetric Features::Surface (mesh based)"], 1.0); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Surface to volume ratio (mesh based) with Large IBSI Phantom Image", 0.698, results["Volumetric Features::Surface to volume ratio (mesh based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Compactness 1 (mesh, mesh based) with Large IBSI Phantom Image", 0.04105, results["Volumetric Features::Compactness 1 (mesh, mesh based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Compactness 2 (mesh, mesh based) with Large IBSI Phantom Image", 0.599, results["Volumetric Features::Compactness 2 (mesh, mesh based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Spherical disproportion (mesh, mesh based) with Large IBSI Phantom Image", 1.18, results["Volumetric Features::Spherical disproportion (mesh, mesh based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Sphericity (mesh, mesh based) with Large IBSI Phantom Image", 0.843, results["Volumetric Features::Sphericity (mesh, mesh based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Asphericity (mesh based) with Large IBSI Phantom Image", 0.186, results["Volumetric Features::Asphericity (mesh, mesh based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Centre of mass shift with Large IBSI Phantom Image", 0.672, results["Volumetric Features::Centre of mass shift"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Maximum 3D diameter with Large IBSI Phantom Image", 11.66, results["Volumetric Features::Maximum 3D diameter"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::PCA Major axis length with Large IBSI Phantom Image", 11.40, results["Volumetric Features::PCA Major axis length"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::PCA Minor axis length with Large IBSI Phantom Image", 9.31, results["Volumetric Features::PCA Minor axis length"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::PCA Least axis length with Large IBSI Phantom Image", 8.54, results["Volumetric Features::PCA Least axis length"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::PCA Elongation with Large IBSI Phantom Image", 0.816, results["Volumetric Features::PCA Elongation"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::PCA Flatness with Large IBSI Phantom Image", 0.749, results["Volumetric Features::PCA Flatness"], 0.01); // These values are obtained by running the filter // They might be wrong! CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Voxel Volume with Large IBSI Phantom Image", 8, results["Volumetric Features::Voxel Volume"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Volume (voxel based) with Large IBSI Phantom Image", 592, results["Volumetric Features::Volume (voxel based)"], 0.1); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Surface (voxel based) with Large IBSI Phantom Image", 488, results["Volumetric Features::Surface (voxel based)"], 1.0); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Centre of mass shift (uncorrected) with Large IBSI Phantom Image", 0.672, results["Volumetric Features::Centre of mass shift (uncorrected)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Bounding Box Volume with Large IBSI Phantom Image", 288, results["Volumetric Features::Bounding Box Volume"], 1.0); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Surface to volume ratio (voxel based) with Large IBSI Phantom Image", 0.824, results["Volumetric Features::Surface to volume ratio (voxel based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Sphericity (voxel based) with Large IBSI Phantom Image", 0.699, results["Volumetric Features::Sphericity (voxel based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Asphericity (voxel based) with Large IBSI Phantom Image", 0.431, results["Volumetric Features::Asphericity (voxel based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Sphericity (mesh based) with Large IBSI Phantom Image", 0.879, results["Volumetric Features::Sphericity (mesh based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Asphericity (mesh based) with Large IBSI Phantom Image", 0.138, results["Volumetric Features::Asphericity (mesh based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Asphericity (mesh based) with Large IBSI Phantom Image", 0.138, results["Volumetric Features::Asphericity (mesh based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Compactness 1 (voxel based) with Large IBSI Phantom Image", 0.031, results["Volumetric Features::Compactness 1 (voxel based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Compactness 1 old (voxel based) with Large IBSI Phantom Image", 5.388, results["Volumetric Features::Compactness 1 old (voxel based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Compactness 2 (voxel based) with Large IBSI Phantom Image", 0.341, results["Volumetric Features::Compactness 2 (voxel based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Compactness 1 (mesh based) with Large IBSI Phantom Image", 0.0437, results["Volumetric Features::Compactness 1 (mesh based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Compactness 2 (mesh based) with Large IBSI Phantom Image", 0.678, results["Volumetric Features::Compactness 2 (mesh based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Spherical disproportion (voxel based) with Large IBSI Phantom Image", 1.43, results["Volumetric Features::Spherical disproportion (voxel based)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::PCA Major axis length (uncorrected) with Large IBSI Phantom Image", 11.40, results["Volumetric Features::PCA Major axis length (uncorrected)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::PCA Minor axis length (uncorrected) with Large IBSI Phantom Image", 9.31, results["Volumetric Features::PCA Minor axis length (uncorrected)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::PCA Least axis length (uncorrected) with Large IBSI Phantom Image", 8.54, results["Volumetric Features::PCA Least axis length (uncorrected)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::PCA Elongation (uncorrected) with Large IBSI Phantom Image", 0.816, results["Volumetric Features::PCA Elongation (uncorrected)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::PCA Flatness (uncorrected) with Large IBSI Phantom Image", 0.749, results["Volumetric Features::PCA Flatness (uncorrected)"], 0.01); CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("Volumetric Features::Compactness 1 old (mesh based) with Large IBSI Phantom Image", 6.278, results["Volumetric Features::Compactness 1 old (mesh based)"], 0.01); } }; MITK_TEST_SUITE_REGISTRATION(mitkGIFVolumetricStatistics ) diff --git a/Modules/CommandLine/include/mitkCommandLineParser.h b/Modules/CommandLine/include/mitkCommandLineParser.h index ddba149101..24cd81b25a 100644 --- a/Modules/CommandLine/include/mitkCommandLineParser.h +++ b/Modules/CommandLine/include/mitkCommandLineParser.h @@ -1,392 +1,391 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ /*========================================================================= Library: CTK Copyright (c) Kitware Inc. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0.txt Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =========================================================================*/ #ifndef __mitkCommandLineParser_h #define __mitkCommandLineParser_h #include #include #include #include /** * * The MITK command line parser, based on the CTK command line parser. * * Use this class to add information about the command line arguments * your program understands and to easily parse them from a given list * of strings. * * This parser provides the following features: * *
    *
  • Add arguments by supplying a long name and/or a short name. * Arguments are validated using a regular expression. They can have * a default value and a help string.
    • *
  • Deprecated arguments.
    • *
  • Custom regular expressions for argument validation.
    • *
  • Set different argument name prefixes for native platform look and feel.
    • *
  • Create a help text for the command line arguments with support for * grouping arguments.
    • *
* * The main difference between the MITK command line parser and the CTK command line * parser is that the former does not depend on Qt. Apart from that an image type was * added and XML output improved for automatic GUI generation. * * std::out is used for output to keep dependencies to a minimum. */ class MITKCOMMANDLINE_EXPORT mitkCommandLineParser { public: enum Type { String = 0, Bool = 1, StringList = 2, Int = 3, Float = 4, Directory = 5, File = 6, Image = 7 }; enum Channel { None = 0, Input = 1, Output = 2 }; typedef std::vector StringContainerType; mitkCommandLineParser(); ~mitkCommandLineParser(); /** * Parse a given list of command line arguments. * * This method parses a list of string elements considering the known arguments * added by calls to addArgument(). If any one of the argument * values does not match the corresponding regular expression, * ok is set to false and an empty map object is returned. * * The keys in the returned map object correspond to the long argument string, * if it is not empty. Otherwise, the short argument string is used as key. The * us::Any values can safely be converted to the type specified in the * addArgument() method call. * * @param arguments A StringContainerType containing command line arguments. * @param ok A pointer to a boolean variable. Will be set to true * if all regular expressions matched, false otherwise. * @return A map object mapping the long argument (if empty, the short one) * to a us::Any containing the value. */ std::map parseArguments(const StringContainerType &arguments, bool *ok = nullptr); /** * Convenient method allowing to parse a given list of command line arguments. * @see parseArguments(const StringContainerType &, bool*) */ std::map parseArguments(int argc, char **argv, bool *ok = nullptr); /** * Returns a detailed error description if a call to parseArguments() * failed. * * @return The error description, empty if no error occured. * @see parseArguments(const StringContainerType&, bool*) */ std::string errorString() const; /** * This method returns all unparsed arguments, i.e. all arguments * for which no long or short name has been registered via a call * to addArgument(). * * @see addArgument() * * @return A list containing unparsed arguments. */ const StringContainerType &unparsedArguments() const; /** * Checks if the given argument has been added via a call * to addArgument(). * * @see addArgument() * * @param argument The argument to be checked. * @return true if the argument was added, false * otherwise. */ bool argumentAdded(const std::string &argument) const; /** * Checks if the given argument has been parsed successfully by a previous * call to parseArguments(). * * @param argument The argument to be checked. * @return true if the argument was parsed, false * otherwise. */ bool argumentParsed(const std::string &argument) const; /** * Adds a command line argument. An argument can have a long name * (like --long-argument-name), a short name (like -l), or both. The type * of the argument can be specified by using the type parameter. * The following types are supported: * * * * * * * * *
Type# of parametersDefault regular exprExample
us::Any::String1.*--test-string StringParameter
us::Any::Bool0does not apply--enable-something
us::Any::StringList-1.*--test-list string1 string2
us::Any::Int1-?[0-9]+--test-int -5
* * The regular expressions are used to validate the parameters of command line * arguments. You can restrict the valid set of parameters by calling * setExactMatchRegularExpression() for your argument. * * Optionally, a help string and a default value can be provided for the argument. If * the us::Any type of the default value does not match type, an * exception is thrown. Arguments with default values are always returned by * parseArguments(). * * You can also declare an argument deprecated, by setting deprecated * to true. Alternatively you can add a deprecated argument by calling * addDeprecatedArgument(). * * If the long or short argument has already been added, or if both are empty strings, * the method call has no effect. * * @param longarg The long argument name. * @param shortarg The short argument name. * @param type The argument type (see the list above for supported types). * @param argLabel The label of this argument, when auto generated interface is used. * @param argHelp A help string describing the argument. * @param defaultValue A default value for the argument. * @param optional * @param ignoreRest All arguments after the current one will be ignored. * @param deprecated Declares the argument deprecated. * @param channel * * @see setExactMatchRegularExpression() * @see addDeprecatedArgument() * @throws std::logic_error If the us::Any type of defaultValue * does not match type, a std::logic_error is thrown. */ void addArgument(const std::string &longarg, const std::string &shortarg, Type type, const std::string &argLabel, const std::string &argHelp = std::string(), const us::Any &defaultValue = us::Any(), bool optional = true, bool ignoreRest = false, bool deprecated = false, mitkCommandLineParser::Channel channel = mitkCommandLineParser::Channel::None); /** * Adds a deprecated command line argument. If a deprecated argument is provided * on the command line, argHelp is displayed in the console and * processing continues with the next argument. * * Deprecated arguments are grouped separately at the end of the help text * returned by helpText(). * * @param longarg The long argument name. * @param shortarg The short argument name. * @param argLabel * @param argHelp A help string describing alternatives to the deprecated argument. */ void addDeprecatedArgument(const std::string &longarg, const std::string &shortarg, const std::string &argLabel, const std::string &argHelp); /** * Returns the vector of current Command line Parameter * */ std::vector < std::map > getArgumentList(); /** * Sets a custom regular expression for validating argument parameters. The method * errorString() can be used the get the last error description. * * @param argument The previously added long or short argument name. * @param expression A regular expression which the arugment parameters must match. * @param exactMatchFailedMessage An error message explaining why the parameter did * not match. * * @return true if the argument was found and the regular expression was set, * false otherwise. * * @see errorString() */ bool setExactMatchRegularExpression(const std::string &argument, const std::string &expression, const std::string &exactMatchFailedMessage); /** * The field width for the argument names without the help text. * * @return The argument names field width in the help text. */ std::string::size_type fieldWidth() const; /** * Creates a help text containing properly formatted argument names and help strings * provided by calls to addArgument(). The arguments can be grouped by * using beginGroup() and endGroup(). * - * @param charPad The padding character. * @return The formatted help text. */ std::string helpText() const; /** * Sets the argument prefix for long and short argument names. This can be used * to create native command line arguments without changing the calls to * addArgument(). For example on Unix-based systems, long argument * names start with "--" and short names with "-", while on Windows argument names * always start with "/". * * Note that all methods in mitkCommandLineParser which take an argument name * expect the name as it was supplied to addArgument. * * Example usage: * * \code * ctkCommandLineParser parser; * parser.setArgumentPrefix("--", "-"); * parser.addArgument("long-argument", "l", us::Any::String); * StringContainerType args; * args << "program name" << "--long-argument Hi"; * parser.parseArguments(args); * \endcode * * @param longPrefix The prefix for long argument names. * @param shortPrefix The prefix for short argument names. */ void setArgumentPrefix(const std::string &longPrefix, const std::string &shortPrefix); /** * Begins a new group for documenting arguments. All newly added arguments via * addArgument() will be put in the new group. You can close the * current group by calling endGroup() or be opening a new group. * * Note that groups cannot be nested and all arguments which do not belong to * a group will be listed at the top of the text created by helpText(). * * @param description The description of the group */ void beginGroup(const std::string &description); /** * Ends the current group. * * @see beginGroup(const std::string&) */ void endGroup(); /** * Can be used to teach the parser to stop parsing the arguments and return False when * an unknown argument is encountered. By default StrictMode is disabled. * * @see parseArguments(const StringContainerType &, bool*) */ void setStrictModeEnabled(bool strictMode); /** * Is used to generate an XML output for any commandline program. */ void generateXmlOutput(); /** * Is used to set the title of the auto generated interface. * * @param title The title of the app. */ void setTitle(std::string title); /** * Is used to set the contributor for the help view in the auto generated interface. * * @param contributor Contributor of the app. */ void setContributor(std::string contributor); /** * Is used to categorize the apps in the commandline module. * * @param category The category of the app. */ void setCategory(std::string category); /** * Is used as the help text in the auto generated interface. * * @param description A short description for the app. */ void setDescription(std::string description); /** * Is used to group several Parameters in one groupbox in the auto generated interface. * Default name is "Parameters", with the tooltip: "Groupbox containing parameters." * * To change the group of several arguments, call this method before the arguments are added. * * @param name The name of the groupbox. * @param tooltip The tooltip of the groupbox. */ void changeParameterGroup(std::string name, std::string tooltip); protected: class ctkInternal; ctkInternal *Internal; std::string Title; std::string Contributor; std::string Category; std::string Description; std::string ParameterGroupName; std::string ParameterGroupDescription; }; #endif diff --git a/Modules/CommandLine/src/mitkCommandLineParser.cpp b/Modules/CommandLine/src/mitkCommandLineParser.cpp index a331d79326..7b663c3464 100644 --- a/Modules/CommandLine/src/mitkCommandLineParser.cpp +++ b/Modules/CommandLine/src/mitkCommandLineParser.cpp @@ -1,1056 +1,1056 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ /*========================================================================= Library: CTK Copyright (c) Kitware Inc. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0.txt Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =========================================================================*/ // STL includes #include #include // MITK includes #include "mitkCommandLineParser.h" using namespace std; namespace { // -------------------------------------------------------------------------- class CommandLineParserArgumentDescription { public: CommandLineParserArgumentDescription(const string &longArg, const string &longArgPrefix, const string &shortArg, const string &shortArgPrefix, mitkCommandLineParser::Type type, const string &argHelp, const string &argLabel, const us::Any &defaultValue, bool ignoreRest, bool deprecated, bool optional, mitkCommandLineParser::Channel channel, string &argGroup, string &groupDescription) : LongArg(longArg), LongArgPrefix(longArgPrefix), ShortArg(shortArg), ShortArgPrefix(shortArgPrefix), ArgHelp(argHelp), ArgLabel(argLabel), ArgGroup(argGroup), ArgGroupDescription(groupDescription), IgnoreRest(ignoreRest), NumberOfParametersToProcess(0), Deprecated(deprecated), Optional(optional), Channel(channel), DefaultValue(defaultValue), Value(type), ValueType(type) { Value = defaultValue; switch (type) { case mitkCommandLineParser::String: { NumberOfParametersToProcess = 1; } break; case mitkCommandLineParser::Bool: { NumberOfParametersToProcess = 0; } break; case mitkCommandLineParser::StringList: { NumberOfParametersToProcess = -1; } break; case mitkCommandLineParser::Int: { NumberOfParametersToProcess = 1; } break; case mitkCommandLineParser::Float: { NumberOfParametersToProcess = 1; } break; case mitkCommandLineParser::Directory: { NumberOfParametersToProcess = 1; } break; case mitkCommandLineParser::File: { NumberOfParametersToProcess = 1; } break; case mitkCommandLineParser::Image: { NumberOfParametersToProcess = 1; } break; default: std::cout << "Type not supported: " << static_cast(type); } } ~CommandLineParserArgumentDescription() {} bool addParameter(const string &value); string helpText(); string LongArg; string LongArgPrefix; string ShortArg; string ShortArgPrefix; string ArgHelp; string ArgLabel; string ArgGroup; string ArgGroupDescription; bool IgnoreRest; int NumberOfParametersToProcess; bool Deprecated; bool Optional; mitkCommandLineParser::Channel Channel; us::Any DefaultValue; us::Any Value; mitkCommandLineParser::Type ValueType; }; // -------------------------------------------------------------------------- bool CommandLineParserArgumentDescription::addParameter(const string &value) { switch (ValueType) { case mitkCommandLineParser::String: { Value = value; } break; case mitkCommandLineParser::Bool: { if (value.compare("true") == 0) Value = true; else Value = false; } break; case mitkCommandLineParser::StringList: { try { mitkCommandLineParser::StringContainerType list = us::any_cast(Value); list.push_back(value); Value = list; } catch (...) { mitkCommandLineParser::StringContainerType list; list.push_back(value); Value = list; } } break; case mitkCommandLineParser::Int: { stringstream ss(value); int i; ss >> i; Value = i; } break; case mitkCommandLineParser::Float: { stringstream ss(value); float f; ss >> f; Value = f; } break; case mitkCommandLineParser::Directory: case mitkCommandLineParser::Image: case mitkCommandLineParser::File: { Value = value; } break; default: return false; } return true; } // -------------------------------------------------------------------------- string CommandLineParserArgumentDescription::helpText() { string text; string shortAndLongArg; if (!this->ShortArg.empty()) { shortAndLongArg = " "; shortAndLongArg += this->ShortArgPrefix; shortAndLongArg += this->ShortArg; } if (!this->LongArg.empty()) { if (this->ShortArg.empty()) shortAndLongArg.append(" "); else shortAndLongArg.append(", "); shortAndLongArg += this->LongArgPrefix; shortAndLongArg += this->LongArg; } text = text + shortAndLongArg + ", " + this->ArgHelp; if (this->Optional) text += " (optional)"; if (!this->DefaultValue.Empty()) { if (this->ValueType == 1) { if (this->DefaultValue.ToString() == "0") text = text + ", (default: false)"; else text = text + ", (default: true)"; } else text = text + ", (default: " + this->DefaultValue.ToString() + ")"; } string value_type = "Unknown"; switch (this->ValueType) { case 0: { value_type = "String"; break; } case 1: { value_type = "Bool"; break; } case 2: { value_type = "StringList"; break; } case 3: { value_type = "Int"; break; } case 4: { value_type = "Float"; break; } case 5: { value_type = "Directory"; break; } case 6: { value_type = "File"; break; } case 7: { value_type = "Image"; } } text = text + ", Type: " + value_type; if (this->Channel == mitkCommandLineParser::Input) text = text + ", Channel: input"; else if (this->Channel == mitkCommandLineParser::Output) text = text + ", Channel: output"; text += "\n"; return text; } } // -------------------------------------------------------------------------- // ctkCommandLineParser::ctkInternal class // -------------------------------------------------------------------------- class mitkCommandLineParser::ctkInternal { public: ctkInternal() : Debug(false), FieldWidth(0), StrictMode(false) {} ~ctkInternal() {} CommandLineParserArgumentDescription *argumentDescription(const string &argument); vector ArgumentDescriptionList; map ArgNameToArgumentDescriptionMap; map> GroupToArgumentDescriptionListMap; StringContainerType UnparsedArguments; StringContainerType ProcessedArguments; string ErrorString; bool Debug; string::size_type FieldWidth; string LongPrefix; string ShortPrefix; string CurrentGroup; string DisableQSettingsLongArg; string DisableQSettingsShortArg; bool StrictMode; }; // -------------------------------------------------------------------------- // ctkCommandLineParser::ctkInternal methods // -------------------------------------------------------------------------- CommandLineParserArgumentDescription *mitkCommandLineParser::ctkInternal::argumentDescription(const string &argument) { string unprefixedArg = argument; if (!LongPrefix.empty() && argument.compare(0, LongPrefix.size(), LongPrefix) == 0) { // Case when (ShortPrefix + UnPrefixedArgument) matches LongPrefix if (argument == LongPrefix && !ShortPrefix.empty() && argument.compare(0, ShortPrefix.size(), ShortPrefix) == 0) { unprefixedArg = argument.substr(ShortPrefix.size(), argument.size()); } else { unprefixedArg = argument.substr(LongPrefix.size(), argument.size()); } } else if (!ShortPrefix.empty() && argument.compare(0, ShortPrefix.size(), ShortPrefix) == 0) { unprefixedArg = argument.substr(ShortPrefix.size(), argument.size()); } else if (!LongPrefix.empty() && !ShortPrefix.empty()) { return nullptr; } if (ArgNameToArgumentDescriptionMap.count(unprefixedArg)) { return this->ArgNameToArgumentDescriptionMap[unprefixedArg]; } return nullptr; } // -------------------------------------------------------------------------- // ctkCommandLineParser methods // -------------------------------------------------------------------------- mitkCommandLineParser::mitkCommandLineParser() { this->Internal = new ctkInternal(); this->Category = string(); this->Title = string(); this->Contributor = string(); this->Description = string(); this->ParameterGroupName = "Parameters"; this->ParameterGroupDescription = "Parameters"; } // -------------------------------------------------------------------------- mitkCommandLineParser::~mitkCommandLineParser() { delete this->Internal; } // -------------------------------------------------------------------------- map mitkCommandLineParser::parseArguments(const StringContainerType &arguments, bool *ok) { // Reset this->Internal->UnparsedArguments.clear(); this->Internal->ProcessedArguments.clear(); this->Internal->ErrorString.clear(); // foreach (CommandLineParserArgumentDescription* desc, this->Internal->ArgumentDescriptionList) for (unsigned int i = 0; i < Internal->ArgumentDescriptionList.size(); i++) { CommandLineParserArgumentDescription *desc = Internal->ArgumentDescriptionList.at(i); desc->Value = us::Any(desc->ValueType); if (!desc->DefaultValue.Empty()) { desc->Value = desc->DefaultValue; } } bool error = false; bool ignoreRest = false; CommandLineParserArgumentDescription *currentArgDesc = nullptr; vector parsedArgDescriptions; for (unsigned int i = 1; i < arguments.size(); ++i) { string argument = arguments.at(i); if (this->Internal->Debug) { std::cout << "Processing" << argument; } if (!argument.compare("--version")) { std::cout << "Git commit hash: " << MITK_REVISION << std::endl; std::cout << "Git branch name: " << MITK_REVISION_NAME << "\n" << std::endl; } if (!argument.compare("--xml") || !argument.compare("-xml") || !argument.compare("--XML") || !argument.compare("-XML")) { this->generateXmlOutput(); return map(); } // should argument be ignored ? if (ignoreRest) { if (this->Internal->Debug) { std::cout << " Skipping: IgnoreRest flag was been set"; } this->Internal->UnparsedArguments.push_back(argument); continue; } // Skip if the argument does not start with the defined prefix if (!(argument.compare(0, Internal->LongPrefix.size(), Internal->LongPrefix) == 0 || argument.compare(0, Internal->ShortPrefix.size(), Internal->ShortPrefix) == 0)) { if (this->Internal->StrictMode) { this->Internal->ErrorString = "Unknown argument "; this->Internal->ErrorString += argument; error = true; break; } if (this->Internal->Debug) { std::cout << " Skipping: It does not start with the defined prefix"; } this->Internal->UnparsedArguments.push_back(argument); continue; } // Skip if argument has already been parsed ... bool alreadyProcessed = false; - for (auto alreadyHandledArgument : Internal->ProcessedArguments) + for (const auto &alreadyHandledArgument : Internal->ProcessedArguments) if (argument.compare(alreadyHandledArgument) == 0) { alreadyProcessed = true; break; } if (alreadyProcessed) { if (this->Internal->StrictMode) { this->Internal->ErrorString = "Argument "; this->Internal->ErrorString += argument; this->Internal->ErrorString += " already processed !"; error = true; break; } if (this->Internal->Debug) { std::cout << " Skipping: Already processed !"; } continue; } // Retrieve corresponding argument description currentArgDesc = this->Internal->argumentDescription(argument); // Is there a corresponding argument description ? if (currentArgDesc) { // If the argument is deprecated, print the help text but continue processing if (currentArgDesc->Deprecated) { std::cout << "Deprecated argument " << argument << ": " << currentArgDesc->ArgHelp; } else { parsedArgDescriptions.push_back(currentArgDesc); } this->Internal->ProcessedArguments.push_back(currentArgDesc->ShortArg); this->Internal->ProcessedArguments.push_back(currentArgDesc->LongArg); int numberOfParametersToProcess = currentArgDesc->NumberOfParametersToProcess; ignoreRest = currentArgDesc->IgnoreRest; if (this->Internal->Debug && ignoreRest) { std::cout << " IgnoreRest flag is True"; } // Is the number of parameters associated with the argument being processed known ? if (numberOfParametersToProcess == 0) { currentArgDesc->addParameter("true"); } else if (numberOfParametersToProcess > 0) { string missingParameterError = "Argument %1 has %2 value(s) associated whereas exacly %3 are expected."; for (int j = 1; j <= numberOfParametersToProcess; ++j) { if (i + j >= arguments.size()) { // this->Internal->ErrorString = // missingParameterError.arg(argument).arg(j-1).arg(numberOfParametersToProcess); // if (this->Internal->Debug) { std::cout << this->Internal->ErrorString; } if (ok) { *ok = false; } return map(); } string parameter = arguments.at(i + j); if (this->Internal->Debug) { std::cout << " Processing parameter" << j << ", value:" << parameter; } if (this->argumentAdded(parameter)) { // this->Internal->ErrorString = // missingParameterError.arg(argument).arg(j-1).arg(numberOfParametersToProcess); // if (this->Internal->Debug) { std::cout << this->Internal->ErrorString; } if (ok) { *ok = false; } return map(); } if (!currentArgDesc->addParameter(parameter)) { // this->Internal->ErrorString = string( // "Value(s) associated with argument %1 are incorrect. %2"). // arg(argument).arg(currentArgDesc->ExactMatchFailedMessage); // if (this->Internal->Debug) { std::cout << this->Internal->ErrorString; } if (ok) { *ok = false; } return map(); } } // Update main loop increment i = i + numberOfParametersToProcess; } else if (numberOfParametersToProcess == -1) { if (this->Internal->Debug) { std::cout << " Proccessing StringList ..."; } int j = 1; while (j + i < arguments.size()) { if (this->argumentAdded(arguments.at(j + i))) { if (this->Internal->Debug) { std::cout << " No more parameter for" << argument; } break; } string parameter = arguments.at(j + i); if (parameter.compare(0, Internal->LongPrefix.size(), Internal->LongPrefix) == 0 || parameter.compare(0, Internal->ShortPrefix.size(), Internal->ShortPrefix) == 0) { j--; break; } if (this->Internal->Debug) { std::cout << " Processing parameter" << j << ", value:" << parameter; } if (!currentArgDesc->addParameter(parameter)) { // this->Internal->ErrorString = string( // "Value(s) associated with argument %1 are incorrect. %2"). // arg(argument).arg(currentArgDesc->ExactMatchFailedMessage); // if (this->Internal->Debug) { std::cout << this->Internal->ErrorString; } if (ok) { *ok = false; } return map(); } j++; } // Update main loop increment i = i + j; } } else { if (this->Internal->StrictMode) { this->Internal->ErrorString = "Unknown argument "; this->Internal->ErrorString += argument; error = true; break; } if (this->Internal->Debug) { std::cout << " Skipping: Unknown argument"; } this->Internal->UnparsedArguments.push_back(argument); } } if (ok) { *ok = !error; } map parsedArguments; int obligatoryArgs = 0; vector::iterator it; for (it = Internal->ArgumentDescriptionList.begin(); it != Internal->ArgumentDescriptionList.end(); ++it) { CommandLineParserArgumentDescription *desc = *it; if (!desc->Optional) obligatoryArgs++; } int parsedObligatoryArgs = 0; for (it = parsedArgDescriptions.begin(); it != parsedArgDescriptions.end(); ++it) { CommandLineParserArgumentDescription *desc = *it; string key; if (!desc->LongArg.empty()) { key = desc->LongArg; } else { key = desc->ShortArg; } if (!desc->Optional) parsedObligatoryArgs++; std::pair elem; elem.first = key; elem.second = desc->Value; parsedArguments.insert(elem); } if (obligatoryArgs > parsedObligatoryArgs) { parsedArguments.clear(); cout << helpText(); } return parsedArguments; } // ------------------------------------------------------------------------- map mitkCommandLineParser::parseArguments(int argc, char **argv, bool *ok) { std::cout << "Running Command Line Utility *" << Title << "*" << std::endl; StringContainerType arguments; // Create a StringContainerType of arguments for (int i = 0; i < argc; ++i) arguments.push_back(argv[i]); return this->parseArguments(arguments, ok); } // ------------------------------------------------------------------------- string mitkCommandLineParser::errorString() const { return this->Internal->ErrorString; } // ------------------------------------------------------------------------- const mitkCommandLineParser::StringContainerType &mitkCommandLineParser::unparsedArguments() const { return this->Internal->UnparsedArguments; } // -------------------------------------------------------------------------- void mitkCommandLineParser::addArgument(const string &longarg, const string &shortarg, Type type, const string &argLabel, const string &argHelp, const us::Any &defaultValue, bool optional, bool ignoreRest, bool deprecated, mitkCommandLineParser::Channel channel) { if (longarg.empty() && shortarg.empty()) { return; } /* Make sure it's not already added */ bool added = (this->Internal->ArgNameToArgumentDescriptionMap.count(longarg) != 0); if (added) { return; } added = (this->Internal->ArgNameToArgumentDescriptionMap.count(shortarg) != 0); if (added) { return; } auto argDesc = new CommandLineParserArgumentDescription(longarg, this->Internal->LongPrefix, shortarg, this->Internal->ShortPrefix, type, argHelp, argLabel, defaultValue, ignoreRest, deprecated, optional, channel, ParameterGroupName, ParameterGroupDescription); std::string::size_type argWidth = 0; if (!longarg.empty()) { this->Internal->ArgNameToArgumentDescriptionMap[longarg] = argDesc; argWidth += longarg.size() + this->Internal->LongPrefix.size(); } if (!shortarg.empty()) { this->Internal->ArgNameToArgumentDescriptionMap[shortarg] = argDesc; argWidth += shortarg.size() + this->Internal->ShortPrefix.size() + 2; } argWidth += 5; // Set the field width for the arguments if (argWidth > this->Internal->FieldWidth) { this->Internal->FieldWidth = argWidth; } this->Internal->ArgumentDescriptionList.push_back(argDesc); this->Internal->GroupToArgumentDescriptionListMap[this->Internal->CurrentGroup].push_back(argDesc); } // -------------------------------------------------------------------------- void mitkCommandLineParser::addDeprecatedArgument(const string &longarg, const string &shortarg, const string &argLabel, const string &argHelp) { addArgument(longarg, shortarg, StringList, argLabel, argHelp, us::Any(), false, true, false); } // -------------------------------------------------------------------------- std::vector < std::map > mitkCommandLineParser::getArgumentList() { std::vector < std::map > parameterList; //for (CommandLineParserArgumentDescription* argument : this->Internal->ArgumentDescriptionList) for (std::size_t i = 0; i< this->Internal->ArgumentDescriptionList.size(); ++i) { CommandLineParserArgumentDescription* argument = this->Internal->ArgumentDescriptionList[i]; std::map tmpMap; //tmpMap["helptext"] = us::Any(argument->helpText); tmpMap["longarg"] = us::Any(argument->LongArg); tmpMap["longargprefix"] = us::Any(argument->LongArgPrefix); tmpMap["shortarg"] = us::Any(argument->ShortArg); tmpMap["shortargprefix"] = us::Any(argument->ShortArgPrefix); tmpMap["arghelp"] = us::Any(argument->ArgHelp); tmpMap["arglabel"] = us::Any(argument->ArgLabel); tmpMap["arggroup"] = us::Any(argument->ArgGroup); tmpMap["arggroupdescription"] = us::Any(argument->ArgGroupDescription); tmpMap["ignorerest"] = us::Any(argument->IgnoreRest); tmpMap["numberofparameterstoprocess"] = us::Any(argument->NumberOfParametersToProcess); tmpMap["deprecated"] = us::Any(argument->Deprecated); tmpMap["optional"] = us::Any(argument->Optional); tmpMap["defaultvalue"] = argument->DefaultValue; tmpMap["value"] = argument->Value; tmpMap["valuetype"] = us::Any(argument->ValueType); tmpMap["channel"] = us::Any(argument->Channel); parameterList.push_back(tmpMap); } return parameterList; } // -------------------------------------------------------------------------- std::string::size_type mitkCommandLineParser::fieldWidth() const { return this->Internal->FieldWidth; } // -------------------------------------------------------------------------- void mitkCommandLineParser::beginGroup(const string &description) { this->Internal->CurrentGroup = description; } // -------------------------------------------------------------------------- void mitkCommandLineParser::endGroup() { this->Internal->CurrentGroup.clear(); } // -------------------------------------------------------------------------- string mitkCommandLineParser::helpText() const { string text; vector deprecatedArgs; text = "Command Line Utility *" + Title + "* in Category *" + Category + "*\n"; text += Description + "\n"; text += Contributor + "\n\n"; text += "Use --xml to generate an XML description parsable as a CTK Command Line Module Plugin.\n"; text += "Use --version to print MITK revision information.\n"; // Loop over grouped argument descriptions map>::iterator it; for (it = Internal->GroupToArgumentDescriptionListMap.begin(); it != Internal->GroupToArgumentDescriptionListMap.end(); ++it) { if (!(*it).first.empty()) { text = text + "\n" + (*it).first + "\n"; } vector::iterator it2; for (it2 = (*it).second.begin(); it2 != (*it).second.end(); ++it2) { CommandLineParserArgumentDescription *argDesc = *it2; if (argDesc->Deprecated) { deprecatedArgs.push_back(argDesc); } else { text += argDesc->helpText(); } } } if (!deprecatedArgs.empty()) { text += "\nDeprecated arguments:\n"; vector::iterator it2; for (it2 = deprecatedArgs.begin(); it2 != deprecatedArgs.end(); ++it2) { CommandLineParserArgumentDescription *argDesc = *it2; text += argDesc->helpText(); } } return text; } // -------------------------------------------------------------------------- bool mitkCommandLineParser::argumentAdded(const string &argument) const { return (this->Internal->ArgNameToArgumentDescriptionMap.count(argument) != 0); } // -------------------------------------------------------------------------- bool mitkCommandLineParser::argumentParsed(const string &argument) const { for (unsigned int i = 0; i < Internal->ProcessedArguments.size(); i++) if (argument.compare(Internal->ProcessedArguments.at(i)) == 0) return true; return false; } // -------------------------------------------------------------------------- void mitkCommandLineParser::setArgumentPrefix(const string &longPrefix, const string &shortPrefix) { this->Internal->LongPrefix = longPrefix; this->Internal->ShortPrefix = shortPrefix; } // -------------------------------------------------------------------------- void mitkCommandLineParser::setStrictModeEnabled(bool strictMode) { this->Internal->StrictMode = strictMode; } void mitkCommandLineParser::generateXmlOutput() { std::stringstream xml; xml << "" << endl; xml << "" << Category << "" << endl; xml << "" << Title << "" << endl; xml << "" << Description << "" << endl; xml << "" << Contributor << "" << endl; xml << "" << endl; std::vector::iterator it; std::string lastParameterGroup = ""; for (it = this->Internal->ArgumentDescriptionList.begin(); it != this->Internal->ArgumentDescriptionList.end(); it++) { std::string type; switch ((*it)->ValueType) { case mitkCommandLineParser::String: type = "string"; break; case mitkCommandLineParser::Bool: type = "boolean"; break; case mitkCommandLineParser::StringList: type = "string-vector"; break; case mitkCommandLineParser::Int: type = "integer"; break; case mitkCommandLineParser::Float: type = "float"; break; case mitkCommandLineParser::Directory: type = "directory"; break; case mitkCommandLineParser::Image: type = "image"; break; case mitkCommandLineParser::File: type = "file"; break; } if (lastParameterGroup.compare((*it)->ArgGroup)) { if (it != this->Internal->ArgumentDescriptionList.begin()) { xml << "" << endl; xml << "" << endl; } xml << "" << endl; xml << "" << (*it)->ArgGroupDescription << "" << endl; lastParameterGroup = (*it)->ArgGroup; } // Skip help item, as it's no use in GUI if ((*it)->ShortArg == "h") continue; auto name = (*it)->LongArg; if (name.empty()) name = (*it)->ShortArg; xml << "<" << type << ">" << endl; xml << "" << name << "" << endl; xml << "" << (*it)->ArgHelp << "" << endl; xml << "" << endl; if (!(*it)->DefaultValue.Empty()) xml << "" << (*it)->DefaultValue.ToString() << "" << endl; xml << "" << (*it)->LongArg << "" << endl; xml << "" << (*it)->ShortArg << "" << endl; if (((*it)->ValueType == mitkCommandLineParser::File || (*it)->ValueType == mitkCommandLineParser::Directory || (*it)->ValueType == mitkCommandLineParser::Image) && (*it)->Channel == mitkCommandLineParser::Channel::Input) { xml << "input" << endl; } else if (((*it)->ValueType == mitkCommandLineParser::File || (*it)->ValueType == mitkCommandLineParser::Directory || (*it)->ValueType == mitkCommandLineParser::Image) && (*it)->Channel == mitkCommandLineParser::Channel::Output) { xml << "output" << endl; } else if ((*it)->Channel == mitkCommandLineParser::Channel::Output || (*it)->Channel == mitkCommandLineParser::Channel::Input) { std::cout << "Only the types Directory, File or Image may be flagged as Input or Output! Ignoring flag for parameter " + name << std::endl; } xml << "" << endl; } xml << "" << endl; xml << "" << endl; cout << xml.str(); } void mitkCommandLineParser::setTitle(string title) { Title = title; } void mitkCommandLineParser::setContributor(string contributor) { Contributor = contributor; } void mitkCommandLineParser::setCategory(string category) { Category = category; } void mitkCommandLineParser::setDescription(string description) { Description = description; } void mitkCommandLineParser::changeParameterGroup(string name, string tooltip) { ParameterGroupName = name; ParameterGroupDescription = tooltip; } diff --git a/Modules/ContourModel/Algorithms/mitkContourModelSubDivisionFilter.cpp b/Modules/ContourModel/Algorithms/mitkContourModelSubDivisionFilter.cpp index dec4e7d708..a7840e854f 100644 --- a/Modules/ContourModel/Algorithms/mitkContourModelSubDivisionFilter.cpp +++ b/Modules/ContourModel/Algorithms/mitkContourModelSubDivisionFilter.cpp @@ -1,202 +1,202 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkContourModelSubDivisionFilter.h" #include #include mitk::ContourModelSubDivisionFilter::ContourModelSubDivisionFilter() { OutputType::Pointer output = dynamic_cast(this->MakeOutput(0).GetPointer()); this->SetNumberOfRequiredInputs(1); this->SetNumberOfIndexedOutputs(1); this->SetNthOutput(0, output.GetPointer()); this->m_InterpolationIterations = 4; } mitk::ContourModelSubDivisionFilter::~ContourModelSubDivisionFilter() { } void mitk::ContourModelSubDivisionFilter::SetInput(const mitk::ContourModelSubDivisionFilter::InputType *input) { this->SetInput(0, input); } void mitk::ContourModelSubDivisionFilter::SetInput(unsigned int idx, const mitk::ContourModelSubDivisionFilter::InputType *input) { if (idx + 1 > this->GetNumberOfInputs()) { this->SetNumberOfRequiredInputs(idx + 1); } if (input != static_cast(this->ProcessObject::GetInput(idx))) { this->ProcessObject::SetNthInput(idx, const_cast(input)); this->Modified(); } } const mitk::ContourModelSubDivisionFilter::InputType *mitk::ContourModelSubDivisionFilter::GetInput(void) { if (this->GetNumberOfInputs() < 1) return nullptr; return static_cast(this->ProcessObject::GetInput(0)); } const mitk::ContourModelSubDivisionFilter::InputType *mitk::ContourModelSubDivisionFilter::GetInput(unsigned int idx) { if (this->GetNumberOfInputs() < 1) return nullptr; return static_cast(this->ProcessObject::GetInput(idx)); } void mitk::ContourModelSubDivisionFilter::GenerateData() { mitk::ContourModel::Pointer input = const_cast(this->GetInput(0)); // mitk::ContourModelSubDivisionFilter::OutputType::Pointer outputContour = this->GetOutput(); mitk::ContourModel::Pointer contour(input); - auto timestep = static_cast(input->GetTimeSteps()); + auto timestep = static_cast(input->GetTimeSteps()); - for (int currentTimestep = 0; currentTimestep < timestep; currentTimestep++) + for (decltype(timestep) currentTimestep = 0; currentTimestep < timestep; currentTimestep++) { if (input->GetNumberOfVertices(currentTimestep) >= 4) { for (int iterations = 0; iterations < this->m_InterpolationIterations; iterations++) { auto it = contour->IteratorBegin(); auto end = contour->IteratorEnd(); auto first = contour->IteratorBegin(); auto last = contour->IteratorEnd() - 1; // tempory contour to store result of a subdivision iteration mitk::ContourModel::Pointer tempContour = mitk::ContourModel::New(); // insert subpoints while (it != end) { // add the current point to the temp contour tempContour->AddVertex((*it)->Coordinates, (*it)->IsControlPoint, currentTimestep); // control points for interpolation auto Ci = it; InputType::VertexIterator CiPlus1; InputType::VertexIterator CiPlus2; InputType::VertexIterator CiMinus1; // consider all possible cases if (it == first) { if (input->IsClosed(currentTimestep)) { CiPlus1 = it + 1; CiPlus2 = it + 2; CiMinus1 = last; } else { CiPlus1 = it + 1; CiPlus2 = it + 2; CiMinus1 = it; } } else if (it == last) { if (input->IsClosed(currentTimestep)) { CiPlus1 = first; CiPlus2 = first + 1; CiMinus1 = it - 1; } else { // don't add point after last break; } } else if (it == (last - 1)) { if (input->IsClosed(currentTimestep)) { CiPlus1 = it + 1; CiPlus2 = first; CiMinus1 = it - 1; } else { CiPlus1 = it + 1; CiPlus2 = it + 1; CiMinus1 = it - 1; } } else { CiPlus1 = it + 1; CiPlus2 = it + 2; CiMinus1 = it - 1; } /* F2i = Ci * F2i+1 = -1/16Ci-1 + 9/16Ci + 9/16Ci+1 - 1/16Ci+2 */ mitk::Point3D subpoint; mitk::Point3D a; a[0] = (-1.0 / 16.0) * (*CiMinus1)->Coordinates[0]; a[1] = (-1.0 / 16.0) * (*CiMinus1)->Coordinates[1]; a[2] = (-1.0 / 16.0) * (*CiMinus1)->Coordinates[2]; mitk::Point3D b; b[0] = (9.0 / 16.0) * (*Ci)->Coordinates[0]; b[1] = (9.0 / 16.0) * (*Ci)->Coordinates[1]; b[2] = (9.0 / 16.0) * (*Ci)->Coordinates[2]; mitk::Point3D c; c[0] = (9.0 / 16.0) * (*CiPlus1)->Coordinates[0]; c[1] = (9.0 / 16.0) * (*CiPlus1)->Coordinates[1]; c[2] = (9.0 / 16.0) * (*CiPlus1)->Coordinates[2]; mitk::Point3D d; d[0] = (-1.0 / 16.0) * (*CiPlus2)->Coordinates[0]; d[1] = (-1.0 / 16.0) * (*CiPlus2)->Coordinates[1]; d[2] = (-1.0 / 16.0) * (*CiPlus2)->Coordinates[2]; subpoint[0] = a[0] + b[0] + c[0] + d[0]; subpoint[1] = a[1] + b[1] + c[1] + d[1]; subpoint[2] = a[2] + b[2] + c[2] + d[2]; InputType::VertexType subdivisionPoint(subpoint, false); // add the new subdivision point to our tempContour tempContour->AddVertex(subdivisionPoint.Coordinates, currentTimestep); it++; } // set the interpolated contour as the contour for the next iteration contour = tempContour; } } else { // filter not executeable - set input to output contour = input; } } // somehow the isClosed property is not set via copy constructor contour->SetClosed(input->IsClosed()); this->SetNthOutput(0, contour); } diff --git a/Modules/ContourModel/Algorithms/mitkContourModelUtils.cpp b/Modules/ContourModel/Algorithms/mitkContourModelUtils.cpp index c2eff3c43f..f96f7a385e 100755 --- a/Modules/ContourModel/Algorithms/mitkContourModelUtils.cpp +++ b/Modules/ContourModel/Algorithms/mitkContourModelUtils.cpp @@ -1,228 +1,238 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include #include #include #include #include #include mitk::ContourModelUtils::ContourModelUtils() { } mitk::ContourModelUtils::~ContourModelUtils() { } mitk::ContourModel::Pointer mitk::ContourModelUtils::ProjectContourTo2DSlice( - Image *slice, ContourModel *contourIn3D, bool, bool) + const Image *slice, const ContourModel *contourIn3D, bool, bool) { if (nullptr == slice || nullptr == contourIn3D) return nullptr; auto projectedContour = ContourModel::New(); projectedContour->Initialize(*contourIn3D); auto sliceGeometry = slice->GetGeometry(); - auto numberOfTimesteps = static_cast(contourIn3D->GetTimeSteps()); + auto numberOfTimesteps = static_cast(contourIn3D->GetTimeSteps()); for (decltype(numberOfTimesteps) t = 0; t < numberOfTimesteps; ++t) { auto iter = contourIn3D->Begin(t); auto end = contourIn3D->End(t); while (iter != end) { const auto ¤tPointIn3D = (*iter)->Coordinates; Point3D projectedPointIn2D; projectedPointIn2D.Fill(0.0); sliceGeometry->WorldToIndex(currentPointIn3D, projectedPointIn2D); projectedContour->AddVertex(projectedPointIn2D, t); ++iter; } } return projectedContour; } mitk::ContourModel::Pointer mitk::ContourModelUtils::BackProjectContourFrom2DSlice( - const BaseGeometry *sliceGeometry, ContourModel *contourIn2D, bool) + const BaseGeometry *sliceGeometry, const ContourModel *contourIn2D, bool) { if (nullptr == sliceGeometry || nullptr == contourIn2D) return nullptr; auto worldContour = ContourModel::New(); worldContour->Initialize(*contourIn2D); - auto numberOfTimesteps = static_cast(contourIn2D->GetTimeSteps()); + auto numberOfTimesteps = static_cast(contourIn2D->GetTimeSteps()); for (decltype(numberOfTimesteps) t = 0; t < numberOfTimesteps; ++t) { auto iter = contourIn2D->Begin(t); auto end = contourIn2D->End(t); while (iter != end) { const auto ¤tPointIn2D = (*iter)->Coordinates; Point3D worldPointIn3D; worldPointIn3D.Fill(0.0); sliceGeometry->IndexToWorld(currentPointIn2D, worldPointIn3D); worldContour->AddVertex(worldPointIn3D, t); ++iter; } } return worldContour; } void mitk::ContourModelUtils::FillContourInSlice( - ContourModel *projectedContour, Image *sliceImage, Image::Pointer workingImage, int paintingPixelValue) + const ContourModel *projectedContour, Image *sliceImage, const Image* workingImage, int paintingPixelValue) { FillContourInSlice(projectedContour, 0, sliceImage, workingImage, paintingPixelValue); } void mitk::ContourModelUtils::FillContourInSlice( - ContourModel *projectedContour, unsigned int t, Image *sliceImage, Image::Pointer workingImage, int paintingPixelValue) + const ContourModel *projectedContour, TimeStepType contourTimeStep, Image *sliceImage, const Image* workingImage, int paintingPixelValue) { + if (nullptr == projectedContour) + { + mitkThrow() << "Cannot fill contour in slice. Passed contour is invalid"; + } + + if (nullptr == sliceImage) + { + mitkThrow() << "Cannot fill contour in slice. Passed slice is invalid"; + } + auto contourModelFilter = mitk::ContourModelToSurfaceFilter::New(); contourModelFilter->SetInput(projectedContour); contourModelFilter->Update(); auto surface = mitk::Surface::New(); surface = contourModelFilter->GetOutput(); - if (nullptr == surface->GetVtkPolyData(t)) + if (nullptr == surface->GetVtkPolyData(contourTimeStep)) { MITK_WARN << "Could not create surface from contour model."; return; } auto surface2D = vtkSmartPointer::New(); - surface2D->SetPoints(surface->GetVtkPolyData(t)->GetPoints()); - surface2D->SetLines(surface->GetVtkPolyData(t)->GetLines()); + surface2D->SetPoints(surface->GetVtkPolyData(contourTimeStep)->GetPoints()); + surface2D->SetLines(surface->GetVtkPolyData(contourTimeStep)->GetLines()); auto image = vtkSmartPointer::New(); image->DeepCopy(sliceImage->GetVtkImageData()); const double FOREGROUND_VALUE = 255.0; const double BACKGROUND_VALUE = 0.0; vtkIdType count = image->GetNumberOfPoints(); for (decltype(count) i = 0; i < count; ++i) image->GetPointData()->GetScalars()->SetTuple1(i, FOREGROUND_VALUE); auto polyDataToImageStencil = vtkSmartPointer::New(); // Set a minimal tolerance, so that clipped pixels will be added to contour as well. polyDataToImageStencil->SetTolerance(mitk::eps); polyDataToImageStencil->SetInputData(surface2D); polyDataToImageStencil->Update(); auto imageStencil = vtkSmartPointer::New(); imageStencil->SetInputData(image); imageStencil->SetStencilConnection(polyDataToImageStencil->GetOutputPort()); imageStencil->ReverseStencilOff(); imageStencil->SetBackgroundValue(BACKGROUND_VALUE); imageStencil->Update(); vtkSmartPointer filledImage = imageStencil->GetOutput(); vtkSmartPointer resultImage = sliceImage->GetVtkImageData(); FillSliceInSlice(filledImage, resultImage, workingImage, paintingPixelValue); sliceImage->SetVolume(resultImage->GetScalarPointer()); } void mitk::ContourModelUtils::FillSliceInSlice( - vtkSmartPointer filledImage, vtkSmartPointer resultImage, mitk::Image::Pointer image, int paintingPixelValue) + vtkSmartPointer filledImage, vtkSmartPointer resultImage, const Image* image, int paintingPixelValue) { - auto labelImage = dynamic_cast(image.GetPointer()); + auto labelImage = dynamic_cast(image); auto numberOfPoints = filledImage->GetNumberOfPoints(); if (nullptr == labelImage) { for (decltype(numberOfPoints) i = 0; i < numberOfPoints; ++i) { if (1 < filledImage->GetPointData()->GetScalars()->GetTuple1(i)) resultImage->GetPointData()->GetScalars()->SetTuple1(i, paintingPixelValue); } } else { auto backgroundValue = labelImage->GetExteriorLabel()->GetValue(); if (paintingPixelValue != backgroundValue) { for (decltype(numberOfPoints) i = 0; i < numberOfPoints; ++i) { if (1 < filledImage->GetPointData()->GetScalars()->GetTuple1(i)) { auto existingValue = resultImage->GetPointData()->GetScalars()->GetTuple1(i); if (!labelImage->GetLabel(existingValue, labelImage->GetActiveLayer())->GetLocked()) resultImage->GetPointData()->GetScalars()->SetTuple1(i, paintingPixelValue); } } } else { auto activePixelValue = labelImage->GetActiveLabel(labelImage->GetActiveLayer())->GetValue(); for (decltype(numberOfPoints) i = 0; i < numberOfPoints; ++i) { if (1 < filledImage->GetPointData()->GetScalars()->GetTuple1(i)) { if (resultImage->GetPointData()->GetScalars()->GetTuple1(i) == activePixelValue) resultImage->GetPointData()->GetScalars()->SetTuple1(i, paintingPixelValue); } } } } } -mitk::ContourModel::Pointer mitk::ContourModelUtils::MoveZerothContourTimeStep(const ContourModel *contour, unsigned int t) +mitk::ContourModel::Pointer mitk::ContourModelUtils::MoveZerothContourTimeStep(const ContourModel *contour, TimeStepType t) { if (nullptr == contour) return nullptr; auto resultContour = ContourModel::New(); resultContour->Expand(t + 1); std::for_each(contour->Begin(), contour->End(), [&resultContour, t](ContourElement::VertexType *vertex) { - resultContour->AddVertex(vertex, t); + resultContour->AddVertex(*vertex, t); }); return resultContour; } -int mitk::ContourModelUtils::GetActivePixelValue(mitk::Image* workingImage) +int mitk::ContourModelUtils::GetActivePixelValue(const Image* workingImage) { - auto* labelSetImage = dynamic_cast(workingImage); + auto labelSetImage = dynamic_cast(workingImage); int activePixelValue = 1; if (nullptr != labelSetImage) { activePixelValue = labelSetImage->GetActiveLabel(labelSetImage->GetActiveLayer())->GetValue(); } return activePixelValue; } diff --git a/Modules/ContourModel/Algorithms/mitkContourModelUtils.h b/Modules/ContourModel/Algorithms/mitkContourModelUtils.h index 61a33c0c87..cfc364b9df 100644 --- a/Modules/ContourModel/Algorithms/mitkContourModelUtils.h +++ b/Modules/ContourModel/Algorithms/mitkContourModelUtils.h @@ -1,106 +1,113 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkContourModelUtils_h #define mitkContourModelUtils_h #include #include #include #include namespace mitk { /** * \brief Helpful methods for working with contours and images * * */ class MITKCONTOURMODEL_EXPORT ContourModelUtils : public itk::Object { public: mitkClassMacroItkParent(ContourModelUtils, itk::Object); /** \brief Projects a contour onto an image point by point. Converts from world to index coordinates. \param slice \param contourIn3D \param correctionForIpSegmentation adds 0.5 to x and y index coordinates (difference between ipSegmentation and MITK contours) \param constrainToInside */ - static ContourModel::Pointer ProjectContourTo2DSlice(Image *slice, - ContourModel *contourIn3D, + static ContourModel::Pointer ProjectContourTo2DSlice(const Image *slice, + const ContourModel *contourIn3D, bool correctionForIpSegmentation, bool constrainToInside); /** \brief Projects a slice index coordinates of a contour back into world coordinates. \param sliceGeometry \param contourIn2D \param correctionForIpSegmentation subtracts 0.5 to x and y index coordinates (difference between ipSegmentation and MITK contours) */ static ContourModel::Pointer BackProjectContourFrom2DSlice(const BaseGeometry *sliceGeometry, - ContourModel *contourIn2D, + const ContourModel *contourIn2D, bool correctionForIpSegmentation = false); /** - \brief Fill a contour in a 2D slice with a specified pixel value at time step 0. + \brief Fill a contour in a 2D slice with a specified pixel value. + This version always uses the contour of time step 0 and fills the image. + \pre sliceImage points to a valid instance + \pre projectedContour points to a valid instance */ - static void FillContourInSlice(ContourModel *projectedContour, + static void FillContourInSlice(const ContourModel *projectedContour, Image *sliceImage, - mitk::Image::Pointer workingImage, + const Image* workingImage, int paintingPixelValue = 1); /** - \brief Fill a contour in a 2D slice with a specified pixel value at a given time step. + \brief Fill a contour in a 2D slice with a specified pixel value. + This overloaded version uses the contour at the passed contourTimeStep + to fill the passed image slice. + \pre sliceImage points to a valid instance + \pre projectedContour points to a valid instance */ - static void FillContourInSlice(ContourModel *projectedContour, - unsigned int timeStep, + static void FillContourInSlice(const ContourModel *projectedContour, + TimeStepType contourTimeStep, Image *sliceImage, - mitk::Image::Pointer workingImage, + const Image* workingImage, int paintingPixelValue = 1); /** \brief Fills a image (filledImage) into another image (resultImage) by incorporating the rules of LabelSet-Images */ static void FillSliceInSlice(vtkSmartPointer filledImage, vtkSmartPointer resultImage, - mitk::Image::Pointer image, + const Image* image, int paintingPixelValue); /** \brief Move the contour in time step 0 to to a new contour model at the given time step. */ - static ContourModel::Pointer MoveZerothContourTimeStep(const ContourModel *contour, unsigned int timeStep); + static ContourModel::Pointer MoveZerothContourTimeStep(const ContourModel *contour, TimeStepType timeStep); /** \brief Retrieves the active pixel value of a (labelset) image. If the image is basic image, the pixel value 1 (one) will be returned. If the image is actually a labelset image, the pixel value of the active label of the active layer will be returned. \param workingImage The (labelset) image to retrieve the active pixel value of. */ - static int GetActivePixelValue(mitk::Image* workingImage); + static int GetActivePixelValue(const Image* workingImage); protected: ContourModelUtils(); ~ContourModelUtils() override; }; } #endif diff --git a/Modules/ContourModel/DataManagement/mitkContourElement.cpp b/Modules/ContourModel/DataManagement/mitkContourElement.cpp index fd14eacedb..bd906acb7b 100644 --- a/Modules/ContourModel/DataManagement/mitkContourElement.cpp +++ b/Modules/ContourModel/DataManagement/mitkContourElement.cpp @@ -1,471 +1,419 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include -mitk::ContourElement::ContourElement() +bool mitk::ContourElement::ContourModelVertex::operator ==(const ContourModelVertex& other) const { - this->m_Vertices = new VertexListType(); - this->m_IsClosed = false; + return this->Coordinates == other.Coordinates && this->IsControlPoint == other.IsControlPoint; +} + +mitk::ContourElement::ConstVertexIterator mitk::ContourElement::ConstIteratorBegin() const +{ + return this->begin(); +} + +mitk::ContourElement::ConstVertexIterator mitk::ContourElement::ConstIteratorEnd() const +{ + return this->end(); +} + +mitk::ContourElement::VertexIterator mitk::ContourElement::IteratorBegin() +{ + return this->begin(); +} + +mitk::ContourElement::VertexIterator mitk::ContourElement::IteratorEnd() +{ + return this->end(); +} + +mitk::ContourElement::ConstVertexIterator mitk::ContourElement::begin() const +{ + return this->m_Vertices.begin(); +} + +mitk::ContourElement::ConstVertexIterator mitk::ContourElement::end() const +{ + return this->m_Vertices.end(); +} + +mitk::ContourElement::VertexIterator mitk::ContourElement::begin() +{ + return this->m_Vertices.begin(); +} + +mitk::ContourElement::VertexIterator mitk::ContourElement::end() +{ + return this->m_Vertices.end(); } mitk::ContourElement::ContourElement(const mitk::ContourElement &other) - : itk::LightObject(), m_Vertices(other.m_Vertices), m_IsClosed(other.m_IsClosed) + : itk::LightObject(), m_IsClosed(other.m_IsClosed) { + for (const auto& v : other.m_Vertices) + { + m_Vertices.push_back(new ContourModelVertex(*v)); + } } -mitk::ContourElement::~ContourElement() +mitk::ContourElement& mitk::ContourElement::operator = (const ContourElement& other) { - delete this->m_Vertices; + if (this != &other) + { + this->Clear(); + for (const auto& v : other.m_Vertices) + { + m_Vertices.push_back(new ContourModelVertex(*v)); + } + } + + this->m_IsClosed = other.m_IsClosed; + return *this; } -void mitk::ContourElement::AddVertex(mitk::Point3D &vertex, bool isControlPoint) +mitk::ContourElement::~ContourElement() { - this->m_Vertices->push_back(new VertexType(vertex, isControlPoint)); + this->Clear(); } -void mitk::ContourElement::AddVertex(VertexType &vertex) +mitk::ContourElement::VertexSizeType mitk::ContourElement::GetSize() const { - this->m_Vertices->push_back(&vertex); + return this->m_Vertices.size(); } -void mitk::ContourElement::AddVertexAtFront(mitk::Point3D &vertex, bool isControlPoint) +void mitk::ContourElement::AddVertex(const mitk::Point3D &vertex, bool isControlPoint) { - this->m_Vertices->push_front(new VertexType(vertex, isControlPoint)); + this->m_Vertices.push_back(new VertexType(vertex, isControlPoint)); } -void mitk::ContourElement::AddVertexAtFront(VertexType &vertex) +void mitk::ContourElement::AddVertexAtFront(const mitk::Point3D &vertex, bool isControlPoint) { - this->m_Vertices->push_front(&vertex); + this->m_Vertices.push_front(new VertexType(vertex, isControlPoint)); } -void mitk::ContourElement::InsertVertexAtIndex(mitk::Point3D &vertex, bool isControlPoint, int index) +void mitk::ContourElement::InsertVertexAtIndex(const mitk::Point3D &vertex, bool isControlPoint, VertexSizeType index) { if (index >= 0 && this->GetSize() > index) { - auto _where = this->m_Vertices->begin(); + auto _where = this->m_Vertices.begin(); _where += index; - this->m_Vertices->insert(_where, new VertexType(vertex, isControlPoint)); + this->m_Vertices.insert(_where, new VertexType(vertex, isControlPoint)); } } -void mitk::ContourElement::SetVertexAt(int pointId, const Point3D &point) +void mitk::ContourElement::SetVertexAt(VertexSizeType pointId, const Point3D &point) { if (pointId >= 0 && this->GetSize() > pointId) { - this->m_Vertices->at(pointId)->Coordinates = point; + this->m_Vertices[pointId]->Coordinates = point; } } -void mitk::ContourElement::SetVertexAt(int pointId, const VertexType *vertex) +void mitk::ContourElement::SetVertexAt(VertexSizeType pointId, const VertexType *vertex) { + if (nullptr == vertex) + { + mitkThrow() << "Cannot set vertex. Passed vertex instance is invalid. Index to set: " << pointId; + } + if (pointId >= 0 && this->GetSize() > pointId) { - this->m_Vertices->at(pointId)->Coordinates = vertex->Coordinates; - this->m_Vertices->at(pointId)->IsControlPoint = vertex->IsControlPoint; + this->m_Vertices[pointId]->Coordinates = vertex->Coordinates; + this->m_Vertices[pointId]->IsControlPoint = vertex->IsControlPoint; } } -mitk::ContourElement::VertexType *mitk::ContourElement::GetVertexAt(int index) +mitk::ContourElement::VertexType *mitk::ContourElement::GetVertexAt(VertexSizeType index) { - return this->m_Vertices->at(index); + return this->m_Vertices.at(index); } -bool mitk::ContourElement::IsEmpty() +const mitk::ContourElement::VertexType* mitk::ContourElement::GetVertexAt(VertexSizeType index) const { - return this->m_Vertices->empty(); + return this->m_Vertices.at(index); +} + +bool mitk::ContourElement::IsEmpty() const +{ + return this->m_Vertices.empty(); } mitk::ContourElement::VertexType *mitk::ContourElement::GetVertexAt(const mitk::Point3D &point, float eps) { /* current version iterates over the whole deque - should some kind of an octree with spatial query*/ if (eps > 0) { // currently no method with better performance is available return BruteForceGetVertexAt(point, eps); } // if eps < 0 return nullptr; } -mitk::ContourElement::VertexType *mitk::ContourElement::BruteForceGetVertexAt(const mitk::Point3D &point, float eps) +mitk::ContourElement::VertexType *mitk::ContourElement::BruteForceGetVertexAt(const mitk::Point3D &point, double eps) { if (eps > 0) { std::deque> nearestlist; - ConstVertexIterator it = this->m_Vertices->begin(); + ConstVertexIterator it = this->m_Vertices.begin(); - ConstVertexIterator end = this->m_Vertices->end(); + ConstVertexIterator end = this->m_Vertices.end(); while (it != end) { mitk::Point3D currentPoint = (*it)->Coordinates; double distance = currentPoint.EuclideanDistanceTo(point); if (distance < eps) { // if list is emtpy, add point to list if (nearestlist.size() < 1) { nearestlist.push_front(std::pair((*it)->Coordinates.EuclideanDistanceTo(point), (*it))); } // found an approximate point - check if current is closer then first in nearestlist else if (distance < nearestlist.front().first) { // found even closer vertex nearestlist.push_front(std::pair((*it)->Coordinates.EuclideanDistanceTo(point), (*it))); } } // if distance > eps it++; } // while if (nearestlist.size() > 0) { /*++++++++++++++++++++ return the nearest active point if one was found++++++++++++++++++*/ auto it = nearestlist.begin(); auto end = nearestlist.end(); while (it != end) { if ((*it).second->IsControlPoint) { return (*it).second; } it++; } /*---------------------------------------------------------------------------------------*/ // return closest point return nearestlist.front().second; } } return nullptr; } -/*mitk::ContourElement::VertexType* mitk::ContourElement::OptimizedGetVertexAt(const mitk::Point3D &point, float eps) -{ - if( (eps > 0) && (this->m_Vertices->size()>0) ) - { - int k = 1; - int dim = 3; - int nPoints = this->m_Vertices->size(); - ANNpointArray pointsArray; - ANNpoint queryPoint; - ANNidxArray indexArray; - ANNdistArray distanceArray; - ANNkd_tree* kdTree; - - queryPoint = annAllocPt(dim); - pointsArray = annAllocPts(nPoints, dim); - indexArray = new ANNidx[k]; - distanceArray = new ANNdist[k]; - - - int i = 0; - - //fill points array with our control points - for(VertexIterator it = this->m_Vertices->begin(); it != this->m_Vertices->end(); it++, i++) - { - mitk::Point3D cur = (*it)->Coordinates; - pointsArray[i][0]= cur[0]; - pointsArray[i][1]= cur[1]; - pointsArray[i][2]= cur[2]; - } - - //create the kd tree - kdTree = new ANNkd_tree(pointsArray,nPoints, dim); - - //fill mitk::Point3D into ANN query point - queryPoint[0] = point[0]; - queryPoint[1] = point[1]; - queryPoint[2] = point[2]; - - //k nearest neighbour search - kdTree->annkSearch(queryPoint, k, indexArray, distanceArray, eps); - - VertexType* ret = nullptr; - - try - { - ret = this->m_Vertices->at(indexArray[0]); - } - catch(std::out_of_range ex) - { - //ret stays nullptr - return ret; - } - - //clean up ANN - delete [] indexArray; - delete [] distanceArray; - delete kdTree; - annClose(); - - return ret; - } - return nullptr; -} -*/ - -mitk::ContourElement::VertexListType *mitk::ContourElement::GetVertexList() +const mitk::ContourElement::VertexListType *mitk::ContourElement::GetVertexList() const { - return this->m_Vertices; + return &(this->m_Vertices); } -bool mitk::ContourElement::IsClosed() +bool mitk::ContourElement::IsClosed() const { return this->m_IsClosed; } -bool mitk::ContourElement::IsNearContour(const mitk::Point3D &point, float eps) +bool mitk::ContourElement::IsNearContour(const mitk::Point3D &point, float eps) const { - ConstVertexIterator it1 = this->m_Vertices->begin(); - ConstVertexIterator it2 = this->m_Vertices->begin(); + ConstVertexIterator it1 = this->m_Vertices.begin(); + ConstVertexIterator it2 = this->m_Vertices.begin(); it2++; // it2 runs one position ahead - ConstVertexIterator end = this->m_Vertices->end(); + ConstVertexIterator end = this->m_Vertices.end(); int counter = 0; for (; it1 != end; it1++, it2++, counter++) { if (it2 == end) - it2 = this->m_Vertices->begin(); + it2 = this->m_Vertices.begin(); mitk::Point3D v1 = (*it1)->Coordinates; mitk::Point3D v2 = (*it2)->Coordinates; const float l2 = v1.SquaredEuclideanDistanceTo(v2); mitk::Vector3D p_v1 = point - v1; mitk::Vector3D v2_v1 = v2 - v1; double tc = (p_v1 * v2_v1) / l2; // take into account we have line segments and not (infinite) lines if (tc < 0.0) tc = 0.0; if (tc > 1.0) tc = 1.0; mitk::Point3D crossPoint = v1 + v2_v1 * tc; double distance = point.SquaredEuclideanDistanceTo(crossPoint); if (distance < eps) { return true; } } return false; } void mitk::ContourElement::Close() { this->m_IsClosed = true; } void mitk::ContourElement::Open() { this->m_IsClosed = false; } void mitk::ContourElement::SetClosed(bool isClosed) { isClosed ? this->Close() : this->Open(); } -mitk::ContourElement::VertexListType *mitk::ContourElement::GetControlVertices() +mitk::ContourElement::VertexListType mitk::ContourElement::GetControlVertices() const { - auto newVertices = new VertexListType(); + VertexListType controlVertices; - auto it = this->m_Vertices->begin(); - auto end = this->m_Vertices->end(); + std::copy_if(this->m_Vertices.begin(), this->m_Vertices.end(), std::back_inserter(controlVertices), [](const VertexType* v) {return v->IsControlPoint; }); - while (it != end) - { - if ((*it)->IsControlPoint) - { - newVertices->push_back((*it)); - } - it++; - } - - return newVertices; + return controlVertices; } -void mitk::ContourElement::Concatenate(mitk::ContourElement *other, bool check) +void mitk::ContourElement::Concatenate(const mitk::ContourElement *other, bool check) { if (other->GetSize() > 0) { - ConstVertexIterator otherIt = other->m_Vertices->begin(); - ConstVertexIterator otherEnd = other->m_Vertices->end(); - while (otherIt != otherEnd) + for (const auto& sourceVertex : other->m_Vertices) { if (check) { - ConstVertexIterator thisIt = this->m_Vertices->begin(); - ConstVertexIterator thisEnd = this->m_Vertices->end(); + auto finding = std::find_if(this->m_Vertices.begin(), this->m_Vertices.end(), [sourceVertex](const VertexType* v) {return sourceVertex->Coordinates == v->Coordinates; }); - bool found = false; - while (thisIt != thisEnd) + if (finding == this->m_Vertices.end()) { - if ((*thisIt)->Coordinates == (*otherIt)->Coordinates) - { - found = true; - break; - } - - thisIt++; + this->m_Vertices.push_back(new ContourModelVertex(*sourceVertex)); } - if (!found) - this->m_Vertices->push_back(*otherIt); } else { - this->m_Vertices->push_back(*otherIt); + this->m_Vertices.push_back(new ContourModelVertex(*sourceVertex)); } - otherIt++; } } } -bool mitk::ContourElement::RemoveVertex(const VertexType *vertex) +mitk::ContourElement::VertexSizeType mitk::ContourElement::GetIndex(const VertexType* vertex) const { - auto it = this->m_Vertices->begin(); + VertexSizeType result = NPOS; - auto end = this->m_Vertices->end(); + auto finding = std::find(this->m_Vertices.begin(), this->m_Vertices.end(), vertex); - // search for vertex and remove it if exists - while (it != end) + if (finding != this->m_Vertices.end()) { - if ((*it) == vertex) - { - this->m_Vertices->erase(it); - return true; - } - - it++; + result = finding - this->m_Vertices.begin(); } - return false; + return result; } -int mitk::ContourElement::GetIndex(const VertexType *vertex) +bool mitk::ContourElement::RemoveVertex(const VertexType *vertex) { - auto it = this->m_Vertices->begin(); + auto finding = std::find(this->m_Vertices.begin(), this->m_Vertices.end(), vertex); - auto end = this->m_Vertices->end(); - - int index = 0; + return RemoveVertexByIterator(finding); +} - // search for vertex - while (it != end) +bool mitk::ContourElement::RemoveVertexAt(VertexSizeType index) +{ + if (index >= 0 && index < this->m_Vertices.size()) { - if ((*it) == vertex) - { - return index; - } - - it++; - ++index; + auto delIter = this->m_Vertices.begin() + index; + return RemoveVertexByIterator(delIter); } - return -1; // not found + return false; } -bool mitk::ContourElement::RemoveVertexAt(int index) +bool mitk::ContourElement::RemoveVertexAt(const mitk::Point3D &point, double eps) { - if (index >= 0 && static_cast(index) < this->m_Vertices->size()) - { - this->m_Vertices->erase(this->m_Vertices->begin() + index); - return true; - } - else + if (eps > 0) { - return false; + auto finding = std::find_if(this->m_Vertices.begin(), this->m_Vertices.end(), [point, eps](const VertexType* v) {return v->Coordinates.EuclideanDistanceTo(point) < eps; }); + + return RemoveVertexByIterator(finding); } + return false; } -bool mitk::ContourElement::RemoveVertexAt(mitk::Point3D &point, float eps) +bool mitk::ContourElement::RemoveVertexByIterator(VertexListType::iterator& iter) { - /* current version iterates over the whole deque - should be some kind of an octree with spatial query*/ - - if (eps > 0) + if (iter != this->m_Vertices.end()) { - auto it = this->m_Vertices->begin(); - - auto end = this->m_Vertices->end(); - - while (it != end) - { - mitk::Point3D currentPoint = (*it)->Coordinates; - - if (currentPoint.EuclideanDistanceTo(point) < eps) - { - // approximate point found - // now erase it - this->m_Vertices->erase(it); - return true; - } - - it++; - } + delete* iter; + this->m_Vertices.erase(iter); + return true; } + return false; } void mitk::ContourElement::Clear() { - this->m_Vertices->clear(); + for (auto vertex : m_Vertices) + { + delete vertex; + } + this->m_Vertices.clear(); } + //---------------------------------------------------------------------- void mitk::ContourElement::RedistributeControlVertices(const VertexType *selected, int period) { int counter = 0; - auto _where = this->m_Vertices->begin(); + auto _where = this->m_Vertices.begin(); if (selected != nullptr) { - while (_where != this->m_Vertices->end()) + auto finding = std::find(this->m_Vertices.begin(), this->m_Vertices.end(), selected); + + if (finding != this->m_Vertices.end()) { - if ((*_where) == selected) - { - break; - } - _where++; + _where = finding; } } auto _iter = _where; - while (_iter != this->m_Vertices->end()) + while (_iter != this->m_Vertices.end()) { div_t divresult; divresult = div(counter, period); (*_iter)->IsControlPoint = (divresult.rem == 0); counter++; _iter++; } _iter = _where; counter = 0; - while (_iter != this->m_Vertices->begin()) + while (_iter != this->m_Vertices.begin()) { div_t divresult; divresult = div(counter, period); (*_iter)->IsControlPoint = (divresult.rem == 0); counter++; _iter--; } } diff --git a/Modules/ContourModel/DataManagement/mitkContourElement.h b/Modules/ContourModel/DataManagement/mitkContourElement.h index 9191b72409..42be258cc3 100644 --- a/Modules/ContourModel/DataManagement/mitkContourElement.h +++ b/Modules/ContourModel/DataManagement/mitkContourElement.h @@ -1,237 +1,260 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 _mitkContourElement_H_ #define _mitkContourElement_H_ #include "mitkCommon.h" #include #include -//#include - #include namespace mitk { /** \brief Represents a contour in 3D space. A ContourElement is consisting of linked vertices implicitely defining the contour. They are stored in a double ended queue making it possible to add vertices at front and end of the contour and to iterate in both directions. To mark a vertex as a special one it can be set as a control point. - \note It is highly not recommend to use this class directly as no secure mechanism is used here. - Use mitk::ContourModel instead providing some additional features. + \note This class assumes that it manages its vertices. So if a vertex instance is added to this + class the ownership of the vertex is transfered to the ContourElement instance. + The ContourElement instance takes care of deleting vertex instances if needed. + It is highly not recommend to use this class directly as it is designed as a internal class of + ContourModel. Therefore it is adviced to use ContourModel if contour representations are needed in + MITK. */ class MITKCONTOURMODEL_EXPORT ContourElement : public itk::LightObject { public: mitkClassMacroItkParent(ContourElement, itk::LightObject); itkFactorylessNewMacro(Self); itkCloneMacro(Self); - // Data container representing vertices - - /** \brief Represents a single vertex of contour. - */ - struct ContourModelVertex + /** \brief Represents a single vertex of a contour. + */ + struct MITKCONTOURMODEL_EXPORT ContourModelVertex { - ContourModelVertex(mitk::Point3D &point, bool active = false) : IsControlPoint(active), Coordinates(point) {} - ContourModelVertex(const ContourModelVertex &other) + ContourModelVertex(const mitk::Point3D& point, bool active = false) : IsControlPoint(active), Coordinates(point) {}; + ContourModelVertex(const ContourModelVertex& other) : IsControlPoint(other.IsControlPoint), Coordinates(other.Coordinates) { - } + }; /** \brief Treat point special. */ bool IsControlPoint; /** \brief Coordinates in 3D space. */ mitk::Point3D Coordinates; + + bool operator ==(const ContourModelVertex& other) const; }; - // END Data container representing vertices - typedef ContourModelVertex VertexType; - typedef std::deque VertexListType; - typedef VertexListType::iterator VertexIterator; - typedef VertexListType::const_iterator ConstVertexIterator; + using VertexType = ContourModelVertex; + using VertexListType = std::deque; + using VertexIterator = VertexListType::iterator; + using ConstVertexIterator = VertexListType::const_iterator; + using VertexSizeType = VertexListType::size_type; - // start of inline methods + /**Indicates an invalid index. + * It is always the maximum of the unsigned int type.*/ + static const VertexSizeType NPOS = -1; + + /** \brief Return a const iterator a the front. + */ + ConstVertexIterator ConstIteratorBegin() const; + /** \brief Return a const iterator a the end. + */ + ConstVertexIterator ConstIteratorEnd() const; + /** \brief Return an iterator a the front. + */ + VertexIterator IteratorBegin(); + /** \brief Return an iterator a the end. + */ + VertexIterator IteratorEnd(); /** \brief Return a const iterator a the front. + * For easier support of stl functionality. */ - virtual ConstVertexIterator ConstIteratorBegin() { return this->m_Vertices->begin(); } + ConstVertexIterator begin() const; /** \brief Return a const iterator a the end. + * For easier support of stl functionality. */ - virtual ConstVertexIterator ConstIteratorEnd() { return this->m_Vertices->end(); } + ConstVertexIterator end() const; /** \brief Return an iterator a the front. + * For easier support of stl functionality. */ - virtual VertexIterator IteratorBegin() { return this->m_Vertices->begin(); } + VertexIterator begin(); /** \brief Return an iterator a the end. + * For easier support of stl functionality. */ - virtual VertexIterator IteratorEnd() { return this->m_Vertices->end(); } + VertexIterator end(); + /** \brief Returns the number of contained vertices. */ - virtual int GetSize() { return this->m_Vertices->size(); } - // end of inline methods + VertexSizeType GetSize() const; /** \brief Add a vertex at the end of the contour \param point - coordinates in 3D space. \param isControlPoint - is the vertex a special control point. */ - virtual void AddVertex(mitk::Point3D &point, bool isControlPoint); - - /** \brief Add a vertex at the end of the contour - \param vertex - a contour element vertex. - */ - virtual void AddVertex(VertexType &vertex); + void AddVertex(const mitk::Point3D &point, bool isControlPoint); /** \brief Add a vertex at the front of the contour \param point - coordinates in 3D space. \param isControlPoint - is the vertex a control point. */ - virtual void AddVertexAtFront(mitk::Point3D &point, bool isControlPoint); - - /** \brief Add a vertex at the front of the contour - \param vertex - a contour element vertex. - */ - virtual void AddVertexAtFront(VertexType &vertex); + void AddVertexAtFront(const mitk::Point3D &point, bool isControlPoint); /** \brief Add a vertex at a given index of the contour \param point - coordinates in 3D space. \param isControlPoint - is the vertex a special control point. \param index - the index to be inserted at. */ - virtual void InsertVertexAtIndex(mitk::Point3D &point, bool isControlPoint, int index); + void InsertVertexAtIndex(const mitk::Point3D &point, bool isControlPoint, VertexSizeType index); /** \brief Set coordinates a given index. \param pointId Index of vertex. \param point Coordinates. */ - virtual void SetVertexAt(int pointId, const mitk::Point3D &point); + void SetVertexAt(VertexSizeType pointId, const mitk::Point3D &point); - /** \brief Set vertex a given index. + /** \brief Set vertex a given index (by copying the values). \param pointId Index of vertex. \param vertex Vertex. + \pre Passed vertex is a valid instance */ - virtual void SetVertexAt(int pointId, const VertexType *vertex); + void SetVertexAt(VertexSizeType pointId, const VertexType* vertex); /** \brief Returns the vertex a given index \param index + \pre index must be valid. */ - virtual VertexType *GetVertexAt(int index); + VertexType* GetVertexAt(VertexSizeType index); + const VertexType* GetVertexAt(VertexSizeType index) const; /** \brief Returns the approximate nearest vertex a given posoition in 3D space \param point - query position in 3D space. \param eps - the error bound for search algorithm. */ - virtual VertexType *GetVertexAt(const mitk::Point3D &point, float eps); + VertexType *GetVertexAt(const mitk::Point3D &point, float eps); /** \brief Returns the index of the given vertex within the contour. \param vertex - the vertex to be searched. - \return index of vertex. -1 if not found. + \return index of vertex. Returns ContourElement::NPOS if not found. */ - virtual int GetIndex(const VertexType *vertex); + VertexSizeType GetIndex(const VertexType *vertex) const; /** \brief Returns the container of the vertices. */ - VertexListType *GetVertexList(); + const VertexListType *GetVertexList() const; /** \brief Returns whether the contour element is empty. */ - bool IsEmpty(); + bool IsEmpty() const; /** \brief Returns if the conour is closed or not. */ - virtual bool IsClosed(); + bool IsClosed() const; /** \brief Returns whether a given point is near a contour, according to eps. \param point - query position in 3D space. \param eps - the error bound for search algorithm. */ - virtual bool IsNearContour(const mitk::Point3D &point, float eps); + bool IsNearContour(const mitk::Point3D &point, float eps) const; /** \brief Close the contour. Connect first with last element. */ - virtual void Close(); + void Close(); /** \brief Open the contour. Disconnect first and last element. */ - virtual void Open(); + void Open(); /** \brief Set the contours IsClosed property. \param isClosed - true = closed; false = open; */ - virtual void SetClosed(bool isClosed); + void SetClosed(bool isClosed); /** \brief Concatenate the contuor with a another contour. - All vertices of the other contour will be added after last vertex. + All vertices of the other contour will be cloned and added after last vertex. \param other - the other contour - \param check - set it true to avoid intersections + \param check - set it true to avoid adding of vertices that are already in the source contour */ - void Concatenate(mitk::ContourElement *other, bool check); + void Concatenate(const mitk::ContourElement *other, bool check); /** \brief Remove the given vertex from the container if exists. \param vertex - the vertex to be removed. */ - virtual bool RemoveVertex(const VertexType *vertex); + bool RemoveVertex(const VertexType *vertex); /** \brief Remove a vertex at given index within the container if exists. \param index - the index where the vertex should be removed. */ - virtual bool RemoveVertexAt(int index); + bool RemoveVertexAt(VertexSizeType index); /** \brief Remove the approximate nearest vertex at given position in 3D space if one exists. \param point - query point in 3D space. \param eps - error bound for search algorithm. */ - virtual bool RemoveVertexAt(mitk::Point3D &point, float eps); + bool RemoveVertexAt(const mitk::Point3D &point, double eps); /** \brief Clear the storage container. */ - virtual void Clear(); + void Clear(); /** \brief Returns the approximate nearest vertex a given posoition in 3D space \param point - query position in 3D space. \param eps - the error bound for search algorithm. */ - VertexType *BruteForceGetVertexAt(const mitk::Point3D &point, float eps); + VertexType *BruteForceGetVertexAt(const mitk::Point3D &point, double eps); - /** \brief Returns the approximate nearest vertex a given posoition in 3D space - \param point - query position in 3D space. - \param eps - the error bound for search algorithm. - */ - // VertexType* OptimizedGetVertexAt(const mitk::Point3D &point, float eps); - - VertexListType *GetControlVertices(); + /** Returns a list pointing to all vertices that are indicated to be control + points. + \remark It is important to note, that the vertex pointers in the returned + list directly point to the vertices stored interanlly. So they are still + owned by the ContourElement instance that returns the list. If one wants + to take over ownership, one has to clone the vertex instances. + */ + VertexListType GetControlVertices() const; /** \brief Uniformly redistribute control points with a given period (in number of vertices) \param vertex - the vertex around which the redistribution is done. \param period - number of vertices between control points. */ void RedistributeControlVertices(const VertexType *vertex, int period); protected: mitkCloneMacro(Self); - ContourElement(); + ContourElement() = default; ContourElement(const mitk::ContourElement &other); - ~ContourElement() override; + ~ContourElement(); + + ContourElement& operator = (const ContourElement & other); + + /** Internal helper function to correctly remove the element indicated by the iterator + from the list. After the call the iterator is invalid. + Caller of the function must ensure that the iterator is valid!. + \result Indicates if the element indicated by the iterator was removed. If iterator points to end it returns false.*/ + bool RemoveVertexByIterator(VertexListType::iterator& iter); - VertexListType *m_Vertices; // double ended queue with vertices - bool m_IsClosed; + VertexListType m_Vertices; // double ended queue with vertices + bool m_IsClosed = false; }; } // namespace mitk #endif // _mitkContourElement_H_ diff --git a/Modules/ContourModel/DataManagement/mitkContourModel.cpp b/Modules/ContourModel/DataManagement/mitkContourModel.cpp index 6d88174b43..d6e04cb150 100644 --- a/Modules/ContourModel/DataManagement/mitkContourModel.cpp +++ b/Modules/ContourModel/DataManagement/mitkContourModel.cpp @@ -1,635 +1,628 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include mitk::ContourModel::ContourModel() : m_UpdateBoundingBox(true) { // set to initial state this->InitializeEmpty(); } -mitk::ContourModel::ContourModel(const mitk::ContourModel &other) - : mitk::BaseData(other), m_ContourSeries(other.m_ContourSeries), m_lineInterpolation(other.m_lineInterpolation) +mitk::ContourModel::ContourModel(const ContourModel &other) + : BaseData(other), m_ContourSeries(other.m_ContourSeries), m_lineInterpolation(other.m_lineInterpolation) { m_SelectedVertex = nullptr; } mitk::ContourModel::~ContourModel() { m_SelectedVertex = nullptr; this->m_ContourSeries.clear(); // TODO check destruction } -void mitk::ContourModel::AddVertex(mitk::Point3D &vertex, int timestep) +void mitk::ContourModel::AddVertex(const Point3D &vertex, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { this->AddVertex(vertex, false, timestep); } } -void mitk::ContourModel::AddVertex(mitk::Point3D &vertex, bool isControlPoint, int timestep) +void mitk::ContourModel::AddVertex(const Point3D &vertex, bool isControlPoint, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { this->m_ContourSeries[timestep]->AddVertex(vertex, isControlPoint); this->InvokeEvent(ContourModelSizeChangeEvent()); this->Modified(); this->m_UpdateBoundingBox = true; } } -void mitk::ContourModel::AddVertex(VertexType &vertex, int timestep) +void mitk::ContourModel::AddVertex(const VertexType &vertex, TimeStepType timestep) { - if (!this->IsEmptyTimeStep(timestep)) - { - this->m_ContourSeries[timestep]->AddVertex(vertex); - this->InvokeEvent(ContourModelSizeChangeEvent()); - this->Modified(); - this->m_UpdateBoundingBox = true; - } -} - -void mitk::ContourModel::AddVertex(const VertexType *vertex, int timestep) -{ - if (vertex != nullptr) - { - this->m_ContourSeries[timestep]->AddVertex(*const_cast(vertex)); - } + this->AddVertex(vertex.Coordinates, vertex.IsControlPoint, timestep); } -void mitk::ContourModel::AddVertexAtFront(mitk::Point3D &vertex, int timestep) +void mitk::ContourModel::AddVertexAtFront(const Point3D &vertex, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { this->AddVertexAtFront(vertex, false, timestep); } } -void mitk::ContourModel::AddVertexAtFront(mitk::Point3D &vertex, bool isControlPoint, int timestep) +void mitk::ContourModel::AddVertexAtFront(const Point3D &vertex, bool isControlPoint, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { this->m_ContourSeries[timestep]->AddVertexAtFront(vertex, isControlPoint); this->InvokeEvent(ContourModelSizeChangeEvent()); this->Modified(); this->m_UpdateBoundingBox = true; } } -void mitk::ContourModel::AddVertexAtFront(VertexType &vertex, int timestep) +void mitk::ContourModel::AddVertexAtFront(const VertexType &vertex, TimeStepType timestep) { - if (!this->IsEmptyTimeStep(timestep)) - { - this->m_ContourSeries[timestep]->AddVertexAtFront(vertex); - this->InvokeEvent(ContourModelSizeChangeEvent()); - this->Modified(); - this->m_UpdateBoundingBox = true; - } + this->AddVertexAtFront(vertex.Coordinates, vertex.IsControlPoint, timestep); } -bool mitk::ContourModel::SetVertexAt(int pointId, const Point3D &point, unsigned int timestep) +bool mitk::ContourModel::SetVertexAt(int pointId, const Point3D &point, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { - if (pointId >= 0 && this->m_ContourSeries[timestep]->GetSize() > pointId) + if (pointId >= 0 && this->m_ContourSeries[timestep]->GetSize() > ContourElement::VertexSizeType(pointId)) { this->m_ContourSeries[timestep]->SetVertexAt(pointId, point); this->Modified(); this->m_UpdateBoundingBox = true; return true; } return false; } return false; } -bool mitk::ContourModel::SetVertexAt(int pointId, const VertexType *vertex, unsigned int timestep) +bool mitk::ContourModel::SetVertexAt(int pointId, const VertexType *vertex, TimeStepType timestep) { if (vertex == nullptr) return false; if (!this->IsEmptyTimeStep(timestep)) { - if (pointId >= 0 && this->m_ContourSeries[timestep]->GetSize() > pointId) + if (pointId >= 0 && this->m_ContourSeries[timestep]->GetSize() > ContourElement::VertexSizeType(pointId)) { this->m_ContourSeries[timestep]->SetVertexAt(pointId, vertex); this->Modified(); this->m_UpdateBoundingBox = true; return true; } return false; } return false; } -void mitk::ContourModel::InsertVertexAtIndex(mitk::Point3D &vertex, int index, bool isControlPoint, int timestep) +void mitk::ContourModel::InsertVertexAtIndex(const Point3D &vertex, int index, bool isControlPoint, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { - if (index >= 0 && this->m_ContourSeries[timestep]->GetSize() > index) + if (index >= 0 && this->m_ContourSeries[timestep]->GetSize() > ContourElement::VertexSizeType(index)) { this->m_ContourSeries[timestep]->InsertVertexAtIndex(vertex, isControlPoint, index); this->InvokeEvent(ContourModelSizeChangeEvent()); this->Modified(); this->m_UpdateBoundingBox = true; } } } -bool mitk::ContourModel::IsEmpty(int timestep) const +void mitk::ContourModel::UpdateContour(const ContourModel* sourceModel, TimeStepType destinationTimeStep, TimeStepType sourceTimeStep) +{ + if (nullptr == sourceModel) + { + mitkThrow() << "Cannot update contour. Passed source model is invalid."; + } + + if (!sourceModel->GetTimeGeometry()->IsValidTimeStep(sourceTimeStep)) + { + mitkThrow() << "Cannot update contour. Source contour time geometry does not support passed time step. Invalid time step: " << sourceTimeStep; + } + + if (!this->GetTimeGeometry()->IsValidTimeStep(destinationTimeStep)) + { + MITK_WARN << "Cannot update contour. Contour time geometry does not support passed time step. Invalid time step: " << destinationTimeStep; + return; + } + + this->Clear(destinationTimeStep); + + std::for_each(sourceModel->Begin(sourceTimeStep), sourceModel->End(sourceTimeStep), [this, destinationTimeStep](ContourElement::VertexType* vertex) { + this->m_ContourSeries[destinationTimeStep]->AddVertex(vertex->Coordinates, vertex->IsControlPoint); + }); + + this->InvokeEvent(ContourModelSizeChangeEvent()); + this->Modified(); + this->m_UpdateBoundingBox = true; +} + +bool mitk::ContourModel::IsEmpty(TimeStepType timestep) const { if (!this->IsEmptyTimeStep(timestep)) { return this->m_ContourSeries[timestep]->IsEmpty(); } return true; } bool mitk::ContourModel::IsEmpty() const { return this->IsEmpty(0); } -int mitk::ContourModel::GetNumberOfVertices(int timestep) const +int mitk::ContourModel::GetNumberOfVertices(TimeStepType timestep) const { if (!this->IsEmptyTimeStep(timestep)) { return this->m_ContourSeries[timestep]->GetSize(); } return -1; } -const mitk::ContourModel::VertexType *mitk::ContourModel::GetVertexAt(int index, int timestep) const +const mitk::ContourModel::VertexType *mitk::ContourModel::GetVertexAt(int index, TimeStepType timestep) const { - if (!this->IsEmptyTimeStep(timestep)) + if (!this->IsEmptyTimeStep(timestep) && this->m_ContourSeries[timestep]->GetSize() > mitk::ContourElement::VertexSizeType(index)) { return this->m_ContourSeries[timestep]->GetVertexAt(index); } return nullptr; } -int mitk::ContourModel::GetIndex(const VertexType *vertex, int timestep) +int mitk::ContourModel::GetIndex(const VertexType *vertex, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { return this->m_ContourSeries[timestep]->GetIndex(vertex); } return -1; } -void mitk::ContourModel::Close(int timestep) +void mitk::ContourModel::Close(TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { this->m_ContourSeries[timestep]->Close(); this->InvokeEvent(ContourModelClosedEvent()); this->Modified(); this->m_UpdateBoundingBox = true; } } -void mitk::ContourModel::Open(int timestep) +void mitk::ContourModel::Open(TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { this->m_ContourSeries[timestep]->Open(); this->InvokeEvent(ContourModelClosedEvent()); this->Modified(); this->m_UpdateBoundingBox = true; } } -void mitk::ContourModel::SetClosed(bool isClosed, int timestep) +void mitk::ContourModel::SetClosed(bool isClosed, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { this->m_ContourSeries[timestep]->SetClosed(isClosed); this->InvokeEvent(ContourModelClosedEvent()); this->Modified(); this->m_UpdateBoundingBox = true; } } bool mitk::ContourModel::IsEmptyTimeStep(unsigned int t) const { return (this->m_ContourSeries.size() <= t); } -bool mitk::ContourModel::IsNearContour(mitk::Point3D &point, float eps, int timestep) +bool mitk::ContourModel::IsNearContour(Point3D &point, float eps, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { return this->m_ContourSeries[timestep]->IsNearContour(point, eps); } return false; } -void mitk::ContourModel::Concatenate(mitk::ContourModel *other, int timestep, bool check) +void mitk::ContourModel::Concatenate(ContourModel *other, TimeStepType timestep, bool check) { if (!this->IsEmptyTimeStep(timestep)) { if (!this->m_ContourSeries[timestep]->IsClosed()) { this->m_ContourSeries[timestep]->Concatenate(other->m_ContourSeries[timestep], check); this->InvokeEvent(ContourModelSizeChangeEvent()); this->Modified(); this->m_UpdateBoundingBox = true; } } } -mitk::ContourModel::VertexIterator mitk::ContourModel::Begin(int timestep) const +mitk::ContourModel::VertexIterator mitk::ContourModel::Begin(TimeStepType timestep) const { return this->IteratorBegin(timestep); } -mitk::ContourModel::VertexIterator mitk::ContourModel::IteratorBegin(int timestep) const +mitk::ContourModel::VertexIterator mitk::ContourModel::IteratorBegin(TimeStepType timestep) const { if (!this->IsEmptyTimeStep(timestep)) { return this->m_ContourSeries[timestep]->IteratorBegin(); } else { mitkThrow() << "No iterator at invalid timestep " << timestep << ". There are only " << this->GetTimeSteps() << " timesteps available."; } } -mitk::ContourModel::VertexIterator mitk::ContourModel::End(int timestep) const +mitk::ContourModel::VertexIterator mitk::ContourModel::End(TimeStepType timestep) const { return this->IteratorEnd(timestep); } -mitk::ContourModel::VertexIterator mitk::ContourModel::IteratorEnd(int timestep) const +mitk::ContourModel::VertexIterator mitk::ContourModel::IteratorEnd(TimeStepType timestep) const { if (!this->IsEmptyTimeStep(timestep)) { return this->m_ContourSeries[timestep]->IteratorEnd(); } else { mitkThrow() << "No iterator at invalid timestep " << timestep << ". There are only " << this->GetTimeSteps() << " timesteps available."; } } bool mitk::ContourModel::IsClosed(int timestep) const { if (!this->IsEmptyTimeStep(timestep)) { return this->m_ContourSeries[timestep]->IsClosed(); } return false; } -bool mitk::ContourModel::SelectVertexAt(mitk::Point3D &point, float eps, int timestep) +bool mitk::ContourModel::SelectVertexAt(Point3D &point, float eps, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { this->m_SelectedVertex = this->m_ContourSeries[timestep]->GetVertexAt(point, eps); } return this->m_SelectedVertex != nullptr; } -bool mitk::ContourModel::SelectVertexAt(int index, int timestep) +bool mitk::ContourModel::SelectVertexAt(int index, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep) && index >= 0) { return (this->m_SelectedVertex = this->m_ContourSeries[timestep]->GetVertexAt(index)); } return false; } -bool mitk::ContourModel::SetControlVertexAt(mitk::Point3D &point, float eps, int timestep) +bool mitk::ContourModel::SetControlVertexAt(Point3D &point, float eps, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { VertexType *vertex = this->m_ContourSeries[timestep]->GetVertexAt(point, eps); if (vertex != nullptr) { vertex->IsControlPoint = true; return true; } } return false; } -bool mitk::ContourModel::SetControlVertexAt(int index, int timestep) +bool mitk::ContourModel::SetControlVertexAt(int index, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep) && index >= 0) { VertexType *vertex = this->m_ContourSeries[timestep]->GetVertexAt(index); if (vertex != nullptr) { vertex->IsControlPoint = true; return true; } } return false; } -bool mitk::ContourModel::RemoveVertex(const VertexType *vertex, int timestep) +bool mitk::ContourModel::RemoveVertex(const VertexType *vertex, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { if (this->m_ContourSeries[timestep]->RemoveVertex(vertex)) { this->Modified(); this->m_UpdateBoundingBox = true; this->InvokeEvent(ContourModelSizeChangeEvent()); return true; } } return false; } -bool mitk::ContourModel::RemoveVertexAt(int index, int timestep) +bool mitk::ContourModel::RemoveVertexAt(int index, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { if (this->m_ContourSeries[timestep]->RemoveVertexAt(index)) { this->Modified(); this->m_UpdateBoundingBox = true; this->InvokeEvent(ContourModelSizeChangeEvent()); return true; } } return false; } -bool mitk::ContourModel::RemoveVertexAt(mitk::Point3D &point, float eps, int timestep) +bool mitk::ContourModel::RemoveVertexAt(Point3D &point, float eps, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { if (this->m_ContourSeries[timestep]->RemoveVertexAt(point, eps)) { this->Modified(); this->m_UpdateBoundingBox = true; this->InvokeEvent(ContourModelSizeChangeEvent()); return true; } } return false; } -void mitk::ContourModel::ShiftSelectedVertex(mitk::Vector3D &translate) +void mitk::ContourModel::ShiftSelectedVertex(Vector3D &translate) { if (this->m_SelectedVertex) { this->ShiftVertex(this->m_SelectedVertex, translate); this->Modified(); this->m_UpdateBoundingBox = true; } } -void mitk::ContourModel::ShiftContour(mitk::Vector3D &translate, int timestep) +void mitk::ContourModel::ShiftContour(Vector3D &translate, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { - VertexListType *vList = this->m_ContourSeries[timestep]->GetVertexList(); - auto it = vList->begin(); - auto end = vList->end(); - // shift all vertices - while (it != end) + for (auto vertex : *(this->m_ContourSeries[timestep])) { - this->ShiftVertex((*it), translate); - it++; + this->ShiftVertex(vertex, translate); } this->Modified(); this->m_UpdateBoundingBox = true; this->InvokeEvent(ContourModelShiftEvent()); } } -void mitk::ContourModel::ShiftVertex(VertexType *vertex, mitk::Vector3D &vector) +void mitk::ContourModel::ShiftVertex(VertexType *vertex, Vector3D &vector) { vertex->Coordinates[0] += vector[0]; vertex->Coordinates[1] += vector[1]; vertex->Coordinates[2] += vector[2]; } -void mitk::ContourModel::Clear(int timestep) +void mitk::ContourModel::Clear(TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { // clear data at timestep this->m_ContourSeries[timestep]->Clear(); - this->InitializeEmpty(); this->Modified(); this->m_UpdateBoundingBox = true; } } void mitk::ContourModel::Expand(unsigned int timeSteps) { std::size_t oldSize = this->m_ContourSeries.size(); if (static_cast(timeSteps) > oldSize) { Superclass::Expand(timeSteps); // insert contours for each new timestep for (std::size_t i = oldSize; i < static_cast(timeSteps); i++) { - m_ContourSeries.push_back(mitk::ContourElement::New()); + m_ContourSeries.push_back(ContourElement::New()); } this->InvokeEvent(ContourModelExpandTimeBoundsEvent()); } } void mitk::ContourModel::SetRequestedRegionToLargestPossibleRegion() { // no support for regions } bool mitk::ContourModel::RequestedRegionIsOutsideOfTheBufferedRegion() { // no support for regions return false; } bool mitk::ContourModel::VerifyRequestedRegion() { // no support for regions return true; } -const mitk::BaseGeometry *mitk::ContourModel::GetUpdatedGeometry(int t) -{ - return Superclass::GetUpdatedGeometry(t); -} - -mitk::BaseGeometry *mitk::ContourModel::GetGeometry(int t) const -{ - return Superclass::GetGeometry(t); -} - void mitk::ContourModel::SetRequestedRegion(const itk::DataObject * /*data*/) { // no support for regions } void mitk::ContourModel::Clear() { // clear data and set to initial state again this->ClearData(); this->InitializeEmpty(); this->Modified(); this->m_UpdateBoundingBox = true; } -void mitk::ContourModel::RedistributeControlVertices(int period, int timestep) +void mitk::ContourModel::RedistributeControlVertices(int period, TimeStepType timestep) { if (!this->IsEmptyTimeStep(timestep)) { this->m_ContourSeries[timestep]->RedistributeControlVertices(this->GetSelectedVertex(), period); this->InvokeEvent(ContourModelClosedEvent()); this->Modified(); this->m_UpdateBoundingBox = true; } } void mitk::ContourModel::ClearData() { // call the superclass, this releases the data of BaseData Superclass::ClearData(); // clear out the time resolved contours this->m_ContourSeries.clear(); } void mitk::ContourModel::Initialize() { this->InitializeEmpty(); this->Modified(); this->m_UpdateBoundingBox = true; } -void mitk::ContourModel::Initialize(mitk::ContourModel &other) +void mitk::ContourModel::Initialize(const ContourModel &other) { - mitk::TimeStepType numberOfTimesteps = other.GetTimeGeometry()->CountTimeSteps(); + TimeStepType numberOfTimesteps = other.GetTimeGeometry()->CountTimeSteps(); this->InitializeTimeGeometry(numberOfTimesteps); - for (mitk::TimeStepType currentTimestep = 0; currentTimestep < numberOfTimesteps; currentTimestep++) + for (TimeStepType currentTimestep = 0; currentTimestep < numberOfTimesteps; currentTimestep++) { - this->m_ContourSeries.push_back(mitk::ContourElement::New()); + this->m_ContourSeries.push_back(ContourElement::New()); this->SetClosed(other.IsClosed(currentTimestep), currentTimestep); } m_SelectedVertex = nullptr; this->m_lineInterpolation = other.m_lineInterpolation; this->Modified(); this->m_UpdateBoundingBox = true; } void mitk::ContourModel::InitializeEmpty() { // clear data at timesteps this->m_ContourSeries.resize(0); - this->m_ContourSeries.push_back(mitk::ContourElement::New()); + this->m_ContourSeries.push_back(ContourElement::New()); // set number of timesteps to one this->InitializeTimeGeometry(1); m_SelectedVertex = nullptr; this->m_lineInterpolation = ContourModel::LINEAR; } void mitk::ContourModel::UpdateOutputInformation() { if (this->GetSource()) { this->GetSource()->UpdateOutputInformation(); } if (this->m_UpdateBoundingBox) { // update the bounds of the geometry according to the stored vertices ScalarType mitkBounds[6]; // calculate the boundingbox at each timestep typedef itk::BoundingBox BoundingBoxType; typedef BoundingBoxType::PointsContainer PointsContainer; int timesteps = this->GetTimeSteps(); // iterate over the timesteps for (int currenTimeStep = 0; currenTimeStep < timesteps; currenTimeStep++) { - if (dynamic_cast(this->GetGeometry(currenTimeStep))) + if (dynamic_cast(this->GetGeometry(currenTimeStep))) { // do not update bounds for 2D geometries, as they are unfortunately defined with min bounds 0! return; } else { // we have a 3D geometry -> let's update bounds // only update bounds if the contour was modified if (this->GetMTime() > this->GetGeometry(currenTimeStep)->GetBoundingBox()->GetMTime()) { mitkBounds[0] = 0.0; mitkBounds[1] = 0.0; mitkBounds[2] = 0.0; mitkBounds[3] = 0.0; mitkBounds[4] = 0.0; mitkBounds[5] = 0.0; BoundingBoxType::Pointer boundingBox = BoundingBoxType::New(); PointsContainer::Pointer points = PointsContainer::New(); auto it = this->IteratorBegin(currenTimeStep); auto end = this->IteratorEnd(currenTimeStep); // fill the boundingbox with the points while (it != end) { Point3D currentP = (*it)->Coordinates; BoundingBoxType::PointType p; p.CastFrom(currentP); points->InsertElement(points->Size(), p); it++; } // construct the new boundingBox boundingBox->SetPoints(points); boundingBox->ComputeBoundingBox(); BoundingBoxType::BoundsArrayType tmp = boundingBox->GetBounds(); mitkBounds[0] = tmp[0]; mitkBounds[1] = tmp[1]; mitkBounds[2] = tmp[2]; mitkBounds[3] = tmp[3]; mitkBounds[4] = tmp[4]; mitkBounds[5] = tmp[5]; // set boundingBox at current timestep BaseGeometry *geometry3d = this->GetGeometry(currenTimeStep); geometry3d->SetBounds(mitkBounds); } } } this->m_UpdateBoundingBox = false; } GetTimeGeometry()->Update(); } -void mitk::ContourModel::ExecuteOperation(mitk::Operation * /*operation*/) +void mitk::ContourModel::ExecuteOperation(Operation * /*operation*/) { // not supported yet } diff --git a/Modules/ContourModel/DataManagement/mitkContourModel.h b/Modules/ContourModel/DataManagement/mitkContourModel.h index 45aae9bcda..d234d9cefb 100644 --- a/Modules/ContourModel/DataManagement/mitkContourModel.h +++ b/Modules/ContourModel/DataManagement/mitkContourModel.h @@ -1,453 +1,437 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef _MITK_CONTOURMODEL_H_ #define _MITK_CONTOURMODEL_H_ #include "mitkBaseData.h" #include "mitkCommon.h" #include #include namespace mitk { /** \brief ContourModel is a structure of linked vertices defining a contour in 3D space. The vertices are stored in a mitk::ContourElement is stored for each timestep. The contour line segments are implicitly defined by the given linked vertices. By default two control points are are linked by a straight line.It is possible to add vertices at front and end of the contour and to iterate in both directions. Points are specified containing coordinates and additional (data) information, see mitk::ContourElement. For accessing a specific vertex either an index or a position in 3D Space can be used. The vertices are best accessed by using a VertexIterator. Interaction with the contour is thus available without any mitk interactor class using the api of ContourModel. It is possible to shift single vertices also as shifting the whole contour. A contour can be either open like a single curved line segment or closed. A closed contour can for example represent a jordan curve. \section mitkContourModelDisplayOptions Display Options The default mappers for this data structure are mitk::ContourModelGLMapper2D and mitk::ContourModelMapper3D. See these classes for display options which can can be set via properties. */ class MITKCONTOURMODEL_EXPORT ContourModel : public BaseData { public: mitkClassMacro(ContourModel, BaseData); itkFactorylessNewMacro(Self); itkCloneMacro(Self); - /*+++++++++++++++ typedefs +++++++++++++++++++++++++++++++*/ - typedef mitk::ContourElement::VertexType VertexType; - typedef mitk::ContourElement::VertexListType VertexListType; - typedef mitk::ContourElement::VertexIterator VertexIterator; - typedef mitk::ContourElement::ConstVertexIterator ConstVertexIterator; - typedef std::vector ContourModelSeries; + /*+++++++++++++++ typedefs +++++++++++++++++++++++++++++++*/ + typedef ContourElement::VertexType VertexType; + typedef ContourElement::VertexListType VertexListType; + typedef ContourElement::VertexIterator VertexIterator; + typedef ContourElement::ConstVertexIterator ConstVertexIterator; + typedef std::vector ContourModelSeries; /*+++++++++++++++ END typedefs ++++++++++++++++++++++++++++*/ /** \brief Possible interpolation of the line segments between control points */ enum LineSegmentInterpolation { LINEAR, B_SPLINE }; /*++++++++++++++++ inline methods +++++++++++++++++++++++*/ /** \brief Get the current selected vertex. */ VertexType *GetSelectedVertex() { return this->m_SelectedVertex; } /** \brief Deselect vertex. */ void Deselect() { this->m_SelectedVertex = nullptr; } /** \brief Set selected vertex as control point */ void SetSelectedVertexAsControlPoint(bool isControlPoint = true) { if (this->m_SelectedVertex) { m_SelectedVertex->IsControlPoint = isControlPoint; this->Modified(); } } /** \brief Set the interpolation of the line segments between control points. */ void SetLineSegmentInterpolation(LineSegmentInterpolation interpolation) { this->m_lineInterpolation = interpolation; this->Modified(); } /** \brief Get the interpolation of the line segments between control points. */ LineSegmentInterpolation GetLineSegmentInterpolation() { return this->m_lineInterpolation; } /*++++++++++++++++ END inline methods +++++++++++++++++++++++*/ /** \brief Add a vertex to the contour at given timestep. The vertex is added at the end of contour. \param vertex - coordinate representation of a control point \param timestep - the timestep at which the vertex will be add ( default 0) @note Adding a vertex to a timestep which exceeds the timebounds of the contour will not be added, the TimeGeometry will not be expanded. */ - void AddVertex(mitk::Point3D &vertex, int timestep = 0); + void AddVertex(const Point3D &vertex, TimeStepType timestep = 0); /** \brief Add a vertex to the contour at given timestep. - The vertex is added at the end of contour. - + A copy of the passed vertex is added at the end of contour. \param vertex - coordinate representation of a control point \param timestep - the timestep at which the vertex will be add ( default 0) - @note Adding a vertex to a timestep which exceeds the timebounds of the contour will not be added, the TimeGeometry will not be expanded. */ - void AddVertex(VertexType &vertex, int timestep = 0); - - /** \brief Add a vertex to the contour at given timestep. - The vertex is added at the end of contour. - - \param vertex - coordinate representation of a control point - \param timestep - the timestep at which the vertex will be add ( default 0) - - @note Adding a vertex to a timestep which exceeds the timebounds of the contour - will not be added, the TimeSlicedGeometry will not be expanded. - */ - void AddVertex(const VertexType *vertex, int timestep = 0); + void AddVertex(const VertexType &vertex, TimeStepType timestep = 0); /** \brief Add a vertex to the contour. - \param vertex - coordinate representation of a control point \param timestep - the timestep at which the vertex will be add ( default 0) \param isControlPoint - specifies the vertex to be handled in a special way (e.g. control points will be rendered). - - @note Adding a vertex to a timestep which exceeds the timebounds of the contour will not be added, the TimeGeometry will not be expanded. */ - void AddVertex(mitk::Point3D &vertex, bool isControlPoint, int timestep = 0); + void AddVertex(const Point3D& vertex, bool isControlPoint, TimeStepType timestep = 0); + + /** Clears the contour of destinationTimeStep and copies + the contour of the passed source model at the sourceTimeStep. + @pre soureModel must point to a valid instance + @pre sourceTimePoint must be valid + @note Updateing a vertex to a timestep which exceeds the timebounds of the contour + will not be added, the TimeGeometry will not be expanded. + */ + void UpdateContour(const ContourModel* sourceModel, TimeStepType destinationTimeStep, TimeStepType sourceTimeStep); /** \brief Add a vertex to the contour at given timestep AT THE FRONT of the contour. The vertex is added at the FRONT of contour. \param vertex - coordinate representation of a control point \param timestep - the timestep at which the vertex will be add ( default 0) @note Adding a vertex to a timestep which exceeds the timebounds of the contour will not be added, the TimeGeometry will not be expanded. */ - void AddVertexAtFront(mitk::Point3D &vertex, int timestep = 0); + void AddVertexAtFront(const Point3D &vertex, TimeStepType timestep = 0); /** \brief Add a vertex to the contour at given timestep AT THE FRONT of the contour. The vertex is added at the FRONT of contour. \param vertex - coordinate representation of a control point \param timestep - the timestep at which the vertex will be add ( default 0) @note Adding a vertex to a timestep which exceeds the timebounds of the contour will not be added, the TimeGeometry will not be expanded. */ - void AddVertexAtFront(VertexType &vertex, int timestep = 0); + void AddVertexAtFront(const VertexType &vertex, TimeStepType timestep = 0); /** \brief Add a vertex to the contour at given timestep AT THE FRONT of the contour. \param vertex - coordinate representation of a control point \param timestep - the timestep at which the vertex will be add ( default 0) \param isControlPoint - specifies the vertex to be handled in a special way (e.g. control points will be rendered). @note Adding a vertex to a timestep which exceeds the timebounds of the contour will not be added, the TimeGeometry will not be expanded. */ - void AddVertexAtFront(mitk::Point3D &vertex, bool isControlPoint, int timestep = 0); + void AddVertexAtFront(const Point3D &vertex, bool isControlPoint, TimeStepType timestep = 0); /** \brief Insert a vertex at given index. */ - void InsertVertexAtIndex(mitk::Point3D &vertex, int index, bool isControlPoint = false, int timestep = 0); + void InsertVertexAtIndex(const Point3D &vertex, int index, bool isControlPoint = false, TimeStepType timestep = 0); /** \brief Set a coordinates for point at given index. */ - bool SetVertexAt(int pointId, const mitk::Point3D &point, unsigned int timestep = 0); + bool SetVertexAt(int pointId, const Point3D &point, TimeStepType timestep = 0); - /** \brief Set a coordinates for point at given index. + /** \brief Set a coordinates and control state for point at given index. */ - bool SetVertexAt(int pointId, const VertexType *vertex, unsigned int timestep = 0); + bool SetVertexAt(int pointId, const VertexType *vertex, TimeStepType timestep = 0); /** \brief Return if the contour is closed or not. */ bool IsClosed(int timestep = 0) const; /** \brief Concatenate two contours. The starting control point of the other will be added at the end of the contour. \param other \param timestep - the timestep at which the vertex will be add ( default 0) \param check - check for intersections ( default false) */ - void Concatenate(mitk::ContourModel *other, int timestep = 0, bool check = false); + void Concatenate(ContourModel *other, TimeStepType timestep = 0, bool check = false); /** \brief Returns a const VertexIterator at the start element of the contour. @throw mitk::Exception if the timestep is invalid. */ - VertexIterator Begin(int timestep = 0) const; + VertexIterator Begin(TimeStepType timestep = 0) const; /** \brief Returns a const VertexIterator at the start element of the contour. @throw mitk::Exception if the timestep is invalid. */ - VertexIterator IteratorBegin(int timestep = 0) const; + VertexIterator IteratorBegin(TimeStepType timestep = 0) const; /** \brief Returns a const VertexIterator at the end element of the contour. @throw mitk::Exception if the timestep is invalid. */ - VertexIterator End(int timestep = 0) const; + VertexIterator End(TimeStepType timestep = 0) const; /** \brief Returns a const VertexIterator at the end element of the contour. @throw mitk::Exception if the timestep is invalid. */ - VertexIterator IteratorEnd(int timestep = 0) const; + VertexIterator IteratorEnd(TimeStepType timestep = 0) const; /** \brief Close the contour. The last control point will be linked with the first point. */ - virtual void Close(int timestep = 0); + virtual void Close(TimeStepType timestep = 0); /** \brief Set isClosed to false contour. The link between the last control point the first point will be removed. */ - virtual void Open(int timestep = 0); + virtual void Open(TimeStepType timestep = 0); /** \brief Set closed property to given boolean. false - The link between the last control point the first point will be removed. true - The last control point will be linked with the first point. */ - virtual void SetClosed(bool isClosed, int timestep = 0); + virtual void SetClosed(bool isClosed, TimeStepType timestep = 0); /** \brief Returns the number of vertices at a given timestep. \param timestep - default = 0 */ - int GetNumberOfVertices(int timestep = 0) const; + int GetNumberOfVertices(TimeStepType timestep = 0) const; /** \brief Returns whether the contour model is empty at a given timestep. \param timestep - default = 0 */ - virtual bool IsEmpty(int timestep) const; + virtual bool IsEmpty(TimeStepType timestep) const; /** \brief Returns whether the contour model is empty. */ bool IsEmpty() const override; /** \brief Returns the vertex at the index position within the container. + * If the index or timestep is invalid a nullptr will be returned. */ - virtual const VertexType *GetVertexAt(int index, int timestep = 0) const; + virtual const VertexType *GetVertexAt(int index, TimeStepType timestep = 0) const; /** \brief Remove a vertex at given timestep within the container. \return index of vertex. -1 if not found. */ - int GetIndex(const VertexType *vertex, int timestep = 0); + int GetIndex(const VertexType *vertex, TimeStepType timestep = 0); /** \brief Check if there isn't something at this timestep. */ bool IsEmptyTimeStep(unsigned int t) const override; /** \brief Check if mouse cursor is near the contour. */ - virtual bool IsNearContour(mitk::Point3D &point, float eps, int timestep); + virtual bool IsNearContour(Point3D &point, float eps, TimeStepType timestep); /** \brief Mark a vertex at an index in the container as selected. */ - bool SelectVertexAt(int index, int timestep = 0); + bool SelectVertexAt(int index, TimeStepType timestep = 0); /** \brief Mark a vertex at an index in the container as control point. */ - bool SetControlVertexAt(int index, int timestep = 0); + bool SetControlVertexAt(int index, TimeStepType timestep = 0); /** \brief Mark a vertex at a given position in 3D space. \param point - query point in 3D space \param eps - radius for nearest neighbour search (error bound). \param timestep - search at this timestep @return true = vertex found; false = no vertex found */ - bool SelectVertexAt(mitk::Point3D &point, float eps, int timestep = 0); + bool SelectVertexAt(Point3D &point, float eps, TimeStepType timestep = 0); /* \pararm point - query point in 3D space \pararm eps - radius for nearest neighbour search (error bound). \pararm timestep - search at this timestep @return true = vertex found; false = no vertex found */ - bool SetControlVertexAt(mitk::Point3D &point, float eps, int timestep = 0); + bool SetControlVertexAt(Point3D &point, float eps, TimeStepType timestep = 0); /** \brief Remove a vertex at given index within the container. @return true = the vertex was successfuly removed; false = wrong index. */ - bool RemoveVertexAt(int index, int timestep = 0); + bool RemoveVertexAt(int index, TimeStepType timestep = 0); /** \brief Remove a vertex at given timestep within the container. @return true = the vertex was successfuly removed. */ - bool RemoveVertex(const VertexType *vertex, int timestep = 0); + bool RemoveVertex(const VertexType *vertex, TimeStepType timestep = 0); /** \brief Remove a vertex at a query position in 3D space. The vertex to be removed will be search by nearest neighbour search. Note that possibly no vertex at this position and eps is stored inside the contour. @return true = the vertex was successfuly removed; false = no vertex found. */ - bool RemoveVertexAt(mitk::Point3D &point, float eps, int timestep = 0); + bool RemoveVertexAt(Point3D &point, float eps, TimeStepType timestep = 0); /** \brief Shift the currently selected vertex by a translation vector. \param translate - the translation vector. */ - void ShiftSelectedVertex(mitk::Vector3D &translate); + void ShiftSelectedVertex(Vector3D &translate); /** \brief Shift the whole contour by a translation vector at given timestep. \param translate - the translation vector. \param timestep - at this timestep the contour will be shifted. */ - void ShiftContour(mitk::Vector3D &translate, int timestep = 0); + void ShiftContour(Vector3D &translate, TimeStepType timestep = 0); /** \brief Clear the storage container at given timestep. All control points are removed at timestep. */ - virtual void Clear(int timestep); + virtual void Clear(TimeStepType timestep); /** \brief Initialize all data objects */ void Initialize() override; /** \brief Initialize object with specs of other contour. Note: No data will be copied. */ - void Initialize(mitk::ContourModel &other); + void Initialize(const ContourModel &other); /*++++++++++++++++++ method inherit from base data +++++++++++++++++++++++++++*/ /** \brief Inherit from base data - no region support available for contourModel objects. */ void SetRequestedRegionToLargestPossibleRegion() override; /** \brief Inherit from base data - no region support available for contourModel objects. */ bool RequestedRegionIsOutsideOfTheBufferedRegion() override; /** \brief Inherit from base data - no region support available for contourModel objects. */ bool VerifyRequestedRegion() override; - /** - \brief Get the updated geometry with recomputed bounds. - */ - virtual const mitk::BaseGeometry *GetUpdatedGeometry(int t = 0); - - /** - \brief Get the BaseGeometry for timestep t. - */ - virtual mitk::BaseGeometry *GetGeometry(int t = 0) const; - /** \brief Inherit from base data - no region support available for contourModel objects. */ void SetRequestedRegion(const itk::DataObject *data) override; /** - \brief Expand the timebounds of the TimeGeometry to given number of timesteps. + \brief Expand the contour model and its TimeGeometry to given number of timesteps. */ void Expand(unsigned int timeSteps) override; /** \brief Update the OutputInformation of a ContourModel object The BoundingBox of the contour will be updated, if necessary. */ void UpdateOutputInformation() override; /** \brief Clear the storage container. The object is set to initial state. All control points are removed and the number of timesteps are set to 1. */ void Clear() override; /** \brief overwrite if the Data can be called by an Interactor (StateMachine). */ void ExecuteOperation(Operation *operation) override; /** \brief Redistributes ontrol vertices with a given period (as number of vertices) \param period - the number of vertices between control points. \param timestep - at this timestep all lines will be rebuilt. */ - virtual void RedistributeControlVertices(int period, int timestep); + virtual void RedistributeControlVertices(int period, TimeStepType timestep); protected: mitkCloneMacro(Self); ContourModel(); - ContourModel(const mitk::ContourModel &other); + ContourModel(const ContourModel &other); ~ContourModel() override; // inherit from BaseData. called by Clear() void ClearData() override; // inherit from BaseData. Initial state of a contour with no vertices and a single timestep. void InitializeEmpty() override; // Shift a vertex - void ShiftVertex(VertexType *vertex, mitk::Vector3D &vector); + static void ShiftVertex(VertexType *vertex, Vector3D &vector); // Storage with time resolved support. ContourModelSeries m_ContourSeries; // The currently selected vertex. VertexType *m_SelectedVertex; // The interpolation of the line segment between control points. LineSegmentInterpolation m_lineInterpolation; // only update the bounding geometry if necessary bool m_UpdateBoundingBox; }; itkEventMacro(ContourModelEvent, itk::AnyEvent); itkEventMacro(ContourModelShiftEvent, ContourModelEvent); itkEventMacro(ContourModelSizeChangeEvent, ContourModelEvent); itkEventMacro(ContourModelAddEvent, ContourModelSizeChangeEvent); itkEventMacro(ContourModelRemoveEvent, ContourModelSizeChangeEvent); itkEventMacro(ContourModelExpandTimeBoundsEvent, ContourModelEvent); itkEventMacro(ContourModelClosedEvent, ContourModelEvent); } #endif diff --git a/Modules/ContourModel/Rendering/mitkContourModelGLMapper2DBase.cpp b/Modules/ContourModel/Rendering/mitkContourModelGLMapper2DBase.cpp index 675fa1b921..980672e655 100644 --- a/Modules/ContourModel/Rendering/mitkContourModelGLMapper2DBase.cpp +++ b/Modules/ContourModel/Rendering/mitkContourModelGLMapper2DBase.cpp @@ -1,396 +1,396 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkContourModelSetGLMapper2D.h" #include "mitkColorProperty.h" #include "mitkContourModelSet.h" #include "mitkPlaneGeometry.h" #include "mitkProperties.h" #include #include "vtkPen.h" #include "vtkContext2D.h" #include "vtkContextDevice2D.h" #include "vtkOpenGLContextDevice2D.h" #include "mitkManualPlacementAnnotationRenderer.h" #include "mitkBaseRenderer.h" #include "mitkContourModel.h" #include "mitkTextAnnotation2D.h" mitk::ContourModelGLMapper2DBase::ContourModelGLMapper2DBase(): m_Initialized(false) { m_PointNumbersAnnotation = mitk::TextAnnotation2D::New(); m_ControlPointNumbersAnnotation = mitk::TextAnnotation2D::New(); } mitk::ContourModelGLMapper2DBase::~ContourModelGLMapper2DBase() { } void mitk::ContourModelGLMapper2DBase::Initialize(mitk::BaseRenderer *) { vtkOpenGLContextDevice2D *device = nullptr; device = vtkOpenGLContextDevice2D::New(); if (device) { this->m_Context->Begin(device); device->Delete(); this->m_Initialized = true; } else { } } void mitk::ContourModelGLMapper2DBase::ApplyColorAndOpacityProperties(mitk::BaseRenderer *renderer, vtkActor * /*actor*/) { float rgba[4] = { 1.0f, 1.0f, 1.0f, 1.0f }; // check for color prop and use it for rendering if it exists GetDataNode()->GetColor(rgba, renderer, "color"); // check for opacity prop and use it for rendering if it exists GetDataNode()->GetOpacity(rgba[3], renderer, "opacity"); if (this->m_Context->GetPen() == nullptr) { return; } this->m_Context->GetPen()->SetColorF((double)rgba[0], (double)rgba[1], (double)rgba[2], (double)rgba[3]); } void mitk::ContourModelGLMapper2DBase::DrawContour(mitk::ContourModel *renderingContour, mitk::BaseRenderer *renderer) { if (std::find(m_RendererList.begin(), m_RendererList.end(), renderer) == m_RendererList.end()) { m_RendererList.push_back(renderer); } mitk::ManualPlacementAnnotationRenderer::AddAnnotation(m_PointNumbersAnnotation.GetPointer(), renderer); m_PointNumbersAnnotation->SetVisibility(false); mitk::ManualPlacementAnnotationRenderer::AddAnnotation(m_ControlPointNumbersAnnotation.GetPointer(), renderer); m_ControlPointNumbersAnnotation->SetVisibility(false); InternalDrawContour(renderingContour, renderer); } void mitk::ContourModelGLMapper2DBase::InternalDrawContour(mitk::ContourModel *renderingContour, mitk::BaseRenderer *renderer) { if (!renderingContour) return; if (!this->m_Initialized) { this->Initialize(renderer); } vtkOpenGLContextDevice2D::SafeDownCast( this->m_Context->GetDevice())->Begin(renderer->GetVtkRenderer()); mitk::DataNode *dataNode = this->GetDataNode(); renderingContour->UpdateOutputInformation(); - unsigned int timestep = renderer->GetTimeStep(); + const auto timestep = this->GetTimestep(); if (!renderingContour->IsEmptyTimeStep(timestep)) { // apply color and opacity read from the PropertyList ApplyColorAndOpacityProperties(renderer); mitk::ColorProperty::Pointer colorprop = dynamic_cast(dataNode->GetProperty("contour.color", renderer)); float opacity = 0.5; dataNode->GetFloatProperty("opacity", opacity, renderer); if (colorprop) { // set the color of the contour double red = colorprop->GetColor().GetRed(); double green = colorprop->GetColor().GetGreen(); double blue = colorprop->GetColor().GetBlue(); this->m_Context->GetPen()->SetColorF(red, green, blue, opacity); } mitk::ColorProperty::Pointer selectedcolor = dynamic_cast(dataNode->GetProperty("contour.points.color", renderer)); if (!selectedcolor) { selectedcolor = mitk::ColorProperty::New(1.0, 0.0, 0.1); } vtkLinearTransform *transform = dataNode->GetVtkTransform(); // ContourModel::OutputType point; mitk::Point3D point; mitk::Point3D p; float vtkp[3]; float lineWidth = 3.0; bool drawit = false; bool isHovering = false; dataNode->GetBoolProperty("contour.hovering", isHovering); if (isHovering) dataNode->GetFloatProperty("contour.hovering.width", lineWidth); else dataNode->GetFloatProperty("contour.width", lineWidth); bool showSegments = false; dataNode->GetBoolProperty("contour.segments.show", showSegments); bool showControlPoints = false; dataNode->GetBoolProperty("contour.controlpoints.show", showControlPoints); bool showPoints = false; dataNode->GetBoolProperty("contour.points.show", showPoints); bool showPointsNumbers = false; dataNode->GetBoolProperty("contour.points.text", showPointsNumbers); bool showControlPointsNumbers = false; dataNode->GetBoolProperty("contour.controlpoints.text", showControlPointsNumbers); bool projectmode = false; dataNode->GetVisibility(projectmode, renderer, "contour.project-onto-plane"); auto pointsIt = renderingContour->IteratorBegin(timestep); Point2D pt2d; // projected_p in display coordinates Point2D lastPt2d; int index = 0; mitk::ScalarType maxDiff = 0.25; while (pointsIt != renderingContour->IteratorEnd(timestep)) { lastPt2d = pt2d; point = (*pointsIt)->Coordinates; itk2vtk(point, vtkp); transform->TransformPoint(vtkp, vtkp); vtk2itk(vtkp, p); renderer->WorldToView(p, pt2d); ScalarType scalardiff = fabs(renderer->GetCurrentWorldPlaneGeometry()->SignedDistance(p)); // project to plane if (projectmode) { drawit = true; } else if (scalardiff < maxDiff) // point is close enough to be drawn { drawit = true; } else { drawit = false; } // draw line if (drawit) { if (showSegments) { // lastPt2d is not valid in first step if (!(pointsIt == renderingContour->IteratorBegin(timestep))) { this->m_Context->GetPen()->SetWidth(lineWidth); this->m_Context->DrawLine(pt2d[0], pt2d[1], lastPt2d[0], lastPt2d[1]); this->m_Context->GetPen()->SetWidth(1); } } if (showControlPoints) { // draw ontrol points if ((*pointsIt)->IsControlPoint) { float pointsize = 4; Point2D tmp; Vector2D horz, vert; horz[1] = 0; vert[0] = 0; horz[0] = pointsize; vert[1] = pointsize; this->m_Context->GetPen()->SetColorF(selectedcolor->GetColor().GetRed(), selectedcolor->GetColor().GetBlue(), selectedcolor->GetColor().GetGreen()); this->m_Context->GetPen()->SetWidth(1); // a rectangle around the point with the selected color auto* rectPts = new float[8]; tmp = pt2d - horz; rectPts[0] = tmp[0]; rectPts[1] = tmp[1]; tmp = pt2d + vert; rectPts[2] = tmp[0]; rectPts[3] = tmp[1]; tmp = pt2d + horz; rectPts[4] = tmp[0]; rectPts[5] = tmp[1]; tmp = pt2d - vert; rectPts[6] = tmp[0]; rectPts[7] = tmp[1]; this->m_Context->DrawPolygon(rectPts,4); // the actual point in the specified color to see the usual color of the point this->m_Context->GetPen()->SetColorF( colorprop->GetColor().GetRed(), colorprop->GetColor().GetGreen(), colorprop->GetColor().GetBlue()); this->m_Context->DrawPoint(pt2d[0], pt2d[1]); } } if (showPoints) { float pointsize = 3; Point2D tmp; Vector2D horz, vert; horz[1] = 0; vert[0] = 0; horz[0] = pointsize; vert[1] = pointsize; this->m_Context->GetPen()->SetColorF(0.0, 0.0, 0.0); this->m_Context->GetPen()->SetWidth(1); // a rectangle around the point with the selected color auto* rectPts = new float[8]; tmp = pt2d - horz; rectPts[0] = tmp[0]; rectPts[1] = tmp[1]; tmp = pt2d + vert; rectPts[2] = tmp[0]; rectPts[3] = tmp[1]; tmp = pt2d + horz; rectPts[4] = tmp[0]; rectPts[5] = tmp[1]; tmp = pt2d - vert; rectPts[6] = tmp[0]; rectPts[7] = tmp[1]; this->m_Context->DrawPolygon(rectPts, 4); // the actual point in the specified color to see the usual color of the point this->m_Context->GetPen()->SetColorF( colorprop->GetColor().GetRed(), colorprop->GetColor().GetGreen(), colorprop->GetColor().GetBlue()); this->m_Context->DrawPoint(pt2d[0], pt2d[1]); } if (showPointsNumbers) { std::string l; std::stringstream ss; ss << index; l.append(ss.str()); float rgb[3]; rgb[0] = 0.0; rgb[1] = 0.0; rgb[2] = 0.0; WriteTextWithAnnotation(m_PointNumbersAnnotation, l.c_str(), rgb, pt2d, renderer); } if (showControlPointsNumbers && (*pointsIt)->IsControlPoint) { std::string l; std::stringstream ss; ss << index; l.append(ss.str()); float rgb[3]; rgb[0] = 1.0; rgb[1] = 1.0; rgb[2] = 0.0; WriteTextWithAnnotation(m_ControlPointNumbersAnnotation, l.c_str(), rgb, pt2d, renderer); } index++; } pointsIt++; } // end while iterate over controlpoints // close contour if necessary if (renderingContour->IsClosed(timestep) && drawit && showSegments) { lastPt2d = pt2d; point = renderingContour->GetVertexAt(0, timestep)->Coordinates; itk2vtk(point, vtkp); transform->TransformPoint(vtkp, vtkp); vtk2itk(vtkp, p); renderer->WorldToDisplay(p, pt2d); this->m_Context->GetPen()->SetWidth(lineWidth); this->m_Context->DrawLine(lastPt2d[0], lastPt2d[1], pt2d[0], pt2d[1]); this->m_Context->GetPen()->SetWidth(1); } // draw selected vertex if exists if (renderingContour->GetSelectedVertex()) { // transform selected vertex point = renderingContour->GetSelectedVertex()->Coordinates; itk2vtk(point, vtkp); transform->TransformPoint(vtkp, vtkp); vtk2itk(vtkp, p); renderer->WorldToDisplay(p, pt2d); ScalarType scalardiff = fabs(renderer->GetCurrentWorldPlaneGeometry()->SignedDistance(p)); //---------------------------------- // draw point if close to plane if (scalardiff < maxDiff) { float pointsize = 5; Point2D tmp; this->m_Context->GetPen()->SetColorF(0.0, 1.0, 0.0); this->m_Context->GetPen()->SetWidth(1); // a rectangle around the point with the selected color auto* rectPts = new float[8]; // a diamond around the point // begin from upper left corner and paint clockwise rectPts[0] = pt2d[0] - pointsize; rectPts[1] = pt2d[1] + pointsize; rectPts[2] = pt2d[0] + pointsize; rectPts[3] = pt2d[1] + pointsize; rectPts[4] = pt2d[0] + pointsize; rectPts[5] = pt2d[1] - pointsize; rectPts[6] = pt2d[0] - pointsize; rectPts[7] = pt2d[1] - pointsize; this->m_Context->DrawPolygon(rectPts, 4); } //------------------------------------ } } this->m_Context->GetDevice()->End(); } void mitk::ContourModelGLMapper2DBase::WriteTextWithAnnotation(TextAnnotationPointerType textAnnotation, const char *text, float rgb[3], Point2D /*pt2d*/, mitk::BaseRenderer * /*renderer*/) { textAnnotation->SetText(text); textAnnotation->SetColor(rgb); textAnnotation->SetOpacity(1); textAnnotation->SetFontSize(16); textAnnotation->SetBoolProperty("drawShadow", false); textAnnotation->SetVisibility(true); } diff --git a/Modules/ContourModel/Rendering/mitkContourModelMapper2D.cpp b/Modules/ContourModel/Rendering/mitkContourModelMapper2D.cpp index 3e2df04f9d..4fdf5d812d 100644 --- a/Modules/ContourModel/Rendering/mitkContourModelMapper2D.cpp +++ b/Modules/ContourModel/Rendering/mitkContourModelMapper2D.cpp @@ -1,372 +1,372 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include #include #include #include #include #include #include #include #include #include mitk::ContourModelMapper2D::ContourModelMapper2D() { } mitk::ContourModelMapper2D::~ContourModelMapper2D() { } const mitk::ContourModel *mitk::ContourModelMapper2D::GetInput(void) { // convient way to get the data from the dataNode return static_cast(GetDataNode()->GetData()); } vtkProp *mitk::ContourModelMapper2D::GetVtkProp(mitk::BaseRenderer *renderer) { // return the actor corresponding to the renderer return m_LSH.GetLocalStorage(renderer)->m_Actor; } void mitk::ContourModelMapper2D::GenerateDataForRenderer(mitk::BaseRenderer *renderer) { /*++ convert the contour to vtkPolyData and set it as input for our mapper ++*/ LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); auto *inputContour = static_cast(GetDataNode()->GetData()); - unsigned int timestep = renderer->GetTimeStep(); + const auto timestep = this->GetTimestep(); // if there's something to be rendered if (inputContour->GetNumberOfVertices(timestep) > 0) { localStorage->m_OutlinePolyData = this->CreateVtkPolyDataFromContour(inputContour, renderer); } this->ApplyContourProperties(renderer); localStorage->m_Mapper->SetInputData(localStorage->m_OutlinePolyData); } void mitk::ContourModelMapper2D::Update(mitk::BaseRenderer *renderer) { bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); if (!visible) return; // check if there is something to be rendered auto *data = static_cast(GetDataNode()->GetData()); if (data == nullptr) { return; } // Calculate time step of the input data for the specified renderer (integer value) this->CalculateTimeStep(renderer); LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); // Check if time step is valid const TimeGeometry *dataTimeGeometry = data->GetTimeGeometry(); if ((dataTimeGeometry == nullptr) || (dataTimeGeometry->CountTimeSteps() == 0) || (!dataTimeGeometry->IsValidTimeStep(renderer->GetTimeStep()))) { // clear the rendered polydata localStorage->m_Mapper->RemoveAllInputs(); // SetInput(vtkSmartPointer::New()); return; } const DataNode *node = this->GetDataNode(); data->UpdateOutputInformation(); // check if something important has changed and we need to rerender if ((localStorage->m_LastUpdateTime < node->GetMTime()) // was the node modified? || (localStorage->m_LastUpdateTime < data->GetPipelineMTime()) // Was the data modified? || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometryUpdateTime()) // was the geometry modified? || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometry()->GetMTime()) || (localStorage->m_LastUpdateTime < node->GetPropertyList()->GetMTime()) // was a property modified? || (localStorage->m_LastUpdateTime < node->GetPropertyList(renderer)->GetMTime())) { this->GenerateDataForRenderer(renderer); } // since we have checked that nothing important has changed, we can set // m_LastUpdateTime to the current time localStorage->m_LastUpdateTime.Modified(); } vtkSmartPointer mitk::ContourModelMapper2D::CreateVtkPolyDataFromContour(mitk::ContourModel *inputContour, mitk::BaseRenderer *renderer) { - unsigned int timestep = this->GetTimestep(); + const auto timestep = this->GetTimestep(); // Create a polydata to store everything in vtkSmartPointer resultingPolyData = vtkSmartPointer::New(); // check for the worldgeometry from the current render window const mitk::PlaneGeometry *currentWorldGeometry = renderer->GetCurrentWorldPlaneGeometry(); if (currentWorldGeometry) { // origin and normal of vtkPlane mitk::Point3D origin = currentWorldGeometry->GetOrigin(); mitk::Vector3D normal = currentWorldGeometry->GetNormal(); // the implicit function to slice through the polyData vtkSmartPointer plane = vtkSmartPointer::New(); plane->SetOrigin(origin[0], origin[1], origin[2]); plane->SetNormal(normal[0], normal[1], normal[2]); /* First of all convert the control points of the contourModel to vtk points * and add lines in between them */ // the points to draw vtkSmartPointer points = vtkSmartPointer::New(); // the lines to connect the points vtkSmartPointer lines = vtkSmartPointer::New(); // Create a polydata to store everything in vtkSmartPointer polyDataIn3D = vtkSmartPointer::New(); vtkSmartPointer appendPoly = vtkSmartPointer::New(); mitk::ContourModel::Pointer renderingContour = mitk::ContourModel::New(); renderingContour = inputContour; bool subdivision = false; this->GetDataNode()->GetBoolProperty("subdivision curve", subdivision, renderer); if (subdivision) { mitk::ContourModel::Pointer subdivContour = mitk::ContourModel::New(); mitk::ContourModelSubDivisionFilter::Pointer subdivFilter = mitk::ContourModelSubDivisionFilter::New(); subdivFilter->SetInput(inputContour); subdivFilter->Update(); subdivContour = subdivFilter->GetOutput(); if (subdivContour->GetNumberOfVertices() == 0) { subdivContour = inputContour; } renderingContour = subdivContour; } // iterate over all control points auto current = renderingContour->IteratorBegin(timestep); auto next = renderingContour->IteratorBegin(timestep); if (next != renderingContour->IteratorEnd(timestep)) { next++; auto end = renderingContour->IteratorEnd(timestep); while (next != end) { mitk::ContourModel::VertexType *currentControlPoint = *current; mitk::ContourModel::VertexType *nextControlPoint = *next; vtkIdType p1 = points->InsertNextPoint(currentControlPoint->Coordinates[0], currentControlPoint->Coordinates[1], currentControlPoint->Coordinates[2]); vtkIdType p2 = points->InsertNextPoint( nextControlPoint->Coordinates[0], nextControlPoint->Coordinates[1], nextControlPoint->Coordinates[2]); // add the line between both contorlPoints lines->InsertNextCell(2); lines->InsertCellPoint(p1); lines->InsertCellPoint(p2); if (currentControlPoint->IsControlPoint) { double coordinates[3]; coordinates[0] = currentControlPoint->Coordinates[0]; coordinates[1] = currentControlPoint->Coordinates[1]; coordinates[2] = currentControlPoint->Coordinates[2]; double distance = plane->DistanceToPlane(coordinates); if (distance < 0.1) { vtkSmartPointer sphere = vtkSmartPointer::New(); sphere->SetRadius(1.2); sphere->SetCenter(coordinates[0], coordinates[1], coordinates[2]); sphere->Update(); appendPoly->AddInputConnection(sphere->GetOutputPort()); } } current++; next++; } // end while (it!=end) // check if last control point is enabled to draw it if ((*current)->IsControlPoint) { double coordinates[3]; coordinates[0] = (*current)->Coordinates[0]; coordinates[1] = (*current)->Coordinates[1]; coordinates[2] = (*current)->Coordinates[2]; double distance = plane->DistanceToPlane(coordinates); if (distance < 0.1) { vtkSmartPointer sphere = vtkSmartPointer::New(); sphere->SetRadius(1.2); sphere->SetCenter(coordinates[0], coordinates[1], coordinates[2]); sphere->Update(); appendPoly->AddInputConnection(sphere->GetOutputPort()); } } /* If the contour is closed an additional line has to be created between the very first point * and the last point */ if (renderingContour->IsClosed(timestep)) { // add a line from the last to the first control point mitk::ContourModel::VertexType *firstControlPoint = *(renderingContour->IteratorBegin(timestep)); mitk::ContourModel::VertexType *lastControlPoint = *(--(renderingContour->IteratorEnd(timestep))); vtkIdType p2 = points->InsertNextPoint( lastControlPoint->Coordinates[0], lastControlPoint->Coordinates[1], lastControlPoint->Coordinates[2]); vtkIdType p1 = points->InsertNextPoint( firstControlPoint->Coordinates[0], firstControlPoint->Coordinates[1], firstControlPoint->Coordinates[2]); // add the line between both contorlPoints lines->InsertNextCell(2); lines->InsertCellPoint(p1); lines->InsertCellPoint(p2); } // end if(isClosed) // Add the points to the dataset polyDataIn3D->SetPoints(points); // Add the lines to the dataset polyDataIn3D->SetLines(lines); // cut through polyData bool useCuttingPlane = false; this->GetDataNode()->GetBoolProperty("use cutting plane", useCuttingPlane, renderer); if (useCuttingPlane) { // slice through the data to get a 2D representation of the (possible) 3D contour // needed because currently there is no outher solution if the contour is within the plane vtkSmartPointer tubeFilter = vtkSmartPointer::New(); tubeFilter->SetInputData(polyDataIn3D); tubeFilter->SetRadius(0.05); // cuts through vtkPolyData with a given implicit function. In our case a plane vtkSmartPointer cutter = vtkSmartPointer::New(); cutter->SetCutFunction(plane); cutter->SetInputConnection(tubeFilter->GetOutputPort()); // we want the scalars of the input - so turn off generating the scalars within vtkCutter cutter->GenerateCutScalarsOff(); cutter->Update(); // set to 2D representation of the contour resultingPolyData = cutter->GetOutput(); } // end if(project contour) else { // set to 3D polyData resultingPolyData = polyDataIn3D; } } // end if (it != end) appendPoly->AddInputData(resultingPolyData); appendPoly->Update(); // return contour with control points return appendPoly->GetOutput(); } else { // return empty polyData return resultingPolyData; } } void mitk::ContourModelMapper2D::ApplyContourProperties(mitk::BaseRenderer *renderer) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); float lineWidth(1.0); if (this->GetDataNode()->GetFloatProperty("width", lineWidth, renderer)) { localStorage->m_Actor->GetProperty()->SetLineWidth(lineWidth); } mitk::ColorProperty::Pointer colorprop = dynamic_cast(GetDataNode()->GetProperty("color", renderer)); if (colorprop) { // set the color of the contour double red = colorprop->GetColor().GetRed(); double green = colorprop->GetColor().GetGreen(); double blue = colorprop->GetColor().GetBlue(); localStorage->m_Actor->GetProperty()->SetColor(red, green, blue); } // make sure that directional lighting isn't used for our contour localStorage->m_Actor->GetProperty()->SetAmbient(1.0); localStorage->m_Actor->GetProperty()->SetDiffuse(0.0); localStorage->m_Actor->GetProperty()->SetSpecular(0.0); } /*+++++++++++++++++++ LocalStorage part +++++++++++++++++++++++++*/ mitk::ContourModelMapper2D::LocalStorage *mitk::ContourModelMapper2D::GetLocalStorage(mitk::BaseRenderer *renderer) { return m_LSH.GetLocalStorage(renderer); } mitk::ContourModelMapper2D::LocalStorage::LocalStorage() { m_Mapper = vtkSmartPointer::New(); m_Actor = vtkSmartPointer::New(); m_OutlinePolyData = vtkSmartPointer::New(); // set the mapper for the actor m_Actor->SetMapper(m_Mapper); } void mitk::ContourModelMapper2D::SetDefaultProperties(mitk::DataNode *node, mitk::BaseRenderer *renderer, bool overwrite) { node->AddProperty("color", ColorProperty::New(0.9, 1.0, 0.1), renderer, overwrite); node->AddProperty("width", mitk::FloatProperty::New(1.0), renderer, overwrite); node->AddProperty("use cutting plane", mitk::BoolProperty::New(true), renderer, overwrite); node->AddProperty("subdivision curve", mitk::BoolProperty::New(false), renderer, overwrite); Superclass::SetDefaultProperties(node, renderer, overwrite); } diff --git a/Modules/ContourModel/Rendering/mitkContourModelMapper3D.cpp b/Modules/ContourModel/Rendering/mitkContourModelMapper3D.cpp index 84e7bacc3b..03fa9641fc 100644 --- a/Modules/ContourModel/Rendering/mitkContourModelMapper3D.cpp +++ b/Modules/ContourModel/Rendering/mitkContourModelMapper3D.cpp @@ -1,233 +1,233 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include #include mitk::ContourModelMapper3D::ContourModelMapper3D() { } mitk::ContourModelMapper3D::~ContourModelMapper3D() { } const mitk::ContourModel *mitk::ContourModelMapper3D::GetInput(void) { // convient way to get the data from the dataNode return static_cast(GetDataNode()->GetData()); } vtkProp *mitk::ContourModelMapper3D::GetVtkProp(mitk::BaseRenderer *renderer) { // return the actor corresponding to the renderer return m_LSH.GetLocalStorage(renderer)->m_Actor; } void mitk::ContourModelMapper3D::GenerateDataForRenderer(mitk::BaseRenderer *renderer) { /* First convert the contourModel to vtkPolyData, then tube filter it and * set it input for our mapper */ LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); auto *inputContour = static_cast(GetDataNode()->GetData()); localStorage->m_OutlinePolyData = this->CreateVtkPolyDataFromContour(inputContour); this->ApplyContourProperties(renderer); // tube filter the polyData localStorage->m_TubeFilter->SetInputData(localStorage->m_OutlinePolyData); float lineWidth(1.0); if (this->GetDataNode()->GetFloatProperty("contour.3D.width", lineWidth, renderer)) { localStorage->m_TubeFilter->SetRadius(lineWidth); } else { localStorage->m_TubeFilter->SetRadius(0.5); } localStorage->m_TubeFilter->CappingOn(); localStorage->m_TubeFilter->SetNumberOfSides(10); localStorage->m_TubeFilter->Update(); localStorage->m_Mapper->SetInputConnection(localStorage->m_TubeFilter->GetOutputPort()); } void mitk::ContourModelMapper3D::Update(mitk::BaseRenderer *renderer) { bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); auto *data = static_cast(GetDataNode()->GetData()); if (data == nullptr) { return; } // Calculate time step of the input data for the specified renderer (integer value) this->CalculateTimeStep(renderer); LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); // Check if time step is valid const TimeGeometry *dataTimeGeometry = data->GetTimeGeometry(); if ((dataTimeGeometry == nullptr) || (dataTimeGeometry->CountTimeSteps() == 0) || (!dataTimeGeometry->IsValidTimePoint(renderer->GetTime())) || (this->GetTimestep() == -1)) { // clear the rendered polydata localStorage->m_Mapper->SetInputData(vtkSmartPointer::New()); return; } const DataNode *node = this->GetDataNode(); data->UpdateOutputInformation(); // check if something important has changed and we need to rerender if ((localStorage->m_LastUpdateTime < node->GetMTime()) // was the node modified? || (localStorage->m_LastUpdateTime < data->GetPipelineMTime()) // Was the data modified? || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometryUpdateTime()) // was the geometry modified? || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometry()->GetMTime()) || (localStorage->m_LastUpdateTime < node->GetPropertyList()->GetMTime()) // was a property modified? || (localStorage->m_LastUpdateTime < node->GetPropertyList(renderer)->GetMTime())) { this->GenerateDataForRenderer(renderer); } // since we have checked that nothing important has changed, we can set // m_LastUpdateTime to the current time localStorage->m_LastUpdateTime.Modified(); } vtkSmartPointer mitk::ContourModelMapper3D::CreateVtkPolyDataFromContour(mitk::ContourModel *inputContour) { - unsigned int timestep = this->GetTimestep(); + const auto timestep = this->GetTimestep(); // the points to draw vtkSmartPointer points = vtkSmartPointer::New(); // the lines to connect the points vtkSmartPointer lines = vtkSmartPointer::New(); // Create a polydata to store everything in vtkSmartPointer polyData = vtkSmartPointer::New(); // iterate over the control points auto current = inputContour->IteratorBegin(timestep); auto next = inputContour->IteratorBegin(timestep); if (next != inputContour->IteratorEnd(timestep)) { next++; auto end = inputContour->IteratorEnd(timestep); while (next != end) { mitk::ContourModel::VertexType *currentControlPoint = *current; mitk::ContourModel::VertexType *nextControlPoint = *next; if (!(currentControlPoint->Coordinates[0] == nextControlPoint->Coordinates[0] && currentControlPoint->Coordinates[1] == nextControlPoint->Coordinates[1] && currentControlPoint->Coordinates[2] == nextControlPoint->Coordinates[2])) { vtkIdType p1 = points->InsertNextPoint(currentControlPoint->Coordinates[0], currentControlPoint->Coordinates[1], currentControlPoint->Coordinates[2]); vtkIdType p2 = points->InsertNextPoint( nextControlPoint->Coordinates[0], nextControlPoint->Coordinates[1], nextControlPoint->Coordinates[2]); // add the line between both contorlPoints lines->InsertNextCell(2); lines->InsertCellPoint(p1); lines->InsertCellPoint(p2); } current++; next++; } if (inputContour->IsClosed(timestep)) { // If the contour is closed add a line from the last to the first control point mitk::ContourModel::VertexType *firstControlPoint = *(inputContour->IteratorBegin(timestep)); mitk::ContourModel::VertexType *lastControlPoint = *(--(inputContour->IteratorEnd(timestep))); if (lastControlPoint->Coordinates[0] != firstControlPoint->Coordinates[0] || lastControlPoint->Coordinates[1] != firstControlPoint->Coordinates[1] || lastControlPoint->Coordinates[2] != firstControlPoint->Coordinates[2]) { vtkIdType p2 = points->InsertNextPoint( lastControlPoint->Coordinates[0], lastControlPoint->Coordinates[1], lastControlPoint->Coordinates[2]); vtkIdType p1 = points->InsertNextPoint( firstControlPoint->Coordinates[0], firstControlPoint->Coordinates[1], firstControlPoint->Coordinates[2]); // add the line to the cellArray lines->InsertNextCell(2); lines->InsertCellPoint(p1); lines->InsertCellPoint(p2); } } // Add the points to the dataset polyData->SetPoints(points); // Add the lines to the dataset polyData->SetLines(lines); } return polyData; } void mitk::ContourModelMapper3D::ApplyContourProperties(mitk::BaseRenderer *renderer) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); mitk::ColorProperty::Pointer colorprop = dynamic_cast(GetDataNode()->GetProperty("contour.color", renderer)); if (colorprop) { // set the color of the contour double red = colorprop->GetColor().GetRed(); double green = colorprop->GetColor().GetGreen(); double blue = colorprop->GetColor().GetBlue(); localStorage->m_Actor->GetProperty()->SetColor(red, green, blue); } } /*+++++++++++++++++++ LocalStorage part +++++++++++++++++++++++++*/ mitk::ContourModelMapper3D::LocalStorage *mitk::ContourModelMapper3D::GetLocalStorage(mitk::BaseRenderer *renderer) { return m_LSH.GetLocalStorage(renderer); } mitk::ContourModelMapper3D::LocalStorage::LocalStorage() { m_Mapper = vtkSmartPointer::New(); m_Actor = vtkSmartPointer::New(); m_OutlinePolyData = vtkSmartPointer::New(); m_TubeFilter = vtkSmartPointer::New(); // set the mapper for the actor m_Actor->SetMapper(m_Mapper); } void mitk::ContourModelMapper3D::SetDefaultProperties(mitk::DataNode *node, mitk::BaseRenderer *renderer, bool overwrite) { node->AddProperty("color", ColorProperty::New(1.0, 0.0, 0.0), renderer, overwrite); node->AddProperty("contour.3D.width", mitk::FloatProperty::New(0.5), renderer, overwrite); Superclass::SetDefaultProperties(node, renderer, overwrite); } diff --git a/Modules/ContourModel/Rendering/mitkContourModelSetMapper3D.cpp b/Modules/ContourModel/Rendering/mitkContourModelSetMapper3D.cpp index 0cd56a24a1..cab6397f83 100644 --- a/Modules/ContourModel/Rendering/mitkContourModelSetMapper3D.cpp +++ b/Modules/ContourModel/Rendering/mitkContourModelSetMapper3D.cpp @@ -1,232 +1,232 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include "mitkSurface.h" #include #include #include #include mitk::ContourModelSetMapper3D::ContourModelSetMapper3D() { } mitk::ContourModelSetMapper3D::~ContourModelSetMapper3D() { } const mitk::ContourModelSet *mitk::ContourModelSetMapper3D::GetInput(void) { // convenient way to get the data from the dataNode return static_cast(GetDataNode()->GetData()); } vtkProp *mitk::ContourModelSetMapper3D::GetVtkProp(mitk::BaseRenderer *renderer) { // return the actor corresponding to the renderer return m_LSH.GetLocalStorage(renderer)->m_Assembly; } void mitk::ContourModelSetMapper3D::GenerateDataForRenderer(mitk::BaseRenderer *renderer) { /* First convert the contourModel to vtkPolyData, then tube filter it and * set it input for our mapper */ LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); auto *contourModelSet = dynamic_cast(this->GetDataNode()->GetData()); if (contourModelSet != nullptr) { vtkSmartPointer points = vtkSmartPointer::New(); vtkSmartPointer cells = vtkSmartPointer::New(); vtkIdType baseIndex = 0; auto it = contourModelSet->Begin(); auto end = contourModelSet->End(); while (it != end) { ContourModel *contourModel = it->GetPointer(); auto vertIt = contourModel->Begin(); auto vertEnd = contourModel->End(); while (vertIt != vertEnd) { points->InsertNextPoint((*vertIt)->Coordinates[0], (*vertIt)->Coordinates[1], (*vertIt)->Coordinates[2]); ++vertIt; } vtkSmartPointer line = vtkSmartPointer::New(); vtkIdList *pointIds = line->GetPointIds(); vtkIdType numPoints = contourModel->GetNumberOfVertices(); pointIds->SetNumberOfIds(numPoints + 1); for (vtkIdType i = 0; i < numPoints; ++i) pointIds->SetId(i, baseIndex + i); pointIds->SetId(numPoints, baseIndex); cells->InsertNextCell(line); baseIndex += numPoints; ++it; } vtkSmartPointer polyData = vtkSmartPointer::New(); polyData->SetPoints(points); polyData->SetLines(cells); vtkSmartPointer mapper = vtkSmartPointer::New(); vtkSmartPointer actor = vtkSmartPointer::New(); actor->SetMapper(mapper); mapper->SetInputData(polyData); localStorage->m_Assembly->AddPart(actor); } this->ApplyContourProperties(renderer); this->ApplyContourModelSetProperties(renderer); } void mitk::ContourModelSetMapper3D::Update(mitk::BaseRenderer *renderer) { bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); auto *data = static_cast(GetDataNode()->GetData()); if (data == nullptr) { return; } // Calculate time step of the input data for the specified renderer (integer value) this->CalculateTimeStep(renderer); LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); if (this->GetTimestep() == -1) { return; } const DataNode *node = this->GetDataNode(); data->UpdateOutputInformation(); // check if something important has changed and we need to rerender if ((localStorage->m_LastUpdateTime < node->GetMTime()) // was the node modified? || (localStorage->m_LastUpdateTime < data->GetPipelineMTime()) // Was the data modified? || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometryUpdateTime()) // was the geometry modified? || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometry()->GetMTime()) || (localStorage->m_LastUpdateTime < node->GetPropertyList()->GetMTime()) // was a property modified? || (localStorage->m_LastUpdateTime < node->GetPropertyList(renderer)->GetMTime())) { this->GenerateDataForRenderer(renderer); } // since we have checked that nothing important has changed, we can set // m_LastUpdateTime to the current time localStorage->m_LastUpdateTime.Modified(); } vtkSmartPointer mitk::ContourModelSetMapper3D::CreateVtkPolyDataFromContour( mitk::ContourModel *inputContour, mitk::BaseRenderer *renderer) { - unsigned int timestep = this->GetTimestep(); + const auto timestep = this->GetTimestep(); LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); localStorage->m_contourToPolyData->SetInput(inputContour); localStorage->m_contourToPolyData->Update(); vtkSmartPointer polyData = vtkSmartPointer::New(); polyData = localStorage->m_contourToPolyData->GetOutput()->GetVtkPolyData(timestep); return polyData; } void mitk::ContourModelSetMapper3D::ApplyContourModelSetProperties(BaseRenderer *renderer) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); DataNode *dataNode = this->GetDataNode(); if (dataNode != nullptr) { float lineWidth = 1; dataNode->GetFloatProperty("contour.3D.width", lineWidth, renderer); vtkSmartPointer collection = vtkSmartPointer::New(); localStorage->m_Assembly->GetActors(collection); collection->InitTraversal(); for (vtkIdType i = 0; i < collection->GetNumberOfItems(); i++) { vtkActor::SafeDownCast(collection->GetNextProp())->GetProperty()->SetLineWidth(lineWidth); } } } void mitk::ContourModelSetMapper3D::ApplyContourProperties(mitk::BaseRenderer *renderer) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); mitk::ColorProperty::Pointer colorprop = dynamic_cast(GetDataNode()->GetProperty("contour.color", renderer)); if (colorprop) { // set the color of the contour double red = colorprop->GetColor().GetRed(); double green = colorprop->GetColor().GetGreen(); double blue = colorprop->GetColor().GetBlue(); vtkSmartPointer collection = vtkSmartPointer::New(); localStorage->m_Assembly->GetActors(collection); collection->InitTraversal(); for (vtkIdType i = 0; i < collection->GetNumberOfItems(); i++) { vtkActor::SafeDownCast(collection->GetNextProp())->GetProperty()->SetColor(red, green, blue); } } } /*+++++++++++++++++++ LocalStorage part +++++++++++++++++++++++++*/ mitk::ContourModelSetMapper3D::LocalStorage *mitk::ContourModelSetMapper3D::GetLocalStorage( mitk::BaseRenderer *renderer) { return m_LSH.GetLocalStorage(renderer); } mitk::ContourModelSetMapper3D::LocalStorage::LocalStorage() { m_Assembly = vtkSmartPointer::New(); m_contourToPolyData = mitk::ContourModelToSurfaceFilter::New(); } void mitk::ContourModelSetMapper3D::SetDefaultProperties(mitk::DataNode *node, mitk::BaseRenderer *renderer, bool overwrite) { node->AddProperty("color", ColorProperty::New(1.0, 0.0, 0.0), renderer, overwrite); node->AddProperty("contour.3D.width", mitk::FloatProperty::New(0.5), renderer, overwrite); Superclass::SetDefaultProperties(node, renderer, overwrite); } diff --git a/Modules/ContourModel/Testing/CMakeLists.txt b/Modules/ContourModel/Testing/CMakeLists.txt index 263e573340..153cd81e2e 100644 --- a/Modules/ContourModel/Testing/CMakeLists.txt +++ b/Modules/ContourModel/Testing/CMakeLists.txt @@ -1,2 +1 @@ MITK_CREATE_MODULE_TESTS() -#mitkAddCustomModuleTest(mitkSegmentationInterpolationTest mitkSegmentationInterpolationTest ${MITK_DATA_DIR}/interpolation_test_manual.nrrd ${MITK_DATA_DIR}/interpolation_test_result.nrrd) diff --git a/Modules/ContourModel/Testing/files.cmake b/Modules/ContourModel/Testing/files.cmake index 8d8021a143..804bb86385 100644 --- a/Modules/ContourModel/Testing/files.cmake +++ b/Modules/ContourModel/Testing/files.cmake @@ -1,13 +1,14 @@ set(MODULE_TESTS + mitkContourElementTest.cpp mitkContourModelTest.cpp mitkContourModelIOTest.cpp mitkContourModelSetTest.cpp ) set(MODULE_IMAGE_TESTS ) set(MODULE_CUSTOM_TESTS ) set(MODULE_TESTIMAGE ) diff --git a/Modules/ContourModel/Testing/mitkContourElementTest.cpp b/Modules/ContourModel/Testing/mitkContourElementTest.cpp new file mode 100644 index 0000000000..b75a434883 --- /dev/null +++ b/Modules/ContourModel/Testing/mitkContourElementTest.cpp @@ -0,0 +1,349 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +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 "mitkContourElement.h" + +#include "mitkTestFixture.h" +#include "mitkTestingMacros.h" +#include + +class mitkContourElementTestSuite : public mitk::TestFixture +{ + CPPUNIT_TEST_SUITE(mitkContourElementTestSuite); + // Test the append method + MITK_TEST(Iterator); + MITK_TEST(AddVertex); + MITK_TEST(AddVertexAtFront); + MITK_TEST(InsertVertexAtIndex); + MITK_TEST(GetSetVertexAt); + MITK_TEST(OpenAndClose); + MITK_TEST(OtherGetters); + MITK_TEST(Concatenate); + MITK_TEST(RemoveVertex); + MITK_TEST(Clear); + MITK_TEST(GetControlVertices); + MITK_TEST(RedistributeControlVertices); + MITK_TEST(Others); + + CPPUNIT_TEST_SUITE_END(); + +private: + mitk::ContourElement::Pointer m_Contour1to4; + mitk::ContourElement::Pointer m_Contour5to6; + mitk::ContourElement::Pointer m_Contour_empty; + mitk::Point3D m_p1; + mitk::Point3D m_p2; + mitk::Point3D m_p3; + mitk::Point3D m_p4; + mitk::Point3D m_p5; + mitk::Point3D m_p6; + mitk::Point3D m_p7; + +public: + static mitk::Point3D GeneratePoint(double val) + { + return mitk::Point3D(val); + } + + void setUp() override + { + m_p1 = GeneratePoint(1); + m_p2 = GeneratePoint(2); + m_p3 = GeneratePoint(3); + m_p4 = GeneratePoint(4); + m_p5 = GeneratePoint(5); + m_p6 = GeneratePoint(6); + m_p7 = GeneratePoint(7); + + m_Contour1to4 = mitk::ContourElement::New(); + m_Contour5to6 = mitk::ContourElement::New(); + m_Contour_empty = mitk::ContourElement::New(); + + m_Contour1to4->AddVertex(m_p1, true); + m_Contour1to4->AddVertex(m_p2, false); + m_Contour1to4->AddVertex(m_p3, true); + m_Contour1to4->AddVertex(m_p4, false); + + m_Contour5to6->AddVertex(m_p5, false); + m_Contour5to6->AddVertex(m_p6, true); + + } + + void tearDown() override {} + + void Iterator() + { + mitk::ContourElement::ConstPointer constcontour = m_Contour5to6.GetPointer(); + CPPUNIT_ASSERT_MESSAGE("Begin does not point to correct element", m_Contour1to4->IteratorBegin().operator*()->Coordinates == m_p1); + CPPUNIT_ASSERT_MESSAGE("Begin does not point to correct element", m_Contour1to4->ConstIteratorBegin().operator*()->Coordinates == m_p1); + CPPUNIT_ASSERT_MESSAGE("Begin does not point to correct element", m_Contour5to6->begin().operator*()->Coordinates == m_p5); + CPPUNIT_ASSERT_MESSAGE("Begin does not point to correct element", constcontour->begin().operator*()->Coordinates == m_p5); + + CPPUNIT_ASSERT_MESSAGE("End does not point to correct element", m_Contour_empty->ConstIteratorBegin() == m_Contour_empty->ConstIteratorEnd()); + CPPUNIT_ASSERT_MESSAGE("End does not point to correct element", m_Contour_empty->IteratorBegin() == m_Contour_empty->IteratorEnd()); + CPPUNIT_ASSERT_MESSAGE("End does not point to correct element", m_Contour_empty->begin() == m_Contour_empty->end()); + } + + void AddVertex() + { + m_Contour_empty->AddVertex(m_p1, false); + CPPUNIT_ASSERT(m_Contour_empty->GetVertexAt(0)->Coordinates == m_p1); + CPPUNIT_ASSERT(m_Contour_empty->GetVertexAt(0)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour_empty->GetSize() == 1); + + m_Contour_empty->AddVertex(m_p7, true); + CPPUNIT_ASSERT(m_Contour_empty->GetVertexAt(0)->Coordinates == m_p1); + CPPUNIT_ASSERT(m_Contour_empty->GetVertexAt(0)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour_empty->GetVertexAt(1)->Coordinates == m_p7); + CPPUNIT_ASSERT(m_Contour_empty->GetVertexAt(1)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour_empty->GetSize() == 2); + } + + void AddVertexAtFront() + { + m_Contour_empty->AddVertexAtFront(m_p1, false); + CPPUNIT_ASSERT(m_Contour_empty->GetVertexAt(0)->Coordinates == m_p1); + CPPUNIT_ASSERT(m_Contour_empty->GetVertexAt(0)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour_empty->GetSize() == 1); + + m_Contour_empty->AddVertexAtFront(m_p7, true); + CPPUNIT_ASSERT(m_Contour_empty->GetVertexAt(1)->Coordinates == m_p1); + CPPUNIT_ASSERT(m_Contour_empty->GetVertexAt(1)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour_empty->GetVertexAt(0)->Coordinates == m_p7); + CPPUNIT_ASSERT(m_Contour_empty->GetVertexAt(0)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour_empty->GetSize() == 2); + } + + void InsertVertexAtIndex() + { + mitk::Point3D outOfBountPoint; + m_Contour1to4->InsertVertexAtIndex(m_p5, false, 0); + m_Contour1to4->InsertVertexAtIndex(m_p7, true, 2); + m_Contour1to4->InsertVertexAtIndex(outOfBountPoint, true, 6); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(0)->Coordinates == m_p5); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(0)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(1)->Coordinates == m_p1); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(1)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(2)->Coordinates == m_p7); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(2)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(3)->Coordinates == m_p2); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(3)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetSize() == 6); + } + + void GetSetVertexAt() + { + mitk::ContourElement::ConstPointer constcontour = m_Contour1to4.GetPointer(); + + auto v0 = m_Contour1to4->GetVertexAt(0); + auto v1 = m_Contour1to4->GetVertexAt(1); + + CPPUNIT_ASSERT(v0->Coordinates == m_p1); + CPPUNIT_ASSERT(v0->IsControlPoint == true); + CPPUNIT_ASSERT(v1->Coordinates == m_p2); + CPPUNIT_ASSERT(v1->IsControlPoint == false); + CPPUNIT_ASSERT(constcontour->GetVertexAt(0)->Coordinates == m_p1); + CPPUNIT_ASSERT(constcontour->GetVertexAt(0)->IsControlPoint == true); + CPPUNIT_ASSERT(constcontour->GetVertexAt(1)->Coordinates == m_p2); + CPPUNIT_ASSERT(constcontour->GetVertexAt(1)->IsControlPoint == false); + + m_Contour1to4->SetVertexAt(0, m_p7); + CPPUNIT_ASSERT(v0->Coordinates == m_p7); + CPPUNIT_ASSERT(v0->IsControlPoint == true); + + m_Contour1to4->SetVertexAt(1, m_Contour5to6->GetVertexAt(1)); + CPPUNIT_ASSERT(v1->Coordinates == m_Contour5to6->GetVertexAt(1)->Coordinates); + CPPUNIT_ASSERT(v1->IsControlPoint == m_Contour5to6->GetVertexAt(1)->IsControlPoint); + CPPUNIT_ASSERT(v1 != m_Contour5to6->GetVertexAt(1)); + + mitk::Point3D search = GeneratePoint(6.05); + + auto finding = m_Contour1to4->GetVertexAt(search, 0.); + CPPUNIT_ASSERT(nullptr == finding); + + finding = m_Contour1to4->GetVertexAt(search, 0.1); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(1) == finding); + } + + void OpenAndClose() + { + CPPUNIT_ASSERT(!m_Contour1to4->IsClosed()); + CPPUNIT_ASSERT(!m_Contour_empty->IsClosed()); + m_Contour1to4->Close(); + m_Contour_empty->SetClosed(true); + CPPUNIT_ASSERT(m_Contour1to4->IsClosed()); + CPPUNIT_ASSERT(m_Contour_empty->IsClosed()); + m_Contour1to4->Open(); + m_Contour_empty->SetClosed(false); + CPPUNIT_ASSERT(!m_Contour1to4->IsClosed()); + CPPUNIT_ASSERT(!m_Contour_empty->IsClosed()); + } + + void OtherGetters() + { + CPPUNIT_ASSERT(m_Contour1to4->GetIndex(m_Contour1to4->GetVertexAt(0)) == 0); + CPPUNIT_ASSERT(m_Contour1to4->GetIndex(m_Contour1to4->GetVertexAt(1)) == 1); + CPPUNIT_ASSERT(m_Contour1to4->GetIndex(m_Contour1to4->GetVertexAt(3)) == 3); + CPPUNIT_ASSERT(m_Contour1to4->GetIndex(m_Contour5to6->GetVertexAt(0)) == mitk::ContourElement::NPOS); + } + + void Concatenate() + { + m_Contour5to6->Concatenate(m_Contour1to4, true); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(0)->Coordinates == m_p5); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(0)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(1)->Coordinates == m_p6); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(1)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(2)->Coordinates == m_p1); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(2)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(3)->Coordinates == m_p2); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(3)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(4)->Coordinates == m_p3); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(4)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(5)->Coordinates == m_p4); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(5)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour5to6->GetSize() == 6); + + m_Contour_empty->AddVertex(m_p1, false); + m_Contour5to6->Concatenate(m_Contour_empty, true); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(0)->Coordinates == m_p5); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(0)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(1)->Coordinates == m_p6); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(1)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(2)->Coordinates == m_p1); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(2)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(3)->Coordinates == m_p2); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(3)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(4)->Coordinates == m_p3); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(4)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(5)->Coordinates == m_p4); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(5)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour5to6->GetSize() == 6); + + m_Contour5to6->Concatenate(m_Contour_empty, false); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(0)->Coordinates == m_p5); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(0)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(1)->Coordinates == m_p6); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(1)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(2)->Coordinates == m_p1); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(2)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(3)->Coordinates == m_p2); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(3)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(4)->Coordinates == m_p3); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(4)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(5)->Coordinates == m_p4); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(5)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(6)->Coordinates == m_p1); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(6)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour5to6->GetSize() == 7); + } + + void RemoveVertex() + { + CPPUNIT_ASSERT(m_Contour1to4->RemoveVertex(m_Contour1to4->GetVertexAt(0))); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(0)->Coordinates == m_p2); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(0)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetSize() == 3); + CPPUNIT_ASSERT(!m_Contour1to4->RemoveVertex(m_Contour5to6->GetVertexAt(0))); + CPPUNIT_ASSERT(m_Contour1to4->GetSize() == 3); + + CPPUNIT_ASSERT(m_Contour1to4->RemoveVertexAt(1)); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(0)->Coordinates == m_p2); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(0)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(1)->Coordinates == m_p4); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(1)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetSize() == 2); + + CPPUNIT_ASSERT(!m_Contour1to4->RemoveVertexAt(2)); + CPPUNIT_ASSERT(m_Contour1to4->GetSize() == 2); + + mitk::Point3D search = GeneratePoint(6.05); + + CPPUNIT_ASSERT(!m_Contour1to4->RemoveVertexAt(search,0.1)); + CPPUNIT_ASSERT(m_Contour1to4->GetSize() == 2); + + CPPUNIT_ASSERT(m_Contour5to6->RemoveVertexAt(search, 0.1)); + CPPUNIT_ASSERT(m_Contour5to6->GetSize() == 1); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(0)->Coordinates == m_p5); + CPPUNIT_ASSERT(m_Contour5to6->GetVertexAt(0)->IsControlPoint == false); + } + + void Clear() + { + m_Contour1to4->Clear(); + CPPUNIT_ASSERT(m_Contour1to4->IsEmpty()); + m_Contour_empty->Clear(); + CPPUNIT_ASSERT(m_Contour_empty->IsEmpty()); + } + + void GetControlVertices() + { + auto controlVs = m_Contour1to4->GetControlVertices(); + CPPUNIT_ASSERT(controlVs.size() == 2); + CPPUNIT_ASSERT(controlVs[0] == m_Contour1to4->GetVertexAt(0)); + CPPUNIT_ASSERT(controlVs[1] == m_Contour1to4->GetVertexAt(2)); + + controlVs = m_Contour_empty->GetControlVertices(); + CPPUNIT_ASSERT(controlVs.empty()); + } + + void RedistributeControlVertices() + { + //just adding more nodes to better check the redistribution + m_Contour1to4->Concatenate(m_Contour1to4, false); + m_Contour1to4->Concatenate(m_Contour1to4, false); + + m_Contour1to4->RedistributeControlVertices(nullptr, 3); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(0)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(1)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(2)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(3)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(4)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(5)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(6)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(7)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(8)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(9)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(10)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(11)->IsControlPoint == false); + + m_Contour1to4->RedistributeControlVertices(m_Contour1to4->GetVertexAt(4), 4); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(0)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(1)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(2)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(3)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(4)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(5)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(6)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(7)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(8)->IsControlPoint == true); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(9)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(10)->IsControlPoint == false); + CPPUNIT_ASSERT(m_Contour1to4->GetVertexAt(11)->IsControlPoint == false); + } + + void Others() + { + CPPUNIT_ASSERT(m_Contour1to4->GetSize() == 4); + CPPUNIT_ASSERT(m_Contour_empty->GetSize() == 0); + CPPUNIT_ASSERT(!m_Contour1to4->IsEmpty()); + CPPUNIT_ASSERT(m_Contour_empty->IsEmpty()); + + mitk::ContourElement::Pointer copyConstructed = m_Contour5to6->Clone(); + CPPUNIT_ASSERT(*(m_Contour5to6->GetVertexAt(0)) == *(copyConstructed->GetVertexAt(0))); + CPPUNIT_ASSERT(*(m_Contour5to6->GetVertexAt(1)) == *(copyConstructed->GetVertexAt(1))); + CPPUNIT_ASSERT(m_Contour5to6->GetSize() == copyConstructed->GetSize()); + } + +}; + +MITK_TEST_SUITE_REGISTRATION(mitkContourElement) diff --git a/Modules/ContourModel/Testing/mitkContourModelTest.cpp b/Modules/ContourModel/Testing/mitkContourModelTest.cpp index 7f2e643776..9464bdcb83 100644 --- a/Modules/ContourModel/Testing/mitkContourModelTest.cpp +++ b/Modules/ContourModel/Testing/mitkContourModelTest.cpp @@ -1,419 +1,483 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include // Add a vertex to the contour and see if size changed static void TestAddVertex() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); - MITK_TEST_CONDITION(contour->GetNumberOfVertices() > 0, "Add a Vertex, size increased"); + MITK_TEST_CONDITION(contour->GetNumberOfVertices() == 1, "Add a Vertex, size increased"); + MITK_TEST_CONDITION(contour->GetVertexAt(0)->Coordinates == p, "Added vertex has the correct value."); + + mitk::Point3D outOfTimeBoundPoint; + outOfTimeBoundPoint[0] = outOfTimeBoundPoint[1] = outOfTimeBoundPoint[2] = 1; + + contour->AddVertex(outOfTimeBoundPoint, mitk::TimeStepType(1)); + + MITK_TEST_CONDITION(contour->GetTimeSteps() == 1, "Add a vertex to an unsupported time step has not changed geometry."); + MITK_TEST_CONDITION(contour->IsEmptyTimeStep(1), "Add a vertex to an unsupported time step has not added an contour element."); + MITK_TEST_CONDITION(contour->GetNumberOfVertices(1) == -1, "Add a vertex to an unsupported time step has not added an contour element."); + + contour->Expand(3); + + mitk::Point3D p2; + p2[0] = p2[1] = p2[2] = 2; + mitk::Point3D p3; + p3[0] = p3[1] = p3[2] = 3; + + contour->AddVertex(p2, mitk::TimeStepType(1)); + contour->AddVertex(mitk::ContourModel::VertexType(p3), mitk::TimeStepType(1)); + + MITK_TEST_CONDITION(!contour->IsEmptyTimeStep(1), "Add a vertex to an unsupported time step has not added an contour element."); + MITK_TEST_CONDITION(contour->GetVertexAt(0,1)->Coordinates == p2, "Add a vertex to the 2nd time step (as Point)."); + MITK_TEST_CONDITION(contour->GetVertexAt(1,1)->Coordinates == p3, "Add a vertex to the 2nd time step via overload (as vertex type)."); + MITK_TEST_CONDITION(contour->GetNumberOfVertices(1) == 2, "Add a vertex to an unsupported time step has not added an contour element."); } // Select a vertex by index. successful if the selected vertex member of the contour is no longer set to null static void TestSelectVertexAtIndex() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); contour->SelectVertexAt(0); MITK_TEST_CONDITION(contour->GetSelectedVertex() != nullptr, "Vertex was selected at index"); } // Select a vertex by worldposition. successful if the selected vertex member of the contour is no longer set to null static void TestSelectVertexAtWorldposition() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); // same point is used here so the epsilon can be chosen very small contour->SelectVertexAt(p, 0.01); MITK_TEST_CONDITION(contour->GetSelectedVertex() != nullptr, "Vertex was selected at position"); } // Move a vertex by a translation vector static void TestMoveSelectedVertex() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); // Same point is used here so the epsilon can be chosen very small contour->SelectVertexAt(p, 0.01); mitk::Vector3D v; v[0] = 1; v[1] = 3; v[2] = -1; contour->ShiftSelectedVertex(v); const mitk::ContourModel::VertexType *vertex = contour->GetSelectedVertex(); bool correctlyMoved = false; correctlyMoved = (vertex->Coordinates)[0] == (v[0]) && (vertex->Coordinates)[1] == (v[1]) && (vertex->Coordinates)[2] == (v[2]); MITK_TEST_CONDITION(correctlyMoved, "Vertex has been moved"); } // Test to move the whole contour /* static void TestMoveContour() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); mitk::Point3D p2; p2[0] = p2[1] = p2[2] = 0; contour->AddVertex(p2); mitk::Vector3D v; v[0] = 1; v[1] = 3; v[2] = -1; contour->ShiftContour(v); mitk::ContourModel::VertexIterator it = contour->IteratorBegin(); mitk::ContourModel::VertexIterator end = contour->IteratorEnd(); bool correctlyMoved = false; while(it != end) { correctlyMoved &= (*it)->Coordinates[0] == (v[0]) && (*it)->Coordinates[1] == (v[1]) && (*it)->Coordinates[2] == (v[2]); } MITK_TEST_CONDITION(correctlyMoved, "Contour has been moved"); } */ // Remove a vertex by index static void TestRemoveVertexAtIndex() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); contour->RemoveVertexAt(0); MITK_TEST_CONDITION(contour->GetNumberOfVertices() == 0, "removed vertex"); } // Remove a vertex by position static void TestRemoveVertexAtWorldPosition() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); contour->RemoveVertexAt(p, 0.01); MITK_TEST_CONDITION(contour->GetNumberOfVertices() == 0, "removed vertex"); } // Check closeable contour static void TestIsclosed() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); mitk::Point3D p2; p2[0] = p2[1] = p2[2] = 1; contour->AddVertex(p2); contour->Close(); MITK_TEST_CONDITION(contour->IsClosed(), "closed contour"); // no vertices should be added to a closed contour int oldNumberOfVertices = contour->GetNumberOfVertices(); mitk::Point3D p3; p3[0] = p3[1] = p3[2] = 4; contour->AddVertex(p3); int newNumberOfVertices = contour->GetNumberOfVertices(); MITK_TEST_CONDITION(oldNumberOfVertices != newNumberOfVertices, "vertices added to closed contour"); } // Test concatenating two contours static void TestConcatenate() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); mitk::Point3D p2; p2[0] = p2[1] = p2[2] = 1; contour->AddVertex(p2); mitk::ContourModel::Pointer contour2 = mitk::ContourModel::New(); mitk::Point3D p3; p3[0] = -2; p3[1] = 10; p3[2] = 0; contour2->AddVertex(p3); mitk::Point3D p4; p4[0] = -3; p4[1] = 6; p4[2] = -5; contour2->AddVertex(p4); contour->Concatenate(contour2); MITK_TEST_CONDITION(contour->GetNumberOfVertices() == 4, "two contours were concatenated"); } // Try to select a vertex at position (within a epsilon of course) where no vertex is. // So the selected verted member should be null. static void TestSelectVertexAtWrongPosition() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); MITK_TEST_CONDITION_REQUIRED(contour->GetSelectedVertex() == nullptr, "selected vertex is nullptr"); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); mitk::Point3D p2; p2[0] = p2[1] = p2[2] = 2; contour->SelectVertexAt(p2, 0.1); MITK_TEST_CONDITION(contour->GetSelectedVertex() == nullptr, "Vertex was not selected"); } static void TestInsertVertex() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); mitk::Point3D p2; p2[0] = p2[1] = p2[2] = 1; contour->AddVertex(p2); mitk::Point3D pointToInsert; pointToInsert[0] = pointToInsert[1] = pointToInsert[2] = 10; contour->InsertVertexAtIndex(pointToInsert, 1); MITK_TEST_CONDITION(contour->GetNumberOfVertices() == 3, "test insert vertex"); MITK_TEST_CONDITION(contour->GetVertexAt(1)->Coordinates == pointToInsert, "compare inserted vertex"); + + mitk::Point3D outOfTimeBoundPoint; + outOfTimeBoundPoint[0] = outOfTimeBoundPoint[1] = outOfTimeBoundPoint[2] = 1; + + contour->InsertVertexAtIndex(outOfTimeBoundPoint, 4, false, mitk::TimeStepType(1)); + + MITK_TEST_CONDITION(contour->GetTimeSteps() == 1, "Insert a vertex to an unsupported time step has not changed geometry."); + MITK_TEST_CONDITION(contour->IsEmptyTimeStep(1), "Insert a vertex to an unsupported time step has not added an contour element."); + MITK_TEST_CONDITION(contour->GetNumberOfVertices(1) == -1, "Insert a vertex to an unsupported time step has not added an contour element."); } // try to access an invalid timestep static void TestInvalidTimeStep() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); mitk::Point3D p2; p2[0] = p2[1] = p2[2] = 1; contour->AddVertex(p2); - int invalidTimeStep = 42; + mitk::TimeStepType invalidTimeStep = 42; MITK_TEST_CONDITION_REQUIRED(contour->IsEmptyTimeStep(invalidTimeStep), "invalid timestep required"); MITK_TEST_FOR_EXCEPTION(std::exception, contour->IteratorBegin(-1)); contour->Close(invalidTimeStep); MITK_TEST_CONDITION(contour->IsClosed() == false, "test close for timestep 0"); MITK_TEST_CONDITION(contour->IsClosed(invalidTimeStep) == false, "test close at invalid timestep"); contour->SetClosed(true, invalidTimeStep); MITK_TEST_CONDITION(contour->GetNumberOfVertices(invalidTimeStep) == -1, "test number of vertices at invalid timestep"); contour->AddVertex(p2, invalidTimeStep); MITK_TEST_CONDITION(contour->GetNumberOfVertices(invalidTimeStep) == -1, "test add vertex at invalid timestep"); contour->InsertVertexAtIndex(p2, 0, false, invalidTimeStep); MITK_TEST_CONDITION(contour->GetNumberOfVertices(invalidTimeStep) == -1, "test insert vertex at invalid timestep"); MITK_TEST_CONDITION(contour->SelectVertexAt(0, invalidTimeStep) == false, "test select vertex at invalid timestep"); MITK_TEST_CONDITION(contour->RemoveVertexAt(0, invalidTimeStep) == false, "test remove vertex at invalid timestep"); + + MITK_TEST_CONDITION(contour->GetVertexAt(0, 5) == nullptr, "Access a vertex on an invalid time step."); + MITK_TEST_CONDITION(contour->GetVertexAt(10, 0) == nullptr, "Access a vertex on an invalid index."); } static void TestEmptyContour() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); MITK_TEST_CONDITION(contour->IteratorBegin() == contour->IteratorEnd(), "test iterator of emtpy contour"); MITK_TEST_CONDITION(contour->GetNumberOfVertices() == 0, "test numberof vertices of empty contour"); } static void TestSetVertices() { mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); mitk::Point3D p; p[0] = p[1] = p[2] = 0; contour->AddVertex(p); mitk::Point3D newCoordinates; newCoordinates[0] = newCoordinates[1] = newCoordinates[2] = 1; contour->SetVertexAt(0, newCoordinates); MITK_TEST_CONDITION(mitk::Equal(contour->GetVertexAt(0)->Coordinates, newCoordinates), "set coordinates"); mitk::ContourModel::Pointer contour2 = mitk::ContourModel::New(); mitk::Point3D p3; p3[0] = -2; p3[1] = 10; p3[2] = 0; contour2->AddVertex(p3); mitk::Point3D p4; p4[0] = -3; p4[1] = 6; p4[2] = -5; contour2->AddVertex(p4); contour->AddVertex(p); - - contour->SetVertexAt(1, contour2->GetVertexAt(1)); + contour->SetVertexAt(1, contour2->GetVertexAt(1), 0); MITK_TEST_CONDITION( mitk::Equal(contour->GetVertexAt(1)->Coordinates, contour2->GetVertexAt(1)->Coordinates), "Use setter and getter combination"); } static void TestContourModelAPI() { mitk::ContourModel::Pointer contour1 = mitk::ContourModel::New(); mitk::Point3D p1; p1[0] = -2; p1[1] = 10; p1[2] = 0; contour1->AddVertex(p1); // adding vertices should always copy the content and not store pointers or references. MITK_TEST_CONDITION(&p1 != &(contour1->GetVertexAt(0)->Coordinates), "copied point"); mitk::Point3D p2; p2[0] = -3; p2[1] = 6; p2[2] = -5; contour1->AddVertex(p2); // test use of setter and getter with const and non-const pointers const mitk::ContourModel::VertexType *vertex = contour1->GetVertexAt(1); MITK_TEST_CONDITION(contour1->GetIndex(vertex) == 1, "Get index"); auto *nonConstVertex = const_cast(vertex); MITK_TEST_CONDITION(contour1->GetIndex(nonConstVertex) == 1, "Get index non-const"); mitk::ContourModel::Pointer contour2 = mitk::ContourModel::New(); - contour2->AddVertex(contour1->GetVertexAt(0)); + contour2->AddVertex(*(contour1->GetVertexAt(0))); MITK_TEST_CONDITION(contour2->GetNumberOfVertices() == 1, "Add call with another contour"); } +static void TestClear() +{ + mitk::ContourModel::Pointer contour = mitk::ContourModel::New(); + contour->Expand(3); + + contour->Expand(3); + mitk::Point3D p; + p[0] = p[1] = p[2] = 0; + contour->AddVertex(p); + p[0] = p[1] = p[2] = 1; + contour->AddVertex(p, mitk::TimeStepType(1)); + p[0] = p[1] = p[2] = 2; + contour->AddVertex(p, mitk::TimeStepType(2)); + + contour->Clear(1); + + MITK_TEST_CONDITION(contour->GetTimeSteps() == 3, "Check time step count stays 3."); + MITK_TEST_CONDITION(!contour->IsEmpty(0), "Check time step 0 is not empty."); + MITK_TEST_CONDITION(contour->IsEmpty(1), "Check time step 1 is empty."); + MITK_TEST_CONDITION(!contour->IsEmpty(2), "Check time step 2 is not empty."); + MITK_TEST_CONDITION(contour->GetVertexAt(0, 2)->Coordinates == p, "compare if vertex at t == 2 is still the same"); + + contour->Clear(); + MITK_TEST_CONDITION(contour->GetTimeSteps() == 1, "Check time step count stays 1."); + MITK_TEST_CONDITION(contour->IsEmpty(0), "Check time step 0 is empty."); +} + int mitkContourModelTest(int /*argc*/, char * /*argv*/ []) { MITK_TEST_BEGIN("mitkContourModelTest") TestAddVertex(); TestSelectVertexAtIndex(); TestSelectVertexAtWorldposition(); TestMoveSelectedVertex(); TestRemoveVertexAtIndex(); TestRemoveVertexAtWorldPosition(); TestIsclosed(); TestConcatenate(); TestInvalidTimeStep(); TestInsertVertex(); TestEmptyContour(); TestSetVertices(); TestSelectVertexAtWrongPosition(); TestContourModelAPI(); + TestClear(); MITK_TEST_END() } diff --git a/Modules/Core/TestingHelper/include/mitkInteractionTestHelper.h b/Modules/Core/TestingHelper/include/mitkInteractionTestHelper.h index 71d54b482a..c1ba0efb79 100644 --- a/Modules/Core/TestingHelper/include/mitkInteractionTestHelper.h +++ b/Modules/Core/TestingHelper/include/mitkInteractionTestHelper.h @@ -1,143 +1,142 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkInteractionTestHelper_h #define mitkInteractionTestHelper_h #include #include #include #include #include class vtkRenderWindow; class vtkRenderer; namespace mitk { /** @brief Creates everything needed to load and playback interaction events. * * The interaction is loaded from an xml file and the event are created. This file is * usually a recorded user interaction with the GUI. This can be done with InteractionEventRecorder * plugin. Also all necessary objects to handle interaction events are generated. * The user of this class is responsible to add the data object to interact with to the data storage * of InteractionTestHelper. And must also make sure that a proper data interactor is associated with the data * object. * * To test a PointSet interaction for instance make sure you have a PointSet node and a PointSetDataInteractor. * Then just add the node to the storage of the your InteractionTestHelper by calling * InteractionTestHelper::AddNodeToStorage. * Use InteractionTestHelper::PlaybackInteraction to execute. The result can afterwards be compared to a reference * object. * * Make sure to destroy the test helper instance after each test, since all render windows and its renderers have to * be * unregistered. * * \sa XML2EventParser * \sa EventFactory * \sa EventRecorder */ class MITKTESTINGHELPER_EXPORT InteractionTestHelper { public: /** * @brief InteractionTestHelper set up all neseccary objects by calling Initialize. * @param interactionXmlFilePath path to xml file containing events and configuration information for the render * windows. */ InteractionTestHelper(const std::string &interactionXmlFilePath); // unregisters all render windows and its renderers. virtual ~InteractionTestHelper(); /** @brief Returns the datastorage, in order to modify the data inside a rendering test. **/ mitk::DataStorage::Pointer GetDataStorage(); /** * @brief AddNodeToStorage Add a node to the datastorage and perform a reinit which is necessary for rendering. * @param node The data you want to add. */ void AddNodeToStorage(mitk::DataNode::Pointer node); /** * @brief PlaybackInteraction playback loaded interaction by passing events to the dispatcher. */ void PlaybackInteraction(); /** * @brief SetTimeStep Sets timesteps of all SliceNavigationControllers to given timestep. * @param newTimeStep new timestep * * Does the same as using ImageNavigators Time slider. Use this if your data was modified in a timestep other than * 0. */ void SetTimeStep(int newTimeStep); typedef std::vector RenderWindowListType; const RenderWindowListType &GetRenderWindowList() { return m_RenderWindowList; } /** * @brief GetRenderWindowByName Get renderWindow by the name of its renderer. * @param name The name of the renderer of the desired renderWindow. * @return nullptr if not found. */ RenderWindow *GetRenderWindowByName(const std::string &name); /** * @brief GetRenderWindowByDefaultViewDirection Get a renderWindow by its default viewdirection. * @param viewDirection * @return nullptr if not found. */ RenderWindow *GetRenderWindowByDefaultViewDirection(mitk::SliceNavigationController::ViewDirection viewDirection); /** * @brief GetRenderWindow Get renderWindow at position 'index'. * @param index Position within the renderWindow list. * @return nullptr if index is out of bounds. */ RenderWindow *GetRenderWindow(unsigned int index); /** * @brief AddDisplayPlaneSubTree * * Creates DisplayPlanes that are shown in a 3D RenderWindow. */ void AddDisplayPlaneSubTree(); void Set3dCameraSettings(); protected: /** * @brief Initialize Internal method to initialize the renderwindow and set the datastorage. * @throws mitk::Exception if interaction xml file can not be loaded. */ void Initialize(const std::string &interactionXmlFilePath); /** * @brief LoadInteraction loads events from xml file. - * @param interactionXmlPath path to xml file with interaction events. */ void LoadInteraction(); mitk::XML2EventParser::EventContainerType m_Events; // List with loaded interaction events std::string m_InteractionFilePath; RenderWindowListType m_RenderWindowList; mitk::DataStorage::Pointer m_DataStorage; mitk::MouseModeSwitcher::Pointer m_MouseModeSwitcher; }; } // namespace mitk #endif diff --git a/Modules/Core/TestingHelper/src/mitkInteractionTestHelper.cpp b/Modules/Core/TestingHelper/src/mitkInteractionTestHelper.cpp index 92578ca3cf..80f98daa8a 100644 --- a/Modules/Core/TestingHelper/src/mitkInteractionTestHelper.cpp +++ b/Modules/Core/TestingHelper/src/mitkInteractionTestHelper.cpp @@ -1,429 +1,429 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // MITK #include #include #include #include #include // VTK #include #include // us #include #include mitk::InteractionTestHelper::InteractionTestHelper(const std::string &interactionXmlFilePath) : m_InteractionFilePath(interactionXmlFilePath) { this->Initialize(interactionXmlFilePath); } void mitk::InteractionTestHelper::Initialize(const std::string &interactionXmlFilePath) { tinyxml2::XMLDocument document; if (tinyxml2::XML_SUCCESS == document.LoadFile(interactionXmlFilePath.c_str())) { // get RenderingManager instance auto rm = mitk::RenderingManager::GetInstance(); // create data storage m_DataStorage = mitk::StandaloneDataStorage::New(); // for each renderer found create a render window and configure for (auto *element = document.FirstChildElement(mitk::InteractionEventConst::xmlTagInteractions().c_str()) ->FirstChildElement(mitk::InteractionEventConst::xmlTagConfigRoot().c_str()) ->FirstChildElement(mitk::InteractionEventConst::xmlTagRenderer().c_str()); element != nullptr; element = element->NextSiblingElement(mitk::InteractionEventConst::xmlTagRenderer().c_str())) { // get name of renderer const char *rendererName = element->Attribute(mitk::InteractionEventConst::xmlEventPropertyRendererName().c_str()); // get view direction mitk::SliceNavigationController::ViewDirection viewDirection = mitk::SliceNavigationController::Axial; if (element->Attribute(mitk::InteractionEventConst::xmlEventPropertyViewDirection().c_str()) != nullptr) { int viewDirectionNum = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlEventPropertyViewDirection().c_str())); viewDirection = static_cast(viewDirectionNum); } // get mapper slot id mitk::BaseRenderer::MapperSlotId mapperID = mitk::BaseRenderer::Standard2D; if (element->Attribute(mitk::InteractionEventConst::xmlEventPropertyMapperID().c_str()) != nullptr) { int mapperIDNum = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlEventPropertyMapperID().c_str())); mapperID = static_cast(mapperIDNum); } // Get Size of Render Windows int size[3]; size[0] = size[1] = size[2] = 0; if (element->Attribute(mitk::InteractionEventConst::xmlRenderSizeX().c_str()) != nullptr) { size[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlRenderSizeX().c_str())); } if (element->Attribute(mitk::InteractionEventConst::xmlRenderSizeY().c_str()) != nullptr) { size[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlRenderSizeY().c_str())); } if (element->Attribute(mitk::InteractionEventConst::xmlRenderSizeZ().c_str()) != nullptr) { size[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlRenderSizeZ().c_str())); } // create renderWindow, renderer and dispatcher auto rw = RenderWindow::New(nullptr, rendererName); // VtkRenderWindow is created within constructor if nullptr if (size[0] != 0 && size[1] != 0) { rw->SetSize(size[0], size[1]); rw->GetRenderer()->Resize(size[0], size[1]); } // set storage of renderer rw->GetRenderer()->SetDataStorage(m_DataStorage); // set view direction to axial rw->GetSliceNavigationController()->SetDefaultViewDirection(viewDirection); // set renderer to render 2D rw->GetRenderer()->SetMapperID(mapperID); rw->GetRenderer()->PrepareRender(); // Some more magic for the 3D render window case: // Camera view direction, position and focal point if (mapperID == mitk::BaseRenderer::Standard3D) { if (element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointX().c_str()) != nullptr) { double cameraFocalPoint[3]; cameraFocalPoint[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointX().c_str())); cameraFocalPoint[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointY().c_str())); cameraFocalPoint[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointZ().c_str())); rw->GetRenderer()->GetVtkRenderer()->GetActiveCamera()->SetFocalPoint(cameraFocalPoint); } if (element->Attribute(mitk::InteractionEventConst::xmlCameraPositionX().c_str()) != nullptr) { double cameraPosition[3]; cameraPosition[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionX().c_str())); cameraPosition[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionY().c_str())); cameraPosition[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionZ().c_str())); rw->GetRenderer()->GetVtkRenderer()->GetActiveCamera()->SetPosition(cameraPosition); } if (element->Attribute(mitk::InteractionEventConst::xmlViewUpX().c_str()) != nullptr) { double viewUp[3]; viewUp[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpX().c_str())); viewUp[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpY().c_str())); viewUp[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpZ().c_str())); rw->GetRenderer()->GetVtkRenderer()->GetActiveCamera()->SetViewUp(viewUp); } } rw->GetVtkRenderWindow()->Render(); rw->GetVtkRenderWindow()->WaitForCompletion(); // connect SliceNavigationControllers to timestep changed event of TimeNavigationController rw->GetSliceNavigationController()->ConnectGeometryTimeEvent(rm->GetTimeNavigationController(), false); rm->GetTimeNavigationController()->ConnectGeometryTimeEvent(rw->GetSliceNavigationController(), false); // add to list of kown render windows m_RenderWindowList.push_back(rw); } // TODO: check the following lines taken from QmitkStdMultiWidget and adapt them to be executed in our code here. // mitkWidget1->GetSliceNavigationController() // ->ConnectGeometrySendEvent(mitk::BaseRenderer::GetInstance(mitkWidget4->GetRenderWindow())); //########### register display interactor to handle scroll events ################## // use MouseModeSwitcher to ensure that the statemachine of DisplayInteractor is loaded correctly m_MouseModeSwitcher = mitk::MouseModeSwitcher::New(); } else { mitkThrow() << "Can not load interaction xml file <" << m_InteractionFilePath << ">"; } // WARNING assumes a 3D window exists !!!! this->AddDisplayPlaneSubTree(); } mitk::InteractionTestHelper::~InteractionTestHelper() { mitk::RenderingManager *rm = mitk::RenderingManager::GetInstance(); // unregister renderers auto it = m_RenderWindowList.begin(); auto end = m_RenderWindowList.end(); for (; it != end; ++it) { rm->GetTimeNavigationController()->Disconnect((*it)->GetSliceNavigationController()); (*it)->GetSliceNavigationController()->Disconnect(rm->GetTimeNavigationController()); mitk::BaseRenderer::RemoveInstance((*it)->GetVtkRenderWindow()); } rm->RemoveAllObservers(); } mitk::DataStorage::Pointer mitk::InteractionTestHelper::GetDataStorage() { return m_DataStorage; } void mitk::InteractionTestHelper::AddNodeToStorage(mitk::DataNode::Pointer node) { this->m_DataStorage->Add(node); this->Set3dCameraSettings(); } void mitk::InteractionTestHelper::PlaybackInteraction() { mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(m_DataStorage); // load events if not loaded yet if (m_Events.empty()) this->LoadInteraction(); auto it = m_RenderWindowList.begin(); auto end = m_RenderWindowList.end(); for (; it != end; ++it) { (*it)->GetRenderer()->PrepareRender(); (*it)->GetVtkRenderWindow()->Render(); (*it)->GetVtkRenderWindow()->WaitForCompletion(); } mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(m_DataStorage); it = m_RenderWindowList.begin(); for (; it != end; ++it) { (*it)->GetVtkRenderWindow()->Render(); (*it)->GetVtkRenderWindow()->WaitForCompletion(); } // mitk::RenderingManager::GetInstance()->ForceImmediateUpdateAll(); // playback all events in queue for (unsigned long i = 0; i < m_Events.size(); ++i) { // let dispatcher of sending renderer process the event m_Events.at(i)->GetSender()->GetDispatcher()->ProcessEvent(m_Events.at(i)); } if (false) { it--; (*it)->GetVtkRenderWindow()->GetInteractor()->Start(); } } void mitk::InteractionTestHelper::LoadInteraction() { // load interaction pattern from xml file std::ifstream xmlStream(m_InteractionFilePath.c_str()); mitk::XML2EventParser parser(xmlStream); m_Events = parser.GetInteractions(); xmlStream.close(); // Avoid VTK warning: Trying to delete object with non-zero reference count. parser.SetReferenceCount(0); } void mitk::InteractionTestHelper::SetTimeStep(int newTimeStep) { mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(m_DataStorage); bool timeStepIsvalid = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetCreatedWorldGeometry()->IsValidTimeStep( newTimeStep); if (timeStepIsvalid) { mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetTime()->SetPos(newTimeStep); } } mitk::RenderWindow *mitk::InteractionTestHelper::GetRenderWindowByName(const std::string &name) { auto it = m_RenderWindowList.begin(); auto end = m_RenderWindowList.end(); for (; it != end; ++it) { if (name.compare((*it)->GetRenderer()->GetName()) == 0) return (*it).GetPointer(); } return nullptr; } mitk::RenderWindow *mitk::InteractionTestHelper::GetRenderWindowByDefaultViewDirection( mitk::SliceNavigationController::ViewDirection viewDirection) { auto it = m_RenderWindowList.begin(); auto end = m_RenderWindowList.end(); for (; it != end; ++it) { if (viewDirection == (*it)->GetSliceNavigationController()->GetDefaultViewDirection()) return (*it).GetPointer(); } return nullptr; } mitk::RenderWindow *mitk::InteractionTestHelper::GetRenderWindow(unsigned int index) { if (index < m_RenderWindowList.size()) { return m_RenderWindowList.at(index).GetPointer(); } else { return nullptr; } } void mitk::InteractionTestHelper::AddDisplayPlaneSubTree() { // add the displayed planes of the multiwidget to a node to which the subtree // @a planesSubTree points ... mitk::PlaneGeometryDataMapper2D::Pointer mapper; mitk::IntProperty::Pointer layer = mitk::IntProperty::New(1000); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetProperty("name", mitk::StringProperty::New("Widgets")); node->SetProperty("helper object", mitk::BoolProperty::New(true)); m_DataStorage->Add(node); for (auto it : m_RenderWindowList) { if (it->GetRenderer()->GetMapperID() == BaseRenderer::Standard3D) continue; // ... of widget 1 mitk::DataNode::Pointer planeNode1 = (mitk::BaseRenderer::GetInstance(it->GetVtkRenderWindow()))->GetCurrentWorldPlaneGeometryNode(); planeNode1->SetProperty("visible", mitk::BoolProperty::New(true)); planeNode1->SetProperty("name", mitk::StringProperty::New("widget1Plane")); planeNode1->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false)); planeNode1->SetProperty("helper object", mitk::BoolProperty::New(true)); planeNode1->SetProperty("layer", layer); planeNode1->SetColor(1.0, 0.0, 0.0); mapper = mitk::PlaneGeometryDataMapper2D::New(); planeNode1->SetMapper(mitk::BaseRenderer::Standard2D, mapper); m_DataStorage->Add(planeNode1, node); } } void mitk::InteractionTestHelper::Set3dCameraSettings() { tinyxml2::XMLDocument document; if (tinyxml2::XML_SUCCESS == document.LoadFile(m_InteractionFilePath.c_str())) { // for each renderer found create a render window and configure for (auto *element = document.FirstChildElement(mitk::InteractionEventConst::xmlTagInteractions().c_str()) ->FirstChildElement(mitk::InteractionEventConst::xmlTagConfigRoot().c_str()) ->FirstChildElement(mitk::InteractionEventConst::xmlTagRenderer().c_str()); element != nullptr; element = element->NextSiblingElement(mitk::InteractionEventConst::xmlTagRenderer().c_str())) { // get name of renderer const char *rendererName = element->Attribute(mitk::InteractionEventConst::xmlEventPropertyRendererName().c_str()); // get mapper slot id mitk::BaseRenderer::MapperSlotId mapperID = mitk::BaseRenderer::Standard2D; if (element->Attribute(mitk::InteractionEventConst::xmlEventPropertyMapperID().c_str()) != nullptr) { int mapperIDNum = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlEventPropertyMapperID().c_str())); mapperID = static_cast(mapperIDNum); } if (mapperID == mitk::BaseRenderer::Standard3D) { RenderWindow *namedRenderer = nullptr; - for (auto it : m_RenderWindowList) + for (const auto &it : m_RenderWindowList) { if (strcmp(it->GetRenderer()->GetName(), rendererName) == 0) { namedRenderer = it.GetPointer(); break; } } if (namedRenderer == nullptr) { MITK_ERROR << "No match for render window was found."; return; } namedRenderer->GetRenderer()->PrepareRender(); if (element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointX().c_str()) != nullptr) { double cameraFocalPoint[3]; cameraFocalPoint[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointX().c_str())); cameraFocalPoint[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointY().c_str())); cameraFocalPoint[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraFocalPointZ().c_str())); namedRenderer->GetRenderer()->GetVtkRenderer()->GetActiveCamera()->SetFocalPoint(cameraFocalPoint); } if (element->Attribute(mitk::InteractionEventConst::xmlCameraPositionX().c_str()) != nullptr) { double cameraPosition[3]; cameraPosition[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionX().c_str())); cameraPosition[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionY().c_str())); cameraPosition[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlCameraPositionZ().c_str())); namedRenderer->GetRenderer()->GetVtkRenderer()->GetActiveCamera()->SetPosition(cameraPosition); } if (element->Attribute(mitk::InteractionEventConst::xmlViewUpX().c_str()) != nullptr) { double viewUp[3]; viewUp[0] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpX().c_str())); viewUp[1] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpY().c_str())); viewUp[2] = std::atoi(element->Attribute(mitk::InteractionEventConst::xmlViewUpZ().c_str())); namedRenderer->GetRenderer()->GetVtkRenderer()->GetActiveCamera()->SetViewUp(viewUp); } namedRenderer->GetVtkRenderWindow()->Render(); } } } } diff --git a/Modules/Core/include/mitkBaseRenderer.h b/Modules/Core/include/mitkBaseRenderer.h index b50a10e5c1..b4015ffd7a 100644 --- a/Modules/Core/include/mitkBaseRenderer.h +++ b/Modules/Core/include/mitkBaseRenderer.h @@ -1,532 +1,532 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 BASERENDERER_H_HEADER_INCLUDED_C1CCA0F4 #define BASERENDERER_H_HEADER_INCLUDED_C1CCA0F4 #include "mitkCameraRotationController.h" #include "mitkDataStorage.h" #include "mitkPlaneGeometry.h" #include "mitkPlaneGeometryData.h" #include "mitkSliceNavigationController.h" #include "mitkTimeGeometry.h" #include "mitkBindDispatcherInteractor.h" #include "mitkDispatcher.h" #include #include #include #include // DEPRECATED #include namespace mitk { class NavigationController; class SliceNavigationController; class CameraRotationController; class CameraController; class DataStorage; class Mapper; class BaseLocalStorageHandler; class KeyEvent; //##Documentation //## @brief Organizes the rendering process //## //## Organizes the rendering process. A Renderer contains a reference to a //## DataStorage and asks the mappers of the data objects to render //## the data into the renderwindow it is associated to. //## //## \#Render() checks if rendering is currently allowed by calling //## RenderWindow::PrepareRendering(). Initialization of a rendering context //## can also be performed in this method. //## //## The actual rendering code has been moved to \#Repaint() //## Both \#Repaint() and \#Update() are declared protected now. //## //## Note: Separation of the Repaint and Update processes (rendering vs //## creating a vtk prop tree) still needs to be worked on. The whole //## rendering process also should be reworked to use VTK based classes for //## both 2D and 3D rendering. //## @ingroup Renderer class MITKCORE_EXPORT BaseRenderer : public itk::Object { public: typedef std::map BaseRendererMapType; static BaseRendererMapType baseRendererMap; static BaseRenderer *GetInstance(vtkRenderWindow *renWin); static void AddInstance(vtkRenderWindow *renWin, BaseRenderer *baseRenderer); static void RemoveInstance(vtkRenderWindow *renWin); static BaseRenderer *GetByName(const std::string &name); static vtkRenderWindow *GetRenderWindowByName(const std::string &name); #pragma GCC visibility push(default) itkEventMacro(RendererResetEvent, itk::AnyEvent); #pragma GCC visibility pop /** Standard class typedefs. */ mitkClassMacroItkParent(BaseRenderer, itk::Object); BaseRenderer(const char *name = nullptr, vtkRenderWindow *renWin = nullptr); //##Documentation //## @brief MapperSlotId defines which kind of mapper (e.g. 2D or 3D) should be used. typedef int MapperSlotId; enum StandardMapperSlot { Standard2D = 1, Standard3D = 2 }; //##Documentation //## @brief Possible view directions for render windows. enum class ViewDirection { AXIAL = 0, SAGITTAL, CORONAL, THREE_D }; virtual void SetDataStorage(DataStorage *storage); ///< set the datastorage that will be used for rendering //##Documentation //## return the DataStorage that is used for rendering virtual DataStorage::Pointer GetDataStorage() const { return m_DataStorage.GetPointer(); } //##Documentation //## @brief Access the RenderWindow into which this renderer renders. vtkRenderWindow *GetRenderWindow() const { return m_RenderWindow; } vtkRenderer *GetVtkRenderer() const { return m_VtkRenderer; } //##Documentation //## @brief Returns the Dispatcher which handles Events for this BaseRenderer Dispatcher::Pointer GetDispatcher() const; //##Documentation //## @brief Default mapper id to use. static const MapperSlotId defaultMapper; //##Documentation //## @brief Do the rendering and flush the result. virtual void Paint(); //##Documentation //## @brief Initialize the RenderWindow. Should only be called from RenderWindow. virtual void Initialize(); //##Documentation //## @brief Called to inform the renderer that the RenderWindow has been resized. virtual void Resize(int w, int h); //##Documentation //## @brief Initialize the renderer with a RenderWindow (@a renderwindow). virtual void InitRenderer(vtkRenderWindow *renderwindow); //##Documentation //## @brief Set the initial size. Called by RenderWindow after it has become //## visible for the first time. virtual void InitSize(int w, int h); //##Documentation //## @brief Draws a point on the widget. //## Should be used during conferences to show the position of the remote mouse virtual void DrawOverlayMouse(Point2D &p2d); //##Documentation //## @brief Set/Get the WorldGeometry (m_WorldGeometry) for 3D and 2D rendering, that describing the //## (maximal) area to be rendered. //## //## Depending of the type of the passed BaseGeometry more or less information can be extracted: //## \li if it is a PlaneGeometry (which is a sub-class of BaseGeometry), m_CurrentWorldPlaneGeometry is //## also set to point to it. m_WorldTimeGeometry is set to nullptr. //## \li if it is a TimeGeometry, m_WorldTimeGeometry is also set to point to it. //## If m_WorldTimeGeometry contains instances of SlicedGeometry3D, m_CurrentWorldPlaneGeometry is set to //## one of geometries stored in the SlicedGeometry3D according to the value of m_Slice; otherwise //## a PlaneGeometry describing the top of the bounding-box of the BaseGeometry is set as the //## m_CurrentWorldPlaneGeometry. //## \li otherwise a PlaneGeometry describing the top of the bounding-box of the BaseGeometry //## is set as the m_CurrentWorldPlaneGeometry. m_WorldTimeGeometry is set to nullptr. //## @todo add calculation of PlaneGeometry describing the top of the bounding-box of the BaseGeometry //## when the passed BaseGeometry is not sliced. //## \sa m_WorldGeometry //## \sa m_WorldTimeGeometry //## \sa m_CurrentWorldPlaneGeometry virtual void SetWorldGeometry3D(const BaseGeometry *geometry); virtual void SetWorldTimeGeometry(const mitk::TimeGeometry *geometry); /** * \deprecatedSince{2013_09} Please use TimeGeometry instead of TimeSlicedGeometry. For more information see * http://www.mitk.org/Development/Refactoring%20of%20the%20Geometry%20Classes%20-%20Part%201 */ DEPRECATED(void SetWorldGeometry3D(TimeSlicedGeometry *geometry)); itkGetConstObjectMacro(WorldTimeGeometry, TimeGeometry); //##Documentation //## @brief Get the current 3D-worldgeometry (m_CurrentWorldGeometry) used for 3D-rendering itkGetConstObjectMacro(CurrentWorldGeometry, BaseGeometry); //##Documentation //## @brief Get the current 2D-worldgeometry (m_CurrentWorldPlaneGeometry) used for 2D-rendering itkGetConstObjectMacro(CurrentWorldPlaneGeometry, PlaneGeometry) /** * \deprecatedSince{2014_10} Please use GetCurrentWorldPlaneGeometry */ DEPRECATED(const PlaneGeometry *GetCurrentWorldGeometry2D()) { return GetCurrentWorldPlaneGeometry(); }; //##Documentation //## Calculates the bounds of the DataStorage (if it contains any valid data), //## creates a geometry from these bounds and sets it as world geometry of the renderer. //## //## Call this method to re-initialize the renderer to the current DataStorage //## (e.g. after loading an additional dataset), to ensure that the view is //## aligned correctly. //## \warning This is not implemented yet. virtual bool SetWorldGeometryToDataStorageBounds() { return false; } //##Documentation //## @brief Set/Get m_Slice which defines together with m_TimeStep the 2D geometry //## stored in m_WorldTimeGeometry used as m_CurrentWorldPlaneGeometry //## //## \sa m_Slice virtual void SetSlice(unsigned int slice); itkGetConstMacro(Slice, unsigned int); //##Documentation //## @brief Set/Get m_TimeStep which defines together with m_Slice the 2D geometry //## stored in m_WorldTimeGeometry used as m_CurrentWorldPlaneGeometry //## //## \sa m_TimeStep virtual void SetTimeStep(unsigned int timeStep); itkGetConstMacro(TimeStep, unsigned int); //##Documentation //## @brief Get the time-step of a BaseData object which //## exists at the time of the currently displayed content //## //## Returns -1 or mitk::BaseData::m_TimeSteps if there //## is no data at the current time. //## \sa GetTimeStep, m_TimeStep - int GetTimeStep(const BaseData *data) const; + TimeStepType GetTimeStep(const BaseData *data) const; //##Documentation //## @brief Get the time in ms of the currently displayed content //## //## \sa GetTimeStep, m_TimeStep ScalarType GetTime() const; //##Documentation //## @brief SetWorldGeometry is called according to the geometrySliceEvent, //## which is supposed to be a SliceNavigationController::GeometrySendEvent virtual void SetGeometry(const itk::EventObject &geometrySliceEvent); //##Documentation //## @brief UpdateWorldGeometry is called to re-read the 2D geometry from the //## slice navigation controller virtual void UpdateGeometry(const itk::EventObject &geometrySliceEvent); //##Documentation //## @brief SetSlice is called according to the geometrySliceEvent, //## which is supposed to be a SliceNavigationController::GeometrySliceEvent virtual void SetGeometrySlice(const itk::EventObject &geometrySliceEvent); //##Documentation //## @brief SetTimeStep is called according to the geometrySliceEvent, //## which is supposed to be a SliceNavigationController::GeometryTimeEvent virtual void SetGeometryTime(const itk::EventObject &geometryTimeEvent); //##Documentation //## @brief Get a DataNode pointing to a data object containing the current 2D-worldgeometry // m_CurrentWorldPlaneGeometry (for 2D rendering) itkGetObjectMacro(CurrentWorldPlaneGeometryNode, DataNode) /** * \deprecatedSince{2014_10} Please use GetCurrentWorldPlaneGeometryNode */ DEPRECATED(DataNode *GetCurrentWorldGeometry2DNode()) { return GetCurrentWorldPlaneGeometryNode(); }; //##Documentation //## @brief Sets timestamp of CurrentWorldPlaneGeometry and forces so reslicing in that renderwindow void SendUpdateSlice(); //##Documentation //## @brief Get timestamp of last call of SetCurrentWorldPlaneGeometry unsigned long GetCurrentWorldPlaneGeometryUpdateTime() { return m_CurrentWorldPlaneGeometryUpdateTime; } /** * \deprecatedSince{2014_10} Please use GetCurrentWorldPlaneGeometryUpdateTime */ DEPRECATED(unsigned long GetCurrentWorldGeometry2DUpdateTime()) { return GetCurrentWorldPlaneGeometryUpdateTime(); }; //##Documentation //## @brief Get timestamp of last change of current TimeStep unsigned long GetTimeStepUpdateTime() { return m_TimeStepUpdateTime; } //##Documentation //## @brief Perform a picking: find the x,y,z world coordinate of a //## display x,y coordinate. //## @warning Has to be overwritten in subclasses for the 3D-case. //## //## Implemented here only for 2D-rendering virtual void PickWorldPoint(const Point2D &diplayPosition, Point3D &worldPosition) const = 0; /** \brief Determines the object (mitk::DataNode) closest to the current * position by means of picking * * \warning Implementation currently empty for 2D rendering; intended to be * implemented for 3D renderers */ virtual DataNode *PickObject(const Point2D & /*displayPosition*/, Point3D & /*worldPosition*/) const { return nullptr; } //##Documentation //## @brief Get the MapperSlotId to use. itkGetMacro(MapperID, MapperSlotId); itkGetConstMacro(MapperID, MapperSlotId); //##Documentation //## @brief Set the MapperSlotId to use. virtual void SetMapperID(MapperSlotId id); virtual int *GetSize() const; virtual int *GetViewportSize() const; void SetSliceNavigationController(SliceNavigationController *SlicenavigationController); itkGetObjectMacro(CameraController, CameraController); itkGetObjectMacro(SliceNavigationController, SliceNavigationController); itkGetObjectMacro(CameraRotationController, CameraRotationController); itkGetMacro(EmptyWorldGeometry, bool); //##Documentation //## @brief Tells if the displayed region is shifted and rescaled if the render window is resized. itkGetMacro(KeepDisplayedRegion, bool) //##Documentation //## @brief Tells if the displayed region should be shifted and rescaled if the render window is resized. itkSetMacro(KeepDisplayedRegion, bool); //##Documentation //## @brief get the name of the Renderer //## @note const char *GetName() const { return m_Name.c_str(); } //##Documentation //## @brief get the x_size of the RendererWindow //## @note int GetSizeX() const { return GetSize()[0]; } //##Documentation //## @brief get the y_size of the RendererWindow //## @note int GetSizeY() const { return GetSize()[1]; } const double *GetBounds() const; void RequestUpdate(); void ForceImmediateUpdate(); /** Returns number of mappers which are visible and have level-of-detail * rendering enabled */ unsigned int GetNumberOfVisibleLODEnabledMappers() const; //##Documentation //## @brief This method converts a display point to the 3D world index //## using the geometry of the renderWindow. void DisplayToWorld(const Point2D &displayPoint, Point3D &worldIndex) const; //##Documentation //## @brief This method converts a display point to the 2D world index, mapped onto the display plane //## using the geometry of the renderWindow. void DisplayToPlane(const Point2D &displayPoint, Point2D &planePointInMM) const; //##Documentation //## @brief This method converts a 3D world index to the display point //## using the geometry of the renderWindow. void WorldToDisplay(const Point3D &worldIndex, Point2D &displayPoint) const; //##Documentation //## @brief This method converts a 3D world index to the point on the viewport //## using the geometry of the renderWindow. void WorldToView(const Point3D &worldIndex, Point2D &viewPoint) const; //##Documentation //## @brief This method converts a 2D plane coordinate to the display point //## using the geometry of the renderWindow. void PlaneToDisplay(const Point2D &planePointInMM, Point2D &displayPoint) const; //##Documentation //## @brief This method converts a 2D plane coordinate to the point on the viewport //## using the geometry of the renderWindow. void PlaneToView(const Point2D &planePointInMM, Point2D &viewPoint) const; double GetScaleFactorMMPerDisplayUnit() const; Point2D GetDisplaySizeInMM() const; Point2D GetViewportSizeInMM() const; Point2D GetOriginInMM() const; itkGetConstMacro(ConstrainZoomingAndPanning, bool) virtual void SetConstrainZoomingAndPanning(bool constrain); /** * \brief Provides (1) world coordinates for a given mouse position and (2) * translates mousePosition to Display coordinates * \deprecated Map2DRendererPositionTo3DWorldPosition is deprecated. Please use DisplayToWorld instead. */ DEPRECATED(virtual Point3D Map2DRendererPositionTo3DWorldPosition(const Point2D &mousePosition) const); protected: ~BaseRenderer() override; //##Documentation //## @brief Call update of all mappers. To be implemented in subclasses. virtual void Update() = 0; vtkRenderWindow *m_RenderWindow; vtkRenderer *m_VtkRenderer; //##Documentation //## @brief MapperSlotId to use. Defines which kind of mapper (e.g., 2D or 3D) shoud be used. MapperSlotId m_MapperID; //##Documentation //## @brief The DataStorage that is used for rendering. DataStorage::Pointer m_DataStorage; //##Documentation //## @brief Timestamp of last call of Update(). unsigned long m_LastUpdateTime; //##Documentation //## @brief CameraController for 3D rendering //## @note preliminary. itk::SmartPointer m_CameraController; SliceNavigationController::Pointer m_SliceNavigationController; CameraRotationController::Pointer m_CameraRotationController; //##Documentation //## @brief Sets m_CurrentWorldPlaneGeometry virtual void SetCurrentWorldPlaneGeometry(const PlaneGeometry *geometry2d); /** * \deprecatedSince{2014_10} Please use SetCurrentWorldPlaneGeometry */ DEPRECATED(void SetCurrentWorldGeometry2D(PlaneGeometry *geometry2d)) { SetCurrentWorldPlaneGeometry(geometry2d); }; //##Documentation //## @brief Sets m_CurrentWorldGeometry virtual void SetCurrentWorldGeometry(const BaseGeometry *geometry); private: //##Documentation //## m_WorldTimeGeometry is set by SetWorldGeometry if the passed BaseGeometry is a //## TimeGeometry (or a sub-class of it). If it contains instances of SlicedGeometry3D, //## m_Slice and m_TimeStep (set via SetSlice and SetTimeStep, respectively) define //## which 2D geometry stored in m_WorldTimeGeometry (if available) //## is used as m_CurrentWorldPlaneGeometry. //## \sa m_CurrentWorldPlaneGeometry TimeGeometry::ConstPointer m_WorldTimeGeometry; //##Documentation //## Pointer to the current 3D-worldgeometry. BaseGeometry::ConstPointer m_CurrentWorldGeometry; //##Documentation //## Pointer to the current 2D-worldgeometry. The 2D-worldgeometry //## describes the maximal area (2D manifold) to be rendered in case we //## are doing 2D-rendering. //## It is const, since we are not allowed to change it (it may be taken //## directly from the geometry of an image-slice and thus it would be //## very strange when suddenly the image-slice changes its geometry). PlaneGeometry::Pointer m_CurrentWorldPlaneGeometry; //##Documentation //## Defines together with m_Slice which 2D geometry stored in m_WorldTimeGeometry //## is used as m_CurrentWorldPlaneGeometry: m_WorldTimeGeometry->GetPlaneGeometry(m_Slice, m_TimeStep). //## \sa m_WorldTimeGeometry unsigned int m_Slice; //##Documentation //## Defines together with m_TimeStep which 2D geometry stored in m_WorldTimeGeometry //## is used as m_CurrentWorldPlaneGeometry: m_WorldTimeGeometry->GetPlaneGeometry(m_Slice, m_TimeStep). //## \sa m_WorldTimeGeometry unsigned int m_TimeStep; //##Documentation //## @brief timestamp of last call of SetWorldGeometry itk::TimeStamp m_CurrentWorldPlaneGeometryUpdateTime; //##Documentation //## @brief timestamp of last change of the current time step itk::TimeStamp m_TimeStepUpdateTime; //##Documentation //## @brief Helper class which establishes connection between Interactors and Dispatcher via a common DataStorage. BindDispatcherInteractor *m_BindDispatcherInteractor; //##Documentation //## @brief Tells if the displayed region should be shifted or rescaled if the render window is resized. bool m_KeepDisplayedRegion; protected: void PrintSelf(std::ostream &os, itk::Indent indent) const override; //##Documentation //## Data object containing the m_CurrentWorldPlaneGeometry defined above. PlaneGeometryData::Pointer m_CurrentWorldPlaneGeometryData; //##Documentation //## DataNode objects containing the m_CurrentWorldPlaneGeometryData defined above. DataNode::Pointer m_CurrentWorldPlaneGeometryNode; //##Documentation //## @brief test only unsigned long m_CurrentWorldPlaneGeometryTransformTime; std::string m_Name; double m_Bounds[6]; bool m_EmptyWorldGeometry; typedef std::set LODEnabledMappersType; /** Number of mappers which are visible and have level-of-detail * rendering enabled */ unsigned int m_NumberOfVisibleLODEnabledMappers; // Local Storage Handling for mappers protected: std::list m_RegisteredLocalStorageHandlers; bool m_ConstrainZoomingAndPanning; public: void RemoveAllLocalStorages(); void RegisterLocalStorageHandler(mitk::BaseLocalStorageHandler *lsh); void UnregisterLocalStorageHandler(mitk::BaseLocalStorageHandler *lsh); }; } // namespace mitk #endif /* BASERENDERER_H_HEADER_INCLUDED_C1CCA0F4 */ diff --git a/Modules/Core/include/mitkIOUtil.h b/Modules/Core/include/mitkIOUtil.h index 24f878efa2..946016eb9c 100644 --- a/Modules/Core/include/mitkIOUtil.h +++ b/Modules/Core/include/mitkIOUtil.h @@ -1,434 +1,456 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 MITKIOUTIL_H #define MITKIOUTIL_H #include #include #include #include #include #include #include #include #include #include namespace us { class ModuleResource; } namespace mitk { /** * \ingroup IO * * \brief A utility class to load and save data from/to the local file system. * * \see QmitkIOUtil */ class MITKCORE_EXPORT IOUtil { public: /**Struct that containes information regarding the current loading process. (e.g. Path that should be loaded, all found readers for the load path,...). It is set be IOUtil and used to pass information via the option callback in load operations. */ struct MITKCORE_EXPORT LoadInfo { LoadInfo(const std::string &path); std::string m_Path; std::vector m_Output; FileReaderSelector m_ReaderSelector; bool m_Cancel; }; /**Struct that is the base class for option callbacks used in load operations. The callback is used by IOUtil, if more than one suitable reader was found or the a reader containes options that can be set. The callback allows to change option settings and select the reader that should be used (via loadInfo). */ struct MITKCORE_EXPORT ReaderOptionsFunctorBase { virtual bool operator()(LoadInfo &loadInfo) const = 0; }; struct MITKCORE_EXPORT SaveInfo { SaveInfo(const BaseData *baseData, const MimeType &mimeType, const std::string &path); bool operator<(const SaveInfo &other) const; /// The BaseData object to save. const BaseData *m_BaseData; /// Contains a set of IFileWriter objects. FileWriterSelector m_WriterSelector; /// The selected mime-type, used to restrict results from FileWriterSelector. MimeType m_MimeType; /// The path to write the BaseData object to. std::string m_Path; /// Flag indicating if sub-sequent save operations are to be canceled. bool m_Cancel; }; /**Struct that is the base class for option callbacks used in save operations. The callback is used by IOUtil, if more than one suitable writer was found or the a writer containes options that can be set. The callback allows to change option settings and select the writer that should be used (via saveInfo). */ struct MITKCORE_EXPORT WriterOptionsFunctorBase { virtual bool operator()(SaveInfo &saveInfo) const = 0; }; /** * Get the file system path where the running executable is located. * * @return The location of the currently running executable, without the filename. */ static std::string GetProgramPath(); /** * Get the default temporary path. * * @return The default path for temporary data. */ static std::string GetTempPath(); /** * Returns the Directory Seperator for the current OS. * * @return the Directory Seperator for the current OS, i.e. "\\" for Windows and "/" otherwise. */ static char GetDirectorySeparator(); /** * Create and open a temporary file. * * This method generates a unique temporary filename from \c templateName, creates * and opens the file using the output stream \c tmpStream and returns the name of * the newly create file. * * The \c templateName argument must contain six consective 'X' characters ("XXXXXX") * and these are replaced with a string that makes the filename unique. * * The file is created with read and write permissions for owner only. * * @param tmpStream The output stream for writing to the temporary file. * @param templateName An optional template for the filename. * @param path An optional path where the temporary file should be created. Defaults * to the default temp path as returned by GetTempPath(). * @return The filename of the created temporary file. * * @throw mitk::Exception if the temporary file could not be created. */ static std::string CreateTemporaryFile(std::ofstream &tmpStream, const std::string &templateName = "XXXXXX", std::string path = std::string()); /** * Create and open a temporary file. * * This method generates a unique temporary filename from \c templateName, creates * and opens the file using the output stream \c tmpStream and the specified open * mode \c mode and returns the name of the newly create file. The open mode is always * OR'd with std::ios_base::out | std::ios_base::trunc. * * The \c templateName argument must contain six consective 'X' characters ("XXXXXX") * and these are replaced with a string that makes the filename unique. * * The file is created with read and write permissions for owner only. * * @param tmpStream The output stream for writing to the temporary file. * @param mode The open mode for the temporary file stream. * @param templateName An optional template for the filename. * @param path An optional path where the temporary file should be created. Defaults * to the default temp path as returned by GetTempPath(). * @return The filename of the created temporary file. * * @throw mitk::Exception if the temporary file could not be created. */ static std::string CreateTemporaryFile(std::ofstream &tmpStream, std::ios_base::openmode mode, const std::string &templateName = "XXXXXX", std::string path = std::string()); /** * Creates an empty temporary file. * * This method generates a unique temporary filename from \c templateName and creates * this file. * * The file is created with read and write permissions for owner only. * * --- * This version is potentially unsafe because the created temporary file is not kept open * and could be used by another process between calling this method and opening the returned * file path for reading or writing. * --- * * @return The filename of the created temporary file. * @param templateName An optional template for the filename. * @param path An optional path where the temporary file should be created. Defaults * to the default temp path as returned by GetTempPath(). * @throw mitk::Exception if the temporary file could not be created. */ static std::string CreateTemporaryFile(const std::string &templateName = "XXXXXX", std::string path = std::string()); /** * Create a temporary directory. * * This method generates a uniquely named temporary directory from \c templateName. * The last set of six consecutive 'X' characters in \c templateName is replaced * with a string that makes the directory name unique. * * The directory is created with read, write and executable permissions for owner only. * * @param templateName An optional template for the directory name. * @param path An optional path where the temporary directory should be created. Defaults * to the default temp path as returned by GetTempPath(). * @return The filename of the created temporary file. * * @throw mitk::Exception if the temporary directory could not be created. */ static std::string CreateTemporaryDirectory(const std::string &templateName = "XXXXXX", std::string path = std::string()); /** * @brief Load a file into the given DataStorage. * * This method calls Load(const std::vector&, DataStorage&) with a * one-element vector. * * @param path The absolute file name including the file extension. * @param storage A DataStorage object to which the loaded data will be added. * @param optionsCallback Pointer to a callback instance. The callback is used by * the load operation if more the suitable reader was found or the reader has options * that can be set. * @return The set of added DataNode objects. * @throws mitk::Exception if \c path could not be loaded. * * @sa Load(const std::vector&, DataStorage&) */ static DataStorage::SetOfObjects::Pointer Load(const std::string &path, DataStorage &storage, const ReaderOptionsFunctorBase *optionsCallback = nullptr); /** * @brief Load a file into the given DataStorage given user defined IFileReader::Options. * * This method calls Load(const std::vector&, DataStorage&) with a * one-element vector. * * @param path The absolute file name including the file extension. * @param options IFileReader option instance that should be used if selected reader * has options. * @param storage A DataStorage object to which the loaded data will be added. * @return The set of added DataNode objects. * @throws mitk::Exception if \c path could not be loaded. * * @sa Load(const std::vector&, DataStorage&) */ static DataStorage::SetOfObjects::Pointer Load(const std::string &path, const IFileReader::Options &options, DataStorage &storage); /** * @brief Load a file and return the loaded data. * * This method calls Load(const std::vector&) with a * one-element vector. * * @param path The absolute file name including the file extension. * @param optionsCallback Pointer to a callback instance. The callback is used by * the load operation if more the suitable reader was found or the reader has options * that can be set. * @return The set of added DataNode objects. * @throws mitk::Exception if \c path could not be loaded. * * @sa Load(const std::vector&, DataStorage&) */ static std::vector Load(const std::string &path, const ReaderOptionsFunctorBase *optionsCallback = nullptr); template static typename T::Pointer Load(const std::string& path, const ReaderOptionsFunctorBase *optionsCallback = nullptr) { return dynamic_cast(Load(path, optionsCallback).at(0).GetPointer()); } /** * @brief Load a file and return the loaded data. * * This method calls Load(const std::vector&) with a * one-element vector. * * @param path The absolute file name including the file extension. * @param options IFileReader option instance that should be used if selected reader * has options. * @return The set of added DataNode objects. * @throws mitk::Exception if \c path could not be loaded. * * @sa Load(const std::vector&, DataStorage&) */ static std::vector Load(const std::string &path, const IFileReader::Options &options); template static typename T::Pointer Load(const std::string& path, const IFileReader::Options &options) { return dynamic_cast(Load(path, options).at(0).GetPointer()); } /** * @brief Loads a list of file paths into the given DataStorage. * * If an entry in \c paths cannot be loaded, this method will continue to load * the remaining entries into \c storage and throw an exception afterwards. * * @param paths A list of absolute file names including the file extension. * @param storage A DataStorage object to which the loaded data will be added. * @param optionsCallback Pointer to a callback instance. The callback is used by * the load operation if more the suitable reader was found or the reader has options * that can be set. * @return The set of added DataNode objects. * @throws mitk::Exception if an entry in \c paths could not be loaded. */ static DataStorage::SetOfObjects::Pointer Load(const std::vector &paths, DataStorage &storage, const ReaderOptionsFunctorBase *optionsCallback = nullptr); static std::vector Load(const std::vector &paths, const ReaderOptionsFunctorBase *optionsCallback = nullptr); /** * @brief Loads the contents of a us::ModuleResource and returns the corresponding mitk::BaseData * @param usResource a ModuleResource, representing a BaseData object * @param mode Optional parameter to set the openmode of the stream * @return The set of loaded BaseData objects. \c Should contain either one or zero elements, since a resource * stream * respresents one object. * @throws mitk::Exception if no reader was found for the stream. */ static std::vector Load(const us::ModuleResource &usResource, std::ios_base::openmode mode = std::ios_base::in); template static typename T::Pointer Load(const us::ModuleResource &usResource, std::ios_base::openmode mode = std::ios_base::in) { return dynamic_cast(Load(usResource, mode).at(0).GetPointer()); } /** * @brief Save a mitk::BaseData instance. * @param data The data to save. * @param path The path to the image including file name and and optional file extension. * If no extension is set, the default extension and mime-type for the * BaseData type of \c data is used. * @param setPathProperty * @throws mitk::Exception if no writer for \c data is available or the writer * is not able to write the image. */ static void Save(const mitk::BaseData *data, const std::string &path, bool setPathProperty = false); /** * @brief Save a mitk::BaseData instance. * @param data The data to save. * @param path The path to the image including file name and an optional file extension. * If no extension is set, the default extension and mime-type for the * BaseData type of \c data is used. * @param options The IFileWriter options to use for the selected writer. * @param setPathProperty * @throws mitk::Exception if no writer for \c data is available or the writer * is not able to write the image. */ static void Save(const mitk::BaseData *data, const std::string &path, const IFileWriter::Options &options, bool setPathProperty = false); /** * @brief Save a mitk::BaseData instance. * @param data The data to save. * @param mimeType The mime-type to use for writing \c data. * @param path The path to the image including file name and an optional file extension. * @param addExtension If \c true, an extension according to the given \c mimeType * is added to \c path if it does not contain one. If \c path already contains * a file name extension, it is not checked for compatibility with \c mimeType. * @param setPathProperty * * @throws mitk::Exception if no writer for the combination of \c data and \c mimeType is * available or the writer is not able to write the image. */ static void Save(const mitk::BaseData *data, const std::string &mimeType, const std::string &path, bool addExtension = true, bool setPathProperty = false); /** * @brief Save a mitk::BaseData instance. * @param data The data to save. * @param mimeType The mime-type to use for writing \c data. * @param path The path to the image including file name and an optional file extension. * @param options Configuration data for the used IFileWriter instance. * @param addExtension If \c true, an extension according to the given \c mimeType * is added to \c path if it does not contain one. If \c path already contains * a file name extension, it is not checked for compatibility with \c mimeType. * @param setPathProperty * * @throws mitk::Exception if no writer for the combination of \c data and \c mimeType is * available or the writer is not able to write the image. */ static void Save(const mitk::BaseData *data, const std::string &mimeType, const std::string &path, const mitk::IFileWriter::Options &options, bool addExtension = true, bool setPathProperty = false); /** * @brief Use SaveInfo objects to save BaseData instances. * * This is a low-level method for directly working with SaveInfo objects. Usually, * the Save() methods taking a BaseData object as an argument are more appropriate. * * @param saveInfos A list of SaveInfo objects for saving contained BaseData objects. * @param setPathProperty * * @see Save(const mitk::BaseData*, const std::string&) */ static void Save(std::vector &saveInfos, bool setPathProperty = false); + /** + * @brief Convert a string encoded with the current code page to an UTF-8 encoded string (Windows) + * + * The conversion happens on Windows only. On all other platforms, the input string + * is returned unmodified as it is assumed to be UTF-8 encoded already. + * + * If the conversion fails, a warning is printed and the input string is returned + * instead. This matches the behavior before this method was introduced. + */ + static std::string Local8BitToUtf8(const std::string& local8BitStr); + + /** + * @brief Convert a UTF-8 encoded string to a string encoded with the current code page (Windows) + * + * The conversion happens on Windows only. On all other platforms, the input string + * is returned unmodified as strings are assumed to be always UTF-8 encoded by default. + * + * If the conversion fails, a warning is printed and the input string is returned + * instead. This matches the behavior before this method was introduced. + */ + static std::string Utf8ToLocal8Bit(const std::string& utf8Str); + protected: static std::string Load(std::vector &loadInfos, DataStorage::SetOfObjects *nodeResult, DataStorage *ds, const ReaderOptionsFunctorBase *optionsCallback); static std::string Save(const BaseData *data, const std::string &mimeType, const std::string &path, WriterOptionsFunctorBase *optionsCallback, bool addExtension, bool setPathProperty); static std::string Save(std::vector &saveInfos, WriterOptionsFunctorBase *optionsCallback, bool setPathProperty); private: struct Impl; }; } #endif // MITKIOUTIL_H diff --git a/Modules/Core/include/mitkMessage.h b/Modules/Core/include/mitkMessage.h index f1c4b48617..47cf00cac8 100644 --- a/Modules/Core/include/mitkMessage.h +++ b/Modules/Core/include/mitkMessage.h @@ -1,697 +1,697 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkMessageHIncluded #define mitkMessageHIncluded #include #include #include /** * Adds a Message<> variable and methods to add/remove message delegates to/from * this variable. */ #define mitkNewMessageMacro(msgHandleObject) \ private: \ ::mitk::Message<> m_##msgHandleObject##Message; \ \ public: \ inline void Add##msgHandleObject##Listener(const ::mitk::MessageAbstractDelegate<> &delegate) \ { \ m_##msgHandleObject##Message += delegate; \ } \ inline void Remove##msgHandleObject##Listener(const ::mitk::MessageAbstractDelegate<> &delegate) \ { \ m_##msgHandleObject##Message -= delegate; \ } #define mitkNewMessageWithReturnMacro(msgHandleObject, returnType) \ private: \ ::mitk::Message m_##msgHandleObject##Message; \ \ public: \ inline void Add##msgHandleObject##Listener(const ::mitk::MessageAbstractDelegate &delegate) \ { \ m_##msgHandleObject##Message += delegate; \ } \ inline void Remove##msgHandleObject##Listener(const ::mitk::MessageAbstractDelegate &delegate) \ { \ m_##msgHandleObject##Message -= delegate; \ } #define mitkNewMessage1Macro(msgHandleObject, type1) \ private: \ ::mitk::Message1 m_##msgHandleObject##Message; \ \ public: \ void Add##msgHandleObject##Listener(const ::mitk::MessageAbstractDelegate1 &delegate) \ { \ m_##msgHandleObject##Message += delegate; \ } \ void Remove##msgHandleObject##Listener(const ::mitk::MessageAbstractDelegate1 &delegate) \ { \ m_##msgHandleObject##Message -= delegate; \ } #define mitkNewMessage2Macro(msgHandleObject, type1, type2) \ private: \ ::mitk::Message2 m_##msgHandleObject##Message; \ \ public: \ void Add##msgHandleObject##Listener(const ::mitk::MessageAbstractDelegate2 &delegate) \ { \ m_##msgHandleObject##Message += delegate; \ } \ void Remove##msgHandleObject##Listener(const ::mitk::MessageAbstractDelegate2 &delegate) \ { \ m_##msgHandleObject##Message -= delegate; \ } namespace mitk { template class MessageAbstractDelegate { public: virtual ~MessageAbstractDelegate() {} virtual A Execute() const = 0; virtual bool operator==(const MessageAbstractDelegate *cmd) const = 0; virtual MessageAbstractDelegate *Clone() const = 0; }; template class MessageAbstractDelegate1 { public: virtual ~MessageAbstractDelegate1() {} virtual A Execute(T t) const = 0; virtual bool operator==(const MessageAbstractDelegate1 *cmd) const = 0; virtual MessageAbstractDelegate1 *Clone() const = 0; }; template class MessageAbstractDelegate2 { public: virtual ~MessageAbstractDelegate2() {} virtual A Execute(T t, U u) const = 0; virtual bool operator==(const MessageAbstractDelegate2 *cmd) const = 0; virtual MessageAbstractDelegate2 *Clone() const = 0; }; template class MessageAbstractDelegate3 { public: virtual ~MessageAbstractDelegate3() {} virtual A Execute(T t, U u, V v) const = 0; virtual bool operator==(const MessageAbstractDelegate3 *cmd) const = 0; virtual MessageAbstractDelegate3 *Clone() const = 0; }; template class MessageAbstractDelegate4 { public: virtual ~MessageAbstractDelegate4() {} virtual A Execute(T t, U u, V v, W w) const = 0; virtual bool operator==(const MessageAbstractDelegate4 *cmd) const = 0; virtual MessageAbstractDelegate4 *Clone() const = 0; }; /** * This class essentially wraps a function pointer with signature * A(R::*function)(). A is the return type of your callback function * and R the type of the class implementing the function. * * Use this class to add a callback function to * messages without parameters. */ template class MessageDelegate : public MessageAbstractDelegate { public: // constructor - takes pointer to an object and pointer to a member and stores // them in two private variables MessageDelegate(R *object, A (R::*memberFunctionPointer)()) : m_Object(object), m_MemberFunctionPointer(memberFunctionPointer) { } ~MessageDelegate() override {} // override function "Call" A Execute() const override { return (m_Object->*m_MemberFunctionPointer)(); // execute member function } bool operator==(const MessageAbstractDelegate *c) const override { const MessageDelegate *cmd = dynamic_cast *>(c); if (!cmd) return false; if ((void *)this->m_Object != (void *)cmd->m_Object) return false; if (this->m_MemberFunctionPointer != cmd->m_MemberFunctionPointer) return false; return true; } MessageAbstractDelegate *Clone() const override { return new MessageDelegate(m_Object, m_MemberFunctionPointer); } private: R *m_Object; // pointer to object A (R::*m_MemberFunctionPointer)(); // pointer to member function }; /** * This class essentially wraps a function pointer with signature * A(R::*function)(T). A is the return type of your callback function, * R the type of the class implementing the function and T the type * of the argument. * * Use this class to add a callback function to * messages with one parameter. * * If you need more parameters, use MessageDelegate2 etc. */ template class MessageDelegate1 : public MessageAbstractDelegate1 { public: // constructor - takes pointer to an object and pointer to a member and stores // them in two private variables MessageDelegate1(R *object, A (R::*memberFunctionPointer)(T)) : m_Object(object), m_MemberFunctionPointer(memberFunctionPointer) { } ~MessageDelegate1() override {} // override function "Call" A Execute(T t) const override { return (m_Object->*m_MemberFunctionPointer)(t); // execute member function } bool operator==(const MessageAbstractDelegate1 *c) const override { const MessageDelegate1 *cmd = dynamic_cast *>(c); if (!cmd) return false; if ((void *)this->m_Object != (void *)cmd->m_Object) return false; if (this->m_MemberFunctionPointer != cmd->m_MemberFunctionPointer) return false; return true; } MessageAbstractDelegate1 *Clone() const override { return new MessageDelegate1(m_Object, m_MemberFunctionPointer); } private: R *m_Object; // pointer to object A (R::*m_MemberFunctionPointer)(T); // pointer to member function }; template class MessageDelegate2 : public MessageAbstractDelegate2 { public: // constructor - takes pointer to an object and pointer to a member and stores // them in two private variables MessageDelegate2(R *object, A (R::*memberFunctionPointer)(T, U)) : m_Object(object), m_MemberFunctionPointer(memberFunctionPointer) { } ~MessageDelegate2() override {} // override function "Call" A Execute(T t, U u) const override { return (m_Object->*m_MemberFunctionPointer)(t, u); // execute member function } bool operator==(const MessageAbstractDelegate2 *c) const override { const MessageDelegate2 *cmd = dynamic_cast *>(c); if (!cmd) return false; if ((void *)this->m_Object != (void *)cmd->m_Object) return false; if (this->m_MemberFunctionPointer != cmd->m_MemberFunctionPointer) return false; return true; } MessageAbstractDelegate2 *Clone() const override { return new MessageDelegate2(m_Object, m_MemberFunctionPointer); } private: R *m_Object; // pointer to object A (R::*m_MemberFunctionPointer)(T, U); // pointer to member function }; template class MessageDelegate3 : public MessageAbstractDelegate3 { public: // constructor - takes pointer to an object and pointer to a member and stores // them in two private variables MessageDelegate3(R *object, A (R::*memberFunctionPointer)(T, U, V)) : m_Object(object), m_MemberFunctionPointer(memberFunctionPointer) { } ~MessageDelegate3() override {} // override function "Call" A Execute(T t, U u, V v) const override { return (m_Object->*m_MemberFunctionPointer)(t, u, v); // execute member function } bool operator==(const MessageAbstractDelegate3 *c) const override { const MessageDelegate3 *cmd = dynamic_cast *>(c); if (!cmd) return false; if ((void *)this->m_Object != (void *)cmd->m_Object) return false; if (this->m_MemberFunctionPointer != cmd->m_MemberFunctionPointer) return false; return true; } MessageAbstractDelegate3 *Clone() const override { return new MessageDelegate3(m_Object, m_MemberFunctionPointer); } private: R *m_Object; // pointer to object A (R::*m_MemberFunctionPointer)(T, U, V); // pointer to member function }; template class MessageDelegate4 : public MessageAbstractDelegate4 { public: // constructor - takes pointer to an object and pointer to a member and stores // them in two private variables MessageDelegate4(R *object, A (R::*memberFunctionPointer)(T, U, V, W)) : m_Object(object), m_MemberFunctionPointer(memberFunctionPointer) { } virtual ~MessageDelegate4() {} // override function "Call" virtual A Execute(T t, U u, V v, W w) const { return (m_Object->*m_MemberFunctionPointer)(t, u, v, w); // execute member function } bool operator==(const MessageAbstractDelegate4 *c) const { const MessageDelegate4 *cmd = dynamic_cast *>(c); if (!cmd) return false; if ((void *)this->m_Object != (void *)cmd->m_Object) return false; if (this->m_MemberFunctionPointer != cmd->m_MemberFunctionPointer) return false; return true; } MessageAbstractDelegate4 *Clone() const { return new MessageDelegate4(m_Object, m_MemberFunctionPointer); } private: R *m_Object; // pointer to object A (R::*m_MemberFunctionPointer)(T, U, V, W); // pointer to member function }; template class MessageBase { public: typedef std::vector ListenerList; virtual ~MessageBase() { for (auto iter = m_Listeners.begin(); iter != m_Listeners.end(); ++iter) { delete *iter; } } MessageBase() {} MessageBase(const MessageBase &o) { for (typename ListenerList::iterator iter = o.m_Listeners.begin(); iter != o.m_Listeners.end(); ++iter) { m_Listeners.push_back((*iter)->Clone()); } } MessageBase &operator=(const MessageBase &o) { MessageBase tmp(o); std::swap(tmp.m_Listeners, this->m_Listeners); return *this; } void AddListener(const AbstractDelegate &delegate) const { AbstractDelegate *msgCmd = delegate.Clone(); m_Mutex.Lock(); for (auto iter = m_Listeners.begin(); iter != m_Listeners.end(); ++iter) { if ((*iter)->operator==(msgCmd)) { delete msgCmd; m_Mutex.Unlock(); return; } } m_Listeners.push_back(msgCmd); m_Mutex.Unlock(); } void operator+=(const AbstractDelegate &delegate) const { this->AddListener(delegate); } void RemoveListener(const AbstractDelegate &delegate) const { m_Mutex.Lock(); for (auto iter = m_Listeners.begin(); iter != m_Listeners.end(); ++iter) { if ((*iter)->operator==(&delegate)) { delete *iter; m_Listeners.erase(iter); m_Mutex.Unlock(); return; } } m_Mutex.Unlock(); } void operator-=(const AbstractDelegate &delegate) const { this->RemoveListener(delegate); } const ListenerList &GetListeners() const { return m_Listeners; } bool HasListeners() const { return !m_Listeners.empty(); } bool IsEmpty() const { return m_Listeners.empty(); } protected: /** * \brief List of listeners. * * This is declared mutable for a reason: Imagine an object that sends out notifications and * someone gets a const Database object, because he/she should not write to the * database. He/she should anyway be able to register for notifications about changes in the database * -- this is why AddListener and RemoveListener are declared const. m_Listeners must be * mutable so that AddListener and RemoveListener can modify it regardless of the object's constness. */ mutable ListenerList m_Listeners; mutable itk::SimpleFastMutexLock m_Mutex; }; /** * \brief Event/message/notification class. * * \sa mitk::BinaryThresholdTool * \sa QmitkBinaryThresholdToolGUI * * This totally ITK, Qt, VTK, whatever toolkit independent class * allows one class to send out messages and another class to * receive these message. This class is templated over the * return type (A) of the callback functions. * There are variations of this class * (Message1, Message2, etc.) for sending * one, two or more parameters along with the messages. * * This is an implementation of the Observer pattern. * * \li There is no guarantee about the order of which observer is notified first. At the moment the observers which * register first will be notified first. * \li Notifications are synchronous, by direct method calls. There is no support for asynchronous messages. * * To conveniently add methods for registering/unregistering observers * to Message variables of your class, you can use the mitkNewMessageMacro * macros. */ template class Message : public MessageBase> { public: typedef MessageBase> Super; typedef typename Super::ListenerList ListenerList; - void Send() + void Send() const { ListenerList listeners; { this->m_Mutex.Lock(); listeners.assign(this->m_Listeners.begin(), this->m_Listeners.end()); this->m_Mutex.Unlock(); } for (auto iter = listeners.begin(); iter != listeners.end(); ++iter) { // notify each listener (*iter)->Execute(); } } - void operator()() { this->Send(); } + void operator()() const { this->Send(); } }; // message with 1 parameter and return type template class Message1 : public MessageBase> { public: typedef MessageBase> Super; typedef typename Super::ListenerList ListenerList; - void Send(T t) + void Send(T t) const { ListenerList listeners; { this->m_Mutex.Lock(); listeners.assign(this->m_Listeners.begin(), this->m_Listeners.end()); this->m_Mutex.Unlock(); } for (auto iter = listeners.begin(); iter != listeners.end(); ++iter) { // notify each listener (*iter)->Execute(t); } } - void operator()(T t) { this->Send(t); } + void operator() (T t) const { this->Send(t); } }; // message with 2 parameters and return type template class Message2 : public MessageBase> { public: typedef MessageBase> Super; typedef typename Super::ListenerList ListenerList; - void Send(T t, U u) + void Send(T t, U u) const { ListenerList listeners; { this->m_Mutex.Lock(); listeners.assign(this->m_Listeners.begin(), this->m_Listeners.end()); this->m_Mutex.Unlock(); } for (auto iter = listeners.begin(); iter != listeners.end(); ++iter) { // notify each listener (*iter)->Execute(t, u); } } - void operator()(T t, U u) { this->Send(t, u); } + void operator()(T t, U u) const { this->Send(t, u); } }; // message with 3 parameters and return type template class Message3 : public MessageBase> { public: typedef MessageBase> Super; typedef typename Super::ListenerList ListenerList; - void Send(T t, U u, V v) + void Send(T t, U u, V v) const { ListenerList listeners; { this->m_Mutex.Lock(); listeners.assign(this->m_Listeners.begin(), this->m_Listeners.end()); this->m_Mutex.Unlock(); } for (typename ListenerList::iterator iter = listeners.begin(); iter != listeners.end(); ++iter) { // notify each listener (*iter)->Execute(t, u, v); } } - void operator()(T t, U u, V v) { this->Send(t, u, v); } + void operator()(T t, U u, V v) const { this->Send(t, u, v); } }; // message with 4 parameters and return type template class Message4 : public MessageBase> { public: typedef MessageBase> Super; typedef typename Super::ListenerList ListenerList; - void Send(T t, U u, V v, W w) + void Send(T t, U u, V v, W w) const { ListenerList listeners; { this->m_Mutex.Lock(); listeners.assign(this->m_Listeners.begin(), this->m_Listeners.end()); this->m_Mutex.Unlock(); } for (typename ListenerList::iterator iter = listeners.begin(); iter != listeners.end(); ++iter) { // notify each listener (*iter)->Execute(t, u, v, w); } } - void operator()(T t, U u, V v, W w) { this->Send(t, u, v, w); } + void operator()(T t, U u, V v, W w) const { this->Send(t, u, v, w); } }; /* Here is an example how to use the macros and templates: * * // An object to be send around * class Law * { * private: * std::string m_Description; * * public: * * Law(const std::string law) : m_Description(law) * { } * * std::string GetDescription() const * { * return m_Description; * } * }; * * // The NewtonMachine will issue specific events * class NewtonMachine * { * mitkNewMessageMacro(AnalysisStarted); * mitkNewMessage1Macro(AnalysisStopped, bool); * mitkNewMessage1Macro(LawDiscovered, const Law&); * * public: * * void StartAnalysis() * { * // send the "started" signal * m_AnalysisStartedMessage(); * * // we found a new law of nature by creating one :-) * Law massLaw("F=ma"); * m_LawDiscoveredMessage(massLaw); * } * * void StopAnalysis() * { * // send the "stop" message with false, indicating * // that no error occured * m_AnalysisStoppedMessage(false); * } * }; * * class Observer * { * private: * * NewtonMachine* m_Machine; * * public: * * Observer(NewtonMachine* machine) : m_Machine(machine) * { * // Add "observers", i.e. function pointers to the machine * m_Machine->AddAnalysisStartedListener( * ::mitk::MessageDelegate(this, &Observer::MachineStarted)); * m_Machine->AddAnalysisStoppedListener( * ::mitk::MessageDelegate1(this, &Observer::MachineStopped)); * m_Machine->AddLawDiscoveredListener( * ::mitk::MessageDelegate1(this, &Observer::LawDiscovered)); * } * * ~Observer() * { * // Always remove your observers when finished * m_Machine->RemoveAnalysisStartedListener( * ::mitk::MessagDelegate(this, &Observer::MachineStarted)); * m_Machine->RemoveAnalysisStoppedListener( * ::mitk::MessageDelegate1(this, &Observer::MachineStopped)); * m_Machine->RemoveLawDiscoveredListener( * ::mitk::MessageDelegate1(this, &Observer::LawDiscovered)); * } * * void MachineStarted() * { * std::cout << "Observed machine has started" << std::endl; * } * * void MachineStopped(bool error) * { * std::cout << "Observed machine stopped " << (error ? "with an error" : "") << std::endl; * } * * void LawDiscovered(const Law& law) * { * std::cout << "New law of nature discovered: " << law.GetDescription() << std::endl; * } * }; * * NewtonMachine newtonMachine; * Observer observer(&newtonMachine); * * // This will send two events to registered observers * newtonMachine.StartAnalysis(); * // This will send one event to registered observers * newtonMachine.StopAnalysis(); * * Another example of how to use these message classes can be * found in the directory Testing, file mitkMessageTest.cpp * */ } // namespace #endif diff --git a/Modules/Core/include/mitkPixelType.h b/Modules/Core/include/mitkPixelType.h index 8717986986..3464c89f37 100644 --- a/Modules/Core/include/mitkPixelType.h +++ b/Modules/Core/include/mitkPixelType.h @@ -1,299 +1,299 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkPixelType_h #define mitkPixelType_h #include "mitkCommon.h" #include "mitkPixelTypeTraits.h" #include #include #include #include #include #include namespace mitk { template std::string PixelComponentTypeToString() { return itk::ImageIOBase::GetComponentTypeAsString(itk::ImageIOBase::MapPixelType::CType); } template std::string PixelTypeToString() { return std::string(); } /** * @brief Class for defining the data type of pixels * * To obtain additional type information not provided by this class * itk::ImageIOBase can be used by passing the return value of * PixelType::GetItkTypeId() to itk::ImageIOBase::SetPixelTypeInfo * and using the itk::ImageIOBase methods GetComponentType, * GetComponentTypeAsString, GetPixelType, GetPixelTypeAsString. * @ingroup Data */ class MITKCORE_EXPORT PixelType { public: typedef itk::ImageIOBase::IOPixelType ItkIOPixelType; typedef itk::ImageIOBase::IOComponentType ItkIOComponentType; PixelType(const mitk::PixelType &aPixelType); PixelType &operator=(const PixelType &other); itk::ImageIOBase::IOPixelType GetPixelType() const; /** * \brief Get the \a component type (the scalar (!) type). Each element * may contain m_NumberOfComponents (more than one) of these scalars. * */ int GetComponentType() const; /** * \brief Returns a string containing the ITK pixel type name. */ std::string GetPixelTypeAsString() const; /** * \brief Returns a string containing the name of the component. */ std::string GetComponentTypeAsString() const; /** * \brief Returns a string representing the pixel type and pixel components. */ std::string GetTypeAsString() const; /** * \brief Get size of the PixelType in bytes * * A RGBA PixelType of floats will return 4 * sizeof(float) */ size_t GetSize() const; /** * \brief Get the number of bits per element (of an * element) * * A vector of double with three components will return * 8*sizeof(double)*3. * \sa GetBitsPerComponent * \sa GetItkTypeId * \sa GetTypeId */ size_t GetBpe() const; /** * \brief Get the number of components of which each element consists * * Each pixel can consist of multiple components, e.g. RGB. */ size_t GetNumberOfComponents() const; /** * \brief Get the number of bits per components * \sa GetBitsPerComponent */ size_t GetBitsPerComponent() const; bool operator==(const PixelType &rhs) const; bool operator!=(const PixelType &rhs) const; ~PixelType(); private: friend PixelType MakePixelType(const itk::ImageIOBase *imageIO); template - friend PixelType MakePixelType(std::size_t numberOfComponents); + friend PixelType MakePixelType(std::size_t numOfComponents); template friend PixelType MakePixelType(); template friend PixelType MakePixelType(size_t); PixelType(const int componentType, const ItkIOPixelType pixelType, std::size_t bytesPerComponent, - std::size_t numberOfComponents, + std::size_t numOfComponents, const std::string &componentTypeName, const std::string &pixelTypeName); // default constructor is disabled on purpose PixelType(void); /** \brief the \a type_info of the scalar (!) component type. Each element may contain m_NumberOfComponents (more than one) of these scalars. */ int m_ComponentType; ItkIOPixelType m_PixelType; std::string m_ComponentTypeName; std::string m_PixelTypeName; std::size_t m_NumberOfComponents; std::size_t m_BytesPerComponent; }; /** * @brief deduct the PixelType for a given vtk image * * @param vtkimagedata the image the PixelType shall be deducted from * @return the mitk::PixelType */ MITKCORE_EXPORT mitk::PixelType MakePixelType(vtkImageData *vtkimagedata); /** * \brief A template method for creating a pixel type. */ template PixelType MakePixelType(std::size_t numOfComponents) { return PixelType(MapPixelType::value>::IOComponentType, MapPixelType::value>::IOPixelType, sizeof(ComponentT), numOfComponents, PixelComponentTypeToString(), PixelTypeToString()); } /** * \brief A template method for creating a pixel type. * * @deprecated, use version with one numOfComponents as function argument instead. */ template PixelType MakePixelType() { return MakePixelType(numOfComponents); } /** * \brief A helper template for compile-time checking of supported ITK image types. * * Unsupported image types will be marked by template specializations with * missing definitions; */ template struct AssertImageTypeIsValid { }; // The itk::VariableLengthVector pixel type is not supported in MITK if it is // used with an itk::Image (it cannot be represented as a mitk::Image object). // Use a itk::VectorImage instead. template struct AssertImageTypeIsValid, VImageDimension>>; /** \brief A template method for creating a MITK pixel type na ITK image type * * \param numOfComponents The number of components for the pixel type of the ITK image */ template PixelType MakePixelType(std::size_t numOfComponents) { AssertImageTypeIsValid(); // define new type, since the ::PixelType is used to distinguish between simple and compound types typedef typename ItkImageType::PixelType ImportPixelType; // get the component type ( is either directly ImportPixelType or ImportPixelType::ValueType for compound types ) typedef typename GetComponentType::ComponentType ComponentT; // The PixelType is the same as the ComponentT for simple types typedef typename ItkImageType::PixelType PixelT; // call the constructor return PixelType(MapPixelType::value>::IOComponentType, MapPixelType::value>::IOPixelType, sizeof(ComponentT), numOfComponents, PixelComponentTypeToString(), PixelTypeToString()); } /** \brief A template method for creating a MITK pixel type from an ITK image * pixel type and dimension * * \param numOfComponents The number of components for the pixel type \c TPixelType */ template PixelType MakePixelType(std::size_t numOfComponents) { typedef typename ImageTypeTrait::ImageType ItkImageType; return MakePixelType(numOfComponents); } /** \brief A template method for creating a MITK pixel type from an ITK image * pixel type and dimension * * For images where the number of components of the pixel type is determined at * runtime (e.g. pixel types like itk::VariableLengthVector) the * MakePixelType(std::size_t) function must be used. */ template PixelType MakePixelType() { if (ImageTypeTrait::IsVectorImage) { mitkThrow() << " Variable pixel type given but the length is not specified. Use the parametric MakePixelType( " "size_t ) method instead."; } // Use the InternalPixelType to get "1" for the number of components in case of // a itk::VectorImage typedef typename ItkImageType::InternalPixelType PixelT; const std::size_t numComp = ComponentsTrait::value, ItkImageType>::Size; // call the constructor return MakePixelType(numComp); } /** * \brief Create a MITK pixel type based on a itk::ImageIOBase object */ inline PixelType MakePixelType(const itk::ImageIOBase *imageIO) { return mitk::PixelType(imageIO->GetComponentType(), imageIO->GetPixelType(), imageIO->GetComponentSize(), imageIO->GetNumberOfComponents(), imageIO->GetComponentTypeAsString(imageIO->GetComponentType()), imageIO->GetPixelTypeAsString(imageIO->GetPixelType())); } /** \brief An interface to the MakePixelType method for creating scalar pixel types. * * Usage: for example MakeScalarPixelType() for a scalar short image */ template PixelType MakeScalarPixelType() { return MakePixelType(); } } // namespace mitk #endif /* mitkPixelType_h */ diff --git a/Modules/Core/include/mitkPlaneGeometry.h b/Modules/Core/include/mitkPlaneGeometry.h index f06e23e30d..7e61246ac8 100644 --- a/Modules/Core/include/mitkPlaneGeometry.h +++ b/Modules/Core/include/mitkPlaneGeometry.h @@ -1,614 +1,614 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ /** * \brief Describes the geometry of a plane object * * Describes a two-dimensional manifold, i.e., to put it simply, * an object that can be described using a 2D coordinate-system. * * PlaneGeometry can map points between 3D world coordinates * (in mm) and the described 2D coordinate-system (in mm) by first projecting * the 3D point onto the 2D manifold and then calculating the 2D-coordinates * (in mm). These 2D-mm-coordinates can be further converted into * 2D-unit-coordinates (e.g., pixels), giving a parameter representation of * the object with parameter values inside a rectangle * (e.g., [0,0]..[width, height]), which is the bounding box (bounding range * in z-direction always [0]..[1]). * * A PlaneGeometry describes the 2D representation within a 3D object (derived from BaseGeometry). For example, * a single CT-image (slice) is 2D in the sense that you can access the * pixels using 2D-coordinates, but is also 3D, as the pixels are really * voxels, thus have an extension (thickness) in the 3rd dimension. * * * Optionally, a reference BaseGeometry can be specified, which usually would * be the geometry associated with the underlying dataset. This is currently * used for calculating the intersection of inclined / rotated planes * (represented as PlaneGeometry) with the bounding box of the associated * BaseGeometry. * * \warning The PlaneGeometry are not necessarily up-to-date and not even * initialized. As described in the previous paragraph, one of the * Generate-/Copy-/UpdateOutputInformation methods have to initialize it. * mitk::BaseData::GetPlaneGeometry() makes sure, that the PlaneGeometry is * up-to-date before returning it (by setting the update extent appropriately * and calling UpdateOutputInformation). * * Rule: everything is in mm (or ms for temporal information) if not * stated otherwise. * \ingroup Geometry */ #ifndef PLANEGEOMETRY_H_HEADER_INCLUDED_C1C68A2C #define PLANEGEOMETRY_H_HEADER_INCLUDED_C1C68A2C #include "mitkBaseGeometry.h" #include "mitkRestorePlanePositionOperation.h" #include #include namespace mitk { template class Line; typedef Line Line3D; class PlaneGeometry; /** \deprecatedSince{2014_10} This class is deprecated. Please use PlaneGeometry instead. */ DEPRECATED(typedef PlaneGeometry Geometry2D); /** * \brief Describes a two-dimensional, rectangular plane * * \ingroup Geometry */ class MITKCORE_EXPORT PlaneGeometry : public BaseGeometry { public: mitkClassMacro(PlaneGeometry, BaseGeometry); /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); enum PlaneOrientation { Axial, Sagittal, Frontal, // also known as "Coronal" in mitk. None // This defines the PlaneGeometry for the 3D renderWindow which // curiously also needs a PlaneGeometry. This should be reconsidered some time. }; virtual void IndexToWorld(const Point2D &pt_units, Point2D &pt_mm) const; virtual void WorldToIndex(const Point2D &pt_mm, Point2D &pt_units) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## @deprecated First parameter (Point2D) is not used. If possible, please use void IndexToWorld(const // mitk::Vector2D& vec_units, mitk::Vector2D& vec_mm) const. //## For further information about coordinates types, please see the Geometry documentation virtual void IndexToWorld(const mitk::Point2D &atPt2d_untis, const mitk::Vector2D &vec_units, mitk::Vector2D &vec_mm) const; //##Documentation //## @brief Convert (continuous or discrete) index coordinates of a \em vector //## \a vec_units to world coordinates (in mm) //## For further information about coordinates types, please see the Geometry documentation virtual void IndexToWorld(const mitk::Vector2D &vec_units, mitk::Vector2D &vec_mm) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## @deprecated First parameter (Point2D) is not used. If possible, please use void WorldToIndex(const // mitk::Vector2D& vec_mm, mitk::Vector2D& vec_units) const. //## For further information about coordinates types, please see the Geometry documentation virtual void WorldToIndex(const mitk::Point2D &atPt2d_mm, const mitk::Vector2D &vec_mm, mitk::Vector2D &vec_units) const; //##Documentation //## @brief Convert world coordinates (in mm) of a \em vector //## \a vec_mm to (continuous!) index coordinates. //## For further information about coordinates types, please see the Geometry documentation virtual void WorldToIndex(const mitk::Vector2D &vec_mm, mitk::Vector2D &vec_units) const; /** * \brief Initialize a plane with orientation \a planeorientation * (default: axial) with respect to \a BaseGeometry (default: identity). * Spacing also taken from \a BaseGeometry. * * \warning A former version of this method created a geometry with unit * spacing. For unit spacing use * * \code * // for in-plane unit spacing: * thisgeometry->SetSizeInUnits(thisgeometry->GetExtentInMM(0), * thisgeometry->GetExtentInMM(1)); * // additionally, for unit spacing in normal direction (former version * // did not do this): * thisgeometry->SetExtentInMM(2, 1.0); * \endcode */ virtual void InitializeStandardPlane(const BaseGeometry *geometry3D, PlaneOrientation planeorientation = Axial, ScalarType zPosition = 0, bool frontside = true, bool rotated = false, bool top = true); /** * \brief Initialize a plane with orientation \a planeorientation * (default: axial) with respect to \a BaseGeometry (default: identity). * Spacing also taken from \a BaseGeometry. * * \param geometry3D * \param top if \a true, create plane at top, otherwise at bottom * (for PlaneOrientation Axial, for other plane locations respectively) * \param planeorientation * \param frontside * \param rotated */ virtual void InitializeStandardPlane(const BaseGeometry *geometry3D, bool top, PlaneOrientation planeorientation = Axial, bool frontside = true, bool rotated = false); /** * \brief Initialize a plane with orientation \a planeorientation * (default: axial) with respect to \a transform (default: identity) * given width and height in units. * * \a Rotated means rotated by 180 degrees (1/2 rotation) within the plane. * Rotation by 90 degrees (1/4 rotation) is not implemented as of now. * * \a Frontside/Backside: * Viewed from below = frontside in the axial case; * (radiologist's view versus neuro-surgeon's view, see: * http://www.itk.org/Wiki/images/e/ed/DICOM-OrientationDiagram-Radiologist-vs-NeuroSurgeon.png ) * Viewed from front = frontside in the coronal case; * Viewed from left = frontside in the sagittal case. * * \a Cave/Caution: Currently only RPI, LAI, LPS and RAS in the three standard planes are covered, * i.e. 12 cases of 144: 3 standard planes * 48 coordinate orientations = 144 cases. */ virtual void InitializeStandardPlane(ScalarType width, ScalarType height, const AffineTransform3D *transform = nullptr, PlaneOrientation planeorientation = Axial, ScalarType zPosition = 0, bool frontside = true, bool rotated = false, bool top = true); /** * \brief Initialize plane with orientation \a planeorientation * (default: axial) given width, height and spacing. * */ virtual void InitializeStandardPlane(ScalarType width, ScalarType height, const Vector3D &spacing, PlaneOrientation planeorientation = Axial, ScalarType zPosition = 0, bool frontside = true, bool rotated = false, bool top = true); /** * \brief Initialize plane by width and height in pixels, right-/down-vector * (itk) to describe orientation in world-space (vectors will be normalized) * and spacing (default: 1.0 mm in all directions). * * The vectors are normalized and multiplied by the respective spacing before * they are set in the matrix. * * This overloaded version of InitializeStandardPlane() creates only righthanded * coordinate orientations, unless spacing contains 1 or 3 negative entries. * */ virtual void InitializeStandardPlane(ScalarType width, ScalarType height, const Vector3D &rightVector, const Vector3D &downVector, const Vector3D *spacing = nullptr); /** * \brief Initialize plane by width and height in pixels, * right-/down-vector (vnl) to describe orientation in world-space (vectors * will be normalized) and spacing (default: 1.0 mm in all directions). * * The vectors are normalized and multiplied by the respective spacing * before they are set in the matrix. * * This overloaded version of InitializeStandardPlane() creates only righthanded * coordinate orientations, unless spacing contains 1 or 3 negative entries. * */ virtual void InitializeStandardPlane(ScalarType width, ScalarType height, const VnlVector &rightVector, const VnlVector &downVector, const Vector3D *spacing = nullptr); /** * \brief Initialize plane by right-/down-vector (itk) and spacing * (default: 1.0 mm in all directions). * * The length of the right-/-down-vector is used as width/height in units, * respectively. Then, the vectors are normalized and multiplied by the * respective spacing before they are set in the matrix. */ virtual void InitializeStandardPlane(const Vector3D &rightVector, const Vector3D &downVector, const Vector3D *spacing = nullptr); /** * \brief Initialize plane by right-/down-vector (vnl) and spacing * (default: 1.0 mm in all directions). * * The length of the right-/-down-vector is used as width/height in units, * respectively. Then, the vectors are normalized and multiplied by the * respective spacing before they are set in the matrix. */ virtual void InitializeStandardPlane(const VnlVector &rightVector, const VnlVector &downVector, const Vector3D *spacing = nullptr); /** * \brief Initialize plane by origin and normal (size is 1.0 mm in * all directions, direction of right-/down-vector valid but * undefined). * \warning This function can only produce righthanded coordinate orientation, not lefthanded. */ virtual void InitializePlane(const Point3D &origin, const Vector3D &normal); /** * \brief Initialize plane by right-/down-vector. * * \warning The vectors are set into the matrix as they are, * \em without normalization! * This function creates a righthanded IndexToWorldTransform, * only a negative thickness could still make it lefthanded. */ void SetMatrixByVectors(const VnlVector &rightVector, const VnlVector &downVector, ScalarType thickness = 1.0); /** * \brief Check if matrix is a rotation matrix: * - determinant is 1? * - R*R^T is ID? * Output warning otherwise. */ - static bool CheckRotationMatrix(AffineTransform3D *transform, double epsilon=mitk::eps); + static bool CheckRotationMatrix(AffineTransform3D *transform, double epsilon=1e-6); /** * \brief Normal of the plane * */ Vector3D GetNormal() const; /** * \brief Normal of the plane as VnlVector * */ VnlVector GetNormalVnl() const; virtual ScalarType SignedDistance(const Point3D &pt3d_mm) const; /** * \brief Calculates, whether a point is below or above the plane. There are two different *calculation methods, with or without consideration of the bounding box. */ virtual bool IsAbove(const Point3D &pt3d_mm, bool considerBoundingBox = false) const; /** * \brief Distance of the point from the plane * (bounding-box \em not considered) * */ ScalarType DistanceFromPlane(const Point3D &pt3d_mm) const; /** * \brief Signed distance of the point from the plane * (bounding-box \em not considered) * * > 0 : point is in the direction of the direction vector. */ inline ScalarType SignedDistanceFromPlane(const Point3D &pt3d_mm) const { ScalarType len = GetNormalVnl().two_norm(); if (len == 0) return 0; return (pt3d_mm - GetOrigin()) * GetNormal() / len; } /** * \brief Distance of the plane from another plane * (bounding-box \em not considered) * * Result is 0 if planes are not parallel. */ ScalarType DistanceFromPlane(const PlaneGeometry *plane) const { return fabs(SignedDistanceFromPlane(plane)); } /** * \brief Signed distance of the plane from another plane * (bounding-box \em not considered) * * Result is 0 if planes are not parallel. */ inline ScalarType SignedDistanceFromPlane(const PlaneGeometry *plane) const { if (IsParallel(plane)) { return SignedDistance(plane->GetOrigin()); } return 0; } /** * \brief Calculate the intersecting line of two planes * * \return \a true planes are intersecting * \return \a false planes do not intersect */ bool IntersectionLine(const PlaneGeometry *plane, Line3D &crossline) const; /** * \brief Calculate two points where another plane intersects the border of this plane * * \return number of intersection points (0..2). First interection point (if existing) * is returned in \a lineFrom, second in \a lineTo. */ unsigned int IntersectWithPlane2D(const PlaneGeometry *plane, Point2D &lineFrom, Point2D &lineTo) const; /** * \brief Calculate the angle between two planes * * \return angle in radiants */ double Angle(const PlaneGeometry *plane) const; /** * \brief Calculate the angle between the plane and a line * * \return angle in radiants */ double Angle(const Line3D &line) const; /** * \brief Calculate intersection point between the plane and a line * * \param line * \param intersectionPoint intersection point * \return \a true if \em unique intersection exists, i.e., if line * is \em not on or parallel to the plane */ bool IntersectionPoint(const Line3D &line, Point3D &intersectionPoint) const; /** * \brief Calculate line parameter of intersection point between the * plane and a line * * \param line * \param t parameter of line: intersection point is * line.GetPoint()+t*line.GetDirection() * \return \a true if \em unique intersection exists, i.e., if line * is \em not on or parallel to the plane */ bool IntersectionPointParam(const Line3D &line, double &t) const; /** * \brief Returns whether the plane is parallel to another plane * * @return true iff the normal vectors both point to the same or exactly oposit direction */ bool IsParallel(const PlaneGeometry *plane) const; /** * \brief Returns whether the point is on the plane * (bounding-box \em not considered) */ bool IsOnPlane(const Point3D &point) const; /** * \brief Returns whether the line is on the plane * (bounding-box \em not considered) */ bool IsOnPlane(const Line3D &line) const; /** * \brief Returns whether the plane is on the plane * (bounding-box \em not considered) * - * @return true iff the normal vector of the planes point to the same or the exactly oposit direction and + * @return true if the normal vector of the planes point to the same or the exactly oposit direction and * the distance of the planes is < eps * */ bool IsOnPlane(const PlaneGeometry *plane) const; /** * \brief Returns the lot from the point to the plane */ Point3D ProjectPointOntoPlane(const Point3D &pt) const; itk::LightObject::Pointer InternalClone() const override; /** Implements operation to re-orient the plane */ void ExecuteOperation(Operation *operation) override; /** * \brief Project a 3D point given in mm (\a pt3d_mm) onto the 2D * geometry. The result is a 2D point in mm (\a pt2d_mm). * * The result is a 2D point in mm (\a pt2d_mm) relative to the upper-left * corner of the geometry. To convert this point into units (e.g., pixels * in case of an image), use WorldToIndex. * \return true projection was possible * \sa Project(const mitk::Point3D &pt3d_mm, mitk::Point3D * &projectedPt3d_mm) */ virtual bool Map(const mitk::Point3D &pt3d_mm, mitk::Point2D &pt2d_mm) const; /** * \brief Converts a 2D point given in mm (\a pt2d_mm) relative to the * upper-left corner of the geometry into the corresponding * world-coordinate (a 3D point in mm, \a pt3d_mm). * * To convert a 2D point given in units (e.g., pixels in case of an * image) into a 2D point given in mm (as required by this method), use * IndexToWorld. */ virtual void Map(const mitk::Point2D &pt2d_mm, mitk::Point3D &pt3d_mm) const; /** * \brief Set the width and height of this 2D-geometry in units by calling * SetBounds. This does \a not change the extent in mm! * * For an image, this is the number of pixels in x-/y-direction. * \note In contrast to calling SetBounds directly, this does \a not change * the extent in mm! */ virtual void SetSizeInUnits(mitk::ScalarType width, mitk::ScalarType height); /** * \brief Project a 3D point given in mm (\a pt3d_mm) onto the 2D * geometry. The result is a 3D point in mm (\a projectedPt3d_mm). * * \return true projection was possible */ virtual bool Project(const mitk::Point3D &pt3d_mm, mitk::Point3D &projectedPt3d_mm) const; /** * \brief Project a 3D vector given in mm (\a vec3d_mm) onto the 2D * geometry. The result is a 2D vector in mm (\a vec2d_mm). * * The result is a 2D vector in mm (\a vec2d_mm) relative to the * upper-left * corner of the geometry. To convert this point into units (e.g., pixels * in case of an image), use WorldToIndex. * \return true projection was possible * \sa Project(const mitk::Vector3D &vec3d_mm, mitk::Vector3D * &projectedVec3d_mm) */ virtual bool Map(const mitk::Point3D &atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector2D &vec2d_mm) const; /** * \brief Converts a 2D vector given in mm (\a vec2d_mm) relative to the * upper-left corner of the geometry into the corresponding * world-coordinate (a 3D vector in mm, \a vec3d_mm). * * To convert a 2D vector given in units (e.g., pixels in case of an * image) into a 2D vector given in mm (as required by this method), use * IndexToWorld. */ virtual void Map(const mitk::Point2D &atPt2d_mm, const mitk::Vector2D &vec2d_mm, mitk::Vector3D &vec3d_mm) const; /** * \brief Project a 3D vector given in mm (\a vec3d_mm) onto the 2D * geometry. The result is a 3D vector in mm (\a projectedVec3d_mm). * * DEPRECATED. Use Project(vector,vector) instead * * \return true projection was possible */ virtual bool Project(const mitk::Point3D &atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const; /** * \brief Project a 3D vector given in mm (\a vec3d_mm) onto the 2D * geometry. The result is a 3D vector in mm (\a projectedVec3d_mm). * * \return true projection was possible */ virtual bool Project(const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const; /** * \brief Distance of the point from the geometry * (bounding-box \em not considered) * */ inline ScalarType Distance(const Point3D &pt3d_mm) const { return fabs(SignedDistance(pt3d_mm)); } /** * \brief Set the geometrical frame of reference in which this PlaneGeometry * is placed. * * This would usually be the BaseGeometry of the underlying dataset, but * setting it is optional. */ void SetReferenceGeometry(const mitk::BaseGeometry *geometry); /** * \brief Get the geometrical frame of reference for this PlaneGeometry. */ const BaseGeometry *GetReferenceGeometry() const; bool HasReferenceGeometry() const; static std::vector< int > CalculateDominantAxes(mitk::AffineTransform3D::MatrixType::InternalMatrixType& rotation_matrix); protected: PlaneGeometry(); PlaneGeometry(const PlaneGeometry &other); ~PlaneGeometry() override; void PrintSelf(std::ostream &os, itk::Indent indent) const override; const mitk::BaseGeometry *m_ReferenceGeometry; //##Documentation //## @brief PreSetSpacing //## //## These virtual function allows a different beahiour in subclasses. //## Do implement them in every subclass of BaseGeometry. If not needed, use //## {Superclass::PreSetSpacing();}; void PreSetSpacing(const mitk::Vector3D &aSpacing) override { Superclass::PreSetSpacing(aSpacing); }; //##Documentation //## @brief CheckBounds //## //## This function is called in SetBounds. Assertions can be implemented in this function (see PlaneGeometry.cpp). //## If you implement this function in a subclass, make sure, that all classes were your class inherits from //## have an implementation of CheckBounds //## (e.g. inheritance BaseGeometry <- A <- B. Implementation of CheckBounds in class B needs implementation in A as // well!) void CheckBounds(const BoundsArrayType &bounds) override; //##Documentation //## @brief CheckIndexToWorldTransform //## //## This function is called in SetIndexToWorldTransform. Assertions can be implemented in this function (see // PlaneGeometry.cpp). //## In Subclasses of BaseGeometry, implement own conditions or call Superclass::CheckBounds(bounds);. void CheckIndexToWorldTransform(mitk::AffineTransform3D *transform) override; private: /** * \brief Compares plane with another plane: \a true if IsOnPlane * (bounding-box \em not considered) */ virtual bool operator==(const PlaneGeometry *) const { return false; }; /** * \brief Compares plane with another plane: \a false if IsOnPlane * (bounding-box \em not considered) */ virtual bool operator!=(const PlaneGeometry *) const { return false; }; }; } // namespace mitk #endif /* PLANEGEOMETRY_H_HEADER_INCLUDED_C1C68A2C */ diff --git a/Modules/Core/include/mitkPoint.h b/Modules/Core/include/mitkPoint.h index a0f0cc3b85..779deb73e8 100644 --- a/Modules/Core/include/mitkPoint.h +++ b/Modules/Core/include/mitkPoint.h @@ -1,135 +1,135 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef MITKPOINT_H_ #define MITKPOINT_H_ #include #include "mitkArray.h" #include "mitkEqual.h" #include "mitkNumericConstants.h" namespace mitk { //##Documentation //##@brief enumeration of the type a point can be enum PointSpecificationType { PTUNDEFINED = 0, PTSTART, PTCORNER, PTEDGE, PTEND }; template class Point : public itk::Point { public: /** Default constructor has nothing to do. */ explicit Point() : itk::Point() {} /** Pass-through constructors for the Array base class. */ template explicit Point(const Point &r) : itk::Point(r) { } template explicit Point(const TPointValueType r[NPointDimension]) : itk::Point(r) { } template - Point(const TPointValueType &v) : itk::Point(v) + explicit Point(const TPointValueType &v) : itk::Point(v) { } Point(const mitk::Point &r) : itk::Point(r) { } Point(const TCoordRep r[NPointDimension]) : itk::Point(r) {} Point(const TCoordRep &v) : itk::Point(v) {} Point(const itk::Point &p) : itk::Point(p) { } /** * Copies the elements from array array to this. * Note that this method will assign doubles to floats without complaining! * * @param array the array whose values shall be copied. Must overload [] operator. */ template void FillPoint(const ArrayType &array) { itk::FixedArray *thisP = dynamic_cast *>(this); mitk::FillArray(*thisP, array); } /** * Copies the values stored in this point into the array array. * * @param array the array which should store the values of this. */ template void ToArray(ArrayType array) const { mitk::ToArray(array, *this); } }; typedef Point Point2D; typedef Point Point3D; typedef Point Point4D; typedef Point Point2I; typedef Point Point3I; typedef Point Point4I; /** * @ingroup MITKTestingAPI * * @param point1 Point to compare. * @param point2 Point to compare. * @param eps Tolerance for floating point comparison. * @param verbose Flag indicating detailed console output. * @return True if points are equal. */ template inline bool Equal(const itk::Point &point1, const itk::Point &point2, TCoordRep eps = mitk::eps, bool verbose = false) { bool isEqual = true; typename itk::Point::VectorType diff = point1 - point2; for (unsigned int i = 0; i < NPointDimension; i++) { if (DifferenceBiggerOrEqualEps(diff[i], eps)) { isEqual = false; break; } } ConditionalOutputOfDifference(point1, point2, eps, verbose, isEqual); return isEqual; } } // namespace mitk #endif /* MITKPOINT_H_ */ diff --git a/Modules/Core/include/mitkVector.h b/Modules/Core/include/mitkVector.h index 095a9de995..e62c166238 100644 --- a/Modules/Core/include/mitkVector.h +++ b/Modules/Core/include/mitkVector.h @@ -1,232 +1,239 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 MITKVECTOR_H_ #define MITKVECTOR_H_ #include #include #include #include "mitkArray.h" #include "mitkEqual.h" #include "mitkExceptionMacro.h" #include "mitkNumericConstants.h" namespace mitk { template class Vector : public itk::Vector { public: /** * @brief Default constructor has nothing to do. */ explicit Vector() : itk::Vector() {} /** * @brief Copy constructor. */ explicit Vector(const mitk::Vector &r) : itk::Vector(r) { } + /** Pass-through assignment operator for the Vector base class. */ + Vector & operator=(const Vector & r) + { + itk::Vector::operator=(r); + return *this; + } + /** * @brief Constructor to convert from itk::Vector to mitk::Vector. */ Vector(const itk::Vector &r) : itk::Vector(r) { } /** * @brief Constructor to convert an array to mitk::Vector * @param r the array. * @attention must have NVectorDimension valid arguments! */ Vector(const TCoordRep r[NVectorDimension]) : itk::Vector(r) { } /** * Constructor to initialize entire vector to one value. */ Vector(const TCoordRep &v) : itk::Vector(v) {} /** * @brief Constructor for vnl_vectors. * @throws mitk::Exception if vnl_vector.size() != NVectorDimension. */ Vector(const vnl_vector &vnlVector) : itk::Vector() { if (vnlVector.size() != NVectorDimension) mitkThrow() << "when constructing mitk::Vector from vnl_vector: sizes didn't match: mitk::Vector " << NVectorDimension << "; vnl_vector " << vnlVector.size(); for (unsigned int var = 0; (var < NVectorDimension) && (var < vnlVector.size()); ++var) { this->SetElement(var, vnlVector.get(var)); } } /** * @brief Constructor for vnl_vector_fixed. */ Vector(const vnl_vector_fixed &vnlVectorFixed) : itk::Vector() { for (unsigned int var = 0; var < NVectorDimension; ++var) { this->SetElement(var, vnlVectorFixed[var]); } }; /** * Copies the elements from array array to this. * Note that this method will assign doubles to floats without complaining! * * @param array the array whose values shall be copied. Must overload [] operator. */ template void FillVector(const ArrayType &array) { itk::FixedArray *thisP = dynamic_cast *>(this); mitk::FillArray(*thisP, array); } /** * Copies the values stored in this vector into the array array.d * * @param array the array which should store the values of this. */ template void ToArray(ArrayType array) const { mitk::ToArray(array, *this); } /** * @brief User defined conversion of mitk::Vector to vnl_vector. * Note: the conversion to mitk::Vector to vnl_vector_fixed has not been implemented since this * would collide with the conversion vnl_vector to vnl_vector_fixed provided by vnl. */ operator vnl_vector() const { return this->GetVnlVector(); } }; // end mitk::Vector // convenience typedefs for often used mitk::Vector representations. typedef Vector Vector2D; typedef Vector Vector3D; typedef Vector Vector4D; // other vector types used in MITK typedef vnl_vector VnlVector; // The equal methods to compare vectors for equality are below: /** * @ingroup MITKTestingAPI * * @param vector1 Vector to compare. * @param vector2 Vector to compare. * @param eps Tolerance for floating point comparison. * @param verbose Flag indicating detailed console output. * @return True if vectors are equal. */ template inline bool Equal(const itk::Vector &vector1, const itk::Vector &vector2, TCoordRep eps = mitk::eps, bool verbose = false) { bool isEqual = true; typename itk::Vector::VectorType diff = vector1 - vector2; for (unsigned int i = 0; i < NPointDimension; i++) { if (DifferenceBiggerOrEqualEps(diff[i], eps)) { isEqual = false; break; } } ConditionalOutputOfDifference(vector1, vector2, eps, verbose, isEqual); return isEqual; } /** * @ingroup MITKTestingAPI * * @param vector1 Vector to compare. * @param vector2 Vector to compare. * @param eps Tolerance for floating point comparison. * @param verbose Flag indicating detailed console output. * @return True if vectors are equal. */ inline bool Equal(const mitk::VnlVector &vector1, const mitk::VnlVector &vector2, ScalarType eps = mitk::eps, bool verbose = false) { bool isEqual = true; mitk::VnlVector diff = vector1 - vector2; for (unsigned int i = 0; i < diff.size(); i++) { if (DifferenceBiggerOrEqualEps(diff[i], eps)) { isEqual = false; break; } } ConditionalOutputOfDifference(vector1, vector2, eps, verbose, isEqual); return isEqual; } /** * @ingroup MITKTestingAPI * * @param vector1 Vector to compare. * @param vector2 Vector to compare. * @param eps Tolerance for floating point comparison. * @param verbose Flag indicating detailed console output. * @return True if vectors are equal. */ template inline bool Equal(const vnl_vector_fixed &vector1, const vnl_vector_fixed &vector2, TCoordRep eps = mitk::eps, bool verbose = false) { vnl_vector_fixed diff = vector1 - vector2; bool isEqual = true; for (unsigned int i = 0; i < diff.size(); i++) { if (DifferenceBiggerOrEqualEps(diff[i], eps)) { isEqual = false; break; } } ConditionalOutputOfDifference(vector1, vector2, eps, verbose, isEqual); return isEqual; } } // end namespace mitk #endif /* MITKVECTOR_H_ */ diff --git a/Modules/Core/src/DataManagement/mitkArbitraryTimeGeometry.cpp b/Modules/Core/src/DataManagement/mitkArbitraryTimeGeometry.cpp index e593a15eca..f287df5d52 100644 --- a/Modules/Core/src/DataManagement/mitkArbitraryTimeGeometry.cpp +++ b/Modules/Core/src/DataManagement/mitkArbitraryTimeGeometry.cpp @@ -1,307 +1,344 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include #include mitk::ArbitraryTimeGeometry::ArbitraryTimeGeometry() = default; mitk::ArbitraryTimeGeometry::~ArbitraryTimeGeometry() = default; void mitk::ArbitraryTimeGeometry::Initialize() { this->ClearAllGeometries(); Geometry3D::Pointer geo = Geometry3D::New(); geo->Initialize(); this->AppendNewTimeStep(geo, 0, 1); Update(); } mitk::TimeStepType mitk::ArbitraryTimeGeometry::CountTimeSteps() const { return static_cast(m_GeometryVector.size()); } mitk::TimePointType mitk::ArbitraryTimeGeometry::GetMinimumTimePoint() const { return m_MinimumTimePoints.empty() ? 0.0 : m_MinimumTimePoints.front(); } mitk::TimePointType mitk::ArbitraryTimeGeometry::GetMaximumTimePoint() const { TimePointType result = 0; if ( !m_MaximumTimePoints.empty() ) { result = m_MaximumTimePoints.back(); } + + /////////////////////////////////////// + // Workarround T27883. See https://phabricator.mitk.org/T27883#219473 for more details. + // This workarround should be removed as soon as T28262 is solved! + if (this->HasCollapsedFinalTimeStep()) + { + result = m_MinimumTimePoints.back() + 1; + } + // End of workarround for T27883 + ////////////////////////////////////// + return result; } mitk::TimePointType mitk::ArbitraryTimeGeometry::GetMinimumTimePoint( TimeStepType step ) const { - TimePointType result = GetMinimumTimePoint(); - if (step > 0 && step <= m_MaximumTimePoints.size()) - { - result = m_MaximumTimePoints[step - 1]; - } - return result; + return step < m_MinimumTimePoints.size() ? m_MinimumTimePoints[step] : 0.0f; }; mitk::TimePointType mitk::ArbitraryTimeGeometry::GetMaximumTimePoint( TimeStepType step ) const { TimePointType result = 0; if (step < m_MaximumTimePoints.size()) { result = m_MaximumTimePoints[step]; } + + /////////////////////////////////////// + // Workarround T27883. See https://phabricator.mitk.org/T27883#219473 for more details. + // This workarround should be removed as soon as T28262 is solved! + if (step + 1 == m_MaximumTimePoints.size() && this->HasCollapsedFinalTimeStep()) + { + result = m_MinimumTimePoints[step] + 1; + } + // End of workarround for T27883 + ////////////////////////////////////// + return result; }; mitk::TimeBounds mitk::ArbitraryTimeGeometry::GetTimeBounds() const { TimeBounds bounds; bounds[0] = this->GetMinimumTimePoint(); bounds[1] = this->GetMaximumTimePoint(); return bounds; } mitk::TimeBounds mitk::ArbitraryTimeGeometry::GetTimeBounds(TimeStepType step) const { TimeBounds bounds; bounds[0] = this->GetMinimumTimePoint( step ); bounds[1] = this->GetMaximumTimePoint( step ); return bounds; } bool mitk::ArbitraryTimeGeometry::IsValidTimePoint(TimePointType timePoint) const { return this->GetMinimumTimePoint() <= timePoint && (timePoint < this->GetMaximumTimePoint() || (this->HasCollapsedFinalTimeStep() && timePoint <= this->GetMaximumTimePoint())); } bool mitk::ArbitraryTimeGeometry::IsValidTimeStep(TimeStepType timeStep) const { return timeStep < this->CountTimeSteps(); } mitk::TimePointType mitk::ArbitraryTimeGeometry::TimeStepToTimePoint( TimeStepType timeStep ) const { TimePointType result = 0.0; if (timeStep < m_MinimumTimePoints.size() ) { result = m_MinimumTimePoints[timeStep]; } return result; } mitk::TimeStepType mitk::ArbitraryTimeGeometry::TimePointToTimeStep(TimePointType timePoint) const { mitk::TimeStepType result = 0; if (timePoint >= GetMinimumTimePoint()) { for (auto pos = m_MaximumTimePoints.cbegin(); pos != m_MaximumTimePoints.cend(); ++pos) { - if (timePoint < *pos || (pos==std::prev(m_MaximumTimePoints.cend()) && timePoint <= *pos && this->HasCollapsedFinalTimeStep())) + /////////////////////////////////////// + // Workarround T27883. See https://phabricator.mitk.org/T27883#219473 for more details. + // The part ("+1.") inline marked as workarround should be removed as soon as T28262 is solved! + if (timePoint < *pos + || (pos == std::prev(m_MaximumTimePoints.cend()) + && timePoint <= *pos +1//<- +1 is the workarround + && this->HasCollapsedFinalTimeStep())) { break; } + // End of workarround for T27883 + ////////////////////////////////////// ++result; } } return result; } mitk::BaseGeometry::Pointer mitk::ArbitraryTimeGeometry::GetGeometryForTimeStep(TimeStepType timeStep) const { if ( IsValidTimeStep( timeStep ) ) { return m_GeometryVector[timeStep]; } else { return nullptr; } } mitk::BaseGeometry::Pointer mitk::ArbitraryTimeGeometry::GetGeometryForTimePoint( TimePointType timePoint ) const { if ( this->IsValidTimePoint( timePoint ) ) { const TimeStepType timeStep = this->TimePointToTimeStep( timePoint ); return this->GetGeometryForTimeStep( timeStep ); } else { return nullptr; } } mitk::BaseGeometry::Pointer mitk::ArbitraryTimeGeometry::GetGeometryCloneForTimeStep( TimeStepType timeStep ) const { if ( timeStep >= m_GeometryVector.size() ) return nullptr; return m_GeometryVector[timeStep]->Clone(); } bool mitk::ArbitraryTimeGeometry::IsValid() const { bool isValid = true; isValid &= m_GeometryVector.size() > 0; return isValid; } void mitk::ArbitraryTimeGeometry::ClearAllGeometries() { m_GeometryVector.clear(); m_MinimumTimePoints.clear(); m_MaximumTimePoints.clear(); } void mitk::ArbitraryTimeGeometry::ReserveSpaceForGeometries( TimeStepType numberOfGeometries ) { m_GeometryVector.reserve( numberOfGeometries ); m_MinimumTimePoints.reserve( numberOfGeometries ); m_MaximumTimePoints.reserve( numberOfGeometries ); } void mitk::ArbitraryTimeGeometry::Expand( mitk::TimeStepType size ) { m_GeometryVector.reserve( size ); const mitk::TimeStepType lastIndex = this->CountTimeSteps() - 1; const TimePointType minTP = this->GetMinimumTimePoint( lastIndex ); TimePointType maxTP = this->GetMaximumTimePoint( lastIndex ); const TimePointType duration = maxTP - minTP; while (m_GeometryVector.size() < size) { m_GeometryVector.push_back( Geometry3D::New().GetPointer() ); m_MinimumTimePoints.push_back( maxTP ); maxTP += duration; m_MaximumTimePoints.push_back( maxTP ); } } void mitk::ArbitraryTimeGeometry::ReplaceTimeStepGeometries(const BaseGeometry *geometry) { for ( auto pos = m_GeometryVector.begin(); pos != m_GeometryVector.end(); ++pos ) { *pos = geometry->Clone(); } } void mitk::ArbitraryTimeGeometry::SetTimeStepGeometry(BaseGeometry *geometry, TimeStepType timeStep) { assert( timeStep <= m_GeometryVector.size() ); if ( timeStep == m_GeometryVector.size() ) { m_GeometryVector.push_back( geometry ); } m_GeometryVector[timeStep] = geometry; } itk::LightObject::Pointer mitk::ArbitraryTimeGeometry::InternalClone() const { itk::LightObject::Pointer parent = Superclass::InternalClone(); ArbitraryTimeGeometry::Pointer newTimeGeometry = dynamic_cast(parent.GetPointer()); newTimeGeometry->m_MinimumTimePoints = this->m_MinimumTimePoints; newTimeGeometry->m_MaximumTimePoints = this->m_MaximumTimePoints; newTimeGeometry->m_GeometryVector.clear(); for (TimeStepType i = 0; i < CountTimeSteps(); ++i) { newTimeGeometry->m_GeometryVector.push_back( this->m_GeometryVector[i]->Clone() ); } return parent; } void mitk::ArbitraryTimeGeometry::AppendNewTimeStep(BaseGeometry *geometry, TimePointType minimumTimePoint, TimePointType maximumTimePoint) { if ( !geometry ) { mitkThrow() << "Cannot append geometry to time geometry. Invalid geometry passed (nullptr pointer)."; } if (maximumTimePoint < minimumTimePoint) { mitkThrow() << "Cannot append geometry to time geometry. Time bound conflict. Maxmimum time point ("< minimumTimePoint ) { mitkThrow() << "Cannot append geometry to time geometry. Time bound conflict new time point and currently last time point overlapp."; } } m_GeometryVector.push_back( geometry ); m_MinimumTimePoints.push_back( minimumTimePoint ); m_MaximumTimePoints.push_back( maximumTimePoint ); } void mitk::ArbitraryTimeGeometry::AppendNewTimeStepClone(const BaseGeometry *geometry, TimePointType minimumTimePoint, TimePointType maximumTimePoint) { BaseGeometry::Pointer clone = geometry->Clone(); this->AppendNewTimeStep(clone, minimumTimePoint, maximumTimePoint); }; void mitk::ArbitraryTimeGeometry::PrintSelf(std::ostream &os, itk::Indent indent) const { Superclass::PrintSelf( os, indent ); os << indent << " MinimumTimePoint: " << this->GetMinimumTimePoint() << " ms" << std::endl; os << indent << " MaximumTimePoint: " << this->GetMaximumTimePoint() << " ms" << std::endl; os << std::endl; os << indent << " min TimeBounds: " << std::endl; for (TimeStepType i = 0; i < m_MinimumTimePoints.size(); ++i) { os << indent.GetNextIndent() << "Step " << i << ": " << m_MinimumTimePoints[i] << " ms" << std::endl; } os << std::endl; os << indent << " max TimeBounds: " << std::endl; for (TimeStepType i = 0; i < m_MaximumTimePoints.size(); ++i) { os << indent.GetNextIndent() << "Step " << i << ": " << m_MaximumTimePoints[i] << " ms" << std::endl; } + /////////////////////////////////////// + // Workarround T27883. See https://phabricator.mitk.org/T27883#219473 for more details. + // This workarround should be removed as soon as T28262 is solved! + if (this->HasCollapsedFinalTimeStep()) + { + os << indent << "Caution: This time geometry has a collapsed finale time step." << std::endl; + os << indent << " Most likely reason is that no duration could be deduced from the original data" << std::endl; + os << indent << " (e.g. DICOM dynamic series stored as single frame images)." << std::endl; + os << indent << " Currently we expand it by 1 ms (see T27883 for more details)." << std::endl; + } + // End of workarround for T27883 + ////////////////////////////////////// } bool mitk::ArbitraryTimeGeometry::HasCollapsedFinalTimeStep() const { bool result = false; if (!m_MaximumTimePoints.empty() && !m_MinimumTimePoints.empty()) { result = m_MinimumTimePoints.back() == m_MaximumTimePoints.back(); } return result; } diff --git a/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp b/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp index 038edbc41b..ba87e198ea 100644 --- a/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp +++ b/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp @@ -1,1096 +1,1096 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include #include #include #include "mitkApplyTransformMatrixOperation.h" #include "mitkBaseGeometry.h" #include "mitkGeometryTransformHolder.h" #include "mitkInteractionConst.h" #include "mitkMatrixConvert.h" #include "mitkModifiedLock.h" #include "mitkPointOperation.h" #include "mitkRestorePlanePositionOperation.h" #include "mitkRotationOperation.h" #include "mitkScaleOperation.h" #include "mitkVector.h" #include "mitkMatrix.h" mitk::BaseGeometry::BaseGeometry() : Superclass(), mitk::OperationActor(), m_FrameOfReferenceID(0), m_IndexToWorldTransformLastModified(0), m_ImageGeometry(false), m_ModifiedLockFlag(false), m_ModifiedCalledFlag(false) { m_GeometryTransform = new GeometryTransformHolder(); Initialize(); } mitk::BaseGeometry::BaseGeometry(const BaseGeometry &other) : Superclass(), mitk::OperationActor(), m_FrameOfReferenceID(other.m_FrameOfReferenceID), m_IndexToWorldTransformLastModified(other.m_IndexToWorldTransformLastModified), m_ImageGeometry(other.m_ImageGeometry), m_ModifiedLockFlag(false), m_ModifiedCalledFlag(false) { m_GeometryTransform = new GeometryTransformHolder(*other.GetGeometryTransformHolder()); other.InitializeGeometry(this); } mitk::BaseGeometry::~BaseGeometry() { delete m_GeometryTransform; } void mitk::BaseGeometry::SetVtkMatrixDeepCopy(vtkTransform *vtktransform) { m_GeometryTransform->SetVtkMatrixDeepCopy(vtktransform); } const mitk::Point3D mitk::BaseGeometry::GetOrigin() const { return m_GeometryTransform->GetOrigin(); } void mitk::BaseGeometry::SetOrigin(const Point3D &origin) { mitk::ModifiedLock lock(this); if (origin != GetOrigin()) { m_GeometryTransform->SetOrigin(origin); Modified(); } } const mitk::Vector3D mitk::BaseGeometry::GetSpacing() const { return m_GeometryTransform->GetSpacing(); } void mitk::BaseGeometry::Initialize() { float b[6] = {0, 1, 0, 1, 0, 1}; SetFloatBounds(b); m_GeometryTransform->Initialize(); m_FrameOfReferenceID = 0; m_ImageGeometry = false; } void mitk::BaseGeometry::SetFloatBounds(const float bounds[6]) { mitk::BoundingBox::BoundsArrayType b; const float *input = bounds; int i = 0; for (mitk::BoundingBox::BoundsArrayType::Iterator it = b.Begin(); i < 6; ++i) *it++ = (mitk::ScalarType)*input++; SetBounds(b); } void mitk::BaseGeometry::SetFloatBounds(const double bounds[6]) { mitk::BoundingBox::BoundsArrayType b; const double *input = bounds; int i = 0; for (mitk::BoundingBox::BoundsArrayType::Iterator it = b.Begin(); i < 6; ++i) *it++ = (mitk::ScalarType)*input++; SetBounds(b); } /** Initialize the geometry */ void mitk::BaseGeometry::InitializeGeometry(BaseGeometry *newGeometry) const { newGeometry->SetBounds(m_BoundingBox->GetBounds()); newGeometry->SetFrameOfReferenceID(GetFrameOfReferenceID()); newGeometry->InitializeGeometryTransformHolder(this); newGeometry->m_ImageGeometry = m_ImageGeometry; } void mitk::BaseGeometry::InitializeGeometryTransformHolder(const BaseGeometry *otherGeometry) { this->m_GeometryTransform->Initialize(otherGeometry->GetGeometryTransformHolder()); } /** Set the bounds */ void mitk::BaseGeometry::SetBounds(const BoundsArrayType &bounds) { mitk::ModifiedLock lock(this); this->CheckBounds(bounds); m_BoundingBox = BoundingBoxType::New(); BoundingBoxType::PointsContainer::Pointer pointscontainer = BoundingBoxType::PointsContainer::New(); BoundingBoxType::PointType p; BoundingBoxType::PointIdentifier pointid; for (pointid = 0; pointid < 2; ++pointid) { unsigned int i; for (i = 0; i < m_NDimensions; ++i) { p[i] = bounds[2 * i + pointid]; } pointscontainer->InsertElement(pointid, p); } m_BoundingBox->SetPoints(pointscontainer); m_BoundingBox->ComputeBoundingBox(); this->Modified(); } void mitk::BaseGeometry::SetIndexToWorldTransform(mitk::AffineTransform3D *transform) { mitk::ModifiedLock lock(this); CheckIndexToWorldTransform(transform); m_GeometryTransform->SetIndexToWorldTransform(transform); Modified(); } void mitk::BaseGeometry::SetIndexToWorldTransformWithoutChangingSpacing(mitk::AffineTransform3D *transform) { // security check mitk::Vector3D originalSpacing = this->GetSpacing(); mitk::ModifiedLock lock(this); CheckIndexToWorldTransform(transform); m_GeometryTransform->SetIndexToWorldTransformWithoutChangingSpacing(transform); Modified(); // Security check. Spacig must not have changed if (!mitk::Equal(originalSpacing, this->GetSpacing())) { MITK_WARN << "Spacing has changed in a method, where the spacing must not change."; assert(false); } } const mitk::BaseGeometry::BoundsArrayType mitk::BaseGeometry::GetBounds() const { assert(m_BoundingBox.IsNotNull()); return m_BoundingBox->GetBounds(); } bool mitk::BaseGeometry::IsValid() const { return true; } void mitk::BaseGeometry::SetSpacing(const mitk::Vector3D &aSpacing, bool enforceSetSpacing) { PreSetSpacing(aSpacing); _SetSpacing(aSpacing, enforceSetSpacing); } void mitk::BaseGeometry::_SetSpacing(const mitk::Vector3D &aSpacing, bool enforceSetSpacing) { m_GeometryTransform->SetSpacing(aSpacing, enforceSetSpacing); } mitk::Vector3D mitk::BaseGeometry::GetAxisVector(unsigned int direction) const { Vector3D frontToBack; frontToBack.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(direction)); frontToBack *= GetExtent(direction); return frontToBack; } mitk::ScalarType mitk::BaseGeometry::GetExtent(unsigned int direction) const { assert(m_BoundingBox.IsNotNull()); if (direction >= m_NDimensions) mitkThrow() << "Direction is too big. This geometry is for 3D Data"; BoundsArrayType bounds = m_BoundingBox->GetBounds(); return bounds[direction * 2 + 1] - bounds[direction * 2]; } bool mitk::BaseGeometry::Is2DConvertable() { bool isConvertableWithoutLoss = true; do { if (this->GetSpacing()[2] != 1) { isConvertableWithoutLoss = false; break; } if (this->GetOrigin()[2] != 0) { isConvertableWithoutLoss = false; break; } mitk::Vector3D col0, col1, col2; col0.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(0)); col1.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(1)); col2.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(2)); if ((col0[2] != 0) || (col1[2] != 0) || (col2[0] != 0) || (col2[1] != 0) || (col2[2] != 1)) { isConvertableWithoutLoss = false; break; } } while (false); return isConvertableWithoutLoss; } mitk::Point3D mitk::BaseGeometry::GetCenter() const { assert(m_BoundingBox.IsNotNull()); Point3D c = m_BoundingBox->GetCenter(); if (m_ImageGeometry) { // Get Center returns the middel of min and max pixel index. In corner based images, this is the right position. // In center based images (imageGeometry == true), the index needs to be shifted back. c[0] -= 0.5; c[1] -= 0.5; c[2] -= 0.5; } this->IndexToWorld(c, c); return c; } double mitk::BaseGeometry::GetDiagonalLength2() const { Vector3D diagonalvector = GetCornerPoint() - GetCornerPoint(false, false, false); return diagonalvector.GetSquaredNorm(); } double mitk::BaseGeometry::GetDiagonalLength() const { return sqrt(GetDiagonalLength2()); } mitk::Point3D mitk::BaseGeometry::GetCornerPoint(int id) const { assert(id >= 0); assert(this->IsBoundingBoxNull() == false); BoundingBox::BoundsArrayType bounds = this->GetBoundingBox()->GetBounds(); Point3D cornerpoint; switch (id) { case 0: FillVector3D(cornerpoint, bounds[0], bounds[2], bounds[4]); break; case 1: FillVector3D(cornerpoint, bounds[0], bounds[2], bounds[5]); break; case 2: FillVector3D(cornerpoint, bounds[0], bounds[3], bounds[4]); break; case 3: FillVector3D(cornerpoint, bounds[0], bounds[3], bounds[5]); break; case 4: FillVector3D(cornerpoint, bounds[1], bounds[2], bounds[4]); break; case 5: FillVector3D(cornerpoint, bounds[1], bounds[2], bounds[5]); break; case 6: FillVector3D(cornerpoint, bounds[1], bounds[3], bounds[4]); break; case 7: FillVector3D(cornerpoint, bounds[1], bounds[3], bounds[5]); break; default: { itkExceptionMacro(<< "A cube only has 8 corners. These are labeled 0-7."); } } if (m_ImageGeometry) { // Here i have to adjust the 0.5 offset manually, because the cornerpoint is the corner of the // bounding box. The bounding box itself is no image, so it is corner-based FillVector3D(cornerpoint, cornerpoint[0] - 0.5, cornerpoint[1] - 0.5, cornerpoint[2] - 0.5); } return this->GetIndexToWorldTransform()->TransformPoint(cornerpoint); } mitk::Point3D mitk::BaseGeometry::GetCornerPoint(bool xFront, bool yFront, bool zFront) const { assert(this->IsBoundingBoxNull() == false); BoundingBox::BoundsArrayType bounds = this->GetBoundingBox()->GetBounds(); Point3D cornerpoint; cornerpoint[0] = (xFront ? bounds[0] : bounds[1]); cornerpoint[1] = (yFront ? bounds[2] : bounds[3]); cornerpoint[2] = (zFront ? bounds[4] : bounds[5]); if (m_ImageGeometry) { // Here i have to adjust the 0.5 offset manually, because the cornerpoint is the corner of the // bounding box. The bounding box itself is no image, so it is corner-based FillVector3D(cornerpoint, cornerpoint[0] - 0.5, cornerpoint[1] - 0.5, cornerpoint[2] - 0.5); } return this->GetIndexToWorldTransform()->TransformPoint(cornerpoint); } mitk::ScalarType mitk::BaseGeometry::GetExtentInMM(int direction) const { return this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(direction).magnitude() * GetExtent(direction); } void mitk::BaseGeometry::SetExtentInMM(int direction, ScalarType extentInMM) { mitk::ModifiedLock lock(this); ScalarType len = GetExtentInMM(direction); if (fabs(len - extentInMM) >= mitk::eps) { AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = m_GeometryTransform->GetVnlMatrix(); if (len > extentInMM) vnlmatrix.set_column(direction, vnlmatrix.get_column(direction) / len * extentInMM); else vnlmatrix.set_column(direction, vnlmatrix.get_column(direction) * extentInMM / len); Matrix3D matrix; matrix = vnlmatrix; m_GeometryTransform->SetMatrix(matrix); Modified(); } } bool mitk::BaseGeometry::IsInside(const mitk::Point3D &p) const { mitk::Point3D index; WorldToIndex(p, index); return IsIndexInside(index); } bool mitk::BaseGeometry::IsIndexInside(const mitk::Point3D &index) const { bool inside = false; // if it is an image geometry, we need to convert the index to discrete values // this is done by applying the rounding function also used in WorldToIndex (see line 323) if (m_ImageGeometry) { mitk::Point3D discretIndex; discretIndex[0] = itk::Math::RoundHalfIntegerUp(index[0]); discretIndex[1] = itk::Math::RoundHalfIntegerUp(index[1]); discretIndex[2] = itk::Math::RoundHalfIntegerUp(index[2]); inside = this->GetBoundingBox()->IsInside(discretIndex); // we have to check if the index is at the upper border of each dimension, // because the boundingbox is not centerbased if (inside) { const BoundingBox::BoundsArrayType &bounds = this->GetBoundingBox()->GetBounds(); if ((discretIndex[0] == bounds[1]) || (discretIndex[1] == bounds[3]) || (discretIndex[2] == bounds[5])) inside = false; } } else inside = this->GetBoundingBox()->IsInside(index); return inside; } void mitk::BaseGeometry::WorldToIndex(const mitk::Point3D &pt_mm, mitk::Point3D &pt_units) const { mitk::Vector3D tempIn, tempOut; const TransformType::OffsetType &offset = this->GetIndexToWorldTransform()->GetOffset(); tempIn = pt_mm.GetVectorFromOrigin() - offset; WorldToIndex(tempIn, tempOut); - pt_units = tempOut; + pt_units = Point3D(tempOut); } void mitk::BaseGeometry::WorldToIndex(const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const { // Get WorldToIndex transform if (m_IndexToWorldTransformLastModified != this->GetIndexToWorldTransform()->GetMTime()) { if (!m_InvertedTransform) { m_InvertedTransform = TransformType::New(); } if (!this->GetIndexToWorldTransform()->GetInverse(m_InvertedTransform.GetPointer())) { itkExceptionMacro("Internal ITK matrix inversion error, cannot proceed."); } m_IndexToWorldTransformLastModified = this->GetIndexToWorldTransform()->GetMTime(); } // Check for valid matrix inversion const TransformType::MatrixType &inverse = m_InvertedTransform->GetMatrix(); if (inverse.GetVnlMatrix().has_nans()) { itkExceptionMacro("Internal ITK matrix inversion error, cannot proceed. Matrix was: " << std::endl << this->GetIndexToWorldTransform()->GetMatrix() << "Suggested inverted matrix is:" << std::endl << inverse); } vec_units = inverse * vec_mm; } void mitk::BaseGeometry::WorldToIndex(const mitk::Point3D & /*atPt3d_mm*/, const mitk::Vector3D &vec_mm, mitk::Vector3D &vec_units) const { MITK_WARN << "Warning! Call of the deprecated function BaseGeometry::WorldToIndex(point, vec, vec). Use " "BaseGeometry::WorldToIndex(vec, vec) instead!"; this->WorldToIndex(vec_mm, vec_units); } mitk::VnlVector mitk::BaseGeometry::GetOriginVnl() const { return GetOrigin().GetVnlVector(); } vtkLinearTransform *mitk::BaseGeometry::GetVtkTransform() const { return m_GeometryTransform->GetVtkTransform(); } void mitk::BaseGeometry::SetIdentity() { mitk::ModifiedLock lock(this); m_GeometryTransform->SetIdentity(); Modified(); } void mitk::BaseGeometry::Compose(const mitk::BaseGeometry::TransformType *other, bool pre) { mitk::ModifiedLock lock(this); m_GeometryTransform->Compose(other, pre); Modified(); } void mitk::BaseGeometry::Compose(const vtkMatrix4x4 *vtkmatrix, bool pre) { mitk::BaseGeometry::TransformType::Pointer itkTransform = mitk::BaseGeometry::TransformType::New(); TransferVtkMatrixToItkTransform(vtkmatrix, itkTransform.GetPointer()); Compose(itkTransform, pre); } void mitk::BaseGeometry::Translate(const Vector3D &vector) { if ((vector[0] != 0) || (vector[1] != 0) || (vector[2] != 0)) { this->SetOrigin(this->GetOrigin() + vector); } } void mitk::BaseGeometry::IndexToWorld(const mitk::Point3D &pt_units, mitk::Point3D &pt_mm) const { pt_mm = this->GetIndexToWorldTransform()->TransformPoint(pt_units); } void mitk::BaseGeometry::IndexToWorld(const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const { vec_mm = this->GetIndexToWorldTransform()->TransformVector(vec_units); } void mitk::BaseGeometry::ExecuteOperation(Operation *operation) { mitk::ModifiedLock lock(this); vtkTransform *vtktransform = vtkTransform::New(); vtktransform->SetMatrix(this->GetVtkMatrix()); switch (operation->GetOperationType()) { case OpNOTHING: break; case OpMOVE: { auto *pointOp = dynamic_cast(operation); if (pointOp == nullptr) { MITK_ERROR << "Point move operation is null!"; return; } mitk::Point3D newPos = pointOp->GetPoint(); ScalarType data[3]; vtktransform->GetPosition(data); vtktransform->PostMultiply(); vtktransform->Translate(newPos[0], newPos[1], newPos[2]); vtktransform->PreMultiply(); break; } case OpSCALE: { auto *scaleOp = dynamic_cast(operation); if (scaleOp == nullptr) { MITK_ERROR << "Scale operation is null!"; return; } mitk::Point3D newScale = scaleOp->GetScaleFactor(); ScalarType scalefactor[3]; scalefactor[0] = 1 + (newScale[0] / GetMatrixColumn(0).magnitude()); scalefactor[1] = 1 + (newScale[1] / GetMatrixColumn(1).magnitude()); scalefactor[2] = 1 + (newScale[2] / GetMatrixColumn(2).magnitude()); mitk::Point3D anchor = scaleOp->GetScaleAnchorPoint(); vtktransform->PostMultiply(); vtktransform->Translate(-anchor[0], -anchor[1], -anchor[2]); vtktransform->Scale(scalefactor[0], scalefactor[1], scalefactor[2]); vtktransform->Translate(anchor[0], anchor[1], anchor[2]); break; } case OpROTATE: { auto *rotateOp = dynamic_cast(operation); if (rotateOp == nullptr) { MITK_ERROR << "Rotation operation is null!"; return; } Vector3D rotationVector = rotateOp->GetVectorOfRotation(); Point3D center = rotateOp->GetCenterOfRotation(); ScalarType angle = rotateOp->GetAngleOfRotation(); vtktransform->PostMultiply(); vtktransform->Translate(-center[0], -center[1], -center[2]); vtktransform->RotateWXYZ(angle, rotationVector[0], rotationVector[1], rotationVector[2]); vtktransform->Translate(center[0], center[1], center[2]); vtktransform->PreMultiply(); break; } case OpRESTOREPLANEPOSITION: { // Copy necessary to avoid vtk warning vtkMatrix4x4 *matrix = vtkMatrix4x4::New(); TransferItkTransformToVtkMatrix( dynamic_cast(operation)->GetTransform().GetPointer(), matrix); vtktransform->SetMatrix(matrix); matrix->Delete(); break; } case OpAPPLYTRANSFORMMATRIX: { auto *applyMatrixOp = dynamic_cast(operation); vtktransform->SetMatrix(applyMatrixOp->GetMatrix()); break; } default: vtktransform->Delete(); return; } this->SetVtkMatrixDeepCopy(vtktransform); Modified(); vtktransform->Delete(); } mitk::VnlVector mitk::BaseGeometry::GetMatrixColumn(unsigned int direction) const { return this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(direction); } mitk::BoundingBox::Pointer mitk::BaseGeometry::CalculateBoundingBoxRelativeToTransform( const mitk::AffineTransform3D *transform) const { mitk::BoundingBox::PointsContainer::Pointer pointscontainer = mitk::BoundingBox::PointsContainer::New(); mitk::BoundingBox::PointIdentifier pointid = 0; unsigned char i; if (transform != nullptr) { mitk::AffineTransform3D::Pointer inverse = mitk::AffineTransform3D::New(); transform->GetInverse(inverse); for (i = 0; i < 8; ++i) pointscontainer->InsertElement(pointid++, inverse->TransformPoint(GetCornerPoint(i))); } else { for (i = 0; i < 8; ++i) pointscontainer->InsertElement(pointid++, GetCornerPoint(i)); } mitk::BoundingBox::Pointer result = mitk::BoundingBox::New(); result->SetPoints(pointscontainer); result->ComputeBoundingBox(); return result; } const std::string mitk::BaseGeometry::GetTransformAsString(TransformType *transformType) { std::ostringstream out; out << '['; for (int i = 0; i < 3; ++i) { out << '['; for (int j = 0; j < 3; ++j) out << transformType->GetMatrix().GetVnlMatrix().get(i, j) << ' '; out << ']'; } out << "]["; for (int i = 0; i < 3; ++i) out << transformType->GetOffset()[i] << ' '; out << "]\0"; return out.str(); } void mitk::BaseGeometry::SetIndexToWorldTransformByVtkMatrix(vtkMatrix4x4 *vtkmatrix) { m_GeometryTransform->SetIndexToWorldTransformByVtkMatrix(vtkmatrix); } void mitk::BaseGeometry::SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(vtkMatrix4x4 *vtkmatrix) { m_GeometryTransform->SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(vtkmatrix); } void mitk::BaseGeometry::IndexToWorld(const mitk::Point3D & /*atPt3d_units*/, const mitk::Vector3D &vec_units, mitk::Vector3D &vec_mm) const { MITK_WARN << "Warning! Call of the deprecated function BaseGeometry::IndexToWorld(point, vec, vec). Use " "BaseGeometry::IndexToWorld(vec, vec) instead!"; // vec_mm = m_IndexToWorldTransform->TransformVector(vec_units); this->IndexToWorld(vec_units, vec_mm); } vtkMatrix4x4 *mitk::BaseGeometry::GetVtkMatrix() { return m_GeometryTransform->GetVtkMatrix(); } bool mitk::BaseGeometry::IsBoundingBoxNull() const { return m_BoundingBox.IsNull(); } bool mitk::BaseGeometry::IsIndexToWorldTransformNull() const { return m_GeometryTransform->IsIndexToWorldTransformNull(); } void mitk::BaseGeometry::ChangeImageGeometryConsideringOriginOffset(const bool isAnImageGeometry) { // If Geometry is switched to ImageGeometry, you have to put an offset to the origin, because // imageGeometries origins are pixel-center-based // ... and remove the offset, if you switch an imageGeometry back to a normal geometry // For more information please see the Geometry documentation page if (m_ImageGeometry == isAnImageGeometry) return; const BoundingBox::BoundsArrayType &boundsarray = this->GetBoundingBox()->GetBounds(); Point3D originIndex; FillVector3D(originIndex, boundsarray[0], boundsarray[2], boundsarray[4]); if (isAnImageGeometry == true) FillVector3D(originIndex, originIndex[0] + 0.5, originIndex[1] + 0.5, originIndex[2] + 0.5); else FillVector3D(originIndex, originIndex[0] - 0.5, originIndex[1] - 0.5, originIndex[2] - 0.5); Point3D originWorld; originWorld = GetIndexToWorldTransform()->TransformPoint(originIndex); // instead could as well call IndexToWorld(originIndex,originWorld); SetOrigin(originWorld); this->SetImageGeometry(isAnImageGeometry); } void mitk::BaseGeometry::PrintSelf(std::ostream &os, itk::Indent indent) const { os << indent << " IndexToWorldTransform: "; if (this->IsIndexToWorldTransformNull()) os << "nullptr" << std::endl; else { // from itk::MatrixOffsetTransformBase unsigned int i, j; os << std::endl; os << indent << "Matrix: " << std::endl; for (i = 0; i < 3; i++) { os << indent.GetNextIndent(); for (j = 0; j < 3; j++) { os << this->GetIndexToWorldTransform()->GetMatrix()[i][j] << " "; } os << std::endl; } os << indent << "Offset: " << this->GetIndexToWorldTransform()->GetOffset() << std::endl; os << indent << "Center: " << this->GetIndexToWorldTransform()->GetCenter() << std::endl; os << indent << "Translation: " << this->GetIndexToWorldTransform()->GetTranslation() << std::endl; os << indent << "Inverse: " << std::endl; for (i = 0; i < 3; i++) { os << indent.GetNextIndent(); for (j = 0; j < 3; j++) { os << this->GetIndexToWorldTransform()->GetInverseMatrix()[i][j] << " "; } os << std::endl; } // from itk::ScalableAffineTransform os << indent << "Scale : "; for (i = 0; i < 3; i++) { os << this->GetIndexToWorldTransform()->GetScale()[i] << " "; } os << std::endl; } os << indent << " BoundingBox: "; if (this->IsBoundingBoxNull()) os << "nullptr" << std::endl; else { os << indent << "( "; for (unsigned int i = 0; i < 3; i++) { os << this->GetBoundingBox()->GetBounds()[2 * i] << "," << this->GetBoundingBox()->GetBounds()[2 * i + 1] << " "; } os << " )" << std::endl; } os << indent << " Origin: " << this->GetOrigin() << std::endl; os << indent << " ImageGeometry: " << this->GetImageGeometry() << std::endl; os << indent << " Spacing: " << this->GetSpacing() << std::endl; } void mitk::BaseGeometry::Modified() const { if (!m_ModifiedLockFlag) Superclass::Modified(); else m_ModifiedCalledFlag = true; } mitk::AffineTransform3D *mitk::BaseGeometry::GetIndexToWorldTransform() { return m_GeometryTransform->GetIndexToWorldTransform(); } const mitk::AffineTransform3D *mitk::BaseGeometry::GetIndexToWorldTransform() const { return m_GeometryTransform->GetIndexToWorldTransform(); } const mitk::GeometryTransformHolder *mitk::BaseGeometry::GetGeometryTransformHolder() const { return m_GeometryTransform; } bool mitk::Equal(const mitk::BaseGeometry::BoundingBoxType &leftHandSide, const mitk::BaseGeometry::BoundingBoxType &rightHandSide, ScalarType eps, bool verbose) { bool result = true; BaseGeometry::BoundsArrayType rightBounds = rightHandSide.GetBounds(); BaseGeometry::BoundsArrayType leftBounds = leftHandSide.GetBounds(); BaseGeometry::BoundsArrayType::Iterator itLeft = leftBounds.Begin(); for (BaseGeometry::BoundsArrayType::Iterator itRight = rightBounds.Begin(); itRight != rightBounds.End(); ++itRight) { if ((!mitk::Equal(*itLeft, *itRight, eps))) { if (verbose) { MITK_INFO << "[( Geometry3D::BoundingBoxType )] bounds are not equal."; MITK_INFO << "rightHandSide is " << setprecision(12) << *itRight << " : leftHandSide is " << *itLeft << " and tolerance is " << eps; } result = false; } itLeft++; } return result; } bool mitk::Equal(const mitk::BaseGeometry &leftHandSide, const mitk::BaseGeometry &rightHandSide, ScalarType coordinateEps, ScalarType directionEps, bool verbose) { bool result = true; // Compare spacings if (!mitk::Equal(leftHandSide.GetSpacing(), rightHandSide.GetSpacing(), coordinateEps)) { if (verbose) { MITK_INFO << "[( Geometry3D )] Spacing differs."; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetSpacing() << " : leftHandSide is " << leftHandSide.GetSpacing() << " and tolerance is " << coordinateEps; } result = false; } // Compare Origins if (!mitk::Equal(leftHandSide.GetOrigin(), rightHandSide.GetOrigin(), coordinateEps)) { if (verbose) { MITK_INFO << "[( Geometry3D )] Origin differs."; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetOrigin() << " : leftHandSide is " << leftHandSide.GetOrigin() << " and tolerance is " << coordinateEps; } result = false; } // Compare Axis and Extents for (unsigned int i = 0; i < 3; ++i) { if (!mitk::Equal(leftHandSide.GetAxisVector(i), rightHandSide.GetAxisVector(i), directionEps)) { if (verbose) { MITK_INFO << "[( Geometry3D )] AxisVector #" << i << " differ"; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetAxisVector(i) << " : leftHandSide is " << leftHandSide.GetAxisVector(i) << " and tolerance is " << directionEps; } result = false; } if (!mitk::Equal(leftHandSide.GetExtent(i), rightHandSide.GetExtent(i), coordinateEps)) { if (verbose) { MITK_INFO << "[( Geometry3D )] Extent #" << i << " differ"; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetExtent(i) << " : leftHandSide is " << leftHandSide.GetExtent(i) << " and tolerance is " << coordinateEps; } result = false; } } // Compare ImageGeometry Flag if (rightHandSide.GetImageGeometry() != leftHandSide.GetImageGeometry()) { if (verbose) { MITK_INFO << "[( Geometry3D )] GetImageGeometry is different."; MITK_INFO << "rightHandSide is " << rightHandSide.GetImageGeometry() << " : leftHandSide is " << leftHandSide.GetImageGeometry(); } result = false; } // Compare FrameOfReference ID if (rightHandSide.GetFrameOfReferenceID() != leftHandSide.GetFrameOfReferenceID()) { if (verbose) { MITK_INFO << "[( Geometry3D )] GetFrameOfReferenceID is different."; MITK_INFO << "rightHandSide is " << rightHandSide.GetFrameOfReferenceID() << " : leftHandSide is " << leftHandSide.GetFrameOfReferenceID(); } result = false; } // Compare BoundingBoxes if (!mitk::Equal(*leftHandSide.GetBoundingBox(), *rightHandSide.GetBoundingBox(), coordinateEps, verbose)) { result = false; } // Compare IndexToWorldTransform Matrix if (!mitk::Equal(*leftHandSide.GetIndexToWorldTransform(), *rightHandSide.GetIndexToWorldTransform(), directionEps, verbose)) { result = false; } return result; } bool mitk::Equal(const mitk::BaseGeometry& leftHandSide, const mitk::BaseGeometry& rightHandSide, ScalarType eps, bool verbose) { return Equal(leftHandSide, rightHandSide, eps, eps, verbose); } bool mitk::Equal(const mitk::BaseGeometry::TransformType &leftHandSide, const mitk::BaseGeometry::TransformType &rightHandSide, ScalarType eps, bool verbose) { // Compare IndexToWorldTransform Matrix if (!mitk::MatrixEqualElementWise(leftHandSide.GetMatrix(), rightHandSide.GetMatrix(), eps)) { if (verbose) { MITK_INFO << "[( Geometry3D::TransformType )] Index to World Transformation matrix differs."; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetMatrix() << " : leftHandSide is " << leftHandSide.GetMatrix() << " and tolerance is " << eps; } return false; } return true; } bool mitk::IsSubGeometry(const mitk::BaseGeometry& testGeo, const mitk::BaseGeometry& referenceGeo, ScalarType coordinateEps, ScalarType directionEps, bool verbose) { bool result = true; // Compare spacings (must be equal) const auto testedSpacing = testGeo.GetSpacing(); if (!mitk::Equal(testedSpacing, referenceGeo.GetSpacing(), coordinateEps)) { if (verbose) { MITK_INFO << "[( Geometry3D )] Spacing differs."; MITK_INFO << "testedGeometry is " << setprecision(12) << testedSpacing << " : referenceGeometry is " << referenceGeo.GetSpacing() << " and tolerance is " << coordinateEps; } result = false; } // Compare ImageGeometry Flag (must be equal) if (referenceGeo.GetImageGeometry() != testGeo.GetImageGeometry()) { if (verbose) { MITK_INFO << "[( Geometry3D )] GetImageGeometry is different."; MITK_INFO << "referenceGeo is " << referenceGeo.GetImageGeometry() << " : testGeo is " << testGeo.GetImageGeometry(); } result = false; } // Compare IndexToWorldTransform Matrix (must be equal -> same axis directions) if (!Equal(*(testGeo.GetIndexToWorldTransform()), *(referenceGeo.GetIndexToWorldTransform()), directionEps, verbose)) { result = false; } for (int i = 0; i<8; ++i) { auto testCorner = testGeo.GetCornerPoint(i); bool isInside = false; mitk::Point3D testCornerIndex; referenceGeo.WorldToIndex(testCorner, testCornerIndex); std::bitset bs(i); //To regard the directionEps, we substract or add it to the index elments //depending on wether it was constructed by a lower or an upper bound value //(see implementation of BaseGeometry::GetCorner()). if (bs.test(0)) { testCornerIndex[2] -= directionEps; } else { testCornerIndex[2] += directionEps; } if (bs.test(1)) { testCornerIndex[1] -= directionEps; } else { testCornerIndex[1] += directionEps; } if (bs.test(2)) { testCornerIndex[0] -= directionEps; } else { testCornerIndex[0] += directionEps; } isInside = referenceGeo.IsIndexInside(testCornerIndex); if (!isInside) { if (verbose) { MITK_INFO << "[( Geometry3D )] corner point is not inside. "; MITK_INFO << "referenceGeo is " << setprecision(12) << referenceGeo << " : tested corner is " << testGeo.GetCornerPoint(i); } result = false; } } // check grid of test geometry is on the grid of the reference geometry. This is important as the // boundingbox is only checked for containing the tested geometry, but if a corner (one is enough // as we know that axis and spacing are equal, due to equal transfor (see above)) of the tested geometry // is on the grid it is really a sub geometry (as they have the same spacing and axis). auto cornerOffset = testGeo.GetCornerPoint(0) - referenceGeo.GetCornerPoint(0); mitk::Vector3D cornerIndexOffset; referenceGeo.WorldToIndex(cornerOffset, cornerIndexOffset); for (unsigned int i = 0; i < 3; ++i) { auto pixelCountContinous = cornerIndexOffset[i]; auto pixelCount = std::round(pixelCountContinous); if (std::abs(pixelCount - pixelCountContinous) > coordinateEps) { if (verbose) { MITK_INFO << "[( Geometry3D )] Tested geometry is not on the grid of the reference geometry. "; MITK_INFO << "referenceGeo is " << setprecision(15) << referenceGeo << " : tested corner offset in pixels is " << pixelCountContinous << " for axis "< #include "mitkGroupTagProperty.h" #include "mitkProperties.h" #include "mitkSmartPointerProperty.h" #include "mitkStringProperty.h" //#include "mitkMaterialProperty.h" #include "mitkColorProperty.h" #include "mitkCoreObjectFactory.h" #include "mitkGenericProperty.h" #include "mitkGeometry3D.h" #include "mitkImageSource.h" #include "mitkLevelWindowProperty.h" #include "mitkRenderingManager.h" mitk::Mapper *mitk::DataNode::GetMapper(MapperSlotId id) const { if ((id >= m_Mappers.size()) || (m_Mappers[id].IsNull())) { if (id >= m_Mappers.capacity()) { // int i, size=id-m_Mappers.capacity()+10; m_Mappers.resize(id + 10); } m_Mappers[id] = CoreObjectFactory::GetInstance()->CreateMapper(const_cast(this), id); } return m_Mappers[id]; } mitk::BaseData *mitk::DataNode::GetData() const { return m_Data; } void mitk::DataNode::SetData(mitk::BaseData *baseData) { if (m_Data != baseData) { m_Mappers.clear(); m_Mappers.resize(10); if (m_Data.IsNotNull() && baseData != nullptr) { // Do previous and new data have same type? Keep existing properties. if (0 == strcmp(m_Data->GetNameOfClass(), baseData->GetNameOfClass())) { m_Data = baseData; } else { m_Data = baseData; this->GetPropertyList()->Clear(); mitk::CoreObjectFactory::GetInstance()->SetDefaultProperties(this); } } else { m_Data = baseData; mitk::CoreObjectFactory::GetInstance()->SetDefaultProperties(this); } m_DataReferenceChangedTime.Modified(); Modified(); } } mitk::DataNode::DataNode() : m_PropertyList(PropertyList::New()), m_PropertyListModifiedObserverTag(0) { m_Mappers.resize(10); // subscribe for modified event itk::MemberCommand::Pointer _PropertyListModifiedCommand = itk::MemberCommand::New(); _PropertyListModifiedCommand->SetCallbackFunction(this, &mitk::DataNode::PropertyListModified); m_PropertyListModifiedObserverTag = m_PropertyList->AddObserver(itk::ModifiedEvent(), _PropertyListModifiedCommand); } mitk::DataNode::~DataNode() { if (m_PropertyList.IsNotNull()) m_PropertyList->RemoveObserver(m_PropertyListModifiedObserverTag); m_Mappers.clear(); m_Data = nullptr; } mitk::DataNode &mitk::DataNode::operator=(const DataNode &right) { mitk::DataNode *node = mitk::DataNode::New(); node->SetData(right.GetData()); return *node; } mitk::DataNode &mitk::DataNode::operator=(mitk::BaseData *right) { mitk::DataNode *node = mitk::DataNode::New(); node->SetData(right); return *node; } #if (_MSC_VER > 1200) || !defined(_MSC_VER) std::istream &mitk::operator>>(std::istream &i, mitk::DataNode::Pointer &dtn) #endif #if ((defined(_MSC_VER)) && (_MSC_VER <= 1200)) std::istream & operator>>(std::istream &i, mitk::DataNode::Pointer &dtn) #endif { dtn = mitk::DataNode::New(); // i >> av.get(); return i; } #if (_MSC_VER > 1200) || !defined(_MSC_VER) std::ostream &mitk::operator<<(std::ostream &o, mitk::DataNode::Pointer &dtn) #endif #if ((defined(_MSC_VER)) && (_MSC_VER <= 1200)) std::ostream & operator<<(std::ostream &o, mitk::DataNode::Pointer &dtn) #endif { if (dtn->GetData() != nullptr) o << dtn->GetData()->GetNameOfClass(); else o << "empty data"; return o; } void mitk::DataNode::SetMapper(MapperSlotId id, mitk::Mapper *mapper) { m_Mappers[id] = mapper; if (mapper != nullptr) mapper->SetDataNode(this); } void mitk::DataNode::UpdateOutputInformation() { if (this->GetSource()) { this->GetSource()->UpdateOutputInformation(); } } void mitk::DataNode::SetRequestedRegionToLargestPossibleRegion() { } bool mitk::DataNode::RequestedRegionIsOutsideOfTheBufferedRegion() { return false; } bool mitk::DataNode::VerifyRequestedRegion() { return true; } void mitk::DataNode::SetRequestedRegion(const itk::DataObject * /*data*/) { } mitk::DataNode::PropertyListKeyNames mitk::DataNode::GetPropertyListNames() const { PropertyListKeyNames result; - for (auto entries : m_MapOfPropertyLists) + for (const auto &entries : m_MapOfPropertyLists) result.push_back(entries.first); return result; } void mitk::DataNode::CopyInformation(const itk::DataObject * /*data*/) { } mitk::PropertyList *mitk::DataNode::GetPropertyList(const mitk::BaseRenderer *renderer) const { if (renderer == nullptr) return m_PropertyList; return this->GetPropertyList(renderer->GetName()); } mitk::PropertyList *mitk::DataNode::GetPropertyList(const std::string &rendererName) const { if (rendererName.empty()) return m_PropertyList; mitk::PropertyList::Pointer &propertyList = m_MapOfPropertyLists[rendererName]; if (propertyList.IsNull()) propertyList = mitk::PropertyList::New(); assert(m_MapOfPropertyLists[rendererName].IsNotNull()); return propertyList; } void mitk::DataNode::ConcatenatePropertyList(PropertyList *pList, bool replace) { m_PropertyList->ConcatenatePropertyList(pList, replace); } mitk::BaseProperty *mitk::DataNode::GetProperty(const char *propertyKey, const mitk::BaseRenderer *renderer, bool fallBackOnDataProperties) const { if (nullptr == propertyKey) return nullptr; if (nullptr != renderer) { auto it = m_MapOfPropertyLists.find(renderer->GetName()); if (m_MapOfPropertyLists.end() != it) { auto property = it->second->GetProperty(propertyKey); if (nullptr != property) return property; } } auto property = m_PropertyList->GetProperty(propertyKey); if (nullptr == property && fallBackOnDataProperties && m_Data.IsNotNull()) property = m_Data->GetProperty(propertyKey); return property; } mitk::DataNode::GroupTagList mitk::DataNode::GetGroupTags() const { GroupTagList groups; const PropertyList::PropertyMap *propertyMap = m_PropertyList->GetMap(); for (auto groupIter = propertyMap->begin(); // m_PropertyList is created in the constructor, so we don't check it here groupIter != propertyMap->end(); ++groupIter) { const BaseProperty *bp = groupIter->second; if (dynamic_cast(bp)) { groups.insert(groupIter->first); } } return groups; } bool mitk::DataNode::GetBoolProperty(const char *propertyKey, bool &boolValue, const mitk::BaseRenderer *renderer) const { mitk::BoolProperty::Pointer boolprop = dynamic_cast(GetProperty(propertyKey, renderer)); if (boolprop.IsNull()) return false; boolValue = boolprop->GetValue(); return true; } bool mitk::DataNode::GetIntProperty(const char *propertyKey, int &intValue, const mitk::BaseRenderer *renderer) const { mitk::IntProperty::Pointer intprop = dynamic_cast(GetProperty(propertyKey, renderer)); if (intprop.IsNull()) return false; intValue = intprop->GetValue(); return true; } bool mitk::DataNode::GetFloatProperty(const char *propertyKey, float &floatValue, const mitk::BaseRenderer *renderer) const { mitk::FloatProperty::Pointer floatprop = dynamic_cast(GetProperty(propertyKey, renderer)); if (floatprop.IsNull()) return false; floatValue = floatprop->GetValue(); return true; } bool mitk::DataNode::GetDoubleProperty(const char *propertyKey, double &doubleValue, const mitk::BaseRenderer *renderer) const { mitk::DoubleProperty::Pointer doubleprop = dynamic_cast(GetProperty(propertyKey, renderer)); if (doubleprop.IsNull()) { // try float instead float floatValue = 0; if (this->GetFloatProperty(propertyKey, floatValue, renderer)) { doubleValue = floatValue; return true; } return false; } doubleValue = doubleprop->GetValue(); return true; } bool mitk::DataNode::GetStringProperty(const char *propertyKey, std::string &string, const mitk::BaseRenderer *renderer) const { mitk::StringProperty::Pointer stringProp = dynamic_cast(GetProperty(propertyKey, renderer)); if (stringProp.IsNull()) { return false; } else { // memcpy((void*)string, stringProp->GetValue(), strlen(stringProp->GetValue()) + 1 ); // looks dangerous string = stringProp->GetValue(); return true; } } bool mitk::DataNode::GetColor(float rgb[3], const mitk::BaseRenderer *renderer, const char *propertyKey) const { mitk::ColorProperty::Pointer colorprop = dynamic_cast(GetProperty(propertyKey, renderer)); if (colorprop.IsNull()) return false; memcpy(rgb, colorprop->GetColor().GetDataPointer(), 3 * sizeof(float)); return true; } bool mitk::DataNode::GetOpacity(float &opacity, const mitk::BaseRenderer *renderer, const char *propertyKey) const { mitk::FloatProperty::Pointer opacityprop = dynamic_cast(GetProperty(propertyKey, renderer)); if (opacityprop.IsNull()) return false; opacity = opacityprop->GetValue(); return true; } bool mitk::DataNode::GetLevelWindow(mitk::LevelWindow &levelWindow, const mitk::BaseRenderer *renderer, const char *propertyKey) const { mitk::LevelWindowProperty::Pointer levWinProp = dynamic_cast(GetProperty(propertyKey, renderer)); if (levWinProp.IsNull()) return false; levelWindow = levWinProp->GetLevelWindow(); return true; } void mitk::DataNode::SetColor(const mitk::Color &color, const mitk::BaseRenderer *renderer, const char *propertyKey) { mitk::ColorProperty::Pointer prop; prop = mitk::ColorProperty::New(color); GetPropertyList(renderer)->SetProperty(propertyKey, prop); } void mitk::DataNode::SetColor( float red, float green, float blue, const mitk::BaseRenderer *renderer, const char *propertyKey) { float color[3]; color[0] = red; color[1] = green; color[2] = blue; SetColor(color, renderer, propertyKey); } void mitk::DataNode::SetColor(const float rgb[3], const mitk::BaseRenderer *renderer, const char *propertyKey) { mitk::ColorProperty::Pointer prop; prop = mitk::ColorProperty::New(rgb); GetPropertyList(renderer)->SetProperty(propertyKey, prop); } void mitk::DataNode::SetVisibility(bool visible, const mitk::BaseRenderer *renderer, const char *propertyKey) { mitk::BoolProperty::Pointer prop; prop = mitk::BoolProperty::New(visible); GetPropertyList(renderer)->SetProperty(propertyKey, prop); } void mitk::DataNode::SetOpacity(float opacity, const mitk::BaseRenderer *renderer, const char *propertyKey) { mitk::FloatProperty::Pointer prop; prop = mitk::FloatProperty::New(opacity); GetPropertyList(renderer)->SetProperty(propertyKey, prop); } void mitk::DataNode::SetLevelWindow(mitk::LevelWindow levelWindow, const mitk::BaseRenderer *renderer, const char *propertyKey) { mitk::LevelWindowProperty::Pointer prop; prop = mitk::LevelWindowProperty::New(levelWindow); GetPropertyList(renderer)->SetProperty(propertyKey, prop); } void mitk::DataNode::SetIntProperty(const char *propertyKey, int intValue, const mitk::BaseRenderer *renderer) { GetPropertyList(renderer)->SetProperty(propertyKey, mitk::IntProperty::New(intValue)); } void mitk::DataNode::SetBoolProperty(const char *propertyKey, bool boolValue, const mitk::BaseRenderer *renderer /*=nullptr*/) { GetPropertyList(renderer)->SetProperty(propertyKey, mitk::BoolProperty::New(boolValue)); } void mitk::DataNode::SetFloatProperty(const char *propertyKey, float floatValue, const mitk::BaseRenderer *renderer /*=nullptr*/) { if (dynamic_cast(this->GetProperty(propertyKey, renderer)) != nullptr) { MITK_WARN << "Setting float property " << propertyKey << " although a double property with the same name already exists"; } GetPropertyList(renderer)->SetProperty(propertyKey, mitk::FloatProperty::New(floatValue)); } void mitk::DataNode::SetDoubleProperty(const char *propertyKey, double doubleValue, const mitk::BaseRenderer *renderer) { if (dynamic_cast(this->GetProperty(propertyKey, renderer)) != nullptr) { MITK_WARN << "Setting double property " << propertyKey << " although a float property with the same name already exists"; } GetPropertyList(renderer)->SetProperty(propertyKey, mitk::DoubleProperty::New(doubleValue)); } void mitk::DataNode::SetStringProperty(const char *propertyKey, const char *stringValue, const mitk::BaseRenderer *renderer /*=nullptr*/) { GetPropertyList(renderer)->SetProperty(propertyKey, mitk::StringProperty::New(stringValue)); } void mitk::DataNode::SetProperty(const char *propertyKey, BaseProperty *propertyValue, const mitk::BaseRenderer *renderer) { GetPropertyList(renderer)->SetProperty(propertyKey, propertyValue); } void mitk::DataNode::ReplaceProperty(const char *propertyKey, BaseProperty *propertyValue, const mitk::BaseRenderer *renderer) { GetPropertyList(renderer)->ReplaceProperty(propertyKey, propertyValue); } void mitk::DataNode::AddProperty(const char *propertyKey, BaseProperty *propertyValue, const mitk::BaseRenderer *renderer, bool overwrite) { if ((overwrite) || (GetProperty(propertyKey, renderer) == nullptr)) { SetProperty(propertyKey, propertyValue, renderer); } } vtkLinearTransform *mitk::DataNode::GetVtkTransform(int t) const { assert(m_Data.IsNotNull()); mitk::BaseGeometry *geometry = m_Data->GetGeometry(t); if (geometry == nullptr) return nullptr; return geometry->GetVtkTransform(); } unsigned long mitk::DataNode::GetMTime() const { unsigned long time = Superclass::GetMTime(); if (m_Data.IsNotNull()) { if ((time < m_Data->GetMTime()) || ((m_Data->GetSource().IsNotNull()) && (time < m_Data->GetSource()->GetMTime()))) { Modified(); return Superclass::GetMTime(); } } return time; } void mitk::DataNode::SetSelected(bool selected, const mitk::BaseRenderer *renderer) { mitk::BoolProperty::Pointer selectedProperty = dynamic_cast(GetProperty("selected")); if (selectedProperty.IsNull()) { selectedProperty = mitk::BoolProperty::New(); selectedProperty->SetValue(false); SetProperty("selected", selectedProperty, renderer); } if (selectedProperty->GetValue() != selected) { selectedProperty->SetValue(selected); itk::ModifiedEvent event; InvokeEvent(event); } } /* class SelectedEvent : public itk::ModifiedEvent { public: typedef SelectedEvent Self; typedef itk::ModifiedEvent Superclass; SelectedEvent(DataNode* dataNode) { m_DataNode = dataNode; }; DataNode* GetDataNode() { return m_DataNode; }; virtual const char * GetEventName() const { return "SelectedEvent"; } virtual bool CheckEvent(const ::itk::EventObject* e) const { return dynamic_cast(e); } virtual ::itk::EventObject* MakeObject() const { return new Self(m_DataNode); } private: DataNode* m_DataNode; SelectedEvent(const Self& event) { m_DataNode = event.m_DataNode; }; void operator=(const Self& event) { m_DataNode = event.m_DataNode; } }; */ bool mitk::DataNode::IsSelected(const mitk::BaseRenderer *renderer) { bool selected; if (!GetBoolProperty("selected", selected, renderer)) return false; return selected; } void mitk::DataNode::SetDataInteractor(const DataInteractor::Pointer interactor) { if (m_DataInteractor == interactor) return; m_DataInteractor = interactor; this->Modified(); mitk::DataNode::InteractorChangedEvent changedEvent; this->InvokeEvent(changedEvent); } mitk::DataInteractor::Pointer mitk::DataNode::GetDataInteractor() const { return m_DataInteractor; } void mitk::DataNode::PropertyListModified(const itk::Object * /*caller*/, const itk::EventObject &) { Modified(); } mitk::BaseProperty::ConstPointer mitk::DataNode::GetConstProperty(const std::string &propertyKey, const std::string &contextName, bool fallBackOnDefaultContext) const { if (propertyKey.empty()) return nullptr; if (!contextName.empty()) { auto propertyListIter = m_MapOfPropertyLists.find(contextName); if (m_MapOfPropertyLists.end() != propertyListIter) { BaseProperty::ConstPointer property = propertyListIter->second->GetProperty(propertyKey); if (property.IsNotNull()) return property; } } if (contextName.empty() || fallBackOnDefaultContext) { BaseProperty::ConstPointer property = m_PropertyList->GetProperty(propertyKey); if (property.IsNull() && m_Data.IsNotNull()) property = m_Data->GetProperty(propertyKey.c_str()); return property; } return nullptr; } mitk::BaseProperty * mitk::DataNode::GetNonConstProperty(const std::string &propertyKey, const std::string &contextName, bool fallBackOnDefaultContext) { if (propertyKey.empty()) return nullptr; if (!contextName.empty()) { auto propertyListIter = m_MapOfPropertyLists.find(contextName); if (m_MapOfPropertyLists.end() != propertyListIter) { auto property = propertyListIter->second->GetProperty(propertyKey); if (nullptr != property) return property; } } if (contextName.empty() || fallBackOnDefaultContext) { auto property = m_PropertyList->GetProperty(propertyKey); if (nullptr == property && m_Data.IsNotNull()) property = m_Data->GetProperty(propertyKey.c_str()); return property; } return nullptr; } void mitk::DataNode::SetProperty(const std::string &propertyKey, BaseProperty *property, const std::string &contextName, bool fallBackOnDefaultContext) { if (propertyKey.empty()) mitkThrow() << "Property key is empty."; if (!contextName.empty()) { auto propertyListIter = m_MapOfPropertyLists.find(contextName); if (m_MapOfPropertyLists.end() != propertyListIter) { propertyListIter->second->SetProperty(propertyKey, property); return; } } if (contextName.empty() || fallBackOnDefaultContext) { m_PropertyList->SetProperty(propertyKey, property); return; } mitkThrow() << "Unknown property context."; } void mitk::DataNode::RemoveProperty(const std::string &propertyKey, const std::string &contextName, bool fallBackOnDefaultContext) { if (propertyKey.empty()) mitkThrow() << "Property key is empty."; if (!contextName.empty()) { auto propertyListIter = m_MapOfPropertyLists.find(contextName); if (m_MapOfPropertyLists.end() != propertyListIter) { propertyListIter->second->RemoveProperty(propertyKey); return; } } if (contextName.empty() || fallBackOnDefaultContext) { m_PropertyList->RemoveProperty(propertyKey); return; } mitkThrow() << "Unknown property context."; } std::vector mitk::DataNode::GetPropertyKeys(const std::string &contextName, bool includeDefaultContext) const { std::vector propertyKeys; if (contextName.empty()) { - for (auto property : *m_PropertyList->GetMap()) + for (const auto &property : *m_PropertyList->GetMap()) propertyKeys.push_back(property.first); return propertyKeys; } auto propertyListIter = m_MapOfPropertyLists.find(contextName); if (m_MapOfPropertyLists.end() != propertyListIter) { - for (auto property : *propertyListIter->second->GetMap()) + for (const auto &property : *propertyListIter->second->GetMap()) propertyKeys.push_back(property.first); } if (includeDefaultContext) { - for (auto property : *m_PropertyList->GetMap()) + for (const auto &property : *m_PropertyList->GetMap()) { auto propertyKeyIter = std::find(propertyKeys.begin(), propertyKeys.end(), property.first); if (propertyKeys.end() == propertyKeyIter) propertyKeys.push_back(property.first); } } return propertyKeys; } std::vector mitk::DataNode::GetPropertyContextNames() const { return this->GetPropertyListNames(); } diff --git a/Modules/Core/src/DataManagement/mitkDataStorage.cpp b/Modules/Core/src/DataManagement/mitkDataStorage.cpp index 890128e9f7..5a555a15da 100644 --- a/Modules/Core/src/DataManagement/mitkDataStorage.cpp +++ b/Modules/Core/src/DataManagement/mitkDataStorage.cpp @@ -1,584 +1,584 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkDataStorage.h" #include "itkCommand.h" #include "itkMutexLockHolder.h" #include "mitkDataNode.h" #include "mitkGroupTagProperty.h" #include "mitkImage.h" #include "mitkNodePredicateBase.h" #include "mitkNodePredicateProperty.h" #include "mitkProperties.h" #include "mitkArbitraryTimeGeometry.h" mitk::DataStorage::DataStorage() : itk::Object(), m_BlockNodeModifiedEvents(false) { } mitk::DataStorage::~DataStorage() { ///// we can not call GetAll() in destructor, because it is implemented in a subclass // SetOfObjects::ConstPointer all = this->GetAll(); // for (SetOfObjects::ConstIterator it = all->Begin(); it != all->End(); ++it) // this->RemoveListeners(it->Value()); // m_NodeModifiedObserverTags.clear(); // m_NodeDeleteObserverTags.clear(); } void mitk::DataStorage::Add(DataNode *node, DataNode *parent) { DataStorage::SetOfObjects::Pointer parents = DataStorage::SetOfObjects::New(); if (parent != nullptr) //< Return empty set if parent is null parents->InsertElement(0, parent); this->Add(node, parents); } void mitk::DataStorage::Remove(const DataStorage::SetOfObjects *nodes) { if (nodes == nullptr) return; for (DataStorage::SetOfObjects::ConstIterator it = nodes->Begin(); it != nodes->End(); it++) this->Remove(it.Value()); } mitk::DataStorage::SetOfObjects::ConstPointer mitk::DataStorage::GetSubset(const NodePredicateBase *condition) const { DataStorage::SetOfObjects::ConstPointer result = this->FilterSetOfObjects(this->GetAll(), condition); return result; } mitk::DataNode *mitk::DataStorage::GetNamedNode(const char *name) const { if (name == nullptr) return nullptr; StringProperty::Pointer s(StringProperty::New(name)); NodePredicateProperty::Pointer p = NodePredicateProperty::New("name", s); DataStorage::SetOfObjects::ConstPointer rs = this->GetSubset(p); if (rs->Size() >= 1) return rs->GetElement(0); else return nullptr; } mitk::DataNode *mitk::DataStorage::GetNode(const NodePredicateBase *condition) const { if (condition == nullptr) return nullptr; DataStorage::SetOfObjects::ConstPointer rs = this->GetSubset(condition); if (rs->Size() >= 1) return rs->GetElement(0); else return nullptr; } mitk::DataNode *mitk::DataStorage::GetNamedDerivedNode(const char *name, const DataNode *sourceNode, bool onlyDirectDerivations) const { if (name == nullptr) return nullptr; StringProperty::Pointer s(StringProperty::New(name)); NodePredicateProperty::Pointer p = NodePredicateProperty::New("name", s); DataStorage::SetOfObjects::ConstPointer rs = this->GetDerivations(sourceNode, p, onlyDirectDerivations); if (rs->Size() >= 1) return rs->GetElement(0); else return nullptr; } void mitk::DataStorage::PrintSelf(std::ostream &os, itk::Indent indent) const { // Superclass::PrintSelf(os, indent); DataStorage::SetOfObjects::ConstPointer all = this->GetAll(); os << indent << "DataStorage " << this << " is managing " << all->Size() << " objects. List of objects:" << std::endl; for (DataStorage::SetOfObjects::ConstIterator allIt = all->Begin(); allIt != all->End(); allIt++) { std::string name; allIt.Value()->GetName(name); std::string datatype; if (allIt.Value()->GetData() != nullptr) datatype = allIt.Value()->GetData()->GetNameOfClass(); os << indent << " " << allIt.Value().GetPointer() << "<" << datatype << ">: " << name << std::endl; DataStorage::SetOfObjects::ConstPointer parents = this->GetSources(allIt.Value()); if (parents->Size() > 0) { os << indent << " Direct sources: "; for (DataStorage::SetOfObjects::ConstIterator parentIt = parents->Begin(); parentIt != parents->End(); parentIt++) os << parentIt.Value().GetPointer() << ", "; os << std::endl; } DataStorage::SetOfObjects::ConstPointer derivations = this->GetDerivations(allIt.Value()); if (derivations->Size() > 0) { os << indent << " Direct derivations: "; for (DataStorage::SetOfObjects::ConstIterator derivationIt = derivations->Begin(); derivationIt != derivations->End(); derivationIt++) os << derivationIt.Value().GetPointer() << ", "; os << std::endl; } } os << std::endl; } mitk::DataStorage::SetOfObjects::ConstPointer mitk::DataStorage::FilterSetOfObjects(const SetOfObjects *set, const NodePredicateBase *condition) const { if (set == nullptr) return nullptr; DataStorage::SetOfObjects::Pointer result = DataStorage::SetOfObjects::New(); for (DataStorage::SetOfObjects::ConstIterator it = set->Begin(); it != set->End(); it++) if (condition == nullptr || condition->CheckNode(it.Value()) == true) // alway copy the set, otherwise the iterator in DataStorage::Remove() will crash result->InsertElement(result->Size(), it.Value()); return DataStorage::SetOfObjects::ConstPointer(result); } const mitk::DataNode::GroupTagList mitk::DataStorage::GetGroupTags() const { DataNode::GroupTagList result; SetOfObjects::ConstPointer all = this->GetAll(); if (all.IsNull()) return result; for (DataStorage::SetOfObjects::ConstIterator nodeIt = all->Begin(); nodeIt != all->End(); nodeIt++) // for each node { PropertyList *pl = nodeIt.Value()->GetPropertyList(); for (auto propIt = pl->GetMap()->begin(); propIt != pl->GetMap()->end(); ++propIt) if (dynamic_cast(propIt->second.GetPointer()) != nullptr) result.insert(propIt->first); } return result; } void mitk::DataStorage::EmitAddNodeEvent(const DataNode *node) { AddNodeEvent.Send(node); } void mitk::DataStorage::EmitRemoveNodeEvent(const DataNode *node) { RemoveNodeEvent.Send(node); } void mitk::DataStorage::OnNodeInteractorChanged(itk::Object *caller, const itk::EventObject &) { const auto *_Node = dynamic_cast(caller); if (_Node) { InteractorChangedNodeEvent.Send(_Node); } } void mitk::DataStorage::OnNodeModifiedOrDeleted(const itk::Object *caller, const itk::EventObject &event) { if (m_BlockNodeModifiedEvents) return; const auto *_Node = dynamic_cast(caller); if (_Node) { const auto *modEvent = dynamic_cast(&event); if (modEvent) ChangedNodeEvent.Send(_Node); else DeleteNodeEvent.Send(_Node); } } void mitk::DataStorage::AddListeners(const DataNode *_Node) { itk::MutexLockHolder locked(m_MutexOne); // node must not be 0 and must not be yet registered auto *NonConstNode = const_cast(_Node); if (_Node && m_NodeModifiedObserverTags.find(NonConstNode) == m_NodeModifiedObserverTags.end()) { itk::MemberCommand::Pointer nodeModifiedCommand = itk::MemberCommand::New(); nodeModifiedCommand->SetCallbackFunction(this, &DataStorage::OnNodeModifiedOrDeleted); m_NodeModifiedObserverTags[NonConstNode] = NonConstNode->AddObserver(itk::ModifiedEvent(), nodeModifiedCommand); itk::MemberCommand::Pointer interactorChangedCommand = itk::MemberCommand::New(); interactorChangedCommand->SetCallbackFunction(this, &DataStorage::OnNodeInteractorChanged); m_NodeInteractorChangedObserverTags[NonConstNode] = NonConstNode->AddObserver(DataNode::InteractorChangedEvent(), interactorChangedCommand); // add itk delete listener on datastorage itk::MemberCommand::Pointer deleteCommand = itk::MemberCommand::New(); deleteCommand->SetCallbackFunction(this, &DataStorage::OnNodeModifiedOrDeleted); // add observer m_NodeDeleteObserverTags[NonConstNode] = NonConstNode->AddObserver(itk::DeleteEvent(), deleteCommand); } } void mitk::DataStorage::RemoveListeners(const DataNode *_Node) { itk::MutexLockHolder locked(m_MutexOne); // node must not be 0 and must be registered auto *NonConstNode = const_cast(_Node); if (_Node && m_NodeModifiedObserverTags.find(NonConstNode) != m_NodeModifiedObserverTags.end()) { // const cast is bad! but sometimes it is necessary. removing an observer does not really // touch the internal state NonConstNode->RemoveObserver(m_NodeModifiedObserverTags.find(NonConstNode)->second); NonConstNode->RemoveObserver(m_NodeDeleteObserverTags.find(NonConstNode)->second); NonConstNode->RemoveObserver(m_NodeInteractorChangedObserverTags.find(NonConstNode)->second); m_NodeModifiedObserverTags.erase(NonConstNode); m_NodeDeleteObserverTags.erase(NonConstNode); m_NodeInteractorChangedObserverTags.erase(NonConstNode); } } mitk::TimeGeometry::ConstPointer mitk::DataStorage::ComputeBoundingGeometry3D(const SetOfObjects *input, const char *boolPropertyKey, const BaseRenderer *renderer, const char *boolPropertyKey2) const { if (input == nullptr) throw std::invalid_argument("DataStorage: input is invalid"); BoundingBox::PointsContainer::Pointer pointscontainer = BoundingBox::PointsContainer::New(); BoundingBox::PointIdentifier pointid = 0; Point3D point; Vector3D minSpacing; minSpacing.Fill(itk::NumericTraits::max()); ScalarType stmax = itk::NumericTraits::max(); ScalarType stmin = itk::NumericTraits::NonpositiveMin(); std::set existingTimePoints; ScalarType maximalTime = 0; // Needed for check of zero bounding boxes ScalarType nullpoint[] = {0, 0, 0, 0, 0, 0}; BoundingBox::BoundsArrayType itkBoundsZero(nullpoint); for (SetOfObjects::ConstIterator it = input->Begin(); it != input->End(); ++it) { DataNode::Pointer node = it->Value(); if ((node.IsNotNull()) && (node->GetData() != nullptr) && (node->GetData()->IsEmpty() == false) && node->IsOn(boolPropertyKey, renderer) && node->IsOn(boolPropertyKey2, renderer)) { const TimeGeometry *timeGeometry = node->GetData()->GetUpdatedTimeGeometry(); if (timeGeometry != nullptr) { // bounding box (only if non-zero) BoundingBox::BoundsArrayType itkBounds = timeGeometry->GetBoundingBoxInWorld()->GetBounds(); if (itkBounds == itkBoundsZero) { continue; } unsigned char i; for (i = 0; i < 8; ++i) { point = timeGeometry->GetCornerPointInWorld(i); if (point[0] * point[0] + point[1] * point[1] + point[2] * point[2] < large) pointscontainer->InsertElement(pointid++, point); else { itkGenericOutputMacro(<< "Unrealistically distant corner point encountered. Ignored. Node: " << node); } } try { // time bounds // iterate over all time steps // Attention: Objects with zero bounding box are not respected in time bound calculation for (TimeStepType i = 0; i < timeGeometry->CountTimeSteps(); i++) { // We must not use 'node->GetData()->GetGeometry(i)->GetSpacing()' here, as it returns the spacing // in its original space, which, in case of an image geometry, can have the values in different // order than in world space. For the further calculations, we need to have the spacing values // in world coordinate order (sag-cor-ax). Vector3D spacing; spacing.Fill(1.0); node->GetData()->GetGeometry(i)->IndexToWorld(spacing, spacing); for (int axis = 0; axis < 3; ++ axis) { ScalarType space = std::abs(spacing[axis]); if (space < minSpacing[axis]) { minSpacing[axis] = space; } } const auto curTimeBounds = timeGeometry->GetTimeBounds(i); if ((curTimeBounds[0] > stmin) && (curTimeBounds[0] < stmax)) { existingTimePoints.insert(curTimeBounds[0]); } if ((curTimeBounds[1] > maximalTime) && (curTimeBounds[1] < stmax)) { maximalTime = curTimeBounds[1]; } } } catch ( const itk::ExceptionObject &e ) { MITK_ERROR << e.GetDescription() << std::endl; } } } } BoundingBox::Pointer result = BoundingBox::New(); result->SetPoints(pointscontainer); result->ComputeBoundingBox(); // compute the number of time steps if (existingTimePoints.empty()) // make sure that there is at least one time sliced geometry in the data storage { existingTimePoints.insert(0.0); maximalTime = 1.0; } ArbitraryTimeGeometry::Pointer timeGeometry = nullptr; if (result->GetPoints()->Size() > 0) { // Initialize a geometry of a single time step Geometry3D::Pointer geometry = Geometry3D::New(); geometry->Initialize(); // correct bounding-box (is now in mm, should be in index-coordinates) // according to spacing BoundingBox::BoundsArrayType bounds = result->GetBounds(); AffineTransform3D::OutputVectorType offset; for (int i = 0; i < 3; ++i) { offset[i] = bounds[i * 2]; bounds[i * 2] = 0.0; bounds[i * 2 + 1] = (bounds[i * 2 + 1] - offset[i]) / minSpacing[i]; } geometry->GetIndexToWorldTransform()->SetOffset(offset); geometry->SetBounds(bounds); geometry->SetSpacing(minSpacing); // Initialize the time sliced geometry auto tsIterator = existingTimePoints.cbegin(); auto tsPredecessor = tsIterator++; auto tsEnd = existingTimePoints.cend(); timeGeometry = ArbitraryTimeGeometry::New(); for (; tsIterator != tsEnd; ++tsIterator, ++tsPredecessor) { timeGeometry->AppendNewTimeStep(geometry, *tsPredecessor, *tsIterator); } timeGeometry->AppendNewTimeStep(geometry, *tsPredecessor, maximalTime); timeGeometry->Update(); } return timeGeometry.GetPointer(); } mitk::TimeGeometry::ConstPointer mitk::DataStorage::ComputeBoundingGeometry3D(const char *boolPropertyKey, const BaseRenderer *renderer, const char *boolPropertyKey2) const { return this->ComputeBoundingGeometry3D(this->GetAll(), boolPropertyKey, renderer, boolPropertyKey2); } mitk::TimeGeometry::ConstPointer mitk::DataStorage::ComputeVisibleBoundingGeometry3D(const BaseRenderer *renderer, const char *boolPropertyKey) { return ComputeBoundingGeometry3D("visible", renderer, boolPropertyKey); } mitk::BoundingBox::Pointer mitk::DataStorage::ComputeBoundingBox(const char *boolPropertyKey, const BaseRenderer *renderer, const char *boolPropertyKey2) { BoundingBox::PointsContainer::Pointer pointscontainer = BoundingBox::PointsContainer::New(); BoundingBox::PointIdentifier pointid = 0; Point3D point; // Needed for check of zero bounding boxes ScalarType nullpoint[] = {0, 0, 0, 0, 0, 0}; BoundingBox::BoundsArrayType itkBoundsZero(nullpoint); SetOfObjects::ConstPointer all = this->GetAll(); for (SetOfObjects::ConstIterator it = all->Begin(); it != all->End(); ++it) { DataNode::Pointer node = it->Value(); if ((node.IsNotNull()) && (node->GetData() != nullptr) && (node->GetData()->IsEmpty() == false) && node->IsOn(boolPropertyKey, renderer) && node->IsOn(boolPropertyKey2, renderer)) { const TimeGeometry *geometry = node->GetData()->GetUpdatedTimeGeometry(); if (geometry != nullptr) { // bounding box (only if non-zero) BoundingBox::BoundsArrayType itkBounds = geometry->GetBoundingBoxInWorld()->GetBounds(); if (itkBounds == itkBoundsZero) { continue; } unsigned char i; for (i = 0; i < 8; ++i) { point = geometry->GetCornerPointInWorld(i); if (point[0] * point[0] + point[1] * point[1] + point[2] * point[2] < large) pointscontainer->InsertElement(pointid++, point); else { itkGenericOutputMacro(<< "Unrealistically distant corner point encountered. Ignored. Node: " << node); } } } } } BoundingBox::Pointer result = BoundingBox::New(); result->SetPoints(pointscontainer); result->ComputeBoundingBox(); return result; } mitk::TimeBounds mitk::DataStorage::ComputeTimeBounds(const char *boolPropertyKey, const BaseRenderer *renderer, const char *boolPropertyKey2) { TimeBounds timeBounds; ScalarType stmin, stmax, cur; stmin = itk::NumericTraits::NonpositiveMin(); stmax = itk::NumericTraits::max(); timeBounds[0] = stmax; timeBounds[1] = stmin; SetOfObjects::ConstPointer all = this->GetAll(); for (SetOfObjects::ConstIterator it = all->Begin(); it != all->End(); ++it) { DataNode::Pointer node = it->Value(); if ((node.IsNotNull()) && (node->GetData() != nullptr) && (node->GetData()->IsEmpty() == false) && node->IsOn(boolPropertyKey, renderer) && node->IsOn(boolPropertyKey2, renderer)) { const TimeGeometry *geometry = node->GetData()->GetUpdatedTimeGeometry(); if (geometry != nullptr) { const TimeBounds &curTimeBounds = geometry->GetTimeBounds(); cur = curTimeBounds[0]; // is it after -infinity, but before everything else that we found until now? if ((cur > stmin) && (cur < timeBounds[0])) timeBounds[0] = cur; cur = curTimeBounds[1]; // is it before infinity, but after everything else that we found until now? if ((cur < stmax) && (cur > timeBounds[1])) timeBounds[1] = cur; } } } if (!(timeBounds[0] < stmax)) { timeBounds[0] = stmin; timeBounds[1] = stmax; } return timeBounds; } void mitk::DataStorage::BlockNodeModifiedEvents(bool block) { m_BlockNodeModifiedEvents = block; } mitk::DataNode::Pointer mitk::FindTopmostVisibleNode(const DataStorage::SetOfObjects::ConstPointer nodes, const Point3D worldPosition, const TimePointType timePoint, const BaseRenderer* baseRender) { if (nodes.IsNull()) { return nullptr; } mitk::DataNode::Pointer topLayerNode = nullptr; int maxLayer = std::numeric_limits::min(); - for (auto node : *nodes) + for (const auto &node : *nodes) { if (node.IsNull()) { continue; } bool isHelperObject = false; node->GetBoolProperty("helper object", isHelperObject); if (isHelperObject) { continue; } auto data = node->GetData(); if (nullptr == data) { continue; } auto geometry = data->GetGeometry(); if (nullptr == geometry || !geometry->IsInside(worldPosition)) { continue; } auto timeGeometry = data->GetUpdatedTimeGeometry(); if (nullptr == timeGeometry) { continue; } if (!timeGeometry->IsValidTimePoint(timePoint)) { continue; } int layer = 0; if (!node->GetIntProperty("layer", layer, baseRender)) { continue; } if (layer <= maxLayer) { continue; } if (!node->IsVisible(baseRender)) { continue; } topLayerNode = node; maxLayer = layer; } return topLayerNode; } diff --git a/Modules/Core/src/DataManagement/mitkGeometryTransformHolder.cpp b/Modules/Core/src/DataManagement/mitkGeometryTransformHolder.cpp index 8d354ca719..a20204ef84 100644 --- a/Modules/Core/src/DataManagement/mitkGeometryTransformHolder.cpp +++ b/Modules/Core/src/DataManagement/mitkGeometryTransformHolder.cpp @@ -1,335 +1,335 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ /* * mitkGeometryTransformHolder.cpp * * Created on: Sep 3, 2014 * Author: wirkert */ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace mitk { void GeometryTransformHolder::CopySpacingFromTransform(const mitk::AffineTransform3D *transform, mitk::Vector3D &spacing) { mitk::AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = transform->GetMatrix().GetVnlMatrix(); spacing[0] = vnlmatrix.get_column(0).magnitude(); spacing[1] = vnlmatrix.get_column(1).magnitude(); spacing[2] = vnlmatrix.get_column(2).magnitude(); } GeometryTransformHolder::GeometryTransformHolder() { m_VtkMatrix = vtkMatrix4x4::New(); m_VtkIndexToWorldTransform = vtkMatrixToLinearTransform::New(); m_VtkIndexToWorldTransform->SetInput(m_VtkMatrix); this->Initialize(); } GeometryTransformHolder::GeometryTransformHolder(const GeometryTransformHolder &other) { m_VtkMatrix = vtkMatrix4x4::New(); m_VtkIndexToWorldTransform = vtkMatrixToLinearTransform::New(); m_VtkIndexToWorldTransform->SetInput(m_VtkMatrix); this->Initialize(&other); } GeometryTransformHolder::~GeometryTransformHolder() { m_VtkMatrix->Delete(); m_VtkIndexToWorldTransform->Delete(); } void GeometryTransformHolder::Initialize() { if (m_IndexToWorldTransform.IsNull()) m_IndexToWorldTransform = TransformType::New(); else m_IndexToWorldTransform->SetIdentity(); m_VtkMatrix->Identity(); } void GeometryTransformHolder::Initialize(const GeometryTransformHolder *other) { Initialize(); if (other->GetIndexToWorldTransform()) { TransformType::Pointer indexToWorldTransform = other->GetIndexToWorldTransform()->Clone(); this->SetIndexToWorldTransform(indexToWorldTransform); } } //##Documentation //## @brief Copy the ITK transform //## (m_IndexToWorldTransform) to the VTK transform //## \sa SetIndexToWorldTransform void GeometryTransformHolder::TransferItkToVtkTransform() { TransferItkTransformToVtkMatrix(m_IndexToWorldTransform.GetPointer(), m_VtkMatrix); } //##Documentation //## @brief Copy the VTK transform //## to the ITK transform (m_IndexToWorldTransform) //## \sa SetIndexToWorldTransform void GeometryTransformHolder::TransferVtkToItkTransform() { TransferVtkMatrixToItkTransform(m_VtkMatrix, m_IndexToWorldTransform.GetPointer()); } //##Documentation //## @brief Get the origin, e.g. the upper-left corner of the plane const Point3D GeometryTransformHolder::GetOrigin() const { - mitk::Point3D origin = this->GetIndexToWorldTransform()->GetOffset(); + Point3D origin = Point3D(this->GetIndexToWorldTransform()->GetOffset()); return origin; } //##Documentation //## @brief Set the origin, i.e. the upper-left corner of the plane //## void GeometryTransformHolder::SetOrigin(const Point3D &origin) { m_IndexToWorldTransform->SetOffset(origin.GetVectorFromOrigin()); TransferItkToVtkTransform(); } //##Documentation //## @brief Get the spacing (size of a pixel). //## const mitk::Vector3D GeometryTransformHolder::GetSpacing() const { mitk::Vector3D spacing; CopySpacingFromTransform(this->GetIndexToWorldTransform(), spacing); return spacing; } //##Documentation //## @brief Set the spacing. //## //##The spacing is also changed in the IndexToWorldTransform. void GeometryTransformHolder::SetSpacing(const mitk::Vector3D &aSpacing, bool enforceSetSpacing) { if (mitk::Equal(this->GetSpacing(), aSpacing) == false || enforceSetSpacing) { assert(aSpacing[0] > 0 && aSpacing[1] > 0 && aSpacing[2] > 0); AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = m_IndexToWorldTransform->GetMatrix().GetVnlMatrix(); mitk::VnlVector col; col = vnlmatrix.get_column(0); col.normalize(); col *= aSpacing[0]; vnlmatrix.set_column(0, col); col = vnlmatrix.get_column(1); col.normalize(); col *= aSpacing[1]; vnlmatrix.set_column(1, col); col = vnlmatrix.get_column(2); col.normalize(); col *= aSpacing[2]; vnlmatrix.set_column(2, col); Matrix3D matrix; matrix = vnlmatrix; AffineTransform3D::Pointer transform = AffineTransform3D::New(); transform->SetMatrix(matrix); transform->SetOffset(m_IndexToWorldTransform->GetOffset()); SetIndexToWorldTransform(transform.GetPointer()); } } //##Documentation //## @brief Get the transformation used to convert from index //## to world coordinates mitk::AffineTransform3D *GeometryTransformHolder::GetIndexToWorldTransform() { return m_IndexToWorldTransform; } //##Documentation //## @brief Get the transformation used to convert from index //## to world coordinates const mitk::AffineTransform3D *GeometryTransformHolder::GetIndexToWorldTransform() const { return m_IndexToWorldTransform; } //## @brief Set the transformation used to convert from index //## to world coordinates. The spacing of the new transform is //## copied to m_spacing. void GeometryTransformHolder::SetIndexToWorldTransform(mitk::AffineTransform3D *transform) { m_IndexToWorldTransform = transform; TransferItkToVtkTransform(); } //##Documentation //## @brief Convenience method for setting the ITK transform //## (m_IndexToWorldTransform) via an vtkMatrix4x4.The spacing of //## the new transform is copied to m_spacing. //## \sa SetIndexToWorldTransform void GeometryTransformHolder::SetIndexToWorldTransformByVtkMatrix(vtkMatrix4x4 *vtkmatrix) { m_VtkMatrix->DeepCopy(vtkmatrix); TransferVtkToItkTransform(); } //## @brief Set the transformation used to convert from index //## to world coordinates.This function keeps the original spacing. void GeometryTransformHolder::SetIndexToWorldTransformWithoutChangingSpacing(mitk::AffineTransform3D *transform) { mitk::Vector3D originalSpacing = this->GetSpacing(); this->SetIndexToWorldTransform(transform); this->SetSpacing(originalSpacing); } //##Documentation //## @brief Convenience method for setting the ITK transform //## (m_IndexToWorldTransform) via an vtkMatrix4x4. This function keeps the original spacing. //## \sa SetIndexToWorldTransform void GeometryTransformHolder::SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(vtkMatrix4x4 *vtkmatrix) { mitk::Vector3D originalSpacing = this->GetSpacing(); this->SetIndexToWorldTransformByVtkMatrix(vtkmatrix); this->SetSpacing(originalSpacing); } //## Get the Vtk Matrix which describes the transform. vtkMatrix4x4 *GeometryTransformHolder::GetVtkMatrix() { return m_VtkMatrix; } //## Get the Vtk Matrix which describes the transform. const vtkMatrix4x4 *GeometryTransformHolder::GetVtkMatrix() const { return m_VtkMatrix; } //##Documentation //## @brief Get the m_IndexToWorldTransform as a vtkLinearTransform vtkLinearTransform *GeometryTransformHolder::GetVtkTransform() const { return (vtkLinearTransform *)m_VtkIndexToWorldTransform; } void GeometryTransformHolder::SetMatrix(Matrix3D &matrix) { m_IndexToWorldTransform->SetMatrix(matrix); TransferItkToVtkTransform(); } void GeometryTransformHolder::SetIdentity() { m_IndexToWorldTransform->SetIdentity(); TransferItkToVtkTransform(); } void GeometryTransformHolder::Compose(const TransformType *other, bool pre) { m_IndexToWorldTransform->Compose(other, pre); TransferItkToVtkTransform(); } void GeometryTransformHolder::SetVtkMatrixDeepCopy(vtkTransform *vtktransform) { m_VtkMatrix->DeepCopy(vtktransform->GetMatrix()); TransferVtkToItkTransform(); } bool GeometryTransformHolder::IsIndexToWorldTransformNull() { return m_IndexToWorldTransform.IsNull(); } AffineTransform3D::MatrixType::InternalMatrixType GeometryTransformHolder::GetVnlMatrix() { return m_IndexToWorldTransform->GetMatrix().GetVnlMatrix(); } } bool mitk::Equal(const mitk::GeometryTransformHolder *leftHandSide, const mitk::GeometryTransformHolder *rightHandSide, ScalarType eps, bool verbose) { if ((leftHandSide == nullptr) || (rightHandSide == nullptr)) { MITK_ERROR << "mitk::Equal(const mitk::Geometry3D *leftHandSide, const mitk::Geometry3D *rightHandSide, ScalarType " "eps, bool verbose) does not with nullptr pointer input."; return false; } return Equal(*leftHandSide, *rightHandSide, eps, verbose); } bool mitk::Equal(const mitk::GeometryTransformHolder &leftHandSide, const mitk::GeometryTransformHolder &rightHandSide, ScalarType eps, bool verbose) { bool result = true; // Compare spacings if (!mitk::Equal(leftHandSide.GetSpacing(), rightHandSide.GetSpacing(), eps)) { if (verbose) { MITK_INFO << "[( Geometry3D )] Spacing differs."; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetSpacing() << " : leftHandSide is " << leftHandSide.GetSpacing() << " and tolerance is " << eps; } result = false; } // Compare Origins if (!mitk::Equal(leftHandSide.GetOrigin(), rightHandSide.GetOrigin(), eps)) { if (verbose) { MITK_INFO << "[( Geometry3D )] Origin differs."; MITK_INFO << "rightHandSide is " << setprecision(12) << rightHandSide.GetOrigin() << " : leftHandSide is " << leftHandSide.GetOrigin() << " and tolerance is " << eps; } result = false; } // Compare IndexToWorldTransform Matrix if (!mitk::Equal(*leftHandSide.GetIndexToWorldTransform(), *rightHandSide.GetIndexToWorldTransform(), eps, verbose)) { result = false; } // Compare vtk Matrix for (int i = 0; i < 4; i++) { for (int j = 0; j < 4; j++) { if (leftHandSide.GetVtkMatrix()->GetElement(i, j) != rightHandSide.GetVtkMatrix()->GetElement(i, j)) { result = false; } } } return result; } diff --git a/Modules/Core/src/DataManagement/mitkPlaneGeometry.cpp b/Modules/Core/src/DataManagement/mitkPlaneGeometry.cpp index 0c68955b41..4a6565d4e7 100644 --- a/Modules/Core/src/DataManagement/mitkPlaneGeometry.cpp +++ b/Modules/Core/src/DataManagement/mitkPlaneGeometry.cpp @@ -1,971 +1,971 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkPlaneGeometry.h" #include "mitkInteractionConst.h" #include "mitkLine.h" #include "mitkPlaneOperation.h" #include #include #include namespace mitk { PlaneGeometry::PlaneGeometry() : Superclass(), m_ReferenceGeometry(nullptr) { Initialize(); } PlaneGeometry::~PlaneGeometry() {} PlaneGeometry::PlaneGeometry(const PlaneGeometry &other) : Superclass(other), m_ReferenceGeometry(other.m_ReferenceGeometry) { } bool PlaneGeometry::CheckRotationMatrix(mitk::AffineTransform3D *transform, double epsilon) { bool rotation = true; auto matrix = transform->GetMatrix().GetVnlMatrix(); matrix.normalize_columns(); auto det = vnl_determinant(matrix); if (fabs(det-1.0) > epsilon) { MITK_WARN << "Invalid rotation matrix! Determinant != 1 (" << det << ")"; rotation = false; } vnl_matrix_fixed id; id.set_identity(); auto should_be_id = matrix*matrix.transpose(); should_be_id -= id; auto max = should_be_id.absolute_value_max(); if (max > epsilon) { MITK_WARN << "Invalid rotation matrix! R*R^T != ID. Max value: " << max << " (should be 0)"; rotation = false; } return rotation; } void PlaneGeometry::CheckIndexToWorldTransform(mitk::AffineTransform3D *transform) { - CheckRotationMatrix(transform); + this->CheckRotationMatrix(transform); } void PlaneGeometry::CheckBounds(const BoundingBox::BoundsArrayType &bounds) { // error: unused parameter 'bounds' // this happens in release mode, where the assert macro is defined empty // hence we "use" the parameter: (void)bounds; // currently the unit rectangle must be starting at the origin [0,0] assert(bounds[0] == 0); assert(bounds[2] == 0); // the unit rectangle must be two-dimensional assert(bounds[1] > 0); assert(bounds[3] > 0); } void PlaneGeometry::IndexToWorld(const Point2D &pt_units, Point2D &pt_mm) const { pt_mm[0] = GetExtentInMM(0) / GetExtent(0) * pt_units[0]; pt_mm[1] = GetExtentInMM(1) / GetExtent(1) * pt_units[1]; } void PlaneGeometry::WorldToIndex(const Point2D &pt_mm, Point2D &pt_units) const { pt_units[0] = pt_mm[0] * (1.0 / (GetExtentInMM(0) / GetExtent(0))); pt_units[1] = pt_mm[1] * (1.0 / (GetExtentInMM(1) / GetExtent(1))); } void PlaneGeometry::IndexToWorld(const Point2D & /*atPt2d_units*/, const Vector2D &vec_units, Vector2D &vec_mm) const { MITK_WARN << "Warning! Call of the deprecated function PlaneGeometry::IndexToWorld(point, vec, vec). Use " "PlaneGeometry::IndexToWorld(vec, vec) instead!"; this->IndexToWorld(vec_units, vec_mm); } void PlaneGeometry::IndexToWorld(const Vector2D &vec_units, Vector2D &vec_mm) const { vec_mm[0] = (GetExtentInMM(0) / GetExtent(0)) * vec_units[0]; vec_mm[1] = (GetExtentInMM(1) / GetExtent(1)) * vec_units[1]; } void PlaneGeometry::WorldToIndex(const Point2D & /*atPt2d_mm*/, const Vector2D &vec_mm, Vector2D &vec_units) const { MITK_WARN << "Warning! Call of the deprecated function PlaneGeometry::WorldToIndex(point, vec, vec). Use " "PlaneGeometry::WorldToIndex(vec, vec) instead!"; this->WorldToIndex(vec_mm, vec_units); } void PlaneGeometry::WorldToIndex(const Vector2D &vec_mm, Vector2D &vec_units) const { vec_units[0] = vec_mm[0] * (1.0 / (GetExtentInMM(0) / GetExtent(0))); vec_units[1] = vec_mm[1] * (1.0 / (GetExtentInMM(1) / GetExtent(1))); } void PlaneGeometry::InitializeStandardPlane(mitk::ScalarType width, ScalarType height, const Vector3D &spacing, PlaneGeometry::PlaneOrientation planeorientation, ScalarType zPosition, bool frontside, bool rotated, bool top) { AffineTransform3D::Pointer transform; transform = AffineTransform3D::New(); AffineTransform3D::MatrixType matrix; AffineTransform3D::MatrixType::InternalMatrixType &vnlmatrix = matrix.GetVnlMatrix(); vnlmatrix.set_identity(); vnlmatrix(0, 0) = spacing[0]; vnlmatrix(1, 1) = spacing[1]; vnlmatrix(2, 2) = spacing[2]; transform->SetIdentity(); transform->SetMatrix(matrix); InitializeStandardPlane(width, height, transform.GetPointer(), planeorientation, zPosition, frontside, rotated, top); } void PlaneGeometry::InitializeStandardPlane(mitk::ScalarType width, mitk::ScalarType height, const AffineTransform3D *transform /* = nullptr */, PlaneGeometry::PlaneOrientation planeorientation /* = Axial */, mitk::ScalarType zPosition /* = 0 */, bool frontside /* = true */, bool rotated /* = false */, bool top /* = true */) { Superclass::Initialize(); /// construct standard view. // We define at the moment "frontside" as: axial from above, // coronal from front (nose), saggital from right. // TODO: Double check with medicals doctors or radiologists [ ]. // We define the orientation in patient's view, e.g. LAI is in a axial cut // (parallel to the triangle ear-ear-nose): // first axis: To the left ear of the patient // seecond axis: To the nose of the patient // third axis: To the legs of the patient. // Options are: L/R left/right; A/P anterior/posterior; I/S inferior/superior // (AKA caudal/cranial). // We note on all cases in the following switch block r.h. for right handed // or l.h. for left handed to describe the different cases. // However, which system is chosen is defined at the end of the switch block. // CAVE / be careful: the vectors right and bottom are relative to the plane // and do NOT describe e.g. the right side of the patient. Point3D origin; /** Bottom means downwards, DV means Direction Vector. Both relative to the image! */ VnlVector rightDV(3), bottomDV(3); /** Origin of this plane is by default a zero vector and implicitly in the top-left corner: */ origin.Fill(0); /** This is different to all definitions in MITK, except the QT mouse clicks. * But it is like this here and we don't want to change a running system. * Just be aware, that IN THIS FUNCTION we define the origin at the top left (e.g. your screen). */ /** NormalDirection defines which axis (i.e. column index in the transform matrix) * is perpendicular to the plane: */ int normalDirection; switch (planeorientation) // Switch through our limited choice of standard planes: { case None: /** Orientation 'None' shall be done like the axial plane orientation, * for whatever reasons. */ case Axial: if (frontside) // Radiologist's view from below. A cut along the triangle ear-ear-nose. { if (rotated == false) /** Origin in the top-left corner, x=[1; 0; 0], y=[0; 1; 0], z=[0; 0; 1], * origin=[0,0,zpos]: LAI (r.h.) * * 0---rightDV----> | * | | * | Picture of a finite, rectangular plane | * | ( insert LOLCAT-scan here ^_^ ) | * | | * v _________________________________________| * */ { FillVector3D(origin, 0, 0, zPosition); FillVector3D(rightDV, 1, 0, 0); FillVector3D(bottomDV, 0, 1, 0); } else // Origin rotated to the bottom-right corner, x=[-1; 0; 0], y=[0; -1; 0], z=[0; 0; 1], // origin=[w,h,zpos]: RPI (r.h.) { // Caveat emptor: Still using top-left as origin of index coordinate system! FillVector3D(origin, width, height, zPosition); FillVector3D(rightDV, -1, 0, 0); FillVector3D(bottomDV, 0, -1, 0); } } else // 'Backside, not frontside.' Neuro-Surgeons's view from above patient. { if (rotated == false) // x=[-1; 0; 0], y=[0; 1; 0], z=[0; 0; 1], origin=[w,0,zpos]: RAS (r.h.) { FillVector3D(origin, width, 0, zPosition); FillVector3D(rightDV, -1, 0, 0); FillVector3D(bottomDV, 0, 1, 0); } else // Origin in the bottom-left corner, x=[1; 0; 0], y=[0; -1; 0], z=[0; 0; 1], // origin=[0,h,zpos]: LPS (r.h.) { FillVector3D(origin, 0, height, zPosition); FillVector3D(rightDV, 1, 0, 0); FillVector3D(bottomDV, 0, -1, 0); } } normalDirection = 2; // That is S=Superior=z=third_axis=middlefinger in righthanded LPS-system. break; // Frontal is known as Coronal in mitk. Plane cuts through patient's ear-ear-heel-heel: case Frontal: if (frontside) { if (rotated == false) // x=[1; 0; 0], y=[0; 0; 1], z=[0; 1; 0], origin=[0,zpos,0]: LAI (r.h.) { FillVector3D(origin, 0, zPosition, 0); FillVector3D(rightDV, 1, 0, 0); FillVector3D(bottomDV, 0, 0, 1); } else // x=[-1;0;0], y=[0;0;-1], z=[0;1;0], origin=[w,zpos,h]: RAS (r.h.) { FillVector3D(origin, width, zPosition, height); FillVector3D(rightDV, -1, 0, 0); FillVector3D(bottomDV, 0, 0, -1); } } else { if (rotated == false) // x=[-1;0;0], y=[0;0;1], z=[0;1;0], origin=[w,zpos,0]: RPI (r.h.) { FillVector3D(origin, width, zPosition, 0); FillVector3D(rightDV, -1, 0, 0); FillVector3D(bottomDV, 0, 0, 1); } else // x=[1;0;0], y=[0;1;0], z=[0;0;-1], origin=[0,zpos,h]: LPS (r.h.) { FillVector3D(origin, 0, zPosition, height); FillVector3D(rightDV, 1, 0, 0); FillVector3D(bottomDV, 0, 0, -1); } } normalDirection = 1; // Normal vector = posterior direction. break; case Sagittal: // Sagittal=Medial plane, the symmetry-plane mirroring your face. if (frontside) { if (rotated == false) // x=[0;1;0], y=[0;0;1], z=[1;0;0], origin=[zpos,0,0]: LAI (r.h.) { FillVector3D(origin, zPosition, 0, 0); FillVector3D(rightDV, 0, 1, 0); FillVector3D(bottomDV, 0, 0, 1); } else // x=[0;-1;0], y=[0;0;-1], z=[1;0;0], origin=[zpos,w,h]: LPS (r.h.) { FillVector3D(origin, zPosition, width, height); FillVector3D(rightDV, 0, -1, 0); FillVector3D(bottomDV, 0, 0, -1); } } else { if (rotated == false) // x=[0;-1;0], y=[0;0;1], z=[1;0;0], origin=[zpos,w,0]: RPI (r.h.) { FillVector3D(origin, zPosition, width, 0); FillVector3D(rightDV, 0, -1, 0); FillVector3D(bottomDV, 0, 0, 1); } else // x=[0;1;0], y=[0;0;-1], z=[1;0;0], origin=[zpos,0,h]: RAS (r.h.) { FillVector3D(origin, zPosition, 0, height); FillVector3D(rightDV, 0, 1, 0); FillVector3D(bottomDV, 0, 0, -1); } } normalDirection = 0; // Normal vector = Lateral direction: Left in a LPS-system. break; default: itkExceptionMacro("unknown PlaneOrientation"); } VnlVector normal(3); FillVector3D(normal, 0, 0, 0); normal[normalDirection] = top ? 1 : -1; if ( transform != nullptr ) { origin = transform->TransformPoint( origin ); rightDV = transform->TransformVector( rightDV ); bottomDV = transform->TransformVector( bottomDV ); normal = transform->TransformVector( normal ); } ScalarType bounds[6] = {0, width, 0, height, 0, 1}; this->SetBounds(bounds); AffineTransform3D::Pointer planeTransform = AffineTransform3D::New(); Matrix3D matrix; matrix.GetVnlMatrix().set_column(0, rightDV); matrix.GetVnlMatrix().set_column(1, bottomDV); matrix.GetVnlMatrix().set_column(2, normal); planeTransform->SetMatrix(matrix); planeTransform->SetOffset(this->GetIndexToWorldTransform()->GetOffset()); this->SetIndexToWorldTransform(planeTransform); this->SetOrigin(origin); } std::vector< int > PlaneGeometry::CalculateDominantAxes(mitk::AffineTransform3D::MatrixType::InternalMatrixType& rotation_matrix) { std::vector< int > axes; bool dominant_axis_error = false; for (int i = 0; i < 3; ++i) { int dominantAxis = itk::Function::Max3( rotation_matrix[0][i], rotation_matrix[1][i], rotation_matrix[2][i] ); for (int j=0; jSetReferenceGeometry(geometry3D); ScalarType width, height; // Inspired by: // http://www.na-mic.org/Wiki/index.php/Coordinate_System_Conversion_Between_ITK_and_Slicer3 mitk::AffineTransform3D::MatrixType matrix = geometry3D->GetIndexToWorldTransform()->GetMatrix(); matrix.GetVnlMatrix().normalize_columns(); mitk::AffineTransform3D::MatrixType::InternalMatrixType inverseMatrix = matrix.GetTranspose(); /// The index of the sagittal, coronal and axial axes in the reference geometry. auto axes = CalculateDominantAxes(inverseMatrix); /// The direction of the sagittal, coronal and axial axes in the reference geometry. /// +1 means that the direction is straight, i.e. greater index translates to greater /// world coordinate. -1 means that the direction is inverted. int directions[3]; ScalarType extents[3]; ScalarType spacings[3]; for (int i=0; i<3; ++i) { int dominantAxis = axes.at(i); directions[i] = itk::Function::Sign(inverseMatrix[dominantAxis][i]); extents[i] = geometry3D->GetExtent(dominantAxis); spacings[i] = geometry3D->GetSpacing()[dominantAxis]; } // matrix(column) = inverseTransformMatrix(row) * flippedAxes * spacing matrix[0][0] = inverseMatrix[axes[0]][0] * directions[0] * spacings[0]; matrix[1][0] = inverseMatrix[axes[0]][1] * directions[0] * spacings[0]; matrix[2][0] = inverseMatrix[axes[0]][2] * directions[0] * spacings[0]; matrix[0][1] = inverseMatrix[axes[1]][0] * directions[1] * spacings[1]; matrix[1][1] = inverseMatrix[axes[1]][1] * directions[1] * spacings[1]; matrix[2][1] = inverseMatrix[axes[1]][2] * directions[1] * spacings[1]; matrix[0][2] = inverseMatrix[axes[2]][0] * directions[2] * spacings[2]; matrix[1][2] = inverseMatrix[axes[2]][1] * directions[2] * spacings[2]; matrix[2][2] = inverseMatrix[axes[2]][2] * directions[2] * spacings[2]; /// The "world origin" is the corner with the lowest physical coordinates. /// We use it as a reference point so that we get the correct anatomical /// orientations. Point3D worldOrigin = geometry3D->GetOrigin(); for (int i = 0; i < 3; ++i) { /// The distance of the plane origin from the world origin in voxels. double offset = directions[i] > 0 ? 0.0 : extents[i]; if (geometry3D->GetImageGeometry()) { offset += directions[i] * 0.5; } for (int j = 0; j < 3; ++j) { worldOrigin[j] -= offset * matrix[j][i]; } } switch(planeorientation) { case None: /** Orientation 'None' shall be done like the axial plane orientation, * for whatever reasons. */ case Axial: width = extents[0]; height = extents[1]; break; case Frontal: width = extents[0]; height = extents[2]; break; case Sagittal: width = extents[1]; height = extents[2]; break; default: itkExceptionMacro("unknown PlaneOrientation"); } ScalarType bounds[6]= { 0, width, 0, height, 0, 1 }; this->SetBounds( bounds ); AffineTransform3D::Pointer transform = AffineTransform3D::New(); transform->SetMatrix(matrix); transform->SetOffset(worldOrigin.GetVectorFromOrigin()); InitializeStandardPlane( width, height, transform, planeorientation, zPosition, frontside, rotated, top); } void PlaneGeometry::InitializeStandardPlane( const BaseGeometry *geometry3D, bool top, PlaneOrientation planeorientation, bool frontside, bool rotated) { /// The index of the sagittal, coronal and axial axes in world coordinate system. int worldAxis; switch(planeorientation) { case None: /** Orientation 'None' shall be done like the axial plane orientation, * for whatever reasons. */ case Axial: worldAxis = 2; break; case Frontal: worldAxis = 1; break; case Sagittal: worldAxis = 0; break; default: itkExceptionMacro("unknown PlaneOrientation"); } // Inspired by: // http://www.na-mic.org/Wiki/index.php/Coordinate_System_Conversion_Between_ITK_and_Slicer3 mitk::AffineTransform3D::ConstPointer affineTransform = geometry3D->GetIndexToWorldTransform(); mitk::AffineTransform3D::MatrixType matrix = affineTransform->GetMatrix(); matrix.GetVnlMatrix().normalize_columns(); mitk::AffineTransform3D::MatrixType::InternalMatrixType inverseMatrix = matrix.GetInverse(); /// The index of the sagittal, coronal and axial axes in the reference geometry. int dominantAxis = CalculateDominantAxes(inverseMatrix).at(worldAxis); ScalarType zPosition = top ? 0.5 : geometry3D->GetExtent(dominantAxis) - 0.5; InitializeStandardPlane(geometry3D, planeorientation, zPosition, frontside, rotated, top); } void PlaneGeometry::InitializeStandardPlane(const Vector3D &rightVector, const Vector3D &downVector, const Vector3D *spacing) { InitializeStandardPlane(rightVector.GetVnlVector(), downVector.GetVnlVector(), spacing); } void PlaneGeometry::InitializeStandardPlane(const VnlVector &rightVector, const VnlVector &downVector, const Vector3D *spacing) { ScalarType width = rightVector.two_norm(); ScalarType height = downVector.two_norm(); InitializeStandardPlane(width, height, rightVector, downVector, spacing); } void PlaneGeometry::InitializeStandardPlane(mitk::ScalarType width, ScalarType height, const Vector3D &rightVector, const Vector3D &downVector, const Vector3D *spacing) { InitializeStandardPlane(width, height, rightVector.GetVnlVector(), downVector.GetVnlVector(), spacing); } void PlaneGeometry::InitializeStandardPlane(mitk::ScalarType width, ScalarType height, const VnlVector &rightVector, const VnlVector &downVector, const Vector3D *spacing) { assert(width > 0); assert(height > 0); VnlVector rightDV = rightVector; rightDV.normalize(); VnlVector downDV = downVector; downDV.normalize(); VnlVector normal = vnl_cross_3d(rightVector, downVector); normal.normalize(); // Crossproduct vnl_cross_3d is always righthanded, but that is okay here // because in this method we create a new IndexToWorldTransform and // spacing with 1 or 3 negative components could still make it lefthanded. if (spacing != nullptr) { rightDV *= (*spacing)[0]; downDV *= (*spacing)[1]; normal *= (*spacing)[2]; } AffineTransform3D::Pointer transform = AffineTransform3D::New(); Matrix3D matrix; matrix.GetVnlMatrix().set_column(0, rightDV); matrix.GetVnlMatrix().set_column(1, downDV); matrix.GetVnlMatrix().set_column(2, normal); transform->SetMatrix(matrix); transform->SetOffset(this->GetIndexToWorldTransform()->GetOffset()); ScalarType bounds[6] = {0, width, 0, height, 0, 1}; this->SetBounds(bounds); this->SetIndexToWorldTransform(transform); } void PlaneGeometry::InitializePlane(const Point3D &origin, const Vector3D &normal) { VnlVector rightVectorVnl(3), downVectorVnl; if (Equal(normal[1], 0.0f) == false) { FillVector3D(rightVectorVnl, 1.0f, -normal[0] / normal[1], 0.0f); rightVectorVnl.normalize(); } else { FillVector3D(rightVectorVnl, 0.0f, 1.0f, 0.0f); } downVectorVnl = vnl_cross_3d(normal.GetVnlVector(), rightVectorVnl); downVectorVnl.normalize(); // Crossproduct vnl_cross_3d is always righthanded. InitializeStandardPlane(rightVectorVnl, downVectorVnl); SetOrigin(origin); } void PlaneGeometry::SetMatrixByVectors(const VnlVector &rightVector, const VnlVector &downVector, ScalarType thickness /* = 1.0 */) { VnlVector normal = vnl_cross_3d(rightVector, downVector); normal.normalize(); normal *= thickness; // Crossproduct vnl_cross_3d is always righthanded, but that is okay here // because in this method we create a new IndexToWorldTransform and // a negative thickness could still make it lefthanded. AffineTransform3D::Pointer transform = AffineTransform3D::New(); Matrix3D matrix; matrix.GetVnlMatrix().set_column(0, rightVector); matrix.GetVnlMatrix().set_column(1, downVector); matrix.GetVnlMatrix().set_column(2, normal); transform->SetMatrix(matrix); transform->SetOffset(this->GetIndexToWorldTransform()->GetOffset()); SetIndexToWorldTransform(transform); } Vector3D PlaneGeometry::GetNormal() const { Vector3D frontToBack; frontToBack.SetVnlVector(this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(2)); return frontToBack; } VnlVector PlaneGeometry::GetNormalVnl() const { return this->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(2); } ScalarType PlaneGeometry::DistanceFromPlane(const Point3D &pt3d_mm) const { return fabs(SignedDistance(pt3d_mm)); } ScalarType PlaneGeometry::SignedDistance(const Point3D &pt3d_mm) const { return SignedDistanceFromPlane(pt3d_mm); } bool PlaneGeometry::IsAbove(const Point3D &pt3d_mm, bool considerBoundingBox) const { if (considerBoundingBox) { Point3D pt3d_units; BaseGeometry::WorldToIndex(pt3d_mm, pt3d_units); return (pt3d_units[2] > this->GetBoundingBox()->GetBounds()[4]); } else return SignedDistanceFromPlane(pt3d_mm) > 0; } bool PlaneGeometry::IntersectionLine(const PlaneGeometry *plane, Line3D &crossline) const { Vector3D normal = this->GetNormal(); normal.Normalize(); Vector3D planeNormal = plane->GetNormal(); planeNormal.Normalize(); Vector3D direction = itk::CrossProduct(normal, planeNormal); if (direction.GetSquaredNorm() < eps) return false; crossline.SetDirection(direction); double N1dN2 = normal * planeNormal; double determinant = 1.0 - N1dN2 * N1dN2; Vector3D origin = this->GetOrigin().GetVectorFromOrigin(); Vector3D planeOrigin = plane->GetOrigin().GetVectorFromOrigin(); double d1 = normal * origin; double d2 = planeNormal * planeOrigin; double c1 = (d1 - d2 * N1dN2) / determinant; double c2 = (d2 - d1 * N1dN2) / determinant; Vector3D p = normal * c1 + planeNormal * c2; crossline.GetPoint().GetVnlVector() = p.GetVnlVector(); return true; } unsigned int PlaneGeometry::IntersectWithPlane2D(const PlaneGeometry *plane, Point2D &lineFrom, Point2D &lineTo) const { Line3D crossline; if (this->IntersectionLine(plane, crossline) == false) return 0; Point2D point2; Vector2D direction2; this->Map(crossline.GetPoint(), point2); this->Map(crossline.GetPoint(), crossline.GetDirection(), direction2); return Line3D::RectangleLineIntersection( 0, 0, GetExtentInMM(0), GetExtentInMM(1), point2, direction2, lineFrom, lineTo); } double PlaneGeometry::Angle(const PlaneGeometry *plane) const { return angle(plane->GetMatrixColumn(2), GetMatrixColumn(2)); } double PlaneGeometry::Angle(const Line3D &line) const { return vnl_math::pi_over_2 - angle(line.GetDirection().GetVnlVector(), GetMatrixColumn(2)); } bool PlaneGeometry::IntersectionPoint(const Line3D &line, Point3D &intersectionPoint) const { Vector3D planeNormal = this->GetNormal(); planeNormal.Normalize(); Vector3D lineDirection = line.GetDirection(); lineDirection.Normalize(); double t = planeNormal * lineDirection; if (fabs(t) < eps) { return false; } Vector3D diff; diff = this->GetOrigin() - line.GetPoint(); t = (planeNormal * diff) / t; intersectionPoint = line.GetPoint() + lineDirection * t; return true; } bool PlaneGeometry::IntersectionPointParam(const Line3D &line, double &t) const { Vector3D planeNormal = this->GetNormal(); Vector3D lineDirection = line.GetDirection(); t = planeNormal * lineDirection; if (fabs(t) < eps) { return false; } Vector3D diff; diff = this->GetOrigin() - line.GetPoint(); t = (planeNormal * diff) / t; return true; } bool PlaneGeometry::IsParallel(const PlaneGeometry *plane) const { return ((Angle(plane) < 10.0 * mitk::sqrteps) || (Angle(plane) > (vnl_math::pi - 10.0 * sqrteps))); } bool PlaneGeometry::IsOnPlane(const Point3D &point) const { return Distance(point) < eps; } bool PlaneGeometry::IsOnPlane(const Line3D &line) const { return ((Distance(line.GetPoint()) < eps) && (Distance(line.GetPoint2()) < eps)); } bool PlaneGeometry::IsOnPlane(const PlaneGeometry *plane) const { return (IsParallel(plane) && (Distance(plane->GetOrigin()) < eps)); } Point3D PlaneGeometry::ProjectPointOntoPlane(const Point3D &pt) const { ScalarType len = this->GetNormalVnl().two_norm(); return pt - this->GetNormal() * this->SignedDistanceFromPlane(pt) / len; } itk::LightObject::Pointer PlaneGeometry::InternalClone() const { Self::Pointer newGeometry = new PlaneGeometry(*this); newGeometry->UnRegister(); return newGeometry.GetPointer(); } void PlaneGeometry::ExecuteOperation(Operation *operation) { vtkTransform *transform = vtkTransform::New(); transform->SetMatrix(this->GetVtkMatrix()); switch (operation->GetOperationType()) { case OpORIENT: { auto *planeOp = dynamic_cast(operation); if (planeOp == nullptr) { return; } Point3D center = planeOp->GetPoint(); Vector3D orientationVector = planeOp->GetNormal(); Vector3D defaultVector; FillVector3D(defaultVector, 0.0, 0.0, 1.0); Vector3D rotationAxis = itk::CrossProduct(orientationVector, defaultVector); // double rotationAngle = acos( orientationVector[2] / orientationVector.GetNorm() ); double rotationAngle = atan2((double)rotationAxis.GetNorm(), (double)(orientationVector * defaultVector)); rotationAngle *= 180.0 / vnl_math::pi; transform->PostMultiply(); transform->Identity(); transform->Translate(center[0], center[1], center[2]); transform->RotateWXYZ(rotationAngle, rotationAxis[0], rotationAxis[1], rotationAxis[2]); transform->Translate(-center[0], -center[1], -center[2]); break; } case OpRESTOREPLANEPOSITION: { auto *op = dynamic_cast(operation); if (op == nullptr) { return; } AffineTransform3D::Pointer transform2 = AffineTransform3D::New(); Matrix3D matrix; matrix.GetVnlMatrix().set_column(0, op->GetTransform()->GetMatrix().GetVnlMatrix().get_column(0)); matrix.GetVnlMatrix().set_column(1, op->GetTransform()->GetMatrix().GetVnlMatrix().get_column(1)); matrix.GetVnlMatrix().set_column(2, op->GetTransform()->GetMatrix().GetVnlMatrix().get_column(2)); transform2->SetMatrix(matrix); Vector3D offset = op->GetTransform()->GetOffset(); transform2->SetOffset(offset); this->SetIndexToWorldTransform(transform2); ScalarType bounds[6] = {0, op->GetWidth(), 0, op->GetHeight(), 0, 1}; this->SetBounds(bounds); this->Modified(); transform->Delete(); return; } default: Superclass::ExecuteOperation(operation); transform->Delete(); return; } this->SetVtkMatrixDeepCopy(transform); this->Modified(); transform->Delete(); } void PlaneGeometry::PrintSelf(std::ostream &os, itk::Indent indent) const { Superclass::PrintSelf(os, indent); os << indent << " ScaleFactorMMPerUnitX: " << GetExtentInMM(0) / GetExtent(0) << std::endl; os << indent << " ScaleFactorMMPerUnitY: " << GetExtentInMM(1) / GetExtent(1) << std::endl; os << indent << " Normal: " << GetNormal() << std::endl; } bool PlaneGeometry::Map(const mitk::Point3D &pt3d_mm, mitk::Point2D &pt2d_mm) const { assert(this->IsBoundingBoxNull() == false); Point3D pt3d_units; Superclass::WorldToIndex(pt3d_mm, pt3d_units); pt2d_mm[0] = pt3d_units[0] * GetExtentInMM(0) / GetExtent(0); pt2d_mm[1] = pt3d_units[1] * GetExtentInMM(1) / GetExtent(1); pt3d_units[2] = 0; return this->GetBoundingBox()->IsInside(pt3d_units); } void PlaneGeometry::Map(const mitk::Point2D &pt2d_mm, mitk::Point3D &pt3d_mm) const { // pt2d_mm is measured from the origin of the world geometry (at leats it called form BaseRendere::Mouse...Event) Point3D pt3d_units; pt3d_units[0] = pt2d_mm[0] / (GetExtentInMM(0) / GetExtent(0)); pt3d_units[1] = pt2d_mm[1] / (GetExtentInMM(1) / GetExtent(1)); pt3d_units[2] = 0; // pt3d_units is a continuos index. We divided it with the Scale Factor (= spacing in x and y) to convert it from mm // to index units. // pt3d_mm = GetIndexToWorldTransform()->TransformPoint(pt3d_units); // now we convert the 3d index to a 3D world point in mm. We could have used IndexToWorld as well as // GetITW->Transform... } void PlaneGeometry::SetSizeInUnits(mitk::ScalarType width, mitk::ScalarType height) { ScalarType bounds[6] = {0, width, 0, height, 0, 1}; ScalarType extent, newextentInMM; if (GetExtent(0) > 0) { extent = GetExtent(0); if (width > extent) newextentInMM = GetExtentInMM(0) / width * extent; else newextentInMM = GetExtentInMM(0) * extent / width; SetExtentInMM(0, newextentInMM); } if (GetExtent(1) > 0) { extent = GetExtent(1); if (width > extent) newextentInMM = GetExtentInMM(1) / height * extent; else newextentInMM = GetExtentInMM(1) * extent / height; SetExtentInMM(1, newextentInMM); } SetBounds(bounds); } bool PlaneGeometry::Project(const mitk::Point3D &pt3d_mm, mitk::Point3D &projectedPt3d_mm) const { assert(this->IsBoundingBoxNull() == false); Point3D pt3d_units; Superclass::WorldToIndex(pt3d_mm, pt3d_units); pt3d_units[2] = 0; projectedPt3d_mm = GetIndexToWorldTransform()->TransformPoint(pt3d_units); return this->GetBoundingBox()->IsInside(pt3d_units); } bool PlaneGeometry::Project(const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const { assert(this->IsBoundingBoxNull() == false); Vector3D vec3d_units; Superclass::WorldToIndex(vec3d_mm, vec3d_units); vec3d_units[2] = 0; projectedVec3d_mm = GetIndexToWorldTransform()->TransformVector(vec3d_units); return true; } bool PlaneGeometry::Project(const mitk::Point3D &atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector3D &projectedVec3d_mm) const { MITK_WARN << "Deprecated function! Call Project(vec3D,vec3D) instead."; assert(this->IsBoundingBoxNull() == false); Vector3D vec3d_units; Superclass::WorldToIndex(atPt3d_mm, vec3d_mm, vec3d_units); vec3d_units[2] = 0; projectedVec3d_mm = GetIndexToWorldTransform()->TransformVector(vec3d_units); Point3D pt3d_units; Superclass::WorldToIndex(atPt3d_mm, pt3d_units); return this->GetBoundingBox()->IsInside(pt3d_units); } bool PlaneGeometry::Map(const mitk::Point3D &atPt3d_mm, const mitk::Vector3D &vec3d_mm, mitk::Vector2D &vec2d_mm) const { Point2D pt2d_mm_start, pt2d_mm_end; Point3D pt3d_mm_end; bool inside = Map(atPt3d_mm, pt2d_mm_start); pt3d_mm_end = atPt3d_mm + vec3d_mm; inside &= Map(pt3d_mm_end, pt2d_mm_end); vec2d_mm = pt2d_mm_end - pt2d_mm_start; return inside; } void PlaneGeometry::Map(const mitk::Point2D & /*atPt2d_mm*/, const mitk::Vector2D & /*vec2d_mm*/, mitk::Vector3D & /*vec3d_mm*/) const { //@todo implement parallel to the other Map method! assert(false); } void PlaneGeometry::SetReferenceGeometry(const mitk::BaseGeometry *geometry) { m_ReferenceGeometry = geometry; } const mitk::BaseGeometry *PlaneGeometry::GetReferenceGeometry() const { return m_ReferenceGeometry; } bool PlaneGeometry::HasReferenceGeometry() const { return (m_ReferenceGeometry != nullptr); } } // namespace diff --git a/Modules/Core/src/DataManagement/mitkPropertyList.cpp b/Modules/Core/src/DataManagement/mitkPropertyList.cpp index 69d6aaed01..d9ad1ac009 100644 --- a/Modules/Core/src/DataManagement/mitkPropertyList.cpp +++ b/Modules/Core/src/DataManagement/mitkPropertyList.cpp @@ -1,376 +1,376 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkPropertyList.h" #include "mitkNumericTypes.h" #include "mitkProperties.h" #include "mitkStringProperty.h" mitk::BaseProperty::ConstPointer mitk::PropertyList::GetConstProperty(const std::string &propertyKey, const std::string &/*contextName*/, bool /*fallBackOnDefaultContext*/) const { PropertyMap::const_iterator it; it = m_Properties.find(propertyKey); if (it != m_Properties.cend()) return it->second.GetPointer(); else return nullptr; }; std::vector mitk::PropertyList::GetPropertyKeys(const std::string &contextName, bool includeDefaultContext) const { std::vector propertyKeys; if (contextName.empty() || includeDefaultContext) { - for (auto property : this->m_Properties) + for (const auto &property : this->m_Properties) propertyKeys.push_back(property.first); } return propertyKeys; }; std::vector mitk::PropertyList::GetPropertyContextNames() const { return std::vector(); }; mitk::BaseProperty *mitk::PropertyList::GetProperty(const std::string &propertyKey) const { PropertyMap::const_iterator it; it = m_Properties.find(propertyKey); if (it != m_Properties.cend()) return it->second; else return nullptr; } mitk::BaseProperty * mitk::PropertyList::GetNonConstProperty(const std::string &propertyKey, const std::string &/*contextName*/, bool /*fallBackOnDefaultContext*/) { return this->GetProperty(propertyKey); } void mitk::PropertyList::SetProperty(const std::string &propertyKey, BaseProperty *property, const std::string &/*contextName*/, bool /*fallBackOnDefaultContext*/) { if (propertyKey.empty()) mitkThrow() << "Property key is empty."; if (!property) return; // make sure that BaseProperty*, which may have just been created and never been // assigned to a SmartPointer, is registered/unregistered properly. If we do not // do that, it will a) not deleted in case it is identical to the old one or // b) possibly deleted when temporarily added to a smartpointer somewhere below. BaseProperty::Pointer tmpSmartPointerToProperty = property; auto it(m_Properties.find(propertyKey)); // Is a property with key @a propertyKey contained in the list? if (it != m_Properties.cend()) { // yes // is the property contained in the list identical to the new one? if (it->second->operator==(*property)) { // yes? do nothing and return. return; } if (it->second->AssignProperty(*property)) { // The assignment was successfull this->Modified(); } else { MITK_ERROR << "In " __FILE__ ", l." << __LINE__ << ": Trying to set existing property " << it->first << " of type " << it->second->GetNameOfClass() << " to a property with different type " << property->GetNameOfClass() << "." << " Use ReplaceProperty() instead." << std::endl; } return; } // no? add it. m_Properties.insert(PropertyMap::value_type(propertyKey, property)); this->Modified(); } void mitk::PropertyList::ReplaceProperty(const std::string &propertyKey, BaseProperty *property) { if (!property) return; auto it(m_Properties.find(propertyKey)); // Is a property with key @a propertyKey contained in the list? if (it != m_Properties.cend()) { it->second = nullptr; m_Properties.erase(it); } // no? add/replace it. m_Properties.insert(PropertyMap::value_type(propertyKey, property)); Modified(); } void mitk::PropertyList::RemoveProperty(const std::string &propertyKey, const std::string &/*contextName*/, bool /*fallBackOnDefaultContext*/) { auto it(m_Properties.find(propertyKey)); // Is a property with key @a propertyKey contained in the list? if (it != m_Properties.cend()) { it->second = nullptr; m_Properties.erase(it); Modified(); } } mitk::PropertyList::PropertyList() { } mitk::PropertyList::PropertyList(const mitk::PropertyList &other) : itk::Object() { for (auto i = other.m_Properties.cbegin(); i != other.m_Properties.cend(); ++i) { m_Properties.insert(std::make_pair(i->first, i->second->Clone())); } } mitk::PropertyList::~PropertyList() { Clear(); } /** * Consider the list as changed when any of the properties has changed recently. */ unsigned long mitk::PropertyList::GetMTime() const { for (auto it = m_Properties.cbegin(); it != m_Properties.cend(); ++it) { if (it->second.IsNull()) { itkWarningMacro(<< "Property '" << it->first << "' contains nothing (nullptr)."); continue; } if (Superclass::GetMTime() < it->second->GetMTime()) { Modified(); break; } } return Superclass::GetMTime(); } bool mitk::PropertyList::DeleteProperty(const std::string &propertyKey) { auto it = m_Properties.find(propertyKey); if (it != m_Properties.end()) { it->second = nullptr; m_Properties.erase(it); Modified(); return true; } return false; } void mitk::PropertyList::Clear() { auto it = m_Properties.begin(), end = m_Properties.end(); while (it != end) { it->second = nullptr; ++it; } m_Properties.clear(); } itk::LightObject::Pointer mitk::PropertyList::InternalClone() const { itk::LightObject::Pointer result(new Self(*this)); result->UnRegister(); return result; } void mitk::PropertyList::ConcatenatePropertyList(PropertyList *pList, bool replace) { if (pList) { const PropertyMap *propertyMap = pList->GetMap(); for (auto iter = propertyMap->cbegin(); // m_PropertyList is created in the constructor, so we don't check it here iter != propertyMap->cend(); ++iter) { const std::string key = iter->first; BaseProperty *value = iter->second; if (replace) { ReplaceProperty(key.c_str(), value); } else { SetProperty(key.c_str(), value); } } } } bool mitk::PropertyList::GetBoolProperty(const char *propertyKey, bool &boolValue) const { BoolProperty *gp = dynamic_cast(GetProperty(propertyKey)); if (gp != nullptr) { boolValue = gp->GetValue(); return true; } return false; // Templated Method does not work on Macs // return GetPropertyValue(propertyKey, boolValue); } bool mitk::PropertyList::GetIntProperty(const char *propertyKey, int &intValue) const { IntProperty *gp = dynamic_cast(GetProperty(propertyKey)); if (gp != nullptr) { intValue = gp->GetValue(); return true; } return false; // Templated Method does not work on Macs // return GetPropertyValue(propertyKey, intValue); } bool mitk::PropertyList::GetFloatProperty(const char *propertyKey, float &floatValue) const { FloatProperty *gp = dynamic_cast(GetProperty(propertyKey)); if (gp != nullptr) { floatValue = gp->GetValue(); return true; } return false; // Templated Method does not work on Macs // return GetPropertyValue(propertyKey, floatValue); } bool mitk::PropertyList::GetStringProperty(const char *propertyKey, std::string &stringValue) const { StringProperty *sp = dynamic_cast(GetProperty(propertyKey)); if (sp != nullptr) { stringValue = sp->GetValue(); return true; } return false; } void mitk::PropertyList::SetIntProperty(const char *propertyKey, int intValue) { SetProperty(propertyKey, mitk::IntProperty::New(intValue)); } void mitk::PropertyList::SetBoolProperty(const char *propertyKey, bool boolValue) { SetProperty(propertyKey, mitk::BoolProperty::New(boolValue)); } void mitk::PropertyList::SetFloatProperty(const char *propertyKey, float floatValue) { SetProperty(propertyKey, mitk::FloatProperty::New(floatValue)); } void mitk::PropertyList::SetStringProperty(const char *propertyKey, const char *stringValue) { SetProperty(propertyKey, mitk::StringProperty::New(stringValue)); } void mitk::PropertyList::Set(const char *propertyKey, bool boolValue) { this->SetBoolProperty(propertyKey, boolValue); } void mitk::PropertyList::Set(const char *propertyKey, int intValue) { this->SetIntProperty(propertyKey, intValue); } void mitk::PropertyList::Set(const char *propertyKey, float floatValue) { this->SetFloatProperty(propertyKey, floatValue); } void mitk::PropertyList::Set(const char *propertyKey, double doubleValue) { this->SetDoubleProperty(propertyKey, doubleValue); } void mitk::PropertyList::Set(const char *propertyKey, const char *stringValue) { this->SetStringProperty(propertyKey, stringValue); } void mitk::PropertyList::Set(const char *propertyKey, const std::string &stringValue) { this->SetStringProperty(propertyKey, stringValue.c_str()); } bool mitk::PropertyList::Get(const char *propertyKey, bool &boolValue) const { return this->GetBoolProperty(propertyKey, boolValue); } bool mitk::PropertyList::Get(const char *propertyKey, int &intValue) const { return this->GetIntProperty(propertyKey, intValue); } bool mitk::PropertyList::Get(const char *propertyKey, float &floatValue) const { return this->GetFloatProperty(propertyKey, floatValue); } bool mitk::PropertyList::Get(const char *propertyKey, double &doubleValue) const { return this->GetDoubleProperty(propertyKey, doubleValue); } bool mitk::PropertyList::Get(const char *propertyKey, std::string &stringValue) const { return this->GetStringProperty(propertyKey, stringValue); } bool mitk::PropertyList::GetDoubleProperty(const char *propertyKey, double &doubleValue) const { DoubleProperty *gp = dynamic_cast(GetProperty(propertyKey)); if (gp != nullptr) { doubleValue = gp->GetValue(); return true; } return false; } void mitk::PropertyList::SetDoubleProperty(const char *propertyKey, double doubleValue) { SetProperty(propertyKey, mitk::DoubleProperty::New(doubleValue)); } diff --git a/Modules/Core/src/DataManagement/mitkSourceImageRelationRule.cpp b/Modules/Core/src/DataManagement/mitkSourceImageRelationRule.cpp index de0916c8d5..b743e4d531 100644 --- a/Modules/Core/src/DataManagement/mitkSourceImageRelationRule.cpp +++ b/Modules/Core/src/DataManagement/mitkSourceImageRelationRule.cpp @@ -1,419 +1,419 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include "mitkSourceImageRelationRule.h" #include "mitkPropertyNameHelper.h" #include "mitkStringProperty.h" #include "mitkTemporoSpatialStringProperty.h" #include "mitkDataNode.h" #include "mitkIdentifiable.h" std::string mitk::SourceImageRelationRule::GenerateRuleID(const std::string& purpose) const { std::string result = "SourceImageRelation"; if (!purpose.empty()) { result += " " + purpose; } return result; } bool mitk::SourceImageRelationRule::IsAbstract() const { return m_PurposeTag.empty(); }; bool mitk::SourceImageRelationRule::IsSupportedRuleID(const RuleIDType& ruleID) const { return ruleID == this->GetRuleID() || (IsAbstract() && ruleID.find("SourceImageRelation ") == 0); }; mitk::SourceImageRelationRule::RuleIDType mitk::SourceImageRelationRule::GetRuleID() const { return this->GenerateRuleID(m_PurposeTag); }; std::string mitk::SourceImageRelationRule::GetDisplayName() const { return m_DisplayName; }; std::string mitk::SourceImageRelationRule::GetSourceRoleName() const { return m_SourceRole; }; std::string mitk::SourceImageRelationRule::GetDestinationRoleName() const { return m_DestinationRole; }; bool mitk::SourceImageRelationRule::IsDestinationCandidate(const IPropertyProvider *owner) const { auto node = dynamic_cast(owner); auto image = nullptr != node ? dynamic_cast(node->GetData()) : dynamic_cast(owner); return image != nullptr; } mitk::SourceImageRelationRule::RelationUIDType mitk::SourceImageRelationRule::Connect(Image *source, const Image *destination) const { return Superclass::Connect(source, destination); }; mitk::SourceImageRelationRule::SourceImageRelationRule() : m_PurposeTag(""), m_DisplayName("Abstract image to image relation"), m_SourceRole("derived data"), m_DestinationRole("source image") {}; mitk::SourceImageRelationRule::SourceImageRelationRule(const RuleIDType &purposeTag) : SourceImageRelationRule(purposeTag, purposeTag + " relation"){}; mitk::SourceImageRelationRule::SourceImageRelationRule(const RuleIDType &purposeTag, const std::string &displayName) : SourceImageRelationRule( purposeTag, displayName, "derived data", "source image"){}; mitk::SourceImageRelationRule::SourceImageRelationRule(const RuleIDType &purposeTag, const std::string &displayName, const std::string &sourceRole, const std::string &destinationRole) : m_PurposeTag(purposeTag), m_DisplayName(displayName), m_SourceRole(sourceRole), m_DestinationRole(destinationRole){}; mitk::SourceImageRelationRule::DataRelationUIDVectorType mitk::SourceImageRelationRule::GetRelationUIDs_DataLayer(const IPropertyProvider* source, const IPropertyProvider* destination, const InstanceIDVectorType& instances_IDLayer) const { DataRelationUIDVectorType result; auto relevantIndicesAndRuleIDs = GetReferenceSequenceIndices(source, destination, instances_IDLayer); auto itemRIIRegExStr = this->GetRIIPropertyRegEx("SourceImageSequenceItem"); auto regEx = std::regex(itemRIIRegExStr); //workaround until T24729 is done. Please remove if T24728 is done auto keys = PropertyRelationRuleBase::GetPropertyKeys(source); //end workaround for T24729 for (const auto &indexNRule : relevantIndicesAndRuleIDs) { bool relationCoveredByRII = false; for (const auto& key : keys) { if (std::regex_match(key, regEx)) { auto sequItemProp = source->GetConstProperty(key); if (sequItemProp.IsNotNull() && sequItemProp->GetValueAsString() == std::to_string(indexNRule.first)) { relationCoveredByRII = true; auto instanceID = GetInstanceIDByPropertyName(key); auto ruleID = GetRuleIDByInstanceID(source, instanceID); if (this->IsSupportedRuleID(ruleID)) { result.emplace_back(this->GetRelationUIDByInstanceID(source, instanceID), ruleID); } } } } if (!relationCoveredByRII) { //the relation is not covered on the RII level, so we generate the property path to the DICOM source reference (this is done via //the SOP Instance UIDs which uniquely identify an DICOM IOD). We use this property path as relation UID because it is identifying //on the data level (even so not long term stable if relations with a lower index are removed). PropertyKeyPath referencedInstanceUIDs; referencedInstanceUIDs.AddElement("DICOM").AddElement("0008").AddSelection("2112", indexNRule.first).AddElement("0008").AddElement("1155"); std::string ruleID = ""; if (!indexNRule.second.empty()) { ruleID = this->GenerateRuleID(indexNRule.second); } result.emplace_back(PropertyKeyPathToPropertyName(referencedInstanceUIDs), ruleID); } } return result; }; std::vector > mitk::SourceImageRelationRule::GetReferenceSequenceIndices(const IPropertyProvider * source, const IPropertyProvider * destination, InstanceIDVectorType ignoreInstances) const { std::vector > result; BaseProperty::ConstPointer destInstanceUIDProp; std::string destinationUID = ""; if (destination) { destInstanceUIDProp = destination->GetConstProperty(GeneratePropertyNameForDICOMTag(0x0008, 0x0018)); if (destInstanceUIDProp.IsNull()) { return result; } auto identifiable = this->CastProviderAsIdentifiable(destination); if (identifiable) { destinationUID= identifiable->GetUID(); } } std::vector ignoreItemIndices; for (const auto& iID : ignoreInstances) { auto sourceImageRefPath = GetRootKeyPath().AddElement(iID).AddElement("SourceImageSequenceItem"); auto imageRefProp = source->GetConstProperty(PropertyKeyPathToPropertyName(sourceImageRefPath)); if (imageRefProp.IsNotNull()) { ignoreItemIndices.emplace_back(imageRefProp->GetValueAsString()); } } PropertyKeyPath referencedInstanceUIDs; referencedInstanceUIDs.AddElement("DICOM").AddElement("0008").AddAnySelection("2112").AddElement("0008").AddElement("1155"); auto sourceRegExStr = PropertyKeyPathToPropertyRegEx(referencedInstanceUIDs); auto regEx = std::regex(sourceRegExStr); std::vector keys; //workaround until T24729 is done. Please remove if T24728 is done keys = PropertyRelationRuleBase::GetPropertyKeys(source); //end workaround for T24729 for (const auto &key : keys) { if (std::regex_match(key, regEx)) { auto refUIDProp = source->GetConstProperty(key); if (destination==nullptr || *refUIDProp == *destInstanceUIDProp) { auto currentKeyPath = PropertyNameToPropertyKeyPath(key); auto currentKeyPathSelection = currentKeyPath.GetNode(2).selection; auto finding = std::find(ignoreItemIndices.begin(), ignoreItemIndices.end(), std::to_string(currentKeyPathSelection)); if (finding == ignoreItemIndices.end()) { PropertyKeyPath purposePath; purposePath.AddElement("DICOM").AddElement("0008").AddSelection("2112", currentKeyPathSelection).AddElement("0040").AddSelection("a170", 0).AddElement("0008").AddElement("0104"); auto purposeProp = source->GetConstProperty(PropertyKeyPathToPropertyName(purposePath)); std::string currentPurpose = ""; if (purposeProp.IsNotNull()) { currentPurpose = purposeProp->GetValueAsString(); } if (this->IsAbstract() || (purposeProp.IsNotNull() && currentPurpose == this->m_PurposeTag)) { result.emplace_back(currentKeyPathSelection, currentPurpose); } } } } } return result; }; /**This mutex is used to guard mitk::SourceImageRelationRule::CreateNewSourceImageSequenceItem by a class wide mutex to avoid racing conditions in a scenario where rules are used concurrently. It is not in the class interface itself, because it is an implementation detail. */ namespace { std::mutex sequenceItemCreationLock; } mitk::PropertyKeyPath::ItemSelectionIndex mitk::SourceImageRelationRule::CreateNewSourceImageSequenceItem( IPropertyOwner *source) const { std::lock_guard guard(sequenceItemCreationLock); ////////////////////////////////////// // Get all existing sequence items std::vector instanceIDs; PropertyKeyPath::ItemSelectionIndex newID = 0; PropertyKeyPath referencedInstanceUIDs; referencedInstanceUIDs.AddElement("DICOM").AddElement("0008").AddAnySelection("2112").AddElement("0008").AddElement("1155"); auto regExStr = PropertyKeyPathToPropertyRegEx(referencedInstanceUIDs); auto regEx = std::regex(regExStr); std::smatch instance_matches; //workaround until T24729 is done. You can use directly source->GetPropertyKeys again, when fixed. const auto keys = GetPropertyKeys(source); //end workaround for T24729 for (const auto &key : keys) { if (std::regex_search(key, instance_matches, regEx)) { if (instance_matches.size()>1) { instanceIDs.push_back(std::stoi(instance_matches[1])); } } } ////////////////////////////////////// // Get new ID std::sort(instanceIDs.begin(), instanceIDs.end()); if (!instanceIDs.empty()) { newID = instanceIDs.back()+1; } ////////////////////////////////////// // reserve new ID PropertyKeyPath newSourceImageSequencePath; newSourceImageSequencePath.AddElement("DICOM").AddElement("0008").AddSelection("2112",newID).AddElement("0008").AddElement("1155"); auto newKey = PropertyKeyPathToPropertyName(newSourceImageSequencePath); source->SetProperty(newKey, mitk::TemporoSpatialStringProperty::New("reserved slot for source image sequence")); return newID; }; void mitk::SourceImageRelationRule::Connect_datalayer(IPropertyOwner * source, const IPropertyProvider * destination, const InstanceIDType & instanceID) const { auto destInstanceUIDProp = destination->GetConstProperty(GeneratePropertyNameForDICOMTag(0x0008,0x0018)); auto destClassUIDProp = destination->GetConstProperty(GeneratePropertyNameForDICOMTag(0x0008, 0x0016)); if (destInstanceUIDProp.IsNotNull() && destClassUIDProp.IsNotNull()) { auto existingRefs = this->GetReferenceSequenceIndices(source, destination); std::string newSelectionIndexStr; if (!existingRefs.empty()) { newSelectionIndexStr = std::to_string(existingRefs[0].first); } else { PropertyKeyPath::ItemSelectionIndex newSelectionIndex = CreateNewSourceImageSequenceItem(source); PropertyKeyPath refInstanceUIDPath; refInstanceUIDPath.AddElement("DICOM").AddElement("0008").AddSelection("2112", newSelectionIndex).AddElement("0008").AddElement("1155"); source->SetProperty(PropertyKeyPathToPropertyName(refInstanceUIDPath), destInstanceUIDProp->Clone()); PropertyKeyPath refClassUIDPath; refClassUIDPath.AddElement("DICOM").AddElement("0008").AddSelection("2112", newSelectionIndex).AddElement("0008").AddElement("1150"); source->SetProperty(PropertyKeyPathToPropertyName(refClassUIDPath), destClassUIDProp->Clone()); PropertyKeyPath purposePath; purposePath.AddElement("DICOM").AddElement("0008").AddSelection("2112", newSelectionIndex).AddElement("0040").AddSelection("a170", 0).AddElement("0008").AddElement("0104"); source->SetProperty(PropertyKeyPathToPropertyName(purposePath), StringProperty::New(m_PurposeTag)); newSelectionIndexStr = std::to_string(newSelectionIndex); } auto sourceImageRefPath = GetRootKeyPath().AddElement(instanceID).AddElement("SourceImageSequenceItem"); source->SetProperty(PropertyKeyPathToPropertyName(sourceImageRefPath), StringProperty::New(newSelectionIndexStr).GetPointer()); } else { MITK_DEBUG << "Cannot connect SourceImageRelationRule on data layer. Passed destination does not have properties for DICOM SOP Instance UIDs(0x0008, 0x0018) and DICOM SOP Class UID(0x0008, 0x0016)"; } }; void mitk::SourceImageRelationRule::Disconnect_datalayer(IPropertyOwner * source, const RelationUIDType & relationUID) const { std::string deletedImageRefSequenceIndexStr = ""; if (relationUID.find("DICOM") == 0) { //relation that is purly data based. auto currentKeyPath = PropertyNameToPropertyKeyPath(relationUID); deletedImageRefSequenceIndexStr = std::to_string(currentKeyPath.GetNode(2).selection); } else { auto sourceImageRefPath = GetRootKeyPath().AddElement(this->GetInstanceIDByRelationUID(source,relationUID)).AddElement("SourceImageSequenceItem"); auto imageRefProp = source->GetConstProperty(PropertyKeyPathToPropertyName(sourceImageRefPath)); if (imageRefProp.IsNotNull()) { deletedImageRefSequenceIndexStr = imageRefProp->GetValueAsString(); } } if(!deletedImageRefSequenceIndexStr.empty()) { auto deletedImageRefSequenceIndex = std::stoull(deletedImageRefSequenceIndexStr); auto refs = GetReferenceSequenceIndices(source); std::sort(refs.begin(), refs.end()); - for (auto refIndex : refs) + for (const auto &refIndex : refs) { if (refIndex.first >= deletedImageRefSequenceIndex) { PropertyKeyPath refDICOMDataPath; refDICOMDataPath.AddElement("DICOM").AddElement("0008").AddSelection("2112", refIndex.first); auto prefix = PropertyKeyPathToPropertyName(refDICOMDataPath); PropertyKeyPath refRelDataPath = GetRootKeyPath().AddAnyElement().AddElement("SourceImageSequenceItem");; auto riiRegEx = std::regex(PropertyKeyPathToPropertyRegEx(refRelDataPath)); //workaround until T24729 is done. You can use directly source->GetPropertyKeys again, when fixed. const auto keys = GetPropertyKeys(source); //end workaround for T24729 for (const auto &key : keys) { if (key.find(prefix) == 0) { //its a relevant DICOM property delete or update if (refIndex.first != deletedImageRefSequenceIndex) { //reindex to close the gap in the dicom sequence. auto newPath = PropertyNameToPropertyKeyPath(key); newPath.GetNode(2).selection = refIndex.first - 1; source->SetProperty(PropertyKeyPathToPropertyName(newPath), source->GetNonConstProperty(key)); } //remove old/outdated data layer information source->RemoveProperty(key); } if (std::regex_match(key, riiRegEx)) { //it is a relevant RII property, remove it or update it. auto imageSequenceItemProp = source->GetConstProperty(key); if (imageSequenceItemProp->GetValueAsString() == deletedImageRefSequenceIndexStr) { source->RemoveProperty(key); } else if (imageSequenceItemProp->GetValueAsString() == std::to_string(refIndex.first)) { //its a relevant data property of the relation rule reindex it. source->SetProperty(key, StringProperty::New(std::to_string(refIndex.first - 1))); } } } } } } }; itk::LightObject::Pointer mitk::SourceImageRelationRule::InternalClone() const { itk::LightObject::Pointer result = Self::New(this->m_PurposeTag, this->m_DisplayName, this->m_SourceRole, this->m_DestinationRole).GetPointer(); return result; }; diff --git a/Modules/Core/src/IO/mitkAbstractFileReader.cpp b/Modules/Core/src/IO/mitkAbstractFileReader.cpp index af38ca14ad..4ac0024740 100644 --- a/Modules/Core/src/IO/mitkAbstractFileReader.cpp +++ b/Modules/Core/src/IO/mitkAbstractFileReader.cpp @@ -1,332 +1,334 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include #include #include #include #include #include #include #include #include namespace mitk { AbstractFileReader::InputStream::InputStream(IFileReader *reader, std::ios_base::openmode mode) : std::istream(nullptr), m_Stream(nullptr) { std::istream *stream = reader->GetInputStream(); if (stream) { this->init(stream->rdbuf()); } else { m_Stream = new std::ifstream(reader->GetInputLocation().c_str(), mode); this->init(m_Stream->rdbuf()); } } AbstractFileReader::InputStream::~InputStream() { delete m_Stream; } class AbstractFileReader::Impl : public FileReaderWriterBase { public: Impl() : FileReaderWriterBase(), m_Stream(nullptr), m_PrototypeFactory(nullptr) {} Impl(const Impl &other) : FileReaderWriterBase(other), m_Stream(nullptr), m_PrototypeFactory(nullptr) {} std::string m_Location; std::string m_TmpFile; std::istream *m_Stream; us::PrototypeServiceFactory *m_PrototypeFactory; us::ServiceRegistration m_Reg; }; AbstractFileReader::AbstractFileReader() : d(new Impl) {} AbstractFileReader::~AbstractFileReader() { UnregisterService(); delete d->m_PrototypeFactory; if (!d->m_TmpFile.empty()) { std::remove(d->m_TmpFile.c_str()); } } AbstractFileReader::AbstractFileReader(const AbstractFileReader &other) : IFileReader(), d(new Impl(*other.d.get())) { } AbstractFileReader::AbstractFileReader(const CustomMimeType &mimeType, const std::string &description) : d(new Impl) { d->SetMimeType(mimeType); d->SetDescription(description); } ////////////////////// Reading ///////////////////////// std::vector AbstractFileReader::Read() { std::vector result = this->DoRead(); const auto options = this->GetOptions(); for (auto& data : result) { data->SetProperty(PropertyKeyPathToPropertyName(IOMetaInformationPropertyConstants::READER_DESCRIPTION()), StringProperty::New(d->GetDescription())); data->SetProperty(PropertyKeyPathToPropertyName(IOMetaInformationPropertyConstants::READER_VERSION()), StringProperty::New(MITK_VERSION_STRING)); data->SetProperty(PropertyKeyPathToPropertyName(IOMetaInformationPropertyConstants::READER_MIME_NAME()), StringProperty::New(d->GetMimeType()->GetName())); data->SetProperty(PropertyKeyPathToPropertyName(IOMetaInformationPropertyConstants::READER_MIME_CATEGORY()), StringProperty::New(d->GetMimeType()->GetCategory())); if (this->GetInputStream() == nullptr) { - data->SetProperty(PropertyKeyPathToPropertyName(IOMetaInformationPropertyConstants::READER_INPUTLOCATION()), StringProperty::New(this->GetInputLocation())); + data->SetProperty(PropertyKeyPathToPropertyName(IOMetaInformationPropertyConstants::READER_INPUTLOCATION()), StringProperty::New(IOUtil::Local8BitToUtf8(this->GetInputLocation()))); } for (const auto& option : options) { auto optionpath = IOMetaInformationPropertyConstants::READER_OPTION_ROOT().AddElement(option.first); data->SetProperty(PropertyKeyPathToPropertyName(optionpath), StringProperty::New(option.second.ToString())); } } return result; } DataStorage::SetOfObjects::Pointer AbstractFileReader::Read(DataStorage &ds) { DataStorage::SetOfObjects::Pointer result = DataStorage::SetOfObjects::New(); std::vector data = this->Read(); for (auto iter = data.begin(); iter != data.end(); ++iter) { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(*iter); this->SetDefaultDataNodeProperties(node, this->GetInputLocation()); ds.Add(node); result->InsertElement(result->Size(), node); } return result; } IFileReader::ConfidenceLevel AbstractFileReader::GetConfidenceLevel() const { if (d->m_Stream) { if (*d->m_Stream) return Supported; } else { if (itksys::SystemTools::FileExists(this->GetInputLocation().c_str(), true)) { return Supported; } } return Unsupported; } //////////// µS Registration & Properties ////////////// us::ServiceRegistration AbstractFileReader::RegisterService(us::ModuleContext *context) { if (d->m_PrototypeFactory) return us::ServiceRegistration(); if (context == nullptr) { context = us::GetModuleContext(); } d->RegisterMimeType(context); if (this->GetMimeType()->GetName().empty()) { MITK_WARN << "Not registering reader due to empty MIME type."; return us::ServiceRegistration(); } struct PrototypeFactory : public us::PrototypeServiceFactory { AbstractFileReader *const m_Prototype; PrototypeFactory(AbstractFileReader *prototype) : m_Prototype(prototype) {} us::InterfaceMap GetService(us::Module * /*module*/, const us::ServiceRegistrationBase & /*registration*/) override { return us::MakeInterfaceMap(m_Prototype->Clone()); } void UngetService(us::Module * /*module*/, const us::ServiceRegistrationBase & /*registration*/, const us::InterfaceMap &service) override { delete us::ExtractInterface(service); } }; d->m_PrototypeFactory = new PrototypeFactory(this); us::ServiceProperties props = this->GetServiceProperties(); d->m_Reg = context->RegisterService(d->m_PrototypeFactory, props); return d->m_Reg; } void AbstractFileReader::UnregisterService() { try { d->m_Reg.Unregister(); } catch (const std::exception &) { } } us::ServiceProperties AbstractFileReader::GetServiceProperties() const { us::ServiceProperties result; result[IFileReader::PROP_DESCRIPTION()] = this->GetDescription(); result[IFileReader::PROP_MIMETYPE()] = this->GetMimeType()->GetName(); result[us::ServiceConstants::SERVICE_RANKING()] = this->GetRanking(); return result; } us::ServiceRegistration AbstractFileReader::RegisterMimeType(us::ModuleContext *context) { return d->RegisterMimeType(context); } std::vector< std::string > AbstractFileReader::GetReadFiles(){ return m_ReadFiles; } void AbstractFileReader::SetMimeType(const CustomMimeType &mimeType) { d->SetMimeType(mimeType); } void AbstractFileReader::SetDescription(const std::string &description) { d->SetDescription(description); } void AbstractFileReader::SetRanking(int ranking) { d->SetRanking(ranking); } int AbstractFileReader::GetRanking() const { return d->GetRanking(); } std::string AbstractFileReader::GetLocalFileName() const { std::string localFileName; if (d->m_Stream) { if (d->m_TmpFile.empty()) { // write the stream contents to temporary file std::string ext = itksys::SystemTools::GetFilenameExtension(this->GetInputLocation()); std::ofstream tmpStream; localFileName = mitk::IOUtil::CreateTemporaryFile( tmpStream, std::ios_base::out | std::ios_base::trunc | std::ios_base::binary, "XXXXXX" + ext); tmpStream << d->m_Stream->rdbuf(); d->m_TmpFile = localFileName; } else { localFileName = d->m_TmpFile; } } else { localFileName = d->m_Location; } return localFileName; } //////////////////////// Options /////////////////////// void AbstractFileReader::SetDefaultOptions(const IFileReader::Options &defaultOptions) { d->SetDefaultOptions(defaultOptions); } IFileReader::Options AbstractFileReader::GetDefaultOptions() const { return d->GetDefaultOptions(); } void AbstractFileReader::SetInput(const std::string &location) { d->m_Location = location; d->m_Stream = nullptr; } void AbstractFileReader::SetInput(const std::string &location, std::istream *is) { if (d->m_Stream != is && !d->m_TmpFile.empty()) { std::remove(d->m_TmpFile.c_str()); d->m_TmpFile.clear(); } d->m_Location = location; d->m_Stream = is; } std::string AbstractFileReader::GetInputLocation() const { return d->m_Location; } std::istream *AbstractFileReader::GetInputStream() const { return d->m_Stream; } MimeType AbstractFileReader::GetRegisteredMimeType() const { return d->GetRegisteredMimeType(); } IFileReader::Options AbstractFileReader::GetOptions() const { return d->GetOptions(); } us::Any AbstractFileReader::GetOption(const std::string &name) const { return d->GetOption(name); } void AbstractFileReader::SetOptions(const Options &options) { d->SetOptions(options); } void AbstractFileReader::SetOption(const std::string &name, const us::Any &value) { d->SetOption(name, value); } ////////////////// MISC ////////////////// void AbstractFileReader::AddProgressCallback(const ProgressCallback &callback) { d->AddProgressCallback(callback); } void AbstractFileReader::RemoveProgressCallback(const ProgressCallback &callback) { d->RemoveProgressCallback(callback); } ////////////////// µS related Getters ////////////////// const CustomMimeType *AbstractFileReader::GetMimeType() const { return d->GetMimeType(); } void AbstractFileReader::SetMimeTypePrefix(const std::string &prefix) { d->SetMimeTypePrefix(prefix); } std::string AbstractFileReader::GetMimeTypePrefix() const { return d->GetMimeTypePrefix(); } std::string AbstractFileReader::GetDescription() const { return d->GetDescription(); } void AbstractFileReader::SetDefaultDataNodeProperties(DataNode *node, const std::string &filePath) { // path if (!filePath.empty()) { - mitk::StringProperty::Pointer pathProp = - mitk::StringProperty::New(itksys::SystemTools::GetFilenamePath(filePath)); - node->SetProperty(StringProperty::PATH, pathProp); + auto path = itksys::SystemTools::GetFilenamePath(filePath); + path = IOUtil::Local8BitToUtf8(path); + node->SetProperty(StringProperty::PATH, mitk::StringProperty::New(path)); } // name already defined? mitk::StringProperty::Pointer nameProp = dynamic_cast(node->GetProperty("name")); if (nameProp.IsNull() || nameProp->GetValue() == DataNode::NO_NAME_VALUE()) { // name already defined in BaseData mitk::StringProperty::Pointer baseDataNameProp = dynamic_cast(node->GetData()->GetProperty("name").GetPointer()); if (baseDataNameProp.IsNull() || baseDataNameProp->GetValue() == DataNode::NO_NAME_VALUE()) { // name neither defined in node, nor in BaseData -> name = filebasename; - nameProp = mitk::StringProperty::New(this->GetRegisteredMimeType().GetFilenameWithoutExtension(filePath)); + auto name = this->GetRegisteredMimeType().GetFilenameWithoutExtension(filePath); + name = IOUtil::Local8BitToUtf8(name); + nameProp = mitk::StringProperty::New(name); node->SetProperty("name", nameProp); } else { // name defined in BaseData! nameProp = mitk::StringProperty::New(baseDataNameProp->GetValue()); node->SetProperty("name", nameProp); } } // visibility if (!node->GetProperty("visible")) { node->SetVisibility(true); } } } diff --git a/Modules/Core/src/IO/mitkIOUtil.cpp b/Modules/Core/src/IO/mitkIOUtil.cpp index 13be752926..7c5f032f04 100644 --- a/Modules/Core/src/IO/mitkIOUtil.cpp +++ b/Modules/Core/src/IO/mitkIOUtil.cpp @@ -1,1027 +1,1062 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkIOUtil.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include // ITK #include // VTK #include #include #include #include #include +#ifdef US_PLATFORM_WINDOWS + +#include + +namespace +{ + std::wstring MultiByteToWideChar(const std::string& mbString, UINT codePage) + { + auto numChars = ::MultiByteToWideChar(codePage, 0, mbString.data(), mbString.size(), nullptr, 0); + + if (0 >= numChars) + mitkThrow() << "Failure to convert multi-byte character string to wide character string"; + + std::wstring wString; + wString.resize(numChars); + + ::MultiByteToWideChar(codePage, 0, mbString.data(), mbString.size(), &wString[0], static_cast(wString.size())); + + return wString; + } + + std::string WideCharToMultiByte(const std::wstring& wString, UINT codePage) + { + auto numChars = ::WideCharToMultiByte(codePage, 0, wString.data(), wString.size(), nullptr, 0, nullptr, nullptr); + + if (0 >= numChars) + mitkThrow() << "Failure to convert wide character string to multi-byte character string"; + + std::string mbString; + mbString.resize(numChars); + + ::WideCharToMultiByte(codePage, 0, wString.data(), wString.size(), &mbString[0], static_cast(mbString.size()), nullptr, nullptr); + + return mbString; + } +} + +#endif + static std::string GetLastErrorStr() { #ifdef US_PLATFORM_POSIX return std::string(strerror(errno)); #else // Retrieve the system error message for the last-error code LPVOID lpMsgBuf; DWORD dw = GetLastError(); FormatMessage(FORMAT_MESSAGE_ALLOCATE_BUFFER | FORMAT_MESSAGE_FROM_SYSTEM | FORMAT_MESSAGE_IGNORE_INSERTS, nullptr, dw, MAKELANGID(LANG_NEUTRAL, SUBLANG_DEFAULT), (LPTSTR)&lpMsgBuf, 0, nullptr); std::string errMsg((LPCTSTR)lpMsgBuf); LocalFree(lpMsgBuf); return errMsg; #endif } #ifdef US_PLATFORM_WINDOWS #include #include // make the posix flags point to the obsolte bsd types on windows #define S_IRUSR S_IREAD #define S_IWUSR S_IWRITE #else #include #include #include #endif #include #include static const char validLetters[] = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789"; // A cross-platform version of the mkstemps function static int mkstemps_compat(char *tmpl, int suffixlen) { static unsigned long long value = 0; int savedErrno = errno; // Lower bound on the number of temporary files to attempt to generate. #define ATTEMPTS_MIN (62 * 62 * 62) /* The number of times to attempt to generate a temporary file. To conform to POSIX, this must be no smaller than TMP_MAX. */ #if ATTEMPTS_MIN < TMP_MAX const unsigned int attempts = TMP_MAX; #else const unsigned int attempts = ATTEMPTS_MIN; #endif const int len = strlen(tmpl); if ((len - suffixlen) < 6 || strncmp(&tmpl[len - 6 - suffixlen], "XXXXXX", 6)) { errno = EINVAL; return -1; } /* This is where the Xs start. */ char *XXXXXX = &tmpl[len - 6 - suffixlen]; /* Get some more or less random data. */ #ifdef US_PLATFORM_WINDOWS { SYSTEMTIME stNow; FILETIME ftNow; // get system time GetSystemTime(&stNow); stNow.wMilliseconds = 500; if (!SystemTimeToFileTime(&stNow, &ftNow)) { errno = -1; return -1; } unsigned long long randomTimeBits = ((static_cast(ftNow.dwHighDateTime) << 32) | static_cast(ftNow.dwLowDateTime)); value = randomTimeBits ^ static_cast(GetCurrentThreadId()); } #else { struct timeval tv; gettimeofday(&tv, nullptr); unsigned long long randomTimeBits = ((static_cast(tv.tv_usec) << 32) | static_cast(tv.tv_sec)); value = randomTimeBits ^ static_cast(getpid()); } #endif for (unsigned int count = 0; count < attempts; value += 7777, ++count) { unsigned long long v = value; /* Fill in the random bits. */ XXXXXX[0] = validLetters[v % 62]; v /= 62; XXXXXX[1] = validLetters[v % 62]; v /= 62; XXXXXX[2] = validLetters[v % 62]; v /= 62; XXXXXX[3] = validLetters[v % 62]; v /= 62; XXXXXX[4] = validLetters[v % 62]; v /= 62; XXXXXX[5] = validLetters[v % 62]; int fd = open(tmpl, O_RDWR | O_CREAT | O_EXCL, S_IRUSR | S_IWUSR); if (fd >= 0) { errno = savedErrno; return fd; } else if (errno != EEXIST) { return -1; } } /* We got out of the loop because we ran out of combinations to try. */ errno = EEXIST; return -1; } // A cross-platform version of the POSIX mkdtemp function static char *mkdtemps_compat(char *tmpl, int suffixlen) { static unsigned long long value = 0; int savedErrno = errno; // Lower bound on the number of temporary dirs to attempt to generate. #define ATTEMPTS_MIN (62 * 62 * 62) /* The number of times to attempt to generate a temporary dir. To conform to POSIX, this must be no smaller than TMP_MAX. */ #if ATTEMPTS_MIN < TMP_MAX const unsigned int attempts = TMP_MAX; #else const unsigned int attempts = ATTEMPTS_MIN; #endif const int len = strlen(tmpl); if ((len - suffixlen) < 6 || strncmp(&tmpl[len - 6 - suffixlen], "XXXXXX", 6)) { errno = EINVAL; return nullptr; } /* This is where the Xs start. */ char *XXXXXX = &tmpl[len - 6 - suffixlen]; /* Get some more or less random data. */ #ifdef US_PLATFORM_WINDOWS { SYSTEMTIME stNow; FILETIME ftNow; // get system time GetSystemTime(&stNow); stNow.wMilliseconds = 500; if (!SystemTimeToFileTime(&stNow, &ftNow)) { errno = -1; return nullptr; } unsigned long long randomTimeBits = ((static_cast(ftNow.dwHighDateTime) << 32) | static_cast(ftNow.dwLowDateTime)); value = randomTimeBits ^ static_cast(GetCurrentThreadId()); } #else { struct timeval tv; gettimeofday(&tv, nullptr); unsigned long long randomTimeBits = ((static_cast(tv.tv_usec) << 32) | static_cast(tv.tv_sec)); value = randomTimeBits ^ static_cast(getpid()); } #endif unsigned int count = 0; for (; count < attempts; value += 7777, ++count) { unsigned long long v = value; /* Fill in the random bits. */ XXXXXX[0] = validLetters[v % 62]; v /= 62; XXXXXX[1] = validLetters[v % 62]; v /= 62; XXXXXX[2] = validLetters[v % 62]; v /= 62; XXXXXX[3] = validLetters[v % 62]; v /= 62; XXXXXX[4] = validLetters[v % 62]; v /= 62; XXXXXX[5] = validLetters[v % 62]; #ifdef US_PLATFORM_WINDOWS int fd = _mkdir(tmpl); //, _S_IREAD | _S_IWRITE | _S_IEXEC); #else int fd = mkdir(tmpl, S_IRUSR | S_IWUSR | S_IXUSR); #endif if (fd >= 0) { errno = savedErrno; return tmpl; } else if (errno != EEXIST) { return nullptr; } } /* We got out of the loop because we ran out of combinations to try. */ errno = EEXIST; return nullptr; } //#endif //************************************************************** // mitk::IOUtil method definitions namespace mitk { struct IOUtil::Impl { struct FixedReaderOptionsFunctor : public ReaderOptionsFunctorBase { FixedReaderOptionsFunctor(const IFileReader::Options &options) : m_Options(options) {} bool operator()(LoadInfo &loadInfo) const override { IFileReader *reader = loadInfo.m_ReaderSelector.GetSelected().GetReader(); if (reader) { reader->SetOptions(m_Options); } return false; } private: const IFileReader::Options &m_Options; }; struct FixedWriterOptionsFunctor : public WriterOptionsFunctorBase { FixedWriterOptionsFunctor(const IFileReader::Options &options) : m_Options(options) {} bool operator()(SaveInfo &saveInfo) const override { IFileWriter *writer = saveInfo.m_WriterSelector.GetSelected().GetWriter(); if (writer) { writer->SetOptions(m_Options); } return false; } private: const IFileWriter::Options &m_Options; }; static BaseData::Pointer LoadBaseDataFromFile(const std::string &path, const ReaderOptionsFunctorBase* optionsCallback = nullptr); - - static void SetDefaultDataNodeProperties(mitk::DataNode *node, const std::string &filePath = std::string()); }; BaseData::Pointer IOUtil::Impl::LoadBaseDataFromFile(const std::string &path, const ReaderOptionsFunctorBase *optionsCallback) { std::vector baseDataList = Load(path, optionsCallback); // The Load(path) call above should throw an exception if nothing could be loaded assert(!baseDataList.empty()); return baseDataList.front(); } + std::string IOUtil::Local8BitToUtf8(const std::string& local8BitStr) + { +#ifdef US_PLATFORM_WINDOWS + try + { + return WideCharToMultiByte(MultiByteToWideChar(local8BitStr, CP_ACP), CP_UTF8); + } + catch (const mitk::Exception&) + { + MITK_WARN << "String conversion from current code page to UTF-8 failed. Input string is returned unmodified."; + } +#endif + + return local8BitStr; + } + + std::string IOUtil::Utf8ToLocal8Bit(const std::string& utf8Str) + { +#ifdef US_PLATFORM_WINDOWS + try + { + return WideCharToMultiByte(MultiByteToWideChar(utf8Str, CP_UTF8), CP_ACP); + } + catch (const mitk::Exception&) + { + MITK_WARN << "String conversion from UTF-8 to current code page failed. Input string is returned unmodified."; + } +#endif + + return utf8Str; + } + #ifdef US_PLATFORM_WINDOWS std::string IOUtil::GetProgramPath() { char path[512]; std::size_t index = std::string(path, GetModuleFileName(nullptr, path, 512)).find_last_of('\\'); return std::string(path, index); } #elif defined(US_PLATFORM_APPLE) #include std::string IOUtil::GetProgramPath() { char path[512]; uint32_t size = sizeof(path); if (_NSGetExecutablePath(path, &size) == 0) { std::size_t index = std::string(path).find_last_of('/'); std::string strPath = std::string(path, index); // const char* execPath = strPath.c_str(); // mitk::StandardFileLocations::GetInstance()->AddDirectoryForSearch(execPath,false); return strPath; } return std::string(); } #else #include #include #include std::string IOUtil::GetProgramPath() { std::stringstream ss; ss << "/proc/" << getpid() << "/exe"; char proc[512] = {0}; ssize_t ch = readlink(ss.str().c_str(), proc, 512); if (ch == -1) return std::string(); std::size_t index = std::string(proc).find_last_of('/'); return std::string(proc, index); } #endif char IOUtil::GetDirectorySeparator() { #ifdef US_PLATFORM_WINDOWS return '\\'; #else return '/'; #endif } std::string IOUtil::GetTempPath() { static std::string result; if (result.empty()) { #ifdef US_PLATFORM_WINDOWS char tempPathTestBuffer[1]; DWORD bufferLength = ::GetTempPath(1, tempPathTestBuffer); if (bufferLength == 0) { mitkThrow() << GetLastErrorStr(); } std::vector tempPath(bufferLength); bufferLength = ::GetTempPath(bufferLength, &tempPath[0]); if (bufferLength == 0) { mitkThrow() << GetLastErrorStr(); } result.assign(tempPath.begin(), tempPath.begin() + static_cast(bufferLength)); #else result = "/tmp/"; #endif } return result; } std::string IOUtil::CreateTemporaryFile(const std::string &templateName, std::string path) { std::ofstream tmpOutputStream; std::string returnValue = CreateTemporaryFile(tmpOutputStream, templateName, path); tmpOutputStream.close(); return returnValue; } std::string IOUtil::CreateTemporaryFile(std::ofstream &f, const std::string &templateName, std::string path) { return CreateTemporaryFile(f, std::ios_base::out | std::ios_base::trunc, templateName, path); } std::string IOUtil::CreateTemporaryFile(std::ofstream &f, std::ios_base::openmode mode, const std::string &templateName, std::string path) { if (path.empty()) { path = GetTempPath(); } path += templateName; std::vector dst_path(path.begin(), path.end()); dst_path.push_back('\0'); std::size_t lastX = path.find_last_of('X'); std::size_t firstX = path.find_last_not_of('X', lastX); int firstNonX = firstX == std::string::npos ? -1 : firstX - 1; while (lastX != std::string::npos && (lastX - firstNonX) < 6) { lastX = path.find_last_of('X', firstX); firstX = path.find_last_not_of('X', lastX); firstNonX = firstX == std::string::npos ? -1 : firstX - 1; } std::size_t suffixlen = lastX == std::string::npos ? path.size() : path.size() - lastX - 1; int fd = mkstemps_compat(&dst_path[0], suffixlen); if (fd != -1) { path.assign(dst_path.begin(), dst_path.end() - 1); f.open(path.c_str(), mode | std::ios_base::out | std::ios_base::trunc); close(fd); } else { mitkThrow() << "Creating temporary file " << &dst_path[0] << " failed: " << GetLastErrorStr(); } return path; } std::string IOUtil::CreateTemporaryDirectory(const std::string &templateName, std::string path) { if (path.empty()) { path = GetTempPath(); } path += GetDirectorySeparator() + templateName; std::vector dst_path(path.begin(), path.end()); dst_path.push_back('\0'); std::size_t lastX = path.find_last_of('X'); std::size_t firstX = path.find_last_not_of('X', lastX); int firstNonX = firstX == std::string::npos ? -1 : firstX - 1; while (lastX != std::string::npos && (lastX - firstNonX) < 6) { lastX = path.find_last_of('X', firstX); firstX = path.find_last_not_of('X', lastX); firstNonX = firstX == std::string::npos ? -1 : firstX - 1; } std::size_t suffixlen = lastX == std::string::npos ? path.size() : path.size() - lastX - 1; if (mkdtemps_compat(&dst_path[0], suffixlen) == nullptr) { mitkThrow() << "Creating temporary directory " << &dst_path[0] << " failed: " << GetLastErrorStr(); } path.assign(dst_path.begin(), dst_path.end() - 1); return path; } DataStorage::SetOfObjects::Pointer IOUtil::Load(const std::string &path, DataStorage &storage, const ReaderOptionsFunctorBase *optionsCallback) { std::vector paths; paths.push_back(path); return Load(paths, storage, optionsCallback); } DataStorage::SetOfObjects::Pointer IOUtil::Load(const std::string &path, const IFileReader::Options &options, DataStorage &storage) { std::vector loadInfos; loadInfos.push_back(LoadInfo(path)); DataStorage::SetOfObjects::Pointer nodeResult = DataStorage::SetOfObjects::New(); Impl::FixedReaderOptionsFunctor optionsCallback(options); std::string errMsg = Load(loadInfos, nodeResult, &storage, &optionsCallback); if (!errMsg.empty()) { mitkThrow() << errMsg; } return nodeResult; } std::vector IOUtil::Load(const std::string &path, const ReaderOptionsFunctorBase *optionsCallback) { std::vector paths; paths.push_back(path); return Load(paths, optionsCallback); } std::vector IOUtil::Load(const std::string &path, const IFileReader::Options &options) { std::vector loadInfos; loadInfos.push_back(LoadInfo(path)); Impl::FixedReaderOptionsFunctor optionsCallback(options); std::string errMsg = Load(loadInfos, nullptr, nullptr, &optionsCallback); if (!errMsg.empty()) { mitkThrow() << errMsg; } return loadInfos.front().m_Output; } DataStorage::SetOfObjects::Pointer IOUtil::Load(const std::vector &paths, DataStorage &storage, const ReaderOptionsFunctorBase *optionsCallback) { DataStorage::SetOfObjects::Pointer nodeResult = DataStorage::SetOfObjects::New(); std::vector loadInfos; - for (auto loadInfo : paths) + for (const auto &loadInfo : paths) { loadInfos.push_back(loadInfo); } std::string errMsg = Load(loadInfos, nodeResult, &storage, optionsCallback); if (!errMsg.empty()) { mitkThrow() << errMsg; } return nodeResult; } std::vector IOUtil::Load(const std::vector &paths, const ReaderOptionsFunctorBase *optionsCallback) { std::vector result; std::vector loadInfos; - for (auto loadInfo : paths) + for (const auto &loadInfo : paths) { loadInfos.push_back(loadInfo); } std::string errMsg = Load(loadInfos, nullptr, nullptr, optionsCallback); if (!errMsg.empty()) { mitkThrow() << errMsg; } for (std::vector::const_iterator iter = loadInfos.begin(), iterEnd = loadInfos.end(); iter != iterEnd; ++iter) { result.insert(result.end(), iter->m_Output.begin(), iter->m_Output.end()); } return result; } std::string IOUtil::Load(std::vector &loadInfos, DataStorage::SetOfObjects *nodeResult, DataStorage *ds, const ReaderOptionsFunctorBase *optionsCallback) { if (loadInfos.empty()) { return "No input files given"; } int filesToRead = loadInfos.size(); mitk::ProgressBar::GetInstance()->AddStepsToDo(2 * filesToRead); std::string errMsg; std::map usedReaderItems; std::vector< std::string > read_files; for (auto &loadInfo : loadInfos) { if(std::find(read_files.begin(), read_files.end(), loadInfo.m_Path) != read_files.end()) continue; std::vector readers = loadInfo.m_ReaderSelector.Get(); if (readers.empty()) { if (!itksys::SystemTools::FileExists(loadInfo.m_Path.c_str())) { errMsg += "File '" + loadInfo.m_Path + "' does not exist\n"; } else { errMsg += "No reader available for '" + loadInfo.m_Path + "'\n"; } continue; } bool callOptionsCallback = readers.size() > 1 || !readers.front().GetReader()->GetOptions().empty(); // check if we already used a reader which should be re-used std::vector currMimeTypes = loadInfo.m_ReaderSelector.GetMimeTypes(); std::string selectedMimeType; for (std::vector::const_iterator mimeTypeIter = currMimeTypes.begin(), mimeTypeIterEnd = currMimeTypes.end(); mimeTypeIter != mimeTypeIterEnd; ++mimeTypeIter) { std::map::const_iterator oldSelectedItemIter = usedReaderItems.find(mimeTypeIter->GetName()); if (oldSelectedItemIter != usedReaderItems.end()) { // we found an already used item for a mime-type which is contained // in the current reader set, check all current readers if there service // id equals the old reader for (std::vector::const_iterator currReaderItem = readers.begin(), currReaderItemEnd = readers.end(); currReaderItem != currReaderItemEnd; ++currReaderItem) { if (currReaderItem->GetMimeType().GetName() == mimeTypeIter->GetName() && currReaderItem->GetServiceId() == oldSelectedItemIter->second.GetServiceId() && currReaderItem->GetConfidenceLevel() >= oldSelectedItemIter->second.GetConfidenceLevel()) { // okay, we used the same reader already, re-use its options selectedMimeType = mimeTypeIter->GetName(); callOptionsCallback = false; loadInfo.m_ReaderSelector.Select(oldSelectedItemIter->second.GetServiceId()); loadInfo.m_ReaderSelector.GetSelected().GetReader()->SetOptions( oldSelectedItemIter->second.GetReader()->GetOptions()); break; } } if (!selectedMimeType.empty()) break; } } if (callOptionsCallback && optionsCallback) { callOptionsCallback = (*optionsCallback)(loadInfo); if (!callOptionsCallback && !loadInfo.m_Cancel) { usedReaderItems.erase(selectedMimeType); FileReaderSelector::Item selectedItem = loadInfo.m_ReaderSelector.GetSelected(); usedReaderItems.insert(std::make_pair(selectedItem.GetMimeType().GetName(), selectedItem)); } } if (loadInfo.m_Cancel) { errMsg += "Reading operation(s) cancelled."; break; } IFileReader *reader = loadInfo.m_ReaderSelector.GetSelected().GetReader(); if (reader == nullptr) { errMsg += "Unexpected nullptr reader."; break; } // Do the actual reading try { DataStorage::SetOfObjects::Pointer nodes; if (ds != nullptr) { nodes = reader->Read(*ds); std::vector< std::string > new_files = reader->GetReadFiles(); read_files.insert( read_files.end(), new_files.begin(), new_files.end() ); } else { nodes = DataStorage::SetOfObjects::New(); std::vector baseData = reader->Read(); for (auto iter = baseData.begin(); iter != baseData.end(); ++iter) { if (iter->IsNotNull()) { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(*iter); nodes->InsertElement(nodes->Size(), node); } } std::vector< std::string > new_files = reader->GetReadFiles(); read_files.insert( read_files.end(), new_files.begin(), new_files.end() ); } for (DataStorage::SetOfObjects::ConstIterator nodeIter = nodes->Begin(), nodeIterEnd = nodes->End(); nodeIter != nodeIterEnd; ++nodeIter) { const mitk::DataNode::Pointer &node = nodeIter->Value(); mitk::BaseData::Pointer data = node->GetData(); if (data.IsNull()) { continue; } - mitk::StringProperty::Pointer pathProp = mitk::StringProperty::New(loadInfo.m_Path); + auto path = Local8BitToUtf8(loadInfo.m_Path); + auto pathProp = mitk::StringProperty::New(path); data->SetProperty("path", pathProp); loadInfo.m_Output.push_back(data); if (nodeResult) { nodeResult->push_back(nodeIter->Value()); } } if (loadInfo.m_Output.empty() || (nodeResult && nodeResult->Size() == 0)) { errMsg += "Unknown read error occurred reading " + loadInfo.m_Path; } } catch (const std::exception &e) { errMsg += "Exception occured when reading file " + loadInfo.m_Path + ":\n" + e.what() + "\n\n"; } mitk::ProgressBar::GetInstance()->Progress(2); --filesToRead; } if (!errMsg.empty()) { MITK_ERROR << errMsg; } mitk::ProgressBar::GetInstance()->Progress(2 * filesToRead); return errMsg; } std::vector IOUtil::Load(const us::ModuleResource &usResource, std::ios_base::openmode mode) { us::ModuleResourceStream resStream(usResource, mode); mitk::CoreServicePointer mimeTypeProvider(mitk::CoreServices::GetMimeTypeProvider()); std::vector mimetypes = mimeTypeProvider->GetMimeTypesForFile(usResource.GetResourcePath()); std::vector data; if (mimetypes.empty()) { mitkThrow() << "No mimetype for resource stream: " << usResource.GetResourcePath(); return data; } mitk::FileReaderRegistry fileReaderRegistry; std::vector> refs = fileReaderRegistry.GetReferences(mimetypes[0]); if (refs.empty()) { mitkThrow() << "No reader available for resource stream: " << usResource.GetResourcePath(); return data; } mitk::IFileReader *reader = fileReaderRegistry.GetReader(refs[0]); reader->SetInput(usResource.GetResourcePath(), &resStream); data = reader->Read(); return data; } void IOUtil::Save(const BaseData *data, const std::string &path, bool setPathProperty) { Save(data, path, IFileWriter::Options(), setPathProperty); } void IOUtil::Save(const BaseData *data, const std::string &path, const IFileWriter::Options &options, bool setPathProperty) { Save(data, std::string(), path, options, setPathProperty); } void IOUtil::Save(const BaseData *data, const std::string &mimeType, const std::string &path, bool addExtension, bool setPathProperty) { Save(data, mimeType, path, IFileWriter::Options(), addExtension, setPathProperty); } void IOUtil::Save(const BaseData *data, const std::string &mimeType, const std::string &path, const IFileWriter::Options &options, bool addExtension, bool setPathProperty) { if ((data == nullptr) || (data->IsEmpty())) mitkThrow() << "BaseData cannotbe null or empty for save methods in IOUtil.h."; std::string errMsg; if (options.empty()) { errMsg = Save(data, mimeType, path, nullptr, addExtension, setPathProperty); } else { Impl::FixedWriterOptionsFunctor optionsCallback(options); errMsg = Save(data, mimeType, path, &optionsCallback, addExtension, setPathProperty); } if (!errMsg.empty()) { mitkThrow() << errMsg; } } void IOUtil::Save(std::vector &saveInfos, bool setPathProperty) { std::string errMsg = Save(saveInfos, nullptr, setPathProperty); if (!errMsg.empty()) { mitkThrow() << errMsg; } } std::string IOUtil::Save(const BaseData *data, const std::string &mimeTypeName, const std::string &path, WriterOptionsFunctorBase *optionsCallback, bool addExtension, bool setPathProperty) { if (path.empty()) { return "No output filename given"; } mitk::CoreServicePointer mimeTypeProvider(mitk::CoreServices::GetMimeTypeProvider()); MimeType mimeType = mimeTypeProvider->GetMimeTypeForName(mimeTypeName); SaveInfo saveInfo(data, mimeType, path); std::string ext = itksys::SystemTools::GetFilenameExtension(path); if (saveInfo.m_WriterSelector.IsEmpty()) { return std::string("No suitable writer found for the current data of type ") + data->GetNameOfClass() + (mimeType.IsValid() ? (std::string(" and mime-type ") + mimeType.GetName()) : std::string()) + (ext.empty() ? std::string() : (std::string(" with extension ") + ext)); } // Add an extension if not already specified if (ext.empty() && addExtension) { saveInfo.m_MimeType.GetExtensions().empty() ? std::string() : "." + saveInfo.m_MimeType.GetExtensions().front(); } std::vector infos; infos.push_back(saveInfo); return Save(infos, optionsCallback, setPathProperty); } std::string IOUtil::Save(std::vector &saveInfos, WriterOptionsFunctorBase *optionsCallback, bool setPathProperty) { if (saveInfos.empty()) { return "No data for saving available"; } int filesToWrite = saveInfos.size(); mitk::ProgressBar::GetInstance()->AddStepsToDo(2 * filesToWrite); std::string errMsg; std::set usedSaveInfos; for (auto &saveInfo : saveInfos) { const std::string baseDataType = saveInfo.m_BaseData->GetNameOfClass(); std::vector writers = saveInfo.m_WriterSelector.Get(); // Error out if no compatible Writer was found if (writers.empty()) { errMsg += std::string("No writer available for ") + baseDataType + " data.\n"; continue; } bool callOptionsCallback = writers.size() > 1 || !writers[0].GetWriter()->GetOptions().empty(); // check if we already used a writer for this base data type // which should be re-used auto oldSaveInfoIter = usedSaveInfos.find(saveInfo); if (oldSaveInfoIter != usedSaveInfos.end()) { // we previously saved a base data object of the same data with the same mime-type, // check if the same writer is contained in the current writer set and if the // confidence level matches FileWriterSelector::Item oldSelectedItem = oldSaveInfoIter->m_WriterSelector.Get(oldSaveInfoIter->m_WriterSelector.GetSelectedId()); for (std::vector::const_iterator currWriterItem = writers.begin(), currWriterItemEnd = writers.end(); currWriterItem != currWriterItemEnd; ++currWriterItem) { if (currWriterItem->GetServiceId() == oldSelectedItem.GetServiceId() && currWriterItem->GetConfidenceLevel() >= oldSelectedItem.GetConfidenceLevel()) { // okay, we used the same writer already, re-use its options callOptionsCallback = false; saveInfo.m_WriterSelector.Select(oldSaveInfoIter->m_WriterSelector.GetSelectedId()); saveInfo.m_WriterSelector.GetSelected().GetWriter()->SetOptions(oldSelectedItem.GetWriter()->GetOptions()); break; } } } if (callOptionsCallback && optionsCallback) { callOptionsCallback = (*optionsCallback)(saveInfo); if (!callOptionsCallback && !saveInfo.m_Cancel) { usedSaveInfos.erase(saveInfo); usedSaveInfos.insert(saveInfo); } } if (saveInfo.m_Cancel) { errMsg += "Writing operation(s) cancelled."; break; } IFileWriter *writer = saveInfo.m_WriterSelector.GetSelected().GetWriter(); if (writer == nullptr) { errMsg += "Unexpected nullptr writer."; break; } // Do the actual writing try { writer->SetOutputLocation(saveInfo.m_Path); writer->Write(); } catch (const std::exception &e) { errMsg += std::string("Exception occurred when writing to ") + saveInfo.m_Path + ":\n" + e.what() + "\n"; } if (setPathProperty) - saveInfo.m_BaseData->GetPropertyList()->SetStringProperty("path", saveInfo.m_Path.c_str()); + saveInfo.m_BaseData->GetPropertyList()->SetStringProperty("path", Local8BitToUtf8(saveInfo.m_Path).c_str()); mitk::ProgressBar::GetInstance()->Progress(2); --filesToWrite; } if (!errMsg.empty()) { MITK_ERROR << errMsg; } mitk::ProgressBar::GetInstance()->Progress(2 * filesToWrite); return errMsg; } - // This method can be removed after the deprecated LoadDataNode() method was removed - void IOUtil::Impl::SetDefaultDataNodeProperties(DataNode *node, const std::string &filePath) - { - // path - mitk::StringProperty::Pointer pathProp = mitk::StringProperty::New(itksys::SystemTools::GetFilenamePath(filePath)); - node->SetProperty(StringProperty::PATH, pathProp); - - // name already defined? - mitk::StringProperty::Pointer nameProp = dynamic_cast(node->GetProperty("name")); - if (nameProp.IsNull() || nameProp->GetValue() == DataNode::NO_NAME_VALUE()) - { - // name already defined in BaseData - mitk::StringProperty::Pointer baseDataNameProp = - dynamic_cast(node->GetData()->GetProperty("name").GetPointer()); - if (baseDataNameProp.IsNull() || baseDataNameProp->GetValue() == DataNode::NO_NAME_VALUE()) - { - // name neither defined in node, nor in BaseData -> name = filename - nameProp = mitk::StringProperty::New(itksys::SystemTools::GetFilenameWithoutExtension(filePath)); - node->SetProperty("name", nameProp); - } - else - { - // name defined in BaseData! - nameProp = mitk::StringProperty::New(baseDataNameProp->GetValue()); - node->SetProperty("name", nameProp); - } - } - - // visibility - if (!node->GetProperty("visible")) - { - node->SetVisibility(true); - } - } - IOUtil::SaveInfo::SaveInfo(const BaseData *baseData, const MimeType &mimeType, const std::string &path) : m_BaseData(baseData), m_WriterSelector(baseData, mimeType.GetName(), path), m_MimeType(mimeType.IsValid() ? mimeType // use the original mime-type : (m_WriterSelector.IsEmpty() ? mimeType // no writer found, use the original invalid mime-type : m_WriterSelector.GetDefault().GetMimeType() // use the found default mime-type )), m_Path(path), m_Cancel(false) { } bool IOUtil::SaveInfo::operator<(const IOUtil::SaveInfo &other) const { int r = strcmp(m_BaseData->GetNameOfClass(), other.m_BaseData->GetNameOfClass()); if (r == 0) { return m_WriterSelector.GetSelected().GetMimeType() < other.m_WriterSelector.GetSelected().GetMimeType(); } return r < 0; } IOUtil::LoadInfo::LoadInfo(const std::string &path) : m_Path(path), m_ReaderSelector(path), m_Cancel(false) {} } diff --git a/Modules/Core/src/IO/mitkItkImageIO.cpp b/Modules/Core/src/IO/mitkItkImageIO.cpp index 55a4b86dc9..78fada2e17 100644 --- a/Modules/Core/src/IO/mitkItkImageIO.cpp +++ b/Modules/Core/src/IO/mitkItkImageIO.cpp @@ -1,724 +1,748 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkItkImageIO.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace mitk { const char *const PROPERTY_NAME_TIMEGEOMETRY_TYPE = "org.mitk.timegeometry.type"; const char *const PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS = "org.mitk.timegeometry.timepoints"; const char *const PROPERTY_KEY_TIMEGEOMETRY_TYPE = "org_mitk_timegeometry_type"; const char *const PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS = "org_mitk_timegeometry_timepoints"; const char* const PROPERTY_KEY_UID = "org_mitk_uid"; ItkImageIO::ItkImageIO(const ItkImageIO &other) : AbstractFileIO(other), m_ImageIO(dynamic_cast(other.m_ImageIO->Clone().GetPointer())) { this->InitializeDefaultMetaDataKeys(); } std::vector ItkImageIO::FixUpImageIOExtensions(const std::string &imageIOName) { std::vector extensions; // Try to fix-up some known ITK image IO classes if (imageIOName == "GiplImageIO") { extensions.push_back("gipl"); extensions.push_back("gipl.gz"); } else if (imageIOName == "GDCMImageIO") { extensions.push_back("gdcm"); extensions.push_back("dcm"); extensions.push_back("DCM"); extensions.push_back("dc3"); extensions.push_back("DC3"); extensions.push_back("ima"); extensions.push_back("img"); } else if (imageIOName == "PNGImageIO") { extensions.push_back("png"); extensions.push_back("PNG"); } else if (imageIOName == "StimulateImageIO") { extensions.push_back("spr"); } else if (imageIOName == "HDF5ImageIO") { extensions.push_back("hdf"); extensions.push_back("h4"); extensions.push_back("hdf4"); extensions.push_back("h5"); extensions.push_back("hdf5"); extensions.push_back("he4"); extensions.push_back("he5"); extensions.push_back("hd5"); } else if ("GE4ImageIO" == imageIOName || "GE5ImageIO" == imageIOName || "Bruker2dseqImageIO" == imageIOName) { extensions.push_back(""); } if (!extensions.empty()) { MITK_DEBUG << "Fixing up known extensions for " << imageIOName; } return extensions; } void ItkImageIO::FixUpCustomMimeTypeName(const std::string &imageIOName, CustomMimeType &customMimeType) { if ("GE4ImageIO" == imageIOName) { customMimeType.SetName(this->AbstractFileReader::GetMimeTypePrefix() + "ge4"); } else if ("GE5ImageIO" == imageIOName) { customMimeType.SetName(this->AbstractFileReader::GetMimeTypePrefix() + "ge5"); } else if ("Bruker2dseqImageIO" == imageIOName) { customMimeType.SetName(this->AbstractFileReader::GetMimeTypePrefix() + "bruker2dseq"); } } ItkImageIO::ItkImageIO(itk::ImageIOBase::Pointer imageIO) : AbstractFileIO(Image::GetStaticNameOfClass()), m_ImageIO(imageIO) { if (m_ImageIO.IsNull()) { mitkThrow() << "ITK ImageIOBase argument must not be nullptr"; } this->AbstractFileReader::SetMimeTypePrefix(IOMimeTypes::DEFAULT_BASE_NAME() + ".image."); this->InitializeDefaultMetaDataKeys(); std::vector readExtensions = m_ImageIO->GetSupportedReadExtensions(); if (readExtensions.empty()) { std::string imageIOName = m_ImageIO->GetNameOfClass(); MITK_DEBUG << "ITK ImageIOBase " << imageIOName << " does not provide read extensions"; readExtensions = FixUpImageIOExtensions(imageIOName); } CustomMimeType customReaderMimeType; customReaderMimeType.SetCategory("Images"); for (std::vector::const_iterator iter = readExtensions.begin(), endIter = readExtensions.end(); iter != endIter; ++iter) { std::string extension = *iter; if (!extension.empty() && extension[0] == '.') { extension.assign(iter->begin() + 1, iter->end()); } customReaderMimeType.AddExtension(extension); } auto extensions = customReaderMimeType.GetExtensions(); if (extensions.empty() || (extensions.size() == 1 && extensions[0].empty())) { std::string imageIOName = m_ImageIO->GetNameOfClass(); FixUpCustomMimeTypeName(imageIOName, customReaderMimeType); } this->AbstractFileReader::SetMimeType(customReaderMimeType); std::vector writeExtensions = imageIO->GetSupportedWriteExtensions(); if (writeExtensions.empty()) { std::string imageIOName = imageIO->GetNameOfClass(); MITK_DEBUG << "ITK ImageIOBase " << imageIOName << " does not provide write extensions"; writeExtensions = FixUpImageIOExtensions(imageIOName); } if (writeExtensions != readExtensions) { CustomMimeType customWriterMimeType; customWriterMimeType.SetCategory("Images"); for (std::vector::const_iterator iter = writeExtensions.begin(), endIter = writeExtensions.end(); iter != endIter; ++iter) { std::string extension = *iter; if (!extension.empty() && extension[0] == '.') { extension.assign(iter->begin() + 1, iter->end()); } customWriterMimeType.AddExtension(extension); } auto extensions = customWriterMimeType.GetExtensions(); if (extensions.empty() || (extensions.size() == 1 && extensions[0].empty())) { std::string imageIOName = m_ImageIO->GetNameOfClass(); FixUpCustomMimeTypeName(imageIOName, customWriterMimeType); } this->AbstractFileWriter::SetMimeType(customWriterMimeType); } std::string description = std::string("ITK ") + imageIO->GetNameOfClass(); this->SetReaderDescription(description); this->SetWriterDescription(description); this->RegisterService(); } ItkImageIO::ItkImageIO(const CustomMimeType &mimeType, itk::ImageIOBase::Pointer imageIO, int rank) : AbstractFileIO(Image::GetStaticNameOfClass(), mimeType, std::string("ITK ") + imageIO->GetNameOfClass()), m_ImageIO(imageIO) { if (m_ImageIO.IsNull()) { mitkThrow() << "ITK ImageIOBase argument must not be nullptr"; } this->AbstractFileReader::SetMimeTypePrefix(IOMimeTypes::DEFAULT_BASE_NAME() + ".image."); this->InitializeDefaultMetaDataKeys(); if (rank) { this->AbstractFileReader::SetRanking(rank); this->AbstractFileWriter::SetRanking(rank); } this->RegisterService(); } std::vector ConvertMetaDataObjectToTimePointList(const itk::MetaDataObjectBase* data) { const auto* timeGeometryTimeData = dynamic_cast*>(data); std::vector result; if (timeGeometryTimeData) { std::string dataStr = timeGeometryTimeData->GetMetaDataObjectValue(); std::stringstream stream(dataStr); TimePointType tp; while (stream >> tp) { result.push_back(tp); } } return result; }; itk::MetaDataObjectBase::Pointer ConvertTimePointListToMetaDataObject(const mitk::TimeGeometry* timeGeometry) { std::stringstream stream; stream << timeGeometry->GetTimeBounds(0)[0]; const auto maxTimePoints = timeGeometry->CountTimeSteps(); for (TimeStepType pos = 0; pos < maxTimePoints; ++pos) { - stream << " " << timeGeometry->GetTimeBounds(pos)[1]; + auto timeBounds = timeGeometry->GetTimeBounds(pos); + + /////////////////////////////////////// + // Workarround T27883. See https://phabricator.mitk.org/T27883#219473 for more details. + // This workarround should be removed as soon as T28262 is solved! + if (pos + 1 == maxTimePoints && timeBounds[0]==timeBounds[1]) + { + timeBounds[1] = timeBounds[0] + 1.; + } + // End of workarround for T27883 + ////////////////////////////////////// + + stream << " " << timeBounds[1]; } auto result = itk::MetaDataObject::New(); result->SetMetaDataObjectValue(stream.str()); return result.GetPointer(); }; std::vector ItkImageIO::DoRead() { std::vector result; mitk::LocaleSwitch localeSwitch("C"); Image::Pointer image = Image::New(); const unsigned int MINDIM = 2; const unsigned int MAXDIM = 4; const std::string path = this->GetLocalFileName(); MITK_INFO << "loading " << path << " via itk::ImageIOFactory... " << std::endl; // Check to see if we can read the file given the name or prefix if (path.empty()) { mitkThrow() << "Empty filename in mitk::ItkImageIO "; } // Got to allocate space for the image. Determine the characteristics of // the image. m_ImageIO->SetFileName(path); m_ImageIO->ReadImageInformation(); unsigned int ndim = m_ImageIO->GetNumberOfDimensions(); if (ndim < MINDIM || ndim > MAXDIM) { MITK_WARN << "Sorry, only dimensions 2, 3 and 4 are supported. The given file has " << ndim << " dimensions! Reading as 4D."; ndim = MAXDIM; } itk::ImageIORegion ioRegion(ndim); itk::ImageIORegion::SizeType ioSize = ioRegion.GetSize(); itk::ImageIORegion::IndexType ioStart = ioRegion.GetIndex(); unsigned int dimensions[MAXDIM]; dimensions[0] = 0; dimensions[1] = 0; dimensions[2] = 0; dimensions[3] = 0; ScalarType spacing[MAXDIM]; spacing[0] = 1.0f; spacing[1] = 1.0f; spacing[2] = 1.0f; spacing[3] = 1.0f; Point3D origin; origin.Fill(0); unsigned int i; for (i = 0; i < ndim; ++i) { ioStart[i] = 0; ioSize[i] = m_ImageIO->GetDimensions(i); if (i < MAXDIM) { dimensions[i] = m_ImageIO->GetDimensions(i); spacing[i] = m_ImageIO->GetSpacing(i); if (spacing[i] <= 0) spacing[i] = 1.0f; } if (i < 3) { origin[i] = m_ImageIO->GetOrigin(i); } } ioRegion.SetSize(ioSize); ioRegion.SetIndex(ioStart); MITK_INFO << "ioRegion: " << ioRegion << std::endl; m_ImageIO->SetIORegion(ioRegion); void *buffer = new unsigned char[m_ImageIO->GetImageSizeInBytes()]; m_ImageIO->Read(buffer); image->Initialize(MakePixelType(m_ImageIO), ndim, dimensions); image->SetImportChannel(buffer, 0, Image::ManageMemory); const itk::MetaDataDictionary &dictionary = m_ImageIO->GetMetaDataDictionary(); // access direction of itk::Image and include spacing mitk::Matrix3D matrix; matrix.SetIdentity(); unsigned int j, itkDimMax3 = (ndim >= 3 ? 3 : ndim); for (i = 0; i < itkDimMax3; ++i) for (j = 0; j < itkDimMax3; ++j) matrix[i][j] = m_ImageIO->GetDirection(j)[i]; // re-initialize PlaneGeometry with origin and direction PlaneGeometry *planeGeometry = image->GetSlicedGeometry(0)->GetPlaneGeometry(0); planeGeometry->SetOrigin(origin); planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix); // re-initialize SlicedGeometry3D SlicedGeometry3D *slicedGeometry = image->GetSlicedGeometry(0); slicedGeometry->InitializeEvenlySpaced(planeGeometry, image->GetDimension(2)); slicedGeometry->SetSpacing(spacing); MITK_INFO << slicedGeometry->GetCornerPoint(false, false, false); MITK_INFO << slicedGeometry->GetCornerPoint(true, true, true); // re-initialize TimeGeometry TimeGeometry::Pointer timeGeometry; if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TYPE) || dictionary.HasKey(PROPERTY_KEY_TIMEGEOMETRY_TYPE)) { // also check for the name because of backwards compatibility. Past code version stored with the name and not with // the key itk::MetaDataObject::ConstPointer timeGeometryTypeData = nullptr; if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TYPE)) { timeGeometryTypeData = dynamic_cast *>(dictionary.Get(PROPERTY_NAME_TIMEGEOMETRY_TYPE)); } else { timeGeometryTypeData = dynamic_cast *>(dictionary.Get(PROPERTY_KEY_TIMEGEOMETRY_TYPE)); } if (timeGeometryTypeData->GetMetaDataObjectValue() == ArbitraryTimeGeometry::GetStaticNameOfClass()) { MITK_INFO << "used time geometry: " << ArbitraryTimeGeometry::GetStaticNameOfClass(); typedef std::vector TimePointVector; TimePointVector timePoints; if (dictionary.HasKey(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS)) { timePoints = ConvertMetaDataObjectToTimePointList(dictionary.Get(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS)); } else if (dictionary.HasKey(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS)) { timePoints = ConvertMetaDataObjectToTimePointList(dictionary.Get(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS)); } if (timePoints.empty()) { MITK_ERROR << "Stored timepoints are empty. Meta information seems to bee invalid. Switch to ProportionalTimeGeometry fallback"; } else if (timePoints.size() - 1 != image->GetDimension(3)) { MITK_ERROR << "Stored timepoints (" << timePoints.size() - 1 << ") and size of image time dimension (" << image->GetDimension(3) << ") do not match. Switch to ProportionalTimeGeometry fallback"; } else { ArbitraryTimeGeometry::Pointer arbitraryTimeGeometry = ArbitraryTimeGeometry::New(); TimePointVector::const_iterator pos = timePoints.begin(); auto prePos = pos++; for (; pos != timePoints.end(); ++prePos, ++pos) { arbitraryTimeGeometry->AppendNewTimeStepClone(slicedGeometry, *prePos, *pos); } timeGeometry = arbitraryTimeGeometry; } } } if (timeGeometry.IsNull()) { // Fallback. If no other valid time geometry has been created, create a ProportionalTimeGeometry MITK_INFO << "used time geometry: " << ProportionalTimeGeometry::GetStaticNameOfClass(); ProportionalTimeGeometry::Pointer propTimeGeometry = ProportionalTimeGeometry::New(); propTimeGeometry->Initialize(slicedGeometry, image->GetDimension(3)); timeGeometry = propTimeGeometry; } image->SetTimeGeometry(timeGeometry); buffer = nullptr; MITK_INFO << "number of image components: " << image->GetPixelType().GetNumberOfComponents(); for (auto iter = dictionary.Begin(), iterEnd = dictionary.End(); iter != iterEnd; ++iter) { if (iter->second->GetMetaDataObjectTypeInfo() == typeid(std::string)) { const std::string &key = iter->first; std::string assumedPropertyName = key; std::replace(assumedPropertyName.begin(), assumedPropertyName.end(), '_', '.'); std::string mimeTypeName = GetMimeType()->GetName(); // Check if there is already a info for the key and our mime type. mitk::CoreServicePointer propPersistenceService(mitk::CoreServices::GetPropertyPersistence()); IPropertyPersistence::InfoResultType infoList = propPersistenceService->GetInfoByKey(key); auto predicate = [&mimeTypeName](const PropertyPersistenceInfo::ConstPointer &x) { return x.IsNotNull() && x->GetMimeTypeName() == mimeTypeName; }; auto finding = std::find_if(infoList.begin(), infoList.end(), predicate); if (finding == infoList.end()) { auto predicateWild = [](const PropertyPersistenceInfo::ConstPointer &x) { return x.IsNotNull() && x->GetMimeTypeName() == PropertyPersistenceInfo::ANY_MIMETYPE_NAME(); }; finding = std::find_if(infoList.begin(), infoList.end(), predicateWild); } PropertyPersistenceInfo::ConstPointer info; if (finding != infoList.end()) { assumedPropertyName = (*finding)->GetName(); info = *finding; } else { // we have not found anything suitable so we generate our own info auto newInfo = PropertyPersistenceInfo::New(); newInfo->SetNameAndKey(assumedPropertyName, key); newInfo->SetMimeTypeName(PropertyPersistenceInfo::ANY_MIMETYPE_NAME()); info = newInfo; } std::string value = dynamic_cast *>(iter->second.GetPointer())->GetMetaDataObjectValue(); mitk::BaseProperty::Pointer loadedProp = info->GetDeserializationFunction()(value); image->SetProperty(assumedPropertyName.c_str(), loadedProp); // Read properties should be persisted unless they are default properties // which are written anyway bool isDefaultKey(false); for (const auto &defaultKey : m_DefaultMetaDataKeys) { if (defaultKey.length() <= assumedPropertyName.length()) { // does the start match the default key if (assumedPropertyName.substr(0, defaultKey.length()).find(defaultKey) != std::string::npos) { isDefaultKey = true; break; } } } if (!isDefaultKey) { propPersistenceService->AddInfo(info); } } } // Handle UID if (dictionary.HasKey(PROPERTY_KEY_UID)) { itk::MetaDataObject::ConstPointer uidData = dynamic_cast*>(dictionary.Get(PROPERTY_KEY_UID)); if (uidData.IsNotNull()) { mitk::UIDManipulator uidManipulator(image); uidManipulator.SetUID(uidData->GetMetaDataObjectValue()); } } MITK_INFO << "...finished!"; result.push_back(image.GetPointer()); return result; } AbstractFileIO::ConfidenceLevel ItkImageIO::GetReaderConfidenceLevel() const { return m_ImageIO->CanReadFile(GetLocalFileName().c_str()) ? IFileReader::Supported : IFileReader::Unsupported; } void ItkImageIO::Write() { const auto *image = dynamic_cast(this->GetInput()); if (image == nullptr) { mitkThrow() << "Cannot write non-image data"; } // Switch the current locale to "C" LocaleSwitch localeSwitch("C"); // Clone the image geometry, because we might have to change it // for writing purposes BaseGeometry::Pointer geometry = image->GetGeometry()->Clone(); // Check if geometry information will be lost if (image->GetDimension() == 2 && !geometry->Is2DConvertable()) { MITK_WARN << "Saving a 2D image with 3D geometry information. Geometry information will be lost! You might " "consider using Convert2Dto3DImageFilter before saving."; // set matrix to identity mitk::AffineTransform3D::Pointer affTrans = mitk::AffineTransform3D::New(); affTrans->SetIdentity(); mitk::Vector3D spacing = geometry->GetSpacing(); mitk::Point3D origin = geometry->GetOrigin(); geometry->SetIndexToWorldTransform(affTrans); geometry->SetSpacing(spacing); geometry->SetOrigin(origin); } LocalFile localFile(this); const std::string path = localFile.GetFileName(); MITK_INFO << "Writing image: " << path << std::endl; try { // Implementation of writer using itkImageIO directly. This skips the use // of templated itkImageFileWriter, which saves the multiplexing on MITK side. const unsigned int dimension = image->GetDimension(); const unsigned int *const dimensions = image->GetDimensions(); const mitk::PixelType pixelType = image->GetPixelType(); const mitk::Vector3D mitkSpacing = geometry->GetSpacing(); const mitk::Point3D mitkOrigin = geometry->GetOrigin(); // Due to templating in itk, we are forced to save a 4D spacing and 4D Origin, // though they are not supported in MITK itk::Vector spacing4D; spacing4D[0] = mitkSpacing[0]; spacing4D[1] = mitkSpacing[1]; spacing4D[2] = mitkSpacing[2]; spacing4D[3] = 1; // There is no support for a 4D spacing. However, we should have a valid value here itk::Vector origin4D; origin4D[0] = mitkOrigin[0]; origin4D[1] = mitkOrigin[1]; origin4D[2] = mitkOrigin[2]; origin4D[3] = 0; // There is no support for a 4D origin. However, we should have a valid value here // Set the necessary information for imageIO m_ImageIO->SetNumberOfDimensions(dimension); m_ImageIO->SetPixelType(pixelType.GetPixelType()); m_ImageIO->SetComponentType(pixelType.GetComponentType() < PixelComponentUserType ? static_cast(pixelType.GetComponentType()) : itk::ImageIOBase::UNKNOWNCOMPONENTTYPE); m_ImageIO->SetNumberOfComponents(pixelType.GetNumberOfComponents()); itk::ImageIORegion ioRegion(dimension); for (unsigned int i = 0; i < dimension; i++) { m_ImageIO->SetDimensions(i, dimensions[i]); m_ImageIO->SetSpacing(i, spacing4D[i]); m_ImageIO->SetOrigin(i, origin4D[i]); mitk::Vector3D mitkDirection; mitkDirection.SetVnlVector(geometry->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i)); itk::Vector direction4D; direction4D[0] = mitkDirection[0]; direction4D[1] = mitkDirection[1]; direction4D[2] = mitkDirection[2]; // MITK only supports a 3x3 direction matrix. Due to templating in itk, however, we must // save a 4x4 matrix for 4D images. in this case, add an homogneous component to the matrix. if (i == 3) { direction4D[3] = 1; // homogenous component } else { direction4D[3] = 0; } vnl_vector axisDirection(dimension); for (unsigned int j = 0; j < dimension; j++) { axisDirection[j] = direction4D[j] / spacing4D[i]; } m_ImageIO->SetDirection(i, axisDirection); ioRegion.SetSize(i, image->GetLargestPossibleRegion().GetSize(i)); ioRegion.SetIndex(i, image->GetLargestPossibleRegion().GetIndex(i)); } // use compression if available m_ImageIO->UseCompressionOn(); m_ImageIO->SetIORegion(ioRegion); m_ImageIO->SetFileName(path); // Handle time geometry const auto *arbitraryTG = dynamic_cast(image->GetTimeGeometry()); if (arbitraryTG) { itk::EncapsulateMetaData(m_ImageIO->GetMetaDataDictionary(), PROPERTY_KEY_TIMEGEOMETRY_TYPE, ArbitraryTimeGeometry::GetStaticNameOfClass()); auto metaTimePoints = ConvertTimePointListToMetaDataObject(arbitraryTG); m_ImageIO->GetMetaDataDictionary().Set(PROPERTY_KEY_TIMEGEOMETRY_TIMEPOINTS, metaTimePoints); } // Handle properties mitk::PropertyList::Pointer imagePropertyList = image->GetPropertyList(); for (const auto &property : *imagePropertyList->GetMap()) { mitk::CoreServicePointer propPersistenceService(mitk::CoreServices::GetPropertyPersistence()); IPropertyPersistence::InfoResultType infoList = propPersistenceService->GetInfo(property.first, GetMimeType()->GetName(), true); if (infoList.empty()) { continue; } - std::string value = infoList.front()->GetSerializationFunction()(property.second); + std::string value = mitk::BaseProperty::VALUE_CANNOT_BE_CONVERTED_TO_STRING; + try + { + value = infoList.front()->GetSerializationFunction()(property.second); + } + catch (const std::exception& e) + { + MITK_ERROR << "Error when serializing content of property. This often indicates the use of an out dated reader. Property will not be stored. Skipped property: " << property.first << ". Reason: " << e.what(); + } + catch (...) + { + MITK_ERROR << "Unkown error when serializing content of property. This often indicates the use of an out dated reader. Property will not be stored. Skipped property: " << property.first; + } if (value == mitk::BaseProperty::VALUE_CANNOT_BE_CONVERTED_TO_STRING) { continue; } std::string key = infoList.front()->GetKey(); itk::EncapsulateMetaData(m_ImageIO->GetMetaDataDictionary(), key, value); } // Handle UID itk::EncapsulateMetaData(m_ImageIO->GetMetaDataDictionary(), PROPERTY_KEY_UID, image->GetUID()); ImageReadAccessor imageAccess(image); LocaleSwitch localeSwitch2("C"); m_ImageIO->Write(imageAccess.GetData()); } catch (const std::exception &e) { mitkThrow() << e.what(); } } AbstractFileIO::ConfidenceLevel ItkImageIO::GetWriterConfidenceLevel() const { // Check if the image dimension is supported const auto *image = dynamic_cast(this->GetInput()); if (image == nullptr) { // We cannot write a null object, DUH! return IFileWriter::Unsupported; } if (!m_ImageIO->SupportsDimension(image->GetDimension())) { // okay, dimension is not supported. We have to look at a special case: // 3D-Image with one slice. We can treat that as a 2D image. if ((image->GetDimension() == 3) && (image->GetSlicedGeometry()->GetSlices() == 1)) return IFileWriter::Supported; else return IFileWriter::Unsupported; } // Check if geometry information will be lost if (image->GetDimension() == 2 && !image->GetGeometry()->Is2DConvertable()) { return IFileWriter::PartiallySupported; } return IFileWriter::Supported; } ItkImageIO *ItkImageIO::IOClone() const { return new ItkImageIO(*this); } void ItkImageIO::InitializeDefaultMetaDataKeys() { this->m_DefaultMetaDataKeys.push_back("NRRD.space"); this->m_DefaultMetaDataKeys.push_back("NRRD.kinds"); this->m_DefaultMetaDataKeys.push_back(PROPERTY_NAME_TIMEGEOMETRY_TYPE); this->m_DefaultMetaDataKeys.push_back(PROPERTY_NAME_TIMEGEOMETRY_TIMEPOINTS); this->m_DefaultMetaDataKeys.push_back("ITK.InputFilterName"); } } diff --git a/Modules/Core/src/IO/mitkPreferenceListReaderOptionsFunctor.cpp b/Modules/Core/src/IO/mitkPreferenceListReaderOptionsFunctor.cpp index 632bf1a0a6..7ac4c6b8b8 100644 --- a/Modules/Core/src/IO/mitkPreferenceListReaderOptionsFunctor.cpp +++ b/Modules/Core/src/IO/mitkPreferenceListReaderOptionsFunctor.cpp @@ -1,88 +1,88 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkPreferenceListReaderOptionsFunctor.h" mitk::PreferenceListReaderOptionsFunctor::PreferenceListReaderOptionsFunctor() { } mitk::PreferenceListReaderOptionsFunctor::PreferenceListReaderOptionsFunctor(const ListType& preference, const IFileReader::Options& options) : m_PreferenceList(preference), m_Options(options) { } mitk::PreferenceListReaderOptionsFunctor::PreferenceListReaderOptionsFunctor(const ListType& preference, const ListType& black) : m_PreferenceList(preference), m_BlackList(black) { } mitk::PreferenceListReaderOptionsFunctor::PreferenceListReaderOptionsFunctor(const ListType& preference, const ListType& black, const IFileReader::Options& options) : m_PreferenceList(preference), m_BlackList(black), m_Options(options) { } bool mitk::PreferenceListReaderOptionsFunctor::operator()(IOUtil::LoadInfo &loadInfo) const { auto readerItems = loadInfo.m_ReaderSelector.Get(); auto selectedID = loadInfo.m_ReaderSelector.GetSelectedId(); //check if the pre selected ID is on the blacklist. If true, "un"select. auto finding = std::find(m_BlackList.begin(), m_BlackList.end(), loadInfo.m_ReaderSelector.GetSelected().GetDescription()); if (finding != m_BlackList.end()) { selectedID = -1; } - for (auto reader : readerItems) + for (const auto &reader : readerItems) { finding = std::find(m_BlackList.begin(), m_BlackList.end(), reader.GetDescription()); if (finding != m_BlackList.end()) { continue; } finding = std::find(m_PreferenceList.begin(), m_PreferenceList.end(), reader.GetDescription()); if (finding != m_PreferenceList.end()) { selectedID = reader.GetServiceId(); break; } if (selectedID==-1) { selectedID = reader.GetServiceId(); } } if (selectedID == -1) { mitkThrow() << "No valid reader found. All available readers are black listed."; } if (!loadInfo.m_ReaderSelector.Select(selectedID)) { MITK_DEBUG << "Was not able to select reader found by the PreferenceListReaderOptionsFunctor"; } auto reader = loadInfo.m_ReaderSelector.GetSelected().GetReader(); if (!m_Options.empty() && nullptr != reader) { reader->SetOptions(m_Options); } return true; } diff --git a/Modules/Core/src/IO/mitkProportionalTimeGeometryToXML.cpp b/Modules/Core/src/IO/mitkProportionalTimeGeometryToXML.cpp index 3b42888705..03a0384d62 100644 --- a/Modules/Core/src/IO/mitkProportionalTimeGeometryToXML.cpp +++ b/Modules/Core/src/IO/mitkProportionalTimeGeometryToXML.cpp @@ -1,164 +1,164 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkProportionalTimeGeometryToXML.h" #include "mitkGeometry3DToXML.h" #include #include tinyxml2::XMLElement *mitk::ProportionalTimeGeometryToXML::ToXML(tinyxml2::XMLDocument& doc, const ProportionalTimeGeometry *timeGeom) { assert(timeGeom); auto *timeGeomElem = doc.NewElement("ProportionalTimeGeometry"); timeGeomElem->SetAttribute("NumberOfTimeSteps", static_cast(timeGeom->CountTimeSteps())); // TinyXML cannot serialize infinity (default value for time step) // So we guard this value and the first time point against serialization problems // by not writing them. The reader can then tell that absence of those values // means "keep the default values" if (timeGeom->GetFirstTimePoint() != -std::numeric_limits::max()) timeGeomElem->SetAttribute("FirstTimePoint", boost::lexical_cast(timeGeom->GetFirstTimePoint()).c_str()); if (timeGeom->GetStepDuration() != std::numeric_limits::infinity()) timeGeomElem->SetAttribute("StepDuration", boost::lexical_cast(timeGeom->GetStepDuration()).c_str()); for (TimeStepType t = 0; t < timeGeom->CountTimeSteps(); ++t) { // add a node for the geometry of each time step const Geometry3D *geom3D(nullptr); if ((geom3D = dynamic_cast(timeGeom->GetGeometryForTimeStep(t).GetPointer()))) { auto *geom3DElement = Geometry3DToXML::ToXML(doc, geom3D); geom3DElement->SetAttribute("TimeStep", static_cast(t)); // mark order for us timeGeomElem->InsertEndChild(geom3DElement); } else { MITK_WARN << "Serializing a ProportionalTimeGeometry that contains something other than Geometry3D!" << " (in time step " << t << ")" << " File will miss information!"; } } return timeGeomElem; } mitk::ProportionalTimeGeometry::Pointer mitk::ProportionalTimeGeometryToXML::FromXML(const tinyxml2::XMLElement *timeGeometryElement) { if (!timeGeometryElement) { MITK_ERROR << "Cannot deserialize ProportionalTimeGeometry from nullptr."; return nullptr; } int numberOfTimeSteps = 0; if (tinyxml2::XML_SUCCESS != timeGeometryElement->QueryIntAttribute("NumberOfTimeSteps", &numberOfTimeSteps)) { MITK_WARN << " found without NumberOfTimeSteps attribute. Counting..."; } // might be missing! TimePointType firstTimePoint; const char* firstTimePoint_s = nullptr; TimePointType stepDuration; const char* stepDuration_s = nullptr; try { firstTimePoint_s = timeGeometryElement->Attribute("FirstTimePoint"); if (nullptr != firstTimePoint_s) { firstTimePoint = boost::lexical_cast(firstTimePoint_s); } else { firstTimePoint = -std::numeric_limits::max(); } stepDuration_s = timeGeometryElement->Attribute("StepDuration"); if (nullptr != stepDuration_s) { stepDuration = boost::lexical_cast(stepDuration_s); } else { stepDuration = std::numeric_limits::infinity(); } } catch ( const boost::bad_lexical_cast &e ) { MITK_ERROR << "Could not parse string as number: " << e.what(); return nullptr; } // list of all geometries with their time steps std::multimap allReadGeometries; int indexForUnlabeledTimeStep(-1); for (auto *currentElement = timeGeometryElement->FirstChildElement(); currentElement != nullptr; currentElement = currentElement->NextSiblingElement()) { // different geometries could have been inside a ProportionalTimeGeometry. // By now, we only support Geometry3D std::string tagName = currentElement->Value(); if (tagName == "Geometry3D") { Geometry3D::Pointer restoredGeometry = Geometry3DToXML::FromXML(currentElement); if (restoredGeometry.IsNotNull()) { int timeStep(-1); if (tinyxml2::XML_SUCCESS != currentElement->QueryIntAttribute("TimeStep", &timeStep)) { timeStep = indexForUnlabeledTimeStep--; // decrement index for next one MITK_WARN << "Found without 'TimeStep' attribute in . No guarantees " "on order anymore."; } if (allReadGeometries.count(static_cast(timeStep)) > 0) { MITK_WARN << "Found tags with identical 'TimeStep' attribute in . No " "guarantees on order anymore."; } allReadGeometries.insert(std::make_pair(static_cast(timeStep), restoredGeometry.GetPointer())); } } else { MITK_WARN << "Found unsupported tag <" << tagName << "> inside . Ignoring."; } } // now add all BaseGeometries that were read to a new instance // of ProportionalTimeGeometry ProportionalTimeGeometry::Pointer newTimeGeometry = ProportionalTimeGeometry::New(); newTimeGeometry->SetFirstTimePoint(firstTimePoint); newTimeGeometry->SetStepDuration(stepDuration); newTimeGeometry->ReserveSpaceForGeometries(allReadGeometries.size()); TimeStepType t(0); - for (auto entry : allReadGeometries) + for (const auto &entry : allReadGeometries) { // We add items with newly assigned time steps. // This avoids great confusion when a file contains // bogus numbers. newTimeGeometry->SetTimeStepGeometry(entry.second, t++); } // Need to re-calculate global bounding box. // This is neither stored in a file, nor done by SetTimeStepGeometry newTimeGeometry->UpdateBoundingBox(); return newTimeGeometry; } diff --git a/Modules/Core/src/Interactions/mitkPointSetDataInteractor.cpp b/Modules/Core/src/Interactions/mitkPointSetDataInteractor.cpp index ac2d921e9a..cfecd85744 100644 --- a/Modules/Core/src/Interactions/mitkPointSetDataInteractor.cpp +++ b/Modules/Core/src/Interactions/mitkPointSetDataInteractor.cpp @@ -1,621 +1,621 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkPointSetDataInteractor.h" #include "mitkMouseMoveEvent.h" #include "mitkInteractionConst.h" // TODO: refactor file #include "mitkInternalEvent.h" #include "mitkOperationEvent.h" #include "mitkRenderingManager.h" #include // #include "mitkBaseRenderer.h" #include "mitkDispatcher.h" #include "mitkUndoController.h" void mitk::PointSetDataInteractor::ConnectActionsAndFunctions() { // Condition which is evaluated before transition is taken // following actions in the statemachine are only executed if it returns TRUE CONNECT_CONDITION("isoverpoint", CheckSelection); CONNECT_FUNCTION("addpoint", AddPoint); CONNECT_FUNCTION("selectpoint", SelectPoint); CONNECT_FUNCTION("unselect", UnSelectPointAtPosition); CONNECT_FUNCTION("unselectAll", UnSelectAll); CONNECT_FUNCTION("initMove", InitMove); CONNECT_FUNCTION("movePoint", MovePoint); CONNECT_FUNCTION("finishMovement", FinishMove); CONNECT_FUNCTION("removePoint", RemovePoint); } void mitk::PointSetDataInteractor::AddPoint(StateMachineAction *stateMachineAction, InteractionEvent *interactionEvent) { unsigned int timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); ScalarType timeInMs = interactionEvent->GetSender()->GetTime(); // disallow adding of new points if maximum number of points is reached if (m_MaxNumberOfPoints > 1 && m_PointSet->GetSize(timeStep) >= m_MaxNumberOfPoints) { return; } // To add a point the minimal information is the position, this method accepts all InteractionsPositionEvents auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { mitk::Point3D itkPoint = positionEvent->GetPositionInWorld(); this->UnselectAll(timeStep, timeInMs); int lastPosition = 0; mitk::PointSet::PointsIterator it, end; it = m_PointSet->Begin(timeStep); end = m_PointSet->End(timeStep); while (it != end) { if (!m_PointSet->IndexExists(lastPosition, timeStep)) break; ++it; ++lastPosition; } // Insert a Point to the PointSet // 2) Create the Operation inserting the point if (m_PointSet->IsEmpty()) { lastPosition = 0; } auto *doOp = new mitk::PointOperation(OpINSERT, timeInMs, itkPoint, lastPosition); // 3) If Undo is enabled, also create the inverse Operation if (m_UndoEnabled) { auto *undoOp = new mitk::PointOperation(OpREMOVE, timeInMs, itkPoint, lastPosition); // 4) Do and Undo Operations are combined in an Operation event which also contains the target of the operations // (here m_PointSet) OperationEvent *operationEvent = new OperationEvent(m_PointSet, doOp, undoOp, "Add point"); // 5) Store the Operation in the UndoController OperationEvent::IncCurrObjectEventId(); m_UndoController->SetOperationEvent(operationEvent); } // 6) Execute the Operation performs the actual insertion of the point into the PointSet m_PointSet->ExecuteOperation(doOp); // 7) If Undo is not enabled the Do-Operation is to be dropped to prevent memory leaks. if (!m_UndoEnabled) delete doOp; RenderingManager::GetInstance()->RequestUpdateAll(); // Check if points form a closed contour now, if so fire an InternalEvent IsClosedContour(stateMachineAction, interactionEvent); if (m_MaxNumberOfPoints > 0 && m_PointSet->GetSize(timeStep) >= m_MaxNumberOfPoints) { // Signal that DataNode is fully filled this->NotifyResultReady(); // Send internal event that can be used by StateMachines to switch in a different state InternalEvent::Pointer event = InternalEvent::New(nullptr, this, "MaximalNumberOfPoints"); positionEvent->GetSender()->GetDispatcher()->QueueEvent(event.GetPointer()); } } } void mitk::PointSetDataInteractor::SelectPoint(StateMachineAction *, InteractionEvent *interactionEvent) { unsigned int timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); ScalarType timeInMs = interactionEvent->GetSender()->GetTime(); auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { Point3D point = positionEvent->GetPositionInWorld(); // iterate over point set and check if it contains a point close enough to the pointer to be selected int index = GetPointIndexByPosition(point, timeStep); if (index != -1) { // first deselect the other points // undoable deselect of all points in the DataList this->UnselectAll(timeStep, timeInMs); auto *doOp = new mitk::PointOperation(OpSELECTPOINT, timeInMs, point, index); /*if (m_UndoEnabled) { PointOperation* undoOp = new mitk::PointOperation(OpDESELECTPOINT,timeInMs,point, index); OperationEvent *operationEvent = new OperationEvent(m_PointSet, doOp, undoOp, "Select Point"); OperationEvent::IncCurrObjectEventId(); m_UndoController->SetOperationEvent(operationEvent); }*/ // execute the Operation m_PointSet->ExecuteOperation(doOp); if (!m_UndoEnabled) delete doOp; RenderingManager::GetInstance()->RequestUpdateAll(); } } } mitk::PointSetDataInteractor::PointSetDataInteractor() : m_MaxNumberOfPoints(0), m_SelectionAccuracy(3.5) { } mitk::PointSetDataInteractor::~PointSetDataInteractor() { } void mitk::PointSetDataInteractor::RemovePoint(StateMachineAction *, InteractionEvent *interactionEvent) { unsigned int timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); ScalarType timeInMs = interactionEvent->GetSender()->GetTime(); auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { mitk::Point3D itkPoint = positionEvent->GetPositionInWorld(); // search the point in the list int position = m_PointSet->SearchPoint(itkPoint, m_SelectionAccuracy, timeStep); if (position >= 0) // found a point { PointSet::PointType pt = m_PointSet->GetPoint(position, timeStep); itkPoint[0] = pt[0]; itkPoint[1] = pt[1]; itkPoint[2] = pt[2]; auto *doOp = new mitk::PointOperation(OpREMOVE, timeInMs, itkPoint, position); if (m_UndoEnabled) // write to UndoMechanism { auto *undoOp = new mitk::PointOperation(OpINSERT, timeInMs, itkPoint, position); OperationEvent *operationEvent = new OperationEvent(m_PointSet, doOp, undoOp, "Remove point"); mitk::OperationEvent::IncCurrObjectEventId(); m_UndoController->SetOperationEvent(operationEvent); } // execute the Operation m_PointSet->ExecuteOperation(doOp); if (!m_UndoEnabled) delete doOp; /*now select the point "position-1", and if it is the first in list, then continue at the last in list*/ // only then a select of a point is possible! if (m_PointSet->GetSize(timeStep) > 0) { this->SelectPoint(m_PointSet->Begin(timeStep)->Index(), timeStep, timeInMs); } } RenderingManager::GetInstance()->RequestUpdateAll(); } } void mitk::PointSetDataInteractor::IsClosedContour(StateMachineAction *, InteractionEvent *interactionEvent) { unsigned int timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { Point3D point = positionEvent->GetPositionInWorld(); // iterate over point set and check if it contains a point close enough to the pointer to be selected if (GetPointIndexByPosition(point, timeStep) != -1 && m_PointSet->GetSize(timeStep) >= 3) { InternalEvent::Pointer event = InternalEvent::New(nullptr, this, "ClosedContour"); positionEvent->GetSender()->GetDispatcher()->QueueEvent(event.GetPointer()); } } } void mitk::PointSetDataInteractor::MovePoint(StateMachineAction *stateMachineAction, InteractionEvent *interactionEvent) { unsigned int timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); ScalarType timeInMs = interactionEvent->GetSender()->GetTime(); auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { IsClosedContour(stateMachineAction, interactionEvent); mitk::Point3D newPoint, resultPoint; newPoint = positionEvent->GetPositionInWorld(); // search the elements in the list that are selected then calculate the // vector, because only with the vector we can move several elements in // the same direction // newPoint - lastPoint = vector // then move all selected and set the lastPoint = newPoint. // then add all vectors to a summeryVector (to be able to calculate the // startpoint for undoOperation) mitk::Vector3D dirVector = newPoint - m_LastPoint; // sum up all Movement for Undo in FinishMovement m_SumVec = m_SumVec + dirVector; mitk::PointSet::PointsIterator it, end; it = m_PointSet->Begin(timeStep); end = m_PointSet->End(timeStep); while (it != end) { int position = it->Index(); if (m_PointSet->GetSelectInfo(position, timeStep)) // if selected { PointSet::PointType pt = m_PointSet->GetPoint(position, timeStep); mitk::Point3D sumVec; sumVec[0] = pt[0]; sumVec[1] = pt[1]; sumVec[2] = pt[2]; resultPoint = sumVec + dirVector; auto *doOp = new mitk::PointOperation(OpMOVE, timeInMs, resultPoint, position); // execute the Operation // here no undo is stored, because the movement-steps aren't interesting. // only the start and the end is interisting to store for undo. m_PointSet->ExecuteOperation(doOp); delete doOp; } ++it; } m_LastPoint = newPoint; // for calculation of the direction vector // Update the display RenderingManager::GetInstance()->RequestUpdateAll(); IsClosedContour(stateMachineAction, interactionEvent); } } void mitk::PointSetDataInteractor::UnSelectPointAtPosition(StateMachineAction *, InteractionEvent *interactionEvent) { unsigned int timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); ScalarType timeInMs = interactionEvent->GetSender()->GetTime(); auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { Point3D point = positionEvent->GetPositionInWorld(); // iterate over point set and check if it contains a point close enough to the pointer to be selected int index = GetPointIndexByPosition(point, timeStep); // here it is ensured that we don't switch from one point being selected to another one being selected, // without accepting the unselect of the current point if (index != -1) { auto *doOp = new mitk::PointOperation(OpDESELECTPOINT, timeInMs, point, index); /*if (m_UndoEnabled) { PointOperation* undoOp = new mitk::PointOperation(OpSELECTPOINT,timeInMs, point, index); OperationEvent *operationEvent = new OperationEvent(m_PointSet, doOp, undoOp, "Unselect Point"); OperationEvent::IncCurrObjectEventId(); m_UndoController->SetOperationEvent(operationEvent); }*/ m_PointSet->ExecuteOperation(doOp); if (!m_UndoEnabled) delete doOp; RenderingManager::GetInstance()->RequestUpdateAll(); } } } void mitk::PointSetDataInteractor::UnSelectAll(mitk::StateMachineAction *, mitk::InteractionEvent *interactionEvent) { unsigned int timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); ScalarType timeInMs = interactionEvent->GetSender()->GetTime(); auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { Point3D positioninWorld = positionEvent->GetPositionInWorld(); PointSet::PointsContainer::Iterator it, end; PointSet::DataType *itkPointSet = m_PointSet->GetPointSet(timeStep); end = itkPointSet->GetPoints()->End(); for (it = itkPointSet->GetPoints()->Begin(); it != end; it++) { int position = it->Index(); // then declare an operation which unselects this point; // UndoOperation as well! if (m_PointSet->GetSelectInfo(position, timeStep)) { float distance = sqrt(positioninWorld.SquaredEuclideanDistanceTo(m_PointSet->GetPoint(position, timeStep))); if (distance > m_SelectionAccuracy) { mitk::Point3D noPoint; noPoint.Fill(0); auto *doOp = new mitk::PointOperation(OpDESELECTPOINT, timeInMs, noPoint, position); /*if ( m_UndoEnabled ) { mitk::PointOperation* undoOp = new mitk::PointOperation(OpSELECTPOINT, timeInMs, noPoint, position); OperationEvent *operationEvent = new OperationEvent( m_PointSet, doOp, undoOp, "Unselect Point" ); OperationEvent::IncCurrObjectEventId(); m_UndoController->SetOperationEvent( operationEvent ); }*/ m_PointSet->ExecuteOperation(doOp); if (!m_UndoEnabled) delete doOp; } } } } else { this->UnselectAll(timeStep, timeInMs); } RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::PointSetDataInteractor::UpdatePointSet(mitk::StateMachineAction *, mitk::InteractionEvent *) { auto *pointSet = dynamic_cast(this->GetDataNode()->GetData()); if (pointSet == nullptr) { MITK_ERROR << "PointSetDataInteractor:: No valid point set ."; return; } m_PointSet = pointSet; } void mitk::PointSetDataInteractor::Abort(StateMachineAction *, InteractionEvent *interactionEvent) { InternalEvent::Pointer event = InternalEvent::New(nullptr, this, IntDeactivateMe); interactionEvent->GetSender()->GetDispatcher()->QueueEvent(event.GetPointer()); } /* * Check whether the DataNode contains a pointset, if not create one and add it. */ void mitk::PointSetDataInteractor::DataNodeChanged() { if (GetDataNode() != nullptr) { auto *points = dynamic_cast(GetDataNode()->GetData()); if (points == nullptr) { m_PointSet = PointSet::New(); GetDataNode()->SetData(m_PointSet); } else { m_PointSet = points; } // load config file parameter: maximal number of points mitk::PropertyList::Pointer properties = GetAttributes(); std::string strNumber; if (properties->GetStringProperty("MaxPoints", strNumber)) { m_MaxNumberOfPoints = atoi(strNumber.c_str()); } } } void mitk::PointSetDataInteractor::InitMove(StateMachineAction *, InteractionEvent *interactionEvent) { auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) return; // start of the Movement is stored to calculate the undoKoordinate // in FinishMovement m_LastPoint = positionEvent->GetPositionInWorld(); // initialize a value to calculate the movement through all // MouseMoveEvents from MouseClick to MouseRelease m_SumVec.Fill(0); GetDataNode()->SetProperty("contourcolor", ColorProperty::New(1.0, 1.0, 1.0)); } void mitk::PointSetDataInteractor::FinishMove(StateMachineAction *, InteractionEvent *interactionEvent) { unsigned int timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); ScalarType timeInMs = interactionEvent->GetSender()->GetTime(); auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { // finish the movement: // the final point is m_LastPoint // m_SumVec stores the movement in a vector // the operation would not be necessary, but we need it for the undo Operation. // m_LastPoint is for the Operation // the point for undoOperation calculates from all selected // elements (point) - m_SumVec // search all selected elements and move them with undo-functionality. mitk::PointSet::PointsIterator it, end; it = m_PointSet->Begin(timeStep); end = m_PointSet->End(timeStep); while (it != end) { int position = it->Index(); if (m_PointSet->GetSelectInfo(position, timeStep)) // if selected { PointSet::PointType pt = m_PointSet->GetPoint(position, timeStep); Point3D itkPoint; itkPoint[0] = pt[0]; itkPoint[1] = pt[1]; itkPoint[2] = pt[2]; auto *doOp = new mitk::PointOperation(OpMOVE, timeInMs, itkPoint, position); if (m_UndoEnabled) //&& (posEvent->GetType() == mitk::Type_MouseButtonRelease) { // set the undo-operation, so the final position is undo-able // calculate the old Position from the already moved position - m_SumVec mitk::Point3D undoPoint = (itkPoint - m_SumVec); auto *undoOp = new mitk::PointOperation(OpMOVE, timeInMs, undoPoint, position); OperationEvent *operationEvent = new OperationEvent(m_PointSet, doOp, undoOp, "Move point"); OperationEvent::IncCurrObjectEventId(); m_UndoController->SetOperationEvent(operationEvent); } // execute the Operation m_PointSet->ExecuteOperation(doOp); if (!m_UndoEnabled) delete doOp; } ++it; } // Update the display RenderingManager::GetInstance()->RequestUpdateAll(); } else { return; } this->NotifyResultReady(); } void mitk::PointSetDataInteractor::SetAccuracy(float accuracy) { m_SelectionAccuracy = accuracy; } void mitk::PointSetDataInteractor::SetMaxPoints(unsigned int maxNumber) { m_MaxNumberOfPoints = maxNumber; } int mitk::PointSetDataInteractor::GetPointIndexByPosition(Point3D position, unsigned int time, float accuracy) { // iterate over point set and check if it contains a point close enough to the pointer to be selected auto *points = dynamic_cast(GetDataNode()->GetData()); int index = -1; if (points == nullptr) { return index; } if (points->GetPointSet(time) == nullptr) return -1; PointSet::PointsContainer *pointsContainer = points->GetPointSet(time)->GetPoints(); float minDistance = m_SelectionAccuracy; if (accuracy != -1) minDistance = accuracy; for (PointSet::PointsIterator it = pointsContainer->Begin(); it != pointsContainer->End(); it++) { float distance = sqrt(position.SquaredEuclideanDistanceTo(points->GetPoint(it->Index(), time))); if (distance < minDistance) // if several points fall within the margin, choose the one with minimal distance to position { index = it->Index(); } } return index; } bool mitk::PointSetDataInteractor::CheckSelection(const mitk::InteractionEvent *interactionEvent) { const auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent != nullptr) { - int timeStep = positionEvent->GetSender()->GetTimeStep(); + const auto timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); Point3D point = positionEvent->GetPositionInWorld(); // iterate over point set and check if it contains a point close enough to the pointer to be selected int index = GetPointIndexByPosition(point, timeStep); if (index != -1) return true; } return false; } void mitk::PointSetDataInteractor::UnselectAll(unsigned int timeStep, ScalarType timeInMs) { auto *pointSet = dynamic_cast(GetDataNode()->GetData()); if (pointSet == nullptr) { return; } mitk::PointSet::DataType *itkPointSet = pointSet->GetPointSet(timeStep); if (itkPointSet == nullptr) { return; } mitk::PointSet::PointsContainer::Iterator it, end; end = itkPointSet->GetPoints()->End(); for (it = itkPointSet->GetPoints()->Begin(); it != end; it++) { int position = it->Index(); PointSet::PointDataType pointData = {0, false, PTUNDEFINED}; itkPointSet->GetPointData(position, &pointData); // then declare an operation which unselects this point; // UndoOperation as well! if (pointData.selected) { mitk::Point3D noPoint; noPoint.Fill(0); auto *doOp = new mitk::PointOperation(OpDESELECTPOINT, timeInMs, noPoint, position); /*if ( m_UndoEnabled ) { mitk::PointOperation *undoOp = new mitk::PointOperation(OpSELECTPOINT, timeInMs, noPoint, position); OperationEvent *operationEvent = new OperationEvent( pointSet, doOp, undoOp, "Unselect Point" ); OperationEvent::IncCurrObjectEventId(); m_UndoController->SetOperationEvent( operationEvent ); }*/ pointSet->ExecuteOperation(doOp); if (!m_UndoEnabled) delete doOp; } } } void mitk::PointSetDataInteractor::SelectPoint(int position, unsigned int timeStep, ScalarType timeInMS) { auto *pointSet = dynamic_cast(this->GetDataNode()->GetData()); // if List is empty, then no selection of a point can be done! if ((pointSet == nullptr) || (pointSet->GetSize(timeStep) <= 0)) { return; } // dummyPoint... not needed anyway mitk::Point3D noPoint; noPoint.Fill(0); auto *doOp = new mitk::PointOperation(OpSELECTPOINT, timeInMS, noPoint, position); /*if ( m_UndoEnabled ) { mitk::PointOperation* undoOp = new mitk::PointOperation(OpDESELECTPOINT,timeInMS, noPoint, position); OperationEvent *operationEvent = new OperationEvent(pointSet, doOp, undoOp, "Select Point"); OperationEvent::IncCurrObjectEventId(); m_UndoController->SetOperationEvent(operationEvent); }*/ pointSet->ExecuteOperation(doOp); if (!m_UndoEnabled) delete doOp; } diff --git a/Modules/Core/src/Rendering/mitkAnnotation.cpp b/Modules/Core/src/Rendering/mitkAnnotation.cpp index 8c7e1e092c..c9ac002908 100644 --- a/Modules/Core/src/Rendering/mitkAnnotation.cpp +++ b/Modules/Core/src/Rendering/mitkAnnotation.cpp @@ -1,348 +1,348 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkAnnotation.h" #include "usGetModuleContext.h" const std::string mitk::Annotation::US_INTERFACE_NAME = "org.mitk.services.Annotation"; const std::string mitk::Annotation::US_PROPKEY_AnnotationNAME = US_INTERFACE_NAME + ".name"; const std::string mitk::Annotation::US_PROPKEY_ID = US_INTERFACE_NAME + ".id"; const std::string mitk::Annotation::US_PROPKEY_MODIFIED = US_INTERFACE_NAME + ".modified"; const std::string mitk::Annotation::US_PROPKEY_RENDERER_ID = US_INTERFACE_NAME + ".rendererId"; const std::string mitk::Annotation::US_PROPKEY_AR_ID = US_INTERFACE_NAME + ".arId"; mitk::Annotation::Annotation() : m_PropertyListModifiedObserverTag(0) { m_PropertyList = mitk::PropertyList::New(); itk::MemberCommand::Pointer _PropertyListModifiedCommand = itk::MemberCommand::New(); _PropertyListModifiedCommand->SetCallbackFunction(this, &mitk::Annotation::PropertyListModified); m_PropertyListModifiedObserverTag = m_PropertyList->AddObserver(itk::ModifiedEvent(), _PropertyListModifiedCommand); this->SetName(this->GetNameOfClass()); this->SetVisibility(true); this->SetOpacity(1.0); } void mitk::Annotation::PropertyListModified(const itk::Object * /*caller*/, const itk::EventObject &) { AnnotationModified(); } mitk::Annotation::~Annotation() { this->UnRegisterMicroservice(); } void mitk::Annotation::SetUSProperty(const std::string &propertyKey, us::Any value) { if (this->m_ServiceRegistration) { us::ServiceProperties props; std::vector propertyKeys; m_ServiceRegistration.GetReference().GetPropertyKeys(propertyKeys); - for (std::string key : propertyKeys) + for (const std::string &key : propertyKeys) { props[key] = m_ServiceRegistration.GetReference().GetProperty(key); } props[propertyKey] = value; m_ServiceRegistration.SetProperties(props); } } void mitk::Annotation::SetProperty(const std::string &propertyKey, const BaseProperty::Pointer &propertyValue) { this->m_PropertyList->SetProperty(propertyKey, propertyValue); } void mitk::Annotation::ReplaceProperty(const std::string &propertyKey, const BaseProperty::Pointer &propertyValue) { this->m_PropertyList->ReplaceProperty(propertyKey, propertyValue); } void mitk::Annotation::AddProperty(const std::string &propertyKey, const BaseProperty::Pointer &propertyValue, bool overwrite) { if ((overwrite) || (GetProperty(propertyKey) == nullptr)) { SetProperty(propertyKey, propertyValue); } } void mitk::Annotation::ConcatenatePropertyList(PropertyList *pList, bool replace) { m_PropertyList->ConcatenatePropertyList(pList, replace); } mitk::BaseProperty *mitk::Annotation::GetProperty(const std::string &propertyKey) const { mitk::BaseProperty::Pointer property = m_PropertyList->GetProperty(propertyKey); if (property.IsNotNull()) return property; // only to satisfy compiler! return nullptr; } bool mitk::Annotation::GetBoolProperty(const std::string &propertyKey, bool &boolValue) const { mitk::BoolProperty::Pointer boolprop = dynamic_cast(GetProperty(propertyKey)); if (boolprop.IsNull()) return false; boolValue = boolprop->GetValue(); return true; } bool mitk::Annotation::GetIntProperty(const std::string &propertyKey, int &intValue) const { mitk::IntProperty::Pointer intprop = dynamic_cast(GetProperty(propertyKey)); if (intprop.IsNull()) return false; intValue = intprop->GetValue(); return true; } bool mitk::Annotation::GetFloatProperty(const std::string &propertyKey, float &floatValue) const { mitk::FloatProperty::Pointer floatprop = dynamic_cast(GetProperty(propertyKey)); if (floatprop.IsNull()) return false; floatValue = floatprop->GetValue(); return true; } bool mitk::Annotation::GetStringProperty(const std::string &propertyKey, std::string &string) const { mitk::StringProperty::Pointer stringProp = dynamic_cast(GetProperty(propertyKey)); if (stringProp.IsNull()) { return false; } else { // memcpy((void*)string, stringProp->GetValue(), strlen(stringProp->GetValue()) + 1 ); // looks dangerous string = stringProp->GetValue(); return true; } } void mitk::Annotation::SetIntProperty(const std::string &propertyKey, int intValue) { this->m_PropertyList->SetProperty(propertyKey, mitk::IntProperty::New(intValue)); Modified(); } void mitk::Annotation::SetBoolProperty(const std::string &propertyKey, bool boolValue) { this->m_PropertyList->SetProperty(propertyKey, mitk::BoolProperty::New(boolValue)); Modified(); } void mitk::Annotation::SetFloatProperty(const std::string &propertyKey, float floatValue) { this->m_PropertyList->SetProperty(propertyKey, mitk::FloatProperty::New(floatValue)); Modified(); } void mitk::Annotation::SetDoubleProperty(const std::string &propertyKey, double doubleValue) { this->m_PropertyList->SetProperty(propertyKey, mitk::DoubleProperty::New(doubleValue)); Modified(); } void mitk::Annotation::SetStringProperty(const std::string &propertyKey, const std::string &stringValue) { this->m_PropertyList->SetProperty(propertyKey, mitk::StringProperty::New(stringValue)); Modified(); } std::string mitk::Annotation::GetName() const { mitk::StringProperty *sp = dynamic_cast(this->GetProperty("name")); if (sp == nullptr) return ""; return sp->GetValue(); } void mitk::Annotation::SetName(const std::string &name) { this->SetStringProperty("name", name); } bool mitk::Annotation::GetName(std::string &nodeName, const std::string &propertyKey) const { return GetStringProperty(propertyKey, nodeName); } void mitk::Annotation::SetText(std::string text) { SetStringProperty("Text", text.c_str()); } std::string mitk::Annotation::GetText() const { std::string text; GetStringProperty("Text", text); return text; } void mitk::Annotation::SetFontSize(int fontSize) { SetIntProperty("FontSize", fontSize); } int mitk::Annotation::GetFontSize() const { int fontSize = 1; GetIntProperty("FontSize", fontSize); return fontSize; } bool mitk::Annotation::GetVisibility(bool &visible, const std::string &propertyKey) const { return GetBoolProperty(propertyKey, visible); } bool mitk::Annotation::IsVisible(const std::string &propertyKey, bool defaultIsOn) const { return IsOn(propertyKey, defaultIsOn); } bool mitk::Annotation::GetColor(float rgb[], const std::string &propertyKey) const { mitk::ColorProperty::Pointer colorprop = dynamic_cast(GetProperty(propertyKey)); if (colorprop.IsNull()) return false; memcpy(rgb, colorprop->GetColor().GetDataPointer(), 3 * sizeof(float)); return true; } void mitk::Annotation::SetColor(const mitk::Color &color, const std::string &propertyKey) { mitk::ColorProperty::Pointer prop; prop = mitk::ColorProperty::New(color); this->m_PropertyList->SetProperty(propertyKey, prop); } void mitk::Annotation::SetColor(float red, float green, float blue, const std::string &propertyKey) { float color[3]; color[0] = red; color[1] = green; color[2] = blue; SetColor(color, propertyKey); } void mitk::Annotation::SetColor(const float rgb[], const std::string &propertyKey) { mitk::ColorProperty::Pointer prop; prop = mitk::ColorProperty::New(rgb); this->m_PropertyList->SetProperty(propertyKey, prop); } bool mitk::Annotation::GetOpacity(float &opacity, const std::string &propertyKey) const { mitk::FloatProperty::Pointer opacityprop = dynamic_cast(GetProperty(propertyKey)); if (opacityprop.IsNull()) return false; opacity = opacityprop->GetValue(); return true; } void mitk::Annotation::SetOpacity(float opacity, const std::string &propertyKey) { mitk::FloatProperty::Pointer prop; prop = mitk::FloatProperty::New(opacity); this->m_PropertyList->SetProperty(propertyKey, prop); } void mitk::Annotation::SetVisibility(bool visible, const std::string &propertyKey) { mitk::BoolProperty::Pointer prop; prop = mitk::BoolProperty::New(visible); this->m_PropertyList->SetProperty(propertyKey, prop); Modified(); } bool mitk::Annotation::BaseLocalStorage::IsGenerateDataRequired(mitk::BaseRenderer *renderer, mitk::Annotation *Annotation) { if (m_LastGenerateDataTime < Annotation->GetMTime()) return true; if (m_LastGenerateDataTime < Annotation->GetPropertyList()->GetMTime()) return true; if (renderer && m_LastGenerateDataTime < renderer->GetTimeStepUpdateTime()) return true; return false; } mitk::Annotation::Bounds mitk::Annotation::GetBoundsOnDisplay(mitk::BaseRenderer *) const { mitk::Annotation::Bounds bounds; bounds.Position[0] = bounds.Position[1] = bounds.Size[0] = bounds.Size[1] = 0; return bounds; } void mitk::Annotation::SetBoundsOnDisplay(mitk::BaseRenderer *, const mitk::Annotation::Bounds &) { } void mitk::Annotation::SetForceInForeground(bool forceForeground) { m_ForceInForeground = forceForeground; } bool mitk::Annotation::IsForceInForeground() const { return m_ForceInForeground; } mitk::PropertyList *mitk::Annotation::GetPropertyList() const { return m_PropertyList; } std::string mitk::Annotation::GetMicroserviceID() { return this->m_ServiceRegistration.GetReference().GetProperty(US_PROPKEY_ID).ToString(); } void mitk::Annotation::RegisterAsMicroservice(us::ServiceProperties props) { if (m_ServiceRegistration != nullptr) m_ServiceRegistration.Unregister(); us::ModuleContext *context = us::GetModuleContext(); // Define ServiceProps mitk::UIDGenerator uidGen = mitk::UIDGenerator("org.mitk.services.Annotation.id_"); props[US_PROPKEY_ID] = uidGen.GetUID(); m_ServiceRegistration = context->RegisterService(this, props); } void mitk::Annotation::UnRegisterMicroservice() { if (m_ServiceRegistration != nullptr) m_ServiceRegistration.Unregister(); m_ServiceRegistration = 0; } void mitk::Annotation::AnnotationModified() { Modified(); this->SetUSProperty(US_PROPKEY_MODIFIED, this->GetMTime()); } diff --git a/Modules/Core/src/Rendering/mitkAnnotationUtils.cpp b/Modules/Core/src/Rendering/mitkAnnotationUtils.cpp index 256bc14643..f67a16d14b 100644 --- a/Modules/Core/src/Rendering/mitkAnnotationUtils.cpp +++ b/Modules/Core/src/Rendering/mitkAnnotationUtils.cpp @@ -1,124 +1,124 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkAnnotationUtils.h" #include "mitkAnnotation.h" #include "vtkCallbackCommand.h" #include "vtkCommand.h" #include namespace mitk { AnnotationUtils::AnnotationUtils() {} AnnotationUtils::~AnnotationUtils() {} AbstractAnnotationRenderer *AnnotationUtils::GetAnnotationRenderer(const std::string &arTypeID, const std::string &rendererID) { // get the context us::ModuleContext *context = us::GetModuleContext(); // specify a filter that defines the requested type std::string filter = "(&(" + AbstractAnnotationRenderer::US_PROPKEY_ID + "=" + arTypeID + ")(" + AbstractAnnotationRenderer::US_PROPKEY_RENDERER_ID + "=" + rendererID + "))"; // find the fitting service std::vector serviceReferences = context->GetServiceReferences(AbstractAnnotationRenderer::US_INTERFACE_NAME, filter); // check if a service reference was found. It is also possible that several // services were found. This is not checked here, just the first one is taken. AbstractAnnotationRenderer *ar = nullptr; if (serviceReferences.size()) { ar = context->GetService(serviceReferences.front()); } // no service reference was found or found service reference has no valid source return ar; } void AnnotationUtils::RegisterAnnotationRenderer(AbstractAnnotationRenderer *annotationRenderer) { static AnnotationRendererServices AnnotationRendererServices; // Define ServiceProps us::ServiceProperties props; props[AbstractAnnotationRenderer::US_PROPKEY_RENDERER_ID] = annotationRenderer->GetRendererID(); props[AbstractAnnotationRenderer::US_PROPKEY_ID] = annotationRenderer->GetID(); us::GetModuleContext()->RegisterService(annotationRenderer, props); AnnotationRendererServices.push_back(std::unique_ptr(annotationRenderer)); } void AnnotationUtils::UpdateAnnotationRenderer(const std::string &rendererID) { for (AbstractAnnotationRenderer *annotationRenderer : GetAnnotationRenderer(rendererID)) { annotationRenderer->Update(); } } void AnnotationUtils::BaseRendererChanged(BaseRenderer *renderer) { for (AbstractAnnotationRenderer *annotationRenderer : GetAnnotationRenderer(renderer->GetName())) { annotationRenderer->CurrentBaseRendererChanged(); } vtkCallbackCommand *renderCallbackCommand = vtkCallbackCommand::New(); renderCallbackCommand->SetCallback(AnnotationUtils::RenderWindowCallback); renderer->GetRenderWindow()->AddObserver(vtkCommand::ModifiedEvent, renderCallbackCommand); renderCallbackCommand->Delete(); } void AnnotationUtils::RenderWindowCallback(vtkObject *caller, unsigned long, void *, void *) { auto *renderWindow = dynamic_cast(caller); if (!renderWindow) return; BaseRenderer *renderer = BaseRenderer::GetInstance(renderWindow); if (nullptr != renderer) { for (AbstractAnnotationRenderer *annotationRenderer : GetAnnotationRenderer(renderer->GetName())) annotationRenderer->OnRenderWindowModified(); } } Annotation *AnnotationUtils::GetAnnotation(const std::string &AnnotationID) { std::string ldapFilter = "(" + Annotation::US_PROPKEY_ID + "=" + AnnotationID + ")"; us::ModuleContext *context = us::GetModuleContext(); std::vector> annotations = context->GetServiceReferences(ldapFilter); Annotation *annotation = nullptr; if (!annotations.empty()) { annotation = us::GetModuleContext()->GetService(annotations.front()); } return annotation; } std::vector AnnotationUtils::GetAnnotationRenderer(const std::string &rendererID) { us::ModuleContext *context = us::GetModuleContext(); // specify a filter that defines the requested type std::string filter = "(&(" + AbstractAnnotationRenderer::US_PROPKEY_ID + "=*)(" + AbstractAnnotationRenderer::US_PROPKEY_RENDERER_ID + "=" + rendererID + "))"; // find the fitting service std::vector serviceReferences = context->GetServiceReferences(AbstractAnnotationRenderer::US_INTERFACE_NAME, filter); std::vector arList; - for (us::ServiceReferenceU service : serviceReferences) + for (const us::ServiceReferenceU &service : serviceReferences) { arList.push_back(context->GetService(service)); } return arList; } } diff --git a/Modules/Core/src/Rendering/mitkBaseRenderer.cpp b/Modules/Core/src/Rendering/mitkBaseRenderer.cpp index ee62b659cd..58f2831295 100644 --- a/Modules/Core/src/Rendering/mitkBaseRenderer.cpp +++ b/Modules/Core/src/Rendering/mitkBaseRenderer.cpp @@ -1,784 +1,784 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkBaseRenderer.h" #include "mitkMapper.h" #include "mitkResliceMethodProperty.h" // Geometries #include "mitkPlaneGeometry.h" #include "mitkSlicedGeometry3D.h" // Controllers #include "mitkCameraController.h" #include "mitkCameraRotationController.h" #include "mitkSliceNavigationController.h" #include "mitkVtkLayerController.h" #include "mitkInteractionConst.h" #include "mitkProperties.h" #include "mitkWeakPointerProperty.h" // VTK #include #include #include #include #include #include #include mitk::BaseRenderer::BaseRendererMapType mitk::BaseRenderer::baseRendererMap; mitk::BaseRenderer *mitk::BaseRenderer::GetInstance(vtkRenderWindow *renWin) { for (auto mapit = baseRendererMap.begin(); mapit != baseRendererMap.end(); ++mapit) { if ((*mapit).first == renWin) return (*mapit).second; } return nullptr; } void mitk::BaseRenderer::AddInstance(vtkRenderWindow *renWin, BaseRenderer *baseRenderer) { if (renWin == nullptr || baseRenderer == nullptr) return; // ensure that no BaseRenderer is managed twice mitk::BaseRenderer::RemoveInstance(renWin); baseRendererMap.insert(BaseRendererMapType::value_type(renWin, baseRenderer)); } void mitk::BaseRenderer::RemoveInstance(vtkRenderWindow *renWin) { auto mapit = baseRendererMap.find(renWin); if (mapit != baseRendererMap.end()) baseRendererMap.erase(mapit); } mitk::BaseRenderer *mitk::BaseRenderer::GetByName(const std::string &name) { for (auto mapit = baseRendererMap.begin(); mapit != baseRendererMap.end(); ++mapit) { if ((*mapit).second->m_Name == name) return (*mapit).second; } return nullptr; } vtkRenderWindow *mitk::BaseRenderer::GetRenderWindowByName(const std::string &name) { for (auto mapit = baseRendererMap.begin(); mapit != baseRendererMap.end(); ++mapit) { if ((*mapit).second->m_Name == name) return (*mapit).first; } return nullptr; } mitk::BaseRenderer::BaseRenderer(const char *name, vtkRenderWindow *renWin) : m_RenderWindow(nullptr), m_VtkRenderer(nullptr), m_MapperID(defaultMapper), m_DataStorage(nullptr), m_LastUpdateTime(0), m_CameraController(nullptr), m_SliceNavigationController(nullptr), m_CameraRotationController(nullptr), m_WorldTimeGeometry(nullptr), m_CurrentWorldGeometry(nullptr), m_CurrentWorldPlaneGeometry(nullptr), m_Slice(0), m_TimeStep(), m_CurrentWorldPlaneGeometryUpdateTime(), m_TimeStepUpdateTime(), m_KeepDisplayedRegion(true), m_CurrentWorldPlaneGeometryData(nullptr), m_CurrentWorldPlaneGeometryNode(nullptr), m_CurrentWorldPlaneGeometryTransformTime(0), m_Name(name), m_EmptyWorldGeometry(true), m_NumberOfVisibleLODEnabledMappers(0) { m_Bounds[0] = 0; m_Bounds[1] = 0; m_Bounds[2] = 0; m_Bounds[3] = 0; m_Bounds[4] = 0; m_Bounds[5] = 0; if (name != nullptr) { m_Name = name; } else { m_Name = "unnamed renderer"; itkWarningMacro(<< "Created unnamed renderer. Bad for serialization. Please choose a name."); } if (renWin != nullptr) { m_RenderWindow = renWin; m_RenderWindow->Register(nullptr); } else { itkWarningMacro(<< "Created mitkBaseRenderer without vtkRenderWindow present."); } // instances.insert( this ); // adding this BaseRenderer to the List of all BaseRenderer m_BindDispatcherInteractor = new mitk::BindDispatcherInteractor(GetName()); WeakPointerProperty::Pointer rendererProp = WeakPointerProperty::New((itk::Object *)this); m_CurrentWorldPlaneGeometry = mitk::PlaneGeometry::New(); m_CurrentWorldPlaneGeometryData = mitk::PlaneGeometryData::New(); m_CurrentWorldPlaneGeometryData->SetPlaneGeometry(m_CurrentWorldPlaneGeometry); m_CurrentWorldPlaneGeometryNode = mitk::DataNode::New(); m_CurrentWorldPlaneGeometryNode->SetData(m_CurrentWorldPlaneGeometryData); m_CurrentWorldPlaneGeometryNode->GetPropertyList()->SetProperty("renderer", rendererProp); m_CurrentWorldPlaneGeometryNode->GetPropertyList()->SetProperty("layer", IntProperty::New(1000)); m_CurrentWorldPlaneGeometryNode->SetProperty("reslice.thickslices", mitk::ResliceMethodProperty::New()); m_CurrentWorldPlaneGeometryNode->SetProperty("reslice.thickslices.num", mitk::IntProperty::New(1)); m_CurrentWorldPlaneGeometryTransformTime = m_CurrentWorldPlaneGeometryNode->GetVtkTransform()->GetMTime(); mitk::SliceNavigationController::Pointer sliceNavigationController = mitk::SliceNavigationController::New(); sliceNavigationController->SetRenderer(this); sliceNavigationController->ConnectGeometrySliceEvent(this); sliceNavigationController->ConnectGeometryUpdateEvent(this); sliceNavigationController->ConnectGeometryTimeEvent(this, false); m_SliceNavigationController = sliceNavigationController; m_CameraRotationController = mitk::CameraRotationController::New(); m_CameraRotationController->SetRenderWindow(m_RenderWindow); m_CameraRotationController->AcquireCamera(); m_CameraController = mitk::CameraController::New(); m_CameraController->SetRenderer(this); m_VtkRenderer = vtkRenderer::New(); m_VtkRenderer->SetMaximumNumberOfPeels(16); if (AntiAliasing::FastApproximate == RenderingManager::GetInstance()->GetAntiAliasing()) m_VtkRenderer->UseFXAAOn(); if (nullptr == mitk::VtkLayerController::GetInstance(m_RenderWindow)) mitk::VtkLayerController::AddInstance(m_RenderWindow, m_VtkRenderer); mitk::VtkLayerController::GetInstance(m_RenderWindow)->InsertSceneRenderer(m_VtkRenderer); } mitk::BaseRenderer::~BaseRenderer() { if (m_VtkRenderer != nullptr) { m_VtkRenderer->Delete(); m_VtkRenderer = nullptr; } if (m_CameraController.IsNotNull()) m_CameraController->SetRenderer(nullptr); mitk::VtkLayerController::RemoveInstance(m_RenderWindow); RemoveAllLocalStorages(); m_DataStorage = nullptr; if (m_BindDispatcherInteractor != nullptr) { delete m_BindDispatcherInteractor; } if (m_RenderWindow != nullptr) { m_RenderWindow->Delete(); m_RenderWindow = nullptr; } } void mitk::BaseRenderer::SetMapperID(MapperSlotId id) { if (m_MapperID != id) { bool useDepthPeeling = Standard3D == id; m_VtkRenderer->SetUseDepthPeeling(useDepthPeeling); m_VtkRenderer->SetUseDepthPeelingForVolumes(useDepthPeeling); m_MapperID = id; this->Modified(); } } void mitk::BaseRenderer::RemoveAllLocalStorages() { this->InvokeEvent(mitk::BaseRenderer::RendererResetEvent()); std::list::iterator it; for (it = m_RegisteredLocalStorageHandlers.begin(); it != m_RegisteredLocalStorageHandlers.end(); ++it) (*it)->ClearLocalStorage(this, false); m_RegisteredLocalStorageHandlers.clear(); } void mitk::BaseRenderer::RegisterLocalStorageHandler(mitk::BaseLocalStorageHandler *lsh) { m_RegisteredLocalStorageHandlers.push_back(lsh); } mitk::Dispatcher::Pointer mitk::BaseRenderer::GetDispatcher() const { return m_BindDispatcherInteractor->GetDispatcher(); } void mitk::BaseRenderer::UnregisterLocalStorageHandler(mitk::BaseLocalStorageHandler *lsh) { m_RegisteredLocalStorageHandlers.remove(lsh); } void mitk::BaseRenderer::SetDataStorage(DataStorage *storage) { if (storage != m_DataStorage && storage != nullptr) { m_DataStorage = storage; m_BindDispatcherInteractor->SetDataStorage(m_DataStorage); this->Modified(); } } const mitk::BaseRenderer::MapperSlotId mitk::BaseRenderer::defaultMapper = 1; void mitk::BaseRenderer::Paint() { } void mitk::BaseRenderer::Initialize() { } void mitk::BaseRenderer::Resize(int w, int h) { this->m_RenderWindow->SetSize(w, h); } void mitk::BaseRenderer::InitRenderer(vtkRenderWindow *renderwindow) { if (m_RenderWindow != renderwindow) { if (m_RenderWindow != nullptr) { m_RenderWindow->Delete(); } m_RenderWindow = renderwindow; if (m_RenderWindow != nullptr) { m_RenderWindow->Register(nullptr); } } RemoveAllLocalStorages(); if (m_CameraController.IsNotNull()) { m_CameraController->SetRenderer(this); } } void mitk::BaseRenderer::InitSize(int w, int h) { this->m_RenderWindow->SetSize(w, h); } void mitk::BaseRenderer::SetSlice(unsigned int slice) { if (m_Slice != slice) { m_Slice = slice; if (m_WorldTimeGeometry.IsNotNull()) { // get world geometry which may be rotated, for the current time step SlicedGeometry3D *slicedWorldGeometry = dynamic_cast(m_WorldTimeGeometry->GetGeometryForTimeStep(m_TimeStep).GetPointer()); if (slicedWorldGeometry != nullptr) { // if slice position is part of the world geometry... if (m_Slice >= slicedWorldGeometry->GetSlices()) // set the current worldplanegeomety as the selected 2D slice of the world geometry m_Slice = slicedWorldGeometry->GetSlices() - 1; SetCurrentWorldPlaneGeometry(slicedWorldGeometry->GetPlaneGeometry(m_Slice)); SetCurrentWorldGeometry(slicedWorldGeometry); } } else Modified(); } } void mitk::BaseRenderer::SetTimeStep(unsigned int timeStep) { if (m_TimeStep != timeStep) { m_TimeStep = timeStep; m_TimeStepUpdateTime.Modified(); if (m_WorldTimeGeometry.IsNotNull()) { if (m_TimeStep >= m_WorldTimeGeometry->CountTimeSteps()) m_TimeStep = m_WorldTimeGeometry->CountTimeSteps() - 1; SlicedGeometry3D *slicedWorldGeometry = dynamic_cast(m_WorldTimeGeometry->GetGeometryForTimeStep(m_TimeStep).GetPointer()); if (slicedWorldGeometry != nullptr) { SetCurrentWorldPlaneGeometry(slicedWorldGeometry->GetPlaneGeometry(m_Slice)); SetCurrentWorldGeometry(slicedWorldGeometry); } } else Modified(); } } -int mitk::BaseRenderer::GetTimeStep(const mitk::BaseData *data) const +mitk::TimeStepType mitk::BaseRenderer::GetTimeStep(const mitk::BaseData *data) const { if ((data == nullptr) || (data->IsInitialized() == false)) { return -1; } return data->GetTimeGeometry()->TimePointToTimeStep(GetTime()); } mitk::ScalarType mitk::BaseRenderer::GetTime() const { if (m_WorldTimeGeometry.IsNull()) { return 0; } else { ScalarType timeInMS = m_WorldTimeGeometry->TimeStepToTimePoint(GetTimeStep()); if (timeInMS == itk::NumericTraits::NonpositiveMin()) return 0; else return timeInMS; } } void mitk::BaseRenderer::SetWorldTimeGeometry(const mitk::TimeGeometry *geometry) { assert(geometry != nullptr); itkDebugMacro("setting WorldTimeGeometry to " << geometry); if (m_WorldTimeGeometry != geometry) { if (geometry->GetBoundingBoxInWorld()->GetDiagonalLength2() == 0) return; m_WorldTimeGeometry = geometry; itkDebugMacro("setting WorldTimeGeometry to " << m_WorldTimeGeometry); if (m_TimeStep >= m_WorldTimeGeometry->CountTimeSteps()) m_TimeStep = m_WorldTimeGeometry->CountTimeSteps() - 1; BaseGeometry *geometry3d; geometry3d = m_WorldTimeGeometry->GetGeometryForTimeStep(m_TimeStep); SetWorldGeometry3D(geometry3d); } } void mitk::BaseRenderer::SetWorldGeometry3D(const mitk::BaseGeometry *geometry) { itkDebugMacro("setting WorldGeometry3D to " << geometry); if (geometry->GetBoundingBox()->GetDiagonalLength2() == 0) return; const SlicedGeometry3D *slicedWorldGeometry; slicedWorldGeometry = dynamic_cast(geometry); PlaneGeometry::ConstPointer geometry2d; if (slicedWorldGeometry != nullptr) { if (m_Slice >= slicedWorldGeometry->GetSlices() && (m_Slice != 0)) m_Slice = slicedWorldGeometry->GetSlices() - 1; geometry2d = slicedWorldGeometry->GetPlaneGeometry(m_Slice); if (geometry2d.IsNull()) { PlaneGeometry::Pointer plane = mitk::PlaneGeometry::New(); plane->InitializeStandardPlane(slicedWorldGeometry); geometry2d = plane; } SetCurrentWorldGeometry(slicedWorldGeometry); } else { geometry2d = dynamic_cast(geometry); if (geometry2d.IsNull()) { PlaneGeometry::Pointer plane = PlaneGeometry::New(); plane->InitializeStandardPlane(geometry); geometry2d = plane; } SetCurrentWorldGeometry(geometry); } SetCurrentWorldPlaneGeometry(geometry2d); // calls Modified() if (m_CurrentWorldPlaneGeometry.IsNull()) itkWarningMacro("m_CurrentWorldPlaneGeometry is nullptr"); } void mitk::BaseRenderer::SetCurrentWorldPlaneGeometry(const mitk::PlaneGeometry *geometry2d) { if (m_CurrentWorldPlaneGeometry != geometry2d) { m_CurrentWorldPlaneGeometry = geometry2d->Clone(); m_CurrentWorldPlaneGeometryData->SetPlaneGeometry(m_CurrentWorldPlaneGeometry); m_CurrentWorldPlaneGeometryUpdateTime.Modified(); Modified(); } } void mitk::BaseRenderer::SendUpdateSlice() { m_CurrentWorldPlaneGeometryUpdateTime.Modified(); } int *mitk::BaseRenderer::GetSize() const { return this->m_RenderWindow->GetSize(); } int *mitk::BaseRenderer::GetViewportSize() const { return this->m_VtkRenderer->GetSize(); } void mitk::BaseRenderer::SetCurrentWorldGeometry(const mitk::BaseGeometry *geometry) { m_CurrentWorldGeometry = geometry; if (geometry == nullptr) { m_Bounds[0] = 0; m_Bounds[1] = 0; m_Bounds[2] = 0; m_Bounds[3] = 0; m_Bounds[4] = 0; m_Bounds[5] = 0; m_EmptyWorldGeometry = true; return; } BoundingBox::Pointer boundingBox = m_CurrentWorldGeometry->CalculateBoundingBoxRelativeToTransform(nullptr); const BoundingBox::BoundsArrayType &worldBounds = boundingBox->GetBounds(); m_Bounds[0] = worldBounds[0]; m_Bounds[1] = worldBounds[1]; m_Bounds[2] = worldBounds[2]; m_Bounds[3] = worldBounds[3]; m_Bounds[4] = worldBounds[4]; m_Bounds[5] = worldBounds[5]; if (boundingBox->GetDiagonalLength2() <= mitk::eps) m_EmptyWorldGeometry = true; else m_EmptyWorldGeometry = false; } void mitk::BaseRenderer::SetGeometry(const itk::EventObject &geometrySendEvent) { const auto *sendEvent = dynamic_cast(&geometrySendEvent); assert(sendEvent != nullptr); SetWorldTimeGeometry(sendEvent->GetTimeGeometry()); } void mitk::BaseRenderer::UpdateGeometry(const itk::EventObject &geometryUpdateEvent) { const auto *updateEvent = dynamic_cast(&geometryUpdateEvent); if (updateEvent == nullptr) return; if (m_CurrentWorldGeometry.IsNotNull()) { auto *slicedWorldGeometry = dynamic_cast(m_CurrentWorldGeometry.GetPointer()); if (slicedWorldGeometry) { PlaneGeometry *geometry2D = slicedWorldGeometry->GetPlaneGeometry(m_Slice); SetCurrentWorldPlaneGeometry(geometry2D); // calls Modified() } } } void mitk::BaseRenderer::SetGeometrySlice(const itk::EventObject &geometrySliceEvent) { const auto *sliceEvent = dynamic_cast(&geometrySliceEvent); assert(sliceEvent != nullptr); SetSlice(sliceEvent->GetPos()); } void mitk::BaseRenderer::SetGeometryTime(const itk::EventObject &geometryTimeEvent) { const auto *timeEvent = dynamic_cast(&geometryTimeEvent); assert(timeEvent != nullptr); SetTimeStep(timeEvent->GetPos()); } const double *mitk::BaseRenderer::GetBounds() const { return m_Bounds; } void mitk::BaseRenderer::DrawOverlayMouse(mitk::Point2D &itkNotUsed(p2d)) { MITK_INFO << "BaseRenderer::DrawOverlayMouse()- should be inconcret implementation OpenGLRenderer." << std::endl; } void mitk::BaseRenderer::RequestUpdate() { SetConstrainZoomingAndPanning(true); RenderingManager::GetInstance()->RequestUpdate(this->m_RenderWindow); } void mitk::BaseRenderer::ForceImmediateUpdate() { RenderingManager::GetInstance()->ForceImmediateUpdate(this->m_RenderWindow); } unsigned int mitk::BaseRenderer::GetNumberOfVisibleLODEnabledMappers() const { return m_NumberOfVisibleLODEnabledMappers; } /*! Sets the new Navigation controller */ void mitk::BaseRenderer::SetSliceNavigationController(mitk::SliceNavigationController *SlicenavigationController) { if (SlicenavigationController == nullptr) return; // copy worldgeometry SlicenavigationController->SetInputWorldTimeGeometry(SlicenavigationController->GetCreatedWorldGeometry()); SlicenavigationController->Update(); // set new m_SliceNavigationController = SlicenavigationController; m_SliceNavigationController->SetRenderer(this); if (m_SliceNavigationController.IsNotNull()) { m_SliceNavigationController->ConnectGeometrySliceEvent(this); m_SliceNavigationController->ConnectGeometryUpdateEvent(this); m_SliceNavigationController->ConnectGeometryTimeEvent(this, false); } } void mitk::BaseRenderer::DisplayToWorld(const Point2D &displayPoint, Point3D &worldIndex) const { if (m_MapperID == BaseRenderer::Standard2D) { double display[3], *world; // For the rigth z-position in display coordinates, take the focal point, convert it to display and use it for // correct depth. double *displayCoord; double cameraFP[4]; // Get camera focal point and position. Convert to display (screen) // coordinates. We need a depth value for z-buffer. this->GetVtkRenderer()->GetActiveCamera()->GetFocalPoint(cameraFP); cameraFP[3] = 0.0; this->GetVtkRenderer()->SetWorldPoint(cameraFP[0], cameraFP[1], cameraFP[2], cameraFP[3]); this->GetVtkRenderer()->WorldToDisplay(); displayCoord = this->GetVtkRenderer()->GetDisplayPoint(); // now convert the display point to world coordinates display[0] = displayPoint[0]; display[1] = displayPoint[1]; display[2] = displayCoord[2]; this->GetVtkRenderer()->SetDisplayPoint(display); this->GetVtkRenderer()->DisplayToWorld(); world = this->GetVtkRenderer()->GetWorldPoint(); for (int i = 0; i < 3; i++) { worldIndex[i] = world[i] / world[3]; } } else if (m_MapperID == BaseRenderer::Standard3D) { PickWorldPoint( displayPoint, worldIndex); // Seems to be the same code as above, but subclasses may contain different implementations. } return; } void mitk::BaseRenderer::DisplayToPlane(const Point2D &displayPoint, Point2D &planePointInMM) const { if (m_MapperID == BaseRenderer::Standard2D) { Point3D worldPoint; this->DisplayToWorld(displayPoint, worldPoint); this->m_CurrentWorldPlaneGeometry->Map(worldPoint, planePointInMM); } else if (m_MapperID == BaseRenderer::Standard3D) { MITK_WARN << "No conversion possible with 3D mapper."; return; } return; } void mitk::BaseRenderer::WorldToDisplay(const Point3D &worldIndex, Point2D &displayPoint) const { double world[4], *display; world[0] = worldIndex[0]; world[1] = worldIndex[1]; world[2] = worldIndex[2]; world[3] = 1.0; this->GetVtkRenderer()->SetWorldPoint(world); this->GetVtkRenderer()->WorldToDisplay(); display = this->GetVtkRenderer()->GetDisplayPoint(); displayPoint[0] = display[0]; displayPoint[1] = display[1]; return; } void mitk::BaseRenderer::WorldToView(const mitk::Point3D &worldIndex, mitk::Point2D &viewPoint) const { double world[4], *view; world[0] = worldIndex[0]; world[1] = worldIndex[1]; world[2] = worldIndex[2]; world[3] = 1.0; this->GetVtkRenderer()->SetWorldPoint(world); this->GetVtkRenderer()->WorldToView(); view = this->GetVtkRenderer()->GetViewPoint(); this->GetVtkRenderer()->ViewToNormalizedViewport(view[0], view[1], view[2]); viewPoint[0] = view[0] * this->GetViewportSize()[0]; viewPoint[1] = view[1] * this->GetViewportSize()[1]; return; } void mitk::BaseRenderer::PlaneToDisplay(const Point2D &planePointInMM, Point2D &displayPoint) const { Point3D worldPoint; this->m_CurrentWorldPlaneGeometry->Map(planePointInMM, worldPoint); this->WorldToDisplay(worldPoint, displayPoint); return; } void mitk::BaseRenderer::PlaneToView(const Point2D &planePointInMM, Point2D &viewPoint) const { Point3D worldPoint; this->m_CurrentWorldPlaneGeometry->Map(planePointInMM, worldPoint); this->WorldToView(worldPoint,viewPoint); return; } double mitk::BaseRenderer::GetScaleFactorMMPerDisplayUnit() const { if (this->GetMapperID() == BaseRenderer::Standard2D) { // GetParallelScale returns half of the height of the render window in mm. // Divided by the half size of the Display size in pixel givest the mm per pixel. return this->GetVtkRenderer()->GetActiveCamera()->GetParallelScale() * 2.0 / GetViewportSize()[1]; } else return 1.0; } mitk::Point2D mitk::BaseRenderer::GetDisplaySizeInMM() const { Point2D dispSizeInMM; dispSizeInMM[0] = GetSizeX() * GetScaleFactorMMPerDisplayUnit(); dispSizeInMM[1] = GetSizeY() * GetScaleFactorMMPerDisplayUnit(); return dispSizeInMM; } mitk::Point2D mitk::BaseRenderer::GetViewportSizeInMM() const { Point2D dispSizeInMM; dispSizeInMM[0] = GetViewportSize()[0] * GetScaleFactorMMPerDisplayUnit(); dispSizeInMM[1] = GetViewportSize()[1] * GetScaleFactorMMPerDisplayUnit(); return dispSizeInMM; } mitk::Point2D mitk::BaseRenderer::GetOriginInMM() const { Point2D originPx; originPx[0] = m_VtkRenderer->GetOrigin()[0]; originPx[1] = m_VtkRenderer->GetOrigin()[1]; Point2D displayGeometryOriginInMM; DisplayToPlane(originPx, displayGeometryOriginInMM); // top left of the render window (Origin) return displayGeometryOriginInMM; } void mitk::BaseRenderer::SetConstrainZoomingAndPanning(bool constrain) { m_ConstrainZoomingAndPanning = constrain; if (m_ConstrainZoomingAndPanning) { this->GetCameraController()->AdjustCameraToPlane(); } } mitk::Point3D mitk::BaseRenderer::Map2DRendererPositionTo3DWorldPosition(const Point2D &mousePosition) const { // DEPRECATED: Map2DRendererPositionTo3DWorldPosition is deprecated. use DisplayToWorldInstead Point3D position; DisplayToWorld(mousePosition, position); return position; } void mitk::BaseRenderer::PrintSelf(std::ostream &os, itk::Indent indent) const { os << indent << " MapperID: " << m_MapperID << std::endl; os << indent << " Slice: " << m_Slice << std::endl; os << indent << " TimeStep: " << m_TimeStep << std::endl; os << indent << " CurrentWorldPlaneGeometry: "; if (m_CurrentWorldPlaneGeometry.IsNull()) os << "nullptr" << std::endl; else m_CurrentWorldPlaneGeometry->Print(os, indent); os << indent << " CurrentWorldPlaneGeometryUpdateTime: " << m_CurrentWorldPlaneGeometryUpdateTime << std::endl; os << indent << " CurrentWorldPlaneGeometryTransformTime: " << m_CurrentWorldPlaneGeometryTransformTime << std::endl; Superclass::PrintSelf(os, indent); } diff --git a/Modules/Core/src/Rendering/mitkImageVtkMapper2D.cpp b/Modules/Core/src/Rendering/mitkImageVtkMapper2D.cpp index 3a4462b53a..5e4e797c38 100644 --- a/Modules/Core/src/Rendering/mitkImageVtkMapper2D.cpp +++ b/Modules/Core/src/Rendering/mitkImageVtkMapper2D.cpp @@ -1,1124 +1,1153 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // MITK #include #include #include #include #include #include #include #include #include #include #include //#include #include "mitkImageStatisticsHolder.h" #include "mitkPlaneClipping.h" #include // MITK Rendering #include "mitkImageVtkMapper2D.h" #include "vtkMitkLevelWindowFilter.h" #include "vtkMitkThickSlicesFilter.h" #include "vtkNeverTranslucentTexture.h" // VTK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // ITK #include #include +namespace +{ + bool IsBinaryImage(mitk::Image* image) + { + if (nullptr != image && image->IsInitialized()) + { + bool isBinary = true; + auto statistics = image->GetStatistics(); + + const auto numTimeSteps = image->GetTimeSteps(); + + for (std::remove_const_t t = 0; t < numTimeSteps; ++t) + { + const auto numChannels = image->GetNumberOfChannels(); + + for (std::remove_const_t c = 0; c < numChannels; ++c) + { + auto minValue = statistics->GetScalarValueMin(t, c); + auto maxValue = statistics->GetScalarValueMax(t, c); + + if (std::abs(maxValue - minValue) < mitk::eps) + continue; + + auto min2ndValue = statistics->GetScalarValue2ndMin(t, c); + auto max2ndValue = statistics->GetScalarValue2ndMax(t, c); + + if (std::abs(maxValue - min2ndValue) < mitk::eps && std::abs(max2ndValue - minValue) < mitk::eps) + continue; + + isBinary = false; + break; + } + + if (!isBinary) + break; + } + + return isBinary; + } + + return false; + } +} + mitk::ImageVtkMapper2D::ImageVtkMapper2D() { } mitk::ImageVtkMapper2D::~ImageVtkMapper2D() { // The 3D RW Mapper (PlaneGeometryDataVtkMapper3D) is listening to this event, // in order to delete the images from the 3D RW. this->InvokeEvent(itk::DeleteEvent()); } // set the two points defining the textured plane according to the dimension and spacing void mitk::ImageVtkMapper2D::GeneratePlane(mitk::BaseRenderer *renderer, double planeBounds[6]) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); float depth = this->CalculateLayerDepth(renderer); // Set the origin to (xMin; yMin; depth) of the plane. This is necessary for obtaining the correct // plane size in crosshair rotation and swivel mode. localStorage->m_Plane->SetOrigin(planeBounds[0], planeBounds[2], depth); // These two points define the axes of the plane in combination with the origin. // Point 1 is the x-axis and point 2 the y-axis. // Each plane is transformed according to the view (axial, coronal and saggital) afterwards. localStorage->m_Plane->SetPoint1(planeBounds[1], planeBounds[2], depth); // P1: (xMax, yMin, depth) localStorage->m_Plane->SetPoint2(planeBounds[0], planeBounds[3], depth); // P2: (xMin, yMax, depth) } float mitk::ImageVtkMapper2D::CalculateLayerDepth(mitk::BaseRenderer *renderer) { // get the clipping range to check how deep into z direction we can render images double maxRange = renderer->GetVtkRenderer()->GetActiveCamera()->GetClippingRange()[1]; // Due to a VTK bug, we cannot use the whole clipping range. /100 is empirically determined float depth = -maxRange * 0.01; // divide by 100 int layer = 0; GetDataNode()->GetIntProperty("layer", layer, renderer); // add the layer property for each image to render images with a higher layer on top of the others depth += layer * 10; //*10: keep some room for each image (e.g. for ODFs in between) if (depth > 0.0f) { depth = 0.0f; MITK_WARN << "Layer value exceeds clipping range. Set to minimum instead."; } return depth; } const mitk::Image *mitk::ImageVtkMapper2D::GetInput(void) { return static_cast(GetDataNode()->GetData()); } vtkProp *mitk::ImageVtkMapper2D::GetVtkProp(mitk::BaseRenderer *renderer) { // return the actor corresponding to the renderer return m_LSH.GetLocalStorage(renderer)->m_PublicActors; } void mitk::ImageVtkMapper2D::GenerateDataForRenderer(mitk::BaseRenderer *renderer) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); auto *image = const_cast(this->GetInput()); mitk::DataNode *datanode = this->GetDataNode(); if (nullptr == image || !image->IsInitialized()) { this->SetToInvalidState(localStorage); return; } // check if there is a valid worldGeometry const PlaneGeometry *worldGeometry = renderer->GetCurrentWorldPlaneGeometry(); if (nullptr == worldGeometry || !worldGeometry->IsValid() || !worldGeometry->HasReferenceGeometry()) { this->SetToInvalidState(localStorage); return; } image->Update(); localStorage->m_PublicActors = localStorage->m_Actors.Get(); // early out if there is no intersection of the current rendering geometry // and the geometry of the image that is to be rendered. if (!RenderingGeometryIntersectsImage(worldGeometry, image->GetSlicedGeometry())) { this->SetToInvalidState(localStorage); return; } // set main input for ExtractSliceFilter localStorage->m_Reslicer->SetInput(image); localStorage->m_Reslicer->SetWorldGeometry(worldGeometry); localStorage->m_Reslicer->SetTimeStep(this->GetTimestep()); // set the transformation of the image to adapt reslice axis localStorage->m_Reslicer->SetResliceTransformByGeometry( image->GetTimeGeometry()->GetGeometryForTimeStep(this->GetTimestep())); // is the geometry of the slice based on the input image or the worldgeometry? bool inPlaneResampleExtentByGeometry = false; datanode->GetBoolProperty("in plane resample extent by geometry", inPlaneResampleExtentByGeometry, renderer); localStorage->m_Reslicer->SetInPlaneResampleExtentByGeometry(inPlaneResampleExtentByGeometry); // Initialize the interpolation mode for resampling; switch to nearest // neighbor if the input image is too small. if ((image->GetDimension() >= 3) && (image->GetDimension(2) > 1)) { VtkResliceInterpolationProperty *resliceInterpolationProperty; datanode->GetProperty(resliceInterpolationProperty, "reslice interpolation", renderer); int interpolationMode = VTK_RESLICE_NEAREST; if (resliceInterpolationProperty != nullptr) { interpolationMode = resliceInterpolationProperty->GetInterpolation(); } switch (interpolationMode) { case VTK_RESLICE_NEAREST: localStorage->m_Reslicer->SetInterpolationMode(ExtractSliceFilter::RESLICE_NEAREST); break; case VTK_RESLICE_LINEAR: localStorage->m_Reslicer->SetInterpolationMode(ExtractSliceFilter::RESLICE_LINEAR); break; case VTK_RESLICE_CUBIC: localStorage->m_Reslicer->SetInterpolationMode(ExtractSliceFilter::RESLICE_CUBIC); break; } } else { localStorage->m_Reslicer->SetInterpolationMode(ExtractSliceFilter::RESLICE_NEAREST); } // set the vtk output property to true, makes sure that no unneeded mitk image convertion // is done. localStorage->m_Reslicer->SetVtkOutputRequest(true); // Thickslicing int thickSlicesMode = 0; int thickSlicesNum = 1; // Thick slices parameters if (image->GetPixelType().GetNumberOfComponents() == 1) // for now only single component are allowed { DataNode *dn = renderer->GetCurrentWorldPlaneGeometryNode(); if (dn) { ResliceMethodProperty *resliceMethodEnumProperty = nullptr; if (dn->GetProperty(resliceMethodEnumProperty, "reslice.thickslices", renderer) && resliceMethodEnumProperty) thickSlicesMode = resliceMethodEnumProperty->GetValueAsId(); IntProperty *intProperty = nullptr; if (dn->GetProperty(intProperty, "reslice.thickslices.num", renderer) && intProperty) { thickSlicesNum = intProperty->GetValue(); if (thickSlicesNum < 1) thickSlicesNum = 1; } } else { MITK_WARN << "no associated widget plane data tree node found"; } } const auto *planeGeometry = dynamic_cast(worldGeometry); if (thickSlicesMode > 0) { double dataZSpacing = 1.0; Vector3D normInIndex, normal; const auto *abstractGeometry = dynamic_cast(worldGeometry); if (abstractGeometry != nullptr) normal = abstractGeometry->GetPlane()->GetNormal(); else { if (planeGeometry != nullptr) { normal = planeGeometry->GetNormal(); } else return; // no fitting geometry set } normal.Normalize(); image->GetTimeGeometry()->GetGeometryForTimeStep(this->GetTimestep())->WorldToIndex(normal, normInIndex); dataZSpacing = 1.0 / normInIndex.GetNorm(); localStorage->m_Reslicer->SetOutputDimensionality(3); localStorage->m_Reslicer->SetOutputSpacingZDirection(dataZSpacing); localStorage->m_Reslicer->SetOutputExtentZDirection(-thickSlicesNum, 0 + thickSlicesNum); // Do the reslicing. Modified() is called to make sure that the reslicer is // executed even though the input geometry information did not change; this // is necessary when the input /em data, but not the /em geometry changes. localStorage->m_TSFilter->SetThickSliceMode(thickSlicesMode - 1); localStorage->m_TSFilter->SetInputData(localStorage->m_Reslicer->GetVtkOutput()); // vtkFilter=>mitkFilter=>vtkFilter update mechanism will fail without calling manually localStorage->m_Reslicer->Modified(); localStorage->m_Reslicer->Update(); localStorage->m_TSFilter->Modified(); localStorage->m_TSFilter->Update(); localStorage->m_ReslicedImage = localStorage->m_TSFilter->GetOutput(); } else { // this is needed when thick mode was enable bevore. These variable have to be reset to default values localStorage->m_Reslicer->SetOutputDimensionality(2); localStorage->m_Reslicer->SetOutputSpacingZDirection(1.0); localStorage->m_Reslicer->SetOutputExtentZDirection(0, 0); localStorage->m_Reslicer->Modified(); // start the pipeline with updating the largest possible, needed if the geometry of the input has changed localStorage->m_Reslicer->UpdateLargestPossibleRegion(); localStorage->m_ReslicedImage = localStorage->m_Reslicer->GetVtkOutput(); } // Bounds information for reslicing (only reuqired if reference geometry // is present) // this used for generating a vtkPLaneSource with the right size double sliceBounds[6]; for (auto &sliceBound : sliceBounds) { sliceBound = 0.0; } localStorage->m_Reslicer->GetClippedPlaneBounds(sliceBounds); // get the spacing of the slice localStorage->m_mmPerPixel = localStorage->m_Reslicer->GetOutputSpacing(); // calculate minimum bounding rect of IMAGE in texture { double textureClippingBounds[6]; for (auto &textureClippingBound : textureClippingBounds) { textureClippingBound = 0.0; } // Calculate the actual bounds of the transformed plane clipped by the // dataset bounding box; this is required for drawing the texture at the // correct position during 3D mapping. mitk::PlaneClipping::CalculateClippedPlaneBounds(image->GetGeometry(), planeGeometry, textureClippingBounds); textureClippingBounds[0] = static_cast(textureClippingBounds[0] / localStorage->m_mmPerPixel[0] + 0.5); textureClippingBounds[1] = static_cast(textureClippingBounds[1] / localStorage->m_mmPerPixel[0] + 0.5); textureClippingBounds[2] = static_cast(textureClippingBounds[2] / localStorage->m_mmPerPixel[1] + 0.5); textureClippingBounds[3] = static_cast(textureClippingBounds[3] / localStorage->m_mmPerPixel[1] + 0.5); // clipping bounds for cutting the image localStorage->m_LevelWindowFilter->SetClippingBounds(textureClippingBounds); } // get the number of scalar components to distinguish between different image types int numberOfComponents = localStorage->m_ReslicedImage->GetNumberOfScalarComponents(); // get the binary property bool binary = false; bool binaryOutline = false; datanode->GetBoolProperty("binary", binary, renderer); if (binary) // binary image { datanode->GetBoolProperty("outline binary", binaryOutline, renderer); if (binaryOutline) // contour rendering { // get pixel type of vtk image itk::ImageIOBase::IOComponentType componentType = static_cast(image->GetPixelType().GetComponentType()); switch (componentType) { case itk::ImageIOBase::UCHAR: // generate contours/outlines localStorage->m_OutlinePolyData = CreateOutlinePolyData(renderer); break; case itk::ImageIOBase::USHORT: // generate contours/outlines localStorage->m_OutlinePolyData = CreateOutlinePolyData(renderer); break; default: binaryOutline = false; this->ApplyLookuptable(renderer); MITK_WARN << "Type of all binary images should be unsigned char or unsigned short. Outline does not work on other pixel types!"; } if (binaryOutline) // binary outline is still true --> add outline { float binaryOutlineWidth = 1.0; if (datanode->GetFloatProperty("outline width", binaryOutlineWidth, renderer)) { float binaryOutlineShadowWidth = 1.5; datanode->GetFloatProperty("outline shadow width", binaryOutlineShadowWidth, renderer); localStorage->m_ShadowOutlineActor->GetProperty()->SetLineWidth(binaryOutlineWidth * binaryOutlineShadowWidth); localStorage->m_ImageActor->GetProperty()->SetLineWidth(binaryOutlineWidth); } } } else // standard binary image { if (numberOfComponents != 1) { MITK_ERROR << "Rendering Error: Binary Images with more then 1 component are not supported!"; } } } this->ApplyOpacity(renderer); this->ApplyRenderingMode(renderer); // do not use a VTK lookup table (we do that ourselves in m_LevelWindowFilter) localStorage->m_Texture->SetColorModeToDirectScalars(); int displayedComponent = 0; if (datanode->GetIntProperty("Image.Displayed Component", displayedComponent, renderer) && numberOfComponents > 1) { localStorage->m_VectorComponentExtractor->SetComponents(displayedComponent); localStorage->m_VectorComponentExtractor->SetInputData(localStorage->m_ReslicedImage); localStorage->m_LevelWindowFilter->SetInputConnection(localStorage->m_VectorComponentExtractor->GetOutputPort(0)); } else { // connect the input with the levelwindow filter localStorage->m_LevelWindowFilter->SetInputData(localStorage->m_ReslicedImage); } // check for texture interpolation property bool textureInterpolation = false; GetDataNode()->GetBoolProperty("texture interpolation", textureInterpolation, renderer); // set the interpolation modus according to the property localStorage->m_Texture->SetInterpolate(textureInterpolation); // connect the texture with the output of the levelwindow filter localStorage->m_Texture->SetInputConnection(localStorage->m_LevelWindowFilter->GetOutputPort()); this->TransformActor(renderer); if (binary && binaryOutline) // connect the mapper with the polyData which contains the lines { // We need the contour for the binary outline property as actor localStorage->m_Mapper->SetInputData(localStorage->m_OutlinePolyData); localStorage->m_ImageActor->SetTexture(nullptr); // no texture for contours bool binaryOutlineShadow = false; datanode->GetBoolProperty("outline binary shadow", binaryOutlineShadow, renderer); if (binaryOutlineShadow) { localStorage->m_ShadowOutlineActor->SetVisibility(true); } else { localStorage->m_ShadowOutlineActor->SetVisibility(false); } } else { // Connect the mapper with the input texture. This is the standard case. // setup the textured plane this->GeneratePlane(renderer, sliceBounds); // set the plane as input for the mapper localStorage->m_Mapper->SetInputConnection(localStorage->m_Plane->GetOutputPort()); // set the texture for the actor localStorage->m_ImageActor->SetTexture(localStorage->m_Texture); localStorage->m_ShadowOutlineActor->SetVisibility(false); } // We have been modified => save this for next Update() localStorage->m_LastUpdateTime.Modified(); } void mitk::ImageVtkMapper2D::ApplyLevelWindow(mitk::BaseRenderer *renderer) { LocalStorage *localStorage = this->GetLocalStorage(renderer); LevelWindow levelWindow; this->GetDataNode()->GetLevelWindow(levelWindow, renderer, "levelwindow"); localStorage->m_LevelWindowFilter->GetLookupTable()->SetRange(levelWindow.GetLowerWindowBound(), levelWindow.GetUpperWindowBound()); mitk::LevelWindow opacLevelWindow; if (this->GetDataNode()->GetLevelWindow(opacLevelWindow, renderer, "opaclevelwindow")) { // pass the opaque level window to the filter localStorage->m_LevelWindowFilter->SetMinOpacity(opacLevelWindow.GetLowerWindowBound()); localStorage->m_LevelWindowFilter->SetMaxOpacity(opacLevelWindow.GetUpperWindowBound()); } else { // no opaque level window localStorage->m_LevelWindowFilter->SetMinOpacity(0.0); localStorage->m_LevelWindowFilter->SetMaxOpacity(255.0); } } void mitk::ImageVtkMapper2D::ApplyColor(mitk::BaseRenderer *renderer) { LocalStorage *localStorage = this->GetLocalStorage(renderer); float rgb[3] = {1.0f, 1.0f, 1.0f}; // check for color prop and use it for rendering if it exists // binary image hovering & binary image selection bool hover = false; bool selected = false; bool binary = false; GetDataNode()->GetBoolProperty("binaryimage.ishovering", hover, renderer); GetDataNode()->GetBoolProperty("selected", selected, renderer); GetDataNode()->GetBoolProperty("binary", binary, renderer); if (binary && hover && !selected) { mitk::ColorProperty::Pointer colorprop = dynamic_cast(GetDataNode()->GetProperty("binaryimage.hoveringcolor", renderer)); if (colorprop.IsNotNull()) { memcpy(rgb, colorprop->GetColor().GetDataPointer(), 3 * sizeof(float)); } else { GetDataNode()->GetColor(rgb, renderer, "color"); } } if (binary && selected) { mitk::ColorProperty::Pointer colorprop = dynamic_cast(GetDataNode()->GetProperty("binaryimage.selectedcolor", renderer)); if (colorprop.IsNotNull()) { memcpy(rgb, colorprop->GetColor().GetDataPointer(), 3 * sizeof(float)); } else { GetDataNode()->GetColor(rgb, renderer, "color"); } } if (!binary || (!hover && !selected)) { GetDataNode()->GetColor(rgb, renderer, "color"); } double rgbConv[3] = {(double)rgb[0], (double)rgb[1], (double)rgb[2]}; // conversion to double for VTK localStorage->m_ShadowOutlineActor->GetProperty()->SetColor(rgbConv); localStorage->m_ImageActor->GetProperty()->SetColor(rgbConv); float shadowRGB[3] = {1.0f, 1.0f, 1.0f}; mitk::ColorProperty::Pointer colorprop = dynamic_cast(GetDataNode()->GetProperty("outline binary shadow color", renderer)); if (colorprop.IsNotNull()) { memcpy(shadowRGB, colorprop->GetColor().GetDataPointer(), 3 * sizeof(float)); } double shadowRGBConv[3] = {(double)shadowRGB[0], (double)shadowRGB[1], (double)shadowRGB[2]}; // conversion to double for VTK localStorage->m_ShadowOutlineActor->GetProperty()->SetColor(shadowRGBConv); } void mitk::ImageVtkMapper2D::ApplyOpacity(mitk::BaseRenderer *renderer) { LocalStorage *localStorage = this->GetLocalStorage(renderer); float opacity = 1.0f; // check for opacity prop and use it for rendering if it exists GetDataNode()->GetOpacity(opacity, renderer, "opacity"); // set the opacity according to the properties localStorage->m_ImageActor->GetProperty()->SetOpacity(opacity); localStorage->m_ShadowOutlineActor->GetProperty()->SetOpacity(opacity); } void mitk::ImageVtkMapper2D::ApplyRenderingMode(mitk::BaseRenderer *renderer) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); bool binary = false; this->GetDataNode()->GetBoolProperty("binary", binary, renderer); if (binary) // is it a binary image? { // for binary images, we always use our default LuT and map every value to (0,1) // the opacity of 0 will always be 0.0. We never a apply a LuT/TfF nor a level window. localStorage->m_LevelWindowFilter->SetLookupTable(localStorage->m_BinaryLookupTable); } else { // all other image types can make use of the rendering mode int renderingMode = mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR; mitk::RenderingModeProperty::Pointer mode = dynamic_cast(this->GetDataNode()->GetProperty("Image Rendering.Mode", renderer)); if (mode.IsNotNull()) { renderingMode = mode->GetRenderingMode(); } switch (renderingMode) { case mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR: MITK_DEBUG << "'Image Rendering.Mode' = LevelWindow_LookupTable_Color"; this->ApplyLookuptable(renderer); this->ApplyLevelWindow(renderer); break; case mitk::RenderingModeProperty::COLORTRANSFERFUNCTION_LEVELWINDOW_COLOR: MITK_DEBUG << "'Image Rendering.Mode' = LevelWindow_ColorTransferFunction_Color"; this->ApplyColorTransferFunction(renderer); this->ApplyLevelWindow(renderer); break; case mitk::RenderingModeProperty::LOOKUPTABLE_COLOR: MITK_DEBUG << "'Image Rendering.Mode' = LookupTable_Color"; this->ApplyLookuptable(renderer); break; case mitk::RenderingModeProperty::COLORTRANSFERFUNCTION_COLOR: MITK_DEBUG << "'Image Rendering.Mode' = ColorTransferFunction_Color"; this->ApplyColorTransferFunction(renderer); break; default: MITK_ERROR << "No valid 'Image Rendering.Mode' set. Using LOOKUPTABLE_LEVELWINDOW_COLOR instead."; this->ApplyLookuptable(renderer); this->ApplyLevelWindow(renderer); break; } } // we apply color for all images (including binaries). this->ApplyColor(renderer); } void mitk::ImageVtkMapper2D::ApplyLookuptable(mitk::BaseRenderer *renderer) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); vtkLookupTable *usedLookupTable = localStorage->m_ColorLookupTable; // If lookup table or transferfunction use is requested... mitk::LookupTableProperty::Pointer lookupTableProp = dynamic_cast(this->GetDataNode()->GetProperty("LookupTable", renderer)); if (lookupTableProp.IsNotNull()) // is a lookuptable set? { usedLookupTable = lookupTableProp->GetLookupTable()->GetVtkLookupTable(); } else { //"Image Rendering.Mode was set to use a lookup table but there is no property 'LookupTable'. // A default (rainbow) lookup table will be used. // Here have to do nothing. Warning for the user has been removed, due to unwanted console output // in every interation of the rendering. } localStorage->m_LevelWindowFilter->SetLookupTable(usedLookupTable); } void mitk::ImageVtkMapper2D::ApplyColorTransferFunction(mitk::BaseRenderer *renderer) { mitk::TransferFunctionProperty::Pointer transferFunctionProp = dynamic_cast( this->GetDataNode()->GetProperty("Image Rendering.Transfer Function", renderer)); if (transferFunctionProp.IsNull()) { MITK_ERROR << "'Image Rendering.Mode'' was set to use a color transfer function but there is no property 'Image " "Rendering.Transfer Function'. Nothing will be done."; return; } LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); // pass the transfer function to our level window filter localStorage->m_LevelWindowFilter->SetLookupTable(transferFunctionProp->GetValue()->GetColorTransferFunction()); localStorage->m_LevelWindowFilter->SetOpacityPiecewiseFunction( transferFunctionProp->GetValue()->GetScalarOpacityFunction()); } void mitk::ImageVtkMapper2D::SetToInvalidState(mitk::ImageVtkMapper2D::LocalStorage* localStorage) { localStorage->m_PublicActors = localStorage->m_EmptyActors.Get(); // set image to nullptr, to clear the texture in 3D, because // the latest image is used there if the plane is out of the geometry // see bug-13275 localStorage->m_ReslicedImage = nullptr; localStorage->m_Mapper->SetInputData(localStorage->m_EmptyPolyData); } void mitk::ImageVtkMapper2D::Update(mitk::BaseRenderer *renderer) { bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); if (!visible) { return; } auto *data = const_cast(this->GetInput()); if (data == nullptr) { return; } // Calculate time step of the input data for the specified renderer (integer value) this->CalculateTimeStep(renderer); LocalStorage* localStorage = m_LSH.GetLocalStorage(renderer); // Check if time step is valid const TimeGeometry *dataTimeGeometry = data->GetTimeGeometry(); if ((dataTimeGeometry == nullptr) || (dataTimeGeometry->CountTimeSteps() == 0) || (!dataTimeGeometry->IsValidTimeStep(this->GetTimestep()))) { this->SetToInvalidState(localStorage); return; } const DataNode *node = this->GetDataNode(); data->UpdateOutputInformation(); // check if something important has changed and we need to rerender if ((localStorage->m_LastUpdateTime < node->GetMTime()) || (localStorage->m_LastUpdateTime < data->GetPipelineMTime()) || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometryUpdateTime()) || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometry()->GetMTime()) || (localStorage->m_LastUpdateTime < node->GetPropertyList()->GetMTime()) || (localStorage->m_LastUpdateTime < node->GetPropertyList(renderer)->GetMTime()) || (localStorage->m_LastUpdateTime < data->GetPropertyList()->GetMTime())) { this->GenerateDataForRenderer(renderer); } // since we have checked that nothing important has changed, we can set // m_LastUpdateTime to the current time localStorage->m_LastUpdateTime.Modified(); } void mitk::ImageVtkMapper2D::SetDefaultProperties(mitk::DataNode *node, mitk::BaseRenderer *renderer, bool overwrite) { mitk::Image::Pointer image = dynamic_cast(node->GetData()); // Properties common for both images and segmentations node->AddProperty("depthOffset", mitk::FloatProperty::New(0.0), renderer, overwrite); node->AddProperty("outline binary", mitk::BoolProperty::New(false), renderer, overwrite); node->AddProperty("outline width", mitk::FloatProperty::New(1.0), renderer, overwrite); node->AddProperty("outline binary shadow", mitk::BoolProperty::New(false), renderer, overwrite); node->AddProperty("outline binary shadow color", ColorProperty::New(0.0, 0.0, 0.0), renderer, overwrite); node->AddProperty("outline shadow width", mitk::FloatProperty::New(1.5), renderer, overwrite); if (image->IsRotated()) node->AddProperty("reslice interpolation", mitk::VtkResliceInterpolationProperty::New(VTK_RESLICE_CUBIC)); else node->AddProperty("reslice interpolation", mitk::VtkResliceInterpolationProperty::New()); node->AddProperty("texture interpolation", mitk::BoolProperty::New(false)); node->AddProperty("in plane resample extent by geometry", mitk::BoolProperty::New(false)); node->AddProperty("bounding box", mitk::BoolProperty::New(false)); mitk::RenderingModeProperty::Pointer renderingModeProperty = mitk::RenderingModeProperty::New(); node->AddProperty("Image Rendering.Mode", renderingModeProperty); // Set default grayscale look-up table mitk::LookupTable::Pointer mitkLut = mitk::LookupTable::New(); mitkLut->SetType(mitk::LookupTable::GRAYSCALE); mitk::LookupTableProperty::Pointer mitkLutProp = mitk::LookupTableProperty::New(); mitkLutProp->SetLookupTable(mitkLut); node->SetProperty("LookupTable", mitkLutProp, renderer); std::string photometricInterpretation; // DICOM tag telling us how pixel values should be displayed if (node->GetStringProperty("dicom.pixel.PhotometricInterpretation", photometricInterpretation)) { // modality provided by DICOM or other reader if (photometricInterpretation.find("MONOCHROME1") != std::string::npos) // meaning: display MINIMUM pixels as WHITE { // Set inverse grayscale look-up table mitkLut->SetType(mitk::LookupTable::INVERSE_GRAYSCALE); mitkLutProp->SetLookupTable(mitkLut); node->SetProperty("LookupTable", mitkLutProp, renderer); renderingModeProperty->SetValue(mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR); // USE lookuptable } // Otherwise do nothing - the default grayscale look-up table has already been set } bool isBinaryImage(false); if (!node->GetBoolProperty("binary", isBinaryImage) && image->GetPixelType().GetNumberOfComponents() == 1) { // ok, property is not set, use heuristic to determine if this // is a binary image mitk::Image::Pointer centralSliceImage; - ScalarType minValue = 0.0; - ScalarType maxValue = 0.0; - ScalarType min2ndValue = 0.0; - ScalarType max2ndValue = 0.0; mitk::ImageSliceSelector::Pointer sliceSelector = mitk::ImageSliceSelector::New(); sliceSelector->SetInput(image); sliceSelector->SetSliceNr(image->GetDimension(2) / 2); sliceSelector->SetTimeNr(image->GetDimension(3) / 2); sliceSelector->SetChannelNr(image->GetDimension(4) / 2); sliceSelector->Update(); centralSliceImage = sliceSelector->GetOutput(); - if (centralSliceImage.IsNotNull() && centralSliceImage->IsInitialized()) - { - minValue = centralSliceImage->GetStatistics()->GetScalarValueMin(); - maxValue = centralSliceImage->GetStatistics()->GetScalarValueMax(); - min2ndValue = centralSliceImage->GetStatistics()->GetScalarValue2ndMin(); - max2ndValue = centralSliceImage->GetStatistics()->GetScalarValue2ndMax(); - } - if ((maxValue == min2ndValue && minValue == max2ndValue) || minValue == maxValue) - { - // centralSlice is strange, lets look at all data - minValue = image->GetStatistics()->GetScalarValueMin(); - maxValue = image->GetStatistics()->GetScalarValueMaxNoRecompute(); - min2ndValue = image->GetStatistics()->GetScalarValue2ndMinNoRecompute(); - max2ndValue = image->GetStatistics()->GetScalarValue2ndMaxNoRecompute(); - } - isBinaryImage = (maxValue == min2ndValue && minValue == max2ndValue); + + isBinaryImage = IsBinaryImage(centralSliceImage); + + if (isBinaryImage) // Potential binary image. Now take a close look. + isBinaryImage = IsBinaryImage(image); } std::string className = image->GetNameOfClass(); if (className != "TensorImage" && className != "OdfImage" && className != "ShImage") { PixelType pixelType = image->GetPixelType(); size_t numComponents = pixelType.GetNumberOfComponents(); if ((pixelType.GetPixelType() == itk::ImageIOBase::VECTOR && numComponents > 1) || numComponents == 2 || numComponents > 4) { node->AddProperty("Image.Displayed Component", mitk::IntProperty::New(0), renderer, overwrite); } } // some more properties specific for a binary... if (isBinaryImage) { node->AddProperty("opacity", mitk::FloatProperty::New(0.3f), renderer, overwrite); node->AddProperty("color", ColorProperty::New(1.0, 0.0, 0.0), renderer, overwrite); node->AddProperty("binaryimage.selectedcolor", ColorProperty::New(1.0, 0.0, 0.0), renderer, overwrite); node->AddProperty("binaryimage.selectedannotationcolor", ColorProperty::New(1.0, 0.0, 0.0), renderer, overwrite); node->AddProperty("binaryimage.hoveringcolor", ColorProperty::New(1.0, 0.0, 0.0), renderer, overwrite); node->AddProperty("binaryimage.hoveringannotationcolor", ColorProperty::New(1.0, 0.0, 0.0), renderer, overwrite); node->AddProperty("binary", mitk::BoolProperty::New(true), renderer, overwrite); node->AddProperty("layer", mitk::IntProperty::New(10), renderer, overwrite); } else //...or image type object { node->AddProperty("opacity", mitk::FloatProperty::New(1.0f), renderer, overwrite); node->AddProperty("color", ColorProperty::New(1.0, 1.0, 1.0), renderer, overwrite); node->AddProperty("binary", mitk::BoolProperty::New(false), renderer, overwrite); node->AddProperty("layer", mitk::IntProperty::New(0), renderer, overwrite); } if (image.IsNotNull() && image->IsInitialized()) { if ((overwrite) || (node->GetProperty("levelwindow", renderer) == nullptr)) { /* initialize level/window from DICOM tags */ mitk::LevelWindow contrast; std::string sLevel = ""; std::string sWindow = ""; if (GetBackwardsCompatibleDICOMProperty( 0x0028, 0x1050, "dicom.voilut.WindowCenter", image->GetPropertyList(), sLevel) && GetBackwardsCompatibleDICOMProperty( 0x0028, 0x1051, "dicom.voilut.WindowWidth", image->GetPropertyList(), sWindow)) { float level = atof(sLevel.c_str()); float window = atof(sWindow.c_str()); std::string sSmallestPixelValueInSeries; std::string sLargestPixelValueInSeries; if (GetBackwardsCompatibleDICOMProperty(0x0028, 0x0108, "dicom.series.SmallestPixelValueInSeries", image->GetPropertyList(), sSmallestPixelValueInSeries) && GetBackwardsCompatibleDICOMProperty(0x0028, 0x0109, "dicom.series.LargestPixelValueInSeries", image->GetPropertyList(), sLargestPixelValueInSeries)) { float smallestPixelValueInSeries = atof(sSmallestPixelValueInSeries.c_str()); float largestPixelValueInSeries = atof(sLargestPixelValueInSeries.c_str()); contrast.SetRangeMinMax(smallestPixelValueInSeries - 1, largestPixelValueInSeries + 1); // why not a little buffer? // might remedy some l/w widget challenges } else { contrast.SetAuto(static_cast(node->GetData()), false, true); // fallback } contrast.SetLevelWindow(level, window, true); } else { contrast.SetAuto(static_cast(node->GetData()), false, true); // fallback } node->SetProperty("levelwindow", LevelWindowProperty::New(contrast), renderer); } if (((overwrite) || (node->GetProperty("opaclevelwindow", renderer) == nullptr)) && (image->GetPixelType().GetPixelType() == itk::ImageIOBase::RGBA) && (image->GetPixelType().GetComponentType() == itk::ImageIOBase::UCHAR)) { mitk::LevelWindow opaclevwin; opaclevwin.SetRangeMinMax(0, 255); opaclevwin.SetWindowBounds(0, 255); mitk::LevelWindowProperty::Pointer prop = mitk::LevelWindowProperty::New(opaclevwin); node->SetProperty("opaclevelwindow", prop, renderer); } } Superclass::SetDefaultProperties(node, renderer, overwrite); } mitk::ImageVtkMapper2D::LocalStorage *mitk::ImageVtkMapper2D::GetLocalStorage(mitk::BaseRenderer *renderer) { return m_LSH.GetLocalStorage(renderer); } const mitk::ImageVtkMapper2D::LocalStorage* mitk::ImageVtkMapper2D::GetConstLocalStorage(mitk::BaseRenderer* renderer) { return m_LSH.GetLocalStorage(renderer); } template vtkSmartPointer mitk::ImageVtkMapper2D::CreateOutlinePolyData(mitk::BaseRenderer *renderer) { LocalStorage *localStorage = this->GetLocalStorage(renderer); // get the min and max index values of each direction int *extent = localStorage->m_ReslicedImage->GetExtent(); int xMin = extent[0]; int xMax = extent[1]; int yMin = extent[2]; int yMax = extent[3]; int *dims = localStorage->m_ReslicedImage->GetDimensions(); // dimensions of the image int line = dims[0]; // how many pixels per line? int x = xMin; // pixel index x int y = yMin; // pixel index y // get the depth for each contour float depth = CalculateLayerDepth(renderer); vtkSmartPointer points = vtkSmartPointer::New(); // the points to draw vtkSmartPointer lines = vtkSmartPointer::New(); // the lines to connect the points // We take the pointer to the first pixel of the image auto* currentPixel = static_cast(localStorage->m_ReslicedImage->GetScalarPointer()); while (y <= yMax) { // if the current pixel value is set to something if ((currentPixel) && (*currentPixel != 0)) { // check in which direction a line is necessary // a line is added if the neighbor of the current pixel has the value 0 // and if the pixel is located at the edge of the image // if vvvvv not the first line vvvvv if (y > yMin && *(currentPixel - line) == 0) { // x direction - bottom edge of the pixel // add the 2 points vtkIdType p1 = points->InsertNextPoint(x * localStorage->m_mmPerPixel[0], y * localStorage->m_mmPerPixel[1], depth); vtkIdType p2 = points->InsertNextPoint((x + 1) * localStorage->m_mmPerPixel[0], y * localStorage->m_mmPerPixel[1], depth); // add the line between both points lines->InsertNextCell(2); lines->InsertCellPoint(p1); lines->InsertCellPoint(p2); } // if vvvvv not the last line vvvvv if (y < yMax && *(currentPixel + line) == 0) { // x direction - top edge of the pixel vtkIdType p1 = points->InsertNextPoint(x * localStorage->m_mmPerPixel[0], (y + 1) * localStorage->m_mmPerPixel[1], depth); vtkIdType p2 = points->InsertNextPoint( (x + 1) * localStorage->m_mmPerPixel[0], (y + 1) * localStorage->m_mmPerPixel[1], depth); lines->InsertNextCell(2); lines->InsertCellPoint(p1); lines->InsertCellPoint(p2); } // if vvvvv not the first pixel vvvvv if ((x > xMin || y > yMin) && *(currentPixel - 1) == 0) { // y direction - left edge of the pixel vtkIdType p1 = points->InsertNextPoint(x * localStorage->m_mmPerPixel[0], y * localStorage->m_mmPerPixel[1], depth); vtkIdType p2 = points->InsertNextPoint(x * localStorage->m_mmPerPixel[0], (y + 1) * localStorage->m_mmPerPixel[1], depth); lines->InsertNextCell(2); lines->InsertCellPoint(p1); lines->InsertCellPoint(p2); } // if vvvvv not the last pixel vvvvv if ((y < yMax || (x < xMax)) && *(currentPixel + 1) == 0) { // y direction - right edge of the pixel vtkIdType p1 = points->InsertNextPoint((x + 1) * localStorage->m_mmPerPixel[0], y * localStorage->m_mmPerPixel[1], depth); vtkIdType p2 = points->InsertNextPoint( (x + 1) * localStorage->m_mmPerPixel[0], (y + 1) * localStorage->m_mmPerPixel[1], depth); lines->InsertNextCell(2); lines->InsertCellPoint(p1); lines->InsertCellPoint(p2); } /* now consider pixels at the edge of the image */ // if vvvvv left edge of image vvvvv if (x == xMin) { // draw left edge of the pixel vtkIdType p1 = points->InsertNextPoint(x * localStorage->m_mmPerPixel[0], y * localStorage->m_mmPerPixel[1], depth); vtkIdType p2 = points->InsertNextPoint(x * localStorage->m_mmPerPixel[0], (y + 1) * localStorage->m_mmPerPixel[1], depth); lines->InsertNextCell(2); lines->InsertCellPoint(p1); lines->InsertCellPoint(p2); } // if vvvvv right edge of image vvvvv if (x == xMax) { // draw right edge of the pixel vtkIdType p1 = points->InsertNextPoint((x + 1) * localStorage->m_mmPerPixel[0], y * localStorage->m_mmPerPixel[1], depth); vtkIdType p2 = points->InsertNextPoint( (x + 1) * localStorage->m_mmPerPixel[0], (y + 1) * localStorage->m_mmPerPixel[1], depth); lines->InsertNextCell(2); lines->InsertCellPoint(p1); lines->InsertCellPoint(p2); } // if vvvvv bottom edge of image vvvvv if (y == yMin) { // draw bottom edge of the pixel vtkIdType p1 = points->InsertNextPoint(x * localStorage->m_mmPerPixel[0], y * localStorage->m_mmPerPixel[1], depth); vtkIdType p2 = points->InsertNextPoint((x + 1) * localStorage->m_mmPerPixel[0], y * localStorage->m_mmPerPixel[1], depth); lines->InsertNextCell(2); lines->InsertCellPoint(p1); lines->InsertCellPoint(p2); } // if vvvvv top edge of image vvvvv if (y == yMax) { // draw top edge of the pixel vtkIdType p1 = points->InsertNextPoint(x * localStorage->m_mmPerPixel[0], (y + 1) * localStorage->m_mmPerPixel[1], depth); vtkIdType p2 = points->InsertNextPoint( (x + 1) * localStorage->m_mmPerPixel[0], (y + 1) * localStorage->m_mmPerPixel[1], depth); lines->InsertNextCell(2); lines->InsertCellPoint(p1); lines->InsertCellPoint(p2); } } // end if currentpixel is set x++; if (x > xMax) { // reached end of line x = xMin; y++; } // Increase the pointer-position to the next pixel. // This is safe, as the while-loop and the x-reset logic above makes // sure we do not exceed the bounds of the image currentPixel++; } // end of while // Create a polydata to store everything in vtkSmartPointer polyData = vtkSmartPointer::New(); // Add the points to the dataset polyData->SetPoints(points); // Add the lines to the dataset polyData->SetLines(lines); return polyData; } void mitk::ImageVtkMapper2D::TransformActor(mitk::BaseRenderer *renderer) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); // get the transformation matrix of the reslicer in order to render the slice as axial, coronal or saggital vtkSmartPointer trans = vtkSmartPointer::New(); vtkSmartPointer matrix = localStorage->m_Reslicer->GetResliceAxes(); trans->SetMatrix(matrix); // transform the plane/contour (the actual actor) to the corresponding view (axial, coronal or saggital) localStorage->m_ImageActor->SetUserTransform(trans); // transform the origin to center based coordinates, because MITK is center based. localStorage->m_ImageActor->SetPosition(-0.5 * localStorage->m_mmPerPixel[0], -0.5 * localStorage->m_mmPerPixel[1], 0.0); localStorage->m_ShadowOutlineActor->SetUserTransform(trans); localStorage->m_ShadowOutlineActor->SetPosition(-0.5 * localStorage->m_mmPerPixel[0], -0.5 * localStorage->m_mmPerPixel[1], 0.0); } bool mitk::ImageVtkMapper2D::RenderingGeometryIntersectsImage(const PlaneGeometry *renderingGeometry, SlicedGeometry3D *imageGeometry) { // if either one of the two geometries is nullptr we return true // for safety reasons if (renderingGeometry == nullptr || imageGeometry == nullptr) return true; // get the distance for the first cornerpoint ScalarType initialDistance = renderingGeometry->SignedDistance(imageGeometry->GetCornerPoint(0)); for (int i = 1; i < 8; i++) { mitk::Point3D cornerPoint = imageGeometry->GetCornerPoint(i); // get the distance to the other cornerpoints ScalarType distance = renderingGeometry->SignedDistance(cornerPoint); // if it has not the same signing as the distance of the first point if (initialDistance * distance < 0) { // we have an intersection and return true return true; } } // all distances have the same sign, no intersection and we return false return false; } mitk::ImageVtkMapper2D::LocalStorage::~LocalStorage() { } mitk::ImageVtkMapper2D::LocalStorage::LocalStorage() : m_VectorComponentExtractor(vtkSmartPointer::New()) { m_LevelWindowFilter = vtkSmartPointer::New(); // Do as much actions as possible in here to avoid double executions. m_Plane = vtkSmartPointer::New(); m_Texture = vtkSmartPointer::New().GetPointer(); m_DefaultLookupTable = vtkSmartPointer::New(); m_BinaryLookupTable = vtkSmartPointer::New(); m_ColorLookupTable = vtkSmartPointer::New(); m_Mapper = vtkSmartPointer::New(); m_ImageActor = vtkSmartPointer::New(); m_ShadowOutlineActor = vtkSmartPointer::New(); m_Actors = vtkSmartPointer::New(); m_EmptyActors = vtkSmartPointer::New(); m_Reslicer = mitk::ExtractSliceFilter::New(); m_TSFilter = vtkSmartPointer::New(); m_OutlinePolyData = vtkSmartPointer::New(); m_ReslicedImage = vtkSmartPointer::New(); m_EmptyPolyData = vtkSmartPointer::New(); // the following actions are always the same and thus can be performed // in the constructor for each image (i.e. the image-corresponding local storage) m_TSFilter->ReleaseDataFlagOn(); mitk::LookupTable::Pointer mitkLUT = mitk::LookupTable::New(); // built a default lookuptable mitkLUT->SetType(mitk::LookupTable::GRAYSCALE); m_DefaultLookupTable = mitkLUT->GetVtkLookupTable(); mitkLUT->SetType(mitk::LookupTable::LEGACY_BINARY); m_BinaryLookupTable = mitkLUT->GetVtkLookupTable(); mitkLUT->SetType(mitk::LookupTable::LEGACY_RAINBOW_COLOR); m_ColorLookupTable = mitkLUT->GetVtkLookupTable(); // do not repeat the texture (the image) m_Texture->RepeatOff(); // set the mapper for the actor m_ImageActor->SetMapper(m_Mapper); m_ShadowOutlineActor->SetMapper(m_Mapper); m_Actors->AddPart(m_ShadowOutlineActor); m_Actors->AddPart(m_ImageActor); m_PublicActors = m_EmptyActors.Get(); } diff --git a/Modules/Core/src/Rendering/mitkPlaneGeometryDataVtkMapper3D.cpp b/Modules/Core/src/Rendering/mitkPlaneGeometryDataVtkMapper3D.cpp index 4db486904d..c49b3d3cc5 100644 --- a/Modules/Core/src/Rendering/mitkPlaneGeometryDataVtkMapper3D.cpp +++ b/Modules/Core/src/Rendering/mitkPlaneGeometryDataVtkMapper3D.cpp @@ -1,582 +1,584 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkPlaneGeometryDataVtkMapper3D.h" #include "mitkImageVtkMapper2D.h" #include "mitkNodePredicateDataType.h" #include "mitkNodePredicateOr.h" #include "mitkSmartPointerProperty.h" #include "mitkSurface.h" #include "mitkVtkRepresentationProperty.h" #include "mitkWeakPointerProperty.h" #include "vtkMitkLevelWindowFilter.h" #include "vtkNeverTranslucentTexture.h" #include #include #include #include #include #include #include #include #include #include #include #include namespace mitk { PlaneGeometryDataVtkMapper3D::PlaneGeometryDataVtkMapper3D() : m_NormalsActorAdded(false), m_DataStorage(nullptr) { m_EdgeTuber = vtkTubeFilter::New(); m_EdgeMapper = vtkPolyDataMapper::New(); m_SurfaceCreator = PlaneGeometryDataToSurfaceFilter::New(); m_SurfaceCreatorBoundingBox = BoundingBox::New(); m_SurfaceCreatorPointsContainer = BoundingBox::PointsContainer::New(); m_Edges = vtkFeatureEdges::New(); m_Edges->BoundaryEdgesOn(); m_Edges->FeatureEdgesOff(); m_Edges->NonManifoldEdgesOff(); m_Edges->ManifoldEdgesOff(); m_EdgeTransformer = vtkTransformPolyDataFilter::New(); m_NormalsTransformer = vtkTransformPolyDataFilter::New(); m_EdgeActor = vtkActor::New(); m_BackgroundMapper = vtkPolyDataMapper::New(); m_BackgroundActor = vtkActor::New(); m_Prop3DAssembly = vtkAssembly::New(); m_ImageAssembly = vtkAssembly::New(); m_SurfaceCreatorBoundingBox->SetPoints(m_SurfaceCreatorPointsContainer); m_Cleaner = vtkCleanPolyData::New(); m_Cleaner->PieceInvariantOn(); m_Cleaner->ConvertLinesToPointsOn(); m_Cleaner->ConvertPolysToLinesOn(); m_Cleaner->ConvertStripsToPolysOn(); m_Cleaner->PointMergingOn(); // Make sure that the FeatureEdge algorithm is initialized with a "valid" // (though empty) input vtkPolyData *emptyPolyData = vtkPolyData::New(); m_Cleaner->SetInputData(emptyPolyData); emptyPolyData->Delete(); m_Edges->SetInputConnection(m_Cleaner->GetOutputPort()); m_EdgeTransformer->SetInputConnection(m_Edges->GetOutputPort()); m_EdgeTuber->SetInputConnection(m_EdgeTransformer->GetOutputPort()); m_EdgeTuber->SetVaryRadiusToVaryRadiusOff(); m_EdgeTuber->SetNumberOfSides(12); m_EdgeTuber->CappingOn(); m_EdgeMapper->SetInputConnection(m_EdgeTuber->GetOutputPort()); m_EdgeMapper->ScalarVisibilityOff(); m_BackgroundMapper->SetInputData(emptyPolyData); m_BackgroundMapper->Update(); m_EdgeActor->SetMapper(m_EdgeMapper); m_BackgroundActor->GetProperty()->SetAmbient(0.5); m_BackgroundActor->GetProperty()->SetColor(0.0, 0.0, 0.0); m_BackgroundActor->GetProperty()->SetOpacity(0.0); m_BackgroundActor->SetMapper(m_BackgroundMapper); vtkProperty *backfaceProperty = m_BackgroundActor->MakeProperty(); backfaceProperty->SetColor(0.0, 0.0, 0.0); m_BackgroundActor->SetBackfaceProperty(backfaceProperty); backfaceProperty->Delete(); m_FrontHedgeHog = vtkHedgeHog::New(); m_BackHedgeHog = vtkHedgeHog::New(); m_FrontNormalsMapper = vtkPolyDataMapper::New(); m_FrontNormalsMapper->SetInputConnection(m_FrontHedgeHog->GetOutputPort()); m_BackNormalsMapper = vtkPolyDataMapper::New(); m_Prop3DAssembly->AddPart(m_EdgeActor); m_Prop3DAssembly->AddPart(m_ImageAssembly); m_FrontNormalsActor = vtkActor::New(); m_FrontNormalsActor->SetMapper(m_FrontNormalsMapper); m_BackNormalsActor = vtkActor::New(); m_BackNormalsActor->SetMapper(m_BackNormalsMapper); m_ImageMapperDeletedCommand = MemberCommandType::New(); m_ImageMapperDeletedCommand->SetCallbackFunction(this, &PlaneGeometryDataVtkMapper3D::ImageMapperDeletedCallback); } PlaneGeometryDataVtkMapper3D::~PlaneGeometryDataVtkMapper3D() { m_ImageAssembly->Delete(); m_Prop3DAssembly->Delete(); m_EdgeTuber->Delete(); m_EdgeMapper->Delete(); m_EdgeTransformer->Delete(); m_Cleaner->Delete(); m_Edges->Delete(); m_NormalsTransformer->Delete(); m_EdgeActor->Delete(); m_BackgroundMapper->Delete(); m_BackgroundActor->Delete(); m_FrontNormalsMapper->Delete(); m_FrontNormalsActor->Delete(); m_FrontHedgeHog->Delete(); m_BackNormalsMapper->Delete(); m_BackNormalsActor->Delete(); m_BackHedgeHog->Delete(); for (auto it = m_ImageActors.begin(); it != m_ImageActors.end(); ++it) it->second.m_Actor->ReleaseGraphicsResources(nullptr); // Delete entries in m_ImageActors list one by one m_ImageActors.clear(); m_DataStorage = nullptr; } vtkProp *PlaneGeometryDataVtkMapper3D::GetVtkProp(mitk::BaseRenderer * /*renderer*/) { if ((this->GetDataNode() != nullptr) && (m_ImageAssembly != nullptr)) { // Do not transform the entire Prop3D assembly, but only the image part // here. The colored frame is transformed elsewhere (via m_EdgeTransformer), // since only vertices should be transformed there, not the poly data // itself, to avoid distortion for anisotropic datasets. m_ImageAssembly->SetUserTransform(this->GetDataNode()->GetVtkTransform()); } return m_Prop3DAssembly; } void PlaneGeometryDataVtkMapper3D::UpdateVtkTransform(mitk::BaseRenderer * /*renderer*/) { m_ImageAssembly->SetUserTransform(this->GetDataNode()->GetVtkTransform(this->GetTimestep())); } const PlaneGeometryData *PlaneGeometryDataVtkMapper3D::GetInput() { return static_cast(GetDataNode()->GetData()); } void PlaneGeometryDataVtkMapper3D::SetDataStorageForTexture(mitk::DataStorage *storage) { if (storage != nullptr && m_DataStorage != storage) { m_DataStorage = storage; this->Modified(); } } void PlaneGeometryDataVtkMapper3D::ImageMapperDeletedCallback(itk::Object *caller, const itk::EventObject & /*event*/) { auto *imageMapper = dynamic_cast(caller); if ((imageMapper != nullptr)) { if (m_ImageActors.count(imageMapper) > 0) { m_ImageActors[imageMapper].m_Sender = nullptr; // sender is already destroying itself m_ImageActors.erase(imageMapper); } } } void PlaneGeometryDataVtkMapper3D::GenerateDataForRenderer(BaseRenderer *renderer) { // Remove all actors from the assembly, and re-initialize it with the // edge actor m_ImageAssembly->GetParts()->RemoveAllItems(); bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); if (!visible) { // visibility has explicitly to be set in the single actors // due to problems when using cell picking: // even if the assembly is invisible, the renderer contains // references to the assemblies parts. During picking the // visibility of each part is checked, and not only for the // whole assembly. m_ImageAssembly->VisibilityOff(); m_EdgeActor->VisibilityOff(); return; } // visibility has explicitly to be set in the single actors // due to problems when using cell picking: // even if the assembly is invisible, the renderer contains // references to the assemblies parts. During picking the // visibility of each part is checked, and not only for the // whole assembly. m_ImageAssembly->VisibilityOn(); bool drawEdges = true; this->GetDataNode()->GetBoolProperty("draw edges", drawEdges, renderer); m_EdgeActor->SetVisibility(drawEdges); PlaneGeometryData::ConstPointer input = this->GetInput(); if (input.IsNotNull() && (input->GetPlaneGeometry() != nullptr)) { SmartPointerProperty::Pointer surfacecreatorprop; surfacecreatorprop = dynamic_cast(GetDataNode()->GetProperty("surfacegeometry", renderer)); if ((surfacecreatorprop.IsNull()) || (surfacecreatorprop->GetSmartPointer().IsNull()) || ((m_SurfaceCreator = dynamic_cast(surfacecreatorprop->GetSmartPointer().GetPointer())) .IsNull())) { m_SurfaceCreator->PlaceByGeometryOn(); surfacecreatorprop = SmartPointerProperty::New(m_SurfaceCreator); GetDataNode()->SetProperty("surfacegeometry", surfacecreatorprop); } m_SurfaceCreator->SetInput(input); int res; if (GetDataNode()->GetIntProperty("xresolution", res, renderer)) { m_SurfaceCreator->SetXResolution(res); } if (GetDataNode()->GetIntProperty("yresolution", res, renderer)) { m_SurfaceCreator->SetYResolution(res); } double tubeRadius = 1.0; // Radius of tubular edge surrounding plane // Clip the PlaneGeometry with the reference geometry bounds (if available) if (input->GetPlaneGeometry()->HasReferenceGeometry()) { const BaseGeometry *referenceGeometry = input->GetPlaneGeometry()->GetReferenceGeometry(); BoundingBox::PointType boundingBoxMin, boundingBoxMax; boundingBoxMin = referenceGeometry->GetBoundingBox()->GetMinimum(); boundingBoxMax = referenceGeometry->GetBoundingBox()->GetMaximum(); if (referenceGeometry->GetImageGeometry()) { for (unsigned int i = 0; i < 3; ++i) { boundingBoxMin[i] -= 0.5; boundingBoxMax[i] -= 0.5; } } m_SurfaceCreatorPointsContainer->CreateElementAt(0) = boundingBoxMin; m_SurfaceCreatorPointsContainer->CreateElementAt(1) = boundingBoxMax; m_SurfaceCreatorBoundingBox->ComputeBoundingBox(); m_SurfaceCreator->SetBoundingBox(m_SurfaceCreatorBoundingBox); tubeRadius = referenceGeometry->GetDiagonalLength() / 450.0; } // If no reference geometry is available, clip with the current global // bounds else if (!m_DataStorage.IsExpired()) { m_SurfaceCreator->SetBoundingBox(m_DataStorage.Lock()->ComputeVisibleBoundingBox(nullptr, "includeInBoundingBox")); tubeRadius = sqrt(m_SurfaceCreator->GetBoundingBox()->GetDiagonalLength2()) / 450.0; } // Calculate the surface of the PlaneGeometry m_SurfaceCreator->Update(); Surface *surface = m_SurfaceCreator->GetOutput(); // Check if there's something to display, otherwise return if ((surface->GetVtkPolyData() == nullptr) || (surface->GetVtkPolyData()->GetNumberOfCells() == 0)) { m_ImageAssembly->VisibilityOff(); return; } // add a graphical representation of the surface normals if requested DataNode *node = this->GetDataNode(); bool displayNormals = false; bool colorTwoSides = false; bool invertNormals = false; node->GetBoolProperty("draw normals 3D", displayNormals, renderer); node->GetBoolProperty("color two sides", colorTwoSides, renderer); node->GetBoolProperty("invert normals", invertNormals, renderer); // if we want to draw the display normals or render two sides we have to get the colors if (displayNormals || colorTwoSides) { // get colors float frontColor[3] = {0.0, 0.0, 1.0}; node->GetColor(frontColor, renderer, "front color"); float backColor[3] = {1.0, 0.0, 0.0}; node->GetColor(backColor, renderer, "back color"); if (displayNormals) { m_NormalsTransformer->SetInputData(surface->GetVtkPolyData()); m_NormalsTransformer->SetTransform(node->GetVtkTransform(this->GetTimestep())); m_FrontHedgeHog->SetInputConnection(m_NormalsTransformer->GetOutputPort()); m_FrontHedgeHog->SetVectorModeToUseNormal(); m_FrontHedgeHog->SetScaleFactor(invertNormals ? 1.0 : -1.0); m_FrontHedgeHog->Update(); m_FrontNormalsActor->GetProperty()->SetColor(frontColor[0], frontColor[1], frontColor[2]); m_BackHedgeHog->SetInputConnection(m_NormalsTransformer->GetOutputPort()); m_BackHedgeHog->SetVectorModeToUseNormal(); m_BackHedgeHog->SetScaleFactor(invertNormals ? -1.0 : 1.0); m_BackHedgeHog->Update(); m_BackNormalsActor->GetProperty()->SetColor(backColor[0], backColor[1], backColor[2]); // if there is no actor added yet, add one if (!m_NormalsActorAdded) { m_Prop3DAssembly->AddPart(m_FrontNormalsActor); m_Prop3DAssembly->AddPart(m_BackNormalsActor); m_NormalsActorAdded = true; } } // if we don't want to display normals AND there is an actor added remove the actor else if (m_NormalsActorAdded) { m_Prop3DAssembly->RemovePart(m_FrontNormalsActor); m_Prop3DAssembly->RemovePart(m_BackNormalsActor); m_NormalsActorAdded = false; } if (colorTwoSides) { if (!invertNormals) { m_BackgroundActor->GetProperty()->SetColor(backColor[0], backColor[1], backColor[2]); m_BackgroundActor->GetBackfaceProperty()->SetColor(frontColor[0], frontColor[1], frontColor[2]); } else { m_BackgroundActor->GetProperty()->SetColor(frontColor[0], frontColor[1], frontColor[2]); m_BackgroundActor->GetBackfaceProperty()->SetColor(backColor[0], backColor[1], backColor[2]); } } } // Add black background for all images (which may be transparent) m_BackgroundMapper->SetInputData(surface->GetVtkPolyData()); // m_ImageAssembly->AddPart(m_BackgroundActor); LayerSortedActorList layerSortedActors; // Traverse the data tree to find nodes resliced by ImageMapperGL2D // use a predicate to get all data nodes which are "images" or inherit from mitk::Image mitk::TNodePredicateDataType::Pointer predicateAllImages = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer all = m_DataStorage.Lock()->GetSubset(predicateAllImages); // process all found images for (mitk::DataStorage::SetOfObjects::ConstIterator it = all->Begin(); it != all->End(); ++it) { DataNode *node = it->Value(); if (node != nullptr) this->ProcessNode(node, renderer, surface, layerSortedActors); } // Add all image actors to the assembly, sorted according to // layer property LayerSortedActorList::iterator actorIt; for (actorIt = layerSortedActors.begin(); actorIt != layerSortedActors.end(); ++actorIt) { m_ImageAssembly->AddPart(actorIt->second); } // Configurate the tube-shaped frame: size according to the surface // bounds, color as specified in the plane's properties vtkPolyData *surfacePolyData = surface->GetVtkPolyData(); m_Cleaner->SetInputData(surfacePolyData); m_EdgeTransformer->SetTransform(this->GetDataNode()->GetVtkTransform(this->GetTimestep())); // Adjust the radius according to extent m_EdgeTuber->SetRadius(tubeRadius); // Get the plane's color and set the tube properties accordingly ColorProperty::Pointer colorProperty; colorProperty = dynamic_cast(this->GetDataNode()->GetProperty("color")); if (colorProperty.IsNotNull()) { const Color &color = colorProperty->GetColor(); m_EdgeActor->GetProperty()->SetColor(color.GetRed(), color.GetGreen(), color.GetBlue()); } else { m_EdgeActor->GetProperty()->SetColor(1.0, 1.0, 1.0); } m_ImageAssembly->SetUserTransform(this->GetDataNode()->GetVtkTransform(this->GetTimestep())); } VtkRepresentationProperty *representationProperty; this->GetDataNode()->GetProperty(representationProperty, "material.representation", renderer); if (representationProperty != nullptr) m_BackgroundActor->GetProperty()->SetRepresentation(representationProperty->GetVtkRepresentation()); } void PlaneGeometryDataVtkMapper3D::ProcessNode(DataNode *node, BaseRenderer *renderer, Surface *surface, LayerSortedActorList &layerSortedActors) { if (node != nullptr) { // we need to get the information from the 2D mapper to render the texture on the 3D plane auto *imageMapper = dynamic_cast(node->GetMapper(1)); // GetMapper(1) provides the 2D mapper for the data node // if there is a 2D mapper, which is not the standard image mapper... if (!imageMapper && node->GetMapper(1)) { //... check if it is the composite mapper std::string cname(node->GetMapper(1)->GetNameOfClass()); if (!cname.compare("CompositeMapper")) // string.compare returns 0 if the two strings are equal. { // get the standard image mapper. // This is a special case in MITK and does only work for the CompositeMapper. imageMapper = dynamic_cast(node->GetMapper(3)); } } if ((node->IsVisible(renderer)) && imageMapper) { WeakPointerProperty::Pointer rendererProp = dynamic_cast(GetDataNode()->GetPropertyList()->GetProperty("renderer")); if (rendererProp.IsNotNull()) { BaseRenderer::Pointer planeRenderer = dynamic_cast(rendererProp->GetWeakPointer().GetPointer()); // Retrieve and update image to be mapped const ImageVtkMapper2D::LocalStorage *localStorage = imageMapper->GetConstLocalStorage(planeRenderer); if (planeRenderer.IsNotNull()) { // perform update of imagemapper if needed (maybe the respective 2D renderwindow is not rendered/update // before) imageMapper->Update(planeRenderer); // If it has not been initialized already in a previous pass, // generate an actor and a texture object to // render the image associated with the ImageVtkMapper2D. vtkActor *imageActor; vtkDataSetMapper *dataSetMapper = nullptr; vtkTexture *texture; if (m_ImageActors.count(imageMapper) == 0) { dataSetMapper = vtkDataSetMapper::New(); texture = vtkNeverTranslucentTexture::New(); texture->RepeatOff(); imageActor = vtkActor::New(); imageActor->SetMapper(dataSetMapper); imageActor->SetTexture(texture); imageActor->GetProperty()->SetOpacity( 0.999); // HACK! otherwise VTK wouldn't recognize this as translucent // surface (if LUT values map to alpha < 255 // improvement: apply "opacity" property onle HERE and also in 2D image mapper. DO NOT change LUT to // achieve // translucent images (see method ChangeOpacity in image mapper 2D) // Make imageActor the sole owner of the mapper and texture // objects dataSetMapper->UnRegister(nullptr); texture->UnRegister(nullptr); // Store the actor so that it may be accessed in following // passes. m_ImageActors[imageMapper].Initialize(imageActor, imageMapper, m_ImageMapperDeletedCommand); } else { // Else, retrieve the actor and associated objects from the // previous pass. imageActor = m_ImageActors[imageMapper].m_Actor; dataSetMapper = (vtkDataSetMapper *)imageActor->GetMapper(); texture = imageActor->GetTexture(); } // Set poly data new each time its object changes (e.g. when // switching between planar and curved geometries) if ((dataSetMapper != nullptr) && (dataSetMapper->GetInput() != surface->GetVtkPolyData())) { dataSetMapper->SetInputData(surface->GetVtkPolyData()); } dataSetMapper->Update(); // Check if the m_ReslicedImage is nullptr. // This is the case when no image geometry is met by // the reslicer. In that case, the texture has to be // empty (black) and we don't have to do anything. // See fixed bug #13275 if (localStorage->m_ReslicedImage != nullptr) { texture->SetInputConnection(localStorage->m_LevelWindowFilter->GetOutputPort()); // do not use a VTK lookup table (we do that ourselves in m_LevelWindowFilter) texture->SetColorModeToDirectScalars(); + auto* property3d = imageActor->GetProperty(); + property3d->LightingOff(); + // re-use properties from the 2D image mapper - auto property = vtkSmartPointer::New(); - localStorage->m_ImageActor->GetProperty()->DeepCopy(property); - property->LightingOff(); - imageActor->SetProperty(property); + auto* property2d = localStorage->m_ImageActor->GetProperty(); + property3d->SetColor(property2d->GetColor()); + property3d->SetOpacity(property2d->GetOpacity()); // Set texture interpolation on/off bool textureInterpolation = node->IsOn("texture interpolation", renderer); texture->SetInterpolate(textureInterpolation); // Store this actor to be added to the actor assembly, sort // by layer int layer = 1; node->GetIntProperty("layer", layer); layerSortedActors.insert(std::pair(layer, imageActor)); } } } } } } void PlaneGeometryDataVtkMapper3D::ActorInfo::Initialize(vtkActor *actor, itk::Object *sender, itk::Command *command) { m_Actor = actor; m_Sender = sender; // Get informed when ImageMapper object is deleted, so that // the data structures built here can be deleted as well m_ObserverID = sender->AddObserver(itk::DeleteEvent(), command); } PlaneGeometryDataVtkMapper3D::ActorInfo::ActorInfo() : m_Actor(nullptr), m_Sender(nullptr), m_ObserverID(0) {} PlaneGeometryDataVtkMapper3D::ActorInfo::~ActorInfo() { if (m_Sender != nullptr) { m_Sender->RemoveObserver(m_ObserverID); } if (m_Actor != nullptr) { m_Actor->ReleaseGraphicsResources(nullptr); m_Actor->Delete(); } } } // namespace mitk diff --git a/Modules/Core/src/Rendering/mitkSurfaceVtkMapper2D.cpp b/Modules/Core/src/Rendering/mitkSurfaceVtkMapper2D.cpp index 3439ff2a22..70fedcf6c8 100644 --- a/Modules/Core/src/Rendering/mitkSurfaceVtkMapper2D.cpp +++ b/Modules/Core/src/Rendering/mitkSurfaceVtkMapper2D.cpp @@ -1,402 +1,417 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkSurfaceVtkMapper2D.h" // MITK includes #include "mitkVtkPropRenderer.h" #include #include #include #include #include #include #include #include #include // VTK includes #include #include #include #include #include #include #include #include #include #include #include // constructor LocalStorage mitk::SurfaceVtkMapper2D::LocalStorage::LocalStorage() { m_Mapper = vtkSmartPointer::New(); m_Mapper->ScalarVisibilityOff(); m_Actor = vtkSmartPointer::New(); m_PropAssembly = vtkSmartPointer::New(); m_PropAssembly->AddPart(m_Actor); m_CuttingPlane = vtkSmartPointer::New(); m_Cutter = vtkSmartPointer::New(); m_Cutter->SetCutFunction(m_CuttingPlane); m_Mapper->SetInputConnection(m_Cutter->GetOutputPort()); m_NormalGlyph = vtkSmartPointer::New(); m_InverseNormalGlyph = vtkSmartPointer::New(); // Source for the glyph filter m_ArrowSource = vtkSmartPointer::New(); // set small default values for fast rendering m_ArrowSource->SetTipRadius(0.05); m_ArrowSource->SetTipLength(0.20); m_ArrowSource->SetTipResolution(5); m_ArrowSource->SetShaftResolution(5); m_ArrowSource->SetShaftRadius(0.01); m_NormalGlyph->SetSourceConnection(m_ArrowSource->GetOutputPort()); m_NormalGlyph->SetVectorModeToUseNormal(); m_NormalGlyph->OrientOn(); m_InverseNormalGlyph->SetSourceConnection(m_ArrowSource->GetOutputPort()); m_InverseNormalGlyph->SetVectorModeToUseNormal(); m_InverseNormalGlyph->OrientOn(); m_NormalMapper = vtkSmartPointer::New(); m_NormalMapper->SetInputConnection(m_NormalGlyph->GetOutputPort()); m_NormalMapper->ScalarVisibilityOff(); m_InverseNormalMapper = vtkSmartPointer::New(); m_InverseNormalMapper->SetInputConnection(m_NormalGlyph->GetOutputPort()); m_InverseNormalMapper->ScalarVisibilityOff(); m_NormalActor = vtkSmartPointer::New(); m_NormalActor->SetMapper(m_NormalMapper); m_InverseNormalActor = vtkSmartPointer::New(); m_InverseNormalActor->SetMapper(m_InverseNormalMapper); m_ReverseSense = vtkSmartPointer::New(); } // destructor LocalStorage mitk::SurfaceVtkMapper2D::LocalStorage::~LocalStorage() { } const mitk::Surface *mitk::SurfaceVtkMapper2D::GetInput() const { return static_cast(GetDataNode()->GetData()); } // constructor PointSetVtkMapper2D mitk::SurfaceVtkMapper2D::SurfaceVtkMapper2D() { } mitk::SurfaceVtkMapper2D::~SurfaceVtkMapper2D() { } // reset mapper so that nothing is displayed e.g. toggle visiblity of the propassembly void mitk::SurfaceVtkMapper2D::ResetMapper(BaseRenderer *renderer) { LocalStorage *ls = m_LSH.GetLocalStorage(renderer); ls->m_PropAssembly->VisibilityOff(); } vtkProp *mitk::SurfaceVtkMapper2D::GetVtkProp(mitk::BaseRenderer *renderer) { LocalStorage *ls = m_LSH.GetLocalStorage(renderer); return ls->m_PropAssembly; } void mitk::SurfaceVtkMapper2D::Update(mitk::BaseRenderer *renderer) { const mitk::DataNode *node = GetDataNode(); + if (node == nullptr) + { + this->ResetMapper(renderer); return; + } + bool visible = true; node->GetVisibility(visible, renderer, "visible"); + if (!visible) + { + this->ResetMapper(renderer); return; + } auto *surface = static_cast(node->GetData()); + if (surface == nullptr) + { + this->ResetMapper(renderer); return; + } - // Calculate time step of the input data for the specified renderer (integer value) - this->CalculateTimeStep(renderer); + const auto* worldGeometry = renderer->GetWorldTimeGeometry(); + const auto timeBounds = worldGeometry->GetTimeBounds(renderer->GetTimeStep()); - // Check if time step is valid - const mitk::TimeGeometry *dataTimeGeometry = surface->GetTimeGeometry(); - if ((dataTimeGeometry == nullptr) || (dataTimeGeometry->CountTimeSteps() == 0) || - (!dataTimeGeometry->IsValidTimeStep(this->GetTimestep()))) + if (!surface->GetTimeGeometry()->IsValidTimePoint(timeBounds[0])) { + this->ResetMapper(renderer); return; } + // Calculate time step of the input data for the specified renderer (integer value) + this->CalculateTimeStep(renderer); + surface->UpdateOutputInformation(); LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); + localStorage->m_PropAssembly->VisibilityOn(); // check if something important has changed and we need to rerender if ((localStorage->m_LastUpdateTime < node->GetMTime()) // was the node modified? || (localStorage->m_LastUpdateTime < surface->GetPipelineMTime()) // Was the data modified? || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometryUpdateTime()) // was the geometry modified? || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometry()->GetMTime()) || (localStorage->m_LastUpdateTime < node->GetPropertyList()->GetMTime()) // was a property modified? || (localStorage->m_LastUpdateTime < node->GetPropertyList(renderer)->GetMTime())) { this->GenerateDataForRenderer(renderer); } // since we have checked that nothing important has changed, we can set // m_LastUpdateTime to the current time localStorage->m_LastUpdateTime.Modified(); } void mitk::SurfaceVtkMapper2D::GenerateDataForRenderer(mitk::BaseRenderer *renderer) { const DataNode *node = GetDataNode(); auto *surface = static_cast(node->GetData()); const TimeGeometry *dataTimeGeometry = surface->GetTimeGeometry(); LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); ScalarType time = renderer->GetTime(); int timestep = 0; if (time > itk::NumericTraits::NonpositiveMin()) timestep = dataTimeGeometry->TimePointToTimeStep(time); vtkSmartPointer inputPolyData = surface->GetVtkPolyData(timestep); if ((inputPolyData == nullptr) || (inputPolyData->GetNumberOfPoints() < 1)) return; // apply color and opacity read from the PropertyList this->ApplyAllProperties(renderer); const PlaneGeometry *planeGeometry = renderer->GetCurrentWorldPlaneGeometry(); if ((planeGeometry == nullptr) || (!planeGeometry->IsValid()) || (!planeGeometry->HasReferenceGeometry())) { return; } if (localStorage->m_Actor->GetMapper() == nullptr) localStorage->m_Actor->SetMapper(localStorage->m_Mapper); double origin[3]; origin[0] = planeGeometry->GetOrigin()[0]; origin[1] = planeGeometry->GetOrigin()[1]; origin[2] = planeGeometry->GetOrigin()[2]; double normal[3]; normal[0] = planeGeometry->GetNormal()[0]; normal[1] = planeGeometry->GetNormal()[1]; normal[2] = planeGeometry->GetNormal()[2]; localStorage->m_CuttingPlane->SetOrigin(origin); localStorage->m_CuttingPlane->SetNormal(normal); // Transform the data according to its geometry. // See UpdateVtkTransform documentation for details. vtkSmartPointer vtktransform = GetDataNode()->GetVtkTransform(this->GetTimestep()); vtkSmartPointer filter = vtkSmartPointer::New(); filter->SetTransform(vtktransform); filter->SetInputData(inputPolyData); localStorage->m_Cutter->SetInputConnection(filter->GetOutputPort()); localStorage->m_Cutter->Update(); bool generateNormals = false; node->GetBoolProperty("draw normals 2D", generateNormals); if (generateNormals) { localStorage->m_NormalGlyph->SetInputConnection(localStorage->m_Cutter->GetOutputPort()); localStorage->m_NormalGlyph->Update(); localStorage->m_NormalMapper->SetInputConnection(localStorage->m_NormalGlyph->GetOutputPort()); localStorage->m_PropAssembly->AddPart(localStorage->m_NormalActor); } else { localStorage->m_NormalGlyph->SetInputConnection(nullptr); localStorage->m_PropAssembly->RemovePart(localStorage->m_NormalActor); } bool generateInverseNormals = false; node->GetBoolProperty("invert normals", generateInverseNormals); if (generateInverseNormals) { localStorage->m_ReverseSense->SetInputConnection(localStorage->m_Cutter->GetOutputPort()); localStorage->m_ReverseSense->ReverseCellsOff(); localStorage->m_ReverseSense->ReverseNormalsOn(); localStorage->m_InverseNormalGlyph->SetInputConnection(localStorage->m_ReverseSense->GetOutputPort()); localStorage->m_InverseNormalGlyph->Update(); localStorage->m_InverseNormalMapper->SetInputConnection(localStorage->m_InverseNormalGlyph->GetOutputPort()); localStorage->m_PropAssembly->AddPart(localStorage->m_InverseNormalActor); } else { localStorage->m_ReverseSense->SetInputConnection(nullptr); localStorage->m_PropAssembly->RemovePart(localStorage->m_InverseNormalActor); } } void mitk::SurfaceVtkMapper2D::FixupLegacyProperties(PropertyList *properties) { // Before bug 18528, "line width" was an IntProperty, now it is a FloatProperty float lineWidth = 1.0f; if (!properties->GetFloatProperty("line width", lineWidth)) { int legacyLineWidth = lineWidth; if (properties->GetIntProperty("line width", legacyLineWidth)) { properties->ReplaceProperty("line width", FloatProperty::New(static_cast(legacyLineWidth))); } } } void mitk::SurfaceVtkMapper2D::ApplyAllProperties(mitk::BaseRenderer *renderer) { const DataNode *node = GetDataNode(); if (node == nullptr) { return; } FixupLegacyProperties(node->GetPropertyList(renderer)); FixupLegacyProperties(node->GetPropertyList()); float lineWidth = 1.0f; node->GetFloatProperty("line width", lineWidth, renderer); LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); // check for color and opacity properties, use it for rendering if they exists float color[3] = {1.0f, 1.0f, 1.0f}; node->GetColor(color, renderer, "color"); float opacity = 1.0f; node->GetOpacity(opacity, renderer, "opacity"); // Pass properties to VTK localStorage->m_Actor->GetProperty()->SetColor(color[0], color[1], color[2]); localStorage->m_Actor->GetProperty()->SetOpacity(opacity); localStorage->m_NormalActor->GetProperty()->SetOpacity(opacity); localStorage->m_InverseNormalActor->GetProperty()->SetOpacity(opacity); localStorage->m_Actor->GetProperty()->SetLineWidth(lineWidth); // By default, the cutter will also copy/compute normals of the cut // to the output polydata. The normals will influence the // vtkPolyDataMapper lightning. To view a clean cut the lighting has // to be disabled. localStorage->m_Actor->GetProperty()->SetLighting(false); // same block for scalar data rendering as in 3D mapper mitk::TransferFunctionProperty::Pointer transferFuncProp; this->GetDataNode()->GetProperty(transferFuncProp, "Surface.TransferFunction", renderer); if (transferFuncProp.IsNotNull()) { localStorage->m_Mapper->SetLookupTable(transferFuncProp->GetValue()->GetColorTransferFunction()); } mitk::LookupTableProperty::Pointer lookupTableProp; this->GetDataNode()->GetProperty(lookupTableProp, "LookupTable", renderer); if (lookupTableProp.IsNotNull()) { localStorage->m_Mapper->SetLookupTable(lookupTableProp->GetLookupTable()->GetVtkLookupTable()); } mitk::LevelWindow levelWindow; if (this->GetDataNode()->GetLevelWindow(levelWindow, renderer, "levelWindow")) { localStorage->m_Mapper->SetScalarRange(levelWindow.GetLowerWindowBound(), levelWindow.GetUpperWindowBound()); } else if (this->GetDataNode()->GetLevelWindow(levelWindow, renderer)) { localStorage->m_Mapper->SetScalarRange(levelWindow.GetLowerWindowBound(), levelWindow.GetUpperWindowBound()); } bool scalarVisibility = false; this->GetDataNode()->GetBoolProperty("scalar visibility", scalarVisibility); localStorage->m_Mapper->SetScalarVisibility((scalarVisibility ? 1 : 0)); if (scalarVisibility) { mitk::VtkScalarModeProperty *scalarMode; if (this->GetDataNode()->GetProperty(scalarMode, "scalar mode", renderer)) localStorage->m_Mapper->SetScalarMode(scalarMode->GetVtkScalarMode()); else localStorage->m_Mapper->SetScalarModeToDefault(); bool colorMode = false; this->GetDataNode()->GetBoolProperty("color mode", colorMode); localStorage->m_Mapper->SetColorMode((colorMode ? 1 : 0)); double scalarsMin = 0; this->GetDataNode()->GetDoubleProperty("ScalarsRangeMinimum", scalarsMin, renderer); double scalarsMax = 1.0; this->GetDataNode()->GetDoubleProperty("ScalarsRangeMaximum", scalarsMax, renderer); localStorage->m_Mapper->SetScalarRange(scalarsMin, scalarsMax); } // color for inverse normals float inverseNormalsColor[3] = {1.0f, 0.0f, 0.0f}; node->GetColor(inverseNormalsColor, renderer, "back color"); localStorage->m_InverseNormalActor->GetProperty()->SetColor( inverseNormalsColor[0], inverseNormalsColor[1], inverseNormalsColor[2]); // color for normals float normalsColor[3] = {0.0f, 1.0f, 0.0f}; node->GetColor(normalsColor, renderer, "front color"); localStorage->m_NormalActor->GetProperty()->SetColor(normalsColor[0], normalsColor[1], normalsColor[2]); // normals scaling float normalScaleFactor = 10.0f; node->GetFloatProperty("front normal lenth (px)", normalScaleFactor, renderer); localStorage->m_NormalGlyph->SetScaleFactor(normalScaleFactor); // inverse normals scaling float inverseNormalScaleFactor = 10.0f; node->GetFloatProperty("back normal lenth (px)", inverseNormalScaleFactor, renderer); localStorage->m_InverseNormalGlyph->SetScaleFactor(inverseNormalScaleFactor); } void mitk::SurfaceVtkMapper2D::SetDefaultProperties(mitk::DataNode *node, mitk::BaseRenderer *renderer, bool overwrite) { mitk::CoreServicePointer aliases(mitk::CoreServices::GetPropertyAliases()); node->AddProperty("line width", FloatProperty::New(2.0f), renderer, overwrite); aliases->AddAlias("line width", "Surface.2D.Line Width", "Surface"); node->AddProperty("scalar mode", VtkScalarModeProperty::New(), renderer, overwrite); node->AddProperty("draw normals 2D", BoolProperty::New(false), renderer, overwrite); aliases->AddAlias("draw normals 2D", "Surface.2D.Normals.Draw Normals", "Surface"); node->AddProperty("invert normals", BoolProperty::New(false), renderer, overwrite); aliases->AddAlias("invert normals", "Surface.2D.Normals.Draw Inverse Normals", "Surface"); node->AddProperty("front color", ColorProperty::New(0.0, 1.0, 0.0), renderer, overwrite); aliases->AddAlias("front color", "Surface.2D.Normals.Normals Color", "Surface"); node->AddProperty("back color", ColorProperty::New(1.0, 0.0, 0.0), renderer, overwrite); aliases->AddAlias("back color", "Surface.2D.Normals.Inverse Normals Color", "Surface"); node->AddProperty("front normal lenth (px)", FloatProperty::New(10.0), renderer, overwrite); aliases->AddAlias("front normal lenth (px)", "Surface.2D.Normals.Normals Scale Factor", "Surface"); node->AddProperty("back normal lenth (px)", FloatProperty::New(10.0), renderer, overwrite); aliases->AddAlias("back normal lenth (px)", "Surface.2D.Normals.Inverse Normals Scale Factor", "Surface"); node->AddProperty("layer", IntProperty::New(100), renderer, overwrite); Superclass::SetDefaultProperties(node, renderer, overwrite); } diff --git a/Modules/Core/src/Rendering/mitkSurfaceVtkMapper3D.cpp b/Modules/Core/src/Rendering/mitkSurfaceVtkMapper3D.cpp index 33016c95e0..43411c4c7a 100644 --- a/Modules/Core/src/Rendering/mitkSurfaceVtkMapper3D.cpp +++ b/Modules/Core/src/Rendering/mitkSurfaceVtkMapper3D.cpp @@ -1,520 +1,530 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkSurfaceVtkMapper3D.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // VTK #include #include #include #include #include #include #include #include #include const mitk::Surface *mitk::SurfaceVtkMapper3D::GetInput() { return static_cast(GetDataNode()->GetData()); } mitk::SurfaceVtkMapper3D::SurfaceVtkMapper3D() { m_GenerateNormals = false; } mitk::SurfaceVtkMapper3D::~SurfaceVtkMapper3D() { } void mitk::SurfaceVtkMapper3D::GenerateDataForRenderer(mitk::BaseRenderer *renderer) { LocalStorage *ls = m_LSH.GetLocalStorage(renderer); bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); if (!visible) { ls->m_Actor->VisibilityOff(); return; } // // set the input-object at time t for the mapper // mitk::Surface::ConstPointer input = this->GetInput(); + + const auto* worldGeometry = renderer->GetWorldTimeGeometry(); + const auto timeBounds = worldGeometry->GetTimeBounds(renderer->GetTimeStep()); + + if (!input->GetTimeGeometry()->IsValidTimePoint(timeBounds[0])) + { + ls->m_Actor->VisibilityOff(); + return; + } + vtkSmartPointer polydata = input->GetVtkPolyData(this->GetTimestep()); if (polydata == nullptr) { ls->m_Actor->VisibilityOff(); return; } if (m_GenerateNormals) { ls->m_VtkPolyDataNormals->SetInputData(polydata); ls->m_VtkPolyDataMapper->SetInputConnection(ls->m_VtkPolyDataNormals->GetOutputPort()); } else { bool depthsorting = false; GetDataNode()->GetBoolProperty("Depth Sorting", depthsorting); if (depthsorting) { ls->m_DepthSort->SetInputData(polydata); ls->m_DepthSort->SetCamera(renderer->GetVtkRenderer()->GetActiveCamera()); ls->m_DepthSort->SetDirectionToBackToFront(); ls->m_DepthSort->Update(); ls->m_VtkPolyDataMapper->SetInputConnection(ls->m_DepthSort->GetOutputPort()); } else { ls->m_VtkPolyDataMapper->SetInputData(polydata); } } // // apply properties read from the PropertyList // ApplyAllProperties(renderer, ls->m_Actor); if (visible) ls->m_Actor->VisibilityOn(); } void mitk::SurfaceVtkMapper3D::ResetMapper(BaseRenderer *renderer) { LocalStorage *ls = m_LSH.GetLocalStorage(renderer); ls->m_Actor->VisibilityOff(); } void mitk::SurfaceVtkMapper3D::ApplyMitkPropertiesToVtkProperty(mitk::DataNode *node, vtkProperty *property, mitk::BaseRenderer *renderer) { // Backface culling { mitk::BoolProperty::Pointer p; node->GetProperty(p, "Backface Culling", renderer); bool useCulling = false; if (p.IsNotNull()) useCulling = p->GetValue(); property->SetBackfaceCulling(useCulling); } // Colors { double ambient[3] = {0.5, 0.5, 0.0}; double diffuse[3] = {0.5, 0.5, 0.0}; double specular[3] = {1.0, 1.0, 1.0}; float coeff_ambient = 0.5f; float coeff_diffuse = 0.5f; float coeff_specular = 0.5f; float power_specular = 10.0f; // Color { mitk::ColorProperty::Pointer p; node->GetProperty(p, "color", renderer); if (p.IsNotNull()) { mitk::Color c = p->GetColor(); ambient[0] = c.GetRed(); ambient[1] = c.GetGreen(); ambient[2] = c.GetBlue(); diffuse[0] = c.GetRed(); diffuse[1] = c.GetGreen(); diffuse[2] = c.GetBlue(); // Setting specular color to the same, make physically no real sense, however vtk rendering slows down, if these // colors are different. specular[0] = c.GetRed(); specular[1] = c.GetGreen(); specular[2] = c.GetBlue(); } } // Ambient { mitk::ColorProperty::Pointer p; node->GetProperty(p, "material.ambientColor", renderer); if (p.IsNotNull()) { mitk::Color c = p->GetColor(); ambient[0] = c.GetRed(); ambient[1] = c.GetGreen(); ambient[2] = c.GetBlue(); } } // Diffuse { mitk::ColorProperty::Pointer p; node->GetProperty(p, "material.diffuseColor", renderer); if (p.IsNotNull()) { mitk::Color c = p->GetColor(); diffuse[0] = c.GetRed(); diffuse[1] = c.GetGreen(); diffuse[2] = c.GetBlue(); } } // Specular { mitk::ColorProperty::Pointer p; node->GetProperty(p, "material.specularColor", renderer); if (p.IsNotNull()) { mitk::Color c = p->GetColor(); specular[0] = c.GetRed(); specular[1] = c.GetGreen(); specular[2] = c.GetBlue(); } } // Ambient coeff { node->GetFloatProperty("material.ambientCoefficient", coeff_ambient, renderer); } // Diffuse coeff { node->GetFloatProperty("material.diffuseCoefficient", coeff_diffuse, renderer); } // Specular coeff { node->GetFloatProperty("material.specularCoefficient", coeff_specular, renderer); } // Specular power { node->GetFloatProperty("material.specularPower", power_specular, renderer); } property->SetAmbient(coeff_ambient); property->SetDiffuse(coeff_diffuse); property->SetSpecular(coeff_specular); property->SetSpecularPower(power_specular); property->SetAmbientColor(ambient); property->SetDiffuseColor(diffuse); property->SetSpecularColor(specular); } // Render mode { // Opacity { float opacity = 1.0f; if (node->GetOpacity(opacity, renderer)) property->SetOpacity(opacity); } // Wireframe line width { float lineWidth = 1; node->GetFloatProperty("material.wireframeLineWidth", lineWidth, renderer); property->SetLineWidth(lineWidth); } // Point size { float pointSize = 1.0f; node->GetFloatProperty("material.pointSize", pointSize, renderer); property->SetPointSize(pointSize); } // Representation { mitk::VtkRepresentationProperty::Pointer p; node->GetProperty(p, "material.representation", renderer); if (p.IsNotNull()) property->SetRepresentation(p->GetVtkRepresentation()); } // Interpolation { mitk::VtkInterpolationProperty::Pointer p; node->GetProperty(p, "material.interpolation", renderer); if (p.IsNotNull()) property->SetInterpolation(p->GetVtkInterpolation()); } } } void mitk::SurfaceVtkMapper3D::ApplyAllProperties(mitk::BaseRenderer *renderer, vtkActor * /*actor*/) { LocalStorage *ls = m_LSH.GetLocalStorage(renderer); Superclass::ApplyColorAndOpacityProperties(renderer, ls->m_Actor); // VTK Properties ApplyMitkPropertiesToVtkProperty(this->GetDataNode(), ls->m_Actor->GetProperty(), renderer); mitk::TransferFunctionProperty::Pointer transferFuncProp; this->GetDataNode()->GetProperty(transferFuncProp, "Surface.TransferFunction", renderer); if (transferFuncProp.IsNotNull()) { ls->m_VtkPolyDataMapper->SetLookupTable(transferFuncProp->GetValue()->GetColorTransferFunction()); } mitk::LookupTableProperty::Pointer lookupTableProp; this->GetDataNode()->GetProperty(lookupTableProp, "LookupTable", renderer); if (lookupTableProp.IsNotNull()) { ls->m_VtkPolyDataMapper->SetLookupTable(lookupTableProp->GetLookupTable()->GetVtkLookupTable()); } mitk::LevelWindow levelWindow; if (this->GetDataNode()->GetLevelWindow(levelWindow, renderer, "levelWindow")) { ls->m_VtkPolyDataMapper->SetScalarRange(levelWindow.GetLowerWindowBound(), levelWindow.GetUpperWindowBound()); } else if (this->GetDataNode()->GetLevelWindow(levelWindow, renderer)) { ls->m_VtkPolyDataMapper->SetScalarRange(levelWindow.GetLowerWindowBound(), levelWindow.GetUpperWindowBound()); } bool scalarVisibility = false; this->GetDataNode()->GetBoolProperty("scalar visibility", scalarVisibility); ls->m_VtkPolyDataMapper->SetScalarVisibility((scalarVisibility ? 1 : 0)); if (scalarVisibility) { mitk::VtkScalarModeProperty *scalarMode; if (this->GetDataNode()->GetProperty(scalarMode, "scalar mode", renderer)) ls->m_VtkPolyDataMapper->SetScalarMode(scalarMode->GetVtkScalarMode()); else ls->m_VtkPolyDataMapper->SetScalarModeToDefault(); bool colorMode = false; this->GetDataNode()->GetBoolProperty("color mode", colorMode); ls->m_VtkPolyDataMapper->SetColorMode((colorMode ? 1 : 0)); double scalarsMin = 0; this->GetDataNode()->GetDoubleProperty("ScalarsRangeMinimum", scalarsMin, renderer); double scalarsMax = 1.0; this->GetDataNode()->GetDoubleProperty("ScalarsRangeMaximum", scalarsMax, renderer); ls->m_VtkPolyDataMapper->SetScalarRange(scalarsMin, scalarsMax); } mitk::SmartPointerProperty::Pointer imagetextureProp = dynamic_cast(GetDataNode()->GetProperty("Surface.Texture", renderer)); if (imagetextureProp.IsNotNull()) { mitk::Image *miktTexture = dynamic_cast(imagetextureProp->GetSmartPointer().GetPointer()); vtkSmartPointer vtkTxture = vtkSmartPointer::New(); // Either select the first slice of a volume if (miktTexture->GetDimension(2) > 1) { MITK_WARN << "3D Textures are not supported by VTK and MITK. The first slice of the volume will be used instead!"; mitk::ImageSliceSelector::Pointer sliceselector = mitk::ImageSliceSelector::New(); sliceselector->SetSliceNr(0); sliceselector->SetChannelNr(0); sliceselector->SetTimeNr(0); sliceselector->SetInput(miktTexture); sliceselector->Update(); vtkTxture->SetInputData(sliceselector->GetOutput()->GetVtkImageData()); } else // or just use the 2D image { vtkTxture->SetInputData(miktTexture->GetVtkImageData()); } // pass the texture to the actor ls->m_Actor->SetTexture(vtkTxture); if (ls->m_VtkPolyDataMapper->GetInput()->GetPointData()->GetTCoords() == nullptr) { MITK_ERROR << "Surface.Texture property was set, but there are no texture coordinates. Please provide texture " "coordinates for the vtkPolyData via vtkPolyData->GetPointData()->SetTCoords()."; } // if no texture is set, this will also remove a previously used texture // and reset the actor to it's default behaviour } else { ls->m_Actor->SetTexture(nullptr); } // deprecated settings bool deprecatedUseCellData = false; this->GetDataNode()->GetBoolProperty("deprecated useCellDataForColouring", deprecatedUseCellData); bool deprecatedUsePointData = false; this->GetDataNode()->GetBoolProperty("deprecated usePointDataForColouring", deprecatedUsePointData); if (deprecatedUseCellData) { ls->m_VtkPolyDataMapper->SetColorModeToDefault(); ls->m_VtkPolyDataMapper->SetScalarRange(0, 255); ls->m_VtkPolyDataMapper->ScalarVisibilityOn(); ls->m_VtkPolyDataMapper->SetScalarModeToUseCellData(); ls->m_Actor->GetProperty()->SetSpecular(1); ls->m_Actor->GetProperty()->SetSpecularPower(50); ls->m_Actor->GetProperty()->SetInterpolationToPhong(); } else if (deprecatedUsePointData) { float scalarsMin = 0; if (dynamic_cast(this->GetDataNode()->GetProperty("ScalarsRangeMinimum")) != nullptr) scalarsMin = dynamic_cast(this->GetDataNode()->GetProperty("ScalarsRangeMinimum"))->GetValue(); float scalarsMax = 0.1; if (dynamic_cast(this->GetDataNode()->GetProperty("ScalarsRangeMaximum")) != nullptr) scalarsMax = dynamic_cast(this->GetDataNode()->GetProperty("ScalarsRangeMaximum"))->GetValue(); ls->m_VtkPolyDataMapper->SetScalarRange(scalarsMin, scalarsMax); ls->m_VtkPolyDataMapper->SetColorModeToMapScalars(); ls->m_VtkPolyDataMapper->ScalarVisibilityOn(); ls->m_Actor->GetProperty()->SetSpecular(1); ls->m_Actor->GetProperty()->SetSpecularPower(50); ls->m_Actor->GetProperty()->SetInterpolationToPhong(); } int deprecatedScalarMode = VTK_COLOR_MODE_DEFAULT; if (this->GetDataNode()->GetIntProperty("deprecated scalar mode", deprecatedScalarMode, renderer)) { ls->m_VtkPolyDataMapper->SetScalarMode(deprecatedScalarMode); ls->m_VtkPolyDataMapper->ScalarVisibilityOn(); ls->m_Actor->GetProperty()->SetSpecular(1); ls->m_Actor->GetProperty()->SetSpecularPower(50); } // Check whether one or more ClippingProperty objects have been defined for // this node. Check both renderer specific and global property lists, since // properties in both should be considered. const PropertyList::PropertyMap *rendererProperties = this->GetDataNode()->GetPropertyList(renderer)->GetMap(); const PropertyList::PropertyMap *globalProperties = this->GetDataNode()->GetPropertyList(nullptr)->GetMap(); // Add clipping planes (if any) ls->m_ClippingPlaneCollection->RemoveAllItems(); PropertyList::PropertyMap::const_iterator it; for (it = rendererProperties->begin(); it != rendererProperties->end(); ++it) { this->CheckForClippingProperty(renderer, (*it).second.GetPointer()); } for (it = globalProperties->begin(); it != globalProperties->end(); ++it) { this->CheckForClippingProperty(renderer, (*it).second.GetPointer()); } if (ls->m_ClippingPlaneCollection->GetNumberOfItems() > 0) { ls->m_VtkPolyDataMapper->SetClippingPlanes(ls->m_ClippingPlaneCollection); } else { ls->m_VtkPolyDataMapper->RemoveAllClippingPlanes(); } } vtkProp *mitk::SurfaceVtkMapper3D::GetVtkProp(mitk::BaseRenderer *renderer) { LocalStorage *ls = m_LSH.GetLocalStorage(renderer); return ls->m_Actor; } void mitk::SurfaceVtkMapper3D::CheckForClippingProperty(mitk::BaseRenderer *renderer, mitk::BaseProperty *property) { LocalStorage *ls = m_LSH.GetLocalStorage(renderer); auto *clippingProperty = dynamic_cast(property); if ((clippingProperty != nullptr) && (clippingProperty->GetClippingEnabled())) { const Point3D &origin = clippingProperty->GetOrigin(); const Vector3D &normal = clippingProperty->GetNormal(); vtkSmartPointer clippingPlane = vtkSmartPointer::New(); clippingPlane->SetOrigin(origin[0], origin[1], origin[2]); clippingPlane->SetNormal(normal[0], normal[1], normal[2]); ls->m_ClippingPlaneCollection->AddItem(clippingPlane); } } void mitk::SurfaceVtkMapper3D::SetDefaultPropertiesForVtkProperty(mitk::DataNode *node, mitk::BaseRenderer *renderer, bool overwrite) { // Shading { node->AddProperty("material.wireframeLineWidth", mitk::FloatProperty::New(1.0f), renderer, overwrite); node->AddProperty("material.pointSize", mitk::FloatProperty::New(1.0f), renderer, overwrite); node->AddProperty("material.ambientCoefficient", mitk::FloatProperty::New(0.05f), renderer, overwrite); node->AddProperty("material.diffuseCoefficient", mitk::FloatProperty::New(0.9f), renderer, overwrite); node->AddProperty("material.specularCoefficient", mitk::FloatProperty::New(1.0f), renderer, overwrite); node->AddProperty("material.specularPower", mitk::FloatProperty::New(16.0f), renderer, overwrite); node->AddProperty("material.representation", mitk::VtkRepresentationProperty::New(), renderer, overwrite); node->AddProperty("material.interpolation", mitk::VtkInterpolationProperty::New(), renderer, overwrite); } } void mitk::SurfaceVtkMapper3D::SetDefaultProperties(mitk::DataNode *node, mitk::BaseRenderer *renderer, bool overwrite) { node->AddProperty("color", mitk::ColorProperty::New(1.0f, 1.0f, 1.0f), renderer, overwrite); node->AddProperty("opacity", mitk::FloatProperty::New(1.0), renderer, overwrite); mitk::SurfaceVtkMapper3D::SetDefaultPropertiesForVtkProperty(node, renderer, overwrite); // Shading node->AddProperty("scalar visibility", mitk::BoolProperty::New(false), renderer, overwrite); node->AddProperty("color mode", mitk::BoolProperty::New(false), renderer, overwrite); node->AddProperty("scalar mode", mitk::VtkScalarModeProperty::New(), renderer, overwrite); mitk::Surface::Pointer surface = dynamic_cast(node->GetData()); if (surface.IsNotNull()) { if ((surface->GetVtkPolyData() != nullptr) && (surface->GetVtkPolyData()->GetPointData() != nullptr) && (surface->GetVtkPolyData()->GetPointData()->GetScalars() != nullptr)) { node->AddProperty("scalar visibility", mitk::BoolProperty::New(true), renderer, overwrite); node->AddProperty("color mode", mitk::BoolProperty::New(true), renderer, overwrite); } } // Backface culling node->AddProperty("Backface Culling", mitk::BoolProperty::New(false), renderer, overwrite); node->AddProperty("Depth Sorting", mitk::BoolProperty::New(false), renderer, overwrite); mitk::CoreServicePointer propDescService(mitk::CoreServices::GetPropertyDescriptions()); propDescService->AddDescription( "Depth Sorting", "Enables correct rendering for transparent objects by ordering polygons according to the distance " "to the camera. It is not recommended to enable this property for large surfaces (rendering might " "be slow)."); Superclass::SetDefaultProperties(node, renderer, overwrite); } diff --git a/Modules/Core/test/mitkArbitraryTimeGeometryTest.cpp b/Modules/Core/test/mitkArbitraryTimeGeometryTest.cpp index b05b96b04c..4935c25e5d 100644 --- a/Modules/Core/test/mitkArbitraryTimeGeometryTest.cpp +++ b/Modules/Core/test/mitkArbitraryTimeGeometryTest.cpp @@ -1,504 +1,532 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkArbitraryTimeGeometry.h" #include "mitkGeometry3D.h" #include "mitkTestFixture.h" #include "mitkTestingMacros.h" #include class mitkArbitraryTimeGeometryTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkArbitraryTimeGeometryTestSuite); // Test the append method MITK_TEST(CountTimeSteps); MITK_TEST(GetMinimumTimePoint); MITK_TEST(GetMaximumTimePoint); MITK_TEST(GetTimeBounds); MITK_TEST(IsValidTimePoint); MITK_TEST(TimeStepToTimePoint); MITK_TEST(TimePointToTimeStep); MITK_TEST(GetGeometryCloneForTimeStep); MITK_TEST(GetGeometryForTimeStep); MITK_TEST(GetGeometryForTimePoint); MITK_TEST(IsValid); MITK_TEST(Expand); MITK_TEST(ReplaceTimeStepGeometries); MITK_TEST(ClearAllGeometries); MITK_TEST(AppendNewTimeStep); MITK_TEST(HasCollapsedFinalTimeStep); CPPUNIT_TEST_SUITE_END(); private: mitk::Geometry3D::Pointer m_Geometry1; mitk::Geometry3D::Pointer m_Geometry2; mitk::Geometry3D::Pointer m_Geometry3; mitk::Geometry3D::Pointer m_Geometry3_5; mitk::Geometry3D::Pointer m_Geometry4; mitk::Geometry3D::Pointer m_Geometry5; mitk::Geometry3D::Pointer m_InvalidGeometry; mitk::Geometry3D::Pointer m_NewGeometry; mitk::TimePointType m_Geometry1MinTP; mitk::TimePointType m_Geometry2MinTP; mitk::TimePointType m_Geometry3MinTP; mitk::TimePointType m_Geometry3_5MinTP; mitk::TimePointType m_Geometry4MinTP; mitk::TimePointType m_Geometry5MinTP; mitk::TimePointType m_NewGeometryMinTP; mitk::TimePointType m_Geometry1MaxTP; mitk::TimePointType m_Geometry2MaxTP; mitk::TimePointType m_Geometry3MaxTP; mitk::TimePointType m_Geometry3_5MaxTP; mitk::TimePointType m_Geometry4MaxTP; mitk::TimePointType m_Geometry5MaxTP; mitk::TimePointType m_NewGeometryMaxTP; mitk::ArbitraryTimeGeometry::Pointer m_emptyTimeGeometry; mitk::ArbitraryTimeGeometry::Pointer m_initTimeGeometry; mitk::ArbitraryTimeGeometry::Pointer m_12345TimeGeometry; mitk::ArbitraryTimeGeometry::Pointer m_123TimeGeometry; mitk::ArbitraryTimeGeometry::Pointer m_123TimeGeometryWithCollapsedEnd; mitk::ArbitraryTimeGeometry::Pointer m_123TimeGeometryWithCollapsedInterim; public: void setUp() override { mitk::TimeBounds bounds; m_Geometry1 = mitk::Geometry3D::New(); m_Geometry2 = mitk::Geometry3D::New(); m_Geometry3 = mitk::Geometry3D::New(); m_Geometry3_5 = mitk::Geometry3D::New(); m_Geometry4 = mitk::Geometry3D::New(); m_Geometry5 = mitk::Geometry3D::New(); m_Geometry1MinTP = 1; m_Geometry2MinTP = 2; m_Geometry3MinTP = 3; m_Geometry3_5MinTP = 3.5; m_Geometry4MinTP = 4; m_Geometry5MinTP = 5; m_Geometry1MaxTP = 1.9; m_Geometry2MaxTP = 2.9; m_Geometry3MaxTP = 3.9; m_Geometry3_5MaxTP = 3.9; m_Geometry4MaxTP = 4.9; m_Geometry5MaxTP = 5.9; m_NewGeometry = mitk::Geometry3D::New(); m_NewGeometryMinTP = 20; m_NewGeometryMaxTP = 21.9; mitk::Point3D origin(42); m_NewGeometry->SetOrigin(origin); m_emptyTimeGeometry = mitk::ArbitraryTimeGeometry::New(); m_emptyTimeGeometry->ClearAllGeometries(); m_initTimeGeometry = mitk::ArbitraryTimeGeometry::New(); m_initTimeGeometry->Initialize(); m_12345TimeGeometry = mitk::ArbitraryTimeGeometry::New(); m_12345TimeGeometry->ClearAllGeometries(); m_12345TimeGeometry->AppendNewTimeStep(m_Geometry1, m_Geometry1MinTP, m_Geometry1MaxTP); m_12345TimeGeometry->AppendNewTimeStep(m_Geometry2, m_Geometry2MinTP, m_Geometry2MaxTP); m_12345TimeGeometry->AppendNewTimeStep(m_Geometry3, m_Geometry3MinTP, m_Geometry3MaxTP); m_12345TimeGeometry->AppendNewTimeStep(m_Geometry4, m_Geometry4MinTP, m_Geometry4MaxTP); m_12345TimeGeometry->AppendNewTimeStep(m_Geometry5, m_Geometry5MinTP, m_Geometry5MaxTP); m_123TimeGeometry = mitk::ArbitraryTimeGeometry::New(); m_123TimeGeometry->ClearAllGeometries(); m_123TimeGeometry->AppendNewTimeStep(m_Geometry1, m_Geometry1MinTP, m_Geometry1MaxTP); m_123TimeGeometry->AppendNewTimeStep(m_Geometry2, m_Geometry2MinTP, m_Geometry2MaxTP); m_123TimeGeometry->AppendNewTimeStep(m_Geometry3, m_Geometry3MinTP, m_Geometry3MaxTP); m_123TimeGeometryWithCollapsedEnd = mitk::ArbitraryTimeGeometry::New(); m_123TimeGeometryWithCollapsedEnd->ClearAllGeometries(); m_123TimeGeometryWithCollapsedEnd->AppendNewTimeStep(m_Geometry1, m_Geometry1MinTP, m_Geometry1MaxTP); m_123TimeGeometryWithCollapsedEnd->AppendNewTimeStep(m_Geometry2, m_Geometry2MinTP, m_Geometry2MaxTP); m_123TimeGeometryWithCollapsedEnd->AppendNewTimeStep(m_Geometry3, m_Geometry3MinTP, m_Geometry3MinTP); m_123TimeGeometryWithCollapsedInterim = mitk::ArbitraryTimeGeometry::New(); m_123TimeGeometryWithCollapsedInterim->ClearAllGeometries(); m_123TimeGeometryWithCollapsedInterim->AppendNewTimeStep(m_Geometry1, m_Geometry1MinTP, m_Geometry1MaxTP); m_123TimeGeometryWithCollapsedInterim->AppendNewTimeStep(m_Geometry2, m_Geometry2MinTP, m_Geometry2MinTP); m_123TimeGeometryWithCollapsedInterim->AppendNewTimeStep(m_Geometry3, m_Geometry3MinTP, m_Geometry3MaxTP); } void tearDown() override {} void CountTimeSteps() { MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->CountTimeSteps() == 0, "Testing CountTimeSteps with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->CountTimeSteps() == 1, "Testing CountTimeSteps with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->CountTimeSteps() == 5, "Testing CountTimeSteps with m_12345TimeGeometry"); } void GetMinimumTimePoint() { MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetMinimumTimePoint() == 0.0, "Testing GetMinimumTimePoint with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetMinimumTimePoint() == 0.0, "Testing GetMinimumTimePoint with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetMinimumTimePoint() == 1.0, "Testing GetMinimumTimePoint with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetMinimumTimePoint(2) == 0.0, "Testing GetMinimumTimePoint(2) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetMinimumTimePoint(2) == 0.0, "Testing GetMinimumTimePoint(2) with m_initTimeGeometry"); - MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetMinimumTimePoint(2) == 2.9, - "Testing GetMinimumTimePoint(2) with m_12345TimeGeometry"); + /////////////////////////////////////// + // Workarround T27883. See https://phabricator.mitk.org/T27883#219473 for more details. + // This workarround should be removed/reevaluated as soon as T28262 is solved and we know + // how time geometries should behave in the future! + MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetMinimumTimePoint(2) == 3.0, + "Testing GetMinimumTimePoint(2) with m_12345TimeGeometry"); + // Deactivated falling original test + // MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetMinimumTimePoint(2) == 2.9, + // "Testing GetMinimumTimePoint(2) with m_12345TimeGeometry"); + // End of workarround for T27883 + ////////////////////////////////////// } void GetMaximumTimePoint() { MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetMaximumTimePoint() == 0.0, "Testing GetMaximumTimePoint with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetMaximumTimePoint() == 1.0, "Testing GetMaximumTimePoint with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetMaximumTimePoint() == 5.9, "Testing GetMaximumTimePoint with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetMaximumTimePoint(2) == 0.0, "Testing GetMaximumTimePoint(2) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetMaximumTimePoint(2) == 0.0, "Testing GetMaximumTimePoint(2) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetMaximumTimePoint(2) == 3.9, "Testing GetMaximumTimePoint(2) with m_12345TimeGeometry"); } void GetTimeBounds() { MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetMaximumTimePoint(2) == 0.0, "Testing GetMaximumTimePoint(2) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetMaximumTimePoint(2) == 0.0, "Testing GetMaximumTimePoint(2) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetMaximumTimePoint(2) == 3.9, "Testing GetMaximumTimePoint(2) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetTimeBounds()[0] == 0.0, "Testing GetTimeBounds lower part with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetTimeBounds()[0] == 0.0, "Testing GetTimeBounds lower part with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetTimeBounds()[0] == 1.0, "Testing GetTimeBounds lower part with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetTimeBounds()[1] == 0.0, "Testing GetTimeBounds with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetTimeBounds()[1] == 1.0, "Testing GetTimeBounds with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetTimeBounds()[1] == 5.9, "Testing GetTimeBounds with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetTimeBounds(3)[0] == 0.0, "Testing GetTimeBounds(3) lower part with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetTimeBounds(3)[0] == 0.0, "Testing GetTimeBounds(3) lower part with m_initTimeGeometry"); - MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetTimeBounds(3)[0] == 3.9, - "Testing GetTimeBounds(3) lower part with m_12345TimeGeometry"); + /////////////////////////////////////// + // Workarround T27883. See https://phabricator.mitk.org/T27883#219473 for more details. + // This workarround should be removed/reevaluated as soon as T28262 is solved and we know + // how time geometries should behave in the future! + MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetTimeBounds(3)[0] == 4.0, + "Testing GetTimeBounds(3) lower part with m_12345TimeGeometry"); + // Deactivated falling original test + // MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetTimeBounds(3)[0] == 3.9, + // "Testing GetTimeBounds(3) lower part with m_12345TimeGeometry"); + // End of workarround for T27883 + ////////////////////////////////////// + MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetTimeBounds(3)[1] == 0.0, "Testing GetTimeBounds(3) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetTimeBounds(3)[1] == 0.0, "Testing GetTimeBounds(3) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetTimeBounds(3)[1] == 4.9, "Testing GetTimeBounds(3) with m_12345TimeGeometry"); } void IsValidTimePoint() { MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->IsValidTimePoint(-1) == false, "Testing IsValidTimePoint(-1) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->IsValidTimePoint(-1) == false, "Testing IsValidTimePoint(-1) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->IsValidTimePoint(-1) == false, "Testing IsValidTimePoint(-1) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->IsValidTimePoint(0) == false, "Testing IsValidTimePoint(0) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->IsValidTimePoint(0) == true, "Testing IsValidTimePoint(0) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->IsValidTimePoint(0) == false, "Testing IsValidTimePoint(0) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->IsValidTimePoint(1) == false, "Testing IsValidTimePoint(1) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->IsValidTimePoint(1) == false, "Testing IsValidTimePoint(1) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->IsValidTimePoint(1) == true, "Testing IsValidTimePoint(1) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->IsValidTimePoint(2.5) == false, "Testing IsValidTimePoint(2.5) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->IsValidTimePoint(2.5) == false, "Testing IsValidTimePoint(2.5) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->IsValidTimePoint(2.5) == true, "Testing IsValidTimePoint(2.5) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->IsValidTimePoint(5.89) == false, "Testing IsValidTimePoint(5.89) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->IsValidTimePoint(5.89) == false, "Testing IsValidTimePoint(5.89) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->IsValidTimePoint(5.89) == true, "Testing IsValidTimePoint(5.89) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->IsValidTimePoint(10) == false, "Testing IsValidTimePoint(10) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->IsValidTimePoint(10) == false, "Testing IsValidTimePoint(10) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->IsValidTimePoint(10) == false, "Testing IsValidTimePoint(10) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->IsValidTimeStep(0) == false, "Testing IsValidTimeStep(0) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->IsValidTimeStep(0) == true, "Testing IsValidTimeStep(0) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->IsValidTimeStep(0) == true, "Testing IsValidTimeStep(0) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->IsValidTimeStep(1) == false, "Testing IsValidTimeStep(1) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->IsValidTimeStep(1) == false, "Testing IsValidTimeStep(1) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->IsValidTimeStep(1) == true, "Testing IsValidTimeStep(1) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->IsValidTimeStep(6) == false, "Testing IsValidTimeStep(6) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->IsValidTimeStep(6) == false, "Testing IsValidTimeStep(6) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->IsValidTimeStep(6) == false, "Testing IsValidTimeStep(6) with m_12345TimeGeometry"); //checked collapsed cases MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometryWithCollapsedInterim->IsValidTimePoint(m_123TimeGeometryWithCollapsedInterim->GetMaximumTimePoint()) == false, "Testing that m_123TimeGeometryWithCollapsedInterim does not inclued the max bound in validity"); MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometryWithCollapsedEnd->IsValidTimePoint(m_123TimeGeometryWithCollapsedEnd->GetMaximumTimePoint()) == true, "Testing that m_123TimeGeometryWithCollapsedEnd does inclued the max bound in validity, because it has an collapsed final time step. (see also T27259)"); } void TimeStepToTimePoint() { MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->TimeStepToTimePoint(0) == 0.0, "Testing TimeStepToTimePoint(0) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->TimeStepToTimePoint(0) == 0.0, "Testing TimeStepToTimePoint(0) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->TimeStepToTimePoint(0) == 1.0, "Testing TimeStepToTimePoint(0) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->TimeStepToTimePoint(1) == 0.0, "Testing TimeStepToTimePoint(1) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->TimeStepToTimePoint(1) == 0.0, "Testing TimeStepToTimePoint(1) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->TimeStepToTimePoint(1) == 2.0, "Testing TimeStepToTimePoint(1) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->TimeStepToTimePoint(6) == 0.0, "Testing TimeStepToTimePoint(6) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->TimeStepToTimePoint(6) == 0.0, "Testing TimeStepToTimePoint(6) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->TimeStepToTimePoint(6) == 0.0, "Testing TimeStepToTimePoint(6) with m_12345TimeGeometry"); } void TimePointToTimeStep() { MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->TimePointToTimeStep(0.0) == 0, "Testing TimePointToTimeStep(0.0) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->TimePointToTimeStep(0.0) == 0, "Testing TimePointToTimeStep(0.0) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->TimePointToTimeStep(0.0) == 0, "Testing TimePointToTimeStep(0.0) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->TimePointToTimeStep(0.5) == 0, "Testing TimePointToTimeStep(0.5) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->TimePointToTimeStep(0.5) == 0, "Testing TimePointToTimeStep(0.5) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->TimePointToTimeStep(0.5) == 0, "Testing TimePointToTimeStep(0.5) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->TimePointToTimeStep(3.5) == 0, "Testing TimePointToTimeStep(3.5) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->TimePointToTimeStep(3.5) == m_initTimeGeometry->CountTimeSteps(), "Testing TimePointToTimeStep(3.5) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->TimePointToTimeStep(3.5) == 2, "Testing TimePointToTimeStep(3.5) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->TimePointToTimeStep(5.8) == 0, "Testing TimePointToTimeStep(5.8) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->TimePointToTimeStep(5.8) == m_initTimeGeometry->CountTimeSteps(), "Testing TimePointToTimeStep(5.8) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->TimePointToTimeStep(5.8) == 4, "Testing TimePointToTimeStep(5.8) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->TimePointToTimeStep(5.9) == m_12345TimeGeometry->CountTimeSteps(), "Testing TimePointToTimeStep(5.9) with m_12345TimeGeometry"); //checked collapsed cases MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometryWithCollapsedInterim->TimePointToTimeStep(m_123TimeGeometryWithCollapsedInterim->GetMaximumTimePoint()) == m_123TimeGeometryWithCollapsedInterim->CountTimeSteps(), "Testing m_123TimeGeometryWithCollapsedInterim does not map the max time poit."); MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometryWithCollapsedEnd->TimePointToTimeStep(m_123TimeGeometryWithCollapsedEnd->GetMaximumTimePoint()) == 2, "Testing that m_123TimeGeometryWithCollapsedEnd does map the max bound, because it has an collapsed final time step. (see also T27259)"); } void GetGeometryCloneForTimeStep() { MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetGeometryCloneForTimeStep(0).IsNull(), "Testing GetGeometryCloneForTimeStep(0) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetGeometryCloneForTimeStep(0).IsNotNull(), "Testing GetGeometryCloneForTimeStep(0) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetGeometryCloneForTimeStep(0).IsNotNull(), "Testing GetGeometryCloneForTimeStep(0) with m_12345TimeGeometry"); } void GetGeometryForTimeStep() { MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetGeometryForTimeStep(0).IsNull(), "Testing GetGeometryForTimePoint(0) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetGeometryForTimeStep(0).IsNotNull(), "Testing GetGeometryForTimePoint(0) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetGeometryForTimeStep(1).IsNull(), "Testing GetGeometryForTimePoint(1) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED( m_12345TimeGeometry->GetGeometryForTimeStep(0).GetPointer() == m_Geometry1.GetPointer(), "Testing GetGeometryForTimePoint(0) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED( m_12345TimeGeometry->GetGeometryForTimeStep(3).GetPointer() == m_Geometry4.GetPointer(), "Testing GetGeometryForTimePoint(3) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED( m_12345TimeGeometry->GetGeometryForTimeStep(4).GetPointer() == m_Geometry5.GetPointer(), "Testing GetGeometryForTimePoint(4) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetGeometryForTimeStep(5).IsNull(), "Testing GetGeometryForTimePoint(5) with m_12345TimeGeometry"); } void GetGeometryForTimePoint() { MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetGeometryForTimePoint(0).IsNull(), "Testing GetGeometryForTimeStep(0) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetGeometryForTimePoint(0).IsNotNull(), "Testing GetGeometryForTimeStep(0) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetGeometryForTimePoint(0).IsNull(), "Testing GetGeometryForTimeStep(0) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetGeometryForTimePoint(1.5).IsNull(), "Testing GetGeometryForTimeStep(1.5) with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->GetGeometryForTimePoint(1.5).IsNull(), "Testing GetGeometryForTimeStep(1.5) with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED( m_12345TimeGeometry->GetGeometryForTimePoint(1.5).GetPointer() == m_Geometry1.GetPointer(), "Testing GetGeometryForTimeStep(1.5) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED( m_12345TimeGeometry->GetGeometryForTimePoint(3.5).GetPointer() == m_Geometry3.GetPointer(), "Testing GetGeometryForTimeStep(3.5) with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetGeometryForTimePoint(5.9).IsNull(), "Testing GetGeometryForTimeStep(5.9) with m_12345TimeGeometry"); } void IsValid() { MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->IsValid() == false, "Testing IsValid() with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->IsValid() == true, "Testing IsValid() with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->IsValid() == true, "Testing IsValid() with m_12345TimeGeometry"); } void Expand() { m_12345TimeGeometry->Expand(3); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->CountTimeSteps() == 5, "Testing Expand(3) doesn't change m_12345TimeGeometry"); m_12345TimeGeometry->Expand(7); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->CountTimeSteps() == 7, "Testing Expand(7) with m_12345TimeGeometry"); } void ReplaceTimeStepGeometries() { // Test replace time step geometries m_12345TimeGeometry->ReplaceTimeStepGeometries(m_NewGeometry); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->CountTimeSteps() == 5, "Testing ReplaceTimeStepGeometries() with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED( m_12345TimeGeometry->GetGeometryForTimeStep(0)->GetOrigin() == m_NewGeometry->GetOrigin(), "Testing ReplaceTimeStepGeometries(): check if first geometry of m_12345TimeGeometry " "was replaced m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED( m_12345TimeGeometry->GetGeometryForTimeStep(4)->GetOrigin() == m_NewGeometry->GetOrigin(), "Testing ReplaceTimeStepGeometries(): check if last geometry of m_12345TimeGeometry " "was replaced m_12345TimeGeometry"); } void ClearAllGeometries() { // Test clear all geometries m_12345TimeGeometry->ClearAllGeometries(); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->CountTimeSteps() == 0, "Testing ClearAllGeometries() with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetMinimumTimePoint() == 0, "Testing ClearAllGeometries() with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->GetMaximumTimePoint() == 0, "Testing ClearAllGeometries() with m_12345TimeGeometry"); } void AppendNewTimeStep() { // Test append MITK_TEST_FOR_EXCEPTION(mitk::Exception, m_123TimeGeometry->AppendNewTimeStep(nullptr, 0, 1)); MITK_TEST_FOR_EXCEPTION(mitk::Exception, m_123TimeGeometry->AppendNewTimeStep(m_Geometry3_5,m_Geometry3_5MinTP,m_Geometry3_5MaxTP)); MITK_TEST_FOR_EXCEPTION(mitk::Exception, m_123TimeGeometry->AppendNewTimeStep(m_Geometry4, m_Geometry4MaxTP, m_Geometry4MinTP)); //valid but inverted bounds m_emptyTimeGeometry->AppendNewTimeStep(m_Geometry4, m_Geometry4MinTP, m_Geometry4MaxTP); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->CountTimeSteps() == 1, "Testing AppendNewTimeStep() with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetMinimumTimePoint() == 4, "Testing ClearAllGeometries() with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->GetMaximumTimePoint() == 4.9, "Testing ClearAllGeometries() with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometry->CountTimeSteps() == 3, "Testing AppendNewTimeStep() with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometry->GetMinimumTimePoint() == 1, "Testing ClearAllGeometries() with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometry->GetMaximumTimePoint() == 3.9, "Testing ClearAllGeometries() with m_emptyTimeGeometry"); m_123TimeGeometry->AppendNewTimeStep(m_Geometry4, m_Geometry4MinTP, m_Geometry4MaxTP); MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometry->CountTimeSteps() == 4, "Testing AppendNewTimeStep() with m_123TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometry->GetMinimumTimePoint() == 1, "Testing AppendNewTimeStep() with m_123TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometry->GetMaximumTimePoint() == 4.9, "Testing AppendNewTimeStep() with m_123TimeGeometry"); - MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometry->GetMinimumTimePoint(3) == 3.9, - "Testing AppendNewTimeStep() with m_123TimeGeometry"); + /////////////////////////////////////// + // Workarround T27883. See https://phabricator.mitk.org/T27883#219473 for more details. + // This workarround should be removed/reevaluated as soon as T28262 is solved and we know + // how time geometries should behave in the future! + MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometry->GetMinimumTimePoint(3) == 4.0, + "Testing AppendNewTimeStep() with m_123TimeGeometry"); + // Deactivated falling original test + // MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometry->GetMinimumTimePoint(3) == 3.9, + // "Testing AppendNewTimeStep() with m_123TimeGeometry"); + // End of workarround for T27883 + ////////////////////////////////////// } void HasCollapsedFinalTimeStep() { MITK_TEST_CONDITION_REQUIRED(m_emptyTimeGeometry->HasCollapsedFinalTimeStep() == false, "Testing HasCollapsedFinalTimeStep() with m_emptyTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_initTimeGeometry->HasCollapsedFinalTimeStep() == false, "Testing HasCollapsedFinalTimeStep() with m_initTimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_12345TimeGeometry->HasCollapsedFinalTimeStep() == false, "Testing HasCollapsedFinalTimeStep() with m_12345TimeGeometry"); MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometryWithCollapsedEnd->HasCollapsedFinalTimeStep() == true, "Testing HasCollapsedFinalTimeStep() with m_123TimeGeometryWithCollapsedEnd"); MITK_TEST_CONDITION_REQUIRED(m_123TimeGeometryWithCollapsedInterim->HasCollapsedFinalTimeStep() == false, "Testing HasCollapsedFinalTimeStep() with m_123TimeGeometryWithCollapsedInterim"); } }; MITK_TEST_SUITE_REGISTRATION(mitkArbitraryTimeGeometry) diff --git a/Modules/Core/test/mitkIOUtilTest.cpp b/Modules/Core/test/mitkIOUtilTest.cpp index 1a7ddd83f3..31fadfb024 100644 --- a/Modules/Core/test/mitkIOUtilTest.cpp +++ b/Modules/Core/test/mitkIOUtilTest.cpp @@ -1,293 +1,311 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include #include #include #include #include #include #include class mitkIOUtilTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkIOUtilTestSuite); MITK_TEST(TestTempMethods); MITK_TEST(TestSaveEmptyData); MITK_TEST(TestLoadAndSaveImage); MITK_TEST(TestNullLoad); MITK_TEST(TestNullSave); MITK_TEST(TestLoadAndSavePointSet); MITK_TEST(TestLoadAndSaveSurface); MITK_TEST(TestTempMethodsForUniqueFilenames); MITK_TEST(TestTempMethodsForUniqueFilenames); MITK_TEST(TestIOMetaInformation); + MITK_TEST(TestUtf8); CPPUNIT_TEST_SUITE_END(); private: std::string m_ImagePath; std::string m_SurfacePath; std::string m_PointSetPath; public: void setUp() override { m_ImagePath = GetTestDataFilePath("Pic3D.nrrd"); m_SurfacePath = GetTestDataFilePath("binary.stl"); m_PointSetPath = GetTestDataFilePath("pointSet.mps"); } void TestSaveEmptyData() { mitk::Surface::Pointer data = mitk::Surface::New(); CPPUNIT_ASSERT_THROW(mitk::IOUtil::Save(data, "/tmp/dummy"), mitk::Exception); } void TestTempMethods() { std::string tmpPath = mitk::IOUtil::GetTempPath(); CPPUNIT_ASSERT(!tmpPath.empty()); std::ofstream tmpFile; std::string tmpFilePath = mitk::IOUtil::CreateTemporaryFile(tmpFile); CPPUNIT_ASSERT(tmpFile && tmpFile.is_open()); CPPUNIT_ASSERT(tmpFilePath.size() > tmpPath.size()); CPPUNIT_ASSERT(tmpFilePath.substr(0, tmpPath.size()) == tmpPath); tmpFile.close(); CPPUNIT_ASSERT(std::remove(tmpFilePath.c_str()) == 0); std::string programPath = mitk::IOUtil::GetProgramPath(); CPPUNIT_ASSERT(!programPath.empty()); std::ofstream tmpFile2; std::string tmpFilePath2 = mitk::IOUtil::CreateTemporaryFile(tmpFile2, "my-XXXXXX", programPath); CPPUNIT_ASSERT(tmpFile2 && tmpFile2.is_open()); CPPUNIT_ASSERT(tmpFilePath2.size() > programPath.size()); CPPUNIT_ASSERT(tmpFilePath2.substr(0, programPath.size()) == programPath); tmpFile2.close(); CPPUNIT_ASSERT(std::remove(tmpFilePath2.c_str()) == 0); std::ofstream tmpFile3; std::string tmpFilePath3 = mitk::IOUtil::CreateTemporaryFile(tmpFile3, std::ios_base::binary, "my-XXXXXX.TXT", programPath); CPPUNIT_ASSERT(tmpFile3 && tmpFile3.is_open()); CPPUNIT_ASSERT(tmpFilePath3.size() > programPath.size()); CPPUNIT_ASSERT(tmpFilePath3.substr(0, programPath.size()) == programPath); CPPUNIT_ASSERT(tmpFilePath3.substr(tmpFilePath3.size() - 13, 3) == "my-"); CPPUNIT_ASSERT(tmpFilePath3.substr(tmpFilePath3.size() - 4) == ".TXT"); tmpFile3.close(); // CPPUNIT_ASSERT(std::remove(tmpFilePath3.c_str()) == 0) std::string tmpFilePath4 = mitk::IOUtil::CreateTemporaryFile(); std::ofstream file; file.open(tmpFilePath4.c_str()); CPPUNIT_ASSERT_MESSAGE("Testing if file exists after CreateTemporaryFile()", file.is_open()); CPPUNIT_ASSERT_THROW(mitk::IOUtil::CreateTemporaryFile(tmpFile2, "XX"), mitk::Exception); std::string tmpDir = mitk::IOUtil::CreateTemporaryDirectory(); CPPUNIT_ASSERT(tmpDir.size() > tmpPath.size()); CPPUNIT_ASSERT(tmpDir.substr(0, tmpPath.size()) == tmpPath); CPPUNIT_ASSERT(itksys::SystemTools::RemoveADirectory(tmpDir.c_str())); std::string tmpDir2 = mitk::IOUtil::CreateTemporaryDirectory("my-XXXXXX", programPath); CPPUNIT_ASSERT(tmpDir2.size() > programPath.size()); CPPUNIT_ASSERT(tmpDir2.substr(0, programPath.size()) == programPath); CPPUNIT_ASSERT(itksys::SystemTools::RemoveADirectory(tmpDir2.c_str())); } void TestTempMethodsForUniqueFilenames() { int numberOfFiles = 100; // create 100 empty files std::vector v100filenames; for (int i = 0; i < numberOfFiles; i++) { v100filenames.push_back(mitk::IOUtil::CreateTemporaryFile()); } // check if all of them are unique for (int i = 0; i < numberOfFiles; i++) for (int j = 0; j < numberOfFiles; j++) { if (i != j) { std::stringstream message; message << "Checking if file " << i << " and file " << j << " are different, which should be the case because each of them should be unique."; CPPUNIT_ASSERT_MESSAGE(message.str(), (v100filenames.at(i) != v100filenames.at(j))); } } // delete all the files / clean up for (int i = 0; i < numberOfFiles; i++) { std::remove(v100filenames.at(i).c_str()); } } void TestLoadAndSaveImage() { mitk::Image::Pointer img1 = mitk::IOUtil::Load(m_ImagePath); CPPUNIT_ASSERT(img1.IsNotNull()); std::ofstream tmpStream; std::string imagePath = mitk::IOUtil::CreateTemporaryFile(tmpStream, "diffpic3d-XXXXXX.nrrd"); tmpStream.close(); std::string imagePath2 = mitk::IOUtil::CreateTemporaryFile(tmpStream, "diffpic3d-XXXXXX.nii.gz"); tmpStream.close(); // the cases where no exception should be thrown CPPUNIT_ASSERT_NO_THROW(mitk::IOUtil::Save(img1, imagePath)); CPPUNIT_ASSERT_NO_THROW(mitk::IOUtil::Save(img1.GetPointer(), imagePath2)); // load data which does not exist CPPUNIT_ASSERT_THROW(mitk::IOUtil::Load("fileWhichDoesNotExist.nrrd"), mitk::Exception); // delete the files after the test is done std::remove(imagePath.c_str()); std::remove(imagePath2.c_str()); mitk::Image::Pointer relativImage = mitk::ImageGenerator::GenerateGradientImage(4, 4, 4, 1); std::string imagePath3 = mitk::IOUtil::CreateTemporaryFile(tmpStream, "XXXXXX.nrrd"); tmpStream.close(); mitk::IOUtil::Save(relativImage, imagePath3); CPPUNIT_ASSERT_NO_THROW(mitk::IOUtil::Load(imagePath3)); std::remove(imagePath3.c_str()); } /** * \brief This method calls all available load methods with a nullpointer and an empty pathand expects an exception **/ void TestNullLoad() { CPPUNIT_ASSERT_THROW(mitk::IOUtil::Load(""), mitk::Exception); } /** * \brief This method calls the save method (to which all other convenience save methods reference) with null *parameters **/ void TestNullSave() { CPPUNIT_ASSERT_THROW(mitk::IOUtil::Save(nullptr, mitk::IOUtil::CreateTemporaryFile()), mitk::Exception); CPPUNIT_ASSERT_THROW(mitk::IOUtil::Save(mitk::Image::New().GetPointer(), ""), mitk::Exception); } void TestLoadAndSavePointSet() { mitk::PointSet::Pointer pointset = mitk::IOUtil::Load(m_PointSetPath); CPPUNIT_ASSERT(pointset.IsNotNull()); std::ofstream tmpStream; std::string pointSetPath = mitk::IOUtil::CreateTemporaryFile(tmpStream, "XXXXXX.mps"); tmpStream.close(); std::string pointSetPathWithDefaultExtension = mitk::IOUtil::CreateTemporaryFile(tmpStream, "XXXXXX.mps"); tmpStream.close(); std::string pointSetPathWithoutDefaultExtension = mitk::IOUtil::CreateTemporaryFile(tmpStream); tmpStream.close(); // the cases where no exception should be thrown CPPUNIT_ASSERT_NO_THROW(mitk::IOUtil::Save(pointset, pointSetPathWithDefaultExtension)); // test if defaultextension is inserted if no extension is present CPPUNIT_ASSERT_NO_THROW(mitk::IOUtil::Save(pointset, pointSetPathWithoutDefaultExtension.c_str())); // delete the files after the test is done std::remove(pointSetPath.c_str()); std::remove(pointSetPathWithDefaultExtension.c_str()); std::remove(pointSetPathWithoutDefaultExtension.c_str()); } void TestLoadAndSaveSurface() { mitk::Surface::Pointer surface = mitk::IOUtil::Load(m_SurfacePath); CPPUNIT_ASSERT(surface.IsNotNull()); std::ofstream tmpStream; std::string surfacePath = mitk::IOUtil::CreateTemporaryFile(tmpStream, "diffsurface-XXXXXX.stl"); // the cases where no exception should be thrown CPPUNIT_ASSERT_NO_THROW(mitk::IOUtil::Save(surface, surfacePath)); // test if exception is thrown as expected on unknown extsension CPPUNIT_ASSERT_THROW(mitk::IOUtil::Save(surface, "testSurface.xXx"), mitk::Exception); // delete the files after the test is done std::remove(surfacePath.c_str()); } std::string GenerateMetaDictKey(const mitk::PropertyKeyPath& propKey) { auto result = mitk::PropertyKeyPathToPropertyName(propKey); std::replace(result.begin(), result.end(), '.', '_'); return result; } std::string GetValueFromMetaDict(const itk::MetaDataDictionary& dict, const mitk::PropertyKeyPath& propKey) { auto metaValueBase = dict.Get(GenerateMetaDictKey(propKey)); auto metaValue = dynamic_cast*>(metaValueBase); return metaValue->GetMetaDataObjectValue(); } void TestIOMetaInformation() { mitk::Image::Pointer img = mitk::IOUtil::Load(m_ImagePath); CPPUNIT_ASSERT(img.IsNotNull()); auto value = img->GetProperty(mitk::PropertyKeyPathToPropertyName(mitk::IOMetaInformationPropertyConstants::READER_DESCRIPTION()).c_str())->GetValueAsString(); CPPUNIT_ASSERT_EQUAL(std::string("ITK NrrdImageIO"), value); value = img->GetProperty(mitk::PropertyKeyPathToPropertyName(mitk::IOMetaInformationPropertyConstants::READER_INPUTLOCATION()).c_str())->GetValueAsString(); CPPUNIT_ASSERT_EQUAL(m_ImagePath, value); value = img->GetProperty(mitk::PropertyKeyPathToPropertyName(mitk::IOMetaInformationPropertyConstants::READER_MIME_CATEGORY()).c_str())->GetValueAsString(); CPPUNIT_ASSERT_EQUAL(std::string("Images"), value); value = img->GetProperty(mitk::PropertyKeyPathToPropertyName(mitk::IOMetaInformationPropertyConstants::READER_MIME_NAME()).c_str())->GetValueAsString(); CPPUNIT_ASSERT_EQUAL(std::string("application/vnd.mitk.image.nrrd"), value); value = img->GetProperty(mitk::PropertyKeyPathToPropertyName(mitk::IOMetaInformationPropertyConstants::READER_VERSION()).c_str())->GetValueAsString(); CPPUNIT_ASSERT_EQUAL(std::string(MITK_VERSION_STRING), value); //check if the information is persistet correctly on save. std::ofstream tmpStream; std::string imagePath = mitk::IOUtil::CreateTemporaryFile(tmpStream, "ioMeta_XXXXXX.nrrd"); tmpStream.close(); mitk::IOUtil::Save(img, imagePath); auto io = itk::NrrdImageIO::New(); io->SetFileName(imagePath); io->ReadImageInformation(); auto metaDict = io->GetMetaDataDictionary(); auto metaValue = GetValueFromMetaDict(metaDict, mitk::IOMetaInformationPropertyConstants::READER_DESCRIPTION()); CPPUNIT_ASSERT_EQUAL(std::string("ITK NrrdImageIO"), metaValue); metaValue = GetValueFromMetaDict(metaDict, mitk::IOMetaInformationPropertyConstants::READER_INPUTLOCATION()); CPPUNIT_ASSERT_EQUAL(m_ImagePath, metaValue); metaValue = GetValueFromMetaDict(metaDict, mitk::IOMetaInformationPropertyConstants::READER_MIME_CATEGORY()); CPPUNIT_ASSERT_EQUAL(std::string("Images"), metaValue); metaValue = GetValueFromMetaDict(metaDict, mitk::IOMetaInformationPropertyConstants::READER_MIME_NAME()); CPPUNIT_ASSERT_EQUAL(std::string("application/vnd.mitk.image.nrrd"), metaValue); metaValue = GetValueFromMetaDict(metaDict, mitk::IOMetaInformationPropertyConstants::READER_VERSION()); CPPUNIT_ASSERT_EQUAL(std::string(MITK_VERSION_STRING), metaValue); // delete the files after the test is done std::remove(imagePath.c_str()); } + void TestUtf8() + { + const std::string utf8Path = u8"UTF-8/\u00c4.nrrd"; // LATIN CAPITAL LETTER A WITH DIAERESIS (U+00C4) + const std::string local8BitPath = mitk::IOUtil::Utf8ToLocal8Bit(utf8Path); + + CPPUNIT_ASSERT(utf8Path == mitk::IOUtil::Local8BitToUtf8(local8BitPath)); + + const std::string path = GetTestDataFilePath(local8BitPath); + + std::fstream file; + file.open(path); + CPPUNIT_ASSERT(file.is_open()); + + auto image = mitk::IOUtil::Load(path); + CPPUNIT_ASSERT(image.IsNotNull()); + } + }; MITK_TEST_SUITE_REGISTRATION(mitkIOUtil) diff --git a/Modules/Core/test/mitkPlaneGeometryTest.cpp b/Modules/Core/test/mitkPlaneGeometryTest.cpp index b10f0e1887..0307e36536 100644 --- a/Modules/Core/test/mitkPlaneGeometryTest.cpp +++ b/Modules/Core/test/mitkPlaneGeometryTest.cpp @@ -1,1093 +1,1093 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkAffineTransform3D.h" #include "mitkBaseGeometry.h" #include "mitkGeometry3D.h" #include "mitkInteractionConst.h" #include "mitkLine.h" #include "mitkPlaneGeometry.h" #include "mitkRotationOperation.h" #include "mitkSlicedGeometry3D.h" #include "mitkThinPlateSplineCurvedGeometry.h" #include #include #include #include #include #include #include #include static const mitk::ScalarType testEps = 1E-9; // the epsilon used in this test == at least float precision. class mitkPlaneGeometryTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkPlaneGeometryTestSuite); MITK_TEST(TestInitializeStandardPlane); MITK_TEST(TestProjectPointOntoPlane); MITK_TEST(TestPlaneGeometryCloning); MITK_TEST(TestInheritance); MITK_TEST(TestSetExtendInMM); MITK_TEST(TestRotate); MITK_TEST(TestClone); MITK_TEST(TestPlaneComparison); MITK_TEST(TestAxialInitialization); MITK_TEST(TestFrontalInitialization); MITK_TEST(TestSaggitalInitialization); MITK_TEST(TestLefthandedCoordinateSystem); MITK_TEST(TestDominantAxesError); MITK_TEST(TestCheckRotationMatrix); // Currently commented out, see See bug 15990 // MITK_TEST(testPlaneGeometryInitializeOrder); MITK_TEST(TestIntersectionPoint); MITK_TEST(TestCase1210); CPPUNIT_TEST_SUITE_END(); private: // private test members that are initialized by setUp() mitk::PlaneGeometry::Pointer planegeometry; mitk::Point3D origin; mitk::Vector3D right, bottom, normal, spacing; mitk::ScalarType width, height; mitk::ScalarType widthInMM, heightInMM, thicknessInMM; public: void setUp() override { planegeometry = mitk::PlaneGeometry::New(); width = 100; widthInMM = width; height = 200; heightInMM = height; thicknessInMM = 1.0; mitk::FillVector3D(origin, 4.5, 7.3, 11.2); mitk::FillVector3D(right, widthInMM, 0, 0); mitk::FillVector3D(bottom, 0, heightInMM, 0); mitk::FillVector3D(normal, 0, 0, thicknessInMM); mitk::FillVector3D(spacing, 1.0, 1.0, thicknessInMM); planegeometry->InitializeStandardPlane(right, bottom); planegeometry->SetOrigin(origin); planegeometry->SetSpacing(spacing); } void tearDown() override {} // This test verifies inheritance behaviour, this test will fail if the behaviour changes in the future void TestInheritance() { mitk::PlaneGeometry::Pointer plane = mitk::PlaneGeometry::New(); mitk::Geometry3D::Pointer g3d = dynamic_cast(plane.GetPointer()); CPPUNIT_ASSERT_MESSAGE("Planegeometry should not be castable to Geometry 3D", g3d.IsNull()); mitk::BaseGeometry::Pointer base = dynamic_cast(plane.GetPointer()); CPPUNIT_ASSERT_MESSAGE("Planegeometry should be castable to BaseGeometry", base.IsNotNull()); g3d = mitk::Geometry3D::New(); base = dynamic_cast(g3d.GetPointer()); CPPUNIT_ASSERT_MESSAGE("Geometry3D should be castable to BaseGeometry", base.IsNotNull()); mitk::SlicedGeometry3D::Pointer sliced = mitk::SlicedGeometry3D::New(); g3d = dynamic_cast(sliced.GetPointer()); CPPUNIT_ASSERT_MESSAGE("SlicedGeometry3D should not be castable to Geometry3D", g3d.IsNull()); mitk::ThinPlateSplineCurvedGeometry::Pointer thin = mitk::ThinPlateSplineCurvedGeometry::New(); plane = dynamic_cast(thin.GetPointer()); CPPUNIT_ASSERT_MESSAGE("AbstractTransformGeometry should be castable to PlaneGeometry", plane.IsNotNull()); plane = mitk::PlaneGeometry::New(); mitk::AbstractTransformGeometry::Pointer atg = dynamic_cast(plane.GetPointer()); CPPUNIT_ASSERT_MESSAGE("PlaneGeometry should not be castable to AbstractTransofrmGeometry", atg.IsNull()); } void TestDominantAxesError() { auto image = mitk::IOUtil::Load(GetTestDataFilePath("NotQuiteARotationMatrix.nrrd")); auto matrix = image->GetGeometry()->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().transpose(); std::vector< int > axes = mitk::PlaneGeometry::CalculateDominantAxes(matrix); CPPUNIT_ASSERT_MESSAGE("Domiant axes cannot be determined in this dataset. Output should be default ordering.", axes.at(0)==0 && axes.at(1)==1 && axes.at(2)==2); } void TestCheckRotationMatrix() { auto image = mitk::IOUtil::Load(GetTestDataFilePath("NotQuiteARotationMatrix.nrrd")); - bool is_rotation = mitk::PlaneGeometry::CheckRotationMatrix(image->GetGeometry()->GetIndexToWorldTransform()); + bool is_rotation = mitk::PlaneGeometry::CheckRotationMatrix(image->GetGeometry()->GetIndexToWorldTransform(), 1e-8); CPPUNIT_ASSERT_MESSAGE("Since the test data matrix is not quite a rotation matrix, this should be detected.", !is_rotation); } void TestLefthandedCoordinateSystem() { /** * @brief This method tests InitializeStandardPlane() and IndexToWorld() * with a left-handed coordinate orientation or indexToWorldMatrix. * * Of course this test does not use standard Parameters, which are right-handed. * See also discussion of bug #11477: http://bugs.mitk.org/show_bug.cgi?id=11477 */ planegeometry = mitk::PlaneGeometry::New(); width = 100; widthInMM = 5; height = 200; heightInMM = 3; thicknessInMM = 1.0; mitk::FillVector3D(right, widthInMM, 0, 0); mitk::FillVector3D(bottom, 0, heightInMM, 0); // This one negative sign results in lefthanded coordinate orientation and det(matrix) < 0. mitk::FillVector3D(normal, 0, 0, -thicknessInMM); mitk::AffineTransform3D::Pointer transform = mitk::AffineTransform3D::New(); mitk::AffineTransform3D::MatrixType matrix; mitk::AffineTransform3D::MatrixType::InternalMatrixType &vnl_matrix = matrix.GetVnlMatrix(); vnl_matrix.set_column(0, right); vnl_matrix.set_column(1, bottom); vnl_matrix.set_column(2, normal); // making sure that we didn't screw up this special test case or else fail deadly: assert(vnl_determinant(vnl_matrix) < 0.0); transform->SetIdentity(); transform->SetMatrix(matrix); planegeometry->InitializeStandardPlane(width, height, transform); // Crux of the matter. CPPUNIT_ASSERT_MESSAGE( "Testing if IndexToWorldMatrix is correct after InitializeStandardPlane( width, height, transform ) ", mitk::MatrixEqualElementWise(planegeometry->GetIndexToWorldTransform()->GetMatrix(), matrix)); mitk::Point3D p_index; p_index[0] = 10.; p_index[1] = 10.; p_index[2] = 0.; mitk::Point3D p_world; mitk::Point3D p_expectedResult; p_expectedResult[0] = 50.; p_expectedResult[1] = 30.; p_expectedResult[2] = 0.; ((mitk::BaseGeometry::Pointer)planegeometry)->IndexToWorld(p_index, p_world); // Crux of the matter. CPPUNIT_ASSERT_MESSAGE("Testing if IndexToWorld(a,b) function works correctly with lefthanded matrix ", mitk::Equal(p_world, p_expectedResult, testEps)); } // See bug 1210 // Test does not use standard Parameters void TestCase1210() { mitk::PlaneGeometry::Pointer planegeometry = mitk::PlaneGeometry::New(); mitk::Point3D origin; mitk::Vector3D right, down, spacing; mitk::FillVector3D(origin, 4.5, 7.3, 11.2); mitk::FillVector3D(right, 1.015625, 1.015625, 1.1999969482421875); mitk::FillVector3D(down, 1.4012984643248170709237295832899161312802619418765e-45, 0, 0); mitk::FillVector3D(spacing, 0, 1.4713633875410579244699160624544119378442750389703e-43, 9.2806360452222355258639080851310540729807238879469e-32); std::cout << "Testing InitializeStandardPlane(rightVector, downVector, spacing = nullptr): " << std::endl; CPPUNIT_ASSERT_NO_THROW(planegeometry->InitializeStandardPlane(right, down, &spacing)); /* std::cout << "Testing width, height and thickness (in units): "; if((mitk::Equal(planegeometry->GetExtent(0),width)==false) || (mitk::Equal(planegeometry->GetExtent(1),height)==false) || (mitk::Equal(planegeometry->GetExtent(2),1)==false) ) { std::cout<<"[FAILED]"<GetExtentInMM(0),widthInMM)==false) || (mitk::Equal(planegeometry->GetExtentInMM(1),heightInMM)==false) || (mitk::Equal(planegeometry->GetExtentInMM(2),thicknessInMM)==false) ) { std::cout<<"[FAILED]"< 0. * */ // Test does not use standard Parameters void TestIntersectionPoint() { // init plane with its parameter mitk::PlaneGeometry::Pointer myPlaneGeometry = mitk::PlaneGeometry::New(); mitk::Point3D origin; origin[0] = 0.0; origin[1] = 2.0; origin[2] = 0.0; mitk::Vector3D normal; normal[0] = 0.0; normal[1] = 1.0; normal[2] = 0.0; myPlaneGeometry->InitializePlane(origin, normal); // generate points and line for intersection testing // point distance of given line > 1 mitk::Point3D pointP1; pointP1[0] = 2.0; pointP1[1] = 1.0; pointP1[2] = 0.0; mitk::Point3D pointP2; pointP2[0] = 2.0; pointP2[1] = 4.0; pointP2[2] = 0.0; mitk::Vector3D lineDirection; lineDirection[0] = pointP2[0] - pointP1[0]; lineDirection[1] = pointP2[1] - pointP1[1]; lineDirection[2] = pointP2[2] - pointP1[2]; mitk::Line3D xingline(pointP1, lineDirection); mitk::Point3D calcXingPoint; myPlaneGeometry->IntersectionPoint(xingline, calcXingPoint); // point distance of given line < 1 mitk::Point3D pointP3; pointP3[0] = 2.0; pointP3[1] = 2.2; pointP3[2] = 0.0; mitk::Point3D pointP4; pointP4[0] = 2.0; pointP4[1] = 1.7; pointP4[2] = 0.0; mitk::Vector3D lineDirection2; lineDirection2[0] = pointP4[0] - pointP3[0]; lineDirection2[1] = pointP4[1] - pointP3[1]; lineDirection2[2] = pointP4[2] - pointP3[2]; mitk::Line3D xingline2(pointP3, lineDirection2); mitk::Point3D calcXingPoint2; myPlaneGeometry->IntersectionPoint(xingline2, calcXingPoint2); // intersection points must be the same CPPUNIT_ASSERT_MESSAGE("Failed to calculate Intersection Point", calcXingPoint == calcXingPoint2); } /** * @brief This method tests method ProjectPointOntoPlane. * * See also bug #3409. */ // Test does not use standard Parameters void TestProjectPointOntoPlane() { mitk::PlaneGeometry::Pointer myPlaneGeometry = mitk::PlaneGeometry::New(); // create normal mitk::Vector3D normal; normal[0] = 0.0; normal[1] = 0.0; normal[2] = 1.0; // create origin mitk::Point3D origin; origin[0] = -27.582859; origin[1] = 50; origin[2] = 200.27742; // initialize plane geometry myPlaneGeometry->InitializePlane(origin, normal); // output to descripe the test std::cout << "Testing PlaneGeometry according to bug #3409" << std::endl; std::cout << "Our normal is: " << normal << std::endl; std::cout << "So ALL projected points should have exactly the same z-value!" << std::endl; // create a number of points mitk::Point3D myPoints[5]; myPoints[0][0] = -27.582859; myPoints[0][1] = 50.00; myPoints[0][2] = 200.27742; myPoints[1][0] = -26.58662; myPoints[1][1] = 50.00; myPoints[1][2] = 200.19026; myPoints[2][0] = -26.58662; myPoints[2][1] = 50.00; myPoints[2][2] = 200.33124; myPoints[3][0] = 104.58662; myPoints[3][1] = 452.12313; myPoints[3][2] = 866.41236; myPoints[4][0] = -207.58662; myPoints[4][1] = 312.00; myPoints[4][2] = -300.12346; // project points onto plane mitk::Point3D myProjectedPoints[5]; for (unsigned int i = 0; i < 5; ++i) { myProjectedPoints[i] = myPlaneGeometry->ProjectPointOntoPlane(myPoints[i]); } // compare z-values with z-value of plane (should be equal) bool allPointsOnPlane = true; for (auto &myProjectedPoint : myProjectedPoints) { if (fabs(myProjectedPoint[2] - origin[2]) > mitk::sqrteps) { allPointsOnPlane = false; } } CPPUNIT_ASSERT_MESSAGE("All points lie not on the same plane", allPointsOnPlane); } void TestPlaneGeometryCloning() { mitk::PlaneGeometry::Pointer geometry2D = createPlaneGeometry(); try { mitk::PlaneGeometry::Pointer clone = geometry2D->Clone(); itk::Matrix matrix = clone->GetIndexToWorldTransform()->GetMatrix(); CPPUNIT_ASSERT_MESSAGE("Test if matrix element exists...", matrix[0][0] == 31); double origin = geometry2D->GetOrigin()[0]; CPPUNIT_ASSERT_MESSAGE("First Point of origin as expected...", mitk::Equal(origin, 8)); double spacing = geometry2D->GetSpacing()[0]; CPPUNIT_ASSERT_MESSAGE("First Point of spacing as expected...", mitk::Equal(spacing, 31)); } catch (...) { CPPUNIT_FAIL("Error during access on a member of cloned geometry"); } // direction [row] [coloum] MITK_TEST_OUTPUT(<< "Casting a rotated 2D ITK Image to a MITK Image and check if Geometry is still same"); } void TestPlaneGeometryInitializeOrder() { mitk::Vector3D mySpacing; mySpacing[0] = 31; mySpacing[1] = 0.1; mySpacing[2] = 5.4; mitk::Point3D myOrigin; myOrigin[0] = 8; myOrigin[1] = 9; myOrigin[2] = 10; mitk::AffineTransform3D::Pointer myTransform = mitk::AffineTransform3D::New(); itk::Matrix transMatrix; transMatrix.Fill(0); transMatrix[0][0] = 1; transMatrix[1][1] = 2; transMatrix[2][2] = 4; myTransform->SetMatrix(transMatrix); mitk::PlaneGeometry::Pointer geometry2D1 = mitk::PlaneGeometry::New(); geometry2D1->SetIndexToWorldTransform(myTransform); geometry2D1->SetSpacing(mySpacing); geometry2D1->SetOrigin(myOrigin); mitk::PlaneGeometry::Pointer geometry2D2 = mitk::PlaneGeometry::New(); geometry2D2->SetSpacing(mySpacing); geometry2D2->SetOrigin(myOrigin); geometry2D2->SetIndexToWorldTransform(myTransform); mitk::PlaneGeometry::Pointer geometry2D3 = mitk::PlaneGeometry::New(); geometry2D3->SetIndexToWorldTransform(myTransform); geometry2D3->SetSpacing(mySpacing); geometry2D3->SetOrigin(myOrigin); geometry2D3->SetIndexToWorldTransform(myTransform); CPPUNIT_ASSERT_MESSAGE("Origin of Geometry 1 matches that of Geometry 2.", mitk::Equal(geometry2D1->GetOrigin(), geometry2D2->GetOrigin())); CPPUNIT_ASSERT_MESSAGE("Origin of Geometry 1 match those of Geometry 3.", mitk::Equal(geometry2D1->GetOrigin(), geometry2D3->GetOrigin())); CPPUNIT_ASSERT_MESSAGE("Origin of Geometry 2 match those of Geometry 3.", mitk::Equal(geometry2D2->GetOrigin(), geometry2D3->GetOrigin())); CPPUNIT_ASSERT_MESSAGE("Spacing of Geometry 1 match those of Geometry 2.", mitk::Equal(geometry2D1->GetSpacing(), geometry2D2->GetSpacing())); CPPUNIT_ASSERT_MESSAGE("Spacing of Geometry 1 match those of Geometry 3.", mitk::Equal(geometry2D1->GetSpacing(), geometry2D3->GetSpacing())); CPPUNIT_ASSERT_MESSAGE("Spacing of Geometry 2 match those of Geometry 3.", mitk::Equal(geometry2D2->GetSpacing(), geometry2D3->GetSpacing())); CPPUNIT_ASSERT_MESSAGE("Transformation of Geometry 1 match those of Geometry 2.", compareMatrix(geometry2D1->GetIndexToWorldTransform()->GetMatrix(), geometry2D2->GetIndexToWorldTransform()->GetMatrix())); CPPUNIT_ASSERT_MESSAGE("Transformation of Geometry 1 match those of Geometry 3.", compareMatrix(geometry2D1->GetIndexToWorldTransform()->GetMatrix(), geometry2D3->GetIndexToWorldTransform()->GetMatrix())); CPPUNIT_ASSERT_MESSAGE("Transformation of Geometry 2 match those of Geometry 3.", compareMatrix(geometry2D2->GetIndexToWorldTransform()->GetMatrix(), geometry2D3->GetIndexToWorldTransform()->GetMatrix())); } void TestInitializeStandardPlane() { CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: width", mitk::Equal(planegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: height", mitk::Equal(planegeometry->GetExtent(1), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: depth", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: width in mm", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: heght in mm", mitk::Equal(planegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: depth in mm", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: AxisVectorRight", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: AxisVectorBottom", mitk::Equal(planegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with default Spacing: AxisVectorNormal", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); mitk::Vector3D spacing; thicknessInMM = 1.5; normal.Normalize(); normal *= thicknessInMM; mitk::FillVector3D(spacing, 1.0, 1.0, thicknessInMM); planegeometry->InitializeStandardPlane(right.GetVnlVector(), bottom.GetVnlVector(), &spacing); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: width", mitk::Equal(planegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: height", mitk::Equal(planegeometry->GetExtent(1), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: depth", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: width in mm", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: height in mm", mitk::Equal(planegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: depth in mm", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: AxisVectorRight", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: AxisVectorBottom", mitk::Equal(planegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing correct Standard Plane initialization with custom Spacing: AxisVectorNormal", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); ; } void TestSetExtendInMM() { normal.Normalize(); normal *= thicknessInMM; planegeometry->SetExtentInMM(2, thicknessInMM); CPPUNIT_ASSERT_MESSAGE("Testing SetExtentInMM(2, ...), querying by GetExtentInMM(2): ", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing SetExtentInMM(2, ...), querying by GetAxisVector(2) and comparing to normal: ", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); planegeometry->SetOrigin(origin); CPPUNIT_ASSERT_MESSAGE("Testing SetOrigin", mitk::Equal(planegeometry->GetOrigin(), origin, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() after SetOrigin: Right", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() after SetOrigin: Bottom", mitk::Equal(planegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() after SetOrigin: Normal", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); mappingTests2D(planegeometry, width, height, widthInMM, heightInMM, origin, right, bottom); } void TestRotate() { // Changing the IndexToWorldTransform to a rotated version by SetIndexToWorldTransform() (keep origin): mitk::AffineTransform3D::Pointer transform = mitk::AffineTransform3D::New(); mitk::AffineTransform3D::MatrixType::InternalMatrixType vnlmatrix; vnlmatrix = planegeometry->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix(); mitk::VnlVector axis(3); mitk::FillVector3D(axis, 1.0, 1.0, 1.0); axis.normalize(); vnl_quaternion rotation(axis, 0.223); vnlmatrix = rotation.rotation_matrix_transpose() * vnlmatrix; mitk::Matrix3D matrix; matrix = vnlmatrix; transform->SetMatrix(matrix); transform->SetOffset(planegeometry->GetIndexToWorldTransform()->GetOffset()); right.SetVnlVector(rotation.rotation_matrix_transpose() * right.GetVnlVector()); bottom.SetVnlVector(rotation.rotation_matrix_transpose() * bottom.GetVnlVector()); normal.SetVnlVector(rotation.rotation_matrix_transpose() * normal.GetVnlVector()); planegeometry->SetIndexToWorldTransform(transform); // The origin changed,because m_Origin=m_IndexToWorldTransform->GetOffset()+GetAxisVector(2)*0.5 // and the AxisVector changes due to the rotation. In other words: the rotation was done around // the corner of the box, not around the planes origin. Now change it to a rotation around // the origin, simply by re-setting the origin to the original one: planegeometry->SetOrigin(origin); CPPUNIT_ASSERT_MESSAGE("Testing whether SetIndexToWorldTransform kept origin: ", mitk::Equal(planegeometry->GetOrigin(), origin, testEps)); mitk::Point2D point; point[0] = 4; point[1] = 3; mitk::Point2D dummy; planegeometry->WorldToIndex(point, dummy); planegeometry->IndexToWorld(dummy, dummy); CPPUNIT_ASSERT_MESSAGE("Testing consistency of index and world coordinates.", dummy == point); CPPUNIT_ASSERT_MESSAGE("Testing width of rotated version: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height of rotated version: ", mitk::Equal(planegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness of rotated version: ", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of rotated version: right ", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of rotated version: bottom", mitk::Equal(planegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of rotated version: normal", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing GetAxisVector(direction).GetNorm() != planegeometry->GetExtentInMM(direction) of rotated version: ", mitk::Equal(planegeometry->GetAxisVector(0).GetNorm(), planegeometry->GetExtentInMM(0), testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing GetAxisVector(direction).GetNorm() != planegeometry->GetExtentInMM(direction) of rotated version: ", mitk::Equal(planegeometry->GetAxisVector(1).GetNorm(), planegeometry->GetExtentInMM(1), testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing GetAxisVector(direction).GetNorm() != planegeometry->GetExtentInMM(direction) of rotated version: ", mitk::Equal(planegeometry->GetAxisVector(2).GetNorm(), planegeometry->GetExtentInMM(2), testEps)); mappingTests2D(planegeometry, width, height, widthInMM, heightInMM, origin, right, bottom); width *= 2; height *= 3; planegeometry->SetSizeInUnits(width, height); CPPUNIT_ASSERT_MESSAGE("Testing SetSizeInUnits() of rotated version: ", mitk::Equal(planegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing SetSizeInUnits() of rotated version: ", mitk::Equal(planegeometry->GetExtent(1), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing SetSizeInUnits() of rotated version: ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width (in mm) of version with changed size in units: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in mm) of version with changed size in units: ", mitk::Equal(planegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness (in mm) of version with changed size in units: ", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of version with changed size in units: right ", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of version with changed size in units: bottom", mitk::Equal(planegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of version with changed size in units: normal", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing GetAxisVector(direction).GetNorm() != planegeometry->GetExtentInMM(direction) of rotated version: ", mitk::Equal(planegeometry->GetAxisVector(0).GetNorm(), planegeometry->GetExtentInMM(0), testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing GetAxisVector(direction).GetNorm() != planegeometry->GetExtentInMM(direction) of rotated version: ", mitk::Equal(planegeometry->GetAxisVector(1).GetNorm(), planegeometry->GetExtentInMM(1), testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing GetAxisVector(direction).GetNorm() != planegeometry->GetExtentInMM(direction) of rotated version: ", mitk::Equal(planegeometry->GetAxisVector(2).GetNorm(), planegeometry->GetExtentInMM(2), testEps)); mappingTests2D(planegeometry, width, height, widthInMM, heightInMM, origin, right, bottom); } void TestClone() { mitk::PlaneGeometry::Pointer clonedplanegeometry = dynamic_cast(planegeometry->Clone().GetPointer()); // Cave: Statement below is negated! CPPUNIT_ASSERT_MESSAGE("Testing Clone(): ", !((clonedplanegeometry.IsNull()) || (clonedplanegeometry->GetReferenceCount() != 1))); CPPUNIT_ASSERT_MESSAGE("Testing origin of cloned version: ", mitk::Equal(clonedplanegeometry->GetOrigin(), origin, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width (in units) of cloned version: ", mitk::Equal(clonedplanegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in units) of cloned version: ", mitk::Equal(clonedplanegeometry->GetExtent(1), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing extent (in units) of cloned version: ", mitk::Equal(clonedplanegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width (in mm) of cloned version: ", mitk::Equal(clonedplanegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in mm) of cloned version: ", mitk::Equal(clonedplanegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness (in mm) of cloned version: ", mitk::Equal(clonedplanegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of cloned version: right", mitk::Equal(clonedplanegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of cloned version: bottom", mitk::Equal(clonedplanegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of cloned version: normal", mitk::Equal(clonedplanegeometry->GetAxisVector(2), normal, testEps)); mappingTests2D(clonedplanegeometry, width, height, widthInMM, heightInMM, origin, right, bottom); } void TestSaggitalInitialization() { mitk::Point3D cornerpoint0 = planegeometry->GetCornerPoint(0); mitk::PlaneGeometry::Pointer clonedplanegeometry = planegeometry->Clone(); // Testing InitializeStandardPlane(clonedplanegeometry, planeorientation = Sagittal, zPosition = 0, frontside=true): planegeometry->InitializeStandardPlane(clonedplanegeometry, mitk::PlaneGeometry::Sagittal); mitk::Vector3D newright, newbottom, newnormal; mitk::ScalarType newthicknessInMM; newright = bottom; newthicknessInMM = widthInMM / width * 1.0; // extent in normal direction is 1; newnormal = right; newnormal.Normalize(); newnormal *= newthicknessInMM; newbottom = normal; newbottom.Normalize(); newbottom *= thicknessInMM; CPPUNIT_ASSERT_MESSAGE("Testing GetCornerPoint(0) of sagitally initialized version:", mitk::Equal(planegeometry->GetCornerPoint(0), cornerpoint0, testEps)); // ok, corner was fine, so we can dare to believe the origin is ok. origin = planegeometry->GetOrigin(); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in units) of sagitally initialized version: ", mitk::Equal(planegeometry->GetExtent(0), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in units) of sagitally initialized version: ", mitk::Equal(planegeometry->GetExtent(1), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in units) of sagitally initialized version: ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in mm) of sagitally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(0), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in mm) of sagitally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(1), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in mm) of sagitally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(2), newthicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of sagitally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(0), newright, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of sagitally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(1), newbottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of sagitally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(2), newnormal, testEps)); mappingTests2D(planegeometry, height, 1, heightInMM, thicknessInMM, origin, newright, newbottom); // set origin back to the one of the axial slice: origin = clonedplanegeometry->GetOrigin(); // Testing backside initialization: InitializeStandardPlane(clonedplanegeometry, planeorientation = Axial, zPosition // = 0, frontside=false, rotated=true): planegeometry->InitializeStandardPlane(clonedplanegeometry, mitk::PlaneGeometry::Axial, 0, false, true); mitk::Point3D backsideorigin; backsideorigin = origin + clonedplanegeometry->GetAxisVector(1); //+clonedplanegeometry->GetAxisVector(2); CPPUNIT_ASSERT_MESSAGE("Testing origin of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetOrigin(), backsideorigin, testEps)); mitk::Point3D backsidecornerpoint0; backsidecornerpoint0 = cornerpoint0 + clonedplanegeometry->GetAxisVector(1); //+clonedplanegeometry->GetAxisVector(2); CPPUNIT_ASSERT_MESSAGE("Testing GetCornerPoint(0) of sagitally initialized version: ", mitk::Equal(planegeometry->GetCornerPoint(0), backsidecornerpoint0, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in units) of backsidedly, axially initialized version " "(should be same as in mm due to unit spacing, except for thickness, which is always 1): ", mitk::Equal(planegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in units) of backsidedly, axially initialized version " "(should be same as in mm due to unit spacing, except for thickness, which is always 1): ", mitk::Equal(planegeometry->GetExtent(1), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in units) of backsidedly, axially initialized version " "(should be same as in mm due to unit spacing, except for thickness, which is always 1): ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in mm) of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in mm) of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width, height and thickness (in mm) of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetAxisVector(1), -bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of backsidedly, axially initialized version: ", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); // T22254: Flipped sign mappingTests2D(planegeometry, width, height, widthInMM, heightInMM, backsideorigin, right, -bottom); } void TestFrontalInitialization() { mitk::Point3D cornerpoint0 = planegeometry->GetCornerPoint(0); mitk::PlaneGeometry::Pointer clonedplanegeometry = dynamic_cast(planegeometry->Clone().GetPointer()); //-------- mitk::Vector3D newright, newbottom, newnormal; mitk::ScalarType newthicknessInMM; // Testing InitializeStandardPlane(clonedplanegeometry, planeorientation = Frontal, zPosition = 0, frontside=true) planegeometry->InitializeStandardPlane(clonedplanegeometry, mitk::PlaneGeometry::Frontal); newright = right; newbottom = normal; newbottom.Normalize(); newbottom *= thicknessInMM; newthicknessInMM = heightInMM / height * 1.0 /*extent in normal direction is 1*/; newnormal = -bottom; newnormal.Normalize(); newnormal *= newthicknessInMM; CPPUNIT_ASSERT_MESSAGE("Testing GetCornerPoint(0) of frontally initialized version: ", mitk::Equal(planegeometry->GetCornerPoint(0), cornerpoint0, testEps)); // ok, corner was fine, so we can dare to believe the origin is ok. origin = planegeometry->GetOrigin(); CPPUNIT_ASSERT_MESSAGE("Testing width (in units) of frontally initialized version: ", mitk::Equal(planegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in units) of frontally initialized version: ", mitk::Equal(planegeometry->GetExtent(1), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness (in units) of frontally initialized version: ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width (in mm) of frontally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in mm) of frontally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(1), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness (in mm) of frontally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(2), newthicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of frontally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(0), newright, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of frontally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(1), newbottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of frontally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(2), -newnormal, testEps)); // T22254: Flipped sign mappingTests2D(planegeometry, width, 1, widthInMM, thicknessInMM, origin, newright, newbottom); // Changing plane to in-plane unit spacing using SetSizeInUnits: planegeometry->SetSizeInUnits(planegeometry->GetExtentInMM(0), planegeometry->GetExtentInMM(1)); CPPUNIT_ASSERT_MESSAGE("Testing origin of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetOrigin(), origin, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in units) of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetExtent(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in units) of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetExtent(1), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in units) of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in mm) of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in mm) of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(1), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in mm) of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(2), newthicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(0), newright, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(1), newbottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(2), -newnormal, testEps)); // T22254: Flipped sign mappingTests2D(planegeometry, widthInMM, thicknessInMM, widthInMM, thicknessInMM, origin, newright, newbottom); // Changing plane to unit spacing also in normal direction using SetExtentInMM(2, 1.0): planegeometry->SetExtentInMM(2, 1.0); newnormal.Normalize(); CPPUNIT_ASSERT_MESSAGE("Testing origin of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetOrigin(), origin, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in units) of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetExtent(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in units) of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetExtent(1), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in units) of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in mm) of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in mm) of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(1), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE( "Testing width, height and thickness (in mm) of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(2), 1.0, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(0), newright, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(1), newbottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of unit spaced, frontally initialized version: ", mitk::Equal(planegeometry->GetAxisVector(2), -newnormal, testEps)); // T22254: Flipped sign mappingTests2D(planegeometry, widthInMM, thicknessInMM, widthInMM, thicknessInMM, origin, newright, newbottom); } void TestAxialInitialization() { mitk::Point3D cornerpoint0 = planegeometry->GetCornerPoint(0); // Clone, move, rotate and test for 'IsParallel' and 'IsOnPlane' mitk::PlaneGeometry::Pointer clonedplanegeometry = dynamic_cast(planegeometry->Clone().GetPointer()); CPPUNIT_ASSERT_MESSAGE("Testing Clone(): ", !((clonedplanegeometry.IsNull()) || (clonedplanegeometry->GetReferenceCount() != 1))); std::cout << "Testing InitializeStandardPlane(clonedplanegeometry, planeorientation = Axial, zPosition = 0, " "frontside=true): " << std::endl; planegeometry->InitializeStandardPlane(clonedplanegeometry); CPPUNIT_ASSERT_MESSAGE("Testing origin of axially initialized version: ", mitk::Equal(planegeometry->GetOrigin(), origin)); CPPUNIT_ASSERT_MESSAGE("Testing GetCornerPoint(0) of axially initialized version: ", mitk::Equal(planegeometry->GetCornerPoint(0), cornerpoint0)); CPPUNIT_ASSERT_MESSAGE("Testing width (in units) of axially initialized version (should be same as in mm due to " "unit spacing, except for thickness, which is always 1): ", mitk::Equal(planegeometry->GetExtent(0), width, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in units) of axially initialized version (should be same as in mm due to " "unit spacing, except for thickness, which is always 1): ", mitk::Equal(planegeometry->GetExtent(1), height, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness (in units) of axially initialized version (should be same as in mm due " "to unit spacing, except for thickness, which is always 1): ", mitk::Equal(planegeometry->GetExtent(2), 1, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing width (in mm) of axially initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(0), widthInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing height (in mm) of axially initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(1), heightInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing thickness (in mm) of axially initialized version: ", mitk::Equal(planegeometry->GetExtentInMM(2), thicknessInMM, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of axially initialized version: ", mitk::Equal(planegeometry->GetAxisVector(0), right, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of axially initialized version: ", mitk::Equal(planegeometry->GetAxisVector(1), bottom, testEps)); CPPUNIT_ASSERT_MESSAGE("Testing GetAxisVector() of axially initialized version: ", mitk::Equal(planegeometry->GetAxisVector(2), normal, testEps)); mappingTests2D(planegeometry, width, height, widthInMM, heightInMM, origin, right, bottom); } void TestPlaneComparison() { // Clone, move, rotate and test for 'IsParallel' and 'IsOnPlane' mitk::PlaneGeometry::Pointer clonedplanegeometry2 = dynamic_cast(planegeometry->Clone().GetPointer()); CPPUNIT_ASSERT_MESSAGE("Testing Clone(): ", !((clonedplanegeometry2.IsNull()) || (clonedplanegeometry2->GetReferenceCount() != 1))); CPPUNIT_ASSERT_MESSAGE("Testing wheter original and clone are at the same position", clonedplanegeometry2->IsOnPlane(planegeometry.GetPointer())); CPPUNIT_ASSERT_MESSAGE(" Asserting that origin is on the plane cloned plane:", clonedplanegeometry2->IsOnPlane(origin)); mitk::VnlVector newaxis(3); mitk::FillVector3D(newaxis, 1.0, 1.0, 1.0); newaxis.normalize(); vnl_quaternion rotation2(newaxis, 0.0); mitk::Vector3D clonednormal = clonedplanegeometry2->GetNormal(); mitk::Point3D clonedorigin = clonedplanegeometry2->GetOrigin(); auto planerot = new mitk::RotationOperation(mitk::OpROTATE, origin, clonedplanegeometry2->GetAxisVector(0), 180.0); clonedplanegeometry2->ExecuteOperation(planerot); CPPUNIT_ASSERT_MESSAGE(" Asserting that a flipped plane is still on the original plane: ", clonedplanegeometry2->IsOnPlane(planegeometry.GetPointer())); clonedorigin += clonednormal; clonedplanegeometry2->SetOrigin(clonedorigin); CPPUNIT_ASSERT_MESSAGE("Testing if the translated (cloned, flipped) plane is parallel to its origin plane: ", clonedplanegeometry2->IsParallel(planegeometry)); delete planerot; planerot = new mitk::RotationOperation(mitk::OpROTATE, origin, clonedplanegeometry2->GetAxisVector(0), 0.5); clonedplanegeometry2->ExecuteOperation(planerot); CPPUNIT_ASSERT_MESSAGE("Testing if a non-paralell plane gets recognized as not paralell [rotation +0.5 degree] : ", !clonedplanegeometry2->IsParallel(planegeometry)); delete planerot; planerot = new mitk::RotationOperation(mitk::OpROTATE, origin, clonedplanegeometry2->GetAxisVector(0), -1.0); clonedplanegeometry2->ExecuteOperation(planerot); CPPUNIT_ASSERT_MESSAGE("Testing if a non-paralell plane gets recognized as not paralell [rotation -0.5 degree] : ", !clonedplanegeometry2->IsParallel(planegeometry)); delete planerot; planerot = new mitk::RotationOperation(mitk::OpROTATE, origin, clonedplanegeometry2->GetAxisVector(0), 360.5); clonedplanegeometry2->ExecuteOperation(planerot); CPPUNIT_ASSERT_MESSAGE("Testing if a non-paralell plane gets recognized as paralell [rotation 360 degree] : ", clonedplanegeometry2->IsParallel(planegeometry)); } private: // helper Methods for the Tests mitk::PlaneGeometry::Pointer createPlaneGeometry() { mitk::Vector3D mySpacing; mySpacing[0] = 31; mySpacing[1] = 0.1; mySpacing[2] = 5.4; mitk::Point3D myOrigin; myOrigin[0] = 8; myOrigin[1] = 9; myOrigin[2] = 10; mitk::AffineTransform3D::Pointer myTransform = mitk::AffineTransform3D::New(); itk::Matrix transMatrix; transMatrix.Fill(0); transMatrix[0][0] = 1; transMatrix[1][1] = 2; transMatrix[2][2] = 4; myTransform->SetMatrix(transMatrix); mitk::PlaneGeometry::Pointer geometry2D = mitk::PlaneGeometry::New(); geometry2D->SetIndexToWorldTransform(myTransform); geometry2D->SetSpacing(mySpacing); geometry2D->SetOrigin(myOrigin); return geometry2D; } bool compareMatrix(itk::Matrix left, itk::Matrix right) { bool equal = true; for (int i = 0; i < 3; ++i) for (int j = 0; j < 3; ++j) equal &= mitk::Equal(left[i][j], right[i][j]); return equal; } /** * This function tests for correct mapping and is called several times from other tests **/ void mappingTests2D(const mitk::PlaneGeometry *planegeometry, const mitk::ScalarType &width, const mitk::ScalarType &height, const mitk::ScalarType &widthInMM, const mitk::ScalarType &heightInMM, const mitk::Point3D &origin, const mitk::Vector3D &right, const mitk::Vector3D &bottom) { std::cout << "Testing mapping Map(pt2d_mm(x=widthInMM/2.3,y=heightInMM/2.5), pt3d_mm) and compare with expected: "; mitk::Point2D pt2d_mm; mitk::Point3D pt3d_mm, expected_pt3d_mm; pt2d_mm[0] = widthInMM / 2.3; pt2d_mm[1] = heightInMM / 2.5; expected_pt3d_mm = origin + right * (pt2d_mm[0] / right.GetNorm()) + bottom * (pt2d_mm[1] / bottom.GetNorm()); planegeometry->Map(pt2d_mm, pt3d_mm); CPPUNIT_ASSERT_MESSAGE( "Testing mapping Map(pt2d_mm(x=widthInMM/2.3,y=heightInMM/2.5), pt3d_mm) and compare with expected", mitk::Equal(pt3d_mm, expected_pt3d_mm, testEps)); std::cout << "Testing mapping Map(pt3d_mm, pt2d_mm) and compare with expected: "; mitk::Point2D testpt2d_mm; planegeometry->Map(pt3d_mm, testpt2d_mm); std::cout << std::setprecision(12) << "Expected pt2d_mm " << pt2d_mm << std::endl; std::cout << std::setprecision(12) << "Result testpt2d_mm " << testpt2d_mm << std::endl; std::cout << std::setprecision(12) << "10*mitk::eps " << 10 * mitk::eps << std::endl; // This eps is temporarily set to 10*mitk::eps. See bug #15037 for details. CPPUNIT_ASSERT_MESSAGE("Testing mapping Map(pt3d_mm, pt2d_mm) and compare with expected", mitk::Equal(pt2d_mm, testpt2d_mm, 10 * mitk::eps)); std::cout << "Testing IndexToWorld(pt2d_units, pt2d_mm) and compare with expected: "; mitk::Point2D pt2d_units; pt2d_units[0] = width / 2.0; pt2d_units[1] = height / 2.0; pt2d_mm[0] = widthInMM / 2.0; pt2d_mm[1] = heightInMM / 2.0; planegeometry->IndexToWorld(pt2d_units, testpt2d_mm); std::cout << std::setprecision(12) << "Expected pt2d_mm " << pt2d_mm << std::endl; std::cout << std::setprecision(12) << "Result testpt2d_mm " << testpt2d_mm << std::endl; std::cout << std::setprecision(12) << "10*mitk::eps " << 10 * mitk::eps << std::endl; // This eps is temporarily set to 10*mitk::eps. See bug #15037 for details. CPPUNIT_ASSERT_MESSAGE("Testing IndexToWorld(pt2d_units, pt2d_mm) and compare with expected: ", mitk::Equal(pt2d_mm, testpt2d_mm, 10 * mitk::eps)); std::cout << "Testing WorldToIndex(pt2d_mm, pt2d_units) and compare with expected: "; mitk::Point2D testpt2d_units; planegeometry->WorldToIndex(pt2d_mm, testpt2d_units); std::cout << std::setprecision(12) << "Expected pt2d_units " << pt2d_units << std::endl; std::cout << std::setprecision(12) << "Result testpt2d_units " << testpt2d_units << std::endl; std::cout << std::setprecision(12) << "10*mitk::eps " << 10 * mitk::eps << std::endl; // This eps is temporarily set to 10*mitk::eps. See bug #15037 for details. CPPUNIT_ASSERT_MESSAGE("Testing WorldToIndex(pt2d_mm, pt2d_units) and compare with expected:", mitk::Equal(pt2d_units, testpt2d_units, 10 * mitk::eps)); } }; MITK_TEST_SUITE_REGISTRATION(mitkPlaneGeometry) diff --git a/Modules/Core/test/mitkPreferenceListReaderOptionsFunctorTest.cpp b/Modules/Core/test/mitkPreferenceListReaderOptionsFunctorTest.cpp index f81ee9152c..0559a8df0f 100644 --- a/Modules/Core/test/mitkPreferenceListReaderOptionsFunctorTest.cpp +++ b/Modules/Core/test/mitkPreferenceListReaderOptionsFunctorTest.cpp @@ -1,219 +1,219 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkPreferenceListReaderOptionsFunctor.h" #include "mitkTestFixture.h" #include "mitkTestingMacros.h" #include #include #include #include #include namespace mitk { class TestFileReaderService : public mitk::AbstractFileReader { public: TestFileReaderService(const std::string &description) : AbstractFileReader(CustomMimeType("TestMimeType"), description) { Options options; options["o1"] = 0; this->SetDefaultOptions(options); m_ServiceRegistration = RegisterService(); }; ~TestFileReaderService() override { }; using AbstractFileReader::Read; std::vector> DoRead() override { std::vector> result; return result; }; ConfidenceLevel GetConfidenceLevel() const override { return Supported; }; private: TestFileReaderService * Clone() const override { return new TestFileReaderService(*this); }; us::ServiceRegistration m_ServiceRegistration; }; } // namespace mitk class mitkPreferenceListReaderOptionsFunctorTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkPreferenceListReaderOptionsFunctorTestSuite); MITK_TEST(UsePreferenceList); MITK_TEST(UseBlackList); MITK_TEST(UseNoList); MITK_TEST(UseBlackAndPreferenceList); MITK_TEST(UseOverlappingBlackAndPreferenceList); MITK_TEST(UsePreferenceListWithInexistantReaders); MITK_TEST(UseAllBlackedList); MITK_TEST(SetOptions); CPPUNIT_TEST_SUITE_END(); private: std::string m_ImagePath; mitk::PreferenceListReaderOptionsFunctor::ListType preference; mitk::PreferenceListReaderOptionsFunctor::ListType black; mitk::PreferenceListReaderOptionsFunctor::ListType emptyList; mitk::TestFileReaderService* m_NormalService; mitk::TestFileReaderService* m_PrefService; mitk::TestFileReaderService* m_BlackService; mitk::CustomMimeType* m_TestMimeType; public: void setUp() override { m_ImagePath = GetTestDataFilePath("BallBinary30x30x30.nrrd"); preference = { "Prefered Test Service" }; black = { "Unwanted Test Service" }; emptyList = {}; m_TestMimeType = new mitk::CustomMimeType("TestMimeType"); m_TestMimeType->AddExtension("nrrd"); m_TestMimeType->SetCategory(mitk::IOMimeTypes::CATEGORY_IMAGES()); m_TestMimeType->SetComment("Test mime type"); us::ModuleContext *context = us::GetModuleContext(); us::ServiceProperties props; props[us::ServiceConstants::SERVICE_RANKING()] = 100; context->RegisterService(m_TestMimeType, props); m_NormalService = new mitk::TestFileReaderService("Normal Test Service"); m_PrefService = new mitk::TestFileReaderService("Prefered Test Service"); m_BlackService = new mitk::TestFileReaderService("Unwanted Test Service"); } void tearDown() override { delete m_PrefService; delete m_BlackService; delete m_NormalService; delete m_TestMimeType; } void UsePreferenceList() { mitk::IOUtil::LoadInfo info(m_ImagePath); mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor(preference, emptyList); CPPUNIT_ASSERT(true == functor(info)); auto description = info.m_ReaderSelector.GetSelected().GetDescription(); CPPUNIT_ASSERT_EQUAL(std::string("Prefered Test Service"), description); CPPUNIT_ASSERT("0" == info.m_ReaderSelector.GetSelected().GetReader()->GetOptions()["o1"].ToString()); } void UseNoList() { mitk::IOUtil::LoadInfo info(m_ImagePath); mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor(emptyList, emptyList); CPPUNIT_ASSERT(true == functor(info)); auto description = info.m_ReaderSelector.GetSelected().GetDescription(); CPPUNIT_ASSERT_EQUAL(std::string("Normal Test Service"), description); } void UseBlackList() { mitk::IOUtil::LoadInfo info(m_ImagePath); mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor(emptyList, black); CPPUNIT_ASSERT(true == functor(info)); auto description = info.m_ReaderSelector.GetSelected().GetDescription(); CPPUNIT_ASSERT(description != "Unwanted Test Service"); } void UseBlackAndPreferenceList() { mitk::IOUtil::LoadInfo info(m_ImagePath); mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor(preference, black); CPPUNIT_ASSERT(true == functor(info)); auto description = info.m_ReaderSelector.GetSelected().GetDescription(); CPPUNIT_ASSERT_EQUAL(std::string("Prefered Test Service"), description); } void UseOverlappingBlackAndPreferenceList() { mitk::IOUtil::LoadInfo info(m_ImagePath); black.push_back("Prefered Test Service"); black.push_back("Normal Test Service"); mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor(preference, black); CPPUNIT_ASSERT(true == functor(info)); auto description = info.m_ReaderSelector.GetSelected().GetDescription(); CPPUNIT_ASSERT_EQUAL(std::string("ITK NrrdImageIO"), description); } void UsePreferenceListWithInexistantReaders() { mitk::IOUtil::LoadInfo info(m_ImagePath); preference.push_back("InexistantReader"); mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor(preference, emptyList); CPPUNIT_ASSERT(true == functor(info)); auto description = info.m_ReaderSelector.GetSelected().GetDescription(); CPPUNIT_ASSERT_EQUAL(std::string("Prefered Test Service"), description); } void UseAllBlackedList() { mitk::IOUtil::LoadInfo info(m_ImagePath); - for (auto reader : info.m_ReaderSelector.Get()) + for (const auto &reader : info.m_ReaderSelector.Get()) { black.push_back(reader.GetDescription()); } mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor(emptyList, black); CPPUNIT_ASSERT_THROW(functor(info), mitk::Exception); } void SetOptions() { mitk::IOUtil::LoadInfo info(m_ImagePath); mitk::IFileReader::Options options; options.insert(std::make_pair("o1", 42)); mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor(preference, options); CPPUNIT_ASSERT(true == functor(info)); auto description = info.m_ReaderSelector.GetSelected().GetDescription(); CPPUNIT_ASSERT_EQUAL(std::string("Prefered Test Service"), description); CPPUNIT_ASSERT("42" == info.m_ReaderSelector.GetSelected().GetReader()->GetOption("o1").ToString()); } }; MITK_TEST_SUITE_REGISTRATION(mitkPreferenceListReaderOptionsFunctor) diff --git a/Modules/CoreCmdApps/CMakeLists.txt b/Modules/CoreCmdApps/CMakeLists.txt index 12d751c887..5841e7e289 100644 --- a/Modules/CoreCmdApps/CMakeLists.txt +++ b/Modules/CoreCmdApps/CMakeLists.txt @@ -1,7 +1,6 @@ option(BUILD_CoreCmdApps "Build command-line apps of the MitkCore module" OFF) if(BUILD_CoreCmdApps OR MITK_BUILD_ALL_APPS) mitkFunctionCreateCommandLineApp(NAME FileConverter) mitkFunctionCreateCommandLineApp(NAME ImageTypeConverter) - mitkFunctionCreateCommandLineApp(NAME RectifyImage) endif() diff --git a/Modules/CoreCmdApps/RectifyImage.cpp b/Modules/CoreCmdApps/RectifyImage.cpp deleted file mode 100644 index 664c13adb0..0000000000 --- a/Modules/CoreCmdApps/RectifyImage.cpp +++ /dev/null @@ -1,194 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include -#include -#include -#include - -template -void RectifyImage(mitk::Image::Pointer inputImage, mitk::Image::Pointer outputImage) -{ - mitk::ImagePixelReadAccessor pixelReadAccess(inputImage); - mitk::ImagePixelWriteAccessor pixelWriteAccess(outputImage); - - const auto DEPTH = static_cast(outputImage->GetDimension(2)); - const auto HEIGHT = static_cast(outputImage->GetDimension(1)); - const auto WIDTH = static_cast(outputImage->GetDimension(0)); - - auto geometry = outputImage->GetGeometry(); - itk::Index<3> index; - mitk::Point3D worldCoords; - - for (index[2] = 0; index[2] < DEPTH; ++index[2]) - { - for (index[1] = 0; index[1] < HEIGHT; ++index[1]) - { - for (index[0] = 0; index[0] < WIDTH; ++index[0]) - { - geometry->IndexToWorld(index, worldCoords); - pixelWriteAccess.SetPixelByIndex(index, pixelReadAccess.GetPixelByWorldCoordinates(worldCoords)); - } - } - } -} - -int main(int argc, char* argv[]) -{ - mitkCommandLineParser parser; - - parser.setTitle("Rectify Image"); - parser.setCategory("Basic Image Processing"); - parser.setDescription("Resample image based on standard world to index transform"); - parser.setContributor("German Cancer Research Center (DKFZ)"); - - parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", mitkCommandLineParser::Image, "Input Image", "Path to input image", us::Any(), false); - parser.addArgument("output", "o", mitkCommandLineParser::Image, "Output Image", "Path to output image", us::Any(), false); - - auto parsedArgs = parser.parseArguments(argc, argv); - - if (2 != parsedArgs.size() || 0 == parsedArgs.count("input") || 0 == parsedArgs.count("output")) - return EXIT_FAILURE; - - auto inputImagePath = us::any_value_to_string(parsedArgs["input"]); - mitk::Image::Pointer inputImage; - - try - { - inputImage = dynamic_cast(mitk::IOUtil::Load(inputImagePath)[0].GetPointer()); - } - catch (const mitk::Exception&) - { - return EXIT_FAILURE; - } - - if (3 != inputImage->GetDimension()) - { - MITK_ERROR << "Only 3-d images are supported."; - return EXIT_FAILURE; - } - - auto inputGeometry = inputImage->GetGeometry(); - - mitk::Point3D minInputIndex; - mitk::FillVector3D(minInputIndex, 0.0, 0.0, 0.0); - - mitk::Point3D minInputIndexInWorld; - inputGeometry->IndexToWorld(minInputIndex, minInputIndexInWorld); - - mitk::Point3D maxInputIndex; - for (int i = 0; i < 3; ++i) - maxInputIndex[i] = inputGeometry->GetExtent(i) - 1; - - mitk::Point3D maxInputIndexInWorld; - inputGeometry->IndexToWorld(maxInputIndex, maxInputIndexInWorld); - - mitk::Point3D minOutputIndexInWorld; - for (int i = 0; i < 3; ++i) - minOutputIndexInWorld[i] = std::min(minInputIndexInWorld[i], maxInputIndexInWorld[i]); - - mitk::Point3D maxOutputIndexInWorld; - for (int i = 0; i < 3; ++i) - maxOutputIndexInWorld[i] = std::max(minInputIndexInWorld[i], maxInputIndexInWorld[i]); - - mitk::Vector3D spacing = inputGeometry->GetSpacing(); - auto transform = inputGeometry->GetIndexToWorldTransform()->Clone(); - auto matrix = transform->GetMatrix(); - - for (int i = 0; i < 3; ++i) - { - for (int j = 0; j < 3; ++j) - { - matrix[i][j] = std::abs(matrix[i][j]) / spacing[j]; - } - } - - transform->SetMatrix(matrix); - spacing = transform->TransformVector(spacing); - - mitk::Vector3D outputExtent = (maxOutputIndexInWorld - minOutputIndexInWorld + spacing); - for (int i = 0; i < 3; ++i) - outputExtent[i] /= spacing[i]; - - mitk::Point3D origin = minOutputIndexInWorld; - - mitk::Vector3D right; - mitk::FillVector3D(right, outputExtent[0], 0.0, 0.0); - - mitk::Vector3D down; - mitk::FillVector3D(down, 0.0, outputExtent[1], 0.0); - - auto planeGeometry = mitk::PlaneGeometry::New(); - planeGeometry->InitializeStandardPlane(right, down, &spacing); - planeGeometry->SetOrigin(origin); - planeGeometry->SetImageGeometry(true); - - auto slicedGeometry = mitk::SlicedGeometry3D::New(); - slicedGeometry->InitializeEvenlySpaced(planeGeometry, static_cast(outputExtent[2])); - - auto outputGeometry = mitk::ProportionalTimeGeometry::New(); - outputGeometry->SetTimeStepGeometry(slicedGeometry, 0); - - auto pixelType = inputImage->GetPixelType(); - - auto outputImage = mitk::Image::New(); - outputImage->Initialize(pixelType, *outputGeometry); - - try - { - switch (pixelType.GetComponentType()) - { - case itk::ImageIOBase::CHAR: - RectifyImage(inputImage, outputImage); - break; - - case itk::ImageIOBase::UCHAR: - RectifyImage(inputImage, outputImage); - break; - - case itk::ImageIOBase::SHORT: - RectifyImage(inputImage, outputImage); - break; - - case itk::ImageIOBase::USHORT: - RectifyImage(inputImage, outputImage); - break; - - default: - MITK_ERROR << "Pixel type is not supported."; - return EXIT_FAILURE; - } - } - catch (const mitk::Exception &e) - { - MITK_ERROR << e.GetDescription(); - return EXIT_FAILURE; - } - - auto outputImagePath = us::any_value_to_string(parsedArgs["output"]); - - try - { - mitk::IOUtil::Save(outputImage, outputImagePath); - } - catch (const mitk::Exception &) - { - return EXIT_FAILURE; - } - - return EXIT_SUCCESS; -} diff --git a/Modules/CppMicroServices/CMakeLists.txt b/Modules/CppMicroServices/CMakeLists.txt index fc114d6bdb..b801ea8334 100644 --- a/Modules/CppMicroServices/CMakeLists.txt +++ b/Modules/CppMicroServices/CMakeLists.txt @@ -1,444 +1,444 @@ project(CppMicroServices) set(${PROJECT_NAME}_MAJOR_VERSION 2) set(${PROJECT_NAME}_MINOR_VERSION 99) set(${PROJECT_NAME}_PATCH_VERSION 0) set(${PROJECT_NAME}_VERSION ${${PROJECT_NAME}_MAJOR_VERSION}.${${PROJECT_NAME}_MINOR_VERSION}.${${PROJECT_NAME}_PATCH_VERSION}) -cmake_minimum_required(VERSION 2.8) -cmake_policy(VERSION 2.8) +cmake_minimum_required(VERSION 2.8.12) +cmake_policy(VERSION 2.8.12) cmake_policy(SET CMP0017 NEW) #----------------------------------------------------------------------------- # Update CMake module path #------------------------------------------------------------------------------ set(US_CMAKE_DIR ${PROJECT_SOURCE_DIR}/cmake) set(CMAKE_MODULE_PATH ${US_CMAKE_DIR} ${CMAKE_MODULE_PATH} ) #----------------------------------------------------------------------------- # CMake function(s) and macro(s) #----------------------------------------------------------------------------- include(CMakeParseArguments) include(CMakePackageConfigHelpers) include(CheckCXXSourceCompiles) include(usFunctionAddResources) include(usFunctionEmbedResources) include(usFunctionGetResourceSource) include(usFunctionCheckResourceLinking) include(usFunctionCheckCompilerFlags) include(usFunctionGetGccVersion) include(usFunctionGenerateModuleInit) include(usMacroCreateModule) if(US_BUILD_TESTING) include(usFunctionCompileSnippets) endif() #----------------------------------------------------------------------------- # Init output directories #----------------------------------------------------------------------------- set(US_ARCHIVE_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/lib") set(US_LIBRARY_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/lib") set(US_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin") foreach(_type ARCHIVE LIBRARY RUNTIME) if(NOT CMAKE_${_type}_OUTPUT_DIRECTORY) set(CMAKE_${_type}_OUTPUT_DIRECTORY ${US_${_type}_OUTPUT_DIRECTORY}) endif() endforeach() #----------------------------------------------------------------------------- # 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() #----------------------------------------------------------------------------- # CMake options #----------------------------------------------------------------------------- function(us_cache_var _var_name _var_default _var_type _var_help) set(_advanced 0) set(_force) foreach(_argn ${ARGN}) if(_argn STREQUAL ADVANCED) set(_advanced 1) elseif(_argn STREQUAL FORCE) set(_force FORCE) endif() endforeach() if(US_IS_EMBEDDED) if(NOT DEFINED ${_var_name} OR _force) set(${_var_name} ${_var_default} PARENT_SCOPE) endif() else() set(${_var_name} ${_var_default} CACHE ${_var_type} "${_var_help}" ${_force}) if(_advanced) mark_as_advanced(${_var_name}) endif() endif() endfunction() # Determine if we are being build inside a larger project if(NOT DEFINED US_IS_EMBEDDED) if(CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME) set(US_IS_EMBEDDED 0) else() set(US_IS_EMBEDDED 1) endif() endif() # Determine the name of the install component for "SDK" artifacts. # The default is "sdk" if(NOT DEFINED US_SDK_INSTALL_COMPONENT) set(US_SDK_INSTALL_COMPONENT COMPONENT sdk) elseif(US_SDK_INSTALL_COMPONENT) set(US_SDK_INSTALL_COMPONENT COMPONENT ${US_SDK_INSTALL_COMPONENT}) endif() us_cache_var(US_ENABLE_AUTOLOADING_SUPPORT OFF BOOL "Enable module auto-loading support") us_cache_var(US_ENABLE_THREADING_SUPPORT OFF BOOL "Enable threading support") us_cache_var(US_ENABLE_DEBUG_OUTPUT OFF BOOL "Enable debug messages" ADVANCED) us_cache_var(US_BUILD_SHARED_LIBS ON BOOL "Build shared libraries") us_cache_var(US_BUILD_TESTING OFF BOOL "Build tests") us_cache_var(US_BUILD_EXAMPLES OFF BOOL "Build example projects") if(US_BUILD_TESTING) enable_testing() endif() if(WIN32 AND NOT CYGWIN) set(default_runtime_install_dir bin/) set(default_library_install_dir bin/) set(default_archive_install_dir lib/) set(default_header_install_dir include/) set(default_auxiliary_install_dir share/) else() set(default_runtime_install_dir bin/) set(default_library_install_dir lib/${PROJECT_NAME}) set(default_archive_install_dir lib/${PROJECT_NAME}) set(default_header_install_dir include/${PROJECT_NAME}) set(default_auxiliary_install_dir share/${PROJECT_NAME}) endif() us_cache_var(RUNTIME_INSTALL_DIR ${default_runtime_install_dir} STRING "Relative install location for binaries" ADVANCED) us_cache_var(LIBRARY_INSTALL_DIR ${default_library_install_dir} STRING "Relative install location for libraries" ADVANCED) us_cache_var(ARCHIVE_INSTALL_DIR ${default_archive_install_dir} STRING "Relative install location for archives" ADVANCED) us_cache_var(HEADER_INSTALL_DIR ${default_header_install_dir} STRING "Relative install location for headers" ADVANCED) us_cache_var(AUXILIARY_INSTALL_DIR ${default_auxiliary_install_dir} STRING "Relative install location for auxiliary files" ADVANCED) set(AUXILIARY_CMAKE_INSTALL_DIR ${AUXILIARY_INSTALL_DIR}/cmake) us_cache_var(US_NAMESPACE "us" STRING "The namespace for the C++ Micro Services symbols") set(BUILD_SHARED_LIBS ${US_BUILD_SHARED_LIBS}) set(US_MODULE_INIT_TEMPLATE "${US_CMAKE_DIR}/usModuleInit.cpp" CACHE INTERNAL "The module initialization template code") set(US_RESOURCE_RC_TEMPLATE "${US_CMAKE_DIR}/us_resources.rc.in" CACHE INTERNAL "The Windows RC resource template") set(US_CMAKE_RESOURCE_DEPENDENCIES_CPP "${US_CMAKE_DIR}/usCMakeResourceDependencies.cpp" CACHE INTERNAL "The dummy resource dependencies code") #----------------------------------------------------------------------------- # US C/CXX Flags #----------------------------------------------------------------------------- if(US_IS_EMBEDDED) set(CMAKE_C_FLAGS) set(CMAKE_C_FLAGS_RELEASE) set(CMAKE_C_FLAGS_DEBUG) set(CMAKE_CXX_FLAGS) set(CMAKE_CXX_FLAGS_RELEASE) set(CMAKE_CXX_FLAGS_DEBUG) set(CMAKE_LINK_FLAGS) set(CMAKE_LINK_FLAGS_RELEASE) set(CMAKE_LINK_FLAGS_DEBUG) endif() # Set C++ compiler flags if(NOT MSVC) foreach(_cxxflag -Werror -Wall -Wextra -Wpointer-arith -Winvalid-pch -Wcast-align -Wwrite-strings -Woverloaded-virtual -Wnon-virtual-dtor -Wold-style-cast -Wstrict-null-sentinel -Wsign-promo -fdiagnostics-show-option -Wno-error=deprecated-copy -Wno-error=implicit-int-float-conversion) usFunctionCheckCompilerFlags(${_cxxflag} US_CXX_FLAGS) endforeach() endif() set(US_HAVE_VISIBILITY_ATTRIBUTE 0) usFunctionCheckCompilerFlags("-fvisibility=hidden -fvisibility-inlines-hidden" _have_visibility) if(_have_visibility) set(US_HAVE_VISIBILITY_ATTRIBUTE 1) endif() if(CMAKE_COMPILER_IS_GNUCXX) usFunctionGetGccVersion(${CMAKE_CXX_COMPILER} GCC_VERSION) if(${GCC_VERSION} VERSION_LESS "4.0.0") message(FATAL_ERROR "gcc version ${GCC_VERSION} not supported. Please use gcc >= 4.") endif() # With older versions of gcc the flag -fstack-protector-all requires an extra dependency to libssp.so. # If the gcc version is lower than 4.4.0 and the build type is Release let's not include the flag. if(${GCC_VERSION} VERSION_GREATER "4.4.0" OR (CMAKE_BUILD_TYPE STREQUAL "Debug" AND ${GCC_VERSION} VERSION_LESS "4.4.0")) usFunctionCheckCompilerFlags("-fstack-protector-all" US_CXX_FLAGS) endif() # Enable visibility support (only for gcc >= 4.5) # We only support hidden visibility with gcc for now. # # Clang has troubles with correctly marking template declarations and explicit template # instantiations as exported across shared library boundaries. Specifically, comparing # type_info objects from STL types does not work (used in us::Any::Type() == typeid(std::string)) # which could be related to the default visibility of STL types declared in libstdc++ and/or libc++ # but also to using RTLD_LOCAL or RTLD_GLOBAL when loading shared libraries via dlopen(). # # See http://comments.gmane.org/gmane.comp.compilers.clang.scm/50028 # and http://llvm.org/bugs/show_bug.cgi?id=10113 # if(_have_visibility AND NOT ${GCC_VERSION} VERSION_LESS "4.5") set(US_CXX_FLAGS "${US_CXX_FLAGS} ${_have_visibility}") else() set(US_GCC_RTTI_WORKAROUND_NEEDED 1) endif() usFunctionCheckCompilerFlags("-O1 -D_FORTIFY_SOURCE=2" _fortify_source_flag) if(_fortify_source_flag) set(US_CXX_FLAGS_RELEASE "${US_CXX_FLAGS_RELEASE} -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=2") endif() endif() if(MSVC) set(US_CXX_FLAGS "/MP /WX /wd4180 /wd4996 /wd4251 /wd4503 ${US_CXX_FLAGS}") endif() set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${US_CXX_FLAGS}") set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} ${US_CXX_FLAGS_RELEASE}") set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${US_C_FLAGS}") set(CMAKE_C_FLAGS_REALEASE "${CMAKE_C_FLAGS_RELEASE} ${US_C_FLAGS_RELEASE}") #----------------------------------------------------------------------------- # US Link Flags #----------------------------------------------------------------------------- set(US_LINK_FLAGS ) if(CMAKE_COMPILER_IS_GNUCXX AND NOT APPLE) foreach(_linkflag -Wl,--no-undefined) set(_add_flag) usFunctionCheckCompilerFlags("${_linkflag}" _add_flag) if(_add_flag) set(US_LINK_FLAGS "${US_LINK_FLAGS} ${_linkflag}") endif() endforeach() endif() usFunctionCheckResourceLinking() #----------------------------------------------------------------------------- # US Header Checks #----------------------------------------------------------------------------- include(CheckIncludeFileCXX) include(CheckCXXSourceCompiles) CHECK_INCLUDE_FILE_CXX(cxxabi.h US_HAVE_CXXABI_H) CHECK_INCLUDE_FILE_CXX(stdint.h US_HAVE_STDINT_H) CHECK_INCLUDE_FILE_CXX(tr1/unordered_map US_HAVE_TR1_UNORDERED_MAP_H) CHECK_INCLUDE_FILE_CXX(tr1/unordered_set US_HAVE_TR1_UNORDERED_SET_H) CHECK_INCLUDE_FILE_CXX(tr1/functional US_HAVE_TR1_FUNCTIONAL_H) CHECK_INCLUDE_FILE_CXX(unordered_map US_HAVE_UNORDERED_MAP_H) CHECK_INCLUDE_FILE_CXX(unordered_set US_HAVE_UNORDERED_SET_H) CHECK_INCLUDE_FILE_CXX(functional US_HAVE_FUNCTIONAL_H) if(US_HAVE_UNORDERED_MAP_H) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::unordered_map m; return 0; }" US_HAVE_TR1_UNORDERED_MAP) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::unordered_map m; return 0; }" US_HAVE_STD_UNORDERED_MAP) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::hash(); return 0; }" US_HAVE_TR1_HASH) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::hash(); return 0; }" US_HAVE_STD_HASH) if(US_HAVE_STD_HASH) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend struct std::hash; }; int main() { return 0; }" US_HAVE_STD_HASH_STRUCT) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend class std::hash; }; int main() { return 0; }" US_HAVE_STD_HASH_CLASS) elseif(US_HAVE_TR1_HASH) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend struct std::tr1::hash; }; int main() { return 0; }" US_HAVE_TR1_HASH_STRUCT) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend class std::tr1::hash; }; int main() { return 0; }" US_HAVE_TR1_HASH_CLASS) endif() elseif(US_HAVE_TR1_UNORDERED_MAP_H) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::unordered_map m; return 0; }" US_HAVE_TR1_UNORDERED_MAP) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::unordered_map m; return 0; }" US_HAVE_STD_UNORDERED_MAP) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::hash(); return 0; }" US_HAVE_TR1_HASH) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::hash(); return 0; }" US_HAVE_STD_HASH) if(US_HAVE_STD_HASH) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend struct std::hash; }; int main() { return 0; }" US_HAVE_STD_HASH_STRUCT) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend class std::hash; }; int main() { return 0; }" US_HAVE_STD_HASH_CLASS) elseif(US_HAVE_TR1_HASH) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend struct std::tr1::hash; }; int main() { return 0; }" US_HAVE_TR1_HASH_STRUCT) CHECK_CXX_SOURCE_COMPILES("#include \nstruct A { friend class std::tr1::hash; }; int main() { return 0; }" US_HAVE_TR1_HASH_CLASS) endif() else() message(SEND_ERROR "The header file \"unordered_map\" is not available.") endif() if(NOT (US_HAVE_TR1_UNORDERED_MAP OR US_HAVE_STD_UNORDERED_MAP)) message(SEND_ERROR "The \"unordered_map\" type is not available.") endif() if(US_HAVE_UNORDERED_SET_H) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::unordered_set s; return 0; }" US_HAVE_TR1_UNORDERED_SET) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::unordered_set s; return 0; }" US_HAVE_STD_UNORDERED_SET) elseif(US_HAVE_TR1_UNORDERED_SET_H) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::unordered_set s; return 0; }" US_HAVE_TR1_UNORDERED_SET) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::unordered_set s; return 0; }" US_HAVE_STD_UNORDERED_SET) else() message(SEND_ERROR "The header file \"unordered_set\" is not available.") endif() if(NOT (US_HAVE_TR1_UNORDERED_SET OR US_HAVE_STD_UNORDERED_SET)) message(SEND_ERROR "The \"unordered_set\" type is not available.") endif() if(NOT (US_HAVE_FUNCTIONAL_H OR US_HAVE_TR1_FUNCTIONAL_H)) message(SEND_ERROR "The header file \"functional\" is not available.") endif() if(US_HAVE_FUNCTIONAL_H) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::function f(main); return 0; }" US_HAVE_TR1_FUNCTION) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::function f(main); return 0; }" US_HAVE_STD_FUNCTION) endif() if((NOT (US_HAVE_STD_FUNCTION OR US_HAVE_TR1_FUNCTION)) AND US_HAVE_TR1_FUNCTIONAL_H) unset(US_HAVE_TR1_FUNCTION CACHE) unset(US_HAVE_STD_FUNCTION CACHE) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::tr1::function f(main); return 0; }" US_HAVE_TR1_FUNCTION) CHECK_CXX_SOURCE_COMPILES("#include \nint main() { std::function f(main); return 0; }" US_HAVE_STD_FUNCTION) endif() if(NOT (US_HAVE_STD_FUNCTION OR US_HAVE_TR1_FUNCTION)) message(SEND_ERROR "The \"function\" type is not available.") endif() #----------------------------------------------------------------------------- # Source directory #----------------------------------------------------------------------------- set(US_INCLUDE_DIRS ${PROJECT_SOURCE_DIR}/third_party ${PROJECT_BINARY_DIR}/include) # Configure CppMicroServicesConfig.cmake for the build tree. # The file is used in sub-directories. set(PACKAGE_CONFIG_INCLUDE_DIR ${US_INCLUDE_DIRS}) set(PACKAGE_CONFIG_RUNTIME_DIR ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}) set(PACKAGE_CONFIG_CMAKE_DIR ${US_CMAKE_DIR}) set(US_RCC_EXECUTABLE_NAME usResourceCompiler CACHE INTERNAL "The target name of the usResourceCompiler executable.") configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/${PROJECT_NAME}Config.cmake.in ${PROJECT_BINARY_DIR}/${PROJECT_NAME}Config.cmake @ONLY ) set(us_global_config_h_file "${PROJECT_BINARY_DIR}/include/usGlobalConfig.h") configure_file(${US_CMAKE_DIR}/usGlobalConfig.h.in ${us_global_config_h_file}) include_directories(${US_INCLUDE_DIRS}) add_subdirectory(tools) add_subdirectory(core) #----------------------------------------------------------------------------- # Documentation #----------------------------------------------------------------------------- add_subdirectory(doc) #----------------------------------------------------------------------------- # Last configuration and install steps #----------------------------------------------------------------------------- # Version information configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/${PROJECT_NAME}ConfigVersion.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake @ONLY ) export(TARGETS ${US_RCC_EXECUTABLE_NAME} FILE ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}Targets.cmake) if(NOT US_NO_INSTALL) install(EXPORT ${PROJECT_NAME}Targets FILE ${PROJECT_NAME}Targets.cmake DESTINATION ${AUXILIARY_CMAKE_INSTALL_DIR}) set(_install_cmake_scripts ${US_MODULE_INIT_TEMPLATE} ${US_CMAKE_RESOURCE_DEPENDENCIES_CPP} ${US_CMAKE_DIR}/usFunctionGenerateModuleInit.cmake ${US_CMAKE_DIR}/usFunctionAddResources.cmake ${US_CMAKE_DIR}/usFunctionEmbedResources.cmake ${US_CMAKE_DIR}/usFunctionGetResourceSource.cmake ${US_CMAKE_DIR}/usFunctionCheckResourceLinking.cmake ${US_CMAKE_DIR}/usFunctionCheckCompilerFlags.cmake ) install(FILES ${_install_cmake_scripts} DESTINATION ${AUXILIARY_CMAKE_INSTALL_DIR}) install(FILES ${us_global_config_h_file} DESTINATION ${HEADER_INSTALL_DIR}) # Configure CppMicroServicesConfig.cmake for the install tree set(CONFIG_INCLUDE_DIR ${HEADER_INSTALL_DIR}) set(CONFIG_RUNTIME_DIR ${RUNTIME_INSTALL_DIR}) set(CONFIG_CMAKE_DIR ${AUXILIARY_CMAKE_INSTALL_DIR}) configure_package_config_file( ${CMAKE_CURRENT_SOURCE_DIR}/${PROJECT_NAME}Config.cmake.in ${PROJECT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/${PROJECT_NAME}Config.cmake INSTALL_DESTINATION ${AUXILIARY_CMAKE_INSTALL_DIR} PATH_VARS CONFIG_INCLUDE_DIR CONFIG_RUNTIME_DIR CONFIG_CMAKE_DIR NO_SET_AND_CHECK_MACRO NO_CHECK_REQUIRED_COMPONENTS_MACRO ) install(FILES ${CMAKE_CURRENT_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/${PROJECT_NAME}Config.cmake ${CMAKE_CURRENT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake DESTINATION ${AUXILIARY_CMAKE_INSTALL_DIR} ${US_SDK_INSTALL_COMPONENT} ) endif() diff --git a/Modules/CppMicroServices/core/doc/doxygen/MicroServices_Resources.md b/Modules/CppMicroServices/core/doc/doxygen/MicroServices_Resources.md index c18d3bb0c9..9cb2102f78 100644 --- a/Modules/CppMicroServices/core/doc/doxygen/MicroServices_Resources.md +++ b/Modules/CppMicroServices/core/doc/doxygen/MicroServices_Resources.md @@ -1,75 +1,75 @@ The Resources System {#MicroServices_Resources} ==================== The C++ Micro Services library provides a generic resources system to embed arbitrary files into a module's shared library (the size limitation per resource is 2GB, due to the used ZIP format). The following features are supported: * Embed arbitrary data into shared or static modules or executables. * Data is embedded in a compressed format (zip) with a configurable compression level. * Resources are accessed via a Module instance, providing individual resource lookup and access for each module. * Resources are managed in a tree hierarchy, modeling the original child - parent relationship on the file-system. * The ModuleResource class provides a high-level API for accessing resource information and traversing the resource tree. * The ModuleResourceStream class provides an STL input stream derived class for the seamless usage of embedded resource data in third-party libraries. The following conventions and limitations apply: * Resource entries are stored with case-insensitive names. On case-sensitive file systemes, adding resources with the same name but different capitalization will lead to an error. * Looking up resources by name at runtime *is* case sensitive. * The CppMicroServices library will search for a valid zip file inside a shared library, starting from the end of the file. If other zip files are embedded in the module as well (e.g. as an additional resource embedded via the Windows RC compiler or using other techniques), it will stop at the first valid zip file and use it a the resource container. Embedding Resources in a %Module -------------------------------- Resources are embedded into a module's shared or static library (or into an executable) by using the `usResourceCompiler` executable. It will create a ZIP archive of all input files and can append it to the module file. -If you are using CMake, consider using the provided `#usFunctionEmbedResources` CMake macro which +If you are using CMake, consider using the provided `usFunctionEmbedResources` CMake macro which handles the invocation of the `usResourceCompiler` executable and sets up the correct file dependencies. Otherwise, you also need to make sure that the set of static modules linked into a shared module or executable is also in the input file list of your `usResourceCompiler` call for that shared module or executable. Here is a full example creating a module and embedding resource data: \include uServices-resources-cmake/CMakeLists_example.txt Accessing Resources at Runtime ------------------------------ Each module provides access to its embedded resources via the Module class which provides methods returning ModuleResource objects. The ModuleResourceStream class provides a std::istream compatible object to access the resource contents. The following example shows how to retrieve a resource from each currently loaded module whose path is specified by a module property: \snippet uServices-resources/main.cpp 2 This example could be enhanced to dynamically react to modules being loaded and unloaded, making use of the popular "extender pattern" from OSGi. Runtime overhead ---------------- The resources system has the following runtime characteristics: * During static initialization of a module, it's ZIP archive header data (if available) is parsed and stored in memory. * Querying `Module` or `ModuleResource` objects for resource information will not extract the embedded resource data and hence only has minimal runtime and memory overhead. * Creating a `ModuleResourceStream` object will allocate memory for the uncompressed resource data and inflate it. The memory will be free'ed after the `ModuleResourceStream` object is destroyed. diff --git a/Modules/CppMicroServices/core/doc/doxygen/MicroServices_TheModuleContext.md b/Modules/CppMicroServices/core/doc/doxygen/MicroServices_TheModuleContext.md index d3dd740cc0..15df41382c 100644 --- a/Modules/CppMicroServices/core/doc/doxygen/MicroServices_TheModuleContext.md +++ b/Modules/CppMicroServices/core/doc/doxygen/MicroServices_TheModuleContext.md @@ -1,38 +1,38 @@ The Module Context {#MicroServices_TheModuleContext} =================== In the context of the C++ Micro Services library, we will call all supported "shared library" types (DLL, DSO, DyLib, etc.) uniformly a *module*. A module accesses the C++ Micro Services API via a ModuleContext object, which is specific to each module. ### Creating a ModuleContext To create a ModuleContext object for a specific library, you have two options. If your project uses -CMake as the build system, use the supplied `#usFunctionGenerateModuleInit` CMake function to automatically +CMake as the build system, use the supplied `usFunctionGenerateModuleInit` CMake function to automatically create a source file and add it to your module's sources: ~~~{.cpp} set(module_srcs ) usFunctionGenerateModuleInit(module_srcs) add_library(mylib ${module_srcs}) set_property(TARGET ${mylib} APPEND PROPERTY COMPILE_DEFINITIONS US_MODULE_NAME=mylib) ~~~ You also need to specify a unique module name by using the `US_MODULE_NAME` compile definition as shown in the last line. The module name must be a valid C identifier and in the case of executables is required to be defined to `main`. If you do not use CMake, you have to add a call to the macro `#US_INITIALIZE_MODULE` in one of the source files of your module: \snippet uServices-modulecontext/main.cpp InitializeModule ### Getting a ModuleContext To retrieve the module specific ModuleContext object from anywhere in your module, use the -`#GetModuleContext` function: +`GetModuleContext` function: \snippet uServices-modulecontext/main.cpp GetModuleContext -Please note that trying to use `#GetModuleContext` without proper initialization code +Please note that trying to use `GetModuleContext` without proper initialization code in the using shared library while either lead to compile or rumtime errors. diff --git a/Modules/CppMicroServices/core/doc/doxygen/examples/MicroServices_Example1.md b/Modules/CppMicroServices/core/doc/doxygen/examples/MicroServices_Example1.md index 8b684bd413..afc7f9c11a 100644 --- a/Modules/CppMicroServices/core/doc/doxygen/examples/MicroServices_Example1.md +++ b/Modules/CppMicroServices/core/doc/doxygen/examples/MicroServices_Example1.md @@ -1,97 +1,97 @@ Example 1 - Service Event Listener {#MicroServices_Example1} ================================== This example creates a simple module that listens for service events. This example does not do much at first, because it only prints out the details of registering and unregistering services. In the next example we will create a module that implements a service, which will cause this module to actually do something. For now, we will just use this example to help us understand the basics of creating a module and its activator. A module gains access to the C++ Micro Services API using a unique instance of ModuleContext. This unique module context can be used during static initialization of the module or at any later point during the life-time of the module. To execute code during static initialization (and de-initialization) time, the module must provide an implementation of the ModuleActivator interface; this interface has two methods, Load() and Unload(), that both receive the module's context and are called when the module is loaded (statically initialized) and unloaded, respectively. \note You do not need to remember the ModuleContext instance within the ModuleActivator::Load() method and provide custom access methods for later retrieval. Use the GetModuleContext() function to easily retrieve the current module's context. In the following source code, our module implements the ModuleActivator interface and uses the context to add itself as a listener for service events (in the `eventlistener/Activator.cpp` file): \snippet eventlistener/Activator.cpp Activator After implementing the C++ source code for the module activator, we must *export* the activator such that the C++ Micro Services library can create an instance of it and call the `Load()` and `Unload()` methods: \dontinclude eventlistener/Activator.cpp \skipline US_EXPORT Now we need to compile the source code. This example uses CMake as the build system and the top-level CMakeLists.txt file could look like this: \dontinclude core/examples/CMakeLists.txt \skip project \until eventlistener and the CMakeLists.txt file in the eventlistener subdirectory is: \include eventlistener/CMakeLists.txt -The call to `#usFunctionGenerateModuleInit` is necessary to integrate the shared +The call to `usFunctionGenerateModuleInit` is necessary to integrate the shared library as a module within the C++ Micro Service library. If you are not using CMake, you have to place a macro call to `#US_INITIALIZE_MODULE` yourself into the module's source code, e.g. in `Activator.cpp`. Have a look at the Getting Started documentation for more details about using CMake or other build systems (e.g. Makefiles) when writing modules. To run the examples contained in the C++ Micro Services library, we use a small driver program called `usCoreExamplesDriver`: \verbatim CppMicroServices-build> bin/usCoreExamplesDriver > h h This help text l Load the module with id or name u Unload the module with id s Print status information q Quit > \endverbatim Typing `s` at the command prompt lists the available, loaded, and unloaded modules. To load the eventlistener module, type `l eventlistener` at the command prompt: \verbatim > s Id | Name | Status ----------------------------------- - | dictionaryclient | - - | dictionaryclient2 | - - | dictionaryclient3 | - - | dictionaryservice | - - | eventlistener | - - | frenchdictionary | - - | spellcheckclient | - - | spellcheckservice | - 1 | CppMicroServices | LOADED > l eventlistener Starting to listen for service events. > \endverbatim The above command loaded the eventlistener module (by loading its shared library). Keep in mind, that this module will not do much at this point since it only listens for service events and we are not registering any services. In the next example we will register a service that will generate an event for this module to receive. To exit the `usCoreExamplesDriver`, use the `q` command. Next: \ref MicroServices_Example2 diff --git a/Modules/DICOM/autoload/DICOMImageIO/src/mitkDICOMImageIOActivator.cpp b/Modules/DICOM/autoload/DICOMImageIO/src/mitkDICOMImageIOActivator.cpp index 95ea5f389d..785e1c0791 100644 --- a/Modules/DICOM/autoload/DICOMImageIO/src/mitkDICOMImageIOActivator.cpp +++ b/Modules/DICOM/autoload/DICOMImageIO/src/mitkDICOMImageIOActivator.cpp @@ -1,123 +1,123 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkDICOMImageIOActivator.h" #include "mitkAutoSelectingDICOMReaderService.h" #include "mitkManualSelectingDICOMReaderService.h" #include "mitkDICOMTagsOfInterestService.h" #include "mitkSimpleVolumeDICOMSeriesReaderService.h" #include "mitkCoreServices.h" #include "mitkPropertyPersistenceInfo.h" #include "mitkDICOMIOMetaInformationPropertyConstants.h" #include "mitkIPropertyPersistence.h" #include "mitkTemporoSpatialStringProperty.h" #include #include void AddPropertyPersistence(const mitk::PropertyKeyPath& propPath, bool temporoSpatial = false) { mitk::CoreServicePointer persistenceService(mitk::CoreServices::GetPropertyPersistence()); mitk::PropertyPersistenceInfo::Pointer info = mitk::PropertyPersistenceInfo::New(); if (propPath.IsExplicit()) { std::string name = mitk::PropertyKeyPathToPropertyName(propPath); std::string key = name; std::replace(key.begin(), key.end(), '.', '_'); info->SetNameAndKey(name, key); } else { std::string key = mitk::PropertyKeyPathToPersistenceKeyRegEx(propPath); std::string keyTemplate = mitk::PropertyKeyPathToPersistenceKeyTemplate(propPath); std::string propRegEx = mitk::PropertyKeyPathToPropertyRegEx(propPath); std::string propTemplate = mitk::PropertyKeyPathToPersistenceNameTemplate(propPath); info->UseRegEx(propRegEx, propTemplate, key, keyTemplate); } if (temporoSpatial) { info->SetDeserializationFunction(mitk::PropertyPersistenceDeserialization::deserializeJSONToTemporoSpatialStringProperty); info->SetSerializationFunction(mitk::PropertyPersistenceSerialization::serializeTemporoSpatialStringPropertyToJSON); } persistenceService->AddInfo(info); } namespace mitk { void DICOMImageIOActivator::Load(us::ModuleContext* context) { m_Context = context; m_AutoSelectingDICOMReader = std::make_unique(); m_SimpleVolumeDICOMSeriesReader = std::make_unique(); m_DICOMTagsOfInterestService = std::make_unique(); context->RegisterService(m_DICOMTagsOfInterestService.get()); DICOMTagPathMapType tagmap = GetDefaultDICOMTagsOfInterest(); - for (auto tag : tagmap) + for (const auto &tag : tagmap) { m_DICOMTagsOfInterestService->AddTagOfInterest(tag.first); } //add properties that should be persistent (if possible/supported by the writer) AddPropertyPersistence(mitk::DICOMIOMetaInformationPropertyConstants::READER_3D_plus_t()); AddPropertyPersistence(mitk::DICOMIOMetaInformationPropertyConstants::READER_CONFIGURATION()); AddPropertyPersistence(mitk::DICOMIOMetaInformationPropertyConstants::READER_DCMTK()); AddPropertyPersistence(mitk::DICOMIOMetaInformationPropertyConstants::READER_FILES(), true); AddPropertyPersistence(mitk::DICOMIOMetaInformationPropertyConstants::READER_GANTRY_TILT_CORRECTED()); AddPropertyPersistence(mitk::DICOMIOMetaInformationPropertyConstants::READER_GDCM()); AddPropertyPersistence(mitk::DICOMIOMetaInformationPropertyConstants::READER_IMPLEMENTATION_LEVEL()); AddPropertyPersistence(mitk::DICOMIOMetaInformationPropertyConstants::READER_IMPLEMENTATION_LEVEL_STRING()); AddPropertyPersistence(mitk::DICOMIOMetaInformationPropertyConstants::READER_PIXEL_SPACING_INTERPRETATION()); AddPropertyPersistence(mitk::DICOMIOMetaInformationPropertyConstants::READER_PIXEL_SPACING_INTERPRETATION_STRING()); //We have to handle ManualSelectingDICOMSeriesReader different then the other //readers. Reason: The reader uses DICOMFileReaderSelector in its constructor. //this class needs to access resources of MitkDICOM module, which might //not be initialized yet (that would lead to a crash, see i.a. T27553). Thus check if the module //is alreade loaded. If not, register a listener and create the reader as soon //as the module is available. auto dicomModule = us::ModuleRegistry::GetModule("MitkDICOM"); if (nullptr == dicomModule) { std::lock_guard lock(m_Mutex); // Listen for events of module life cycle. m_Context->AddModuleListener(this, &DICOMImageIOActivator::EnsureManualSelectingDICOMSeriesReader); } else { m_ManualSelectingDICOMSeriesReader = std::make_unique(); } } void DICOMImageIOActivator::Unload(us::ModuleContext*) { } void DICOMImageIOActivator::EnsureManualSelectingDICOMSeriesReader(const us::ModuleEvent event) { //We have to handle ManualSelectingDICOMSeriesReader different then the other //readers. For more details see the explanations in the constructor. std::lock_guard lock(m_Mutex); if (nullptr == m_ManualSelectingDICOMSeriesReader && event.GetModule()->GetName()=="MitkDICOM" && event.GetType() == us::ModuleEvent::LOADED) { m_ManualSelectingDICOMSeriesReader = std::make_unique(); } } } US_EXPORT_MODULE_ACTIVATOR(mitk::DICOMImageIOActivator) diff --git a/Modules/DICOM/src/mitkDICOMFilesHelper.cpp b/Modules/DICOM/src/mitkDICOMFilesHelper.cpp index 5cd3ed1ba2..d3e3d09f45 100644 --- a/Modules/DICOM/src/mitkDICOMFilesHelper.cpp +++ b/Modules/DICOM/src/mitkDICOMFilesHelper.cpp @@ -1,80 +1,80 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkDICOMFilesHelper.h" #include #include #include #include mitk::DICOMFilePathList mitk::GetDICOMFilesInSameDirectory(const std::string& filePath) { DICOMFilePathList result; if (!filePath.empty()) { std::string dir = filePath; if (!itksys::SystemTools::FileIsDirectory(filePath)) { dir = itksys::SystemTools::GetFilenamePath(filePath); } gdcm::Directory directoryLister; directoryLister.Load(dir.c_str(), false); // non-recursive result = FilterForDICOMFiles(directoryLister.GetFilenames()); } return result; }; mitk::DICOMFilePathList mitk::FilterForDICOMFiles(const DICOMFilePathList& fileList) { mitk::DICOMFilePathList result; itk::GDCMImageIO::Pointer io = itk::GDCMImageIO::New(); - for (auto aFile : fileList) + for (const auto &aFile : fileList) { if (io->CanReadFile(aFile.c_str())) { result.push_back(aFile); } } return result; }; mitk::DICOMFilePathList mitk::FilterDICOMFilesForSameSeries(const std::string& refFilePath, const DICOMFilePathList& fileList) { auto dicomFiles = FilterForDICOMFiles(fileList); //use the gdcm scanner directly instead of our wrapping classes, as it is a very simple task //and I want to spare the indirection/overhead. gdcm::Scanner scanner; const gdcm::Tag seriesInstanceUIDTag(0x0020, 0x000e); scanner.AddTag(seriesInstanceUIDTag); //Series Instance UID; scanner.Scan({ refFilePath }); auto uid = scanner.GetValue(refFilePath.c_str(), seriesInstanceUIDTag); if (uid != nullptr) { const std::string refUID = uid; scanner.Scan(dicomFiles); return scanner.GetAllFilenamesFromTagToValue(seriesInstanceUIDTag, refUID.c_str()); } return mitk::DICOMFilePathList(); } diff --git a/Modules/DICOM/src/mitkDICOMImageBlockDescriptor.cpp b/Modules/DICOM/src/mitkDICOMImageBlockDescriptor.cpp index 69ca0c9109..df4fa8ed0a 100644 --- a/Modules/DICOM/src/mitkDICOMImageBlockDescriptor.cpp +++ b/Modules/DICOM/src/mitkDICOMImageBlockDescriptor.cpp @@ -1,913 +1,913 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkDICOMImageBlockDescriptor.h" #include "mitkStringProperty.h" #include "mitkLevelWindowProperty.h" #include "mitkPropertyKeyPath.h" #include "mitkDICOMIOMetaInformationPropertyConstants.h" #include #include #include #include mitk::DICOMImageBlockDescriptor::DICOMImageBlockDescriptor() : m_ReaderImplementationLevel( SOPClassUnknown ) , m_PropertyList( PropertyList::New() ) , m_TagCache( nullptr ) , m_PropertiesOutOfDate( true ) { m_PropertyFunctor = &mitk::DICOMImageBlockDescriptor::GetPropertyForDICOMValues; } mitk::DICOMImageBlockDescriptor::~DICOMImageBlockDescriptor() { } mitk::DICOMImageBlockDescriptor::DICOMImageBlockDescriptor( const DICOMImageBlockDescriptor& other ) : m_ImageFrameList( other.m_ImageFrameList ) , m_MitkImage( other.m_MitkImage ) , m_SliceIsLoaded( other.m_SliceIsLoaded ) , m_ReaderImplementationLevel( other.m_ReaderImplementationLevel ) , m_TiltInformation( other.m_TiltInformation ) , m_PropertyList( other.m_PropertyList->Clone() ) , m_TagCache( other.m_TagCache ) , m_PropertiesOutOfDate( other.m_PropertiesOutOfDate ) , m_AdditionalTagMap(other.m_AdditionalTagMap) , m_FoundAdditionalTags(other.m_FoundAdditionalTags) , m_PropertyFunctor(other.m_PropertyFunctor) { if ( m_MitkImage ) { m_MitkImage = m_MitkImage->Clone(); } } mitk::DICOMImageBlockDescriptor& mitk::DICOMImageBlockDescriptor:: operator=( const DICOMImageBlockDescriptor& other ) { if ( this != &other ) { m_ImageFrameList = other.m_ImageFrameList; m_MitkImage = other.m_MitkImage; m_SliceIsLoaded = other.m_SliceIsLoaded; m_ReaderImplementationLevel = other.m_ReaderImplementationLevel; m_TiltInformation = other.m_TiltInformation; m_AdditionalTagMap = other.m_AdditionalTagMap; m_FoundAdditionalTags = other.m_FoundAdditionalTags; m_PropertyFunctor = other.m_PropertyFunctor; if ( other.m_PropertyList ) { m_PropertyList = other.m_PropertyList->Clone(); } if ( other.m_MitkImage ) { m_MitkImage = other.m_MitkImage->Clone(); } m_TagCache = other.m_TagCache; m_PropertiesOutOfDate = other.m_PropertiesOutOfDate; } return *this; } mitk::DICOMTagList mitk::DICOMImageBlockDescriptor::GetTagsOfInterest() { DICOMTagList completeList; completeList.push_back( DICOMTag( 0x0018, 0x1164 ) ); // pixel spacing completeList.push_back( DICOMTag( 0x0028, 0x0030 ) ); // imager pixel spacing completeList.push_back( DICOMTag( 0x0008, 0x0018 ) ); // sop instance UID completeList.push_back( DICOMTag( 0x0008, 0x0016 ) ); // sop class UID completeList.push_back( DICOMTag( 0x0020, 0x0011 ) ); // series number completeList.push_back( DICOMTag( 0x0008, 0x1030 ) ); // study description completeList.push_back( DICOMTag( 0x0008, 0x103e ) ); // series description completeList.push_back( DICOMTag( 0x0008, 0x0060 ) ); // modality completeList.push_back( DICOMTag( 0x0018, 0x0024 ) ); // sequence name completeList.push_back( DICOMTag( 0x0020, 0x0037 ) ); // image orientation completeList.push_back( DICOMTag( 0x0020, 0x1041 ) ); // slice location completeList.push_back( DICOMTag( 0x0020, 0x0012 ) ); // acquisition number completeList.push_back( DICOMTag( 0x0020, 0x0013 ) ); // instance number completeList.push_back( DICOMTag( 0x0020, 0x0032 ) ); // image position patient completeList.push_back( DICOMTag( 0x0028, 0x1050 ) ); // window center completeList.push_back( DICOMTag( 0x0028, 0x1051 ) ); // window width completeList.push_back( DICOMTag( 0x0008, 0x0008 ) ); // image type completeList.push_back( DICOMTag( 0x0028, 0x0004 ) ); // photometric interpretation return completeList; } void mitk::DICOMImageBlockDescriptor::SetAdditionalTagsOfInterest( const AdditionalTagsMapType& tagMap) { m_AdditionalTagMap = tagMap; } void mitk::DICOMImageBlockDescriptor::SetTiltInformation( const GantryTiltInformation& info ) { m_TiltInformation = info; } const mitk::GantryTiltInformation mitk::DICOMImageBlockDescriptor::GetTiltInformation() const { return m_TiltInformation; } void mitk::DICOMImageBlockDescriptor::SetImageFrameList( const DICOMImageFrameList& framelist ) { m_ImageFrameList = framelist; m_SliceIsLoaded.resize( framelist.size() ); m_SliceIsLoaded.assign( framelist.size(), false ); m_PropertiesOutOfDate = true; } const mitk::DICOMImageFrameList& mitk::DICOMImageBlockDescriptor::GetImageFrameList() const { return m_ImageFrameList; } void mitk::DICOMImageBlockDescriptor::SetMitkImage( Image::Pointer image ) { if ( m_MitkImage != image ) { if ( m_TagCache.IsExpired() ) { MITK_ERROR << "Unable to describe MITK image with properties without a tag-cache object!"; m_MitkImage = nullptr; return; } if ( m_ImageFrameList.empty() ) { MITK_ERROR << "Unable to describe MITK image with properties without a frame list!"; m_MitkImage = nullptr; return; } // Should verify that the image matches m_ImageFrameList and m_TagCache // however, this is hard to do without re-analyzing all // TODO we should at least make sure that the number of frames is identical (plus rows/columns, // orientation) // without gantry tilt correction, we can also check image origin m_MitkImage = this->DescribeImageWithProperties( this->FixupSpacing( image ) ); } } mitk::Image::Pointer mitk::DICOMImageBlockDescriptor::GetMitkImage() const { return m_MitkImage; } mitk::Image::Pointer mitk::DICOMImageBlockDescriptor::FixupSpacing( Image* mitkImage ) { if ( mitkImage ) { Vector3D imageSpacing = mitkImage->GetGeometry()->GetSpacing(); ScalarType desiredSpacingX = imageSpacing[0]; ScalarType desiredSpacingY = imageSpacing[1]; this->GetDesiredMITKImagePixelSpacing( desiredSpacingX, desiredSpacingY ); // prefer pixel spacing over imager pixel spacing if ( desiredSpacingX <= 0 || desiredSpacingY <= 0 ) { return mitkImage; } MITK_DEBUG << "Loaded image with spacing " << imageSpacing[0] << ", " << imageSpacing[1]; MITK_DEBUG << "Found correct spacing info " << desiredSpacingX << ", " << desiredSpacingY; imageSpacing[0] = desiredSpacingX; imageSpacing[1] = desiredSpacingY; mitkImage->GetGeometry()->SetSpacing( imageSpacing ); } return mitkImage; } void mitk::DICOMImageBlockDescriptor::SetSliceIsLoaded( unsigned int index, bool isLoaded ) { if ( index < m_SliceIsLoaded.size() ) { m_SliceIsLoaded[index] = isLoaded; } else { std::stringstream ss; ss << "Index " << index << " out of range (" << m_SliceIsLoaded.size() << " indices reserved)"; throw std::invalid_argument( ss.str() ); } } bool mitk::DICOMImageBlockDescriptor::IsSliceLoaded( unsigned int index ) const { if ( index < m_SliceIsLoaded.size() ) { return m_SliceIsLoaded[index]; } else { std::stringstream ss; ss << "Index " << index << " out of range (" << m_SliceIsLoaded.size() << " indices reserved)"; throw std::invalid_argument( ss.str() ); } } bool mitk::DICOMImageBlockDescriptor::AllSlicesAreLoaded() const { bool allLoaded = true; for ( auto iter = m_SliceIsLoaded.cbegin(); iter != m_SliceIsLoaded.cend(); ++iter ) { allLoaded &= *iter; } return allLoaded; } /* PS defined IPS defined PS==IPS 0 0 --> UNKNOWN spacing, loader will invent 0 1 --> spacing as at detector surface 1 0 --> spacing as in patient 1 1 0 --> detector surface spacing CORRECTED for geometrical magnifications: spacing as in patient 1 1 1 --> detector surface spacing NOT corrected for geometrical magnifications: spacing as at detector */ mitk::PixelSpacingInterpretation mitk::DICOMImageBlockDescriptor::GetPixelSpacingInterpretation() const { if ( m_ImageFrameList.empty() || m_TagCache.IsExpired() ) { MITK_ERROR << "Invalid call to GetPixelSpacingInterpretation. Need to have initialized tag-cache!"; return SpacingUnknown; } const std::string pixelSpacing = this->GetPixelSpacing(); const std::string imagerPixelSpacing = this->GetImagerPixelSpacing(); if ( pixelSpacing.empty() ) { if ( imagerPixelSpacing.empty() ) { return SpacingUnknown; } else { return SpacingAtDetector; } } else // Pixel Spacing defined { if ( imagerPixelSpacing.empty() ) { return SpacingInPatient; } else if ( pixelSpacing != imagerPixelSpacing ) { return SpacingInPatient; } else { return SpacingAtDetector; } } } std::string mitk::DICOMImageBlockDescriptor::GetPixelSpacing() const { if ( m_ImageFrameList.empty() || m_TagCache.IsExpired() ) { MITK_ERROR << "Invalid call to GetPixelSpacing. Need to have initialized tag-cache!"; return std::string( "" ); } static const DICOMTag tagPixelSpacing( 0x0028, 0x0030 ); return m_TagCache.Lock()->GetTagValue( m_ImageFrameList.front(), tagPixelSpacing ).value; } std::string mitk::DICOMImageBlockDescriptor::GetImagerPixelSpacing() const { if ( m_ImageFrameList.empty() || m_TagCache.IsExpired() ) { MITK_ERROR << "Invalid call to GetImagerPixelSpacing. Need to have initialized tag-cache!"; return std::string( "" ); } static const DICOMTag tagImagerPixelSpacing( 0x0018, 0x1164 ); return m_TagCache.Lock()->GetTagValue( m_ImageFrameList.front(), tagImagerPixelSpacing ).value; } void mitk::DICOMImageBlockDescriptor::GetDesiredMITKImagePixelSpacing( ScalarType& spacingX, ScalarType& spacingY ) const { const std::string pixelSpacing = this->GetPixelSpacing(); // preference for "in patient" pixel spacing if ( !DICOMStringToSpacing( pixelSpacing, spacingX, spacingY ) ) { const std::string imagerPixelSpacing = this->GetImagerPixelSpacing(); // fallback to "on detector" spacing if ( !DICOMStringToSpacing( imagerPixelSpacing, spacingX, spacingY ) ) { // at this point we have no hints whether the spacing is correct // do a quick sanity check and either trust in the input or set both to 1 // We assume neither spacing to be negative, zero or unexpectedly large for // medical images if (spacingX < mitk::eps || spacingX > 1000 || spacingY < mitk::eps || spacingY > 1000) { spacingX = spacingY = 1.0; } } } } void mitk::DICOMImageBlockDescriptor::SetProperty( const std::string& key, BaseProperty* value ) { m_PropertyList->SetProperty( key, value ); } mitk::BaseProperty* mitk::DICOMImageBlockDescriptor::GetProperty( const std::string& key ) const { this->UpdateImageDescribingProperties(); return m_PropertyList->GetProperty( key ); } std::string mitk::DICOMImageBlockDescriptor::GetPropertyAsString( const std::string& key ) const { this->UpdateImageDescribingProperties(); const mitk::BaseProperty::Pointer property = m_PropertyList->GetProperty( key ); if ( property.IsNotNull() ) { return property->GetValueAsString(); } else { return std::string( "" ); } } void mitk::DICOMImageBlockDescriptor::SetFlag( const std::string& key, bool value ) { m_PropertyList->ReplaceProperty( key, BoolProperty::New( value ) ); } bool mitk::DICOMImageBlockDescriptor::GetFlag( const std::string& key, bool defaultValue ) const { this->UpdateImageDescribingProperties(); BoolProperty::ConstPointer boolProp = dynamic_cast( this->GetProperty( key ) ); if ( boolProp.IsNotNull() ) { return boolProp->GetValue(); } else { return defaultValue; } } void mitk::DICOMImageBlockDescriptor::SetIntProperty( const std::string& key, int value ) { m_PropertyList->ReplaceProperty( key, IntProperty::New( value ) ); } int mitk::DICOMImageBlockDescriptor::GetIntProperty( const std::string& key, int defaultValue ) const { this->UpdateImageDescribingProperties(); IntProperty::ConstPointer intProp = dynamic_cast( this->GetProperty( key ) ); if ( intProp.IsNotNull() ) { return intProp->GetValue(); } else { return defaultValue; } } double mitk::DICOMImageBlockDescriptor::stringtodouble( const std::string& str ) const { double d; std::string trimmedstring( str ); try { trimmedstring = trimmedstring.erase( trimmedstring.find_last_not_of( " \n\r\t" ) + 1 ); } catch ( ... ) { // no last not of } std::string firstcomponent( trimmedstring ); try { firstcomponent = trimmedstring.erase( trimmedstring.find_first_of( "\\" ) ); } catch ( ... ) { // no last not of } std::istringstream converter( firstcomponent ); if ( !firstcomponent.empty() && ( converter >> d ) && converter.eof() ) { return d; } else { throw std::invalid_argument( "Argument is not a convertable number" ); } } mitk::Image::Pointer mitk::DICOMImageBlockDescriptor::DescribeImageWithProperties( Image* mitkImage ) { // TODO: this is a collection of properties that have been provided by the // legacy DicomSeriesReader. // We should at some point clean up this collection and name them in a more // consistent way! if ( !mitkImage ) return mitkImage; mitkImage->SetProperty(PropertyKeyPathToPropertyName(DICOMIOMetaInformationPropertyConstants::READER_FILES()), this->GetProperty("filenamesForSlices")); mitkImage->SetProperty(PropertyKeyPathToPropertyName(DICOMIOMetaInformationPropertyConstants::READER_PIXEL_SPACING_INTERPRETATION_STRING()), StringProperty::New(PixelSpacingInterpretationToString(this->GetPixelSpacingInterpretation()))); mitkImage->SetProperty(PropertyKeyPathToPropertyName(DICOMIOMetaInformationPropertyConstants::READER_PIXEL_SPACING_INTERPRETATION()), GenericProperty::New(this->GetPixelSpacingInterpretation())); mitkImage->SetProperty(PropertyKeyPathToPropertyName(DICOMIOMetaInformationPropertyConstants::READER_IMPLEMENTATION_LEVEL_STRING()), StringProperty::New(ReaderImplementationLevelToString(m_ReaderImplementationLevel))); mitkImage->SetProperty(PropertyKeyPathToPropertyName(DICOMIOMetaInformationPropertyConstants::READER_IMPLEMENTATION_LEVEL()), GenericProperty::New(m_ReaderImplementationLevel)); mitkImage->SetProperty(PropertyKeyPathToPropertyName(DICOMIOMetaInformationPropertyConstants::READER_GANTRY_TILT_CORRECTED()), BoolProperty::New(this->GetTiltInformation().IsRegularGantryTilt())); mitkImage->SetProperty(PropertyKeyPathToPropertyName(DICOMIOMetaInformationPropertyConstants::READER_3D_plus_t()), BoolProperty::New(this->GetFlag("3D+t", false))); mitkImage->SetProperty(PropertyKeyPathToPropertyName(DICOMIOMetaInformationPropertyConstants::READER_GDCM()), StringProperty::New(gdcm::Version::GetVersion())); mitkImage->SetProperty(PropertyKeyPathToPropertyName(DICOMIOMetaInformationPropertyConstants::READER_DCMTK()), StringProperty::New(PACKAGE_VERSION)); // get all found additional tags of interest - for (auto tag : m_FoundAdditionalTags) + for (const auto &tag : m_FoundAdditionalTags) { BaseProperty* prop = this->GetProperty(tag); if (prop) { mitkImage->SetProperty(tag.c_str(), prop); } } ///////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////// //// Deprecated properties should be removed sooner then later (see above) ///////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////// // first part: add some tags that describe individual slices // these propeties are defined at analysis time (see UpdateImageDescribingProperties()) const char* propertyKeySliceLocation = "dicom.image.0020.1041"; const char* propertyKeyInstanceNumber = "dicom.image.0020.0013"; const char* propertyKeySOPInstanceUID = "dicom.image.0008.0018"; mitkImage->SetProperty( propertyKeySliceLocation, this->GetProperty( "sliceLocationForSlices" ) ); mitkImage->SetProperty( propertyKeyInstanceNumber, this->GetProperty( "instanceNumberForSlices" ) ); mitkImage->SetProperty( propertyKeySOPInstanceUID, this->GetProperty( "SOPInstanceUIDForSlices" ) ); mitkImage->SetProperty( "files", this->GetProperty( "filenamesForSlices_deprecated" ) ); // second part: add properties that describe the whole image block mitkImage->SetProperty( "dicomseriesreader.SOPClassUID", StringProperty::New( this->GetSOPClassUID() ) ); mitkImage->SetProperty( "dicomseriesreader.SOPClass", StringProperty::New( this->GetSOPClassUIDAsName() ) ); mitkImage->SetProperty( "dicomseriesreader.PixelSpacingInterpretationString", StringProperty::New( PixelSpacingInterpretationToString( this->GetPixelSpacingInterpretation() ) ) ); mitkImage->SetProperty( "dicomseriesreader.PixelSpacingInterpretation", GenericProperty::New( this->GetPixelSpacingInterpretation() ) ); mitkImage->SetProperty( "dicomseriesreader.ReaderImplementationLevelString", StringProperty::New( ReaderImplementationLevelToString( m_ReaderImplementationLevel ) ) ); mitkImage->SetProperty( "dicomseriesreader.ReaderImplementationLevel", GenericProperty::New( m_ReaderImplementationLevel ) ); mitkImage->SetProperty( "dicomseriesreader.GantyTiltCorrected", BoolProperty::New( this->GetTiltInformation().IsRegularGantryTilt() ) ); mitkImage->SetProperty( "dicomseriesreader.3D+t", BoolProperty::New( this->GetFlag( "3D+t", false ) ) ); // level window const std::string windowCenter = this->GetPropertyAsString( "windowCenter" ); const std::string windowWidth = this->GetPropertyAsString( "windowWidth" ); try { const double level = stringtodouble( windowCenter ); const double window = stringtodouble( windowWidth ); mitkImage->SetProperty( "levelwindow", LevelWindowProperty::New( LevelWindow( level, window ) ) ); } catch ( ... ) { // nothing, no levelwindow to be predicted... } const std::string modality = this->GetPropertyAsString( "modality" ); mitkImage->SetProperty( "modality", StringProperty::New( modality ) ); mitkImage->SetProperty( "dicom.pixel.PhotometricInterpretation", this->GetProperty( "photometricInterpretation" ) ); mitkImage->SetProperty( "dicom.image.imagetype", this->GetProperty( "imagetype" ) ); mitkImage->SetProperty( "dicom.study.StudyDescription", this->GetProperty( "studyDescription" ) ); mitkImage->SetProperty( "dicom.series.SeriesDescription", this->GetProperty( "seriesDescription" ) ); mitkImage->SetProperty( "dicom.pixel.Rows", this->GetProperty( "rows" ) ); mitkImage->SetProperty( "dicom.pixel.Columns", this->GetProperty( "columns" ) ); // fourth part: get something from ImageIO. BUT this needs to be created elsewhere. or not at all! return mitkImage; } void mitk::DICOMImageBlockDescriptor::SetReaderImplementationLevel( const ReaderImplementationLevel& level ) { m_ReaderImplementationLevel = level; } mitk::ReaderImplementationLevel mitk::DICOMImageBlockDescriptor::GetReaderImplementationLevel() const { return m_ReaderImplementationLevel; } std::string mitk::DICOMImageBlockDescriptor::GetSOPClassUID() const { if ( !m_ImageFrameList.empty() && !m_TagCache.IsExpired() ) { static const DICOMTag tagSOPClassUID( 0x0008, 0x0016 ); return m_TagCache.Lock()->GetTagValue( m_ImageFrameList.front(), tagSOPClassUID ).value; } else { MITK_ERROR << "Invalid call to DICOMImageBlockDescriptor::GetSOPClassUID(). Need to have initialized tag-cache!"; return std::string( "" ); } } std::string mitk::DICOMImageBlockDescriptor::GetSOPClassUIDAsName() const { if ( !m_ImageFrameList.empty() && !m_TagCache.IsExpired() ) { gdcm::UIDs uidKnowledge; uidKnowledge.SetFromUID( this->GetSOPClassUID().c_str() ); const char* name = uidKnowledge.GetName(); if ( name ) { return std::string( name ); } else { return std::string( "" ); } } else { MITK_ERROR << "Invalid call to DICOMImageBlockDescriptor::GetSOPClassUIDAsName(). Need to have " "initialized tag-cache!"; return std::string( "" ); } } int mitk::DICOMImageBlockDescriptor::GetNumberOfTimeSteps() const { int result = 1; this->m_PropertyList->GetIntProperty("timesteps", result); return result; }; int mitk::DICOMImageBlockDescriptor::GetNumberOfFramesPerTimeStep() const { const int numberOfTimesteps = this->GetNumberOfTimeSteps(); int numberOfFramesPerTimestep = this->m_ImageFrameList.size() / numberOfTimesteps; assert(int(double((double)this->m_ImageFrameList.size() / (double)numberOfTimesteps)) == numberOfFramesPerTimestep); // this should hold return numberOfFramesPerTimestep; }; void mitk::DICOMImageBlockDescriptor::SetTagCache( DICOMTagCache* privateCache ) { // this must only be used during loading and never afterwards m_TagCache = privateCache; } #define printPropertyRange( label, property_name ) \ \ { \ const std::string first = this->GetPropertyAsString( #property_name "First" ); \ const std::string last = this->GetPropertyAsString( #property_name "Last" ); \ if ( !first.empty() || !last.empty() ) \ { \ if ( first == last ) \ { \ os << " " label ": '" << first << "'" << std::endl; \ } \ else \ { \ os << " " label ": '" << first << "' - '" << last << "'" << std::endl; \ } \ } \ \ } #define printProperty( label, property_name ) \ \ { \ const std::string first = this->GetPropertyAsString( #property_name ); \ if ( !first.empty() ) \ { \ os << " " label ": '" << first << "'" << std::endl; \ } \ \ } #define printBool( label, commands ) \ \ { \ os << " " label ": '" << ( commands ? "yes" : "no" ) << "'" << std::endl; \ \ } void mitk::DICOMImageBlockDescriptor::Print(std::ostream& os, bool filenameDetails) const { os << " Number of Frames: '" << m_ImageFrameList.size() << "'" << std::endl; os << " SOP class: '" << this->GetSOPClassUIDAsName() << "'" << std::endl; printProperty( "Series Number", seriesNumber ); printProperty( "Study Description", studyDescription ); printProperty( "Series Description", seriesDescription ); printProperty( "Modality", modality ); printProperty( "Sequence Name", sequenceName ); printPropertyRange( "Slice Location", sliceLocation ); printPropertyRange( "Acquisition Number", acquisitionNumber ); printPropertyRange( "Instance Number", instanceNumber ); printPropertyRange( "Image Position", imagePositionPatient ); printProperty( "Image Orientation", orientation ); os << " Pixel spacing interpretation: '" << PixelSpacingInterpretationToString( this->GetPixelSpacingInterpretation() ) << "'" << std::endl; printBool( "Gantry Tilt", this->GetTiltInformation().IsRegularGantryTilt() ) // printBool("3D+t", this->GetFlag("3D+t",false)) // os << " MITK image loaded: '" << (this->GetMitkImage().IsNotNull() ? "yes" : "no") << "'" << // std::endl; if ( filenameDetails ) { os << " Files in this image block:" << std::endl; for ( auto frameIter = m_ImageFrameList.begin(); frameIter != m_ImageFrameList.end(); ++frameIter ) { os << " " << ( *frameIter )->Filename; if ( ( *frameIter )->FrameNo > 0 ) { os << ", " << ( *frameIter )->FrameNo; } os << std::endl; } } } #define storeTagValueToProperty( tag_name, tag_g, tag_e ) \ \ { \ const DICOMTag t( tag_g, tag_e ); \ const std::string tagValue = tagCache->GetTagValue( firstFrame, t ).value; \ const_cast( this ) \ ->SetProperty( #tag_name, StringProperty::New( tagValue ) ); \ \ } #define storeTagValueRangeToProperty( tag_name, tag_g, tag_e ) \ \ { \ const DICOMTag t( tag_g, tag_e ); \ const std::string tagValueFirst = tagCache->GetTagValue( firstFrame, t ).value; \ const std::string tagValueLast = tagCache->GetTagValue( lastFrame, t ).value; \ const_cast( this ) \ ->SetProperty( #tag_name "First", StringProperty::New( tagValueFirst ) ); \ const_cast( this ) \ ->SetProperty( #tag_name "Last", StringProperty::New( tagValueLast ) ); \ \ } void mitk::DICOMImageBlockDescriptor::UpdateImageDescribingProperties() const { if ( !m_PropertiesOutOfDate ) return; if ( !m_ImageFrameList.empty() ) { if ( m_TagCache.IsExpired() ) { MITK_ERROR << "Invalid call to DICOMImageBlockDescriptor::UpdateImageDescribingProperties(). Need to " "have initialized tag-cache!"; return; } auto tagCache = m_TagCache.Lock(); if (tagCache.IsNull()) { MITK_ERROR << "Invalid call to DICOMImageBlockDescriptor::UpdateImageDescribingProperties(). Need to " "have initialized tag-cache!"; return; } const DICOMImageFrameInfo::Pointer firstFrame = m_ImageFrameList.front(); const DICOMImageFrameInfo::Pointer lastFrame = m_ImageFrameList.back(); // see macros above storeTagValueToProperty( seriesNumber, 0x0020, 0x0011 ); storeTagValueToProperty( studyDescription, 0x0008, 0x1030 ); storeTagValueToProperty( seriesDescription, 0x0008, 0x103e ); storeTagValueToProperty( modality, 0x0008, 0x0060 ); storeTagValueToProperty( sequenceName, 0x0018, 0x0024 ); storeTagValueToProperty( orientation, 0x0020, 0x0037 ); storeTagValueToProperty( rows, 0x0028, 0x0010 ); storeTagValueToProperty( columns, 0x0028, 0x0011 ); storeTagValueRangeToProperty( sliceLocation, 0x0020, 0x1041 ); storeTagValueRangeToProperty( acquisitionNumber, 0x0020, 0x0012 ); storeTagValueRangeToProperty( instanceNumber, 0x0020, 0x0013 ); storeTagValueRangeToProperty( imagePositionPatient, 0x0020, 0x0032 ); storeTagValueToProperty( windowCenter, 0x0028, 0x1050 ); storeTagValueToProperty( windowWidth, 0x0028, 0x1051 ); storeTagValueToProperty( imageType, 0x0008, 0x0008 ); storeTagValueToProperty( photometricInterpretation, 0x0028, 0x0004 ); // some per-image attributes // frames are just numbered starting from 0. timestep 1 (the second time-step) has frames starting at // (number-of-frames-per-timestep) // std::string propertyKeySliceLocation = "dicom.image.0020.1041"; // std::string propertyKeyInstanceNumber = "dicom.image.0020.0013"; // std::string propertyKeySOPInstanceNumber = "dicom.image.0008.0018"; StringLookupTable sliceLocationForSlices; StringLookupTable instanceNumberForSlices; StringLookupTable SOPInstanceUIDForSlices; StringLookupTable filenamesForSlices_deprecated; DICOMCachedValueLookupTable filenamesForSlices; const DICOMTag tagSliceLocation( 0x0020, 0x1041 ); const DICOMTag tagInstanceNumber( 0x0020, 0x0013 ); const DICOMTag tagSOPInstanceNumber( 0x0008, 0x0018 ); std::unordered_map additionalTagResultList; unsigned int slice(0); int timePoint(-1); const int framesPerTimeStep = this->GetNumberOfFramesPerTimeStep(); for ( auto frameIter = m_ImageFrameList.begin(); frameIter != m_ImageFrameList.end(); ++slice, ++frameIter ) { unsigned int zSlice = slice%framesPerTimeStep; if ( zSlice == 0) { timePoint++; } const std::string sliceLocation = tagCache->GetTagValue( *frameIter, tagSliceLocation ).value; sliceLocationForSlices.SetTableValue( slice, sliceLocation ); const std::string instanceNumber = tagCache->GetTagValue( *frameIter, tagInstanceNumber ).value; instanceNumberForSlices.SetTableValue( slice, instanceNumber ); const std::string sopInstanceUID = tagCache->GetTagValue( *frameIter, tagSOPInstanceNumber ).value; SOPInstanceUIDForSlices.SetTableValue( slice, sopInstanceUID ); const std::string filename = ( *frameIter )->Filename; filenamesForSlices_deprecated.SetTableValue( slice, filename ); filenamesForSlices.SetTableValue(slice, { static_cast(timePoint), zSlice, filename }); MITK_DEBUG << "Tag info for slice " << slice << ": SL '" << sliceLocation << "' IN '" << instanceNumber << "' SOP instance UID '" << sopInstanceUID << "'"; for (const auto& tag : m_AdditionalTagMap) { const DICOMTagCache::FindingsListType findings = tagCache->GetTagValue( *frameIter, tag.first ); for (const auto& finding : findings) { if (finding.isValid) { std::string propKey = (tag.second.empty()) ? DICOMTagPathToPropertyName(finding.path) : tag.second; DICOMCachedValueInfo info{ static_cast(timePoint), zSlice, finding.value }; additionalTagResultList[propKey].SetTableValue(slice, info); } } } } // add property or properties with proper names auto* thisInstance = const_cast( this ); thisInstance->SetProperty( "sliceLocationForSlices", StringLookupTableProperty::New( sliceLocationForSlices ) ); thisInstance->SetProperty( "instanceNumberForSlices", StringLookupTableProperty::New( instanceNumberForSlices ) ); thisInstance->SetProperty( "SOPInstanceUIDForSlices", StringLookupTableProperty::New( SOPInstanceUIDForSlices ) ); thisInstance->SetProperty( "filenamesForSlices_deprecated", StringLookupTableProperty::New( filenamesForSlices_deprecated ) ); thisInstance->SetProperty("filenamesForSlices", m_PropertyFunctor(filenamesForSlices)); //add properties for additional tags of interest for ( auto iter = additionalTagResultList.cbegin(); iter != additionalTagResultList.cend(); ++iter ) { thisInstance->SetProperty( iter->first, m_PropertyFunctor( iter->second ) ); thisInstance->m_FoundAdditionalTags.insert(m_FoundAdditionalTags.cend(),iter->first); } m_PropertiesOutOfDate = false; } } mitk::BaseProperty::Pointer mitk::DICOMImageBlockDescriptor::GetPropertyForDICOMValues(const DICOMCachedValueLookupTable& cacheLookupTable) { const auto& lookupTable = cacheLookupTable.GetLookupTable(); typedef std::pair PairType; if ( std::adjacent_find( lookupTable.cbegin(), lookupTable.cend(), []( const PairType& lhs, const PairType& rhs ) { return lhs.second.Value != rhs.second.Value; } ) == lookupTable.cend() ) { return static_cast( mitk::StringProperty::New(cacheLookupTable.GetTableValue(0).Value).GetPointer()); } StringLookupTable stringTable; - for (auto element : lookupTable) + for (const auto &element : lookupTable) { stringTable.SetTableValue(element.first, element.second.Value); } return static_cast( mitk::StringLookupTableProperty::New(stringTable).GetPointer()); } void mitk::DICOMImageBlockDescriptor::SetTagLookupTableToPropertyFunctor( TagLookupTableToPropertyFunctor functor ) { if ( functor != nullptr ) { m_PropertyFunctor = functor; } } mitk::BaseProperty::ConstPointer mitk::DICOMImageBlockDescriptor::GetConstProperty(const std::string &propertyKey, const std::string &/*contextName*/, bool /*fallBackOnDefaultContext*/) const { this->UpdateImageDescribingProperties(); return m_PropertyList->GetConstProperty(propertyKey); }; std::vector mitk::DICOMImageBlockDescriptor::GetPropertyKeys(const std::string &/*contextName*/, bool /*includeDefaultContext*/) const { this->UpdateImageDescribingProperties(); return m_PropertyList->GetPropertyKeys(); }; std::vector mitk::DICOMImageBlockDescriptor::GetPropertyContextNames() const { return std::vector(); }; diff --git a/Modules/DICOM/src/mitkDICOMProperty.cpp b/Modules/DICOM/src/mitkDICOMProperty.cpp index c82c2923ba..89ecf35724 100644 --- a/Modules/DICOM/src/mitkDICOMProperty.cpp +++ b/Modules/DICOM/src/mitkDICOMProperty.cpp @@ -1,55 +1,55 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkDICOMProperty.h" mitk::BaseProperty::Pointer mitk::GetDICOMPropertyForDICOMValuesFunctor(const mitk::DICOMCachedValueLookupTable& cacheLookupTable) { const auto& lookupTable = cacheLookupTable.GetLookupTable(); mitk::DICOMProperty::Pointer prop = mitk::DICOMProperty::New(); - for (auto element : lookupTable) + for (const auto &element : lookupTable) { prop->SetValue(element.second.TimePoint, element.second.SliceInTimePoint, element.second.Value); } return prop.GetPointer(); } std::map< std::string, mitk::BaseProperty::Pointer> mitk::GetPropertyByDICOMTagPath(const mitk::PropertyList* list, const mitk::DICOMTagPath& path) { std::map< std::string, mitk::BaseProperty::Pointer> result; for (const auto& iter : *(list->GetMap())) { DICOMTagPath propPath = PropertyNameToDICOMTagPath(iter.first); if (!propPath.IsEmpty() && path.Equals(propPath)) { result.insert(iter); } } return result; }; std::map< std::string, mitk::BaseProperty::Pointer> mitk::GetPropertyByDICOMTagPath(const mitk::BaseData* data, const mitk::DICOMTagPath& path) { std::map< std::string, mitk::BaseProperty::Pointer> result; if (data) { result = GetPropertyByDICOMTagPath(data->GetPropertyList(), path); } return result; }; diff --git a/Modules/DICOMPM/autoload/DICOMPMIO/mitkDICOMPMIO.cpp b/Modules/DICOMPM/autoload/DICOMPMIO/mitkDICOMPMIO.cpp index b03d29e22e..1d25a7e344 100644 --- a/Modules/DICOMPM/autoload/DICOMPMIO/mitkDICOMPMIO.cpp +++ b/Modules/DICOMPM/autoload/DICOMPMIO/mitkDICOMPMIO.cpp @@ -1,217 +1,217 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef __mitkDICOMPMIO__cpp #define __mitkDICOMPMIO__cpp #include "mitkDICOMPMIO.h" #include "mitkDICOMPMIOMimeTypes.h" #include #include #include #include #include #include #include #include #include #include "mitkParamapPresetsParser.h" // us #include #include // model fit parameters #include "mitkModelFitConstants.h" namespace mitk { DICOMPMIO::DICOMPMIO() : AbstractFileIO(Image::GetStaticNameOfClass(), mitk::MitkDICOMPMIOMimeTypes::DICOMPM_MIMETYPE_NAME(), "DICOM PM") { AbstractFileWriter::SetRanking(10); AbstractFileReader::SetRanking(10); this->RegisterService(); } IFileIO::ConfidenceLevel DICOMPMIO::GetWriterConfidenceLevel() const { if (AbstractFileIO::GetWriterConfidenceLevel() == Unsupported) return Unsupported; const Image *PMinput = static_cast(this->GetInput()); if (PMinput) { auto modalityProperty = PMinput->GetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0060).c_str()); if (modalityProperty.IsNotNull()) { std::string modality = modalityProperty->GetValueAsString(); if (modality == "PM") { return Supported; } else return Unsupported; } else return Unsupported; } else return Unsupported; } void DICOMPMIO::Write() { ValidateOutputLocation(); mitk::LocaleSwitch localeSwitch("C"); LocalFile localFile(this); const std::string path = localFile.GetFileName(); auto PMinput = dynamic_cast(this->GetInput()); if (PMinput == nullptr) mitkThrow() << "Cannot write non-image data"; // Get DICOM information from referenced image vector> dcmDatasetsSourceImage; std::unique_ptr readFileFormat(new DcmFileFormat()); try { // Generate dcmdataset witk DICOM tags from property list; ATM the source are the filepaths from the // property list mitk::StringLookupTableProperty::Pointer filesProp = dynamic_cast(PMinput->GetProperty("referenceFiles").GetPointer()); if (filesProp.IsNull()) { mitkThrow() << "No property with dicom file path."; return; } // returns a list of all referenced files StringLookupTable filesLut = filesProp->GetValue(); const StringLookupTable::LookupTableType &lookUpTableMap = filesLut.GetLookupTable(); - for (auto it : lookUpTableMap) + for (const auto &it : lookUpTableMap) { const char *fileName = (it.second).c_str(); if (readFileFormat->loadFile(fileName, EXS_Unknown).good()) { std::unique_ptr readDCMDataset(readFileFormat->getAndRemoveDataset()); dcmDatasetsSourceImage.push_back(std::move(readDCMDataset)); } } } catch (const std::exception &e) { MITK_ERROR << "An error occurred while getting the dicom information: " << e.what() << endl; return; } mitk::Image *mitkPMImage = const_cast(PMinput); // Cast input PMinput to itk image ImageToItk::Pointer PMimageToItkFilter = ImageToItk::New(); PMimageToItkFilter->SetInput(mitkPMImage); // Cast from original itk type to dcmqi input itk image type typedef itk::CastImageFilter castItkImageFilterType; castItkImageFilterType::Pointer castFilter = castItkImageFilterType::New(); castFilter->SetInput(PMimageToItkFilter->GetOutput()); castFilter->Update(); PMitkInternalImageType::Pointer itkParamapImage = castFilter->GetOutput(); // Create PM meta information const std::string tmpMetaInfoFile = this->CreateMetaDataJsonFilePM(); // Convert itk PM images to dicom image MITK_INFO << "Writing PM image: " << path << std::endl; try { // convert from unique to raw pointer vector rawVecDataset; for ( const auto& dcmDataSet : dcmDatasetsSourceImage ) { rawVecDataset.push_back( dcmDataSet.get() ); } std::unique_ptr PMconverter(new dcmqi::ParaMapConverter()); std::unique_ptr PMresult (PMconverter->itkimage2paramap(itkParamapImage, rawVecDataset, tmpMetaInfoFile)); // Write dicom file DcmFileFormat dcmFileFormat(PMresult.get()); std::string filePath = path.substr(0, path.find_last_of(".")); filePath = filePath + ".dcm"; dcmFileFormat.saveFile(filePath.c_str(), EXS_LittleEndianExplicit); } catch (const std::exception &e) { MITK_ERROR << "An error occurred during writing the DICOM Paramap: " << e.what() << endl; return; } } const std::string mitk::DICOMPMIO::CreateMetaDataJsonFilePM() const { const mitk::Image *PMimage = dynamic_cast(this->GetInput()); dcmqi::JSONParametricMapMetaInformationHandler PMhandler; // Get Metadata from modelFitConstants std::string parameterName; PMimage->GetPropertyList()->GetStringProperty(ModelFitConstants::PARAMETER_NAME_PROPERTY_NAME().c_str(), parameterName); std::string modelName; PMimage->GetPropertyList()->GetStringProperty(ModelFitConstants::MODEL_NAME_PROPERTY_NAME().c_str(), modelName); mitk::ParamapPresetsParser* pmPresets = mitk::ParamapPresetsParser::New(); // Here the mitkParamapPresets.xml file containing the Coding Schmeme Designator and Code Value are parsed and the relevant values extracted pmPresets->LoadPreset(); auto pmType_parameterName = pmPresets->GetType(parameterName); auto pmType_modelName = pmPresets->GetType(modelName); // Pass codes to Paramap Converter PMhandler.setDerivedPixelContrast("TCS"); PMhandler.setFrameLaterality("U"); PMhandler.setQuantityValueCode(pmType_parameterName.codeValue, pmType_parameterName.codeScheme, parameterName); PMhandler.setMeasurementMethodCode(pmType_modelName.codeValue, pmType_modelName.codeScheme, modelName); PMhandler.setMeasurementUnitsCode("/min", "UCUM", "/m"); PMhandler.setSeriesNumber("1"); PMhandler.setInstanceNumber("1"); PMhandler.setDerivationCode("129104", "DCM", "Perfusion image analysis"); PMhandler.setRealWorldValueSlope("1"); return PMhandler.getJSONOutputAsString(); } std::vector DICOMPMIO::DoRead() { mitk::LocaleSwitch localeSwitch("C"); std::vector result; return result; } IFileIO::ConfidenceLevel DICOMPMIO::GetReaderConfidenceLevel() const { return Unsupported; } DICOMPMIO *DICOMPMIO::IOClone() const { return new DICOMPMIO(*this); } } // namespace #endif //__mitkDICOMPMIO__cpp diff --git a/Modules/DICOMTesting/src/mitkTestDICOMLoading.cpp b/Modules/DICOMTesting/src/mitkTestDICOMLoading.cpp index ed2c8e71b0..9d63c65aa9 100644 --- a/Modules/DICOMTesting/src/mitkTestDICOMLoading.cpp +++ b/Modules/DICOMTesting/src/mitkTestDICOMLoading.cpp @@ -1,572 +1,585 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ //#define MBILOG_ENABLE_DEBUG #include "mitkTestDICOMLoading.h" #include "mitkDICOMIOMetaInformationPropertyConstants.h" #include "mitkDICOMProperty.h" +#include "mitkArbitraryTimeGeometry.h" #include #include #include #include "itksys/SystemTools.hxx" mitk::TestDICOMLoading::TestDICOMLoading() :m_PreviousCLocale(nullptr) { } void mitk::TestDICOMLoading::SetDefaultLocale() { // remember old locale only once if (m_PreviousCLocale == nullptr) { m_PreviousCLocale = setlocale(LC_NUMERIC, nullptr); // set to "C" setlocale(LC_NUMERIC, "C"); m_PreviousCppLocale = std::cin.getloc(); std::locale l( "C" ); std::cin.imbue(l); std::cout.imbue(l); } } void mitk::TestDICOMLoading::ResetUserLocale() { if (m_PreviousCLocale) { setlocale(LC_NUMERIC, m_PreviousCLocale); std::cin.imbue(m_PreviousCppLocale); std::cout.imbue(m_PreviousCppLocale); m_PreviousCLocale = nullptr; } } mitk::TestDICOMLoading::ImageList mitk::TestDICOMLoading ::LoadFiles( const StringList& files ) { for (auto iter = files.begin(); iter != files.end(); ++iter) { MITK_DEBUG << "File " << *iter; } ImageList result; ClassicDICOMSeriesReader::Pointer reader = this->BuildDICOMReader(); reader->SetTagLookupTableToPropertyFunctor(mitk::GetDICOMPropertyForDICOMValuesFunctor); reader->SetInputFiles( files ); reader->AnalyzeInputFiles(); reader->PrintOutputs(std::cout,true); reader->LoadImages(); unsigned int numberOfImages = reader->GetNumberOfOutputs(); for (unsigned imageIndex = 0; imageIndex < numberOfImages; ++imageIndex) { const DICOMImageBlockDescriptor& block = reader->GetOutput(imageIndex); result.push_back( block.GetMitkImage() ); } return result; } mitk::ClassicDICOMSeriesReader::Pointer mitk::TestDICOMLoading ::BuildDICOMReader() { ClassicDICOMSeriesReader::Pointer reader = ClassicDICOMSeriesReader::New(); reader->SetFixTiltByShearing(true); return reader; } mitk::Image::Pointer mitk::TestDICOMLoading ::DecorateVerifyCachedImage( const StringList& files, mitk::DICOMTagCache* tagCache, mitk::Image::Pointer cachedImage ) { DICOMImageBlockDescriptor block; DICOMImageFrameList framelist; for (auto iter = files.begin(); iter != files.end(); ++iter) { framelist.push_back( DICOMImageFrameInfo::New(*iter) ); } block.SetImageFrameList( framelist ); block.SetTagCache( tagCache ); block.SetMitkImage( cachedImage ); // this should/will create a propertylist describing the image slices return block.GetMitkImage(); } mitk::Image::Pointer mitk::TestDICOMLoading ::DecorateVerifyCachedImage( const StringList& files, mitk::Image::Pointer cachedImage ) { ClassicDICOMSeriesReader::Pointer reader = this->BuildDICOMReader(); reader->SetTagLookupTableToPropertyFunctor(mitk::GetDICOMPropertyForDICOMValuesFunctor); reader->SetInputFiles( files ); reader->AnalyzeInputFiles(); // This just creates a "tag cache and a nice DICOMImageBlockDescriptor. // Both of these could also be produced in a different way. The only // important thing is, that the DICOMImageBlockDescriptor knows a // tag-cache object when PropertyDecorateCachedMitkImageForImageBlockDescriptor // is called. if ( reader->GetNumberOfOutputs() != 1 ) { MITK_ERROR << "Reader produce " << reader->GetNumberOfOutputs() << " images instead of 1 expected.."; return nullptr; } DICOMImageBlockDescriptor block = reader->GetOutput(0); // creates a block copy block.SetMitkImage( cachedImage ); // this should/will create a propertylist describing the image slices return block.GetMitkImage(); } std::string mitk::TestDICOMLoading::ComponentTypeToString(int type) { if (type == itk::ImageIOBase::UCHAR) return "UCHAR"; else if (type == itk::ImageIOBase::CHAR) return "CHAR"; else if (type == itk::ImageIOBase::USHORT) return "USHORT"; else if (type == itk::ImageIOBase::SHORT) return "SHORT"; else if (type == itk::ImageIOBase::UINT) return "UINT"; else if (type == itk::ImageIOBase::INT) return "INT"; else if (type == itk::ImageIOBase::ULONG) return "ULONG"; else if (type == itk::ImageIOBase::LONG) return "LONG"; else if (type == itk::ImageIOBase::FLOAT) return "FLOAT"; else if (type == itk::ImageIOBase::DOUBLE) return "DOUBLE"; else return "UNKNOWN"; } // add a line to stringstream result (see DumpImageInformation #define DumpLine(field, data) DumpILine(0, field, data) // add an indented(!) line to stringstream result (see DumpImageInformation #define DumpILine(indent, field, data) \ { \ std::string DumpLine_INDENT; DumpLine_INDENT.resize(indent, ' ' ); \ result << DumpLine_INDENT << field << ": " << data << "\n"; \ } std::string mitk::TestDICOMLoading::DumpImageInformation( const Image* image ) { std::stringstream result; if (image == nullptr) return result.str(); SetDefaultLocale(); // basic image data DumpLine( "Pixeltype", ComponentTypeToString(image->GetPixelType().GetComponentType()) ); DumpLine( "BitsPerPixel", image->GetPixelType().GetBpe() ); DumpLine( "Dimension", image->GetDimension() ); result << "Dimensions: "; for (unsigned int dim = 0; dim < image->GetDimension(); ++dim) result << image->GetDimension(dim) << " "; result << "\n"; // geometry data result << "Geometry: \n"; const TimeGeometry* timeGeometry = image->GetTimeGeometry(); BaseGeometry* geometry = timeGeometry->GetGeometryForTimeStep(0); if (geometry) { AffineTransform3D* transform = geometry->GetIndexToWorldTransform(); if (transform) { result << " " << "Matrix: "; const AffineTransform3D::MatrixType& matrix = transform->GetMatrix(); for (unsigned int i = 0; i < 3; ++i) for (unsigned int j = 0; j < 3; ++j) result << matrix[i][j] << " "; result << "\n"; result << " " << "Offset: "; const AffineTransform3D::OutputVectorType& offset = transform->GetOffset(); for (unsigned int i = 0; i < 3; ++i) result << offset[i] << " "; result << "\n"; result << " " << "Center: "; const AffineTransform3D::InputPointType& center = transform->GetCenter(); for (unsigned int i = 0; i < 3; ++i) result << center[i] << " "; result << "\n"; result << " " << "Translation: "; const AffineTransform3D::OutputVectorType& translation = transform->GetTranslation(); for (unsigned int i = 0; i < 3; ++i) result << translation[i] << " "; result << "\n"; result << " " << "Scale: "; const double* scale = transform->GetScale(); for (unsigned int i = 0; i < 3; ++i) result << scale[i] << " "; result << "\n"; result << " " << "Origin: "; const Point3D& origin = geometry->GetOrigin(); for (unsigned int i = 0; i < 3; ++i) result << origin[i] << " "; result << "\n"; result << " " << "Spacing: "; const Vector3D& spacing = geometry->GetSpacing(); for (unsigned int i = 0; i < 3; ++i) result << spacing[i] << " "; result << "\n"; result << " " << "TimeBounds: "; - const TimeBounds timeBounds = timeGeometry->GetTimeBounds(); + /////////////////////////////////////// + // Workarround T27883. See https://phabricator.mitk.org/T27883#219473 for more details. + // This workarround should be removed as soon as T28262 is solved! + TimeBounds timeBounds = timeGeometry->GetTimeBounds(); + auto atg = dynamic_cast(timeGeometry); + if (atg && atg->HasCollapsedFinalTimeStep()) + { + timeBounds[1] = timeBounds[1] - 1.; + } + //Original code: + //const TimeBounds timeBounds = timeGeometry->GetTimeBounds(); + // + // End of workarround for T27883 + ////////////////////////////////////// for (unsigned int i = 0; i < 2; ++i) - result << timeBounds[i] << " "; + result << timeBounds[i] << " "; result << "\n"; - } } // io dicom meta information AddPropertyToDump(mitk::DICOMIOMetaInformationPropertyConstants::READER_CONFIGURATION(), image, result); AddPropertyToDump(mitk::DICOMIOMetaInformationPropertyConstants::READER_FILES(), image, result); AddPropertyToDump(mitk::DICOMIOMetaInformationPropertyConstants::READER_GANTRY_TILT_CORRECTED(), image, result); AddPropertyToDump(mitk::DICOMIOMetaInformationPropertyConstants::READER_IMPLEMENTATION_LEVEL(), image, result); AddPropertyToDump(mitk::DICOMIOMetaInformationPropertyConstants::READER_IMPLEMENTATION_LEVEL_STRING(), image, result); AddPropertyToDump(mitk::DICOMIOMetaInformationPropertyConstants::READER_PIXEL_SPACING_INTERPRETATION(), image, result); AddPropertyToDump(mitk::DICOMIOMetaInformationPropertyConstants::READER_PIXEL_SPACING_INTERPRETATION_STRING(), image, result); AddPropertyToDump(mitk::DICOMIOMetaInformationPropertyConstants::READER_3D_plus_t(), image, result); AddPropertyToDump(mitk::DICOMIOMetaInformationPropertyConstants::READER_DCMTK(), image, result); AddPropertyToDump(mitk::DICOMIOMetaInformationPropertyConstants::READER_GDCM(), image, result); ResetUserLocale(); return result.str(); } void mitk::TestDICOMLoading::AddPropertyToDump(const mitk::PropertyKeyPath& key, const mitk::Image* image, std::stringstream& result) { auto propKey = mitk::PropertyKeyPathToPropertyName(key); auto prop = image->GetProperty(propKey.c_str()); if (prop.IsNotNull()) { auto value = prop->GetValueAsString(); auto dicomProp = dynamic_cast< mitk::DICOMProperty*>(prop.GetPointer()); if (dicomProp != nullptr) { auto strippedProp = dicomProp->Clone(); if (key == mitk::DICOMIOMetaInformationPropertyConstants::READER_FILES()) {//strip dicom file information from path to ensure generalized dump files auto timePoints = strippedProp->GetAvailableTimeSteps(); for (auto timePoint : timePoints) { auto slices = strippedProp->GetAvailableSlices(timePoint); for (auto slice : slices) { auto value = strippedProp->GetValue(timePoint, slice); value = itksys::SystemTools::GetFilenameName(value); strippedProp->SetValue(timePoint, slice, value); } } } value = mitk::PropertyPersistenceSerialization::serializeTemporoSpatialStringPropertyToJSON(strippedProp); } result << propKey << ": " << value << "\n"; } } std::string mitk::TestDICOMLoading::trim(const std::string& pString, const std::string& pWhitespace) { const size_t beginStr = pString.find_first_not_of(pWhitespace); if (beginStr == std::string::npos) { // no content return ""; } const size_t endStr = pString.find_last_not_of(pWhitespace); const size_t range = endStr - beginStr + 1; return pString.substr(beginStr, range); } std::string mitk::TestDICOMLoading::reduce(const std::string& pString, const std::string& pFill, const std::string& pWhitespace) { // trim first std::string result(trim(pString, pWhitespace)); // replace sub ranges size_t beginSpace = result.find_first_of(pWhitespace); while (beginSpace != std::string::npos) { const size_t endSpace = result.find_first_not_of(pWhitespace, beginSpace); const size_t range = endSpace - beginSpace; result.replace(beginSpace, range, pFill); const size_t newStart = beginSpace + pFill.length(); beginSpace = result.find_first_of(pWhitespace, newStart); } return result; } bool mitk::TestDICOMLoading::CompareSpacedValueFields( const std::string& reference, const std::string& test, double /*eps*/ ) { bool result(true); // tokenize string, compare each token, if possible by float comparison std::stringstream referenceStream(reduce(reference)); std::stringstream testStream(reduce(test)); std::string refToken; std::string testToken; while ( std::getline( referenceStream, refToken, ' ' ) && std::getline ( testStream, testToken, ' ' ) ) { float refNumber; float testNumber; if ( this->StringToNumber(refToken, refNumber) ) { if ( this->StringToNumber(testToken, testNumber) ) { // print-out compared tokens if DEBUG output allowed MITK_DEBUG << "Reference Token '" << refToken << "'" << " value " << refNumber << ", test Token '" << testToken << "'" << " value " << testNumber; bool old_result = result; result &= ( std::abs(refNumber - testNumber) < 0.0001f /*mitk::eps*/ ); // log the token/number which causes the test to fail if( old_result != result) { MITK_ERROR << std::setprecision(16) << "Reference Token '" << refToken << "'" << " value " << refNumber << ", test Token '" << testToken << "'" << " value " << testNumber; MITK_ERROR << "[FALSE] - difference: " << std::setprecision(16) << std::abs(refNumber - testNumber) << " EPS: " << 0.0001f; //mitk::eps; } } else { MITK_ERROR << refNumber << " cannot be compared to '" << testToken << "'"; } } else { MITK_DEBUG << "Token '" << refToken << "'" << " handled as string"; result &= refToken == testToken; } } if ( std::getline( referenceStream, refToken, ' ' ) ) { MITK_ERROR << "Reference string still had values when test string was already parsed: ref '" << reference << "', test '" << test << "'"; result = false; } else if ( std::getline( testStream, testToken, ' ' ) ) { MITK_ERROR << "Test string still had values when reference string was already parsed: ref '" << reference << "', test '" << test << "'"; result = false; } return result; } bool mitk::TestDICOMLoading::CompareImageInformationDumps( const std::string& referenceDump, const std::string& testDump ) { KeyValueMap reference = ParseDump(referenceDump); KeyValueMap test = ParseDump(testDump); bool testResult(true); // verify all expected values for (KeyValueMap::const_iterator refIter = reference.begin(); refIter != reference.end(); ++refIter) { const std::string& refKey = refIter->first; const std::string& refValue = refIter->second; if ( test.find(refKey) != test.end() ) { const std::string& testValue = test[refKey]; if (refKey == mitk::PropertyKeyPathToPropertyName(mitk::DICOMIOMetaInformationPropertyConstants::READER_DCMTK())) { //check dcmtk version always against the current version of the system bool thisTestResult = testValue == std::string(" ") + PACKAGE_VERSION; testResult &= thisTestResult; MITK_DEBUG << refKey << ": '" << PACKAGE_VERSION << "' == '" << testValue << "' ? " << (thisTestResult ? "YES" : "NO"); } else if (refKey == mitk::PropertyKeyPathToPropertyName(mitk::DICOMIOMetaInformationPropertyConstants::READER_GDCM())) {//check gdcm version always against the current version of the system bool thisTestResult = testValue == std::string(" ") + gdcm::Version::GetVersion(); testResult &= thisTestResult; MITK_DEBUG << refKey << ": '" << gdcm::Version::GetVersion() << "' == '" << testValue << "' ? " << (thisTestResult ? "YES" : "NO"); } else { bool thisTestResult = CompareSpacedValueFields(refValue, testValue); testResult &= thisTestResult; MITK_DEBUG << refKey << ": '" << refValue << "' == '" << testValue << "' ? " << (thisTestResult ? "YES" : "NO"); } } else { MITK_ERROR << "Reference dump contains a key'" << refKey << "' (value '" << refValue << "')." ; MITK_ERROR << "This key is expected to be generated for tests (but was not). Most probably you need to update your test data."; return false; } } // now check test dump does not contain any additional keys for (KeyValueMap::const_iterator testIter = test.begin(); testIter != test.end(); ++testIter) { const std::string& key = testIter->first; const std::string& value = testIter->second; if (key == mitk::PropertyKeyPathToPropertyName(mitk::DICOMIOMetaInformationPropertyConstants::READER_DCMTK())) {//check dcmtk version always against the current version of the system bool thisTestResult = value == std::string(" ")+PACKAGE_VERSION; testResult &= thisTestResult; MITK_DEBUG << key << ": '" << PACKAGE_VERSION << "' == '" << value << "' ? " << (thisTestResult ? "YES" : "NO"); } else if (key == mitk::PropertyKeyPathToPropertyName(mitk::DICOMIOMetaInformationPropertyConstants::READER_GDCM())) {//check gdcm version always against the current version of the system bool thisTestResult = value == std::string(" ") + gdcm::Version::GetVersion(); testResult &= thisTestResult; MITK_DEBUG << key << ": '" << gdcm::Version::GetVersion() << "' == '" << value << "' ? " << (thisTestResult ? "YES" : "NO"); } else if ( reference.find(key) == reference.end() ) { MITK_ERROR << "Test dump contains an unexpected key'" << key << "' (value '" << value << "')." ; MITK_ERROR << "This key is not expected. Most probably you need to update your test data."; return false; } } return testResult; } mitk::TestDICOMLoading::KeyValueMap mitk::TestDICOMLoading::ParseDump( const std::string& dump ) { KeyValueMap parsedResult; std::string shredder(dump); std::stack surroundingKeys; std::stack expectedIndents; expectedIndents.push(0); while (true) { std::string::size_type newLinePos = shredder.find( '\n' ); if (newLinePos == std::string::npos || newLinePos == 0) break; std::string line = shredder.substr( 0, newLinePos ); shredder = shredder.erase( 0, newLinePos+1 ); std::string::size_type keyPosition = line.find_first_not_of( ' ' ); std::string::size_type colonPosition = line.find( ':' ); std::string key = line.substr(keyPosition, colonPosition - keyPosition); std::string::size_type firstSpacePosition = key.find_first_of(" "); if (firstSpacePosition != std::string::npos) { key.erase(firstSpacePosition); } if ( keyPosition > expectedIndents.top() ) { // more indent than before expectedIndents.push(keyPosition); } else { if (!surroundingKeys.empty()) { surroundingKeys.pop(); // last of same length } while (expectedIndents.top() != keyPosition) { expectedIndents.pop(); if (!surroundingKeys.empty()) { surroundingKeys.pop(); } }; // unwind until current indent is found } if (!surroundingKeys.empty()) { key = surroundingKeys.top() + "." + key; // construct current key name } surroundingKeys.push(key); // this is the new embracing key std::string value = line.substr(colonPosition+1); MITK_DEBUG << " Key: '" << key << "' value '" << value << "'" ; parsedResult[key] = value; // store parsing result } return parsedResult; } diff --git a/Modules/DICOMUI/src/QmitkDicomLocalStorageWidget.cpp b/Modules/DICOMUI/src/QmitkDicomLocalStorageWidget.cpp index ba2679faa5..975912427f 100644 --- a/Modules/DICOMUI/src/QmitkDicomLocalStorageWidget.cpp +++ b/Modules/DICOMUI/src/QmitkDicomLocalStorageWidget.cpp @@ -1,228 +1,228 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Qmitk #include "QmitkDicomLocalStorageWidget.h" //#include // Qt #include #include #include #include const std::string QmitkDicomLocalStorageWidget::Widget_ID = "org.mitk.Widgets.QmitkDicomLocalStorageWidget"; QmitkDicomLocalStorageWidget::QmitkDicomLocalStorageWidget(QWidget *parent) : QWidget(parent), m_LocalIndexer(new ctkDICOMIndexer(parent)), m_Controls(nullptr) { CreateQtPartControl(this); } QmitkDicomLocalStorageWidget::~QmitkDicomLocalStorageWidget() { m_LocalDatabase->closeDatabase(); } void QmitkDicomLocalStorageWidget::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { m_Controls = new Ui::QmitkDicomLocalStorageWidgetControls; m_Controls->setupUi(parent); connect(m_Controls->deleteButton, SIGNAL(clicked()), this, SLOT(OnDeleteButtonClicked())); connect(m_Controls->viewInternalDataButton, SIGNAL(clicked()), this, SLOT(OnViewButtonClicked())); connect(m_Controls->ctkDicomBrowser, SIGNAL(seriesSelectionChanged(const QStringList &)), this, SLOT(OnSeriesSelectionChanged(const QStringList &))); connect(m_Controls->ctkDicomBrowser, SIGNAL(seriesSelectionChanged(const QStringList &)), this, SLOT(OnSeriesSelectionChanged(const QStringList &))); connect( m_Controls->ctkDicomBrowser, SIGNAL(seriesDoubleClicked(const QModelIndex &)), this, SLOT(OnViewButtonClicked())); connect(m_LocalIndexer, SIGNAL(indexingComplete(int, int, int, int)), this, SIGNAL(SignalFinishedImport())); m_Controls->ctkDicomBrowser->setTableOrientation(Qt::Vertical); } } void QmitkDicomLocalStorageWidget::OnStartDicomImport(const QString &dicomData) { if (m_LocalDatabase->isOpen()) { m_LocalIndexer->addDirectory(dicomData); } } void QmitkDicomLocalStorageWidget::OnStartDicomImport(const QStringList &dicomData) { if (m_LocalDatabase->isOpen()) { m_LocalIndexer->addListOfFiles( dicomData); } } void QmitkDicomLocalStorageWidget::OnDeleteButtonClicked() { if (!this->DeletePatients()) { if (!this->DeleteStudies()) { this->DeleteSeries(); } } m_Controls->ctkDicomBrowser->updateTableViews(); } bool QmitkDicomLocalStorageWidget::DeletePatients() { auto selectedPatientUIDs = m_Controls->ctkDicomBrowser->currentPatientsSelection(); if (!selectedPatientUIDs.empty()) { QStringList studyUIDs; - for (const auto &patientUID : selectedPatientUIDs) + for (const auto &patientUID : qAsConst(selectedPatientUIDs)) studyUIDs.append(m_LocalDatabase->studiesForPatient(patientUID)); QStringList seriesUIDs; for (const auto &studyUID : studyUIDs) seriesUIDs.append(m_LocalDatabase->seriesForStudy(studyUID)); auto answer = QMessageBox::question(nullptr, "Delete Patients", QString("Do you really want to delete %1 %2, containing %3 series in %4 %5?") .arg(selectedPatientUIDs.count()) .arg(selectedPatientUIDs.count() != 1 ? "patients" : "patient") .arg(seriesUIDs.count()) .arg(studyUIDs.count()) .arg(studyUIDs.count() != 1 ? "studies" : "study"), QMessageBox::Yes | QMessageBox::No, QMessageBox::No); if (answer == QMessageBox::Yes) { - for (const auto &patientUID : selectedPatientUIDs) + for (const auto &patientUID : qAsConst(selectedPatientUIDs)) m_LocalDatabase->removePatient(patientUID); } return true; } return false; } bool QmitkDicomLocalStorageWidget::DeleteStudies() { auto selectedStudyUIDs = m_Controls->ctkDicomBrowser->currentStudiesSelection(); if (!selectedStudyUIDs.empty()) { QStringList seriesUIDs; - for (const auto &studyUID : selectedStudyUIDs) + for (const auto &studyUID : qAsConst(selectedStudyUIDs)) seriesUIDs.append(m_LocalDatabase->seriesForStudy(studyUID)); auto answer = QMessageBox::question(nullptr, "Delete Studies", QString("Do you really want to delete %1 %2, containing %3 series?") .arg(selectedStudyUIDs.count()) .arg(selectedStudyUIDs.count() != 1 ? "studies" : "study") .arg(seriesUIDs.count()), QMessageBox::Yes | QMessageBox::No, QMessageBox::No); if (answer == QMessageBox::Yes) { - for (const auto &studyUID : selectedStudyUIDs) + for (const auto &studyUID : qAsConst(selectedStudyUIDs)) m_LocalDatabase->removeStudy(studyUID); } return true; } return false; } bool QmitkDicomLocalStorageWidget::DeleteSeries() { auto selectedSeriesUIDs = m_Controls->ctkDicomBrowser->currentSeriesSelection(); if (!selectedSeriesUIDs.empty()) { auto answer = QMessageBox::question(nullptr, "Delete Series", QString("Do you really want to delete %1 series?").arg(selectedSeriesUIDs.count()), QMessageBox::Yes | QMessageBox::No, QMessageBox::No); if (answer == QMessageBox::Yes) { - for (const auto &seriesUID : selectedSeriesUIDs) + for (const auto &seriesUID : qAsConst(selectedSeriesUIDs)) m_LocalDatabase->removeSeries(seriesUID); } return true; } return false; } void QmitkDicomLocalStorageWidget::OnViewButtonClicked() { QStringList uids = m_Controls->ctkDicomBrowser->currentSeriesSelection(); QString uid; foreach (uid, uids) { QStringList filesForSeries = m_LocalDatabase->filesForSeries(uid); QHash eventProperty; eventProperty.insert("FilesForSeries", filesForSeries); if (!filesForSeries.isEmpty()) { QString modality = m_LocalDatabase->fileValue(filesForSeries.at(0), "0008,0060"); eventProperty.insert("Modality", modality); } emit SignalDicomToDataManager(eventProperty); } } void QmitkDicomLocalStorageWidget::SetDatabaseDirectory(QString newDatatbaseDirectory) { QDir databaseDirecory = QDir(newDatatbaseDirectory); if (!databaseDirecory.exists()) { databaseDirecory.mkpath(databaseDirecory.absolutePath()); } QString newDatatbaseFile = databaseDirecory.absolutePath() + QString("/ctkDICOM.sql"); this->SetDatabase(newDatatbaseFile); } void QmitkDicomLocalStorageWidget::SetDatabase(QString databaseFile) { m_LocalDatabase = new ctkDICOMDatabase(databaseFile); m_LocalDatabase->setParent(this); m_Controls->ctkDicomBrowser->setDICOMDatabase(m_LocalDatabase); m_LocalIndexer->setDatabase(m_LocalDatabase); } void QmitkDicomLocalStorageWidget::OnSeriesSelectionChanged(const QStringList &s) { m_Controls->viewInternalDataButton->setEnabled((s.size() != 0)); } diff --git a/Modules/DataTypesExt/include/mitkCompressedImageContainer.h b/Modules/DataTypesExt/include/mitkCompressedImageContainer.h index 71d5d9878e..32ead859c3 100644 --- a/Modules/DataTypesExt/include/mitkCompressedImageContainer.h +++ b/Modules/DataTypesExt/include/mitkCompressedImageContainer.h @@ -1,80 +1,80 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkCompressedImageContainer_h_Included #define mitkCompressedImageContainer_h_Included #include "MitkDataTypesExtExports.h" #include "mitkCommon.h" #include "mitkGeometry3D.h" #include "mitkImage.h" #include "mitkImageDataItem.h" #include #include namespace mitk { /** \brief Holds one (compressed) mitk::Image Uses zlib to compress the data of an mitk::Image. $Author$ */ class MITKDATATYPESEXT_EXPORT CompressedImageContainer : public itk::Object { public: mitkClassMacroItkParent(CompressedImageContainer, itk::Object); itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** * \brief Creates a compressed version of the image. * * Will not hold any further SmartPointers to the image. * */ - void SetImage(Image *); + void SetImage(const Image *); /** * \brief Creates a full mitk::Image from its compressed version. * * This Method hold no buffer, so the uncompression algorithm will be * executed every time you call this method. Don't overdo it. * */ - Image::Pointer GetImage(); + Image::Pointer GetImage() const; protected: CompressedImageContainer(); // purposely hidden ~CompressedImageContainer() override; PixelType *m_PixelType; unsigned int m_ImageDimension; std::vector m_ImageDimensions; unsigned long m_OneTimeStepImageSizeInBytes; unsigned int m_NumberOfTimeSteps; /// one for each timestep. first = pointer to compressed data; second = size of buffer in bytes std::vector> m_ByteBuffers; BaseGeometry::Pointer m_ImageGeometry; }; } // namespace #endif diff --git a/Modules/DataTypesExt/src/mitkCompressedImageContainer.cpp b/Modules/DataTypesExt/src/mitkCompressedImageContainer.cpp index bfad62d7ef..7d11a9e9a9 100644 --- a/Modules/DataTypesExt/src/mitkCompressedImageContainer.cpp +++ b/Modules/DataTypesExt/src/mitkCompressedImageContainer.cpp @@ -1,178 +1,178 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkCompressedImageContainer.h" #include "mitkImageReadAccessor.h" #include "itk_zlib.h" #include mitk::CompressedImageContainer::CompressedImageContainer() : m_PixelType(nullptr), m_ImageGeometry(nullptr) { } mitk::CompressedImageContainer::~CompressedImageContainer() { for (auto iter = m_ByteBuffers.begin(); iter != m_ByteBuffers.end(); ++iter) { free(iter->first); } delete m_PixelType; } -void mitk::CompressedImageContainer::SetImage(Image *image) +void mitk::CompressedImageContainer::SetImage(const Image *image) { for (auto iter = m_ByteBuffers.begin(); iter != m_ByteBuffers.end(); ++iter) { free(iter->first); } m_ByteBuffers.clear(); // Compress diff image using zlib (will be restored on demand) // determine memory size occupied by voxel data m_ImageDimension = image->GetDimension(); m_ImageDimensions.clear(); m_PixelType = new mitk::PixelType(image->GetPixelType()); m_OneTimeStepImageSizeInBytes = m_PixelType->GetSize(); // bits per element divided by 8 for (unsigned int i = 0; i < m_ImageDimension; ++i) { unsigned int currentImageDimension = image->GetDimension(i); m_ImageDimensions.push_back(currentImageDimension); if (i < 3) { m_OneTimeStepImageSizeInBytes *= currentImageDimension; // only the 3D memory size } } m_ImageGeometry = image->GetGeometry(); m_NumberOfTimeSteps = 1; if (m_ImageDimension > 3) { m_NumberOfTimeSteps = image->GetDimension(3); } for (unsigned int timestep = 0; timestep < m_NumberOfTimeSteps; ++timestep) { // allocate a buffer as specified by zlib unsigned long bufferSize = m_OneTimeStepImageSizeInBytes + static_cast(m_OneTimeStepImageSizeInBytes * 0.2) + 12; auto *byteBuffer = (unsigned char *)malloc(bufferSize); if (itk::Object::GetDebug()) { // compress image here into a buffer MITK_INFO << "Using ZLib version: '" << zlibVersion() << "'" << std::endl << "Attempting to compress " << m_OneTimeStepImageSizeInBytes << " image bytes into a buffer of size " << bufferSize << std::endl; } ImageReadAccessor imgAcc(image, image->GetVolumeData(timestep)); ::Bytef *dest(byteBuffer); ::uLongf destLen(bufferSize); auto *source((unsigned char *)imgAcc.GetData()); ::uLongf sourceLen(m_OneTimeStepImageSizeInBytes); int zlibRetVal = ::compress(dest, &destLen, source, sourceLen); if (itk::Object::GetDebug()) { if (zlibRetVal == Z_OK) { MITK_INFO << "Success, using " << destLen << " bytes of the buffer (ratio " << ((double)destLen / (double)sourceLen) << ")" << std::endl; } else { switch (zlibRetVal) { case Z_MEM_ERROR: MITK_ERROR << "not enough memory" << std::endl; break; case Z_BUF_ERROR: MITK_ERROR << "output buffer too small" << std::endl; break; default: MITK_ERROR << "other, unspecified error" << std::endl; break; } } } // only use the neccessary amount of memory, realloc the buffer! byteBuffer = (unsigned char *)realloc(byteBuffer, destLen); bufferSize = destLen; // MITK_INFO << "Using " << bufferSize << " bytes to store compressed image (" << destLen << " needed)" << // std::endl; m_ByteBuffers.push_back(std::pair(byteBuffer, bufferSize)); } } -mitk::Image::Pointer mitk::CompressedImageContainer::GetImage() +mitk::Image::Pointer mitk::CompressedImageContainer::GetImage() const { if (m_ByteBuffers.empty()) return nullptr; // uncompress image data, create an Image Image::Pointer image = Image::New(); unsigned int dims[20]; // more than 20 dimensions and bang for (unsigned int dim = 0; dim < m_ImageDimension; ++dim) dims[dim] = m_ImageDimensions[dim]; image->Initialize(*m_PixelType, m_ImageDimension, dims); // this IS needed, right ?? But it does allocate memory -> // does create one big lump of memory (also in windows) unsigned int timeStep(0); for (auto iter = m_ByteBuffers.begin(); iter != m_ByteBuffers.end(); ++iter, ++timeStep) { ImageReadAccessor imgAcc(image, image->GetVolumeData(timeStep)); auto *dest((unsigned char *)imgAcc.GetData()); ::uLongf destLen(m_OneTimeStepImageSizeInBytes); ::Bytef *source(iter->first); ::uLongf sourceLen(iter->second); int zlibRetVal = ::uncompress(dest, &destLen, source, sourceLen); if (itk::Object::GetDebug()) { if (zlibRetVal == Z_OK) { MITK_INFO << "Success, destLen now " << destLen << " bytes" << std::endl; } else { switch (zlibRetVal) { case Z_DATA_ERROR: MITK_ERROR << "compressed data corrupted" << std::endl; break; case Z_MEM_ERROR: MITK_ERROR << "not enough memory" << std::endl; break; case Z_BUF_ERROR: MITK_ERROR << "output buffer too small" << std::endl; break; default: MITK_ERROR << "other, unspecified error" << std::endl; break; } } } } image->SetGeometry(m_ImageGeometry); image->Modified(); return image; } diff --git a/Modules/Gizmo/src/mitkGizmoInteractor.cpp b/Modules/Gizmo/src/mitkGizmoInteractor.cpp index a682f70a24..7749ad82de 100644 --- a/Modules/Gizmo/src/mitkGizmoInteractor.cpp +++ b/Modules/Gizmo/src/mitkGizmoInteractor.cpp @@ -1,465 +1,465 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkGizmoInteractor.h" #include "mitkGizmoMapper2D.h" // MITK includes #include #include #include #include #include #include #include #include #include #include // VTK includes #include #include #include #include #include #include #include #include #include mitk::GizmoInteractor::GizmoInteractor() { m_ColorForHighlight[0] = 1.0; m_ColorForHighlight[1] = 0.5; m_ColorForHighlight[2] = 0.0; m_ColorForHighlight[3] = 1.0; // TODO if we want to get this configurable, the this is the recipe: // - make the 2D mapper add corresponding properties to control "enabled" and "color" // - make the interactor evaluate those properties // - in an ideal world, modify the state machine on the fly and skip mouse move handling } mitk::GizmoInteractor::~GizmoInteractor() { } void mitk::GizmoInteractor::ConnectActionsAndFunctions() { CONNECT_CONDITION("PickedHandle", HasPickedHandle); CONNECT_FUNCTION("DecideInteraction", DecideInteraction); CONNECT_FUNCTION("MoveAlongAxis", MoveAlongAxis); CONNECT_FUNCTION("RotateAroundAxis", RotateAroundAxis); CONNECT_FUNCTION("MoveFreely", MoveFreely); CONNECT_FUNCTION("ScaleEqually", ScaleEqually); CONNECT_FUNCTION("FeedUndoStack", FeedUndoStack); } void mitk::GizmoInteractor::SetGizmoNode(DataNode *node) { DataInteractor::SetDataNode(node); m_Gizmo = dynamic_cast(node->GetData()); // setup picking from just this object m_Picker.clear(); } void mitk::GizmoInteractor::SetManipulatedObjectNode(DataNode *node) { if (node && node->GetData()) { m_ManipulatedObjectGeometry = node->GetData()->GetGeometry(); } } bool mitk::GizmoInteractor::HasPickedHandle(const InteractionEvent *interactionEvent) { auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr || m_Gizmo.IsNull() || m_ManipulatedObjectGeometry.IsNull() || interactionEvent->GetSender()->GetRenderWindow()->GetNeverRendered()) { return false; } if (interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D) { m_PickedHandle = PickFrom2D(positionEvent); } else { m_PickedHandle = PickFrom3D(positionEvent); } UpdateHandleHighlight(); return m_PickedHandle != Gizmo::NoHandle; } void mitk::GizmoInteractor::DecideInteraction(StateMachineAction *, InteractionEvent *interactionEvent) { assert(m_PickedHandle != Gizmo::NoHandle); auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) { return; } // if something relevant was picked, we calculate a number of // important points and axes for the upcoming geometry manipulations // note initial state m_InitialClickPosition2D = positionEvent->GetPointerPositionOnScreen(); m_InitialClickPosition3D = positionEvent->GetPositionInWorld(); auto renderer = positionEvent->GetSender()->GetVtkRenderer(); renderer->SetWorldPoint(m_InitialClickPosition3D[0], m_InitialClickPosition3D[1], m_InitialClickPosition3D[2], 0); renderer->WorldToDisplay(); m_InitialClickPosition2DZ = renderer->GetDisplayPoint()[2]; m_InitialGizmoCenter3D = m_Gizmo->GetCenter(); positionEvent->GetSender()->WorldToDisplay(m_InitialGizmoCenter3D, m_InitialGizmoCenter2D); m_InitialManipulatedObjectGeometry = m_ManipulatedObjectGeometry->Clone(); switch ( m_PickedHandle ) { case Gizmo::MoveAlongAxisX: case Gizmo::RotateAroundAxisX: case Gizmo::ScaleX: m_AxisOfMovement = m_InitialManipulatedObjectGeometry->GetAxisVector(0); break; case Gizmo::MoveAlongAxisY: case Gizmo::RotateAroundAxisY: case Gizmo::ScaleY: m_AxisOfMovement = m_InitialManipulatedObjectGeometry->GetAxisVector(1); break; case Gizmo::MoveAlongAxisZ: case Gizmo::RotateAroundAxisZ: case Gizmo::ScaleZ: m_AxisOfMovement = m_InitialManipulatedObjectGeometry->GetAxisVector(2); break; default: break; } m_AxisOfMovement.Normalize(); m_AxisOfRotation = m_AxisOfMovement; // for translation: test whether the user clicked into the "object's real" axis direction // or into the other one Vector3D intendedAxis = m_InitialClickPosition3D - m_InitialGizmoCenter3D; if ( intendedAxis * m_AxisOfMovement < 0 ) { m_AxisOfMovement *= -1.0; } // for rotation: test whether the axis of rotation is more looking in the direction // of the camera or in the opposite vtkCamera *camera = renderer->GetActiveCamera(); vtkVector3d cameraDirection(camera->GetDirectionOfProjection()); double angle_rad = vtkMath::AngleBetweenVectors(cameraDirection.GetData(), m_AxisOfRotation.GetDataPointer()); if ( angle_rad < vtkMath::Pi() / 2.0 ) { m_AxisOfRotation *= -1.0; } InternalEvent::Pointer decision; switch (m_PickedHandle) { case Gizmo::MoveAlongAxisX: case Gizmo::MoveAlongAxisY: case Gizmo::MoveAlongAxisZ: decision = InternalEvent::New(interactionEvent->GetSender(), this, "StartTranslationAlongAxis"); break; case Gizmo::RotateAroundAxisX: case Gizmo::RotateAroundAxisY: case Gizmo::RotateAroundAxisZ: decision = InternalEvent::New(interactionEvent->GetSender(), this, "StartRotationAroundAxis"); break; case Gizmo::MoveFreely: decision = InternalEvent::New(interactionEvent->GetSender(), this, "MoveFreely"); break; case Gizmo::ScaleX: case Gizmo::ScaleY: case Gizmo::ScaleZ: // Implementation note: Why didn't we implement per-axis scaling yet? // When this was implemented, the mitk::ScaleOperation was able to only describe // uniform scaling around a central point. Since we use operations for all modifications // in order to have undo/redo working, any axis-specific scaling should also // use operations. // Consequence: enhance ScaleOperation when there is need to have scaling per axis. decision = InternalEvent::New(interactionEvent->GetSender(), this, "ScaleEqually"); break; default: break; } interactionEvent->GetSender()->GetDispatcher()->QueueEvent(decision); } void mitk::GizmoInteractor::MoveAlongAxis(StateMachineAction *, InteractionEvent *interactionEvent) { auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) { return; } Point2D currentPosition2D = positionEvent->GetPointerPositionOnScreen(); // re-use the initial z value to calculate movements parallel to the camera plane auto renderer = positionEvent->GetSender()->GetVtkRenderer(); renderer->SetDisplayPoint(currentPosition2D[0], currentPosition2D[1], m_InitialClickPosition2DZ); renderer->DisplayToWorld(); vtkVector3d worldPointVTK(renderer->GetWorldPoint()); Point3D worldPointITK(worldPointVTK.GetData()); Vector3D freeMouseMovement3D(worldPointITK - m_InitialClickPosition3D); double projectedMouseMovement3D = freeMouseMovement3D * m_AxisOfMovement; Vector3D appliedMovement3D = projectedMouseMovement3D * m_AxisOfMovement; ApplyTranslationToManipulatedObject(appliedMovement3D); RenderingManager::GetInstance()->ForceImmediateUpdateAll(); } void mitk::GizmoInteractor::RotateAroundAxis(StateMachineAction *, InteractionEvent *interactionEvent) { auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) { return; } Vector2D originalVector = m_InitialClickPosition2D - m_InitialGizmoCenter2D; Vector2D currentVector = positionEvent->GetPointerPositionOnScreen() - m_InitialGizmoCenter2D; originalVector.Normalize(); currentVector.Normalize(); double angle_rad = std::atan2(currentVector[1], currentVector[0]) - std::atan2(originalVector[1], originalVector[0]); ApplyRotationToManipulatedObject(vtkMath::DegreesFromRadians(angle_rad)); RenderingManager::GetInstance()->ForceImmediateUpdateAll(); } void mitk::GizmoInteractor::MoveFreely(StateMachineAction *, InteractionEvent *interactionEvent) { auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) { return; } Point2D currentPosition2D = positionEvent->GetPointerPositionOnScreen(); // re-use the initial z value to really move parallel to the camera plane auto renderer = positionEvent->GetSender()->GetVtkRenderer(); renderer->SetDisplayPoint(currentPosition2D[0], currentPosition2D[1], m_InitialClickPosition2DZ); renderer->DisplayToWorld(); vtkVector3d worldPointVTK(renderer->GetWorldPoint()); Point3D worldPointITK(worldPointVTK.GetData()); Vector3D movementITK(worldPointITK - m_InitialClickPosition3D); ApplyTranslationToManipulatedObject(movementITK); RenderingManager::GetInstance()->ForceImmediateUpdateAll(); } void mitk::GizmoInteractor::ScaleEqually(StateMachineAction *, InteractionEvent *interactionEvent) { auto positionEvent = dynamic_cast(interactionEvent); if (positionEvent == nullptr) { return; } Point2D currentPosition2D = positionEvent->GetPointerPositionOnScreen(); double relativeSize = (currentPosition2D - m_InitialGizmoCenter2D).GetNorm() / (m_InitialClickPosition2D - m_InitialGizmoCenter2D).GetNorm(); ApplyEqualScalingToManipulatedObject(relativeSize); RenderingManager::GetInstance()->ForceImmediateUpdateAll(); } void mitk::GizmoInteractor::ApplyTranslationToManipulatedObject(const Vector3D &translation) { assert(m_ManipulatedObjectGeometry.IsNotNull()); auto manipulatedGeometry = m_InitialManipulatedObjectGeometry->Clone(); - m_FinalDoOperation.reset(new PointOperation(OpMOVE, translation)); + m_FinalDoOperation.reset(new PointOperation(OpMOVE, Point3D(translation))); if (m_UndoEnabled) { - m_FinalUndoOperation.reset(new PointOperation(OpMOVE, -translation)); + m_FinalUndoOperation.reset(new PointOperation(OpMOVE, Point3D(-translation))); } manipulatedGeometry->ExecuteOperation(m_FinalDoOperation.get()); m_ManipulatedObjectGeometry->SetIndexToWorldTransform(manipulatedGeometry->GetIndexToWorldTransform()); } void mitk::GizmoInteractor::ApplyEqualScalingToManipulatedObject(double scalingFactor) { assert(m_ManipulatedObjectGeometry.IsNotNull()); auto manipulatedGeometry = m_InitialManipulatedObjectGeometry->Clone(); m_FinalDoOperation.reset(new ScaleOperation(OpSCALE, scalingFactor - 1.0, m_InitialGizmoCenter3D)); if (m_UndoEnabled) { m_FinalUndoOperation.reset(new ScaleOperation(OpSCALE, -(scalingFactor - 1.0), m_InitialGizmoCenter3D)); } manipulatedGeometry->ExecuteOperation(m_FinalDoOperation.get()); m_ManipulatedObjectGeometry->SetIndexToWorldTransform(manipulatedGeometry->GetIndexToWorldTransform()); } void mitk::GizmoInteractor::ApplyRotationToManipulatedObject(double angle_deg) { assert(m_ManipulatedObjectGeometry.IsNotNull()); auto manipulatedGeometry = m_InitialManipulatedObjectGeometry->Clone(); m_FinalDoOperation.reset(new RotationOperation(OpROTATE, m_InitialGizmoCenter3D, m_AxisOfRotation, angle_deg)); if (m_UndoEnabled) { m_FinalUndoOperation.reset(new RotationOperation(OpROTATE, m_InitialGizmoCenter3D, m_AxisOfRotation, -angle_deg)); } manipulatedGeometry->ExecuteOperation(m_FinalDoOperation.get()); m_ManipulatedObjectGeometry->SetIndexToWorldTransform(manipulatedGeometry->GetIndexToWorldTransform()); } void mitk::GizmoInteractor::FeedUndoStack(StateMachineAction *, InteractionEvent *) { if (m_UndoEnabled) { OperationEvent *operationEvent = new OperationEvent(m_ManipulatedObjectGeometry, // OperationEvent will destroy operations! // --> release() and not get() m_FinalDoOperation.release(), m_FinalUndoOperation.release(), "Direct geometry manipulation"); mitk::OperationEvent::IncCurrObjectEventId(); // save each modification individually m_UndoController->SetOperationEvent(operationEvent); } } mitk::Gizmo::HandleType mitk::GizmoInteractor::PickFrom2D(const InteractionPositionEvent *positionEvent) { BaseRenderer *renderer = positionEvent->GetSender(); auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard2D); auto gizmo_mapper = dynamic_cast(mapper); auto &picker = m_Picker[renderer]; if (picker == nullptr) { picker = vtkSmartPointer::New(); picker->SetTolerance(0.005); if (gizmo_mapper) { // doing this each time is bizarre picker->AddPickList(gizmo_mapper->GetVtkProp(renderer)); picker->PickFromListOn(); } } auto displayPosition = positionEvent->GetPointerPositionOnScreen(); picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer()); vtkIdType pickedPointID = picker->GetPointId(); if (pickedPointID == -1) { return Gizmo::NoHandle; } vtkPolyData *polydata = gizmo_mapper->GetVtkPolyData(renderer); if (polydata && polydata->GetPointData() && polydata->GetPointData()->GetScalars()) { double dataValue = polydata->GetPointData()->GetScalars()->GetTuple1(pickedPointID); return m_Gizmo->GetHandleFromPointDataValue(dataValue); } return Gizmo::NoHandle; } mitk::Gizmo::HandleType mitk::GizmoInteractor::PickFrom3D(const InteractionPositionEvent *positionEvent) { BaseRenderer *renderer = positionEvent->GetSender(); auto &picker = m_Picker[renderer]; if (picker == nullptr) { picker = vtkSmartPointer::New(); picker->SetTolerance(0.005); auto mapper = GetDataNode()->GetMapper(BaseRenderer::Standard3D); auto vtk_mapper = dynamic_cast(mapper); if (vtk_mapper) { // doing this each time is bizarre picker->AddPickList(vtk_mapper->GetVtkProp(renderer)); picker->PickFromListOn(); } } auto displayPosition = positionEvent->GetPointerPositionOnScreen(); picker->Pick(displayPosition[0], displayPosition[1], 0, positionEvent->GetSender()->GetVtkRenderer()); vtkIdType pickedPointID = picker->GetPointId(); if (pickedPointID == -1) { return Gizmo::NoHandle; } // _something_ picked return m_Gizmo->GetHandleFromPointID(pickedPointID); } void mitk::GizmoInteractor::UpdateHandleHighlight() { if (m_HighlightedHandle != m_PickedHandle) { auto node = GetDataNode(); if (node == nullptr) return; auto base_prop = node->GetProperty("LookupTable"); if (base_prop == nullptr) return; auto lut_prop = dynamic_cast(base_prop); if (lut_prop == nullptr) return; auto lut = lut_prop->GetLookupTable(); if (lut == nullptr) return; // Table size is expected to constructed as one entry per gizmo-part enum value assert(lut->GetVtkLookupTable()->GetNumberOfTableValues() > std::max(m_PickedHandle, m_HighlightedHandle)); // Reset previously overwritten color if (m_HighlightedHandle != Gizmo::NoHandle) { lut->SetTableValue(m_HighlightedHandle, m_ColorReplacedByHighlight); } // Overwrite currently highlighted color if (m_PickedHandle != Gizmo::NoHandle) { lut->GetTableValue(m_PickedHandle, m_ColorReplacedByHighlight); lut->SetTableValue(m_PickedHandle, m_ColorForHighlight); } // Mark node modified to allow repaint node->Modified(); RenderingManager::GetInstance()->RequestUpdateAll(RenderingManager::REQUEST_UPDATE_ALL); m_HighlightedHandle = m_PickedHandle; } } diff --git a/Modules/IGT/Algorithms/mitkNavigationDataToIGTLMessageFilter.cpp b/Modules/IGT/Algorithms/mitkNavigationDataToIGTLMessageFilter.cpp index 300ed54246..186d9fc2fc 100644 --- a/Modules/IGT/Algorithms/mitkNavigationDataToIGTLMessageFilter.cpp +++ b/Modules/IGT/Algorithms/mitkNavigationDataToIGTLMessageFilter.cpp @@ -1,319 +1,319 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkNavigationDataToIGTLMessageFilter.h" #include "igtlQuaternionTrackingDataMessage.h" #include "igtlTrackingDataMessage.h" #include "igtlTransformMessage.h" #include "igtlPositionMessage.h" #include #include mitk::NavigationDataToIGTLMessageFilter::NavigationDataToIGTLMessageFilter() { mitk::IGTLMessage::Pointer output = mitk::IGTLMessage::New(); this->SetNumberOfRequiredOutputs(1); this->SetNthOutput(0, output.GetPointer()); this->SetNumberOfRequiredInputs(1); // m_OperationMode = Mode3D; m_CurrentTimeStep = 0; // m_RingBufferSize = 50; //the default ring buffer size // m_NumberForMean = 100; } mitk::NavigationDataToIGTLMessageFilter::~NavigationDataToIGTLMessageFilter() { } void mitk::NavigationDataToIGTLMessageFilter::GenerateData() { switch (m_OperationMode) { case ModeSendQTDataMsg: this->GenerateDataModeSendQTDataMsg(); break; case ModeSendTDataMsg: this->GenerateDataModeSendTDataMsg(); break; case ModeSendQTransMsg: this->GenerateDataModeSendQTransMsg(); break; case ModeSendTransMsg: this->GenerateDataModeSendTransMsg(); break; default: break; } } void mitk::NavigationDataToIGTLMessageFilter::SetInput(const NavigationData* nd) { // Process object is not const-correct so the const_cast is required here this->ProcessObject::SetNthInput(0, const_cast(nd)); this->CreateOutputsForAllInputs(); } void mitk::NavigationDataToIGTLMessageFilter::SetInput(unsigned int idx, const NavigationData* nd) { // Process object is not const-correct so the const_cast is required here this->ProcessObject::SetNthInput(idx, const_cast(nd)); this->CreateOutputsForAllInputs(); } const mitk::NavigationData* mitk::NavigationDataToIGTLMessageFilter::GetInput(void) { if (this->GetNumberOfInputs() < 1) return nullptr; return static_cast(this->ProcessObject::GetInput(0)); } const mitk::NavigationData* mitk::NavigationDataToIGTLMessageFilter::GetInput(unsigned int idx) { if (this->GetNumberOfInputs() < 1) return nullptr; return static_cast(this->ProcessObject::GetInput(idx)); } void mitk::NavigationDataToIGTLMessageFilter::CreateOutputsForAllInputs() { switch (m_OperationMode) { case ModeSendQTDataMsg: // create one message output for all navigation data inputs this->SetNumberOfIndexedOutputs(1); // set the type for this filter this->SetType("QTDATA"); break; case ModeSendTDataMsg: // create one message output for all navigation data inputs this->SetNumberOfIndexedOutputs(1); // set the type for this filter this->SetType("TDATA"); break; case ModeSendQTransMsg: // create one message output for all navigation data input together this->SetNumberOfIndexedOutputs(1); // set the type for this filter this->SetType("POSITION"); break; case ModeSendTransMsg: // create one message output for each navigation data input this->SetNumberOfIndexedOutputs(this->GetNumberOfIndexedInputs()); // set the type for this filter this->SetType("TRANS"); break; default: break; } for (unsigned int idx = 0; idx < this->GetNumberOfIndexedOutputs(); ++idx) { if (this->GetOutput(idx) == nullptr) { DataObjectPointer newOutput = this->MakeOutput(idx); this->SetNthOutput(idx, newOutput); } this->Modified(); } } void ConvertAffineTransformationIntoIGTLMatrix(mitk::AffineTransform3D* trans, igtl::Matrix4x4 igtlTransform) { const mitk::AffineTransform3D::MatrixType& matrix = trans->GetMatrix(); mitk::Vector3D position = trans->GetOffset(); //copy the data into a matrix type that igtl understands for (unsigned int r = 0; r < 3; r++) { for (unsigned int c = 0; c < 3; c++) { igtlTransform[r][c] = matrix(r, c); } igtlTransform[r][3] = position[r]; } for (unsigned int c = 0; c < 3; c++) { igtlTransform[3][c] = 0.0; } igtlTransform[3][3] = 1.0; } void mitk::NavigationDataToIGTLMessageFilter::GenerateDataModeSendQTransMsg() { // for each output message for (unsigned int i = 0; i < this->GetNumberOfIndexedInputs(); ++i) { mitk::IGTLMessage* output = this->GetOutput(i); assert(output); const mitk::NavigationData* input = this->GetInput(i); assert(input); // do not add navigation data to message if input is invalid if (input->IsDataValid() == false) continue; //get the navigation data components mitk::NavigationData::PositionType pos = input->GetPosition(); mitk::NavigationData::OrientationType ori = input->GetOrientation(); //insert this information into the message igtl::PositionMessage::Pointer posMsg = igtl::PositionMessage::New(); posMsg->SetPosition(pos[0], pos[1], pos[2]); posMsg->SetQuaternion(ori[0], ori[1], ori[2], ori[3]); igtl::TimeStamp::Pointer timestamp = ConvertToIGTLTimeStamp(input->GetIGTTimeStamp()); posMsg->SetTimeStamp(timestamp); posMsg->SetDeviceName(input->GetName()); posMsg->Pack(); //add the igtl message to the mitk::IGTLMessage output->SetMessage(posMsg.GetPointer()); } } void mitk::NavigationDataToIGTLMessageFilter::GenerateDataModeSendTransMsg() { // for each output message for (unsigned int i = 0; i < this->GetNumberOfIndexedInputs(); ++i) { mitk::IGTLMessage* output = this->GetOutput(i); assert(output); const mitk::NavigationData* input = this->GetInput(i); assert(input); // do not add navigation data to message if input is invalid if (input->IsDataValid() == false) continue; //get the navigation data components mitk::AffineTransform3D::Pointer transform = input->GetAffineTransform3D(); - mitk::NavigationData::PositionType position = transform->GetOffset(); + mitk::NavigationData::PositionType position = Point3D(transform->GetOffset()); //convert the transform into a igtl type igtl::Matrix4x4 igtlTransform; ConvertAffineTransformationIntoIGTLMatrix(transform, igtlTransform); //insert this information into the message igtl::TransformMessage::Pointer transMsg = igtl::TransformMessage::New(); transMsg->SetMatrix(igtlTransform); transMsg->SetPosition(position[0], position[1], position[2]); igtl::TimeStamp::Pointer timestamp = ConvertToIGTLTimeStamp(input->GetIGTTimeStamp()); transMsg->SetTimeStamp(timestamp); transMsg->SetDeviceName(input->GetName()); transMsg->Pack(); //add the igtl message to the mitk::IGTLMessage output->SetMessage(transMsg.GetPointer()); } } igtl::TimeStamp::Pointer mitk::NavigationDataToIGTLMessageFilter::ConvertToIGTLTimeStamp(double IGTTimeStamp) { igtl::TimeStamp::Pointer timestamp = igtl::TimeStamp::New(); timestamp->SetTime(IGTTimeStamp / 1000, (int)(IGTTimeStamp) % 1000); return timestamp; } void mitk::NavigationDataToIGTLMessageFilter::GenerateDataModeSendQTDataMsg() { mitk::IGTLMessage* output = this->GetOutput(); assert(output); //create a output igtl message igtl::QuaternionTrackingDataMessage::Pointer qtdMsg = igtl::QuaternionTrackingDataMessage::New(); mitk::NavigationData::PositionType pos; mitk::NavigationData::OrientationType ori; for (unsigned int index = 0; index < this->GetNumberOfIndexedInputs(); index++) { const mitk::NavigationData* nd = GetInput(index); assert(nd); //get the navigation data components pos = nd->GetPosition(); ori = nd->GetOrientation(); //insert the information into the tracking element igtl::QuaternionTrackingDataElement::Pointer tde = igtl::QuaternionTrackingDataElement::New(); tde->SetPosition(pos[0], pos[1], pos[2]); tde->SetQuaternion(ori[0], ori[1], ori[2], ori[3]); tde->SetName(nd->GetName()); //insert this element into the tracking data message qtdMsg->AddQuaternionTrackingDataElement(tde); MITK_INFO << ConvertToIGTLTimeStamp(nd->GetIGTTimeStamp()); } qtdMsg->Pack(); //add the igtl message to the mitk::IGTLMessage output->SetMessage(qtdMsg.GetPointer()); } void mitk::NavigationDataToIGTLMessageFilter::GenerateDataModeSendTDataMsg() { igtl::TrackingDataMessage::Pointer tdMsg = igtl::TrackingDataMessage::New(); mitk::IGTLMessage* output = this->GetOutput(0); assert(output); // for each output message for (unsigned int i = 0; i < this->GetNumberOfIndexedInputs(); ++i) { const mitk::NavigationData* input = this->GetInput(i); assert(input); // do not add navigation data to message if input is invalid if (input->IsDataValid() == false) continue; //get the navigation data components mitk::AffineTransform3D::Pointer transform = input->GetAffineTransform3D(); - mitk::NavigationData::PositionType position = transform->GetOffset(); + mitk::NavigationData::PositionType position = Point3D(transform->GetOffset()); //convert the transform into a igtl type igtl::Matrix4x4 igtlTransform; ConvertAffineTransformationIntoIGTLMatrix(transform, igtlTransform); //insert this information into the message igtl::TrackingDataElement::Pointer tde = igtl::TrackingDataElement::New(); tde->SetMatrix(igtlTransform); tde->SetPosition(position[0], position[1], position[2]); tde->SetName(input->GetName()); tde->SetType(igtl::TrackingDataElement::TYPE_6D); tdMsg->AddTrackingDataElement(tde); } //use time stamp from first input igtl::TimeStamp::Pointer timestamp = ConvertToIGTLTimeStamp(this->GetInput(0)->GetIGTTimeStamp()); tdMsg->SetTimeStamp(timestamp); //tdMsg->SetDeviceName("MITK OpenIGTLink Connection"); tdMsg->Pack(); tdMsg->SetDeviceName("MITK OpenIGTLink Source"); output->SetMessage(tdMsg.GetPointer()); } void mitk::NavigationDataToIGTLMessageFilter::SetOperationMode(OperationMode mode) { m_OperationMode = mode; this->Modified(); } void mitk::NavigationDataToIGTLMessageFilter::ConnectTo( mitk::NavigationDataSource* UpstreamFilter) { for (DataObjectPointerArraySizeType i = 0; i < UpstreamFilter->GetNumberOfOutputs(); i++) { this->SetInput(i, UpstreamFilter->GetOutput(i)); } } diff --git a/Modules/IGT/CMakeLists.txt b/Modules/IGT/CMakeLists.txt index 51ae8db7fe..79ab9c6f5c 100644 --- a/Modules/IGT/CMakeLists.txt +++ b/Modules/IGT/CMakeLists.txt @@ -1,61 +1,54 @@ include(MITKIGTHardware.cmake) if(MITK_USE_MICRON_TRACKER) set(ADDITIONAL_INCLUDE_DIRS ${ADDITIONAL_INCLUDE_DIRS} ${MITK_MICRON_TRACKER_INCLUDE_DIR}) set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_MICRON_TRACKER_LIB}) -endif(MITK_USE_MICRON_TRACKER) +endif() if(MITK_USE_OPTITRACK_TRACKER) set(ADDITIONAL_INCLUDE_DIRS ${ADDITIONAL_INCLUDE_DIRS} ${MITK_OPTITRACK_TRACKER_INCLUDE_DIR}) set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_OPTITRACK_TRACKER_LIB}) add_definitions( -DMITK_USE_OPTITRACK_TRACKER ) -endif(MITK_USE_OPTITRACK_TRACKER) +endif() if(MITK_USE_MICROBIRD_TRACKER) set(ADDITIONAL_INCLUDE_DIRS ${ADDITIONAL_INCLUDE_DIRS} ${MITK_USE_MICROBIRD_TRACKER_INCLUDE_DIR}) set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_USE_MICROBIRD_TRACKER_LIB}) -endif(MITK_USE_MICROBIRD_TRACKER) +endif() if(MITK_USE_POLHEMUS_TRACKER) set(ADDITIONAL_INCLUDE_DIRS ${ADDITIONAL_INCLUDE_DIRS} ${MITK_POLHEMUS_TRACKER_INCLUDE_DIR}) set(ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ${MITK_POLHEMUS_TRACKER_LIB}) -endif(MITK_USE_POLHEMUS_TRACKER) +endif() -MITK_CREATE_MODULE( +mitk_create_module( INCLUDE_DIRS PUBLIC Algorithms Common DataManagement ExceptionHandling IO Rendering TrackingDevices TestingHelper PRIVATE ${ADDITIONAL_INCLUDE_DIRS} DEPENDS PUBLIC MitkImageStatistics MitkSceneSerialization MitkIGTBase MitkOpenIGTLink PACKAGE_DEPENDS PRIVATE ITK|RegistrationCommon OpenIGTLink tinyxml2 ADDITIONAL_LIBS "${ADDITIONAL_LIBS}" ) if(MitkIGT_IS_ENABLED) MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/ClaronMicron.stl ) MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/IntuitiveDaVinci.stl ) MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAurora.stl ) MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAurora_Dome.stl ) MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAuroraCompactFG_Dome.stl ) MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAuroraPlanarFG_Dome.stl ) MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAuroraTabletopFG_Dome.stl ) MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIAuroraTabletopFG_Prototype_Dome.stl ) MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIPolarisOldModel.stl ) MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIPolarisSpectra.stl ) MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIPolarisSpectraExtendedPyramid.stl ) MITK_INSTALL(FILES ${MITK_SOURCE_DIR}/Modules/IGT/Resources/NDIPolarisVicra.stl ) endif() -if(NOT MODULE_IS_ENABLED) - message(STATUS "IGTTutorialStep1 won't be built. Missing: ${_RESULT}") -else() -## create IGT config -configure_file(mitkIGTConfig.h.in ${PROJECT_BINARY_DIR}/mitkIGTConfig.h @ONLY) - -add_subdirectory(autoload/DeviceRegistry) - -add_subdirectory(Tutorial) - -add_subdirectory(Testing) +if(MODULE_IS_ENABLED) + configure_file(mitkIGTConfig.h.in ${PROJECT_BINARY_DIR}/mitkIGTConfig.h @ONLY) + add_subdirectory(autoload/DeviceRegistry) + add_subdirectory(Tutorial) + add_subdirectory(Testing) endif() - diff --git a/Modules/IGT/Testing/mitkNavigationDataReferenceTransformFilterTest.cpp b/Modules/IGT/Testing/mitkNavigationDataReferenceTransformFilterTest.cpp index f76ed9bae0..3c557e6186 100644 --- a/Modules/IGT/Testing/mitkNavigationDataReferenceTransformFilterTest.cpp +++ b/Modules/IGT/Testing/mitkNavigationDataReferenceTransformFilterTest.cpp @@ -1,223 +1,223 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkNavigationDataReferenceTransformFilter.h" #include "mitkNavigationData.h" #include "mitkTestingMacros.h" #include #include /**Documentation * test for the class "NavigationDataReferenceTransformFilter". */ int mitkNavigationDataReferenceTransformFilterTest(int /* argc */, char* /*argv*/[]) { MITK_TEST_BEGIN("NavigationDataReferenceTransformFilter") // let's create an object of our class mitk::NavigationDataReferenceTransformFilter::Pointer myFilter = mitk::NavigationDataReferenceTransformFilter::New(); // first test: did this work? // using MITK_TEST_CONDITION_REQUIRED makes the test stop after failure, since // it makes no sense to continue without an object. MITK_TEST_CONDITION_REQUIRED(myFilter.IsNotNull(),"Testing instantiation"); /*create helper objects: positions of the ND sources*/ mitk::Point3D sourcePos1,sourcePos2, sourcePos3, targetPos1, targetPos2, targetPos3; mitk::FillVector3D(sourcePos1, 11.1, 11.1, 11.1); mitk::FillVector3D(sourcePos2, 22.2, 22.2, 22.2); mitk::FillVector3D(sourcePos3, 33.3, 33.3, 33.3); mitk::FillVector3D(targetPos1, -1.1, -2.2, -3.3); mitk::FillVector3D(targetPos2, -4.4, -5.5, -6.6); mitk::FillVector3D(targetPos3, -7.7, -8.8, -9.9); /*create helper objects: orientations of the ND sources*/ mitk::NavigationData::OrientationType sourceOri1(0.1, 0.1, 0.1, 0.1); mitk::NavigationData::OrientationType sourceOri2(0.2, 0.2, 0.2, 0.2); mitk::NavigationData::OrientationType sourceOri3(0.3, 0.3, 0.3, 0.3); mitk::NavigationData::OrientationType targetOri1(0.4, 0.4, 0.4, 0.4); mitk::NavigationData::OrientationType targetOri2(0.5, 0.5, 0.5, 0.5); mitk::NavigationData::OrientationType targetOri3(0.6, 0.6, 0.6, 0.6); /*create helper objects: ND position accurancy and validity bool*/ mitk::ScalarType initialError(0.0); bool initialValid(true); /*create helper objects: NDs for the source and target NDs*/ mitk::NavigationData::Pointer snd1 = mitk::NavigationData::New(); snd1->SetPosition(sourcePos1); snd1->SetOrientation(sourceOri1); snd1->SetPositionAccuracy(initialError); snd1->SetDataValid(initialValid); mitk::NavigationData::Pointer snd2 = mitk::NavigationData::New(); snd2->SetPosition(sourcePos2); snd2->SetOrientation(sourceOri2); snd2->SetPositionAccuracy(initialError); snd2->SetDataValid(initialValid); mitk::NavigationData::Pointer snd3 = mitk::NavigationData::New(); snd3->SetPosition(sourcePos3); snd3->SetOrientation(sourceOri3); snd3->SetPositionAccuracy(initialError); snd3->SetDataValid(initialValid); mitk::NavigationData::Pointer tnd1 = mitk::NavigationData::New(); tnd1->SetPosition(targetPos1); tnd1->SetOrientation(targetOri1); tnd1->SetPositionAccuracy(initialError); tnd1->SetDataValid(initialValid); mitk::NavigationData::Pointer tnd2 = mitk::NavigationData::New(); tnd2->SetPosition(targetPos2); tnd2->SetOrientation(targetOri2); tnd2->SetPositionAccuracy(initialError); tnd2->SetDataValid(initialValid); mitk::NavigationData::Pointer tnd3 = mitk::NavigationData::New(); tnd3->SetPosition(targetPos3); tnd3->SetOrientation(targetOri3); tnd3->SetPositionAccuracy(initialError); tnd3->SetDataValid(initialValid); std::vector emptySourceNDs; std::vector oneSourceNDs; oneSourceNDs.push_back(snd1); std::vector twoSourceNDs; twoSourceNDs.push_back(snd1); twoSourceNDs.push_back(snd2); std::vector threeSourceNDs; threeSourceNDs.push_back(snd1); threeSourceNDs.push_back(snd2); threeSourceNDs.push_back(snd3); std::vector emptyTargetNDs; std::vector oneTargetNDs; oneTargetNDs.push_back(tnd1); std::vector twoTargetNDs; twoTargetNDs.push_back(tnd1); twoTargetNDs.push_back(tnd2); std::vector threeTargetNDs; threeTargetNDs.push_back(tnd1); threeTargetNDs.push_back(tnd2); threeTargetNDs.push_back(tnd3); // ------------------ setting no NDs ------------------ myFilter->SetSourceNavigationDatas(emptySourceNDs); MITK_TEST_CONDITION_REQUIRED(myFilter->GetSourceLandmarks()->IsEmpty() == true, "Testing behaviour if setting no source NDs"); myFilter->SetSourceNavigationDatas(emptyTargetNDs); MITK_TEST_CONDITION_REQUIRED(myFilter->GetTargetLandmarks()->IsEmpty() == true, "Testing behaviour if setting no target NDs"); // ------------------ setting one ND ------------------ myFilter->SetSourceNavigationDatas(oneSourceNDs); MITK_TEST_CONDITION_REQUIRED(myFilter->GetSourceLandmarks()->GetSize() == 3, "Testing if 3 source points are generated from one source ND"); myFilter->SetTargetNavigationDatas(oneTargetNDs); MITK_TEST_CONDITION_REQUIRED(myFilter->GetTargetLandmarks()->GetSize() == 3, "Testing if 3 target points are generated from one target ND"); // ------------------ setting two NDs ------------------ myFilter->SetSourceNavigationDatas(twoSourceNDs); MITK_TEST_CONDITION_REQUIRED(myFilter->GetSourceLandmarks()->GetSize() == 6, "Testing if 6 source points are generated from two source NDs"); myFilter->SetTargetNavigationDatas(twoTargetNDs); MITK_TEST_CONDITION_REQUIRED(myFilter->GetTargetLandmarks()->GetSize() == 6, "Testing if 6 target points are generated from two target NDs"); // ------------------ setting three NDs ------------------ myFilter->SetSourceNavigationDatas(threeSourceNDs); MITK_TEST_CONDITION_REQUIRED(myFilter->GetSourceLandmarks()->GetSize() == 3, "Testing if 3 source NDs are passed to 3 source points"); myFilter->SetTargetNavigationDatas(threeTargetNDs); MITK_TEST_CONDITION_REQUIRED(myFilter->GetTargetLandmarks()->GetSize() == 3, "Testing if 3 target NDs are passed to 3 target points"); // ------------------ setting different number of NDs for source and target ------------------ bool firstInitialize = myFilter->InitializeTransform(); myFilter->SetTargetNavigationDatas(twoTargetNDs); MITK_TEST_CONDITION_REQUIRED((firstInitialize == true && myFilter->InitializeTransform() == false), "Testing if initialization is denied, if different number of source and target NDs are set"); // ------------------ reinit of this filter ------------------ bool sourcePointsSet = myFilter->GetSourceLandmarks()->GetSize() > 0; bool targetPointsSet = myFilter->GetTargetLandmarks()->GetSize() > 0; MITK_TEST_CONDITION_REQUIRED(sourcePointsSet && targetPointsSet, "Testing if there are source and target landmarks set in the superclass"); myFilter->ReinitFilter(); bool sourcePointsCleared = myFilter->GetSourceLandmarks()->GetSize() == 0; bool targetPointsCleared = myFilter->GetTargetLandmarks()->GetSize() == 0; MITK_TEST_CONDITION_REQUIRED(sourcePointsCleared && targetPointsCleared, "Testing if reinit of filter was successful"); // ------------------ testing the point generation ------------------ myFilter->SetSourceNavigationDatas(oneSourceNDs); // set the ND with sourcePos1 and sourceOri1 for that the points will be generated itk::QuaternionRigidTransform::Pointer quaternionTransform = itk::QuaternionRigidTransform::New(); vnl_quaternion const vnlQuatIn(sourceOri1.x(), sourceOri1.y(), sourceOri1.z(), sourceOri1.r()); quaternionTransform->SetRotation(vnlQuatIn); mitk::Point3D pointA; mitk::Point3D pointB; mitk::Point3D pointC; //initializing three points with position(0|0|0) pointA.Fill(0); pointB.Fill(0); pointC.Fill(0); // changing position off all points in order to make them orthogonal pointA[0] = 1; pointB[1] = 1; pointC[2] = 1; // quaternion transform the points pointA = quaternionTransform->GetMatrix() * pointA; pointB = quaternionTransform->GetMatrix() * pointB; pointC = quaternionTransform->GetMatrix() * pointC; // now subtract them from the filter landmarks and compare them to the source pos - pointA = myFilter->GetSourceLandmarks()->GetPoint(0)-pointA; - pointB = myFilter->GetSourceLandmarks()->GetPoint(1)-pointB; - pointC = myFilter->GetSourceLandmarks()->GetPoint(2)-pointC; + pointA = mitk::Point3D(myFilter->GetSourceLandmarks()->GetPoint(0)-pointA); + pointB = mitk::Point3D(myFilter->GetSourceLandmarks()->GetPoint(1)-pointB); + pointC = mitk::Point3D(myFilter->GetSourceLandmarks()->GetPoint(2)-pointC); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(sourcePos1,pointA,mitk::eps,true), "Testing if point generation of first point is correct"); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(sourcePos1,pointB,mitk::eps,true), "Testing if point generation of second point is correct"); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(sourcePos1,pointC,mitk::eps,true), "Testing if point generation of third point is correct"); // deleting helper objects myFilter = nullptr; quaternionTransform = nullptr; snd1 = nullptr; snd2 = nullptr; snd3 = nullptr; tnd1 = nullptr; tnd2 = nullptr; tnd3 = nullptr; // always end with this! MITK_TEST_END(); } diff --git a/Modules/IGTBase/include/mitkNavigationDataSet.h b/Modules/IGTBase/include/mitkNavigationDataSet.h index c7475addf8..e69b031e5a 100644 --- a/Modules/IGTBase/include/mitkNavigationDataSet.h +++ b/Modules/IGTBase/include/mitkNavigationDataSet.h @@ -1,170 +1,161 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef MITKNAVIGATIONDATASET_H_HEADER_INCLUDED_ #define MITKNAVIGATIONDATASET_H_HEADER_INCLUDED_ #include #include "mitkBaseData.h" #include "mitkNavigationData.h" namespace mitk { /** * \brief Data structure which stores streams of mitk::NavigationData for * multiple tools. * * Use mitk::NavigationDataRecorder to create these sets easily from pipelines. * Use mitk::NavigationDataPlayer to stream from these sets easily. * */ class MITKIGTBASE_EXPORT NavigationDataSet : public BaseData { public: /** * \brief This iterator iterates over the distinct time steps in this set. * * It returns an array of the length equal to GetNumberOfTools(), containing a * mitk::NavigationData for each tool.. */ typedef std::vector< std::vector >::iterator NavigationDataSetIterator; /** * \brief This iterator iterates over the distinct time steps in this set. And is const. * * It returns an array of the length equal to GetNumberOfTools(), containing a * mitk::NavigationData for each tool.. */ typedef std::vector< std::vector >::const_iterator NavigationDataSetConstIterator; mitkClassMacro(NavigationDataSet, BaseData); mitkNewMacro1Param(Self, unsigned int); /** * \brief Add mitk::NavigationData of the given tool to the Set. * * @param navigationDatas vector of mitk::NavigationData objects to be added. Make sure that the size of the * vector equals the number of tools given in the constructor * @return true if object was be added to the set successfully, false otherwise */ bool AddNavigationDatas( std::vector navigationDatas ); /** * \brief Get mitk::NavigationData from the given tool at given index. * * @param toolIndex Index of the tool from which mitk::NavigationData should be returned. * @param index Index of the mitk::NavigationData object that should be returned. * @return mitk::NavigationData at the specified indices, 0 if there is no object at the indices. */ NavigationData::Pointer GetNavigationDataForIndex( unsigned int index, unsigned int toolIndex ) const; - ///** - //* \brief Get last mitk::Navigation object for given tool whose timestamp is less than the given timestamp. - //* @param toolIndex Index of the tool from which mitk::NavigationData should be returned. - //* @param timestamp Timestamp for selecting last object before. - //* @return Last mitk::NavigationData with timestamp less than given timestamp, 0 if there is no adequate object. - //*/ - // Method not yet supported! - //NavigationData::Pointer GetNavigationDataBeforeTimestamp( mitk::NavigationData::TimeStampType timestamp , unsigned int toolIndex ) const; - /** * \brief Returns a vector that contains all tracking data for a given tool. * * This is a relatively expensive operation, as it requires the construction of a new vector. * * @param toolIndex Index of the tool for which the stream should be returned. * @return Returns a vector that contains all tracking data for a given tool. */ virtual std::vector< mitk::NavigationData::Pointer > GetDataStreamForTool(unsigned int toolIndex); /** * \brief Returns a vector that contains NavigationDatas for each tool for a given timestep. * * If GetNumberOFTools() equals four, then 4 NavigationDatas will be returned. * * @param index Index of the timeStep for which the datas should be returned. cannot be larger than mitk::NavigationDataSet::Size() * @return Returns a vector that contains all tracking data for a given tool. */ virtual std::vector< mitk::NavigationData::Pointer > GetTimeStep(unsigned int index) const; /** * \brief Returns the number of tools for which NavigationDatas are stored in this set. * * This is always equal to the number given in the constructor of this class. * * @return the number of tools for which NavigationDatas are stored in this set. */ unsigned int GetNumberOfTools() const; /** * \brief Returns the number of time steps stored in this NavigationDataSet. * * This is not the total number of Navigation Datas stored in this set, but the number stored for each tool. * i.e. the total number of NavigationDatas equals Size() * GetNumberOfTools(); * * @return Returns the number of time steps stored in this NavigationDataSet. */ unsigned int Size() const; /** * \brief Returns an iterator pointing to the first TimeStep. * * @return Returns an iterator pointing to the first TimeStep. */ virtual NavigationDataSetConstIterator Begin() const; /** * \brief Returns an iterator pointing behind to the last TimeStep. * * @return Returns an iterator pointing behind to the last TimeStep. */ virtual NavigationDataSetConstIterator End() const; // virtual methods, that need to be implemented, but aren't reasonable for NavigationData void SetRequestedRegionToLargestPossibleRegion( ) override; bool RequestedRegionIsOutsideOfTheBufferedRegion( ) override; bool VerifyRequestedRegion( ) override; void SetRequestedRegion( const itk::DataObject *data ) override; /** * \brief This overrid is probably a little hacky. See Bug 19086. */ bool IsEmpty() const override; //Converts Navigation Data for each tool to a Point Set and adds it to the data storage void ConvertNavigationDataToPointSet() const; protected: /** * \brief Constructs set with fixed number of tools. * @param numTools How many tools are used with this mitk::NavigationDataSet. */ NavigationDataSet( unsigned int numTools ); ~NavigationDataSet( ) override; /** * \brief Holds all the mitk::NavigationData objects managed by this class. * * The first dimension is the index of the navigation data, the second is the * tool to which this data belongs. i.e. the first dimension is usually the longer one. */ std::vector > m_NavigationDataVectors; /** * \brief The Number of Tools that this class is going to support. */ unsigned int m_NumberOfTools; }; } #endif // MITKNAVIGATIONDATASET_H_HEADER_INCLUDED_ diff --git a/Modules/IGTUI/Qmitk/QmitkNavigationToolCreationWidget.cpp b/Modules/IGTUI/Qmitk/QmitkNavigationToolCreationWidget.cpp index 60cb9e101c..11fa90a23f 100644 --- a/Modules/IGTUI/Qmitk/QmitkNavigationToolCreationWidget.cpp +++ b/Modules/IGTUI/Qmitk/QmitkNavigationToolCreationWidget.cpp @@ -1,393 +1,393 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkNavigationToolCreationWidget.h" //mitk headers #include #include #include #include #include "mitkTrackingDeviceTypeCollection.h" //qt headers #include #include #include #include #include //poco headers #include const std::string QmitkNavigationToolCreationWidget::VIEW_ID = "org.mitk.views.navigationtoolcreationwizardwidget"; QmitkNavigationToolCreationWidget::QmitkNavigationToolCreationWidget(QWidget* parent, Qt::WindowFlags f) : QWidget(parent, f) { m_Controls = nullptr; m_ToolToBeEdited = mitk::NavigationTool::New(); m_FinalTool = mitk::NavigationTool::New(); m_ToolTransformationWidget = new QmitkInteractiveTransformationWidget(); m_Controls = nullptr; CreateQtPartControl(this); CreateConnections(); this->InitializeUIToolLandmarkLists(); Initialize(nullptr, ""); //Default values, which are not stored in tool m_Controls->m_CalibrationFileName->setText("none"); m_Controls->m_Surface_Use_Sphere->setChecked(true); m_Controls->m_CalibrationLandmarksList->EnableEditButton(false); m_Controls->m_RegistrationLandmarksList->EnableEditButton(false); RefreshTrackingDeviceCollection(); OnSurfaceUseToggled(); } QmitkNavigationToolCreationWidget::~QmitkNavigationToolCreationWidget() { m_Controls->m_CalibrationLandmarksList->SetPointSetNode(nullptr); m_Controls->m_RegistrationLandmarksList->SetPointSetNode(nullptr); delete m_ToolTransformationWidget; } void QmitkNavigationToolCreationWidget::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkNavigationToolCreationWidgetControls; m_Controls->setupUi(parent); } } void QmitkNavigationToolCreationWidget::CreateConnections() { if (m_Controls) { connect((QObject*)(m_Controls->m_TrackingDeviceTypeChooser), SIGNAL(currentIndexChanged(int)), this, SLOT(GetValuesFromGuiElements())); connect((QObject*)(m_Controls->m_ToolNameEdit), SIGNAL(textChanged(const QString)), this, SLOT(GetValuesFromGuiElements())); connect((QObject*)(m_Controls->m_ToolTypeChooser), SIGNAL(currentIndexChanged(int)), this, SLOT(GetValuesFromGuiElements())); connect((QObject*)(m_Controls->m_IdentifierEdit), SIGNAL(textChanged(const QString)), this, SLOT(GetValuesFromGuiElements())); connect((QObject*)(m_Controls->m_SerialNumberEdit), SIGNAL(textChanged(const QString)), this, SLOT(GetValuesFromGuiElements())); connect((QObject*)(m_Controls->m_ToolAxisX), SIGNAL(valueChanged(int)), this, SLOT(GetValuesFromGuiElements())); connect((QObject*)(m_Controls->m_ToolAxisY), SIGNAL(valueChanged(int)), this, SLOT(GetValuesFromGuiElements())); connect((QObject*)(m_Controls->m_ToolAxisZ), SIGNAL(valueChanged(int)), this, SLOT(GetValuesFromGuiElements())); //Buttons connect((QObject*)(m_Controls->m_LoadCalibrationFile), SIGNAL(clicked()), this, SLOT(OnLoadCalibrationFile())); connect(m_Controls->m_Surface_Use_Other, SIGNAL(toggled(bool)), this, SLOT(OnSurfaceUseToggled())); connect(m_Controls->m_Surface_Load_File, SIGNAL(toggled(bool)), this, SLOT(OnSurfaceUseToggled())); connect((QObject*)(m_Controls->m_LoadSurface), SIGNAL(clicked()), this, SLOT(OnLoadSurface())); connect((QObject*)(m_Controls->m_EditToolTip), SIGNAL(clicked()), this, SLOT(OnEditToolTip())); connect((QObject*)(m_ToolTransformationWidget), SIGNAL(EditToolTipFinished(mitk::AffineTransform3D::Pointer)), this, SLOT(OnEditToolTipFinished(mitk::AffineTransform3D::Pointer))); connect((QObject*)(m_Controls->m_cancel), SIGNAL(clicked()), this, SLOT(OnCancel())); connect((QObject*)(m_Controls->m_finished), SIGNAL(clicked()), this, SLOT(OnFinished())); } } void QmitkNavigationToolCreationWidget::Initialize(mitk::DataStorage* dataStorage, const std::string& supposedIdentifier, const std::string& supposedName) { m_DataStorage = dataStorage; //initialize UI components m_Controls->m_SurfaceChooser->SetDataStorage(m_DataStorage); m_Controls->m_SurfaceChooser->SetAutoSelectNewItems(true); m_Controls->m_SurfaceChooser->SetPredicate(mitk::NodePredicateDataType::New("Surface")); //Create new tool, which should be edited/created m_ToolToBeEdited = nullptr;//Reset m_ToolToBeEdited = mitk::NavigationTool::New();//Reinitialize m_ToolToBeEdited->SetIdentifier(supposedIdentifier); m_ToolToBeEdited->GetDataNode()->SetName(supposedName); this->SetDefaultData(m_ToolToBeEdited); } void QmitkNavigationToolCreationWidget::ShowToolPreview(std::string _name) { m_DataStorage->Add(m_ToolToBeEdited->GetDataNode()); m_ToolToBeEdited->GetDataNode()->SetName(_name); //change color to blue m_ToolToBeEdited->GetDataNode()->SetProperty("color", mitk::ColorProperty::New(0, 0, 1)); //Global Reinit to show new tool mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(m_DataStorage); } void QmitkNavigationToolCreationWidget::SetDefaultData(mitk::NavigationTool::Pointer DefaultTool) { //Set Members. This can either be the new initialized tool from call of Initialize() or a tool which already exists in the toolStorage m_ToolToBeEdited = DefaultTool->Clone(); //Set all gui variables SetGuiElements(); } void QmitkNavigationToolCreationWidget::SetGuiElements() { //Block signals, so that we don't call SetGuiElements again. This is undone at the end of this function! m_Controls->m_TrackingDeviceTypeChooser->blockSignals(true); m_Controls->m_ToolNameEdit->blockSignals(true); m_Controls->m_ToolTypeChooser->blockSignals(true); m_Controls->m_IdentifierEdit->blockSignals(true); m_Controls->m_SerialNumberEdit->blockSignals(true); m_Controls->m_ToolAxisX->blockSignals(true); m_Controls->m_ToolAxisY->blockSignals(true); m_Controls->m_ToolAxisZ->blockSignals(true); //DeviceType int index = m_Controls->m_TrackingDeviceTypeChooser->findText(QString::fromStdString(m_ToolToBeEdited->GetTrackingDeviceType())); if (index >= 0) { m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(index); } m_Controls->m_ToolNameEdit->setText(QString(m_ToolToBeEdited->GetToolName().c_str())); m_Controls->m_CalibrationFileName->setText(QString(m_ToolToBeEdited->GetCalibrationFile().c_str())); FillUIToolLandmarkLists(m_ToolToBeEdited->GetToolControlPoints(), m_ToolToBeEdited->GetToolLandmarks()); switch (m_ToolToBeEdited->GetType()) { case mitk::NavigationTool::Instrument: m_Controls->m_ToolTypeChooser->setCurrentIndex(0); break; case mitk::NavigationTool::Fiducial: m_Controls->m_ToolTypeChooser->setCurrentIndex(1); break; case mitk::NavigationTool::Skinmarker: m_Controls->m_ToolTypeChooser->setCurrentIndex(2); break; case mitk::NavigationTool::Unknown: m_Controls->m_ToolTypeChooser->setCurrentIndex(3); break; } m_Controls->m_IdentifierEdit->setText(QString(m_ToolToBeEdited->GetIdentifier().c_str())); m_Controls->m_SerialNumberEdit->setText(QString(m_ToolToBeEdited->GetSerialNumber().c_str())); QString _label = "(" + QString::number(m_ToolToBeEdited->GetToolTipPosition()[0], 'f', 1) + ", " + QString::number(m_ToolToBeEdited->GetToolTipPosition()[1], 'f', 1) + ", " + QString::number(m_ToolToBeEdited->GetToolTipPosition()[2], 'f', 1) + "), quat: [" + QString::number(m_ToolToBeEdited->GetToolAxisOrientation()[0], 'f', 2) + ", " + QString::number(m_ToolToBeEdited->GetToolAxisOrientation()[1], 'f', 2) + ", " + QString::number(m_ToolToBeEdited->GetToolAxisOrientation()[2], 'f', 2) + ", " + QString::number(m_ToolToBeEdited->GetToolAxisOrientation()[3], 'f', 2) + "]"; m_Controls->m_ToolTipLabel->setText(_label); //Undo block signals. Don't remove it, if signals are still blocked at the beginning of this function! m_Controls->m_TrackingDeviceTypeChooser->blockSignals(false); m_Controls->m_ToolNameEdit->blockSignals(false); m_Controls->m_ToolTypeChooser->blockSignals(false); m_Controls->m_IdentifierEdit->blockSignals(false); m_Controls->m_SerialNumberEdit->blockSignals(false); m_Controls->m_ToolAxisX->blockSignals(false); m_Controls->m_ToolAxisY->blockSignals(false); m_Controls->m_ToolAxisZ->blockSignals(false); } void QmitkNavigationToolCreationWidget::OnSurfaceUseToggled() { if (m_Controls->m_Surface_Use_Sphere->isChecked()) m_ToolToBeEdited->SetDefaultSurface(); m_Controls->m_SurfaceChooser->setEnabled(m_Controls->m_Surface_Use_Other->isChecked()); m_Controls->m_LoadSurface->setEnabled(m_Controls->m_Surface_Load_File->isChecked()); //Global Reinit to show tool surface preview mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(m_DataStorage); } void QmitkNavigationToolCreationWidget::OnLoadSurface() { std::string filename = QFileDialog::getOpenFileName(nullptr, tr("Open Surface"), QmitkIGTCommonHelper::GetLastFileLoadPath(), tr("STL (*.stl)")).toLatin1().data(); QmitkIGTCommonHelper::SetLastFileLoadPathByFileName(QString::fromStdString(filename)); mitk::Surface::Pointer surface; try { surface = mitk::IOUtil::Load(filename.c_str()); } catch (mitk::Exception &e) { MITK_ERROR << "Exception occured: " << e.what(); return; } m_ToolToBeEdited->GetDataNode()->SetData(surface); //Global Reinit to show tool surface or preview mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(m_DataStorage); } void QmitkNavigationToolCreationWidget::OnLoadCalibrationFile() { QString fileName = QFileDialog::getOpenFileName(nullptr, tr("Open Calibration File"), QmitkIGTCommonHelper::GetLastFileLoadPath(), "*.*"); QmitkIGTCommonHelper::SetLastFileLoadPathByFileName(fileName); m_Controls->m_CalibrationFileName->setText(fileName); m_ToolToBeEdited->SetCalibrationFile(fileName.toStdString()); } void QmitkNavigationToolCreationWidget::GetValuesFromGuiElements() { //Tracking Device m_ToolToBeEdited->SetTrackingDeviceType(m_Controls->m_TrackingDeviceTypeChooser->currentText().toStdString()); //m_ToolToBeEdited->GetDataNode()->SetName(m_Controls->m_ToolNameEdit->text().toStdString()); //Tool Landmarks mitk::PointSet::Pointer toolCalLandmarks, toolRegLandmarks; GetUIToolLandmarksLists(toolCalLandmarks, toolRegLandmarks); m_ToolToBeEdited->SetToolControlPoints(toolCalLandmarks); m_ToolToBeEdited->SetToolLandmarks(toolRegLandmarks); //Advanced if (m_Controls->m_ToolTypeChooser->currentText() == "Instrument") m_ToolToBeEdited->SetType(mitk::NavigationTool::Instrument); else if (m_Controls->m_ToolTypeChooser->currentText() == "Fiducial") m_ToolToBeEdited->SetType(mitk::NavigationTool::Fiducial); else if (m_Controls->m_ToolTypeChooser->currentText() == "Skinmarker") m_ToolToBeEdited->SetType(mitk::NavigationTool::Skinmarker); else m_FinalTool->SetType(mitk::NavigationTool::Unknown); m_ToolToBeEdited->SetIdentifier(m_Controls->m_IdentifierEdit->text().toLatin1().data()); m_ToolToBeEdited->SetSerialNumber(m_Controls->m_SerialNumberEdit->text().toLatin1().data()); ////Tool Axis //mitk::Point3D toolAxis; //toolAxis.SetElement(0, (m_Controls->m_ToolAxisX->value())); //toolAxis.SetElement(1, (m_Controls->m_ToolAxisY->value())); //toolAxis.SetElement(2, (m_Controls->m_ToolAxisZ->value())); //m_ToolToBeEdited->SetToolAxis(toolAxis); } mitk::NavigationTool::Pointer QmitkNavigationToolCreationWidget::GetCreatedTool() { return m_FinalTool; } void QmitkNavigationToolCreationWidget::OnFinished() { if (m_Controls->m_Surface_Use_Other->isChecked()) m_ToolToBeEdited->GetDataNode()->SetData(m_Controls->m_SurfaceChooser->GetSelectedNode()->GetData()); //here we create a new tool m_FinalTool = m_ToolToBeEdited->Clone(); //Set the correct name of data node, cause the m_ToolToBeEdited was called "Tool preview" m_FinalTool->GetDataNode()->SetName(m_Controls->m_ToolNameEdit->text().toStdString()); emit NavigationToolFinished(); } void QmitkNavigationToolCreationWidget::OnCancel() { Initialize(nullptr, "");//Reset everything to a fresh tool, like it was done in the constructor emit Canceled(); } void QmitkNavigationToolCreationWidget::SetTrackingDeviceType(mitk::TrackingDeviceType type, bool changeable /*= true*/) { //Adapt Gui int index = m_Controls->m_TrackingDeviceTypeChooser->findText(QString::fromStdString(type)); if (index >= 0) { m_Controls->m_TrackingDeviceTypeChooser->setCurrentIndex(index); } m_Controls->m_TrackingDeviceTypeChooser->setEditable(changeable); //Set data to member m_ToolToBeEdited->SetTrackingDeviceType(type); } //################################################################################## //############################## internal help methods ############################# //################################################################################## void QmitkNavigationToolCreationWidget::MessageBox(std::string s) { QMessageBox msgBox; msgBox.setText(s.c_str()); msgBox.exec(); } void QmitkNavigationToolCreationWidget::OnEditToolTip() { m_ToolTransformationWidget->SetToolToEdit(m_ToolToBeEdited); m_ToolTransformationWidget->SetDefaultRotation(m_ToolToBeEdited->GetToolAxisOrientation()); m_ToolTransformationWidget->SetDefaultOffset(m_ToolToBeEdited->GetToolTipPosition()); m_ToolTransformationWidget->open(); } void QmitkNavigationToolCreationWidget::OnEditToolTipFinished(mitk::AffineTransform3D::Pointer toolTip) { //if user pressed cancle, nullptr is returned. Do nothing. Else, set values. if (toolTip) { - m_ToolToBeEdited->SetToolTipPosition(toolTip->GetOffset()); + m_ToolToBeEdited->SetToolTipPosition(mitk::Point3D(toolTip->GetOffset())); mitk::NavigationData::Pointer tempND = mitk::NavigationData::New(toolTip);//Convert to Navigation data for simple transversion to quaternion m_ToolToBeEdited->SetToolAxisOrientation(tempND->GetOrientation()); //Update Label QString _label = "(" + QString::number(m_ToolToBeEdited->GetToolTipPosition()[0], 'f', 1) + ", " + QString::number(m_ToolToBeEdited->GetToolTipPosition()[1], 'f', 1) + ", " + QString::number(m_ToolToBeEdited->GetToolTipPosition()[2], 'f', 1) + "), quat: [" + QString::number(m_ToolToBeEdited->GetToolAxisOrientation()[0], 'f', 2) + ", " + QString::number(m_ToolToBeEdited->GetToolAxisOrientation()[1], 'f', 2) + ", " + QString::number(m_ToolToBeEdited->GetToolAxisOrientation()[2], 'f', 2) + ", " + QString::number(m_ToolToBeEdited->GetToolAxisOrientation()[3], 'f', 2) + "]"; m_Controls->m_ToolTipLabel->setText(_label); } } void QmitkNavigationToolCreationWidget::FillUIToolLandmarkLists(mitk::PointSet::Pointer calLandmarks, mitk::PointSet::Pointer regLandmarks) { m_calLandmarkNode->SetData(calLandmarks); m_regLandmarkNode->SetData(regLandmarks); m_Controls->m_CalibrationLandmarksList->SetPointSetNode(m_calLandmarkNode); m_Controls->m_RegistrationLandmarksList->SetPointSetNode(m_regLandmarkNode); } void QmitkNavigationToolCreationWidget::GetUIToolLandmarksLists(mitk::PointSet::Pointer& calLandmarks, mitk::PointSet::Pointer& regLandmarks) { calLandmarks = dynamic_cast(m_calLandmarkNode->GetData()); regLandmarks = dynamic_cast(m_regLandmarkNode->GetData()); } void QmitkNavigationToolCreationWidget::InitializeUIToolLandmarkLists() { m_calLandmarkNode = mitk::DataNode::New(); m_regLandmarkNode = mitk::DataNode::New(); FillUIToolLandmarkLists(mitk::PointSet::New(), mitk::PointSet::New()); } void QmitkNavigationToolCreationWidget::RefreshTrackingDeviceCollection() { us::ModuleContext* context = us::GetModuleContext(); std::vector > refs = context->GetServiceReferences(); if (refs.empty()) { MITK_WARN << "No tracking device service found!"; return; } mitk::TrackingDeviceTypeCollection* _DeviceTypeCollection = context->GetService(refs.front()); for (auto name : _DeviceTypeCollection->GetTrackingDeviceTypeNames()) { //if the device is not included yet, add name to comboBox and widget to stackedWidget if (m_Controls->m_TrackingDeviceTypeChooser->findText(QString::fromStdString(name)) == -1) { m_Controls->m_TrackingDeviceTypeChooser->addItem(QString::fromStdString(name)); } } } diff --git a/Modules/IOExt/Internal/mitkUnstructuredGridVtkWriter.txx b/Modules/IOExt/Internal/mitkUnstructuredGridVtkWriter.txx index 3f44c734b9..9e3d6f9376 100644 --- a/Modules/IOExt/Internal/mitkUnstructuredGridVtkWriter.txx +++ b/Modules/IOExt/Internal/mitkUnstructuredGridVtkWriter.txx @@ -1,196 +1,196 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef _MITK_UNSTRUCTURED_GRID_VTKWRITER_TXX_ #define _MITK_UNSTRUCTURED_GRID_VTKWRITER_TXX_ #include #include #include #include #include #include #include #include #include #include #include namespace mitk { template UnstructuredGridVtkWriter::UnstructuredGridVtkWriter() : m_Success(false) { this->SetNumberOfRequiredInputs(1); } template UnstructuredGridVtkWriter::~UnstructuredGridVtkWriter() { } template void UnstructuredGridVtkWriter::GenerateData() { m_Success = false; if (m_FileName == "") { itkWarningMacro(<< "Sorry, filename has not been set!"); return; } mitk::UnstructuredGrid::Pointer input = const_cast(this->GetInput()); if (input.IsNull()) { itkWarningMacro(<< "Sorry, input to mitk::UnstructuredGridVtkWriter is NULL"); return; } VTKWRITER *unstructuredGridWriter = VTKWRITER::New(); vtkTransformFilter *transformPointSet = vtkTransformFilter::New(); vtkUnstructuredGrid *unstructuredGrid; BaseGeometry *geometry; if (input->GetTimeGeometry()->CountTimeSteps() > 1) { int t, timesteps; timesteps = input->GetTimeGeometry()->CountTimeSteps(); for (t = 0; t < timesteps; ++t) { std::ostringstream filename; geometry = input->GetGeometry(t); if (input->GetTimeGeometry()->IsValidTimeStep(t)) { - const mitk::TimeBounds &timebounds = input->GetTimeGeometry()->GetTimeBounds(t); + const mitk::TimeBounds timebounds = input->GetTimeGeometry()->GetTimeBounds(t); filename << m_FileName.c_str() << "_S" << std::setprecision(0) << timebounds[0] << "_E" << std::setprecision(0) << timebounds[1] << "_T" << t << GetDefaultExtension(); } else { itkWarningMacro(<< "Error on write: TimeGeometry invalid of unstructured grid " << filename.str() << "."); filename << m_FileName.c_str() << "_T" << t << GetDefaultExtension(); } transformPointSet->SetInputData(input->GetVtkUnstructuredGrid(t)); transformPointSet->SetTransform(geometry->GetVtkTransform()); transformPointSet->UpdateWholeExtent(); unstructuredGrid = static_cast(transformPointSet->GetOutput()); unstructuredGridWriter->SetFileName(filename.str().c_str()); unstructuredGridWriter->SetInputData(unstructuredGrid); ExecuteWrite(unstructuredGridWriter); } } else { geometry = input->GetGeometry(); transformPointSet->SetInputData(input->GetVtkUnstructuredGrid()); transformPointSet->SetTransform(geometry->GetVtkTransform()); transformPointSet->UpdateWholeExtent(); unstructuredGrid = static_cast(transformPointSet->GetOutput()); unstructuredGridWriter->SetFileName(m_FileName.c_str()); unstructuredGridWriter->SetInputData(unstructuredGrid); ExecuteWrite(unstructuredGridWriter); } transformPointSet->Delete(); unstructuredGridWriter->Delete(); m_Success = true; } template void UnstructuredGridVtkWriter::ExecuteWrite(VTKWRITER *vtkWriter) { struct stat fileStatus; time_t timeBefore = 0; if (!stat(vtkWriter->GetFileName(), &fileStatus)) { timeBefore = fileStatus.st_mtime; } if (!vtkWriter->Write()) { itkExceptionMacro(<< "Error during unstructured grid writing."); } // check if file can be written because vtkWriter doesn't check that if (stat(vtkWriter->GetFileName(), &fileStatus) || (timeBefore == fileStatus.st_mtime)) { itkExceptionMacro(<< "Error during unstructured grid writing: file could not be written"); } } template void UnstructuredGridVtkWriter::SetInput(BaseData *input) { this->ProcessObject::SetNthInput(0, input); } template const UnstructuredGrid *UnstructuredGridVtkWriter::GetInput() { if (this->GetNumberOfInputs() < 1) { return nullptr; } else { return dynamic_cast(this->ProcessObject::GetInput(0)); } } template bool UnstructuredGridVtkWriter::CanWriteBaseDataType(BaseData::Pointer data) { return (dynamic_cast(data.GetPointer()) != nullptr); } template void UnstructuredGridVtkWriter::DoWrite(BaseData::Pointer data) { if (CanWriteBaseDataType(data)) { this->SetInput(dynamic_cast(data.GetPointer())); this->Update(); } } template std::vector UnstructuredGridVtkWriter::GetPossibleFileExtensions() { throw std::exception(); // no specialization available! } template const char *UnstructuredGridVtkWriter::GetDefaultFilename() { throw std::exception(); // no specialization available! } template const char *UnstructuredGridVtkWriter::GetFileDialogPattern() { throw std::exception(); // no specialization available! } template const char *UnstructuredGridVtkWriter::GetDefaultExtension() { throw std::exception(); // no specialization available! } } #endif diff --git a/Modules/ImageStatistics/mitkImageStatisticsContainer.cpp b/Modules/ImageStatistics/mitkImageStatisticsContainer.cpp index 34f21704af..6b8851bdd4 100644 --- a/Modules/ImageStatistics/mitkImageStatisticsContainer.cpp +++ b/Modules/ImageStatistics/mitkImageStatisticsContainer.cpp @@ -1,240 +1,240 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include namespace mitk { ImageStatisticsContainer::ImageStatisticsContainer() { this->Reset(); } // The order is derived from the old (<2018) image statistics plugin. const ImageStatisticsContainer::ImageStatisticsObject::StatisticNameVector ImageStatisticsContainer::ImageStatisticsObject::m_DefaultNames = {ImageStatisticsConstants::MEAN(), ImageStatisticsConstants::MEDIAN(), ImageStatisticsConstants::STANDARDDEVIATION(), ImageStatisticsConstants::RMS(), ImageStatisticsConstants::MAXIMUM(), ImageStatisticsConstants::MAXIMUMPOSITION(), ImageStatisticsConstants::MINIMUM(), ImageStatisticsConstants::MINIMUMPOSITION(), ImageStatisticsConstants::NUMBEROFVOXELS(), ImageStatisticsConstants::VOLUME(), ImageStatisticsConstants::SKEWNESS(), ImageStatisticsConstants::KURTOSIS(), ImageStatisticsConstants::UNIFORMITY(), ImageStatisticsConstants::ENTROPY(), ImageStatisticsConstants::MPP(), ImageStatisticsConstants::UPP()}; ImageStatisticsContainer::ImageStatisticsObject::ImageStatisticsObject() { Reset(); } void ImageStatisticsContainer::ImageStatisticsObject::AddStatistic(const std::string &key, StatisticsVariantType value) { m_Statistics.emplace(key, value); if (std::find(m_DefaultNames.cbegin(), m_DefaultNames.cend(), key) == m_DefaultNames.cend()) { if (std::find(m_CustomNames.cbegin(), m_CustomNames.cend(), key) == m_CustomNames.cend()) { m_CustomNames.emplace_back(key); } } } const ImageStatisticsContainer::ImageStatisticsObject::StatisticNameVector & ImageStatisticsContainer::ImageStatisticsObject::GetDefaultStatisticNames() { return m_DefaultNames; } const ImageStatisticsContainer::ImageStatisticsObject::StatisticNameVector & ImageStatisticsContainer::ImageStatisticsObject::GetCustomStatisticNames() const { return m_CustomNames; } ImageStatisticsContainer::ImageStatisticsObject::StatisticNameVector ImageStatisticsContainer::ImageStatisticsObject::GetAllStatisticNames() const { StatisticNameVector names = GetDefaultStatisticNames(); names.insert(names.cend(), m_CustomNames.cbegin(), m_CustomNames.cend()); return names; } ImageStatisticsContainer::ImageStatisticsObject::StatisticNameVector ImageStatisticsContainer::ImageStatisticsObject::GetExistingStatisticNames() const { StatisticNameVector names; std::transform(m_Statistics.begin(), m_Statistics.end(), std::back_inserter(names), [](const auto &pair) { return pair.first; }); return names; } bool ImageStatisticsContainer::ImageStatisticsObject::HasStatistic(const std::string &name) const { return m_Statistics.find(name) != m_Statistics.cend(); } ImageStatisticsContainer::StatisticsVariantType ImageStatisticsContainer::ImageStatisticsObject::GetValueNonConverted( const std::string &name) const { if (HasStatistic(name)) { return m_Statistics.find(name)->second; } else { mitkThrow() << "invalid statistic key, could not find"; } } void ImageStatisticsContainer::ImageStatisticsObject::Reset() { m_Statistics.clear(); m_CustomNames.clear(); } bool ImageStatisticsContainer::TimeStepExists(TimeStepType timeStep) const { return m_TimeStepMap.find(timeStep) != m_TimeStepMap.end(); } const ImageStatisticsContainer::HistogramType* ImageStatisticsContainer::GetHistogramForTimeStep(TimeStepType timeStep) const { return this->GetStatisticsForTimeStep(timeStep).m_Histogram; } const ImageStatisticsContainer::ImageStatisticsObject &ImageStatisticsContainer::GetStatisticsForTimeStep( TimeStepType timeStep) const { auto it = m_TimeStepMap.find(timeStep); if (it != m_TimeStepMap.end()) { return it->second; } mitkThrow() << "StatisticsObject for timeStep " << timeStep << " not found!"; } void ImageStatisticsContainer::SetStatisticsForTimeStep(TimeStepType timeStep, ImageStatisticsObject statistics) { if (timeStep < this->GetTimeSteps()) { m_TimeStepMap.emplace(timeStep, statistics); this->Modified(); } else { mitkThrow() << "Given timeStep " << timeStep << " out of timeStep geometry bounds. TimeSteps in geometry: " << this->GetTimeSteps(); } } void ImageStatisticsContainer::PrintSelf(std::ostream &os, itk::Indent indent) const { Superclass::PrintSelf(os, indent); for (unsigned int i = 0; i < this->GetTimeSteps(); i++) { auto statisticsValues = GetStatisticsForTimeStep(i); os << std::endl << indent << "Statistics instance for timeStep " << i << ":"; auto statisticKeys = statisticsValues.GetExistingStatisticNames(); os << std::endl << indent << "Number of entries: " << statisticKeys.size(); for (const auto &aKey : statisticKeys) { os << std::endl << indent.GetNextIndent() << aKey << ": " << statisticsValues.GetValueNonConverted(aKey); } } } unsigned int ImageStatisticsContainer::GetNumberOfTimeSteps() const { return this->GetTimeSteps(); } void ImageStatisticsContainer::Reset() { for (auto iter = m_TimeStepMap.begin(); iter != m_TimeStepMap.end(); iter++) { iter->second.Reset(); } } itk::LightObject::Pointer ImageStatisticsContainer::InternalClone() const { itk::LightObject::Pointer ioPtr = Superclass::InternalClone(); Self::Pointer rval = dynamic_cast(ioPtr.GetPointer()); if (rval.IsNull()) { itkExceptionMacro(<< "downcast to type " << "StatisticsContainer" << " failed."); } rval->SetTimeStepMap(m_TimeStepMap); rval->SetTimeGeometry(this->GetTimeGeometry()->Clone()); return ioPtr; } void ImageStatisticsContainer::SetTimeStepMap(TimeStepMapType map) { m_TimeStepMap = map; } ImageStatisticsContainer::ImageStatisticsObject::StatisticNameVector GetAllStatisticNames( const ImageStatisticsContainer *container) { ImageStatisticsContainer::ImageStatisticsObject::StatisticNameVector names = ImageStatisticsContainer::ImageStatisticsObject::GetDefaultStatisticNames(); if (container) { std::set customKeys; for (unsigned int i = 0; i < container->GetTimeSteps(); i++) { auto statisticKeys = container->GetStatisticsForTimeStep(i).GetCustomStatisticNames(); customKeys.insert(statisticKeys.cbegin(), statisticKeys.cend()); } names.insert(names.cend(), customKeys.cbegin(), customKeys.cend()); } return names; } ImageStatisticsContainer::ImageStatisticsObject::StatisticNameVector GetAllStatisticNames( std::vector containers) { ImageStatisticsContainer::ImageStatisticsObject::StatisticNameVector names = ImageStatisticsContainer::ImageStatisticsObject::GetDefaultStatisticNames(); std::set customKeys; - for (auto container : containers) + for (const auto &container : containers) { for (unsigned int i = 0; i < container->GetTimeSteps(); i++) { if(container->TimeStepExists(i)) { auto statisticKeys = container->GetStatisticsForTimeStep(i).GetCustomStatisticNames(); customKeys.insert(statisticKeys.cbegin(), statisticKeys.cend()); } } } names.insert(names.end(), customKeys.begin(), customKeys.end()); return names; }; } // namespace mitk diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkDataGeneratorBase.cpp b/Modules/ImageStatisticsUI/Qmitk/QmitkDataGeneratorBase.cpp index f32be6e324..5b8d159cba 100644 --- a/Modules/ImageStatisticsUI/Qmitk/QmitkDataGeneratorBase.cpp +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkDataGeneratorBase.cpp @@ -1,275 +1,275 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkDataGeneratorBase.h" #include "QmitkDataGenerationJobBase.h" #include "mitkDataNode.h" #include "mitkProperties.h" #include "mitkImageStatisticsContainerManager.h" #include QmitkDataGeneratorBase::QmitkDataGeneratorBase(mitk::DataStorage::Pointer storage, QObject* parent) : QObject(parent) { this->SetDataStorage(storage); } QmitkDataGeneratorBase::QmitkDataGeneratorBase(QObject* parent): QObject(parent) {} QmitkDataGeneratorBase::~QmitkDataGeneratorBase() { auto dataStorage = m_Storage.Lock(); if (dataStorage.IsNotNull()) { // remove "change node listener" from data storage dataStorage->ChangedNodeEvent.RemoveListener( mitk::MessageDelegate1(this, &QmitkDataGeneratorBase::NodeAddedOrModified)); } } mitk::DataStorage::Pointer QmitkDataGeneratorBase::GetDataStorage() const { return m_Storage.Lock(); } bool QmitkDataGeneratorBase::GetAutoUpdate() const { return m_AutoUpdate; } bool QmitkDataGeneratorBase::IsGenerating() const { return m_WIP; } void QmitkDataGeneratorBase::SetDataStorage(mitk::DataStorage* storage) { if (storage == m_Storage) return; std::lock_guard mutexguard(m_DataMutex); auto oldStorage = m_Storage.Lock(); if (oldStorage.IsNotNull()) { // remove "change node listener" from old data storage oldStorage->ChangedNodeEvent.RemoveListener( mitk::MessageDelegate1(this, &QmitkDataGeneratorBase::NodeAddedOrModified)); } m_Storage = storage; auto newStorage = m_Storage.Lock(); if (newStorage.IsNotNull()) { // add change node listener for new data storage newStorage->ChangedNodeEvent.AddListener( mitk::MessageDelegate1(this, &QmitkDataGeneratorBase::NodeAddedOrModified)); } } void QmitkDataGeneratorBase::SetAutoUpdate(bool autoUpdate) { m_AutoUpdate = autoUpdate; } void QmitkDataGeneratorBase::OnJobError(QString error, const QmitkDataGenerationJobBase* failedJob) const { emit JobError(error, failedJob); } void QmitkDataGeneratorBase::OnFinalResultsAvailable(JobResultMapType results, const QmitkDataGenerationJobBase *job) const { auto resultnodes = mitk::DataStorage::SetOfObjects::New(); - for (auto pos : results) + for (const auto &pos : results) { resultnodes->push_back(this->PrepareResultForStorage(pos.first, pos.second, job)); } { std::lock_guard mutexguard(m_DataMutex); auto storage = m_Storage.Lock(); if (storage.IsNotNull()) { m_AddingToStorage = true; for (auto pos = resultnodes->Begin(); pos != resultnodes->End(); ++pos) { storage->Add(pos->Value()); } m_AddingToStorage = false; } } emit NewDataAvailable(resultnodes.GetPointer()); if (!resultnodes->empty()) { this->EnsureRecheckingAndGeneration(); } } void QmitkDataGeneratorBase::NodeAddedOrModified(const mitk::DataNode* node) { if (!m_AddingToStorage) { if (this->ChangedNodeIsRelevant(node)) { this->EnsureRecheckingAndGeneration(); } } } void QmitkDataGeneratorBase::EnsureRecheckingAndGeneration() const { m_RestartGeneration = true; if (!m_InGenerate) { this->Generate(); } } bool QmitkDataGeneratorBase::Generate() const { bool everythingValid = false; if (m_InGenerate) { m_RestartGeneration = true; } else { m_InGenerate = true; m_RestartGeneration = true; while (m_RestartGeneration) { m_RestartGeneration = false; everythingValid = DoGenerate(); } m_InGenerate = false; } return everythingValid; } mitk::DataNode::Pointer QmitkDataGeneratorBase::CreateWIPDataNode(mitk::BaseData* dataDummy, const std::string& nodeName) { if (!dataDummy) { mitkThrow() << "data is nullptr"; } auto interimResultNode = mitk::DataNode::New(); interimResultNode->SetProperty("helper object", mitk::BoolProperty::New(true)); dataDummy->SetProperty(mitk::STATS_GENERATION_STATUS_PROPERTY_NAME.c_str(), mitk::StringProperty::New(mitk::STATS_GENERATION_STATUS_VALUE_PENDING)); interimResultNode->SetVisibility(false); interimResultNode->SetData(dataDummy); if (!nodeName.empty()) { interimResultNode->SetName(nodeName); } return interimResultNode; } QmitkDataGeneratorBase::InputPairVectorType QmitkDataGeneratorBase::FilterImageROICombinations(InputPairVectorType&& imageROICombinations) const { std::lock_guard mutexguard(m_DataMutex); InputPairVectorType filteredImageROICombinations; auto storage = m_Storage.Lock(); if (storage.IsNotNull()) { for (auto inputPair : imageROICombinations) { if (storage->Exists(inputPair.first) && (inputPair.second.IsNull() || storage->Exists(inputPair.second))) { filteredImageROICombinations.emplace_back(inputPair); } else { MITK_DEBUG << "Ignore pair because at least one of the nodes is not in storage. Pair: " << GetPairDescription(inputPair); } } } return filteredImageROICombinations; } std::string QmitkDataGeneratorBase::GetPairDescription(const InputPairVectorType::value_type& imageAndSeg) const { if (imageAndSeg.second.IsNotNull()) { return imageAndSeg.first->GetName() + " and ROI " + imageAndSeg.second->GetName(); } else { return imageAndSeg.first->GetName(); } } bool QmitkDataGeneratorBase::DoGenerate() const { auto filteredImageROICombinations = FilterImageROICombinations(this->GetAllImageROICombinations()); QThreadPool* threadPool = QThreadPool::globalInstance(); bool everythingValid = true; for (const auto& imageAndSeg : filteredImageROICombinations) { MITK_DEBUG << "checking node " << GetPairDescription(imageAndSeg); if (!this->IsValidResultAvailable(imageAndSeg.first.GetPointer(), imageAndSeg.second.GetPointer())) { this->IndicateFutureResults(imageAndSeg.first.GetPointer(), imageAndSeg.second.GetPointer()); if (everythingValid) { m_WIP = true; everythingValid = false; } MITK_DEBUG << "No valid result available. Requesting next necessary job." << imageAndSeg.first->GetName(); auto nextJob = this->GetNextMissingGenerationJob(imageAndSeg.first.GetPointer(), imageAndSeg.second.GetPointer()); //other jobs are pending, nothing has to be done if (nextJob.first==nullptr && nextJob.second.IsNotNull()) { MITK_DEBUG << "Last generation job still running, pass on till job is finished..."; } else if(nextJob.first != nullptr && nextJob.second.IsNotNull()) { MITK_DEBUG << "Next generation job started..."; nextJob.first->setAutoDelete(true); nextJob.second->GetData()->SetProperty(mitk::STATS_GENERATION_STATUS_PROPERTY_NAME.c_str(), mitk::StringProperty::New(mitk::STATS_GENERATION_STATUS_VALUE_WORK_IN_PROGRESS)); connect(nextJob.first, &QmitkDataGenerationJobBase::Error, this, &QmitkDataGeneratorBase::OnJobError, Qt::BlockingQueuedConnection); connect(nextJob.first, &QmitkDataGenerationJobBase::ResultsAvailable, this, &QmitkDataGeneratorBase::OnFinalResultsAvailable, Qt::BlockingQueuedConnection); emit DataGenerationStarted(imageAndSeg.first.GetPointer(), imageAndSeg.second.GetPointer(), nextJob.first); threadPool->start(nextJob.first); } } else { this->RemoveObsoleteDataNodes(imageAndSeg.first.GetPointer(), imageAndSeg.second.GetPointer()); } } if (everythingValid && m_WIP) { m_WIP = false; emit GenerationFinished(); } return everythingValid; } diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.cpp b/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.cpp index e893386303..25ad5e8ad8 100644 --- a/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.cpp +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.cpp @@ -1,228 +1,229 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkHistogramVisualizationWidget.h" #include QmitkHistogramVisualizationWidget::QmitkHistogramVisualizationWidget(QWidget* parent) : QWidget(parent) { m_Controls.setupUi(this); m_Controls.checkBoxShowSubchart->setChecked(false); m_Controls.spinBoxNBins->setValue(m_DefaultNBins); m_Controls.spinBoxNBins->setMinimum(m_MinNBins); m_Controls.spinBoxNBins->setMaximum(m_MaxNBins); m_Controls.chartWidget->SetXAxisLabel("Gray value"); m_Controls.chartWidget->SetYAxisLabel("Frequency"); + m_Controls.chartWidget->SetShowLegend(false); SetGUIElementsEnabled(false); CreateConnections(); } void QmitkHistogramVisualizationWidget::SetHistogram(itk::Statistics::Histogram::ConstPointer histogram, const std::string& dataLabel) { if (histogram == nullptr) return; bool histogramWasEmpty = m_Histograms.empty(); if (m_Histograms.find(dataLabel) == m_Histograms.end()) { m_Histograms.insert(std::make_pair(dataLabel, histogram)); m_Controls.chartWidget->AddData2D(ConvertHistogramToPairList(histogram), dataLabel); m_Controls.chartWidget->SetChartType(dataLabel, QmitkChartWidget::ChartType::bar); } else { m_Histograms[dataLabel] = histogram; m_Controls.chartWidget->UpdateData2D(ConvertHistogramToPairList(histogram), dataLabel); } if (m_Histograms.empty() != histogramWasEmpty) { m_Controls.chartWidget->Show(m_Controls.checkBoxShowSubchart->isChecked()); SetGUIElementsEnabled(!m_Histograms.empty()); } } void QmitkHistogramVisualizationWidget::Reset() { m_Controls.chartWidget->Clear(); SetGUIElementsEnabled(false); } int QmitkHistogramVisualizationWidget::GetBins() { return m_Controls.spinBoxNBins->value(); } void QmitkHistogramVisualizationWidget::ResetDefault() { m_Controls.checkBoxUseDefaultNBins->setChecked(true); m_Controls.spinBoxNBins->setEnabled(false); m_Controls.spinBoxNBins->setValue(100); m_Controls.checkBoxShowSubchart->setChecked(false); } void QmitkHistogramVisualizationWidget::SetTheme(QmitkChartWidget::ColorTheme style) { m_Controls.chartWidget->SetTheme(style); } void QmitkHistogramVisualizationWidget::CreateConnections() { connect(m_Controls.buttonCopyHistogramToClipboard, &QPushButton::clicked, this, &QmitkHistogramVisualizationWidget::OnClipboardButtonClicked); connect(m_Controls.checkBoxUseDefaultNBins, &QCheckBox::clicked, this, &QmitkHistogramVisualizationWidget::OnDefaultNBinsCheckBoxChanged); connect(m_Controls.spinBoxNBins, &QSpinBox::editingFinished, this, &QmitkHistogramVisualizationWidget::OnNBinsSpinBoxValueChanged); connect(m_Controls.checkBoxShowSubchart, &QCheckBox::clicked, this, &QmitkHistogramVisualizationWidget::OnShowSubchartCheckBoxChanged); connect(m_Controls.checkBoxViewMinMax, &QCheckBox::clicked, this, &QmitkHistogramVisualizationWidget::OnViewMinMaxCheckBoxChanged); connect(m_Controls.doubleSpinBoxMaxValue, &QSpinBox::editingFinished, this, &QmitkHistogramVisualizationWidget::OnMaxValueSpinBoxValueChanged); connect(m_Controls.doubleSpinBoxMinValue, &QSpinBox::editingFinished, this, &QmitkHistogramVisualizationWidget::OnMinValueSpinBoxValueChanged); } void QmitkHistogramVisualizationWidget::SetGUIElementsEnabled(bool enabled) { this->setEnabled(enabled); m_Controls.tabWidgetPlot->setEnabled(enabled); m_Controls.checkBoxShowSubchart->setEnabled(enabled); m_Controls.checkBoxUseDefaultNBins->setEnabled(enabled); m_Controls.spinBoxNBins->setEnabled(!m_Controls.checkBoxUseDefaultNBins->isChecked()); m_Controls.buttonCopyHistogramToClipboard->setEnabled(enabled); m_Controls.checkBoxViewMinMax->setEnabled(enabled); m_Controls.doubleSpinBoxMaxValue->setEnabled(m_Controls.checkBoxViewMinMax->isChecked()); m_Controls.doubleSpinBoxMinValue->setEnabled(m_Controls.checkBoxViewMinMax->isChecked()); } std::vector< std::pair > QmitkHistogramVisualizationWidget::ConvertHistogramToPairList(itk::Statistics::Histogram::ConstPointer histogram) const { std::map histogramMap; if (histogram) { auto endIt = histogram->End(); auto it = histogram->Begin(); // generating Lists of measurement and frequencies for (; it != endIt; ++it) { double frequency = it.GetFrequency(); double measurement = it.GetMeasurementVector()[0]; histogramMap.emplace(measurement, frequency); } } std::vector< std::pair > histogram_list; for(auto iter = histogramMap.begin(); iter != histogramMap.end(); ++iter) histogram_list.emplace_back( iter->first, iter->second ); return histogram_list; } void QmitkHistogramVisualizationWidget::OnClipboardButtonClicked() { if (!m_Histograms.empty()) { QString clipboard; for (const auto& histogram : m_Histograms) { clipboard.append(QString::fromStdString(histogram.first)); clipboard.append("Measurement \t Frequency\n"); auto iter = histogram.second->Begin(); auto iterEnd = histogram.second->End(); for (; iter != iterEnd; ++iter) { clipboard = clipboard.append("%L1 \t %L2\n") .arg(iter.GetMeasurementVector()[0], 0, 'f', 2) .arg(iter.GetFrequency()); } clipboard.append("\n\n"); } QApplication::clipboard()->clear(); QApplication::clipboard()->setText(clipboard, QClipboard::Clipboard); } } void QmitkHistogramVisualizationWidget::OnDefaultNBinsCheckBoxChanged() { if (m_Controls.checkBoxUseDefaultNBins->isChecked()) { m_Controls.spinBoxNBins->setEnabled(false); if (m_Controls.spinBoxNBins->value() != static_cast(m_DefaultNBins) ) { m_Controls.spinBoxNBins->setValue(m_DefaultNBins); OnNBinsSpinBoxValueChanged(); } } else { m_Controls.spinBoxNBins->setEnabled(true); } } void QmitkHistogramVisualizationWidget::OnNBinsSpinBoxValueChanged() { emit RequestHistogramUpdate(m_Controls.spinBoxNBins->value()); } void QmitkHistogramVisualizationWidget::OnShowSubchartCheckBoxChanged() { m_Controls.chartWidget->Show(m_Controls.checkBoxShowSubchart->isChecked()); } void QmitkHistogramVisualizationWidget::OnViewMinMaxCheckBoxChanged() { double min = std::numeric_limits::max(); double max = std::numeric_limits::lowest(); for (const auto& histogram : m_Histograms) { auto aMin = histogram.second->GetBinMin(0, 0); if (min > aMin) min = aMin; auto maxVector = histogram.second->GetDimensionMaxs(0); if (m_Controls.checkBoxUseDefaultNBins->isChecked()) { max = std::max(max, maxVector[m_DefaultNBins - 1]); } else { max = std::max(max, maxVector[m_Controls.spinBoxNBins->value() - 1]); } } if (!m_Controls.checkBoxViewMinMax->isChecked()) { m_Controls.doubleSpinBoxMaxValue->setEnabled(false); m_Controls.doubleSpinBoxMinValue->setEnabled(false); m_Controls.chartWidget->Reload(); } else { m_Controls.doubleSpinBoxMinValue->setMinimum(min); m_Controls.doubleSpinBoxMinValue->setValue(min); m_Controls.doubleSpinBoxMaxValue->setMaximum(max); m_Controls.doubleSpinBoxMaxValue->setValue(max); m_Controls.doubleSpinBoxMaxValue->setEnabled(true); m_Controls.doubleSpinBoxMinValue->setEnabled(true); } } void QmitkHistogramVisualizationWidget::OnMinValueSpinBoxValueChanged() { m_Controls.doubleSpinBoxMaxValue->setMinimum(m_Controls.doubleSpinBoxMinValue->value()+1); m_Controls.chartWidget->SetMinMaxValueXView(m_Controls.doubleSpinBoxMinValue->value(),m_Controls.doubleSpinBoxMaxValue->value()); m_Controls.chartWidget->Show(); } void QmitkHistogramVisualizationWidget::OnMaxValueSpinBoxValueChanged() { m_Controls.doubleSpinBoxMinValue->setMaximum(m_Controls.doubleSpinBoxMaxValue->value()-1); m_Controls.chartWidget->SetMinMaxValueXView(m_Controls.doubleSpinBoxMinValue->value(),m_Controls.doubleSpinBoxMaxValue->value()); m_Controls.chartWidget->Show(); } diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsTreeModel.cpp b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsTreeModel.cpp index f0b184289b..56bb7ac961 100644 --- a/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsTreeModel.cpp +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsTreeModel.cpp @@ -1,425 +1,425 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkImageStatisticsTreeModel.h" #include "QmitkImageStatisticsTreeItem.h" #include "itkMutexLockHolder.h" #include "mitkImageStatisticsContainerManager.h" #include "mitkProportionalTimeGeometry.h" #include "mitkStatisticsToImageRelationRule.h" #include "mitkStatisticsToMaskRelationRule.h" #include "QmitkStyleManager.h" QmitkImageStatisticsTreeModel::QmitkImageStatisticsTreeModel(QObject *parent) : QmitkAbstractDataStorageModel(parent) { m_RootItem = new QmitkImageStatisticsTreeItem(); } QmitkImageStatisticsTreeModel ::~QmitkImageStatisticsTreeModel() { // set data storage to nullptr so that the event listener gets removed this->SetDataStorage(nullptr); delete m_RootItem; }; void QmitkImageStatisticsTreeModel::DataStorageChanged() { emit beginResetModel(); UpdateByDataStorage(); emit endResetModel(); emit modelChanged(); } void QmitkImageStatisticsTreeModel::NodePredicateChanged() { emit beginResetModel(); UpdateByDataStorage(); emit endResetModel(); emit modelChanged(); } int QmitkImageStatisticsTreeModel::columnCount(const QModelIndex& /*parent*/) const { int columns = m_StatisticNames.size() + 1; return columns; } int QmitkImageStatisticsTreeModel::rowCount(const QModelIndex &parent) const { QmitkImageStatisticsTreeItem *parentItem; if (parent.column() > 0) return 0; if (!parent.isValid()) parentItem = m_RootItem; else parentItem = static_cast(parent.internalPointer()); return parentItem->childCount(); } QVariant QmitkImageStatisticsTreeModel::data(const QModelIndex &index, int role) const { if (!index.isValid()) return QVariant(); QmitkImageStatisticsTreeItem* item = static_cast(index.internalPointer()); if (role == Qt::DisplayRole) { return item->data(index.column()); } else if (role == Qt::DecorationRole && index.column() == 0 && item->isWIP() && item->childCount()==0) { return QVariant(QmitkStyleManager::ThemeIcon(QStringLiteral(":/Qmitk/hourglass-half-solid.svg"))); } return QVariant(); } QModelIndex QmitkImageStatisticsTreeModel::index(int row, int column, const QModelIndex &parent) const { if (!hasIndex(row, column, parent)) return QModelIndex(); QmitkImageStatisticsTreeItem *parentItem; if (!parent.isValid()) parentItem = m_RootItem; else parentItem = static_cast(parent.internalPointer()); QmitkImageStatisticsTreeItem *childItem = parentItem->child(row); if (childItem) return createIndex(row, column, childItem); else return QModelIndex(); } QModelIndex QmitkImageStatisticsTreeModel::parent(const QModelIndex &child) const { if (!child.isValid()) return QModelIndex(); QmitkImageStatisticsTreeItem *childItem = static_cast(child.internalPointer()); QmitkImageStatisticsTreeItem *parentItem = childItem->parentItem(); if (parentItem == m_RootItem) return QModelIndex(); return createIndex(parentItem->row(), 0, parentItem); } Qt::ItemFlags QmitkImageStatisticsTreeModel::flags(const QModelIndex &index) const { if (!index.isValid()) return nullptr; return QAbstractItemModel::flags(index); } QVariant QmitkImageStatisticsTreeModel::headerData(int section, Qt::Orientation orientation, int role) const { if ((Qt::DisplayRole == role) && (Qt::Horizontal == orientation)) { if (section == 0) { return m_HeaderFirstColumn; } else { return QVariant(m_StatisticNames.at(section - 1).c_str()); } } return QVariant(); } void QmitkImageStatisticsTreeModel::SetImageNodes(const std::vector &nodes) { std::vector> tempNodes; for (const auto &node : nodes) { auto data = node->GetData(); if (data) { auto timeSteps = data->GetTimeSteps(); for (unsigned int i = 0; i < timeSteps; i++) { tempNodes.push_back(std::make_pair(node, i)); } } } emit beginResetModel(); m_TimeStepResolvedImageNodes = std::move(tempNodes); m_ImageNodes = nodes; UpdateByDataStorage(); emit endResetModel(); emit modelChanged(); } void QmitkImageStatisticsTreeModel::SetMaskNodes(const std::vector &nodes) { std::vector> tempNodes; for (const auto &node : nodes) { auto data = node->GetData(); if (data) { auto timeSteps = data->GetTimeSteps(); // special case: apply one mask to each timestep of an 4D image if (timeSteps == 1 && m_TimeStepResolvedImageNodes.size() > 1) { timeSteps = m_TimeStepResolvedImageNodes.size(); } for (unsigned int i = 0; i < timeSteps; i++) { tempNodes.push_back(std::make_pair(node, i)); } } } emit beginResetModel(); m_TimeStepResolvedMaskNodes = std::move(tempNodes); m_MaskNodes = nodes; UpdateByDataStorage(); emit endResetModel(); emit modelChanged(); } void QmitkImageStatisticsTreeModel::Clear() { emit beginResetModel(); m_Statistics.clear(); m_ImageNodes.clear(); m_TimeStepResolvedImageNodes.clear(); m_MaskNodes.clear(); m_StatisticNames.clear(); emit endResetModel(); emit modelChanged(); } void QmitkImageStatisticsTreeModel::SetIgnoreZeroValueVoxel(bool _arg) { if (m_IgnoreZeroValueVoxel != _arg) { emit beginResetModel(); m_IgnoreZeroValueVoxel = _arg; UpdateByDataStorage(); emit endResetModel(); emit modelChanged(); } } bool QmitkImageStatisticsTreeModel::GetIgnoreZeroValueVoxel() const { return this->m_IgnoreZeroValueVoxel; } void QmitkImageStatisticsTreeModel::SetHistogramNBins(unsigned int nbins) { if (m_HistogramNBins != nbins) { emit beginResetModel(); m_HistogramNBins = nbins; UpdateByDataStorage(); emit endResetModel(); emit modelChanged(); } } unsigned int QmitkImageStatisticsTreeModel::GetHistogramNBins() const { return this->m_HistogramNBins; } void QmitkImageStatisticsTreeModel::UpdateByDataStorage() { StatisticsContainerVector newStatistics; auto datamanager = m_DataStorage.Lock(); if (datamanager.IsNotNull()) { for (const auto &image : m_ImageNodes) { if (m_MaskNodes.empty()) { auto stats = mitk::ImageStatisticsContainerManager::GetImageStatistics(datamanager, image->GetData(), nullptr, m_IgnoreZeroValueVoxel, m_HistogramNBins, true, false); if (stats.IsNotNull()) { newStatistics.emplace_back(stats); } } else { for (const auto &mask : m_MaskNodes) { auto stats = mitk::ImageStatisticsContainerManager::GetImageStatistics(datamanager, image->GetData(), mask->GetData(), m_IgnoreZeroValueVoxel, m_HistogramNBins, true, false); if (stats.IsNotNull()) { newStatistics.emplace_back(stats); } } } } if (!newStatistics.empty()) { emit dataAvailable(); } } { itk::MutexLockHolder locked(m_Mutex); m_Statistics = newStatistics; } m_StatisticNames = mitk::GetAllStatisticNames(m_Statistics); BuildHierarchicalModel(); } void QmitkImageStatisticsTreeModel::BuildHierarchicalModel() { // reset old model delete m_RootItem; m_RootItem = new QmitkImageStatisticsTreeItem(); bool hasMask = false; bool hasMultipleTimesteps = false; std::map dataNodeToTreeItem; - for (auto statistic : m_Statistics) + for (const auto &statistic : m_Statistics) { bool isWIP = statistic->GetProperty(mitk::STATS_GENERATION_STATUS_PROPERTY_NAME.c_str()).IsNotNull(); // get the connected image data node/mask data node auto imageRule = mitk::StatisticsToImageRelationRule::New(); auto imageOfStatisticsPredicate = imageRule->GetDestinationsDetector(statistic); auto imageFinding = std::find_if(m_ImageNodes.begin(), m_ImageNodes.end(), [&imageOfStatisticsPredicate](const mitk::DataNode::ConstPointer& testNode) { return imageOfStatisticsPredicate->CheckNode(testNode); }); auto maskRule = mitk::StatisticsToMaskRelationRule::New(); auto maskOfStatisticsPredicate = maskRule->GetDestinationsDetector(statistic); auto maskFinding = std::find_if(m_MaskNodes.begin(), m_MaskNodes.end(), [&maskOfStatisticsPredicate](const mitk::DataNode::ConstPointer& testNode) { return maskOfStatisticsPredicate->CheckNode(testNode); }); if (imageFinding == m_ImageNodes.end()) { mitkThrow() << "no image found connected to statistic" << statistic << " Aborting."; } auto& image = *imageFinding; // image: 1. hierarchy level QmitkImageStatisticsTreeItem *imageItem = nullptr; auto search = dataNodeToTreeItem.find(image); // the tree item was created previously if (search != dataNodeToTreeItem.end()) { imageItem = search->second; } // create the tree item else { QString imageLabel = QString::fromStdString(image->GetName()); if (statistic->GetTimeSteps() == 1 && maskFinding == m_MaskNodes.end()) { auto statisticsObject = statistic->GetStatisticsForTimeStep(0); imageItem = new QmitkImageStatisticsTreeItem(statisticsObject, m_StatisticNames, imageLabel, isWIP, m_RootItem); } else { imageItem = new QmitkImageStatisticsTreeItem(m_StatisticNames, imageLabel, isWIP, m_RootItem); } m_RootItem->appendChild(imageItem); dataNodeToTreeItem.emplace(image, imageItem); } // mask: 2. hierarchy level (optional, only if mask exists) QmitkImageStatisticsTreeItem *lastParent = nullptr; if (maskFinding != m_MaskNodes.end()) { auto& mask = *maskFinding; QString maskLabel = QString::fromStdString(mask->GetName()); QmitkImageStatisticsTreeItem *maskItem; // add statistical values directly in this hierarchy level if (statistic->GetTimeSteps() == 1) { auto statisticsObject = statistic->GetStatisticsForTimeStep(0); maskItem = new QmitkImageStatisticsTreeItem(statisticsObject, m_StatisticNames, maskLabel, isWIP, imageItem); } else { maskItem = new QmitkImageStatisticsTreeItem(m_StatisticNames, maskLabel, isWIP, imageItem); } imageItem->appendChild(maskItem); lastParent = maskItem; hasMask = true; } else { lastParent = imageItem; } // 3. hierarchy level (optional, only if >1 timestep) if (statistic->GetTimeSteps() > 1) { for (unsigned int i = 0; i < statistic->GetTimeSteps(); i++) { QString timeStepLabel = "[" + QString::number(i) + "] " + QString::number(statistic->GetTimeGeometry()->TimeStepToTimePoint(i)) + " ms"; if (statistic->TimeStepExists(i)) { auto statisticsItem = new QmitkImageStatisticsTreeItem( statistic->GetStatisticsForTimeStep(i), m_StatisticNames, timeStepLabel, isWIP, lastParent); lastParent->appendChild(statisticsItem); } } hasMultipleTimesteps = true; } } QString headerString = "Images"; if (hasMask) { headerString += "/Masks"; } if (hasMultipleTimesteps) { headerString += "/Timesteps"; } m_HeaderFirstColumn = headerString; } void QmitkImageStatisticsTreeModel::NodeRemoved(const mitk::DataNode *) { emit beginResetModel(); UpdateByDataStorage(); emit endResetModel(); emit modelChanged(); } void QmitkImageStatisticsTreeModel::NodeAdded(const mitk::DataNode *) { emit beginResetModel(); UpdateByDataStorage(); emit endResetModel(); emit modelChanged(); } void QmitkImageStatisticsTreeModel::NodeChanged(const mitk::DataNode *) { emit beginResetModel(); UpdateByDataStorage(); emit endResetModel(); emit modelChanged(); } diff --git a/Modules/LegacyIO/mitkImageWriter.cpp b/Modules/LegacyIO/mitkImageWriter.cpp index 4cec0c6130..1b80e14b55 100644 --- a/Modules/LegacyIO/mitkImageWriter.cpp +++ b/Modules/LegacyIO/mitkImageWriter.cpp @@ -1,476 +1,476 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkImageWriter.h" #include "mitkImage.h" #include "mitkImageAccessByItk.h" #include "mitkImageReadAccessor.h" #include "mitkImageTimeSelector.h" #include "mitkItkPictureWrite.h" #include #include #include mitk::ImageWriter::ImageWriter() : m_UseCompression(true) { this->SetNumberOfRequiredInputs(1); m_MimeType = ""; SetDefaultExtension(); } mitk::ImageWriter::~ImageWriter() { } void mitk::ImageWriter::SetFileName(const char *fileName) { if (fileName && (fileName == this->m_FileName)) { return; } if (fileName) { this->m_FileName = fileName; this->m_FileNameWithoutExtension = this->m_FileName; this->m_Extension.clear(); std::size_t pos = this->m_FileName.find_last_of("/\\"); if (pos != std::string::npos) { std::size_t ppos = this->m_FileName.find_first_of('.', pos); if (ppos != std::string::npos) { this->m_FileNameWithoutExtension = this->m_FileName.substr(0, ppos); this->m_Extension = this->m_FileName.substr(ppos); } } } else { this->m_FileName.clear(); this->m_FileNameWithoutExtension.clear(); this->m_Extension.clear(); } this->Modified(); } void mitk::ImageWriter::SetFileName(const std::string &fileName) { this->SetFileName(fileName.c_str()); } void mitk::ImageWriter::SetExtension(const char *extension) { if (extension && (extension == this->m_Extension)) { return; } if (extension) { this->m_Extension = extension; this->m_FileName = this->m_FileNameWithoutExtension + this->m_Extension; } else { this->m_Extension.clear(); this->m_FileName = this->m_FileNameWithoutExtension; } this->Modified(); } void mitk::ImageWriter::SetExtension(const std::string &extension) { this->SetFileName(extension.c_str()); } void mitk::ImageWriter::SetDefaultExtension() { this->m_Extension = ".mhd"; this->m_FileName = this->m_FileNameWithoutExtension + this->m_Extension; this->Modified(); } #include #include #include static void writeVti(const char *filename, mitk::Image *image, int t = 0) { vtkXMLImageDataWriter *vtkwriter = vtkXMLImageDataWriter::New(); vtkwriter->SetFileName(filename); vtkwriter->SetInputData(image->GetVtkImageData(t)); vtkwriter->Write(); vtkwriter->Delete(); } #include void mitk::ImageWriter::WriteByITK(mitk::Image *image, const std::string &fileName) { MITK_INFO << "Writing image: " << fileName << std::endl; // Pictures and picture series like .png are written via a different mechanism then volume images. // So, they are still multiplexed and thus not support vector images. if (fileName.find(".png") != std::string::npos || fileName.find(".tif") != std::string::npos || fileName.find(".jpg") != std::string::npos || fileName.find(".bmp") != std::string::npos) { try { // switch processing of single/multi-component images if (image->GetPixelType(0).GetNumberOfComponents() == 1) { AccessByItk_1(image, _mitkItkPictureWrite, fileName); } else { AccessFixedPixelTypeByItk_1(image, _mitkItkPictureWriteComposite, MITK_ACCESSBYITK_PIXEL_TYPES_SEQ MITK_ACCESSBYITK_COMPOSITE_PIXEL_TYPES_SEQ, fileName); } } catch (itk::ExceptionObject &e) { std::cerr << "Caught " << e.what() << std::endl; } catch (std::exception &e) { std::cerr << "Caught std::exception " << e.what() << std::endl; } return; } // Implementation of writer using itkImageIO directly. This skips the use // of templated itkImageFileWriter, which saves the multiplexing on MITK side. unsigned int dimension = image->GetDimension(); unsigned int *dimensions = image->GetDimensions(); mitk::PixelType pixelType = image->GetPixelType(); mitk::Vector3D mitkSpacing = image->GetGeometry()->GetSpacing(); mitk::Point3D mitkOrigin = image->GetGeometry()->GetOrigin(); // Due to templating in itk, we are forced to save a 4D spacing and 4D Origin, though they are not supported in MITK itk::Vector spacing4D; spacing4D[0] = mitkSpacing[0]; spacing4D[1] = mitkSpacing[1]; spacing4D[2] = mitkSpacing[2]; spacing4D[3] = 1; // There is no support for a 4D spacing. However, we should have an valid value here itk::Vector origin4D; origin4D[0] = mitkOrigin[0]; origin4D[1] = mitkOrigin[1]; origin4D[2] = mitkOrigin[2]; origin4D[3] = 0; // There is no support for a 4D origin. However, we should have an valid value here itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(fileName.c_str(), itk::ImageIOFactory::WriteMode); if (imageIO.IsNull()) { itkExceptionMacro(<< "Error: Could not create itkImageIO via factory for file " << fileName); } // Set the necessary information for imageIO imageIO->SetNumberOfDimensions(dimension); imageIO->SetPixelType(pixelType.GetPixelType()); imageIO->SetComponentType(pixelType.GetComponentType() < PixelComponentUserType ? static_cast(pixelType.GetComponentType()) : itk::ImageIOBase::UNKNOWNCOMPONENTTYPE); imageIO->SetNumberOfComponents(pixelType.GetNumberOfComponents()); itk::ImageIORegion ioRegion(dimension); for (unsigned int i = 0; i < dimension; i++) { imageIO->SetDimensions(i, dimensions[i]); imageIO->SetSpacing(i, spacing4D[i]); imageIO->SetOrigin(i, origin4D[i]); mitk::Vector3D mitkDirection; mitkDirection.SetVnlVector( image->GetGeometry()->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix().get_column(i)); itk::Vector direction4D; direction4D[0] = mitkDirection[0]; direction4D[1] = mitkDirection[1]; direction4D[2] = mitkDirection[2]; // MITK only supports a 3x3 direction matrix. Due to templating in itk, however, we must // save a 4x4 matrix for 4D images. in this case, add an homogneous component to the matrix. if (i == 3) direction4D[3] = 1; // homogenous component else direction4D[3] = 0; vnl_vector axisDirection(dimension); for (unsigned int j = 0; j < dimension; j++) { axisDirection[j] = direction4D[j] / spacing4D[i]; } imageIO->SetDirection(i, axisDirection); ioRegion.SetSize(i, image->GetLargestPossibleRegion().GetSize(i)); ioRegion.SetIndex(i, image->GetLargestPossibleRegion().GetIndex(i)); } // use compression if available imageIO->SetUseCompression(m_UseCompression); imageIO->SetIORegion(ioRegion); imageIO->SetFileName(fileName); ImageReadAccessor imageAccess(image); imageIO->Write(imageAccess.GetData()); } void mitk::ImageWriter::GenerateData() { mitk::LocaleSwitch localeSwitch("C"); if (m_FileName == "") { itkWarningMacro(<< "Sorry, filename has not been set!"); return; } FILE *tempFile = fopen(m_FileName.c_str(), "w"); if (tempFile == nullptr) { itkExceptionMacro(<< "File location not writeable"); return; } fclose(tempFile); remove(m_FileName.c_str()); // Creating clone of input image, since i might change the geometry mitk::Image::Pointer input = this->GetInput()->Clone(); // Check if geometry information will be lost if (input->GetDimension() == 2) { if (!input->GetGeometry()->Is2DConvertable()) { MITK_WARN << "Saving a 2D image with 3D geometry information. Geometry information will be lost! You might " "consider using Convert2Dto3DImageFilter before saving."; // set matrix to identity mitk::AffineTransform3D::Pointer affTrans = mitk::AffineTransform3D::New(); affTrans->SetIdentity(); mitk::Vector3D spacing = input->GetGeometry()->GetSpacing(); mitk::Point3D origin = input->GetGeometry()->GetOrigin(); input->GetGeometry()->SetIndexToWorldTransform(affTrans); input->GetGeometry()->SetSpacing(spacing); input->GetGeometry()->SetOrigin(origin); } } bool vti = (m_Extension.find(".vti") != std::string::npos); // If the extension is NOT .pic and NOT .nrrd and NOT .nii and NOT .nii.gz the following block is entered if (m_Extension.find(".pic") == std::string::npos && m_Extension.find(".nrrd") == std::string::npos && m_Extension.find(".nii") == std::string::npos && m_Extension.find(".nii.gz") == std::string::npos) { if (input->GetDimension() > 3) { int t, timesteps; timesteps = input->GetDimension(3); ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New(); timeSelector->SetInput(input); mitk::Image::Pointer image = timeSelector->GetOutput(); for (t = 0; t < timesteps; ++t) { std::ostringstream filename; timeSelector->SetTimeNr(t); timeSelector->Update(); if (input->GetTimeGeometry()->IsValidTimeStep(t)) { - const mitk::TimeBounds &timebounds = input->GetTimeGeometry()->GetTimeBounds(t); + const mitk::TimeBounds timebounds = input->GetTimeGeometry()->GetTimeBounds(t); filename << m_FileNameWithoutExtension << "_S" << std::setprecision(0) << timebounds[0] << "_E" << std::setprecision(0) << timebounds[1] << "_T" << t << m_Extension; } else { itkWarningMacro(<< "Error on write: TimeGeometry invalid of image " << filename.str() << "."); filename << m_FileNameWithoutExtension << "_T" << t << m_Extension; } if (vti) { writeVti(filename.str().c_str(), input, t); } else { WriteByITK(image, filename.str()); } } } else if (vti) { writeVti(m_FileName.c_str(), input); } else { WriteByITK(input, m_FileName); } } else { // use the PicFileWriter for the .pic data type if (m_Extension.find(".pic") != std::string::npos) { /* PicFileWriter::Pointer picWriter = PicFileWriter::New(); size_t found; found = m_FileName.find( m_Extension ); // !!! HAS to be at the very end of the filename (not somewhere in the middle) if( m_FileName.length() > 3 && found != m_FileName.length() - 4 ) { //if Extension not in Filename std::ostringstream filename; filename << m_FileName.c_str() << m_Extension; picWriter->SetFileName( filename.str().c_str() ); } else { picWriter->SetFileName( m_FileName.c_str() ); } picWriter->SetInputImage( input ); picWriter->Write(); */ } // use the ITK .nrrd Image writer if (m_Extension.find(".nrrd") != std::string::npos || m_Extension.find(".nii") != std::string::npos || m_Extension.find(".nii.gz") != std::string::npos) { WriteByITK(input, this->m_FileName); } } m_MimeType = "application/MITK.Pic"; } bool mitk::ImageWriter::CanWriteDataType(DataNode *input) { if (input) { return this->CanWriteBaseDataType(input->GetData()); } return false; } void mitk::ImageWriter::SetInput(DataNode *input) { if (input && CanWriteDataType(input)) this->ProcessObject::SetNthInput(0, dynamic_cast(input->GetData())); } std::string mitk::ImageWriter::GetWritenMIMEType() { return m_MimeType; } std::vector mitk::ImageWriter::GetPossibleFileExtensions() { std::vector possibleFileExtensions; possibleFileExtensions.push_back(".pic"); possibleFileExtensions.push_back(".pic.gz"); possibleFileExtensions.push_back(".bmp"); possibleFileExtensions.push_back(".dcm"); possibleFileExtensions.push_back(".DCM"); possibleFileExtensions.push_back(".dicom"); possibleFileExtensions.push_back(".DICOM"); possibleFileExtensions.push_back(".gipl"); possibleFileExtensions.push_back(".gipl.gz"); possibleFileExtensions.push_back(".mha"); possibleFileExtensions.push_back(".nii"); possibleFileExtensions.push_back(".nii.gz"); possibleFileExtensions.push_back(".nrrd"); possibleFileExtensions.push_back(".nhdr"); possibleFileExtensions.push_back(".png"); possibleFileExtensions.push_back(".PNG"); possibleFileExtensions.push_back(".spr"); possibleFileExtensions.push_back(".mhd"); possibleFileExtensions.push_back(".vtk"); possibleFileExtensions.push_back(".vti"); possibleFileExtensions.push_back(".hdr"); possibleFileExtensions.push_back(".img"); possibleFileExtensions.push_back(".img.gz"); possibleFileExtensions.push_back(".png"); possibleFileExtensions.push_back(".tif"); possibleFileExtensions.push_back(".jpg"); return possibleFileExtensions; } std::string mitk::ImageWriter::GetSupportedBaseData() const { return Image::GetStaticNameOfClass(); } std::string mitk::ImageWriter::GetFileExtension() { return m_Extension; } void mitk::ImageWriter::SetInput(mitk::Image *image) { this->ProcessObject::SetNthInput(0, image); } const mitk::Image *mitk::ImageWriter::GetInput() { if (this->GetNumberOfInputs() < 1) { return nullptr; } else { return static_cast(this->ProcessObject::GetInput(0)); } } const char *mitk::ImageWriter::GetDefaultFilename() { return "Image.nrrd"; } const char *mitk::ImageWriter::GetFileDialogPattern() { return "Nearly Raw Raster Data (*.nrrd);;" "NIfTI format (*.nii *.nii.gz);;" "VTK Image Data Files (*.vti);;" "NRRD with detached header (*.nhdr);;" "Analyze Format (*.hdr);;" "MetaImage (*.mhd);;" "Sets of 2D slices (*.png *.tiff *.jpg *.jpeg *.bmp);;" "DICOM (*.dcm *.DCM *.dicom *.DICOM);;" "UMDS GIPL Format Files (*.gipl *.gipl.gz)"; } const char *mitk::ImageWriter::GetDefaultExtension() { return ".nrrd"; } bool mitk::ImageWriter::CanWriteBaseDataType(BaseData::Pointer data) { return dynamic_cast(data.GetPointer()); } void mitk::ImageWriter::DoWrite(BaseData::Pointer data) { if (this->CanWriteBaseDataType(data)) { this->SetInput(dynamic_cast(data.GetPointer())); this->Update(); } } void mitk::ImageWriter::SetUseCompression(bool useCompression) { m_UseCompression = useCompression; } diff --git a/Modules/LegacyIO/mitkSurfaceVtkWriter.txx b/Modules/LegacyIO/mitkSurfaceVtkWriter.txx index 82b0c18fab..3072e4634c 100644 --- a/Modules/LegacyIO/mitkSurfaceVtkWriter.txx +++ b/Modules/LegacyIO/mitkSurfaceVtkWriter.txx @@ -1,171 +1,171 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkSurfaceVtkWriter.h" #include #include #include #include #include #include #include #include #include template mitk::SurfaceVtkWriter::SurfaceVtkWriter() : m_WriterWriteHasReturnValue(false) { this->SetNumberOfRequiredInputs(1); m_VtkWriter = vtkSmartPointer::New(); // enable to write ascii-formatted-file // m_VtkWriter->SetFileTypeToASCII(); SetDefaultExtension(); // and information about the Writer's Write() method } template mitk::SurfaceVtkWriter::~SurfaceVtkWriter() { } template void mitk::SurfaceVtkWriter::SetDefaultExtension() { m_Extension = ".vtk"; } template void mitk::SurfaceVtkWriter::ExecuteWrite(VtkWriterType *vtkWriter) { if (vtkWriter->Write() == 0 || vtkWriter->GetErrorCode() != 0) { itkExceptionMacro(<< "Error during surface writing: " << vtkErrorCode::GetStringFromErrorCode(vtkWriter->GetErrorCode())); } } template void mitk::SurfaceVtkWriter::GenerateData() { if (m_FileName == "") { itkWarningMacro(<< "Sorry, filename has not been set!"); return; } mitk::Surface::Pointer input = const_cast(this->GetInput()); vtkSmartPointer transformPolyData = vtkSmartPointer::New(); vtkPolyData *polyData; BaseGeometry *geometry; unsigned int t, timesteps = input->GetTimeGeometry()->CountTimeSteps(); for (t = 0; t < timesteps; ++t) { // surfaces do not have to exist in all timeteps; therefor, only write valid surfaces if (input->GetVtkPolyData(t) == nullptr) continue; std::ostringstream filename; filename.imbue(::std::locale::classic()); geometry = input->GetGeometry(t); if (timesteps > 1) { if (input->GetTimeGeometry()->IsValidTimeStep(t)) { - const TimeBounds &timebounds = input->GetTimeGeometry()->GetTimeBounds(t); + const TimeBounds timebounds = input->GetTimeGeometry()->GetTimeBounds(t); filename << m_FileName.c_str() << "_S" << std::setprecision(0) << timebounds[0] << "_E" << std::setprecision(0) << timebounds[1] << "_T" << t << m_Extension; } else { itkWarningMacro(<< "Error on write: TimeGeometry invalid of surface " << filename.str() << "."); filename << m_FileName.c_str() << "_T" << t << m_Extension; } m_VtkWriter->SetFileName(filename.str().c_str()); } else m_VtkWriter->SetFileName(m_FileName.c_str()); transformPolyData->SetInputData(input->GetVtkPolyData(t)); transformPolyData->SetTransform(geometry->GetVtkTransform()); transformPolyData->UpdateWholeExtent(); polyData = transformPolyData->GetOutput(); m_VtkWriter->SetInputData(polyData); ExecuteWrite(m_VtkWriter); } m_MimeType = "application/MITK.Surface"; } template void mitk::SurfaceVtkWriter::SetInput(mitk::Surface *surface) { this->ProcessObject::SetNthInput(0, surface); } template const mitk::Surface *mitk::SurfaceVtkWriter::GetInput() { if (this->GetNumberOfInputs() < 1) { return nullptr; } else { return static_cast(this->ProcessObject::GetInput(0)); } } template bool mitk::SurfaceVtkWriter::CanWriteDataType(DataNode *input) { if (input) { BaseData *data = input->GetData(); if (data) { Surface::Pointer surface = dynamic_cast(data); if (surface.IsNotNull()) { SetDefaultExtension(); return true; } } } return false; } template void mitk::SurfaceVtkWriter::SetInput(DataNode *input) { if (input && CanWriteDataType(input)) SetInput(dynamic_cast(input->GetData())); } template std::string mitk::SurfaceVtkWriter::GetWritenMIMEType() { return m_MimeType; } template std::string mitk::SurfaceVtkWriter::GetFileExtension() { return m_Extension; } diff --git a/Modules/MatchPointRegistration/CMakeLists.txt b/Modules/MatchPointRegistration/CMakeLists.txt index 71204d9f1a..577f222225 100644 --- a/Modules/MatchPointRegistration/CMakeLists.txt +++ b/Modules/MatchPointRegistration/CMakeLists.txt @@ -1,29 +1,29 @@ -MITK_CREATE_MODULE( +mitk_create_module( INCLUDE_DIRS PUBLIC algorithms PRIVATE src/Helper src/Rendering DEPENDS MitkCore MitkSceneSerializationBase PACKAGE_DEPENDS PUBLIC MatchPoint PRIVATE VTK|ImagingGeneral+ImagingHybrid ) if(TARGET ${MODULE_TARGET}) set(ALG_PROFILE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/algorithms) include(${MatchPoint_SOURCE_DIR}/CMake/mapFunctionCreateAlgorithmProfile.cmake) file(GLOB ALG_PROFILE_FILES LIST_DIRECTORIES false RELATIVE ${ALG_PROFILE_DIR} "${ALG_PROFILE_DIR}/*.profile") foreach(profile_file ${ALG_PROFILE_FILES}) get_filename_component(profile_name ${profile_file} NAME_WE) - MESSAGE(STATUS "... generate MDRA profile ${profile_name} (from ${profile_file})...") + message(STATUS "Generate MDRA profile ${profile_name} (from ${profile_file})") CREATE_ALGORITHM_PROFILE(${profile_name} ${ALG_PROFILE_DIR}/${profile_file}) - endforeach(profile_file) + endforeach() - ADD_SUBDIRECTORY(autoload/IO) - ADD_SUBDIRECTORY(deployment) + add_subdirectory(autoload/IO) + add_subdirectory(deployment) if(BUILD_TESTING) - ADD_SUBDIRECTORY(Testing) - endif(BUILD_TESTING) - ADD_SUBDIRECTORY(cmdapps) + add_subdirectory(Testing) + endif() + add_subdirectory(cmdapps) endif() diff --git a/Modules/MatchPointRegistration/src/Rendering/mitkRegEvaluationMapper2D.cpp b/Modules/MatchPointRegistration/src/Rendering/mitkRegEvaluationMapper2D.cpp index 32ff499f6b..a2938eb0c8 100644 --- a/Modules/MatchPointRegistration/src/Rendering/mitkRegEvaluationMapper2D.cpp +++ b/Modules/MatchPointRegistration/src/Rendering/mitkRegEvaluationMapper2D.cpp @@ -1,836 +1,836 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ //MITK #include #include #include #include #include #include #include #include #include #include #include #include "mitkImageStatisticsHolder.h" #include "mitkPlaneClipping.h" #include "mitkRegVisPropertyTags.h" #include "mitkRegVisHelper.h" #include "mitkRegEvalStyleProperty.h" #include "mitkRegEvalWipeStyleProperty.h" //MITK Rendering #include "mitkRegEvaluationMapper2D.h" #include "vtkMitkThickSlicesFilter.h" #include "vtkMitkLevelWindowFilter.h" #include "vtkNeverTranslucentTexture.h" //VTK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include //ITK #include #include //MatchPoint #include #include mitk::RegEvaluationMapper2D::RegEvaluationMapper2D() { } mitk::RegEvaluationMapper2D::~RegEvaluationMapper2D() { } //set the two points defining the textured plane according to the dimension and spacing void mitk::RegEvaluationMapper2D::GeneratePlane(mitk::BaseRenderer* renderer, double planeBounds[6]) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); float depth = this->CalculateLayerDepth(renderer); //Set the origin to (xMin; yMin; depth) of the plane. This is necessary for obtaining the correct //plane size in crosshair rotation and swivel mode. localStorage->m_Plane->SetOrigin(planeBounds[0], planeBounds[2], depth); //These two points define the axes of the plane in combination with the origin. //Point 1 is the x-axis and point 2 the y-axis. //Each plane is transformed according to the view (axial, coronal and saggital) afterwards. localStorage->m_Plane->SetPoint1(planeBounds[1] , planeBounds[2], depth); //P1: (xMax, yMin, depth) localStorage->m_Plane->SetPoint2(planeBounds[0], planeBounds[3], depth); //P2: (xMin, yMax, depth) } float mitk::RegEvaluationMapper2D::CalculateLayerDepth(mitk::BaseRenderer* renderer) { //get the clipping range to check how deep into z direction we can render images double maxRange = renderer->GetVtkRenderer()->GetActiveCamera()->GetClippingRange()[1]; //Due to a VTK bug, we cannot use the whole clipping range. /100 is empirically determined float depth = -maxRange*0.01; // divide by 100 int layer = 0; GetDataNode()->GetIntProperty( "layer", layer, renderer); //add the layer property for each image to render images with a higher layer on top of the others depth += layer*10; //*10: keep some room for each image (e.g. for ODFs in between) if(depth > 0.0f) { depth = 0.0f; MITK_WARN << "Layer value exceeds clipping range. Set to minimum instead."; } return depth; } const mitk::Image* mitk::RegEvaluationMapper2D::GetTargetImage( void ) { const mitk::RegEvaluationObject* evalObj = dynamic_cast< const mitk::RegEvaluationObject* >( GetDataNode()->GetData() ); if (evalObj) { return evalObj->GetTargetImage(); } return nullptr; } const mitk::Image* mitk::RegEvaluationMapper2D::GetMovingImage( void ) { const mitk::RegEvaluationObject* evalObj = dynamic_cast< const mitk::RegEvaluationObject* >( GetDataNode()->GetData() ); if (evalObj) { return evalObj->GetMovingImage(); } return nullptr; } const mitk::DataNode* mitk::RegEvaluationMapper2D::GetTargetNode(void) { const mitk::RegEvaluationObject* evalObj = dynamic_cast< const mitk::RegEvaluationObject* >(GetDataNode()->GetData()); if (evalObj) { return evalObj->GetTargetNode(); } return nullptr; } const mitk::DataNode* mitk::RegEvaluationMapper2D::GetMovingNode(void) { const mitk::RegEvaluationObject* evalObj = dynamic_cast< const mitk::RegEvaluationObject* >(GetDataNode()->GetData()); if (evalObj) { return evalObj->GetMovingNode(); } return nullptr; } const mitk::MAPRegistrationWrapper* mitk::RegEvaluationMapper2D::GetRegistration( void ) { const mitk::RegEvaluationObject* evalObj = dynamic_cast< const mitk::RegEvaluationObject* >( GetDataNode()->GetData() ); if (evalObj) { return evalObj->GetRegistration(); } return nullptr; } vtkProp* mitk::RegEvaluationMapper2D::GetVtkProp(mitk::BaseRenderer* renderer) { //return the actor corresponding to the renderer return m_LSH.GetLocalStorage(renderer)->m_Actors; } void mitk::RegEvaluationMapper2D::GenerateDataForRenderer( mitk::BaseRenderer *renderer ) { bool updated = false; LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); mitk::Image::Pointer targetInput = const_cast< mitk::Image * >( this->GetTargetImage() ); mitk::DataNode* datanode = this->GetDataNode(); if ( targetInput.IsNull() || targetInput->IsInitialized() == false ) { return; } mitk::Image::ConstPointer movingInput = this->GetMovingImage(); if ( movingInput.IsNull() || movingInput->IsInitialized() == false ) { return; } mitk::MAPRegistrationWrapper::ConstPointer reg = this->GetRegistration(); //check if there is a valid worldGeometry const PlaneGeometry *worldGeometry = renderer->GetCurrentWorldPlaneGeometry(); if( ( worldGeometry == nullptr ) || ( !worldGeometry->IsValid() ) || ( !worldGeometry->HasReferenceGeometry() )) { return; } if(targetInput->GetMTime()>localStorage->m_LastUpdateTime || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometryUpdateTime()) //was the geometry modified? || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometry()->GetMTime())) { //target input has been modified -> reslice target input targetInput->Update(); // early out if there is no intersection of the current rendering geometry // and the geometry of the image that is to be rendered. if ( !RenderingGeometryIntersectsImage( worldGeometry, targetInput->GetSlicedGeometry() ) ) { // set image to nullptr, to clear the texture in 3D, because // the latest image is used there if the plane is out of the geometry // see bug-13275 localStorage->m_EvaluationImage = nullptr; localStorage->m_Mapper->SetInputData( localStorage->m_EmptyPolyData ); return; } //set main input for ExtractSliceFilter localStorage->m_Reslicer->SetInput(targetInput); localStorage->m_Reslicer->SetWorldGeometry(worldGeometry); localStorage->m_Reslicer->SetTimeStep( this->GetTimestep() ); //set the transformation of the image to adapt reslice axis localStorage->m_Reslicer->SetResliceTransformByGeometry( targetInput->GetTimeGeometry()->GetGeometryForTimeStep( this->GetTimestep() ) ); //is the geometry of the slice based on the input image or the worldgeometry? bool inPlaneResampleExtentByGeometry = false; datanode->GetBoolProperty("in plane resample extent by geometry", inPlaneResampleExtentByGeometry, renderer); localStorage->m_Reslicer->SetInPlaneResampleExtentByGeometry(inPlaneResampleExtentByGeometry); // Initialize the interpolation mode for resampling; switch to nearest // neighbor if the input image is too small. if ( (targetInput->GetDimension() >= 3) && (targetInput->GetDimension(2) > 1) ) { VtkResliceInterpolationProperty *resliceInterpolationProperty; datanode->GetProperty( resliceInterpolationProperty, "reslice interpolation" ); int interpolationMode = VTK_RESLICE_NEAREST; if ( resliceInterpolationProperty != nullptr ) { interpolationMode = resliceInterpolationProperty->GetInterpolation(); } switch ( interpolationMode ) { case VTK_RESLICE_NEAREST: localStorage->m_Reslicer->SetInterpolationMode(ExtractSliceFilter::RESLICE_NEAREST); break; case VTK_RESLICE_LINEAR: localStorage->m_Reslicer->SetInterpolationMode(ExtractSliceFilter::RESLICE_LINEAR); break; case VTK_RESLICE_CUBIC: localStorage->m_Reslicer->SetInterpolationMode(ExtractSliceFilter::RESLICE_CUBIC); break; } } else { localStorage->m_Reslicer->SetInterpolationMode(ExtractSliceFilter::RESLICE_NEAREST); } //this is needed when thick mode was enable bevore. These variable have to be reset to default values localStorage->m_Reslicer->SetOutputDimensionality( 2 ); localStorage->m_Reslicer->SetOutputSpacingZDirection(1.0); localStorage->m_Reslicer->SetOutputExtentZDirection( 0, 0 ); localStorage->m_Reslicer->Modified(); //start the pipeline with updating the largest possible, needed if the geometry of the input has changed localStorage->m_Reslicer->UpdateLargestPossibleRegion(); localStorage->m_slicedTargetImage = localStorage->m_Reslicer->GetOutput(); updated = true; } if(updated || movingInput->GetMTime() > localStorage->m_LastUpdateTime || reg->GetMTime() > localStorage->m_LastUpdateTime) { //Map moving image localStorage->m_slicedMappedImage = mitk::ImageMappingHelper::map(movingInput,reg,false,0,localStorage->m_slicedTargetImage->GetGeometry(),false,0); updated = true; } // Bounds information for reslicing (only required if reference geometry // is present) //this used for generating a vtkPLaneSource with the right size double sliceBounds[6] = { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 }; if (updated || (localStorage->m_LastUpdateTime < datanode->GetPropertyList()->GetMTime()) //was a property modified? || (localStorage->m_LastUpdateTime < datanode->GetPropertyList(renderer)->GetMTime()) || (localStorage->m_LastUpdateTime < this->GetTargetNode()->GetMTime()) || (localStorage->m_LastUpdateTime < this->GetMovingNode()->GetMTime())) { localStorage->m_Reslicer->GetClippedPlaneBounds(sliceBounds); //get the spacing of the slice localStorage->m_mmPerPixel = localStorage->m_Reslicer->GetOutputSpacing(); // calculate minimum bounding rect of IMAGE in texture { double textureClippingBounds[6] = { 0.0, 0.0, 0.0, 0.0, 0.0, 0.0 }; // Calculate the actual bounds of the transformed plane clipped by the // dataset bounding box; this is required for drawing the texture at the // correct position during 3D mapping. const PlaneGeometry *planeGeometry = dynamic_cast(worldGeometry); mitk::PlaneClipping::CalculateClippedPlaneBounds(targetInput->GetGeometry(), planeGeometry, textureClippingBounds); textureClippingBounds[0] = static_cast(textureClippingBounds[0] / localStorage->m_mmPerPixel[0] + 0.5); textureClippingBounds[1] = static_cast(textureClippingBounds[1] / localStorage->m_mmPerPixel[0] + 0.5); textureClippingBounds[2] = static_cast(textureClippingBounds[2] / localStorage->m_mmPerPixel[1] + 0.5); textureClippingBounds[3] = static_cast(textureClippingBounds[3] / localStorage->m_mmPerPixel[1] + 0.5); //clipping bounds for cutting the image localStorage->m_TargetLevelWindowFilter->SetClippingBounds(textureClippingBounds); localStorage->m_MappedLevelWindowFilter->SetClippingBounds(textureClippingBounds); } this->ApplyLookuptable(renderer, this->GetTargetNode(), localStorage->m_TargetLevelWindowFilter); this->ApplyLookuptable(renderer, this->GetMovingNode(), localStorage->m_MappedLevelWindowFilter); this->ApplyLevelWindow(renderer, this->GetTargetNode(), localStorage->m_TargetLevelWindowFilter); this->ApplyLevelWindow(renderer, this->GetMovingNode(), localStorage->m_MappedLevelWindowFilter); //connect the input with the levelwindow filter localStorage->m_TargetLevelWindowFilter->SetInputData(localStorage->m_slicedTargetImage->GetVtkImageData()); localStorage->m_MappedLevelWindowFilter->SetInputData(localStorage->m_slicedMappedImage->GetVtkImageData()); localStorage->m_TargetExtractFilter->SetInputConnection(localStorage->m_TargetLevelWindowFilter->GetOutputPort()); localStorage->m_MappedExtractFilter->SetInputConnection(localStorage->m_MappedLevelWindowFilter->GetOutputPort()); localStorage->m_TargetExtractFilter->SetComponents(0); localStorage->m_MappedExtractFilter->SetComponents(0); updated = true; } //Generate evaluation image bool isStyleOutdated = mitk::PropertyIsOutdated(datanode,mitk::nodeProp_RegEvalStyle,localStorage->m_LastUpdateTime); bool isBlendOutdated = mitk::PropertyIsOutdated(datanode,mitk::nodeProp_RegEvalBlendFactor,localStorage->m_LastUpdateTime); bool isCheckerOutdated = mitk::PropertyIsOutdated(datanode,mitk::nodeProp_RegEvalCheckerCount,localStorage->m_LastUpdateTime); bool isWipeStyleOutdated = mitk::PropertyIsOutdated(datanode,mitk::nodeProp_RegEvalWipeStyle,localStorage->m_LastUpdateTime); bool isContourOutdated = mitk::PropertyIsOutdated(datanode,mitk::nodeProp_RegEvalTargetContour,localStorage->m_LastUpdateTime); bool isPositionOutdated = mitk::PropertyIsOutdated(datanode, mitk::nodeProp_RegEvalCurrentPosition, localStorage->m_LastUpdateTime); if (updated || isStyleOutdated || isBlendOutdated || isCheckerOutdated || isWipeStyleOutdated || isContourOutdated || isPositionOutdated) { mitk::RegEvalStyleProperty::Pointer evalStyleProp = mitk::RegEvalStyleProperty::New(); datanode->GetProperty(evalStyleProp, mitk::nodeProp_RegEvalStyle); switch (evalStyleProp->GetValueAsId()) { case 0 : { PrepareBlend(datanode, localStorage); break; } case 1 : { PrepareColorBlend(localStorage); break; } case 2 : { PrepareCheckerBoard(datanode, localStorage); break; } case 3 : { const PlaneGeometry *worldGeometry = renderer->GetCurrentWorldPlaneGeometry(); Point3D currentPos3D; datanode->GetPropertyValue(mitk::nodeProp_RegEvalCurrentPosition, currentPos3D); Point2D currentPos2D; worldGeometry->Map(currentPos3D, currentPos2D); Point2D currentIndex2D; worldGeometry->WorldToIndex(currentPos2D, currentIndex2D); PrepareWipe(datanode, localStorage, currentIndex2D); break; } case 4 : { PrepareDifference(localStorage); break; } case 5 : { PrepareContour(datanode, localStorage); break; } } updated = true; } if(updated || (localStorage->m_LastUpdateTime < datanode->GetPropertyList()->GetMTime()) //was a property modified? || (localStorage->m_LastUpdateTime < datanode->GetPropertyList(renderer)->GetMTime()) ) { this->ApplyOpacity( renderer ); // do not use a VTK lookup table (we do that ourselves in m_LevelWindowFilter) localStorage->m_Texture->SetColorModeToDirectScalars(); // check for texture interpolation property bool textureInterpolation = false; GetDataNode()->GetBoolProperty( "texture interpolation", textureInterpolation, renderer ); //set the interpolation modus according to the property localStorage->m_Texture->SetInterpolate(textureInterpolation); // connect the texture with the output of the levelwindow filter localStorage->m_Texture->SetInputData(localStorage->m_EvaluationImage); this->TransformActor( renderer ); vtkActor* contourShadowActor = dynamic_cast (localStorage->m_Actors->GetParts()->GetItemAsObject(0)); //Connect the mapper with the input texture. This is the standard case. //setup the textured plane this->GeneratePlane( renderer, sliceBounds ); //set the plane as input for the mapper localStorage->m_Mapper->SetInputConnection(localStorage->m_Plane->GetOutputPort()); //set the texture for the actor localStorage->m_Actor->SetTexture(localStorage->m_Texture); contourShadowActor->SetVisibility( false ); // We have been modified => save this for next Update() localStorage->m_LastUpdateTime.Modified(); } } void mitk::RegEvaluationMapper2D::PrepareContour( mitk::DataNode* datanode, LocalStorage * localStorage ) { bool targetContour = true; datanode->GetBoolProperty(mitk::nodeProp_RegEvalTargetContour,targetContour); vtkSmartPointer magFilter = vtkSmartPointer::New(); if(targetContour) { magFilter->SetInputConnection(localStorage->m_TargetExtractFilter->GetOutputPort()); } else { magFilter->SetInputConnection(localStorage->m_MappedExtractFilter->GetOutputPort()); } vtkSmartPointer appendFilter = vtkSmartPointer::New(); appendFilter->AddInputConnection(magFilter->GetOutputPort()); appendFilter->AddInputConnection(magFilter->GetOutputPort()); if(targetContour) { appendFilter->AddInputConnection(localStorage->m_MappedExtractFilter->GetOutputPort()); } else { appendFilter->AddInputConnection(localStorage->m_TargetExtractFilter->GetOutputPort()); } appendFilter->Update(); localStorage->m_EvaluationImage = appendFilter->GetOutput(); } void mitk::RegEvaluationMapper2D::PrepareDifference( LocalStorage * localStorage ) { vtkSmartPointer diffFilter = vtkSmartPointer::New(); vtkSmartPointer minFilter = vtkSmartPointer::New(); vtkSmartPointer maxFilter = vtkSmartPointer::New(); minFilter->SetInputConnection(0, localStorage->m_TargetExtractFilter->GetOutputPort()); minFilter->SetInputConnection(1, localStorage->m_MappedExtractFilter->GetOutputPort()); minFilter->SetOperationToMin(); maxFilter->SetInputConnection(0, localStorage->m_TargetExtractFilter->GetOutputPort()); maxFilter->SetInputConnection(1, localStorage->m_MappedExtractFilter->GetOutputPort()); maxFilter->SetOperationToMax(); diffFilter->SetInputConnection(0, maxFilter->GetOutputPort()); diffFilter->SetInputConnection(1, minFilter->GetOutputPort()); diffFilter->SetOperationToSubtract(); diffFilter->Update(); localStorage->m_EvaluationImage = diffFilter->GetOutput(); } void mitk::RegEvaluationMapper2D::PrepareWipe(mitk::DataNode* datanode, LocalStorage * localStorage, const Point2D& currentIndex2D) { mitk::RegEvalWipeStyleProperty::Pointer evalWipeStyleProp = mitk::RegEvalWipeStyleProperty::New(); datanode->GetProperty(evalWipeStyleProp, mitk::nodeProp_RegEvalWipeStyle); vtkSmartPointer wipedFilter = vtkSmartPointer::New(); wipedFilter->SetInputConnection(0, localStorage->m_TargetLevelWindowFilter->GetOutputPort()); wipedFilter->SetInputConnection(1, localStorage->m_MappedLevelWindowFilter->GetOutputPort()); wipedFilter->SetPosition(currentIndex2D[0], currentIndex2D[1]); if (evalWipeStyleProp->GetValueAsId() == 0) { wipedFilter->SetWipeToQuad(); } else if (evalWipeStyleProp->GetValueAsId() == 1) { wipedFilter->SetWipeToHorizontal(); } else if (evalWipeStyleProp->GetValueAsId() == 2) { wipedFilter->SetWipeToVertical(); } wipedFilter->Update(); localStorage->m_EvaluationImage = wipedFilter->GetOutput(); } void mitk::RegEvaluationMapper2D::PrepareCheckerBoard( mitk::DataNode* datanode, LocalStorage * localStorage ) { int checkerCount = 5; datanode->GetIntProperty(mitk::nodeProp_RegEvalCheckerCount,checkerCount); vtkSmartPointer checkerboardFilter = vtkSmartPointer::New(); checkerboardFilter->SetInputConnection(0, localStorage->m_TargetLevelWindowFilter->GetOutputPort()); checkerboardFilter->SetInputConnection(1, localStorage->m_MappedLevelWindowFilter->GetOutputPort()); checkerboardFilter->SetNumberOfDivisions(checkerCount, checkerCount, 1); checkerboardFilter->Update(); localStorage->m_EvaluationImage = checkerboardFilter->GetOutput(); } void mitk::RegEvaluationMapper2D::PrepareColorBlend( LocalStorage * localStorage ) { vtkSmartPointer appendFilter = vtkSmartPointer::New(); //red channel appendFilter->AddInputConnection(localStorage->m_MappedExtractFilter->GetOutputPort()); //green channel appendFilter->AddInputConnection(localStorage->m_MappedExtractFilter->GetOutputPort()); //blue channel appendFilter->AddInputConnection(localStorage->m_TargetExtractFilter->GetOutputPort()); appendFilter->Update(); localStorage->m_EvaluationImage = appendFilter->GetOutput(); } void mitk::RegEvaluationMapper2D::PrepareBlend( mitk::DataNode* datanode, LocalStorage * localStorage ) { int blendfactor = 50; datanode->GetIntProperty(mitk::nodeProp_RegEvalBlendFactor,blendfactor); vtkSmartPointer blendFilter = vtkSmartPointer::New(); blendFilter->AddInputConnection(localStorage->m_TargetExtractFilter->GetOutputPort()); blendFilter->AddInputConnection(localStorage->m_MappedExtractFilter->GetOutputPort()); blendFilter->SetWeight(0, (100 - blendfactor) / 100.); blendFilter->SetWeight(1,blendfactor/100.); blendFilter->Update(); localStorage->m_EvaluationImage = blendFilter->GetOutput(); } void mitk::RegEvaluationMapper2D::ApplyLevelWindow(mitk::BaseRenderer *renderer, const mitk::DataNode* dataNode, vtkMitkLevelWindowFilter* levelFilter) { LevelWindow levelWindow; dataNode->GetLevelWindow(levelWindow, renderer, "levelwindow"); levelFilter->GetLookupTable()->SetRange(levelWindow.GetLowerWindowBound(), levelWindow.GetUpperWindowBound()); mitk::LevelWindow opacLevelWindow; if (dataNode->GetLevelWindow(opacLevelWindow, renderer, "opaclevelwindow")) { //pass the opaque level window to the filter levelFilter->SetMinOpacity(opacLevelWindow.GetLowerWindowBound()); levelFilter->SetMaxOpacity(opacLevelWindow.GetUpperWindowBound()); } else { //no opaque level window levelFilter->SetMinOpacity(0.0); levelFilter->SetMaxOpacity(255.0); } } void mitk::RegEvaluationMapper2D::ApplyLookuptable(mitk::BaseRenderer* renderer, const mitk::DataNode* dataNode, vtkMitkLevelWindowFilter* levelFilter) { LocalStorage* localStorage = m_LSH.GetLocalStorage(renderer); vtkLookupTable* usedLookupTable = localStorage->m_ColorLookupTable; // If lookup table or transferfunction use is requested... mitk::LookupTableProperty::Pointer lookupTableProp = dynamic_cast(dataNode->GetProperty("LookupTable")); if (lookupTableProp.IsNotNull()) // is a lookuptable set? { usedLookupTable = lookupTableProp->GetLookupTable()->GetVtkLookupTable(); } else { //"Image Rendering.Mode was set to use a lookup table but there is no property 'LookupTable'. //A default (rainbow) lookup table will be used. //Here have to do nothing. Warning for the user has been removed, due to unwanted console output //in every interation of the rendering. } levelFilter->SetLookupTable(usedLookupTable); } void mitk::RegEvaluationMapper2D::ApplyOpacity( mitk::BaseRenderer* renderer ) { LocalStorage* localStorage = this->GetLocalStorage( renderer ); float opacity = 1.0f; // check for opacity prop and use it for rendering if it exists GetDataNode()->GetOpacity( opacity, renderer, "opacity" ); //set the opacity according to the properties localStorage->m_Actor->GetProperty()->SetOpacity(opacity); if ( localStorage->m_Actors->GetParts()->GetNumberOfItems() > 1 ) { dynamic_cast( localStorage->m_Actors->GetParts()->GetItemAsObject(0) )->GetProperty()->SetOpacity(opacity); } } void mitk::RegEvaluationMapper2D::Update(mitk::BaseRenderer* renderer) { bool visible = true; GetDataNode()->GetVisibility(visible, renderer, "visible"); if ( !visible ) { return; } mitk::Image* data = const_cast( this->GetTargetImage() ); if ( data == nullptr ) { return; } // Calculate time step of the input data for the specified renderer (integer value) this->CalculateTimeStep( renderer ); // Check if time step is valid const TimeGeometry *dataTimeGeometry = data->GetTimeGeometry(); if ( ( dataTimeGeometry == nullptr ) || ( dataTimeGeometry->CountTimeSteps() == 0 ) || ( !dataTimeGeometry->IsValidTimeStep( this->GetTimestep() ) ) ) { return; } const DataNode *node = this->GetDataNode(); data->UpdateOutputInformation(); LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); //check if something important has changed and we need to rerender if ( (localStorage->m_LastUpdateTime < node->GetMTime()) //was the node modified? || (localStorage->m_LastUpdateTime < data->GetPipelineMTime()) //Was the data modified? || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometryUpdateTime()) //was the geometry modified? || (localStorage->m_LastUpdateTime < renderer->GetCurrentWorldPlaneGeometry()->GetMTime()) || (localStorage->m_LastUpdateTime < node->GetPropertyList()->GetMTime()) //was a property modified? || (localStorage->m_LastUpdateTime < node->GetPropertyList(renderer)->GetMTime()) || (localStorage->m_LastUpdateTime < this->GetTargetNode()->GetMTime()) //was the target node modified? || (localStorage->m_LastUpdateTime < this->GetMovingNode()->GetMTime()) //was the moving node modified? || (localStorage->m_LastUpdateTime < this->GetTargetNode()->GetPropertyList()->GetMTime()) //was a target node property modified? || (localStorage->m_LastUpdateTime < this->GetTargetNode()->GetPropertyList(renderer)->GetMTime()) || (localStorage->m_LastUpdateTime < this->GetMovingNode()->GetPropertyList()->GetMTime()) //was a moving node property modified? || (localStorage->m_LastUpdateTime < this->GetMovingNode()->GetPropertyList(renderer)->GetMTime())) { this->GenerateDataForRenderer( renderer ); } // since we have checked that nothing important has changed, we can set // m_LastUpdateTime to the current time localStorage->m_LastUpdateTime.Modified(); } void mitk::RegEvaluationMapper2D::SetDefaultProperties(mitk::DataNode* node, mitk::BaseRenderer* renderer, bool overwrite) { mitk::RegEvaluationObject* regEval = dynamic_cast(node->GetData()); if(!regEval) { return; } // Properties common for both images and segmentations node->AddProperty( "depthOffset", mitk::FloatProperty::New( 0.0 ), renderer, overwrite ); if(regEval->GetTargetImage() && regEval->GetTargetImage()->IsRotated()) node->AddProperty( "reslice interpolation", mitk::VtkResliceInterpolationProperty::New(VTK_RESLICE_CUBIC) ); else node->AddProperty( "reslice interpolation", mitk::VtkResliceInterpolationProperty::New() ); node->AddProperty( "texture interpolation", mitk::BoolProperty::New( false ) ); // set to user configurable default value (see global options) node->AddProperty( "in plane resample extent by geometry", mitk::BoolProperty::New( false ) ); node->AddProperty( "bounding box", mitk::BoolProperty::New( false ) ); mitk::RenderingModeProperty::Pointer renderingModeProperty = mitk::RenderingModeProperty::New(); node->AddProperty( "Image Rendering.Mode", renderingModeProperty); // Set default grayscale look-up table mitk::LookupTable::Pointer mitkLut = mitk::LookupTable::New(); mitk::LookupTableProperty::Pointer mitkLutProp = mitk::LookupTableProperty::New(); mitkLutProp->SetLookupTable(mitkLut); node->SetProperty("LookupTable", mitkLutProp); node->AddProperty( "opacity", mitk::FloatProperty::New(1.0f), renderer, overwrite ); node->AddProperty( "color", ColorProperty::New(1.0,1.0,1.0), renderer, overwrite ); node->AddProperty( "binary", mitk::BoolProperty::New( false ), renderer, overwrite ); node->AddProperty("layer", mitk::IntProperty::New(0), renderer, overwrite); node->AddProperty(mitk::nodeProp_RegEvalStyle, mitk::RegEvalStyleProperty::New(0), renderer, overwrite); node->AddProperty(mitk::nodeProp_RegEvalBlendFactor, mitk::IntProperty::New(50), renderer, overwrite); node->AddProperty(mitk::nodeProp_RegEvalCheckerCount, mitk::IntProperty::New(3), renderer, overwrite); node->AddProperty(mitk::nodeProp_RegEvalTargetContour, mitk::BoolProperty::New(true), renderer, overwrite); node->AddProperty(mitk::nodeProp_RegEvalWipeStyle, mitk::RegEvalWipeStyleProperty::New(0), renderer, overwrite); - node->AddProperty(mitk::nodeProp_RegEvalCurrentPosition, mitk::GenericProperty::New(mitk::Point3D()), renderer, overwrite); + node->AddProperty(mitk::nodeProp_RegEvalCurrentPosition, mitk::Point3dProperty::New(mitk::Point3D()), renderer, overwrite); Superclass::SetDefaultProperties(node, renderer, overwrite); } mitk::RegEvaluationMapper2D::LocalStorage* mitk::RegEvaluationMapper2D::GetLocalStorage(mitk::BaseRenderer* renderer) { return m_LSH.GetLocalStorage(renderer); } void mitk::RegEvaluationMapper2D::TransformActor(mitk::BaseRenderer* renderer) { LocalStorage *localStorage = m_LSH.GetLocalStorage(renderer); //get the transformation matrix of the reslicer in order to render the slice as axial, coronal or saggital vtkSmartPointer trans = vtkSmartPointer::New(); vtkSmartPointer matrix = localStorage->m_Reslicer->GetResliceAxes(); trans->SetMatrix(matrix); //transform the plane/contour (the actual actor) to the corresponding view (axial, coronal or saggital) localStorage->m_Actor->SetUserTransform(trans); //transform the origin to center based coordinates, because MITK is center based. localStorage->m_Actor->SetPosition( -0.5*localStorage->m_mmPerPixel[0], -0.5*localStorage->m_mmPerPixel[1], 0.0); if ( localStorage->m_Actors->GetNumberOfPaths() > 1 ) { vtkActor* secondaryActor = dynamic_cast( localStorage->m_Actors->GetParts()->GetItemAsObject(0) ); secondaryActor->SetUserTransform(trans); secondaryActor->SetPosition( -0.5*localStorage->m_mmPerPixel[0], -0.5*localStorage->m_mmPerPixel[1], 0.0); } } bool mitk::RegEvaluationMapper2D::RenderingGeometryIntersectsImage( const PlaneGeometry* renderingGeometry, SlicedGeometry3D* imageGeometry ) { // if either one of the two geometries is nullptr we return true // for safety reasons if ( renderingGeometry == nullptr || imageGeometry == nullptr ) return true; // get the distance for the first cornerpoint ScalarType initialDistance = renderingGeometry->SignedDistance( imageGeometry->GetCornerPoint( 0 ) ); for( int i=1; i<8; i++ ) { mitk::Point3D cornerPoint = imageGeometry->GetCornerPoint( i ); // get the distance to the other cornerpoints ScalarType distance = renderingGeometry->SignedDistance( cornerPoint ); // if it has not the same signing as the distance of the first point if ( initialDistance * distance < 0 ) { // we have an intersection and return true return true; } } // all distances have the same sign, no intersection and we return false return false; } mitk::RegEvaluationMapper2D::LocalStorage::~LocalStorage() { } mitk::RegEvaluationMapper2D::LocalStorage::LocalStorage() { m_TargetLevelWindowFilter = vtkSmartPointer::New(); m_MappedLevelWindowFilter = vtkSmartPointer::New(); m_TargetExtractFilter = vtkSmartPointer::New(); m_MappedExtractFilter = vtkSmartPointer::New(); m_mmPerPixel = nullptr; //Do as much actions as possible in here to avoid double executions. m_Plane = vtkSmartPointer::New(); //m_Texture = vtkSmartPointer::New().GetPointer(); m_Texture = vtkSmartPointer::New().GetPointer(); m_DefaultLookupTable = vtkSmartPointer::New(); m_ColorLookupTable = vtkSmartPointer::New(); m_Mapper = vtkSmartPointer::New(); m_Actor = vtkSmartPointer::New(); m_Actors = vtkSmartPointer::New(); m_Reslicer = mitk::ExtractSliceFilter::New(); m_EvaluationImage = vtkSmartPointer::New(); m_EmptyPolyData = vtkSmartPointer::New(); mitk::LookupTable::Pointer mitkLUT = mitk::LookupTable::New(); //built a default lookuptable mitkLUT->SetType(mitk::LookupTable::GRAYSCALE); m_DefaultLookupTable = mitkLUT->GetVtkLookupTable(); mitkLUT->SetType(mitk::LookupTable::JET); m_ColorLookupTable = mitkLUT->GetVtkLookupTable(); //do not repeat the texture (the image) m_Texture->RepeatOff(); //set the mapper for the actor m_Actor->SetMapper( m_Mapper ); vtkSmartPointer outlineShadowActor = vtkSmartPointer::New(); outlineShadowActor->SetMapper( m_Mapper ); m_Actors->AddPart( outlineShadowActor ); m_Actors->AddPart( m_Actor ); } diff --git a/Modules/MatchPointRegistrationUI/Qmitk/QmitkRegEvalSettingsWidget.h b/Modules/MatchPointRegistrationUI/Qmitk/QmitkRegEvalSettingsWidget.h index abbb5628ee..293db09e8c 100644 --- a/Modules/MatchPointRegistrationUI/Qmitk/QmitkRegEvalSettingsWidget.h +++ b/Modules/MatchPointRegistrationUI/Qmitk/QmitkRegEvalSettingsWidget.h @@ -1,70 +1,69 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QMITK_REG_EVAL_SETTINGS_WIDGET_H #define QMITK_REG_EVAL_SETTINGS_WIDGET_H #include #include "ui_QmitkRegEvalSettingsWidget.h" #include #include /** * \class QmitkRegEvalSettingsWidget * \brief Widget that views the information and profile of an algorithm stored in an DLLInfo object. */ class MITKMATCHPOINTREGISTRATIONUI_EXPORT QmitkRegEvalSettingsWidget : public QWidget, private Ui::QmitkRegEvalSettingsWidget { Q_OBJECT public: QmitkRegEvalSettingsWidget(QWidget *parent = nullptr); /** * Configures the passed settings according to the current state of the * widget. - * \param pointer to a instance based on QmitkMappingJobSettings. * \pre settings must point to a valid instance.. */ void ConfigureControls(); public Q_SLOTS: /** * \brief Slot that can be used to set the node that should be configured by the widget.*/ void SetNode(mitk::DataNode *node); signals: void SettingsChanged(mitk::DataNode *node); protected Q_SLOTS: void OnComboStyleChanged(int); void OnBlend50Pushed(); void OnBlendTargetPushed(); void OnBlendMovingPushed(); void OnBlendTogglePushed(); void OnSlideBlendChanged(int); void OnSpinBlendChanged(int); void OnSpinCheckerChanged(int); void OnWipeStyleChanged(); void OnContourStyleChanged(); private: mitk::DataNode::Pointer m_selectedEvalNode; bool m_internalBlendUpdate; bool m_internalUpdate; }; #endif // QmitkRegEvalSettingsWidget_H diff --git a/Modules/ModelFit/src/Common/mitkModelFitCmdAppsHelper.cpp b/Modules/ModelFit/src/Common/mitkModelFitCmdAppsHelper.cpp index 2dc1760558..31e2352642 100644 --- a/Modules/ModelFit/src/Common/mitkModelFitCmdAppsHelper.cpp +++ b/Modules/ModelFit/src/Common/mitkModelFitCmdAppsHelper.cpp @@ -1,120 +1,120 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 std::string sanitizeString(const std::string& path) { auto result = path; std::string illegalChars = "\\/:?\"<>|%* "; for (auto &c : result) { bool found = illegalChars.find(c) != std::string::npos; if (found){ c = '_'; } } return result; } MITKMODELFIT_EXPORT std::string mitk::generateModelFitResultImagePath(const std::string& outputPathTemplate, const std::string& parameterName) { std::string ext = ::itksys::SystemTools::GetFilenameLastExtension(outputPathTemplate); std::string dir = itksys::SystemTools::GetFilenamePath(outputPathTemplate); dir = itksys::SystemTools::ConvertToOutputPath(dir); std::string rootName = itksys::SystemTools::GetFilenameWithoutLastExtension(outputPathTemplate); std::string fileName = rootName + "_" + sanitizeString(parameterName) + ext; std::string fullOutPath = itksys::SystemTools::ConvertToOutputPath(dir + "/" + fileName); return fullOutPath; } std::string convertParameterTypeToStr(mitk::modelFit::Parameter::Type type) { switch (type) { case mitk::modelFit::Parameter::ParameterType: return "parameter"; case mitk::modelFit::Parameter::DerivedType: return "derived"; case mitk::modelFit::Parameter::CriterionType: return "criterion"; case mitk::modelFit::Parameter::EvaluationType: return "evaluation"; default: return "unkown"; } } MITKMODELFIT_EXPORT void mitk::storeModelFitResultImage(const std::string& outputPathTemplate, const std::string& parameterName, mitk::Image* image, mitk::modelFit::Parameter::Type nodeType, const mitk::modelFit::ModelFitInfo* modelFitInfo) { mitk::modelFit::SetModelFitDataProperties(image, parameterName, nodeType, modelFitInfo); storeParameterResultImage(outputPathTemplate, parameterName, image, nodeType); } MITKMODELFIT_EXPORT void mitk::storeParameterResultImage(const std::string& outputPathTemplate, const std::string& parameterName, mitk::Image* image, mitk::modelFit::Parameter::Type parameterType) { std::string fullOutPath = generateModelFitResultImagePath(outputPathTemplate, parameterName); mitk::IOUtil::Save(image, fullOutPath); std::cout << "Store result " << convertParameterTypeToStr(parameterType) << ": " << parameterName << " -> " << fullOutPath << std::endl; } MITKMODELFIT_EXPORT void mitk::storeModelFitGeneratorResults(const std::string& outputPathTemplate, mitk::ParameterFitImageGeneratorBase* generator, const mitk::modelFit::ModelFitInfo* fitSession) { if (generator) { - for (auto imageIterator : generator->GetParameterImages()) + for (const auto &imageIterator : generator->GetParameterImages()) { storeModelFitResultImage(outputPathTemplate, imageIterator.first, imageIterator.second, mitk::modelFit::Parameter::ParameterType, fitSession); } - for (auto imageIterator : generator->GetDerivedParameterImages()) + for (const auto &imageIterator : generator->GetDerivedParameterImages()) { storeModelFitResultImage(outputPathTemplate, imageIterator.first, imageIterator.second, mitk::modelFit::Parameter::DerivedType, fitSession); } - for (auto imageIterator : generator->GetCriterionImages()) + for (const auto &imageIterator : generator->GetCriterionImages()) { storeModelFitResultImage(outputPathTemplate, imageIterator.first, imageIterator.second, mitk::modelFit::Parameter::CriterionType, fitSession); } - for (auto imageIterator : generator->GetEvaluationParameterImages()) + for (const auto &imageIterator : generator->GetEvaluationParameterImages()) { storeModelFitResultImage(outputPathTemplate, imageIterator.first, imageIterator.second, mitk::modelFit::Parameter::EvaluationType, fitSession); } } } MITKMODELFIT_EXPORT void mitk::previewModelFitGeneratorResults(const std::string& outputPathTemplate, mitk::ParameterFitImageGeneratorBase* generator) { if (generator) { - for (auto aName : generator->GetParameterNames()) + for (const auto &aName : generator->GetParameterNames()) { std::cout << "Store result " << convertParameterTypeToStr(modelFit::Parameter::ParameterType) << ": " << aName << " -> " << generateModelFitResultImagePath(outputPathTemplate, aName) << std::endl; } - for (auto aName : generator->GetDerivedParameterNames()) + for (const auto &aName : generator->GetDerivedParameterNames()) { std::cout << "Store result " << convertParameterTypeToStr(modelFit::Parameter::DerivedType) << ": " << aName << " -> " << generateModelFitResultImagePath(outputPathTemplate, aName) << std::endl; } - for (auto aName : generator->GetCriterionNames()) + for (const auto &aName : generator->GetCriterionNames()) { std::cout << "Store result " << convertParameterTypeToStr(modelFit::Parameter::CriterionType) << ": " << aName << " -> " << generateModelFitResultImagePath(outputPathTemplate, aName) << std::endl; } - for (auto aName : generator->GetEvaluationParameterNames()) + for (const auto &aName : generator->GetEvaluationParameterNames()) { std::cout << "Store result " << convertParameterTypeToStr(modelFit::Parameter::EvaluationType) << ": " << aName << " -> " << generateModelFitResultImagePath(outputPathTemplate, aName) << std::endl; } std::cout << "Preview done." << std::endl; } } diff --git a/Modules/ModelFitUI/Qmitk/QmitkFitPlotDataModel.cpp b/Modules/ModelFitUI/Qmitk/QmitkFitPlotDataModel.cpp index 6c0e0e2b86..b405653fad 100644 --- a/Modules/ModelFitUI/Qmitk/QmitkFitPlotDataModel.cpp +++ b/Modules/ModelFitUI/Qmitk/QmitkFitPlotDataModel.cpp @@ -1,280 +1,280 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkExceptionMacro.h" #include "QmitkFitPlotDataModel.h" QmitkFitPlotDataModel:: QmitkFitPlotDataModel(QObject* parent) : QAbstractTableModel(parent) { } const mitk::ModelFitPlotData* QmitkFitPlotDataModel:: GetPlotData() const { return &m_PlotData; }; void QmitkFitPlotDataModel:: SetPlotData(const mitk::ModelFitPlotData* data) { emit beginResetModel(); m_PlotData = *data; emit endResetModel(); }; const std::string& QmitkFitPlotDataModel:: GetXName() const { return m_XName; }; void QmitkFitPlotDataModel:: SetXName(const std::string& xName) { emit beginResetModel(); m_XName = xName; emit endResetModel(); }; int QmitkFitPlotDataModel:: rowCount(const QModelIndex&) const { //we assume that all plots have the same nr of values (except the interpolated signal which will be ignored). //Thus we have only to check one plot. Reason: One fit is always derived from one input data and therefore //all derived data should have the same size. auto plot = GetCurveByColumn(0); if (plot.second) { return plot.second->GetValues().size(); } return 0; } std::pair QmitkFitPlotDataModel::GetPositionalCurvePoint(const mitk::PlotDataCurve* curve) const { for (auto collection : this->m_PlotData.positionalPlots) { - for (auto aCurve : collection.second.second->CastToSTLContainer()) + for (const auto &aCurve : collection.second.second->CastToSTLContainer()) { if (curve == aCurve.second.GetPointer()) { return std::make_pair(true, collection); } } } return std::make_pair(false, mitk::ModelFitPlotData::PositionalCollectionMap::value_type()); } int QmitkFitPlotDataModel:: columnCount(const QModelIndex& parent) const { if (parent.isValid()) { return 0; } else { auto size = this->m_PlotData.currentPositionPlots->size() + this->m_PlotData.staticPlots->size(); if (mitk::ModelFitPlotData::GetInterpolatedSignalPlot(this->m_PlotData.currentPositionPlots)) { //don't take the interpolated signal into account size -= 1; } if (mitk::ModelFitPlotData::GetInterpolatedSignalPlot(this->m_PlotData.staticPlots)) { //don't take the interpolated signal into account size -= 1; } for (const auto& coll : this->m_PlotData.positionalPlots) { size += coll.second.second->size(); if (mitk::ModelFitPlotData::GetInterpolatedSignalPlot(coll.second.second)) { //don't take the interpolated signal into account size -= 1; } } return size+2; } } bool GetCurveFromCollection(const mitk::PlotDataCurveCollection* collection, std::size_t index, std::pair& finding, std::size_t& actualCount) { actualCount = 0; for (const auto& iter : *(collection)) { if (iter.first != mitk::MODEL_FIT_PLOT_INTERPOLATED_SIGNAL_NAME()) { if (actualCount == index) { finding = std::make_pair(iter.first, iter.second.GetPointer()); return true; } ++actualCount; } } return false; } std::pair QmitkFitPlotDataModel:: GetCurveByColumn(int col) const { if (col == 1) { /*the x axis is needed so just get the first signal.*/ col = 0; } else if (col > 1) { /*a normal signal is requested, correct the column index to ignore the timestep and timepoint column*/ col -= 2; } std::pair finding; std::size_t actualCount; if (GetCurveFromCollection(this->m_PlotData.currentPositionPlots.GetPointer(), col, finding, actualCount)) { return finding; } col -= actualCount; - for (auto collection : this->m_PlotData.positionalPlots) + for (const auto &collection : this->m_PlotData.positionalPlots) { if (GetCurveFromCollection(collection.second.second.GetPointer(), col, finding, actualCount)) { return finding; } col -= actualCount; } GetCurveFromCollection(this->m_PlotData.staticPlots.GetPointer(), col, finding, actualCount); return finding; }; QVariant QmitkFitPlotDataModel:: data(const QModelIndex& index, int role) const { if (!index.isValid()) { return QVariant(); } QVariant result; if (index.column() == 0) { if (role == Qt::DisplayRole || role == Qt::EditRole) { result = QVariant(QString::number(index.row())); } else if (role == Qt::ToolTipRole) { result = QVariant("Index in plot."); } } else if (index.column() == 1) { auto finding = GetCurveByColumn(index.column()); if (role == Qt::DisplayRole || role == Qt::EditRole) { if (finding.second && index.row() < static_cast(finding.second->GetValues().size())) { result = QVariant(QString::number(finding.second->GetValues()[index.row()].first)); } } else if (role == Qt::ToolTipRole) { result = QVariant("x value in plot."); } } else { auto finding = GetCurveByColumn(index.column()); if (role == Qt::DisplayRole || role == Qt::EditRole) { if (finding.second && index.row() < static_cast(finding.second->GetValues().size())) { result = QVariant(QString::number(finding.second->GetValues()[index.row()].second)); } } else if (role == Qt::ToolTipRole) { result = QVariant("This is a value of the respective curve."); } } return result; } Qt::ItemFlags QmitkFitPlotDataModel:: flags(const QModelIndex& index) const { Qt::ItemFlags flags = QAbstractItemModel::flags(index); return flags; } QVariant QmitkFitPlotDataModel:: headerData(int section, Qt::Orientation orientation, int role) const { if ((Qt::DisplayRole == role) && (Qt::Horizontal == orientation)) { if (section == 0) { return QVariant("#"); } else if (section == 1) { return QVariant(QString::fromStdString(m_XName)); } else { auto finding = GetCurveByColumn(section); auto pointFinding = GetPositionalCurvePoint(finding.second); std::ostringstream nameStrm; nameStrm.imbue(std::locale("C")); nameStrm << finding.first; if (pointFinding.first) { nameStrm << " @ " << mitk::ModelFitPlotData::GetPositionalCollectionName(pointFinding.second); } return QVariant(QString::fromStdString(nameStrm.str())); } } return QVariant(); } bool QmitkFitPlotDataModel:: setData(const QModelIndex&, const QVariant&, int) { return false; }; diff --git a/Modules/Multilabel/Testing/mitkLabelSetImageTest.cpp b/Modules/Multilabel/Testing/mitkLabelSetImageTest.cpp index 8637823ce0..97516291b0 100644 --- a/Modules/Multilabel/Testing/mitkLabelSetImageTest.cpp +++ b/Modules/Multilabel/Testing/mitkLabelSetImageTest.cpp @@ -1,435 +1,442 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include #include #include class mitkLabelSetImageTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkLabelSetImageTestSuite); MITK_TEST(TestInitialize); MITK_TEST(TestAddLayer); MITK_TEST(TestGetActiveLabelSet); MITK_TEST(TestGetActiveLabel); MITK_TEST(TestInitializeByLabeledImage); MITK_TEST(TestGetLabelSet); MITK_TEST(TestGetLabel); MITK_TEST(TestSetExteriorLabel); MITK_TEST(TestGetTotalNumberOfLabels); MITK_TEST(TestExistsLabel); MITK_TEST(TestExistsLabelSet); MITK_TEST(TestSetActiveLayer); MITK_TEST(TestRemoveLayer); MITK_TEST(TestRemoveLabels); MITK_TEST(TestMergeLabel); CPPUNIT_TEST_SUITE_END(); private: mitk::LabelSetImage::Pointer m_LabelSetImage; public: void setUp() override { // Create a new labelset image m_LabelSetImage = mitk::LabelSetImage::New(); mitk::Image::Pointer regularImage = mitk::Image::New(); unsigned int dimensions[3] = { 96, 128, 52 }; regularImage->Initialize(mitk::MakeScalarPixelType(), 3, dimensions); m_LabelSetImage->Initialize(regularImage); } void tearDown() override { // Delete LabelSetImage m_LabelSetImage = nullptr; } void TestInitialize() { // LabelSet image should always has the pixel type mitk::Label::PixelType CPPUNIT_ASSERT_MESSAGE("LabelSetImage has wrong pixel type", m_LabelSetImage->GetPixelType() == mitk::MakeScalarPixelType()); mitk::Image::Pointer regularImage = mitk::Image::New(); unsigned int dimensions[3] = { 96, 128, 52 }; regularImage->Initialize(mitk::MakeScalarPixelType(), 3, dimensions); mitk::BaseGeometry::Pointer regularImageGeo = regularImage->GetGeometry(); mitk::BaseGeometry::Pointer labelImageGeo = m_LabelSetImage->GetGeometry(); MITK_ASSERT_EQUAL(labelImageGeo, regularImageGeo, "LabelSetImage has wrong geometry"); // By default one layer containing the exterior label should be added CPPUNIT_ASSERT_MESSAGE("Image was not correctly initialized - number of layers is not one", m_LabelSetImage->GetNumberOfLayers() == 1); CPPUNIT_ASSERT_MESSAGE("Image was not correctly initialized - active layer has wrong ID", m_LabelSetImage->GetActiveLayer() == 0); CPPUNIT_ASSERT_MESSAGE("Image was not correctly initialized - active label is not the exterior label", m_LabelSetImage->GetActiveLabel()->GetValue() == 0); } void TestAddLayer() { CPPUNIT_ASSERT_MESSAGE("Number of layers is not zero", m_LabelSetImage->GetNumberOfLayers() == 1); m_LabelSetImage->AddLayer(); CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - number of layers is not one", m_LabelSetImage->GetNumberOfLayers() == 2); CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - active layer has wrong ID", m_LabelSetImage->GetActiveLayer() == 1); CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - active label is not the exterior label", m_LabelSetImage->GetActiveLabel()->GetValue() == 0); mitk::LabelSet::Pointer newlayer = mitk::LabelSet::New(); mitk::Label::Pointer label1 = mitk::Label::New(); label1->SetName("Label1"); label1->SetValue(1); mitk::Label::Pointer label2 = mitk::Label::New(); label2->SetName("Label2"); label2->SetValue(200); newlayer->AddLabel(label1); newlayer->AddLabel(label2); newlayer->SetActiveLabel(200); unsigned int layerID = m_LabelSetImage->AddLayer(newlayer); CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - number of layers is not two", m_LabelSetImage->GetNumberOfLayers() == 3); CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - active layer has wrong ID", m_LabelSetImage->GetActiveLayer() == layerID); CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - active label is wrong", m_LabelSetImage->GetActiveLabel(layerID)->GetValue() == 200); } void TestGetActiveLabelSet() { mitk::LabelSet::Pointer newlayer = mitk::LabelSet::New(); mitk::Label::Pointer label1 = mitk::Label::New(); label1->SetName("Label1"); label1->SetValue(1); mitk::Label::Pointer label2 = mitk::Label::New(); label2->SetName("Label2"); label2->SetValue(200); newlayer->AddLabel(label1); newlayer->AddLabel(label2); newlayer->SetActiveLabel(200); unsigned int layerID = m_LabelSetImage->AddLayer(newlayer); mitk::LabelSet::Pointer activeLayer = m_LabelSetImage->GetActiveLabelSet(); CPPUNIT_ASSERT_MESSAGE("Wrong layer ID was returned", layerID == 1); CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(*newlayer, *activeLayer, 0.00001, true)); + + mitk::LabelSet::ConstPointer constActiveLayer = const_cast(m_LabelSetImage.GetPointer())->GetActiveLabelSet(); + CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(*newlayer, *constActiveLayer, 0.00001, true)); } void TestGetActiveLabel() { mitk::Label::Pointer label1 = mitk::Label::New(); label1->SetName("Label1"); mitk::Label::PixelType value1 = 1; label1->SetValue(value1); mitk::Label::Pointer label2 = mitk::Label::New(); label2->SetName("Label2"); mitk::Label::PixelType value2 = 200; label2->SetValue(value2); m_LabelSetImage->GetActiveLabelSet()->AddLabel(label1); m_LabelSetImage->GetActiveLabelSet()->AddLabel(label2); m_LabelSetImage->GetActiveLabelSet()->SetActiveLabel(1); CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - active label is wrong", m_LabelSetImage->GetActiveLabel()->GetValue() == value1); m_LabelSetImage->GetActiveLabelSet()->SetActiveLabel(value2); CPPUNIT_ASSERT_MESSAGE("Layer was not added correctly to image - active label is wrong", m_LabelSetImage->GetActiveLabel()->GetValue() == value2); + + CPPUNIT_ASSERT_MESSAGE("Active Label was not correctly retreived with const getter", + const_cast(m_LabelSetImage.GetPointer())->GetActiveLabel()->GetValue() == value2); + } void TestInitializeByLabeledImage() { mitk::Image::Pointer image = mitk::IOUtil::Load(GetTestDataFilePath("Multilabel/LabelSetTestInitializeImage.nrrd")); m_LabelSetImage->InitializeByLabeledImage(image); CPPUNIT_ASSERT_MESSAGE("Image - number of labels is not 6", m_LabelSetImage->GetNumberOfLabels() == 6); } void TestGetLabelSet() { // Test get non existing lset mitk::LabelSet::ConstPointer lset = m_LabelSetImage->GetLabelSet(10000); CPPUNIT_ASSERT_MESSAGE("Non existing labelset is not nullptr", lset.IsNull()); lset = m_LabelSetImage->GetLabelSet(0); CPPUNIT_ASSERT_MESSAGE("Existing labelset is nullptr", lset.IsNotNull()); } void TestGetLabel() { mitk::Label::Pointer label1 = mitk::Label::New(); label1->SetName("Label1"); mitk::Label::PixelType value1 = 1; label1->SetValue(value1); mitk::Label::Pointer label2 = mitk::Label::New(); label2->SetName("Label2"); mitk::Label::PixelType value2 = 200; label2->SetValue(value2); m_LabelSetImage->GetActiveLabelSet()->AddLabel(label1); m_LabelSetImage->AddLayer(); m_LabelSetImage->GetLabelSet(1)->AddLabel(label2); CPPUNIT_ASSERT_MESSAGE("Wrong label retrieved for active layer", mitk::Equal(*m_LabelSetImage->GetLabel(1), *label1, 0.0001, true)); CPPUNIT_ASSERT_MESSAGE("Wrong label retrieved for layer 1", mitk::Equal(*m_LabelSetImage->GetLabel(200, 1), *label2, 0.0001, true)); // Try to get a non existing label mitk::Label *label3 = m_LabelSetImage->GetLabel(1000); CPPUNIT_ASSERT_MESSAGE("Non existing label should be nullptr", label3 == nullptr); // Try to get a label from a non existing layer label3 = m_LabelSetImage->GetLabel(200, 1000); CPPUNIT_ASSERT_MESSAGE("Label from non existing layer should be nullptr", label3 == nullptr); } void TestSetExteriorLabel() { mitk::Label::Pointer exteriorLabel = mitk::Label::New(); exteriorLabel->SetName("MyExteriorSpecialLabel"); mitk::Label::PixelType value1 = 10000; exteriorLabel->SetValue(value1); m_LabelSetImage->SetExteriorLabel(exteriorLabel); CPPUNIT_ASSERT_MESSAGE("Wrong label retrieved for layer 1", mitk::Equal(*m_LabelSetImage->GetExteriorLabel(), *exteriorLabel, 0.0001, true)); // Exterior label should be set automatically for each new layer m_LabelSetImage->AddLayer(); CPPUNIT_ASSERT_MESSAGE("Wrong label retrieved for layer 1", mitk::Equal(*m_LabelSetImage->GetLabel(10000, 1), *exteriorLabel, 0.0001, true)); } void TestGetTotalNumberOfLabels() { mitk::Label::Pointer label1 = mitk::Label::New(); label1->SetName("Label1"); mitk::Label::PixelType value1 = 1; label1->SetValue(value1); mitk::Label::Pointer label2 = mitk::Label::New(); label2->SetName("Label2"); mitk::Label::PixelType value2 = 200; label2->SetValue(value2); m_LabelSetImage->GetActiveLabelSet()->AddLabel(label1); m_LabelSetImage->AddLayer(); m_LabelSetImage->GetLabelSet(1)->AddLabel(label2); CPPUNIT_ASSERT_MESSAGE( "Wrong total number of labels", m_LabelSetImage->GetTotalNumberOfLabels() == 4); // added 2 labels + 2 exterior default labels } void TestExistsLabel() { mitk::Label::Pointer label = mitk::Label::New(); label->SetName("Label2"); mitk::Label::PixelType value = 200; label->SetValue(value); m_LabelSetImage->AddLayer(); m_LabelSetImage->GetLabelSet(1)->AddLabel(label); m_LabelSetImage->SetActiveLayer(0); CPPUNIT_ASSERT_MESSAGE("Existing label was not found", m_LabelSetImage->ExistLabel(value) == true); CPPUNIT_ASSERT_MESSAGE("Non existing label was found", m_LabelSetImage->ExistLabel(10000) == false); } void TestExistsLabelSet() { // Cache active layer mitk::LabelSet::ConstPointer activeLayer = m_LabelSetImage->GetActiveLabelSet(); // Add new layer mitk::LabelSet::Pointer newlayer = mitk::LabelSet::New(); mitk::Label::Pointer label1 = mitk::Label::New(); label1->SetName("Label1"); label1->SetValue(1); mitk::Label::Pointer label2 = mitk::Label::New(); label2->SetName("Label2"); label2->SetValue(200); newlayer->AddLabel(label1); newlayer->AddLabel(label2); newlayer->SetActiveLabel(200); m_LabelSetImage->AddLayer(newlayer); CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(0) == true); CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(1) == true); CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(20) == false); } void TestSetActiveLayer() { // Cache active layer mitk::LabelSet::ConstPointer activeLayer = m_LabelSetImage->GetActiveLabelSet(); // Add new layer mitk::LabelSet::Pointer newlayer = mitk::LabelSet::New(); mitk::Label::Pointer label1 = mitk::Label::New(); label1->SetName("Label1"); label1->SetValue(1); mitk::Label::Pointer label2 = mitk::Label::New(); label2->SetName("Label2"); label2->SetValue(200); newlayer->AddLabel(label1); newlayer->AddLabel(label2); newlayer->SetActiveLabel(200); unsigned int layerID = m_LabelSetImage->AddLayer(newlayer); // Set initial layer as active layer m_LabelSetImage->SetActiveLayer(0); CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(*activeLayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true)); // Set previously added layer as active layer m_LabelSetImage->SetActiveLayer(layerID); CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(*newlayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true)); // Set a non existing layer as active layer - nothing should change m_LabelSetImage->SetActiveLayer(10000); CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(*newlayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true)); } void TestRemoveLayer() { // Cache active layer mitk::LabelSet::ConstPointer activeLayer = m_LabelSetImage->GetActiveLabelSet(); // Add new layers m_LabelSetImage->AddLayer(); mitk::LabelSet::Pointer newlayer = mitk::LabelSet::New(); mitk::Label::Pointer label1 = mitk::Label::New(); label1->SetName("Label1"); label1->SetValue(1); mitk::Label::Pointer label2 = mitk::Label::New(); label2->SetName("Label2"); label2->SetValue(200); newlayer->AddLabel(label1); newlayer->AddLabel(label2); newlayer->SetActiveLabel(200); m_LabelSetImage->AddLayer(newlayer); CPPUNIT_ASSERT_MESSAGE("Wrong active labelset returned", mitk::Equal(*newlayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true)); m_LabelSetImage->RemoveLayer(); CPPUNIT_ASSERT_MESSAGE("Wrong number of layers, after a layer was removed", m_LabelSetImage->GetNumberOfLayers() == 2); CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(2) == false); CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(1) == true); CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(0) == true); m_LabelSetImage->RemoveLayer(); CPPUNIT_ASSERT_MESSAGE("Wrong number of layers, after a layer was removed", m_LabelSetImage->GetNumberOfLayers() == 1); CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(1) == false); CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(0) == true); CPPUNIT_ASSERT_MESSAGE("Wrong active layer", mitk::Equal(*activeLayer, *m_LabelSetImage->GetActiveLabelSet(), 0.00001, true)); m_LabelSetImage->RemoveLayer(); CPPUNIT_ASSERT_MESSAGE("Wrong number of layers, after a layer was removed", m_LabelSetImage->GetNumberOfLayers() == 0); CPPUNIT_ASSERT_MESSAGE("Check for existing layer failed", m_LabelSetImage->ExistLabelSet(0) == false); CPPUNIT_ASSERT_MESSAGE("Active layers is not nullptr although all layer have been removed", m_LabelSetImage->GetActiveLabelSet() == nullptr); } void TestRemoveLabels() { mitk::Image::Pointer image = mitk::IOUtil::Load(GetTestDataFilePath("Multilabel/LabelSetTestInitializeImage.nrrd")); m_LabelSetImage->InitializeByLabeledImage(image); CPPUNIT_ASSERT_MESSAGE("Image - number of labels is not 6", m_LabelSetImage->GetNumberOfLabels() == 6); // 2ndMin because of the exterior label = 0 CPPUNIT_ASSERT_MESSAGE("Labels with value 1 and 3 was not remove from the image", m_LabelSetImage->GetStatistics()->GetScalarValue2ndMin() == 1); CPPUNIT_ASSERT_MESSAGE("Label with value 7 was not remove from the image", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 7); CPPUNIT_ASSERT_MESSAGE("Label with ID 3 does not exists after initialization", m_LabelSetImage->ExistLabel(3) == true); CPPUNIT_ASSERT_MESSAGE("Label with ID 7 does not exists after initialization", m_LabelSetImage->ExistLabel(7) == true); std::vector labelsToBeRemoved; labelsToBeRemoved.push_back(1); labelsToBeRemoved.push_back(3); labelsToBeRemoved.push_back(7); m_LabelSetImage->RemoveLabels(labelsToBeRemoved); CPPUNIT_ASSERT_MESSAGE("Wrong number of labels after some have been removed", m_LabelSetImage->GetNumberOfLabels() == 3); // Values within the image are 0, 1, 3, 5, 6, 7 - New Min/Max value should be 5 / 6 // 2ndMin because of the exterior label = 0 CPPUNIT_ASSERT_MESSAGE("Labels with value 1 and 3 was not remove from the image", m_LabelSetImage->GetStatistics()->GetScalarValue2ndMin() == 5); CPPUNIT_ASSERT_MESSAGE("Label with value 7 was not remove from the image", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 6); } void TestMergeLabel() { mitk::Image::Pointer image = mitk::IOUtil::Load(GetTestDataFilePath("Multilabel/LabelSetTestInitializeImage.nrrd")); m_LabelSetImage = nullptr; m_LabelSetImage = mitk::LabelSetImage::New(); m_LabelSetImage->InitializeByLabeledImage(image); CPPUNIT_ASSERT_MESSAGE("Image - number of labels is not 6", m_LabelSetImage->GetNumberOfLabels() == 6); // 2ndMin because of the exterior label = 0 CPPUNIT_ASSERT_MESSAGE("Wrong MIN value", m_LabelSetImage->GetStatistics()->GetScalarValueMin() == 0); CPPUNIT_ASSERT_MESSAGE("Wrong MAX value", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 7); m_LabelSetImage->GetActiveLabelSet()->SetActiveLabel(6); // Merge label 7 with label 0. Result should be that label 7 is not present any more m_LabelSetImage->MergeLabel(6, 7); CPPUNIT_ASSERT_MESSAGE("Label with value 7 was not remove from the image", m_LabelSetImage->GetStatistics()->GetScalarValueMax() == 6); m_LabelSetImage->GetStatistics()->GetScalarValue2ndMax(); // Count all pixels with value 7 = 823 // Count all pixels with value 6 = 507 // Check if merge label has 507 + 823 = 1330 pixels CPPUNIT_ASSERT_MESSAGE("Label with value 7 was not remove from the image", m_LabelSetImage->GetStatistics()->GetCountOfMaxValuedVoxels() == 1330); } }; MITK_TEST_SUITE_REGISTRATION(mitkLabelSetImage) diff --git a/Modules/Multilabel/autoload/DICOMSegIO/mitkDICOMSegmentationIO.cpp b/Modules/Multilabel/autoload/DICOMSegIO/mitkDICOMSegmentationIO.cpp index a8caa81a5f..ec08b5baf2 100644 --- a/Modules/Multilabel/autoload/DICOMSegIO/mitkDICOMSegmentationIO.cpp +++ b/Modules/Multilabel/autoload/DICOMSegIO/mitkDICOMSegmentationIO.cpp @@ -1,704 +1,704 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 __mitkDICOMSegmentationIO__cpp #define __mitkDICOMSegmentationIO__cpp #include "mitkDICOMSegmentationIO.h" #include "mitkDICOMSegIOMimeTypes.h" #include "mitkDICOMSegmentationConstants.h" #include #include #include #include #include #include #include #include // itk #include // dcmqi #include // us #include #include namespace mitk { DICOMSegmentationIO::DICOMSegmentationIO() : AbstractFileIO(LabelSetImage::GetStaticNameOfClass(), mitk::MitkDICOMSEGIOMimeTypes::DICOMSEG_MIMETYPE_NAME(), "DICOM Segmentation") { AbstractFileWriter::SetRanking(10); AbstractFileReader::SetRanking(10); this->RegisterService(); } std::vector DICOMSegmentationIO::GetDICOMTagsOfInterest() { std::vector result; result.emplace_back(DICOMSegmentationConstants::SEGMENT_SEQUENCE_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENT_NUMBER_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENT_LABEL_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENT_ALGORITHM_TYPE_PATH()); result.emplace_back(DICOMSegmentationConstants::ANATOMIC_REGION_SEQUENCE_PATH()); result.emplace_back(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_VALUE_PATH()); result.emplace_back(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_SCHEME_PATH()); result.emplace_back(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_MEANING_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENTED_PROPERTY_CATEGORY_SEQUENCE_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_VALUE_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_SCHEME_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_MEANING_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENTED_PROPERTY_TYPE_SEQUENCE_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_VALUE_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_SCHEME_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_MEANING_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENTED_PROPERTY_MODIFIER_SEQUENCE_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_VALUE_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_SCHEME_PATH()); result.emplace_back(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_MEANING_PATH()); return result; } IFileIO::ConfidenceLevel DICOMSegmentationIO::GetWriterConfidenceLevel() const { if (AbstractFileIO::GetWriterConfidenceLevel() == Unsupported) return Unsupported; // Check if the input file is a segmentation const LabelSetImage *input = static_cast(this->GetInput()); if (input) { if ((input->GetDimension() != 3)) { MITK_INFO << "DICOM segmentation writer is tested only with 3D images, sorry."; return Unsupported; } // Check if input file has dicom information for the referenced image (original DICOM image, e.g. CT) Still necessary, see write() mitk::StringLookupTableProperty::Pointer dicomFilesProp = dynamic_cast(input->GetProperty("referenceFiles").GetPointer()); if (dicomFilesProp.IsNotNull()) return Supported; } return Unsupported; } void DICOMSegmentationIO::Write() { ValidateOutputLocation(); mitk::LocaleSwitch localeSwitch("C"); LocalFile localFile(this); const std::string path = localFile.GetFileName(); auto input = dynamic_cast(this->GetInput()); if (input == nullptr) mitkThrow() << "Cannot write non-image data"; // Get DICOM information from referenced image vector> dcmDatasetsSourceImage; std::unique_ptr readFileFormat(new DcmFileFormat()); try { // TODO: Generate dcmdataset witk DICOM tags from property list; ATM the source are the filepaths from the // property list mitk::StringLookupTableProperty::Pointer filesProp = dynamic_cast(input->GetProperty("referenceFiles").GetPointer()); if (filesProp.IsNull()) { mitkThrow() << "No property with dicom file path."; return; } StringLookupTable filesLut = filesProp->GetValue(); const StringLookupTable::LookupTableType &lookUpTableMap = filesLut.GetLookupTable(); - for (auto it : lookUpTableMap) + for (const auto &it : lookUpTableMap) { const char *fileName = (it.second).c_str(); if (readFileFormat->loadFile(fileName, EXS_Unknown).good()) { std::unique_ptr readDCMDataset(readFileFormat->getAndRemoveDataset()); dcmDatasetsSourceImage.push_back(std::move(readDCMDataset)); } } } catch (const std::exception &e) { MITK_ERROR << "An error occurred while getting the dicom informations: " << e.what() << endl; return; } // Iterate over all layers. For each a dcm file will be generated for (unsigned int layer = 0; layer < input->GetNumberOfLayers(); ++layer) { vector segmentations; try { // Hack: Remove the const attribute to switch between the layer images. Normally you could get the different // layer images by input->GetLayerImage(layer) mitk::LabelSetImage *mitkLayerImage = const_cast(input); mitkLayerImage->SetActiveLayer(layer); // Cast mitk layer image to itk ImageToItk::Pointer imageToItkFilter = ImageToItk::New(); imageToItkFilter->SetInput(mitkLayerImage); // Cast from original itk type to dcmqi input itk image type typedef itk::CastImageFilter castItkImageFilterType; castItkImageFilterType::Pointer castFilter = castItkImageFilterType::New(); castFilter->SetInput(imageToItkFilter->GetOutput()); castFilter->Update(); itkInternalImageType::Pointer itkLabelImage = castFilter->GetOutput(); itkLabelImage->DisconnectPipeline(); // Iterate over all labels. For each label a segmentation image will be created const LabelSet *labelSet = input->GetLabelSet(layer); auto labelIter = labelSet->IteratorConstBegin(); // Ignore background label ++labelIter; for (; labelIter != labelSet->IteratorConstEnd(); ++labelIter) { // Thresold over the image with the given label value itk::ThresholdImageFilter::Pointer thresholdFilter = itk::ThresholdImageFilter::New(); thresholdFilter->SetInput(itkLabelImage); thresholdFilter->ThresholdOutside(labelIter->first, labelIter->first); thresholdFilter->SetOutsideValue(0); thresholdFilter->Update(); itkInternalImageType::Pointer segmentImage = thresholdFilter->GetOutput(); segmentImage->DisconnectPipeline(); segmentations.push_back(segmentImage); } } catch (const itk::ExceptionObject &e) { MITK_ERROR << e.GetDescription() << endl; return; } // Create segmentation meta information const std::string tmpMetaInfoFile = this->CreateMetaDataJsonFile(layer); MITK_INFO << "Writing image: " << path << std::endl; try { //TODO is there a better way? Interface expects a vector of raw pointer. vector rawVecDataset; for (const auto& dcmDataSet : dcmDatasetsSourceImage) rawVecDataset.push_back(dcmDataSet.get()); // Convert itk segmentation images to dicom image std::unique_ptr converter = std::make_unique(); std::unique_ptr result(converter->itkimage2dcmSegmentation(rawVecDataset, segmentations, tmpMetaInfoFile, false)); // Write dicom file DcmFileFormat dcmFileFormat(result.get()); std::string filePath = path.substr(0, path.find_last_of(".")); // If there is more than one layer, we have to write more than 1 dicom file if (input->GetNumberOfLayers() != 1) filePath = filePath + std::to_string(layer) + ".dcm"; else filePath = filePath + ".dcm"; dcmFileFormat.saveFile(filePath.c_str(), EXS_LittleEndianExplicit); } catch (const std::exception &e) { MITK_ERROR << "An error occurred during writing the DICOM Seg: " << e.what() << endl; return; } } // Write a dcm file for the next layer } IFileIO::ConfidenceLevel DICOMSegmentationIO::GetReaderConfidenceLevel() const { if (AbstractFileIO::GetReaderConfidenceLevel() == Unsupported) return Unsupported; const std::string fileName = this->GetLocalFileName(); DcmFileFormat dcmFileFormat; OFCondition status = dcmFileFormat.loadFile(fileName.c_str()); if (status.bad()) return Unsupported; OFString modality; if (dcmFileFormat.getDataset()->findAndGetOFString(DCM_Modality, modality).good()) { if (modality.compare("SEG") == 0) return Supported; else return Unsupported; } return Unsupported; } std::vector DICOMSegmentationIO::DoRead() { mitk::LocaleSwitch localeSwitch("C"); LabelSetImage::Pointer labelSetImage; std::vector result; const std::string path = this->GetLocalFileName(); MITK_INFO << "loading " << path << std::endl; if (path.empty()) mitkThrow() << "Empty filename in mitk::ItkImageIO "; try { // Get the dcm data set from file path DcmFileFormat dcmFileFormat; OFCondition status = dcmFileFormat.loadFile(path.c_str()); if (status.bad()) mitkThrow() << "Can't read the input file!"; DcmDataset *dataSet = dcmFileFormat.getDataset(); if (dataSet == nullptr) mitkThrow() << "Can't read data from input file!"; //=============================== dcmqi part ==================================== // Read the DICOM SEG images (segItkImages) and DICOM tags (metaInfo) std::unique_ptr converter = std::make_unique(); pair, string> dcmqiOutput = converter->dcmSegmentation2itkimage(dataSet); map segItkImages = dcmqiOutput.first; dcmqi::JSONSegmentationMetaInformationHandler metaInfo(dcmqiOutput.second.c_str()); metaInfo.read(); MITK_INFO << "Input " << metaInfo.getJSONOutputAsString(); //=============================================================================== // Get the label information from segment attributes for each itk image vector>::const_iterator segmentIter = metaInfo.segmentsAttributesMappingList.begin(); // For each itk image add a layer to the LabelSetImage output for (auto &element : segItkImages) { // Get the labeled image and cast it to mitkImage typedef itk::CastImageFilter castItkImageFilterType; castItkImageFilterType::Pointer castFilter = castItkImageFilterType::New(); castFilter->SetInput(element.second); castFilter->Update(); Image::Pointer layerImage; CastToMitkImage(castFilter->GetOutput(), layerImage); // Get pixel value of the label itkInternalImageType::ValueType segValue = 1; typedef itk::ImageRegionIterator IteratorType; // Iterate over the image to find the pixel value of the label IteratorType iter(element.second, element.second->GetLargestPossibleRegion()); iter.GoToBegin(); while (!iter.IsAtEnd()) { itkInputImageType::PixelType value = iter.Get(); if (value != 0) { segValue = value; break; } ++iter; } // Get Segment information map map segmentMap = (*segmentIter); map::const_iterator segmentMapIter = (*segmentIter).begin(); dcmqi::SegmentAttributes *segmentAttribute = (*segmentMapIter).second; OFString labelName; if (segmentAttribute->getSegmentedPropertyTypeCodeSequence() != nullptr) { segmentAttribute->getSegmentedPropertyTypeCodeSequence()->getCodeMeaning(labelName); if (segmentAttribute->getSegmentedPropertyTypeModifierCodeSequence() != nullptr) { OFString modifier; segmentAttribute->getSegmentedPropertyTypeModifierCodeSequence()->getCodeMeaning(modifier); labelName.append(" (").append(modifier).append(")"); } } else { labelName = std::to_string(segmentAttribute->getLabelID()).c_str(); if (labelName.empty()) labelName = "Unnamed"; } float tmp[3] = { 0.0, 0.0, 0.0 }; if (segmentAttribute->getRecommendedDisplayRGBValue() != nullptr) { tmp[0] = segmentAttribute->getRecommendedDisplayRGBValue()[0] / 255.0; tmp[1] = segmentAttribute->getRecommendedDisplayRGBValue()[1] / 255.0; tmp[2] = segmentAttribute->getRecommendedDisplayRGBValue()[2] / 255.0; } Label *newLabel = nullptr; // If labelSetImage do not exists (first image) if (labelSetImage.IsNull()) { // Initialize the labelSetImage with the read image labelSetImage = LabelSetImage::New(); labelSetImage->InitializeByLabeledImage(layerImage); // Already a label was generated, so set the information to this newLabel = labelSetImage->GetActiveLabel(labelSetImage->GetActiveLayer()); newLabel->SetName(labelName.c_str()); newLabel->SetColor(Color(tmp)); newLabel->SetValue(segValue); } else { // Add a new layer to the labelSetImage. Background label is set automatically labelSetImage->AddLayer(layerImage); // Add new label newLabel = new Label; newLabel->SetName(labelName.c_str()); newLabel->SetColor(Color(tmp)); newLabel->SetValue(segValue); labelSetImage->GetLabelSet(labelSetImage->GetActiveLayer())->AddLabel(newLabel); } // Add some more label properties this->SetLabelProperties(newLabel, segmentAttribute); ++segmentIter; } labelSetImage->GetLabelSet()->SetAllLabelsVisible(true); // Add some general DICOM Segmentation properties mitk::IDICOMTagsOfInterest *toiSrv = GetDicomTagsOfInterestService(); auto tagsOfInterest = toiSrv->GetTagsOfInterest(); DICOMTagPathList tagsOfInterestList; for (const auto &tag : tagsOfInterest) { tagsOfInterestList.push_back(tag.first); } mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New(); scanner->SetInputFiles({ GetInputLocation() }); scanner->AddTagPaths(tagsOfInterestList); scanner->Scan(); mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList(); if (frames.empty()) { MITK_ERROR << "Error reading the DICOM Seg file" << std::endl; return result; } auto findings = ExtractPathsOfInterest(tagsOfInterestList, frames); SetProperties(labelSetImage, findings); // Set active layer to the first layer of the labelset image if (labelSetImage->GetNumberOfLayers() > 1 && labelSetImage->GetActiveLayer() != 0) labelSetImage->SetActiveLayer(0); } catch (const std::exception &e) { MITK_ERROR << "An error occurred while reading the DICOM Seg file: " << e.what(); return result; } catch (...) { MITK_ERROR << "An error occurred in dcmqi while reading the DICOM Seg file"; return result; } result.push_back(labelSetImage.GetPointer()); return result; } const std::string mitk::DICOMSegmentationIO::CreateMetaDataJsonFile(int layer) { const mitk::LabelSetImage *image = dynamic_cast(this->GetInput()); const std::string output; dcmqi::JSONSegmentationMetaInformationHandler handler; // 1. Metadata attributes that will be listed in the resulting DICOM SEG object std::string contentCreatorName; if (!image->GetPropertyList()->GetStringProperty(GeneratePropertyNameForDICOMTag(0x0070, 0x0084).c_str(), contentCreatorName)) contentCreatorName = "MITK"; handler.setContentCreatorName(contentCreatorName); std::string clinicalTrailSeriesId; if (!image->GetPropertyList()->GetStringProperty(GeneratePropertyNameForDICOMTag(0x0012, 0x0071).c_str(), clinicalTrailSeriesId)) clinicalTrailSeriesId = "Session 1"; handler.setClinicalTrialSeriesID(clinicalTrailSeriesId); std::string clinicalTrialTimePointID; if (!image->GetPropertyList()->GetStringProperty(GeneratePropertyNameForDICOMTag(0x0012, 0x0050).c_str(), clinicalTrialTimePointID)) clinicalTrialTimePointID = "0"; handler.setClinicalTrialTimePointID(clinicalTrialTimePointID); std::string clinicalTrialCoordinatingCenterName = ""; if (!image->GetPropertyList()->GetStringProperty(GeneratePropertyNameForDICOMTag(0x0012, 0x0060).c_str(), clinicalTrialCoordinatingCenterName)) clinicalTrialCoordinatingCenterName = "Unknown"; handler.setClinicalTrialCoordinatingCenterName(clinicalTrialCoordinatingCenterName); std::string seriesDescription; if (!image->GetPropertyList()->GetStringProperty("name", seriesDescription)) seriesDescription = "MITK Segmentation"; handler.setSeriesDescription(seriesDescription); handler.setSeriesNumber("0" + std::to_string(layer)); handler.setInstanceNumber("1"); handler.setBodyPartExamined(""); const LabelSet *labelSet = image->GetLabelSet(layer); auto labelIter = labelSet->IteratorConstBegin(); // Ignore background label ++labelIter; for (; labelIter != labelSet->IteratorConstEnd(); ++labelIter) { const Label *label = labelIter->second; if (label != nullptr) { TemporoSpatialStringProperty *segmentNumberProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_NUMBER_PATH()).c_str())); TemporoSpatialStringProperty *segmentLabelProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_LABEL_PATH()).c_str())); TemporoSpatialStringProperty *algorithmTypeProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_ALGORITHM_TYPE_PATH()).c_str())); TemporoSpatialStringProperty *segmentCategoryCodeValueProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_VALUE_PATH()).c_str())); TemporoSpatialStringProperty *segmentCategoryCodeSchemeProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_SCHEME_PATH()).c_str())); TemporoSpatialStringProperty *segmentCategoryCodeMeaningProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_MEANING_PATH()).c_str())); TemporoSpatialStringProperty *segmentTypeCodeValueProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_VALUE_PATH()).c_str())); TemporoSpatialStringProperty *segmentTypeCodeSchemeProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_SCHEME_PATH()).c_str())); TemporoSpatialStringProperty *segmentTypeCodeMeaningProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_MEANING_PATH()).c_str())); TemporoSpatialStringProperty *segmentModifierCodeValueProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_VALUE_PATH()).c_str())); TemporoSpatialStringProperty *segmentModifierCodeSchemeProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_SCHEME_PATH()).c_str())); TemporoSpatialStringProperty *segmentModifierCodeMeaningProp = dynamic_cast(label->GetProperty( mitk::DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_MEANING_PATH()).c_str())); dcmqi::SegmentAttributes *segmentAttribute = nullptr; if (segmentNumberProp->GetValue() == "") { MITK_ERROR << "Something went wrong with the label ID."; } else { int labelId = std::stoi(segmentNumberProp->GetValue()); segmentAttribute = handler.createAndGetNewSegment(labelId); } if (segmentAttribute != nullptr) { segmentAttribute->setSegmentDescription(segmentLabelProp->GetValueAsString()); segmentAttribute->setSegmentAlgorithmType(algorithmTypeProp->GetValueAsString()); segmentAttribute->setSegmentAlgorithmName("MITK Segmentation"); if (segmentCategoryCodeValueProp != nullptr && segmentCategoryCodeSchemeProp != nullptr && segmentCategoryCodeMeaningProp != nullptr) segmentAttribute->setSegmentedPropertyCategoryCodeSequence( segmentCategoryCodeValueProp->GetValueAsString(), segmentCategoryCodeSchemeProp->GetValueAsString(), segmentCategoryCodeMeaningProp->GetValueAsString()); else // some default values segmentAttribute->setSegmentedPropertyCategoryCodeSequence( "M-01000", "SRT", "Morphologically Altered Structure"); if (segmentTypeCodeValueProp != nullptr && segmentTypeCodeSchemeProp != nullptr && segmentTypeCodeMeaningProp != nullptr) { segmentAttribute->setSegmentedPropertyTypeCodeSequence(segmentTypeCodeValueProp->GetValueAsString(), segmentTypeCodeSchemeProp->GetValueAsString(), segmentTypeCodeMeaningProp->GetValueAsString()); handler.setBodyPartExamined(segmentTypeCodeMeaningProp->GetValueAsString()); } else { // some default values segmentAttribute->setSegmentedPropertyTypeCodeSequence("M-03000", "SRT", "Mass"); handler.setBodyPartExamined("Mass"); } if (segmentModifierCodeValueProp != nullptr && segmentModifierCodeSchemeProp != nullptr && segmentModifierCodeMeaningProp != nullptr) segmentAttribute->setSegmentedPropertyTypeModifierCodeSequence( segmentModifierCodeValueProp->GetValueAsString(), segmentModifierCodeSchemeProp->GetValueAsString(), segmentModifierCodeMeaningProp->GetValueAsString()); Color color = label->GetColor(); segmentAttribute->setRecommendedDisplayRGBValue(color[0] * 255, color[1] * 255, color[2] * 255); } } } return handler.getJSONOutputAsString(); } void mitk::DICOMSegmentationIO::SetLabelProperties(mitk::Label *label, dcmqi::SegmentAttributes *segmentAttribute) { // Segment Number:Identification number of the segment.The value of Segment Number(0062, 0004) shall be unique // within the Segmentation instance in which it is created label->SetProperty(DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_NUMBER_PATH()).c_str(), TemporoSpatialStringProperty::New(std::to_string(label->GetValue()))); // Segment Label: User-defined label identifying this segment. label->SetProperty(DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_LABEL_PATH()).c_str(), TemporoSpatialStringProperty::New(label->GetName())); // Segment Algorithm Type: Type of algorithm used to generate the segment. if (!segmentAttribute->getSegmentAlgorithmType().empty()) label->SetProperty(DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_ALGORITHM_TYPE_PATH()).c_str(), TemporoSpatialStringProperty::New(segmentAttribute->getSegmentAlgorithmType())); // Add Segmented Property Category Code Sequence tags auto categoryCodeSequence = segmentAttribute->getSegmentedPropertyCategoryCodeSequence(); if (categoryCodeSequence != nullptr) { OFString codeValue; // (0008,0100) Code Value categoryCodeSequence->getCodeValue(codeValue); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_VALUE_PATH()).c_str(), TemporoSpatialStringProperty::New(codeValue.c_str())); OFString codeScheme; // (0008,0102) Coding Scheme Designator categoryCodeSequence->getCodingSchemeDesignator(codeScheme); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_SCHEME_PATH()).c_str(), TemporoSpatialStringProperty::New(codeScheme.c_str())); OFString codeMeaning; // (0008,0104) Code Meaning categoryCodeSequence->getCodeMeaning(codeMeaning); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_MEANING_PATH()).c_str(), TemporoSpatialStringProperty::New(codeMeaning.c_str())); } // Add Segmented Property Type Code Sequence tags auto typeCodeSequence = segmentAttribute->getSegmentedPropertyTypeCodeSequence(); if (typeCodeSequence != nullptr) { OFString codeValue; // (0008,0100) Code Value typeCodeSequence->getCodeValue(codeValue); label->SetProperty(DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_VALUE_PATH()).c_str(), TemporoSpatialStringProperty::New(codeValue.c_str())); OFString codeScheme; // (0008,0102) Coding Scheme Designator typeCodeSequence->getCodingSchemeDesignator(codeScheme); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_SCHEME_PATH()).c_str(), TemporoSpatialStringProperty::New(codeScheme.c_str())); OFString codeMeaning; // (0008,0104) Code Meaning typeCodeSequence->getCodeMeaning(codeMeaning); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_MEANING_PATH()).c_str(), TemporoSpatialStringProperty::New(codeMeaning.c_str())); } // Add Segmented Property Type Modifier Code Sequence tags auto modifierCodeSequence = segmentAttribute->getSegmentedPropertyTypeModifierCodeSequence(); if (modifierCodeSequence != nullptr) { OFString codeValue; // (0008,0100) Code Value modifierCodeSequence->getCodeValue(codeValue); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_VALUE_PATH()).c_str(), TemporoSpatialStringProperty::New(codeValue.c_str())); OFString codeScheme; // (0008,0102) Coding Scheme Designator modifierCodeSequence->getCodingSchemeDesignator(codeScheme); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_SCHEME_PATH()).c_str(), TemporoSpatialStringProperty::New(codeScheme.c_str())); OFString codeMeaning; // (0008,0104) Code Meaning modifierCodeSequence->getCodeMeaning(codeMeaning); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_MODIFIER_CODE_MEANING_PATH()).c_str(), TemporoSpatialStringProperty::New(codeMeaning.c_str())); } // Add Atomic RegionSequence tags auto atomicRegionSequence = segmentAttribute->getAnatomicRegionSequence(); if (atomicRegionSequence != nullptr) { OFString codeValue; // (0008,0100) Code Value atomicRegionSequence->getCodeValue(codeValue); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_VALUE_PATH()).c_str(), TemporoSpatialStringProperty::New(codeValue.c_str())); OFString codeScheme; // (0008,0102) Coding Scheme Designator atomicRegionSequence->getCodingSchemeDesignator(codeScheme); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_SCHEME_PATH()).c_str(), TemporoSpatialStringProperty::New(codeScheme.c_str())); OFString codeMeaning; // (0008,0104) Code Meaning atomicRegionSequence->getCodeMeaning(codeMeaning); label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::ANATOMIC_REGION_CODE_MEANING_PATH()).c_str(), TemporoSpatialStringProperty::New(codeMeaning.c_str())); } } DICOMSegmentationIO *DICOMSegmentationIO::IOClone() const { return new DICOMSegmentationIO(*this); } } // namespace #endif //__mitkDICOMSegmentationIO__cpp diff --git a/Modules/Multilabel/mitkLabelSetImage.cpp b/Modules/Multilabel/mitkLabelSetImage.cpp index 71a099210e..8ebc7838fb 100644 --- a/Modules/Multilabel/mitkLabelSetImage.cpp +++ b/Modules/Multilabel/mitkLabelSetImage.cpp @@ -1,989 +1,1012 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkLabelSetImage.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkImagePixelReadAccessor.h" #include "mitkImagePixelWriteAccessor.h" #include "mitkInteractionConst.h" #include "mitkLookupTableProperty.h" #include "mitkPadImageFilter.h" #include "mitkRenderingManager.h" #include "mitkDICOMSegmentationPropertyHelper.h" #include "mitkDICOMQIPropertyHelper.h" #include #include #include #include #include #include //#include #include template void SetToZero(itk::Image *source) { source->FillBuffer(0); } template void CreateLabelMaskProcessing(mitk::Image *layerImage, mitk::Image *mask, mitk::LabelSet::PixelType index) { mitk::ImagePixelReadAccessor readAccessor(layerImage); mitk::ImagePixelWriteAccessor writeAccessor(mask); std::size_t numberOfPixels = 1; for (int dim = 0; dim < static_cast(VImageDimension); ++dim) numberOfPixels *= static_cast(readAccessor.GetDimension(dim)); auto src = readAccessor.GetData(); auto dest = writeAccessor.GetData(); for (std::size_t i = 0; i < numberOfPixels; ++i) { if (index == *(src + i)) *(dest + i) = 1; } } mitk::LabelSetImage::LabelSetImage() : mitk::Image(), m_ActiveLayer(0), m_activeLayerInvalid(false), m_ExteriorLabel(nullptr) { // Iniitlaize Background Label mitk::Color color; color.Set(0, 0, 0); m_ExteriorLabel = mitk::Label::New(); m_ExteriorLabel->SetColor(color); m_ExteriorLabel->SetName("Exterior"); m_ExteriorLabel->SetOpacity(0.0); m_ExteriorLabel->SetLocked(false); m_ExteriorLabel->SetValue(0); // Add some DICOM Tags as properties to segmentation image DICOMSegmentationPropertyHelper::DeriveDICOMSegmentationProperties(this); } mitk::LabelSetImage::LabelSetImage(const mitk::LabelSetImage &other) : Image(other), m_ActiveLayer(other.GetActiveLayer()), m_activeLayerInvalid(false), m_ExteriorLabel(other.GetExteriorLabel()->Clone()) { for (unsigned int i = 0; i < other.GetNumberOfLayers(); i++) { // Clone LabelSet data mitk::LabelSet::Pointer lsClone = other.GetLabelSet(i)->Clone(); // add modified event listener to LabelSet (listen to LabelSet changes) itk::SimpleMemberCommand::Pointer command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &mitk::LabelSetImage::OnLabelSetModified); lsClone->AddObserver(itk::ModifiedEvent(), command); m_LabelSetContainer.push_back(lsClone); // clone layer Image data mitk::Image::Pointer liClone = other.GetLayerImage(i)->Clone(); m_LayerContainer.push_back(liClone); } // Add some DICOM Tags as properties to segmentation image DICOMSegmentationPropertyHelper::DeriveDICOMSegmentationProperties(this); } void mitk::LabelSetImage::OnLabelSetModified() { Superclass::Modified(); } void mitk::LabelSetImage::SetExteriorLabel(mitk::Label *label) { m_ExteriorLabel = label; } mitk::Label *mitk::LabelSetImage::GetExteriorLabel() { return m_ExteriorLabel; } const mitk::Label *mitk::LabelSetImage::GetExteriorLabel() const { return m_ExteriorLabel; } void mitk::LabelSetImage::Initialize(const mitk::Image *other) { mitk::PixelType pixelType(mitk::MakeScalarPixelType()); if (other->GetDimension() == 2) { const unsigned int dimensions[] = {other->GetDimension(0), other->GetDimension(1), 1}; Superclass::Initialize(pixelType, 3, dimensions); } else { Superclass::Initialize(pixelType, other->GetDimension(), other->GetDimensions()); } auto originalGeometry = other->GetTimeGeometry()->Clone(); this->SetTimeGeometry(originalGeometry); // initialize image memory to zero if (4 == this->GetDimension()) { AccessFixedDimensionByItk(this, SetToZero, 4); } else { AccessByItk(this, SetToZero); } // Transfer some general DICOM properties from the source image to derived image (e.g. Patient information,...) DICOMQIPropertyHelper::DeriveDICOMSourceProperties(other, this); // Add a inital LabelSet ans corresponding image data to the stack AddLayer(); } mitk::LabelSetImage::~LabelSetImage() { m_LabelSetContainer.clear(); } mitk::Image *mitk::LabelSetImage::GetLayerImage(unsigned int layer) { return m_LayerContainer[layer]; } const mitk::Image *mitk::LabelSetImage::GetLayerImage(unsigned int layer) const { return m_LayerContainer[layer]; } unsigned int mitk::LabelSetImage::GetActiveLayer() const { return m_ActiveLayer; } unsigned int mitk::LabelSetImage::GetNumberOfLayers() const { return m_LabelSetContainer.size(); } void mitk::LabelSetImage::RemoveLayer() { int layerToDelete = GetActiveLayer(); // remove all observers from active label set GetLabelSet(layerToDelete)->RemoveAllObservers(); // set the active layer to one below, if exists. if (layerToDelete != 0) { SetActiveLayer(layerToDelete - 1); } else { // we are deleting layer zero, it should not be copied back into the vector m_activeLayerInvalid = true; } // remove labelset and image data m_LabelSetContainer.erase(m_LabelSetContainer.begin() + layerToDelete); m_LayerContainer.erase(m_LayerContainer.begin() + layerToDelete); if (layerToDelete == 0) { this->SetActiveLayer(layerToDelete); } this->Modified(); } unsigned int mitk::LabelSetImage::AddLayer(mitk::LabelSet::Pointer lset) { mitk::Image::Pointer newImage = mitk::Image::New(); newImage->Initialize(this->GetPixelType(), this->GetDimension(), this->GetDimensions(), this->GetImageDescriptor()->GetNumberOfChannels()); newImage->SetTimeGeometry(this->GetTimeGeometry()->Clone()); if (newImage->GetDimension() < 4) { AccessByItk(newImage, SetToZero); } else { AccessFixedDimensionByItk(newImage, SetToZero, 4); } unsigned int newLabelSetId = this->AddLayer(newImage, lset); return newLabelSetId; } unsigned int mitk::LabelSetImage::AddLayer(mitk::Image::Pointer layerImage, mitk::LabelSet::Pointer lset) { unsigned int newLabelSetId = m_LayerContainer.size(); // Add labelset to layer mitk::LabelSet::Pointer ls; if (lset.IsNotNull()) { ls = lset; } else { ls = mitk::LabelSet::New(); ls->AddLabel(GetExteriorLabel()); ls->SetActiveLabel(0 /*Exterior Label*/); } ls->SetLayer(newLabelSetId); // Add exterior Label to label set // mitk::Label::Pointer exteriorLabel = CreateExteriorLabel(); // push a new working image for the new layer m_LayerContainer.push_back(layerImage); // push a new labelset for the new layer m_LabelSetContainer.push_back(ls); // add modified event listener to LabelSet (listen to LabelSet changes) itk::SimpleMemberCommand::Pointer command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &mitk::LabelSetImage::OnLabelSetModified); ls->AddObserver(itk::ModifiedEvent(), command); SetActiveLayer(newLabelSetId); // MITK_INFO << GetActiveLayer(); this->Modified(); return newLabelSetId; } void mitk::LabelSetImage::AddLabelSetToLayer(const unsigned int layerIdx, const mitk::LabelSet::Pointer labelSet) { if (m_LayerContainer.size() <= layerIdx) { mitkThrow() << "Trying to add labelSet to non-existing layer."; } if (layerIdx < m_LabelSetContainer.size()) { m_LabelSetContainer[layerIdx] = labelSet; } else { while (layerIdx >= m_LabelSetContainer.size()) { mitk::LabelSet::Pointer defaultLabelSet = mitk::LabelSet::New(); defaultLabelSet->AddLabel(GetExteriorLabel()); defaultLabelSet->SetActiveLabel(0 /*Exterior Label*/); defaultLabelSet->SetLayer(m_LabelSetContainer.size()); m_LabelSetContainer.push_back(defaultLabelSet); } m_LabelSetContainer.push_back(labelSet); } } void mitk::LabelSetImage::SetActiveLayer(unsigned int layer) { try { if (4 == this->GetDimension()) { if ((layer != GetActiveLayer() || m_activeLayerInvalid) && (layer < this->GetNumberOfLayers())) { BeforeChangeLayerEvent.Send(); if (m_activeLayerInvalid) { // We should not write the invalid layer back to the vector m_activeLayerInvalid = false; } else { AccessFixedDimensionByItk_n(this, ImageToLayerContainerProcessing, 4, (GetActiveLayer())); } m_ActiveLayer = layer; // only at this place m_ActiveLayer should be manipulated!!! Use Getter and Setter AccessFixedDimensionByItk_n(this, LayerContainerToImageProcessing, 4, (GetActiveLayer())); AfterChangeLayerEvent.Send(); } } else { if ((layer != GetActiveLayer() || m_activeLayerInvalid) && (layer < this->GetNumberOfLayers())) { BeforeChangeLayerEvent.Send(); if (m_activeLayerInvalid) { // We should not write the invalid layer back to the vector m_activeLayerInvalid = false; } else { AccessByItk_1(this, ImageToLayerContainerProcessing, GetActiveLayer()); } m_ActiveLayer = layer; // only at this place m_ActiveLayer should be manipulated!!! Use Getter and Setter AccessByItk_1(this, LayerContainerToImageProcessing, GetActiveLayer()); AfterChangeLayerEvent.Send(); } } } catch (itk::ExceptionObject &e) { mitkThrow() << e.GetDescription(); } this->Modified(); } void mitk::LabelSetImage::Concatenate(mitk::LabelSetImage *other) { const unsigned int *otherDims = other->GetDimensions(); const unsigned int *thisDims = this->GetDimensions(); if ((otherDims[0] != thisDims[0]) || (otherDims[1] != thisDims[1]) || (otherDims[2] != thisDims[2])) mitkThrow() << "Dimensions do not match."; try { int numberOfLayers = other->GetNumberOfLayers(); for (int layer = 0; layer < numberOfLayers; ++layer) { this->SetActiveLayer(layer); AccessByItk_1(this, ConcatenateProcessing, other); mitk::LabelSet *ls = other->GetLabelSet(layer); auto it = ls->IteratorConstBegin(); auto end = ls->IteratorConstEnd(); it++; // skip exterior while (it != end) { GetLabelSet()->AddLabel((it->second)); // AddLabelEvent.Send(); it++; } } } catch (itk::ExceptionObject &e) { mitkThrow() << e.GetDescription(); } this->Modified(); } void mitk::LabelSetImage::ClearBuffer() { try { AccessByItk(this, ClearBufferProcessing); this->Modified(); } catch (itk::ExceptionObject &e) { mitkThrow() << e.GetDescription(); } } bool mitk::LabelSetImage::ExistLabel(PixelType pixelValue) const { bool exist = false; for (unsigned int lidx = 0; lidx < GetNumberOfLayers(); lidx++) exist |= m_LabelSetContainer[lidx]->ExistLabel(pixelValue); return exist; } bool mitk::LabelSetImage::ExistLabel(PixelType pixelValue, unsigned int layer) const { bool exist = m_LabelSetContainer[layer]->ExistLabel(pixelValue); return exist; } bool mitk::LabelSetImage::ExistLabelSet(unsigned int layer) const { return layer < m_LabelSetContainer.size(); } void mitk::LabelSetImage::MergeLabel(PixelType pixelValue, PixelType sourcePixelValue, unsigned int layer) { try { AccessByItk_2(this, MergeLabelProcessing, pixelValue, sourcePixelValue); } catch (itk::ExceptionObject &e) { mitkThrow() << e.GetDescription(); } GetLabelSet(layer)->SetActiveLabel(pixelValue); Modified(); } void mitk::LabelSetImage::MergeLabels(PixelType pixelValue, std::vector& vectorOfSourcePixelValues, unsigned int layer) { try { for (unsigned int idx = 0; idx < vectorOfSourcePixelValues.size(); idx++) { AccessByItk_2(this, MergeLabelProcessing, pixelValue, vectorOfSourcePixelValues[idx]); } } catch (itk::ExceptionObject &e) { mitkThrow() << e.GetDescription(); } GetLabelSet(layer)->SetActiveLabel(pixelValue); Modified(); } void mitk::LabelSetImage::RemoveLabels(std::vector &VectorOfLabelPixelValues, unsigned int layer) { for (unsigned int idx = 0; idx < VectorOfLabelPixelValues.size(); idx++) { GetLabelSet(layer)->RemoveLabel(VectorOfLabelPixelValues[idx]); EraseLabel(VectorOfLabelPixelValues[idx], layer); } } void mitk::LabelSetImage::EraseLabels(std::vector &VectorOfLabelPixelValues, unsigned int layer) { for (unsigned int i = 0; i < VectorOfLabelPixelValues.size(); i++) { this->EraseLabel(VectorOfLabelPixelValues[i], layer); } } void mitk::LabelSetImage::EraseLabel(PixelType pixelValue, unsigned int layer) { try { - AccessByItk_2(this, EraseLabelProcessing, pixelValue, layer); + if (4 == this->GetDimension()) + { + AccessFixedDimensionByItk_2(this, EraseLabelProcessing, 4, pixelValue, layer); + } + else + { + AccessByItk_2(this, EraseLabelProcessing, pixelValue, layer); + } } - catch (itk::ExceptionObject &e) + catch (const itk::ExceptionObject &e) { mitkThrow() << e.GetDescription(); } Modified(); } mitk::Label *mitk::LabelSetImage::GetActiveLabel(unsigned int layer) { if (m_LabelSetContainer.size() <= layer) return nullptr; else - return m_LabelSetContainer[layer]->GetActiveLabel();; + return m_LabelSetContainer[layer]->GetActiveLabel(); +} + +const mitk::Label* mitk::LabelSetImage::GetActiveLabel(unsigned int layer) const +{ + if (m_LabelSetContainer.size() <= layer) + return nullptr; + else + return m_LabelSetContainer[layer]->GetActiveLabel(); } mitk::Label *mitk::LabelSetImage::GetLabel(PixelType pixelValue, unsigned int layer) const { if (m_LabelSetContainer.size() <= layer) return nullptr; else return m_LabelSetContainer[layer]->GetLabel(pixelValue); } mitk::LabelSet *mitk::LabelSetImage::GetLabelSet(unsigned int layer) { if (m_LabelSetContainer.size() <= layer) return nullptr; else return m_LabelSetContainer[layer].GetPointer(); } const mitk::LabelSet *mitk::LabelSetImage::GetLabelSet(unsigned int layer) const { if (m_LabelSetContainer.size() <= layer) return nullptr; else return m_LabelSetContainer[layer].GetPointer(); } mitk::LabelSet *mitk::LabelSetImage::GetActiveLabelSet() { if (m_LabelSetContainer.size() == 0) return nullptr; else return m_LabelSetContainer[GetActiveLayer()].GetPointer(); } +const mitk::LabelSet* mitk::LabelSetImage::GetActiveLabelSet() const +{ + if (m_LabelSetContainer.size() == 0) + return nullptr; + else + return m_LabelSetContainer[GetActiveLayer()].GetPointer(); +} + void mitk::LabelSetImage::UpdateCenterOfMass(PixelType pixelValue, unsigned int layer) { if (4 == this->GetDimension()) { AccessFixedDimensionByItk_2(this, CalculateCenterOfMassProcessing, 4, pixelValue, layer); } else { AccessByItk_2(this, CalculateCenterOfMassProcessing, pixelValue, layer); } } unsigned int mitk::LabelSetImage::GetNumberOfLabels(unsigned int layer) const { return m_LabelSetContainer[layer]->GetNumberOfLabels(); } unsigned int mitk::LabelSetImage::GetTotalNumberOfLabels() const { unsigned int totalLabels(0); auto layerIter = m_LabelSetContainer.begin(); for (; layerIter != m_LabelSetContainer.end(); ++layerIter) totalLabels += (*layerIter)->GetNumberOfLabels(); return totalLabels; } void mitk::LabelSetImage::MaskStamp(mitk::Image *mask, bool forceOverwrite) { try { mitk::PadImageFilter::Pointer padImageFilter = mitk::PadImageFilter::New(); padImageFilter->SetInput(0, mask); padImageFilter->SetInput(1, this); padImageFilter->SetPadConstant(0); padImageFilter->SetBinaryFilter(false); padImageFilter->SetLowerThreshold(0); padImageFilter->SetUpperThreshold(1); padImageFilter->Update(); mitk::Image::Pointer paddedMask = padImageFilter->GetOutput(); if (paddedMask.IsNull()) return; AccessByItk_2(this, MaskStampProcessing, paddedMask, forceOverwrite); } catch (...) { mitkThrow() << "Could not stamp the provided mask on the selected label."; } } mitk::Image::Pointer mitk::LabelSetImage::CreateLabelMask(PixelType index, bool useActiveLayer, unsigned int layer) { auto previousActiveLayer = this->GetActiveLayer(); auto mask = mitk::Image::New(); try { mask->Initialize(this); auto byteSize = sizeof(LabelSetImage::PixelType); for (unsigned int dim = 0; dim < mask->GetDimension(); ++dim) byteSize *= mask->GetDimension(dim); { ImageWriteAccessor accessor(mask); memset(accessor.GetData(), 0, byteSize); } if (!useActiveLayer) this->SetActiveLayer(layer); if (4 == this->GetDimension()) { ::CreateLabelMaskProcessing<4>(this, mask, index); } else if (3 == this->GetDimension()) { ::CreateLabelMaskProcessing(this, mask, index); } else { mitkThrow(); } } catch (...) { if (!useActiveLayer) this->SetActiveLayer(previousActiveLayer); mitkThrow() << "Could not create a mask out of the selected label."; } if (!useActiveLayer) this->SetActiveLayer(previousActiveLayer); return mask; } void mitk::LabelSetImage::InitializeByLabeledImage(mitk::Image::Pointer image) { if (image.IsNull() || image->IsEmpty() || !image->IsInitialized()) mitkThrow() << "Invalid labeled image."; try { this->Initialize(image); unsigned int byteSize = sizeof(LabelSetImage::PixelType); for (unsigned int dim = 0; dim < image->GetDimension(); ++dim) { byteSize *= image->GetDimension(dim); } mitk::ImageWriteAccessor *accessor = new mitk::ImageWriteAccessor(static_cast(this)); memset(accessor->GetData(), 0, byteSize); delete accessor; auto geometry = image->GetTimeGeometry()->Clone(); this->SetTimeGeometry(geometry); if (image->GetDimension() == 3) { AccessTwoImagesFixedDimensionByItk(this, image, InitializeByLabeledImageProcessing, 3); } else if (image->GetDimension() == 4) { AccessTwoImagesFixedDimensionByItk(this, image, InitializeByLabeledImageProcessing, 4); } else { mitkThrow() << image->GetDimension() << "-dimensional label set images not yet supported"; } } catch (...) { mitkThrow() << "Could not intialize by provided labeled image."; } this->Modified(); } template void mitk::LabelSetImage::InitializeByLabeledImageProcessing(LabelSetImageType *labelSetImage, ImageType *image) { typedef itk::ImageRegionConstIteratorWithIndex SourceIteratorType; typedef itk::ImageRegionIterator TargetIteratorType; TargetIteratorType targetIter(labelSetImage, labelSetImage->GetRequestedRegion()); targetIter.GoToBegin(); SourceIteratorType sourceIter(image, image->GetRequestedRegion()); sourceIter.GoToBegin(); while (!sourceIter.IsAtEnd()) { auto sourceValue = static_cast(sourceIter.Get()); targetIter.Set(sourceValue); if (!this->ExistLabel(sourceValue)) { std::stringstream name; name << "object-" << sourceValue; double rgba[4]; m_LabelSetContainer[this->GetActiveLayer()]->GetLookupTable()->GetTableValue(sourceValue, rgba); mitk::Color color; color.SetRed(rgba[0]); color.SetGreen(rgba[1]); color.SetBlue(rgba[2]); auto label = mitk::Label::New(); label->SetName(name.str().c_str()); label->SetColor(color); label->SetOpacity(rgba[3]); label->SetValue(sourceValue); this->GetLabelSet()->AddLabel(label); if (GetActiveLabelSet()->GetNumberOfLabels() >= mitk::Label::MAX_LABEL_VALUE || sourceValue >= mitk::Label::MAX_LABEL_VALUE) this->AddLayer(); } ++sourceIter; ++targetIter; } } template void mitk::LabelSetImage::MaskStampProcessing(ImageType *itkImage, mitk::Image *mask, bool forceOverwrite) { typename ImageType::Pointer itkMask; mitk::CastToItkImage(mask, itkMask); typedef itk::ImageRegionConstIterator SourceIteratorType; typedef itk::ImageRegionIterator TargetIteratorType; SourceIteratorType sourceIter(itkMask, itkMask->GetLargestPossibleRegion()); sourceIter.GoToBegin(); TargetIteratorType targetIter(itkImage, itkImage->GetLargestPossibleRegion()); targetIter.GoToBegin(); int activeLabel = this->GetActiveLabel(GetActiveLayer())->GetValue(); while (!sourceIter.IsAtEnd()) { PixelType sourceValue = sourceIter.Get(); PixelType targetValue = targetIter.Get(); if ((sourceValue != 0) && (forceOverwrite || !this->GetLabel(targetValue)->GetLocked())) // skip exterior and locked labels { targetIter.Set(activeLabel); } ++sourceIter; ++targetIter; } this->Modified(); } template void mitk::LabelSetImage::CalculateCenterOfMassProcessing(ImageType *itkImage, PixelType pixelValue, unsigned int layer) { // for now, we just retrieve the voxel in the middle typedef itk::ImageRegionConstIterator IteratorType; IteratorType iter(itkImage, itkImage->GetLargestPossibleRegion()); iter.GoToBegin(); std::vector indexVector; while (!iter.IsAtEnd()) { // TODO fix comparison warning more effective if (iter.Get() == pixelValue) { indexVector.push_back(iter.GetIndex()); } ++iter; } mitk::Point3D pos; pos.Fill(0.0); if (!indexVector.empty()) { typename itk::ImageRegionConstIteratorWithIndex::IndexType centerIndex; centerIndex = indexVector.at(indexVector.size() / 2); if (centerIndex.GetIndexDimension() == 3) { pos[0] = centerIndex[0]; pos[1] = centerIndex[1]; pos[2] = centerIndex[2]; } else return; } GetLabelSet(layer)->GetLabel(pixelValue)->SetCenterOfMassIndex(pos); this->GetSlicedGeometry()->IndexToWorld(pos, pos); // TODO: TimeGeometry? GetLabelSet(layer)->GetLabel(pixelValue)->SetCenterOfMassCoordinates(pos); } template void mitk::LabelSetImage::ClearBufferProcessing(ImageType *itkImage) { itkImage->FillBuffer(0); } // todo: concatenate all layers and not just the active one template void mitk::LabelSetImage::ConcatenateProcessing(ImageType *itkTarget, mitk::LabelSetImage *other) { typename ImageType::Pointer itkSource = ImageType::New(); mitk::CastToItkImage(other, itkSource); typedef itk::ImageRegionConstIterator ConstIteratorType; typedef itk::ImageRegionIterator IteratorType; ConstIteratorType sourceIter(itkSource, itkSource->GetLargestPossibleRegion()); IteratorType targetIter(itkTarget, itkTarget->GetLargestPossibleRegion()); int numberOfTargetLabels = this->GetNumberOfLabels(GetActiveLayer()) - 1; // skip exterior sourceIter.GoToBegin(); targetIter.GoToBegin(); while (!sourceIter.IsAtEnd()) { PixelType sourceValue = sourceIter.Get(); PixelType targetValue = targetIter.Get(); if ((sourceValue != 0) && !this->GetLabel(targetValue)->GetLocked()) // skip exterior and locked labels { targetIter.Set(sourceValue + numberOfTargetLabels); } ++sourceIter; ++targetIter; } } template void mitk::LabelSetImage::LayerContainerToImageProcessing(itk::Image *target, unsigned int layer) { typedef itk::Image ImageType; typename ImageType::Pointer itkSource; // mitk::CastToItkImage(m_LayerContainer[layer], itkSource); itkSource = ImageToItkImage(m_LayerContainer[layer]); typedef itk::ImageRegionConstIterator SourceIteratorType; typedef itk::ImageRegionIterator TargetIteratorType; SourceIteratorType sourceIter(itkSource, itkSource->GetLargestPossibleRegion()); sourceIter.GoToBegin(); TargetIteratorType targetIter(target, target->GetLargestPossibleRegion()); targetIter.GoToBegin(); while (!sourceIter.IsAtEnd()) { targetIter.Set(sourceIter.Get()); ++sourceIter; ++targetIter; } } template void mitk::LabelSetImage::ImageToLayerContainerProcessing(itk::Image *source, unsigned int layer) const { typedef itk::Image ImageType; typename ImageType::Pointer itkTarget; // mitk::CastToItkImage(m_LayerContainer[layer], itkTarget); itkTarget = ImageToItkImage(m_LayerContainer[layer]); typedef itk::ImageRegionConstIterator SourceIteratorType; typedef itk::ImageRegionIterator TargetIteratorType; SourceIteratorType sourceIter(source, source->GetLargestPossibleRegion()); sourceIter.GoToBegin(); TargetIteratorType targetIter(itkTarget, itkTarget->GetLargestPossibleRegion()); targetIter.GoToBegin(); while (!sourceIter.IsAtEnd()) { targetIter.Set(sourceIter.Get()); ++sourceIter; ++targetIter; } } template void mitk::LabelSetImage::EraseLabelProcessing(ImageType *itkImage, PixelType pixelValue, unsigned int /*layer*/) { typedef itk::ImageRegionIterator IteratorType; IteratorType iter(itkImage, itkImage->GetLargestPossibleRegion()); iter.GoToBegin(); while (!iter.IsAtEnd()) { PixelType value = iter.Get(); if (value == pixelValue) { iter.Set(0); } ++iter; } } template void mitk::LabelSetImage::MergeLabelProcessing(ImageType *itkImage, PixelType pixelValue, PixelType index) { typedef itk::ImageRegionIterator IteratorType; IteratorType iter(itkImage, itkImage->GetLargestPossibleRegion()); iter.GoToBegin(); while (!iter.IsAtEnd()) { if (iter.Get() == index) { iter.Set(pixelValue); } ++iter; } } bool mitk::Equal(const mitk::LabelSetImage &leftHandSide, const mitk::LabelSetImage &rightHandSide, ScalarType eps, bool verbose) { bool returnValue = true; /* LabelSetImage members */ MITK_INFO(verbose) << "--- LabelSetImage Equal ---"; // number layers returnValue = leftHandSide.GetNumberOfLayers() == rightHandSide.GetNumberOfLayers(); if (!returnValue) { MITK_INFO(verbose) << "Number of layers not equal."; return false; } // total number labels returnValue = leftHandSide.GetTotalNumberOfLabels() == rightHandSide.GetTotalNumberOfLabels(); if (!returnValue) { MITK_INFO(verbose) << "Total number of labels not equal."; return false; } // active layer returnValue = leftHandSide.GetActiveLayer() == rightHandSide.GetActiveLayer(); if (!returnValue) { MITK_INFO(verbose) << "Active layer not equal."; return false; } if (4 == leftHandSide.GetDimension()) { MITK_INFO(verbose) << "Can not compare image data for 4D images - skipping check."; } else { // working image data returnValue = mitk::Equal((const mitk::Image &)leftHandSide, (const mitk::Image &)rightHandSide, eps, verbose); if (!returnValue) { MITK_INFO(verbose) << "Working image data not equal."; return false; } } for (unsigned int layerIndex = 0; layerIndex < leftHandSide.GetNumberOfLayers(); layerIndex++) { if (4 == leftHandSide.GetDimension()) { MITK_INFO(verbose) << "Can not compare image data for 4D images - skipping check."; } else { // layer image data returnValue = mitk::Equal(*leftHandSide.GetLayerImage(layerIndex), *rightHandSide.GetLayerImage(layerIndex), eps, verbose); if (!returnValue) { MITK_INFO(verbose) << "Layer image data not equal."; return false; } } // layer labelset data returnValue = mitk::Equal(*leftHandSide.GetLabelSet(layerIndex), *rightHandSide.GetLabelSet(layerIndex), eps, verbose); if (!returnValue) { MITK_INFO(verbose) << "Layer labelset data not equal."; return false; } } return returnValue; } diff --git a/Modules/Multilabel/mitkLabelSetImage.h b/Modules/Multilabel/mitkLabelSetImage.h index e65e6752e8..2d02b05287 100644 --- a/Modules/Multilabel/mitkLabelSetImage.h +++ b/Modules/Multilabel/mitkLabelSetImage.h @@ -1,340 +1,342 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 __mitkLabelSetImage_H_ #define __mitkLabelSetImage_H_ #include #include #include namespace mitk { //##Documentation //## @brief LabelSetImage class for handling labels and layers in a segmentation session. //## //## Handles operations for adding, removing, erasing and editing labels and layers. //## @ingroup Data class MITKMULTILABEL_EXPORT LabelSetImage : public Image { public: mitkClassMacro(LabelSetImage, Image); itkNewMacro(Self); typedef mitk::Label::PixelType PixelType; /** * \brief BeforeChangeLayerEvent (e.g. used for GUI integration) * As soon as active labelset should be changed, the signal emits. * Emitted by SetActiveLayer(int layer); */ Message<> BeforeChangeLayerEvent; /** * \brief AfterchangeLayerEvent (e.g. used for GUI integration) * As soon as active labelset was changed, the signal emits. * Emitted by SetActiveLayer(int layer); */ Message<> AfterChangeLayerEvent; /** * @brief Initialize an empty mitk::LabelSetImage using the information * of an mitk::Image * @param image the image which is used for initializing the mitk::LabelSetImage */ using mitk::Image::Initialize; void Initialize(const mitk::Image *image) override; /** * \brief */ void Concatenate(mitk::LabelSetImage *image); /** * \brief */ void ClearBuffer(); /** * @brief Merges the mitk::Label with a given target value with the active label * * @param pixelValue the value of the label that should be the new merged label * @param sourcePixelValue the value of the label that should be merged into the specified one * @param layer the layer in which the merge should be performed */ void MergeLabel(PixelType pixelValue, PixelType sourcePixelValue, unsigned int layer = 0); /** * @brief Merges a list of mitk::Labels with the mitk::Label that has a specific value * * @param pixelValue the value of the label that should be the new merged label * @param vectorOfSourcePixelValues the list of label values that should be merge into the specified one * @param layer the layer in which the merge should be performed */ void MergeLabels(PixelType pixelValue, std::vector& vectorOfSourcePixelValues, unsigned int layer = 0); /** * \brief */ void UpdateCenterOfMass(PixelType pixelValue, unsigned int layer = 0); /** * @brief Removes labels from the mitk::LabelSet of given layer. * Calls mitk::LabelSetImage::EraseLabels() which also removes the labels from within the image. * @param VectorOfLabelPixelValues a list of labels to be removed * @param layer the layer in which the labels should be removed */ void RemoveLabels(std::vector &VectorOfLabelPixelValues, unsigned int layer = 0); /** * @brief Erases the label with the given value in the given layer from the underlying image. * The label itself will not be erased from the respective mitk::LabelSet. In order to * remove the label itself use mitk::LabelSetImage::RemoveLabels() * @param pixelValue the label which will be remove from the image * @param layer the layer in which the label should be removed */ void EraseLabel(PixelType pixelValue, unsigned int layer = 0); /** * @brief Similar to mitk::LabelSetImage::EraseLabel() this funtion erase a list of labels from the image * @param VectorOfLabelPixelValues the list of labels that should be remove * @param layer the layer for which the labels should be removed */ void EraseLabels(std::vector &VectorOfLabelPixelValues, unsigned int layer = 0); /** * \brief Returns true if the value exists in one of the labelsets*/ bool ExistLabel(PixelType pixelValue) const; /** * @brief Checks if a label exists in a certain layer * @param pixelValue the label value * @param layer the layer in which should be searched for the label * @return true if the label exists otherwise false */ bool ExistLabel(PixelType pixelValue, unsigned int layer) const; /** * \brief Returns true if the labelset exists*/ bool ExistLabelSet(unsigned int layer) const; /** * @brief Returns the active label of a specific layer * @param layer the layer ID for which the active label should be returned * @return the active label of the specified layer */ mitk::Label *GetActiveLabel(unsigned int layer = 0); + const mitk::Label* GetActiveLabel(unsigned int layer = 0) const; /** * @brief Returns the mitk::Label with the given pixelValue and for the given layer * @param pixelValue the pixel value of the label * @param layer the layer in which the labels should be located * @return the mitk::Label if available otherwise nullptr */ mitk::Label *GetLabel(PixelType pixelValue, unsigned int layer = 0) const; /** * @brief Returns the currently active mitk::LabelSet * @return the mitk::LabelSet of the active layer or nullptr if non is present */ mitk::LabelSet *GetActiveLabelSet(); + const mitk::LabelSet* GetActiveLabelSet() const; /** * @brief Gets the mitk::LabelSet for the given layer * @param layer the layer for which the mitk::LabelSet should be retrieved * @return the respective mitk::LabelSet or nullptr if non exists for the given layer */ mitk::LabelSet *GetLabelSet(unsigned int layer = 0); const mitk::LabelSet *GetLabelSet(unsigned int layer = 0) const; /** * @brief Gets the ID of the currently active layer * @return the ID of the active layer */ unsigned int GetActiveLayer() const; /** * @brief Get the number of all existing mitk::Labels for a given layer * @param layer the layer ID for which the active mitk::Labels should be retrieved * @return the number of all existing mitk::Labels for the given layer */ unsigned int GetNumberOfLabels(unsigned int layer = 0) const; /** * @brief Returns the number of all labels summed up across all layers * @return the overall number of labels across all layers */ unsigned int GetTotalNumberOfLabels() const; // This function will need to be ported to an external class // it requires knowledge of pixeltype and dimension and includes // too much algorithm to be sensibly part of a data class ///** // * \brief */ // void SurfaceStamp(mitk::Surface* surface, bool forceOverwrite); /** * \brief */ mitk::Image::Pointer CreateLabelMask(PixelType index, bool useActiveLayer = true, unsigned int layer = 0); /** * @brief Initialize a new mitk::LabelSetImage by an given image. * For all distinct pixel values of the parameter image new labels will * be created. If the number of distinct pixel values exceeds mitk::Label::MAX_LABEL_VALUE * a new layer will be created * @param image the image which is used for initialization */ void InitializeByLabeledImage(mitk::Image::Pointer image); /** * \brief */ void MaskStamp(mitk::Image *mask, bool forceOverwrite); /** * \brief */ void SetActiveLayer(unsigned int layer); /** * \brief */ unsigned int GetNumberOfLayers() const; /** * @brief Adds a new layer to the LabelSetImage. The new layer will be set as the active one * @param layer a mitk::LabelSet which will be set as new layer. * @return the layer ID of the new layer */ unsigned int AddLayer(mitk::LabelSet::Pointer layer = nullptr); /** * \brief Add a layer based on a provided mitk::Image * \param layerImage is added to the vector of label images * \param lset a label set that will be added to the new layer if provided *\return the layer ID of the new layer */ unsigned int AddLayer(mitk::Image::Pointer layerImage, mitk::LabelSet::Pointer lset = nullptr); /** * \brief Add a LabelSet to an existing layer * * This will replace an existing labelSet if one exists. Throws an exceptions if you are trying * to add a labelSet to a non-existing layer. * * If there are no labelSets for layers with an id less than layerIdx default ones will be added * for them. * * \param layerIdx The index of the layer the LabelSet should be added to * \param labelSet The LabelSet that should be added */ void AddLabelSetToLayer(const unsigned int layerIdx, const mitk::LabelSet::Pointer labelSet); /** * @brief Removes the active layer and the respective mitk::LabelSet and image information. * The new active layer is the one below, if exists */ void RemoveLayer(); /** * \brief */ mitk::Image *GetLayerImage(unsigned int layer); const mitk::Image *GetLayerImage(unsigned int layer) const; void OnLabelSetModified(); /** * @brief Sets the label which is used as default exterior label when creating a new layer * @param label the label which will be used as new exterior label */ void SetExteriorLabel(mitk::Label *label); /** * @brief Gets the mitk::Label which is used as default exterior label * @return the exterior mitk::Label */ mitk::Label *GetExteriorLabel(); const mitk::Label *GetExteriorLabel() const; protected: mitkCloneMacro(Self); LabelSetImage(); LabelSetImage(const LabelSetImage &other); ~LabelSetImage() override; template void ChangeLayerProcessing(ImageType1 *source, ImageType2 *target); template void LayerContainerToImageProcessing(itk::Image *source, unsigned int layer); template void ImageToLayerContainerProcessing(itk::Image *source, unsigned int layer) const; template void CalculateCenterOfMassProcessing(ImageType *input, PixelType index, unsigned int layer); template void ClearBufferProcessing(ImageType *input); template void EraseLabelProcessing(ImageType *input, PixelType index, unsigned int layer); // template < typename ImageType > // void ReorderLabelProcessing( ImageType* input, int index, int layer); template void MergeLabelProcessing(ImageType *input, PixelType pixelValue, PixelType index); template void ConcatenateProcessing(ImageType *input, mitk::LabelSetImage *other); template void MaskStampProcessing(ImageType *input, mitk::Image *mask, bool forceOverwrite); template void InitializeByLabeledImageProcessing(LabelSetImageType *input, ImageType *other); std::vector m_LabelSetContainer; std::vector m_LayerContainer; int m_ActiveLayer; bool m_activeLayerInvalid; mitk::Label::Pointer m_ExteriorLabel; }; /** * @brief Equal A function comparing two label set images for beeing equal in meta- and imagedata * * @ingroup MITKTestingAPI * * Following aspects are tested for equality: * - LabelSetImage members * - working image data * - layer image data * - labels in label set * * @param rightHandSide An image to be compared * @param leftHandSide An image to be compared * @param eps Tolerance for comparison. You can use mitk::eps in most cases. * @param verbose Flag indicating if the user wants detailed console output or not. * @return true, if all subsequent comparisons are true, false otherwise */ MITKMULTILABEL_EXPORT bool Equal(const mitk::LabelSetImage &leftHandSide, const mitk::LabelSetImage &rightHandSide, ScalarType eps, bool verbose); } // namespace mitk #endif // __mitkLabelSetImage_H_ diff --git a/Modules/Multilabel/mitkLabelSetImageToSurfaceFilter.h b/Modules/Multilabel/mitkLabelSetImageToSurfaceFilter.h index 034a04bcf1..c30ca766b1 100644 --- a/Modules/Multilabel/mitkLabelSetImageToSurfaceFilter.h +++ b/Modules/Multilabel/mitkLabelSetImageToSurfaceFilter.h @@ -1,157 +1,157 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef _mitkLabelSetImageToSurfaceFilter_H_ #define _mitkLabelSetImageToSurfaceFilter_H_ #include "MitkMultilabelExports.h" #include "mitkLabelSetImage.h" #include "mitkSurface.h" #include #include #include #include namespace mitk { /** * Generates surface meshes from a labelset image. * If you want to calculate a surface representation for all available labels, * you may call GenerateAllLabelsOn(). */ class MITKMULTILABEL_EXPORT LabelSetImageToSurfaceFilter : public SurfaceSource { public: mitkClassMacro(LabelSetImageToSurfaceFilter, SurfaceSource); itkNewMacro(Self); typedef LabelSetImage::PixelType LabelType; typedef std::map LabelMapType; typedef std::map IndexToLabelMapType; /** * Returns a const pointer to the labelset image set as input */ const mitk::Image *GetInput(void); /** * Set the labelset image to create a surface from. */ using ProcessObject::SetInput; virtual void SetInput(const mitk::Image *image); // virtual void SetObserver(mitk::ProcessObserver::Pointer observer); /** * Set whether you want to extract all labesl (true) or a single one. */ itkSetMacro(GenerateAllLabels, bool); /** * @returns if all labels or only a specific label should be * extracted. */ itkGetMacro(GenerateAllLabels, bool); itkBooleanMacro(GenerateAllLabels); /** * Set the label you want to extract. This method only has an effect, * if GenerateAllLabels() is set to false * @param _arg the label to extract, by default 1 */ itkSetMacro(RequestedLabel, int); /** * Returns the label you want to extract. This method only has an effect, * if GenerateAllLabels() is set to false - * @returns _arg the label to extract, by default 1 + * @return the label to extract, by default 1 */ itkGetMacro(RequestedLabel, int); /** * Sets the label value of the background. No surface will be generated for this label. * @param _arg the label of the background, by default 0 */ itkSetMacro(BackgroundLabel, int); /** * Gets the label value of the background. No surface will be generated for this label. - * @param _arg the label of the background, by default 0 + * @return the label of the background, by default 0 */ itkGetMacro(BackgroundLabel, int); /** * Sets whether to provide a smoothed surface */ itkSetMacro(UseSmoothing, int); /** * Sets the Sigma used in the gaussian smoothing */ itkSetMacro(Sigma, float); protected: LabelSetImageToSurfaceFilter(); ~LabelSetImageToSurfaceFilter() override; /** * Transforms a point by a 4x4 matrix */ template inline void mitkVtkLinearTransformPoint(T1 matrix[4][4], T2 in[3], T3 out[3]) { T3 x = matrix[0][0] * in[0] + matrix[0][1] * in[1] + matrix[0][2] * in[2] + matrix[0][3]; T3 y = matrix[1][0] * in[0] + matrix[1][1] * in[1] + matrix[1][2] * in[2] + matrix[1][3]; T3 z = matrix[2][0] * in[0] + matrix[2][1] * in[1] + matrix[2][2] * in[2] + matrix[2][3]; out[0] = x; out[1] = y; out[2] = z; } mitk::Image::Pointer m_ResultImage; template void InternalProcessing(const itk::Image *input, mitk::Surface *surface); bool m_GenerateAllLabels; int m_RequestedLabel; int m_BackgroundLabel; int m_UseSmoothing; float m_Sigma; LabelMapType m_AvailableLabels; IndexToLabelMapType m_IndexToLabels; mitk::Vector3D m_InputImageSpacing; void GenerateData() override; void GenerateOutputInformation() override; // mitk::ProcessObserver::Pointer m_Observer; }; } // end of namespace mitk #endif //_mitkLabelSetImageToSurfaceFilter_H_ diff --git a/Modules/OpenCL/mitkOclFilter.h b/Modules/OpenCL/mitkOclFilter.h index 4de5217d7a..b958ffaf56 100644 --- a/Modules/OpenCL/mitkOclFilter.h +++ b/Modules/OpenCL/mitkOclFilter.h @@ -1,159 +1,157 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef __mitkOclFilter_h #define __mitkOclFilter_h #include "mitkOclUtils.h" #include "mitkCommon.h" #include #include #include 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 CStringList; typedef std::vector 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 - * - * @param preambel e.g. defines for the shader code */ 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 // __mitkOclFilter_h diff --git a/Modules/Pharmacokinetics/src/Functors/mitkCurveParameterFunctor.cpp b/Modules/Pharmacokinetics/src/Functors/mitkCurveParameterFunctor.cpp index 4a61df2446..f4b5db81cf 100644 --- a/Modules/Pharmacokinetics/src/Functors/mitkCurveParameterFunctor.cpp +++ b/Modules/Pharmacokinetics/src/Functors/mitkCurveParameterFunctor.cpp @@ -1,137 +1,137 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkCurveParameterFunctor.h" mitk::SimpleFunctorBase::OutputPixelVectorType mitk::CurveParameterFunctor::Compute(const mitk::SimpleFunctorBase::InputPixelVectorType& value) const { if (this->m_Grid.GetSize() == 0) { itkExceptionMacro("Error. Cannot compute Curve Description Parameters. No Curve Grid set!"); } if (this->m_DescriptorMap.size() == 0) { itkGenericExceptionMacro( << "Error. Cannot compute Curve Description Parameters. No Parameters registered!"); } CurveDescriptionParameterBase::CurveType sample(value.size()); for (CurveDescriptionParameterBase::CurveType::SizeValueType i = 0; i < sample.Size(); ++i) { sample[i] = value [i]; } mitk::SimpleFunctorBase::OutputPixelVectorType result; result.reserve(m_DescriptorMap.size()); //we will have at least this number of values unsigned int i = 0; for (DescriptionParameterMapType::const_iterator pos = m_DescriptorMap.begin(); pos != m_DescriptorMap.end(); ++pos, ++i) { CurveDescriptionParameterBase* paramFct = const_cast (pos->second.GetPointer()); CurveDescriptionParameterBase::DescriptionParameterResultsType fctResults = paramFct->GetCurveDescriptionParameter(sample, this->m_Grid); result.insert(result.end(), fctResults.begin(), fctResults.end()); } if (this->GetDescriptionParameterNames().size() != result.size()) { itkGenericExceptionMacro( << "Error. Curve parameter functor has an invalid state. Number of parameter names and number of computed values does not match. Names count: " << this->GetDescriptionParameterNames().size() << "; value count: " << result.size()); } return result; }; unsigned int mitk::CurveParameterFunctor::GetNumberOfOutputs() const { return GetDescriptionParameterNames().size(); }; mitk::CurveParameterFunctor::GridArrayType mitk::CurveParameterFunctor::GetGrid() const { return m_Grid; }; void mitk::CurveParameterFunctor::ResetDescriptionParameters() { m_DescriptorMap.clear(); }; void mitk::CurveParameterFunctor::RegisterDescriptionParameter(const std::string& parameterName, CurveDescriptionParameterBase* parameterFunction) { CurveDescriptionParameterBase::Pointer paramFunctPtr = parameterFunction; m_DescriptorMap.insert(std::make_pair(parameterName, paramFunctPtr)); }; mitk::CurveParameterFunctor::ParameterNamesType mitk::CurveParameterFunctor::GetDescriptionParameterNames() const { ParameterNamesType result; - for (auto descriptor : m_DescriptorMap) + for (const auto &descriptor : m_DescriptorMap) { CurveDescriptionParameterBase::DescriptionParameterNamesType fctResults = descriptor.second->GetDescriptionParameterName(); if (fctResults.size() > 1) { - for (auto fctName : fctResults) + for (const auto &fctName : fctResults) { result.push_back(descriptor.first + "_" + fctName); } } else { //if the descriptor has only one parameter just use the registered descriptor name. result.push_back(descriptor.first); } } return result; }; const mitk::CurveDescriptionParameterBase* mitk::CurveParameterFunctor::GetDescriptionParameterFunction(const std::string& parameterName) const { const CurveDescriptionParameterBase* result = nullptr; DescriptionParameterMapType::const_iterator pos = m_DescriptorMap.find(parameterName); if (pos != m_DescriptorMap.end()) { result = (pos->second).GetPointer(); } return result; }; mitk::CurveParameterFunctor:: CurveParameterFunctor() {}; mitk::CurveParameterFunctor:: ~CurveParameterFunctor() {}; diff --git a/Modules/PharmacokineticsUI/Qmitk/QmitkDescriptionParameterBackgroundJob.cpp b/Modules/PharmacokineticsUI/Qmitk/QmitkDescriptionParameterBackgroundJob.cpp index 0ab7b626ff..bd0a16a8d3 100644 --- a/Modules/PharmacokineticsUI/Qmitk/QmitkDescriptionParameterBackgroundJob.cpp +++ b/Modules/PharmacokineticsUI/Qmitk/QmitkDescriptionParameterBackgroundJob.cpp @@ -1,123 +1,123 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkDescriptionParameterBackgroundJob.h" #include "mitkModelFitInfo.h" void DescriptionParameterBackgroundJob::OnComputeEvent(::itk::Object* caller, const itk::EventObject& event) { itk::ProgressEvent progressEvent; itk::InitializeEvent initEvent; itk::StartEvent startEvent; itk::EndEvent endEvent; if (progressEvent.CheckEvent(&event)) { mitk::DescriptionParameterImageGeneratorBase* castedReporter = dynamic_cast(caller); emit JobProgress(castedReporter->GetProgress()); } else if (initEvent.CheckEvent(&event)) { emit JobStatusChanged(QString("Initializing description parameter generator")); } else if (startEvent.CheckEvent(&event)) { emit JobStatusChanged(QString("Started parameter computation process.")); } else if (endEvent.CheckEvent(&event)) { emit JobStatusChanged(QString("Finished parameter computation process.")); } } DescriptionParameterBackgroundJob:: DescriptionParameterBackgroundJob(mitk::DescriptionParameterImageGeneratorBase* generator, mitk::DataNode* parentNode) { if (!generator) { mitkThrow() << "Cannot create description parameter background job. Passed fit generator is NULL."; } m_Generator = generator; m_ParentNode = parentNode; m_spCommand = ::itk::MemberCommand::New(); m_spCommand->SetCallbackFunction(this, &DescriptionParameterBackgroundJob::OnComputeEvent); m_ObserverID = m_Generator->AddObserver(::itk::AnyEvent(), m_spCommand); }; mitk::DataNode* DescriptionParameterBackgroundJob:: GetParentNode() const { return m_ParentNode; }; DescriptionParameterBackgroundJob:: ~DescriptionParameterBackgroundJob() { m_Generator->RemoveObserver(m_ObserverID); }; mitk::modelFit::ModelFitResultNodeVectorType DescriptionParameterBackgroundJob::CreateResultNodes( const mitk::DescriptionParameterImageGeneratorBase::ParameterImageMapType& paramimages) { mitk::modelFit::ModelFitResultNodeVectorType results; - for (auto image : paramimages) + for (const auto &image : paramimages) { if (image.second.IsNull()) { mitkThrow() << "Cannot generate result node. Passed parameterImage is null. parameter name: " << image.first; } mitk::DataNode::Pointer result = mitk::DataNode::New(); result->SetData(image.second); result->SetName(image.first); result->SetVisibility(true); results.push_back(result); } return results; }; void DescriptionParameterBackgroundJob:: run() { try { emit JobStatusChanged(QString("Started session...")); m_Generator->Generate(); emit JobStatusChanged(QString("Generate result nodes.")); m_Results = CreateResultNodes(m_Generator->GetParameterImages()); emit ResultsAreAvailable(m_Results, this); } catch (::std::exception& e) { emit Error(QString("Error while processing data. Details: ") + QString::fromLatin1(e.what())); } catch (...) { emit Error(QString("Unkown error when processing the data.")); } emit Finished(); }; diff --git a/Modules/QtWidgets/include/QmitkRenderWindow.h b/Modules/QtWidgets/include/QmitkRenderWindow.h index 124352da5a..668cbc7e69 100644 --- a/Modules/QtWidgets/include/QmitkRenderWindow.h +++ b/Modules/QtWidgets/include/QmitkRenderWindow.h @@ -1,158 +1,156 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QMITKRENDERWINDOW_H #define QMITKRENDERWINDOW_H #include "mitkRenderWindowBase.h" #include "QmitkRenderWindowMenu.h" #include #include #include #include "mitkBaseRenderer.h" #include "mitkInteractionEventConst.h" class QDragEnterEvent; class QDropEvent; class QInputEvent; class QMouseEvent; /** * \ingroup QmitkModule * \brief MITK implementation of the QVTKWidget */ class MITKQTWIDGETS_EXPORT QmitkRenderWindow : public QVTKOpenGLNativeWidget, public mitk::RenderWindowBase { Q_OBJECT public: QmitkRenderWindow( QWidget *parent = nullptr, const QString &name = "unnamed renderwindow", mitk::VtkPropRenderer *renderer = nullptr); ~QmitkRenderWindow() override; /** * \brief Whether Qt events should be passed to parent (default: true) * * With introduction of the QVTKWidget the behaviour regarding Qt events changed. * QVTKWidget "accepts" Qt events like mouse clicks (i.e. set an "accepted" flag). * When this flag is set, Qt fininshed handling of this event -- otherwise it is * reached through to the widget's parent. * * This reaching through to the parent was implicitly required by QmitkMaterialWidget / QmitkMaterialShowCase. * * The default behaviour of QmitkRenderWindow is now to clear the "accepted" flag * of Qt events after they were handled by QVTKWidget. This way parents can also * handle events. * * If you don't want this behaviour, call SetResendQtEvents(true) on your render window. */ virtual void SetResendQtEvents(bool resend); // Set Layout Index to define the Layout Type void SetLayoutIndex(QmitkRenderWindowMenu::LayoutIndex layoutIndex); // Get Layout Index to define the Layout Type QmitkRenderWindowMenu::LayoutIndex GetLayoutIndex(); // MenuWidget need to update the Layout Design List when Layout had changed void UpdateLayoutDesignList(QmitkRenderWindowMenu::LayoutDesign layoutDesign); void UpdateCrosshairVisibility(bool); void UpdateCrosshairRotationMode(int); // Activate or Deactivate MenuWidget. void ActivateMenuWidget(bool state); bool GetActivateMenuWidgetFlag() { return m_MenuWidgetActivated; } // Get it from the QVTKWidget parent vtkRenderWindow *GetVtkRenderWindow() override { return this->renderWindow(); } vtkRenderWindowInteractor *GetVtkRenderWindowInteractor() override { return nullptr; } protected: // catch-all event handler bool event(QEvent *e) override; // overloaded move handler void moveEvent(QMoveEvent *event) override; // overloaded show handler void showEvent(QShowEvent *event) override; // overloaded enter handler void enterEvent(QEvent *) override; // overloaded leave handler void leaveEvent(QEvent *) override; // Overloaded resize handler, see decs in QVTKOpenGLWidget. // Basically, we have to ensure the VTK rendering is updated for each change in window size. void resizeGL(int w, int h) override; /// \brief Simply says we accept the event type. void dragEnterEvent(QDragEnterEvent *event) override; /// \brief If the dropped type is application/x-mitk-datanodes we process the request by converting to mitk::DataNode /// pointers and emitting the NodesDropped signal. void dropEvent(QDropEvent *event) override; - void AdjustRenderWindowMenuVisibility(const QPoint &pos); - Q_SIGNALS: void LayoutDesignChanged(QmitkRenderWindowMenu::LayoutDesign); void ResetView(); void CrosshairRotationModeChanged(int); void CrosshairVisibilityChanged(bool); void moved(); /// \brief Emits a signal to say that this window has had the following nodes dropped on it. void NodesDropped(QmitkRenderWindow *thisWindow, std::vector nodes); void mouseEvent(QMouseEvent *); private Q_SLOTS: void DeferredHideMenu(); private: // Helper Functions to Convert Qt-Events to Mitk-Events mitk::Point2D GetMousePosition(QMouseEvent *me) const; mitk::Point2D GetMousePosition(QWheelEvent *we) const; mitk::InteractionEvent::MouseButtons GetEventButton(QMouseEvent *me) const; mitk::InteractionEvent::MouseButtons GetButtonState(QMouseEvent *me) const; mitk::InteractionEvent::ModifierKeys GetModifiers(QInputEvent *me) const; mitk::InteractionEvent::MouseButtons GetButtonState(QWheelEvent *we) const; std::string GetKeyLetter(QKeyEvent *ke) const; int GetDelta(QWheelEvent *we) const; bool m_ResendQtEvents; QmitkRenderWindowMenu *m_MenuWidget; bool m_MenuWidgetActivated; QmitkRenderWindowMenu::LayoutIndex m_LayoutIndex; vtkSmartPointer m_InternalRenderWindow; }; #endif // QMITKRENDERWINDOW_H diff --git a/Modules/QtWidgets/include/QmitkRenderWindowMenu.h b/Modules/QtWidgets/include/QmitkRenderWindowMenu.h index 705ffc8a19..275f0176cd 100644 --- a/Modules/QtWidgets/include/QmitkRenderWindowMenu.h +++ b/Modules/QtWidgets/include/QmitkRenderWindowMenu.h @@ -1,214 +1,194 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QMITKRENDERWINDOWMENU_H #define QMITKRENDERWINDOWMENU_H -#if defined(_WIN32) || defined(__APPLE__) -#define QMITK_USE_EXTERNAL_RENDERWINDOW_MENU -#endif - // mitk qtwidgets module #include "MitkQtWidgetsExports.h" #include "QmitkMultiWidgetLayoutManager.h" // mitk core #include // qt #include #include #include #include #include #include #include #include /** * \ingroup QmitkModule * \brief The QmitkRenderWindowMenu is a popup Widget which shows * up when the mouse cursor enter a QmitkRenderWindow. * The Menu Widget is located in the right top corner of each * RenderWindow. It includes different settings. For example * the layout design can be changed with the setting button. Switching * between full-screen mode and layout design can be done * with the full-screen button. * The popup Widget can be deactivated with ActivateMenuWidget(false) in * QmitkRenderWindow. * * \sa QmitkRenderWindow * */ class MITKQTWIDGETS_EXPORT QmitkRenderWindowMenu : public QWidget { Q_OBJECT public: using LayoutIndex = mitk::BaseRenderer::ViewDirection; using LayoutDesign = QmitkMultiWidgetLayoutManager::LayoutDesign; QmitkRenderWindowMenu(QWidget *parent = nullptr, Qt::WindowFlags f = nullptr, mitk::BaseRenderer *b = nullptr); ~QmitkRenderWindowMenu() override; /*! Return visibility of settings menu. The menu is connected with m_SettingsButton and includes layout direction (axial, coronal .. ) and layout design (standard layout, 2D images top, 3D bottom ... ). */ bool GetSettingsMenuVisibilty() { if (m_LayoutActionsMenu == nullptr) return false; else return m_LayoutActionsMenu->isVisible(); } /*! Set layout index. Defines layout direction (axial, coronal, sagital or threeD) of the parent. */ void SetLayoutIndex(LayoutIndex layoutIndex); /*! Return layout direction of parent (axial, coronal, sagital or threeD) */ LayoutIndex GetLayoutIndex() { return m_Layout; } /*! Update list of layout design (standard layout, 2D images top, 3D bottom ..). Set action of current layout design to disable and all other to enable. */ void UpdateLayoutDesignList(LayoutDesign layoutDesign); void UpdateCrosshairVisibility(bool visible); void UpdateCrosshairRotationMode(int mode); /*! Move menu widget to correct position (right upper corner). E.g. it is necessary when the full-screen mode is activated.*/ -#ifdef QMITK_USE_EXTERNAL_RENDERWINDOW_MENU - void MoveWidgetToCorrectPos(float opacity); -#else - void MoveWidgetToCorrectPos(float /*opacity*/); -#endif + void MoveWidgetToCorrectPos(); void ShowMenu(); void HideMenu(); protected: /*! Reimplemented from QWidget. The paint event is a request to repaint all or part of a widget.*/ void paintEvent(QPaintEvent *event) override; void CreateMenuWidget(); /*! Create settings menu which contains layout direction and the different layout designs. */ void CreateSettingsWidget(); /*! Change Icon of full-screen button depending on full-screen mode. */ void ChangeFullScreenIcon(); Q_SIGNALS: void ResetView(); // == "global reinit" void CrosshairVisibilityChanged(bool); // \brief int parameters are enum from QmitkStdMultiWidget void CrosshairRotationModeChanged(int); /*! emit signal, when layout design changed by the setting menu.*/ void LayoutDesignChanged(LayoutDesign layoutDesign); -public Q_SLOTS: - - void DeferredShowMenu(); - void DeferredHideMenu(); - /*! This method is responsible for non fluttering of - the renderWindowMenu when mouse cursor moves along the renderWindowMenu*/ - void smoothHide(); - protected Q_SLOTS: - void enterEvent(QEvent * /*e*/) override; - void leaveEvent(QEvent * /*e*/) override; - /// this function is continuously called by a timer /// to do the auto rotation void AutoRotateNextStep(); /// this function is invoked when the auto-rotate action /// is clicked void OnAutoRotationActionTriggered(); void OnTSNumChanged(int); void OnCrosshairMenuAboutToShow(); void OnCrosshairVisibilityChanged(bool); void OnCrosshairRotationModeSelected(QAction *); /*! slot for activating/deactivating the full-screen mode. The slot is connected to the clicked() event of m_FullScreenButton. Activating the full-screen maximize the current widget, deactivating restore If layout design changed by the settings menu, the full-Screen mode is automatically switched to false. */ void OnFullScreenButton(bool checked); /*! Slot for opening setting menu. The slot is connected to the clicked() event of m_SettingsButton. The settings menu includes different layout directions (axial, coronal, sagittal and 3D) as well all layout design (standard layout, 2D images top, 3D bottom ..)*/ void OnLayoutDesignButton(bool checked); void OnSetLayout(LayoutDesign layoutDesign); protected: QToolButton* m_CrosshairModeButton; QToolButton* m_FullScreenButton; QToolButton* m_LayoutDesignButton; QMenu* m_LayoutActionsMenu; QAction* m_DefaultLayoutAction; QAction* m_All2DTop3DBottomLayoutAction; QAction* m_All2DLeft3DRightLayoutAction; QAction* m_OneBigLayoutAction; QAction* m_Only2DHorizontalLayoutAction; QAction* m_Only2DVerticalLayoutAction; QAction* m_OneTop3DBottomLayoutAction; QAction* m_OneLeft3DRightLayoutAction; QAction* m_AllHorizontalLayoutAction; QAction* m_AllVerticalLayoutAction; QAction* m_RemoveOneLayoutAction; QLabel *m_TSLabel; QMenu *m_CrosshairMenu; /*! Flag if full-screen mode is activated or deactivated. */ bool m_FullScreenMode; private: mitk::BaseRenderer::Pointer m_Renderer; QTimer* m_AutoRotationTimer; - QTimer* m_HideTimer; QWidget *m_Parent; //memory because mode is set to default for slice num = 1 static unsigned int m_DefaultThickMode; int m_CrosshairRotationMode; bool m_CrosshairVisibility; LayoutIndex m_Layout; LayoutDesign m_LayoutDesign; LayoutDesign m_OldLayoutDesign; }; #endif // QMITKRENDERWINDOWMENU_H diff --git a/Modules/QtWidgets/src/QmitkAbstractNodeSelectionWidget.cpp b/Modules/QtWidgets/src/QmitkAbstractNodeSelectionWidget.cpp index 39acb451f4..1b3d6c9e98 100644 --- a/Modules/QtWidgets/src/QmitkAbstractNodeSelectionWidget.cpp +++ b/Modules/QtWidgets/src/QmitkAbstractNodeSelectionWidget.cpp @@ -1,426 +1,426 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkAbstractNodeSelectionWidget.h" #include "QmitkModelViewSelectionConnector.h" QmitkAbstractNodeSelectionWidget::QmitkAbstractNodeSelectionWidget(QWidget* parent) : QWidget(parent) , m_InvalidInfo("Error. Select data.") , m_EmptyInfo("Empty. Make a selection.") , m_PopUpTitel("Select a data node") , m_PopUpHint("") , m_IsOptional(false) , m_SelectOnlyVisibleNodes(true) , m_DataStorageDeletedTag(0) , m_LastEmissionAllowance(true) , m_RecursionGuard(false) { } QmitkAbstractNodeSelectionWidget::~QmitkAbstractNodeSelectionWidget() { auto dataStorage = m_DataStorage.Lock(); if (dataStorage.IsNotNull()) { // remove Listener for the data storage itself dataStorage->RemoveObserver(m_DataStorageDeletedTag); // remove "add node listener" from data storage dataStorage->AddNodeEvent.RemoveListener( mitk::MessageDelegate1(this, &QmitkAbstractNodeSelectionWidget::NodeAddedToStorage)); // remove "remove node listener" from data storage dataStorage->RemoveNodeEvent.RemoveListener( mitk::MessageDelegate1(this, &QmitkAbstractNodeSelectionWidget::NodeRemovedFromStorage)); } for (auto& node : m_CurrentInternalSelection) { this->RemoveNodeObserver(node); } } QmitkAbstractNodeSelectionWidget::NodeList QmitkAbstractNodeSelectionWidget::GetSelectedNodes() const { return this->CompileEmitSelection(); } QmitkAbstractNodeSelectionWidget::ConstNodeStdVector QmitkAbstractNodeSelectionWidget::GetSelectedNodesStdVector() const { auto result = this->GetSelectedNodes(); return ConstNodeStdVector(result.begin(), result.end()); } void QmitkAbstractNodeSelectionWidget::SetDataStorage(mitk::DataStorage* dataStorage) { if (m_DataStorage == dataStorage) { return; } auto oldStorage = m_DataStorage.Lock(); if (oldStorage.IsNotNull()) { // remove Listener for the data storage itself oldStorage->RemoveObserver(m_DataStorageDeletedTag); // remove "add node listener" from old data storage oldStorage->AddNodeEvent.RemoveListener( mitk::MessageDelegate1(this, &QmitkAbstractNodeSelectionWidget::NodeAddedToStorage)); // remove "remove node listener" from old data storage oldStorage->RemoveNodeEvent.RemoveListener( mitk::MessageDelegate1(this, &QmitkAbstractNodeSelectionWidget::NodeRemovedFromStorage)); } m_DataStorage = dataStorage; auto newStorage = m_DataStorage.Lock(); if (newStorage.IsNotNull()) { // add Listener for the data storage itself auto command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkAbstractNodeSelectionWidget::SetDataStorageDeleted); m_DataStorageDeletedTag = newStorage->AddObserver(itk::DeleteEvent(), command); // add "add node listener" for new data storage newStorage->AddNodeEvent.AddListener( mitk::MessageDelegate1(this, &QmitkAbstractNodeSelectionWidget::NodeAddedToStorage)); // add remove node listener for new data storage newStorage->RemoveNodeEvent.AddListener( mitk::MessageDelegate1(this, &QmitkAbstractNodeSelectionWidget::NodeRemovedFromStorage)); } this->OnDataStorageChanged(); this->HandleChangeOfInternalSelection({}); } void QmitkAbstractNodeSelectionWidget::SetNodePredicate(const mitk::NodePredicateBase* nodePredicate) { if (m_NodePredicate != nodePredicate) { m_NodePredicate = nodePredicate; this->OnNodePredicateChanged(); NodeList newInternalNodes; for (auto& node : m_CurrentInternalSelection) { if (m_NodePredicate.IsNull() || m_NodePredicate->CheckNode(node)) { newInternalNodes.append(node); } } if (!m_SelectOnlyVisibleNodes) { for (auto& node : m_CurrentExternalSelection) { if (!newInternalNodes.contains(node) && (m_NodePredicate.IsNull() || m_NodePredicate->CheckNode(node))) { newInternalNodes.append(node); } } } this->HandleChangeOfInternalSelection(newInternalNodes); } } void QmitkAbstractNodeSelectionWidget::HandleChangeOfInternalSelection(NodeList newInternalSelection) { if (!EqualNodeSelections(m_CurrentInternalSelection, newInternalSelection)) { this->ReviseSelectionChanged(m_CurrentInternalSelection, newInternalSelection); this->SetCurrentInternalSelection(newInternalSelection); this->OnInternalSelectionChanged(); auto newEmission = this->CompileEmitSelection(); this->EmitSelection(newEmission); this->UpdateInfo(); } } void QmitkAbstractNodeSelectionWidget::SetCurrentSelection(NodeList selectedNodes) { if (!m_RecursionGuard) { m_CurrentExternalSelection = selectedNodes; auto dataStorage = m_DataStorage.Lock(); NodeList newInternalSelection; - for (auto node : selectedNodes) + for (const auto &node : qAsConst(selectedNodes)) { if (dataStorage.IsNotNull() && dataStorage->Exists(node) && (m_NodePredicate.IsNull() || m_NodePredicate->CheckNode(node))) { newInternalSelection.append(node); } } this->HandleChangeOfInternalSelection(newInternalSelection); } } const mitk::NodePredicateBase* QmitkAbstractNodeSelectionWidget::GetNodePredicate() const { return m_NodePredicate; } QString QmitkAbstractNodeSelectionWidget::GetInvalidInfo() const { return m_InvalidInfo; } QString QmitkAbstractNodeSelectionWidget::GetEmptyInfo() const { return m_EmptyInfo; } QString QmitkAbstractNodeSelectionWidget::GetPopUpTitel() const { return m_PopUpTitel; } QString QmitkAbstractNodeSelectionWidget::GetPopUpHint() const { return m_PopUpHint; } bool QmitkAbstractNodeSelectionWidget::GetSelectionIsOptional() const { return m_IsOptional; } bool QmitkAbstractNodeSelectionWidget::GetSelectOnlyVisibleNodes() const { return m_SelectOnlyVisibleNodes; } void QmitkAbstractNodeSelectionWidget::SetSelectOnlyVisibleNodes(bool selectOnlyVisibleNodes) { if (m_SelectOnlyVisibleNodes != selectOnlyVisibleNodes) { m_SelectOnlyVisibleNodes = selectOnlyVisibleNodes; auto newEmission = this->CompileEmitSelection(); this->EmitSelection(newEmission); } } void QmitkAbstractNodeSelectionWidget::SetInvalidInfo(QString info) { m_InvalidInfo = info; this->UpdateInfo(); } void QmitkAbstractNodeSelectionWidget::SetEmptyInfo(QString info) { m_EmptyInfo = info; this->UpdateInfo(); } void QmitkAbstractNodeSelectionWidget::SetPopUpTitel(QString info) { m_PopUpTitel = info; } void QmitkAbstractNodeSelectionWidget::SetPopUpHint(QString info) { m_PopUpHint = info; } void QmitkAbstractNodeSelectionWidget::SetSelectionIsOptional(bool isOptional) { m_IsOptional = isOptional; this->UpdateInfo(); } void QmitkAbstractNodeSelectionWidget::SetDataStorageDeleted() { this->OnDataStorageChanged(); this->HandleChangeOfInternalSelection({}); } void QmitkAbstractNodeSelectionWidget::ReviseSelectionChanged(const NodeList& /*oldInternalSelection*/, NodeList& /*newInternalSelection*/) { } bool QmitkAbstractNodeSelectionWidget::AllowEmissionOfSelection(const NodeList& /*emissionCandidates*/) const { return true; } void QmitkAbstractNodeSelectionWidget::EmitSelection(const NodeList& emissionCandidates) { m_LastEmissionAllowance = this->AllowEmissionOfSelection(emissionCandidates); if (m_LastEmissionAllowance && !EqualNodeSelections(m_LastEmission, emissionCandidates)) { m_RecursionGuard = true; emit CurrentSelectionChanged(emissionCandidates); m_RecursionGuard = false; m_LastEmission = emissionCandidates; } } void QmitkAbstractNodeSelectionWidget::SetCurrentInternalSelection(NodeList selectedNodes) { for (auto& node : m_CurrentInternalSelection) { this->RemoveNodeObserver(node); } m_CurrentInternalSelection = selectedNodes; for (auto& node : m_CurrentInternalSelection) { this->AddNodeObserver(node); } } const QmitkAbstractNodeSelectionWidget::NodeList& QmitkAbstractNodeSelectionWidget::GetCurrentInternalSelection() const { return m_CurrentInternalSelection; } const QmitkAbstractNodeSelectionWidget::NodeList& QmitkAbstractNodeSelectionWidget::GetCurrentExternalSelection() const { return m_CurrentExternalSelection; } void QmitkAbstractNodeSelectionWidget::OnNodePredicateChanged() { } void QmitkAbstractNodeSelectionWidget::OnDataStorageChanged() { } void QmitkAbstractNodeSelectionWidget::OnInternalSelectionChanged() { } void QmitkAbstractNodeSelectionWidget::NodeAddedToStorage(const mitk::DataNode* node) { this->OnNodeAddedToStorage(node); } void QmitkAbstractNodeSelectionWidget::OnNodeAddedToStorage(const mitk::DataNode* /*node*/) { } void QmitkAbstractNodeSelectionWidget::NodeRemovedFromStorage(const mitk::DataNode* node) { this->OnNodeRemovedFromStorage(node); this->RemoveNodeFromSelection(node); } void QmitkAbstractNodeSelectionWidget::OnNodeRemovedFromStorage(const mitk::DataNode* /*node*/) { } QmitkAbstractNodeSelectionWidget::NodeList QmitkAbstractNodeSelectionWidget::CompileEmitSelection() const { NodeList result = m_CurrentInternalSelection; if (!m_SelectOnlyVisibleNodes) { - for (auto node : m_CurrentExternalSelection) + for (const auto &node : m_CurrentExternalSelection) { if (!result.contains(node) && m_NodePredicate.IsNotNull() && !m_NodePredicate->CheckNode(node)) { result.append(node); } } } return result; } void QmitkAbstractNodeSelectionWidget::RemoveNodeFromSelection(const mitk::DataNode* node) { auto newSelection = m_CurrentInternalSelection; auto finding = std::find(std::begin(newSelection), std::end(newSelection), node); if (finding != std::end(newSelection)) { newSelection.erase(finding); this->HandleChangeOfInternalSelection(newSelection); } } void QmitkAbstractNodeSelectionWidget::OnNodeModified(const itk::Object * caller, const itk::EventObject & event) { if (itk::ModifiedEvent().CheckEvent(&event)) { auto node = dynamic_cast(caller); if (node) { if (m_NodePredicate.IsNotNull() && !m_NodePredicate->CheckNode(node)) { this->RemoveNodeFromSelection(node); } else { auto oldAllowance = m_LastEmissionAllowance; auto newEmission = this->CompileEmitSelection(); auto nonConstNode = const_cast(node); if (newEmission.contains(nonConstNode) && (oldAllowance != this->AllowEmissionOfSelection(newEmission))) { this->EmitSelection(newEmission); this->UpdateInfo(); } } } } } void QmitkAbstractNodeSelectionWidget::AddNodeObserver(mitk::DataNode* node) { if (node) { auto modifiedCommand = itk::MemberCommand::New(); modifiedCommand->SetCallbackFunction(this, &QmitkAbstractNodeSelectionWidget::OnNodeModified); auto nodeModifiedObserverTag = node->AddObserver(itk::ModifiedEvent(), modifiedCommand); m_NodeObserverTags.insert(std::make_pair(node, nodeModifiedObserverTag)); } } void QmitkAbstractNodeSelectionWidget::RemoveNodeObserver(mitk::DataNode* node) { if (node) { auto finding = m_NodeObserverTags.find(node); if (finding != std::end(m_NodeObserverTags)) { node->RemoveObserver(finding->second); } else { MITK_ERROR << "Selection widget is in a wrong state. A node should be removed from the internal selection but seems to have no observer. Node:" << node; } m_NodeObserverTags.erase(node); } } diff --git a/Modules/QtWidgets/src/QmitkDataStorageFavoriteNodesInspector.cpp b/Modules/QtWidgets/src/QmitkDataStorageFavoriteNodesInspector.cpp index f64a2a8146..271e19c06d 100644 --- a/Modules/QtWidgets/src/QmitkDataStorageFavoriteNodesInspector.cpp +++ b/Modules/QtWidgets/src/QmitkDataStorageFavoriteNodesInspector.cpp @@ -1,55 +1,55 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include "QmitkDataStorageDefaultListModel.h" #include "mitkNodePredicateAnd.h" #include "QPushButton" #include "QmitkStyleManager.h" QmitkDataStorageFavoriteNodesInspector::QmitkDataStorageFavoriteNodesInspector(QWidget* parent/* = nullptr*/) : QmitkDataStorageListInspector(parent) { auto favoriteNodesButton = new QPushButton(parent); QmitkDataStorageListInspector::m_Controls.verticalLayout->addWidget(favoriteNodesButton, 0, Qt::AlignRight); favoriteNodesButton->setIcon(QmitkStyleManager::ThemeIcon(QStringLiteral(":/Qmitk/favorite_remove.svg"))); favoriteNodesButton->setIconSize(QSize(24, 24)); favoriteNodesButton->setToolTip("Remove selected nodes as favorite"); m_FavoriteNodeSelectionPredicate = mitk::NodePredicateProperty::New("org.mitk.selection.favorite", mitk::BoolProperty::New(true)); m_NodePredicate = m_FavoriteNodeSelectionPredicate; connect(favoriteNodesButton, &QPushButton::clicked, this, &QmitkDataStorageFavoriteNodesInspector::OnFavoriteNodesButtonClicked); } void QmitkDataStorageFavoriteNodesInspector::SetNodePredicate(const mitk::NodePredicateBase* nodePredicate) { mitk::NodePredicateAnd::Pointer combinedPredicate = mitk::NodePredicateAnd::New(); combinedPredicate->AddPredicate(m_FavoriteNodeSelectionPredicate); combinedPredicate->AddPredicate(nodePredicate); QmitkDataStorageListInspector::SetNodePredicate(combinedPredicate); } void QmitkDataStorageFavoriteNodesInspector::OnFavoriteNodesButtonClicked() { auto selectedNodes = GetSelectedNodes(); - for (auto node : selectedNodes) + for (auto node : qAsConst(selectedNodes)) { node->SetBoolProperty("org.mitk.selection.favorite", false); } } diff --git a/Modules/QtWidgets/src/QmitkDnDDataNodeWidget.cpp b/Modules/QtWidgets/src/QmitkDnDDataNodeWidget.cpp index 6a0cfcde32..2b48e0e411 100644 --- a/Modules/QtWidgets/src/QmitkDnDDataNodeWidget.cpp +++ b/Modules/QtWidgets/src/QmitkDnDDataNodeWidget.cpp @@ -1,66 +1,69 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include // mitk qt widgets module #include "QmitkMimeTypes.h" // qt #include +#include +#include +#include QmitkDnDDataNodeWidget::QmitkDnDDataNodeWidget(QWidget* parent /*= nullptr*/) : QFrame(parent) { this->setAcceptDrops(true); } QmitkDnDDataNodeWidget::~QmitkDnDDataNodeWidget() { // nothing here } void QmitkDnDDataNodeWidget::dragEnterEvent(QDragEnterEvent* event) { if (this != event->source()) { event->acceptProposedAction(); } else { event->ignore(); } } void QmitkDnDDataNodeWidget::dragMoveEvent(QDragMoveEvent* event) { if (event->mimeData()->hasFormat(QmitkMimeTypes::DataNodePtrs)) { event->acceptProposedAction(); } else { event->ignore(); } } void QmitkDnDDataNodeWidget::dropEvent(QDropEvent* event) { QList dataNodeList = QmitkMimeTypes::ToDataNodePtrList(event->mimeData()); if (!dataNodeList.empty()) { emit NodesDropped(dataNodeList.toVector().toStdVector()); } event->acceptProposedAction(); } diff --git a/Modules/QtWidgets/src/QmitkIOUtil.cpp b/Modules/QtWidgets/src/QmitkIOUtil.cpp index 3754154f2e..f25869f0e2 100644 --- a/Modules/QtWidgets/src/QmitkIOUtil.cpp +++ b/Modules/QtWidgets/src/QmitkIOUtil.cpp @@ -1,586 +1,586 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkIOUtil.h" #include "mitkCoreServices.h" #include "mitkCustomMimeType.h" #include "mitkFileReaderRegistry.h" #include "mitkFileWriterRegistry.h" #include "mitkIMimeTypeProvider.h" #include "mitkMimeType.h" #include #include #include "QmitkFileReaderOptionsDialog.h" #include "QmitkFileWriterOptionsDialog.h" // QT #include #include #include #include #include // ITK #include #include struct QmitkIOUtil::Impl { struct ReaderOptionsDialogFunctor : public ReaderOptionsFunctorBase { bool operator()(LoadInfo &loadInfo) const override { QmitkFileReaderOptionsDialog dialog(loadInfo); if (dialog.exec() == QDialog::Accepted) { return !dialog.ReuseOptions(); } else { loadInfo.m_Cancel = true; return true; } } }; struct WriterOptionsDialogFunctor : public WriterOptionsFunctorBase { bool operator()(SaveInfo &saveInfo) const override { QmitkFileWriterOptionsDialog dialog(saveInfo); if (dialog.exec() == QDialog::Accepted) { return !dialog.ReuseOptions(); } else { saveInfo.m_Cancel = true; return true; } } }; //! Filename characters that are not valid - depending on the platform (Windows, Posix) static QString s_InvalidFilenameCharacters; //! Return 'true' when: //! - the specified filename contains characters not accepted by the file system (see s_InvalidFilenameCharacters) //! - filename starts or ends in space characters //! //! This test is not exhaustive but just excluding the most common problems. static bool IsIllegalFilename(const QString &fullFilename) { QFileInfo fi(fullFilename); auto filename = fi.fileName(); - for (const auto &ch : s_InvalidFilenameCharacters) + for (const auto &ch : qAsConst(s_InvalidFilenameCharacters)) { if (filename.contains(ch)) { return true; } } if (filename.startsWith(' ' || filename.endsWith(' '))) { return true; } return false; } }; // Impl #if defined(_WIN32) || defined(_WIN64) QString QmitkIOUtil::Impl::s_InvalidFilenameCharacters = "<>:\"/\\|?*"; #else QString QmitkIOUtil::Impl::s_InvalidFilenameCharacters = "/"; #endif struct MimeTypeComparison : public std::unary_function { MimeTypeComparison(const std::string &mimeTypeName) : m_Name(mimeTypeName) {} bool operator()(const mitk::MimeType &mimeType) const { return mimeType.GetName() == m_Name; } const std::string m_Name; }; QString QmitkIOUtil::GetFileOpenFilterString() { QString filters; mitk::CoreServicePointer mimeTypeProvider(mitk::CoreServices::GetMimeTypeProvider()); std::vector categories = mimeTypeProvider->GetCategories(); for (std::vector::iterator cat = categories.begin(); cat != categories.end(); ++cat) { QSet filterExtensions; std::vector mimeTypes = mimeTypeProvider->GetMimeTypesForCategory(*cat); for (std::vector::iterator mt = mimeTypes.begin(); mt != mimeTypes.end(); ++mt) { std::vector extensions = mt->GetExtensions(); for (std::vector::iterator ext = extensions.begin(); ext != extensions.end(); ++ext) { filterExtensions << QString::fromStdString(*ext); } } QString filter = QString::fromStdString(*cat) + " ("; foreach (const QString &extension, filterExtensions) { filter += "*." + extension + " "; } filter = filter.replace(filter.size() - 1, 1, ')'); filters += ";;" + filter; } filters.prepend("All (*)"); return filters; } QList QmitkIOUtil::Load(const QStringList &paths, QWidget *parent) { std::vector loadInfos; foreach (const QString &file, paths) { loadInfos.push_back(LoadInfo(file.toLocal8Bit().constData())); } Impl::ReaderOptionsDialogFunctor optionsCallback; std::string errMsg = Load(loadInfos, nullptr, nullptr, &optionsCallback); if (!errMsg.empty()) { QMessageBox::warning(parent, "Error reading files", QString::fromStdString(errMsg)); mitkThrow() << errMsg; } QList qResult; for (std::vector::const_iterator iter = loadInfos.begin(), iterEnd = loadInfos.end(); iter != iterEnd; ++iter) { for (const auto &elem : iter->m_Output) { qResult << elem; } } return qResult; } mitk::DataStorage::SetOfObjects::Pointer QmitkIOUtil::Load(const QStringList &paths, mitk::DataStorage &storage, QWidget *parent) { std::vector loadInfos; foreach (const QString &file, paths) { loadInfos.push_back(LoadInfo(file.toLocal8Bit().constData())); } mitk::DataStorage::SetOfObjects::Pointer nodeResult = mitk::DataStorage::SetOfObjects::New(); Impl::ReaderOptionsDialogFunctor optionsCallback; std::string errMsg = Load(loadInfos, nodeResult, &storage, &optionsCallback); if (!errMsg.empty()) { QMessageBox::warning(parent, "Error reading files", QString::fromStdString(errMsg)); } return nodeResult; } QList QmitkIOUtil::Load(const QString &path, QWidget *parent) { QStringList paths; paths << path; return Load(paths, parent); } mitk::DataStorage::SetOfObjects::Pointer QmitkIOUtil::Load(const QString &path, mitk::DataStorage &storage, QWidget *parent) { QStringList paths; paths << path; return Load(paths, storage, parent); } QString QmitkIOUtil::Save(const mitk::BaseData *data, const QString &defaultBaseName, const QString &defaultPath, QWidget *parent, bool setPathProperty) { std::vector dataVector; dataVector.push_back(data); QStringList defaultBaseNames; defaultBaseNames.push_back(defaultBaseName); return Save(dataVector, defaultBaseNames, defaultPath, parent, setPathProperty).back(); } QStringList QmitkIOUtil::Save(const std::vector &data, const QStringList &defaultBaseNames, const QString &defaultPath, QWidget *parent, bool setPathProperty) { QStringList fileNames; QString currentPath = defaultPath; std::vector saveInfos; int counter = 0; for (std::vector::const_iterator dataIter = data.begin(), dataIterEnd = data.end(); dataIter != dataIterEnd; ++dataIter, ++counter) { SaveInfo saveInfo(*dataIter, mitk::MimeType(), std::string()); SaveFilter filters(saveInfo); // If there is only the "__all__" filter string, it means there is no writer for this base data if (filters.Size() < 2) { QMessageBox::warning( parent, "Saving not possible", QString("No writer available for type \"%1\"").arg(QString::fromStdString((*dataIter)->GetNameOfClass()))); continue; } // Construct a default path and file name QString filterString = filters.ToString(); QString selectedFilter = filters.GetDefaultFilter(); QString fileName = currentPath; QString dialogTitle = "Save " + QString::fromStdString((*dataIter)->GetNameOfClass()); if (counter < defaultBaseNames.size()) { dialogTitle += " \"" + defaultBaseNames[counter] + "\""; fileName += QDir::separator() + defaultBaseNames[counter]; // We do not append an extension to the file name by default. The extension // is chosen by the user by either selecting a filter or writing the // extension in the file name himself (in the file save dialog). /* QString defaultExt = filters.GetDefaultExtension(); if (!defaultExt.isEmpty()) { fileName += "." + defaultExt; } */ } // Ask the user for a file name QString nextName = QFileDialog::getSaveFileName(parent, dialogTitle, fileName, filterString, &selectedFilter); if (Impl::IsIllegalFilename(nextName)) { QMessageBox::warning( parent, "Saving not possible", QString("File \"%2\" contains invalid characters.\n\nPlease avoid any of \"%1\"") .arg(Impl::s_InvalidFilenameCharacters.split("", QString::SkipEmptyParts).join(" ")) .arg(nextName)); continue; } if (nextName.isEmpty()) { // We stop asking for further file names, but we still save the // data where the user already confirmed the save dialog. break; } fileName = nextName; std::string stdFileName = fileName.toLocal8Bit().constData(); QFileInfo fileInfo(fileName); currentPath = fileInfo.absolutePath(); QString suffix = fileInfo.completeSuffix(); mitk::MimeType filterMimeType = filters.GetMimeTypeForFilter(selectedFilter); mitk::MimeType selectedMimeType; if (fileInfo.exists() && !fileInfo.isFile()) { QMessageBox::warning(parent, "Saving not possible", QString("The path \"%1\" is not a file").arg(fileName)); continue; } // Theoretically, the user could have entered an extension that does not match the selected filter // The extension then has prioritry over the filter // Check if one of the available mime-types match the filename std::vector filterMimeTypes = filters.GetMimeTypes(); for (std::vector::const_iterator mimeTypeIter = filterMimeTypes.begin(), mimeTypeIterEnd = filterMimeTypes.end(); mimeTypeIter != mimeTypeIterEnd; ++mimeTypeIter) { if (mimeTypeIter->MatchesExtension(stdFileName)) { selectedMimeType = *mimeTypeIter; break; } } if (!selectedMimeType.IsValid()) { // The file name either does not contain an extension or the // extension is unknown. // If the file already exists, we stop here because we are unable // to (over)write the file without adding a custom suffix. If the file // does not exist, we add the default extension from the currently // selected filter. If the "All" filter was selected, we only add the // default extensions if the file name itself does not already contain // an extension. if (!fileInfo.exists()) { if (filterMimeType == SaveFilter::ALL_MIMETYPE()) { if (suffix.isEmpty()) { // Use the highest ranked mime-type from the list selectedMimeType = filters.GetDefaultMimeType(); } } else { selectedMimeType = filterMimeType; } if (selectedMimeType.IsValid()) { suffix = QString::fromStdString(selectedMimeType.GetExtensions().front()); fileName += "." + suffix; stdFileName = fileName.toLocal8Bit().constData(); // We changed the file name (added a suffix) so ask in case // the file aready exists. fileInfo = QFileInfo(fileName); if (fileInfo.exists()) { if (!fileInfo.isFile()) { QMessageBox::warning( parent, "Saving not possible", QString("The path \"%1\" is not a file").arg(fileName)); continue; } if (QMessageBox::question( parent, "Replace File", QString("A file named \"%1\" already exists. Do you want to replace it?").arg(fileName)) == QMessageBox::No) { continue; } } } } } if (!selectedMimeType.IsValid()) { // The extension/filename is not valid (no mime-type found), bail out QMessageBox::warning( parent, "Saving not possible", QString("No mime-type available which can handle \"%1\".").arg(fileName)); continue; } if (!QFileInfo(fileInfo.absolutePath()).isWritable()) { QMessageBox::warning(parent, "Saving not possible", QString("The path \"%1\" is not writable").arg(fileName)); continue; } fileNames.push_back(fileName); saveInfo.m_Path = stdFileName; saveInfo.m_MimeType = selectedMimeType; // pre-select the best writer for the chosen mime-type saveInfo.m_WriterSelector.Select(selectedMimeType.GetName()); saveInfos.push_back(saveInfo); } if (!saveInfos.empty()) { Impl::WriterOptionsDialogFunctor optionsCallback; std::string errMsg = Save(saveInfos, &optionsCallback, setPathProperty); if (!errMsg.empty()) { QMessageBox::warning(parent, "Error writing files", QString::fromStdString(errMsg)); mitkThrow() << errMsg; } } return fileNames; } void QmitkIOUtil::SaveBaseDataWithDialog(mitk::BaseData *data, std::string fileName, QWidget * /*parent*/) { Save(data, fileName); } void QmitkIOUtil::SaveSurfaceWithDialog(mitk::Surface::Pointer surface, std::string fileName, QWidget * /*parent*/) { Save(surface, fileName); } void QmitkIOUtil::SaveImageWithDialog(mitk::Image::Pointer image, std::string fileName, QWidget * /*parent*/) { Save(image, fileName); } void QmitkIOUtil::SavePointSetWithDialog(mitk::PointSet::Pointer pointset, std::string fileName, QWidget * /*parent*/) { Save(pointset, fileName); } struct QmitkIOUtil::SaveFilter::Impl { Impl(const mitk::IOUtil::SaveInfo &saveInfo) : m_SaveInfo(saveInfo) { // Add an artifical filter for "All" m_MimeTypes.push_back(ALL_MIMETYPE()); m_FilterStrings.push_back("All (*.*)"); // Get all writers and their mime types for the given base data type // (this is sorted already) std::vector mimeTypes = saveInfo.m_WriterSelector.GetMimeTypes(); for (std::vector::const_reverse_iterator iter = mimeTypes.rbegin(), iterEnd = mimeTypes.rend(); iter != iterEnd; ++iter) { QList filterExtensions; mitk::MimeType mimeType = *iter; std::vector extensions = mimeType.GetExtensions(); for (auto &extension : extensions) { filterExtensions << QString::fromStdString(extension); } if (m_DefaultExtension.isEmpty()) { m_DefaultExtension = QString::fromStdString(extensions.front()); } QString filter = QString::fromStdString(mimeType.GetComment()) + " ("; foreach (const QString &extension, filterExtensions) { filter += "*." + extension + " "; } filter = filter.replace(filter.size() - 1, 1, ')'); m_MimeTypes.push_back(mimeType); m_FilterStrings.push_back(filter); } } const mitk::IOUtil::SaveInfo m_SaveInfo; std::vector m_MimeTypes; QStringList m_FilterStrings; QString m_DefaultExtension; }; mitk::MimeType QmitkIOUtil::SaveFilter::ALL_MIMETYPE() { static mitk::CustomMimeType allMimeType(std::string("__all__")); return mitk::MimeType(allMimeType, -1, -1); } QmitkIOUtil::SaveFilter::SaveFilter(const QmitkIOUtil::SaveFilter &other) : d(new Impl(*other.d)) { } QmitkIOUtil::SaveFilter::SaveFilter(const SaveInfo &saveInfo) : d(new Impl(saveInfo)) { } QmitkIOUtil::SaveFilter &QmitkIOUtil::SaveFilter::operator=(const QmitkIOUtil::SaveFilter &other) { d.reset(new Impl(*other.d)); return *this; } std::vector QmitkIOUtil::SaveFilter::GetMimeTypes() const { return d->m_MimeTypes; } QString QmitkIOUtil::SaveFilter::GetFilterForMimeType(const std::string &mimeType) const { std::vector::const_iterator iter = std::find_if(d->m_MimeTypes.begin(), d->m_MimeTypes.end(), MimeTypeComparison(mimeType)); if (iter == d->m_MimeTypes.end()) { return QString(); } int index = static_cast(iter - d->m_MimeTypes.begin()); if (index < 0 || index >= d->m_FilterStrings.size()) { return QString(); } return d->m_FilterStrings[index]; } mitk::MimeType QmitkIOUtil::SaveFilter::GetMimeTypeForFilter(const QString &filter) const { int index = d->m_FilterStrings.indexOf(filter); if (index < 0) { return mitk::MimeType(); } return d->m_MimeTypes[index]; } QString QmitkIOUtil::SaveFilter::GetDefaultFilter() const { if (d->m_FilterStrings.size() > 1) { return d->m_FilterStrings.at(1); } else if (d->m_FilterStrings.size() > 0) { return d->m_FilterStrings.front(); } return QString(); } QString QmitkIOUtil::SaveFilter::GetDefaultExtension() const { return d->m_DefaultExtension; } mitk::MimeType QmitkIOUtil::SaveFilter::GetDefaultMimeType() const { if (d->m_MimeTypes.size() > 1) { return d->m_MimeTypes.at(1); } else if (d->m_MimeTypes.size() > 0) { return d->m_MimeTypes.front(); } return mitk::MimeType(); } QString QmitkIOUtil::SaveFilter::ToString() const { return d->m_FilterStrings.join(";;"); } int QmitkIOUtil::SaveFilter::Size() const { return d->m_FilterStrings.size(); } bool QmitkIOUtil::SaveFilter::IsEmpty() const { return d->m_FilterStrings.isEmpty(); } bool QmitkIOUtil::SaveFilter::ContainsMimeType(const std::string &mimeType) { return std::find_if(d->m_MimeTypes.begin(), d->m_MimeTypes.end(), MimeTypeComparison(mimeType)) != d->m_MimeTypes.end(); } diff --git a/Modules/QtWidgets/src/QmitkModelViewSelectionConnector.cpp b/Modules/QtWidgets/src/QmitkModelViewSelectionConnector.cpp index 93a75e0e09..a52e840471 100644 --- a/Modules/QtWidgets/src/QmitkModelViewSelectionConnector.cpp +++ b/Modules/QtWidgets/src/QmitkModelViewSelectionConnector.cpp @@ -1,185 +1,185 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 common plugin #include "QmitkModelViewSelectionConnector.h" // qt widgets module #include "QmitkCustomVariants.h" #include "QmitkEnums.h" QmitkModelViewSelectionConnector::QmitkModelViewSelectionConnector() : m_Model(nullptr) , m_View(nullptr) , m_SelectOnlyVisibleNodes(false) { // nothing here } void QmitkModelViewSelectionConnector::SetView(QAbstractItemView* view) { if (nullptr != m_View) { disconnect(m_View->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), this, SLOT(ChangeModelSelection(const QItemSelection&, const QItemSelection&))); } // reset model-view pair and check for valid function argument m_View = nullptr; if (nullptr == view) { mitkThrow() << "Invalid item view. To use the model-view selection connector please specify a valid 'QAbstractItemView'."; } auto storageModel = dynamic_cast(view->model()); if (storageModel == nullptr) { mitkThrow() << "Invalid data model. To use the model-view selection connector please set a valid 'QmitkAbstractDataStorageModel' for the given item view."; } // a valid item view and a valid data model was found m_View = view; m_Model = storageModel; connect(m_View->selectionModel(), SIGNAL(selectionChanged(const QItemSelection&, const QItemSelection&)), SLOT(ChangeModelSelection(const QItemSelection&, const QItemSelection&))); } void QmitkModelViewSelectionConnector::SetSelectOnlyVisibleNodes(bool selectOnlyVisibleNodes) { m_SelectOnlyVisibleNodes = selectOnlyVisibleNodes; } void QmitkModelViewSelectionConnector::SetCurrentSelection(QList selectedNodes) { if (nullptr == m_Model || nullptr == m_View) { return; } // filter input nodes and return the modified input node list QList filteredNodes = FilterNodeList(selectedNodes); bool equal = EqualNodeSelections(this->GetInternalSelectedNodes(), filteredNodes); if (equal) { return; } if (!m_SelectOnlyVisibleNodes) { // store the unmodified selection m_NonVisibleSelection = selectedNodes; // remove the nodes in the original selection that are already contained in the filtered input node list // this will keep the selection of the original nodes that are not presented by the current view unmodified, but allows to change the selection of the filtered nodes // later, the nodes of the 'm_NonVisibleSelection' member have to be added again to the list of selected (filtered) nodes, if a selection is sent from the current view (see 'ModelSelectionChanged') auto lambda = [&filteredNodes](mitk::DataNode::Pointer original) { return filteredNodes.contains(original); }; m_NonVisibleSelection.erase(std::remove_if(m_NonVisibleSelection.begin(), m_NonVisibleSelection.end(), lambda), m_NonVisibleSelection.end()); } // create new selection by retrieving the corresponding indices of the (filtered) nodes QItemSelection newCurrentSelection; - for (const auto& node : filteredNodes) + for (const auto& node : qAsConst(filteredNodes)) { QModelIndexList matched = m_Model->match(m_Model->index(0, 0), QmitkDataNodeRole, QVariant::fromValue(node), 1, Qt::MatchRecursive); if (!matched.empty()) { newCurrentSelection.select(matched.front(), matched.front()); } } m_View->selectionModel()->select(newCurrentSelection, QItemSelectionModel::ClearAndSelect); } void QmitkModelViewSelectionConnector::ChangeModelSelection(const QItemSelection& /*selected*/, const QItemSelection& /*deselected*/) { emit CurrentSelectionChanged(GetSelectedNodes()); } bool QmitkModelViewSelectionConnector::GetSelectOnlyVisibleNodes() const { return m_SelectOnlyVisibleNodes; } QList QmitkModelViewSelectionConnector::GetSelectedNodes() const { auto nodes = GetInternalSelectedNodes(); if (!m_SelectOnlyVisibleNodes) { // add the non-visible nodes from the original selection nodes.append(m_NonVisibleSelection); } return nodes; } QList QmitkModelViewSelectionConnector::GetInternalSelectedNodes() const { if (nullptr == m_Model || nullptr == m_View) { return QList(); } QList nodes; QModelIndexList selectedIndexes = m_View->selectionModel()->selectedIndexes(); - for (const auto& index : selectedIndexes) + for (const auto& index : qAsConst(selectedIndexes)) { QVariant qvariantDataNode = m_Model->data(index, QmitkDataNodeRole); if (qvariantDataNode.canConvert()) { nodes.push_back(qvariantDataNode.value()); } } return nodes; } QList QmitkModelViewSelectionConnector::FilterNodeList(const QList& nodes) const { if (nodes.isEmpty()) { return QList(); } if (nullptr == m_Model) { return nodes; } auto nodePredicate = m_Model->GetNodePredicate(); if (nullptr == nodePredicate) { // no filter set return nodes; } QList result; for (const auto& node : nodes) { if (true == nodePredicate->CheckNode(node)) { result.push_back(node); } } return result; } bool MITKQTWIDGETS_EXPORT EqualNodeSelections(const QList& selection1, const QList& selection2) { if (selection1.size() == selection2.size()) { // lambda to compare node pointer inside both lists auto lambda = [](mitk::DataNode::Pointer lhs, mitk::DataNode::Pointer rhs) { return lhs == rhs; }; return std::is_permutation(selection1.begin(), selection1.end(), selection2.begin(), selection2.end(), lambda); } return false; } diff --git a/Modules/QtWidgets/src/QmitkMultiWidgetLayoutSelectionWidget.cpp b/Modules/QtWidgets/src/QmitkMultiWidgetLayoutSelectionWidget.cpp index d47adcc5f5..0575c4a260 100644 --- a/Modules/QtWidgets/src/QmitkMultiWidgetLayoutSelectionWidget.cpp +++ b/Modules/QtWidgets/src/QmitkMultiWidgetLayoutSelectionWidget.cpp @@ -1,76 +1,76 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkMultiWidgetLayoutSelectionWidget.h" QmitkMultiWidgetLayoutSelectionWidget::QmitkMultiWidgetLayoutSelectionWidget(QWidget* parent/* = 0*/) : QWidget(parent) { Init(); } void QmitkMultiWidgetLayoutSelectionWidget::Init() { ui.setupUi(this); auto stylesheet = "QTableWidget::item{background-color: white;}\nQTableWidget::item:selected{background-color: #1C97EA;}"; ui.tableWidget->setStyleSheet(stylesheet); connect(ui.tableWidget, &QTableWidget::itemSelectionChanged, this, &QmitkMultiWidgetLayoutSelectionWidget::OnTableItemSelectionChanged); connect(ui.setLayoutPushButton, &QPushButton::clicked, this, &QmitkMultiWidgetLayoutSelectionWidget::OnSetLayoutButtonClicked); } void QmitkMultiWidgetLayoutSelectionWidget::OnTableItemSelectionChanged() { QItemSelectionModel* selectionModel = ui.tableWidget->selectionModel(); int row = 0; int column = 0; QModelIndexList indices = selectionModel->selectedIndexes(); if (indices.size() > 0) { row = indices[0].row(); column = indices[0].column(); QModelIndex topLeft = ui.tableWidget->model()->index(0, 0, QModelIndex()); QModelIndex bottomRight = ui.tableWidget->model()->index(row, column, QModelIndex()); QItemSelection cellSelection; cellSelection.select(topLeft, bottomRight); selectionModel->select(cellSelection, QItemSelectionModel::Select); } } void QmitkMultiWidgetLayoutSelectionWidget::OnSetLayoutButtonClicked() { int row = 0; int column = 0; QModelIndexList indices = ui.tableWidget->selectionModel()->selectedIndexes(); if (indices.size() > 0) { // find largest row and column - for (const auto& modelIndex : indices) + for (const auto& modelIndex : qAsConst(indices)) { if (modelIndex.row() > row) { row = modelIndex.row(); } if (modelIndex.column() > column) { column = modelIndex.column(); } } close(); emit LayoutSet(row+1, column+1); } } diff --git a/Modules/QtWidgets/src/QmitkPropertyItemModel.cpp b/Modules/QtWidgets/src/QmitkPropertyItemModel.cpp index f65d8888e1..66b89810ff 100644 --- a/Modules/QtWidgets/src/QmitkPropertyItemModel.cpp +++ b/Modules/QtWidgets/src/QmitkPropertyItemModel.cpp @@ -1,474 +1,474 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkPropertyItemModel.h" #include "QmitkPropertyItem.h" #include #include #include #include #include #include #include #include namespace { QColor MitkToQt(const mitk::Color& color) { return QColor(color.GetRed() * 255, color.GetGreen() * 255, color.GetBlue() * 255); } mitk::BaseProperty* GetBaseProperty(const QVariant& data) { return data.isValid() ? reinterpret_cast(data.value()) : nullptr; } mitk::Color QtToMitk(const QColor& color) { mitk::Color mitkColor; mitkColor.SetRed(color.red() / 255.0f); mitkColor.SetGreen(color.green() / 255.0f); mitkColor.SetBlue(color.blue() / 255.0f); return mitkColor; } } class PropertyEqualTo { public: PropertyEqualTo(const mitk::BaseProperty *property) : m_Property(property) {} bool operator()(const mitk::PropertyList::PropertyMapElementType &pair) const { return pair.second.GetPointer() == m_Property; } private: const mitk::BaseProperty *m_Property; }; QmitkPropertyItemModel::QmitkPropertyItemModel(QObject *parent) : QAbstractItemModel(parent), m_PropertyAliases(mitk::CoreServices::GetPropertyAliases()), m_PropertyFilters(mitk::CoreServices::GetPropertyFilters()) { this->CreateRootItem(); } QmitkPropertyItemModel::~QmitkPropertyItemModel() { this->SetNewPropertyList(nullptr); } int QmitkPropertyItemModel::columnCount(const QModelIndex &parent) const { if (parent.isValid()) return static_cast(parent.internalPointer())->GetColumnCount(); else return m_RootItem->GetColumnCount(); } void QmitkPropertyItemModel::CreateRootItem() { QList rootData; rootData << "Property" << "Value"; m_RootItem.reset(new QmitkPropertyItem(rootData)); this->beginResetModel(); this->endResetModel(); } QVariant QmitkPropertyItemModel::data(const QModelIndex &index, int role) const { if (!index.isValid()) return QVariant(); mitk::BaseProperty *property = index.column() == 1 ? GetBaseProperty(static_cast(index.internalPointer())->GetData(1)) : nullptr; if (role == Qt::DisplayRole) { if (index.column() == 0) { return static_cast(index.internalPointer())->GetData(0); } else if (index.column() == 1 && property != nullptr) { if (auto colorProperty = dynamic_cast(property)) return MitkToQt(colorProperty->GetValue()); else if (dynamic_cast(property) == nullptr) return QString::fromStdString(property->GetValueAsString()); } } else if (index.column() == 1 && property != nullptr) { if (role == Qt::CheckStateRole) { if (auto boolProperty = dynamic_cast(property)) return boolProperty->GetValue() ? Qt::Checked : Qt::Unchecked; } else if (role == Qt::EditRole) { if (dynamic_cast(property) != nullptr) { return QString::fromStdString(property->GetValueAsString()); } else if (auto intProperty = dynamic_cast(property)) { return intProperty->GetValue(); } else if (auto floatProperty = dynamic_cast(property)) { return floatProperty->GetValue(); } else if (auto doubleProperty = dynamic_cast(property)) { return doubleProperty->GetValue(); } else if (auto enumProperty = dynamic_cast(property)) { QStringList values; for (mitk::EnumerationProperty::EnumConstIterator it = enumProperty->Begin(); it != enumProperty->End(); it++) values << QString::fromStdString(it->second); return values; } else if (auto colorProperty = dynamic_cast(property)) { return MitkToQt(colorProperty->GetValue()); } } else if (role == mitk::PropertyRole) { return QVariant::fromValue(property); } } return QVariant(); } QModelIndex QmitkPropertyItemModel::FindProperty(const mitk::BaseProperty *property) { if (property == nullptr) return QModelIndex(); if (m_PropertyList.IsExpired()) return QModelIndex(); auto propertyMap = m_PropertyList.Lock()->GetMap(); auto it = std::find_if(propertyMap->begin(), propertyMap->end(), PropertyEqualTo(property)); if (it == propertyMap->end()) return QModelIndex(); QString name = QString::fromStdString(it->first); if (!name.contains('.')) { QModelIndexList item = this->match(index(0, 0), Qt::DisplayRole, name, 1, Qt::MatchExactly); if (!item.empty()) return item[0]; } else { QStringList names = name.split('.'); QModelIndexList items = this->match(index(0, 0), Qt::DisplayRole, names.last(), -1, Qt::MatchRecursive | Qt::MatchExactly); - for (auto item : items) + for (auto item : qAsConst(items)) { QModelIndex candidate = item; for (int i = names.length() - 1; i != 0; --i) { QModelIndex parent = item.parent(); if (parent.parent() == QModelIndex()) { if (parent.data() != names.first()) break; return candidate; } if (parent.data() != names[i - 1]) break; item = parent; } } } return QModelIndex(); } Qt::ItemFlags QmitkPropertyItemModel::flags(const QModelIndex &index) const { Qt::ItemFlags flags = QAbstractItemModel::flags(index); if (index.column() == 1) { if (index.data(Qt::EditRole).isValid()) flags |= Qt::ItemIsEditable; if (index.data(Qt::CheckStateRole).isValid()) flags |= Qt::ItemIsUserCheckable; } return flags; } mitk::PropertyList *QmitkPropertyItemModel::GetPropertyList() const { return m_PropertyList.Lock().GetPointer(); } QVariant QmitkPropertyItemModel::headerData(int section, Qt::Orientation orientation, int role) const { if (orientation == Qt::Horizontal && role == Qt::DisplayRole) return m_RootItem->GetData(section); return QVariant(); } QModelIndex QmitkPropertyItemModel::index(int row, int column, const QModelIndex &parent) const { if (!this->hasIndex(row, column, parent)) return QModelIndex(); QmitkPropertyItem *parentItem = parent.isValid() ? static_cast(parent.internalPointer()) : m_RootItem.get(); QmitkPropertyItem *childItem = parentItem->GetChild(row); return childItem != nullptr ? this->createIndex(row, column, childItem) : QModelIndex(); } void QmitkPropertyItemModel::OnPropertyListModified() { this->SetNewPropertyList(m_PropertyList.Lock()); } void QmitkPropertyItemModel::OnPropertyListDeleted() { this->CreateRootItem(); } void QmitkPropertyItemModel::OnPropertyModified(const itk::Object *property, const itk::EventObject &) { QModelIndex index = this->FindProperty(static_cast(property)); if (index != QModelIndex()) emit dataChanged(index, index); } QModelIndex QmitkPropertyItemModel::parent(const QModelIndex &child) const { if (!child.isValid()) return QModelIndex(); QmitkPropertyItem *parentItem = static_cast(child.internalPointer())->GetParent(); if (parentItem == m_RootItem.get()) return QModelIndex(); return this->createIndex(parentItem->GetRow(), 0, parentItem); } int QmitkPropertyItemModel::rowCount(const QModelIndex &parent) const { if (parent.column() > 0) return 0; QmitkPropertyItem *parentItem = parent.isValid() ? static_cast(parent.internalPointer()) : m_RootItem.get(); return parentItem->GetChildCount(); } bool QmitkPropertyItemModel::setData(const QModelIndex &index, const QVariant &value, int role) { if (!index.isValid() || index.column() != 1 || (role != Qt::EditRole && role != Qt::CheckStateRole)) return false; mitk::BaseProperty *property = GetBaseProperty(static_cast(index.internalPointer())->GetData(1)); if (property == nullptr) return false; if (mitk::BoolProperty *boolProperty = dynamic_cast(property)) { boolProperty->SetValue(value.toInt() == Qt::Checked ? true : false); } else if (mitk::StringProperty *stringProperty = dynamic_cast(property)) { stringProperty->SetValue(value.toString().toStdString()); } else if (mitk::IntProperty *intProperty = dynamic_cast(property)) { intProperty->SetValue(value.toInt()); } else if (mitk::FloatProperty *floatProperty = dynamic_cast(property)) { floatProperty->SetValue(value.toFloat()); } else if (mitk::DoubleProperty *doubleProperty = dynamic_cast(property)) { doubleProperty->SetValue(value.toDouble()); } else if (mitk::EnumerationProperty *enumProperty = dynamic_cast(property)) { std::string selection = value.toString().toStdString(); if (selection != enumProperty->GetValueAsString() && enumProperty->IsValidEnumerationValue(selection)) enumProperty->SetValue(selection); } else if (mitk::ColorProperty *colorProperty = dynamic_cast(property)) { colorProperty->SetValue(QtToMitk(value.value())); } auto propertyList = m_PropertyList.Lock(); propertyList->Modified(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); return true; } void QmitkPropertyItemModel::SetNewPropertyList(mitk::PropertyList *newPropertyList) { typedef mitk::PropertyList::PropertyMap PropertyMap; this->beginResetModel(); if (!m_PropertyList.IsExpired()) { auto propertyList = m_PropertyList.Lock(); propertyList->RemoveObserver(m_PropertyListDeletedTag); propertyList->RemoveObserver(m_PropertyListModifiedTag); const PropertyMap *propertyMap = m_PropertyList.Lock()->GetMap(); for (PropertyMap::const_iterator propertyIt = propertyMap->begin(); propertyIt != propertyMap->end(); ++propertyIt) { std::map::const_iterator tagIt = m_PropertyModifiedTags.find(propertyIt->first); if (tagIt != m_PropertyModifiedTags.end()) propertyIt->second->RemoveObserver(tagIt->second); tagIt = m_PropertyDeletedTags.find(propertyIt->first); if (tagIt != m_PropertyDeletedTags.end()) propertyIt->second->RemoveObserver(tagIt->second); } m_PropertyModifiedTags.clear(); m_PropertyDeletedTags.clear(); } m_PropertyList = newPropertyList; if (!m_PropertyList.IsExpired()) { auto onPropertyListModified = itk::SimpleMemberCommand::New(); onPropertyListModified->SetCallbackFunction(this, &QmitkPropertyItemModel::OnPropertyListModified); m_PropertyListModifiedTag = m_PropertyList.Lock()->AddObserver(itk::ModifiedEvent(), onPropertyListModified); auto onPropertyListDeleted = itk::SimpleMemberCommand::New(); onPropertyListDeleted->SetCallbackFunction(this, &QmitkPropertyItemModel::OnPropertyListDeleted); m_PropertyListDeletedTag = m_PropertyList.Lock()->AddObserver(itk::DeleteEvent(), onPropertyListDeleted); auto modifiedCommand = itk::MemberCommand::New(); modifiedCommand->SetCallbackFunction(this, &QmitkPropertyItemModel::OnPropertyModified); const PropertyMap *propertyMap = m_PropertyList.Lock()->GetMap(); for (PropertyMap::const_iterator it = propertyMap->begin(); it != propertyMap->end(); ++it) m_PropertyModifiedTags.insert( std::make_pair(it->first, it->second->AddObserver(itk::ModifiedEvent(), modifiedCommand))); } this->CreateRootItem(); if (m_PropertyList != nullptr && !m_PropertyList.Lock()->IsEmpty()) { mitk::PropertyList::PropertyMap filteredProperties; bool filterProperties = false; if (m_PropertyFilters->HasFilter() || m_PropertyFilters->HasFilter(m_ClassName.toStdString())) { filteredProperties = m_PropertyFilters->ApplyFilter(*m_PropertyList.Lock()->GetMap(), m_ClassName.toStdString()); filterProperties = true; } const mitk::PropertyList::PropertyMap *propertyMap = !filterProperties ? m_PropertyList.Lock()->GetMap() : &filteredProperties; mitk::PropertyList::PropertyMap::const_iterator end = propertyMap->end(); for (mitk::PropertyList::PropertyMap::const_iterator iter = propertyMap->begin(); iter != end; ++iter) { std::vector aliases; aliases = m_PropertyAliases->GetAliases(iter->first, m_ClassName.toStdString()); if (aliases.empty() && !m_ClassName.isEmpty()) aliases = m_PropertyAliases->GetAliases(iter->first); if (aliases.empty()) { QList data; data << QString::fromStdString(iter->first) << QVariant::fromValue((reinterpret_cast(iter->second.GetPointer()))); m_RootItem->AppendChild(new QmitkPropertyItem(data)); } else { std::vector::const_iterator end = aliases.end(); for (std::vector::const_iterator aliasIter = aliases.begin(); aliasIter != end; ++aliasIter) { QList data; data << QString::fromStdString(*aliasIter) << QVariant::fromValue((reinterpret_cast(iter->second.GetPointer()))); m_RootItem->AppendChild(new QmitkPropertyItem(data)); } } } } this->endResetModel(); } void QmitkPropertyItemModel::SetPropertyList(mitk::PropertyList *propertyList, const QString &className) { if (m_PropertyList != propertyList) { m_ClassName = className; this->SetNewPropertyList(propertyList); } } void QmitkPropertyItemModel::Update() { this->SetNewPropertyList(m_PropertyList.Lock()); } diff --git a/Modules/QtWidgets/src/QmitkRenderWindow.cpp b/Modules/QtWidgets/src/QmitkRenderWindow.cpp index bf51c1fc4a..eecc0b070f 100644 --- a/Modules/QtWidgets/src/QmitkRenderWindow.cpp +++ b/Modules/QtWidgets/src/QmitkRenderWindow.cpp @@ -1,468 +1,464 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkRenderWindow.h" #include "mitkInteractionKeyEvent.h" #include "mitkInternalEvent.h" #include "mitkMouseDoubleClickEvent.h" #include "mitkMouseMoveEvent.h" #include "mitkMousePressEvent.h" #include "mitkMouseReleaseEvent.h" #include "mitkMouseWheelEvent.h" #include #include #include #include #include #include #include #include #include #include #include "QmitkMimeTypes.h" #include "QmitkRenderWindowMenu.h" QmitkRenderWindow::QmitkRenderWindow(QWidget *parent, const QString &name, mitk::VtkPropRenderer *) : QVTKOpenGLNativeWidget(parent) , m_ResendQtEvents(true) , m_MenuWidget(nullptr) , m_MenuWidgetActivated(false) , m_LayoutIndex(QmitkRenderWindowMenu::LayoutIndex::AXIAL) { m_InternalRenderWindow = vtkSmartPointer::New(); m_InternalRenderWindow->SetMultiSamples(0); m_InternalRenderWindow->SetAlphaBitPlanes(0); setRenderWindow(m_InternalRenderWindow); Initialize(name.toStdString().c_str()); setFocusPolicy(Qt::StrongFocus); setMouseTracking(true); QSizePolicy sizePolicy(QSizePolicy::Expanding, QSizePolicy::Expanding); setSizePolicy(sizePolicy); } QmitkRenderWindow::~QmitkRenderWindow() { Destroy(); // Destroy mitkRenderWindowBase } void QmitkRenderWindow::SetResendQtEvents(bool resend) { m_ResendQtEvents = resend; } void QmitkRenderWindow::SetLayoutIndex(QmitkRenderWindowMenu::LayoutIndex layoutIndex) { m_LayoutIndex = layoutIndex; if (nullptr != m_MenuWidget) { m_MenuWidget->SetLayoutIndex(layoutIndex); } } QmitkRenderWindowMenu::LayoutIndex QmitkRenderWindow::GetLayoutIndex() { if (nullptr != m_MenuWidget) { return m_MenuWidget->GetLayoutIndex(); } else { return QmitkRenderWindowMenu::LayoutIndex::AXIAL; } } void QmitkRenderWindow::UpdateLayoutDesignList(QmitkRenderWindowMenu::LayoutDesign layoutDesign) { if (nullptr != m_MenuWidget) { m_MenuWidget->UpdateLayoutDesignList(layoutDesign); } } void QmitkRenderWindow::UpdateCrosshairVisibility(bool visible) { m_MenuWidget->UpdateCrosshairVisibility(visible); } void QmitkRenderWindow::UpdateCrosshairRotationMode(int mode) { m_MenuWidget->UpdateCrosshairRotationMode(mode); } void QmitkRenderWindow::ActivateMenuWidget(bool state) { if (nullptr == m_MenuWidget) { m_MenuWidget = new QmitkRenderWindowMenu(this, nullptr, m_Renderer); m_MenuWidget->SetLayoutIndex(m_LayoutIndex); } m_MenuWidgetActivated = state; if (m_MenuWidgetActivated) { connect(m_MenuWidget, &QmitkRenderWindowMenu::LayoutDesignChanged, this, &QmitkRenderWindow::LayoutDesignChanged); connect(m_MenuWidget, &QmitkRenderWindowMenu::ResetView, this, &QmitkRenderWindow::ResetView); connect(m_MenuWidget, &QmitkRenderWindowMenu::CrosshairVisibilityChanged, this, &QmitkRenderWindow::CrosshairVisibilityChanged); connect(m_MenuWidget, &QmitkRenderWindowMenu::CrosshairRotationModeChanged, this, &QmitkRenderWindow::CrosshairRotationModeChanged); } else { disconnect(m_MenuWidget, &QmitkRenderWindowMenu::LayoutDesignChanged, this, &QmitkRenderWindow::LayoutDesignChanged); disconnect(m_MenuWidget, &QmitkRenderWindowMenu::ResetView, this, &QmitkRenderWindow::ResetView); disconnect(m_MenuWidget, &QmitkRenderWindowMenu::CrosshairVisibilityChanged, this, &QmitkRenderWindow::CrosshairVisibilityChanged); disconnect(m_MenuWidget, &QmitkRenderWindowMenu::CrosshairRotationModeChanged, this, &QmitkRenderWindow::CrosshairRotationModeChanged); m_MenuWidget->hide(); } } void QmitkRenderWindow::moveEvent(QMoveEvent *event) { QVTKOpenGLNativeWidget::moveEvent(event); // after a move the overlays need to be positioned emit moved(); } void QmitkRenderWindow::showEvent(QShowEvent *event) { QVTKOpenGLNativeWidget::showEvent(event); // this singleshot is necessary to have the overlays positioned correctly after initial show // simple call of moved() is no use here!! QTimer::singleShot(0, this, SIGNAL(moved())); } bool QmitkRenderWindow::event(QEvent* e) { mitk::InteractionEvent::Pointer mitkEvent = nullptr; switch (e->type()) { case QEvent::MouseMove: { auto me = static_cast(e); - this->AdjustRenderWindowMenuVisibility(me->pos()); mitkEvent = mitk::MouseMoveEvent::New(m_Renderer, GetMousePosition(me), GetButtonState(me), GetModifiers(me)); break; } case QEvent::MouseButtonPress: { auto me = static_cast(e); mitkEvent = mitk::MousePressEvent::New( m_Renderer, GetMousePosition(me), GetButtonState(me), GetModifiers(me), GetEventButton(me)); break; } case QEvent::MouseButtonRelease: { auto me = static_cast(e); mitkEvent = mitk::MouseReleaseEvent::New( m_Renderer, GetMousePosition(me), GetButtonState(me), GetModifiers(me), GetEventButton(me)); break; } case QEvent::MouseButtonDblClick: { auto me = static_cast(e); mitkEvent = mitk::MouseDoubleClickEvent::New( m_Renderer, GetMousePosition(me), GetButtonState(me), GetModifiers(me), GetEventButton(me)); break; } case QEvent::Wheel: { auto we = static_cast(e); mitkEvent = mitk::MouseWheelEvent::New( m_Renderer, GetMousePosition(we), GetButtonState(we), GetModifiers(we), GetDelta(we)); break; } case QEvent::KeyPress: { auto ke = static_cast(e); mitkEvent = mitk::InteractionKeyEvent::New(m_Renderer, GetKeyLetter(ke), GetModifiers(ke)); break; } + case QEvent::Resize: + { + if (nullptr != m_MenuWidget) + m_MenuWidget->MoveWidgetToCorrectPos(); + } default: { break; } } if (mitkEvent != nullptr) { if (this->HandleEvent(mitkEvent.GetPointer())) { return m_ResendQtEvents ? false : true; } } return QVTKOpenGLNativeWidget::event(e); } void QmitkRenderWindow::enterEvent(QEvent *e) { // TODO implement new event QVTKOpenGLNativeWidget::enterEvent(e); + + if (nullptr != m_MenuWidget) + m_MenuWidget->ShowMenu(); } void QmitkRenderWindow::leaveEvent(QEvent *e) { mitk::InternalEvent::Pointer internalEvent = mitk::InternalEvent::New(this->m_Renderer, nullptr, "LeaveRenderWindow"); this->HandleEvent(internalEvent.GetPointer()); if (nullptr != m_MenuWidget) - { - m_MenuWidget->smoothHide(); - } + m_MenuWidget->HideMenu(); QVTKOpenGLNativeWidget::leaveEvent(e); } void QmitkRenderWindow::resizeGL(int w, int h) { QVTKOpenGLNativeWidget::resizeGL(w, h); mitk::RenderingManager::GetInstance()->ForceImmediateUpdate(renderWindow()); } void QmitkRenderWindow::dragEnterEvent(QDragEnterEvent *event) { if (event->mimeData()->hasFormat("application/x-mitk-datanodes")) { event->accept(); } } void QmitkRenderWindow::dropEvent(QDropEvent *event) { QList dataNodeList = QmitkMimeTypes::ToDataNodePtrList(event->mimeData()); if (!dataNodeList.empty()) { emit NodesDropped(this, dataNodeList.toVector().toStdVector()); } } -void QmitkRenderWindow::AdjustRenderWindowMenuVisibility(const QPoint & /*pos*/) -{ - if (nullptr != m_MenuWidget) - { - m_MenuWidget->ShowMenu(); - m_MenuWidget->MoveWidgetToCorrectPos(1.0f); - } -} - void QmitkRenderWindow::DeferredHideMenu() { MITK_DEBUG << "QmitkRenderWindow::DeferredHideMenu"; if (nullptr != m_MenuWidget) { m_MenuWidget->HideMenu(); } } mitk::Point2D QmitkRenderWindow::GetMousePosition(QMouseEvent *me) const { mitk::Point2D point; point[0] = me->x(); // We need to convert the y component, as the display and vtk have other definitions for the y direction point[1] = m_Renderer->GetSizeY() - me->y(); return point; } mitk::Point2D QmitkRenderWindow::GetMousePosition(QWheelEvent *we) const { mitk::Point2D point; point[0] = we->x(); // We need to convert the y component, as the display and vtk have other definitions for the y direction point[1] = m_Renderer->GetSizeY() - we->y(); return point; } mitk::InteractionEvent::MouseButtons QmitkRenderWindow::GetEventButton(QMouseEvent *me) const { mitk::InteractionEvent::MouseButtons eventButton; switch (me->button()) { case Qt::LeftButton: eventButton = mitk::InteractionEvent::LeftMouseButton; break; case Qt::RightButton: eventButton = mitk::InteractionEvent::RightMouseButton; break; case Qt::MidButton: eventButton = mitk::InteractionEvent::MiddleMouseButton; break; default: eventButton = mitk::InteractionEvent::NoButton; break; } return eventButton; } mitk::InteractionEvent::MouseButtons QmitkRenderWindow::GetButtonState(QMouseEvent *me) const { mitk::InteractionEvent::MouseButtons buttonState = mitk::InteractionEvent::NoButton; if (me->buttons() & Qt::LeftButton) { buttonState = buttonState | mitk::InteractionEvent::LeftMouseButton; } if (me->buttons() & Qt::RightButton) { buttonState = buttonState | mitk::InteractionEvent::RightMouseButton; } if (me->buttons() & Qt::MidButton) { buttonState = buttonState | mitk::InteractionEvent::MiddleMouseButton; } return buttonState; } mitk::InteractionEvent::ModifierKeys QmitkRenderWindow::GetModifiers(QInputEvent *me) const { mitk::InteractionEvent::ModifierKeys modifiers = mitk::InteractionEvent::NoKey; if (me->modifiers() & Qt::ALT) { modifiers = modifiers | mitk::InteractionEvent::AltKey; } if (me->modifiers() & Qt::CTRL) { modifiers = modifiers | mitk::InteractionEvent::ControlKey; } if (me->modifiers() & Qt::SHIFT) { modifiers = modifiers | mitk::InteractionEvent::ShiftKey; } return modifiers; } mitk::InteractionEvent::MouseButtons QmitkRenderWindow::GetButtonState(QWheelEvent *we) const { mitk::InteractionEvent::MouseButtons buttonState = mitk::InteractionEvent::NoButton; if (we->buttons() & Qt::LeftButton) { buttonState = buttonState | mitk::InteractionEvent::LeftMouseButton; } if (we->buttons() & Qt::RightButton) { buttonState = buttonState | mitk::InteractionEvent::RightMouseButton; } if (we->buttons() & Qt::MidButton) { buttonState = buttonState | mitk::InteractionEvent::MiddleMouseButton; } return buttonState; } std::string QmitkRenderWindow::GetKeyLetter(QKeyEvent *ke) const { // Converting Qt Key Event to string element. std::string key = ""; int tkey = ke->key(); if (tkey < 128) { // standard ascii letter key = (char)toupper(tkey); } else { // special keys switch (tkey) { case Qt::Key_Return: key = mitk::InteractionEvent::KeyReturn; break; case Qt::Key_Enter: key = mitk::InteractionEvent::KeyEnter; break; case Qt::Key_Escape: key = mitk::InteractionEvent::KeyEsc; break; case Qt::Key_Delete: key = mitk::InteractionEvent::KeyDelete; break; case Qt::Key_Up: key = mitk::InteractionEvent::KeyArrowUp; break; case Qt::Key_Down: key = mitk::InteractionEvent::KeyArrowDown; break; case Qt::Key_Left: key = mitk::InteractionEvent::KeyArrowLeft; break; case Qt::Key_Right: key = mitk::InteractionEvent::KeyArrowRight; break; case Qt::Key_F1: key = mitk::InteractionEvent::KeyF1; break; case Qt::Key_F2: key = mitk::InteractionEvent::KeyF2; break; case Qt::Key_F3: key = mitk::InteractionEvent::KeyF3; break; case Qt::Key_F4: key = mitk::InteractionEvent::KeyF4; break; case Qt::Key_F5: key = mitk::InteractionEvent::KeyF5; break; case Qt::Key_F6: key = mitk::InteractionEvent::KeyF6; break; case Qt::Key_F7: key = mitk::InteractionEvent::KeyF7; break; case Qt::Key_F8: key = mitk::InteractionEvent::KeyF8; break; case Qt::Key_F9: key = mitk::InteractionEvent::KeyF9; break; case Qt::Key_F10: key = mitk::InteractionEvent::KeyF10; break; case Qt::Key_F11: key = mitk::InteractionEvent::KeyF11; break; case Qt::Key_F12: key = mitk::InteractionEvent::KeyF12; break; case Qt::Key_End: key = mitk::InteractionEvent::KeyEnd; break; case Qt::Key_Home: key = mitk::InteractionEvent::KeyPos1; break; case Qt::Key_Insert: key = mitk::InteractionEvent::KeyInsert; break; case Qt::Key_PageDown: key = mitk::InteractionEvent::KeyPageDown; break; case Qt::Key_PageUp: key = mitk::InteractionEvent::KeyPageUp; break; case Qt::Key_Space: key = mitk::InteractionEvent::KeySpace; break; } } return key; } int QmitkRenderWindow::GetDelta(QWheelEvent *we) const { return we->delta(); } diff --git a/Modules/QtWidgets/src/QmitkRenderWindowMenu.cpp b/Modules/QtWidgets/src/QmitkRenderWindowMenu.cpp index 59c39115ef..b75f46182c 100644 --- a/Modules/QtWidgets/src/QmitkRenderWindowMenu.cpp +++ b/Modules/QtWidgets/src/QmitkRenderWindowMenu.cpp @@ -1,658 +1,578 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkRenderWindowMenu.h" // mitk core #include "mitkProperties.h" #include "mitkResliceMethodProperty.h" // qt #include #include #include #include #include #include #include #include #include //#include"iconClose.xpm" #include "iconCrosshairMode.xpm" #include "iconFullScreen.xpm" //#include"iconHoriSplit.xpm" #include "iconSettings.xpm" //#include"iconVertiSplit.xpm" #include "iconLeaveFullScreen.xpm" // c++ #include unsigned int QmitkRenderWindowMenu::m_DefaultThickMode(1); -#ifdef QMITK_USE_EXTERNAL_RENDERWINDOW_MENU -QmitkRenderWindowMenu::QmitkRenderWindowMenu(QWidget* parent, - Qt::WindowFlags, - mitk::BaseRenderer* baseRenderer) - : QWidget(nullptr, Qt::Tool | Qt::FramelessWindowHint) - -#else QmitkRenderWindowMenu::QmitkRenderWindowMenu(QWidget* parent, Qt::WindowFlags flags, mitk::BaseRenderer* baseRenderer) : QWidget(parent, flags) -#endif - , m_LayoutActionsMenu(nullptr) , m_CrosshairMenu(nullptr) , m_FullScreenMode(false) , m_Renderer(baseRenderer) , m_Parent(parent) , m_CrosshairRotationMode(0) , m_CrosshairVisibility(true) , m_Layout(LayoutIndex::AXIAL) , m_LayoutDesign(LayoutDesign::DEFAULT) , m_OldLayoutDesign(LayoutDesign::DEFAULT) { CreateMenuWidget(); setMinimumWidth(61); // DIRTY.. If you add or remove a button, you need to change the size. setMaximumWidth(61); setAutoFillBackground(true); -// Else part fixes the render window menu issue on Linux bug but caused bugs on macOS and Windows -// for macOS see bug 3192 -// for Windows see bug 12130 -//... so macOS and Windows must be treated differently: -#if defined(Q_OS_MAC) - this->show(); - this->setWindowOpacity(0.0f); -#else - this->setVisible(false); -#endif + this->hide(); m_AutoRotationTimer = new QTimer(this); m_AutoRotationTimer->setInterval(75); - m_HideTimer = new QTimer(this); - m_HideTimer->setSingleShot(true); - connect(m_AutoRotationTimer, &QTimer::timeout, this, &QmitkRenderWindowMenu::AutoRotateNextStep); - connect(m_HideTimer, &QTimer::timeout, this, &QmitkRenderWindowMenu::DeferredHideMenu); connect(m_Parent, &QObject::destroyed, this, &QmitkRenderWindowMenu::deleteLater); } QmitkRenderWindowMenu::~QmitkRenderWindowMenu() { if (m_AutoRotationTimer->isActive()) { m_AutoRotationTimer->stop(); } } void QmitkRenderWindowMenu::SetLayoutIndex(LayoutIndex layoutIndex) { m_Layout = layoutIndex; } void QmitkRenderWindowMenu::UpdateLayoutDesignList(LayoutDesign layoutDesign) { m_LayoutDesign = layoutDesign; if (nullptr == m_LayoutActionsMenu) { CreateSettingsWidget(); } m_DefaultLayoutAction->setEnabled(true); m_All2DTop3DBottomLayoutAction->setEnabled(true); m_All2DLeft3DRightLayoutAction->setEnabled(true); m_OneBigLayoutAction->setEnabled(true); m_Only2DHorizontalLayoutAction->setEnabled(true); m_Only2DVerticalLayoutAction->setEnabled(true); m_OneTop3DBottomLayoutAction->setEnabled(true); m_OneLeft3DRightLayoutAction->setEnabled(true); m_AllHorizontalLayoutAction->setEnabled(true); m_AllVerticalLayoutAction->setEnabled(true); m_RemoveOneLayoutAction->setEnabled(true); switch (m_LayoutDesign) { case LayoutDesign::DEFAULT: { m_DefaultLayoutAction->setEnabled(false); break; } case LayoutDesign::ALL_2D_TOP_3D_BOTTOM: { m_All2DTop3DBottomLayoutAction->setEnabled(false); break; } case LayoutDesign::ALL_2D_LEFT_3D_RIGHT: { m_All2DLeft3DRightLayoutAction->setEnabled(false); break; } case LayoutDesign::ONE_BIG: { m_OneBigLayoutAction->setEnabled(false); break; } case LayoutDesign::ONLY_2D_HORIZONTAL: { m_Only2DHorizontalLayoutAction->setEnabled(false); break; } case LayoutDesign::ONLY_2D_VERTICAL: { m_Only2DVerticalLayoutAction->setEnabled(false); break; } case LayoutDesign::ONE_TOP_3D_BOTTOM: { m_OneTop3DBottomLayoutAction->setEnabled(false); break; } case LayoutDesign::ONE_LEFT_3D_RIGHT: { m_OneLeft3DRightLayoutAction->setEnabled(false); break; } case LayoutDesign::ALL_HORIZONTAL: { m_AllHorizontalLayoutAction->setEnabled(false); break; } case LayoutDesign::ALL_VERTICAL: { m_AllVerticalLayoutAction->setEnabled(false); break; } case LayoutDesign::REMOVE_ONE: { m_RemoveOneLayoutAction->setEnabled(false); break; } case LayoutDesign::NONE: { break; } } } void QmitkRenderWindowMenu::UpdateCrosshairVisibility(bool visible) { m_CrosshairVisibility = visible; } void QmitkRenderWindowMenu::UpdateCrosshairRotationMode(int mode) { m_CrosshairRotationMode = mode; } -#ifdef QMITK_USE_EXTERNAL_RENDERWINDOW_MENU -void QmitkRenderWindowMenu::MoveWidgetToCorrectPos(float opacity) -#else -void QmitkRenderWindowMenu::MoveWidgetToCorrectPos(float /*opacity*/) -#endif +void QmitkRenderWindowMenu::MoveWidgetToCorrectPos() { -#ifdef QMITK_USE_EXTERNAL_RENDERWINDOW_MENU - int X = floor(double(this->m_Parent->width() - this->width() - 8.0)); - int Y = 7; - - QPoint pos = this->m_Parent->mapToGlobal(QPoint(0, 0)); - - this->move(X + pos.x(), Y + pos.y()); + int moveX = floor(static_cast(this->m_Parent->width()) - static_cast(this->width()) - 4.0); + this->move(moveX, 3); - if (opacity < 0) - opacity = 0; - else if (opacity > 1) - opacity = 1; + auto cursorPos = this->mapFromGlobal(QCursor::pos()); - this->setWindowOpacity(opacity); -#else - int moveX = floor(double(this->m_Parent->width() - this->width() - 4.0)); - this->move(moveX, 3); - this->show(); -#endif + if (cursorPos.x() < 0 || cursorPos.x() >= this->width() || + cursorPos.y() < 0 || cursorPos.y() >= this->height()) + { + this->HideMenu(); + } + else + { + this->ShowMenu(); + } } void QmitkRenderWindowMenu::ShowMenu() { MITK_DEBUG << "menu showMenu"; - DeferredShowMenu(); + this->show(); + this->raise(); } void QmitkRenderWindowMenu::HideMenu() { MITK_DEBUG << "menu hideEvent"; - DeferredHideMenu(); + this->hide(); } void QmitkRenderWindowMenu::paintEvent(QPaintEvent * /*e*/) { QPainter painter(this); QColor semiTransparentColor = Qt::black; semiTransparentColor.setAlpha(255); painter.fillRect(rect(), semiTransparentColor); } void QmitkRenderWindowMenu::CreateMenuWidget() { QHBoxLayout *layout = new QHBoxLayout(this); layout->setAlignment(Qt::AlignRight); layout->setContentsMargins(1, 1, 1, 1); QSize size(13, 13); m_CrosshairMenu = new QMenu(this); connect(m_CrosshairMenu, &QMenu::aboutToShow, this, &QmitkRenderWindowMenu::OnCrosshairMenuAboutToShow); m_CrosshairModeButton = new QToolButton(this); m_CrosshairModeButton->setMaximumSize(15, 15); m_CrosshairModeButton->setIconSize(size); m_CrosshairModeButton->setMenu(m_CrosshairMenu); m_CrosshairModeButton->setIcon(QIcon(QPixmap(iconCrosshairMode_xpm))); m_CrosshairModeButton->setPopupMode(QToolButton::InstantPopup); m_CrosshairModeButton->setStyleSheet("QToolButton::menu-indicator { image: none; }"); m_CrosshairModeButton->setAutoRaise(true); layout->addWidget(m_CrosshairModeButton); m_FullScreenButton = new QToolButton(this); m_FullScreenButton->setMaximumSize(15, 15); m_FullScreenButton->setIconSize(size); m_FullScreenButton->setIcon(QIcon(QPixmap(iconFullScreen_xpm))); m_FullScreenButton->setAutoRaise(true); layout->addWidget(m_FullScreenButton); m_LayoutDesignButton = new QToolButton(this); m_LayoutDesignButton->setMaximumSize(15, 15); m_LayoutDesignButton->setIconSize(size); m_LayoutDesignButton->setIcon(QIcon(QPixmap(iconSettings_xpm))); m_LayoutDesignButton->setAutoRaise(true); layout->addWidget(m_LayoutDesignButton); connect(m_FullScreenButton, &QToolButton::clicked, this, &QmitkRenderWindowMenu::OnFullScreenButton); connect(m_LayoutDesignButton, &QToolButton::clicked, this, &QmitkRenderWindowMenu::OnLayoutDesignButton); } void QmitkRenderWindowMenu::CreateSettingsWidget() { m_LayoutActionsMenu = new QMenu(this); m_DefaultLayoutAction = new QAction("Standard layout", m_LayoutActionsMenu); m_DefaultLayoutAction->setDisabled(true); m_All2DTop3DBottomLayoutAction = new QAction("All 2D top, 3D bottom", m_LayoutActionsMenu); m_All2DTop3DBottomLayoutAction->setDisabled(false); m_All2DLeft3DRightLayoutAction = new QAction("All 2D left, 3D right", m_LayoutActionsMenu); m_All2DLeft3DRightLayoutAction->setDisabled(false); m_OneBigLayoutAction = new QAction("This big", m_LayoutActionsMenu); m_OneBigLayoutAction->setDisabled(false); m_Only2DHorizontalLayoutAction = new QAction("Only 2D horizontal", m_LayoutActionsMenu); m_Only2DHorizontalLayoutAction->setDisabled(false); m_Only2DVerticalLayoutAction = new QAction("Only 2D vertical", m_LayoutActionsMenu); m_Only2DVerticalLayoutAction->setDisabled(false); m_OneTop3DBottomLayoutAction = new QAction("This top, 3D bottom", m_LayoutActionsMenu); m_OneTop3DBottomLayoutAction->setDisabled(false); m_OneLeft3DRightLayoutAction = new QAction("This left, 3D right", m_LayoutActionsMenu); m_OneLeft3DRightLayoutAction->setDisabled(false); m_AllHorizontalLayoutAction = new QAction("All horizontal", m_LayoutActionsMenu); m_AllHorizontalLayoutAction->setDisabled(false); m_AllVerticalLayoutAction = new QAction("All vertical", m_LayoutActionsMenu); m_AllVerticalLayoutAction->setDisabled(false); m_RemoveOneLayoutAction = new QAction("Remove this", m_LayoutActionsMenu); m_RemoveOneLayoutAction->setDisabled(false); m_LayoutActionsMenu->addAction(m_DefaultLayoutAction); m_LayoutActionsMenu->addAction(m_All2DTop3DBottomLayoutAction); m_LayoutActionsMenu->addAction(m_All2DLeft3DRightLayoutAction); m_LayoutActionsMenu->addAction(m_OneBigLayoutAction); m_LayoutActionsMenu->addAction(m_Only2DHorizontalLayoutAction); m_LayoutActionsMenu->addAction(m_Only2DVerticalLayoutAction); m_LayoutActionsMenu->addAction(m_OneTop3DBottomLayoutAction); m_LayoutActionsMenu->addAction(m_OneLeft3DRightLayoutAction); m_LayoutActionsMenu->addAction(m_AllHorizontalLayoutAction); m_LayoutActionsMenu->addAction(m_AllVerticalLayoutAction); m_LayoutActionsMenu->addAction(m_RemoveOneLayoutAction); m_LayoutActionsMenu->setVisible(false); connect(m_DefaultLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::DEFAULT); }); connect(m_All2DTop3DBottomLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ALL_2D_TOP_3D_BOTTOM); }); connect(m_All2DLeft3DRightLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ALL_2D_LEFT_3D_RIGHT); }); connect(m_OneBigLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ONE_BIG); }); connect(m_Only2DHorizontalLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ONLY_2D_HORIZONTAL); }); connect(m_Only2DVerticalLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ONLY_2D_VERTICAL); }); connect(m_OneTop3DBottomLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ONE_TOP_3D_BOTTOM); }); connect(m_OneLeft3DRightLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ONE_LEFT_3D_RIGHT); }); connect(m_AllHorizontalLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ALL_HORIZONTAL); }); connect(m_AllVerticalLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::ALL_VERTICAL); }); connect(m_RemoveOneLayoutAction, &QAction::triggered, [this]() { this->OnSetLayout(LayoutDesign::REMOVE_ONE); }); } void QmitkRenderWindowMenu::ChangeFullScreenIcon() { m_FullScreenButton->setIcon(m_FullScreenMode ? QPixmap(iconLeaveFullScreen_xpm) : QPixmap(iconFullScreen_xpm)); } -void QmitkRenderWindowMenu::DeferredShowMenu() -{ - MITK_DEBUG << "deferred show menu"; - m_HideTimer->stop(); - - // Else part fixes the render window menu issue on Linux bug but caused bugs on macOS and Windows - // for macOS see bug 3192 - // for Windows see bug 12130 - //... so macOS and Windows must be treated differently: -#if defined(Q_OS_MAC) - this->setWindowOpacity(1.0f); -#else - this->setVisible(true); - this->raise(); -#endif -} - -void QmitkRenderWindowMenu::DeferredHideMenu() -{ - MITK_DEBUG << "menu deferredhidemenu"; - // Else part fixes the render window menu issue on Linux bug but caused bugs on macOS and Windows - // for macOS see bug 3192 - // for Windows see bug 12130 - //... so macOS and Windows must be treated differently: -#if defined(Q_OS_MAC) - this->setWindowOpacity(0.0f); -#else - this->setVisible(false); -#endif -} - -void QmitkRenderWindowMenu::smoothHide() -{ - MITK_DEBUG << "menu leaveEvent"; - m_HideTimer->start(10); -} - -void QmitkRenderWindowMenu::enterEvent(QEvent * /*e*/) -{ - MITK_DEBUG << "menu enterEvent"; - DeferredShowMenu(); -} - -void QmitkRenderWindowMenu::leaveEvent(QEvent * /*e*/) -{ - MITK_DEBUG << "menu leaveEvent"; - smoothHide(); -} - void QmitkRenderWindowMenu::AutoRotateNextStep() { if (m_Renderer->GetCameraRotationController()) { m_Renderer->GetCameraRotationController()->GetSlice()->Next(); } } void QmitkRenderWindowMenu::OnAutoRotationActionTriggered() { if (m_AutoRotationTimer->isActive()) { m_AutoRotationTimer->stop(); m_Renderer->GetCameraRotationController()->GetSlice()->PingPongOff(); } else { m_Renderer->GetCameraRotationController()->GetSlice()->PingPongOn(); m_AutoRotationTimer->start(); } } void QmitkRenderWindowMenu::OnTSNumChanged(int num) { MITK_DEBUG << "Thickslices num: " << num << " on renderer " << m_Renderer.GetPointer(); if (m_Renderer.IsNotNull()) { unsigned int thickSlicesMode = 0; // determine the state of the thick-slice mode mitk::ResliceMethodProperty *resliceMethodEnumProperty = nullptr; if(m_Renderer->GetCurrentWorldPlaneGeometryNode()->GetProperty(resliceMethodEnumProperty, "reslice.thickslices") && resliceMethodEnumProperty) { thickSlicesMode = resliceMethodEnumProperty->GetValueAsId(); if(thickSlicesMode!=0) m_DefaultThickMode = thickSlicesMode; } if(thickSlicesMode==0 && num>0) //default mode only for single slices { thickSlicesMode = m_DefaultThickMode; //mip default m_Renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices.showarea", mitk::BoolProperty::New(true)); } if(num<1) { thickSlicesMode = 0; m_Renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices.showarea", mitk::BoolProperty::New(false)); } m_Renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices", mitk::ResliceMethodProperty::New(thickSlicesMode)); m_Renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices.num", mitk::IntProperty::New(num)); m_TSLabel->setText(QString::number(num * 2 + 1)); m_Renderer->SendUpdateSlice(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkRenderWindowMenu::OnCrosshairMenuAboutToShow() { QMenu *crosshairModesMenu = m_CrosshairMenu; crosshairModesMenu->clear(); QAction *resetViewAction = new QAction(crosshairModesMenu); resetViewAction->setText("Reset view"); crosshairModesMenu->addAction(resetViewAction); connect(resetViewAction, &QAction::triggered, this, &QmitkRenderWindowMenu::ResetView); // Show hide crosshairs { QAction *showHideCrosshairVisibilityAction = new QAction(crosshairModesMenu); showHideCrosshairVisibilityAction->setText("Show crosshair"); showHideCrosshairVisibilityAction->setCheckable(true); showHideCrosshairVisibilityAction->setChecked(m_CrosshairVisibility); crosshairModesMenu->addAction(showHideCrosshairVisibilityAction); connect(showHideCrosshairVisibilityAction, &QAction::toggled, this, &QmitkRenderWindowMenu::OnCrosshairVisibilityChanged); } // Rotation mode { QAction *rotationGroupSeparator = new QAction(crosshairModesMenu); rotationGroupSeparator->setSeparator(true); rotationGroupSeparator->setText("Rotation mode"); crosshairModesMenu->addAction(rotationGroupSeparator); QActionGroup *rotationModeActionGroup = new QActionGroup(crosshairModesMenu); rotationModeActionGroup->setExclusive(true); QAction *noCrosshairRotation = new QAction(crosshairModesMenu); noCrosshairRotation->setActionGroup(rotationModeActionGroup); noCrosshairRotation->setText("No crosshair rotation"); noCrosshairRotation->setCheckable(true); noCrosshairRotation->setChecked(m_CrosshairRotationMode == 0); noCrosshairRotation->setData(0); crosshairModesMenu->addAction(noCrosshairRotation); QAction *singleCrosshairRotation = new QAction(crosshairModesMenu); singleCrosshairRotation->setActionGroup(rotationModeActionGroup); singleCrosshairRotation->setText("Crosshair rotation"); singleCrosshairRotation->setCheckable(true); singleCrosshairRotation->setChecked(m_CrosshairRotationMode == 1); singleCrosshairRotation->setData(1); crosshairModesMenu->addAction(singleCrosshairRotation); QAction *coupledCrosshairRotation = new QAction(crosshairModesMenu); coupledCrosshairRotation->setActionGroup(rotationModeActionGroup); coupledCrosshairRotation->setText("Coupled crosshair rotation"); coupledCrosshairRotation->setCheckable(true); coupledCrosshairRotation->setChecked(m_CrosshairRotationMode == 2); coupledCrosshairRotation->setData(2); crosshairModesMenu->addAction(coupledCrosshairRotation); QAction *swivelMode = new QAction(crosshairModesMenu); swivelMode->setActionGroup(rotationModeActionGroup); swivelMode->setText("Swivel mode"); swivelMode->setCheckable(true); swivelMode->setChecked(m_CrosshairRotationMode == 3); swivelMode->setData(3); crosshairModesMenu->addAction(swivelMode); connect(rotationModeActionGroup, &QActionGroup::triggered, this, &QmitkRenderWindowMenu::OnCrosshairRotationModeSelected); } // auto rotation support if (m_Renderer.IsNotNull() && m_Renderer->GetMapperID() == mitk::BaseRenderer::Standard3D) { QAction *autoRotationGroupSeparator = new QAction(crosshairModesMenu); autoRotationGroupSeparator->setSeparator(true); crosshairModesMenu->addAction(autoRotationGroupSeparator); QAction *autoRotationAction = crosshairModesMenu->addAction("Auto Rotation"); autoRotationAction->setCheckable(true); autoRotationAction->setChecked(m_AutoRotationTimer->isActive()); connect(autoRotationAction, &QAction::triggered, this, &QmitkRenderWindowMenu::OnAutoRotationActionTriggered); } // Thickslices support if (m_Renderer.IsNotNull() && m_Renderer->GetMapperID() == mitk::BaseRenderer::Standard2D) { QAction *thickSlicesGroupSeparator = new QAction(crosshairModesMenu); thickSlicesGroupSeparator->setSeparator(true); thickSlicesGroupSeparator->setText("ThickSlices mode"); crosshairModesMenu->addAction(thickSlicesGroupSeparator); QActionGroup *thickSlicesActionGroup = new QActionGroup(crosshairModesMenu); thickSlicesActionGroup->setExclusive(true); int currentMode = 0; { mitk::ResliceMethodProperty::Pointer m = dynamic_cast( m_Renderer->GetCurrentWorldPlaneGeometryNode()->GetProperty("reslice.thickslices")); if (m.IsNotNull()) currentMode = m->GetValueAsId(); } int currentNum = 1; { mitk::IntProperty::Pointer m = dynamic_cast( m_Renderer->GetCurrentWorldPlaneGeometryNode()->GetProperty("reslice.thickslices.num")); if (m.IsNotNull()) { currentNum = m->GetValue(); } } if (currentMode == 0) currentNum = 0; QSlider *m_TSSlider = new QSlider(crosshairModesMenu); m_TSSlider->setMinimum(0); m_TSSlider->setMaximum(50); m_TSSlider->setValue(currentNum); m_TSSlider->setOrientation(Qt::Horizontal); connect(m_TSSlider, &QSlider::valueChanged, this, &QmitkRenderWindowMenu::OnTSNumChanged); QHBoxLayout *tsLayout = new QHBoxLayout; tsLayout->setContentsMargins(4, 4, 4, 4); tsLayout->addWidget(new QLabel("TS: ")); tsLayout->addWidget(m_TSSlider); tsLayout->addWidget(m_TSLabel = new QLabel(QString::number(currentNum * 2 + 1), this)); QWidget *tsWidget = new QWidget; tsWidget->setLayout(tsLayout); QWidgetAction *m_TSSliderAction = new QWidgetAction(crosshairModesMenu); m_TSSliderAction->setDefaultWidget(tsWidget); crosshairModesMenu->addAction(m_TSSliderAction); } } void QmitkRenderWindowMenu::OnCrosshairVisibilityChanged(bool visible) { UpdateCrosshairVisibility(visible); emit CrosshairVisibilityChanged(m_CrosshairVisibility); } void QmitkRenderWindowMenu::OnCrosshairRotationModeSelected(QAction *action) { UpdateCrosshairRotationMode(action->data().toInt()); emit CrosshairRotationModeChanged(m_CrosshairRotationMode); } void QmitkRenderWindowMenu::OnFullScreenButton(bool /*checked*/) { if (!m_FullScreenMode) { m_FullScreenMode = true; m_OldLayoutDesign = m_LayoutDesign; emit LayoutDesignChanged(LayoutDesign::ONE_BIG); } else { m_FullScreenMode = false; emit LayoutDesignChanged(m_OldLayoutDesign); } - MoveWidgetToCorrectPos(1.0f); + MoveWidgetToCorrectPos(); ChangeFullScreenIcon(); - - DeferredShowMenu(); + ShowMenu(); } void QmitkRenderWindowMenu::OnLayoutDesignButton(bool /*checked*/) { if (nullptr == m_LayoutActionsMenu) { CreateSettingsWidget(); } QPoint point = mapToGlobal(m_LayoutDesignButton->geometry().topLeft()); m_LayoutActionsMenu->setVisible(true); m_LayoutActionsMenu->exec(point); } void QmitkRenderWindowMenu::OnSetLayout(LayoutDesign layoutDesign) { m_FullScreenMode = false; ChangeFullScreenIcon(); m_LayoutDesign = layoutDesign; emit LayoutDesignChanged(m_LayoutDesign); - DeferredShowMenu(); + ShowMenu(); } diff --git a/Modules/QtWidgets/src/mitkDataStorageInspectorGenerator.cpp b/Modules/QtWidgets/src/mitkDataStorageInspectorGenerator.cpp index fad908465e..9f1ab8d13c 100644 --- a/Modules/QtWidgets/src/mitkDataStorageInspectorGenerator.cpp +++ b/Modules/QtWidgets/src/mitkDataStorageInspectorGenerator.cpp @@ -1,57 +1,57 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "usModuleContext.h" #include "usGetModuleContext.h" #include "mitkLogMacros.h" #include "mitkDataStorageInspectorGenerator.h" mitk::IDataStorageInspectorProvider* mitk::DataStorageInspectorGenerator::GetProvider(const IDType& id) { mitk::IDataStorageInspectorProvider* result = nullptr; std::string filter = "(" + mitk::IDataStorageInspectorProvider::PROP_INSPECTOR_ID() + "=" + id + ")"; std::vector > providerRegisters = us::GetModuleContext()->GetServiceReferences(filter); if (!providerRegisters.empty()) { if (providerRegisters.size() > 1) { MITK_WARN << "Multiple provider for class id'" << id << "' found. Using just one."; } result = us::GetModuleContext()->GetService(providerRegisters.front()); } return result; }; mitk::DataStorageInspectorGenerator::ProviderMapType mitk::DataStorageInspectorGenerator::GetProviders() { std::vector > providerRegisters = us::GetModuleContext()->GetServiceReferences(); ProviderMapType result; - for (auto regs : providerRegisters) + for (const auto ®s : providerRegisters) { auto provider = us::GetModuleContext()->GetService(regs); result.insert(std::make_pair(provider->GetInspectorID(), provider)); } return result; }; mitk::DataStorageInspectorGenerator::DataStorageInspectorGenerator() = default; mitk::DataStorageInspectorGenerator::~DataStorageInspectorGenerator() = default; diff --git a/Modules/QtWidgetsExt/src/QmitkPointListView.cpp b/Modules/QtWidgetsExt/src/QmitkPointListView.cpp index 8e16d207eb..9ecf11704a 100644 --- a/Modules/QtWidgetsExt/src/QmitkPointListView.cpp +++ b/Modules/QtWidgetsExt/src/QmitkPointListView.cpp @@ -1,334 +1,335 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkPointListView.h" #include "QmitkEditPointDialog.h" #include "QmitkPointListModel.h" #include "QmitkRenderWindow.h" #include "QmitkStdMultiWidget.h" #include "mitkRenderingManager.h" #include #include #include #include #include QmitkPointListView::QmitkPointListView(QWidget *parent) : QListView(parent), m_PointListModel(new QmitkPointListModel()), m_SelfCall(false), m_showFading(false), m_MultiWidget(nullptr) { QListView::setAlternatingRowColors(true); QListView::setSelectionBehavior(QAbstractItemView::SelectItems); QListView::setSelectionMode(QAbstractItemView::SingleSelection); QListView::setModel(m_PointListModel); QString tooltip = QString("Use the F2/F3 keys to move a point up/down, the Del key to remove a point\nand the mouse " "wheel to change the timestep.\n\nTimeStep:\t%1") .arg(0); QListView::setToolTip(tooltip); this->setContextMenuPolicy(Qt::CustomContextMenu); this->setMinimumHeight(40); this->setSizePolicy(QSizePolicy::Ignored, QSizePolicy::Ignored); connect(m_PointListModel, SIGNAL(SignalUpdateSelection()), this, SLOT(OnPointSetSelectionChanged())); connect(this, SIGNAL(doubleClicked(const QModelIndex &)), this, SLOT(OnPointDoubleClicked(const QModelIndex &))); connect(QListView::selectionModel(), SIGNAL(selectionChanged(const QItemSelection &, const QItemSelection &)), this, SLOT(OnListViewSelectionChanged(const QItemSelection &, const QItemSelection &))); - connect(this, SIGNAL(customContextMenuRequested(const QPoint &)), this, SLOT(ctxMenu(const QPoint &))); + // T28213: Every single action in the context menu is either not implemented or working. Implement/fix or remove in future. + // connect(this, SIGNAL(customContextMenuRequested(const QPoint &)), this, SLOT(ctxMenu(const QPoint &))); } QmitkPointListView::~QmitkPointListView() { delete m_PointListModel; } void QmitkPointListView::SetPointSetNode(mitk::DataNode *pointSetNode) { m_PointListModel->SetPointSetNode(pointSetNode); } const mitk::PointSet *QmitkPointListView::GetPointSet() const { return m_PointListModel->GetPointSet(); } void QmitkPointListView::SetMultiWidget(QmitkStdMultiWidget *multiWidget) { m_MultiWidget = multiWidget; if (nullptr != m_MultiWidget) { AddSliceNavigationController(m_MultiWidget->GetRenderWindow1()->GetSliceNavigationController()); AddSliceNavigationController(m_MultiWidget->GetRenderWindow2()->GetSliceNavigationController()); AddSliceNavigationController(m_MultiWidget->GetRenderWindow3()->GetSliceNavigationController()); } } QmitkStdMultiWidget *QmitkPointListView::GetMultiWidget() const { return m_MultiWidget; } void QmitkPointListView::OnPointDoubleClicked(const QModelIndex &index) { mitk::PointSet::PointType p; mitk::PointSet::PointIdentifier id; m_PointListModel->GetPointForModelIndex(index, p, id); QmitkEditPointDialog _EditPointDialog(this); _EditPointDialog.SetPoint(m_PointListModel->GetPointSet(), id, m_PointListModel->GetTimeStep()); _EditPointDialog.exec(); } void QmitkPointListView::OnPointSetSelectionChanged() { const mitk::PointSet *pointSet = m_PointListModel->GetPointSet(); if (pointSet == nullptr) return; // update this view's selection status as a result to changes in the point set data structure m_SelfCall = true; int timeStep = m_PointListModel->GetTimeStep(); if (pointSet->GetNumberOfSelected(timeStep) > 1) { MITK_ERROR << "Point set has multiple selected points. This view is not designed for more than one selected point."; } int selectedIndex = pointSet->SearchSelectedPoint(timeStep); if (selectedIndex == -1) // no selected point is found { m_SelfCall = false; return; } QModelIndex index; bool modelIndexOkay = m_PointListModel->GetModelIndexForPointID(selectedIndex, index); if (modelIndexOkay == true) QListView::selectionModel()->select(index, QItemSelectionModel::ClearAndSelect); emit SignalPointSelectionChanged(); m_SelfCall = false; } void QmitkPointListView::OnListViewSelectionChanged(const QItemSelection &selected, const QItemSelection & /*deselected*/) { if (m_SelfCall) return; mitk::PointSet *pointSet = const_cast(m_PointListModel->GetPointSet()); if (pointSet == nullptr) return; // (take care that this widget doesn't react to self-induced changes by setting m_SelfCall) m_SelfCall = true; // update selection of all points in pointset: select the one(s) that are selected in the view, deselect all others QModelIndexList selectedIndexes = selected.indexes(); // only call setSelectInfo on a point set with 'selected = true' if you deselcted the other entries int indexToSelect = -1; for (mitk::PointSet::PointsContainer::Iterator it = pointSet->GetPointSet(m_PointListModel->GetTimeStep())->GetPoints()->Begin(); it != pointSet->GetPointSet(m_PointListModel->GetTimeStep())->GetPoints()->End(); ++it) { QModelIndex index; if (m_PointListModel->GetModelIndexForPointID(it->Index(), index)) { if (selectedIndexes.indexOf(index) != -1) // index is found in the selected indices list { indexToSelect = it->Index(); } else { pointSet->SetSelectInfo(it->Index(), false, m_PointListModel->GetTimeStep()); } } } // force selection of only one index after deselecting the others if (indexToSelect > -1) { pointSet->SetSelectInfo(indexToSelect, true, m_PointListModel->GetTimeStep()); mitk::Point3D p = pointSet->GetPoint(indexToSelect, m_PointListModel->GetTimeStep()); for (auto snc : m_Sncs) snc->SelectSliceByPoint(p); } m_SelfCall = false; emit SignalPointSelectionChanged(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPointListView::keyPressEvent(QKeyEvent *e) { if (m_PointListModel == nullptr) return; int key = e->key(); switch (key) { case Qt::Key_F2: m_PointListModel->MoveSelectedPointUp(); break; case Qt::Key_F3: m_PointListModel->MoveSelectedPointDown(); break; case Qt::Key_Delete: m_PointListModel->RemoveSelectedPoint(); break; default: break; } } void QmitkPointListView::wheelEvent(QWheelEvent *event) { if (!m_PointListModel || !m_PointListModel->GetPointSet() || (int)(m_PointListModel->GetPointSet()->GetTimeSteps()) == 1) return; int whe = event->delta(); mitk::PointSet::Pointer ps = dynamic_cast(m_PointListModel->GetPointSet()); unsigned int numberOfTS = ps->GetTimeSteps(); if (numberOfTS == 1) return; int currentTS = this->m_PointListModel->GetTimeStep(); if (whe > 0) { if ((currentTS + 1 >= (int)numberOfTS)) return; this->m_PointListModel->SetTimeStep(++currentTS); } else { if ((currentTS <= 0)) return; this->m_PointListModel->SetTimeStep(--currentTS); } QString tooltip = QString("Use the F2/F3 keys to move a point up/down, the Del key to remove a point\nand the mouse " "wheel to change the timestep.\n\nTimeStep:\t%1") .arg(currentTS); this->setToolTip(tooltip); emit SignalTimeStepChanged(currentTS); } void QmitkPointListView::ctxMenu(const QPoint &pos) { QMenu *menu = new QMenu; // add Fading check QAction *showFading = new QAction(this); showFading->setCheckable(false); // TODO: reset when fading is working showFading->setEnabled(false); // TODO: reset when fading is working showFading->setText("Fade TimeStep"); connect(showFading, SIGNAL(triggered(bool)), this, SLOT(SetFading(bool))); menu->addAction(showFading); // add Clear action QAction *clearList = new QAction(this); clearList->setText("Clear List"); connect(clearList, SIGNAL(triggered()), this, SLOT(ClearPointList())); menu->addAction(clearList); // add Clear TimeStep action QAction *clearTS = new QAction(this); clearTS->setText("Clear current time step"); connect(clearTS, SIGNAL(triggered()), this, SLOT(ClearPointListTS())); menu->addAction(clearTS); menu->exec(this->mapToGlobal(pos)); } void QmitkPointListView::SetFading(bool onOff) { m_showFading = onOff; } void QmitkPointListView::ClearPointList() { if (!m_PointListModel->GetPointSet()) return; mitk::PointSet::Pointer curPS = m_PointListModel->GetPointSet(); if (curPS->GetSize() == 0) return; switch (QMessageBox::question(this, tr("Clear Points"), tr("Remove all points from the displayed list?"), QMessageBox::Yes | QMessageBox::No, QMessageBox::No)) { case QMessageBox::Yes: { mitk::PointSet::PointsIterator it; mitk::PointSet::PointsContainer *curPsPoints; while (!curPS->IsEmptyTimeStep(0)) { curPsPoints = curPS->GetPointSet()->GetPoints(); it = curPsPoints->Begin(); curPS->SetSelectInfo(it->Index(), true); m_PointListModel->RemoveSelectedPoint(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); break; } case QMessageBox::No: default: break; } } void QmitkPointListView::ClearPointListTS() { } void QmitkPointListView::AddSliceNavigationController(mitk::SliceNavigationController *snc) { if (snc == nullptr) return; m_Sncs.insert(snc); } void QmitkPointListView::RemoveSliceNavigationController(mitk::SliceNavigationController *snc) { if (snc == nullptr) return; m_Sncs.erase(snc); } diff --git a/Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.cpp b/Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.cpp index 921e4d6556..50f4a52ad0 100644 --- a/Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.cpp +++ b/Modules/RT/autoload/DICOMRTIO/mitkRTDoseReaderService.cpp @@ -1,168 +1,171 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include #include #include #include #include #include #include #include #include #include +#include +#include #include #include #include namespace mitk { RTDoseReaderService::RTDoseReaderService() : AbstractFileReader(CustomMimeType(mitk::DICOMRTMimeTypes::DICOMRT_DOSE_MIMETYPE_NAME()), mitk::DICOMRTMimeTypes::DICOMRT_DOSE_MIMETYPE_DESCRIPTION()) { m_FileReaderServiceReg = RegisterService(); } RTDoseReaderService::RTDoseReaderService(const RTDoseReaderService& other) : mitk::AbstractFileReader(other) { } RTDoseReaderService::~RTDoseReaderService() {} template void RTDoseReaderService::MultiplyGridScaling(itk::Image* image, float gridscale) { typedef itk::Image OutputImageType; typedef itk::Image InputImageType; typedef itk::CastImageFilter CastFilterType; typedef itk::ShiftScaleImageFilter ScaleFilterType; typename CastFilterType::Pointer castFilter = CastFilterType::New(); typename ScaleFilterType::Pointer scaleFilter = ScaleFilterType::New(); castFilter->SetInput(image); scaleFilter->SetInput(castFilter->GetOutput()); scaleFilter->SetScale(gridscale); scaleFilter->Update(); typename OutputImageType::Pointer scaledOutput = scaleFilter->GetOutput(); this->scaledDoseImage = mitk::Image::New(); mitk::CastToMitkImage(scaledOutput, this->scaledDoseImage); } std::vector > RTDoseReaderService::DoRead() { std::vector > result; mitk::IDICOMTagsOfInterest* toiSrv = GetDicomTagsOfInterestService(); auto tagsOfInterest = toiSrv->GetTagsOfInterest(); DICOMTagPathList tagsOfInterestList; for (const auto& tag : tagsOfInterest) { tagsOfInterestList.push_back(tag.first); } std::string location = GetInputLocation(); mitk::DICOMFileReaderSelector::Pointer selector = mitk::DICOMFileReaderSelector::New(); selector->LoadBuiltIn3DConfigs(); selector->SetInputFiles({ location }); mitk::DICOMFileReader::Pointer reader = selector->GetFirstReaderWithMinimumNumberOfOutputImages(); reader->SetAdditionalTagsOfInterest(toiSrv->GetTagsOfInterest()); + reader->SetTagLookupTableToPropertyFunctor(mitk::GetDICOMPropertyForDICOMValuesFunctor); reader->SetInputFiles({ location }); reader->AnalyzeInputFiles(); reader->LoadImages(); if (reader->GetNumberOfOutputs() == 0) { MITK_ERROR << "Could not determine a DICOM reader for this file" << std::endl; return result; } mitk::DICOMDCMTKTagScanner::Pointer scanner = mitk::DICOMDCMTKTagScanner::New(); scanner->SetInputFiles({ location }); scanner->AddTagPaths(tagsOfInterestList); scanner->Scan(); mitk::DICOMDatasetAccessingImageFrameList frames = scanner->GetFrameInfoList(); if (frames.empty()) { MITK_ERROR << "Error reading the RTDOSE file" << std::endl; return result; } const mitk::DICOMImageBlockDescriptor& desc = reader->GetOutput(0); mitk::Image::Pointer originalImage = desc.GetMitkImage(); if (originalImage.IsNull()) { MITK_ERROR << "Error reading the RTDOSE file in mitk::DicomFileReader" << std::endl; return result; } DcmFileFormat fileformat; OFCondition outp = fileformat.loadFile(location.c_str(), EXS_Unknown); if (outp.bad()) { MITK_ERROR << "Error reading the RTDOSE file in DCMTK" << std::endl; return result; } DcmDataset *dataset = fileformat.getDataset(); DRTDoseIOD doseObject; OFCondition DCMTKresult = doseObject.read(*dataset); if (DCMTKresult.bad()) { MITK_ERROR << "Error reading the RTDOSE file in DCMTK" << std::endl; return result; } auto findingsGridScaling = frames.front()->GetTagValueAsString(DICOMTagPath(0x3004, 0x000e)); //(0x3004, 0x000e) is grid scaling double gridScaling; if (findingsGridScaling.empty()) { MITK_ERROR << "Could not find DoseGridScaling tag" << std::endl; return result; } else { gridScaling = boost::lexical_cast(findingsGridScaling.front().value); } AccessByItk_1(originalImage, MultiplyGridScaling, gridScaling); auto statistics = this->scaledDoseImage->GetStatistics(); double maxDose = statistics->GetScalarValueMax(); this->scaledDoseImage->SetPropertyList(originalImage->GetPropertyList()); - this->scaledDoseImage->SetProperty(mitk::RTConstants::PRESCRIBED_DOSE_PROPERTY_NAME.c_str(), mitk::GenericProperty::New(0.8*maxDose)); + this->scaledDoseImage->SetProperty(mitk::RTConstants::PRESCRIBED_DOSE_PROPERTY_NAME.c_str(), mitk::DoubleProperty::New(0.8*maxDose)); auto findings = ExtractPathsOfInterest(tagsOfInterestList, frames); SetProperties(this->scaledDoseImage, findings); result.push_back(this->scaledDoseImage.GetPointer()); return result; } RTDoseReaderService* RTDoseReaderService::Clone() const { return new RTDoseReaderService(*this); } } diff --git a/Modules/RT/test/mitkRTDoseReaderServiceTest.cpp b/Modules/RT/test/mitkRTDoseReaderServiceTest.cpp index f6d984d8f0..ac49052143 100644 --- a/Modules/RT/test/mitkRTDoseReaderServiceTest.cpp +++ b/Modules/RT/test/mitkRTDoseReaderServiceTest.cpp @@ -1,70 +1,70 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include -#include +#include #include "mitkTemporoSpatialStringProperty.h" #include class mitkRTDoseReaderServiceTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkRTDoseReaderServiceTestSuite); MITK_TEST(TestDoseImage); MITK_TEST(TestProperties); CPPUNIT_TEST_SUITE_END(); private: mitk::Image::ConstPointer m_doseImage; mitk::Image::ConstPointer m_referenceImage; public: void setUp() override { m_referenceImage = mitk::IOUtil::Load(GetTestDataFilePath("RT/Dose/RT_Dose.nrrd")); m_doseImage = mitk::IOUtil::Load(GetTestDataFilePath("RT/Dose/RD.dcm")); } void TestDoseImage() { CPPUNIT_ASSERT_EQUAL_MESSAGE("image should not be null", m_doseImage.IsNotNull(), true); CPPUNIT_ASSERT_EQUAL_MESSAGE("reference image and image should be equal", true, mitk::Equal(*m_doseImage, *m_referenceImage, mitk::eps, true)); } void TestProperties() { CheckStringProperty("DICOM.0008.0060", "RTDOSE"); //Modality auto prescibedDoseProperty = m_doseImage->GetProperty(mitk::RTConstants::PRESCRIBED_DOSE_PROPERTY_NAME.c_str()); - auto prescribedDoseGenericProperty = dynamic_cast*>(prescibedDoseProperty.GetPointer()); + auto prescribedDoseGenericProperty = dynamic_cast(prescibedDoseProperty.GetPointer()); double actualPrescribedDose = prescribedDoseGenericProperty->GetValue(); double expectedPrescribedDose = 65535 * 0.0010494648*0.8; CPPUNIT_ASSERT_DOUBLES_EQUAL_MESSAGE("prescribed dose property is not as expected", expectedPrescribedDose, actualPrescribedDose, 1e-5); CheckStringProperty("DICOM.0020.000D", "1.2.826.0.1.3680043.8.176.2013826104517910.408.3433258507"); //StudyInstanceUID CheckStringProperty("DICOM.3004.000E", "0.0010494648"); //DoseGridScaling CheckStringProperty("DICOM.300C.0002.[0].0008.1155", "1.2.826.0.1.3680043.8.176.2013826104526987.672.1228523524"); //ReferencedRTPlanSequence.ReferencedSOPInstanceUID } void CheckStringProperty(const std::string& propertyName, const std::string& expectedPropertyValue) { auto actualProperty = m_doseImage->GetProperty(propertyName.c_str()); CPPUNIT_ASSERT_EQUAL_MESSAGE("Property not found: " + propertyName, actualProperty.IsNotNull(), true); auto actualTemporoSpatialStringProperty = dynamic_cast(actualProperty.GetPointer()); CPPUNIT_ASSERT_EQUAL_MESSAGE("Property has not type string: " + propertyName, actualTemporoSpatialStringProperty != nullptr, true); std::string actualStringProperty = actualTemporoSpatialStringProperty->GetValue(); CPPUNIT_ASSERT_EQUAL_MESSAGE(propertyName + " is not as expected", actualStringProperty, expectedPropertyValue); } }; MITK_TEST_SUITE_REGISTRATION(mitkRTDoseReaderService) diff --git a/Modules/RenderWindowManagerUI/src/QmitkRenderWindowDataStorageListModel.cpp b/Modules/RenderWindowManagerUI/src/QmitkRenderWindowDataStorageListModel.cpp index 52df4f37ec..67c0c79336 100644 --- a/Modules/RenderWindowManagerUI/src/QmitkRenderWindowDataStorageListModel.cpp +++ b/Modules/RenderWindowManagerUI/src/QmitkRenderWindowDataStorageListModel.cpp @@ -1,354 +1,354 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // render window manager UI module #include "QmitkRenderWindowDataStorageListModel.h" // qt widgets module #include "QmitkCustomVariants.h" #include "QmitkEnums.h" #include "QmitkMimeTypes.h" #include "QmitkNodeDescriptorManager.h" QmitkRenderWindowDataStorageListModel::QmitkRenderWindowDataStorageListModel(QObject* parent /*= nullptr*/) : QmitkAbstractDataStorageModel(parent) { m_RenderWindowLayerController = std::make_unique(); } void QmitkRenderWindowDataStorageListModel::DataStorageChanged() { m_RenderWindowLayerController->SetDataStorage(m_DataStorage.Lock()); UpdateModelData(); } void QmitkRenderWindowDataStorageListModel::NodePredicateChanged() { UpdateModelData(); } void QmitkRenderWindowDataStorageListModel::NodeAdded(const mitk::DataNode* node) { // add a node to each render window specific list (or to a global list initially) AddDataNodeToAllRenderer(const_cast(node)); UpdateModelData(); } void QmitkRenderWindowDataStorageListModel::NodeChanged(const mitk::DataNode* /*node*/) { // nothing here, since the "'NodeChanged'-event is currently sent far too often } void QmitkRenderWindowDataStorageListModel::NodeRemoved(const mitk::DataNode* /*node*/) { // update model data to create a new list without the removed data node UpdateModelData(); } QModelIndex QmitkRenderWindowDataStorageListModel::index(int row, int column, const QModelIndex& parent) const { bool hasIndex = this->hasIndex(row, column, parent); if (hasIndex) { return this->createIndex(row, column); } return QModelIndex(); } QModelIndex QmitkRenderWindowDataStorageListModel::parent(const QModelIndex& /*child*/) const { return QModelIndex(); } int QmitkRenderWindowDataStorageListModel::rowCount(const QModelIndex& parent /*= QModelIndex()*/) const { if (parent.isValid()) { return 0; } return static_cast(m_LayerStack.size()); } int QmitkRenderWindowDataStorageListModel::columnCount(const QModelIndex& parent /*= QModelIndex()*/) const { if (parent.isValid()) { return 0; } return 1; } QVariant QmitkRenderWindowDataStorageListModel::data(const QModelIndex& index, int role) const { if (m_BaseRenderer.IsExpired()) { return QVariant(); } auto baseRenderer = m_BaseRenderer.Lock(); if (!index.isValid() || this != index.model()) { return QVariant(); } if (index.row() < 0 || index.row() >= static_cast(m_LayerStack.size())) { return QVariant(); } mitk::RenderWindowLayerUtilities::LayerStack::const_iterator layerStackIt = m_LayerStack.begin(); std::advance(layerStackIt, index.row()); mitk::DataNode* dataNode = layerStackIt->second; if (Qt::CheckStateRole == role) { bool visibility = false; dataNode->GetVisibility(visibility, baseRenderer); if (visibility) { return Qt::Checked; } else { return Qt::Unchecked; } } else if (Qt::DisplayRole == role) { return QVariant(QString::fromStdString(dataNode->GetName())); } else if (Qt::ToolTipRole == role) { return QVariant("Name of the data node."); } else if (Qt::DecorationRole == role) { QmitkNodeDescriptor* nodeDescriptor = QmitkNodeDescriptorManager::GetInstance()->GetDescriptor(dataNode); return nodeDescriptor->GetIcon(dataNode); } else if (Qt::UserRole == role || QmitkDataNodeRawPointerRole == role) { // user role always returns a reference to the data node, // which can be used to modify the data node in the data storage return QVariant::fromValue(dataNode); } else if (QmitkDataNodeRole == role) { return QVariant::fromValue(mitk::DataNode::Pointer(dataNode)); } return QVariant(); } bool QmitkRenderWindowDataStorageListModel::setData(const QModelIndex& index, const QVariant& value, int role /*= Qt::EditRole*/) { if (m_BaseRenderer.IsExpired()) { return false; } auto baseRenderer = m_BaseRenderer.Lock(); if (!index.isValid() || this != index.model()) { return false; } if (index.row() < 0 || index.row() >= static_cast(m_LayerStack.size())) { return false; } mitk::RenderWindowLayerUtilities::LayerStack::const_iterator layerStackIt = m_LayerStack.begin(); std::advance(layerStackIt, index.row()); mitk::DataNode* dataNode = layerStackIt->second; if (Qt::CheckStateRole == role) { Qt::CheckState newCheckState = static_cast(value.toInt()); bool isVisible = newCheckState; dataNode->SetVisibility(isVisible, baseRenderer); emit dataChanged(index, index); mitk::RenderingManager::GetInstance()->RequestUpdate(baseRenderer->GetRenderWindow()); return true; } return false; } Qt::ItemFlags QmitkRenderWindowDataStorageListModel::flags(const QModelIndex &index) const { if (this != index.model()) { return Qt::NoItemFlags; } if (!index.isValid()) { return Qt::ItemIsDropEnabled; } return Qt::ItemIsEnabled | Qt::ItemIsSelectable | Qt::ItemIsUserCheckable | Qt::ItemIsDragEnabled | Qt::ItemIsDropEnabled; } Qt::DropActions QmitkRenderWindowDataStorageListModel::supportedDropActions() const { return Qt::CopyAction | Qt::MoveAction; } Qt::DropActions QmitkRenderWindowDataStorageListModel::supportedDragActions() const { return Qt::CopyAction | Qt::MoveAction; } QStringList QmitkRenderWindowDataStorageListModel::mimeTypes() const { QStringList types = QAbstractItemModel::mimeTypes(); types << QmitkMimeTypes::DataNodePtrs; return types; } QMimeData* QmitkRenderWindowDataStorageListModel::mimeData(const QModelIndexList& indexes) const { QMimeData* mimeData = new QMimeData(); QByteArray encodedData; QDataStream stream(&encodedData, QIODevice::WriteOnly); for (const auto& index : indexes) { if (index.isValid()) { auto dataNode = data(index, QmitkDataNodeRawPointerRole).value(); stream << reinterpret_cast(dataNode); } } mimeData->setData(QmitkMimeTypes::DataNodePtrs, encodedData); return mimeData; } bool QmitkRenderWindowDataStorageListModel::dropMimeData(const QMimeData* data, Qt::DropAction action, int /*row*/, int column, const QModelIndex& parent) { if (m_BaseRenderer.IsExpired()) { return false; } auto baseRenderer = m_BaseRenderer.Lock(); if (action == Qt::IgnoreAction) { return true; } if (!data->hasFormat(QmitkMimeTypes::DataNodePtrs)) { return false; } if (column > 0) { return false; } if (parent.isValid()) { int layer = -1; auto dataNode = this->data(parent, QmitkDataNodeRawPointerRole).value(); if (nullptr != dataNode) { dataNode->GetIntProperty("layer", layer, baseRenderer); } auto dataNodeList = QmitkMimeTypes::ToDataNodePtrList(data); - for (const auto& dataNode : dataNodeList) + for (const auto& dataNode : qAsConst(dataNodeList)) { m_RenderWindowLayerController->MoveNodeToPosition(dataNode, layer, baseRenderer); } UpdateModelData(); return true; } return false; } void QmitkRenderWindowDataStorageListModel::SetControlledRenderer(mitk::RenderWindowLayerUtilities::RendererVector controlledRenderer) { m_RenderWindowLayerController->SetControlledRenderer(controlledRenderer); if (!m_DataStorage.IsExpired()) { auto dataStorage = m_DataStorage.Lock(); mitk::DataStorage::SetOfObjects::ConstPointer allDataNodes = dataStorage->GetAll(); for (mitk::DataStorage::SetOfObjects::ConstIterator it = allDataNodes->Begin(); it != allDataNodes->End(); ++it) { mitk::DataNode::Pointer dataNode = it->Value(); if (dataNode.IsNull()) { continue; } AddDataNodeToAllRenderer(dataNode); } } } void QmitkRenderWindowDataStorageListModel::SetCurrentRenderer(mitk::BaseRenderer* baseRenderer) { if (m_BaseRenderer == baseRenderer) { return; } m_BaseRenderer = baseRenderer; if (!m_BaseRenderer.IsExpired()) { UpdateModelData(); } } mitk::BaseRenderer* QmitkRenderWindowDataStorageListModel::GetCurrentRenderer() const { if (m_BaseRenderer.IsExpired()) { return nullptr; } return m_BaseRenderer.Lock().GetPointer(); } void QmitkRenderWindowDataStorageListModel::AddDataNodeToAllRenderer(mitk::DataNode* dataNode) { m_RenderWindowLayerController->InsertLayerNode(dataNode); } void QmitkRenderWindowDataStorageListModel::UpdateModelData() { if (!m_DataStorage.IsExpired()) { auto dataStorage = m_DataStorage.Lock(); if (!m_BaseRenderer.IsExpired()) { auto baseRenderer = m_BaseRenderer.Lock(); // update the model, so that it will be filled with the nodes of the new data storage beginResetModel(); // get the current layer stack of the given base renderer m_LayerStack = mitk::RenderWindowLayerUtilities::GetLayerStack(dataStorage, baseRenderer, true); endResetModel(); } } } diff --git a/Modules/RenderWindowManagerUI/src/QmitkRenderWindowDataStorageTreeModel.cpp b/Modules/RenderWindowManagerUI/src/QmitkRenderWindowDataStorageTreeModel.cpp index c453dbdc5c..8274403471 100644 --- a/Modules/RenderWindowManagerUI/src/QmitkRenderWindowDataStorageTreeModel.cpp +++ b/Modules/RenderWindowManagerUI/src/QmitkRenderWindowDataStorageTreeModel.cpp @@ -1,601 +1,601 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // render window manager UI module #include "QmitkRenderWindowDataStorageTreeModel.h" // mitk core #include // qt widgets module #include "QmitkCustomVariants.h" #include "QmitkEnums.h" #include "QmitkMimeTypes.h" #include "QmitkNodeDescriptorManager.h" QmitkRenderWindowDataStorageTreeModel::QmitkRenderWindowDataStorageTreeModel(QObject* parent /*= nullptr*/) : QmitkAbstractDataStorageModel(parent) , m_Root(nullptr) { m_RenderWindowLayerController = std::make_unique(); ResetTree(); } void QmitkRenderWindowDataStorageTreeModel::DataStorageChanged() { m_RenderWindowLayerController->SetDataStorage(m_DataStorage.Lock()); ResetTree(); UpdateModelData(); } void QmitkRenderWindowDataStorageTreeModel::NodePredicateChanged() { ResetTree(); UpdateModelData(); } void QmitkRenderWindowDataStorageTreeModel::NodeAdded(const mitk::DataNode* node) { for (const auto renderer : m_ControlledRenderer) { // add the node to each render window mitk::RenderWindowLayerUtilities::SetRenderWindowProperties(const_cast(node), renderer); } if (!m_BaseRenderer.IsExpired()) { auto baseRenderer = m_BaseRenderer.Lock(); AddNodeInternal(node, baseRenderer); } } void QmitkRenderWindowDataStorageTreeModel::NodeChanged(const mitk::DataNode* node) { auto item = m_Root->Find(node); if (nullptr != item) { auto parentItem = item->GetParent(); // as the root node should not be removed one should always have a parent item if (nullptr == parentItem) { return; } auto index = createIndex(item->GetIndex(), 0, item); emit dataChanged(index, index); } } void QmitkRenderWindowDataStorageTreeModel::NodeRemoved(const mitk::DataNode* node) { RemoveNodeInternal(node); } QModelIndex QmitkRenderWindowDataStorageTreeModel::index(int row, int column, const QModelIndex& parent) const { auto item = GetItemByIndex(parent); if (nullptr != item) { item = item->GetChild(row); } if (nullptr == item) { return QModelIndex(); } return createIndex(row, column, item); } QModelIndex QmitkRenderWindowDataStorageTreeModel::parent(const QModelIndex& parent) const { auto item = GetItemByIndex(parent); if (nullptr != item) { item = item->GetParent(); } if(nullptr == item) { return QModelIndex(); } if (item == m_Root) { return QModelIndex(); } return createIndex(item->GetIndex(), 0, item); } int QmitkRenderWindowDataStorageTreeModel::rowCount(const QModelIndex& parent /*= QModelIndex()*/) const { auto item = GetItemByIndex(parent); if (nullptr == item) { return 0; } return item->GetChildCount(); } int QmitkRenderWindowDataStorageTreeModel::columnCount(const QModelIndex&/* parent = QModelIndex()*/) const { if (0 == m_Root->GetChildCount()) { // no items stored, no need to display columns return 0; } return 1; } QVariant QmitkRenderWindowDataStorageTreeModel::data(const QModelIndex& index, int role) const { if (m_BaseRenderer.IsExpired()) { return QVariant(); } auto baseRenderer = m_BaseRenderer.Lock(); if (!index.isValid() || this != index.model()) { return QVariant(); } auto item = GetItemByIndex(index); if (nullptr == item) { return QVariant(); } auto dataNode = item->GetDataNode(); if (nullptr == dataNode) { return QVariant(); } if (Qt::CheckStateRole == role) { bool visibility = false; dataNode->GetVisibility(visibility, baseRenderer); if (visibility) { return Qt::Checked; } else { return Qt::Unchecked; } } else if (Qt::DisplayRole == role) { return QVariant(QString::fromStdString(dataNode->GetName())); } else if (Qt::ToolTipRole == role) { return QVariant("Name of the data node."); } else if (Qt::DecorationRole == role) { QmitkNodeDescriptor* nodeDescriptor = QmitkNodeDescriptorManager::GetInstance()->GetDescriptor(dataNode); return nodeDescriptor->GetIcon(dataNode); } else if (Qt::UserRole == role || QmitkDataNodeRawPointerRole == role) { // user role always returns a reference to the data node, // which can be used to modify the data node in the data storage return QVariant::fromValue(dataNode); } else if (QmitkDataNodeRole == role) { return QVariant::fromValue(mitk::DataNode::Pointer(dataNode)); } return QVariant(); } bool QmitkRenderWindowDataStorageTreeModel::setData(const QModelIndex& index, const QVariant& value, int role /*= Qt::EditRole*/) { if (m_BaseRenderer.IsExpired()) { return false; } auto baseRenderer = m_BaseRenderer.Lock(); if (!index.isValid() || this != index.model()) { return false; } auto item = GetItemByIndex(index); if (nullptr == item) { return false; } auto dataNode = item->GetDataNode(); if (nullptr == dataNode) { return false; } if (Qt::EditRole == role && !value.toString().isEmpty()) { dataNode->SetName(value.toString().toStdString().c_str()); emit dataChanged(index, index); return true; } if (Qt::CheckStateRole == role) { Qt::CheckState newCheckState = static_cast(value.toInt()); bool isVisible = newCheckState; dataNode->SetVisibility(isVisible, baseRenderer); emit dataChanged(index, index); mitk::RenderingManager::GetInstance()->RequestUpdate(baseRenderer->GetRenderWindow()); return true; } return false; } Qt::ItemFlags QmitkRenderWindowDataStorageTreeModel::flags(const QModelIndex& index) const { if (this != index.model()) { return Qt::NoItemFlags; } if (!index.isValid()) { return Qt::ItemIsDropEnabled; } auto item = GetItemByIndex(index); if (nullptr == item) { return Qt::NoItemFlags; } const auto dataNode = item->GetDataNode(); if (m_NodePredicate.IsNull() || m_NodePredicate->CheckNode(dataNode)) { return Qt::ItemIsEnabled | Qt::ItemIsSelectable | Qt::ItemIsUserCheckable | Qt::ItemIsDragEnabled | Qt::ItemIsDropEnabled; } return Qt::NoItemFlags; } Qt::DropActions QmitkRenderWindowDataStorageTreeModel::supportedDropActions() const { return Qt::CopyAction | Qt::MoveAction; } Qt::DropActions QmitkRenderWindowDataStorageTreeModel::supportedDragActions() const { return Qt::CopyAction | Qt::MoveAction; } QStringList QmitkRenderWindowDataStorageTreeModel::mimeTypes() const { QStringList types = QAbstractItemModel::mimeTypes(); types << QmitkMimeTypes::DataNodePtrs; return types; } QMimeData* QmitkRenderWindowDataStorageTreeModel::mimeData(const QModelIndexList& indexes) const { QMimeData* mimeData = new QMimeData(); QByteArray encodedData; QDataStream stream(&encodedData, QIODevice::WriteOnly); for (const auto& index : indexes) { if (index.isValid()) { auto dataNode = data(index, QmitkDataNodeRawPointerRole).value(); stream << reinterpret_cast(dataNode); } } mimeData->setData(QmitkMimeTypes::DataNodePtrs, encodedData); return mimeData; } bool QmitkRenderWindowDataStorageTreeModel::dropMimeData(const QMimeData* data, Qt::DropAction action, int /*row*/, int /*column*/, const QModelIndex& parent) { if (m_BaseRenderer.IsExpired()) { return false; } auto baseRenderer = m_BaseRenderer.Lock(); if (action == Qt::IgnoreAction) { return true; } if (!data->hasFormat(QmitkMimeTypes::DataNodePtrs)) { return false; } if (!parent.isValid()) { return false; } int layer = -1; auto dataNode = this->data(parent, QmitkDataNodeRawPointerRole).value(); if (nullptr != dataNode) { dataNode->GetIntProperty("layer", layer, baseRenderer); } auto dataNodeList = QmitkMimeTypes::ToDataNodePtrList(data); - for (const auto& dataNode : dataNodeList) + for (const auto& dataNode : qAsConst(dataNodeList)) { m_RenderWindowLayerController->MoveNodeToPosition(dataNode, layer, baseRenderer); } ResetTree(); UpdateModelData(); AdjustLayerProperty(); return true; } void QmitkRenderWindowDataStorageTreeModel::SetControlledRenderer(mitk::RenderWindowLayerUtilities::RendererVector controlledRenderer) { m_RenderWindowLayerController->SetControlledRenderer(controlledRenderer); m_ControlledRenderer = controlledRenderer; ResetTree(); if (m_DataStorage.IsExpired()) { return; } auto dataStorage = m_DataStorage.Lock(); for (const auto& renderer : controlledRenderer) { if (nullptr == renderer) { continue; } auto allDataNodes = dataStorage->GetAll(); for (const auto& dataNode : *allDataNodes) { // add the node to each render window mitk::RenderWindowLayerUtilities::SetRenderWindowProperties(dataNode, renderer); } } } void QmitkRenderWindowDataStorageTreeModel::SetCurrentRenderer(mitk::BaseRenderer* baseRenderer) { if (m_BaseRenderer == baseRenderer) { return; } // base renderer changed // reset tree to build a new renderer-specific item hierarchy m_BaseRenderer = baseRenderer; ResetTree(); UpdateModelData(); } mitk::BaseRenderer* QmitkRenderWindowDataStorageTreeModel::GetCurrentRenderer() const { if (m_BaseRenderer.IsExpired()) { return nullptr; } return m_BaseRenderer.Lock().GetPointer(); } void QmitkRenderWindowDataStorageTreeModel::ResetTree() { beginResetModel(); if (nullptr != m_Root) { m_Root->Delete(); } mitk::DataNode::Pointer rootDataNode = mitk::DataNode::New(); rootDataNode->SetName("Data Storage"); m_Root = new QmitkDataStorageTreeModelInternalItem(rootDataNode); endResetModel(); } void QmitkRenderWindowDataStorageTreeModel::UpdateModelData() { if (!m_DataStorage.IsExpired()) { auto dataStorage = m_DataStorage.Lock(); if (!m_BaseRenderer.IsExpired()) { auto baseRenderer = m_BaseRenderer.Lock(); mitk::NodePredicateAnd::Pointer combinedNodePredicate = mitk::RenderWindowLayerUtilities::GetRenderWindowPredicate(baseRenderer); auto filteredDataNodes = dataStorage->GetSubset(combinedNodePredicate); for (const auto& dataNode : *filteredDataNodes) { AddNodeInternal(dataNode, baseRenderer); } } } } void QmitkRenderWindowDataStorageTreeModel::AdjustLayerProperty() { if (m_BaseRenderer.IsExpired()) { return; } auto baseRenderer = m_BaseRenderer.Lock(); std::vector treeAsVector; TreeToVector(m_Root, treeAsVector); int i = treeAsVector.size() - 1; for (auto it = treeAsVector.begin(); it != treeAsVector.end(); ++it) { auto dataNode = (*it)->GetDataNode(); dataNode->SetIntProperty("layer", i, baseRenderer); --i; } } void QmitkRenderWindowDataStorageTreeModel::TreeToVector(QmitkDataStorageTreeModelInternalItem* parent, std::vector& treeAsVector) const { QmitkDataStorageTreeModelInternalItem* item; for (int i = 0; i < parent->GetChildCount(); ++i) { item = parent->GetChild(i); TreeToVector(item, treeAsVector); treeAsVector.push_back(item); } } void QmitkRenderWindowDataStorageTreeModel::AddNodeInternal(const mitk::DataNode* dataNode, const mitk::BaseRenderer* renderer) { if (nullptr == dataNode || m_DataStorage.IsExpired() || nullptr != m_Root->Find(dataNode)) { return; } // find out if we have a root node auto parentItem = m_Root; QModelIndex index; auto parentDataNode = GetParentNode(dataNode); if (nullptr != parentDataNode) // no top level data node { parentItem = m_Root->Find(parentDataNode); if (nullptr == parentItem) { // parent node not contained in the tree; add it NodeAdded(parentDataNode); parentItem = m_Root->Find(parentDataNode); if (nullptr == parentItem) { // could not find and add the parent tree; abort return; } } // get the index of this parent with the help of the grand parent index = createIndex(parentItem->GetIndex(), 0, parentItem); } int firstRowWithASiblingBelow = 0; int nodeLayer = -1; dataNode->GetIntProperty("layer", nodeLayer, renderer); for (const auto& siblingItem : parentItem->GetChildren()) { int siblingLayer = -1; auto siblingNode = siblingItem->GetDataNode(); if (nullptr != siblingNode) { siblingNode->GetIntProperty("layer", siblingLayer, renderer); } if (nodeLayer > siblingLayer) { break; } ++firstRowWithASiblingBelow; } beginInsertRows(index, firstRowWithASiblingBelow, firstRowWithASiblingBelow); auto newNode = new QmitkDataStorageTreeModelInternalItem(const_cast(dataNode)); parentItem->InsertChild(newNode, firstRowWithASiblingBelow); endInsertRows(); } void QmitkRenderWindowDataStorageTreeModel::RemoveNodeInternal(const mitk::DataNode* dataNode) { if (nullptr == dataNode || nullptr == m_Root) { return; } auto item = m_Root->Find(dataNode); if (nullptr == item) { return; } auto parentItem = item->GetParent(); auto parentIndex = GetIndexByItem(parentItem); auto children = item->GetChildren(); beginRemoveRows(parentIndex, item->GetIndex(), item->GetIndex()); parentItem->RemoveChild(item); delete item; endRemoveRows(); if (!children.empty()) { // rebuild tree because children could not be at the top level ResetTree(); UpdateModelData(); } } mitk::DataNode* QmitkRenderWindowDataStorageTreeModel::GetParentNode(const mitk::DataNode* node) const { mitk::DataNode* dataNode = nullptr; if (m_DataStorage.IsExpired()) { return dataNode; } auto sources = m_DataStorage.Lock()->GetSources(node); if (sources->empty()) { return dataNode; } return sources->front(); } QmitkDataStorageTreeModelInternalItem* QmitkRenderWindowDataStorageTreeModel::GetItemByIndex(const QModelIndex& index) const { if (index.isValid()) { return static_cast(index.internalPointer()); } return m_Root; } QModelIndex QmitkRenderWindowDataStorageTreeModel::GetIndexByItem(QmitkDataStorageTreeModelInternalItem* item) const { if (item == m_Root) { return QModelIndex(); } return createIndex(item->GetIndex(), 0, item); } diff --git a/Modules/SceneSerialization/src/mitkSceneIO.cpp b/Modules/SceneSerialization/src/mitkSceneIO.cpp index 04db6cf399..888eda6c5c 100644 --- a/Modules/SceneSerialization/src/mitkSceneIO.cpp +++ b/Modules/SceneSerialization/src/mitkSceneIO.cpp @@ -1,575 +1,575 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include #include #include #include "mitkBaseDataSerializer.h" #include "mitkPropertyListSerializer.h" #include "mitkSceneIO.h" #include "mitkSceneReader.h" #include "mitkBaseRenderer.h" #include "mitkProgressBar.h" #include "mitkRenderingManager.h" #include "mitkStandaloneDataStorage.h" #include #include #include #include #include #include #include "itksys/SystemTools.hxx" #include mitk::SceneIO::SceneIO() : m_WorkingDirectory(""), m_UnzipErrors(0) { } mitk::SceneIO::~SceneIO() { } std::string mitk::SceneIO::CreateEmptyTempDirectory() { mitk::UIDGenerator uidGen; // std::string returnValue = mitk::StandardFileLocations::GetInstance()->GetOptionDirectory() + // Poco::Path::separator() + "SceneIOTemp" + uidGen.GetUID(); std::string returnValue = Poco::Path::temp() + "SceneIOTemp" + uidGen.GetUID(); std::string uniquename = returnValue + Poco::Path::separator(); Poco::File tempdir(uniquename); try { bool existsNot = tempdir.createDirectory(); if (!existsNot) { MITK_ERROR << "Warning: Directory already exitsts: " << uniquename << " (choosing another)"; returnValue = mitk::StandardFileLocations::GetInstance()->GetOptionDirectory() + Poco::Path::separator() + "SceneIOTempDirectory" + uidGen.GetUID(); uniquename = returnValue + Poco::Path::separator(); Poco::File tempdir2(uniquename); if (!tempdir2.createDirectory()) { MITK_ERROR << "Warning: Second directory also already exitsts: " << uniquename; } } } catch (std::exception &e) { MITK_ERROR << "Could not create temporary directory " << uniquename << ":" << e.what(); return ""; } return returnValue; } mitk::DataStorage::Pointer mitk::SceneIO::LoadScene(const std::string &filename, DataStorage *pStorage, bool clearStorageFirst) { mitk::LocaleSwitch localeSwitch("C"); // prepare data storage DataStorage::Pointer storage = pStorage; if (storage.IsNull()) { storage = StandaloneDataStorage::New().GetPointer(); } // test input filename if (filename.empty()) { MITK_ERROR << "No filename given. Not possible to load scene."; return storage; } // test if filename can be read std::ifstream file(filename.c_str(), std::ios::binary); if (!file.good()) { MITK_ERROR << "Cannot open '" << filename << "' for reading"; return storage; } // get new temporary directory m_WorkingDirectory = CreateEmptyTempDirectory(); if (m_WorkingDirectory.empty()) { MITK_ERROR << "Could not create temporary directory. Cannot open scene files."; return storage; } // unzip all filenames contents to temp dir m_UnzipErrors = 0; Poco::Zip::Decompress unzipper(file, Poco::Path(m_WorkingDirectory)); unzipper.EError += Poco::Delegate>( this, &SceneIO::OnUnzipError); unzipper.EOk += Poco::Delegate>( this, &SceneIO::OnUnzipOk); unzipper.decompressAllFiles(); unzipper.EError -= Poco::Delegate>( this, &SceneIO::OnUnzipError); unzipper.EOk -= Poco::Delegate>( this, &SceneIO::OnUnzipOk); if (m_UnzipErrors) { MITK_ERROR << "There were " << m_UnzipErrors << " errors unzipping '" << filename << "'. Will attempt to read whatever could be unzipped."; } // transcode locale-dependent string m_WorkingDirectory = Poco::Path::transcode (m_WorkingDirectory); auto indexFile = m_WorkingDirectory + mitk::IOUtil::GetDirectorySeparator() + "index.xml"; storage = LoadSceneUnzipped(indexFile, storage, clearStorageFirst); // delete temp directory try { Poco::File deleteDir(m_WorkingDirectory); deleteDir.remove(true); // recursive } catch (...) { MITK_ERROR << "Could not delete temporary directory " << m_WorkingDirectory; } // return new data storage, even if empty or uncomplete (return as much as possible but notify calling method) return storage; } mitk::DataStorage::Pointer mitk::SceneIO::LoadSceneUnzipped(const std::string &indexfilename, DataStorage *pStorage, bool clearStorageFirst) { mitk::LocaleSwitch localeSwitch("C"); // prepare data storage DataStorage::Pointer storage = pStorage; if (storage.IsNull()) { storage = StandaloneDataStorage::New().GetPointer(); } if (clearStorageFirst) { try { storage->Remove(storage->GetAll()); } catch (...) { MITK_ERROR << "DataStorage cannot be cleared properly."; } } // test input filename if (indexfilename.empty()) { MITK_ERROR << "No filename given. Not possible to load scene."; return storage; } // transcode locale-dependent string std::string tempfilename; std::string workingDir; itksys::SystemTools::SplitProgramPath(indexfilename, workingDir, tempfilename); // test if index.xml exists // parse index.xml with TinyXML tinyxml2::XMLDocument document; if (tinyxml2::XML_SUCCESS != document.LoadFile(indexfilename.c_str())) { MITK_ERROR << "Could not open/read/parse " << workingDir << mitk::IOUtil::GetDirectorySeparator() << "index.xml\nTinyXML reports: " << document.ErrorStr() << std::endl; return storage; } SceneReader::Pointer reader = SceneReader::New(); if (!reader->LoadScene(document, workingDir, storage)) { MITK_ERROR << "There were errors while loading scene file " << indexfilename << ". Your data may be corrupted"; } // return new data storage, even if empty or uncomplete (return as much as possible but notify calling method) return storage; } bool mitk::SceneIO::SaveScene(DataStorage::SetOfObjects::ConstPointer sceneNodes, const DataStorage *storage, const std::string &filename) { if (!sceneNodes) { MITK_ERROR << "No set of nodes given. Not possible to save scene."; return false; } if (!storage) { MITK_ERROR << "No data storage given. Not possible to save scene."; // \TODO: Technically, it would be possible to // save the nodes without their relation return false; } if (filename.empty()) { MITK_ERROR << "No filename given. Not possible to save scene."; return false; } mitk::LocaleSwitch localeSwitch("C"); try { m_FailedNodes = DataStorage::SetOfObjects::New(); m_FailedProperties = PropertyList::New(); // start XML DOM tinyxml2::XMLDocument document; document.InsertEndChild(document.NewDeclaration()); auto *version = document.NewElement("Version"); version->SetAttribute("Writer", __FILE__); version->SetAttribute("Revision", "$Revision: 17055 $"); version->SetAttribute("FileVersion", 1); document.InsertEndChild(version); // DataStorage::SetOfObjects::ConstPointer sceneNodes = storage->GetSubset( predicate ); if (sceneNodes.IsNull()) { MITK_WARN << "Saving empty scene to " << filename; } else { if (sceneNodes->size() == 0) { MITK_WARN << "Saving empty scene to " << filename; } MITK_INFO << "Storing scene with " << sceneNodes->size() << " objects to " << filename; m_WorkingDirectory = CreateEmptyTempDirectory(); if (m_WorkingDirectory.empty()) { MITK_ERROR << "Could not create temporary directory. Cannot create scene files."; return false; } ProgressBar::GetInstance()->AddStepsToDo(sceneNodes->size()); // find out about dependencies typedef std::map UIDMapType; typedef std::map> SourcesMapType; UIDMapType nodeUIDs; // for dependencies: ID of each node SourcesMapType sourceUIDs; // for dependencies: IDs of a node's parent nodes UIDGenerator nodeUIDGen("OBJECT_"); for (auto iter = sceneNodes->begin(); iter != sceneNodes->end(); ++iter) { DataNode *node = iter->GetPointer(); if (!node) continue; // unlikely event that we get a nullptr pointer as an object for saving. just ignore // generate UIDs for all source objects DataStorage::SetOfObjects::ConstPointer sourceObjects = storage->GetSources(node); for (auto sourceIter = sourceObjects->begin(); sourceIter != sourceObjects->end(); ++sourceIter) { if (std::find(sceneNodes->begin(), sceneNodes->end(), *sourceIter) == sceneNodes->end()) continue; // source is not saved, so don't generate a UID for this source // create a uid for the parent object if (nodeUIDs[*sourceIter].empty()) { nodeUIDs[*sourceIter] = nodeUIDGen.GetUID(); } // store this dependency for writing sourceUIDs[node].push_back(nodeUIDs[*sourceIter]); } if (nodeUIDs[node].empty()) { nodeUIDs[node] = nodeUIDGen.GetUID(); } } // write out objects, dependencies and properties for (auto iter = sceneNodes->begin(); iter != sceneNodes->end(); ++iter) { DataNode *node = iter->GetPointer(); if (node) { auto *nodeElement = document.NewElement("node"); std::string filenameHint(node->GetName()); filenameHint = itksys::SystemTools::MakeCindentifier( filenameHint.c_str()); // escape filename <-- only allow [A-Za-z0-9_], replace everything else with _ // store dependencies auto searchUIDIter = nodeUIDs.find(node); if (searchUIDIter != nodeUIDs.end()) { // store this node's ID nodeElement->SetAttribute("UID", searchUIDIter->second.c_str()); } auto searchSourcesIter = sourceUIDs.find(node); if (searchSourcesIter != sourceUIDs.end()) { // store all source IDs for (auto sourceUIDIter = searchSourcesIter->second.begin(); sourceUIDIter != searchSourcesIter->second.end(); ++sourceUIDIter) { auto *uidElement = document.NewElement("source"); uidElement->SetAttribute("UID", sourceUIDIter->c_str()); nodeElement->InsertEndChild(uidElement); } } // store basedata if (BaseData *data = node->GetData()) { // std::string filenameHint( node->GetName() ); bool error(false); auto *dataElement = SaveBaseData(document, data, filenameHint, error); // returns a reference to a file if (error) { m_FailedNodes->push_back(node); } // store basedata properties PropertyList *propertyList = data->GetPropertyList(); if (propertyList && !propertyList->IsEmpty()) { auto *baseDataPropertiesElement = SavePropertyList(document, propertyList, filenameHint + "-data"); // returns a reference to a file dataElement->InsertEndChild(baseDataPropertiesElement); } nodeElement->InsertEndChild(dataElement); } // store all renderwindow specific propertylists mitk::DataNode::PropertyListKeyNames propertyListKeys = node->GetPropertyListNames(); - for (auto renderWindowName : propertyListKeys) + for (const auto &renderWindowName : propertyListKeys) { PropertyList *propertyList = node->GetPropertyList(renderWindowName); if (propertyList && !propertyList->IsEmpty()) { auto *renderWindowPropertiesElement = SavePropertyList(document, propertyList, filenameHint + "-" + renderWindowName); // returns a reference to a file renderWindowPropertiesElement->SetAttribute("renderwindow", renderWindowName.c_str()); nodeElement->InsertEndChild(renderWindowPropertiesElement); } } // don't forget the renderwindow independent list PropertyList *propertyList = node->GetPropertyList(); if (propertyList && !propertyList->IsEmpty()) { auto *propertiesElement = SavePropertyList(document, propertyList, filenameHint + "-node"); // returns a reference to a file nodeElement->InsertEndChild(propertiesElement); } document.InsertEndChild(nodeElement); } else { MITK_WARN << "Ignoring nullptr node during scene serialization."; } ProgressBar::GetInstance()->Progress(); } // end for all nodes } // end if sceneNodes std::string defaultLocale_WorkingDirectory = Poco::Path::transcode( m_WorkingDirectory ); auto xmlFilename = defaultLocale_WorkingDirectory + Poco::Path::separator() + "index.xml"; if (tinyxml2::XML_SUCCESS != document.SaveFile(xmlFilename.c_str())) { MITK_ERROR << "Could not write scene to " << defaultLocale_WorkingDirectory << Poco::Path::separator() << "index.xml" << "\nTinyXML reports '" << document.ErrorStr() << "'"; return false; } else { try { Poco::File deleteFile(filename.c_str()); if (deleteFile.exists()) { deleteFile.remove(); } // create zip at filename std::ofstream file(filename.c_str(), std::ios::binary | std::ios::out); if (!file.good()) { MITK_ERROR << "Could not open a zip file for writing: '" << filename << "'"; return false; } else { Poco::Zip::Compress zipper(file, true); Poco::Path tmpdir(m_WorkingDirectory); zipper.addRecursive(tmpdir); zipper.close(); } try { Poco::File deleteDir(m_WorkingDirectory); deleteDir.remove(true); // recursive } catch (...) { MITK_ERROR << "Could not delete temporary directory " << m_WorkingDirectory; return false; // ok? } } catch (std::exception &e) { MITK_ERROR << "Could not create ZIP file from " << m_WorkingDirectory << "\nReason: " << e.what(); return false; } return true; } } catch (std::exception &e) { MITK_ERROR << "Caught exception during saving temporary files to disk. Error description: '" << e.what() << "'"; return false; } } tinyxml2::XMLElement *mitk::SceneIO::SaveBaseData(tinyxml2::XMLDocument &doc, BaseData *data, const std::string &filenamehint, bool &error) { assert(data); error = true; // find correct serializer // the serializer must // - create a file containing all information to recreate the BaseData object --> needs to know where to put this // file (and a filename?) // - TODO what to do about writers that creates one file per timestep? auto *element = doc.NewElement("data"); element->SetAttribute("type", data->GetNameOfClass()); // construct name of serializer class std::string serializername(data->GetNameOfClass()); serializername += "Serializer"; std::list thingsThatCanSerializeThis = itk::ObjectFactoryBase::CreateAllInstance(serializername.c_str()); if (thingsThatCanSerializeThis.size() < 1) { MITK_ERROR << "No serializer found for " << data->GetNameOfClass() << ". Skipping object"; } for (auto iter = thingsThatCanSerializeThis.begin(); iter != thingsThatCanSerializeThis.end(); ++iter) { if (auto *serializer = dynamic_cast(iter->GetPointer())) { serializer->SetData(data); serializer->SetFilenameHint(filenamehint); std::string defaultLocale_WorkingDirectory = Poco::Path::transcode( m_WorkingDirectory ); serializer->SetWorkingDirectory(defaultLocale_WorkingDirectory); try { std::string writtenfilename = serializer->Serialize(); element->SetAttribute("file", writtenfilename.c_str()); error = false; } catch (std::exception &e) { MITK_ERROR << "Serializer " << serializer->GetNameOfClass() << " failed: " << e.what(); } break; } } element->SetAttribute("UID", data->GetUID().c_str()); return element; } tinyxml2::XMLElement *mitk::SceneIO::SavePropertyList(tinyxml2::XMLDocument &doc, PropertyList *propertyList, const std::string &filenamehint) { assert(propertyList); // - TODO what to do about shared properties (same object in two lists or behind several keys)? auto *element = doc.NewElement("properties"); // construct name of serializer class PropertyListSerializer::Pointer serializer = PropertyListSerializer::New(); serializer->SetPropertyList(propertyList); serializer->SetFilenameHint(filenamehint); std::string defaultLocale_WorkingDirectory = Poco::Path::transcode( m_WorkingDirectory ); serializer->SetWorkingDirectory(defaultLocale_WorkingDirectory); try { std::string writtenfilename = serializer->Serialize(); element->SetAttribute("file", writtenfilename.c_str()); PropertyList::Pointer failedProperties = serializer->GetFailedProperties(); if (failedProperties.IsNotNull()) { // move failed properties to global list m_FailedProperties->ConcatenatePropertyList(failedProperties, true); } } catch (std::exception &e) { MITK_ERROR << "Serializer " << serializer->GetNameOfClass() << " failed: " << e.what(); } return element; } const mitk::SceneIO::FailedBaseDataListType *mitk::SceneIO::GetFailedNodes() { return m_FailedNodes.GetPointer(); } const mitk::PropertyList *mitk::SceneIO::GetFailedProperties() { return m_FailedProperties; } void mitk::SceneIO::OnUnzipError(const void * /*pSender*/, std::pair &info) { ++m_UnzipErrors; MITK_ERROR << "Error while unzipping: " << info.second; } void mitk::SceneIO::OnUnzipOk(const void * /*pSender*/, std::pair & /*info*/) { // MITK_INFO << "Unzipped ok: " << info.second.toString(); } diff --git a/Modules/SceneSerialization/src/mitkSceneReaderV1.cpp b/Modules/SceneSerialization/src/mitkSceneReaderV1.cpp index 155f8f20f4..c55bf4e681 100644 --- a/Modules/SceneSerialization/src/mitkSceneReaderV1.cpp +++ b/Modules/SceneSerialization/src/mitkSceneReaderV1.cpp @@ -1,430 +1,457 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkSceneReaderV1.h" #include "Poco/Path.h" #include "mitkBaseRenderer.h" #include "mitkIOUtil.h" #include "mitkProgressBar.h" #include "mitkPropertyListDeserializer.h" #include "mitkSerializerMacros.h" #include #include #include MITK_REGISTER_SERIALIZER(SceneReaderV1) namespace { typedef std::pair> NodesAndParentsPair; bool NodeSortByLayerIsLessThan(const NodesAndParentsPair &left, const NodesAndParentsPair &right) { if (left.first.IsNotNull() && right.first.IsNotNull()) { int leftLayer; int rightLayer; if (left.first->GetIntProperty("layer", leftLayer) && right.first->GetIntProperty("layer", rightLayer)) { return leftLayer < rightLayer; } else { // fall back to name sort return left.first->GetName() < right.first->GetName(); } } // in all other cases, fall back to stupid pointer comparison // this is not reasonable but at least answers the sorting // question clearly return left.first.GetPointer() < right.first.GetPointer(); } + + // This is a workaround until we are able to save time-related information in an + // actual file format of surfaces. + void ApplyProportionalTimeGeometryProperties(mitk::BaseData* data) + { + if (nullptr == data) + return; + + auto properties = data->GetPropertyList(); + + if (properties.IsNull()) + return; + + auto* geometry = dynamic_cast(data->GetTimeGeometry()); + + if (nullptr == geometry) + return; + + float value = 0.0f; + + if (properties->GetFloatProperty("ProportionalTimeGeometry.FirstTimePoint", value)) + geometry->SetFirstTimePoint(value); + + if (properties->GetFloatProperty("ProportionalTimeGeometry.StepDuration", value)) + geometry->SetStepDuration(value); + } } bool mitk::SceneReaderV1::LoadScene(tinyxml2::XMLDocument &document, const std::string &workingDirectory, DataStorage *storage) { assert(storage); bool error(false); // TODO prepare to detect errors (such as cycles) from wrongly written or edited xml files // Get number of elements to initialze progress bar // 1. if there is a element, // - construct a name for the appropriate serializer // - try to instantiate this serializer via itk object factory // - if serializer could be created, use it to read the file into a BaseData object // - if successful, call the new node's SetData(..) // create a node for the tag "data" and test if node was created typedef std::vector DataNodeVector; DataNodeVector DataNodes; unsigned int listSize = 0; for (auto *element = document.FirstChildElement("node"); element != nullptr; element = element->NextSiblingElement("node")) { ++listSize; } ProgressBar::GetInstance()->AddStepsToDo(listSize * 2); for (auto *element = document.FirstChildElement("node"); element != nullptr; element = element->NextSiblingElement("node")) { DataNodes.push_back(LoadBaseDataFromDataTag(element->FirstChildElement("data"), workingDirectory, error)); ProgressBar::GetInstance()->Progress(); } // iterate all nodes // first level nodes should be elements auto nit = DataNodes.begin(); for (auto *element = document.FirstChildElement("node"); element != nullptr || nit != DataNodes.end(); element = element->NextSiblingElement("node"), ++nit) { mitk::DataNode::Pointer node = *nit; // in case dataXmlElement is valid test whether it containts the "properties" child tag // and process further if and only if yes auto *dataXmlElement = element->FirstChildElement("data"); if (dataXmlElement && dataXmlElement->FirstChildElement("properties")) { auto *baseDataElement = dataXmlElement->FirstChildElement("properties"); if (node->GetData()) { DecorateBaseDataWithProperties(node->GetData(), baseDataElement, workingDirectory); + ApplyProportionalTimeGeometryProperties(node->GetData()); } else { MITK_WARN << "BaseData properties stored in scene file, but BaseData could not be read" << std::endl; } } // 2. check child nodes const char *uida = element->Attribute("UID"); std::string uid(""); if (uida) { uid = uida; m_NodeForID[uid] = node.GetPointer(); m_IDForNode[node.GetPointer()] = uid; } else { MITK_ERROR << "No UID found for current node. Node will have no parents."; error = true; } // 3. if there are nodes, // - instantiate the appropriate PropertyListDeSerializer // - use them to construct PropertyList objects // - add these properties to the node (if necessary, use renderwindow name) bool success = DecorateNodeWithProperties(node, element, workingDirectory); if (!success) { MITK_ERROR << "Could not load properties for node."; error = true; } // remember node for later adding to DataStorage m_OrderedNodePairs.push_back(std::make_pair(node, std::list())); // 4. if there are elements, remember parent objects for (auto *source = element->FirstChildElement("source"); source != nullptr; source = source->NextSiblingElement("source")) { const char *sourceUID = source->Attribute("UID"); if (sourceUID) { m_OrderedNodePairs.back().second.push_back(std::string(sourceUID)); } } ProgressBar::GetInstance()->Progress(); } // end for all // sort our nodes by their "layer" property // (to be inserted in that order) m_OrderedNodePairs.sort(&NodeSortByLayerIsLessThan); // remove all unknown parent UIDs for (auto nodesIter = m_OrderedNodePairs.begin(); nodesIter != m_OrderedNodePairs.end(); ++nodesIter) { for (auto parentsIter = nodesIter->second.begin(); parentsIter != nodesIter->second.end();) { if (m_NodeForID.find(*parentsIter) == m_NodeForID.end()) { parentsIter = nodesIter->second.erase(parentsIter); MITK_WARN << "Found a DataNode with unknown parents. Will add it to DataStorage without any parent objects."; error = true; } else { ++parentsIter; } } } // repeat the following loop ... // ... for all created nodes unsigned int lastMapSize(0); while (lastMapSize != m_OrderedNodePairs .size()) // this is to prevent infinite loops; each iteration must at least add one node to DataStorage { lastMapSize = m_OrderedNodePairs.size(); // iterate (layer) ordered nodes backwards // we insert the highest layers first for (auto nodesIter = m_OrderedNodePairs.begin(); nodesIter != m_OrderedNodePairs.end(); ++nodesIter) { bool addThisNode(true); // if any parent node is not yet in DataStorage, skip node for now and check later for (auto parentsIter = nodesIter->second.begin(); parentsIter != nodesIter->second.end(); ++parentsIter) { if (!storage->Exists(m_NodeForID[*parentsIter])) { addThisNode = false; break; } } if (addThisNode) { DataStorage::SetOfObjects::Pointer parents = DataStorage::SetOfObjects::New(); for (auto parentsIter = nodesIter->second.begin(); parentsIter != nodesIter->second.end(); ++parentsIter) { parents->push_back(m_NodeForID[*parentsIter]); } // if all parents are found in datastorage (or are unknown), add node to DataStorage storage->Add(nodesIter->first, parents); // remove this node from m_OrderedNodePairs m_OrderedNodePairs.erase(nodesIter); // break this for loop because iterators are probably invalid break; } } } // All nodes that are still in m_OrderedNodePairs at this point are not part of a proper directed graph structure. // We'll add such nodes without any parent information. for (auto nodesIter = m_OrderedNodePairs.begin(); nodesIter != m_OrderedNodePairs.end(); ++nodesIter) { storage->Add(nodesIter->first); MITK_WARN << "Encountered node that is not part of a directed graph structure. Will be added to DataStorage " "without parents."; error = true; } return !error; } mitk::DataNode::Pointer mitk::SceneReaderV1::LoadBaseDataFromDataTag(const tinyxml2::XMLElement *dataElement, const std::string &workingDirectory, bool &error) { DataNode::Pointer node; if (dataElement) { const char *filename = dataElement->Attribute("file"); if (filename && strlen(filename) != 0) { try { std::vector baseData = IOUtil::Load(workingDirectory + Poco::Path::separator() + filename); if (baseData.size() > 1) { MITK_WARN << "Discarding multiple base data results from " << filename << " except the first one."; } node = DataNode::New(); node->SetData(baseData.front()); } catch (std::exception &e) { MITK_ERROR << "Error during attempt to read '" << filename << "'. Exception says: " << e.what(); error = true; } if (node.IsNull()) { MITK_ERROR << "Error during attempt to read '" << filename << "'. Factory returned nullptr object."; error = true; } } const char* dataUID = dataElement->Attribute("UID"); if (!error && dataUID != nullptr) { UIDManipulator manip(node->GetData()); manip.SetUID(dataUID); } } // in case there was no element we create a new empty node (for appending a propertylist later) if (node.IsNull()) { node = DataNode::New(); } return node; } void mitk::SceneReaderV1::ClearNodePropertyListWithExceptions(DataNode &node, PropertyList &propertyList) { // Basically call propertyList.Clear(), but implement exceptions (see bug 19354) BaseData *data = node.GetData(); PropertyList::Pointer propertiesToKeep = PropertyList::New(); if (dynamic_cast(data)) { /* Older scene files (before changes of bug 17547) could contain a RenderingMode property with value "LevelWindow_Color". Since bug 17547 this value has been removed and replaced by the default value LookupTable_LevelWindow_Color. This new default value does only result in "black-to-white" CT images (or others) if there is a corresponding lookup table. Such a lookup table is provided as a default value by the Image mapper. Since that value was never present in older scene files, we do well in not removing the new default value here. Otherwise the mapper would fall back to another default which is all the colors of the rainbow :-( */ BaseProperty::Pointer lutProperty = propertyList.GetProperty("LookupTable"); propertiesToKeep->SetProperty("LookupTable", lutProperty); /* Older scene files (before changes of T14807) may contain multi-component images without the "Image.Displayed Component" property. As the treatment as multi-component image and the corresponding visualization options hinges on that property we should not delete it, if it was added by the mapper. This is a fix for the issue reported in T19919. */ BaseProperty::Pointer compProperty = propertyList.GetProperty("Image.Displayed Component"); if (compProperty.IsNotNull()) { propertiesToKeep->SetProperty("Image.Displayed Component", compProperty); } } propertyList.Clear(); propertyList.ConcatenatePropertyList(propertiesToKeep); } bool mitk::SceneReaderV1::DecorateNodeWithProperties(DataNode *node, const tinyxml2::XMLElement *nodeElement, const std::string &workingDirectory) { assert(node); assert(nodeElement); bool error(false); for (auto *properties = nodeElement->FirstChildElement("properties"); properties != nullptr; properties = properties->NextSiblingElement("properties")) { const char *propertiesfilea(properties->Attribute("file")); std::string propertiesfile(propertiesfilea ? propertiesfilea : ""); const char *renderwindowa(properties->Attribute("renderwindow")); std::string renderwindow(renderwindowa ? renderwindowa : ""); PropertyList::Pointer propertyList = node->GetPropertyList(renderwindow); // DataNode implementation always returns a propertylist ClearNodePropertyListWithExceptions(*node, *propertyList); // use deserializer to construct new properties PropertyListDeserializer::Pointer deserializer = PropertyListDeserializer::New(); deserializer->SetFilename(workingDirectory + Poco::Path::separator() + propertiesfile); bool success = deserializer->Deserialize(); error |= !success; PropertyList::Pointer readProperties = deserializer->GetOutput(); if (readProperties.IsNotNull()) { propertyList->ConcatenatePropertyList(readProperties, true); // true = replace } else { MITK_ERROR << "Property list reader did not return a property list. This is an implementation error. Please tell " "your developer."; error = true; } } return !error; } bool mitk::SceneReaderV1::DecorateBaseDataWithProperties(BaseData::Pointer data, const tinyxml2::XMLElement *baseDataNodeElem, const std::string &workingDir) { // check given variables, initialize error variable assert(baseDataNodeElem); bool error(false); // get the file name stored in the tag const char *baseDataPropertyFile(baseDataNodeElem->Attribute("file")); // check if the filename was found if (baseDataPropertyFile) { // PropertyList::Pointer dataPropList = data->GetPropertyList(); PropertyListDeserializer::Pointer propertyDeserializer = PropertyListDeserializer::New(); // initialize the property reader propertyDeserializer->SetFilename(workingDir + Poco::Path::separator() + baseDataPropertyFile); bool ioSuccess = propertyDeserializer->Deserialize(); error = !ioSuccess; // get the output PropertyList::Pointer inProperties = propertyDeserializer->GetOutput(); // store the read-in properties to the given node or throw error otherwise if (inProperties.IsNotNull()) { data->SetPropertyList(inProperties); } else { MITK_ERROR << "The property deserializer did not return a (valid) property list."; error = true; } } else { MITK_ERROR << "Function DecorateBaseDataWithProperties(...) called with false XML element. \n \t ->Given element " "does not contain a 'file' attribute. \n"; error = true; } return !error; } diff --git a/Modules/SceneSerialization/test/mitkDataStorageCompare.cpp b/Modules/SceneSerialization/test/mitkDataStorageCompare.cpp index 0bb249821c..b058f76d52 100644 --- a/Modules/SceneSerialization/test/mitkDataStorageCompare.cpp +++ b/Modules/SceneSerialization/test/mitkDataStorageCompare.cpp @@ -1,538 +1,538 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkDataStorageCompare.h" #include "mitkBaseDataCompare.h" #include "mitkBaseRenderer.h" #include "mitkMapper.h" #include "usGetModuleContext.h" #include "usLDAPFilter.h" #include "usModuleContext.h" mitk::DataStorageCompare::DataStorageCompare(const mitk::DataStorage *reference, const mitk::DataStorage *test, Tests flags, double eps) : m_Eps(eps), m_TestAspects(flags), m_ReferenceDS(reference), m_TestDS(test), m_HierarchyPassed(true), m_DataPassed(true), m_PropertiesPassed(true), m_MappersPassed(true), m_InteractorsPassed(true), m_AspectsFailed(0) { BaseDataCompare::RegisterCoreEquals(); } bool mitk::DataStorageCompare::CompareVerbose() { return Compare(true); } bool mitk::DataStorageCompare::Compare(bool verbose) { DescribeHierarchyOfNodes(m_ReferenceDS, m_RefNodesByHierarchy); DescribeHierarchyOfNodes(m_TestDS, m_TestNodesByHierarchy); m_HierarchyPassed = true; m_DataPassed = true; m_PropertiesPassed = true; m_MappersPassed = true; m_InteractorsPassed = true; m_AspectsFailed = 0; if (m_TestAspects & CMP_Hierarchy) m_HierarchyPassed = CompareHierarchy(verbose); if (m_TestAspects != CMP_Nothing) CompareDataNodes(verbose); if ((m_TestAspects & CMP_Data) && !m_DataPassed) ++m_AspectsFailed; if ((m_TestAspects & CMP_Properties) && !m_PropertiesPassed) ++m_AspectsFailed; if ((m_TestAspects & CMP_Mappers) && !m_MappersPassed) ++m_AspectsFailed; if ((m_TestAspects & CMP_Interactors) && !m_InteractorsPassed) ++m_AspectsFailed; if (verbose) Report(); return m_AspectsFailed == 0; } void mitk::DataStorageCompare::Report() { MITK_INFO << "Comparison results:"; MITK_INFO << " Hierarchy comparison: " << (m_TestAspects & CMP_Hierarchy ? (m_HierarchyPassed ? "pass" : "fail") : "skipped"); MITK_INFO << " Data comparison: " << (m_TestAspects & CMP_Data ? (m_DataPassed ? "pass" : "fail") : "skipped"); MITK_INFO << " Properties comparison: " << (m_TestAspects & CMP_Properties ? (m_PropertiesPassed ? "pass" : "fail") : "skipped"); MITK_INFO << " Mappers comparison: " << (m_TestAspects & CMP_Mappers ? (m_MappersPassed ? "pass" : "fail") : "skipped"); MITK_INFO << " Interactors comparison: " << (m_TestAspects & CMP_Interactors ? (m_InteractorsPassed ? "pass" : "fail") : "skipped"); if (m_AspectsFailed == 0) MITK_INFO << " Summary: ALL PASSED"; else MITK_INFO << " Summary: " << m_AspectsFailed << " failures"; } void mitk::DataStorageCompare::DescribeHierarchyOfNodes(DataStorage::ConstPointer storage, HierarchyDescriptorMap &result) { result.clear(); if (storage.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer allNodes = storage->GetAll(); for (auto node : *allNodes) { std::string descriptor = GenerateHierarchyDescriptor(node, storage); result.insert(std::make_pair(descriptor, node)); } } std::string mitk::DataStorageCompare::GenerateNodeDescriptor(mitk::DataNode::Pointer node) { if (node.IsNull()) return "nullptr"; std::string thisDataDescriptor = "nullptr"; mitk::BaseData *data = node->GetData(); if (data != nullptr) thisDataDescriptor = data->GetNameOfClass(); std::string thisNodeName = node->GetName(); std::string thisNodesDescriptor = std::string("_") + thisDataDescriptor + "_(" + thisNodeName + ")"; return thisNodesDescriptor; } std::string mitk::DataStorageCompare::GenerateHierarchyDescriptor(mitk::DataNode::Pointer node, mitk::DataStorage::ConstPointer storage) { std::string thisNodesDescriptor = GenerateNodeDescriptor(node); mitk::DataStorage::SetOfObjects::ConstPointer parents = storage->GetSources(node, nullptr, true); // direct sources without filter // construct descriptors for parents std::vector parentDescriptors; - for (auto parent : *parents) + for (const auto &parent : *parents) parentDescriptors.push_back(GenerateHierarchyDescriptor(parent, storage)); // sort descriptors (we don't want to rely on potentially random order of parents) std::sort(parentDescriptors.begin(), parentDescriptors.end()); // construct a string from all sorted parent descriptors if (!parentDescriptors.empty()) { thisNodesDescriptor += " <("; - for (auto descriptor : parentDescriptors) + for (const auto &descriptor : parentDescriptors) { if (descriptor != parentDescriptors.front()) // join by '+' { thisNodesDescriptor += " + "; } thisNodesDescriptor += descriptor; } thisNodesDescriptor += ")"; } return thisNodesDescriptor; } bool mitk::DataStorageCompare::CompareHierarchy(bool verbose) { int numberOfMisMatches = 0; // check for each reference storage entry // if it can be found in test storage with // an identical hierarchy descriptor. // Compare just counts because there might be // multiple nodes that have the same name / type / etc. - for (auto entry : m_RefNodesByHierarchy) + for (const auto &entry : m_RefNodesByHierarchy) { const std::string &key = entry.first; const mitk::DataNode::Pointer &node = entry.second; unsigned int timesInReference = m_RefNodesByHierarchy.count(key); unsigned int timesInTest = m_TestNodesByHierarchy.count(key); if (timesInTest != timesInReference) { ++numberOfMisMatches; if (verbose) { MITK_WARN << "### Hierarchy mismatch problem"; MITK_WARN << " Reference storage has " << timesInReference << " node(s), test storage " << timesInTest; MITK_WARN << " Node name '" << node->GetName() << "'"; MITK_WARN << " Reference hierarchy descriptor: " << key; } } } // test also keys that are _only_ in test! - for (auto entry : m_TestNodesByHierarchy) + for (const auto &entry : m_TestNodesByHierarchy) { const std::string &key = entry.first; const mitk::DataNode::Pointer &node = entry.second; unsigned int timesInReference = m_RefNodesByHierarchy.count(key); unsigned int timesInTest = m_TestNodesByHierarchy.count(key); // we already tested all items in reference storage. // Here we want to test additional items in test storage. if (timesInTest > timesInReference) { ++numberOfMisMatches; if (verbose) { MITK_WARN << "### Hierarchy mismatch problem"; MITK_WARN << " Test storage has more nodes (" << timesInReference << ") than reference storage (" << timesInTest << ")"; MITK_WARN << " Node name '" << node->GetName() << "'"; MITK_WARN << " Reference hierarchy descriptor: " << key; } } } // for debug purposes we provide a dump of the test storage // in error cases. This can be compared to the test case // by a programmer. if (verbose && numberOfMisMatches > 0) { MITK_WARN << "Dumping test storage because there were errors:"; - for (auto entry : m_TestNodesByHierarchy) + for (const auto &entry : m_TestNodesByHierarchy) { const std::string &key = entry.first; const mitk::DataNode::Pointer &node = entry.second; MITK_WARN << " Test node '" << node->GetName() << "', hierarchy : " << key; } } return numberOfMisMatches == 0; } bool mitk::DataStorageCompare::AreNodesEqual(const mitk::DataNode *reference, const mitk::DataNode *test, bool verbose) { if (reference == nullptr && test == nullptr) return true; if (reference == nullptr && test != nullptr) { if (verbose) MITK_WARN << " Reference node is nullptr, test node is not (type " << test->GetNameOfClass() << ")"; return false; } if (reference != nullptr && test == nullptr) { if (verbose) MITK_WARN << " Test node is nullptr, reference node is not (type " << reference->GetNameOfClass() << ")"; return false; } if (m_TestAspects & CMP_Data) m_DataPassed &= IsDataEqual(reference->GetData(), test->GetData(), verbose); if (m_TestAspects & CMP_Properties) m_PropertiesPassed &= ArePropertyListsEqual(*reference, *test, verbose); if (m_TestAspects & CMP_Mappers) m_MappersPassed &= AreMappersEqual(*reference, *test, verbose); // .. add interactors/mappers // two real nodes, need to really compare return m_AspectsFailed == 0; } bool mitk::DataStorageCompare::IsDataEqual(const mitk::BaseData *reference, const mitk::BaseData *test, bool verbose) { // early-out for nullptrs if (reference == nullptr && test == nullptr) return true; if (reference == nullptr && test != nullptr) { if (verbose) MITK_WARN << " Reference data is nullptr, test data is not (type " << test->GetNameOfClass() << ")"; return false; } if (reference != nullptr && test == nullptr) { if (verbose) MITK_WARN << " Test data is nullptr, reference data is not (type " << reference->GetNameOfClass() << ")"; return false; } // two real BaseData objects, need to really compare if (reference->GetNameOfClass() != test->GetNameOfClass()) { if (verbose) MITK_WARN << " Mismatch: Reference data is '" << reference->GetNameOfClass() << "', " << "test data is '" << test->GetNameOfClass() << "'"; return false; } try { std::string ldapFilter = std::string("(basedata=") + reference->GetNameOfClass() + "*)"; std::vector> comparators = us::GetModuleContext()->GetServiceReferences(ldapFilter); if (comparators.empty()) { // bad, no comparator found, cannot compare MITK_ERROR << "Comparison error: no comparator for objects of type '" << reference->GetNameOfClass() << "'"; return false; } else if (comparators.size() > 1) { MITK_WARN << "Comparison warning: multiple comparisons possible for objects of type '" << reference->GetNameOfClass() << "'. Using just one."; // bad, multiple comparators, need to add ranking or something } auto *comparator = us::GetModuleContext()->GetService(comparators.front()); if (!comparator) { MITK_ERROR << "Service lookup error, cannot get comparator for class " << reference->GetNameOfClass(); } return comparator->AreEqual(reference, test, m_Eps, verbose); } catch (std::exception &e) { MITK_ERROR << "Exception during comparison: " << e.what(); return false; } } bool mitk::DataStorageCompare::ArePropertyListsEqual(const mitk::DataNode &reference, const mitk::DataNode &test, bool verbose) { DataNode::PropertyListKeyNames refListNames = reference.GetPropertyListNames(); DataNode::PropertyListKeyNames testListNames = test.GetPropertyListNames(); // add the empty names to treat all lists equally refListNames.push_back(""); testListNames.push_back(""); // verify that list names are identical bool error = false; if (refListNames.size() != testListNames.size()) { - for (auto name : refListNames) + for (const auto &name : refListNames) if (std::find(testListNames.begin(), testListNames.end(), name) == testListNames.end()) { MITK_WARN << "Propertylist '" << name << "' from reference node (" << reference.GetName() << ") not found in test node."; error = true; } - for (auto name : testListNames) + for (const auto &name : testListNames) if (std::find(refListNames.begin(), refListNames.end(), name) == refListNames.end()) { MITK_WARN << "Propertylist '" << name << "' did not exist in reference node (" << reference.GetName() << "), but is present in test node."; error = true; } if (error) return false; } // compare each list - for (auto name : refListNames) + for (const auto &name : refListNames) { if (!ArePropertyListsEqual(*(reference.GetPropertyList(name)), *(test.GetPropertyList(name)), verbose)) { MITK_WARN << "Property mismatch while comparing propertylist '" << name << "'. See messages above."; error = true; } } return !error; } bool mitk::DataStorageCompare::ArePropertyListsEqual(const mitk::PropertyList &reference, const mitk::PropertyList &test, bool verbose) { const mitk::PropertyList::PropertyMap *refMap = reference.GetMap(); bool error = false; - for (auto refEntry : *refMap) + for (const auto &refEntry : *refMap) { std::string propertyKey = refEntry.first; BaseProperty::Pointer refProperty = refEntry.second; BaseProperty::Pointer testProperty = test.GetProperty(propertyKey); if (testProperty.IsNull()) { if (verbose) MITK_WARN << "Property '" << propertyKey << "' not found in test, only in reference."; error = true; } else { if (!(*refProperty == *testProperty)) { if (verbose) { MITK_WARN << "Property '" << propertyKey << "' does not match original."; MITK_WARN << "Reference was: " << refProperty->GetValueAsString(); MITK_WARN << "Test was:" << testProperty->GetValueAsString(); } error = true; } } } return !error; } bool mitk::DataStorageCompare::AreMappersEqual(const mitk::DataNode &reference, const mitk::DataNode &test, bool verbose) { bool error = false; mitk::Mapper *refMapper2D = reference.GetMapper(mitk::BaseRenderer::Standard2D); mitk::Mapper *testMapper2D = test.GetMapper(mitk::BaseRenderer::Standard2D); if (refMapper2D == nullptr && testMapper2D == nullptr) { ; // ok } else if (refMapper2D != nullptr && testMapper2D == nullptr) { if (verbose) { MITK_WARN << "Mapper for 2D was '" << refMapper2D->GetNameOfClass() << "' in reference, is 'nullptr" << "' in test (DataNode '" << reference.GetName() << "')"; } error = true; } else if (refMapper2D == nullptr && testMapper2D != nullptr) { if (verbose) { MITK_WARN << "Mapper for 2D was 'nullptr" << "' in reference, is '" << testMapper2D->GetNameOfClass() << "' in test (DataNode '" << reference.GetName() << "')"; } error = true; } // else both are valid pointers, we just compare the type else if (refMapper2D->GetNameOfClass() != testMapper2D->GetNameOfClass()) { if (verbose) { MITK_WARN << "Mapper for 2D was '" << refMapper2D->GetNameOfClass() << "' in reference, is '" << testMapper2D->GetNameOfClass() << "' in test (DataNode '" << reference.GetName() << "')"; } error = true; } mitk::Mapper *refMapper3D = reference.GetMapper(mitk::BaseRenderer::Standard3D); mitk::Mapper *testMapper3D = test.GetMapper(mitk::BaseRenderer::Standard3D); if (refMapper3D == nullptr && testMapper3D == nullptr) { ; // ok } else if (refMapper3D != nullptr && testMapper3D == nullptr) { if (verbose) { MITK_WARN << "Mapper for 3D was '" << refMapper3D->GetNameOfClass() << "' in reference, is 'nullptr" << "' in test (DataNode '" << reference.GetName() << "')"; } error = true; } else if (refMapper3D == nullptr && testMapper3D != nullptr) { if (verbose) { MITK_WARN << "Mapper for 3D was 'nullptr" << "' in reference, is '" << testMapper3D->GetNameOfClass() << "' in test (DataNode '" << reference.GetName() << "')"; } error = true; } // else both are valid pointers, we just compare the type else if (refMapper3D->GetNameOfClass() != testMapper3D->GetNameOfClass()) { if (verbose) { MITK_WARN << "Mapper for 3D was '" << refMapper3D->GetNameOfClass() << "' in reference, is '" << testMapper3D->GetNameOfClass() << "' in test (DataNode '" << reference.GetName() << "')"; } error = true; } return !error; } bool mitk::DataStorageCompare::CompareDataNodes(bool verbose) { int numberOfMisMatches = 0; - for (auto entry : m_RefNodesByHierarchy) + for (const auto &entry : m_RefNodesByHierarchy) { const std::string &key = entry.first; const mitk::DataNode::Pointer &refNode = entry.second; unsigned int timesInReference = m_RefNodesByHierarchy.count(key); unsigned int timesInTest = m_TestNodesByHierarchy.count(key); if (timesInReference == 1 && timesInTest == 1) { // go on an compare those two auto testEntry = m_TestNodesByHierarchy.find(key); mitk::DataNode::Pointer testNode = testEntry->second; if (!AreNodesEqual(refNode, testNode, verbose)) { ++numberOfMisMatches; if (verbose) { MITK_WARN << "### DataNode mismatch problem"; MITK_WARN << " Node '" << key << "' did not compare to equal (see warnings above)."; } } } else { ++numberOfMisMatches; if (verbose) { MITK_WARN << "### DataNode mismatch problem"; MITK_WARN << " Reference storage has " << timesInReference << " node(s), test storage " << timesInTest; MITK_WARN << " This does not match or we don't know how to figure out comparison partners"; } } } return numberOfMisMatches == 0; } diff --git a/Modules/Segmentation/Algorithms/mitkContourUtils.h b/Modules/Segmentation/Algorithms/mitkContourUtils.h index 3040e042fa..66bb8b4a97 100644 --- a/Modules/Segmentation/Algorithms/mitkContourUtils.h +++ b/Modules/Segmentation/Algorithms/mitkContourUtils.h @@ -1,71 +1,73 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkContourUtilshIncludett #define mitkContourUtilshIncludett #include "mitkContour.h" #include "mitkContourModel.h" #include "mitkImage.h" #include namespace mitk { /** * \brief Helpful methods for working with contours and images * * Legacy support for mitk::Contour * TODO remove this class when mitk::Contour is removed */ class MITKSEGMENTATION_EXPORT ContourUtils : public itk::Object { public: mitkClassMacroItkParent(ContourUtils, itk::Object); itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** \brief Projects a contour onto an image point by point. Converts from world to index coordinates. \param slice \param contourIn3D \param correctionForIpSegmentation adds 0.5 to x and y index coordinates (difference between ipSegmentation and MITK contours) \param constrainToInside */ ContourModel::Pointer ProjectContourTo2DSlice(Image *slice, Contour *contourIn3D, bool correctionForIpSegmentation, bool constrainToInside); /** \brief Projects a slice index coordinates of a contour back into world coordinates. - \param correctionForIpSegmentation subtracts 0.5 to x and y index coordinates (difference between + \param sliceGeometry + \param contourIn2D + \param correctionForIpSegmentation subtracts 0.5 to x and y index coordinates (difference between ipSegmentation and MITK contours) */ ContourModel::Pointer BackProjectContourFrom2DSlice(const BaseGeometry *sliceGeometry, Contour *contourIn2D, bool correctionForIpSegmentation = false); /** \brief Fill a contour in a 2D slice with a specified pixel value. */ void FillContourInSlice(Contour *projectedContour, Image *sliceImage, int paintingPixelValue = 1); protected: ContourUtils(); ~ContourUtils() override; }; } #endif diff --git a/Modules/Segmentation/Algorithms/mitkDiffSliceOperation.cpp b/Modules/Segmentation/Algorithms/mitkDiffSliceOperation.cpp index 1b0c4598da..bab4084f3e 100644 --- a/Modules/Segmentation/Algorithms/mitkDiffSliceOperation.cpp +++ b/Modules/Segmentation/Algorithms/mitkDiffSliceOperation.cpp @@ -1,100 +1,100 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkDiffSliceOperation.h" #include #include mitk::DiffSliceOperation::DiffSliceOperation() : Operation(1) { m_TimeStep = 0; m_zlibSliceContainer = nullptr; m_Image = nullptr; m_WorldGeometry = nullptr; m_SliceGeometry = nullptr; m_ImageIsValid = false; m_DeleteObserverTag = 0; } -mitk::DiffSliceOperation::DiffSliceOperation(mitk::Image *imageVolume, - Image *slice, - SlicedGeometry3D *sliceGeometry, - unsigned int timestep, - BaseGeometry *currentWorldGeometry) +mitk::DiffSliceOperation::DiffSliceOperation(Image *imageVolume, + const Image *slice, + const SlicedGeometry3D *sliceGeometry, + TimeStepType timestep, + const BaseGeometry *currentWorldGeometry) : Operation(1) { m_WorldGeometry = currentWorldGeometry->Clone(); /* Quick fix for bug 12338. Guard object - fix this when clone method of PlaneGeometry is cloning the reference geometry (see bug 13392)*/ // xxxx m_GuardReferenceGeometry = mitk::BaseGeometry::New(); - m_GuardReferenceGeometry = dynamic_cast(m_WorldGeometry.GetPointer())->GetReferenceGeometry(); + m_GuardReferenceGeometry = dynamic_cast(m_WorldGeometry.GetPointer())->GetReferenceGeometry(); /*---------------------------------------------------------------------------------------------------*/ m_SliceGeometry = sliceGeometry->Clone(); m_TimeStep = timestep; m_zlibSliceContainer = CompressedImageContainer::New(); m_zlibSliceContainer->SetImage(slice); m_Image = imageVolume; m_DeleteObserverTag = 0; if (m_Image) { /*add an observer to listen to the delete event of the image, this is necessary because the operation is then * invalid*/ itk::SimpleMemberCommand::Pointer command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &DiffSliceOperation::OnImageDeleted); // get the id of the observer, used to remove it later on m_DeleteObserverTag = imageVolume->AddObserver(itk::DeleteEvent(), command); m_ImageIsValid = true; } else m_ImageIsValid = false; } mitk::DiffSliceOperation::~DiffSliceOperation() { m_WorldGeometry = nullptr; m_zlibSliceContainer = nullptr; if (m_ImageIsValid) { // if the image is still there, we have to remove the observer from it m_Image->RemoveObserver(m_DeleteObserverTag); } m_Image = nullptr; } mitk::Image::Pointer mitk::DiffSliceOperation::GetSlice() { Image::Pointer image = m_zlibSliceContainer->GetImage(); return image; } bool mitk::DiffSliceOperation::IsValid() { return m_ImageIsValid && m_zlibSliceContainer.IsNotNull() && (m_WorldGeometry.IsNotNull()); // TODO improve } void mitk::DiffSliceOperation::OnImageDeleted() { // if our imageVolume is removed e.g. from the datastorage the operation is no lnger valid m_ImageIsValid = false; } diff --git a/Modules/Segmentation/Algorithms/mitkDiffSliceOperation.h b/Modules/Segmentation/Algorithms/mitkDiffSliceOperation.h index 1ed4d8aa0c..9647976b40 100644 --- a/Modules/Segmentation/Algorithms/mitkDiffSliceOperation.h +++ b/Modules/Segmentation/Algorithms/mitkDiffSliceOperation.h @@ -1,109 +1,101 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkDiffSliceOperation_h_Included #define mitkDiffSliceOperation_h_Included #include "mitkCompressedImageContainer.h" #include #include #include namespace mitk { class Image; /** \brief An Operation for applying an edited slice to the volume. \sa DiffSliceOperationApplier The information for the operation is specified by properties: imageVolume the volume where the slice was extracted from. slice the slice to be applied. timestep the timestep in an 4D image. currentWorldGeometry specifies the axis where the slice has to be applied in the volume. This Operation can be used to realize undo-redo functionality for e.g. segmentation purposes. */ class MITKSEGMENTATION_EXPORT DiffSliceOperation : public Operation { public: mitkClassMacro(DiffSliceOperation, OperationActor); // itkFactorylessNewMacro(Self) // itkCloneMacro(Self) // mitkNewMacro4Param(DiffSliceOperation,mitk::Image,mitk::Image,unsigned int, mitk::PlaneGeometry); /** \brief Creates an empty instance. Note that it is not valid yet. The properties of the object have to be set. */ DiffSliceOperation(); /** \brief */ DiffSliceOperation(mitk::Image *imageVolume, - mitk::Image *slice, - SlicedGeometry3D *sliceGeometry, - unsigned int timestep, - BaseGeometry *currentWorldGeometry); + const mitk::Image *slice, + const SlicedGeometry3D *sliceGeometry, + const TimeStepType timestep, + const BaseGeometry *currentWorldGeometry); /** \brief Check if it is a valid operation.*/ bool IsValid(); - /** \brief Set the image volume.*/ - void SetImage(mitk::Image *image) { this->m_Image = image; } /** \brief Get th image volume.*/ mitk::Image *GetImage() { return this->m_Image; } - /** \brief Set thee slice to be applied.*/ - void SetImage(vtkImageData *slice) { this->m_Slice = slice; } + const mitk::Image* GetImage() const { return this->m_Image; } + /** \brief Get the slice that is applied in the operation.*/ Image::Pointer GetSlice(); - /** \brief Get timeStep.*/ - void SetTimeStep(unsigned int timestep) { this->m_TimeStep = timestep; } /** \brief Set timeStep*/ - unsigned int GetTimeStep() { return this->m_TimeStep; } - /** \brief Set the axis where the slice has to be applied in the volume.*/ - void SetSliceGeometry(SlicedGeometry3D *sliceGeometry) { this->m_SliceGeometry = sliceGeometry; } + TimeStepType GetTimeStep() const { return this->m_TimeStep; } /** \brief Get the axis where the slice has to be applied in the volume.*/ - SlicedGeometry3D *GetSliceGeometry() { return this->m_SliceGeometry; } - /** \brief Set the axis where the slice has to be applied in the volume.*/ - void SetCurrentWorldGeometry(BaseGeometry *worldGeometry) { this->m_WorldGeometry = worldGeometry; } + const SlicedGeometry3D *GetSliceGeometry() const { return this->m_SliceGeometry; } /** \brief Get the axis where the slice has to be applied in the volume.*/ - BaseGeometry *GetWorldGeometry() { return this->m_WorldGeometry; } + const BaseGeometry *GetWorldGeometry() const { return this->m_WorldGeometry; } protected: ~DiffSliceOperation() override; /** \brief Callback for image observer.*/ void OnImageDeleted(); CompressedImageContainer::Pointer m_zlibSliceContainer; mitk::Image *m_Image; vtkSmartPointer m_Slice; - SlicedGeometry3D::Pointer m_SliceGeometry; + SlicedGeometry3D::ConstPointer m_SliceGeometry; - unsigned int m_TimeStep; + TimeStepType m_TimeStep; - BaseGeometry::Pointer m_WorldGeometry; + BaseGeometry::ConstPointer m_WorldGeometry; bool m_ImageIsValid; unsigned long m_DeleteObserverTag; mitk::BaseGeometry::ConstPointer m_GuardReferenceGeometry; }; } #endif diff --git a/Modules/Segmentation/Algorithms/mitkDiffSliceOperationApplier.cpp b/Modules/Segmentation/Algorithms/mitkDiffSliceOperationApplier.cpp index b34a65bc09..6c666c1b36 100644 --- a/Modules/Segmentation/Algorithms/mitkDiffSliceOperationApplier.cpp +++ b/Modules/Segmentation/Algorithms/mitkDiffSliceOperationApplier.cpp @@ -1,89 +1,89 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkDiffSliceOperationApplier.h" #include "mitkDiffSliceOperation.h" #include "mitkRenderingManager.h" #include "mitkSegTool2D.h" #include #include // VTK #include mitk::DiffSliceOperationApplier::DiffSliceOperationApplier() { } mitk::DiffSliceOperationApplier::~DiffSliceOperationApplier() { } void mitk::DiffSliceOperationApplier::ExecuteOperation(Operation *operation) { auto *imageOperation = dynamic_cast(operation); // as we only support DiffSliceOperation return if operation is not type of DiffSliceOperation if (!imageOperation) return; // chak if the operation is valid if (imageOperation->IsValid()) { // the actual overwrite filter (vtk) vtkSmartPointer reslice = vtkSmartPointer::New(); mitk::Image::Pointer slice = imageOperation->GetSlice(); // Set the slice as 'input' reslice->SetInputSlice(slice->GetVtkImageData()); // set overwrite mode to true to write back to the image volume reslice->SetOverwriteMode(true); reslice->Modified(); // a wrapper for vtkImageOverwrite mitk::ExtractSliceFilter::Pointer extractor = mitk::ExtractSliceFilter::New(reslice); extractor->SetInput(imageOperation->GetImage()); extractor->SetTimeStep(imageOperation->GetTimeStep()); - extractor->SetWorldGeometry(dynamic_cast(imageOperation->GetWorldGeometry())); + extractor->SetWorldGeometry(dynamic_cast(imageOperation->GetWorldGeometry())); extractor->SetVtkOutputRequest(true); extractor->SetResliceTransformByGeometry(imageOperation->GetImage()->GetGeometry(imageOperation->GetTimeStep())); extractor->Modified(); extractor->Update(); // make sure the modification is rendered RenderingManager::GetInstance()->RequestUpdateAll(); imageOperation->GetImage()->Modified(); mitk::ExtractSliceFilter::Pointer extractor2 = mitk::ExtractSliceFilter::New(); extractor2->SetInput(imageOperation->GetImage()); extractor2->SetTimeStep(imageOperation->GetTimeStep()); - extractor2->SetWorldGeometry(dynamic_cast(imageOperation->GetWorldGeometry())); + extractor2->SetWorldGeometry(dynamic_cast(imageOperation->GetWorldGeometry())); extractor2->SetResliceTransformByGeometry(imageOperation->GetImage()->GetGeometry(imageOperation->GetTimeStep())); extractor2->Modified(); extractor2->Update(); // TODO Move this code to SurfaceInterpolationController! mitk::Image::Pointer slice2 = extractor2->GetOutput(); - mitk::PlaneGeometry::Pointer plane = dynamic_cast(imageOperation->GetWorldGeometry()); + mitk::PlaneGeometry::ConstPointer plane = dynamic_cast(imageOperation->GetWorldGeometry()); slice2->DisconnectPipeline(); mitk::SegTool2D::UpdateSurfaceInterpolation(slice2, imageOperation->GetImage(), plane, true); } } mitk::DiffSliceOperationApplier *mitk::DiffSliceOperationApplier::GetInstance() { static auto *s_Instance = new DiffSliceOperationApplier(); return s_Instance; } diff --git a/Modules/Segmentation/Algorithms/mitkImageLiveWireContourModelFilter.h b/Modules/Segmentation/Algorithms/mitkImageLiveWireContourModelFilter.h index 1b923b58b2..b3c2f482d5 100644 --- a/Modules/Segmentation/Algorithms/mitkImageLiveWireContourModelFilter.h +++ b/Modules/Segmentation/Algorithms/mitkImageLiveWireContourModelFilter.h @@ -1,162 +1,156 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 _mitkImageLiveWireContourModelFilter_h__ #define _mitkImageLiveWireContourModelFilter_h__ #include "mitkCommon.h" #include "mitkContourModel.h" #include "mitkContourModelSource.h" #include #include #include #include #include #include namespace mitk { /** \brief Calculates a LiveWire contour between two points in an image. For defining costs between two pixels specific features are extraced from the image and tranformed into a single cost value. \sa ShortestPathCostFunctionLiveWire The filter is able to create dynamic cost tranfer map and thus use on the fly training. \note On the fly training will only be used for next update. The computation uses the last calculated segment to map cost according to features in the area of the segment. - For time resolved purposes use ImageLiveWireContourModelFilter::SetTimestep( unsigned int ) to create the LiveWire - contour - at a specific timestep. + Caution: time support currently not available. Filter will always work on the first + timestep in its current implementation. \ingroup ContourModelFilters \ingroup Process */ class MITKSEGMENTATION_EXPORT ImageLiveWireContourModelFilter : public ContourModelSource { public: mitkClassMacro(ImageLiveWireContourModelFilter, ContourModelSource); itkFactorylessNewMacro(Self); itkCloneMacro(Self); typedef ContourModel OutputType; typedef OutputType::Pointer OutputTypePointer; typedef mitk::Image InputType; typedef itk::Image InternalImageType; typedef itk::ShortestPathImageFilter ShortestPathImageFilterType; typedef itk::ShortestPathCostFunctionLiveWire CostFunctionType; typedef std::vector> ShortestPathType; /** \brief start point in world coordinates*/ itkSetMacro(StartPoint, mitk::Point3D); itkGetMacro(StartPoint, mitk::Point3D); /** \brief end point in woorld coordinates*/ itkSetMacro(EndPoint, mitk::Point3D); itkGetMacro(EndPoint, mitk::Point3D); /** \brief Create dynamic cost tranfer map - use on the fly training. \note On the fly training will be used for next update only. The computation uses the last calculated segment to map cost according to features in the area of the segment. */ itkSetMacro(UseDynamicCostMap, bool); itkGetMacro(UseDynamicCostMap, bool); - /** \brief Actual time step - */ - itkSetMacro(TimeStep, unsigned int); - itkGetMacro(TimeStep, unsigned int); - /** \brief Clear all repulsive points used in the cost function */ void ClearRepulsivePoints(); /** \brief Set a vector with repulsive points to use in the cost function */ void SetRepulsivePoints(const ShortestPathType &points); /** \brief Add a single repulsive point to the cost function */ void AddRepulsivePoint(const itk::Index<2> &idx); /** \brief Remove a single repulsive point from the cost function */ void RemoveRepulsivePoint(const itk::Index<2> &idx); virtual void SetInput(const InputType *input); using Superclass::SetInput; virtual void SetInput(unsigned int idx, const InputType *input); const InputType *GetInput(void); const InputType *GetInput(unsigned int idx); virtual OutputType *GetOutput(); virtual void DumpMaskImage(); /** \brief Create dynamic cost tranfer map - on the fly training*/ bool CreateDynamicCostMap(mitk::ContourModel *path = nullptr); protected: ImageLiveWireContourModelFilter(); ~ImageLiveWireContourModelFilter() override; void GenerateOutputInformation() override{}; void GenerateData() override; void UpdateLiveWire(); /** \brief start point in worldcoordinates*/ mitk::Point3D m_StartPoint; /** \brief end point in woorldcoordinates*/ mitk::Point3D m_EndPoint; /** \brief Start point in index*/ mitk::Point3D m_StartPointInIndex; /** \brief End point in index*/ mitk::Point3D m_EndPointInIndex; /** \brief The cost function to compute costs between two pixels*/ CostFunctionType::Pointer m_CostFunction; /** \brief Shortest path filter according to cost function m_CostFunction*/ ShortestPathImageFilterType::Pointer m_ShortestPathFilter; /** \brief Flag to use a dynmic cost map or not*/ bool m_UseDynamicCostMap; unsigned int m_TimeStep; template void ItkPreProcessImage(const itk::Image *inputImage); template void CreateDynamicCostMapByITK(const itk::Image *inputImage, mitk::ContourModel *path = nullptr); InternalImageType::Pointer m_InternalImage; }; } #endif diff --git a/Modules/Segmentation/Interactions/mitkAdaptiveRegionGrowingTool.cpp b/Modules/Segmentation/Interactions/mitkAdaptiveRegionGrowingTool.cpp index 64de93da55..d4a109ccfe 100644 --- a/Modules/Segmentation/Interactions/mitkAdaptiveRegionGrowingTool.cpp +++ b/Modules/Segmentation/Interactions/mitkAdaptiveRegionGrowingTool.cpp @@ -1,117 +1,120 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkAdaptiveRegionGrowingTool.h" #include "mitkImage.h" #include "mitkProperties.h" #include "mitkToolManager.h" // us #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, AdaptiveRegionGrowingTool, "AdaptiveRegionGrowingTool"); } mitk::AdaptiveRegionGrowingTool::AdaptiveRegionGrowingTool() { m_PointSetNode = mitk::DataNode::New(); m_PointSetNode->GetPropertyList()->SetProperty("name", mitk::StringProperty::New("3D_Regiongrowing_Seedpoint")); m_PointSetNode->GetPropertyList()->SetProperty("helper object", mitk::BoolProperty::New(true)); m_PointSet = mitk::PointSet::New(); m_PointSetNode->SetData(m_PointSet); } mitk::AdaptiveRegionGrowingTool::~AdaptiveRegionGrowingTool() { } bool mitk::AdaptiveRegionGrowingTool::CanHandle(const BaseData* referenceData, const BaseData* /*workingData*/) const { if (referenceData == nullptr) return false; auto *image = dynamic_cast(referenceData); if (image == nullptr) return false; if (image->GetDimension() < 3) return false; + if (image->GetTimeSteps() > 1) //release quickfix for T28275 + return false; + return true; } const char **mitk::AdaptiveRegionGrowingTool::GetXPM() const { return nullptr; } const char *mitk::AdaptiveRegionGrowingTool::GetName() const { return "Region Growing 3D"; } us::ModuleResource mitk::AdaptiveRegionGrowingTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("RegionGrowing_48x48.png"); return resource; } void mitk::AdaptiveRegionGrowingTool::Activated() { Superclass::Activated(); if (!GetDataStorage()->Exists(m_PointSetNode)) GetDataStorage()->Add(m_PointSetNode, GetWorkingData()); m_SeedPointInteractor = mitk::SinglePointDataInteractor::New(); m_SeedPointInteractor->LoadStateMachine("PointSet.xml"); m_SeedPointInteractor->SetEventConfig("PointSetConfig.xml"); m_SeedPointInteractor->SetDataNode(m_PointSetNode); } void mitk::AdaptiveRegionGrowingTool::Deactivated() { m_PointSet->Clear(); GetDataStorage()->Remove(m_PointSetNode); Superclass::Deactivated(); } void mitk::AdaptiveRegionGrowingTool::ConfirmSegmentation() { m_ToolManager->ActivateTool(-1); } mitk::DataNode *mitk::AdaptiveRegionGrowingTool::GetReferenceData() { return this->m_ToolManager->GetReferenceData(0); } mitk::DataStorage *mitk::AdaptiveRegionGrowingTool::GetDataStorage() { return this->m_ToolManager->GetDataStorage(); } mitk::DataNode *mitk::AdaptiveRegionGrowingTool::GetWorkingData() { return this->m_ToolManager->GetWorkingData(0); } mitk::DataNode::Pointer mitk::AdaptiveRegionGrowingTool::GetPointSetNode() { return m_PointSetNode; } diff --git a/Modules/Segmentation/Interactions/mitkAutoSegmentationTool.cpp b/Modules/Segmentation/Interactions/mitkAutoSegmentationTool.cpp index 96ba360d0f..647fa8b80d 100644 --- a/Modules/Segmentation/Interactions/mitkAutoSegmentationTool.cpp +++ b/Modules/Segmentation/Interactions/mitkAutoSegmentationTool.cpp @@ -1,97 +1,130 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkAutoSegmentationTool.h" #include "mitkImage.h" #include "mitkToolManager.h" #include mitk::AutoSegmentationTool::AutoSegmentationTool() : Tool("dummy"), m_OverwriteExistingSegmentation(false) { } +mitk::AutoSegmentationTool::AutoSegmentationTool(const char* interactorType, const us::Module* interactorModule) : Tool(interactorType, interactorModule), m_OverwriteExistingSegmentation(false) +{ +} + mitk::AutoSegmentationTool::~AutoSegmentationTool() { } +void mitk::AutoSegmentationTool::Activated() +{ + Superclass::Activated(); + + m_NoneOverwriteTargetSegmentationNode = nullptr; +} + +void mitk::AutoSegmentationTool::Deactivated() +{ + m_NoneOverwriteTargetSegmentationNode = nullptr; + + Superclass::Deactivated(); +} + const char *mitk::AutoSegmentationTool::GetGroup() const { return "autoSegmentation"; } mitk::Image::ConstPointer mitk::AutoSegmentationTool::GetImageByTimeStep(const mitk::Image* image, unsigned int timestep) { if (nullptr == image) return image; if (image->GetDimension() != 4) return image; mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(image); imageTimeSelector->SetTimeNr(static_cast(timestep)); imageTimeSelector->UpdateLargestPossibleRegion(); return imageTimeSelector->GetOutput(); } mitk::Image::ConstPointer mitk::AutoSegmentationTool::GetImageByTimePoint(const mitk::Image* image, TimePointType timePoint) { if (nullptr == image) return image; if (!image->GetTimeGeometry()->IsValidTimePoint(timePoint)) return nullptr; return AutoSegmentationTool::GetImageByTimeStep(image, image->GetTimeGeometry()->TimePointToTimeStep(timePoint)); } void mitk::AutoSegmentationTool::SetOverwriteExistingSegmentation(bool overwrite) { - m_OverwriteExistingSegmentation = overwrite; + if (m_OverwriteExistingSegmentation != overwrite) + { + m_OverwriteExistingSegmentation = overwrite; + m_NoneOverwriteTargetSegmentationNode = nullptr; + } } std::string mitk::AutoSegmentationTool::GetCurrentSegmentationName() { if (m_ToolManager->GetWorkingData(0)) return m_ToolManager->GetWorkingData(0)->GetName(); else return ""; } -mitk::DataNode *mitk::AutoSegmentationTool::GetTargetSegmentationNode() +mitk::DataNode *mitk::AutoSegmentationTool::GetTargetSegmentationNode() const { mitk::DataNode::Pointer segmentationNode = m_ToolManager->GetWorkingData(0); if (!m_OverwriteExistingSegmentation) { - mitk::DataNode::Pointer refNode = m_ToolManager->GetReferenceData(0); - if (refNode.IsNull()) + if (m_NoneOverwriteTargetSegmentationNode.IsNull()) { - // TODO create and use segmentation exceptions instead!! - MITK_ERROR << "No valid reference data!"; - return nullptr; + mitk::DataNode::Pointer refNode = m_ToolManager->GetReferenceData(0); + if (refNode.IsNull()) + { + // TODO create and use segmentation exceptions instead!! + MITK_ERROR << "No valid reference data!"; + return nullptr; + } + + std::string nodename = refNode->GetName() + "_" + this->GetName(); + mitk::Color color; + color.SetRed(1); + color.SetBlue(0); + color.SetGreen(0); + //create a new segmentation node based on the current segmentation as template + m_NoneOverwriteTargetSegmentationNode = CreateEmptySegmentationNode(dynamic_cast(segmentationNode->GetData()), nodename, color); } - - std::string nodename = refNode->GetName() + "_" + this->GetName(); - mitk::Color color; - color.SetRed(1); - color.SetBlue(0); - color.SetGreen(0); - //create a new segmentation node based on the current segmentation as template - segmentationNode = CreateEmptySegmentationNode(dynamic_cast(segmentationNode->GetData()), nodename, color); - - m_ToolManager->GetDataStorage()->Add(segmentationNode, refNode); + segmentationNode = m_NoneOverwriteTargetSegmentationNode; } return segmentationNode; } + +void mitk::AutoSegmentationTool::EnsureTargetSegmentationNodeInDataStorage() const +{ + auto targetNode = this->GetTargetSegmentationNode(); + if (!m_ToolManager->GetDataStorage()->Exists(targetNode)) + { + m_ToolManager->GetDataStorage()->Add(targetNode, m_ToolManager->GetReferenceData(0)); + } +} diff --git a/Modules/Segmentation/Interactions/mitkAutoSegmentationTool.h b/Modules/Segmentation/Interactions/mitkAutoSegmentationTool.h index dfb36b908c..69624986c8 100644 --- a/Modules/Segmentation/Interactions/mitkAutoSegmentationTool.h +++ b/Modules/Segmentation/Interactions/mitkAutoSegmentationTool.h @@ -1,71 +1,84 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkAutoSegmentationTool_h_Included #define mitkAutoSegmentationTool_h_Included #include "mitkCommon.h" #include "mitkTool.h" #include namespace mitk { class Image; /** \brief Superclass for tool that create a new segmentation without user interaction in render windows This class is undocumented. Ask the creator ($Author$) to supply useful comments. */ class MITKSEGMENTATION_EXPORT AutoSegmentationTool : public Tool { public: mitkClassMacro(AutoSegmentationTool, Tool); + void Activated() override; + void Deactivated() override; + /** This function controls wether a confirmed segmentation should replace the old * segmentation/working node (true) or if it should be stored as new and additional * node (false). */ void SetOverwriteExistingSegmentation(bool overwrite); /** * @brief Gets the name of the currently selected segmentation node * @return the name of the segmentation node or an empty string if * none is selected */ std::string GetCurrentSegmentationName(); /** - * @brief Depending on the selected mode either returns the currently selected segmentation - * or creates a new one from the selected reference data and adds the new segmentation - * to the datastorage + * @brief Depending on the selected mode either returns the currently selected segmentation node + * or (if overwrite mode is false) creates a new one from the selected reference data. + * @remark Please keep in mind that new created nodes are not automatically added to the data storage. + * Derived tools can call EnsureTargetSegmentationNodeInDataStorage to ensure it as soon as it is clear + * that the target segmentation node will be/is confirmed. * @return a mitk::DataNode which contains a segmentation image */ - virtual mitk::DataNode *GetTargetSegmentationNode(); + virtual DataNode *GetTargetSegmentationNode() const; protected: AutoSegmentationTool(); // purposely hidden + AutoSegmentationTool(const char* interactorType, const us::Module* interactorModule = nullptr); // purposely hidden ~AutoSegmentationTool() override; const char *GetGroup() const override; /** Helper that extracts the image for the passed timestep, if the image has multiple time steps.*/ static Image::ConstPointer GetImageByTimeStep(const Image* image, unsigned int timestep); /** Helper that extracts the image for the passed time point, if the image has multiple time steps.*/ static Image::ConstPointer GetImageByTimePoint(const Image* image, TimePointType timePoint); + void EnsureTargetSegmentationNodeInDataStorage() const; + bool m_OverwriteExistingSegmentation; + + private: + /**Contains the node returned by GetTargetSementationNode if m_OverwriteExistingSegmentation == false. Then + * GetTargetSegmentation generates a new target segmentation node.*/ + mutable DataNode::Pointer m_NoneOverwriteTargetSegmentationNode; }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.cpp b/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.cpp index e8554c2228..1c52e44aad 100644 --- a/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.cpp +++ b/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.cpp @@ -1,478 +1,523 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkAutoSegmentationWithPreviewTool.h" #include "mitkToolManager.h" #include "mitkColorProperty.h" #include "mitkLevelWindowProperty.h" #include "mitkProperties.h" #include "mitkDataStorage.h" #include "mitkRenderingManager.h" #include #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkImageStatisticsHolder.h" #include "mitkImageTimeSelector.h" #include "mitkLabelSetImage.h" #include "mitkMaskAndCutRoiImageFilter.h" #include "mitkPadImageFilter.h" #include "mitkNodePredicateGeometry.h" +#include "mitkSegTool2D.h" mitk::AutoSegmentationWithPreviewTool::AutoSegmentationWithPreviewTool(bool lazyDynamicPreviews): m_LazyDynamicPreviews(lazyDynamicPreviews) { m_ProgressCommand = mitk::ToolCommand::New(); } +mitk::AutoSegmentationWithPreviewTool::AutoSegmentationWithPreviewTool(bool lazyDynamicPreviews, const char* interactorType, const us::Module* interactorModule) : AutoSegmentationTool(interactorType, interactorModule), m_LazyDynamicPreviews(lazyDynamicPreviews) +{ + m_ProgressCommand = mitk::ToolCommand::New(); +} + + mitk::AutoSegmentationWithPreviewTool::~AutoSegmentationWithPreviewTool() { } bool mitk::AutoSegmentationWithPreviewTool::CanHandle(const BaseData* referenceData, const BaseData* workingData) const { if (!Superclass::CanHandle(referenceData, workingData)) return false; if (workingData == nullptr) return true; auto* labelSet = dynamic_cast(workingData); if (labelSet != nullptr) return true; auto* image = dynamic_cast(workingData); if (image == nullptr) return false; //if it is a normal image and not a label set image is used as working data //it must have the same pixel type as a label set. return MakeScalarPixelType< DefaultSegmentationDataType >() == image->GetPixelType(); } void mitk::AutoSegmentationWithPreviewTool::Activated() { Superclass::Activated(); m_ToolManager->RoiDataChanged += mitk::MessageDelegate(this, &mitk::AutoSegmentationWithPreviewTool::OnRoiDataChanged); m_ToolManager->SelectedTimePointChanged += mitk::MessageDelegate(this, &mitk::AutoSegmentationWithPreviewTool::OnTimePointChanged); m_ReferenceDataNode = m_ToolManager->GetReferenceData(0); m_SegmentationInputNode = m_ReferenceDataNode; - m_LastTimePointOfUpdate = 0; + m_LastTimePointOfUpdate = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); if (m_PreviewSegmentationNode.IsNull()) { m_PreviewSegmentationNode = DataNode::New(); m_PreviewSegmentationNode->SetProperty("color", ColorProperty::New(0.0, 1.0, 0.0)); m_PreviewSegmentationNode->SetProperty("name", StringProperty::New(std::string(this->GetName())+" preview")); m_PreviewSegmentationNode->SetProperty("opacity", FloatProperty::New(0.3)); m_PreviewSegmentationNode->SetProperty("binary", BoolProperty::New(true)); m_PreviewSegmentationNode->SetProperty("helper object", BoolProperty::New(true)); } if (m_SegmentationInputNode.IsNotNull()) { this->ResetPreviewNode(); this->InitiateToolByInput(); } else { m_ToolManager->ActivateTool(-1); } } void mitk::AutoSegmentationWithPreviewTool::Deactivated() { m_ToolManager->RoiDataChanged -= mitk::MessageDelegate(this, &mitk::AutoSegmentationWithPreviewTool::OnRoiDataChanged); m_ToolManager->SelectedTimePointChanged -= mitk::MessageDelegate(this, &mitk::AutoSegmentationWithPreviewTool::OnTimePointChanged); m_SegmentationInputNode = nullptr; m_ReferenceDataNode = nullptr; + m_WorkingPlaneGeometry = nullptr; try { if (DataStorage *storage = m_ToolManager->GetDataStorage()) { storage->Remove(m_PreviewSegmentationNode); RenderingManager::GetInstance()->RequestUpdateAll(); } } catch (...) { // don't care } if (m_PreviewSegmentationNode.IsNotNull()) { m_PreviewSegmentationNode->SetData(nullptr); } Superclass::Deactivated(); } void mitk::AutoSegmentationWithPreviewTool::ConfirmSegmentation() { if (m_LazyDynamicPreviews && m_CreateAllTimeSteps) { // The tool should create all time steps but is currently in lazy mode, // thus ensure that a preview for all time steps is available. this->UpdatePreview(true); } CreateResultSegmentationFromPreview(); RenderingManager::GetInstance()->RequestUpdateAll(); if (!m_KeepActiveAfterAccept) { m_ToolManager->ActivateTool(-1); } } void mitk::AutoSegmentationWithPreviewTool::InitiateToolByInput() { //default implementation does nothing. //implement in derived classes to change behavior } mitk::Image* mitk::AutoSegmentationWithPreviewTool::GetPreviewSegmentation() { if (m_PreviewSegmentationNode.IsNull()) { return nullptr; } return dynamic_cast(m_PreviewSegmentationNode->GetData()); } mitk::DataNode* mitk::AutoSegmentationWithPreviewTool::GetPreviewSegmentationNode() { return m_PreviewSegmentationNode; } const mitk::Image* mitk::AutoSegmentationWithPreviewTool::GetSegmentationInput() const { if (m_SegmentationInputNode.IsNull()) { return nullptr; } return dynamic_cast(m_SegmentationInputNode->GetData()); } const mitk::Image* mitk::AutoSegmentationWithPreviewTool::GetReferenceData() const { if (m_ReferenceDataNode.IsNull()) { return nullptr; } return dynamic_cast(m_ReferenceDataNode->GetData()); } void mitk::AutoSegmentationWithPreviewTool::ResetPreviewNode() { itk::RGBPixel previewColor; previewColor[0] = 0.0f; previewColor[1] = 1.0f; previewColor[2] = 0.0f; const auto image = this->GetSegmentationInput(); if (nullptr != image) { mitk::LabelSetImage::ConstPointer workingImage = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); if (workingImage.IsNotNull()) { auto newPreviewImage = workingImage->Clone(); if (newPreviewImage.IsNull()) { MITK_ERROR << "Cannot create preview helper objects. Unable to clone working image"; return; } m_PreviewSegmentationNode->SetData(newPreviewImage); // Let's paint the feedback node green... newPreviewImage->GetActiveLabel()->SetColor(previewColor); newPreviewImage->GetActiveLabelSet()->UpdateLookupTable(newPreviewImage->GetActiveLabel()->GetValue()); } else { mitk::Image::ConstPointer workingImageBin = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); if (workingImageBin.IsNotNull()) { auto newPreviewImage = workingImageBin->Clone(); if (newPreviewImage.IsNull()) { MITK_ERROR << "Cannot create preview helper objects. Unable to clone working image"; return; } m_PreviewSegmentationNode->SetData(newPreviewImage->Clone()); } else { mitkThrow() << "Tool is an invalid state. Cannot setup preview node. Working data is an unsupported class and should have not been accepted by CanHandle()."; } } m_PreviewSegmentationNode->SetColor(previewColor); m_PreviewSegmentationNode->SetOpacity(0.5); int layer(50); m_ReferenceDataNode->GetIntProperty("layer", layer); m_PreviewSegmentationNode->SetIntProperty("layer", layer + 1); if (DataStorage *ds = m_ToolManager->GetDataStorage()) { if (!ds->Exists(m_PreviewSegmentationNode)) ds->Add(m_PreviewSegmentationNode, m_ReferenceDataNode); } } } template static void ITKSetVolume(const itk::Image *originalImage, mitk::Image *segmentation, unsigned int timeStep) { auto constPixelContainer = originalImage->GetPixelContainer(); //have to make a const cast because itk::PixelContainer does not provide a const correct access :( auto pixelContainer = const_cast::PixelContainer*>(constPixelContainer); segmentation->SetVolume((void *)pixelContainer->GetBufferPointer(), timeStep); } void mitk::AutoSegmentationWithPreviewTool::TransferImageAtTimeStep(const Image* sourceImage, Image* destinationImage, const TimeStepType timeStep) { try { - Image::ConstPointer image3D = this->GetImageByTimeStep(sourceImage, timeStep); + Image::ConstPointer sourceImageAtTimeStep = this->GetImageByTimeStep(sourceImage, timeStep); - if (image3D->GetPixelType() != destinationImage->GetPixelType()) + if (sourceImageAtTimeStep->GetPixelType() != destinationImage->GetPixelType()) { mitkThrow() << "Cannot transfer images. Tool is in an invalid state, source image and destination image do not have the same pixel type. " << "Source pixel type: " << sourceImage->GetPixelType().GetTypeAsString() << "; destination pixel type: " << destinationImage->GetPixelType().GetTypeAsString(); } if (!Equal(*(sourceImage->GetGeometry(timeStep)), *(destinationImage->GetGeometry(timeStep)), NODE_PREDICATE_GEOMETRY_DEFAULT_CHECK_PRECISION, false)) { mitkThrow() << "Cannot transfer images. Tool is in an invalid state, source image and destination image do not have the same geometry."; } - if (image3D->GetDimension() == 2) + if (nullptr != this->GetWorkingPlaneGeometry()) { - AccessFixedDimensionByItk_2( - image3D, ITKSetVolume, 2, destinationImage, timeStep); + auto sourceSlice = SegTool2D::GetAffectedImageSliceAs2DImage(this->GetWorkingPlaneGeometry(), sourceImage, timeStep); + SegTool2D::WriteBackSegmentationResult(this->GetTargetSegmentationNode(), m_WorkingPlaneGeometry, sourceSlice, timeStep); } else - { - AccessFixedDimensionByItk_2( - image3D, ITKSetVolume, 3, destinationImage, timeStep); + { //take care of the full segmentation volume + if (sourceImageAtTimeStep->GetDimension() == 2) + { + AccessFixedDimensionByItk_2( + sourceImageAtTimeStep, ITKSetVolume, 2, destinationImage, timeStep); + } + else + { + AccessFixedDimensionByItk_2( + sourceImageAtTimeStep, ITKSetVolume, 3, destinationImage, timeStep); + } } } catch (...) { Tool::ErrorMessage("Error accessing single time steps of the original image. Cannot create segmentation."); throw; } } void mitk::AutoSegmentationWithPreviewTool::CreateResultSegmentationFromPreview() { const auto segInput = this->GetSegmentationInput(); auto previewImage = this->GetPreviewSegmentation(); if (nullptr != segInput && nullptr != previewImage) { DataNode::Pointer resultSegmentationNode = GetTargetSegmentationNode(); if (resultSegmentationNode.IsNotNull()) { const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); auto resultSegmentation = dynamic_cast(resultSegmentationNode->GetData()); // REMARK: the following code in this scope assumes that previewImage and resultSegmentation // are clones of the working image (segmentation provided to the tool). Therefore they have // the same time geometry. if (previewImage->GetTimeSteps() != resultSegmentation->GetTimeSteps()) { mitkThrow() << "Cannot perform threshold. Internal tool state is invalid." << " Preview segmentation and segmentation result image have different time geometries."; } if (m_CreateAllTimeSteps) { for (unsigned int timeStep = 0; timeStep < previewImage->GetTimeSteps(); ++timeStep) { - TransferImageAtTimeStep(previewImage, resultSegmentation, timeStep); + this->TransferImageAtTimeStep(previewImage, resultSegmentation, timeStep); } } else { const auto timeStep = resultSegmentation->GetTimeGeometry()->TimePointToTimeStep(timePoint); - TransferImageAtTimeStep(previewImage, resultSegmentation, timeStep); + this->TransferImageAtTimeStep(previewImage, resultSegmentation, timeStep); } // since we are maybe working on a smaller image, pad it to the size of the original image if (m_ReferenceDataNode.GetPointer() != m_SegmentationInputNode.GetPointer()) { mitk::PadImageFilter::Pointer padFilter = mitk::PadImageFilter::New(); padFilter->SetInput(0, resultSegmentation); padFilter->SetInput(1, dynamic_cast(m_ReferenceDataNode->GetData())); padFilter->SetBinaryFilter(true); padFilter->SetUpperThreshold(1); padFilter->SetLowerThreshold(1); padFilter->Update(); resultSegmentationNode->SetData(padFilter->GetOutput()); } m_ToolManager->SetWorkingData(resultSegmentationNode); m_ToolManager->GetWorkingData(0)->Modified(); + this->EnsureTargetSegmentationNodeInDataStorage(); } } } void mitk::AutoSegmentationWithPreviewTool::OnRoiDataChanged() { mitk::DataNode::ConstPointer node = m_ToolManager->GetRoiData(0); if (node.IsNotNull()) { mitk::MaskAndCutRoiImageFilter::Pointer roiFilter = mitk::MaskAndCutRoiImageFilter::New(); mitk::Image::Pointer image = dynamic_cast(m_SegmentationInputNode->GetData()); if (image.IsNull()) return; roiFilter->SetInput(image); roiFilter->SetRegionOfInterest(node->GetData()); roiFilter->Update(); mitk::DataNode::Pointer tmpNode = mitk::DataNode::New(); tmpNode->SetData(roiFilter->GetOutput()); m_SegmentationInputNode = tmpNode; } else m_SegmentationInputNode = m_ReferenceDataNode; this->ResetPreviewNode(); this->InitiateToolByInput(); this->UpdatePreview(); } void mitk::AutoSegmentationWithPreviewTool::OnTimePointChanged() { if (m_IsTimePointChangeAware && m_PreviewSegmentationNode.IsNotNull() && m_SegmentationInputNode.IsNotNull()) { const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); const bool isStaticSegOnDynamicImage = m_PreviewSegmentationNode->GetData()->GetTimeSteps() == 1 && m_SegmentationInputNode->GetData()->GetTimeSteps() > 1; if (timePoint!=m_LastTimePointOfUpdate && (isStaticSegOnDynamicImage || m_LazyDynamicPreviews)) { //we only need to update either because we are lazzy //or because we have a static segmentation with a dynamic image this->UpdatePreview(); } } } void mitk::AutoSegmentationWithPreviewTool::UpdatePreview(bool ignoreLazyPreviewSetting) { const auto inputImage = this->GetSegmentationInput(); auto previewImage = this->GetPreviewSegmentation(); int progress_steps = 200; this->CurrentlyBusy.Send(true); + m_IsUpdating = true; this->UpdatePrepare(); const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); try { if (nullptr != inputImage && nullptr != previewImage) { m_ProgressCommand->AddStepsToDo(progress_steps); if (previewImage->GetTimeSteps() > 1 && (ignoreLazyPreviewSetting || !m_LazyDynamicPreviews)) { - for (unsigned int timeStep = 0; timeStep < inputImage->GetTimeSteps(); ++timeStep) + for (unsigned int timeStep = 0; timeStep < previewImage->GetTimeSteps(); ++timeStep) { - auto feedBackImage3D = this->GetImageByTimeStep(inputImage, timeStep); - - this->DoUpdatePreview(feedBackImage3D, previewImage, timeStep); + Image::ConstPointer feedBackImage; + auto previewTimePoint = previewImage->GetTimeGeometry()->TimeStepToTimePoint(timeStep); + auto inputTimeStep = inputImage->GetTimeGeometry()->TimePointToTimeStep(previewTimePoint); + + if (nullptr != this->GetWorkingPlaneGeometry()) + { //only extract a specific slice defined by the working plane as feedback image. + feedBackImage = SegTool2D::GetAffectedImageSliceAs2DImage(this->GetWorkingPlaneGeometry(), inputImage, inputTimeStep); + } + else + { //work on the whole feedback image + feedBackImage = this->GetImageByTimeStep(inputImage, inputTimeStep); + } + + this->DoUpdatePreview(feedBackImage, previewImage, timeStep); } } else { - auto feedBackImage3D = this->GetImageByTimePoint(inputImage, timePoint); + Image::ConstPointer feedBackImage; + if (nullptr != this->GetWorkingPlaneGeometry()) + { + feedBackImage = SegTool2D::GetAffectedImageSliceAs2DImageByTimePoint(this->GetWorkingPlaneGeometry(), inputImage, timePoint); + } + else + { + feedBackImage = this->GetImageByTimePoint(inputImage, timePoint); + } + auto timeStep = previewImage->GetTimeGeometry()->TimePointToTimeStep(timePoint); - this->DoUpdatePreview(feedBackImage3D, previewImage, timeStep); + this->DoUpdatePreview(feedBackImage, previewImage, timeStep); } RenderingManager::GetInstance()->RequestUpdateAll(); } } catch (itk::ExceptionObject & excep) { MITK_ERROR << "Exception caught: " << excep.GetDescription(); m_ProgressCommand->SetProgress(progress_steps); std::string msg = excep.GetDescription(); ErrorMessage.Send(msg); } catch (...) { m_ProgressCommand->SetProgress(progress_steps); + m_IsUpdating = false; CurrentlyBusy.Send(false); throw; } this->UpdateCleanUp(); m_LastTimePointOfUpdate = timePoint; m_ProgressCommand->SetProgress(progress_steps); + m_IsUpdating = false; CurrentlyBusy.Send(false); } +bool mitk::AutoSegmentationWithPreviewTool::IsUpdating() const +{ + return m_IsUpdating; +} + void mitk::AutoSegmentationWithPreviewTool::UpdatePrepare() { // default implementation does nothing //reimplement in derived classes for special behavior } void mitk::AutoSegmentationWithPreviewTool::UpdateCleanUp() { // default implementation does nothing //reimplement in derived classes for special behavior } mitk::TimePointType mitk::AutoSegmentationWithPreviewTool::GetLastTimePointOfUpdate() const { return m_LastTimePointOfUpdate; } diff --git a/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.h b/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.h index 848ff0c005..b3cad84572 100644 --- a/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.h +++ b/Modules/Segmentation/Interactions/mitkAutoSegmentationWithPreviewTool.h @@ -1,152 +1,169 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef mitkAutoSegmentationWithPreviewTool_h_Included #define mitkAutoSegmentationWithPreviewTool_h_Included #include "mitkAutoSegmentationTool.h" #include "mitkCommon.h" #include "mitkDataNode.h" #include "mitkToolCommand.h" #include namespace mitk { /** \brief Base class for any auto segmentation tool that provides a preview of the new segmentation. This tool class implements a lot basic logic to handle auto segmentation tools with preview, Time point and ROI support. Derived classes will ask to update the segmentation preview if needed (e.g. because the ROI or the current time point has changed) or because derived tools indicated the need to update themselves. This class also takes care to properly transfer a confirmed preview into the segementation result. \ingroup ToolManagerEtAl \sa mitk::Tool \sa QmitkInteractiveSegmentation */ class MITKSEGMENTATION_EXPORT AutoSegmentationWithPreviewTool : public AutoSegmentationTool { public: mitkClassMacro(AutoSegmentationWithPreviewTool, AutoSegmentationTool); void Activated() override; void Deactivated() override; void ConfirmSegmentation(); itkSetMacro(CreateAllTimeSteps, bool); itkGetMacro(CreateAllTimeSteps, bool); itkBooleanMacro(CreateAllTimeSteps); itkSetMacro(KeepActiveAfterAccept, bool); itkGetMacro(KeepActiveAfterAccept, bool); itkBooleanMacro(KeepActiveAfterAccept); itkSetMacro(IsTimePointChangeAware, bool); itkGetMacro(IsTimePointChangeAware, bool); itkBooleanMacro(IsTimePointChangeAware); bool CanHandle(const BaseData* referenceData, const BaseData* workingData) const override; /** Triggers the actualization of the preview * @param ignoreLazyPreviewSetting If set true UpdatePreview will always * generate the preview for all time steps. If set to false, UpdatePreview * will regard the setting specified by the constructor. * To define the update generation for time steps implement DoUpdatePreview. * To alter what should be done directly before or after the update of the preview, * reimplement UpdatePrepare() or UpdateCleanUp().*/ void UpdatePreview(bool ignoreLazyPreviewSetting = false); + /** Indicate if currently UpdatePreview is triggered (true) or not (false).*/ + bool IsUpdating() const; + protected: mitk::ToolCommand::Pointer m_ProgressCommand; /** Member is always called if GetSegmentationInput() has changed * (e.g. because a new ROI was defined, or on activation) to give derived * classes the posibility to initiate their state accordingly. * Reimplement this function to implement special behavior. */ virtual void InitiateToolByInput(); virtual void UpdatePrepare(); virtual void UpdateCleanUp(); /** This function does the real work. Here the preview for a given * input image should be computed and stored in the also passed * preview image at the passed time step. */ virtual void DoUpdatePreview(const Image* inputAtTimeStep, Image* previewImage, TimeStepType timeStep) = 0; - AutoSegmentationWithPreviewTool(bool lazyDynamicPreviews = false); + AutoSegmentationWithPreviewTool(bool lazyDynamicPreviews = false); // purposely hidden + AutoSegmentationWithPreviewTool(bool lazyDynamicPreviews, const char* interactorType, const us::Module* interactorModule = nullptr); // purposely hidden + ~AutoSegmentationWithPreviewTool() override; /** Returns the image that contains the preview of the current segmentation. * Returns null if the node is not set or does not contain an image.*/ Image* GetPreviewSegmentation(); DataNode* GetPreviewSegmentationNode(); /** Returns the input that should be used for any segmentation/preview or tool update. * It is either the data of ReferenceDataNode itself or a part of it defined by a ROI mask * provided by the tool manager. Derived classes should regard this as the relevant * input data for any processing. * Returns null if the node is not set or does not contain an image.*/ const Image* GetSegmentationInput() const; /** Returns the image that is provided by the ReferenceDataNode. * Returns null if the node is not set or does not contain an image.*/ const Image* GetReferenceData() const; /** Resets the preview node so it is empty and ready to be filled by the tool*/ void ResetPreviewNode(); TimePointType GetLastTimePointOfUpdate() const; + itkSetObjectMacro(WorkingPlaneGeometry, PlaneGeometry); + itkGetConstObjectMacro(WorkingPlaneGeometry, PlaneGeometry); + private: void TransferImageAtTimeStep(const Image* sourceImage, Image* destinationImage, const TimeStepType timeStep); void CreateResultSegmentationFromPreview(); void OnRoiDataChanged(); void OnTimePointChanged(); /** Node that containes the preview data generated and managed by this class or derived ones.*/ DataNode::Pointer m_PreviewSegmentationNode; /** The reference data recieved from ToolManager::GetReferenceData when tool was activated.*/ DataNode::Pointer m_ReferenceDataNode; /** Node that containes the data that should be used as input for any auto segmentation. It might * be the same like m_ReferenceDataNode (if no ROI is set) or a sub region (if ROI is set).*/ DataNode::Pointer m_SegmentationInputNode; /** Indicates if Accepting the threshold should transfer/create the segmentations of all time steps (true) or only of the currently selected timepoint (false).*/ bool m_CreateAllTimeSteps = false; /** Indicates if the tool should kept active after accepting the segmentation or not.*/ bool m_KeepActiveAfterAccept = false; /** Relevant if the working data / preview image has multiple time steps (dynamic segmentations). * This flag has to be set by derived classes accordingly to there way to generate dynamic previews. * If LazyDynamicPreview is true, the tool generates only the preview for the current time step. * Therefore it always has to update the preview if current time point has changed and it has to (re)compute * all timeframes if ConfirmSegmentation() is called.*/ bool m_LazyDynamicPreviews = false; bool m_IsTimePointChangeAware = true; TimePointType m_LastTimePointOfUpdate = 0.; + + bool m_IsUpdating = false; + + /** This variable indicates if for the tool a working plane geometry is defined. + * If a working plane is defined the tool will only work an the slice of the input + * and the segmentation. Thus only the relevant input slice will be passed to + * DoUpdatePreview(...) and only the relevant slice of the preview will be transfered when + * ConfirmSegmentation() is called.*/ + PlaneGeometry::Pointer m_WorkingPlaneGeometry; }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkContourModelInteractor.cpp b/Modules/Segmentation/Interactions/mitkContourModelInteractor.cpp index 92dba4c9a5..e608aaec13 100644 --- a/Modules/Segmentation/Interactions/mitkContourModelInteractor.cpp +++ b/Modules/Segmentation/Interactions/mitkContourModelInteractor.cpp @@ -1,164 +1,164 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkContourModelInteractor.h" #include "mitkToolManager.h" #include "mitkBaseRenderer.h" #include "mitkRenderingManager.h" #include #include mitk::ContourModelInteractor::ContourModelInteractor() { } void mitk::ContourModelInteractor::ConnectActionsAndFunctions() { CONNECT_CONDITION("checkisOverPoint", OnCheckPointClick); CONNECT_CONDITION("mouseMove", IsHovering); CONNECT_FUNCTION("movePoints", OnMovePoint); CONNECT_FUNCTION("deletePoint", OnDeletePoint); CONNECT_FUNCTION("finish", OnFinishEditing); } mitk::ContourModelInteractor::~ContourModelInteractor() { } bool mitk::ContourModelInteractor::OnCheckPointClick(const InteractionEvent *interactionEvent) { const auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return false; - int timestep = positionEvent->GetSender()->GetTimeStep(); + const auto timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); auto *contour = dynamic_cast(this->GetDataNode()->GetData()); contour->Deselect(); mitk::Point3D click = positionEvent->GetPositionInWorld(); - if (contour->SelectVertexAt(click, 1.5, timestep)) + if (contour->SelectVertexAt(click, 1.5, timeStep)) { contour->SetSelectedVertexAsControlPoint(); mitk::RenderingManager::GetInstance()->RequestUpdate(interactionEvent->GetSender()->GetRenderWindow()); m_lastMousePosition = click; - auto *contourGeometry = dynamic_cast(contour->GetGeometry(timestep)); + auto *contourGeometry = dynamic_cast(contour->GetGeometry(timeStep)); if (contourGeometry->IsInside(click)) { m_lastMousePosition = click; return true; } else return false; } else { return false; } return true; } void mitk::ContourModelInteractor::OnDeletePoint(StateMachineAction *, InteractionEvent *) { auto *contour = dynamic_cast(this->GetDataNode()->GetData()); contour->RemoveVertex(contour->GetSelectedVertex()); } bool mitk::ContourModelInteractor::IsHovering(const InteractionEvent *interactionEvent) { const auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return false; - int timestep = positionEvent->GetSender()->GetTimeStep(); + const auto timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); auto *contour = dynamic_cast(this->GetDataNode()->GetData()); mitk::Point3D currentPosition = positionEvent->GetPositionInWorld(); bool isHover = false; this->GetDataNode()->GetBoolProperty("contour.hovering", isHover, positionEvent->GetSender()); - if (contour->IsNearContour(currentPosition, 1.5, timestep)) + if (contour->IsNearContour(currentPosition, 1.5, timeStep)) { if (isHover == false) { this->GetDataNode()->SetBoolProperty("contour.hovering", true); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } } else { if (isHover == true) { this->GetDataNode()->SetBoolProperty("contour.hovering", false); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } } return false; } void mitk::ContourModelInteractor::OnMovePoint(StateMachineAction *, InteractionEvent *interactionEvent) { const auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; auto *contour = dynamic_cast(this->GetDataNode()->GetData()); mitk::Vector3D translation; mitk::Point3D currentPosition = positionEvent->GetPositionInWorld(); translation[0] = currentPosition[0] - this->m_lastMousePosition[0]; translation[1] = currentPosition[1] - this->m_lastMousePosition[1]; translation[2] = currentPosition[2] - this->m_lastMousePosition[2]; contour->ShiftSelectedVertex(translation); this->m_lastMousePosition = positionEvent->GetPositionInWorld(); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } void mitk::ContourModelInteractor::OnMoveContour(StateMachineAction *, InteractionEvent *interactionEvent) { const auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; - int timestep = positionEvent->GetSender()->GetTimeStep(); + const auto timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); auto *contour = dynamic_cast(this->GetDataNode()->GetData()); mitk::Vector3D translation; mitk::Point3D currentPosition = positionEvent->GetPositionInWorld(); translation[0] = currentPosition[0] - this->m_lastMousePosition[0]; translation[1] = currentPosition[1] - this->m_lastMousePosition[1]; translation[2] = currentPosition[2] - this->m_lastMousePosition[2]; - contour->ShiftContour(translation, timestep); + contour->ShiftContour(translation, timeStep); this->m_lastMousePosition = positionEvent->GetPositionInWorld(); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } void mitk::ContourModelInteractor::OnFinishEditing(StateMachineAction *, InteractionEvent *interactionEvent) { auto *contour = dynamic_cast(this->GetDataNode()->GetData()); contour->Deselect(); mitk::RenderingManager::GetInstance()->RequestUpdate(interactionEvent->GetSender()->GetRenderWindow()); } diff --git a/Modules/Segmentation/Interactions/mitkContourModelLiveWireInteractor.cpp b/Modules/Segmentation/Interactions/mitkContourModelLiveWireInteractor.cpp index 695b2969ef..e2e0e95b68 100644 --- a/Modules/Segmentation/Interactions/mitkContourModelLiveWireInteractor.cpp +++ b/Modules/Segmentation/Interactions/mitkContourModelLiveWireInteractor.cpp @@ -1,482 +1,485 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkContourModelLiveWireInteractor.h" #include "mitkInteractionPositionEvent.h" #include "mitkToolManager.h" #include "mitkBaseRenderer.h" #include "mitkRenderingManager.h" #include #include "mitkIOUtil.h" mitk::ContourModelLiveWireInteractor::ContourModelLiveWireInteractor() : ContourModelInteractor() { m_LiveWireFilter = mitk::ImageLiveWireContourModelFilter::New(); m_NextActiveVertexDown.Fill(0); m_NextActiveVertexUp.Fill(0); } mitk::ContourModelLiveWireInteractor::~ContourModelLiveWireInteractor() { } void mitk::ContourModelLiveWireInteractor::ConnectActionsAndFunctions() { CONNECT_CONDITION("checkisOverPoint", OnCheckPointClick); CONNECT_CONDITION("mouseMove", IsHovering); CONNECT_FUNCTION("movePoint", OnMovePoint); CONNECT_FUNCTION("deletePoint", OnDeletePoint); CONNECT_FUNCTION("finish", OnFinishEditing); } bool mitk::ContourModelLiveWireInteractor::OnCheckPointClick(const InteractionEvent *interactionEvent) { const auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return false; - int timestep = positionEvent->GetSender()->GetTimeStep(); + const auto timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); auto *contour = dynamic_cast(this->GetDataNode()->GetData()); if (contour == nullptr) { MITK_ERROR << "Invalid Contour"; return false; } contour->Deselect(); // Check distance to any vertex. // Transition YES if click close to a vertex mitk::Point3D click = positionEvent->GetPositionInWorld(); - if (contour->SelectVertexAt(click, 1.5, timestep)) + if (contour->SelectVertexAt(click, 1.5, timeStep)) { contour->SetSelectedVertexAsControlPoint(false); m_ContourLeft = mitk::ContourModel::New(); // get coordinates of next active vertex downwards from selected vertex - int downIndex = this->SplitContourFromSelectedVertex(contour, m_ContourLeft, false, timestep); + int downIndex = this->SplitContourFromSelectedVertex(contour, m_ContourLeft, false, timeStep); m_NextActiveVertexDownIter = contour->IteratorBegin() + downIndex; m_NextActiveVertexDown = (*m_NextActiveVertexDownIter)->Coordinates; m_ContourRight = mitk::ContourModel::New(); // get coordinates of next active vertex upwards from selected vertex - int upIndex = this->SplitContourFromSelectedVertex(contour, m_ContourRight, true, timestep); + int upIndex = this->SplitContourFromSelectedVertex(contour, m_ContourRight, true, timeStep); m_NextActiveVertexUpIter = contour->IteratorBegin() + upIndex; m_NextActiveVertexUp = (*m_NextActiveVertexUpIter)->Coordinates; // clear previous void positions this->m_LiveWireFilter->ClearRepulsivePoints(); // set the current contour as void positions in the cost map // start with down side - auto iter = contour->IteratorBegin(timestep); + auto iter = contour->IteratorBegin(timeStep); for (; iter != m_NextActiveVertexDownIter; iter++) { itk::Index<2> idx; this->m_WorkingSlice->GetGeometry()->WorldToIndex((*iter)->Coordinates, idx); this->m_LiveWireFilter->AddRepulsivePoint(idx); } // continue with upper side iter = m_NextActiveVertexUpIter + 1; - for (; iter != contour->IteratorEnd(timestep); iter++) + for (; iter != contour->IteratorEnd(timeStep); iter++) { itk::Index<2> idx; this->m_WorkingSlice->GetGeometry()->WorldToIndex((*iter)->Coordinates, idx); this->m_LiveWireFilter->AddRepulsivePoint(idx); } // clear container with void points between neighboring control points m_ContourBeingModified.clear(); // let us have the selected point as a control point contour->SetSelectedVertexAsControlPoint(true); // finally, return true to pass this condition return true; } else { // do not pass condition return false; } mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); return true; } void mitk::ContourModelLiveWireInteractor::SetEditingContourModelNode(mitk::DataNode *_arg) { if (this->m_EditingContourNode != _arg) { this->m_EditingContourNode = _arg; } } void mitk::ContourModelLiveWireInteractor::SetWorkingImage(mitk::Image *_arg) { if (this->m_WorkingSlice != _arg) { this->m_WorkingSlice = _arg; this->m_LiveWireFilter->SetInput(this->m_WorkingSlice); } } void mitk::ContourModelLiveWireInteractor::OnDeletePoint(StateMachineAction *, InteractionEvent *interactionEvent) { - int timestep = interactionEvent->GetSender()->GetTimeStep(); + const auto timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); auto *contour = dynamic_cast(this->GetDataNode()->GetData()); if (contour == nullptr) { MITK_ERROR << "Invalid Contour!"; return; } if (contour->GetSelectedVertex()) { mitk::ContourModel::Pointer newContour = mitk::ContourModel::New(); newContour->Expand(contour->GetTimeSteps()); + newContour->SetTimeGeometry(contour->GetTimeGeometry()->Clone()); - newContour->Concatenate(m_ContourLeft, timestep); + newContour->Concatenate(m_ContourLeft, timeStep); // recompute contour between neighbored two active control points this->m_LiveWireFilter->SetStartPoint(this->m_NextActiveVertexDown); this->m_LiveWireFilter->SetEndPoint(this->m_NextActiveVertexUp); // this->m_LiveWireFilter->ClearRepulsivePoints(); this->m_LiveWireFilter->Update(); mitk::ContourModel *liveWireContour = this->m_LiveWireFilter->GetOutput(); assert(liveWireContour); - if (liveWireContour->IsEmpty(timestep)) + if (liveWireContour->IsEmpty(timeStep)) return; - liveWireContour->RemoveVertexAt(0, timestep); - liveWireContour->RemoveVertexAt(liveWireContour->GetNumberOfVertices(timestep) - 1, timestep); + liveWireContour->RemoveVertexAt(0, timeStep); + liveWireContour->RemoveVertexAt(liveWireContour->GetNumberOfVertices(timeStep) - 1, timeStep); // insert new live wire computed points - newContour->Concatenate(liveWireContour, timestep); + newContour->Concatenate(liveWireContour, timeStep); // insert right side of original contour - newContour->Concatenate(this->m_ContourRight, timestep); + newContour->Concatenate(this->m_ContourRight, timeStep); - newContour->SetClosed(contour->IsClosed(timestep), timestep); + newContour->SetClosed(contour->IsClosed(timeStep), timeStep); // instead of leaving a single point, delete all points - if (newContour->GetNumberOfVertices(timestep) <= 2) + if (newContour->GetNumberOfVertices(timeStep) <= 2) { - newContour->Clear(timestep); + newContour->Clear(timeStep); } this->GetDataNode()->SetData(newContour); mitk::RenderingManager::GetInstance()->RequestUpdate(interactionEvent->GetSender()->GetRenderWindow()); } } void mitk::ContourModelLiveWireInteractor::OnMovePoint(StateMachineAction *, InteractionEvent *interactionEvent) { const auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; - int timestep = positionEvent->GetSender()->GetTimeStep(); + const auto timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); mitk::Point3D currentPosition = positionEvent->GetPositionInWorld(); auto *contour = dynamic_cast(this->GetDataNode()->GetData()); if (contour == nullptr) { MITK_ERROR << "invalid contour"; return; } mitk::ContourModel::Pointer editingContour = mitk::ContourModel::New(); editingContour->Expand(contour->GetTimeSteps()); + editingContour->SetTimeGeometry(contour->GetTimeGeometry()->Clone()); // recompute left live wire, i.e. the contour between previous active vertex and selected vertex this->m_LiveWireFilter->SetStartPoint(this->m_NextActiveVertexDown); this->m_LiveWireFilter->SetEndPoint(currentPosition); // remove void positions between previous active vertex and next active vertex. if (!m_ContourBeingModified.empty()) { std::vector>::const_iterator iter = m_ContourBeingModified.begin(); for (; iter != m_ContourBeingModified.end(); iter++) { this->m_LiveWireFilter->RemoveRepulsivePoint((*iter)); } } // update to get the left livewire. Remember that the points in the rest of the contour are already // set as void positions in the filter this->m_LiveWireFilter->Update(); mitk::ContourModel::Pointer leftLiveWire = this->m_LiveWireFilter->GetOutput(); assert(leftLiveWire); - if (!leftLiveWire->IsEmpty(timestep)) - leftLiveWire->RemoveVertexAt(0, timestep); + if (!leftLiveWire->IsEmpty(timeStep)) + leftLiveWire->RemoveVertexAt(0, timeStep); - editingContour->Concatenate(leftLiveWire, timestep); + editingContour->Concatenate(leftLiveWire, timeStep); // the new index of the selected vertex unsigned int selectedVertexIndex = - this->m_ContourLeft->GetNumberOfVertices(timestep) + leftLiveWire->GetNumberOfVertices(timestep) - 1; + this->m_ContourLeft->GetNumberOfVertices(timeStep) + leftLiveWire->GetNumberOfVertices(timeStep) - 1; // at this point the container has to be empty m_ContourBeingModified.clear(); // add points from left live wire contour - auto iter = leftLiveWire->IteratorBegin(timestep); - for (; iter != leftLiveWire->IteratorEnd(timestep); iter++) + auto iter = leftLiveWire->IteratorBegin(timeStep); + for (; iter != leftLiveWire->IteratorEnd(timeStep); iter++) { itk::Index<2> idx; this->m_WorkingSlice->GetGeometry()->WorldToIndex((*iter)->Coordinates, idx); this->m_LiveWireFilter->AddRepulsivePoint(idx); // add indices m_ContourBeingModified.push_back(idx); } // recompute right live wire, i.e. the contour between selected vertex and next active vertex this->m_LiveWireFilter->SetStartPoint(currentPosition); this->m_LiveWireFilter->SetEndPoint(m_NextActiveVertexUp); // update filter with all contour points set as void but the right live wire portion to be calculated now this->m_LiveWireFilter->Update(); mitk::ContourModel::Pointer rightLiveWire = this->m_LiveWireFilter->GetOutput(); assert(rightLiveWire); // reject strange paths - if (abs(rightLiveWire->GetNumberOfVertices(timestep) - leftLiveWire->GetNumberOfVertices(timestep)) > 50) + if (abs(rightLiveWire->GetNumberOfVertices(timeStep) - leftLiveWire->GetNumberOfVertices(timeStep)) > 50) { return; } - if (!leftLiveWire->IsEmpty(timestep)) - leftLiveWire->SetControlVertexAt(leftLiveWire->GetNumberOfVertices() - 1, timestep); + if (!leftLiveWire->IsEmpty(timeStep)) + leftLiveWire->SetControlVertexAt(leftLiveWire->GetNumberOfVertices() - 1, timeStep); - if (!rightLiveWire->IsEmpty(timestep)) - rightLiveWire->RemoveVertexAt(0, timestep); + if (!rightLiveWire->IsEmpty(timeStep)) + rightLiveWire->RemoveVertexAt(0, timeStep); - editingContour->Concatenate(rightLiveWire, timestep); + editingContour->Concatenate(rightLiveWire, timeStep); m_EditingContourNode->SetData(editingContour); mitk::ContourModel::Pointer newContour = mitk::ContourModel::New(); newContour->Expand(contour->GetTimeSteps()); + newContour->SetTimeGeometry(contour->GetTimeGeometry()->Clone()); // concatenate left original contour - newContour->Concatenate(this->m_ContourLeft, timestep); + newContour->Concatenate(this->m_ContourLeft, timeStep); - newContour->Concatenate(editingContour, timestep, true); + newContour->Concatenate(editingContour, timeStep, true); // set last inserted vertex as selected - newContour->SelectVertexAt(selectedVertexIndex, timestep); + newContour->SelectVertexAt(selectedVertexIndex, timeStep); // set as control point newContour->SetSelectedVertexAsControlPoint(true); // concatenate right original contour - newContour->Concatenate(this->m_ContourRight, timestep); + newContour->Concatenate(this->m_ContourRight, timeStep); - newContour->SetClosed(contour->IsClosed(timestep), timestep); + newContour->SetClosed(contour->IsClosed(timeStep), timeStep); this->GetDataNode()->SetData(newContour); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } bool mitk::ContourModelLiveWireInteractor::IsHovering(const InteractionEvent *interactionEvent) { const auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return false; - int timestep = positionEvent->GetSender()->GetTimeStep(); + const auto timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); auto *contour = dynamic_cast(this->GetDataNode()->GetData()); mitk::Point3D currentPosition = positionEvent->GetPositionInWorld(); bool isHover = false; this->GetDataNode()->GetBoolProperty("contour.hovering", isHover, positionEvent->GetSender()); - if (contour->IsNearContour(currentPosition, 1.5, timestep)) + if (contour->IsNearContour(currentPosition, 1.5, timeStep)) { if (isHover == false) { this->GetDataNode()->SetBoolProperty("contour.hovering", true); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } } else { if (isHover == true) { this->GetDataNode()->SetBoolProperty("contour.hovering", false); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } } return false; } int mitk::ContourModelLiveWireInteractor::SplitContourFromSelectedVertex(mitk::ContourModel *srcContour, mitk::ContourModel *destContour, bool fromSelectedUpwards, int timestep) { auto end = srcContour->IteratorEnd(); auto begin = srcContour->IteratorBegin(); // search next active control point to left and rigth and set as start and end point for filter auto itSelected = begin; // move iterator to position while ((*itSelected) != srcContour->GetSelectedVertex()) { itSelected++; } // CASE search upwards for next control point if (fromSelectedUpwards) { auto itUp = itSelected; if (itUp != end) { itUp++; // step once up otherwise the loop breaks immediately } while (itUp != end && !((*itUp)->IsControlPoint)) { itUp++; } auto it = itUp; if (itSelected != begin) { // copy the rest of the original contour while (it != end) { destContour->AddVertex((*it)->Coordinates, (*it)->IsControlPoint, timestep); it++; } } // else do not copy the contour // return the offset of iterator at one before next-vertex-upwards if (itUp != begin) { return std::distance(begin, itUp) - 1; } else { return std::distance(begin, itUp); } } else // CASE search downwards for next control point { auto itDown = itSelected; auto it = srcContour->IteratorBegin(); if (itSelected != begin) { if (itDown != begin) { itDown--; // step once down otherwise the the loop breaks immediately } while (itDown != begin && !((*itDown)->IsControlPoint)) { itDown--; } if (it != end) // if not empty { // always add the first vertex destContour->AddVertex((*it)->Coordinates, (*it)->IsControlPoint, timestep); it++; } // copy from begin to itDown while (it <= itDown) { destContour->AddVertex((*it)->Coordinates, (*it)->IsControlPoint, timestep); it++; } } else { // if selected vertex is the first element search from end of contour downwards itDown = end; itDown--; while (!((*itDown)->IsControlPoint) && itDown != begin) { itDown--; } // move one forward as we don't want the first control point it++; // move iterator to second control point while ((it != end) && !((*it)->IsControlPoint)) { it++; } // copy from begin to itDown while (it <= itDown) { // copy the contour from second control point to itDown destContour->AddVertex((*it)->Coordinates, (*it)->IsControlPoint, timestep); it++; } } /* //add vertex at itDown - it's not considered during while loop if( it != begin && it != end) { //destContour->AddVertex( (*it)->Coordinates, (*it)->IsControlPoint, timestep); } */ // return the offset of iterator at one after next-vertex-downwards if (itDown != end) { return std::distance(begin, itDown); // + 1;//index of next vertex } else { return std::distance(begin, itDown) - 1; } } } void mitk::ContourModelLiveWireInteractor::OnFinishEditing(StateMachineAction *, InteractionEvent *interactionEvent) { - int timestep = interactionEvent->GetSender()->GetTimeStep(); + const auto timeStep = interactionEvent->GetSender()->GetTimeStep(GetDataNode()->GetData()); auto *editingContour = dynamic_cast(this->m_EditingContourNode->GetData()); - editingContour->Clear(timestep); + editingContour->Clear(timeStep); mitk::RenderingManager::GetInstance()->RequestUpdate(interactionEvent->GetSender()->GetRenderWindow()); } diff --git a/Modules/Segmentation/Interactions/mitkContourTool.cpp b/Modules/Segmentation/Interactions/mitkContourTool.cpp index 3cc6e941fe..41ec690074 100644 --- a/Modules/Segmentation/Interactions/mitkContourTool.cpp +++ b/Modules/Segmentation/Interactions/mitkContourTool.cpp @@ -1,180 +1,111 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkContourTool.h" -#include "mitkAbstractTransformGeometry.h" -#include "mitkOverwriteDirectedPlaneImageFilter.h" -#include "mitkOverwriteSliceImageFilter.h" -#include "mitkToolManager.h" - -#include "mitkBaseRenderer.h" -#include "mitkRenderingManager.h" - -#include "mitkInteractionEvent.h" -#include "mitkStateMachineAction.h" - mitk::ContourTool::ContourTool(int paintingPixelValue) : FeedbackContourTool("PressMoveReleaseWithCTRLInversion"), m_PaintingPixelValue(paintingPixelValue) { } mitk::ContourTool::~ContourTool() { } void mitk::ContourTool::ConnectActionsAndFunctions() { CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed); CONNECT_FUNCTION("Move", OnMouseMoved); CONNECT_FUNCTION("Release", OnMouseReleased); CONNECT_FUNCTION("InvertLogic", OnInvertLogic); } void mitk::ContourTool::Activated() { Superclass::Activated(); } void mitk::ContourTool::Deactivated() { Superclass::Deactivated(); } /** Just show the contour, insert the first point. */ void mitk::ContourTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent) { auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; m_LastEventSender = positionEvent->GetSender(); m_LastEventSlice = m_LastEventSender->GetSlice(); - int timestep = positionEvent->GetSender()->GetTimeStep(); - - ContourModel *contour = FeedbackContourTool::GetFeedbackContour(); - // Clear feedback contour - contour->Initialize(); - // expand time bounds because our contour was initialized - contour->Expand(timestep + 1); - // draw as a closed contour - contour->SetClosed(true, timestep); - // add first mouse position + this->ClearsCurrentFeedbackContour(true); mitk::Point3D point = positionEvent->GetPositionInWorld(); - contour->AddVertex(point, timestep); + this->AddVertexToCurrentFeedbackContour(point); FeedbackContourTool::SetFeedbackContourVisible(true); assert(positionEvent->GetSender()->GetRenderWindow()); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } /** Insert the point to the feedback contour. */ void mitk::ContourTool::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent) { auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; - int timestep = positionEvent->GetSender()->GetTimeStep(); - - ContourModel *contour = FeedbackContourTool::GetFeedbackContour(); mitk::Point3D point = positionEvent->GetPositionInWorld(); - contour->AddVertex(point, timestep); + this->AddVertexToCurrentFeedbackContour(point); assert(positionEvent->GetSender()->GetRenderWindow()); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } /** Close the contour, project it to the image slice and fill it in 2D. */ void mitk::ContourTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent) { - // 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's - // working image corresponds to that - FeedbackContourTool::SetFeedbackContourVisible(false); - auto *positionEvent = dynamic_cast(interactionEvent); - // const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return; assert(positionEvent->GetSender()->GetRenderWindow()); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); - DataNode *workingNode(m_ToolManager->GetWorkingData(0)); - if (!workingNode) - return; - - auto workingImage = dynamic_cast(workingNode->GetData()); - const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry())); - if (!workingImage || !planeGeometry) - return; - - const auto *abstractTransformGeometry( - dynamic_cast(positionEvent->GetSender()->GetCurrentWorldPlaneGeometry())); - if (!workingImage || abstractTransformGeometry) - return; - - // 2. Slice is known, now we try to get it as a 2D image and project the contour into index coordinates of this slice - Image::Pointer slice = SegTool2D::GetAffectedImageSliceAs2DImage(positionEvent, workingImage); - - if (slice.IsNull()) - { - MITK_ERROR << "Unable to extract slice." << std::endl; - return; - } - - ContourModel *feedbackContour = FeedbackContourTool::GetFeedbackContour(); - ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice( - slice, feedbackContour, true, false); // true: actually no idea why this is neccessary, but it works :-( - - if (projectedContour.IsNull()) - return; - - int timestep = positionEvent->GetSender()->GetTimeStep(); - int activePixelValue = ContourModelUtils::GetActivePixelValue(workingImage); - - // m_PaintingPixelValue only decides whether to paint or erase - mitk::ContourModelUtils::FillContourInSlice( - projectedContour, timestep, slice, workingImage, m_PaintingPixelValue * activePixelValue); - - // this->WriteBackSegmentationResult(positionEvent, slice); - SegTool2D::WriteBackSegmentationResult(positionEvent, slice); - - // 4. Make sure the result is drawn again --> is visible then. - assert(positionEvent->GetSender()->GetRenderWindow()); + this->WriteBackFeedbackContourAsSegmentationResult(positionEvent, m_PaintingPixelValue); } /** Called when the CTRL key is pressed. Will change the painting pixel value from 0 to 1 or from 1 to 0. */ void mitk::ContourTool::OnInvertLogic(StateMachineAction *, InteractionEvent *) { // Inversion only for 0 and 1 as painting values if (m_PaintingPixelValue == 1) { m_PaintingPixelValue = 0; FeedbackContourTool::SetFeedbackContourColor(1.0, 0.0, 0.0); } else if (m_PaintingPixelValue == 0) { m_PaintingPixelValue = 1; FeedbackContourTool::SetFeedbackContourColorDefault(); } } diff --git a/Modules/Segmentation/Interactions/mitkCorrectorTool2D.cpp b/Modules/Segmentation/Interactions/mitkCorrectorTool2D.cpp deleted file mode 100644 index 0e928ed279..0000000000 --- a/Modules/Segmentation/Interactions/mitkCorrectorTool2D.cpp +++ /dev/null @@ -1,204 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -All rights reserved. - -Use of this source code is governed by a 3-clause BSD license that can be -found in the LICENSE file. - -============================================================================*/ - -#include "mitkCorrectorTool2D.h" -#include "mitkCorrectorAlgorithm.h" - -#include "mitkAbstractTransformGeometry.h" -#include "mitkBaseRenderer.h" -#include "mitkImageReadAccessor.h" -#include "mitkLabelSetImage.h" -#include "mitkRenderingManager.h" -#include "mitkToolManager.h" - -#include "mitkCorrectorTool2D.xpm" -#include "mitkLabelSetImage.h" - -// us -#include -#include -#include -#include - -namespace mitk -{ - MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, CorrectorTool2D, "Correction tool"); -} - -mitk::CorrectorTool2D::CorrectorTool2D(int paintingPixelValue) - : FeedbackContourTool("PressMoveRelease"), m_PaintingPixelValue(paintingPixelValue) -{ - GetFeedbackContour()->SetClosed(false); // don't close the contour to a polygon -} - -mitk::CorrectorTool2D::~CorrectorTool2D() -{ -} - -void mitk::CorrectorTool2D::ConnectActionsAndFunctions() -{ - CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed); - CONNECT_FUNCTION("Move", OnMouseMoved); - CONNECT_FUNCTION("Release", OnMouseReleased); -} - -const char **mitk::CorrectorTool2D::GetXPM() const -{ - return mitkCorrectorTool2D_xpm; -} - -us::ModuleResource mitk::CorrectorTool2D::GetIconResource() const -{ - us::Module *module = us::GetModuleContext()->GetModule(); - us::ModuleResource resource = module->GetResource("Correction_48x48.png"); - return resource; -} - -us::ModuleResource mitk::CorrectorTool2D::GetCursorIconResource() const -{ - us::Module *module = us::GetModuleContext()->GetModule(); - us::ModuleResource resource = module->GetResource("Correction_Cursor_32x32.png"); - return resource; -} - -const char *mitk::CorrectorTool2D::GetName() const -{ - return "Correction"; -} - -void mitk::CorrectorTool2D::Activated() -{ - Superclass::Activated(); -} - -void mitk::CorrectorTool2D::Deactivated() -{ - Superclass::Deactivated(); -} - -void mitk::CorrectorTool2D::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent) -{ - auto *positionEvent = dynamic_cast(interactionEvent); - if (!positionEvent) - return; - - m_LastEventSender = positionEvent->GetSender(); - m_LastEventSlice = m_LastEventSender->GetSlice(); - - int timestep = positionEvent->GetSender()->GetTimeStep(); - ContourModel *contour = FeedbackContourTool::GetFeedbackContour(); - contour->Initialize(); - contour->Expand(timestep + 1); - contour->SetClosed(false, timestep); - mitk::Point3D point = positionEvent->GetPositionInWorld(); - contour->AddVertex(point, timestep); - - FeedbackContourTool::SetFeedbackContourVisible(true); -} - -void mitk::CorrectorTool2D::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent) -{ - auto *positionEvent = dynamic_cast(interactionEvent); - if (!positionEvent) - return; - - int timestep = positionEvent->GetSender()->GetTimeStep(); - ContourModel *contour = FeedbackContourTool::GetFeedbackContour(); - mitk::Point3D point = positionEvent->GetPositionInWorld(); - contour->AddVertex(point, timestep); - - assert(positionEvent->GetSender()->GetRenderWindow()); - mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); -} - -void mitk::CorrectorTool2D::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent) -{ - // 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's - // working image corresponds to that - FeedbackContourTool::SetFeedbackContourVisible(false); - - auto *positionEvent = dynamic_cast(interactionEvent); - // const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); - if (!positionEvent) - return; - - assert(positionEvent->GetSender()->GetRenderWindow()); - mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); - - DataNode *workingNode(m_ToolManager->GetWorkingData(0)); - if (!workingNode) - return; - - auto *workingImage = dynamic_cast(workingNode->GetData()); - const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry())); - if (!workingImage || !planeGeometry) - return; - - const auto *abstractTransformGeometry( - dynamic_cast(positionEvent->GetSender()->GetCurrentWorldPlaneGeometry())); - if (!workingImage || abstractTransformGeometry) - return; - - // 2. Slice is known, now we try to get it as a 2D image and project the contour into index coordinates of this slice - m_WorkingSlice = FeedbackContourTool::GetAffectedImageSliceAs2DImage(positionEvent, workingImage); - - if (m_WorkingSlice.IsNull()) - { - MITK_ERROR << "Unable to extract slice." << std::endl; - return; - } - - int timestep = positionEvent->GetSender()->GetTimeStep(); - mitk::ContourModel::Pointer singleTimestepContour = mitk::ContourModel::New(); - - auto it = FeedbackContourTool::GetFeedbackContour()->Begin(timestep); - auto end = FeedbackContourTool::GetFeedbackContour()->End(timestep); - - while (it != end) - { - singleTimestepContour->AddVertex((*it)->Coordinates); - it++; - } - - CorrectorAlgorithm::Pointer algorithm = CorrectorAlgorithm::New(); - algorithm->SetInput(m_WorkingSlice); - algorithm->SetContour(singleTimestepContour); - - int activePixelValue = ContourModelUtils::GetActivePixelValue(workingImage); - algorithm->SetFillColor(activePixelValue); - - try - { - algorithm->UpdateLargestPossibleRegion(); - } - catch (std::exception &e) - { - MITK_ERROR << "Caught exception '" << e.what() << "'" << std::endl; - } - - mitk::Image::Pointer resultSlice = mitk::Image::New(); - resultSlice->Initialize(algorithm->GetOutput()); - - auto* labelSetImage = dynamic_cast(workingImage); - if (nullptr != labelSetImage) - { - mitk::Image::Pointer erg1 = FeedbackContourTool::GetAffectedImageSliceAs2DImage(positionEvent, workingImage); - SegTool2D::WritePreviewOnWorkingImage(erg1, algorithm->GetOutput(), workingImage, activePixelValue, 0); - SegTool2D::WriteBackSegmentationResult(positionEvent, erg1); - } - else - { - mitk::ImageReadAccessor imAccess(algorithm->GetOutput()); - resultSlice->SetVolume(imAccess.GetData()); - this->WriteBackSegmentationResult(positionEvent, resultSlice); - } -} diff --git a/Modules/Segmentation/Interactions/mitkCorrectorTool2D.h b/Modules/Segmentation/Interactions/mitkCorrectorTool2D.h deleted file mode 100644 index da1147cd25..0000000000 --- a/Modules/Segmentation/Interactions/mitkCorrectorTool2D.h +++ /dev/null @@ -1,84 +0,0 @@ -/*============================================================================ - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center (DKFZ) -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 mitkCorrectorTool2D_h_Included -#define mitkCorrectorTool2D_h_Included - -#include "mitkCommon.h" -#include "mitkFeedbackContourTool.h" -#include - -namespace us -{ - class ModuleResource; -} - -namespace mitk -{ - class Image; - class StateMachineAction; - class InteractionEvent; - - /** - \brief Corrector tool for 2D binary segmentations - - \sa FeedbackContourTool - \sa ExtractImageFilter - \sa OverwriteSliceImageFilter - - \ingroup Interaction - \ingroup ToolManagerEtAl - - Lets the user draw a (multi-point) line and intelligently decides what to do. The underlying algorithm - tests if the line begins and ends inside or outside a segmentation and either adds or subtracts a piece of - segmentation. - - Algorithm is implemented in CorrectorAlgorithm (so that it could be reimplemented in a more modern fashion some - time). - - \warning Only to be instantiated by mitk::ToolManager. - - $Author$ - */ - class MITKSEGMENTATION_EXPORT CorrectorTool2D : public FeedbackContourTool - { - public: - mitkClassMacro(CorrectorTool2D, FeedbackContourTool); - itkFactorylessNewMacro(Self); - itkCloneMacro(Self); - - const char **GetXPM() const override; - us::ModuleResource GetCursorIconResource() const override; - us::ModuleResource GetIconResource() const override; - - const char *GetName() const override; - - protected: - CorrectorTool2D(int paintingPixelValue = 1); // purposely hidden - ~CorrectorTool2D() override; - - void ConnectActionsAndFunctions() override; - - void Activated() override; - void Deactivated() override; - - virtual void OnMousePressed(StateMachineAction *, InteractionEvent *); - virtual void OnMouseMoved(StateMachineAction *, InteractionEvent *); - virtual void OnMouseReleased(StateMachineAction *, InteractionEvent *); - int m_PaintingPixelValue; - - Image::Pointer m_WorkingSlice; - }; - -} // namespace - -#endif diff --git a/Modules/Segmentation/Interactions/mitkCorrectorTool2D.xpm b/Modules/Segmentation/Interactions/mitkCorrectorTool2D.xpm deleted file mode 100644 index 4e9c2f50f1..0000000000 --- a/Modules/Segmentation/Interactions/mitkCorrectorTool2D.xpm +++ /dev/null @@ -1,38 +0,0 @@ -/* XPM */ -static const char * mitkCorrectorTool2D_xpm[] = { -/* columns rows colors chars-per-pixel */ -"24 24 8 1", -" c #00A9D3", -". c #00AAD2", -"X c #00ABD2", -"o c #00AAD3", -"O c #00ABD3", -"+ c #00AAD4", -"@ c #00ABD5", -"# c None", -/* pixels */ -"########################", -"########################", -"########################", -"####################X###", -"###O oooooO#########o###", -"###################o####", -"##################o#####", -"#################o######", -"############### oo######", -"#############ooo########", -"###########+o ##########", -"########oo+#############", -"######oo################", -"##################o#####", -"####o############@o#####", -"###o#############@o#####", -"###o########### oo+ +##", -"##o###########.o.ooo..##", -"##o##############@o#####", -"#################@o#####", -"##o##############O #####", -"########################", -"########################", -"########################" -}; diff --git a/Modules/Segmentation/Interactions/mitkDrawPaintbrushTool.cpp b/Modules/Segmentation/Interactions/mitkDrawPaintbrushTool.cpp index 9f15b3765d..644e2de507 100644 --- a/Modules/Segmentation/Interactions/mitkDrawPaintbrushTool.cpp +++ b/Modules/Segmentation/Interactions/mitkDrawPaintbrushTool.cpp @@ -1,58 +1,59 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkDrawPaintbrushTool.h" #include "mitkDrawPaintbrushTool.xpm" // us #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, DrawPaintbrushTool, "Paintbrush drawing tool"); } mitk::DrawPaintbrushTool::DrawPaintbrushTool() : PaintbrushTool(1) { + FeedbackContourTool::SetFeedbackContourColorDefault(); } mitk::DrawPaintbrushTool::~DrawPaintbrushTool() { } const char **mitk::DrawPaintbrushTool::GetXPM() const { return mitkDrawPaintbrushTool_xpm; } us::ModuleResource mitk::DrawPaintbrushTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("Paint_48x48.png"); return resource; } us::ModuleResource mitk::DrawPaintbrushTool::GetCursorIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("Paint_Cursor_32x32.png"); return resource; } const char *mitk::DrawPaintbrushTool::GetName() const { return "Paint"; } diff --git a/Modules/Segmentation/Interactions/mitkFastMarchingBaseTool.cpp b/Modules/Segmentation/Interactions/mitkFastMarchingBaseTool.cpp new file mode 100644 index 0000000000..1ded558ddc --- /dev/null +++ b/Modules/Segmentation/Interactions/mitkFastMarchingBaseTool.cpp @@ -0,0 +1,335 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#include "mitkFastMarchingBaseTool.h" +#include "mitkToolManager.h" + +#include "mitkBaseRenderer.h" +#include "mitkInteractionConst.h" +#include "mitkRenderingManager.h" +#include "mitkInteractionPositionEvent.h" + +#include "mitkImageAccessByItk.h" + +#include "mitkSegTool2D.h" + +#include + +// itk filter +#include "itkBinaryThresholdImageFilter.h" +#include "itkCurvatureAnisotropicDiffusionImageFilter.h" +#include "itkGradientMagnitudeRecursiveGaussianImageFilter.h" +#include "itkSigmoidImageFilter.h" + +// us +#include +#include +#include +#include + + +mitk::FastMarchingBaseTool::FastMarchingBaseTool(unsigned int toolDim) + : AutoSegmentationWithPreviewTool(false, "FastMarchingTool"), + m_LowerThreshold(0), + m_UpperThreshold(200), + m_StoppingValue(100), + m_Sigma(1.0), + m_Alpha(-0.5), + m_Beta(3.0), + m_ToolDimension(toolDim) +{ +} + +mitk::FastMarchingBaseTool::~FastMarchingBaseTool() +{ +} + +bool mitk::FastMarchingBaseTool::CanHandle(const BaseData* referenceData, const BaseData* workingData) const +{ + if(!Superclass::CanHandle(referenceData, workingData)) + return false; + + if (referenceData == nullptr) + return false; + + auto *image = dynamic_cast(referenceData); + + if (image == nullptr) + return false; + + if (image->GetDimension() < 3) + return false; + + return true; +} + +const char **mitk::FastMarchingBaseTool::GetXPM() const +{ + return nullptr; // mitkFastMarchingBaseTool_xpm; +} + +us::ModuleResource mitk::FastMarchingBaseTool::GetIconResource() const +{ + us::Module *module = us::GetModuleContext()->GetModule(); + us::ModuleResource resource = module->GetResource("FastMarching_48x48.png"); + return resource; +} + +us::ModuleResource mitk::FastMarchingBaseTool::GetCursorIconResource() const +{ + us::Module* module = us::GetModuleContext()->GetModule(); + us::ModuleResource resource = module->GetResource("FastMarching_Cursor_32x32.png"); + return resource; +} + +void mitk::FastMarchingBaseTool::SetUpperThreshold(double value) +{ + m_UpperThreshold = value / 10.0; +} + +void mitk::FastMarchingBaseTool::SetLowerThreshold(double value) +{ + m_LowerThreshold = value / 10.0; +} + +void mitk::FastMarchingBaseTool::SetBeta(double value) +{ + if (m_Beta != value) + { + m_Beta = value; + } +} + +void mitk::FastMarchingBaseTool::SetSigma(double value) +{ + if (m_Sigma != value) + { + if (value > 0.0) + { + m_Sigma = value; + } + } +} + +void mitk::FastMarchingBaseTool::SetAlpha(double value) +{ + if (m_Alpha != value) + { + m_Alpha = value; + } +} + +void mitk::FastMarchingBaseTool::SetStoppingValue(double value) +{ + if (m_StoppingValue != value) + { + m_StoppingValue = value; + } +} + +void mitk::FastMarchingBaseTool::Activated() +{ + Superclass::Activated(); + + m_SeedsAsPointSet = mitk::PointSet::New(); + //ensure that the seed points are visible for all timepoints. + dynamic_cast(m_SeedsAsPointSet->GetTimeGeometry())->SetStepDuration(std::numeric_limits::max()); + + m_SeedsAsPointSetNode = mitk::DataNode::New(); + m_SeedsAsPointSetNode->SetData(m_SeedsAsPointSet); + m_SeedsAsPointSetNode->SetName(std::string(this->GetName()) + "_PointSet"); + m_SeedsAsPointSetNode->SetBoolProperty("helper object", true); + m_SeedsAsPointSetNode->SetColor(0.0, 1.0, 0.0); + m_SeedsAsPointSetNode->SetVisibility(true); + + m_ToolManager->GetDataStorage()->Add(m_SeedsAsPointSetNode, m_ToolManager->GetWorkingData(0)); +} + +void mitk::FastMarchingBaseTool::Deactivated() +{ + this->ClearSeeds(); + + m_ToolManager->GetDataStorage()->Remove(m_SeedsAsPointSetNode); + m_SeedsAsPointSetNode = nullptr; + m_SeedsAsPointSet = nullptr; + + Superclass::Deactivated(); +} + +void mitk::FastMarchingBaseTool::ConnectActionsAndFunctions() +{ + CONNECT_FUNCTION("ShiftSecondaryButtonPressed", OnAddPoint); + CONNECT_FUNCTION("ShiftPrimaryButtonPressed", OnAddPoint); + CONNECT_FUNCTION("DeletePoint", OnDelete); +} + +void mitk::FastMarchingBaseTool::OnAddPoint(StateMachineAction*, InteractionEvent* interactionEvent) +{ + if (!this->IsUpdating() && m_SeedsAsPointSet.IsNotNull()) + { + const auto positionEvent = dynamic_cast(interactionEvent); + + if (positionEvent != nullptr) + { + auto workingPlaneGeometry = positionEvent->GetSender()->GetCurrentWorldPlaneGeometry(); + + // if click was on another plane and we are in 2D mode we should reset the seeds + if (m_ToolDimension == 2 && ( nullptr == this->GetWorkingPlaneGeometry() || !this->GetWorkingPlaneGeometry()->IsOnPlane(workingPlaneGeometry))) + { + this->ClearSeeds(); + this->SetWorkingPlaneGeometry(workingPlaneGeometry->Clone()); + } + + m_SeedsAsPointSet->InsertPoint(m_SeedsAsPointSet->GetSize(), positionEvent->GetPositionInWorld()); + + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + + this->UpdatePreview(); + } + } +} + +void mitk::FastMarchingBaseTool::OnDelete(StateMachineAction*, InteractionEvent* /*interactionEvent*/) +{ + if (!this->IsUpdating() && m_SeedsAsPointSet.IsNotNull()) + { + // delete last seed point + if (this->m_SeedsAsPointSet->GetSize() > 0) + { + m_SeedsAsPointSet->RemovePointAtEnd(0); + + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + + this->UpdatePreview(); + } + } +} + +void mitk::FastMarchingBaseTool::ClearSeeds() +{ + if (this->m_SeedsAsPointSet.IsNotNull()) + { + // renew pointset + this->m_SeedsAsPointSet = mitk::PointSet::New(); + //ensure that the seed points are visible for all timepoints. + dynamic_cast(m_SeedsAsPointSet->GetTimeGeometry())->SetStepDuration(std::numeric_limits::max()); + this->m_SeedsAsPointSetNode->SetData(this->m_SeedsAsPointSet); + } +} + +template +void mitk::FastMarchingBaseTool::DoITKFastMarching(const itk::Image* inputImage, + Image* previewImage, unsigned int timeStep, const BaseGeometry* inputGeometry) +{ + // typedefs for itk pipeline + typedef itk::Image InputImageType; + + typedef float InternalPixelType; + typedef itk::Image InternalImageType; + + typedef mitk::Tool::DefaultSegmentationDataType OutputPixelType; + typedef itk::Image OutputImageType; + + typedef itk::CurvatureAnisotropicDiffusionImageFilter SmoothingFilterType; + typedef itk::GradientMagnitudeRecursiveGaussianImageFilter GradientFilterType; + typedef itk::SigmoidImageFilter SigmoidFilterType; + typedef itk::BinaryThresholdImageFilter ThresholdingFilterType; + + typedef itk::FastMarchingImageFilter FastMarchingFilterType; + typedef typename FastMarchingFilterType::NodeContainer NodeContainer; + typedef typename FastMarchingFilterType::NodeType NodeType; + + //convert point set seed into trialpoint + typename NodeContainer::Pointer trialPoints = NodeContainer::New(); + trialPoints->Initialize(); + + for (auto pos = m_SeedsAsPointSet->Begin(); pos != m_SeedsAsPointSet->End(); ++pos) + { + mitk::Point3D clickInIndex; + + inputGeometry->WorldToIndex(pos->Value(), clickInIndex); + itk::Index seedPosition; + for (unsigned int dim = 0; dim < VImageDimension; ++dim) + { + seedPosition[dim] = clickInIndex[dim]; + } + + NodeType node; + const double seedValue = 0.0; + node.SetValue(seedValue); + node.SetIndex(seedPosition); + trialPoints->InsertElement(trialPoints->Size(), node); + } + + // assemble pipeline + auto smoothFilter = SmoothingFilterType::New(); + smoothFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand); + smoothFilter->SetTimeStep(0.05); + smoothFilter->SetNumberOfIterations(2); + smoothFilter->SetConductanceParameter(9.0); + + auto gradientMagnitudeFilter = GradientFilterType::New(); + gradientMagnitudeFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand); + gradientMagnitudeFilter->SetSigma(m_Sigma); + + auto sigmoidFilter = SigmoidFilterType::New(); + sigmoidFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand); + sigmoidFilter->SetAlpha(m_Alpha); + sigmoidFilter->SetBeta(m_Beta); + sigmoidFilter->SetOutputMinimum(0.0); + sigmoidFilter->SetOutputMaximum(1.0); + + auto fastMarchingFilter = FastMarchingFilterType::New(); + fastMarchingFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand); + fastMarchingFilter->SetStoppingValue(m_StoppingValue); + fastMarchingFilter->SetTrialPoints(trialPoints); + + auto thresholdFilter = ThresholdingFilterType::New(); + thresholdFilter->SetLowerThreshold(m_LowerThreshold); + thresholdFilter->SetUpperThreshold(m_UpperThreshold); + thresholdFilter->SetOutsideValue(0); + thresholdFilter->SetInsideValue(1.0); + + // set up pipeline + smoothFilter->SetInput(inputImage); + gradientMagnitudeFilter->SetInput(smoothFilter->GetOutput()); + sigmoidFilter->SetInput(gradientMagnitudeFilter->GetOutput()); + fastMarchingFilter->SetInput(sigmoidFilter->GetOutput()); + thresholdFilter->SetInput(fastMarchingFilter->GetOutput()); + thresholdFilter->Update(); + + if (nullptr == this->GetWorkingPlaneGeometry()) + { + previewImage->SetVolume((void*)(thresholdFilter->GetOutput()->GetPixelContainer()->GetBufferPointer()), timeStep); + } + else + { + mitk::Image::Pointer sliceImage = mitk::Image::New(); + mitk::CastToMitkImage(thresholdFilter->GetOutput(), sliceImage); + SegTool2D::WriteSliceToVolume(previewImage, this->GetWorkingPlaneGeometry(), sliceImage, timeStep, false); + } +} + +void mitk::FastMarchingBaseTool::DoUpdatePreview(const Image* inputAtTimeStep, Image* previewImage, TimeStepType timeStep) +{ + if (nullptr != inputAtTimeStep && nullptr != previewImage && m_SeedsAsPointSet.IsNotNull() && m_SeedsAsPointSet->GetSize()>0) + { + if (nullptr == this->GetWorkingPlaneGeometry()) + { + AccessFixedDimensionByItk_n(inputAtTimeStep, DoITKFastMarching, 3, (previewImage, timeStep, inputAtTimeStep->GetGeometry())); + } + else + { + AccessFixedDimensionByItk_n(inputAtTimeStep, DoITKFastMarching, 2, (previewImage, timeStep, inputAtTimeStep->GetGeometry())); + } + } +} diff --git a/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.h b/Modules/Segmentation/Interactions/mitkFastMarchingBaseTool.h similarity index 67% copy from Modules/Segmentation/Interactions/mitkFastMarchingTool3D.h copy to Modules/Segmentation/Interactions/mitkFastMarchingBaseTool.h index 652e0d550b..ebec9fd0b2 100644 --- a/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.h +++ b/Modules/Segmentation/Interactions/mitkFastMarchingBaseTool.h @@ -1,124 +1,118 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkFastMarchingTool3D_h_Included -#define mitkFastMarchingTool3D_h_Included +#ifndef mitkFastMarchingBaseTool_h_Included +#define mitkFastMarchingBaseTool_h_Included #include "mitkAutoSegmentationWithPreviewTool.h" #include "mitkDataNode.h" #include "mitkPointSet.h" #include "mitkPointSetDataInteractor.h" #include "mitkToolCommand.h" #include "itkImage.h" #include "itkFastMarchingImageFilter.h" #include namespace us { class ModuleResource; } namespace mitk { /** - \brief FastMarching semgentation tool. + \brief FastMarching semgentation tool base class. The segmentation is done by setting one or more seed points on the image and adapting the time range and threshold. The pipeline is: Smoothing->GradientMagnitude->SigmoidFunction->FastMarching->Threshold The resulting binary image is seen as a segmentation of an object. For detailed documentation see ITK Software Guide section 9.3.1 Fast Marching Segmentation. */ - class MITKSEGMENTATION_EXPORT FastMarchingTool3D : public AutoSegmentationWithPreviewTool + class MITKSEGMENTATION_EXPORT FastMarchingBaseTool : public AutoSegmentationWithPreviewTool { public: - mitkClassMacro(FastMarchingTool3D, AutoSegmentationWithPreviewTool); - itkFactorylessNewMacro(Self); - itkCloneMacro(Self); + mitkClassMacro(FastMarchingBaseTool, AutoSegmentationWithPreviewTool); bool CanHandle(const BaseData* referenceData, const BaseData* workingData) const override; /* icon stuff */ const char **GetXPM() const override; - const char *GetName() const override; + us::ModuleResource GetCursorIconResource() const override; us::ModuleResource GetIconResource() const override; void Activated() override; void Deactivated() override; /// \brief Set parameter used in Threshold filter. void SetUpperThreshold(double); /// \brief Set parameter used in Threshold filter. void SetLowerThreshold(double); /// \brief Set parameter used in Fast Marching filter. void SetStoppingValue(double); /// \brief Set parameter used in Gradient Magnitude filter. void SetSigma(double); /// \brief Set parameter used in Fast Marching filter. void SetAlpha(double); /// \brief Set parameter used in Fast Marching filter. void SetBeta(double); /// \brief Clear all seed points. void ClearSeeds(); + protected: - FastMarchingTool3D(); - ~FastMarchingTool3D() override; + FastMarchingBaseTool(unsigned int toolDim); + ~FastMarchingBaseTool() override; + + void ConnectActionsAndFunctions() override; /// \brief Add point action of StateMachine pattern - virtual void OnAddPoint(); + virtual void OnAddPoint(StateMachineAction*, InteractionEvent* interactionEvent); /// \brief Delete action of StateMachine pattern - virtual void OnDelete(); + virtual void OnDelete(StateMachineAction*, InteractionEvent* interactionEvent); - void UpdatePrepare() override; - void UpdateCleanUp() override; void DoUpdatePreview(const Image* inputAtTimeStep, Image* previewImage, TimeStepType timeStep) override; template void DoITKFastMarching(const itk::Image* inputImage, - mitk::Image* segmentation, unsigned int timeStep); + Image* segmentation, unsigned int timeStep, const BaseGeometry* inputGeometry); float m_LowerThreshold; // used in Threshold filter float m_UpperThreshold; // used in Threshold filter float m_StoppingValue; // used in Fast Marching filter float m_Sigma; // used in GradientMagnitude filter float m_Alpha; // used in Sigmoid filter float m_Beta; // used in Sigmoid filter - typedef float InternalPixelType; - typedef itk::Image InternalImageType; - typedef itk::FastMarchingImageFilter FastMarchingFilterType; - typedef FastMarchingFilterType::NodeContainer NodeContainer; - typedef FastMarchingFilterType::NodeType NodeType; + DataNode::Pointer m_SeedsAsPointSetNode; // used to visualize the seed points + PointSet::Pointer m_SeedsAsPointSet; - NodeContainer::Pointer m_SeedContainer; // seed points for FastMarching + private: + /** Indicating if the tool is used in 2D mode (just segment the current slice) + * or 3D mode (segment the whole current volume),*/ + unsigned int m_ToolDimension; - mitk::DataNode::Pointer m_SeedsAsPointSetNode; // used to visualize the seed points - mitk::PointSet::Pointer m_SeedsAsPointSet; - mitk::PointSetDataInteractor::Pointer m_SeedPointInteractor; - unsigned int m_PointSetAddObserverTag; - unsigned int m_PointSetRemoveObserverTag; }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkFastMarchingTool.cpp b/Modules/Segmentation/Interactions/mitkFastMarchingTool.cpp index b4220d6acb..95eb57c850 100644 --- a/Modules/Segmentation/Interactions/mitkFastMarchingTool.cpp +++ b/Modules/Segmentation/Interactions/mitkFastMarchingTool.cpp @@ -1,483 +1,34 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkFastMarchingTool.h" -#include "mitkToolManager.h" -#include "mitkBaseRenderer.h" -#include "mitkInteractionConst.h" -#include "mitkRenderingManager.h" - -#include "itkOrImageFilter.h" -#include "mitkImageTimeSelector.h" - -// us -#include -#include -#include -#include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, FastMarchingTool, "FastMarching2D tool"); } mitk::FastMarchingTool::FastMarchingTool() - : FeedbackContourTool("FastMarchingTool"), - m_NeedUpdate(true), - m_CurrentTimeStep(0), - m_PositionEvent(nullptr), - m_LowerThreshold(0), - m_UpperThreshold(200), - m_StoppingValue(100), - m_Sigma(1.0), - m_Alpha(-0.5), - m_Beta(3.0) + : FastMarchingBaseTool(2) { } mitk::FastMarchingTool::~FastMarchingTool() { - if (this->m_SmoothFilter.IsNotNull()) - this->m_SmoothFilter->RemoveAllObservers(); - - if (this->m_SigmoidFilter.IsNotNull()) - this->m_SigmoidFilter->RemoveAllObservers(); - - if (this->m_GradientMagnitudeFilter.IsNotNull()) - this->m_GradientMagnitudeFilter->RemoveAllObservers(); - - if (this->m_FastMarchingFilter.IsNotNull()) - this->m_FastMarchingFilter->RemoveAllObservers(); -} - -void mitk::FastMarchingTool::ConnectActionsAndFunctions() -{ - CONNECT_FUNCTION("ShiftSecondaryButtonPressed", OnAddPoint); - CONNECT_FUNCTION("ShiftPrimaryButtonPressed", OnAddPoint); - CONNECT_FUNCTION("DeletePoint", OnDelete); -} - -const char **mitk::FastMarchingTool::GetXPM() const -{ - return nullptr; // mitkFastMarchingTool_xpm; -} - -us::ModuleResource mitk::FastMarchingTool::GetIconResource() const -{ - us::Module *module = us::GetModuleContext()->GetModule(); - us::ModuleResource resource = module->GetResource("FastMarching_48x48.png"); - return resource; -} - -us::ModuleResource mitk::FastMarchingTool::GetCursorIconResource() const -{ - us::Module *module = us::GetModuleContext()->GetModule(); - us::ModuleResource resource = module->GetResource("FastMarching_Cursor_32x32.png"); - return resource; } const char *mitk::FastMarchingTool::GetName() const { return "2D Fast Marching"; } -void mitk::FastMarchingTool::BuildITKPipeline() -{ - m_ReferenceImageSliceAsITK = InternalImageType::New(); - - m_ReferenceImageSlice = GetAffectedReferenceSlice(m_PositionEvent); - CastToItkImage(m_ReferenceImageSlice, m_ReferenceImageSliceAsITK); - - m_ProgressCommand = mitk::ToolCommand::New(); - - m_SmoothFilter = SmoothingFilterType::New(); - m_SmoothFilter->SetInput(m_ReferenceImageSliceAsITK); - m_SmoothFilter->SetTimeStep(0.05); - m_SmoothFilter->SetNumberOfIterations(2); - m_SmoothFilter->SetConductanceParameter(9.0); - - m_GradientMagnitudeFilter = GradientFilterType::New(); - m_GradientMagnitudeFilter->SetSigma(m_Sigma); - - m_SigmoidFilter = SigmoidFilterType::New(); - m_SigmoidFilter->SetAlpha(m_Alpha); - m_SigmoidFilter->SetBeta(m_Beta); - m_SigmoidFilter->SetOutputMinimum(0.0); - m_SigmoidFilter->SetOutputMaximum(1.0); - - m_FastMarchingFilter = FastMarchingFilterType::New(); - m_FastMarchingFilter->SetStoppingValue(m_StoppingValue); - - m_ThresholdFilter = ThresholdingFilterType::New(); - m_ThresholdFilter->SetLowerThreshold(m_LowerThreshold); - m_ThresholdFilter->SetUpperThreshold(m_UpperThreshold); - m_ThresholdFilter->SetOutsideValue(0); - m_ThresholdFilter->SetInsideValue(1.0); - - m_SeedContainer = NodeContainer::New(); - m_SeedContainer->Initialize(); - m_FastMarchingFilter->SetTrialPoints(m_SeedContainer); - - if (this->m_SmoothFilter.IsNotNull()) - this->m_SmoothFilter->RemoveAllObservers(); - - if (this->m_SigmoidFilter.IsNotNull()) - this->m_SigmoidFilter->RemoveAllObservers(); - - if (this->m_GradientMagnitudeFilter.IsNotNull()) - this->m_GradientMagnitudeFilter->RemoveAllObservers(); - - if (this->m_FastMarchingFilter.IsNotNull()) - this->m_FastMarchingFilter->RemoveAllObservers(); - - m_SmoothFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand); - m_GradientMagnitudeFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand); - m_SigmoidFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand); - m_FastMarchingFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand); - - m_SmoothFilter->SetInput(m_ReferenceImageSliceAsITK); - m_GradientMagnitudeFilter->SetInput(m_SmoothFilter->GetOutput()); - m_SigmoidFilter->SetInput(m_GradientMagnitudeFilter->GetOutput()); - m_FastMarchingFilter->SetInput(m_SigmoidFilter->GetOutput()); - m_ThresholdFilter->SetInput(m_FastMarchingFilter->GetOutput()); - m_ReferenceImageSliceAsITK = InternalImageType::New(); -} - -void mitk::FastMarchingTool::SetUpperThreshold(double value) -{ - if (m_UpperThreshold != value) - { - m_UpperThreshold = value / 10.0; - m_ThresholdFilter->SetUpperThreshold(m_UpperThreshold); - m_NeedUpdate = true; - } -} - -void mitk::FastMarchingTool::SetLowerThreshold(double value) -{ - if (m_LowerThreshold != value) - { - m_LowerThreshold = value / 10.0; - m_ThresholdFilter->SetLowerThreshold(m_LowerThreshold); - m_NeedUpdate = true; - } -} - -void mitk::FastMarchingTool::SetBeta(double value) -{ - if (m_Beta != value) - { - m_Beta = value; - m_SigmoidFilter->SetBeta(m_Beta); - m_NeedUpdate = true; - } -} - -void mitk::FastMarchingTool::SetSigma(double value) -{ - if (m_Sigma != value) - { - m_Sigma = value; - m_GradientMagnitudeFilter->SetSigma(m_Sigma); - m_NeedUpdate = true; - } -} - -void mitk::FastMarchingTool::SetAlpha(double value) -{ - if (m_Alpha != value) - { - m_Alpha = value; - m_SigmoidFilter->SetAlpha(m_Alpha); - m_NeedUpdate = true; - } -} - -void mitk::FastMarchingTool::SetStoppingValue(double value) -{ - if (m_StoppingValue != value) - { - m_StoppingValue = value; - m_FastMarchingFilter->SetStoppingValue(m_StoppingValue); - m_NeedUpdate = true; - } -} - -void mitk::FastMarchingTool::Activated() -{ - Superclass::Activated(); - - m_ResultImageNode = mitk::DataNode::New(); - m_ResultImageNode->SetName("FastMarching_Preview"); - m_ResultImageNode->SetBoolProperty("helper object", true); - m_ResultImageNode->SetColor(0.0, 1.0, 0.0); - m_ResultImageNode->SetVisibility(true); - m_ToolManager->GetDataStorage()->Add(this->m_ResultImageNode, m_ToolManager->GetReferenceData(0)); - - m_SeedsAsPointSet = mitk::PointSet::New(); - m_SeedsAsPointSetNode = mitk::DataNode::New(); - m_SeedsAsPointSetNode->SetData(m_SeedsAsPointSet); - m_SeedsAsPointSetNode->SetName("Seeds_Preview"); - m_SeedsAsPointSetNode->SetBoolProperty("helper object", true); - m_SeedsAsPointSetNode->SetColor(0.0, 1.0, 0.0); - m_SeedsAsPointSetNode->SetVisibility(true); - m_ToolManager->GetDataStorage()->Add(this->m_SeedsAsPointSetNode, m_ToolManager->GetReferenceData(0)); - - this->Initialize(); -} - -void mitk::FastMarchingTool::Deactivated() -{ - m_ToolManager->GetDataStorage()->Remove(this->m_ResultImageNode); - m_ToolManager->GetDataStorage()->Remove(this->m_SeedsAsPointSetNode); - this->ClearSeeds(); - m_ResultImageNode = nullptr; - m_SeedsAsPointSetNode = nullptr; - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - - Superclass::Deactivated(); -} - -void mitk::FastMarchingTool::Initialize() -{ - m_ReferenceImage = dynamic_cast(m_ToolManager->GetReferenceData(0)->GetData()); - if (m_ReferenceImage->GetTimeGeometry()->CountTimeSteps() > 1) - { - mitk::ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New(); - timeSelector->SetInput(m_ReferenceImage); - timeSelector->SetTimeNr(m_CurrentTimeStep); - timeSelector->UpdateLargestPossibleRegion(); - m_ReferenceImage = timeSelector->GetOutput(); - } - m_NeedUpdate = true; -} - -void mitk::FastMarchingTool::ConfirmSegmentation() -{ - // combine preview image with current working segmentation - if (dynamic_cast(m_ResultImageNode->GetData())) - { - // logical or combination of preview and segmentation slice - - Image::Pointer workingImageSlice; - - Image::Pointer workingImage = dynamic_cast(this->m_ToolManager->GetWorkingData(0)->GetData()); - TimePointType referenceImageTimePoint = m_ReferenceImage->GetTimeGeometry()->TimeStepToTimePoint(m_CurrentTimeStep); - TimeStepType workingImageTimeStep = workingImage->GetTimeGeometry()->TimePointToTimeStep(referenceImageTimePoint); - workingImageSlice = GetAffectedImageSliceAs2DImage(m_WorkingPlane, workingImage, workingImageTimeStep); - - Image::Pointer segmentationResult = Image::New(); - - bool isDeprecatedUnsignedCharSegmentation = - (workingImage->GetPixelType().GetComponentType() == itk::ImageIOBase::UCHAR); - - if (isDeprecatedUnsignedCharSegmentation) - { - typedef itk::Image OutputUCharImageType; - OutputUCharImageType::Pointer workingImageSliceInITK = OutputUCharImageType::New(); - - CastToItkImage(workingImageSlice, workingImageSliceInITK); - - typedef itk::OrImageFilter OrImageFilterType; - OrImageFilterType::Pointer orFilter = OrImageFilterType::New(); - - orFilter->SetInput1(m_ThresholdFilter->GetOutput()); - orFilter->SetInput2(workingImageSliceInITK); - orFilter->Update(); - - mitk::CastToMitkImage(orFilter->GetOutput(), segmentationResult); - } - else - { - OutputImageType::Pointer workingImageSliceInITK = OutputImageType::New(); - - CastToItkImage(workingImageSlice, workingImageSliceInITK); - - typedef itk::OrImageFilter OrImageFilterType; - OrImageFilterType::Pointer orFilter = OrImageFilterType::New(); - - orFilter->SetInput(0, m_ThresholdFilter->GetOutput()); - orFilter->SetInput(1, workingImageSliceInITK); - orFilter->Update(); - - mitk::CastToMitkImage(orFilter->GetOutput(), segmentationResult); - } - - segmentationResult->GetGeometry()->SetOrigin(workingImageSlice->GetGeometry()->GetOrigin()); - segmentationResult->GetGeometry()->SetIndexToWorldTransform( - workingImageSlice->GetGeometry()->GetIndexToWorldTransform()); - - // write to segmentation volume and hide preview image - // again, current time step is not considered - this->WriteBackSegmentationResult(m_WorkingPlane, segmentationResult, workingImageTimeStep); - this->m_ResultImageNode->SetVisibility(false); - - this->ClearSeeds(); - } - - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - m_ToolManager->ActivateTool(-1); -} - -void mitk::FastMarchingTool::OnAddPoint(StateMachineAction *, InteractionEvent *interactionEvent) -{ - // Add a new seed point for FastMarching algorithm - auto *positionEvent = dynamic_cast(interactionEvent); - // const PositionEvent* p = dynamic_cast(stateEvent->GetEvent()); - if (positionEvent == nullptr) - return; - - if (m_PositionEvent.IsNotNull()) - m_PositionEvent = nullptr; - - m_PositionEvent = - InteractionPositionEvent::New(positionEvent->GetSender(), positionEvent->GetPointerPositionOnScreen()); - - // if click was on another renderwindow or slice then reset pipeline and preview - if ((m_LastEventSender != m_PositionEvent->GetSender()) || - (m_LastEventSlice != m_PositionEvent->GetSender()->GetSlice())) - { - this->BuildITKPipeline(); - this->ClearSeeds(); - } - - m_LastEventSender = m_PositionEvent->GetSender(); - m_LastEventSlice = m_LastEventSender->GetSlice(); - m_WorkingPlane = positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()->Clone(); - - mitk::Point3D clickInIndex; - - m_ReferenceImageSlice->GetGeometry()->WorldToIndex(m_PositionEvent->GetPositionInWorld(), clickInIndex); - itk::Index<2> seedPosition; - seedPosition[0] = clickInIndex[0]; - seedPosition[1] = clickInIndex[1]; - - NodeType node; - const double seedValue = 0.0; - node.SetValue(seedValue); - node.SetIndex(seedPosition); - this->m_SeedContainer->InsertElement(this->m_SeedContainer->Size(), node); - m_FastMarchingFilter->Modified(); - - m_SeedsAsPointSet->InsertPoint(m_SeedsAsPointSet->GetSize(), m_PositionEvent->GetPositionInWorld()); - - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - - m_NeedUpdate = true; - - this->Update(); - - m_ReadyMessage.Send(); -} - -void mitk::FastMarchingTool::OnDelete(StateMachineAction *, InteractionEvent *) -{ - // delete last seed point - if (!(this->m_SeedContainer->empty())) - { - // delete last element of seeds container - this->m_SeedContainer->pop_back(); - m_FastMarchingFilter->Modified(); - - // delete last point in pointset - somehow ugly - m_SeedsAsPointSet->GetPointSet()->GetPoints()->DeleteIndex(m_SeedsAsPointSet->GetSize() - 1); - - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - - m_NeedUpdate = true; - - this->Update(); - } -} - -void mitk::FastMarchingTool::Update() -{ - const unsigned int progress_steps = 20; - - // update FastMarching pipeline and show result - if (m_NeedUpdate) - { - m_ProgressCommand->AddStepsToDo(progress_steps); - CurrentlyBusy.Send(true); - try - { - m_ThresholdFilter->Update(); - } - catch (itk::ExceptionObject &excep) - { - MITK_ERROR << "Exception caught: " << excep.GetDescription(); - - // progress by max step count, will force - m_ProgressCommand->SetProgress(progress_steps); - CurrentlyBusy.Send(false); - - std::string msg = excep.GetDescription(); - ErrorMessage.Send(msg); - - return; - } - m_ProgressCommand->SetProgress(progress_steps); - CurrentlyBusy.Send(false); - - // make output visible - mitk::Image::Pointer result = mitk::Image::New(); - CastToMitkImage(m_ThresholdFilter->GetOutput(), result); - result->GetGeometry()->SetOrigin(m_ReferenceImageSlice->GetGeometry()->GetOrigin()); - result->GetGeometry()->SetIndexToWorldTransform(m_ReferenceImageSlice->GetGeometry()->GetIndexToWorldTransform()); - m_ResultImageNode->SetData(result); - m_ResultImageNode->SetVisibility(true); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - } -} - -void mitk::FastMarchingTool::ClearSeeds() -{ - // clear seeds for FastMarching as well as the PointSet for visualization - if (this->m_SeedContainer.IsNotNull()) - this->m_SeedContainer->Initialize(); - - if (this->m_SeedsAsPointSet.IsNotNull()) - { - this->m_SeedsAsPointSet = mitk::PointSet::New(); - this->m_SeedsAsPointSetNode->SetData(this->m_SeedsAsPointSet); - m_SeedsAsPointSetNode->SetName("Seeds_Preview"); - m_SeedsAsPointSetNode->SetBoolProperty("helper object", true); - m_SeedsAsPointSetNode->SetColor(0.0, 1.0, 0.0); - m_SeedsAsPointSetNode->SetVisibility(true); - } - - if (this->m_FastMarchingFilter.IsNotNull()) - m_FastMarchingFilter->Modified(); - - this->m_NeedUpdate = true; -} - -void mitk::FastMarchingTool::Reset() -{ - // clear all seeds and preview empty result - this->ClearSeeds(); - - m_ResultImageNode->SetVisibility(false); - - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); -} - -void mitk::FastMarchingTool::SetCurrentTimeStep(int t) -{ - if (m_CurrentTimeStep != t) - { - m_CurrentTimeStep = t; - - this->Initialize(); - } -} diff --git a/Modules/Segmentation/Interactions/mitkFastMarchingTool.h b/Modules/Segmentation/Interactions/mitkFastMarchingTool.h index e98b2fba71..9aa06c0b1a 100644 --- a/Modules/Segmentation/Interactions/mitkFastMarchingTool.h +++ b/Modules/Segmentation/Interactions/mitkFastMarchingTool.h @@ -1,175 +1,48 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkFastMarchingTool_h_Included #define mitkFastMarchingTool_h_Included -#include "mitkDataNode.h" -#include "mitkFeedbackContourTool.h" -#include "mitkPointSet.h" -#include "mitkToolCommand.h" -#include - -#include "mitkMessage.h" - -#include "itkImage.h" +#include "mitkFastMarchingBaseTool.h" -// itk filter -#include "itkBinaryThresholdImageFilter.h" -#include "itkCurvatureAnisotropicDiffusionImageFilter.h" -#include "itkFastMarchingImageFilter.h" -#include "itkGradientMagnitudeRecursiveGaussianImageFilter.h" -#include "itkSigmoidImageFilter.h" - -namespace us -{ - class ModuleResource; -} +#include namespace mitk { - class StateMachineAction; - class InteractionEvent; - /** \brief FastMarching semgentation tool. The segmentation is done by setting one or more seed points on the image and adapting the time range and threshold. The pipeline is: Smoothing->GradientMagnitude->SigmoidFunction->FastMarching->Threshold The resulting binary image is seen as a segmentation of an object. For detailed documentation see ITK Software Guide section 9.3.1 Fast Marching Segmentation. */ - class MITKSEGMENTATION_EXPORT FastMarchingTool : public FeedbackContourTool + class MITKSEGMENTATION_EXPORT FastMarchingTool : public FastMarchingBaseTool { - mitkNewMessageMacro(Ready); - public: - mitkClassMacro(FastMarchingTool, FeedbackContourTool); + mitkClassMacro(FastMarchingTool, FastMarchingBaseTool); itkFactorylessNewMacro(Self); itkCloneMacro(Self); - /* typedefs for itk pipeline */ - typedef float InternalPixelType; - typedef itk::Image InternalImageType; - typedef mitk::Tool::DefaultSegmentationDataType OutputPixelType; - typedef itk::Image OutputImageType; - - typedef itk::BinaryThresholdImageFilter ThresholdingFilterType; - typedef itk::CurvatureAnisotropicDiffusionImageFilter SmoothingFilterType; - typedef itk::GradientMagnitudeRecursiveGaussianImageFilter GradientFilterType; - typedef itk::SigmoidImageFilter SigmoidFilterType; - typedef itk::FastMarchingImageFilter FastMarchingFilterType; - typedef FastMarchingFilterType::NodeContainer NodeContainer; - typedef FastMarchingFilterType::NodeType NodeType; - - /* icon stuff */ - const char **GetXPM() const override; const char *GetName() const override; - us::ModuleResource GetCursorIconResource() const override; - us::ModuleResource GetIconResource() const override; - - /// \brief Set parameter used in Threshold filter. - void SetUpperThreshold(double); - - /// \brief Set parameter used in Threshold filter. - void SetLowerThreshold(double); - - /// \brief Set parameter used in Fast Marching filter. - void SetStoppingValue(double); - - /// \brief Set parameter used in Gradient Magnitude filter. - void SetSigma(double); - - /// \brief Set parameter used in Fast Marching filter. - void SetAlpha(double); - - /// \brief Set parameter used in Fast Marching filter. - void SetBeta(double); - - /// \brief Adds the feedback image to the current working image. - virtual void ConfirmSegmentation(); - - /// \brief Set the working time step. - virtual void SetCurrentTimeStep(int t); - - /// \brief Clear all seed points. - void ClearSeeds(); - - /// \brief Updates the itk pipeline and shows the result of FastMarching. - void Update(); - protected: FastMarchingTool(); ~FastMarchingTool() override; - - void ConnectActionsAndFunctions() override; - - // virtual float CanHandleEvent( StateEvent const *stateEvent) const; - - void Activated() override; - void Deactivated() override; - virtual void Initialize(); - - virtual void BuildITKPipeline(); - - /// \brief Add point action of StateMachine pattern - virtual void OnAddPoint(StateMachineAction *, InteractionEvent *interactionEvent); - - /// \brief Delete action of StateMachine pattern - virtual void OnDelete(StateMachineAction *, InteractionEvent *interactionEvent); - - /// \brief Reset all relevant inputs of the itk pipeline. - void Reset(); - - mitk::ToolCommand::Pointer m_ProgressCommand; - - Image::Pointer m_ReferenceImage; - Image::Pointer m_ReferenceImageSlice; - - bool m_NeedUpdate; - - int m_CurrentTimeStep; - - mitk::InteractionPositionEvent::Pointer m_PositionEvent; - - float m_LowerThreshold; // used in Threshold filter - float m_UpperThreshold; // used in Threshold filter - float m_StoppingValue; // used in Fast Marching filter - float m_Sigma; // used in GradientMagnitude filter - float m_Alpha; // used in Sigmoid filter - float m_Beta; // used in Sigmoid filter - - NodeContainer::Pointer m_SeedContainer; // seed points for FastMarching - - InternalImageType::Pointer m_ReferenceImageSliceAsITK; // the reference image as itk::Image - - mitk::DataNode::Pointer m_ResultImageNode; // holds the result as a preview image - - mitk::DataNode::Pointer m_SeedsAsPointSetNode; // used to visualize the seed points - mitk::PointSet::Pointer m_SeedsAsPointSet; - - ThresholdingFilterType::Pointer m_ThresholdFilter; - SmoothingFilterType::Pointer m_SmoothFilter; - GradientFilterType::Pointer m_GradientMagnitudeFilter; - SigmoidFilterType::Pointer m_SigmoidFilter; - FastMarchingFilterType::Pointer m_FastMarchingFilter; - - private: - PlaneGeometry::Pointer m_WorkingPlane; }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.cpp b/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.cpp index 8ada9faf2b..0de2aacf30 100644 --- a/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.cpp +++ b/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.cpp @@ -1,334 +1,32 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkFastMarchingTool3D.h" -#include "mitkToolManager.h" - -#include "mitkBaseRenderer.h" -#include "mitkInteractionConst.h" -#include "mitkRenderingManager.h" - -#include "mitkImageAccessByItk.h" - -// itk filter -#include "itkBinaryThresholdImageFilter.h" -#include "itkCurvatureAnisotropicDiffusionImageFilter.h" -#include "itkGradientMagnitudeRecursiveGaussianImageFilter.h" -#include "itkSigmoidImageFilter.h" - -// us -#include -#include -#include -#include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, FastMarchingTool3D, "FastMarching3D tool"); } mitk::FastMarchingTool3D::FastMarchingTool3D() - : AutoSegmentationWithPreviewTool(), - m_LowerThreshold(0), - m_UpperThreshold(200), - m_StoppingValue(100), - m_Sigma(1.0), - m_Alpha(-0.5), - m_Beta(3.0), - m_PointSetAddObserverTag(0), - m_PointSetRemoveObserverTag(0) + : FastMarchingBaseTool(3) { } mitk::FastMarchingTool3D::~FastMarchingTool3D() { } -bool mitk::FastMarchingTool3D::CanHandle(const BaseData* referenceData, const BaseData* workingData) const -{ - if(!Superclass::CanHandle(referenceData, workingData)) - return false; - - if (referenceData == nullptr) - return false; - - auto *image = dynamic_cast(referenceData); - - if (image == nullptr) - return false; - - if (image->GetDimension() < 3) - return false; - - return true; -} - -const char **mitk::FastMarchingTool3D::GetXPM() const -{ - return nullptr; // mitkFastMarchingTool3D_xpm; -} - -us::ModuleResource mitk::FastMarchingTool3D::GetIconResource() const -{ - us::Module *module = us::GetModuleContext()->GetModule(); - us::ModuleResource resource = module->GetResource("FastMarching_48x48.png"); - return resource; -} - const char *mitk::FastMarchingTool3D::GetName() const { return "Fast Marching 3D"; } - -void mitk::FastMarchingTool3D::SetUpperThreshold(double value) -{ - m_UpperThreshold = value / 10.0; -} - -void mitk::FastMarchingTool3D::SetLowerThreshold(double value) -{ - m_LowerThreshold = value / 10.0; -} - -void mitk::FastMarchingTool3D::SetBeta(double value) -{ - if (m_Beta != value) - { - m_Beta = value; - } -} - -void mitk::FastMarchingTool3D::SetSigma(double value) -{ - if (m_Sigma != value) - { - if (value > 0.0) - { - m_Sigma = value; - } - } -} - -void mitk::FastMarchingTool3D::SetAlpha(double value) -{ - if (m_Alpha != value) - { - m_Alpha = value; - } -} - -void mitk::FastMarchingTool3D::SetStoppingValue(double value) -{ - if (m_StoppingValue != value) - { - m_StoppingValue = value; - } -} - -void mitk::FastMarchingTool3D::Activated() -{ - Superclass::Activated(); - - m_SeedsAsPointSet = mitk::PointSet::New(); - m_SeedsAsPointSetNode = mitk::DataNode::New(); - m_SeedsAsPointSetNode->SetData(m_SeedsAsPointSet); - m_SeedsAsPointSetNode->SetName("3D_FastMarching_PointSet"); - m_SeedsAsPointSetNode->SetBoolProperty("helper object", true); - m_SeedsAsPointSetNode->SetColor(0.0, 1.0, 0.0); - m_SeedsAsPointSetNode->SetVisibility(true); - - // Create PointSetData Interactor - m_SeedPointInteractor = mitk::PointSetDataInteractor::New(); - // Load the according state machine for regular point set interaction - m_SeedPointInteractor->LoadStateMachine("PointSet.xml"); - // Set the configuration file that defines the triggers for the transitions - m_SeedPointInteractor->SetEventConfig("PointSetConfig.xml"); - // set the DataNode (which already is added to the DataStorage - m_SeedPointInteractor->SetDataNode(m_SeedsAsPointSetNode); - - m_ToolManager->GetDataStorage()->Add(m_SeedsAsPointSetNode, m_ToolManager->GetWorkingData(0)); - - m_SeedContainer = NodeContainer::New(); - m_SeedContainer->Initialize(); - - itk::SimpleMemberCommand::Pointer pointAddedCommand = - itk::SimpleMemberCommand::New(); - pointAddedCommand->SetCallbackFunction(this, &mitk::FastMarchingTool3D::OnAddPoint); - m_PointSetAddObserverTag = m_SeedsAsPointSet->AddObserver(mitk::PointSetAddEvent(), pointAddedCommand); - - itk::SimpleMemberCommand::Pointer pointRemovedCommand = - itk::SimpleMemberCommand::New(); - pointRemovedCommand->SetCallbackFunction(this, &mitk::FastMarchingTool3D::OnDelete); - m_PointSetRemoveObserverTag = m_SeedsAsPointSet->AddObserver(mitk::PointSetRemoveEvent(), pointRemovedCommand); -} - -void mitk::FastMarchingTool3D::Deactivated() -{ - this->ClearSeeds(); - - // Deactivate Interaction - m_SeedPointInteractor->SetDataNode(nullptr); - m_ToolManager->GetDataStorage()->Remove(m_SeedsAsPointSetNode); - m_SeedsAsPointSetNode = nullptr; - m_SeedsAsPointSet->RemoveObserver(m_PointSetAddObserverTag); - m_SeedsAsPointSet->RemoveObserver(m_PointSetRemoveObserverTag); - m_SeedsAsPointSet = nullptr; - - Superclass::Deactivated(); -} - -void mitk::FastMarchingTool3D::OnAddPoint() -{ - // Add a new seed point for FastMarching algorithm - mitk::Point3D clickInIndex; - - this->GetReferenceData()->GetGeometry()->WorldToIndex(m_SeedsAsPointSet->GetPoint(m_SeedsAsPointSet->GetSize() - 1), - clickInIndex); - itk::Index<3> seedPosition; - seedPosition[0] = clickInIndex[0]; - seedPosition[1] = clickInIndex[1]; - seedPosition[2] = clickInIndex[2]; - - NodeType node; - const double seedValue = 0.0; - node.SetValue(seedValue); - node.SetIndex(seedPosition); - this->m_SeedContainer->InsertElement(this->m_SeedContainer->Size(), node); - - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - - this->UpdatePreview(); -} - -void mitk::FastMarchingTool3D::OnDelete() -{ - // delete last seed point - if (!(this->m_SeedContainer->empty())) - { - // delete last element of seeds container - this->m_SeedContainer->pop_back(); - - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - - this->UpdatePreview(); - } -} - -void mitk::FastMarchingTool3D::ClearSeeds() -{ - // clear seeds for FastMarching as well as the PointSet for visualization - if (this->m_SeedContainer.IsNotNull()) - this->m_SeedContainer->Initialize(); - - if (this->m_SeedsAsPointSet.IsNotNull()) - { - // remove observers from current pointset - m_SeedsAsPointSet->RemoveObserver(m_PointSetAddObserverTag); - m_SeedsAsPointSet->RemoveObserver(m_PointSetRemoveObserverTag); - - // renew pointset - this->m_SeedsAsPointSet = mitk::PointSet::New(); - this->m_SeedsAsPointSetNode->SetData(this->m_SeedsAsPointSet); - m_SeedsAsPointSetNode->SetName("Seeds_Preview"); - m_SeedsAsPointSetNode->SetBoolProperty("helper object", true); - m_SeedsAsPointSetNode->SetColor(0.0, 1.0, 0.0); - m_SeedsAsPointSetNode->SetVisibility(true); - - // add callback function for adding and removing points - itk::SimpleMemberCommand::Pointer pointAddedCommand = - itk::SimpleMemberCommand::New(); - pointAddedCommand->SetCallbackFunction(this, &mitk::FastMarchingTool3D::OnAddPoint); - m_PointSetAddObserverTag = m_SeedsAsPointSet->AddObserver(mitk::PointSetAddEvent(), pointAddedCommand); - - itk::SimpleMemberCommand::Pointer pointRemovedCommand = - itk::SimpleMemberCommand::New(); - pointRemovedCommand->SetCallbackFunction(this, &mitk::FastMarchingTool3D::OnDelete); - m_PointSetRemoveObserverTag = m_SeedsAsPointSet->AddObserver(mitk::PointSetRemoveEvent(), pointRemovedCommand); - } -} - -template -void mitk::FastMarchingTool3D::DoITKFastMarching(const itk::Image* inputImage, - mitk::Image* segmentation, unsigned int timeStep) -{ - typedef itk::Image InputImageType; - - /* typedefs for itk pipeline */ - - typedef mitk::Tool::DefaultSegmentationDataType OutputPixelType; - typedef itk::Image OutputImageType; - - typedef itk::CurvatureAnisotropicDiffusionImageFilter SmoothingFilterType; - typedef itk::GradientMagnitudeRecursiveGaussianImageFilter GradientFilterType; - typedef itk::SigmoidImageFilter SigmoidFilterType; - typedef itk::BinaryThresholdImageFilter ThresholdingFilterType; - - auto smoothFilter = SmoothingFilterType::New(); - smoothFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand); - smoothFilter->SetTimeStep(0.05); - smoothFilter->SetNumberOfIterations(2); - smoothFilter->SetConductanceParameter(9.0); - - auto gradientMagnitudeFilter = GradientFilterType::New(); - gradientMagnitudeFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand); - gradientMagnitudeFilter->SetSigma(m_Sigma); - - auto sigmoidFilter = SigmoidFilterType::New(); - sigmoidFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand); - sigmoidFilter->SetAlpha(m_Alpha); - sigmoidFilter->SetBeta(m_Beta); - sigmoidFilter->SetOutputMinimum(0.0); - sigmoidFilter->SetOutputMaximum(1.0); - - auto fastMarchingFilter = FastMarchingFilterType::New(); - fastMarchingFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand); - fastMarchingFilter->SetStoppingValue(m_StoppingValue); - fastMarchingFilter->SetTrialPoints(m_SeedContainer); - - auto thresholdFilter = ThresholdingFilterType::New(); - thresholdFilter->SetLowerThreshold(m_LowerThreshold); - thresholdFilter->SetUpperThreshold(m_UpperThreshold); - thresholdFilter->SetOutsideValue(0); - thresholdFilter->SetInsideValue(1.0); - - // set up pipeline - smoothFilter->SetInput(inputImage); - gradientMagnitudeFilter->SetInput(smoothFilter->GetOutput()); - sigmoidFilter->SetInput(gradientMagnitudeFilter->GetOutput()); - fastMarchingFilter->SetInput(sigmoidFilter->GetOutput()); - thresholdFilter->SetInput(fastMarchingFilter->GetOutput()); - thresholdFilter->Update(); - - segmentation->SetVolume((void*)(thresholdFilter->GetOutput()->GetPixelContainer()->GetBufferPointer()), timeStep); -} - -void mitk::FastMarchingTool3D::UpdatePrepare() -{ - // remove interaction with poinset while updating - if (m_SeedPointInteractor.IsNotNull()) - m_SeedPointInteractor->SetDataNode(nullptr); -} - -void mitk::FastMarchingTool3D::UpdateCleanUp() -{ - // add interaction with poinset again - if (m_SeedPointInteractor.IsNotNull()) - m_SeedPointInteractor->SetDataNode(m_SeedsAsPointSetNode); -} - -void mitk::FastMarchingTool3D::DoUpdatePreview(const Image* inputAtTimeStep, Image* previewImage, TimeStepType timeStep) -{ - if (nullptr != inputAtTimeStep && nullptr != previewImage && m_SeedContainer.IsNotNull()) - { - AccessFixedDimensionByItk_n(inputAtTimeStep, DoITKFastMarching, 3, (previewImage, timeStep)); - } -} diff --git a/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.h b/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.h index 652e0d550b..88b82a6038 100644 --- a/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.h +++ b/Modules/Segmentation/Interactions/mitkFastMarchingTool3D.h @@ -1,124 +1,49 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkFastMarchingTool3D_h_Included #define mitkFastMarchingTool3D_h_Included -#include "mitkAutoSegmentationWithPreviewTool.h" -#include "mitkDataNode.h" -#include "mitkPointSet.h" -#include "mitkPointSetDataInteractor.h" -#include "mitkToolCommand.h" - -#include "itkImage.h" -#include "itkFastMarchingImageFilter.h" +#include "mitkFastMarchingBaseTool.h" #include -namespace us -{ - class ModuleResource; -} - namespace mitk { /** \brief FastMarching semgentation tool. The segmentation is done by setting one or more seed points on the image and adapting the time range and threshold. The pipeline is: Smoothing->GradientMagnitude->SigmoidFunction->FastMarching->Threshold The resulting binary image is seen as a segmentation of an object. For detailed documentation see ITK Software Guide section 9.3.1 Fast Marching Segmentation. */ - class MITKSEGMENTATION_EXPORT FastMarchingTool3D : public AutoSegmentationWithPreviewTool + class MITKSEGMENTATION_EXPORT FastMarchingTool3D : public FastMarchingBaseTool { public: - mitkClassMacro(FastMarchingTool3D, AutoSegmentationWithPreviewTool); + mitkClassMacro(FastMarchingTool3D, FastMarchingBaseTool); itkFactorylessNewMacro(Self); itkCloneMacro(Self); - bool CanHandle(const BaseData* referenceData, const BaseData* workingData) const override; - /* icon stuff */ - const char **GetXPM() const override; const char *GetName() const override; - us::ModuleResource GetIconResource() const override; - - void Activated() override; - void Deactivated() override; - - /// \brief Set parameter used in Threshold filter. - void SetUpperThreshold(double); - - /// \brief Set parameter used in Threshold filter. - void SetLowerThreshold(double); - - /// \brief Set parameter used in Fast Marching filter. - void SetStoppingValue(double); - - /// \brief Set parameter used in Gradient Magnitude filter. - void SetSigma(double); - - /// \brief Set parameter used in Fast Marching filter. - void SetAlpha(double); - - /// \brief Set parameter used in Fast Marching filter. - void SetBeta(double); - - /// \brief Clear all seed points. - void ClearSeeds(); protected: FastMarchingTool3D(); ~FastMarchingTool3D() override; - - /// \brief Add point action of StateMachine pattern - virtual void OnAddPoint(); - - /// \brief Delete action of StateMachine pattern - virtual void OnDelete(); - - void UpdatePrepare() override; - void UpdateCleanUp() override; - void DoUpdatePreview(const Image* inputAtTimeStep, Image* previewImage, TimeStepType timeStep) override; - - template - void DoITKFastMarching(const itk::Image* inputImage, - mitk::Image* segmentation, unsigned int timeStep); - - float m_LowerThreshold; // used in Threshold filter - float m_UpperThreshold; // used in Threshold filter - float m_StoppingValue; // used in Fast Marching filter - float m_Sigma; // used in GradientMagnitude filter - float m_Alpha; // used in Sigmoid filter - float m_Beta; // used in Sigmoid filter - - typedef float InternalPixelType; - typedef itk::Image InternalImageType; - typedef itk::FastMarchingImageFilter FastMarchingFilterType; - typedef FastMarchingFilterType::NodeContainer NodeContainer; - typedef FastMarchingFilterType::NodeType NodeType; - - NodeContainer::Pointer m_SeedContainer; // seed points for FastMarching - - mitk::DataNode::Pointer m_SeedsAsPointSetNode; // used to visualize the seed points - mitk::PointSet::Pointer m_SeedsAsPointSet; - mitk::PointSetDataInteractor::Pointer m_SeedPointInteractor; - unsigned int m_PointSetAddObserverTag; - unsigned int m_PointSetRemoveObserverTag; }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkFeedbackContourTool.cpp b/Modules/Segmentation/Interactions/mitkFeedbackContourTool.cpp index 4cea251184..c6eb82b51a 100644 --- a/Modules/Segmentation/Interactions/mitkFeedbackContourTool.cpp +++ b/Modules/Segmentation/Interactions/mitkFeedbackContourTool.cpp @@ -1,140 +1,278 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkFeedbackContourTool.h" #include "mitkToolManager.h" #include "mitkColorProperty.h" #include "mitkProperties.h" #include "mitkStringProperty.h" #include "mitkBaseRenderer.h" #include "mitkDataStorage.h" #include "mitkRenderingManager.h" +#include "mitkAbstractTransformGeometry.h" + mitk::FeedbackContourTool::FeedbackContourTool(const char *type) : SegTool2D(type), m_FeedbackContourVisible(false) { - m_FeedbackContour = ContourModel::New(); - m_FeedbackContour->SetClosed(true); m_FeedbackContourNode = DataNode::New(); - m_FeedbackContourNode->SetData(m_FeedbackContour); m_FeedbackContourNode->SetProperty("name", StringProperty::New("One of FeedbackContourTool's feedback nodes")); m_FeedbackContourNode->SetProperty("visible", BoolProperty::New(true)); m_FeedbackContourNode->SetProperty("helper object", BoolProperty::New(true)); m_FeedbackContourNode->SetProperty("layer", IntProperty::New(1000)); m_FeedbackContourNode->SetProperty("contour.project-onto-plane", BoolProperty::New(false)); m_FeedbackContourNode->SetProperty("contour.width", FloatProperty::New(1.0)); // set to max short, max int doesn't work, max value somewhere hardcoded? m_FeedbackContourNode->SetProperty("layer", IntProperty::New(std::numeric_limits::max())); m_FeedbackContourNode->SetProperty("fixedLayer", BoolProperty::New(true)); - + this->InitializeFeedbackContour(true); SetFeedbackContourColorDefault(); } mitk::FeedbackContourTool::~FeedbackContourTool() { } void mitk::FeedbackContourTool::SetFeedbackContourColor(float r, float g, float b) { m_FeedbackContourNode->SetProperty("contour.color", ColorProperty::New(r, g, b)); } void mitk::FeedbackContourTool::SetFeedbackContourColorDefault() { m_FeedbackContourNode->SetProperty("contour.color", ColorProperty::New(0.0 / 255.0, 255.0 / 255.0, 0.0 / 255.0)); } void mitk::FeedbackContourTool::Deactivated() { Superclass::Deactivated(); DataStorage *storage = m_ToolManager->GetDataStorage(); if (storage && m_FeedbackContourNode.IsNotNull()) { storage->Remove(m_FeedbackContourNode); m_FeedbackContour->Clear(); SetFeedbackContourVisible(false); } } void mitk::FeedbackContourTool::Activated() { Superclass::Activated(); - - SetFeedbackContourVisible(true); + this->InitializeFeedbackContour(true); + this->SetFeedbackContourVisible(true); } -mitk::ContourModel *mitk::FeedbackContourTool::GetFeedbackContour() +const mitk::ContourModel *mitk::FeedbackContourTool::GetFeedbackContour() const { return m_FeedbackContour; } -void mitk::FeedbackContourTool::SetFeedbackContour(ContourModel::Pointer contour) +void mitk::FeedbackContourTool::InitializeFeedbackContour(bool isClosed) { - m_FeedbackContour = contour; + m_FeedbackContour = ContourModel::New(); + m_FeedbackContour->SetClosed(isClosed); + + auto workingImage = this->GetWorkingData(); + + if (nullptr != workingImage) + { + m_FeedbackContour->Expand(workingImage->GetTimeSteps()); + + auto contourTimeGeometry = workingImage->GetTimeGeometry()->Clone(); + contourTimeGeometry->ReplaceTimeStepGeometries(m_FeedbackContour->GetGeometry()); + m_FeedbackContour->SetTimeGeometry(contourTimeGeometry); + + for (unsigned int t = 0; t < m_FeedbackContour->GetTimeSteps(); ++t) + { + m_FeedbackContour->SetClosed(isClosed, t); + } + } + m_FeedbackContourNode->SetData(m_FeedbackContour); } +void mitk::FeedbackContourTool::ClearsCurrentFeedbackContour(bool isClosed) +{ + if (!m_FeedbackContour->GetTimeGeometry()->IsValidTimePoint(this->GetLastTimePointTriggered())) + { + MITK_WARN << "Cannot clear feedback contour at current time step. Feedback contour is in invalid state as its time geometry does not support current selected time point. Invalid time point: " << this->GetLastTimePointTriggered(); + return; + } + + auto feedbackTimeStep = m_FeedbackContour->GetTimeGeometry()->TimePointToTimeStep(this->GetLastTimePointTriggered()); + m_FeedbackContour->Clear(feedbackTimeStep); + m_FeedbackContour->SetClosed(isClosed, feedbackTimeStep); +} + +void mitk::FeedbackContourTool::UpdateCurrentFeedbackContour(const ContourModel* sourceModel, TimeStepType sourceTimeStep) +{ + if (nullptr == sourceModel) + return; + + if (!m_FeedbackContour->GetTimeGeometry()->IsValidTimePoint(this->GetLastTimePointTriggered())) + { + MITK_WARN << "Cannot update feedback contour. Feedback contour is in invalid state as its time geometry does not support current selected time point. Invalid time point: "<GetLastTimePointTriggered(); + return; + } + + auto feedbackTimeStep = m_FeedbackContour->GetTimeGeometry()->TimePointToTimeStep(this->GetLastTimePointTriggered()); + this->UpdateFeedbackContour(sourceModel, feedbackTimeStep, sourceTimeStep); +} + +void mitk::FeedbackContourTool::UpdateFeedbackContour(const ContourModel* sourceModel, TimeStepType feedbackTimeStep, TimeStepType sourceTimeStep) +{ + if (nullptr == sourceModel) + return; + + if (!sourceModel->GetTimeGeometry()->IsValidTimeStep(sourceTimeStep)) + { + MITK_WARN << "Cannot update feedback contour. Source contour time geometry does not support passed time step. Invalid time step: " << sourceTimeStep; + return; + } + + if (!m_FeedbackContour->GetTimeGeometry()->IsValidTimeStep(feedbackTimeStep)) + { + MITK_WARN << "Cannot update feedback contour. Feedback contour time geometry does not support passed time step. Invalid time step: "<UpdateContour(sourceModel, feedbackTimeStep, sourceTimeStep); +} + +void mitk::FeedbackContourTool::AddVertexToCurrentFeedbackContour(const Point3D& point) +{ + if (!m_FeedbackContour->GetTimeGeometry()->IsValidTimePoint(this->GetLastTimePointTriggered())) + { + MITK_WARN << "Cannot add vertex to feedback contour. Feedback contour is in invalid state as its time geometry does not support current selected time point. Invalid time point: " << this->GetLastTimePointTriggered(); + return; + } + + auto feedbackTimeStep = m_FeedbackContour->GetTimeGeometry()->TimePointToTimeStep(this->GetLastTimePointTriggered()); + this->AddVertexToFeedbackContour(point, feedbackTimeStep); +}; + +/** Adds a vertex to the feedback contour for the passed time step. If time step is invalid, nothing will be added.*/ +void mitk::FeedbackContourTool::AddVertexToFeedbackContour(const Point3D& point, TimeStepType feedbackTimeStep) +{ + if (!m_FeedbackContour->GetTimeGeometry()->IsValidTimeStep(feedbackTimeStep)) + { + MITK_WARN << "Cannot add vertex to feedback contour. Feedback contour time geometry does not support passed time step. Invalid time step: " << feedbackTimeStep; + return; + } + + m_FeedbackContour->AddVertex(point, feedbackTimeStep); +} + + void mitk::FeedbackContourTool::SetFeedbackContourVisible(bool visible) { if (m_FeedbackContourVisible == visible) return; // nothing changed if (DataStorage *storage = m_ToolManager->GetDataStorage()) { if (visible) { // Add the feedback contour node as a derived node of the first working data. // If there is no working data, the node is added at the top level. - storage->Add(m_FeedbackContourNode, m_ToolManager->GetWorkingData(0)); + storage->Add(m_FeedbackContourNode, this->GetWorkingDataNode()); } else { storage->Remove(m_FeedbackContourNode); } } m_FeedbackContourVisible = visible; } -mitk::ContourModel::Pointer mitk::FeedbackContourTool::ProjectContourTo2DSlice(Image *slice, - ContourModel *contourIn3D, +mitk::ContourModel::Pointer mitk::FeedbackContourTool::ProjectContourTo2DSlice(const Image *slice, + const ContourModel *contourIn3D, bool correctionForIpSegmentation, bool constrainToInside) { return mitk::ContourModelUtils::ProjectContourTo2DSlice( slice, contourIn3D, correctionForIpSegmentation, constrainToInside); } mitk::ContourModel::Pointer mitk::FeedbackContourTool::BackProjectContourFrom2DSlice(const BaseGeometry *sliceGeometry, - ContourModel *contourIn2D, + const ContourModel *contourIn2D, bool correctionForIpSegmentation) { return mitk::ContourModelUtils::BackProjectContourFrom2DSlice( sliceGeometry, contourIn2D, correctionForIpSegmentation); } +void mitk::FeedbackContourTool::WriteBackFeedbackContourAsSegmentationResult(const InteractionPositionEvent* positionEvent, int paintingPixelValue, bool setInvisibleAfterSuccess) +{ + if (!positionEvent) + return; + + auto workingImage = this->GetWorkingData(); + const auto planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry())); + + if (!workingImage || !planeGeometry) + return; + + const auto* abstractTransformGeometry( + dynamic_cast(positionEvent->GetSender()->GetCurrentWorldPlaneGeometry())); + if (nullptr != abstractTransformGeometry) + return; + + Image::Pointer slice = FeedbackContourTool::GetAffectedWorkingSlice(positionEvent); + + if (slice.IsNull()) + { + MITK_ERROR << "Unable to extract slice." << std::endl; + return; + } + + const auto feedbackContour = FeedbackContourTool::GetFeedbackContour(); + auto contourTimeStep = positionEvent->GetSender()->GetTimeStep(feedbackContour); + + ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice( + slice, feedbackContour, false, false); // false: don't add 0.5 (done by FillContourInSlice) + // false: don't constrain the contour to the image's inside + + if (projectedContour.IsNull()) + return; + + auto activePixelValue = ContourModelUtils::GetActivePixelValue(workingImage); + + mitk::ContourModelUtils::FillContourInSlice( + projectedContour, contourTimeStep, slice, workingImage, paintingPixelValue * activePixelValue); + + this->WriteBackSegmentationResult(positionEvent, slice); + + if (setInvisibleAfterSuccess) + { + this->SetFeedbackContourVisible(false); + } +} + + void mitk::FeedbackContourTool::FillContourInSlice(ContourModel *projectedContour, Image *sliceImage, int paintingPixelValue) { this->FillContourInSlice(projectedContour, 0, sliceImage, paintingPixelValue); } void mitk::FeedbackContourTool::FillContourInSlice(ContourModel *projectedContour, unsigned int timeStep, Image *sliceImage, int paintingPixelValue) { mitk::ContourModelUtils::FillContourInSlice(projectedContour, timeStep, sliceImage, sliceImage, paintingPixelValue); } diff --git a/Modules/Segmentation/Interactions/mitkFeedbackContourTool.h b/Modules/Segmentation/Interactions/mitkFeedbackContourTool.h index 945c4911fd..60c6b60f34 100644 --- a/Modules/Segmentation/Interactions/mitkFeedbackContourTool.h +++ b/Modules/Segmentation/Interactions/mitkFeedbackContourTool.h @@ -1,118 +1,149 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkFeedbackContourTool_h_Included #define mitkFeedbackContourTool_h_Included #include "mitkCommon.h" #include "mitkContourModelUtils.h" #include "mitkContourUtils.h" //TODO remove legacy support #include "mitkImage.h" #include "mitkSegTool2D.h" #include #include "mitkDataNode.h" #include "mitkImageCast.h" namespace mitk { /** \brief Base class for tools that use a contour for feedback \sa Tool \sa ContourModel \ingroup Interaction \ingroup ToolManagerEtAl Implements helper methods, that might be of use to all kind of 2D segmentation tools that use a contour for user feedback. - Providing a feedback contour that might be added or removed from the visible scene (SetFeedbackContourVisible). - Filling of a contour into a 2D slice These helper methods are actually implemented in ContourUtils now. FeedbackContourTool only forwards such requests. \warning Only to be instantiated by mitk::ToolManager. $Author: nolden $ */ class MITKSEGMENTATION_EXPORT FeedbackContourTool : public SegTool2D { public: mitkClassMacro(FeedbackContourTool, SegTool2D); protected: FeedbackContourTool(); // purposely hidden FeedbackContourTool(const char *); // purposely hidden ~FeedbackContourTool() override; - ContourModel *GetFeedbackContour(); - void SetFeedbackContour(ContourModel::Pointer); + const ContourModel *GetFeedbackContour() const; + + /** (Re)initialize the feesback contour by creating a new instance. + * It is assured that the new instance as the same time geometry than + * the working image.*/ + void InitializeFeedbackContour(bool isClosed); + + /** Clears the current time step of the feedback contour and resets its closed state.*/ + void ClearsCurrentFeedbackContour(bool isClosed); + + /** Updates the feedback contour of the currently selected time point. The update will be done + * by clearing all existings vertices at the current time point and copying the vertics of the + * source model at the specified source time step.*/ + void UpdateCurrentFeedbackContour(const ContourModel* sourceModel, TimeStepType sourceTimeStep = 0); + /** Updates the feedback contour at the time step specified by feedbackTimeStep. The update will be done + * by clearing all existings vertices at feedbackTimeStep and copying the vertics of the + * source model at the specified source time step.*/ + void UpdateFeedbackContour(const ContourModel* sourceModel, TimeStepType feedbackTimeStep, TimeStepType sourceTimeStep = 0); + + /** Adds a vertex to the feedback contour for the current time point. */ + void AddVertexToCurrentFeedbackContour(const Point3D& point); + + /** Adds a vertex to the feedback contour for the passed time step. If time step is invalid, nothing will be added.*/ + void AddVertexToFeedbackContour(const Point3D& point, TimeStepType feedbackTimeStep); void SetFeedbackContourVisible(bool); /// Provide values from 0.0 (black) to 1.0 (full color) void SetFeedbackContourColor(float r, float g, float b); void SetFeedbackContourColorDefault(); void Deactivated() override; void Activated() override; /** \brief Projects a contour onto an image point by point. Converts from world to index coordinates. \param slice \param contourIn3D \param correctionForIpSegmentation adds 0.5 to x and y index coordinates (difference between ipSegmentation and MITK contours) \param constrainToInside */ - ContourModel::Pointer ProjectContourTo2DSlice(Image *slice, - ContourModel *contourIn3D, + ContourModel::Pointer ProjectContourTo2DSlice(const Image *slice, + const ContourModel *contourIn3D, bool correctionForIpSegmentation = false, bool constrainToInside = true); /** \brief Projects a slice index coordinates of a contour back into world coordinates. \param sliceGeometry \param contourIn2D \param correctionForIpSegmentation subtracts 0.5 to x and y index coordinates (difference between ipSegmentation and MITK contours) */ ContourModel::Pointer BackProjectContourFrom2DSlice(const BaseGeometry *sliceGeometry, - ContourModel *contourIn2D, + const ContourModel *contourIn2D, bool correctionForIpSegmentation = false); + /** Helper methods that checks all precondition and if they are fullfilled does the following: + * 1. Gets the contour of the time point specified by positionEvent. + * 2. Gets the affacted working slice of the time point specified by positionEvent. + * 3. projects the contour onto the working slice and then fills it with the passed paintingPixelValue (adjusted by the current active lable value) + * to the slice. + * 4. writes the slice back into the working image using SegTool2D::WriteBackSegmentationResult().*/ + void WriteBackFeedbackContourAsSegmentationResult(const InteractionPositionEvent* positionEvent, int paintingPixelValue, bool setInvisibleAfterSuccess = true); + /** \brief Fill a contour in a 2D slice with a specified pixel value. */ void FillContourInSlice(ContourModel *projectedContour, Image *sliceImage, int paintingPixelValue = 1); /** \brief Fill a contour in a 2D slice with a specified pixel value at a given time step. */ void FillContourInSlice(ContourModel *projectedContour, unsigned int timeStep, Image *sliceImage, int paintingPixelValue = 1); + private: ContourModel::Pointer m_FeedbackContour; DataNode::Pointer m_FeedbackContourNode; bool m_FeedbackContourVisible; }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp index a75e5bd1ce..5870887320 100644 --- a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp +++ b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.cpp @@ -1,593 +1,620 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, LiveWireTool2D, "LiveWire tool"); } mitk::LiveWireTool2D::LiveWireTool2D() : SegTool2D("LiveWireTool"), m_CreateAndUseDynamicCosts(false) { } mitk::LiveWireTool2D::~LiveWireTool2D() { this->ClearSegmentation(); } void mitk::LiveWireTool2D::RemoveHelperObjects() { auto dataStorage = m_ToolManager->GetDataStorage(); if (nullptr == dataStorage) return; for (const auto &editingContour : m_EditingContours) dataStorage->Remove(editingContour.first); for (const auto &workingContour : m_WorkingContours) dataStorage->Remove(workingContour.first); if (m_EditingContourNode.IsNotNull()) dataStorage->Remove(m_EditingContourNode); if (m_LiveWireContourNode.IsNotNull()) dataStorage->Remove(m_LiveWireContourNode); if (m_ContourNode.IsNotNull()) dataStorage->Remove(m_ContourNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::LiveWireTool2D::ReleaseHelperObjects() { this->RemoveHelperObjects(); m_EditingContours.clear(); m_WorkingContours.clear(); m_EditingContourNode = nullptr; m_EditingContour = nullptr; m_LiveWireContourNode = nullptr; m_LiveWireContour = nullptr; m_ContourNode = nullptr; m_Contour = nullptr; } void mitk::LiveWireTool2D::ReleaseInteractors() { this->EnableContourLiveWireInteraction(false); m_LiveWireInteractors.clear(); } void mitk::LiveWireTool2D::ConnectActionsAndFunctions() { CONNECT_CONDITION("CheckContourClosed", OnCheckPoint); CONNECT_FUNCTION("InitObject", OnInitLiveWire); CONNECT_FUNCTION("AddPoint", OnAddPoint); CONNECT_FUNCTION("CtrlAddPoint", OnAddPoint); CONNECT_FUNCTION("MovePoint", OnMouseMoveNoDynamicCosts); CONNECT_FUNCTION("FinishContour", OnFinish); CONNECT_FUNCTION("DeletePoint", OnLastSegmentDelete); CONNECT_FUNCTION("CtrlMovePoint", OnMouseMoved); } const char **mitk::LiveWireTool2D::GetXPM() const { return mitkLiveWireTool2D_xpm; } us::ModuleResource mitk::LiveWireTool2D::GetIconResource() const { return us::GetModuleContext()->GetModule()->GetResource("LiveWire_48x48.png"); } us::ModuleResource mitk::LiveWireTool2D::GetCursorIconResource() const { return us::GetModuleContext()->GetModule()->GetResource("LiveWire_Cursor_32x32.png"); } const char *mitk::LiveWireTool2D::GetName() const { return "Live Wire"; } void mitk::LiveWireTool2D::Activated() { Superclass::Activated(); this->ResetToStartState(); this->EnableContourLiveWireInteraction(true); } void mitk::LiveWireTool2D::Deactivated() { this->ConfirmSegmentation(); Superclass::Deactivated(); } -void mitk::LiveWireTool2D::EnableContourLiveWireInteraction(bool on) +void mitk::LiveWireTool2D::UpdateLiveWireContour() { - for (const auto &interactor : m_LiveWireInteractors) - interactor->EnableInteraction(on); + if (m_Contour.IsNotNull()) + { + auto timeGeometry = m_Contour->GetTimeGeometry()->Clone(); + m_LiveWireContour = this->m_LiveWireFilter->GetOutput(); + m_LiveWireContour->SetTimeGeometry(timeGeometry); //needed because the results of the filter are always from 0 ms to 1 ms and the filter also resets its outputs. + m_LiveWireContourNode->SetData(this->m_LiveWireContour); + } } -void mitk::LiveWireTool2D::ConfirmSegmentation() +void mitk::LiveWireTool2D::OnTimePointChanged() { - auto referenceNode = m_ToolManager->GetReferenceData(0); - auto workingNode = m_ToolManager->GetWorkingData(0); - - if (nullptr == referenceNode || nullptr == workingNode) + auto reference = this->GetReferenceData(); + if (nullptr == reference || m_PlaneGeometry.IsNull() || m_LiveWireFilter.IsNull() || m_LiveWireContourNode.IsNull()) return; - auto referenceImage = dynamic_cast(referenceNode->GetData()); - auto workingImage = dynamic_cast(workingNode->GetData()); + auto timeStep = reference->GetTimeGeometry()->TimePointToTimeStep(this->GetLastTimePointTriggered()); - if (nullptr == referenceImage || nullptr == workingImage) - return; + m_ReferenceDataSlice = GetAffectedImageSliceAs2DImageByTimePoint(m_PlaneGeometry, reference, timeStep); + m_LiveWireFilter->SetInput(m_ReferenceDataSlice); + + m_LiveWireFilter->Update(); - std::vector sliceInfos; - sliceInfos.reserve(m_WorkingContours.size()); + this->UpdateLiveWireContour(); - for (const auto &workingContour : m_WorkingContours) - { - auto contour = dynamic_cast(workingContour.first->GetData()); + RenderingManager::GetInstance()->RequestUpdateAll(); +}; - if (nullptr == contour) - continue; - const auto numberOfTimeSteps = contour->GetTimeSteps(); +void mitk::LiveWireTool2D::EnableContourLiveWireInteraction(bool on) +{ + for (const auto &interactor : m_LiveWireInteractors) + interactor->EnableInteraction(on); +} + +void mitk::LiveWireTool2D::ConfirmSegmentation() +{ + auto referenceImage = this->GetReferenceData(); + auto workingImage = this->GetWorkingData(); + + if (nullptr != referenceImage && nullptr != workingImage) + { + std::vector sliceInfos; + sliceInfos.reserve(m_WorkingContours.size()); + + const auto currentTimePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); + TimeStepType workingImageTimeStep = workingImage->GetTimeGeometry()->TimePointToTimeStep(currentTimePoint); - for (std::remove_const_t t = 0; t < numberOfTimeSteps; ++t) + for (const auto &workingContour : m_WorkingContours) { - if (contour->IsEmptyTimeStep(t)) + auto contour = dynamic_cast(workingContour.first->GetData()); + + if (nullptr == contour || contour->IsEmpty()) continue; - TimePointType referenceImageTimePoint = referenceImage->GetTimeGeometry()->TimeStepToTimePoint(t); - TimeStepType workingImageTimeStep = workingImage->GetTimeGeometry()->TimePointToTimeStep(referenceImageTimePoint); + auto sameSlicePredicate = [&workingContour, workingImageTimeStep](const SliceInformation& si) { return workingContour.second->IsOnPlane(si.plane) && workingImageTimeStep == si.timestep; }; + + auto finding = std::find_if(sliceInfos.begin(), sliceInfos.end(), sameSlicePredicate); + if (finding == sliceInfos.end()) + { + auto workingSlice = this->GetAffectedImageSliceAs2DImage(workingContour.second, workingImage, workingImageTimeStep)->Clone(); + sliceInfos.emplace_back(workingSlice, workingContour.second, workingImageTimeStep); + finding = std::prev(sliceInfos.end()); + } + + //cast const away is OK in this case, because these are all slices created and manipulated + //localy in this function call. And we want to keep the high constness of SliceInformation for + //public interfaces. + auto workingSlice = const_cast(finding->slice.GetPointer()); - auto workingSlice = this->GetAffectedImageSliceAs2DImage(workingContour.second, workingImage, workingImageTimeStep); auto projectedContour = ContourModelUtils::ProjectContourTo2DSlice(workingSlice, contour, true, false); int activePixelValue = ContourModelUtils::GetActivePixelValue(workingImage); ContourModelUtils::FillContourInSlice( - projectedContour, referenceImageTimePoint, workingSlice, workingImage, activePixelValue); - - sliceInfos.emplace_back(workingSlice, workingContour.second, referenceImageTimePoint); - this->WriteSliceToVolume(sliceInfos.back()); + projectedContour, workingSlice, workingImage, activePixelValue); } + + this->WriteBackSegmentationResults(sliceInfos); } - this->WriteBackSegmentationResult(sliceInfos, false); this->ClearSegmentation(); } void mitk::LiveWireTool2D::ClearSegmentation() { this->ReleaseHelperObjects(); this->ReleaseInteractors(); this->ResetToStartState(); } bool mitk::LiveWireTool2D::IsPositionEventInsideImageRegion(mitk::InteractionPositionEvent *positionEvent, mitk::BaseData *data) { bool isPositionEventInsideImageRegion = nullptr != data && data->GetGeometry()->IsInside(positionEvent->GetPositionInWorld()); if (!isPositionEventInsideImageRegion) MITK_WARN("LiveWireTool2D") << "PositionEvent is outside ImageRegion!"; return isPositionEventInsideImageRegion; } +mitk::ContourModel::Pointer mitk::LiveWireTool2D::CreateNewContour() const +{ + auto workingData = this->GetWorkingData(); + if (nullptr == workingData) + { + this->InteractiveSegmentationBugMessage("Cannot create new contour. No valid working data is set. Application is in invalid state."); + mitkThrow() << "Cannot create new contour. No valid working data is set. Application is in invalid state."; + } + + auto contour = ContourModel::New(); + + //generate a time geometry that is always visible as the working contour should always be. + auto contourTimeGeometry = ProportionalTimeGeometry::New(); + contourTimeGeometry->SetStepDuration(std::numeric_limits::max()); + contourTimeGeometry->SetTimeStepGeometry(contour->GetTimeGeometry()->GetGeometryForTimeStep(0)->Clone(), 0); + contour->SetTimeGeometry(contourTimeGeometry); + + return contour; +} + void mitk::LiveWireTool2D::OnInitLiveWire(StateMachineAction *, InteractionEvent *interactionEvent) { auto positionEvent = dynamic_cast(interactionEvent); if (nullptr == positionEvent) return; - auto workingDataNode = m_ToolManager->GetWorkingData(0); + auto workingDataNode = this->GetWorkingDataNode(); if (!IsPositionEventInsideImageRegion(positionEvent, workingDataNode->GetData())) { this->ResetToStartState(); return; } m_LastEventSender = positionEvent->GetSender(); m_LastEventSlice = m_LastEventSender->GetSlice(); - auto t = positionEvent->GetSender()->GetTimeStep(); - - m_Contour = mitk::ContourModel::New(); - m_Contour->Expand(t + 1); + m_Contour = this->CreateNewContour(); m_ContourNode = mitk::DataNode::New(); m_ContourNode->SetData(m_Contour); m_ContourNode->SetName("working contour node"); m_ContourNode->SetProperty("layer", IntProperty::New(100)); m_ContourNode->AddProperty("fixedLayer", BoolProperty::New(true)); m_ContourNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_ContourNode->AddProperty("contour.color", ColorProperty::New(1.0f, 1.0f, 0.0f), nullptr, true); m_ContourNode->AddProperty("contour.points.color", ColorProperty::New(1.0f, 0.0f, 0.1f), nullptr, true); m_ContourNode->AddProperty("contour.controlpoints.show", BoolProperty::New(true), nullptr, true); - m_LiveWireContour = mitk::ContourModel::New(); - m_LiveWireContour->Expand(t + 1); + m_LiveWireContour = this->CreateNewContour(); m_LiveWireContourNode = mitk::DataNode::New(); m_LiveWireContourNode->SetData(m_LiveWireContour); m_LiveWireContourNode->SetName("active livewire node"); m_LiveWireContourNode->SetProperty("layer", IntProperty::New(101)); m_LiveWireContourNode->AddProperty("fixedLayer", BoolProperty::New(true)); m_LiveWireContourNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_LiveWireContourNode->AddProperty("contour.color", ColorProperty::New(0.1f, 1.0f, 0.1f), nullptr, true); m_LiveWireContourNode->AddProperty("contour.width", mitk::FloatProperty::New(4.0f), nullptr, true); - m_EditingContour = mitk::ContourModel::New(); - m_EditingContour->Expand(t + 1); + m_EditingContour = this->CreateNewContour(); m_EditingContourNode = mitk::DataNode::New(); m_EditingContourNode->SetData(m_EditingContour); m_EditingContourNode->SetName("editing node"); m_EditingContourNode->SetProperty("layer", IntProperty::New(102)); m_EditingContourNode->AddProperty("fixedLayer", BoolProperty::New(true)); m_EditingContourNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_EditingContourNode->AddProperty("contour.color", ColorProperty::New(0.1f, 1.0f, 0.1f), nullptr, true); m_EditingContourNode->AddProperty("contour.points.color", ColorProperty::New(0.0f, 0.0f, 1.0f), nullptr, true); m_EditingContourNode->AddProperty("contour.width", mitk::FloatProperty::New(4.0f), nullptr, true); auto dataStorage = m_ToolManager->GetDataStorage(); dataStorage->Add(m_ContourNode, workingDataNode); dataStorage->Add(m_LiveWireContourNode, workingDataNode); dataStorage->Add(m_EditingContourNode, workingDataNode); // Set current slice as input for ImageToLiveWireContourFilter - m_WorkingSlice = this->GetAffectedReferenceSlice(positionEvent); + m_ReferenceDataSlice = this->GetAffectedReferenceSlice(positionEvent); - auto origin = m_WorkingSlice->GetSlicedGeometry()->GetOrigin(); - m_WorkingSlice->GetSlicedGeometry()->WorldToIndex(origin, origin); - m_WorkingSlice->GetSlicedGeometry()->IndexToWorld(origin, origin); - m_WorkingSlice->GetSlicedGeometry()->SetOrigin(origin); + auto origin = m_ReferenceDataSlice->GetSlicedGeometry()->GetOrigin(); + m_ReferenceDataSlice->GetSlicedGeometry()->WorldToIndex(origin, origin); + m_ReferenceDataSlice->GetSlicedGeometry()->IndexToWorld(origin, origin); + m_ReferenceDataSlice->GetSlicedGeometry()->SetOrigin(origin); m_LiveWireFilter = ImageLiveWireContourModelFilter::New(); - m_LiveWireFilter->SetInput(m_WorkingSlice); + m_LiveWireFilter->SetInput(m_ReferenceDataSlice); // Map click to pixel coordinates auto click = positionEvent->GetPositionInWorld(); itk::Index<3> idx; - m_WorkingSlice->GetGeometry()->WorldToIndex(click, idx); + m_ReferenceDataSlice->GetGeometry()->WorldToIndex(click, idx); // Get the pixel with the highest gradient in a 7x7 region itk::Index<3> indexWithHighestGradient; - AccessFixedDimensionByItk_2(m_WorkingSlice, FindHighestGradientMagnitudeByITK, 2, idx, indexWithHighestGradient); + AccessFixedDimensionByItk_2(m_ReferenceDataSlice, FindHighestGradientMagnitudeByITK, 2, idx, indexWithHighestGradient); click[0] = indexWithHighestGradient[0]; click[1] = indexWithHighestGradient[1]; click[2] = indexWithHighestGradient[2]; - m_WorkingSlice->GetGeometry()->IndexToWorld(click, click); + m_ReferenceDataSlice->GetGeometry()->IndexToWorld(click, click); // Set initial start point - m_Contour->AddVertex(click, true, t); + m_Contour->AddVertex(click, true); m_LiveWireFilter->SetStartPoint(click); // Remember PlaneGeometry to determine if events were triggered in the same plane m_PlaneGeometry = interactionEvent->GetSender()->GetCurrentWorldPlaneGeometry(); m_CreateAndUseDynamicCosts = true; mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } void mitk::LiveWireTool2D::OnAddPoint(StateMachineAction *, InteractionEvent *interactionEvent) { // Complete LiveWire interaction for the last segment. Add current LiveWire contour to // the finished contour and reset to start a new segment and computation. auto positionEvent = dynamic_cast(interactionEvent); if (nullptr == positionEvent) return; if (m_PlaneGeometry.IsNotNull()) { // Check if the point is in the correct slice if (m_PlaneGeometry->DistanceFromPlane(positionEvent->GetPositionInWorld()) > mitk::sqrteps) return; } - auto t = static_cast(positionEvent->GetSender()->GetTimeStep()); - // Add repulsive points to avoid getting the same path again std::for_each(m_LiveWireContour->IteratorBegin(), m_LiveWireContour->IteratorEnd(), [this](ContourElement::VertexType *vertex) { ImageLiveWireContourModelFilter::InternalImageType::IndexType idx; - this->m_WorkingSlice->GetGeometry()->WorldToIndex(vertex->Coordinates, idx); + this->m_ReferenceDataSlice->GetGeometry()->WorldToIndex(vertex->Coordinates, idx); this->m_LiveWireFilter->AddRepulsivePoint(idx); }); // Remove duplicate first vertex, it's already contained in m_Contour - m_LiveWireContour->RemoveVertexAt(0, t); + m_LiveWireContour->RemoveVertexAt(0); // Set last point as control point - m_LiveWireContour->SetControlVertexAt(m_LiveWireContour->GetNumberOfVertices(t) - 1, t); + m_LiveWireContour->SetControlVertexAt(m_LiveWireContour->GetNumberOfVertices() - 1); // Merge contours - m_Contour->Concatenate(m_LiveWireContour, t); + m_Contour->Concatenate(m_LiveWireContour); // Clear the LiveWire contour and reset the corresponding DataNode - m_LiveWireContour->Clear(t); + m_LiveWireContour->Clear(); // Set new start point m_LiveWireFilter->SetStartPoint(positionEvent->GetPositionInWorld()); if (m_CreateAndUseDynamicCosts) { // Use dynamic cost map for next update m_LiveWireFilter->CreateDynamicCostMap(m_Contour); m_LiveWireFilter->SetUseDynamicCostMap(true); } mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } void mitk::LiveWireTool2D::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent) { // Compute LiveWire segment from last control point to current mouse position auto positionEvent = dynamic_cast(interactionEvent); if (nullptr == positionEvent) return; - auto t = positionEvent->GetSender()->GetTimeStep(); - m_LiveWireFilter->SetEndPoint(positionEvent->GetPositionInWorld()); - m_LiveWireFilter->SetTimeStep(t); m_LiveWireFilter->Update(); - m_LiveWireContour = this->m_LiveWireFilter->GetOutput(); - m_LiveWireContourNode->SetData(this->m_LiveWireContour); + this->UpdateLiveWireContour(); RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } void mitk::LiveWireTool2D::OnMouseMoveNoDynamicCosts(StateMachineAction *, InteractionEvent *interactionEvent) { m_LiveWireFilter->SetUseDynamicCostMap(false); this->OnMouseMoved(nullptr, interactionEvent); m_LiveWireFilter->SetUseDynamicCostMap(true); } bool mitk::LiveWireTool2D::OnCheckPoint(const InteractionEvent *interactionEvent) { // Check double click on first control point to finish the LiveWire tool auto positionEvent = dynamic_cast(interactionEvent); if (nullptr == positionEvent) return false; - auto t = static_cast(positionEvent->GetSender()->GetTimeStep()); - mitk::Point3D click = positionEvent->GetPositionInWorld(); - mitk::Point3D first = this->m_Contour->GetVertexAt(0, t)->Coordinates; + mitk::Point3D first = this->m_Contour->GetVertexAt(0)->Coordinates; return first.EuclideanDistanceTo(click) < 4.5; } void mitk::LiveWireTool2D::OnFinish(StateMachineAction *, InteractionEvent *interactionEvent) { // Finish LiveWire tool interaction auto positionEvent = dynamic_cast(interactionEvent); if (nullptr == positionEvent) return; - // Have to do that here so that the m_LastEventSender is set correctly - mitk::SegTool2D::AddContourmarker(); - - auto t = static_cast(positionEvent->GetSender()->GetTimeStep()); - // Remove last control point added by double click - m_Contour->RemoveVertexAt(m_Contour->GetNumberOfVertices(t) - 1, t); + m_Contour->RemoveVertexAt(m_Contour->GetNumberOfVertices() - 1); // Save contour and corresponding plane geometry to list this->m_WorkingContours.emplace_back(std::make_pair(m_ContourNode, positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()->Clone())); this->m_EditingContours.emplace_back(std::make_pair(m_EditingContourNode, positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()->Clone())); m_LiveWireFilter->SetUseDynamicCostMap(false); this->FinishTool(); } void mitk::LiveWireTool2D::FinishTool() { - auto numberOfTimesteps = static_cast(m_Contour->GetTimeGeometry()->CountTimeSteps()); + auto numberOfTimesteps = static_cast(m_Contour->GetTimeSteps()); for (int i = 0; i <= numberOfTimesteps; ++i) m_Contour->Close(i); m_ToolManager->GetDataStorage()->Remove(m_LiveWireContourNode); m_LiveWireContourNode = nullptr; m_LiveWireContour = nullptr; m_ContourInteractor = mitk::ContourModelLiveWireInteractor::New(); m_ContourInteractor->SetDataNode(m_ContourNode); m_ContourInteractor->LoadStateMachine("ContourModelModificationInteractor.xml", us::GetModuleContext()->GetModule()); m_ContourInteractor->SetEventConfig("ContourModelModificationConfig.xml", us::GetModuleContext()->GetModule()); - m_ContourInteractor->SetWorkingImage(this->m_WorkingSlice); + m_ContourInteractor->SetWorkingImage(this->m_ReferenceDataSlice); m_ContourInteractor->SetEditingContourModelNode(this->m_EditingContourNode); m_ContourNode->SetDataInteractor(m_ContourInteractor.GetPointer()); this->m_LiveWireInteractors.push_back(m_ContourInteractor); } void mitk::LiveWireTool2D::OnLastSegmentDelete(StateMachineAction *, InteractionEvent *interactionEvent) { - int t = static_cast(interactionEvent->GetSender()->GetTimeStep()); - // If last point of current contour will be removed go to start state and remove nodes - if (m_Contour->GetNumberOfVertices(t) <= 1) + if (m_Contour->GetNumberOfVertices() <= 1) { auto dataStorage = m_ToolManager->GetDataStorage(); dataStorage->Remove(m_LiveWireContourNode); dataStorage->Remove(m_ContourNode); dataStorage->Remove(m_EditingContourNode); - m_LiveWireContour = mitk::ContourModel::New(); + m_LiveWireContour = this->CreateNewContour(); m_LiveWireContourNode->SetData(m_LiveWireContour); - m_Contour = mitk::ContourModel::New(); + m_Contour = this->CreateNewContour(); m_ContourNode->SetData(m_Contour); this->ResetToStartState(); } else // Remove last segment from contour and reset LiveWire contour { - m_LiveWireContour = mitk::ContourModel::New(); + m_LiveWireContour = this->CreateNewContour(); m_LiveWireContourNode->SetData(m_LiveWireContour); - auto newContour = mitk::ContourModel::New(); - newContour->Expand(m_Contour->GetTimeSteps()); + auto newContour = this->CreateNewContour(); auto begin = m_Contour->IteratorBegin(); // Iterate from last point to next active point auto newLast = m_Contour->IteratorBegin() + (m_Contour->GetNumberOfVertices() - 1); // Go at least one down if (newLast != begin) --newLast; // Search next active control point while (newLast != begin && !((*newLast)->IsControlPoint)) --newLast; // Set position of start point for LiveWire filter to coordinates of the new last point m_LiveWireFilter->SetStartPoint((*newLast)->Coordinates); auto it = m_Contour->IteratorBegin(); // Fll new Contour while (it <= newLast) { - newContour->AddVertex((*it)->Coordinates, (*it)->IsControlPoint, t); + newContour->AddVertex((*it)->Coordinates, (*it)->IsControlPoint); ++it; } newContour->SetClosed(m_Contour->IsClosed()); m_ContourNode->SetData(newContour); m_Contour = newContour; mitk::RenderingManager::GetInstance()->RequestUpdate(interactionEvent->GetSender()->GetRenderWindow()); } } template void mitk::LiveWireTool2D::FindHighestGradientMagnitudeByITK(itk::Image *inputImage, itk::Index<3> &index, itk::Index<3> &returnIndex) { typedef itk::Image InputImageType; typedef typename InputImageType::IndexType IndexType; const auto MAX_X = inputImage->GetLargestPossibleRegion().GetSize()[0]; const auto MAX_Y = inputImage->GetLargestPossibleRegion().GetSize()[1]; returnIndex[0] = index[0]; returnIndex[1] = index[1]; returnIndex[2] = 0.0; double gradientMagnitude = 0.0; double maxGradientMagnitude = 0.0; // The size and thus the region of 7x7 is only used to calculate the gradient magnitude in that region, // not for searching the maximum value. // Maximum value in each direction for size typename InputImageType::SizeType size; size[0] = 7; size[1] = 7; // Minimum value in each direction for startRegion IndexType startRegion; startRegion[0] = index[0] - 3; startRegion[1] = index[1] - 3; if (startRegion[0] < 0) startRegion[0] = 0; if (startRegion[1] < 0) startRegion[1] = 0; if (MAX_X - index[0] < 7) startRegion[0] = MAX_X - 7; if (MAX_Y - index[1] < 7) startRegion[1] = MAX_Y - 7; index[0] = startRegion[0] + 3; index[1] = startRegion[1] + 3; typename InputImageType::RegionType region; region.SetSize(size); region.SetIndex(startRegion); typedef typename itk::GradientMagnitudeImageFilter GradientMagnitudeFilterType; typename GradientMagnitudeFilterType::Pointer gradientFilter = GradientMagnitudeFilterType::New(); gradientFilter->SetInput(inputImage); gradientFilter->GetOutput()->SetRequestedRegion(region); gradientFilter->Update(); typename InputImageType::Pointer gradientMagnitudeImage; gradientMagnitudeImage = gradientFilter->GetOutput(); IndexType currentIndex; currentIndex[0] = 0; currentIndex[1] = 0; // Search max (approximate) gradient magnitude for (int x = -1; x <= 1; ++x) { currentIndex[0] = index[0] + x; for (int y = -1; y <= 1; ++y) { currentIndex[1] = index[1] + y; gradientMagnitude = gradientMagnitudeImage->GetPixel(currentIndex); // Check for new max if (maxGradientMagnitude < gradientMagnitude) { maxGradientMagnitude = gradientMagnitude; returnIndex[0] = currentIndex[0]; returnIndex[1] = currentIndex[1]; returnIndex[2] = 0.0; } } currentIndex[1] = index[1]; } } diff --git a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.h b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.h index 45ebf5f865..dff07f7a0b 100644 --- a/Modules/Segmentation/Interactions/mitkLiveWireTool2D.h +++ b/Modules/Segmentation/Interactions/mitkLiveWireTool2D.h @@ -1,125 +1,139 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkLiveWireTool2D_h #define mitkLiveWireTool2D_h #include #include namespace mitk { /** \brief A 2D segmentation tool based on a LiveWire approach. The contour between the last point and the current mouse position is computed by searching the shortest path according to specific features of the image. The contour thus tends to snap to the boundary of objects. + The tool always assumes that unconfirmed contours are always defined for the + current time point. So the time step in which the contours will be stored as + segmentations will be determined when the contours got confirmed. Then they + will be transfered to the slices of the currently selected time step. + Changing the time point/time step while tool is active will updated the working + slice the live wire filter. So the behavior of the active live wire contour is + always WYSIWYG (What you see is what you get). + \sa SegTool2D \sa ImageLiveWireContourModelFilter \ingroup Interaction \ingroup ToolManagerEtAl \warning Only to be instantiated by mitk::ToolManager. */ class MITKSEGMENTATION_EXPORT LiveWireTool2D : public SegTool2D { public: mitkClassMacro(LiveWireTool2D, SegTool2D); itkFactorylessNewMacro(Self); us::ModuleResource GetCursorIconResource() const override; us::ModuleResource GetIconResource() const override; const char *GetName() const override; const char **GetXPM() const override; /// \brief Convert all current contours to binary segmentations. void ConfirmSegmentation(); /// \brief Delete all current contours. void ClearSegmentation(); protected: LiveWireTool2D(); ~LiveWireTool2D() override; void ConnectActionsAndFunctions() override; void Activated() override; void Deactivated() override; + void UpdateLiveWireContour(); + void OnTimePointChanged() override; private: /// \brief Initialize tool. void OnInitLiveWire(StateMachineAction *, InteractionEvent *interactionEvent); /// \brief Add a control point and finish current segment. void OnAddPoint(StateMachineAction *, InteractionEvent *interactionEvent); /// \brief Actual LiveWire computation. void OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent); /// \brief Check double click on first control point to finish the LiveWire tool. bool OnCheckPoint(const InteractionEvent *interactionEvent); /// \brief Finish LiveWire tool. void OnFinish(StateMachineAction *, InteractionEvent *interactionEvent); /// \brief Close the contour. void OnLastSegmentDelete(StateMachineAction *, InteractionEvent *interactionEvent); /// \brief Don't use dynamic cost map for LiveWire calculation. void OnMouseMoveNoDynamicCosts(StateMachineAction *, InteractionEvent *interactionEvent); /// \brief Finish contour interaction. void FinishTool(); void EnableContourLiveWireInteraction(bool on); bool IsPositionEventInsideImageRegion(InteractionPositionEvent *positionEvent, BaseData *data); void ReleaseInteractors(); void ReleaseHelperObjects(); void RemoveHelperObjects(); template void FindHighestGradientMagnitudeByITK(itk::Image *inputImage, itk::Index<3> &index, itk::Index<3> &returnIndex); + ContourModel::Pointer CreateNewContour() const; + mitk::ContourModel::Pointer m_Contour; mitk::DataNode::Pointer m_ContourNode; mitk::ContourModel::Pointer m_LiveWireContour; mitk::DataNode::Pointer m_LiveWireContourNode; mitk::ContourModel::Pointer m_EditingContour; mitk::DataNode::Pointer m_EditingContourNode; mitk::ContourModelLiveWireInteractor::Pointer m_ContourInteractor; - mitk::Image::Pointer m_WorkingSlice; + /** Slice of the reference data the tool is currently actively working on to + define contours.*/ + mitk::Image::Pointer m_ReferenceDataSlice; mitk::ImageLiveWireContourModelFilter::Pointer m_LiveWireFilter; bool m_CreateAndUseDynamicCosts; std::vector> m_WorkingContours; std::vector> m_EditingContours; std::vector m_LiveWireInteractors; PlaneGeometry::ConstPointer m_PlaneGeometry; }; } #endif diff --git a/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp b/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp index de9837ba8d..54231db23f 100644 --- a/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp +++ b/Modules/Segmentation/Interactions/mitkPaintbrushTool.cpp @@ -1,587 +1,566 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkPaintbrushTool.h" -#include "ipSegmentation.h" #include "mitkAbstractTransformGeometry.h" #include "mitkBaseRenderer.h" -#include "mitkImageDataItem.h" -#include "mitkOverwriteSliceImageFilter.h" #include "mitkToolManager.h" #include "mitkContourModelUtils.h" #include "mitkLevelWindowProperty.h" int mitk::PaintbrushTool::m_Size = 1; mitk::PaintbrushTool::PaintbrushTool(int paintingPixelValue) : FeedbackContourTool("PressMoveReleaseWithCTRLInversionAllMouseMoves"), m_PaintingPixelValue(paintingPixelValue), m_LastContourSize(0) // other than initial mitk::PaintbrushTool::m_Size (around l. 28) { m_MasterContour = ContourModel::New(); m_MasterContour->Initialize(); m_CurrentPlane = nullptr; m_WorkingNode = DataNode::New(); m_WorkingNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(mitk::LevelWindow(0, 1))); m_WorkingNode->SetProperty("binary", mitk::BoolProperty::New(true)); } mitk::PaintbrushTool::~PaintbrushTool() { } void mitk::PaintbrushTool::ConnectActionsAndFunctions() { CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed); CONNECT_FUNCTION("Move", OnPrimaryButtonPressedMoved); CONNECT_FUNCTION("MouseMove", OnMouseMoved); CONNECT_FUNCTION("Release", OnMouseReleased); CONNECT_FUNCTION("InvertLogic", OnInvertLogic); } void mitk::PaintbrushTool::Activated() { Superclass::Activated(); FeedbackContourTool::SetFeedbackContourVisible(true); SizeChanged.Send(m_Size); m_ToolManager->WorkingDataChanged += mitk::MessageDelegate(this, &mitk::PaintbrushTool::OnToolManagerWorkingDataModified); } void mitk::PaintbrushTool::Deactivated() { FeedbackContourTool::SetFeedbackContourVisible(false); if (m_ToolManager->GetDataStorage()->Exists(m_WorkingNode)) m_ToolManager->GetDataStorage()->Remove(m_WorkingNode); m_WorkingSlice = nullptr; m_CurrentPlane = nullptr; m_ToolManager->WorkingDataChanged -= mitk::MessageDelegate(this, &mitk::PaintbrushTool::OnToolManagerWorkingDataModified); Superclass::Deactivated(); } void mitk::PaintbrushTool::SetSize(int value) { m_Size = value; } mitk::Point2D mitk::PaintbrushTool::upperLeft(mitk::Point2D p) { p[0] -= 0.5; p[1] += 0.5; return p; } void mitk::PaintbrushTool::UpdateContour(const InteractionPositionEvent *positionEvent) { // MITK_INFO<<"Update..."; // examine stateEvent and create a contour that matches the pixel mask that we are going to draw // mitk::InteractionPositionEvent* positionEvent = dynamic_cast( interactionEvent ); // const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); if (!positionEvent) return; // Get Spacing of current Slice // mitk::Vector3D vSpacing = m_WorkingSlice->GetSlicedGeometry()->GetPlaneGeometry(0)->GetSpacing(); // // Draw a contour in Square according to selected brush size // int radius = (m_Size) / 2; float fradius = static_cast(m_Size) / 2.0f; ContourModel::Pointer contourInImageIndexCoordinates = ContourModel::New(); // estimate center point of the brush ( relative to the pixel the mouse points on ) // -- left upper corner for even sizes, // -- midpoint for uneven sizes mitk::Point2D centerCorrection; centerCorrection.Fill(0); // even --> correction of [+0.5, +0.5] bool evenSize = ((m_Size % 2) == 0); if (evenSize) { centerCorrection[0] += 0.5; centerCorrection[1] += 0.5; } // we will compute the control points for the upper left quarter part of a circle contour std::vector quarterCycleUpperRight; std::vector quarterCycleLowerRight; std::vector quarterCycleLowerLeft; std::vector quarterCycleUpperLeft; mitk::Point2D curPoint; bool curPointIsInside = true; curPoint[0] = 0; curPoint[1] = radius; quarterCycleUpperRight.push_back(upperLeft(curPoint)); // to estimate if a pixel is inside the circle, we need to compare against the 'outer radius' // i.e. the distance from the midpoint [0,0] to the border of the pixel [0,radius] // const float outer_radius = static_cast(radius) + 0.5; while (curPoint[1] > 0) { // Move right until pixel is outside circle float curPointX_squared = 0.0f; float curPointY_squared = (curPoint[1] - centerCorrection[1]) * (curPoint[1] - centerCorrection[1]); while (curPointIsInside) { // increment posX and chec curPoint[0]++; curPointX_squared = (curPoint[0] - centerCorrection[0]) * (curPoint[0] - centerCorrection[0]); const float len = sqrt(curPointX_squared + curPointY_squared); if (len > fradius) { // found first Pixel in this horizontal line, that is outside the circle curPointIsInside = false; } } quarterCycleUpperRight.push_back(upperLeft(curPoint)); // Move down until pixel is inside circle while (!curPointIsInside) { // increment posX and chec curPoint[1]--; curPointY_squared = (curPoint[1] - centerCorrection[1]) * (curPoint[1] - centerCorrection[1]); const float len = sqrt(curPointX_squared + curPointY_squared); if (len <= fradius) { // found first Pixel in this horizontal line, that is outside the circle curPointIsInside = true; quarterCycleUpperRight.push_back(upperLeft(curPoint)); } // Quarter cycle is full, when curPoint y position is 0 if (curPoint[1] <= 0) break; } } // QuarterCycle is full! Now copy quarter cycle to other quarters. if (!evenSize) { std::vector::const_iterator it = quarterCycleUpperRight.begin(); while (it != quarterCycleUpperRight.end()) { mitk::Point2D p; p = *it; // the contour points in the lower right corner have same position but with negative y values p[1] *= -1; quarterCycleLowerRight.push_back(p); // the contour points in the lower left corner have same position // but with both x,y negative p[0] *= -1; quarterCycleLowerLeft.push_back(p); // the contour points in the upper left corner have same position // but with x negative p[1] *= -1; quarterCycleUpperLeft.push_back(p); it++; } } else { std::vector::const_iterator it = quarterCycleUpperRight.begin(); while (it != quarterCycleUpperRight.end()) { mitk::Point2D p, q; p = *it; q = p; // the contour points in the lower right corner have same position but with negative y values q[1] *= -1; // correct for moved offset if size even = the midpoint is not the midpoint of the current pixel // but its upper rigt corner q[1] += 1; quarterCycleLowerRight.push_back(q); q = p; // the contour points in the lower left corner have same position // but with both x,y negative q[1] = -1.0f * q[1] + 1; q[0] = -1.0f * q[0] + 1; quarterCycleLowerLeft.push_back(q); // the contour points in the upper left corner have same position // but with x negative q = p; q[0] *= -1; q[0] += 1; quarterCycleUpperLeft.push_back(q); it++; } } // fill contour with poins in right ordering, starting with the upperRight block mitk::Point3D tempPoint; for (unsigned int i = 0; i < quarterCycleUpperRight.size(); i++) { tempPoint[0] = quarterCycleUpperRight[i][0]; tempPoint[1] = quarterCycleUpperRight[i][1]; tempPoint[2] = 0; contourInImageIndexCoordinates->AddVertex(tempPoint); } // the lower right has to be parsed in reverse order for (int i = quarterCycleLowerRight.size() - 1; i >= 0; i--) { tempPoint[0] = quarterCycleLowerRight[i][0]; tempPoint[1] = quarterCycleLowerRight[i][1]; tempPoint[2] = 0; contourInImageIndexCoordinates->AddVertex(tempPoint); } for (unsigned int i = 0; i < quarterCycleLowerLeft.size(); i++) { tempPoint[0] = quarterCycleLowerLeft[i][0]; tempPoint[1] = quarterCycleLowerLeft[i][1]; tempPoint[2] = 0; contourInImageIndexCoordinates->AddVertex(tempPoint); } // the upper left also has to be parsed in reverse order for (int i = quarterCycleUpperLeft.size() - 1; i >= 0; i--) { tempPoint[0] = quarterCycleUpperLeft[i][0]; tempPoint[1] = quarterCycleUpperLeft[i][1]; tempPoint[2] = 0; contourInImageIndexCoordinates->AddVertex(tempPoint); } m_MasterContour = contourInImageIndexCoordinates; } /** Just show the contour, get one point as the central point and add surrounding points to the contour. */ void mitk::PaintbrushTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent) { if (m_WorkingSlice.IsNull()) return; auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; m_WorkingSlice->GetGeometry()->WorldToIndex(positionEvent->GetPositionInWorld(), m_LastPosition); // create new working node // a fresh node is needed to only display the actual drawing process for // the undo function if (m_ToolManager->GetDataStorage()->Exists(m_WorkingNode)) m_ToolManager->GetDataStorage()->Remove(m_WorkingNode); m_WorkingSlice = nullptr; m_CurrentPlane = nullptr; m_WorkingNode = DataNode::New(); m_WorkingNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(mitk::LevelWindow(0, 1))); m_WorkingNode->SetProperty("binary", mitk::BoolProperty::New(true)); this->m_WorkingNode->SetVisibility(true); m_LastEventSender = positionEvent->GetSender(); m_LastEventSlice = m_LastEventSender->GetSlice(); m_MasterContour->SetClosed(true); this->MouseMoved(interactionEvent, true); } void mitk::PaintbrushTool::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent) { MouseMoved(interactionEvent, false); } void mitk::PaintbrushTool::OnPrimaryButtonPressedMoved(StateMachineAction *, InteractionEvent *interactionEvent) { MouseMoved(interactionEvent, true); } /** Insert the point to the feedback contour,finish to build the contour and at the same time the painting function */ void mitk::PaintbrushTool::MouseMoved(mitk::InteractionEvent *interactionEvent, bool leftMouseButtonPressed) { auto *positionEvent = dynamic_cast(interactionEvent); CheckIfCurrentSliceHasChanged(positionEvent); if (m_LastContourSize != m_Size) { UpdateContour(positionEvent); m_LastContourSize = m_Size; } Point3D worldCoordinates = positionEvent->GetPositionInWorld(); Point3D indexCoordinates; m_WorkingSlice->GetGeometry()->WorldToIndex(worldCoordinates, indexCoordinates); // round to nearest voxel center (abort if this hasn't changed) if (m_Size % 2 == 0) // even { indexCoordinates[0] = std::round(indexCoordinates[0]); indexCoordinates[1] = std::round(indexCoordinates[1]); } else // odd { indexCoordinates[0] = std::round(indexCoordinates[0]); indexCoordinates[1] = std::round(indexCoordinates[1]); } static Point3D lastPos; // uninitialized: if somebody finds out how this can be initialized in a one-liner, tell me if (fabs(indexCoordinates[0] - lastPos[0]) > mitk::eps || fabs(indexCoordinates[1] - lastPos[1]) > mitk::eps || fabs(indexCoordinates[2] - lastPos[2]) > mitk::eps || leftMouseButtonPressed) { lastPos = indexCoordinates; } else { return; } - int t = positionEvent->GetSender()->GetTimeStep(); - auto contour = ContourModel::New(); contour->SetClosed(true); auto it = m_MasterContour->Begin(); auto end = m_MasterContour->End(); while (it != end) { auto point = (*it)->Coordinates; point[0] += indexCoordinates[0]; point[1] += indexCoordinates[1]; contour->AddVertex(point); ++it; } if (leftMouseButtonPressed) { const double dist = indexCoordinates.EuclideanDistanceTo(m_LastPosition); const double radius = static_cast(m_Size) / 2.0; DataNode *workingNode(m_ToolManager->GetWorkingData(0)); auto workingImage = dynamic_cast(workingNode->GetData()); int activePixelValue = ContourModelUtils::GetActivePixelValue(workingImage); // m_PaintingPixelValue only decides whether to paint or erase mitk::ContourModelUtils::FillContourInSlice( contour, m_WorkingSlice, workingImage, m_PaintingPixelValue * activePixelValue); m_WorkingNode->SetData(m_WorkingSlice); m_WorkingNode->Modified(); // if points are >= radius away draw rectangle to fill empty holes // in between the 2 points if (dist > radius) { const mitk::Point3D ¤tPos = indexCoordinates; mitk::Point3D direction; mitk::Point3D vertex; mitk::Point3D normal; direction[0] = indexCoordinates[0] - m_LastPosition[0]; direction[1] = indexCoordinates[1] - m_LastPosition[1]; direction[2] = indexCoordinates[2] - m_LastPosition[2]; direction[0] = direction.GetVnlVector().normalize()[0]; direction[1] = direction.GetVnlVector().normalize()[1]; direction[2] = direction.GetVnlVector().normalize()[2]; // 90 degrees rotation of direction normal[0] = -1.0 * direction[1]; normal[1] = direction[0]; contour->Clear(); // upper left corner vertex[0] = m_LastPosition[0] + (normal[0] * radius); vertex[1] = m_LastPosition[1] + (normal[1] * radius); contour->AddVertex(vertex); // upper right corner vertex[0] = currentPos[0] + (normal[0] * radius); vertex[1] = currentPos[1] + (normal[1] * radius); contour->AddVertex(vertex); // lower right corner vertex[0] = currentPos[0] - (normal[0] * radius); vertex[1] = currentPos[1] - (normal[1] * radius); contour->AddVertex(vertex); // lower left corner vertex[0] = m_LastPosition[0] - (normal[0] * radius); vertex[1] = m_LastPosition[1] - (normal[1] * radius); contour->AddVertex(vertex); mitk::ContourModelUtils::FillContourInSlice(contour, m_WorkingSlice, workingImage, m_PaintingPixelValue * activePixelValue); m_WorkingNode->SetData(m_WorkingSlice); m_WorkingNode->Modified(); } } else { // switched from different renderwindow // no activate hover highlighting. Otherwise undo / redo wont work this->m_WorkingNode->SetVisibility(false); } m_LastPosition = indexCoordinates; // visualize contour - ContourModel::Pointer displayContour = FeedbackContourTool::GetFeedbackContour(); - displayContour->Clear(); - ContourModel::Pointer tmp = FeedbackContourTool::BackProjectContourFrom2DSlice(m_WorkingSlice->GetGeometry(), contour); - // copy transformed contour into display contour - it = tmp->Begin(); - end = tmp->End(); - - while (it != end) - { - Point3D point = (*it)->Coordinates; - - displayContour->AddVertex(point, t); - it++; - } - - m_FeedbackContourNode->GetData()->Modified(); + this->UpdateCurrentFeedbackContour(tmp); assert(positionEvent->GetSender()->GetRenderWindow()); - RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } void mitk::PaintbrushTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent) { // When mouse is released write segmentationresult back into image auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; this->WriteBackSegmentationResult(positionEvent, m_WorkingSlice->Clone()); // deactivate visibility of helper node m_WorkingNode->SetVisibility(false); RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } /** Called when the CTRL key is pressed. Will change the painting pixel value from 0 to 1 or from 1 to 0. */ void mitk::PaintbrushTool::OnInvertLogic(StateMachineAction *, InteractionEvent *) { // Inversion only for 0 and 1 as painting values if (m_PaintingPixelValue == 1) { m_PaintingPixelValue = 0; FeedbackContourTool::SetFeedbackContourColor(1.0, 0.0, 0.0); } else if (m_PaintingPixelValue == 0) { m_PaintingPixelValue = 1; FeedbackContourTool::SetFeedbackContourColorDefault(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::PaintbrushTool::CheckIfCurrentSliceHasChanged(const InteractionPositionEvent *event) { const PlaneGeometry *planeGeometry((event->GetSender()->GetCurrentWorldPlaneGeometry())); const auto *abstractTransformGeometry( dynamic_cast(event->GetSender()->GetCurrentWorldPlaneGeometry())); DataNode *workingNode(m_ToolManager->GetWorkingData(0)); if (!workingNode) return; Image::Pointer image = dynamic_cast(workingNode->GetData()); if (!image || !planeGeometry || abstractTransformGeometry) return; if (m_CurrentPlane.IsNull() || m_WorkingSlice.IsNull()) { m_CurrentPlane = planeGeometry; m_WorkingSlice = SegTool2D::GetAffectedImageSliceAs2DImage(event, image)->Clone(); m_WorkingNode->ReplaceProperty("color", workingNode->GetProperty("color")); m_WorkingNode->SetData(m_WorkingSlice); } else { bool isSameSlice(false); isSameSlice = mitk::MatrixEqualElementWise(planeGeometry->GetIndexToWorldTransform()->GetMatrix(), m_CurrentPlane->GetIndexToWorldTransform()->GetMatrix()); isSameSlice = mitk::Equal(planeGeometry->GetIndexToWorldTransform()->GetOffset(), m_CurrentPlane->GetIndexToWorldTransform()->GetOffset()); if (!isSameSlice) { m_ToolManager->GetDataStorage()->Remove(m_WorkingNode); m_CurrentPlane = nullptr; m_WorkingSlice = nullptr; m_WorkingNode = nullptr; m_CurrentPlane = planeGeometry; m_WorkingSlice = SegTool2D::GetAffectedImageSliceAs2DImage(event, image)->Clone(); m_WorkingNode = mitk::DataNode::New(); m_WorkingNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(mitk::LevelWindow(0, 1))); m_WorkingNode->SetProperty("binary", mitk::BoolProperty::New(true)); m_WorkingNode->SetData(m_WorkingSlice); // So that the paintbrush contour vanished in the previous render window RenderingManager::GetInstance()->RequestUpdateAll(); } } if (!m_ToolManager->GetDataStorage()->Exists(m_WorkingNode)) { m_WorkingNode->SetProperty("outline binary", mitk::BoolProperty::New(true)); m_WorkingNode->SetProperty("color", workingNode->GetProperty("color")); m_WorkingNode->SetProperty("name", mitk::StringProperty::New("Paintbrush_Node")); m_WorkingNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_WorkingNode->SetProperty("opacity", mitk::FloatProperty::New(0.8)); m_WorkingNode->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false)); m_WorkingNode->SetVisibility( false, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget3"))); m_ToolManager->GetDataStorage()->Add(m_WorkingNode); } } void mitk::PaintbrushTool::OnToolManagerWorkingDataModified() { // Here we simply set the current working slice to null. The next time the mouse is moved // within a renderwindow a new slice will be extracted from the new working data m_WorkingSlice = nullptr; } diff --git a/Modules/Segmentation/Interactions/mitkPaintbrushTool.h b/Modules/Segmentation/Interactions/mitkPaintbrushTool.h index b63fdfc0a5..b8c4074376 100644 --- a/Modules/Segmentation/Interactions/mitkPaintbrushTool.h +++ b/Modules/Segmentation/Interactions/mitkPaintbrushTool.h @@ -1,103 +1,101 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkPaintbrushTool_h_Included #define mitkPaintbrushTool_h_Included #include "mitkCommon.h" #include "mitkFeedbackContourTool.h" -#include "mitkPointOperation.h" -#include "mitkPointSet.h" #include namespace mitk { class StateMachineAction; class InteractionEvent; class InteractionPositionEvent; /** \brief Paintbrush tool for InteractiveSegmentation \sa FeedbackContourTool \sa ExtractImageFilter \sa OverwriteSliceImageFilter \ingroup Interaction \ingroup ToolManagerEtAl Simple paintbrush drawing tool. Right now there are only circular pens of varying size. \warning Only to be instantiated by mitk::ToolManager. $Author: maleike $ */ class MITKSEGMENTATION_EXPORT PaintbrushTool : public FeedbackContourTool { public: // sent when the pen size is changed or should be updated in a GUI. Message1 SizeChanged; mitkClassMacro(PaintbrushTool, FeedbackContourTool); void SetSize(int value); protected: PaintbrushTool(int paintingPixelValue = 1); // purposely hidden ~PaintbrushTool() override; void ConnectActionsAndFunctions() override; void Activated() override; void Deactivated() override; virtual void OnMousePressed(StateMachineAction *, InteractionEvent *); virtual void OnMouseMoved(StateMachineAction *, InteractionEvent *); virtual void OnPrimaryButtonPressedMoved(StateMachineAction *, InteractionEvent *); virtual void MouseMoved(mitk::InteractionEvent *interactionEvent, bool leftMouseButtonPressed); virtual void OnMouseReleased(StateMachineAction *, InteractionEvent *); virtual void OnInvertLogic(StateMachineAction *, InteractionEvent *); /** * \todo This is a possible place where to introduce * different types of pens */ void UpdateContour(const InteractionPositionEvent *); /** * Little helper function. Returns the upper left corner of the given pixel. */ mitk::Point2D upperLeft(mitk::Point2D p); /** * Checks if the current slice has changed */ void CheckIfCurrentSliceHasChanged(const InteractionPositionEvent *event); void OnToolManagerWorkingDataModified(); int m_PaintingPixelValue; static int m_Size; ContourModel::Pointer m_MasterContour; int m_LastContourSize; Image::Pointer m_WorkingSlice; PlaneGeometry::ConstPointer m_CurrentPlane; DataNode::Pointer m_WorkingNode; mitk::Point3D m_LastPosition; }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkPickingTool.cpp b/Modules/Segmentation/Interactions/mitkPickingTool.cpp index 1e903db63c..e2bfed1ca1 100644 --- a/Modules/Segmentation/Interactions/mitkPickingTool.cpp +++ b/Modules/Segmentation/Interactions/mitkPickingTool.cpp @@ -1,253 +1,269 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkPickingTool.h" #include "mitkProperties.h" #include "mitkToolManager.h" // us #include #include #include #include #include "mitkITKImageImport.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkImageTimeSelector.h" #include "mitkImageTimeSelector.h" #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, PickingTool, "PickingTool"); } mitk::PickingTool::PickingTool() : m_WorkingData(nullptr) { m_PointSetNode = mitk::DataNode::New(); m_PointSetNode->GetPropertyList()->SetProperty("name", mitk::StringProperty::New("Picking_Seedpoint")); m_PointSetNode->GetPropertyList()->SetProperty("helper object", mitk::BoolProperty::New(true)); m_PointSet = mitk::PointSet::New(); m_PointSetNode->SetData(m_PointSet); // Watch for point added or modified itk::SimpleMemberCommand::Pointer pointAddedCommand = itk::SimpleMemberCommand::New(); pointAddedCommand->SetCallbackFunction(this, &mitk::PickingTool::OnPointAdded); m_PointSetAddObserverTag = m_PointSet->AddObserver(mitk::PointSetAddEvent(), pointAddedCommand); // create new node for picked region m_ResultNode = mitk::DataNode::New(); // set some properties m_ResultNode->SetProperty("name", mitk::StringProperty::New("result")); m_ResultNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_ResultNode->SetProperty("color", mitk::ColorProperty::New(0, 1, 0)); m_ResultNode->SetProperty("layer", mitk::IntProperty::New(1)); m_ResultNode->SetProperty("opacity", mitk::FloatProperty::New(0.33f)); } mitk::PickingTool::~PickingTool() { m_PointSet->RemoveObserver(m_PointSetAddObserverTag); } +bool mitk::PickingTool::CanHandle(const BaseData* referenceData, const BaseData* workingData) const +{ + if (!Superclass::CanHandle(referenceData,workingData)) + return false; + + auto* image = dynamic_cast(referenceData); + + if (image == nullptr) + return false; + + if (image->GetTimeSteps() > 1) //release quickfix for T28248 + return false; + + return true; +} + const char **mitk::PickingTool::GetXPM() const { return nullptr; } const char *mitk::PickingTool::GetName() const { return "Picking"; } us::ModuleResource mitk::PickingTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("Pick_48x48.png"); return resource; } void mitk::PickingTool::Activated() { Superclass::Activated(); DataStorage *dataStorage = this->GetDataStorage(); m_WorkingData = this->GetWorkingData(); // add to datastorage and enable interaction if (!dataStorage->Exists(m_PointSetNode)) dataStorage->Add(m_PointSetNode, m_WorkingData); m_SeedPointInteractor = mitk::SinglePointDataInteractor::New(); m_SeedPointInteractor->LoadStateMachine("PointSet.xml"); m_SeedPointInteractor->SetEventConfig("PointSetConfig.xml"); m_SeedPointInteractor->SetDataNode(m_PointSetNode); // now add result to data tree dataStorage->Add(m_ResultNode, m_WorkingData); } void mitk::PickingTool::Deactivated() { m_PointSet->Clear(); // remove from data storage and disable interaction GetDataStorage()->Remove(m_PointSetNode); GetDataStorage()->Remove(m_ResultNode); Superclass::Deactivated(); } mitk::DataNode *mitk::PickingTool::GetReferenceData() { return this->m_ToolManager->GetReferenceData(0); } mitk::DataStorage *mitk::PickingTool::GetDataStorage() { return this->m_ToolManager->GetDataStorage(); } mitk::DataNode *mitk::PickingTool::GetWorkingData() { return this->m_ToolManager->GetWorkingData(0); } mitk::DataNode::Pointer mitk::PickingTool::GetPointSetNode() { return m_PointSetNode; } void mitk::PickingTool::OnPointAdded() { if (m_WorkingData != this->GetWorkingData()) { DataStorage *dataStorage = this->GetDataStorage(); if (dataStorage->Exists(m_PointSetNode)) { dataStorage->Remove(m_PointSetNode); dataStorage->Add(m_PointSetNode, this->GetWorkingData()); } if (dataStorage->Exists(m_ResultNode)) { dataStorage->Remove(m_ResultNode); dataStorage->Add(m_ResultNode, this->GetWorkingData()); } m_WorkingData = this->GetWorkingData(); } // Perform region growing/picking int timeStep = mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget0"))->GetTimeStep(); mitk::PointSet::PointType seedPoint = m_PointSet->GetPointSet(timeStep)->GetPoints()->Begin().Value(); // as we want to pick a region from our segmentation image use the working data from ToolManager mitk::Image::Pointer orgImage = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); if (orgImage.IsNotNull()) { if (orgImage->GetDimension() == 4) { // there may be 4D segmentation data even though we currently don't support that mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(orgImage); timeSelector->SetTimeNr(timeStep); timeSelector->UpdateLargestPossibleRegion(); mitk::Image *timedImage = timeSelector->GetOutput(); AccessByItk_2(timedImage, StartRegionGrowing, timedImage->GetGeometry(), seedPoint); } else if (orgImage->GetDimension() == 3) { AccessByItk_2(orgImage, StartRegionGrowing, orgImage->GetGeometry(), seedPoint); } this->m_PointSet->Clear(); } } template void mitk::PickingTool::StartRegionGrowing(itk::Image *itkImage, mitk::BaseGeometry *imageGeometry, mitk::PointSet::PointType seedPoint) { typedef itk::Image InputImageType; typedef typename InputImageType::IndexType IndexType; typedef itk::ConnectedThresholdImageFilter RegionGrowingFilterType; typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New(); // convert world coordinates to image indices IndexType seedIndex; imageGeometry->WorldToIndex(seedPoint, seedIndex); // perform region growing in desired segmented region regionGrower->SetInput(itkImage); regionGrower->AddSeed(seedIndex); // TODO: conversion added to silence warning and // maintain existing behaviour, should be fixed // since it's not correct e.g. for signed char regionGrower->SetLower(static_cast(1)); regionGrower->SetUpper(static_cast(255)); try { regionGrower->Update(); } catch (const itk::ExceptionObject &) { return; // can't work } catch (...) { return; } // Store result and preview mitk::Image::Pointer resultImage = mitk::ImportItkImage(regionGrower->GetOutput(), imageGeometry)->Clone(); mitk::LabelSetImage::Pointer resultLabelSetImage = mitk::LabelSetImage::New(); resultLabelSetImage->InitializeByLabeledImage(resultImage); m_ResultNode->SetData(resultLabelSetImage); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void mitk::PickingTool::ConfirmSegmentation() { mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetProperty("name", mitk::StringProperty::New(m_WorkingData->GetName() + "_picked")); float rgb[3] = {1.0f, 0.0f, 0.0f}; m_WorkingData->GetColor(rgb); newNode->SetProperty("color", mitk::ColorProperty::New(rgb)); float opacity = 1.0f; m_WorkingData->GetOpacity(opacity, nullptr); newNode->SetProperty("opacity", mitk::FloatProperty::New(opacity)); newNode->SetData(m_ResultNode->GetData()); GetDataStorage()->Add(newNode, this->GetReferenceData()); m_WorkingData->SetVisibility(false); m_ResultNode->SetData(nullptr); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } diff --git a/Modules/Segmentation/Interactions/mitkPickingTool.h b/Modules/Segmentation/Interactions/mitkPickingTool.h index a5172832c0..a619ecbf3d 100644 --- a/Modules/Segmentation/Interactions/mitkPickingTool.h +++ b/Modules/Segmentation/Interactions/mitkPickingTool.h @@ -1,93 +1,95 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkPickingTool_h_Included #define mitkPickingTool_h_Included #include "itkImage.h" #include "mitkAutoSegmentationTool.h" #include "mitkCommon.h" #include "mitkDataStorage.h" #include "mitkPointSet.h" #include "mitkSinglePointDataInteractor.h" #include namespace us { class ModuleResource; } namespace mitk { /** \brief Extracts a single region from a segmentation image and creates a new image with same geometry of the input image. The region is extracted in 3D space. This is done by performing region growing within the desired region. Use shift click to add the seed point. \ingroup ToolManagerEtAl \sa mitk::Tool \sa QmitkInteractiveSegmentation */ class MITKSEGMENTATION_EXPORT PickingTool : public AutoSegmentationTool { public: mitkClassMacro(PickingTool, AutoSegmentationTool); itkFactorylessNewMacro(Self); itkCloneMacro(Self); const char **GetXPM() const override; const char *GetName() const override; us::ModuleResource GetIconResource() const override; void Activated() override; void Deactivated() override; + bool CanHandle(const BaseData* referenceData, const BaseData* workingData) const override; + virtual DataNode::Pointer GetPointSetNode(); mitk::DataNode *GetReferenceData(); mitk::DataNode *GetWorkingData(); mitk::DataStorage *GetDataStorage(); void ConfirmSegmentation(); protected: PickingTool(); // purposely hidden ~PickingTool() override; // Callback for point add event of PointSet void OnPointAdded(); // Observer id long m_PointSetAddObserverTag; mitk::DataNode::Pointer m_ResultNode; // itk regrowing template void StartRegionGrowing(itk::Image *itkImage, mitk::BaseGeometry *imageGeometry, mitk::PointSet::PointType seedPoint); // seed point PointSet::Pointer m_PointSet; SinglePointDataInteractor::Pointer m_SeedPointInteractor; DataNode::Pointer m_PointSetNode; DataNode *m_WorkingData; }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp index 7a46716569..3e2617f963 100644 --- a/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp +++ b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp @@ -1,650 +1,573 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkRegionGrowingTool.h" -#include "mitkApplicationCursor.h" #include "mitkBaseRenderer.h" -#include "mitkImageDataItem.h" #include "mitkImageToContourModelFilter.h" -#include "mitkOverwriteSliceImageFilter.h" #include "mitkRegionGrowingTool.xpm" #include "mitkRenderingManager.h" #include "mitkToolManager.h" -#include "mitkExtractDirectedPlaneImageFilterNew.h" -#include "mitkLabelSetImage.h" -#include "mitkOverwriteDirectedPlaneImageFilter.h" - // us #include #include #include #include // ITK #include "mitkITKImageImport.h" #include "mitkImageAccessByItk.h" #include #include -#include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, RegionGrowingTool, "Region growing tool"); } #define ROUND(a) ((a) > 0 ? (int)((a) + 0.5) : -(int)(0.5 - (a))) mitk::RegionGrowingTool::RegionGrowingTool() : FeedbackContourTool("PressMoveRelease"), m_SeedValue(0), m_ScreenYDifference(0), m_ScreenXDifference(0), m_MouseDistanceScaleFactor(0.5), m_PaintingPixelValue(0), m_FillFeedbackContour(true), m_ConnectedComponentValue(1) { } mitk::RegionGrowingTool::~RegionGrowingTool() { } void mitk::RegionGrowingTool::ConnectActionsAndFunctions() { CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed); CONNECT_FUNCTION("Move", OnMouseMoved); CONNECT_FUNCTION("Release", OnMouseReleased); } const char **mitk::RegionGrowingTool::GetXPM() const { return mitkRegionGrowingTool_xpm; } us::ModuleResource mitk::RegionGrowingTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("RegionGrowing_48x48.png"); return resource; } us::ModuleResource mitk::RegionGrowingTool::GetCursorIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("RegionGrowing_Cursor_32x32.png"); return resource; } const char *mitk::RegionGrowingTool::GetName() const { return "Region Growing"; } void mitk::RegionGrowingTool::Activated() { Superclass::Activated(); } void mitk::RegionGrowingTool::Deactivated() { Superclass::Deactivated(); } // Get the average pixel value of square/cube with radius=neighborhood around index template void mitk::RegionGrowingTool::GetNeighborhoodAverage(const itk::Image *itkImage, const itk::Index& index, ScalarType *result, unsigned int neighborhood) { // maybe assert that image dimension is only 2 or 3? auto neighborhoodInt = (int)neighborhood; TPixel averageValue(0); unsigned int numberOfPixels = (2 * neighborhood + 1) * (2 * neighborhood + 1); if (imageDimension == 3) { numberOfPixels *= (2 * neighborhood + 1); } MITK_DEBUG << "Getting neighborhood of " << numberOfPixels << " pixels around " << index; itk::Index currentIndex; for (int i = (0 - neighborhoodInt); i <= neighborhoodInt; ++i) { currentIndex[0] = index[0] + i; for (int j = (0 - neighborhoodInt); j <= neighborhoodInt; ++j) { currentIndex[1] = index[1] + j; if (imageDimension == 3) { for (int k = (0 - neighborhoodInt); k <= neighborhoodInt; ++k) { currentIndex[2] = index[2] + k; if (itkImage->GetLargestPossibleRegion().IsInside(currentIndex)) { averageValue += itkImage->GetPixel(currentIndex); } else { numberOfPixels -= 1; } } } else { if (itkImage->GetLargestPossibleRegion().IsInside(currentIndex)) { averageValue += itkImage->GetPixel(currentIndex); } else { numberOfPixels -= 1; } } } } *result = (ScalarType)averageValue; *result /= numberOfPixels; } // Check whether index lies inside a segmentation template void mitk::RegionGrowingTool::IsInsideSegmentation(const itk::Image *itkImage, const itk::Index& index, bool *result) { if (itkImage->GetPixel(index) > 0) { *result = true; } else { *result = false; } } // Do the region growing (i.e. call an ITK filter that does it) template void mitk::RegionGrowingTool::StartRegionGrowing(const itk::Image *inputImage, const itk::Index& seedIndex, const std::array& thresholds, mitk::Image::Pointer &outputImage) { MITK_DEBUG << "Starting region growing at index " << seedIndex << " with lower threshold " << thresholds[0] << " and upper threshold " << thresholds[1]; typedef itk::Image InputImageType; typedef itk::Image OutputImageType; typedef itk::ConnectedThresholdImageFilter RegionGrowingFilterType; typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New(); // perform region growing in desired segmented region regionGrower->SetInput(inputImage); regionGrower->SetSeed(seedIndex); regionGrower->SetLower(thresholds[0]); regionGrower->SetUpper(thresholds[1]); try { regionGrower->Update(); } catch (...) { return; // Should we do something? } typename OutputImageType::Pointer resultImage = regionGrower->GetOutput(); // Smooth result: Every pixel is replaced by the majority of the neighborhood typedef itk::NeighborhoodIterator NeighborhoodIteratorType; typedef itk::ImageRegionIterator ImageIteratorType; typename NeighborhoodIteratorType::RadiusType radius; radius.Fill(2); // for now, maybe make this something the user can adjust in the preferences? typedef itk::ImageDuplicator< OutputImageType > DuplicatorType; typename DuplicatorType::Pointer duplicator = DuplicatorType::New(); duplicator->SetInputImage(resultImage); duplicator->Update(); typename OutputImageType::Pointer resultDup = duplicator->GetOutput(); NeighborhoodIteratorType neighborhoodIterator(radius, resultDup, resultDup->GetRequestedRegion()); ImageIteratorType imageIterator(resultImage, resultImage->GetRequestedRegion()); for (neighborhoodIterator.GoToBegin(), imageIterator.GoToBegin(); !neighborhoodIterator.IsAtEnd(); ++neighborhoodIterator, ++imageIterator) { DefaultSegmentationDataType voteYes(0); DefaultSegmentationDataType voteNo(0); for (unsigned int i = 0; i < neighborhoodIterator.Size(); ++i) { if (neighborhoodIterator.GetPixel(i) > 0) { voteYes += 1; } else { voteNo += 1; } } if (voteYes > voteNo) { imageIterator.Set(1); } else { imageIterator.Set(0); } } if (resultImage.IsNull()) { MITK_DEBUG << "Region growing result is empty."; } // Can potentially have multiple regions, use connected component image filter to label disjunct regions typedef itk::ConnectedComponentImageFilter ConnectedComponentImageFilterType; typename ConnectedComponentImageFilterType::Pointer connectedComponentFilter = ConnectedComponentImageFilterType::New(); connectedComponentFilter->SetInput(resultImage); connectedComponentFilter->Update(); typename OutputImageType::Pointer resultImageCC = connectedComponentFilter->GetOutput(); m_ConnectedComponentValue = resultImageCC->GetPixel(seedIndex); outputImage = mitk::GrabItkImageMemory(resultImageCC); } template void mitk::RegionGrowingTool::CalculateInitialThresholds(const itk::Image*) { LevelWindow levelWindow; m_ToolManager->GetReferenceData(0)->GetLevelWindow(levelWindow); m_ThresholdExtrema[0] = static_cast(std::numeric_limits::lowest()); m_ThresholdExtrema[1] = static_cast(std::numeric_limits::max()); const ScalarType lowerWindowBound = std::max(m_ThresholdExtrema[0], levelWindow.GetLowerWindowBound()); const ScalarType upperWindowBound = std::min(m_ThresholdExtrema[1], levelWindow.GetUpperWindowBound()); if (m_SeedValue < lowerWindowBound) { m_InitialThresholds = { m_ThresholdExtrema[0], lowerWindowBound }; } else if (m_SeedValue > upperWindowBound) { m_InitialThresholds = { upperWindowBound, m_ThresholdExtrema[1] }; } else { const ScalarType range = 0.1 * (upperWindowBound - lowerWindowBound); // 10% of the visible window m_InitialThresholds[0] = std::min(std::max(lowerWindowBound, m_SeedValue - 0.5 * range), upperWindowBound - range); m_InitialThresholds[1] = m_InitialThresholds[0] + range; } } void mitk::RegionGrowingTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent) { auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; m_LastEventSender = positionEvent->GetSender(); m_LastEventSlice = m_LastEventSender->GetSlice(); - m_LastScreenPosition = positionEvent->GetPointerPositionOnScreen(); + m_LastScreenPosition = Point2I(positionEvent->GetPointerPositionOnScreen()); // ReferenceSlice is from the underlying image, WorkingSlice from the active segmentation (can be empty) m_ReferenceSlice = FeedbackContourTool::GetAffectedReferenceSlice(positionEvent); m_WorkingSlice = FeedbackContourTool::GetAffectedWorkingSlice(positionEvent); if (m_WorkingSlice.IsNotNull()) // can't do anything without a working slice (i.e. a possibly empty segmentation) { // 2. Determine if the user clicked inside or outside of the segmentation/working slice (i.e. the whole volume) mitk::BaseGeometry::Pointer workingSliceGeometry; workingSliceGeometry = m_WorkingSlice->GetGeometry(); workingSliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), m_SeedPoint); itk::Index<2> indexInWorkingSlice2D; indexInWorkingSlice2D[0] = m_SeedPoint[0]; indexInWorkingSlice2D[1] = m_SeedPoint[1]; if (workingSliceGeometry->IsIndexInside(m_SeedPoint)) { MITK_DEBUG << "OnMousePressed: point " << positionEvent->GetPositionInWorld() << " (index coordinates " << m_SeedPoint << ") is inside working slice"; // 3. determine the pixel value under the last click to determine what to do bool inside(true); AccessFixedDimensionByItk_2(m_WorkingSlice, IsInsideSegmentation, 2, indexInWorkingSlice2D, &inside); m_PaintingPixelValue = inside ? 0 : 1; if (inside) { MITK_DEBUG << "Clicked inside segmentation"; // For now, we're doing nothing when the user clicks inside the segmentation. Behaviour can be implemented via // OnMousePressedInside() // When you do, be sure to remove the m_PaintingPixelValue check in OnMouseMoved() and OnMouseReleased() return; } else { MITK_DEBUG << "Clicked outside of segmentation"; OnMousePressedOutside(nullptr, interactionEvent); } } } } // Use this to implement a behaviour for when the user clicks inside a segmentation (for example remove something) // Old IpPic code is kept as comment for reference void mitk::RegionGrowingTool::OnMousePressedInside() { // mitk::InteractionPositionEvent* positionEvent = dynamic_cast( interactionEvent // ); // //const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); // checked in // OnMousePressed // // 3.1.1. Create a skeletonization of the segmentation and try to find a nice cut // // apply the skeletonization-and-cut algorithm // // generate contour to remove // // set m_ReferenceSlice = nullptr so nothing will happen during mouse move // // remember to fill the contour with 0 in mouserelease // mitkIpPicDescriptor* segmentationHistory = ipMITKSegmentationCreateGrowerHistory( workingPicSlice, // m_LastWorkingSeed, nullptr ); // free again // if (segmentationHistory) // { // tCutResult cutContour = ipMITKSegmentationGetCutPoints( workingPicSlice, segmentationHistory, // initialWorkingOffset ); // tCutResult is a ipSegmentation type // mitkIpPicFree( segmentationHistory ); // if (cutContour.cutIt) // { // int timestep = positionEvent->GetSender()->GetTimeStep(); // // 3.1.2 copy point from float* to mitk::Contour // ContourModel::Pointer contourInImageIndexCoordinates = ContourModel::New(); // contourInImageIndexCoordinates->Expand(timestep + 1); // contourInImageIndexCoordinates->SetClosed(true, timestep); // Point3D newPoint; // for (int index = 0; index < cutContour.deleteSize; ++index) // { // newPoint[0] = cutContour.deleteCurve[ 2 * index + 0 ] - 0.5;//correction is needed because the // output of the algorithm is center based // newPoint[1] = cutContour.deleteCurve[ 2 * index + 1 ] - 0.5;//and we want our contour displayed // corner based. // newPoint[2] = 0.0; // contourInImageIndexCoordinates->AddVertex( newPoint, timestep ); // } // free(cutContour.traceline); // free(cutContour.deleteCurve); // perhaps visualize this for fun? // free(cutContour.onGradient); // ContourModel::Pointer contourInWorldCoordinates = FeedbackContourTool::BackProjectContourFrom2DSlice( // m_WorkingSlice->GetGeometry(), contourInImageIndexCoordinates, true ); // true: sub 0.5 for // ipSegmentation correction // FeedbackContourTool::SetFeedbackContour( contourInWorldCoordinates ); // FeedbackContourTool::SetFeedbackContourVisible(true); // mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); // m_FillFeedbackContour = true; // } // else // { // m_FillFeedbackContour = false; // } // } // else // { // m_FillFeedbackContour = false; // } // m_ReferenceSlice = nullptr; // return true; } void mitk::RegionGrowingTool::OnMousePressedOutside(StateMachineAction *, InteractionEvent *interactionEvent) { auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent) { // Get geometry and indices mitk::BaseGeometry::Pointer workingSliceGeometry; workingSliceGeometry = m_WorkingSlice->GetGeometry(); itk::Index<2> indexInWorkingSlice2D; indexInWorkingSlice2D[0] = m_SeedPoint[0]; indexInWorkingSlice2D[1] = m_SeedPoint[1]; mitk::BaseGeometry::Pointer referenceSliceGeometry; referenceSliceGeometry = m_ReferenceSlice->GetGeometry(); itk::Index<3> indexInReferenceSlice; itk::Index<2> indexInReferenceSlice2D; referenceSliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), indexInReferenceSlice); indexInReferenceSlice2D[0] = indexInReferenceSlice[0]; indexInReferenceSlice2D[1] = indexInReferenceSlice[1]; // Get seed neighborhood ScalarType averageValue(0); AccessFixedDimensionByItk_3(m_ReferenceSlice, GetNeighborhoodAverage, 2, indexInReferenceSlice2D, &averageValue, 1); m_SeedValue = averageValue; MITK_DEBUG << "Seed value is " << m_SeedValue; // Calculate initial thresholds AccessFixedDimensionByItk(m_ReferenceSlice, CalculateInitialThresholds, 2); m_Thresholds[0] = m_InitialThresholds[0]; m_Thresholds[1] = m_InitialThresholds[1]; // Perform region growing mitk::Image::Pointer resultImage = mitk::Image::New(); AccessFixedDimensionByItk_3( m_ReferenceSlice, StartRegionGrowing, 2, indexInWorkingSlice2D, m_Thresholds, resultImage); resultImage->SetGeometry(workingSliceGeometry); // Extract contour if (resultImage.IsNotNull() && m_ConnectedComponentValue >= 1) { float isoOffset = 0.33; mitk::ImageToContourModelFilter::Pointer contourExtractor = mitk::ImageToContourModelFilter::New(); contourExtractor->SetInput(resultImage); contourExtractor->SetContourValue(m_ConnectedComponentValue - isoOffset); contourExtractor->Update(); ContourModel::Pointer resultContour = ContourModel::New(); resultContour = contourExtractor->GetOutput(); // Show contour if (resultContour.IsNotNull()) { ContourModel::Pointer resultContourWorld = FeedbackContourTool::BackProjectContourFrom2DSlice( workingSliceGeometry, FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, resultContour)); - // this is not a beautiful solution, just one that works, check T22412 for details - auto t = positionEvent->GetSender()->GetTimeStep(); - - FeedbackContourTool::SetFeedbackContour(0 != t - ? ContourModelUtils::MoveZerothContourTimeStep(resultContourWorld, t) - : resultContourWorld); + FeedbackContourTool::UpdateCurrentFeedbackContour(resultContourWorld); FeedbackContourTool::SetFeedbackContourVisible(true); mitk::RenderingManager::GetInstance()->RequestUpdate(m_LastEventSender->GetRenderWindow()); } } } } void mitk::RegionGrowingTool::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent) { // Until OnMousePressedInside() implements a behaviour, we're just returning here whenever m_PaintingPixelValue is 0, // i.e. when the user clicked inside the segmentation if (m_PaintingPixelValue == 0) { return; } auto *positionEvent = dynamic_cast(interactionEvent); if (m_ReferenceSlice.IsNotNull() && positionEvent) { // Get geometry and indices mitk::BaseGeometry::Pointer workingSliceGeometry; workingSliceGeometry = m_WorkingSlice->GetGeometry(); itk::Index<2> indexInWorkingSlice2D; indexInWorkingSlice2D[0] = m_SeedPoint[0]; indexInWorkingSlice2D[1] = m_SeedPoint[1]; m_ScreenYDifference += positionEvent->GetPointerPositionOnScreen()[1] - m_LastScreenPosition[1]; m_ScreenXDifference += positionEvent->GetPointerPositionOnScreen()[0] - m_LastScreenPosition[0]; - m_LastScreenPosition = positionEvent->GetPointerPositionOnScreen(); + m_LastScreenPosition = Point2I(positionEvent->GetPointerPositionOnScreen()); // Moving the mouse up and down adjusts the width of the threshold window, // moving it left and right shifts the threshold window m_Thresholds[0] = std::min(m_SeedValue, m_InitialThresholds[0] - (m_ScreenYDifference - m_ScreenXDifference) * m_MouseDistanceScaleFactor); m_Thresholds[1] = std::max(m_SeedValue, m_InitialThresholds[1] + (m_ScreenYDifference + m_ScreenXDifference) * m_MouseDistanceScaleFactor); // Do not exceed the pixel type extrema of the reference slice, though m_Thresholds[0] = std::max(m_ThresholdExtrema[0], m_Thresholds[0]); m_Thresholds[1] = std::min(m_ThresholdExtrema[1], m_Thresholds[1]); // Perform region growing again and show the result mitk::Image::Pointer resultImage = mitk::Image::New(); AccessFixedDimensionByItk_3( m_ReferenceSlice, StartRegionGrowing, 2, indexInWorkingSlice2D, m_Thresholds, resultImage); resultImage->SetGeometry(workingSliceGeometry); // Update the contour if (resultImage.IsNotNull() && m_ConnectedComponentValue >= 1) { float isoOffset = 0.33; mitk::ImageToContourModelFilter::Pointer contourExtractor = mitk::ImageToContourModelFilter::New(); contourExtractor->SetInput(resultImage); contourExtractor->SetContourValue(m_ConnectedComponentValue - isoOffset); contourExtractor->Update(); ContourModel::Pointer resultContour = ContourModel::New(); resultContour = contourExtractor->GetOutput(); // Show contour if (resultContour.IsNotNull()) { ContourModel::Pointer resultContourWorld = FeedbackContourTool::BackProjectContourFrom2DSlice( workingSliceGeometry, FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, resultContour)); - // this is not a beautiful solution, just one that works, check T22412 for details - int timestep = positionEvent->GetSender()->GetTimeStep(); - if (0 != timestep) - { - int size = resultContourWorld->GetNumberOfVertices(0); - auto resultContourTimeWorld = mitk::ContourModel::New(); - resultContourTimeWorld->Expand(timestep + 1); - for (int loop = 0; loop < size; ++loop) - { - resultContourTimeWorld->AddVertex(resultContourWorld->GetVertexAt(loop, 0), timestep); - } - FeedbackContourTool::SetFeedbackContour(resultContourTimeWorld); - } - else - { - FeedbackContourTool::SetFeedbackContour(resultContourWorld); - } + FeedbackContourTool::UpdateCurrentFeedbackContour(resultContourWorld); FeedbackContourTool::SetFeedbackContourVisible(true); mitk::RenderingManager::GetInstance()->ForceImmediateUpdate(positionEvent->GetSender()->GetRenderWindow()); } } } } void mitk::RegionGrowingTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent) { // Until OnMousePressedInside() implements a behaviour, we're just returning here whenever m_PaintingPixelValue is 0, // i.e. when the user clicked inside the segmentation if (m_PaintingPixelValue == 0) { return; } auto *positionEvent = dynamic_cast(interactionEvent); if (m_WorkingSlice.IsNotNull() && m_FillFeedbackContour && positionEvent) { - // Project contour into working slice - ContourModel *feedbackContour(FeedbackContourTool::GetFeedbackContour()); - - ContourModel::Pointer projectedContour; - - // this is not a beautiful solution, just one that works, check T22412 for details - int timestep = positionEvent->GetSender()->GetTimeStep(); - if (0 != timestep) - { - int size = feedbackContour->GetNumberOfVertices(timestep); - auto feedbackContourTime = mitk::ContourModel::New(); - feedbackContourTime->Expand(timestep + 1); - for (int loop = 0; loop < size; ++loop) - { - feedbackContourTime->AddVertex(feedbackContour->GetVertexAt(loop, timestep), 0); - } - - projectedContour = - FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, feedbackContourTime, false, false); - } - else - { - projectedContour = - FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, feedbackContour, false, false); - } - - // If there is a projected contour, fill it - if (projectedContour.IsNotNull()) - { - mitk::DataNode *workingNode(m_ToolManager->GetWorkingData(0)); - if (nullptr == workingNode) - { - return; - } - - auto workingImage = dynamic_cast(workingNode->GetData()); - if (nullptr == workingImage) - { - return; - } - - // m_PaintingPixelValue only decides whether to paint or erase - int activePixelValue = ContourModelUtils::GetActivePixelValue(workingImage); - mitk::ContourModelUtils::FillContourInSlice( - projectedContour, 0, m_WorkingSlice, workingImage, m_PaintingPixelValue * activePixelValue); - - this->WriteBackSegmentationResult(positionEvent, m_WorkingSlice); - FeedbackContourTool::SetFeedbackContourVisible(false); - } + this->WriteBackFeedbackContourAsSegmentationResult(positionEvent, m_PaintingPixelValue); m_ScreenYDifference = 0; m_ScreenXDifference = 0; } } diff --git a/Modules/Segmentation/Interactions/mitkSegTool2D.cpp b/Modules/Segmentation/Interactions/mitkSegTool2D.cpp index cd83b0f699..57ddfb9e90 100644 --- a/Modules/Segmentation/Interactions/mitkSegTool2D.cpp +++ b/Modules/Segmentation/Interactions/mitkSegTool2D.cpp @@ -1,629 +1,834 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkSegTool2D.h" #include "mitkToolManager.h" #include "mitkBaseRenderer.h" #include "mitkDataStorage.h" #include "mitkPlaneGeometry.h" -#include "mitkExtractDirectedPlaneImageFilter.h" -#include "mitkExtractImageFilter.h" - // Include of the new ImageExtractor -#include "mitkExtractDirectedPlaneImageFilterNew.h" #include "mitkMorphologicalOperations.h" -#include "mitkOverwriteDirectedPlaneImageFilter.h" -#include "mitkOverwriteSliceImageFilter.h" #include "mitkPlanarCircle.h" #include "usGetModuleContext.h" // Includes for 3DSurfaceInterpolation #include "mitkImageTimeSelector.h" #include "mitkImageToContourFilter.h" #include "mitkSurfaceInterpolationController.h" // includes for resling and overwriting #include #include #include #include - #include "mitkOperationEvent.h" #include "mitkUndoController.h" #include #include "mitkAbstractTransformGeometry.h" -#include "mitkImageAccessByItk.h" -#include "mitkImageCast.h" -#include "mitkImageToItk.h" #include "mitkLabelSetImage.h" +#include "mitkContourModelUtils.h" + +#include "itkImageRegionIterator.h" + #define ROUND(a) ((a) > 0 ? (int)((a) + 0.5) : -(int)(0.5 - (a))) bool mitk::SegTool2D::m_SurfaceInterpolationEnabled = true; +mitk::SegTool2D::SliceInformation::SliceInformation(const mitk::Image* aSlice, const mitk::PlaneGeometry* aPlane, mitk::TimeStepType aTimestep) : + slice(aSlice), plane(aPlane), timestep(aTimestep) +{ +} + mitk::SegTool2D::SegTool2D(const char *type, const us::Module *interactorModule) - : Tool(type, interactorModule), m_LastEventSender(nullptr), m_LastEventSlice(0), m_Contourmarkername("Position"), m_ShowMarkerNodes(false) + : Tool(type, interactorModule), m_Contourmarkername("Position") { Tool::m_EventConfig = "DisplayConfigMITKNoCrosshair.xml"; } mitk::SegTool2D::~SegTool2D() { } bool mitk::SegTool2D::FilterEvents(InteractionEvent *interactionEvent, DataNode *) { const auto *positionEvent = dynamic_cast(interactionEvent); bool isValidEvent = (positionEvent && // Only events of type mitk::InteractionPositionEvent interactionEvent->GetSender()->GetMapperID() == BaseRenderer::Standard2D // Only events from the 2D renderwindows ); return isValidEvent; } bool mitk::SegTool2D::DetermineAffectedImageSlice(const Image *image, const PlaneGeometry *plane, int &affectedDimension, int &affectedSlice) { assert(image); assert(plane); // compare normal of plane to the three axis vectors of the image Vector3D normal = plane->GetNormal(); Vector3D imageNormal0 = image->GetSlicedGeometry()->GetAxisVector(0); Vector3D imageNormal1 = image->GetSlicedGeometry()->GetAxisVector(1); Vector3D imageNormal2 = image->GetSlicedGeometry()->GetAxisVector(2); normal.Normalize(); imageNormal0.Normalize(); imageNormal1.Normalize(); imageNormal2.Normalize(); imageNormal0.SetVnlVector(vnl_cross_3d(normal.GetVnlVector(), imageNormal0.GetVnlVector())); imageNormal1.SetVnlVector(vnl_cross_3d(normal.GetVnlVector(), imageNormal1.GetVnlVector())); imageNormal2.SetVnlVector(vnl_cross_3d(normal.GetVnlVector(), imageNormal2.GetVnlVector())); double eps(0.00001); // axial if (imageNormal2.GetNorm() <= eps) { affectedDimension = 2; } // sagittal else if (imageNormal1.GetNorm() <= eps) { affectedDimension = 1; } // frontal else if (imageNormal0.GetNorm() <= eps) { affectedDimension = 0; } else { affectedDimension = -1; // no idea return false; } // determine slice number in image BaseGeometry *imageGeometry = image->GetGeometry(0); Point3D testPoint = imageGeometry->GetCenter(); Point3D projectedPoint; plane->Project(testPoint, projectedPoint); Point3D indexPoint; imageGeometry->WorldToIndex(projectedPoint, indexPoint); affectedSlice = ROUND(indexPoint[affectedDimension]); MITK_DEBUG << "indexPoint " << indexPoint << " affectedDimension " << affectedDimension << " affectedSlice " << affectedSlice; // check if this index is still within the image if (affectedSlice < 0 || affectedSlice >= static_cast(image->GetDimension(affectedDimension))) return false; return true; } void mitk::SegTool2D::UpdateSurfaceInterpolation(const Image *slice, const Image *workingImage, const PlaneGeometry *plane, bool detectIntersection) +{ + std::vector slices = { SliceInformation(slice, plane, 0)}; + Self::UpdateSurfaceInterpolation(slices, workingImage, detectIntersection); +} + +void mitk::SegTool2D::RemoveContourFromInterpolator(const SliceInformation& sliceInfo) +{ + mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo; + contourInfo.contourNormal = sliceInfo.plane->GetNormal(); + contourInfo.contourPoint = sliceInfo.plane->GetOrigin(); + mitk::SurfaceInterpolationController::GetInstance()->RemoveContour(contourInfo); +} + +void mitk::SegTool2D::UpdateSurfaceInterpolation(const std::vector& sliceInfos, + const Image* workingImage, + bool detectIntersection) { if (!m_SurfaceInterpolationEnabled) return; + //Remark: the ImageTimeSelector is just needed to extract a timestep/channel of + //the image in order to get the image dimension (time dimension and channel dimension + //stripped away). Therfore it is OK to always use time step 0 and channel 0 + mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); + timeSelector->SetInput(workingImage); + timeSelector->SetTimeNr(0); + timeSelector->SetChannelNr(0); + timeSelector->Update(); + const auto dimRefImg = timeSelector->GetOutput()->GetDimension(); + + if (dimRefImg != 3) + return; + + std::vector contourList; + contourList.reserve(sliceInfos.size()); + ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New(); - mitk::Surface::Pointer contour; + + std::vector relevantSlices = sliceInfos; if (detectIntersection) { - // Test whether there is something to extract or whether the slice just contains intersections of others - mitk::Image::Pointer slice2 = slice->Clone(); - mitk::MorphologicalOperations::Erode(slice2, 2, mitk::MorphologicalOperations::Ball); + relevantSlices.clear(); - contourExtractor->SetInput(slice2); - contourExtractor->Update(); - contour = contourExtractor->GetOutput(); - - if (contour->GetVtkPolyData()->GetNumberOfPoints() == 0) + for (const auto& sliceInfo : sliceInfos) { - // Remove contour! - mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo; - contourInfo.contourNormal = plane->GetNormal(); - contourInfo.contourPoint = plane->GetOrigin(); - mitk::SurfaceInterpolationController::GetInstance()->RemoveContour(contourInfo); - return; + // Test whether there is something to extract or whether the slice just contains intersections of others + mitk::Image::Pointer slice2 = sliceInfo.slice->Clone(); + mitk::MorphologicalOperations::Erode(slice2, 2, mitk::MorphologicalOperations::Ball); + + contourExtractor->SetInput(slice2); + contourExtractor->Update(); + mitk::Surface::Pointer contour = contourExtractor->GetOutput(); + + if (contour->GetVtkPolyData()->GetNumberOfPoints() == 0) + { + Self::RemoveContourFromInterpolator(sliceInfo); + } + else + { + relevantSlices.push_back(sliceInfo); + } } } - contourExtractor->SetInput(slice); - contourExtractor->Update(); - contour = contourExtractor->GetOutput(); - - mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); - timeSelector->SetInput(workingImage); - timeSelector->SetTimeNr(0); - timeSelector->SetChannelNr(0); - timeSelector->Update(); - Image::Pointer dimRefImg = timeSelector->GetOutput(); + if (relevantSlices.empty()) + return; - if (contour->GetVtkPolyData()->GetNumberOfPoints() != 0 && dimRefImg->GetDimension() == 3) + for (const auto& sliceInfo : relevantSlices) { - mitk::SurfaceInterpolationController::GetInstance()->AddNewContour(contour); - contour->DisconnectPipeline(); - } - else - { - // Remove contour! - mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo; - contourInfo.contourNormal = plane->GetNormal(); - contourInfo.contourPoint = plane->GetOrigin(); - mitk::SurfaceInterpolationController::GetInstance()->RemoveContour(contourInfo); + + contourExtractor->SetInput(sliceInfo.slice); + contourExtractor->Update(); + mitk::Surface::Pointer contour = contourExtractor->GetOutput(); + + if (contour->GetVtkPolyData()->GetNumberOfPoints() == 0) + { + Self::RemoveContourFromInterpolator(sliceInfo); + } + else + { + contour->DisconnectPipeline(); + contourList.push_back(contour); + } } + mitk::SurfaceInterpolationController::GetInstance()->AddNewContours(contourList); } + + mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImage(const InteractionPositionEvent *positionEvent, const Image *image, unsigned int component /*= 0*/) { if (!positionEvent) { return nullptr; } assert(positionEvent->GetSender()); // sure, right? - unsigned int timeStep = positionEvent->GetSender()->GetTimeStep(image); // get the timestep of the visible part (time-wise) of the image + const auto timeStep = positionEvent->GetSender()->GetTimeStep(image); // get the timestep of the visible part (time-wise) of the image return GetAffectedImageSliceAs2DImage(positionEvent->GetSender()->GetCurrentWorldPlaneGeometry(), image, timeStep, component); } -mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImage(const PlaneGeometry *planeGeometry, const Image *image, unsigned int timeStep, unsigned int component /*= 0*/) +mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImageByTimePoint(const PlaneGeometry* planeGeometry, const Image* image, TimePointType timePoint, unsigned int component /*= 0*/) +{ + if (!image || !planeGeometry) + { + return nullptr; + } + + if (!image->GetTimeGeometry()->IsValidTimePoint(timePoint)) + return nullptr; + + return SegTool2D::GetAffectedImageSliceAs2DImage(planeGeometry, image, image->GetTimeGeometry()->TimePointToTimeStep(timePoint), component); +} + + +mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImage(const PlaneGeometry *planeGeometry, const Image *image, TimeStepType timeStep, unsigned int component /*= 0*/) { if (!image || !planeGeometry) { return nullptr; } // Make sure that for reslicing and overwriting the same alogrithm is used. We can specify the mode of the vtk reslicer vtkSmartPointer reslice = vtkSmartPointer::New(); // set to false to extract a slice reslice->SetOverwriteMode(false); reslice->Modified(); // use ExtractSliceFilter with our specific vtkImageReslice for overwriting and extracting mitk::ExtractSliceFilter::Pointer extractor = mitk::ExtractSliceFilter::New(reslice); extractor->SetInput(image); extractor->SetTimeStep(timeStep); extractor->SetWorldGeometry(planeGeometry); extractor->SetVtkOutputRequest(false); extractor->SetResliceTransformByGeometry(image->GetTimeGeometry()->GetGeometryForTimeStep(timeStep)); // additionally extract the given component // default is 0; the extractor checks for multi-component images extractor->SetComponent(component); extractor->Modified(); extractor->Update(); Image::Pointer slice = extractor->GetOutput(); return slice; } -mitk::Image::Pointer mitk::SegTool2D::GetAffectedWorkingSlice(const InteractionPositionEvent *positionEvent) +mitk::Image::Pointer mitk::SegTool2D::GetAffectedWorkingSlice(const InteractionPositionEvent *positionEvent) const { - DataNode *workingNode(m_ToolManager->GetWorkingData(0)); + const auto workingNode = this->GetWorkingDataNode(); if (!workingNode) { return nullptr; } - auto *workingImage = dynamic_cast(workingNode->GetData()); + const auto *workingImage = dynamic_cast(workingNode->GetData()); if (!workingImage) { return nullptr; } return GetAffectedImageSliceAs2DImage(positionEvent, workingImage); } -mitk::Image::Pointer mitk::SegTool2D::GetAffectedReferenceSlice(const InteractionPositionEvent *positionEvent) +mitk::Image::Pointer mitk::SegTool2D::GetAffectedReferenceSlice(const InteractionPositionEvent *positionEvent) const { - DataNode *referenceNode(m_ToolManager->GetReferenceData(0)); + DataNode* referenceNode = this->GetReferenceDataNode(); if (!referenceNode) { return nullptr; } auto *referenceImage = dynamic_cast(referenceNode->GetData()); if (!referenceImage) { return nullptr; } int displayedComponent = 0; if (referenceNode->GetIntProperty("Image.Displayed Component", displayedComponent)) { // found the displayed component return GetAffectedImageSliceAs2DImage(positionEvent, referenceImage, displayedComponent); } else { return GetAffectedImageSliceAs2DImage(positionEvent, referenceImage); } } -void mitk::SegTool2D::WriteBackSegmentationResult(const InteractionPositionEvent *positionEvent, Image *slice) +mitk::Image::Pointer mitk::SegTool2D::GetAffectedReferenceSlice(const PlaneGeometry* planeGeometry, TimeStepType timeStep) const +{ + DataNode* referenceNode = this->GetReferenceDataNode(); + if (!referenceNode) + { + return nullptr; + } + + auto* referenceImage = dynamic_cast(referenceNode->GetData()); + if (!referenceImage) + { + return nullptr; + } + + int displayedComponent = 0; + if (referenceNode->GetIntProperty("Image.Displayed Component", displayedComponent)) + { + // found the displayed component + return GetAffectedImageSliceAs2DImage(planeGeometry, referenceImage, timeStep, displayedComponent); + } + else + { + return GetAffectedImageSliceAs2DImage(planeGeometry, referenceImage, timeStep); + } +} + +void mitk::SegTool2D::Activated() +{ + Superclass::Activated(); + + m_ToolManager->SelectedTimePointChanged += + mitk::MessageDelegate(this, &mitk::SegTool2D::OnTimePointChangedInternal); + + m_LastTimePointTriggered = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); +} + +void mitk::SegTool2D::Deactivated() +{ + m_ToolManager->SelectedTimePointChanged -= + mitk::MessageDelegate(this, &mitk::SegTool2D::OnTimePointChangedInternal); + Superclass::Deactivated(); +} + +void mitk::SegTool2D::OnTimePointChangedInternal() +{ + if (m_IsTimePointChangeAware && nullptr != this->GetWorkingDataNode()) + { + const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); + + if (timePoint != m_LastTimePointTriggered) + { + m_LastTimePointTriggered = timePoint; + this->OnTimePointChanged(); + } + } +} + +void mitk::SegTool2D::OnTimePointChanged() +{ + //default implementation does nothing +} + +mitk::DataNode* mitk::SegTool2D::GetWorkingDataNode() const +{ + if (nullptr != m_ToolManager) + { + return m_ToolManager->GetWorkingData(0); + } + return nullptr; +} + +mitk::Image* mitk::SegTool2D::GetWorkingData() const +{ + auto node = this->GetWorkingDataNode(); + if (nullptr != node) + { + return dynamic_cast(node->GetData()); + } + return nullptr; +} + +mitk::DataNode* mitk::SegTool2D::GetReferenceDataNode() const +{ + if (nullptr != m_ToolManager) + { + return m_ToolManager->GetReferenceData(0); + } + return nullptr; +} + +mitk::Image* mitk::SegTool2D::GetReferenceData() const +{ + auto node = this->GetReferenceDataNode(); + if (nullptr != node) + { + return dynamic_cast(node->GetData()); + } + return nullptr; +} + + +void mitk::SegTool2D::WriteBackSegmentationResult(const InteractionPositionEvent *positionEvent, const Image * segmentationResult) { if (!positionEvent) return; const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry())); const auto *abstractTransformGeometry( dynamic_cast(positionEvent->GetSender()->GetCurrentWorldPlaneGeometry())); - if (planeGeometry && slice && !abstractTransformGeometry) + if (planeGeometry && segmentationResult && !abstractTransformGeometry) { - DataNode *workingNode(m_ToolManager->GetWorkingData(0)); + const auto workingNode = this->GetWorkingDataNode(); auto *image = dynamic_cast(workingNode->GetData()); - unsigned int timeStep = positionEvent->GetSender()->GetTimeStep(image); - this->WriteBackSegmentationResult(planeGeometry, slice, timeStep); + const auto timeStep = positionEvent->GetSender()->GetTimeStep(image); + this->WriteBackSegmentationResult(planeGeometry, segmentationResult, timeStep); } } +void mitk::SegTool2D::WriteBackSegmentationResult(const DataNode* workingNode, const PlaneGeometry* planeGeometry, const Image* segmentationResult, TimeStepType timeStep) +{ + if (!planeGeometry || !segmentationResult) + return; + + SliceInformation sliceInfo(segmentationResult, const_cast(planeGeometry), timeStep); + Self::WriteBackSegmentationResults(workingNode, { sliceInfo }, true); +} + void mitk::SegTool2D::WriteBackSegmentationResult(const PlaneGeometry *planeGeometry, - Image *slice, - unsigned int timeStep) + const Image * segmentationResult, + TimeStepType timeStep) { - if (!planeGeometry || !slice) + if (!planeGeometry || !segmentationResult) return; - SliceInformation sliceInfo(slice, const_cast(planeGeometry), timeStep); - this->WriteSliceToVolume(sliceInfo); - DataNode *workingNode(m_ToolManager->GetWorkingData(0)); - auto *image = dynamic_cast(workingNode->GetData()); + SliceInformation sliceInfo(segmentationResult, const_cast(planeGeometry), timeStep); + WriteBackSegmentationResults({ sliceInfo }, true); +} - this->UpdateSurfaceInterpolation(slice, image, planeGeometry, false); +void mitk::SegTool2D::WriteBackSegmentationResults(const std::vector &sliceList, + bool writeSliceToVolume) +{ + if (sliceList.empty()) + { + return; + } - if (m_SurfaceInterpolationEnabled) - this->AddContourmarker(); + if (nullptr == m_LastEventSender) + { + MITK_WARN << "Cannot write tool results. Tool seems to be in an invalid state, as no interaction event was recieved but is expected."; + return; + } - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + const auto workingNode = this->GetWorkingDataNode(); + + mitk::SegTool2D::WriteBackSegmentationResults(workingNode, sliceList, writeSliceToVolume); + + // the first geometry is needed otherwise restoring the position is not working + const auto* plane3 = + dynamic_cast(dynamic_cast( + m_LastEventSender->GetSliceNavigationController()->GetCurrentGeometry3D()) + ->GetPlaneGeometry(0)); + unsigned int slicePosition = m_LastEventSender->GetSliceNavigationController()->GetSlice()->GetPos(); + + /* A cleaner solution would be to add a contour marker for each slice info. It currently + does not work as the contour markers expect that the plane is always the plane of slice 0. + Had not the time to do it properly no. Should be solved by T28146*/ + this->AddContourmarker(plane3, slicePosition); } -void mitk::SegTool2D::WriteBackSegmentationResult(const std::vector &sliceList, - bool writeSliceToVolume) +void mitk::SegTool2D::WriteBackSegmentationResults(const DataNode* workingNode, const std::vector& sliceList, bool writeSliceToVolume) { - std::vector contourList; - contourList.reserve(sliceList.size()); - ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New(); + if (sliceList.empty()) + { + return; + } + + if (nullptr == workingNode) + { + mitkThrow() << "Cannot write slice to working node. Working node is invalid."; + } - DataNode *workingNode(m_ToolManager->GetWorkingData(0)); - auto *image = dynamic_cast(workingNode->GetData()); + auto* image = dynamic_cast(workingNode->GetData()); - mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); - timeSelector->SetInput(image); - timeSelector->SetTimeNr(0); - timeSelector->SetChannelNr(0); - timeSelector->Update(); - Image::Pointer dimRefImg = timeSelector->GetOutput(); + if (nullptr == image) + { + mitkThrow() << "Cannot write slice to working node. Working node does not contain an image."; + } - for (unsigned int i = 0; i < sliceList.size(); ++i) + for (const auto& sliceInfo : sliceList) { - SliceInformation currentSliceInfo = sliceList.at(i); - if (writeSliceToVolume) - this->WriteSliceToVolume(currentSliceInfo); - if (m_SurfaceInterpolationEnabled && dimRefImg->GetDimension() == 3) + if (writeSliceToVolume && nullptr != sliceInfo.plane && sliceInfo.slice.IsNotNull()) { - currentSliceInfo.slice->DisconnectPipeline(); - contourExtractor->SetInput(currentSliceInfo.slice); - contourExtractor->Update(); - mitk::Surface::Pointer contour = contourExtractor->GetOutput(); - contour->DisconnectPipeline(); - - contourList.push_back(contour); + mitk::SegTool2D::WriteSliceToVolume(image, sliceInfo, true); } } - mitk::SurfaceInterpolationController::GetInstance()->AddNewContours(contourList); + + mitk::SegTool2D::UpdateSurfaceInterpolation(sliceList, image, false); + + // also mark its node as modified (T27308). Can be removed if T27307 + // is properly solved + if (workingNode != nullptr) workingNode->Modified(); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } -void mitk::SegTool2D::WriteSliceToVolume(const mitk::SegTool2D::SliceInformation &sliceInfo) +void mitk::SegTool2D::WriteSliceToVolume(Image* workingImage, const PlaneGeometry* planeGeometry, const Image* slice, TimeStepType timeStep, bool allowUndo) { - DataNode *workingNode(m_ToolManager->GetWorkingData(0)); - auto *image = dynamic_cast(workingNode->GetData()); + SliceInformation sliceInfo(slice, planeGeometry, timeStep); + WriteSliceToVolume(workingImage, sliceInfo , allowUndo); +} - /*============= BEGIN undo/redo feature block ========================*/ - // Create undo operation by caching the not yet modified slices - mitk::Image::Pointer originalSlice = GetAffectedImageSliceAs2DImage(sliceInfo.plane, image, sliceInfo.timestep); - auto *undoOperation = - new DiffSliceOperation(image, - originalSlice, - dynamic_cast(originalSlice->GetGeometry()), - sliceInfo.timestep, - sliceInfo.plane); - /*============= END undo/redo feature block ========================*/ +void mitk::SegTool2D::WriteSliceToVolume(Image* workingImage, const SliceInformation &sliceInfo, bool allowUndo) +{ + if (nullptr == workingImage) + { + mitkThrow() << "Cannot write slice to working node. Working node does not contain an image."; + } + + DiffSliceOperation* undoOperation = nullptr; + + if (allowUndo) + { + /*============= BEGIN undo/redo feature block ========================*/ + // Create undo operation by caching the not yet modified slices + mitk::Image::Pointer originalSlice = GetAffectedImageSliceAs2DImage(sliceInfo.plane, workingImage, sliceInfo.timestep); + undoOperation = + new DiffSliceOperation(workingImage, + originalSlice, + dynamic_cast(originalSlice->GetGeometry()), + sliceInfo.timestep, + sliceInfo.plane); + /*============= END undo/redo feature block ========================*/ + } // Make sure that for reslicing and overwriting the same alogrithm is used. We can specify the mode of the vtk // reslicer vtkSmartPointer reslice = vtkSmartPointer::New(); // Set the slice as 'input' - reslice->SetInputSlice(sliceInfo.slice->GetVtkImageData()); + // casting const away is needed and OK as long the OverwriteMode of + // mitkVTKImageOverwrite is true. + // Reason: because then the input slice is not touched but + // used to overwrite the input of the ExtractSliceFilter. + auto noneConstSlice = const_cast(sliceInfo.slice.GetPointer()); + reslice->SetInputSlice(noneConstSlice->GetVtkImageData()); // set overwrite mode to true to write back to the image volume reslice->SetOverwriteMode(true); reslice->Modified(); mitk::ExtractSliceFilter::Pointer extractor = mitk::ExtractSliceFilter::New(reslice); - extractor->SetInput(image); + extractor->SetInput(workingImage); extractor->SetTimeStep(sliceInfo.timestep); extractor->SetWorldGeometry(sliceInfo.plane); extractor->SetVtkOutputRequest(false); - extractor->SetResliceTransformByGeometry(image->GetGeometry(sliceInfo.timestep)); + extractor->SetResliceTransformByGeometry(workingImage->GetGeometry(sliceInfo.timestep)); extractor->Modified(); extractor->Update(); // the image was modified within the pipeline, but not marked so - image->Modified(); - image->GetVtkImageData()->Modified(); - - // also mark its node as modified (T27308). Can be removed if T27307 - // is properly solved - if (workingNode != nullptr) workingNode->Modified(); - - /*============= BEGIN undo/redo feature block ========================*/ - // specify the undo operation with the edited slice - auto *doOperation = - new DiffSliceOperation(image, - extractor->GetOutput(), - dynamic_cast(sliceInfo.slice->GetGeometry()), - sliceInfo.timestep, - sliceInfo.plane); - - // create an operation event for the undo stack - OperationEvent *undoStackItem = - new OperationEvent(DiffSliceOperationApplier::GetInstance(), doOperation, undoOperation, "Segmentation"); + workingImage->Modified(); + workingImage->GetVtkImageData()->Modified(); - // add it to the undo controller - UndoStackItem::IncCurrObjectEventId(); - UndoStackItem::IncCurrGroupEventId(); - UndoController::GetCurrentUndoModel()->SetOperationEvent(undoStackItem); + if (allowUndo) + { + /*============= BEGIN undo/redo feature block ========================*/ + // specify the redo operation with the edited slice + auto* doOperation = + new DiffSliceOperation(workingImage, + extractor->GetOutput(), + dynamic_cast(sliceInfo.slice->GetGeometry()), + sliceInfo.timestep, + sliceInfo.plane); + + // create an operation event for the undo stack + OperationEvent* undoStackItem = + new OperationEvent(DiffSliceOperationApplier::GetInstance(), doOperation, undoOperation, "Segmentation"); + + // add it to the undo controller + UndoStackItem::IncCurrObjectEventId(); + UndoStackItem::IncCurrGroupEventId(); + UndoController::GetCurrentUndoModel()->SetOperationEvent(undoStackItem); + /*============= END undo/redo feature block ========================*/ + } - // clear the pointers as the operation are stored in the undocontroller and also deleted from there - undoOperation = nullptr; - doOperation = nullptr; - /*============= END undo/redo feature block ========================*/ } + void mitk::SegTool2D::SetShowMarkerNodes(bool status) { m_ShowMarkerNodes = status; } void mitk::SegTool2D::SetEnable3DInterpolation(bool enabled) { m_SurfaceInterpolationEnabled = enabled; } -int mitk::SegTool2D::AddContourmarker() + +int mitk::SegTool2D::AddContourmarker(const PlaneGeometry* planeGeometry, unsigned int sliceIndex) { - if (m_LastEventSender == nullptr) + if (planeGeometry == nullptr) return -1; us::ServiceReference serviceRef = us::GetModuleContext()->GetServiceReference(); PlanePositionManagerService *service = us::GetModuleContext()->GetService(serviceRef); - unsigned int slicePosition = m_LastEventSender->GetSliceNavigationController()->GetSlice()->GetPos(); - - // the first geometry is needed otherwise restoring the position is not working - const auto *plane = - dynamic_cast(dynamic_cast( - m_LastEventSender->GetSliceNavigationController()->GetCurrentGeometry3D()) - ->GetPlaneGeometry(0)); - unsigned int size = service->GetNumberOfPlanePositions(); - unsigned int id = service->AddNewPlanePosition(plane, slicePosition); + unsigned int id = service->AddNewPlanePosition(planeGeometry, sliceIndex); mitk::PlanarCircle::Pointer contourMarker = mitk::PlanarCircle::New(); mitk::Point2D p1; - plane->Map(plane->GetCenter(), p1); + planeGeometry->Map(planeGeometry->GetCenter(), p1); mitk::Point2D p2 = p1; - p2[0] -= plane->GetSpacing()[0]; - p2[1] -= plane->GetSpacing()[1]; + p2[0] -= planeGeometry->GetSpacing()[0]; + p2[1] -= planeGeometry->GetSpacing()[1]; contourMarker->PlaceFigure(p1); contourMarker->SetCurrentControlPoint(p1); - contourMarker->SetPlaneGeometry(const_cast(plane)); + contourMarker->SetPlaneGeometry(planeGeometry->Clone()); std::stringstream markerStream; - mitk::DataNode *workingNode(m_ToolManager->GetWorkingData(0)); + auto workingNode = this->GetWorkingDataNode(); markerStream << m_Contourmarkername; markerStream << " "; markerStream << id + 1; DataNode::Pointer rotatedContourNode = DataNode::New(); rotatedContourNode->SetData(contourMarker); rotatedContourNode->SetProperty("name", StringProperty::New(markerStream.str())); rotatedContourNode->SetProperty("isContourMarker", BoolProperty::New(true)); rotatedContourNode->SetBoolProperty("PlanarFigureInitializedWindow", true, m_LastEventSender); rotatedContourNode->SetProperty("includeInBoundingBox", BoolProperty::New(false)); rotatedContourNode->SetProperty("helper object", mitk::BoolProperty::New(!m_ShowMarkerNodes)); rotatedContourNode->SetProperty("planarfigure.drawcontrolpoints", BoolProperty::New(false)); rotatedContourNode->SetProperty("planarfigure.drawname", BoolProperty::New(false)); rotatedContourNode->SetProperty("planarfigure.drawoutline", BoolProperty::New(false)); rotatedContourNode->SetProperty("planarfigure.drawshadow", BoolProperty::New(false)); - if (plane) + if (planeGeometry) { if (id == size) { m_ToolManager->GetDataStorage()->Add(rotatedContourNode, workingNode); } else { mitk::NodePredicateProperty::Pointer isMarker = mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true)); mitk::DataStorage::SetOfObjects::ConstPointer markers = m_ToolManager->GetDataStorage()->GetDerivations(workingNode, isMarker); for (auto iter = markers->begin(); iter != markers->end(); ++iter) { std::string nodeName = (*iter)->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int markerId = atof(nodeName.substr(t + 1).c_str()) - 1; if (id == markerId) { return id; } } m_ToolManager->GetDataStorage()->Add(rotatedContourNode, workingNode); } } return id; } -void mitk::SegTool2D::InteractiveSegmentationBugMessage(const std::string &message) +void mitk::SegTool2D::InteractiveSegmentationBugMessage(const std::string &message) const { MITK_ERROR << "********************************************************************************" << std::endl << " " << message << std::endl << "********************************************************************************" << std::endl << " " << std::endl << " If your image is rotated or the 2D views don't really contain the patient image, try to press the " "button next to the image selection. " << std::endl << " " << std::endl << " Please file a BUG REPORT: " << std::endl << " https://phabricator.mitk.org/" << std::endl << " Contain the following information:" << std::endl << " - What image were you working on?" << std::endl << " - Which region of the image?" << std::endl << " - Which tool did you use?" << std::endl << " - What did you do?" << std::endl << " - What happened (not)? What did you expect?" << std::endl; } template void InternalWritePreviewOnWorkingImage(itk::Image *targetSlice, const mitk::Image *sourceSlice, mitk::Image *originalImage, int overwritevalue) { typedef itk::Image SliceType; typename SliceType::Pointer sourceSliceITK; CastToItkImage(sourceSlice, sourceSliceITK); // now the original slice and the ipSegmentation-painted slice are in the same format, and we can just copy all pixels // that are non-zero typedef itk::ImageRegionIterator OutputIteratorType; typedef itk::ImageRegionConstIterator InputIteratorType; InputIteratorType inputIterator(sourceSliceITK, sourceSliceITK->GetLargestPossibleRegion()); OutputIteratorType outputIterator(targetSlice, targetSlice->GetLargestPossibleRegion()); outputIterator.GoToBegin(); inputIterator.GoToBegin(); auto *workingImage = dynamic_cast(originalImage); assert(workingImage); int activePixelValue = workingImage->GetActiveLabel()->GetValue(); if (activePixelValue == 0) // if exterior is the active label { while (!outputIterator.IsAtEnd()) { if (inputIterator.Get() != 0) { outputIterator.Set(overwritevalue); } ++outputIterator; ++inputIterator; } } else if (overwritevalue != 0) // if we are not erasing { while (!outputIterator.IsAtEnd()) { auto targetValue = static_cast(outputIterator.Get()); if (inputIterator.Get() != 0) { if (!workingImage->GetLabel(targetValue)->GetLocked()) { outputIterator.Set(overwritevalue); } } if (targetValue == overwritevalue) { outputIterator.Set(inputIterator.Get()); } ++outputIterator; ++inputIterator; } } else // if we are erasing { while (!outputIterator.IsAtEnd()) { const int targetValue = outputIterator.Get(); if (inputIterator.Get() != 0) { if (targetValue == activePixelValue) outputIterator.Set(overwritevalue); } ++outputIterator; ++inputIterator; } } } void mitk::SegTool2D::WritePreviewOnWorkingImage( - Image *targetSlice, Image *sourceSlice, mitk::Image *workingImage, int paintingPixelValue, int) + Image *targetSlice, const Image *sourceSlice, const Image *workingImage, int paintingPixelValue) { - if ((!targetSlice) || (!sourceSlice)) - return; - AccessFixedDimensionByItk_3( - targetSlice, InternalWritePreviewOnWorkingImage, 2, sourceSlice, workingImage, paintingPixelValue); + if (nullptr == targetSlice) + { + mitkThrow() << "Cannot write preview on working image. Target slice does not point to a valid instance."; + } + + if (nullptr == sourceSlice) + { + mitkThrow() << "Cannot write preview on working image. Source slice does not point to a valid instance."; + } + + if (nullptr == workingImage) + { + mitkThrow() << "Cannot write preview on working image. Working image does not point to a valid instance."; + } + + auto constVtkSource = sourceSlice->GetVtkImageData(); + /*Need to const cast because Vtk interface does not support const correctly. + (or I am not experienced enough to use it correctly)*/ + auto nonConstVtkSource = const_cast(constVtkSource); + + ContourModelUtils::FillSliceInSlice(nonConstVtkSource, targetSlice->GetVtkImageData(), workingImage, paintingPixelValue); } diff --git a/Modules/Segmentation/Interactions/mitkSegTool2D.h b/Modules/Segmentation/Interactions/mitkSegTool2D.h index 474b90fae7..1c58bbf035 100644 --- a/Modules/Segmentation/Interactions/mitkSegTool2D.h +++ b/Modules/Segmentation/Interactions/mitkSegTool2D.h @@ -1,199 +1,294 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkSegTool2D_h_Included #define mitkSegTool2D_h_Included #include "mitkCommon.h" #include "mitkImage.h" #include "mitkTool.h" #include #include "mitkInteractionPositionEvent.h" #include "mitkInteractionConst.h" #include "mitkPlanePositionManager.h" #include "mitkRestorePlanePositionOperation.h" #include namespace mitk { class BaseRenderer; /** \brief Abstract base class for segmentation tools. \sa Tool \ingroup Interaction \ingroup ToolManagerEtAl Implements 2D segmentation specific helper methods, that might be of use to all kind of 2D segmentation tools. At the moment these are: - Determination of the slice where the user paints upon (DetermineAffectedImageSlice) - Projection of a 3D contour onto a 2D plane/slice SegTool2D tries to structure the interaction a bit. If you pass "PressMoveRelease" as the interaction type of your derived tool, you might implement the methods OnMousePressed, OnMouseMoved, and OnMouseReleased. Yes, your guess about when they are called is correct. \warning Only to be instantiated by mitk::ToolManager. $Author$ */ class MITKSEGMENTATION_EXPORT SegTool2D : public Tool { public: mitkClassMacro(SegTool2D, Tool); /** \brief Calculates for a given Image and PlaneGeometry, which slice of the image (in index corrdinates) is meant by the plane. \return false, if no slice direction seems right (e.g. rotated planes) \param image \param plane \param affectedDimension The image dimension, which is constant for all points in the plane, e.g. Axial --> 2 \param affectedSlice The index of the image slice */ static bool DetermineAffectedImageSlice(const Image *image, const PlaneGeometry *plane, int &affectedDimension, int &affectedSlice); /** * @brief Updates the surface interpolation by extracting the contour form the given slice. * @param slice the slice from which the contour should be extracted * @param workingImage the segmentation image * @param plane the plane in which the slice lies * @param detectIntersection if true the slice is eroded before contour extraction. If the slice is empty after the * erosion it is most * likely an intersecting contour an will not be added to the SurfaceInterpolationController */ static void UpdateSurfaceInterpolation(const Image *slice, const Image *workingImage, const PlaneGeometry *plane, bool detectIntersection); + /** + * \brief Extract the slice of an image that the user just scribbles on. The given component denotes the vector component of an vector image. + * + * \param positionEvent Event that specifies the plane that should be used to slice + * \param image Image that should be sliced + * \param component The component to be extracted of a given multi-component image. -1 is the default parameter to denote an invalid component. + * + * \return 'nullptr' if SegTool2D is either unable to determine which slice was affected, or if there was some problem + * getting the image data at that position. + */ + static Image::Pointer GetAffectedImageSliceAs2DImage(const InteractionPositionEvent* positionEvent, const Image* image, unsigned int component = 0); + + /** + * \brief Extract the slice of an image cut by given plane. The given component denotes the vector component of a vector image. + * + * \param planeGeometry Geometry defining the slice that should be cut out. + * \param image Image that should be sliced + * \param timeStep TimeStep of the image that shold be sliced + * \param component The component to be extracted of a given multi-component image. -1 is the default parameter to denote an invalid component. + * + * \return 'nullptr' if SegTool2D is either unable to determine which slice was affected, or if there was some problem + * getting the image data at that position. + */ + static Image::Pointer GetAffectedImageSliceAs2DImage(const PlaneGeometry* planeGeometry, + const Image* image, + TimeStepType timeStep, + unsigned int component = 0); + static Image::Pointer GetAffectedImageSliceAs2DImageByTimePoint(const PlaneGeometry* planeGeometry, + const Image* image, + TimePointType timePoint, + unsigned int component = 0); + + /** Convenience overloaded version that can be called for a given planeGeometry, slice image and time step. + * Calls static WriteBackSegmentationResults*/ + static void WriteBackSegmentationResult(const DataNode* workingNode, const PlaneGeometry* planeGeometry, const Image* segmentationResult, TimeStepType timeStep); + + /** Convenience overloaded version that can be called for a given planeGeometry, slice image and time step. + * For more details see protected WriteSliceToVolume version.*/ + static void WriteSliceToVolume(Image* workingImage, const PlaneGeometry* planeGeometry, const Image* slice, TimeStepType timeStep, bool allowUndo); + void SetShowMarkerNodes(bool); /** * \brief Enables or disables the 3D interpolation after writing back the 2D segmentation result, and defaults to * true. */ void SetEnable3DInterpolation(bool); + void Activated() override; + void Deactivated() override; + + itkSetMacro(IsTimePointChangeAware, bool); + itkGetMacro(IsTimePointChangeAware, bool); + itkBooleanMacro(IsTimePointChangeAware); + protected: SegTool2D(); // purposely hidden SegTool2D(const char *, const us::Module *interactorModule = nullptr); // purposely hidden ~SegTool2D() override; + /** + * @brief returns the segmentation node that should be modified by the tool. + */ + DataNode* GetWorkingDataNode() const; + Image* GetWorkingData() const; + + DataNode* GetReferenceDataNode() const; + Image* GetReferenceData() const; + + /** + * This function can be reimplemented by derived classes to react on changes of the current + * time point. Default implementation does nothing.*/ + virtual void OnTimePointChanged(); + struct SliceInformation { - mitk::Image::Pointer slice; - mitk::PlaneGeometry *plane; - unsigned int timestep; - - SliceInformation() {} - SliceInformation(mitk::Image *slice, mitk::PlaneGeometry *plane, unsigned int timestep) - { - this->slice = slice; - this->plane = plane; - this->timestep = timestep; - } + mitk::Image::ConstPointer slice; + const mitk::PlaneGeometry *plane = nullptr; + mitk::TimeStepType timestep = 0; + + SliceInformation() = default; + SliceInformation(const mitk::Image* aSlice, const mitk::PlaneGeometry* aPlane, mitk::TimeStepType aTimestep); }; /** - * \brief Filters events that cannot be handle by 2D segmentation tools - * - * Current an event is discarded if it was not sent by a 2D renderwindow and if it is - * not of type InteractionPositionEvent - */ - bool FilterEvents(InteractionEvent *interactionEvent, DataNode *dataNode) override; + * @brief Updates the surface interpolation by extracting the contour form the given slice. + * @param sliceInfos vector of slice information instances from which the contours should be extracted + * @param workingImage the segmentation image + * @param detectIntersection if true the slice is eroded before contour extraction. If the slice is empty after the + * erosion it is most + * likely an intersecting contour an will not be added to the SurfaceInterpolationController + */ + static void UpdateSurfaceInterpolation(const std::vector& sliceInfos, + const Image* workingImage, + bool detectIntersection); - /** - * \brief Extract the slice of an image that the user just scribbles on. The given component denotes the vector component of a dwi-image. - * - * \param positionEvent - * \param image - * \param component The component to be extracted of a given multi-component image. -1 is the default parameter to denote an invalid component. - * - * \return 'nullptr' if SegTool2D is either unable to determine which slice was affected, or if there was some problem - * getting the image data at that position. - */ - Image::Pointer GetAffectedImageSliceAs2DImage(const InteractionPositionEvent *positionEvent, const Image *image, unsigned int component = 0); /** - * \brief Extract the slice of an image cut by given plane. The given component denotes the vector component of a dwi-image. - * - * \param planeGeometry - * \param image - * \param timeStep - * \param component The component to be extracted of a given multi-component image. -1 is the default parameter to denote an invalid component. + * \brief Filters events that cannot be handled by 2D segmentation tools * - * \return 'nullptr' if SegTool2D is either unable to determine which slice was affected, or if there was some problem - * getting the image data at that position. + * Currently an event is discarded if it was not sent by a 2D renderwindow and if it is + * not of type InteractionPositionEvent */ - Image::Pointer GetAffectedImageSliceAs2DImage(const PlaneGeometry *planeGeometry, - const Image *image, - unsigned int timeStep, - unsigned int component = 0); + bool FilterEvents(InteractionEvent *interactionEvent, DataNode *dataNode) override; /** \brief Extract the slice of the currently selected working image that the user just scribbles on. \return nullptr if SegTool2D is either unable to determine which slice was affected, or if there was some problem getting the image data at that position, or just no working image is selected. */ - Image::Pointer GetAffectedWorkingSlice(const InteractionPositionEvent *); + Image::Pointer GetAffectedWorkingSlice(const InteractionPositionEvent *) const; /** \brief Extract the slice of the currently selected reference image that the user just scribbles on. \return nullptr if SegTool2D is either unable to determine which slice was affected, or if there was some problem getting the image data at that position, or just no reference image is selected. */ - Image::Pointer GetAffectedReferenceSlice(const InteractionPositionEvent *); - - void WriteBackSegmentationResult(const InteractionPositionEvent *, Image *); - - void WriteBackSegmentationResult(const PlaneGeometry *planeGeometry, Image *, unsigned int timeStep); + Image::Pointer GetAffectedReferenceSlice(const InteractionPositionEvent *) const; + /** Overload version that gets the reference slice passed on the passed plane geometry and timestep.*/ + Image::Pointer GetAffectedReferenceSlice(const PlaneGeometry* planeGeometry, TimeStepType timeStep) const; + + /** Convenience version that can be called for a given event (which is used to deduce timepoint and plane) and a slice image. + * Calls non static WriteBackSegmentationResults*/ + void WriteBackSegmentationResult(const InteractionPositionEvent *, const Image* segmentationResult); + + /** Convenience version that can be called for a given planeGeometry, slice image and time step. + * Calls non static WriteBackSegmentationResults*/ + void WriteBackSegmentationResult(const PlaneGeometry *planeGeometry, const Image* segmentationResult, TimeStepType timeStep); + + /** Overloaded version that calls the static version and also adds the contour markers. + * @remark If the sliceList is empty, this function does nothing.*/ + void WriteBackSegmentationResults(const std::vector &sliceList, bool writeSliceToVolume = true); + + /** \brief Writes all provided source slices into the data of the passed workingNode. + * The function does the following: 1) for every passed slice write it to workingNode (and generate and undo/redo step); + * 2) update the surface interpolation and 3) marke the node as modified. + * @param workingNode Pointer to the node that contains the working image. + * @param sliceList Vector of all slices that should be written into the workingNode. If the list is + * empty, the function call does nothing. + * @param writeSliceToVolume If set to false the write operation (WriteSliceToVolume will be skipped) + * and only the surface interpolation will be updated. + * @pre workingNode must point to a valid instance and contain an image instance as data.*/ + static void WriteBackSegmentationResults(const DataNode* workingNode, const std::vector& sliceList, bool writeSliceToVolume = true); + + /** Writes the provided source slice into the target slice with the given pixel value. + * If passed workingImage is a LabelSetImage the label set rules will be applied when + * writing all non zero source pixels into the target slice (e.g. locked lables will not be touched) + * with the given paintingPixelValue. + * @param targetSlice Pointer to the slice that should be filled with the content of the sourceSlice. + * @param sourceSlice Pointer to the slice that is the source/preview every pixel will be (tried to be) transfered . + * @param workingImage Will be used to check if LabeSetImageRules have to be applied and the label set state. + * @param paintingPixelValue Value that will be used to paint onto target slice. + * @pre targetSlice must point to a valid instance. + * @pre sourceSlice must point to a valid instance. + * @pre workingImage must point to a valid instance.*/ + static void WritePreviewOnWorkingImage( + Image *targetSlice, const Image *sourceSlice, const Image *workingImage, int paintingPixelValue); + + /** Writes a provided slice into the passed working image. The content of working image that is covered + * by the slice will be completly overwritten. If asked for it also generates the needed + * undo/redo steps. + * @param workingImage Pointer to the image that is the target of the write operation. + * @param sliceInfo SliceInfo instance that containes the slice image, the defining plane geometry and time step. + * @param allowUndo Indicates if undo/redo operations should be registered for the write operation + * performed by this call. true: undo/redo will be generated; false: no undo/redo will be generated, so + * this operation cannot be revoked by the user. + * @pre workingImage must point to a valid instance.*/ + static void WriteSliceToVolume(Image* workingImage, const SliceInformation &sliceInfo, bool allowUndo); - void WriteBackSegmentationResult(const std::vector &sliceList, bool writeSliceToVolume = true); - - void WritePreviewOnWorkingImage( - Image *targetSlice, Image *sourceSlice, Image *workingImage, int paintingPixelValue, int timestep); - - void WriteSliceToVolume(const SliceInformation &sliceInfo); /** \brief Adds a new node called Contourmarker to the datastorage which holds a mitk::PlanarFigure. - By selecting this node the slicestack will be reoriented according to the PlanarFigure's Geometry + By selecting this node the slicestack will be reoriented according to the passed + PlanarFigure's Geometry */ - int AddContourmarker(); + int AddContourmarker(const PlaneGeometry* planeGeometry, unsigned int sliceIndex); - void InteractiveSegmentationBugMessage(const std::string &message); + void InteractiveSegmentationBugMessage(const std::string &message) const; - BaseRenderer *m_LastEventSender; - unsigned int m_LastEventSlice; + BaseRenderer *m_LastEventSender = nullptr; + unsigned int m_LastEventSlice = 0; + + itkGetMacro(LastTimePointTriggered, TimePointType); private: + /** Internal method that gets triggered as soon as the tool manager indicates a + * time point change. If the time point has changed since last time and tool + * is set to be time point change aware, OnTimePointChanged() will be called.*/ + void OnTimePointChangedInternal(); + + static void RemoveContourFromInterpolator(const SliceInformation& sliceInfo); + // The prefix of the contourmarkername. Suffix is a consecutive number const std::string m_Contourmarkername; - bool m_ShowMarkerNodes; + bool m_ShowMarkerNodes = false; static bool m_SurfaceInterpolationEnabled; + + bool m_IsTimePointChangeAware = true; + + TimePointType m_LastTimePointTriggered = 0.; }; } // namespace #endif diff --git a/Modules/Segmentation/Interactions/mitkSegmentationInteractor.cpp b/Modules/Segmentation/Interactions/mitkSegmentationInteractor.cpp index 4aec82aba5..1b67d32f1f 100644 --- a/Modules/Segmentation/Interactions/mitkSegmentationInteractor.cpp +++ b/Modules/Segmentation/Interactions/mitkSegmentationInteractor.cpp @@ -1,63 +1,63 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkSegmentationInteractor.h" #include "mitkInteractionPositionEvent.h" #include "mitkLabelSetImage.h" #include "mitkToolManager.h" #include "mitkToolManagerProvider.h" #include #include void mitk::SegmentationInteractor::ConnectActionsAndFunctions() { Superclass::ConnectActionsAndFunctions(); // CONNECT_FUNCTION("change_active_label", ChangeActiveLabel); } bool mitk::SegmentationInteractor::ChangeActiveLabel(StateMachineAction *, InteractionEvent *interactionEvent) { BaseRenderer::Pointer sender = interactionEvent->GetSender(); auto *positionEvent = static_cast(interactionEvent); // MLI TODO // m_LastDisplayCoordinate = m_CurrentDisplayCoordinate; // m_CurrentDisplayCoordinate = positionEvent->GetPointerPositionOnScreen(); auto *toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager( mitk::ToolManagerProvider::MULTILABEL_SEGMENTATION); assert(toolManager); DataNode *workingNode(toolManager->GetWorkingData(0)); if (workingNode) { auto *workingImage = dynamic_cast(workingNode->GetData()); assert(workingImage); - int timestep = positionEvent->GetSender()->GetTimeStep(); + const auto timestep = positionEvent->GetSender()->GetTimeStep(workingImage); int pixelValue = static_cast(workingImage->GetPixelValueByWorldCoordinate(positionEvent->GetPositionInWorld(), timestep)); workingImage->GetActiveLabelSet()->SetActiveLabel(pixelValue); // can be the background // Call Events // workingImage->ActiveLabelEvent.Send(pixelValue); // MLI TODO // toolManager->WorkingDataModified.Send(); } RenderingManager::GetInstance()->RequestUpdateAll(); return true; } diff --git a/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp b/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp index bf0bbfe459..da8a94ed20 100644 --- a/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp +++ b/Modules/Segmentation/Interactions/mitkSetRegionTool.cpp @@ -1,176 +1,138 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkSetRegionTool.h" #include "mitkToolManager.h" #include "mitkBaseRenderer.h" -#include "mitkImageDataItem.h" -#include "mitkLabelSetImage.h" #include -#include #include #include #include mitk::SetRegionTool::SetRegionTool(int paintingPixelValue) : FeedbackContourTool("PressMoveRelease"), m_PaintingPixelValue(paintingPixelValue) { } mitk::SetRegionTool::~SetRegionTool() { } void mitk::SetRegionTool::ConnectActionsAndFunctions() { CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed); CONNECT_FUNCTION("Release", OnMouseReleased); CONNECT_FUNCTION("Move", OnMouseMoved); } void mitk::SetRegionTool::Activated() { Superclass::Activated(); } void mitk::SetRegionTool::Deactivated() { Superclass::Deactivated(); } void mitk::SetRegionTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent) { auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; m_LastEventSender = positionEvent->GetSender(); m_LastEventSlice = m_LastEventSender->GetSlice(); // 1. Get the working image Image::Pointer workingSlice = FeedbackContourTool::GetAffectedWorkingSlice(positionEvent); if (workingSlice.IsNull()) return; // can't do anything without the segmentation // if click was outside the image, don't continue const BaseGeometry *sliceGeometry = workingSlice->GetGeometry(); itk::Index<3> projectedPointIn2D; sliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), projectedPointIn2D); if (!sliceGeometry->IsIndexInside(projectedPointIn2D)) { MITK_WARN << "Point outside of segmentation slice." << std::endl; return; // can't use that as a seed point } typedef itk::Image InputImageType; typedef InputImageType::IndexType IndexType; typedef itk::ConnectedThresholdImageFilter RegionGrowingFilterType; RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New(); // convert world coordinates to image indices IndexType seedIndex; sliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), seedIndex); // perform region growing in desired segmented region InputImageType::Pointer itkImage = InputImageType::New(); CastToItkImage(workingSlice, itkImage); regionGrower->SetInput(itkImage); regionGrower->AddSeed(seedIndex); InputImageType::PixelType bound = itkImage->GetPixel(seedIndex); regionGrower->SetLower(bound); regionGrower->SetUpper(bound); regionGrower->SetReplaceValue(1); itk::BinaryFillholeImageFilter::Pointer fillHolesFilter = itk::BinaryFillholeImageFilter::New(); fillHolesFilter->SetInput(regionGrower->GetOutput()); fillHolesFilter->SetForegroundValue(1); // Store result and preview mitk::Image::Pointer resultImage = mitk::GrabItkImageMemory(fillHolesFilter->GetOutput()); resultImage->SetGeometry(workingSlice->GetGeometry()); // Get the current working color DataNode *workingNode(m_ToolManager->GetWorkingData(0)); if (!workingNode) return; mitk::ImageToContourModelFilter::Pointer contourextractor = mitk::ImageToContourModelFilter::New(); contourextractor->SetInput(resultImage); contourextractor->Update(); mitk::ContourModel::Pointer awesomeContour = contourextractor->GetOutput(); - auto t = positionEvent->GetSender()->GetTimeStep(); - FeedbackContourTool::SetFeedbackContour(0 != t - ? ContourModelUtils::MoveZerothContourTimeStep(awesomeContour, t) - : awesomeContour); + this->UpdateCurrentFeedbackContour(awesomeContour); FeedbackContourTool::SetFeedbackContourVisible(true); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); } void mitk::SetRegionTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent) { auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; assert(positionEvent->GetSender()->GetRenderWindow()); // 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's // working image corresponds to that - FeedbackContourTool::SetFeedbackContourVisible(false); mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow()); - int timeStep = positionEvent->GetSender()->GetTimeStep(); - - DataNode *workingNode(m_ToolManager->GetWorkingData(0)); - if (!workingNode) - return; - - auto *image = dynamic_cast(workingNode->GetData()); - const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry())); - if (!image || !planeGeometry) - return; - - Image::Pointer slice = FeedbackContourTool::GetAffectedImageSliceAs2DImage(positionEvent, image); - - if (slice.IsNull()) - { - MITK_ERROR << "Unable to extract slice." << std::endl; - return; - } - - ContourModel *feedbackContour(FeedbackContourTool::GetFeedbackContour()); - ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice( - slice, feedbackContour, false, false); // false: don't add 0.5 (done by FillContourInSlice) - // false: don't constrain the contour to the image's inside - if (projectedContour.IsNull()) - return; - - int activePixelValue = ContourModelUtils::GetActivePixelValue(image); - - mitk::ContourModelUtils::FillContourInSlice( - projectedContour, timeStep, slice, image, m_PaintingPixelValue * activePixelValue); - - this->WriteBackSegmentationResult(positionEvent, slice); + this->WriteBackFeedbackContourAsSegmentationResult(positionEvent, m_PaintingPixelValue); } void mitk::SetRegionTool::OnMouseMoved(mitk::StateMachineAction *, mitk::InteractionEvent *) { } diff --git a/Modules/Segmentation/Interactions/mitkTool.cpp b/Modules/Segmentation/Interactions/mitkTool.cpp index 2c2f32e1e5..5f15bc5dbf 100644 --- a/Modules/Segmentation/Interactions/mitkTool.cpp +++ b/Modules/Segmentation/Interactions/mitkTool.cpp @@ -1,333 +1,333 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkTool.h" #include #include "mitkDisplayInteractor.h" #include "mitkDisplayActionEventBroadcast.h" #include "mitkImageReadAccessor.h" #include "mitkImageWriteAccessor.h" #include "mitkLevelWindowProperty.h" #include "mitkLookupTableProperty.h" #include "mitkProperties.h" #include "mitkVtkResliceInterpolationProperty.h" #include // us #include #include // itk #include mitk::Tool::Tool(const char *type, const us::Module *interactorModule) : m_EventConfig("DisplayConfigMITK.xml"), m_ToolManager(nullptr), m_PredicateImages(NodePredicateDataType::New("Image")), // for reference images m_PredicateDim3(NodePredicateDimension::New(3, 1)), m_PredicateDim4(NodePredicateDimension::New(4, 1)), m_PredicateDimension(mitk::NodePredicateOr::New(m_PredicateDim3, m_PredicateDim4)), m_PredicateImage3D(NodePredicateAnd::New(m_PredicateImages, m_PredicateDimension)), m_PredicateBinary(NodePredicateProperty::New("binary", BoolProperty::New(true))), m_PredicateNotBinary(NodePredicateNot::New(m_PredicateBinary)), m_PredicateSegmentation(NodePredicateProperty::New("segmentation", BoolProperty::New(true))), m_PredicateNotSegmentation(NodePredicateNot::New(m_PredicateSegmentation)), m_PredicateHelper(NodePredicateProperty::New("helper object", BoolProperty::New(true))), m_PredicateNotHelper(NodePredicateNot::New(m_PredicateHelper)), m_PredicateImageColorful(NodePredicateAnd::New(m_PredicateNotBinary, m_PredicateNotSegmentation)), m_PredicateImageColorfulNotHelper(NodePredicateAnd::New(m_PredicateImageColorful, m_PredicateNotHelper)), m_PredicateReference(NodePredicateAnd::New(m_PredicateImage3D, m_PredicateImageColorfulNotHelper)), m_IsSegmentationPredicate( NodePredicateAnd::New(NodePredicateOr::New(m_PredicateBinary, m_PredicateSegmentation), m_PredicateNotHelper)), m_InteractorType(type), m_DisplayInteractorConfigs(), m_InteractorModule(interactorModule) { } mitk::Tool::~Tool() { } bool mitk::Tool::CanHandle(const BaseData* referenceData, const BaseData* /*workingData*/) const { if (referenceData == nullptr) return false; return true; } void mitk::Tool::InitializeStateMachine() { if (m_InteractorType.empty()) return; try { auto isThisModule = nullptr == m_InteractorModule; auto module = isThisModule ? us::GetModuleContext()->GetModule() : m_InteractorModule; LoadStateMachine(m_InteractorType + ".xml", module); SetEventConfig(isThisModule ? "SegmentationToolsConfig.xml" : m_InteractorType + "Config.xml", module); } catch (const std::exception &e) { MITK_ERROR << "Could not load statemachine pattern " << m_InteractorType << ".xml with exception: " << e.what(); } } void mitk::Tool::Notify(InteractionEvent *interactionEvent, bool isHandled) { // to use the state machine pattern, // the event is passed to the state machine interface to be handled if (!isHandled) { this->HandleEvent(interactionEvent, nullptr); } } void mitk::Tool::ConnectActionsAndFunctions() { } bool mitk::Tool::FilterEvents(InteractionEvent *, DataNode *) { return true; } const char *mitk::Tool::GetGroup() const { return "default"; } void mitk::Tool::SetToolManager(ToolManager *manager) { m_ToolManager = manager; } void mitk::Tool::Activated() { // As a legacy solution the display interaction of the new interaction framework is disabled here to avoid conflicts // with tools // Note: this only affects InteractionEventObservers (formerly known as Listeners) all DataNode specific interaction // will still be enabled m_DisplayInteractorConfigs.clear(); std::vector> listEventObserver = us::GetModuleContext()->GetServiceReferences(); for (auto it = listEventObserver.begin(); it != listEventObserver.end(); ++it) { auto displayInteractor = dynamic_cast(us::GetModuleContext()->GetService(*it)); if (displayInteractor != nullptr) { // remember the original configuration m_DisplayInteractorConfigs.insert(std::make_pair(*it, displayInteractor->GetEventConfig())); // here the alternative configuration is loaded displayInteractor->SetEventConfig(m_EventConfig.c_str()); } auto displayActionEventBroadcast = dynamic_cast(us::GetModuleContext()->GetService(*it)); if (displayActionEventBroadcast != nullptr) { // remember the original configuration m_DisplayInteractorConfigs.insert(std::make_pair(*it, displayActionEventBroadcast->GetEventConfig())); // here the alternative configuration is loaded displayActionEventBroadcast->SetEventConfig(m_EventConfig.c_str()); } } } void mitk::Tool::Deactivated() { // Re-enabling InteractionEventObservers that have been previously disabled for legacy handling of Tools // in new interaction framework for (auto it = m_DisplayInteractorConfigs.begin(); it != m_DisplayInteractorConfigs.end(); ++it) { if (it->first) { auto displayInteractor = static_cast(us::GetModuleContext()->GetService(it->first)); if (displayInteractor != nullptr) { // here the regular configuration is loaded again displayInteractor->SetEventConfig(it->second); } auto displayActionEventBroadcast = dynamic_cast(us::GetModuleContext()->GetService(it->first)); if (displayActionEventBroadcast != nullptr) { // here the regular configuration is loaded again displayActionEventBroadcast->SetEventConfig(it->second); } } } m_DisplayInteractorConfigs.clear(); } itk::Object::Pointer mitk::Tool::GetGUI(const std::string &toolkitPrefix, const std::string &toolkitPostfix) { itk::Object::Pointer object; std::string classname = this->GetNameOfClass(); std::string guiClassname = toolkitPrefix + classname + toolkitPostfix; std::list allGUIs = itk::ObjectFactoryBase::CreateAllInstance(guiClassname.c_str()); for (auto iter = allGUIs.begin(); iter != allGUIs.end(); ++iter) { if (object.IsNull()) { object = dynamic_cast(iter->GetPointer()); } else { MITK_ERROR << "There is more than one GUI for " << classname << " (several factories claim ability to produce a " << guiClassname << " ) " << std::endl; return nullptr; // people should see and fix this error } } return object; } mitk::NodePredicateBase::ConstPointer mitk::Tool::GetReferenceDataPreference() const { return m_PredicateReference.GetPointer(); } mitk::NodePredicateBase::ConstPointer mitk::Tool::GetWorkingDataPreference() const { return m_IsSegmentationPredicate.GetPointer(); } mitk::DataNode::Pointer mitk::Tool::CreateEmptySegmentationNode(const Image *original, const std::string &organName, - const mitk::Color &color) + const mitk::Color &color) const { // we NEED a reference image for size etc. if (!original) return nullptr; // actually create a new empty segmentation PixelType pixelType(mitk::MakeScalarPixelType()); LabelSetImage::Pointer segmentation = LabelSetImage::New(); if (original->GetDimension() == 2) { const unsigned int dimensions[] = {original->GetDimension(0), original->GetDimension(1), 1}; segmentation->Initialize(pixelType, 3, dimensions); segmentation->AddLayer(); } else { segmentation->Initialize(original); } mitk::Label::Pointer label = mitk::Label::New(); label->SetName(organName); label->SetColor(color); label->SetValue(1); segmentation->GetActiveLabelSet()->AddLabel(label); segmentation->GetActiveLabelSet()->SetActiveLabel(1); unsigned int byteSize = sizeof(mitk::Label::PixelType); if (segmentation->GetDimension() < 4) { for (unsigned int dim = 0; dim < segmentation->GetDimension(); ++dim) { byteSize *= segmentation->GetDimension(dim); } mitk::ImageWriteAccessor writeAccess(segmentation.GetPointer(), segmentation->GetVolumeData(0)); memset(writeAccess.GetData(), 0, byteSize); } else { // if we have a time-resolved image we need to set memory to 0 for each time step for (unsigned int dim = 0; dim < 3; ++dim) { byteSize *= segmentation->GetDimension(dim); } for (unsigned int volumeNumber = 0; volumeNumber < segmentation->GetDimension(3); volumeNumber++) { mitk::ImageWriteAccessor writeAccess(segmentation.GetPointer(), segmentation->GetVolumeData(volumeNumber)); memset(writeAccess.GetData(), 0, byteSize); } } if (original->GetTimeGeometry()) { TimeGeometry::Pointer originalGeometry = original->GetTimeGeometry()->Clone(); segmentation->SetTimeGeometry(originalGeometry); } else { Tool::ErrorMessage("Original image does not have a 'Time sliced geometry'! Cannot create a segmentation."); return nullptr; } return CreateSegmentationNode(segmentation, organName, color); } mitk::DataNode::Pointer mitk::Tool::CreateSegmentationNode(Image *image, const std::string &organName, - const mitk::Color &color) + const mitk::Color &color) const { if (!image) return nullptr; // decorate the datatreenode with some properties DataNode::Pointer segmentationNode = DataNode::New(); segmentationNode->SetData(image); // name segmentationNode->SetProperty("name", StringProperty::New(organName)); // visualization properties segmentationNode->SetProperty("binary", BoolProperty::New(true)); segmentationNode->SetProperty("color", ColorProperty::New(color)); mitk::LookupTable::Pointer lut = mitk::LookupTable::New(); lut->SetType(mitk::LookupTable::MULTILABEL); mitk::LookupTableProperty::Pointer lutProp = mitk::LookupTableProperty::New(); lutProp->SetLookupTable(lut); segmentationNode->SetProperty("LookupTable", lutProp); segmentationNode->SetProperty("texture interpolation", BoolProperty::New(false)); segmentationNode->SetProperty("layer", IntProperty::New(10)); segmentationNode->SetProperty("levelwindow", LevelWindowProperty::New(LevelWindow(0.5, 1))); segmentationNode->SetProperty("opacity", FloatProperty::New(0.3)); segmentationNode->SetProperty("segmentation", BoolProperty::New(true)); segmentationNode->SetProperty("reslice interpolation", VtkResliceInterpolationProperty::New()); // otherwise -> segmentation appears in 2 // slices sometimes (only visual effect, not // different data) // For MITK-3M3 release, the volume of all segmentations should be shown segmentationNode->SetProperty("showVolume", BoolProperty::New(true)); return segmentationNode; } us::ModuleResource mitk::Tool::GetIconResource() const { // Each specific tool should load its own resource. This one will be invalid return us::ModuleResource(); } us::ModuleResource mitk::Tool::GetCursorIconResource() const { // Each specific tool should load its own resource. This one will be invalid return us::ModuleResource(); } diff --git a/Modules/Segmentation/Interactions/mitkTool.h b/Modules/Segmentation/Interactions/mitkTool.h index 16b2cf15a9..ddc998b8d0 100644 --- a/Modules/Segmentation/Interactions/mitkTool.h +++ b/Modules/Segmentation/Interactions/mitkTool.h @@ -1,270 +1,269 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 mitkTool_h_Included #define mitkTool_h_Included #include "itkObjectFactoryBase.h" #include "itkVersion.h" #include "mitkCommon.h" #include "mitkDataNode.h" #include "mitkEventStateMachine.h" #include "mitkInteractionEventObserver.h" #include "mitkLabelSetImage.h" #include "mitkMessage.h" #include "mitkNodePredicateAnd.h" #include "mitkNodePredicateDataType.h" #include "mitkNodePredicateDimension.h" #include "mitkNodePredicateNot.h" #include "mitkNodePredicateOr.h" #include "mitkNodePredicateProperty.h" #include "mitkToolEvents.h" #include "mitkToolFactoryMacro.h" #include #include #include #include #include #include #include "usServiceRegistration.h" namespace us { class ModuleResource; } namespace mitk { class ToolManager; /** \brief Base class of all tools used by mitk::ToolManager. \sa ToolManager \sa SegTool2D \ingroup Interaction \ingroup ToolManagerEtAl Every tool is a mitk::StateMachine, which can follow any transition pattern that it likes. One important thing to know is, that every derived tool should always call SuperClass::Deactivated() at the end of its own implementation of Deactivated, because mitk::Tool resets the StateMachine in this method. Only if you are very sure that you covered all possible things that might happen to your own tool, you should consider not to reset the StateMachine from time to time. To learn about the MITK implementation of state machines in general, have a look at \ref InteractionPage. To derive a non-abstract tool, you inherit from mitk::Tool (or some other base class further down the inheritance tree), and in your own parameterless constructor (that is called from the itkFactorylessNewMacro that you use) you pass a StateMachine pattern name to the superclass. Names for valid patterns can be found in StateMachine.xml (which might be enhanced by you). You have to implement at least GetXPM() and GetName() to provide some identification. Each Tool knows its ToolManager, which can provide the data that the tool should work on. \warning Only to be instantiated by mitk::ToolManager (because SetToolManager has to be called). All other uses are unsupported. $Author$ */ class MITKSEGMENTATION_EXPORT Tool : public EventStateMachine, public InteractionEventObserver { public: typedef mitk::Label::PixelType DefaultSegmentationDataType; /** * \brief To let GUI process new events (e.g. qApp->processEvents() ) */ Message<> GUIProcessEventsMessage; /** * \brief To send error messages (to be shown by some GUI) */ Message1 ErrorMessage; /** * \brief To send whether the tool is busy (to be shown by some GUI) */ Message1 CurrentlyBusy; /** * \brief To send general messages (to be shown by some GUI) */ Message1 GeneralMessage; mitkClassMacro(Tool, EventStateMachine); // no New(), there should only be subclasses /** \brief Returns an icon in the XPM format. This icon has to fit into some kind of button in most applications, so make it smaller than 25x25 pixels. XPM is e.g. supported by The Gimp. But if you open any XPM file in your text editor, you will see that you could also "draw" it with an editor. */ virtual const char **GetXPM() const = 0; /** * \brief Returns the path of an icon. * * This icon is preferred to the XPM icon. */ virtual std::string GetIconPath() const { return ""; } /** * \brief Returns the path of a cursor icon. * */ virtual us::ModuleResource GetCursorIconResource() const; /** * @brief Returns the tool button icon of the tool wrapped by a usModuleResource * @return a valid ModuleResource or an invalid if this function * is not reimplemented */ virtual us::ModuleResource GetIconResource() const; /** \brief Returns the name of this tool. Make it short! This name has to fit into some kind of button in most applications, so take some time to think of a good name! */ virtual const char *GetName() const = 0; /** \brief Name of a group. You can group several tools by assigning a group name. Graphical tool selectors might use this information to group tools. (What other reason could there be?) */ virtual const char *GetGroup() const; virtual void InitializeStateMachine(); /** * \brief Interface for GUI creation. * * This is the basic interface for creation of a GUI object belonging to one tool. * * Tools that support a GUI (e.g. for display/editing of parameters) should follow some rules: * * - A Tool and its GUI are two separate classes * - There may be several instances of a GUI at the same time. * - mitk::Tool is toolkit (Qt, wxWidgets, etc.) independent, the GUI part is of course dependent * - The GUI part inherits both from itk::Object and some GUI toolkit class * - The GUI class name HAS to be constructed like "toolkitPrefix" tool->GetClassName() + "toolkitPostfix", e.g. * MyTool -> wxMyToolGUI * - For each supported toolkit there is a base class for tool GUIs, which contains some convenience methods * - Tools notify the GUI about changes using ITK events. The GUI must observe interesting events. * - The GUI base class may convert all ITK events to the GUI toolkit's favoured messaging system (Qt -> signals) * - Calling methods of a tool by its GUI is done directly. * In some cases GUIs don't want to be notified by the tool when they cause a change in a tool. * There is a macro CALL_WITHOUT_NOTICE(method()), which will temporarily disable all notifications during a * method call. */ virtual itk::Object::Pointer GetGUI(const std::string &toolkitPrefix, const std::string &toolkitPostfix); virtual NodePredicateBase::ConstPointer GetReferenceDataPreference() const; virtual NodePredicateBase::ConstPointer GetWorkingDataPreference() const; DataNode::Pointer CreateEmptySegmentationNode(const Image *original, const std::string &organName, - const mitk::Color &color); - DataNode::Pointer CreateSegmentationNode(Image *image, const std::string &organName, const mitk::Color &color); + const mitk::Color &color) const; + DataNode::Pointer CreateSegmentationNode(Image *image, const std::string &organName, const mitk::Color &color) const; /** Function used to check if a tool can handle the referenceData and (if specified) the working data. @pre referenceData must be a valid pointer @param referenceData Pointer to the data that should be checked as valid reference for the tool. @param workingData Pointer to the data that should be checked as valid working data for this tool. This parameter can be null if no working data is specified so far.*/ virtual bool CanHandle(const BaseData *referenceData, const BaseData *workingData) const; protected: friend class ToolManager; virtual void SetToolManager(ToolManager *); void ConnectActionsAndFunctions() override; /** \brief Called when the tool gets activated. Derived tools should call their parents implementation at the beginning of the overriding function. */ virtual void Activated(); /** \brief Called when the tool gets deactivated. Derived tools should call their parents implementation at the end of the overriding function. */ virtual void Deactivated(); /** \brief Let subclasses change their event configuration. */ std::string m_EventConfig; - Tool(); // purposely hidden Tool(const char *, const us::Module *interactorModule = nullptr); // purposely hidden ~Tool() override; void Notify(InteractionEvent *interactionEvent, bool isHandled) override; bool FilterEvents(InteractionEvent *, DataNode *) override; ToolManager *m_ToolManager; private: // for reference data NodePredicateDataType::Pointer m_PredicateImages; NodePredicateDimension::Pointer m_PredicateDim3; NodePredicateDimension::Pointer m_PredicateDim4; NodePredicateOr::Pointer m_PredicateDimension; NodePredicateAnd::Pointer m_PredicateImage3D; NodePredicateProperty::Pointer m_PredicateBinary; NodePredicateNot::Pointer m_PredicateNotBinary; NodePredicateProperty::Pointer m_PredicateSegmentation; NodePredicateNot::Pointer m_PredicateNotSegmentation; NodePredicateProperty::Pointer m_PredicateHelper; NodePredicateNot::Pointer m_PredicateNotHelper; NodePredicateAnd::Pointer m_PredicateImageColorful; NodePredicateAnd::Pointer m_PredicateImageColorfulNotHelper; NodePredicateAnd::Pointer m_PredicateReference; // for working data NodePredicateAnd::Pointer m_IsSegmentationPredicate; std::string m_InteractorType; std::map m_DisplayInteractorConfigs; const us::Module *m_InteractorModule; }; } // namespace #endif diff --git a/Modules/Segmentation/Resources/Correction_48x48.png b/Modules/Segmentation/Resources/Correction_48x48.png deleted file mode 100644 index d2b1508cfd..0000000000 Binary files a/Modules/Segmentation/Resources/Correction_48x48.png and /dev/null differ diff --git a/Modules/Segmentation/Resources/Correction_Cursor_32x32.png b/Modules/Segmentation/Resources/Correction_Cursor_32x32.png deleted file mode 100644 index beb67b0a85..0000000000 Binary files a/Modules/Segmentation/Resources/Correction_Cursor_32x32.png and /dev/null differ diff --git a/Modules/Segmentation/files.cmake b/Modules/Segmentation/files.cmake index 3bce31c9b5..68d22a6ccc 100644 --- a/Modules/Segmentation/files.cmake +++ b/Modules/Segmentation/files.cmake @@ -1,118 +1,116 @@ set(CPP_FILES Algorithms/mitkCalculateSegmentationVolume.cpp Algorithms/mitkContourModelSetToImageFilter.cpp Algorithms/mitkContourSetToPointSetFilter.cpp Algorithms/mitkContourUtils.cpp Algorithms/mitkCorrectorAlgorithm.cpp Algorithms/mitkDiffImageApplier.cpp Algorithms/mitkDiffSliceOperation.cpp Algorithms/mitkDiffSliceOperationApplier.cpp Algorithms/mitkFeatureBasedEdgeDetectionFilter.cpp Algorithms/mitkImageLiveWireContourModelFilter.cpp Algorithms/mitkImageToContourFilter.cpp #Algorithms/mitkImageToContourModelFilter.cpp Algorithms/mitkImageToLiveWireContourFilter.cpp Algorithms/mitkManualSegmentationToSurfaceFilter.cpp Algorithms/mitkOtsuSegmentationFilter.cpp Algorithms/mitkOverwriteDirectedPlaneImageFilter.cpp Algorithms/mitkOverwriteSliceImageFilter.cpp Algorithms/mitkSegmentationObjectFactory.cpp Algorithms/mitkShapeBasedInterpolationAlgorithm.cpp Algorithms/mitkShowSegmentationAsSmoothedSurface.cpp Algorithms/mitkShowSegmentationAsSurface.cpp Algorithms/mitkVtkImageOverwrite.cpp Controllers/mitkSegmentationInterpolationController.cpp Controllers/mitkToolManager.cpp Controllers/mitkSegmentationModuleActivator.cpp Controllers/mitkToolManagerProvider.cpp DataManagement/mitkContour.cpp DataManagement/mitkContourSet.cpp DataManagement/mitkExtrudedContour.cpp Interactions/mitkAdaptiveRegionGrowingTool.cpp Interactions/mitkAddContourTool.cpp Interactions/mitkAutoCropTool.cpp Interactions/mitkAutoSegmentationTool.cpp Interactions/mitkAutoSegmentationWithPreviewTool.cpp Interactions/mitkAutoMLSegmentationWithPreviewTool.cpp Interactions/mitkBinaryThresholdBaseTool.cpp Interactions/mitkBinaryThresholdTool.cpp Interactions/mitkBinaryThresholdULTool.cpp Interactions/mitkCalculateGrayValueStatisticsTool.cpp Interactions/mitkCalculateVolumetryTool.cpp Interactions/mitkContourModelInteractor.cpp Interactions/mitkContourModelLiveWireInteractor.cpp Interactions/mitkLiveWireTool2D.cpp Interactions/mitkContourTool.cpp - Interactions/mitkCorrectorTool2D.cpp Interactions/mitkCreateSurfaceTool.cpp Interactions/mitkDrawPaintbrushTool.cpp Interactions/mitkErasePaintbrushTool.cpp Interactions/mitkEraseRegionTool.cpp + Interactions/mitkFastMarchingBaseTool.cpp Interactions/mitkFastMarchingTool.cpp Interactions/mitkFastMarchingTool3D.cpp Interactions/mitkFeedbackContourTool.cpp Interactions/mitkFillRegionTool.cpp Interactions/mitkOtsuTool3D.cpp Interactions/mitkPaintbrushTool.cpp Interactions/mitkPixelManipulationTool.cpp Interactions/mitkRegionGrowingTool.cpp Interactions/mitkSegmentationsProcessingTool.cpp Interactions/mitkSetRegionTool.cpp Interactions/mitkSegTool2D.cpp Interactions/mitkSubtractContourTool.cpp Interactions/mitkTool.cpp Interactions/mitkToolCommand.cpp Interactions/mitkWatershedTool.cpp Interactions/mitkPickingTool.cpp Interactions/mitkSegmentationInteractor.cpp #SO Rendering/mitkContourMapper2D.cpp Rendering/mitkContourSetMapper2D.cpp Rendering/mitkContourSetVtkMapper3D.cpp Rendering/mitkContourVtkMapper3D.cpp SegmentationUtilities/BooleanOperations/mitkBooleanOperation.cpp SegmentationUtilities/MorphologicalOperations/mitkMorphologicalOperations.cpp #Added from ML Controllers/mitkSliceBasedInterpolationController.cpp Algorithms/mitkSurfaceStampImageFilter.cpp ) set(RESOURCE_FILES Add_48x48.png Add_Cursor_32x32.png - Correction_48x48.png - Correction_Cursor_32x32.png Erase_48x48.png Erase_Cursor_32x32.png FastMarching_48x48.png FastMarching_Cursor_32x32.png Fill_48x48.png Fill_Cursor_32x32.png LiveWire_48x48.png LiveWire_Cursor_32x32.png Otsu_48x48.png Paint_48x48.png Paint_Cursor_32x32.png Pick_48x48.png RegionGrowing_48x48.png RegionGrowing_Cursor_32x32.png Subtract_48x48.png Subtract_Cursor_32x32.png Threshold_48x48.png TwoThresholds_48x48.png Watershed_48x48.png Watershed_Cursor_32x32.png Wipe_48x48.png Wipe_Cursor_32x32.png Interactions/dummy.xml Interactions/LiveWireTool.xml Interactions/FastMarchingTool.xml Interactions/PressMoveRelease.xml Interactions/PressMoveReleaseAndPointSetting.xml Interactions/PressMoveReleaseWithCTRLInversion.xml Interactions/PressMoveReleaseWithCTRLInversionAllMouseMoves.xml Interactions/SegmentationToolsConfig.xml Interactions/ContourModelModificationConfig.xml Interactions/ContourModelModificationInteractor.xml ) diff --git a/Modules/SegmentationUI/Qmitk/QmitkAutoMLSegmentationToolGUIBase.cpp b/Modules/SegmentationUI/Qmitk/QmitkAutoMLSegmentationToolGUIBase.cpp new file mode 100644 index 0000000000..b332866f6f --- /dev/null +++ b/Modules/SegmentationUI/Qmitk/QmitkAutoMLSegmentationToolGUIBase.cpp @@ -0,0 +1,95 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +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 "QmitkAutoMLSegmentationToolGUIBase.h" +#include "mitkAutoMLSegmentationWithPreviewTool.h" + +#include + +QmitkAutoMLSegmentationToolGUIBase::QmitkAutoMLSegmentationToolGUIBase() : QmitkAutoSegmentationToolGUIBase(false) +{ + auto enableOtsuDelegate = [this](bool enabled) + { + bool result = enabled; + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) + { + result = !tool->GetSelectedLabels().empty() && enabled; + } + else + { + result = false; + } + + return result; + }; + + m_EnableConfirmSegBtnFnc = enableOtsuDelegate; +} + +void QmitkAutoMLSegmentationToolGUIBase::ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool) +{ + Superclass::ConnectNewTool(newTool); + this->EnableWidgets(true); +} + +void QmitkAutoMLSegmentationToolGUIBase::InitializeUI(QBoxLayout* mainLayout) +{ + m_LabelSelectionList = new QmitkSimpleLabelSetListWidget(this); + m_LabelSelectionList->setObjectName(QString::fromUtf8("m_LabelSelectionList")); + QSizePolicy sizePolicy2(QSizePolicy::Minimum, QSizePolicy::MinimumExpanding); + sizePolicy2.setHorizontalStretch(0); + sizePolicy2.setVerticalStretch(0); + sizePolicy2.setHeightForWidth(m_LabelSelectionList->sizePolicy().hasHeightForWidth()); + m_LabelSelectionList->setSizePolicy(sizePolicy2); + m_LabelSelectionList->setMaximumSize(QSize(10000000, 10000000)); + + mainLayout->addWidget(m_LabelSelectionList); + + connect(m_LabelSelectionList, &QmitkSimpleLabelSetListWidget::SelectedLabelsChanged, this, &QmitkAutoMLSegmentationToolGUIBase::OnLabelSelectionChanged); + + Superclass::InitializeUI(mainLayout); +} + +void QmitkAutoMLSegmentationToolGUIBase::OnLabelSelectionChanged(const QmitkSimpleLabelSetListWidget::LabelVectorType& selectedLabels) +{ + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) + { + mitk::AutoMLSegmentationWithPreviewTool::SelectedLabelVectorType labelIDs; + for (const auto& label : selectedLabels) + { + labelIDs.push_back(label->GetValue()); + } + + tool->SetSelectedLabels(labelIDs); + tool->UpdatePreview(); + this->EnableWidgets(true); //used to actualize the ConfirmSeg btn via the delegate; + } +} + +void QmitkAutoMLSegmentationToolGUIBase::EnableWidgets(bool enabled) +{ + Superclass::EnableWidgets(enabled); + if (nullptr != m_LabelSelectionList) + { + m_LabelSelectionList->setEnabled(enabled); + } +} + +void QmitkAutoMLSegmentationToolGUIBase::SetLabelSetPreview(const mitk::LabelSetImage* preview) +{ + if (nullptr != m_LabelSelectionList) + { + m_LabelSelectionList->SetLabelSetImage(preview); + } +} diff --git a/Modules/SegmentationUI/Qmitk/QmitkAutoMLSegmentationToolGUIBase.h b/Modules/SegmentationUI/Qmitk/QmitkAutoMLSegmentationToolGUIBase.h new file mode 100644 index 0000000000..76bf69cea8 --- /dev/null +++ b/Modules/SegmentationUI/Qmitk/QmitkAutoMLSegmentationToolGUIBase.h @@ -0,0 +1,53 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#ifndef QmitkAutoMLSegmentationToolGUIBase_h_Included +#define QmitkAutoMLSegmentationToolGUIBase_h_Included + +#include "QmitkAutoSegmentationToolGUIBase.h" + +#include "QmitkSimpleLabelSetListWidget.h" + +#include + +/** + \ingroup org_mitk_gui_qt_interactivesegmentation_internal + \brief GUI for tools based on mitk::AutoMLSegmentationWithPreviewTool. + + This GUI offers an additional list to select the label that should be confirmed. +*/ +class MITKSEGMENTATIONUI_EXPORT QmitkAutoMLSegmentationToolGUIBase : public QmitkAutoSegmentationToolGUIBase +{ + Q_OBJECT + +public: + mitkClassMacro(QmitkAutoMLSegmentationToolGUIBase, QmitkAutoSegmentationToolGUIBase); + +protected slots : + + void OnLabelSelectionChanged(const QmitkSimpleLabelSetListWidget::LabelVectorType& selectedLabels); + +protected: + QmitkAutoMLSegmentationToolGUIBase(); + ~QmitkAutoMLSegmentationToolGUIBase() = default; + + void InitializeUI(QBoxLayout* mainLayout) override; + void ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool) override; + + void EnableWidgets(bool enabled) override; + void SetLabelSetPreview(const mitk::LabelSetImage* preview); + +private: + QmitkSimpleLabelSetListWidget* m_LabelSelectionList = nullptr; +}; + +#endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.cpp b/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.cpp new file mode 100644 index 0000000000..19e7da115e --- /dev/null +++ b/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.cpp @@ -0,0 +1,155 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +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 "QmitkAutoSegmentationToolGUIBase.h" + +#include +#include +#include +#include +#include + +bool DefaultEnableConfirmSegBtnFunction(bool enabled) +{ + return enabled; +} + +QmitkAutoSegmentationToolGUIBase::QmitkAutoSegmentationToolGUIBase(bool mode2D) : QmitkToolGUI(), m_EnableConfirmSegBtnFnc(DefaultEnableConfirmSegBtnFunction), m_Mode2D(mode2D) +{ + connect(this, SIGNAL(NewToolAssociated(mitk::Tool *)), this, SLOT(OnNewToolAssociated(mitk::Tool *))); +} + +QmitkAutoSegmentationToolGUIBase::~QmitkAutoSegmentationToolGUIBase() +{ + if (m_Tool.IsNotNull()) + { + m_Tool->CurrentlyBusy -= mitk::MessageDelegate1(this, &QmitkAutoSegmentationToolGUIBase::BusyStateChanged); + } +} + +void QmitkAutoSegmentationToolGUIBase::OnNewToolAssociated(mitk::Tool *tool) +{ + if (m_Tool.IsNotNull()) + { + this->DisconnectOldTool(m_Tool); + } + + m_Tool = dynamic_cast(tool); + + if (nullptr == m_MainLayout) + { + // create the visible widgets + m_MainLayout = new QVBoxLayout(this); + m_ConfirmSegBtn = new QPushButton("Confirm Segmentation", this); + connect(m_ConfirmSegBtn, SIGNAL(clicked()), this, SLOT(OnAcceptPreview())); + + m_CheckProcessAll = new QCheckBox("Process all time steps", this); + m_CheckProcessAll->setChecked(false); + m_CheckProcessAll->setToolTip("Process all time steps of the dynamic segmentation and not just the currently visible time step."); + m_CheckProcessAll->setVisible(!m_Mode2D); + //remark: keept m_CheckProcessAll deactivated in 2D because in this refactoring + //it should be kept to the status quo and it was not clear how interpolation + //would behave. As soon as it is sorted out we can remove that "feature switch" + //or the comment. + + m_CheckCreateNew = new QCheckBox("Create as new segmentation", this); + m_CheckCreateNew->setChecked(false); + m_CheckCreateNew->setToolTip("Add the confirmed segmentation as a new segmentation instead of overwriting the currently selected."); + m_CheckCreateNew->setVisible(!m_Mode2D); + //remark: keept m_CheckCreateNew deactivated in 2D because in this refactoring + //it should be kept to the status quo and it was not clear how interpolation + //would behave. As soon as it is sorted out we can remove that "feature switch" + //or the comment. + + this->InitializeUI(m_MainLayout); + + m_MainLayout->addWidget(m_ConfirmSegBtn); + m_MainLayout->addWidget(m_CheckProcessAll); + m_MainLayout->addWidget(m_CheckCreateNew); + } + + if (m_Tool.IsNotNull()) + { + this->ConnectNewTool(m_Tool); + } +} + +void QmitkAutoSegmentationToolGUIBase::OnAcceptPreview() +{ + if (m_Tool.IsNotNull()) + { + if (m_CheckCreateNew->isChecked()) + { + m_Tool->SetOverwriteExistingSegmentation(false); + } + else + { + m_Tool->SetOverwriteExistingSegmentation(true); + } + + m_Tool->SetCreateAllTimeSteps(m_CheckProcessAll->isChecked()); + + m_ConfirmSegBtn->setEnabled(false); + m_Tool->ConfirmSegmentation(); + } +} + +void QmitkAutoSegmentationToolGUIBase::DisconnectOldTool(mitk::AutoSegmentationWithPreviewTool* oldTool) +{ + oldTool->CurrentlyBusy -= mitk::MessageDelegate1(this, &QmitkAutoSegmentationToolGUIBase::BusyStateChanged); +} + +void QmitkAutoSegmentationToolGUIBase::ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool) +{ + newTool->CurrentlyBusy += + mitk::MessageDelegate1(this, &QmitkAutoSegmentationToolGUIBase::BusyStateChanged); + + newTool->SetOverwriteExistingSegmentation(true); + m_CheckProcessAll->setVisible(newTool->GetTargetSegmentationNode()->GetData()->GetTimeSteps() > 1); +} + +void QmitkAutoSegmentationToolGUIBase::InitializeUI(QBoxLayout* /*mainLayout*/) +{ + //default implementation does nothing +} + +void QmitkAutoSegmentationToolGUIBase::BusyStateChanged(bool isBusy) +{ + if (isBusy) + { + QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); + } + else + { + QApplication::restoreOverrideCursor(); + } + this->EnableWidgets(!isBusy); + } + +void QmitkAutoSegmentationToolGUIBase::EnableWidgets(bool enabled) +{ + if (nullptr != m_MainLayout) + { + if (nullptr != m_ConfirmSegBtn) + { + m_ConfirmSegBtn->setEnabled(m_EnableConfirmSegBtnFnc(enabled)); + } + if (nullptr != m_CheckProcessAll) + { + m_CheckProcessAll->setEnabled(enabled); + } + if (nullptr != m_CheckCreateNew) + { + m_CheckCreateNew->setEnabled(enabled); + } + } +} diff --git a/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.h b/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.h new file mode 100644 index 0000000000..6501a2e1b5 --- /dev/null +++ b/Modules/SegmentationUI/Qmitk/QmitkAutoSegmentationToolGUIBase.h @@ -0,0 +1,81 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +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 QmitkAutoSegmentationToolGUIBase_h_Included +#define QmitkAutoSegmentationToolGUIBase_h_Included + +#include "QmitkToolGUI.h" + +#include "mitkAutoSegmentationWithPreviewTool.h" + +#include + +class QCheckBox; +class QPushButton; +class QBoxLayout; + +/** + \ingroup org_mitk_gui_qt_interactivesegmentation_internal + \brief GUI base clase for tools derived from mitk::AutoSegmentationTool. +*/ +class MITKSEGMENTATIONUI_EXPORT QmitkAutoSegmentationToolGUIBase : public QmitkToolGUI +{ + Q_OBJECT + +public: + mitkClassMacro(QmitkAutoSegmentationToolGUIBase, QmitkToolGUI); + itkCloneMacro(Self); + + itkGetConstMacro(Mode2D, bool); + +protected slots: + + void OnNewToolAssociated(mitk::Tool *); + + void OnAcceptPreview(); + +protected: + QmitkAutoSegmentationToolGUIBase(bool mode2D); + ~QmitkAutoSegmentationToolGUIBase() override; + + virtual void DisconnectOldTool(mitk::AutoSegmentationWithPreviewTool* oldTool); + virtual void ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool); + virtual void InitializeUI(QBoxLayout* mainLayout); + + void BusyStateChanged(bool isBusy) override; + + using EnableConfirmSegBtnFunctionType = std::function; + EnableConfirmSegBtnFunctionType m_EnableConfirmSegBtnFnc; + + virtual void EnableWidgets(bool enabled); + + template + TTool* GetConnectedToolAs() + { + return dynamic_cast(m_Tool.GetPointer()); + }; + + + +private: + QCheckBox* m_CheckProcessAll = nullptr; + QCheckBox* m_CheckCreateNew = nullptr; + QPushButton* m_ConfirmSegBtn = nullptr; + QBoxLayout* m_MainLayout = nullptr; + + /**Indicates if the tool is in 2D or 3D mode.*/ + bool m_Mode2D; + + mitk::AutoSegmentationWithPreviewTool::Pointer m_Tool; +}; + +#endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUI.cpp index 7c720d4a58..fc1cdf2592 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUI.cpp @@ -1,168 +1,31 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkBinaryThresholdToolGUI.h" #include #include #include #include #include MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkBinaryThresholdToolGUI, "") QmitkBinaryThresholdToolGUI::QmitkBinaryThresholdToolGUI() - : QmitkToolGUI() + : QmitkBinaryThresholdToolGUIBase(false) { - // create the visible widgets - QBoxLayout *mainLayout = new QVBoxLayout(this); - - QLabel *label = new QLabel("Threshold :", this); - QFont f = label->font(); - f.setBold(false); - label->setFont(f); - mainLayout->addWidget(label); - - QBoxLayout *layout = new QHBoxLayout(); - - m_ThresholdSlider = new ctkSliderWidget(); - connect( - m_ThresholdSlider, SIGNAL(valueChanged(double)), this, SLOT(OnSliderValueChanged(double))); - layout->addWidget(m_ThresholdSlider); - mainLayout->addLayout(layout); - m_ThresholdSlider->setSingleStep(0.01); - - QPushButton *okButton = new QPushButton("Confirm Segmentation", this); - connect(okButton, SIGNAL(clicked()), this, SLOT(OnAcceptThresholdPreview())); - okButton->setFont(f); - mainLayout->addWidget(okButton); - - m_CheckProcessAll = new QCheckBox("Process all time steps", this); - m_CheckProcessAll->setChecked(false); - m_CheckProcessAll->setToolTip("Process/overwrite all time steps of the dynamic segmentation and not just the currently visible time step."); - - mainLayout->addWidget(m_CheckProcessAll); - - m_CheckCreateNew = new QCheckBox("Create as new segmentation", this); - m_CheckCreateNew->setChecked(false); - m_CheckCreateNew->setToolTip("Add the confirmed segmentation as a new segmentation instead of overwriting the currently selected."); - mainLayout->addWidget(m_CheckCreateNew); - - connect(this, SIGNAL(NewToolAssociated(mitk::Tool *)), this, SLOT(OnNewToolAssociated(mitk::Tool *))); } QmitkBinaryThresholdToolGUI::~QmitkBinaryThresholdToolGUI() { - if (m_BinaryThresholdTool.IsNotNull()) - { - m_BinaryThresholdTool->CurrentlyBusy -= - mitk::MessageDelegate1(this, &QmitkBinaryThresholdToolGUI::BusyStateChanged); - m_BinaryThresholdTool->IntervalBordersChanged -= - mitk::MessageDelegate3( - this, &QmitkBinaryThresholdToolGUI::OnThresholdingIntervalBordersChanged); - m_BinaryThresholdTool->ThresholdingValuesChanged -= mitk::MessageDelegate2( - this, &QmitkBinaryThresholdToolGUI::OnThresholdingValuesChanged); - } } -void QmitkBinaryThresholdToolGUI::OnNewToolAssociated(mitk::Tool *tool) -{ - if (m_BinaryThresholdTool.IsNotNull()) - { - m_BinaryThresholdTool->CurrentlyBusy -= - mitk::MessageDelegate1(this, &QmitkBinaryThresholdToolGUI::BusyStateChanged); - m_BinaryThresholdTool->IntervalBordersChanged -= - mitk::MessageDelegate3( - this, &QmitkBinaryThresholdToolGUI::OnThresholdingIntervalBordersChanged); - m_BinaryThresholdTool->ThresholdingValuesChanged -= mitk::MessageDelegate2( - this, &QmitkBinaryThresholdToolGUI::OnThresholdingValuesChanged); - } - - m_BinaryThresholdTool = dynamic_cast(tool); - - if (m_BinaryThresholdTool.IsNotNull()) - { - m_BinaryThresholdTool->CurrentlyBusy += - mitk::MessageDelegate1(this, &QmitkBinaryThresholdToolGUI::BusyStateChanged); - m_BinaryThresholdTool->IntervalBordersChanged += - mitk::MessageDelegate3( - this, &QmitkBinaryThresholdToolGUI::OnThresholdingIntervalBordersChanged); - m_BinaryThresholdTool->ThresholdingValuesChanged += mitk::MessageDelegate2( - this, &QmitkBinaryThresholdToolGUI::OnThresholdingValuesChanged); - - m_BinaryThresholdTool->SetOverwriteExistingSegmentation(true); - m_CheckProcessAll->setVisible(m_BinaryThresholdTool->GetTargetSegmentationNode()->GetData()->GetTimeSteps()>1); - } -} - -void QmitkBinaryThresholdToolGUI::OnAcceptThresholdPreview() -{ - if (m_BinaryThresholdTool.IsNotNull()) - { - if (m_CheckCreateNew->isChecked()) - { - m_BinaryThresholdTool->SetOverwriteExistingSegmentation(false); - } - else - { - m_BinaryThresholdTool->SetOverwriteExistingSegmentation(true); - } - - m_BinaryThresholdTool->SetCreateAllTimeSteps(m_CheckProcessAll->isChecked()); - - this->thresholdAccepted(); - m_BinaryThresholdTool->ConfirmSegmentation(); - } -} - -void QmitkBinaryThresholdToolGUI::OnThresholdingIntervalBordersChanged(double lower, double upper, bool isFloat) -{ - m_InternalUpdate = true; - if (!isFloat) - { - m_ThresholdSlider->setRange(int(lower), int(upper)); - m_ThresholdSlider->setSingleStep(1); - m_ThresholdSlider->setDecimals(0); - } - else - { - m_ThresholdSlider->setRange(lower, upper); - } - m_InternalUpdate = false; -} - -void QmitkBinaryThresholdToolGUI::OnThresholdingValuesChanged(mitk::ScalarType lower, mitk::ScalarType /*upper*/) -{ - m_ThresholdSlider->setValue(lower); -} - -void QmitkBinaryThresholdToolGUI::OnSliderValueChanged(double value) -{ - if (m_BinaryThresholdTool.IsNotNull() && !m_InternalUpdate) - { - m_BinaryThresholdTool->SetThresholdValue(value); - } -} - -void QmitkBinaryThresholdToolGUI::BusyStateChanged(bool value) -{ - if (value) - { - QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); - } - else - { - QApplication::restoreOverrideCursor(); - } - - m_ThresholdSlider->setEnabled(!value); -} diff --git a/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUI.h index 5696c1ff98..e62d8fc8fc 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUI.h @@ -1,80 +1,50 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkBinaryThresholdToolGUI_h_Included #define QmitkBinaryThresholdToolGUI_h_Included -#include "QmitkToolGUI.h" +#include "QmitkBinaryThresholdToolGUIBase.h" #include "mitkBinaryThresholdTool.h" #include #include "ctkSliderWidget.h" #include /** \ingroup org_mitk_gui_qt_interactivesegmentation_internal \brief GUI for mitk::BinaryThresholdTool. This GUI shows a slider to change the tool's threshold and an OK button to accept a preview for actual thresholding. There is only a slider for INT values in QT. So, if the working image has a float/double pixeltype, we need to convert the original float intensity into a respective int value for the slider. The slider range is then between 0 and 99. If the pixeltype is INT, then we do not need any conversion. Last contributor: $Author$ */ -class MITKSEGMENTATIONUI_EXPORT QmitkBinaryThresholdToolGUI : public QmitkToolGUI +class MITKSEGMENTATIONUI_EXPORT QmitkBinaryThresholdToolGUI : public QmitkBinaryThresholdToolGUIBase { Q_OBJECT public: - mitkClassMacro(QmitkBinaryThresholdToolGUI, QmitkToolGUI); + mitkClassMacro(QmitkBinaryThresholdToolGUI, QmitkBinaryThresholdToolGUIBase); itkFactorylessNewMacro(Self); itkCloneMacro(Self); - void OnThresholdingIntervalBordersChanged(double lower, double upper, bool isFloat); - void OnThresholdingValuesChanged(mitk::ScalarType lower, mitk::ScalarType upper); - -signals: - - /// \brief Emitted when threshold Accepted - void thresholdAccepted(); - - /// \brief Emitted when threshold Canceled - void thresholdCanceled(); - -public slots: - -protected slots: - - void OnNewToolAssociated(mitk::Tool *); - void OnAcceptThresholdPreview(); - - void OnSliderValueChanged(double value); - protected: QmitkBinaryThresholdToolGUI(); ~QmitkBinaryThresholdToolGUI() override; - - void BusyStateChanged(bool) override; - - ctkSliderWidget* m_ThresholdSlider = nullptr; - QCheckBox* m_CheckProcessAll = nullptr; - QCheckBox* m_CheckCreateNew = nullptr; - - bool m_InternalUpdate = false; - - mitk::BinaryThresholdTool::Pointer m_BinaryThresholdTool; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUIBase.cpp b/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUIBase.cpp new file mode 100644 index 0000000000..930eacadb7 --- /dev/null +++ b/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUIBase.cpp @@ -0,0 +1,187 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +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 "QmitkBinaryThresholdToolGUIBase.h" + +#include "mitkBinaryThresholdBaseTool.h" +#include "mitkBinaryThresholdTool.h" + +#include +#include +#include +#include + +QmitkBinaryThresholdToolGUIBase::QmitkBinaryThresholdToolGUIBase(bool ulMode) : QmitkAutoSegmentationToolGUIBase(false), m_ULMode(ulMode) +{ +} + +QmitkBinaryThresholdToolGUIBase::~QmitkBinaryThresholdToolGUIBase() +{ + auto tool = this->GetConnectedToolAs(); + + if (nullptr != tool) + { + tool->IntervalBordersChanged -= + mitk::MessageDelegate3( + this, &QmitkBinaryThresholdToolGUIBase::OnThresholdingIntervalBordersChanged); + tool->ThresholdingValuesChanged -= + mitk::MessageDelegate2( + this, &QmitkBinaryThresholdToolGUIBase::OnThresholdingValuesChanged); + } +} + +void QmitkBinaryThresholdToolGUIBase::OnThresholdingIntervalBordersChanged(double lower, double upper, bool isFloat) +{ + m_InternalUpdate = true; + + if (m_ULMode) + { + if (!isFloat) + { + m_ThresholdRange->setRange(int(lower), int(upper)); + m_ThresholdRange->setSingleStep(1); + m_ThresholdRange->setDecimals(0); + } + else + { + m_ThresholdRange->setRange(lower, upper); + } + } + else + { + if (!isFloat) + { + m_ThresholdSlider->setRange(int(lower), int(upper)); + m_ThresholdSlider->setSingleStep(1); + m_ThresholdSlider->setDecimals(0); + } + else + { + m_ThresholdSlider->setRange(lower, upper); + } + } + + m_InternalUpdate = false; +} + +void QmitkBinaryThresholdToolGUIBase::OnThresholdingValuesChanged(mitk::ScalarType lower, mitk::ScalarType upper) +{ + if (m_ULMode) + { + m_ThresholdRange->setValues(lower, upper); + } + else + { + m_ThresholdSlider->setValue(lower); + } +} + +void QmitkBinaryThresholdToolGUIBase::OnThresholdRangeChanged(double min, double max) +{ + auto tool = this->GetConnectedToolAs(); + + if (nullptr != tool && !m_InternalUpdate) + { + tool->SetThresholdValues(min, max); + } +} + +void QmitkBinaryThresholdToolGUIBase::OnThresholdSliderChanged(double value) +{ + auto tool = this->GetConnectedToolAs(); + + if (nullptr != tool && !m_InternalUpdate) + { + tool->SetThresholdValue(value); + } +} + +void QmitkBinaryThresholdToolGUIBase::DisconnectOldTool(mitk::AutoSegmentationWithPreviewTool* oldTool) +{ + Superclass::DisconnectOldTool(oldTool); + + auto tool = dynamic_cast(oldTool); + + if (nullptr != tool) + { + tool->IntervalBordersChanged -= + mitk::MessageDelegate3( + this, &QmitkBinaryThresholdToolGUIBase::OnThresholdingIntervalBordersChanged); + tool->ThresholdingValuesChanged -= + mitk::MessageDelegate2( + this, &QmitkBinaryThresholdToolGUIBase::OnThresholdingValuesChanged); + } +} + +void QmitkBinaryThresholdToolGUIBase::ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool) +{ + Superclass::ConnectNewTool(newTool); + + auto tool = dynamic_cast(newTool); + + if (nullptr != tool) + { + tool->IntervalBordersChanged += + mitk::MessageDelegate3( + this, &QmitkBinaryThresholdToolGUIBase::OnThresholdingIntervalBordersChanged); + tool->ThresholdingValuesChanged += + mitk::MessageDelegate2( + this, &QmitkBinaryThresholdToolGUIBase::OnThresholdingValuesChanged); + } +} + +void QmitkBinaryThresholdToolGUIBase::InitializeUI(QBoxLayout* mainLayout) +{ + QLabel* label = new QLabel("Threshold :", this); + QFont f = label->font(); + f.setBold(false); + label->setFont(f); + mainLayout->addWidget(label); + + QBoxLayout* layout = new QHBoxLayout(); + + if (m_ULMode) + { + m_ThresholdRange = new ctkRangeWidget(); + connect( + m_ThresholdRange, SIGNAL(valuesChanged(double, double)), this, SLOT(OnThresholdRangeChanged(double, double))); + layout->addWidget(m_ThresholdRange); + m_ThresholdRange->setSingleStep(0.01); + } + else + { + m_ThresholdSlider = new ctkSliderWidget(); + connect( + m_ThresholdSlider, SIGNAL(valueChanged(double)), this, SLOT(OnThresholdSliderChanged(double))); + layout->addWidget(m_ThresholdSlider); + m_ThresholdSlider->setSingleStep(0.01); + } + + mainLayout->addLayout(layout); + + Superclass::InitializeUI(mainLayout); +} + +void QmitkBinaryThresholdToolGUIBase::BusyStateChanged(bool value) +{ + Superclass::BusyStateChanged(value); + + if (m_ThresholdRange) + { + m_ThresholdRange->setEnabled(!value); + } + + if (m_ThresholdSlider) + { + m_ThresholdSlider->setEnabled(!value); + } +} diff --git a/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUIBase.h b/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUIBase.h new file mode 100644 index 0000000000..47f25dd544 --- /dev/null +++ b/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdToolGUIBase.h @@ -0,0 +1,63 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#ifndef QmitkBinaryThresholdToolGUIBase_h_Included +#define QmitkBinaryThresholdToolGUIBase_h_Included + +#include "QmitkAutoSegmentationToolGUIBase.h" +#include "ctkRangeWidget.h" +#include "ctkSliderWidget.h" + +#include + +/** + \ingroup org_mitk_gui_qt_interactivesegmentation_internal + \brief Base GUI for mitk::BinaryThresholdTool. + + This GUI shows a slider to change the tool's threshold and an OK button to accept a preview for actual thresholding. +*/ +class MITKSEGMENTATIONUI_EXPORT QmitkBinaryThresholdToolGUIBase : public QmitkAutoSegmentationToolGUIBase +{ + Q_OBJECT + +public: + mitkClassMacro(QmitkBinaryThresholdToolGUIBase, QmitkAutoSegmentationToolGUIBase); + + void OnThresholdingIntervalBordersChanged(double lower, double upper, bool isFloat); + void OnThresholdingValuesChanged(mitk::ScalarType lower, mitk::ScalarType upper); + +protected slots: + + void OnThresholdRangeChanged(double min, double max); + void OnThresholdSliderChanged(double value); + +protected: + QmitkBinaryThresholdToolGUIBase(bool ulMode); + ~QmitkBinaryThresholdToolGUIBase() override; + + void DisconnectOldTool(mitk::AutoSegmentationWithPreviewTool* oldTool) override; + void ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool) override; + void InitializeUI(QBoxLayout* mainLayout) override; + + void BusyStateChanged(bool) override; + + ctkRangeWidget* m_ThresholdRange = nullptr; + ctkSliderWidget* m_ThresholdSlider = nullptr; + + /** Indicates if the tool UI is used for a tool with upper an lower threshold (true) + ore only with one threshold (false)*/ + bool m_ULMode; + + bool m_InternalUpdate = false; +}; + +#endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdULToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdULToolGUI.cpp index 5954acff4c..1eab27a6fb 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdULToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdULToolGUI.cpp @@ -1,163 +1,30 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkBinaryThresholdULToolGUI.h" #include #include #include #include #include MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkBinaryThresholdULToolGUI, "") -QmitkBinaryThresholdULToolGUI::QmitkBinaryThresholdULToolGUI() : QmitkToolGUI() +QmitkBinaryThresholdULToolGUI::QmitkBinaryThresholdULToolGUI() : QmitkBinaryThresholdToolGUIBase(true) { - // create the visible widgets - QBoxLayout *mainLayout = new QVBoxLayout(this); - - QLabel *label = new QLabel("Threshold :", this); - QFont f = label->font(); - f.setBold(false); - label->setFont(f); - mainLayout->addWidget(label); - - QBoxLayout *layout = new QHBoxLayout(); - - m_DoubleThresholdSlider = new ctkRangeWidget(); - connect( - m_DoubleThresholdSlider, SIGNAL(valuesChanged(double, double)), this, SLOT(OnThresholdsChanged(double, double))); - layout->addWidget(m_DoubleThresholdSlider); - mainLayout->addLayout(layout); - m_DoubleThresholdSlider->setSingleStep(0.01); - - QPushButton *okButton = new QPushButton("Confirm Segmentation", this); - connect(okButton, SIGNAL(clicked()), this, SLOT(OnAcceptThresholdPreview())); - okButton->setFont(f); - mainLayout->addWidget(okButton); - - m_CheckProcessAll = new QCheckBox("Process all time steps", this); - m_CheckProcessAll->setChecked(false); - m_CheckProcessAll->setToolTip("Process/overwrite all time steps of the dynamic segmentation and not just the currently visible time step."); - mainLayout->addWidget(m_CheckProcessAll); - - m_CheckCreateNew = new QCheckBox("Create as new segmentation", this); - m_CheckCreateNew->setChecked(false); - m_CheckCreateNew->setToolTip("Add the confirmed segmentation as a new segmentation instead of overwriting the currently selected."); - mainLayout->addWidget(m_CheckCreateNew); - - connect(this, SIGNAL(NewToolAssociated(mitk::Tool *)), this, SLOT(OnNewToolAssociated(mitk::Tool *))); } QmitkBinaryThresholdULToolGUI::~QmitkBinaryThresholdULToolGUI() { - if (m_BinaryThresholdULTool.IsNotNull()) - { - m_BinaryThresholdULTool->CurrentlyBusy -= - mitk::MessageDelegate1(this, &QmitkBinaryThresholdULToolGUI::BusyStateChanged); - m_BinaryThresholdULTool->IntervalBordersChanged -= - mitk::MessageDelegate3( - this, &QmitkBinaryThresholdULToolGUI::OnThresholdingIntervalBordersChanged); - m_BinaryThresholdULTool->ThresholdingValuesChanged -= - mitk::MessageDelegate2( - this, &QmitkBinaryThresholdULToolGUI::OnThresholdingValuesChanged); - } -} - -void QmitkBinaryThresholdULToolGUI::OnNewToolAssociated(mitk::Tool *tool) -{ - if (m_BinaryThresholdULTool.IsNotNull()) - { - m_BinaryThresholdULTool->CurrentlyBusy -= - mitk::MessageDelegate1(this, &QmitkBinaryThresholdULToolGUI::BusyStateChanged); - m_BinaryThresholdULTool->IntervalBordersChanged -= - mitk::MessageDelegate3( - this, &QmitkBinaryThresholdULToolGUI::OnThresholdingIntervalBordersChanged); - m_BinaryThresholdULTool->ThresholdingValuesChanged -= - mitk::MessageDelegate2( - this, &QmitkBinaryThresholdULToolGUI::OnThresholdingValuesChanged); - } - - m_BinaryThresholdULTool = dynamic_cast(tool); - - if (m_BinaryThresholdULTool.IsNotNull()) - { - m_BinaryThresholdULTool->CurrentlyBusy += - mitk::MessageDelegate1(this, &QmitkBinaryThresholdULToolGUI::BusyStateChanged); - m_BinaryThresholdULTool->IntervalBordersChanged += - mitk::MessageDelegate3( - this, &QmitkBinaryThresholdULToolGUI::OnThresholdingIntervalBordersChanged); - m_BinaryThresholdULTool->ThresholdingValuesChanged += - mitk::MessageDelegate2( - this, &QmitkBinaryThresholdULToolGUI::OnThresholdingValuesChanged); - - m_BinaryThresholdULTool->SetOverwriteExistingSegmentation(true); - m_CheckProcessAll->setVisible(m_BinaryThresholdULTool->GetTargetSegmentationNode()->GetData()->GetTimeSteps() > 1); - } -} - -void QmitkBinaryThresholdULToolGUI::OnAcceptThresholdPreview() -{ - if (m_BinaryThresholdULTool.IsNotNull()) - { - if (m_CheckCreateNew->isChecked()) - { - m_BinaryThresholdULTool->SetOverwriteExistingSegmentation(false); - } - else - { - m_BinaryThresholdULTool->SetOverwriteExistingSegmentation(true); - } - - m_BinaryThresholdULTool->SetCreateAllTimeSteps(m_CheckProcessAll->isChecked()); - - m_BinaryThresholdULTool->ConfirmSegmentation(); - } -} - -void QmitkBinaryThresholdULToolGUI::OnThresholdingIntervalBordersChanged(double lower, double upper, bool isFloat) -{ - if (!isFloat) - { - m_DoubleThresholdSlider->setRange(int(lower), int(upper)); - m_DoubleThresholdSlider->setSingleStep(1); - m_DoubleThresholdSlider->setDecimals(0); - } - else - { - m_DoubleThresholdSlider->setRange(lower, upper); - } } -void QmitkBinaryThresholdULToolGUI::OnThresholdingValuesChanged(mitk::ScalarType lower, mitk::ScalarType upper) -{ - m_DoubleThresholdSlider->setValues(lower, upper); -} - -void QmitkBinaryThresholdULToolGUI::OnThresholdsChanged(double min, double max) -{ - m_BinaryThresholdULTool->SetThresholdValues(min, max); -} - -void QmitkBinaryThresholdULToolGUI::BusyStateChanged(bool value) -{ - if (value) - { - QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); - } - else - { - QApplication::restoreOverrideCursor(); - } - - m_DoubleThresholdSlider->setEnabled(!value); -} diff --git a/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdULToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdULToolGUI.h index ec0c130821..b903df1e58 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdULToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkBinaryThresholdULToolGUI.h @@ -1,68 +1,42 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 QmitkBinaryThresholdULToolGUI_h_Included #define QmitkBinaryThresholdULToolGUI_h_Included -#include "QmitkToolGUI.h" -#include "ctkRangeWidget.h" -#include -#include "mitkBinaryThresholdULTool.h" +#include "QmitkBinaryThresholdToolGUIBase.h" #include /** \ingroup org_mitk_gui_qt_interactivesegmentation_internal \brief GUI for mitk::BinaryThresholdTool. This GUI shows a slider to change the tool's threshold and an OK button to accept a preview for actual thresholding. Last contributor: $Author$ */ -class MITKSEGMENTATIONUI_EXPORT QmitkBinaryThresholdULToolGUI : public QmitkToolGUI +class MITKSEGMENTATIONUI_EXPORT QmitkBinaryThresholdULToolGUI : public QmitkBinaryThresholdToolGUIBase { Q_OBJECT public: - mitkClassMacro(QmitkBinaryThresholdULToolGUI, QmitkToolGUI); + mitkClassMacro(QmitkBinaryThresholdULToolGUI, QmitkBinaryThresholdToolGUIBase); itkFactorylessNewMacro(Self); itkCloneMacro(Self); - void OnThresholdingIntervalBordersChanged(double lower, double upper, bool isFloat); - void OnThresholdingValuesChanged(mitk::ScalarType lower, mitk::ScalarType upper); - -signals: - -public slots: - -protected slots: - - void OnNewToolAssociated(mitk::Tool *); - - void OnAcceptThresholdPreview(); - - void OnThresholdsChanged(double min, double max); - protected: QmitkBinaryThresholdULToolGUI(); ~QmitkBinaryThresholdULToolGUI() override; - - void BusyStateChanged(bool) override; - - ctkRangeWidget *m_DoubleThresholdSlider; - QCheckBox* m_CheckProcessAll = nullptr; - QCheckBox* m_CheckCreateNew = nullptr; - - mitk::BinaryThresholdULTool::Pointer m_BinaryThresholdULTool; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkFastMarchingTool3DGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkFastMarchingTool3DGUI.cpp index b83f50a5eb..165cd8bde0 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkFastMarchingTool3DGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkFastMarchingTool3DGUI.cpp @@ -1,361 +1,20 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkFastMarchingTool3DGUI.h" -#include "QmitkConfirmSegmentationDialog.h" - -#include "mitkBaseRenderer.h" -#include "mitkStepper.h" -#include -#include -#include -#include -#include -#include -#include -#include -#include - MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkFastMarchingTool3DGUI, "") -QmitkFastMarchingTool3DGUI::QmitkFastMarchingTool3DGUI() : QmitkToolGUI() -{ - this->setContentsMargins(0, 0, 0, 0); - - // create the visible widgets - QVBoxLayout *widgetLayout = new QVBoxLayout(this); - widgetLayout->setContentsMargins(0, 0, 0, 0); - - QFont fntHelp; - fntHelp.setBold(true); - - QLabel *lblHelp = new QLabel(this); - lblHelp->setText("Press shift-click to add seeds repeatedly."); - lblHelp->setFont(fntHelp); - - widgetLayout->addWidget(lblHelp); - - // Sigma controls - { - QHBoxLayout *hlayout = new QHBoxLayout(); - hlayout->setSpacing(2); - - QLabel *lbl = new QLabel(this); - lbl->setText("Sigma: "); - hlayout->addWidget(lbl); - - QSpacerItem *sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); - hlayout->addItem(sp2); - - widgetLayout->addItem(hlayout); - } - - m_slSigma = new ctkSliderWidget(this); - m_slSigma->setMinimum(0.1); - m_slSigma->setMaximum(5.0); - m_slSigma->setPageStep(0.1); - m_slSigma->setSingleStep(0.01); - m_slSigma->setValue(1.0); - m_slSigma->setTracking(false); - m_slSigma->setToolTip("The \"sigma\" parameter in the Gradient Magnitude filter."); - connect(m_slSigma, SIGNAL(valueChanged(double)), this, SLOT(OnSigmaChanged(double))); - widgetLayout->addWidget(m_slSigma); - - // Alpha controls - { - QHBoxLayout *hlayout = new QHBoxLayout(); - hlayout->setSpacing(2); - - QLabel *lbl = new QLabel(this); - lbl->setText("Alpha: "); - hlayout->addWidget(lbl); - - QSpacerItem *sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); - hlayout->addItem(sp2); - - widgetLayout->addItem(hlayout); - } - - m_slAlpha = new ctkSliderWidget(this); - m_slAlpha->setMinimum(-10); - m_slAlpha->setMaximum(0); - m_slAlpha->setPageStep(0.1); - m_slAlpha->setSingleStep(0.01); - m_slAlpha->setValue(-2.5); - m_slAlpha->setTracking(false); - m_slAlpha->setToolTip("The \"alpha\" parameter in the Sigmoid mapping filter."); - connect(m_slAlpha, SIGNAL(valueChanged(double)), this, SLOT(OnAlphaChanged(double))); - widgetLayout->addWidget(m_slAlpha); - - // Beta controls - { - QHBoxLayout *hlayout = new QHBoxLayout(); - hlayout->setSpacing(2); - - QLabel *lbl = new QLabel(this); - lbl->setText("Beta: "); - hlayout->addWidget(lbl); - - QSpacerItem *sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); - hlayout->addItem(sp2); - - widgetLayout->addLayout(hlayout); - } - - m_slBeta = new ctkSliderWidget(this); - m_slBeta->setMinimum(0); - m_slBeta->setMaximum(100); - m_slBeta->setPageStep(0.1); - m_slBeta->setSingleStep(0.01); - m_slBeta->setValue(3.5); - m_slBeta->setTracking(false); - m_slBeta->setToolTip("The \"beta\" parameter in the Sigmoid mapping filter."); - connect(m_slBeta, SIGNAL(valueChanged(double)), this, SLOT(OnBetaChanged(double))); - widgetLayout->addWidget(m_slBeta); - - // stopping value controls - { - QHBoxLayout *hlayout = new QHBoxLayout(); - hlayout->setSpacing(2); - - QLabel *lbl = new QLabel(this); - lbl->setText("Stopping value: "); - hlayout->addWidget(lbl); - - QSpacerItem *sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); - hlayout->addItem(sp2); - - widgetLayout->addLayout(hlayout); - } - - m_slStoppingValue = new ctkSliderWidget(this); - m_slStoppingValue->setMinimum(0); - m_slStoppingValue->setMaximum(10000); - m_slStoppingValue->setPageStep(10); - m_slStoppingValue->setSingleStep(1); - m_slStoppingValue->setValue(2000); - m_slStoppingValue->setDecimals(0); - m_slStoppingValue->setTracking(false); - m_slStoppingValue->setToolTip("The \"stopping value\" parameter in the fast marching 3D algorithm"); - connect(m_slStoppingValue, SIGNAL(valueChanged(double)), this, SLOT(OnStoppingValueChanged(double))); - widgetLayout->addWidget(m_slStoppingValue); - - // threshold controls - { - QHBoxLayout *hlayout = new QHBoxLayout(); - hlayout->setSpacing(2); - - QLabel *lbl = new QLabel(this); - lbl->setText("Threshold: "); - hlayout->addWidget(lbl); - - QSpacerItem *sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); - hlayout->addItem(sp2); - - widgetLayout->addLayout(hlayout); - } - - m_slwThreshold = new ctkRangeWidget(this); - m_slwThreshold->setMinimum(-100); - m_slwThreshold->setMaximum(5000); - m_slwThreshold->setMinimumValue(-100); - m_slwThreshold->setMaximumValue(2000); - m_slwThreshold->setDecimals(0); - m_slwThreshold->setTracking(false); - m_slwThreshold->setToolTip("The lower and upper thresholds for the final thresholding"); - connect(m_slwThreshold, SIGNAL(valuesChanged(double, double)), this, SLOT(OnThresholdChanged(double, double))); - widgetLayout->addWidget(m_slwThreshold); - - m_btClearSeeds = new QPushButton("Clear"); - m_btClearSeeds->setToolTip("Clear current result and start over again"); - m_btClearSeeds->setEnabled(false); - widgetLayout->addWidget(m_btClearSeeds); - connect(m_btClearSeeds, SIGNAL(clicked()), this, SLOT(OnClearSeeds())); - - m_btConfirm = new QPushButton("Confirm Segmentation"); - m_btConfirm->setToolTip("Incorporate current result in your working session."); - m_btConfirm->setEnabled(false); - widgetLayout->addWidget(m_btConfirm); - connect(m_btConfirm, SIGNAL(clicked()), this, SLOT(OnConfirmSegmentation())); - - m_CheckProcessAll = new QCheckBox("Process all time steps", this); - m_CheckProcessAll->setChecked(false); - m_CheckProcessAll->setToolTip("Process/overwrite all time steps of the dynamic segmentation and not just the currently visible time step."); - widgetLayout->addWidget(m_CheckProcessAll); - - m_CheckCreateNew = new QCheckBox("Create as new segmentation", this); - m_CheckCreateNew->setChecked(false); - m_CheckCreateNew->setToolTip("Add the confirmed segmentation as a new segmentation instead of overwriting the currently selected."); - widgetLayout->addWidget(m_CheckCreateNew); - - connect(this, SIGNAL(NewToolAssociated(mitk::Tool *)), this, SLOT(OnNewToolAssociated(mitk::Tool *))); - - m_slSigma->setDecimals(2); - m_slBeta->setDecimals(2); - m_slAlpha->setDecimals(2); - - this->EnableWidgets(false); -} - -QmitkFastMarchingTool3DGUI::~QmitkFastMarchingTool3DGUI() -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->CurrentlyBusy -= - mitk::MessageDelegate1(this, &QmitkFastMarchingTool3DGUI::BusyStateChanged); - } -} - -void QmitkFastMarchingTool3DGUI::OnNewToolAssociated(mitk::Tool *tool) -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->CurrentlyBusy -= - mitk::MessageDelegate1(this, &QmitkFastMarchingTool3DGUI::BusyStateChanged); - } - - m_FastMarchingTool = dynamic_cast(tool); - - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->CurrentlyBusy += - mitk::MessageDelegate1(this, &QmitkFastMarchingTool3DGUI::BusyStateChanged); - - m_FastMarchingTool->SetLowerThreshold(m_slwThreshold->minimumValue()); - m_FastMarchingTool->SetUpperThreshold(m_slwThreshold->maximumValue()); - m_FastMarchingTool->SetStoppingValue(m_slStoppingValue->value()); - m_FastMarchingTool->SetSigma(m_slSigma->value()); - m_FastMarchingTool->SetAlpha(m_slAlpha->value()); - m_FastMarchingTool->SetBeta(m_slBeta->value()); - m_FastMarchingTool->SetOverwriteExistingSegmentation(true); - m_FastMarchingTool->ClearSeeds(); - m_CheckProcessAll->setVisible(m_FastMarchingTool->GetTargetSegmentationNode()->GetData()->GetTimeSteps() > 1); - } -} - -void QmitkFastMarchingTool3DGUI::Update() -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->SetLowerThreshold(m_slwThreshold->minimumValue()); - m_FastMarchingTool->SetUpperThreshold(m_slwThreshold->maximumValue()); - m_FastMarchingTool->SetStoppingValue(m_slStoppingValue->value()); - m_FastMarchingTool->SetSigma(m_slSigma->value()); - m_FastMarchingTool->SetAlpha(m_slAlpha->value()); - m_FastMarchingTool->SetBeta(m_slBeta->value()); - m_FastMarchingTool->UpdatePreview(); - } -} - -void QmitkFastMarchingTool3DGUI::OnThresholdChanged(double lower, double upper) -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->SetLowerThreshold(lower); - m_FastMarchingTool->SetUpperThreshold(upper); - this->Update(); - } -} - -void QmitkFastMarchingTool3DGUI::OnBetaChanged(double value) -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->SetBeta(value); - this->Update(); - } -} - -void QmitkFastMarchingTool3DGUI::OnSigmaChanged(double value) +QmitkFastMarchingTool3DGUI::QmitkFastMarchingTool3DGUI() : QmitkFastMarchingToolGUIBase(false) { - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->SetSigma(value); - this->Update(); - } } -void QmitkFastMarchingTool3DGUI::OnAlphaChanged(double value) -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->SetAlpha(value); - this->Update(); - } -} - -void QmitkFastMarchingTool3DGUI::OnStoppingValueChanged(double value) -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->SetStoppingValue(value); - this->Update(); - } -} - -void QmitkFastMarchingTool3DGUI::OnConfirmSegmentation() -{ - if (m_FastMarchingTool.IsNotNull()) - { - if (m_CheckCreateNew->isChecked()) - { - m_FastMarchingTool->SetOverwriteExistingSegmentation(false); - } - else - { - m_FastMarchingTool->SetOverwriteExistingSegmentation(true); - } - - m_FastMarchingTool->SetCreateAllTimeSteps(m_CheckProcessAll->isChecked()); - - m_btConfirm->setEnabled(false); - m_FastMarchingTool->ConfirmSegmentation(); - } -} - -void QmitkFastMarchingTool3DGUI::OnClearSeeds() -{ - // event from image navigator recieved - timestep has changed - m_FastMarchingTool->ClearSeeds(); - m_btClearSeeds->setEnabled(false); - m_btConfirm->setEnabled(false); - this->EnableWidgets(false); - this->Update(); -} - -void QmitkFastMarchingTool3DGUI::BusyStateChanged(bool value) -{ - if (value) - { - QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); - this->EnableWidgets(false); - } - else - { - QApplication::restoreOverrideCursor(); - this->EnableWidgets(true); - } -} - -void QmitkFastMarchingTool3DGUI::EnableWidgets(bool enable) -{ - m_slSigma->setEnabled(enable); - m_slAlpha->setEnabled(enable); - m_slBeta->setEnabled(enable); - m_slStoppingValue->setEnabled(enable); - m_slwThreshold->setEnabled(enable); - m_btClearSeeds->setEnabled(enable); - m_btConfirm->setEnabled(enable); - m_CheckCreateNew->setEnabled(enable); - m_CheckProcessAll->setEnabled(enable); -} diff --git a/Modules/SegmentationUI/Qmitk/QmitkFastMarchingTool3DGUI.h b/Modules/SegmentationUI/Qmitk/QmitkFastMarchingTool3DGUI.h index a02b18de12..42f2c60ecb 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkFastMarchingTool3DGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkFastMarchingTool3DGUI.h @@ -1,79 +1,38 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 QmitkFastMarchingTool3DGUI_h_Included #define QmitkFastMarchingTool3DGUI_h_Included -#include "QmitkToolGUI.h" -#include "mitkFastMarchingTool3D.h" +#include "QmitkFastMarchingToolGUIBase.h" #include -class ctkSliderWidget; -class ctkRangeWidget; -class QPushButton; -class QCheckBox; - /** \ingroup org_mitk_gui_qt_interactivesegmentation_internal -\brief GUI for mitk::FastMarchingTool. +\brief GUI for mitk::FastMarchingTool3D. \sa mitk::FastMarchingTool */ -class MITKSEGMENTATIONUI_EXPORT QmitkFastMarchingTool3DGUI : public QmitkToolGUI +class MITKSEGMENTATIONUI_EXPORT QmitkFastMarchingTool3DGUI : public QmitkFastMarchingToolGUIBase { Q_OBJECT public: - mitkClassMacro(QmitkFastMarchingTool3DGUI, QmitkToolGUI); + mitkClassMacro(QmitkFastMarchingTool3DGUI, QmitkFastMarchingToolGUIBase); itkFactorylessNewMacro(Self); itkCloneMacro(Self); - void OnThresholdChanged(int current); - -protected slots: - - void OnNewToolAssociated(mitk::Tool *); - - void OnThresholdChanged(double, double); - void OnAlphaChanged(double); - void OnBetaChanged(double); - void OnSigmaChanged(double); - void OnStoppingValueChanged(double); - void OnConfirmSegmentation(); - void OnClearSeeds(); - protected: QmitkFastMarchingTool3DGUI(); - ~QmitkFastMarchingTool3DGUI() override; - - void BusyStateChanged(bool) override; - - void Update(); - - ctkRangeWidget *m_slwThreshold; - ctkSliderWidget *m_slStoppingValue; - ctkSliderWidget *m_slSigma; - ctkSliderWidget *m_slAlpha; - ctkSliderWidget *m_slBeta; - - QPushButton *m_btConfirm; - QPushButton *m_btClearSeeds; - - QCheckBox* m_CheckProcessAll = nullptr; - QCheckBox* m_CheckCreateNew = nullptr; - - mitk::FastMarchingTool3D::Pointer m_FastMarchingTool; - -private: - void EnableWidgets(bool); + ~QmitkFastMarchingTool3DGUI() = default; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUI.cpp index f02ff0523b..08670906f7 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUI.cpp @@ -1,350 +1,31 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkFastMarchingToolGUI.h" #include "QmitkNewSegmentationDialog.h" #include "mitkBaseRenderer.h" #include "mitkStepper.h" #include #include #include #include #include #include #include #include MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkFastMarchingToolGUI, "") -QmitkFastMarchingToolGUI::QmitkFastMarchingToolGUI() : QmitkToolGUI(), m_TimeIsConnected(false) -{ - this->setContentsMargins(0, 0, 0, 0); - - // create the visible widgets - QVBoxLayout *widgetLayout = new QVBoxLayout(this); - widgetLayout->setContentsMargins(0, 0, 0, 0); - - QFont fntHelp; - fntHelp.setBold(true); - - QLabel *lblHelp = new QLabel(this); - lblHelp->setText("Press shift-click to add seeds repeatedly."); - lblHelp->setFont(fntHelp); - - widgetLayout->addWidget(lblHelp); - - // Sigma controls - { - QHBoxLayout *hlayout = new QHBoxLayout(); - hlayout->setSpacing(2); - - QLabel *lbl = new QLabel(this); - lbl->setText("Sigma: "); - hlayout->addWidget(lbl); - - QSpacerItem *sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); - hlayout->addItem(sp2); - - widgetLayout->addItem(hlayout); - } - - m_slSigma = new ctkSliderWidget(this); - m_slSigma->setMinimum(0.1); - m_slSigma->setMaximum(5.0); - m_slSigma->setPageStep(0.1); - m_slSigma->setSingleStep(0.01); - m_slSigma->setValue(1.0); - m_slSigma->setTracking(false); - m_slSigma->setToolTip("The \"sigma\" parameter in the Gradient Magnitude filter."); - connect(m_slSigma, SIGNAL(valueChanged(double)), this, SLOT(OnSigmaChanged(double))); - widgetLayout->addWidget(m_slSigma); - - // Alpha controls - { - QHBoxLayout *hlayout = new QHBoxLayout(); - hlayout->setSpacing(2); - - QLabel *lbl = new QLabel(this); - lbl->setText("Alpha: "); - hlayout->addWidget(lbl); - - QSpacerItem *sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); - hlayout->addItem(sp2); - - widgetLayout->addItem(hlayout); - } - - m_slAlpha = new ctkSliderWidget(this); - m_slAlpha->setMinimum(-10); - m_slAlpha->setMaximum(0); - m_slAlpha->setPageStep(0.1); - m_slAlpha->setSingleStep(0.01); - m_slAlpha->setValue(-2.5); - m_slAlpha->setTracking(false); - m_slAlpha->setToolTip("The \"alpha\" parameter in the Sigmoid mapping filter."); - connect(m_slAlpha, SIGNAL(valueChanged(double)), this, SLOT(OnAlphaChanged(double))); - widgetLayout->addWidget(m_slAlpha); - - // Beta controls - { - QHBoxLayout *hlayout = new QHBoxLayout(); - hlayout->setSpacing(2); - - QLabel *lbl = new QLabel(this); - lbl->setText("Beta: "); - hlayout->addWidget(lbl); - - QSpacerItem *sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); - hlayout->addItem(sp2); - - widgetLayout->addLayout(hlayout); - } - - m_slBeta = new ctkSliderWidget(this); - m_slBeta->setMinimum(0); - m_slBeta->setMaximum(100); - m_slBeta->setPageStep(0.1); - m_slBeta->setSingleStep(0.01); - m_slBeta->setValue(3.5); - m_slBeta->setTracking(false); - m_slBeta->setToolTip("The \"beta\" parameter in the Sigmoid mapping filter."); - connect(m_slBeta, SIGNAL(valueChanged(double)), this, SLOT(OnBetaChanged(double))); - widgetLayout->addWidget(m_slBeta); - - // stopping value controls - { - QHBoxLayout *hlayout = new QHBoxLayout(); - hlayout->setSpacing(2); - - QLabel *lbl = new QLabel(this); - lbl->setText("Stopping value: "); - hlayout->addWidget(lbl); - - QSpacerItem *sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); - hlayout->addItem(sp2); - - widgetLayout->addLayout(hlayout); - } - - m_slStoppingValue = new ctkSliderWidget(this); - m_slStoppingValue->setMinimum(0); - m_slStoppingValue->setMaximum(10000); - m_slStoppingValue->setPageStep(10); - m_slStoppingValue->setSingleStep(1); - m_slStoppingValue->setValue(2000); - m_slStoppingValue->setDecimals(0); - m_slStoppingValue->setTracking(false); - m_slStoppingValue->setToolTip("The \"stopping value\" parameter in the fast marching 3D algorithm"); - connect(m_slStoppingValue, SIGNAL(valueChanged(double)), this, SLOT(OnStoppingValueChanged(double))); - widgetLayout->addWidget(m_slStoppingValue); - - // threshold controls - { - QHBoxLayout *hlayout = new QHBoxLayout(); - hlayout->setSpacing(2); - - QLabel *lbl = new QLabel(this); - lbl->setText("Threshold: "); - hlayout->addWidget(lbl); - - QSpacerItem *sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); - hlayout->addItem(sp2); - - widgetLayout->addLayout(hlayout); - } - - m_slwThreshold = new ctkRangeWidget(this); - m_slwThreshold->setMinimum(-100); - m_slwThreshold->setMaximum(5000); - m_slwThreshold->setMinimumValue(-100); - m_slwThreshold->setMaximumValue(2000); - m_slwThreshold->setDecimals(0); - m_slwThreshold->setTracking(false); - m_slwThreshold->setToolTip("The lower and upper thresholds for the final thresholding"); - connect(m_slwThreshold, SIGNAL(valuesChanged(double, double)), this, SLOT(OnThresholdChanged(double, double))); - widgetLayout->addWidget(m_slwThreshold); - - m_btClearSeeds = new QPushButton("Clear"); - m_btClearSeeds->setToolTip("Clear current result and start over again"); - m_btClearSeeds->setEnabled(false); - widgetLayout->addWidget(m_btClearSeeds); - connect(m_btClearSeeds, SIGNAL(clicked()), this, SLOT(OnClearSeeds())); - - m_btConfirm = new QPushButton("Confirm Segmentation"); - m_btConfirm->setToolTip("Incorporate current result in your working session."); - m_btConfirm->setEnabled(false); - widgetLayout->addWidget(m_btConfirm); - connect(m_btConfirm, SIGNAL(clicked()), this, SLOT(OnConfirmSegmentation())); - - connect(this, SIGNAL(NewToolAssociated(mitk::Tool *)), this, SLOT(OnNewToolAssociated(mitk::Tool *))); - - m_slAlpha->setDecimals(2); - m_slSigma->setDecimals(2); - m_slBeta->setDecimals(2); - - this->EnableWidgets(false); -} - -QmitkFastMarchingToolGUI::~QmitkFastMarchingToolGUI() -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->CurrentlyBusy -= - mitk::MessageDelegate1(this, &QmitkFastMarchingToolGUI::BusyStateChanged); - m_FastMarchingTool->RemoveReadyListener( - mitk::MessageDelegate(this, &QmitkFastMarchingToolGUI::OnFastMarchingToolReady)); - } -} - -void QmitkFastMarchingToolGUI::OnNewToolAssociated(mitk::Tool *tool) -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->CurrentlyBusy -= - mitk::MessageDelegate1(this, &QmitkFastMarchingToolGUI::BusyStateChanged); - m_FastMarchingTool->RemoveReadyListener( - mitk::MessageDelegate(this, &QmitkFastMarchingToolGUI::OnFastMarchingToolReady)); - } - - m_FastMarchingTool = dynamic_cast(tool); - - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->CurrentlyBusy += - mitk::MessageDelegate1(this, &QmitkFastMarchingToolGUI::BusyStateChanged); - m_FastMarchingTool->AddReadyListener( - mitk::MessageDelegate(this, &QmitkFastMarchingToolGUI::OnFastMarchingToolReady)); - - // listen to timestep change events - mitk::BaseRenderer::Pointer renderer; - renderer = mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget0")); - if (renderer.IsNotNull() && !m_TimeIsConnected) - { - new QmitkStepperAdapter(this, renderer->GetSliceNavigationController()->GetTime(), "stepper"); - // connect(m_TimeStepper, SIGNAL(Refetch()), this, SLOT(Refetch())); - m_TimeIsConnected = true; - } - } -} - -void QmitkFastMarchingToolGUI::Update() -{ - m_FastMarchingTool->SetLowerThreshold(this->m_slwThreshold->minimumValue()); - m_FastMarchingTool->SetUpperThreshold(this->m_slwThreshold->maximumValue()); - m_FastMarchingTool->SetStoppingValue(this->m_slStoppingValue->value()); - m_FastMarchingTool->SetSigma(this->m_slSigma->value()); - m_FastMarchingTool->SetAlpha(this->m_slAlpha->value()); - m_FastMarchingTool->SetBeta(this->m_slBeta->value()); - m_FastMarchingTool->Update(); -} - -void QmitkFastMarchingToolGUI::OnThresholdChanged(double lower, double upper) -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->SetLowerThreshold(lower); - m_FastMarchingTool->SetUpperThreshold(upper); - this->Update(); - } -} - -void QmitkFastMarchingToolGUI::OnBetaChanged(double value) -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->SetBeta(value); - this->Update(); - } -} - -void QmitkFastMarchingToolGUI::OnSigmaChanged(double value) -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->SetSigma(value); - this->Update(); - } -} - -void QmitkFastMarchingToolGUI::OnAlphaChanged(double value) -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->SetAlpha(value); - this->Update(); - } -} - -void QmitkFastMarchingToolGUI::OnStoppingValueChanged(double value) -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_FastMarchingTool->SetStoppingValue(value); - this->Update(); - } -} - -void QmitkFastMarchingToolGUI::OnConfirmSegmentation() -{ - if (m_FastMarchingTool.IsNotNull()) - { - m_btConfirm->setEnabled(false); - m_FastMarchingTool->ConfirmSegmentation(); - } -} - -void QmitkFastMarchingToolGUI::SetStepper(mitk::Stepper *stepper) -{ - this->m_TimeStepper = stepper; -} - -void QmitkFastMarchingToolGUI::Refetch() -{ - // event from image navigator recieved - timestep has changed - m_FastMarchingTool->SetCurrentTimeStep(m_TimeStepper->GetPos()); -} - -void QmitkFastMarchingToolGUI::OnClearSeeds() -{ - // event from image navigator recieved - timestep has changed - m_FastMarchingTool->ClearSeeds(); - m_btClearSeeds->setEnabled(false); - m_btConfirm->setEnabled(false); - this->EnableWidgets(false); - this->Update(); -} - -void QmitkFastMarchingToolGUI::BusyStateChanged(bool value) -{ - if (value) - QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); - else - QApplication::restoreOverrideCursor(); -} - -void QmitkFastMarchingToolGUI::OnFastMarchingToolReady() -{ - this->EnableWidgets(true); - this->m_btClearSeeds->setEnabled(true); - this->m_btConfirm->setEnabled(true); -} - -void QmitkFastMarchingToolGUI::EnableWidgets(bool enable) -{ - m_slSigma->setEnabled(enable); - m_slAlpha->setEnabled(enable); - m_slBeta->setEnabled(enable); - m_slStoppingValue->setEnabled(enable); - m_slwThreshold->setEnabled(enable); -} +QmitkFastMarchingToolGUI::QmitkFastMarchingToolGUI() : QmitkFastMarchingToolGUIBase(true) +{} diff --git a/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUI.h index 6d1ede7b3d..72340f6114 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUI.h @@ -1,84 +1,38 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 QmitkFastMarchingToolGUI_h_Included #define QmitkFastMarchingToolGUI_h_Included -#include "QmitkToolGUI.h" -#include "mitkFastMarchingTool.h" +#include "QmitkFastMarchingToolGUIBase.h" #include -class ctkSliderWidget; -class ctkRangeWidget; -class QPushButton; - -#include "QmitkStepperAdapter.h" - /** \ingroup org_mitk_gui_qt_interactivesegmentation_internal -\brief GUI for mitk::FastMarchingTool. +\brief GUI for mitk::FastMarchingTool in 2D. \sa mitk::FastMarchingTool */ -class MITKSEGMENTATIONUI_EXPORT QmitkFastMarchingToolGUI : public QmitkToolGUI +class MITKSEGMENTATIONUI_EXPORT QmitkFastMarchingToolGUI : public QmitkFastMarchingToolGUIBase { Q_OBJECT public: - mitkClassMacro(QmitkFastMarchingToolGUI, QmitkToolGUI); + mitkClassMacro(QmitkFastMarchingToolGUI, QmitkFastMarchingToolGUIBase); itkFactorylessNewMacro(Self); itkCloneMacro(Self); - void OnThresholdChanged(int current); - -protected slots: - - void OnNewToolAssociated(mitk::Tool *); - - void OnThresholdChanged(double, double); - void OnAlphaChanged(double); - void OnBetaChanged(double); - void OnSigmaChanged(double); - void OnStoppingValueChanged(double); - void OnConfirmSegmentation(); - void Refetch(); - void SetStepper(mitk::Stepper *); - void OnClearSeeds(); - protected: QmitkFastMarchingToolGUI(); - ~QmitkFastMarchingToolGUI() override; - - void Update(); - - void BusyStateChanged(bool) override; - - ctkRangeWidget *m_slwThreshold; - ctkSliderWidget *m_slStoppingValue; - ctkSliderWidget *m_slSigma; - ctkSliderWidget *m_slAlpha; - ctkSliderWidget *m_slBeta; - - QPushButton *m_btConfirm; - QPushButton *m_btClearSeeds; - - mitk::FastMarchingTool::Pointer m_FastMarchingTool; - - bool m_TimeIsConnected; - mitk::Stepper::Pointer m_TimeStepper; - - void OnFastMarchingToolReady(); - -private: - void EnableWidgets(bool); + ~QmitkFastMarchingToolGUI() = default; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUIBase.cpp b/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUIBase.cpp new file mode 100644 index 0000000000..1bd272c0f5 --- /dev/null +++ b/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUIBase.cpp @@ -0,0 +1,296 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +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 "QmitkFastMarchingToolGUIBase.h" + +#include "mitkBaseRenderer.h" +#include "mitkStepper.h" +#include +#include +#include +#include +#include +#include +#include +#include + +QmitkFastMarchingToolGUIBase::QmitkFastMarchingToolGUIBase(bool mode2D) : QmitkAutoSegmentationToolGUIBase(mode2D) +{ +} + +QmitkFastMarchingToolGUIBase::~QmitkFastMarchingToolGUIBase() +{ +} + +void QmitkFastMarchingToolGUIBase::Update() +{ + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) + { + tool->SetLowerThreshold(m_slwThreshold->minimumValue()); + tool->SetUpperThreshold(m_slwThreshold->maximumValue()); + tool->SetStoppingValue(m_slStoppingValue->value()); + tool->SetSigma(m_slSigma->value()); + tool->SetAlpha(m_slAlpha->value()); + tool->SetBeta(m_slBeta->value()); + tool->UpdatePreview(); + } +} + +void QmitkFastMarchingToolGUIBase::OnThresholdChanged(double lower, double upper) +{ + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) + { + tool->SetLowerThreshold(lower); + tool->SetUpperThreshold(upper); + this->Update(); + } +} + +void QmitkFastMarchingToolGUIBase::OnBetaChanged(double value) +{ + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) + { + tool->SetBeta(value); + this->Update(); + } +} + +void QmitkFastMarchingToolGUIBase::OnSigmaChanged(double value) +{ + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) + { + tool->SetSigma(value); + this->Update(); + } +} + +void QmitkFastMarchingToolGUIBase::OnAlphaChanged(double value) +{ + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) + { + tool->SetAlpha(value); + this->Update(); + } +} + +void QmitkFastMarchingToolGUIBase::OnStoppingValueChanged(double value) +{ + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) + { + tool->SetStoppingValue(value); + this->Update(); + } +} + +void QmitkFastMarchingToolGUIBase::OnClearSeeds() +{ + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) + { + tool->ClearSeeds(); + this->EnableWidgets(false); + this->Update(); + } +} + +void QmitkFastMarchingToolGUIBase::ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool) +{ + Superclass::ConnectNewTool(newTool); + + auto tool = dynamic_cast(newTool); + if (nullptr != tool) + { + tool->SetLowerThreshold(m_slwThreshold->minimumValue()); + tool->SetUpperThreshold(m_slwThreshold->maximumValue()); + tool->SetStoppingValue(m_slStoppingValue->value()); + tool->SetSigma(m_slSigma->value()); + tool->SetAlpha(m_slAlpha->value()); + tool->SetBeta(m_slBeta->value()); + tool->ClearSeeds(); + } +} + +void QmitkFastMarchingToolGUIBase::InitializeUI(QBoxLayout* mainLayout) +{ + mainLayout->setContentsMargins(0, 0, 0, 0); + + QFont fntHelp; + fntHelp.setBold(true); + + QLabel* lblHelp = new QLabel(this); + lblHelp->setText("Press shift-click to add seeds repeatedly."); + lblHelp->setFont(fntHelp); + + mainLayout->addWidget(lblHelp); + + // Sigma controls + { + QHBoxLayout* hlayout = new QHBoxLayout(); + hlayout->setSpacing(2); + + QLabel* lbl = new QLabel(this); + lbl->setText("Sigma: "); + hlayout->addWidget(lbl); + + QSpacerItem* sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); + hlayout->addItem(sp2); + + mainLayout->addItem(hlayout); + } + + m_slSigma = new ctkSliderWidget(this); + m_slSigma->setMinimum(0.1); + m_slSigma->setMaximum(5.0); + m_slSigma->setPageStep(0.1); + m_slSigma->setSingleStep(0.01); + m_slSigma->setValue(1.0); + m_slSigma->setTracking(false); + m_slSigma->setToolTip("The \"sigma\" parameter in the Gradient Magnitude filter."); + connect(m_slSigma, SIGNAL(valueChanged(double)), this, SLOT(OnSigmaChanged(double))); + mainLayout->addWidget(m_slSigma); + + // Alpha controls + { + QHBoxLayout* hlayout = new QHBoxLayout(); + hlayout->setSpacing(2); + + QLabel* lbl = new QLabel(this); + lbl->setText("Alpha: "); + hlayout->addWidget(lbl); + + QSpacerItem* sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); + hlayout->addItem(sp2); + + mainLayout->addItem(hlayout); + } + + m_slAlpha = new ctkSliderWidget(this); + m_slAlpha->setMinimum(-10); + m_slAlpha->setMaximum(0); + m_slAlpha->setPageStep(0.1); + m_slAlpha->setSingleStep(0.01); + m_slAlpha->setValue(-2.5); + m_slAlpha->setTracking(false); + m_slAlpha->setToolTip("The \"alpha\" parameter in the Sigmoid mapping filter."); + connect(m_slAlpha, SIGNAL(valueChanged(double)), this, SLOT(OnAlphaChanged(double))); + mainLayout->addWidget(m_slAlpha); + + // Beta controls + { + QHBoxLayout* hlayout = new QHBoxLayout(); + hlayout->setSpacing(2); + + QLabel* lbl = new QLabel(this); + lbl->setText("Beta: "); + hlayout->addWidget(lbl); + + QSpacerItem* sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); + hlayout->addItem(sp2); + + mainLayout->addLayout(hlayout); + } + + m_slBeta = new ctkSliderWidget(this); + m_slBeta->setMinimum(0); + m_slBeta->setMaximum(100); + m_slBeta->setPageStep(0.1); + m_slBeta->setSingleStep(0.01); + m_slBeta->setValue(3.5); + m_slBeta->setTracking(false); + m_slBeta->setToolTip("The \"beta\" parameter in the Sigmoid mapping filter."); + connect(m_slBeta, SIGNAL(valueChanged(double)), this, SLOT(OnBetaChanged(double))); + mainLayout->addWidget(m_slBeta); + + // stopping value controls + { + QHBoxLayout* hlayout = new QHBoxLayout(); + hlayout->setSpacing(2); + + QLabel* lbl = new QLabel(this); + lbl->setText("Stopping value: "); + hlayout->addWidget(lbl); + + QSpacerItem* sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); + hlayout->addItem(sp2); + + mainLayout->addLayout(hlayout); + } + + m_slStoppingValue = new ctkSliderWidget(this); + m_slStoppingValue->setMinimum(0); + m_slStoppingValue->setMaximum(10000); + m_slStoppingValue->setPageStep(10); + m_slStoppingValue->setSingleStep(1); + m_slStoppingValue->setValue(2000); + m_slStoppingValue->setDecimals(0); + m_slStoppingValue->setTracking(false); + m_slStoppingValue->setToolTip("The \"stopping value\" parameter in the fast marching 3D algorithm"); + connect(m_slStoppingValue, SIGNAL(valueChanged(double)), this, SLOT(OnStoppingValueChanged(double))); + mainLayout->addWidget(m_slStoppingValue); + + // threshold controls + { + QHBoxLayout* hlayout = new QHBoxLayout(); + hlayout->setSpacing(2); + + QLabel* lbl = new QLabel(this); + lbl->setText("Threshold: "); + hlayout->addWidget(lbl); + + QSpacerItem* sp2 = new QSpacerItem(40, 20, QSizePolicy::Expanding, QSizePolicy::Minimum); + hlayout->addItem(sp2); + + mainLayout->addLayout(hlayout); + } + + m_slwThreshold = new ctkRangeWidget(this); + m_slwThreshold->setMinimum(-100); + m_slwThreshold->setMaximum(5000); + m_slwThreshold->setMinimumValue(-100); + m_slwThreshold->setMaximumValue(2000); + m_slwThreshold->setDecimals(0); + m_slwThreshold->setTracking(false); + m_slwThreshold->setToolTip("The lower and upper thresholds for the final thresholding"); + connect(m_slwThreshold, SIGNAL(valuesChanged(double, double)), this, SLOT(OnThresholdChanged(double, double))); + mainLayout->addWidget(m_slwThreshold); + + m_btClearSeeds = new QPushButton("Clear"); + m_btClearSeeds->setToolTip("Clear current result and start over again"); + m_btClearSeeds->setEnabled(false); + mainLayout->addWidget(m_btClearSeeds); + connect(m_btClearSeeds, SIGNAL(clicked()), this, SLOT(OnClearSeeds())); + + m_slSigma->setDecimals(2); + m_slBeta->setDecimals(2); + m_slAlpha->setDecimals(2); + + this->EnableWidgets(false); + + Superclass::InitializeUI(mainLayout); +} + +void QmitkFastMarchingToolGUIBase::EnableWidgets(bool enable) +{ + Superclass::EnableWidgets(enable); + m_slSigma->setEnabled(enable); + m_slAlpha->setEnabled(enable); + m_slBeta->setEnabled(enable); + m_slStoppingValue->setEnabled(enable); + m_slwThreshold->setEnabled(enable); + m_btClearSeeds->setEnabled(enable); +} diff --git a/Modules/SegmentationUI/Qmitk/QmitkFastMarchingTool3DGUI.h b/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUIBase.h similarity index 58% copy from Modules/SegmentationUI/Qmitk/QmitkFastMarchingTool3DGUI.h copy to Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUIBase.h index a02b18de12..669ef27155 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkFastMarchingTool3DGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkFastMarchingToolGUIBase.h @@ -1,79 +1,67 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ -#ifndef QmitkFastMarchingTool3DGUI_h_Included -#define QmitkFastMarchingTool3DGUI_h_Included +#ifndef QmitkFastMarchingToolGUIBase_h_Included +#define QmitkFastMarchingToolGUIBase_h_Included -#include "QmitkToolGUI.h" +#include "QmitkAutoSegmentationToolGUIBase.h" #include "mitkFastMarchingTool3D.h" #include class ctkSliderWidget; class ctkRangeWidget; class QPushButton; -class QCheckBox; /** \ingroup org_mitk_gui_qt_interactivesegmentation_internal -\brief GUI for mitk::FastMarchingTool. +\brief Base GUI for mitk::FastMarchingTool (2D and 3D). \sa mitk::FastMarchingTool */ -class MITKSEGMENTATIONUI_EXPORT QmitkFastMarchingTool3DGUI : public QmitkToolGUI +class MITKSEGMENTATIONUI_EXPORT QmitkFastMarchingToolGUIBase : public QmitkAutoSegmentationToolGUIBase { Q_OBJECT public: - mitkClassMacro(QmitkFastMarchingTool3DGUI, QmitkToolGUI); - itkFactorylessNewMacro(Self); - itkCloneMacro(Self); - - void OnThresholdChanged(int current); + mitkClassMacro(QmitkFastMarchingToolGUIBase, QmitkAutoSegmentationToolGUIBase); protected slots: - void OnNewToolAssociated(mitk::Tool *); - void OnThresholdChanged(double, double); void OnAlphaChanged(double); void OnBetaChanged(double); void OnSigmaChanged(double); void OnStoppingValueChanged(double); - void OnConfirmSegmentation(); void OnClearSeeds(); protected: - QmitkFastMarchingTool3DGUI(); - ~QmitkFastMarchingTool3DGUI() override; + QmitkFastMarchingToolGUIBase(bool mode2D); + ~QmitkFastMarchingToolGUIBase() override; + + void ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool) override; + void InitializeUI(QBoxLayout* mainLayout) override; - void BusyStateChanged(bool) override; + void EnableWidgets(bool) override; void Update(); ctkRangeWidget *m_slwThreshold; ctkSliderWidget *m_slStoppingValue; ctkSliderWidget *m_slSigma; ctkSliderWidget *m_slAlpha; ctkSliderWidget *m_slBeta; - QPushButton *m_btConfirm; QPushButton *m_btClearSeeds; - QCheckBox* m_CheckProcessAll = nullptr; - QCheckBox* m_CheckCreateNew = nullptr; - - mitk::FastMarchingTool3D::Pointer m_FastMarchingTool; - private: - void EnableWidgets(bool); }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp index 9e925b66ba..6533d2e726 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp @@ -1,194 +1,129 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkOtsuTool3DGUI.h" +#include "mitkOtsuTool3D.h" #include MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkOtsuTool3DGUI, "") -QmitkOtsuTool3DGUI::QmitkOtsuTool3DGUI() : QmitkToolGUI(), m_NumberOfRegions(0) +QmitkOtsuTool3DGUI::QmitkOtsuTool3DGUI() : QmitkAutoMLSegmentationToolGUIBase() +{ +} + +void QmitkOtsuTool3DGUI::ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool) +{ + Superclass::ConnectNewTool(newTool); + + newTool->IsTimePointChangeAwareOff(); + m_FirstPreviewComputation = true; +} + +void QmitkOtsuTool3DGUI::InitializeUI(QBoxLayout* mainLayout) { m_Controls.setupUi(this); + mainLayout->addLayout(m_Controls.verticalLayout); - connect(m_Controls.previewButton, SIGNAL(clicked()), this, SLOT(OnSpinboxValueAccept())); - connect(m_Controls.m_selectionListWidget, &QmitkSimpleLabelSetListWidget::SelectedLabelsChanged, this, &QmitkOtsuTool3DGUI::OnRegionSelectionChanged); + connect(m_Controls.previewButton, SIGNAL(clicked()), this, SLOT(OnPreviewBtnClicked())); connect(m_Controls.m_Spinbox, SIGNAL(valueChanged(int)), this, SLOT(OnRegionSpinboxChanged(int))); - connect(m_Controls.m_ConfSegButton, SIGNAL(clicked()), this, SLOT(OnSegmentationRegionAccept())); - connect(this, SIGNAL(NewToolAssociated(mitk::Tool *)), this, SLOT(OnNewToolAssociated(mitk::Tool *))); connect(m_Controls.advancedSettingsButton, SIGNAL(toggled(bool)), this, SLOT(OnAdvancedSettingsButtonToggled(bool))); this->OnAdvancedSettingsButtonToggled(false); -} -QmitkOtsuTool3DGUI::~QmitkOtsuTool3DGUI() -{ - if (m_OtsuTool3DTool.IsNotNull()) - { - m_OtsuTool3DTool->CurrentlyBusy -= - mitk::MessageDelegate1(this, &QmitkOtsuTool3DGUI::BusyStateChanged); - } + Superclass::InitializeUI(mainLayout); } void QmitkOtsuTool3DGUI::OnRegionSpinboxChanged(int numberOfRegions) { // we have to change to minimum number of histogram bins accordingly int curBinValue = m_Controls.m_BinsSpinBox->value(); if (curBinValue < numberOfRegions) m_Controls.m_BinsSpinBox->setValue(numberOfRegions); } -void QmitkOtsuTool3DGUI::OnRegionSelectionChanged(const QmitkSimpleLabelSetListWidget::LabelVectorType& selectedLabels) -{ - if (m_OtsuTool3DTool.IsNotNull()) - { - mitk::AutoMLSegmentationWithPreviewTool::SelectedLabelVectorType labelIDs; - for (const auto& label : selectedLabels) - { - labelIDs.push_back(label->GetValue()); - } - - m_OtsuTool3DTool->SetSelectedLabels(labelIDs); - m_OtsuTool3DTool->UpdatePreview(); - - m_Controls.m_ConfSegButton->setEnabled(!labelIDs.empty()); - } -} - void QmitkOtsuTool3DGUI::OnAdvancedSettingsButtonToggled(bool toggled) { m_Controls.m_ValleyCheckbox->setVisible(toggled); m_Controls.binLabel->setVisible(toggled); m_Controls.m_BinsSpinBox->setVisible(toggled); - if (toggled) + auto tool = this->GetConnectedToolAs(); + if (toggled && nullptr != tool) { - int max = m_OtsuTool3DTool->GetMaxNumberOfBins(); + int max = tool->GetMaxNumberOfBins(); if (max >= m_Controls.m_BinsSpinBox->minimum()) { m_Controls.m_BinsSpinBox->setMaximum(max); } } } -void QmitkOtsuTool3DGUI::OnNewToolAssociated(mitk::Tool *tool) +void QmitkOtsuTool3DGUI::OnPreviewBtnClicked() { - if (m_OtsuTool3DTool.IsNotNull()) - { - m_OtsuTool3DTool->CurrentlyBusy -= - mitk::MessageDelegate1(this, &QmitkOtsuTool3DGUI::BusyStateChanged); - } - - m_OtsuTool3DTool = dynamic_cast(tool); - - if (m_OtsuTool3DTool.IsNotNull()) + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) { - m_OtsuTool3DTool->CurrentlyBusy += - mitk::MessageDelegate1(this, &QmitkOtsuTool3DGUI::BusyStateChanged); - - m_OtsuTool3DTool->SetOverwriteExistingSegmentation(true); - m_OtsuTool3DTool->IsTimePointChangeAwareOff(); - m_Controls.m_CheckProcessAll->setVisible(m_OtsuTool3DTool->GetTargetSegmentationNode()->GetData()->GetTimeSteps() > 1); - } -} - -void QmitkOtsuTool3DGUI::OnSegmentationRegionAccept() -{ - QString segName = QString::fromStdString(m_OtsuTool3DTool->GetCurrentSegmentationName()); - - if (m_OtsuTool3DTool.IsNotNull()) - { - if (this->m_Controls.m_CheckCreateNew->isChecked()) - { - m_OtsuTool3DTool->SetOverwriteExistingSegmentation(false); - } - else - { - m_OtsuTool3DTool->SetOverwriteExistingSegmentation(true); - } - - m_OtsuTool3DTool->SetCreateAllTimeSteps(this->m_Controls.m_CheckProcessAll->isChecked()); - - this->m_Controls.m_ConfSegButton->setEnabled(false); - m_OtsuTool3DTool->ConfirmSegmentation(); - } -} + if (!m_FirstPreviewComputation && + (tool->GetNumberOfRegions() == static_cast(m_Controls.m_Spinbox->value()) && + tool->GetUseValley() == m_Controls.m_ValleyCheckbox->isChecked() && + tool->GetNumberOfBins() == static_cast(m_Controls.m_BinsSpinBox->value()))) + return; -void QmitkOtsuTool3DGUI::OnSpinboxValueAccept() -{ - if (m_NumberOfRegions == m_Controls.m_Spinbox->value() && - m_UseValleyEmphasis == m_Controls.m_ValleyCheckbox->isChecked() && - m_NumberOfBins == m_Controls.m_BinsSpinBox->value()) - return; + m_FirstPreviewComputation = false; - if (m_OtsuTool3DTool.IsNotNull()) - { try { int proceed; QMessageBox *messageBox = new QMessageBox(QMessageBox::Question, nullptr, "The otsu segmentation computation may take several minutes depending " "on the number of Regions you selected. Proceed anyway?", QMessageBox::Ok | QMessageBox::Cancel); if (m_Controls.m_Spinbox->value() >= 5) { proceed = messageBox->exec(); if (proceed != QMessageBox::Ok) return; } - m_NumberOfRegions = m_Controls.m_Spinbox->value(); - m_UseValleyEmphasis = m_Controls.m_ValleyCheckbox->isChecked(); - m_NumberOfBins = m_Controls.m_BinsSpinBox->value(); - m_OtsuTool3DTool->SetNumberOfRegions(m_NumberOfRegions); - m_OtsuTool3DTool->SetUseValley(m_UseValleyEmphasis); - m_OtsuTool3DTool->SetNumberOfBins(m_NumberOfBins); + tool->SetNumberOfRegions(static_cast(m_Controls.m_Spinbox->value())); + tool->SetUseValley(m_Controls.m_ValleyCheckbox->isChecked()); + tool->SetNumberOfBins(static_cast(m_Controls.m_BinsSpinBox->value())); - m_OtsuTool3DTool->UpdatePreview(); + tool->UpdatePreview(); } catch (...) { this->setCursor(Qt::ArrowCursor); QMessageBox *messageBox = new QMessageBox(QMessageBox::Critical, nullptr, "itkOtsuFilter error: image dimension must be in {2, 3} and no RGB images can be handled."); messageBox->exec(); delete messageBox; return; } - m_Controls.m_selectionListWidget->SetLabelSetImage(m_OtsuTool3DTool->GetMLPreview()); - m_OtsuTool3DTool->IsTimePointChangeAwareOn(); + this->SetLabelSetPreview(tool->GetMLPreview()); + tool->IsTimePointChangeAwareOn(); } } -void QmitkOtsuTool3DGUI::BusyStateChanged(bool value) +void QmitkOtsuTool3DGUI::EnableWidgets(bool enabled) { - if (value) - { - QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); - } - else - { - QApplication::restoreOverrideCursor(); - } - - m_Controls.m_ValleyCheckbox->setEnabled(!value); - m_Controls.binLabel->setEnabled(!value); - m_Controls.m_BinsSpinBox->setEnabled(!value); - m_Controls.m_ConfSegButton->setEnabled(!m_OtsuTool3DTool->GetSelectedLabels().empty() && !value); - m_Controls.m_CheckProcessAll->setEnabled(!value); - m_Controls.m_CheckCreateNew->setEnabled(!value); - m_Controls.previewButton->setEnabled(!value); + Superclass::EnableWidgets(enabled); + m_Controls.m_ValleyCheckbox->setEnabled(enabled); + m_Controls.binLabel->setEnabled(enabled); + m_Controls.m_BinsSpinBox->setEnabled(enabled); + m_Controls.previewButton->setEnabled(enabled); } diff --git a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.h b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.h index e7a3762c43..f9d87fd615 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.h @@ -1,75 +1,64 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 QmitkOtsuTool3DGUI_h_Included #define QmitkOtsuTool3DGUI_h_Included -#include "QmitkToolGUI.h" -#include "mitkOtsuTool3D.h" +#include "QmitkAutoMLSegmentationToolGUIBase.h" #include "ui_QmitkOtsuToolWidgetControls.h" #include -#include /** \ingroup org_mitk_gui_qt_interactivesegmentation_internal \brief GUI for mitk::. \sa mitk:: This GUI shows ... Last contributor: $Author$ */ -class MITKSEGMENTATIONUI_EXPORT QmitkOtsuTool3DGUI : public QmitkToolGUI +class MITKSEGMENTATIONUI_EXPORT QmitkOtsuTool3DGUI : public QmitkAutoMLSegmentationToolGUIBase { Q_OBJECT public: - mitkClassMacro(QmitkOtsuTool3DGUI, QmitkToolGUI); + mitkClassMacro(QmitkOtsuTool3DGUI, QmitkAutoMLSegmentationToolGUIBase); itkFactorylessNewMacro(Self); itkCloneMacro(Self); protected slots : - void OnNewToolAssociated(mitk::Tool *); - - void OnSpinboxValueAccept(); - - void OnSegmentationRegionAccept(); - - void OnRegionSelectionChanged(const QmitkSimpleLabelSetListWidget::LabelVectorType& selectedLabels); + void OnPreviewBtnClicked(); void OnRegionSpinboxChanged(int); private slots: void OnAdvancedSettingsButtonToggled(bool toggled); protected: QmitkOtsuTool3DGUI(); - ~QmitkOtsuTool3DGUI() override; + ~QmitkOtsuTool3DGUI() = default; - void BusyStateChanged(bool value) override; + void ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool) override; + void InitializeUI(QBoxLayout* mainLayout) override; - mitk::OtsuTool3D::Pointer m_OtsuTool3DTool; + void EnableWidgets(bool enabled) override; Ui_QmitkOtsuToolWidgetControls m_Controls; - int m_NumberOfRegions; - - bool m_UseValleyEmphasis; - - int m_NumberOfBins; + bool m_FirstPreviewComputation = true; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui b/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui index d01d26178d..8137fb2d3f 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui +++ b/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui @@ -1,253 +1,205 @@ QmitkOtsuToolWidgetControls 0 0 699 352 0 0 100 0 100000 100000 QmitkOtsuToolWidget + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + QLayout::SetNoConstraint 0 0 Number of Regions: 0 0 40 16777215 2 32 Qt::Horizontal 40 20 0 0 0 32 Advanced settings Qt::ToolButtonTextBesideIcon true 2 4096 128 Use Valley Emphasis Number of Histogram Bins: Qt::Horizontal 40 20 - - - - - 0 - 0 - - - - - 10000000 - 10000000 - - - - 0 0 100000 16777215 Preview - - - - false - - - - 0 - 0 - - - - - 100000 - 16777215 - - - - Confirm Segmentation - - - - - - - Process/overwrite all time steps of the dynamic segmentation and not just the currently visible time step. - - - Process all time steps - - - - - - - Add the confirmed segmentation as a new segmentation instead of overwriting the currently selected. - - - Create as new segmentation - - - ctkExpandButton QToolButton
ctkExpandButton.h
 - - QmitkSimpleLabelSetListWidget - QWidget -
QmitkSimpleLabelSetListWidget.h
- diff --git a/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.cpp b/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.cpp index 22865bf8b4..6820efbc3b 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.cpp @@ -1,1385 +1,1405 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkSlicesInterpolator.h" #include "QmitkSelectableGLWidget.h" #include "QmitkStdMultiWidget.h" #include "mitkApplyDiffImageOperation.h" #include "mitkColorProperty.h" #include "mitkCoreObjectFactory.h" #include "mitkDiffImageApplier.h" #include "mitkInteractionConst.h" #include "mitkLevelWindowProperty.h" #include "mitkOperationEvent.h" #include "mitkOverwriteSliceImageFilter.h" #include "mitkProgressBar.h" #include "mitkProperties.h" #include "mitkRenderingManager.h" #include "mitkSegTool2D.h" #include "mitkSliceNavigationController.h" #include "mitkSurfaceToImageFilter.h" #include "mitkToolManager.h" #include "mitkUndoController.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include -//#define ROUND(a) ((a)>0 ? (int)((a)+0.5) : -(int)(0.5-(a))) +#include + +namespace +{ + template + itk::SmartPointer GetData(const mitk::DataNode* dataNode) + { + return nullptr != dataNode + ? dynamic_cast(dataNode->GetData()) + : nullptr; + } +} float SURFACE_COLOR_RGB[3] = {0.49f, 1.0f, 0.16f}; const std::map QmitkSlicesInterpolator::createActionToSliceDimension() { std::map actionToSliceDimension; foreach (mitk::SliceNavigationController *slicer, m_ControllerToDeleteObserverTag.keys()) { actionToSliceDimension[new QAction(QString::fromStdString(slicer->GetViewDirectionAsString()), nullptr)] = slicer; } return actionToSliceDimension; } QmitkSlicesInterpolator::QmitkSlicesInterpolator(QWidget *parent, const char * /*name*/) : QWidget(parent), // ACTION_TO_SLICEDIMENSION( createActionToSliceDimension() ), m_Interpolator(mitk::SegmentationInterpolationController::New()), m_SurfaceInterpolator(mitk::SurfaceInterpolationController::GetInstance()), m_ToolManager(nullptr), m_Initialized(false), m_LastSNC(nullptr), m_LastSliceIndex(0), m_2DInterpolationEnabled(false), m_3DInterpolationEnabled(false), m_FirstRun(true) { m_GroupBoxEnableExclusiveInterpolationMode = new QGroupBox("Interpolation", this); QVBoxLayout *vboxLayout = new QVBoxLayout(m_GroupBoxEnableExclusiveInterpolationMode); m_EdgeDetector = mitk::FeatureBasedEdgeDetectionFilter::New(); m_PointScorer = mitk::PointCloudScoringFilter::New(); m_CmbInterpolation = new QComboBox(m_GroupBoxEnableExclusiveInterpolationMode); m_CmbInterpolation->addItem("Disabled"); m_CmbInterpolation->addItem("2-Dimensional"); m_CmbInterpolation->addItem("3-Dimensional"); vboxLayout->addWidget(m_CmbInterpolation); m_BtnApply2D = new QPushButton("Confirm for single slice", m_GroupBoxEnableExclusiveInterpolationMode); vboxLayout->addWidget(m_BtnApply2D); m_BtnApplyForAllSlices2D = new QPushButton("Confirm for all slices", m_GroupBoxEnableExclusiveInterpolationMode); vboxLayout->addWidget(m_BtnApplyForAllSlices2D); m_BtnApply3D = new QPushButton("Confirm", m_GroupBoxEnableExclusiveInterpolationMode); vboxLayout->addWidget(m_BtnApply3D); - m_BtnSuggestPlane = new QPushButton("Suggest a plane", m_GroupBoxEnableExclusiveInterpolationMode); - vboxLayout->addWidget(m_BtnSuggestPlane); + // T28261 + // m_BtnSuggestPlane = new QPushButton("Suggest a plane", m_GroupBoxEnableExclusiveInterpolationMode); + // vboxLayout->addWidget(m_BtnSuggestPlane); m_BtnReinit3DInterpolation = new QPushButton("Reinit Interpolation", m_GroupBoxEnableExclusiveInterpolationMode); vboxLayout->addWidget(m_BtnReinit3DInterpolation); m_ChkShowPositionNodes = new QCheckBox("Show Position Nodes", m_GroupBoxEnableExclusiveInterpolationMode); vboxLayout->addWidget(m_ChkShowPositionNodes); this->HideAllInterpolationControls(); connect(m_CmbInterpolation, SIGNAL(currentIndexChanged(int)), this, SLOT(OnInterpolationMethodChanged(int))); connect(m_BtnApply2D, SIGNAL(clicked()), this, SLOT(OnAcceptInterpolationClicked())); connect(m_BtnApplyForAllSlices2D, SIGNAL(clicked()), this, SLOT(OnAcceptAllInterpolationsClicked())); connect(m_BtnApply3D, SIGNAL(clicked()), this, SLOT(OnAccept3DInterpolationClicked())); - connect(m_BtnSuggestPlane, SIGNAL(clicked()), this, SLOT(OnSuggestPlaneClicked())); + // T28261 + // connect(m_BtnSuggestPlane, SIGNAL(clicked()), this, SLOT(OnSuggestPlaneClicked())); connect(m_BtnReinit3DInterpolation, SIGNAL(clicked()), this, SLOT(OnReinit3DInterpolation())); connect(m_ChkShowPositionNodes, SIGNAL(toggled(bool)), this, SLOT(OnShowMarkers(bool))); connect(m_ChkShowPositionNodes, SIGNAL(toggled(bool)), this, SIGNAL(SignalShowMarkerNodes(bool))); QHBoxLayout *layout = new QHBoxLayout(this); layout->addWidget(m_GroupBoxEnableExclusiveInterpolationMode); this->setLayout(layout); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSlicesInterpolator::OnInterpolationInfoChanged); InterpolationInfoChangedObserverTag = m_Interpolator->AddObserver(itk::ModifiedEvent(), command); itk::ReceptorMemberCommand::Pointer command2 = itk::ReceptorMemberCommand::New(); command2->SetCallbackFunction(this, &QmitkSlicesInterpolator::OnSurfaceInterpolationInfoChanged); SurfaceInterpolationInfoChangedObserverTag = m_SurfaceInterpolator->AddObserver(itk::ModifiedEvent(), command2); // feedback node and its visualization properties m_FeedbackNode = mitk::DataNode::New(); mitk::CoreObjectFactory::GetInstance()->SetDefaultProperties(m_FeedbackNode); m_FeedbackNode->SetProperty("binary", mitk::BoolProperty::New(true)); m_FeedbackNode->SetProperty("outline binary", mitk::BoolProperty::New(true)); m_FeedbackNode->SetProperty("color", mitk::ColorProperty::New(255.0, 255.0, 0.0)); m_FeedbackNode->SetProperty("texture interpolation", mitk::BoolProperty::New(false)); m_FeedbackNode->SetProperty("layer", mitk::IntProperty::New(20)); m_FeedbackNode->SetProperty("levelwindow", mitk::LevelWindowProperty::New(mitk::LevelWindow(0, 1))); m_FeedbackNode->SetProperty("name", mitk::StringProperty::New("Interpolation feedback")); m_FeedbackNode->SetProperty("opacity", mitk::FloatProperty::New(0.8)); m_FeedbackNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_InterpolatedSurfaceNode = mitk::DataNode::New(); m_InterpolatedSurfaceNode->SetProperty("color", mitk::ColorProperty::New(SURFACE_COLOR_RGB)); m_InterpolatedSurfaceNode->SetProperty("name", mitk::StringProperty::New("Surface Interpolation feedback")); m_InterpolatedSurfaceNode->SetProperty("opacity", mitk::FloatProperty::New(0.5)); m_InterpolatedSurfaceNode->SetProperty("line width", mitk::FloatProperty::New(4.0f)); m_InterpolatedSurfaceNode->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false)); m_InterpolatedSurfaceNode->SetProperty("helper object", mitk::BoolProperty::New(true)); m_InterpolatedSurfaceNode->SetVisibility(false); m_3DContourNode = mitk::DataNode::New(); m_3DContourNode->SetProperty("color", mitk::ColorProperty::New(0.0, 0.0, 0.0)); m_3DContourNode->SetProperty("hidden object", mitk::BoolProperty::New(true)); m_3DContourNode->SetProperty("name", mitk::StringProperty::New("Drawn Contours")); m_3DContourNode->SetProperty("material.representation", mitk::VtkRepresentationProperty::New(VTK_WIREFRAME)); m_3DContourNode->SetProperty("material.wireframeLineWidth", mitk::FloatProperty::New(2.0f)); m_3DContourNode->SetProperty("3DContourContainer", mitk::BoolProperty::New(true)); m_3DContourNode->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(false)); m_3DContourNode->SetVisibility( false, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget0"))); m_3DContourNode->SetVisibility( false, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget1"))); m_3DContourNode->SetVisibility( false, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget2"))); m_3DContourNode->SetVisibility( false, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget3"))); QWidget::setContentsMargins(0, 0, 0, 0); if (QWidget::layout() != nullptr) { QWidget::layout()->setContentsMargins(0, 0, 0, 0); } // For running 3D Interpolation in background // create a QFuture and a QFutureWatcher connect(&m_Watcher, SIGNAL(started()), this, SLOT(StartUpdateInterpolationTimer())); connect(&m_Watcher, SIGNAL(finished()), this, SLOT(OnSurfaceInterpolationFinished())); connect(&m_Watcher, SIGNAL(finished()), this, SLOT(StopUpdateInterpolationTimer())); m_Timer = new QTimer(this); connect(m_Timer, SIGNAL(timeout()), this, SLOT(ChangeSurfaceColor())); } void QmitkSlicesInterpolator::SetDataStorage(mitk::DataStorage::Pointer storage) { if (m_DataStorage == storage) { return; } if (m_DataStorage.IsNotNull()) { m_DataStorage->RemoveNodeEvent.RemoveListener( mitk::MessageDelegate1(this, &QmitkSlicesInterpolator::NodeRemoved) ); } m_DataStorage = storage; m_SurfaceInterpolator->SetDataStorage(storage); if (m_DataStorage.IsNotNull()) { m_DataStorage->RemoveNodeEvent.AddListener( mitk::MessageDelegate1(this, &QmitkSlicesInterpolator::NodeRemoved) ); } } mitk::DataStorage *QmitkSlicesInterpolator::GetDataStorage() { if (m_DataStorage.IsNotNull()) { return m_DataStorage; } else { return nullptr; } } void QmitkSlicesInterpolator::Initialize(mitk::ToolManager *toolManager, const QList &controllers) { Q_ASSERT(!controllers.empty()); if (m_Initialized) { // remove old observers Uninitialize(); } m_ToolManager = toolManager; if (m_ToolManager) { // set enabled only if a segmentation is selected mitk::DataNode *node = m_ToolManager->GetWorkingData(0); QWidget::setEnabled(node != nullptr); // react whenever the set of selected segmentation changes m_ToolManager->WorkingDataChanged += mitk::MessageDelegate(this, &QmitkSlicesInterpolator::OnToolManagerWorkingDataModified); m_ToolManager->ReferenceDataChanged += mitk::MessageDelegate( this, &QmitkSlicesInterpolator::OnToolManagerReferenceDataModified); // connect to the slice navigation controller. after each change, call the interpolator foreach (mitk::SliceNavigationController *slicer, controllers) { // Has to be initialized m_LastSNC = slicer; m_TimePoints.insert(slicer, slicer->GetSelectedTimePoint()); itk::MemberCommand::Pointer deleteCommand = itk::MemberCommand::New(); deleteCommand->SetCallbackFunction(this, &QmitkSlicesInterpolator::OnSliceNavigationControllerDeleted); m_ControllerToDeleteObserverTag.insert(slicer, slicer->AddObserver(itk::DeleteEvent(), deleteCommand)); itk::MemberCommand::Pointer timeChangedCommand = itk::MemberCommand::New(); timeChangedCommand->SetCallbackFunction(this, &QmitkSlicesInterpolator::OnTimeChanged); m_ControllerToTimeObserverTag.insert( slicer, slicer->AddObserver(mitk::SliceNavigationController::TimeGeometryEvent(nullptr, 0), timeChangedCommand)); itk::MemberCommand::Pointer sliceChangedCommand = itk::MemberCommand::New(); sliceChangedCommand->SetCallbackFunction(this, &QmitkSlicesInterpolator::OnSliceChanged); m_ControllerToSliceObserverTag.insert( slicer, slicer->AddObserver(mitk::SliceNavigationController::GeometrySliceEvent(nullptr, 0), sliceChangedCommand)); } ACTION_TO_SLICEDIMENSION = createActionToSliceDimension(); } m_Initialized = true; } void QmitkSlicesInterpolator::Uninitialize() { if (m_ToolManager.IsNotNull()) { m_ToolManager->WorkingDataChanged -= mitk::MessageDelegate(this, &QmitkSlicesInterpolator::OnToolManagerWorkingDataModified); m_ToolManager->ReferenceDataChanged -= mitk::MessageDelegate( this, &QmitkSlicesInterpolator::OnToolManagerReferenceDataModified); } foreach (mitk::SliceNavigationController *slicer, m_ControllerToSliceObserverTag.keys()) { slicer->RemoveObserver(m_ControllerToDeleteObserverTag.take(slicer)); slicer->RemoveObserver(m_ControllerToTimeObserverTag.take(slicer)); slicer->RemoveObserver(m_ControllerToSliceObserverTag.take(slicer)); } ACTION_TO_SLICEDIMENSION.clear(); m_ToolManager = nullptr; m_Initialized = false; } QmitkSlicesInterpolator::~QmitkSlicesInterpolator() { if (m_Initialized) { // remove old observers Uninitialize(); } WaitForFutures(); if (m_DataStorage.IsNotNull()) { m_DataStorage->RemoveNodeEvent.RemoveListener( mitk::MessageDelegate1(this, &QmitkSlicesInterpolator::NodeRemoved) ); if (m_DataStorage->Exists(m_3DContourNode)) m_DataStorage->Remove(m_3DContourNode); if (m_DataStorage->Exists(m_InterpolatedSurfaceNode)) m_DataStorage->Remove(m_InterpolatedSurfaceNode); } // remove observer m_Interpolator->RemoveObserver(InterpolationInfoChangedObserverTag); m_SurfaceInterpolator->RemoveObserver(SurfaceInterpolationInfoChangedObserverTag); delete m_Timer; } /** External enableization... */ void QmitkSlicesInterpolator::setEnabled(bool enable) { QWidget::setEnabled(enable); // Set the gui elements of the different interpolation modi enabled if (enable) { if (m_2DInterpolationEnabled) { this->Show2DInterpolationControls(true); m_Interpolator->Activate2DInterpolation(true); } else if (m_3DInterpolationEnabled) { this->Show3DInterpolationControls(true); this->Show3DInterpolationResult(true); } } // Set all gui elements of the interpolation disabled else { this->HideAllInterpolationControls(); this->Show3DInterpolationResult(false); } } void QmitkSlicesInterpolator::On2DInterpolationEnabled(bool status) { OnInterpolationActivated(status); m_Interpolator->Activate2DInterpolation(status); } void QmitkSlicesInterpolator::On3DInterpolationEnabled(bool status) { On3DInterpolationActivated(status); } void QmitkSlicesInterpolator::OnInterpolationDisabled(bool status) { if (status) { OnInterpolationActivated(!status); On3DInterpolationActivated(!status); this->Show3DInterpolationResult(false); } } void QmitkSlicesInterpolator::HideAllInterpolationControls() { this->Show2DInterpolationControls(false); this->Show3DInterpolationControls(false); } void QmitkSlicesInterpolator::Show2DInterpolationControls(bool show) { m_BtnApply2D->setVisible(show); m_BtnApplyForAllSlices2D->setVisible(show); } void QmitkSlicesInterpolator::Show3DInterpolationControls(bool show) { m_BtnApply3D->setVisible(show); - m_BtnSuggestPlane->setVisible(show); + + // T28261 + // m_BtnSuggestPlane->setVisible(show); + m_ChkShowPositionNodes->setVisible(show); m_BtnReinit3DInterpolation->setVisible(show); } void QmitkSlicesInterpolator::OnInterpolationMethodChanged(int index) { switch (index) { case 0: // Disabled m_GroupBoxEnableExclusiveInterpolationMode->setTitle("Interpolation"); this->HideAllInterpolationControls(); this->OnInterpolationActivated(false); this->On3DInterpolationActivated(false); this->Show3DInterpolationResult(false); m_Interpolator->Activate2DInterpolation(false); break; case 1: // 2D m_GroupBoxEnableExclusiveInterpolationMode->setTitle("Interpolation (Enabled)"); this->HideAllInterpolationControls(); this->Show2DInterpolationControls(true); this->OnInterpolationActivated(true); this->On3DInterpolationActivated(false); m_Interpolator->Activate2DInterpolation(true); break; case 2: // 3D m_GroupBoxEnableExclusiveInterpolationMode->setTitle("Interpolation (Enabled)"); this->HideAllInterpolationControls(); this->Show3DInterpolationControls(true); this->OnInterpolationActivated(false); this->On3DInterpolationActivated(true); m_Interpolator->Activate2DInterpolation(false); break; default: MITK_ERROR << "Unknown interpolation method!"; m_CmbInterpolation->setCurrentIndex(0); break; } } void QmitkSlicesInterpolator::OnShowMarkers(bool state) { mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = m_DataStorage->GetSubset(mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true))); for (mitk::DataStorage::SetOfObjects::ConstIterator it = allContourMarkers->Begin(); it != allContourMarkers->End(); ++it) { it->Value()->SetProperty("helper object", mitk::BoolProperty::New(!state)); } } void QmitkSlicesInterpolator::OnToolManagerWorkingDataModified() { if (m_ToolManager->GetWorkingData(0) != nullptr) { m_Segmentation = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); m_BtnReinit3DInterpolation->setEnabled(true); } else { // If no workingdata is set, remove the interpolation feedback this->GetDataStorage()->Remove(m_FeedbackNode); m_FeedbackNode->SetData(nullptr); this->GetDataStorage()->Remove(m_3DContourNode); m_3DContourNode->SetData(nullptr); this->GetDataStorage()->Remove(m_InterpolatedSurfaceNode); m_InterpolatedSurfaceNode->SetData(nullptr); m_BtnReinit3DInterpolation->setEnabled(false); return; } // Updating the current selected segmentation for the 3D interpolation SetCurrentContourListID(); if (m_2DInterpolationEnabled) { OnInterpolationActivated(true); // re-initialize if needed } this->CheckSupportedImageDimension(); } void QmitkSlicesInterpolator::OnToolManagerReferenceDataModified() { } void QmitkSlicesInterpolator::OnTimeChanged(itk::Object *sender, const itk::EventObject &e) { // Check if we really have a GeometryTimeEvent if (!dynamic_cast(&e)) return; mitk::SliceNavigationController *slicer = dynamic_cast(sender); Q_ASSERT(slicer); const auto timePoint = slicer->GetSelectedTimePoint(); m_TimePoints[slicer] = timePoint; m_SurfaceInterpolator->SetCurrentTimePoint(timePoint); if (m_LastSNC == slicer) { slicer->SendSlice(); // will trigger a new interpolation } } void QmitkSlicesInterpolator::OnSliceChanged(itk::Object *sender, const itk::EventObject &e) { // Check whether we really have a GeometrySliceEvent if (!dynamic_cast(&e)) return; mitk::SliceNavigationController *slicer = dynamic_cast(sender); if (TranslateAndInterpolateChangedSlice(e, slicer)) { slicer->GetRenderer()->RequestUpdate(); } } bool QmitkSlicesInterpolator::TranslateAndInterpolateChangedSlice(const itk::EventObject &e, mitk::SliceNavigationController *slicer) { if (!m_2DInterpolationEnabled) return false; try { const mitk::SliceNavigationController::GeometrySliceEvent &event = dynamic_cast(e); mitk::TimeGeometry *tsg = event.GetTimeGeometry(); if (tsg && m_TimePoints.contains(slicer) && tsg->IsValidTimePoint(m_TimePoints[slicer])) { mitk::SlicedGeometry3D *slicedGeometry = dynamic_cast(tsg->GetGeometryForTimePoint(m_TimePoints[slicer]).GetPointer()); if (slicedGeometry) { m_LastSNC = slicer; mitk::PlaneGeometry *plane = dynamic_cast(slicedGeometry->GetPlaneGeometry(event.GetPos())); if (plane) Interpolate(plane, m_TimePoints[slicer], slicer); return true; } } } catch (const std::bad_cast &) { return false; // so what } return false; } void QmitkSlicesInterpolator::Interpolate(mitk::PlaneGeometry *plane, mitk::TimePointType timePoint, mitk::SliceNavigationController *slicer) { if (m_ToolManager) { mitk::DataNode *node = m_ToolManager->GetWorkingData(0); if (node) { m_Segmentation = dynamic_cast(node->GetData()); if (m_Segmentation) { if (!m_Segmentation->GetTimeGeometry()->IsValidTimePoint(timePoint)) { MITK_WARN << "Cannot interpolate segmentation. Passed time point is not within the time bounds of WorkingImage. Time point: " << timePoint; return; } const auto timeStep = m_Segmentation->GetTimeGeometry()->TimePointToTimeStep(timePoint); int clickedSliceDimension(-1); int clickedSliceIndex(-1); // calculate real slice position, i.e. slice of the image and not slice of the TimeSlicedGeometry mitk::SegTool2D::DetermineAffectedImageSlice(m_Segmentation, plane, clickedSliceDimension, clickedSliceIndex); mitk::Image::Pointer interpolation = m_Interpolator->Interpolate(clickedSliceDimension, clickedSliceIndex, plane, timeStep); m_FeedbackNode->SetData(interpolation); m_LastSNC = slicer; m_LastSliceIndex = clickedSliceIndex; } } } } void QmitkSlicesInterpolator::OnSurfaceInterpolationFinished() { mitk::Surface::Pointer interpolatedSurface = m_SurfaceInterpolator->GetInterpolationResult(); mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); if (interpolatedSurface.IsNotNull() && workingNode && workingNode->IsVisible( mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget2")))) { m_BtnApply3D->setEnabled(true); - m_BtnSuggestPlane->setEnabled(true); + + // T28261 + // m_BtnSuggestPlane->setEnabled(true); + m_InterpolatedSurfaceNode->SetData(interpolatedSurface); m_3DContourNode->SetData(m_SurfaceInterpolator->GetContoursAsSurface()); this->Show3DInterpolationResult(true); if (!m_DataStorage->Exists(m_InterpolatedSurfaceNode)) { m_DataStorage->Add(m_InterpolatedSurfaceNode); } if (!m_DataStorage->Exists(m_3DContourNode)) { m_DataStorage->Add(m_3DContourNode, workingNode); } } else if (interpolatedSurface.IsNull()) { m_BtnApply3D->setEnabled(false); - m_BtnSuggestPlane->setEnabled(false); + + // T28261 + // m_BtnSuggestPlane->setEnabled(false); if (m_DataStorage->Exists(m_InterpolatedSurfaceNode)) { this->Show3DInterpolationResult(false); } } m_BtnReinit3DInterpolation->setEnabled(true); foreach (mitk::SliceNavigationController *slicer, m_ControllerToTimeObserverTag.keys()) { slicer->GetRenderer()->RequestUpdate(); } } void QmitkSlicesInterpolator::OnAcceptInterpolationClicked() { if (m_Segmentation && m_FeedbackNode->GetData()) { // Make sure that for reslicing and overwriting the same alogrithm is used. We can specify the mode of the vtk // reslicer vtkSmartPointer reslice = vtkSmartPointer::New(); // Set slice as input mitk::Image::Pointer slice = dynamic_cast(m_FeedbackNode->GetData()); reslice->SetInputSlice(slice->GetSliceData()->GetVtkImageAccessor(slice)->GetVtkImageData()); // set overwrite mode to true to write back to the image volume reslice->SetOverwriteMode(true); reslice->Modified(); const auto timePoint = m_LastSNC->GetSelectedTimePoint(); if (!m_Segmentation->GetTimeGeometry()->IsValidTimePoint(timePoint)) { MITK_WARN << "Cannot accept interpolation. Time point selected by SliceNavigationController is not within the time bounds of segmentation. Time point: " << timePoint; return; } mitk::ExtractSliceFilter::Pointer extractor = mitk::ExtractSliceFilter::New(reslice); extractor->SetInput(m_Segmentation); const auto timeStep = m_Segmentation->GetTimeGeometry()->TimePointToTimeStep(timePoint); extractor->SetTimeStep(timeStep); extractor->SetWorldGeometry(m_LastSNC->GetCurrentPlaneGeometry()); extractor->SetVtkOutputRequest(true); extractor->SetResliceTransformByGeometry(m_Segmentation->GetTimeGeometry()->GetGeometryForTimeStep(timeStep)); extractor->Modified(); extractor->Update(); // the image was modified within the pipeline, but not marked so m_Segmentation->Modified(); m_Segmentation->GetVtkImageData()->Modified(); m_FeedbackNode->SetData(nullptr); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkSlicesInterpolator::AcceptAllInterpolations(mitk::SliceNavigationController *slicer) { /* * What exactly is done here: * 1. We create an empty diff image for the current segmentation * 2. All interpolated slices are written into the diff image * 3. Then the diffimage is applied to the original segmentation */ if (m_Segmentation) { mitk::Image::Pointer image3D = m_Segmentation; unsigned int timeStep(0); const auto timePoint = slicer->GetSelectedTimePoint(); if (m_Segmentation->GetDimension() == 4) { if (!m_Segmentation->GetTimeGeometry()->IsValidTimePoint(timePoint)) { MITK_WARN << "Cannot accept all interpolations. Time point selected by passed SliceNavigationController is not within the time bounds of segmentation. Time point: " << timePoint; return; } timeStep = m_Segmentation->GetTimeGeometry()->TimePointToTimeStep(timePoint); mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(m_Segmentation); timeSelector->SetTimeNr(timeStep); timeSelector->Update(); image3D = timeSelector->GetOutput(); } // create a empty diff image for the undo operation mitk::Image::Pointer diffImage = mitk::Image::New(); diffImage->Initialize(image3D); // Create scope for ImageWriteAccessor so that the accessor is destroyed // after the image is initialized. Otherwise later image access will lead to an error { mitk::ImageWriteAccessor imAccess(diffImage); // Set all pixels to zero mitk::PixelType pixelType(mitk::MakeScalarPixelType()); // For legacy purpose support former pixel type of segmentations (before multilabel) if (m_Segmentation->GetImageDescriptor()->GetChannelDescriptor().GetPixelType().GetComponentType() == itk::ImageIOBase::UCHAR) { pixelType = mitk::MakeScalarPixelType(); } memset(imAccess.GetData(), 0, (pixelType.GetBpe() >> 3) * diffImage->GetDimension(0) * diffImage->GetDimension(1) * diffImage->GetDimension(2)); } // Since we need to shift the plane it must be clone so that the original plane isn't altered mitk::PlaneGeometry::Pointer reslicePlane = slicer->GetCurrentPlaneGeometry()->Clone(); int sliceDimension(-1); int sliceIndex(-1); mitk::SegTool2D::DetermineAffectedImageSlice(m_Segmentation, reslicePlane, sliceDimension, sliceIndex); unsigned int zslices = m_Segmentation->GetDimension(sliceDimension); mitk::ProgressBar::GetInstance()->AddStepsToDo(zslices); mitk::Point3D origin = reslicePlane->GetOrigin(); unsigned int totalChangedSlices(0); for (unsigned int sliceIndex = 0; sliceIndex < zslices; ++sliceIndex) { // Transforming the current origin of the reslice plane // so that it matches the one of the next slice m_Segmentation->GetSlicedGeometry()->WorldToIndex(origin, origin); origin[sliceDimension] = sliceIndex; m_Segmentation->GetSlicedGeometry()->IndexToWorld(origin, origin); reslicePlane->SetOrigin(origin); // Set the slice as 'input' mitk::Image::Pointer interpolation = m_Interpolator->Interpolate(sliceDimension, sliceIndex, reslicePlane, timeStep); if (interpolation.IsNotNull()) // we don't check if interpolation is necessary/sensible - but m_Interpolator does { // Setting up the reslicing pipeline which allows us to write the interpolation results back into // the image volume vtkSmartPointer reslice = vtkSmartPointer::New(); // set overwrite mode to true to write back to the image volume reslice->SetInputSlice(interpolation->GetSliceData()->GetVtkImageAccessor(interpolation)->GetVtkImageData()); reslice->SetOverwriteMode(true); reslice->Modified(); mitk::ExtractSliceFilter::Pointer diffslicewriter = mitk::ExtractSliceFilter::New(reslice); diffslicewriter->SetInput(diffImage); diffslicewriter->SetTimeStep(0); diffslicewriter->SetWorldGeometry(reslicePlane); diffslicewriter->SetVtkOutputRequest(true); diffslicewriter->SetResliceTransformByGeometry(diffImage->GetTimeGeometry()->GetGeometryForTimeStep(0)); diffslicewriter->Modified(); diffslicewriter->Update(); ++totalChangedSlices; } mitk::ProgressBar::GetInstance()->Progress(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (totalChangedSlices > 0) { // store undo stack items if (true) { // create do/undo operations mitk::ApplyDiffImageOperation *doOp = new mitk::ApplyDiffImageOperation(mitk::OpTEST, m_Segmentation, diffImage, timeStep); mitk::ApplyDiffImageOperation *undoOp = new mitk::ApplyDiffImageOperation(mitk::OpTEST, m_Segmentation, diffImage, timeStep); undoOp->SetFactor(-1.0); std::stringstream comment; comment << "Confirm all interpolations (" << totalChangedSlices << ")"; mitk::OperationEvent *undoStackItem = new mitk::OperationEvent(mitk::DiffImageApplier::GetInstanceForUndo(), doOp, undoOp, comment.str()); mitk::OperationEvent::IncCurrGroupEventId(); mitk::OperationEvent::IncCurrObjectEventId(); mitk::UndoController::GetCurrentUndoModel()->SetOperationEvent(undoStackItem); // acutally apply the changes here to the original image mitk::DiffImageApplier::GetInstanceForUndo()->ExecuteOperation(doOp); } } m_FeedbackNode->SetData(nullptr); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkSlicesInterpolator::FinishInterpolation(mitk::SliceNavigationController *slicer) { // this redirect is for calling from outside if (slicer == nullptr) OnAcceptAllInterpolationsClicked(); else AcceptAllInterpolations(slicer); } void QmitkSlicesInterpolator::OnAcceptAllInterpolationsClicked() { QMenu orientationPopup(this); std::map::const_iterator it; for (it = ACTION_TO_SLICEDIMENSION.begin(); it != ACTION_TO_SLICEDIMENSION.end(); it++) orientationPopup.addAction(it->first); connect(&orientationPopup, SIGNAL(triggered(QAction *)), this, SLOT(OnAcceptAllPopupActivated(QAction *))); orientationPopup.exec(QCursor::pos()); } void QmitkSlicesInterpolator::OnAccept3DInterpolationClicked() { - if (m_InterpolatedSurfaceNode.IsNotNull() && m_InterpolatedSurfaceNode->GetData()) + auto referenceImage = GetData(m_ToolManager->GetReferenceData(0)); + + auto* segmentationDataNode = m_ToolManager->GetWorkingData(0); + auto segmentation = GetData(segmentationDataNode); + + if (referenceImage.IsNull() || segmentation.IsNull()) + return; + + const auto* segmentationGeometry = segmentation->GetTimeGeometry(); + const auto timePoint = m_LastSNC->GetSelectedTimePoint(); + + if (!referenceImage->GetTimeGeometry()->IsValidTimePoint(timePoint) || + !segmentationGeometry->IsValidTimePoint(timePoint)) { - mitk::DataNode *segmentationNode = m_ToolManager->GetWorkingData(0); - mitk::Image *currSeg = dynamic_cast(segmentationNode->GetData()); + MITK_WARN << "Cannot accept interpolation. Current time point is not within the time bounds of the patient image and segmentation."; + return; + } - mitk::SurfaceToImageFilter::Pointer s2iFilter = mitk::SurfaceToImageFilter::New(); - s2iFilter->MakeOutputBinaryOn(); - if (currSeg->GetPixelType().GetComponentType() == itk::ImageIOBase::USHORT) - s2iFilter->SetUShortBinaryPixelType(true); - s2iFilter->SetInput(dynamic_cast(m_InterpolatedSurfaceNode->GetData())); + auto interpolatedSurface = GetData(m_InterpolatedSurfaceNode); - // check if ToolManager holds valid ReferenceData - if (m_ToolManager->GetReferenceData(0) == nullptr || m_ToolManager->GetWorkingData(0) == nullptr) - { - return; - } - s2iFilter->SetImage(dynamic_cast(m_ToolManager->GetReferenceData(0)->GetData())); - s2iFilter->Update(); + if (interpolatedSurface.IsNull()) + return; - mitk::Image::Pointer newSeg = s2iFilter->GetOutput(); + auto surfaceToImageFilter = mitk::SurfaceToImageFilter::New(); - const auto timePoint = m_LastSNC->GetSelectedTimePoint(); - if (!m_ToolManager->GetReferenceData(0)->GetData()->GetTimeGeometry()->IsValidTimePoint(timePoint) || - !m_ToolManager->GetWorkingData(0)->GetData()->GetTimeGeometry()->IsValidTimePoint(timePoint)) - { - MITK_WARN << "Cannot accept interpolation. Time point selected by SliceNavigationController is not within the time bounds of reference or working image. Time point: " << timePoint; - return; - } + surfaceToImageFilter->SetImage(referenceImage); + surfaceToImageFilter->SetMakeOutputBinary(true); + surfaceToImageFilter->SetUShortBinaryPixelType(itk::ImageIOBase::USHORT == segmentation->GetPixelType().GetComponentType()); + surfaceToImageFilter->SetInput(interpolatedSurface); + surfaceToImageFilter->Update(); - const auto newTimeStep = newSeg->GetTimeGeometry()->TimePointToTimeStep(timePoint); - mitk::ImageReadAccessor readAccess(newSeg, newSeg->GetVolumeData(newTimeStep)); - const void *cPointer = readAccess.GetData(); + mitk::Image::Pointer interpolatedSegmentation = surfaceToImageFilter->GetOutput(); - if (currSeg && cPointer) - { - const auto curTimeStep = currSeg->GetTimeGeometry()->TimePointToTimeStep(timePoint); - currSeg->SetVolume(cPointer, curTimeStep, 0); - } - else - { - return; - } + auto timeStep = interpolatedSegmentation->GetTimeGeometry()->TimePointToTimeStep(timePoint); + mitk::ImageReadAccessor readAccessor(interpolatedSegmentation, interpolatedSegmentation->GetVolumeData(timeStep)); + const auto* dataPointer = readAccessor.GetData(); - m_CmbInterpolation->setCurrentIndex(0); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - mitk::DataNode::Pointer segSurface = mitk::DataNode::New(); - float rgb[3]; - segmentationNode->GetColor(rgb); - segSurface->SetColor(rgb); - segSurface->SetData(m_InterpolatedSurfaceNode->GetData()); - std::stringstream stream; - stream << segmentationNode->GetName(); - stream << "_"; - stream << "3D-interpolation"; - segSurface->SetName(stream.str()); - segSurface->SetProperty("opacity", mitk::FloatProperty::New(0.7)); - segSurface->SetProperty("includeInBoundingBox", mitk::BoolProperty::New(true)); - segSurface->SetProperty("3DInterpolationResult", mitk::BoolProperty::New(true)); - segSurface->SetVisibility(false); - m_DataStorage->Add(segSurface, segmentationNode); - this->Show3DInterpolationResult(false); + if (nullptr == dataPointer) + return; + + timeStep = segmentationGeometry->TimePointToTimeStep(timePoint); + segmentation->SetVolume(dataPointer, timeStep, 0); + + m_CmbInterpolation->setCurrentIndex(0); + this->Show3DInterpolationResult(false); + + std::string name = segmentationDataNode->GetName() + "_3D-interpolation"; + mitk::TimeBounds timeBounds; + + if (1 < interpolatedSurface->GetTimeSteps()) + { + name += "_t" + std::to_string(timeStep); + + auto* polyData = vtkPolyData::New(); + polyData->DeepCopy(interpolatedSurface->GetVtkPolyData(timeStep)); + + auto surface = mitk::Surface::New(); + surface->SetVtkPolyData(polyData); + + interpolatedSurface = surface; + timeBounds = segmentationGeometry->GetTimeBounds(timeStep); } + else + { + timeBounds = segmentationGeometry->GetTimeBounds(0); + } + + auto* surfaceGeometry = static_cast(interpolatedSurface->GetTimeGeometry()); + surfaceGeometry->SetFirstTimePoint(timeBounds[0]); + surfaceGeometry->SetStepDuration(timeBounds[1] - timeBounds[0]); + + // Typical file formats for surfaces do not save any time-related information. As a workaround at least for MITK scene files, we have the + // possibility to seralize this information as properties. + + interpolatedSurface->SetProperty("ProportionalTimeGeometry.FirstTimePoint", mitk::FloatProperty::New(surfaceGeometry->GetFirstTimePoint())); + interpolatedSurface->SetProperty("ProportionalTimeGeometry.StepDuration", mitk::FloatProperty::New(surfaceGeometry->GetStepDuration())); + + auto interpolatedSurfaceDataNode = mitk::DataNode::New(); + + interpolatedSurfaceDataNode->SetData(interpolatedSurface); + interpolatedSurfaceDataNode->SetName(name); + interpolatedSurfaceDataNode->SetOpacity(0.7f); + + std::array rgb; + segmentationDataNode->GetColor(rgb.data()); + interpolatedSurfaceDataNode->SetColor(rgb.data()); + + m_DataStorage->Add(interpolatedSurfaceDataNode, segmentationDataNode); } void ::QmitkSlicesInterpolator::OnSuggestPlaneClicked() { if (m_PlaneWatcher.isRunning()) m_PlaneWatcher.waitForFinished(); m_PlaneFuture = QtConcurrent::run(this, &QmitkSlicesInterpolator::RunPlaneSuggestion); m_PlaneWatcher.setFuture(m_PlaneFuture); } void ::QmitkSlicesInterpolator::RunPlaneSuggestion() { if (m_FirstRun) mitk::ProgressBar::GetInstance()->AddStepsToDo(7); else mitk::ProgressBar::GetInstance()->AddStepsToDo(3); m_EdgeDetector->SetSegmentationMask(m_Segmentation); m_EdgeDetector->SetInput(dynamic_cast(m_ToolManager->GetReferenceData(0)->GetData())); m_EdgeDetector->Update(); mitk::UnstructuredGrid::Pointer uGrid = mitk::UnstructuredGrid::New(); uGrid->SetVtkUnstructuredGrid(m_EdgeDetector->GetOutput()->GetVtkUnstructuredGrid()); mitk::ProgressBar::GetInstance()->Progress(); mitk::Surface::Pointer surface = dynamic_cast(m_InterpolatedSurfaceNode->GetData()); vtkSmartPointer vtkpoly = surface->GetVtkPolyData(); vtkSmartPointer vtkpoints = vtkpoly->GetPoints(); vtkSmartPointer vGrid = vtkSmartPointer::New(); vtkSmartPointer verts = vtkSmartPointer::New(); verts->GetPointIds()->SetNumberOfIds(vtkpoints->GetNumberOfPoints()); for (int i = 0; i < vtkpoints->GetNumberOfPoints(); i++) { verts->GetPointIds()->SetId(i, i); } vGrid->Allocate(1); vGrid->InsertNextCell(verts->GetCellType(), verts->GetPointIds()); vGrid->SetPoints(vtkpoints); mitk::UnstructuredGrid::Pointer interpolationGrid = mitk::UnstructuredGrid::New(); interpolationGrid->SetVtkUnstructuredGrid(vGrid); m_PointScorer->SetInput(0, uGrid); m_PointScorer->SetInput(1, interpolationGrid); m_PointScorer->Update(); mitk::UnstructuredGrid::Pointer scoredGrid = mitk::UnstructuredGrid::New(); scoredGrid = m_PointScorer->GetOutput(); mitk::ProgressBar::GetInstance()->Progress(); double spacing = mitk::SurfaceInterpolationController::GetInstance()->GetDistanceImageSpacing(); mitk::UnstructuredGridClusteringFilter::Pointer clusterFilter = mitk::UnstructuredGridClusteringFilter::New(); clusterFilter->SetInput(scoredGrid); clusterFilter->SetMeshing(false); clusterFilter->SetMinPts(4); clusterFilter->Seteps(spacing); clusterFilter->Update(); mitk::ProgressBar::GetInstance()->Progress(); // Create plane suggestion mitk::BaseRenderer::Pointer br = mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget0")); mitk::PlaneProposer planeProposer; std::vector grids = clusterFilter->GetAllClusters(); planeProposer.SetUnstructuredGrids(grids); mitk::SliceNavigationController::Pointer snc = br->GetSliceNavigationController(); planeProposer.SetSliceNavigationController(snc); planeProposer.SetUseDistances(true); try { planeProposer.CreatePlaneInfo(); } catch (const mitk::Exception &e) { MITK_ERROR << e.what(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); m_FirstRun = false; } void QmitkSlicesInterpolator::OnReinit3DInterpolation() { mitk::NodePredicateProperty::Pointer pred = mitk::NodePredicateProperty::New("3DContourContainer", mitk::BoolProperty::New(true)); mitk::DataStorage::SetOfObjects::ConstPointer contourNodes = m_DataStorage->GetDerivations(m_ToolManager->GetWorkingData(0), pred); if (contourNodes->Size() != 0) { m_BtnApply3D->setEnabled(true); m_3DContourNode = contourNodes->at(0); mitk::Surface::Pointer contours = dynamic_cast(m_3DContourNode->GetData()); if (contours) mitk::SurfaceInterpolationController::GetInstance()->ReinitializeInterpolation(contours); m_BtnReinit3DInterpolation->setEnabled(false); } else { m_BtnApply3D->setEnabled(false); QMessageBox errorInfo; errorInfo.setWindowTitle("Reinitialize surface interpolation"); errorInfo.setIcon(QMessageBox::Information); errorInfo.setText("No contours available for the selected segmentation!"); errorInfo.exec(); } } void QmitkSlicesInterpolator::OnAcceptAllPopupActivated(QAction *action) { try { std::map::const_iterator iter = ACTION_TO_SLICEDIMENSION.find(action); if (iter != ACTION_TO_SLICEDIMENSION.end()) { mitk::SliceNavigationController *slicer = iter->second; AcceptAllInterpolations(slicer); } } catch (...) { /* Showing message box with possible memory error */ QMessageBox errorInfo; errorInfo.setWindowTitle("Interpolation Process"); errorInfo.setIcon(QMessageBox::Critical); errorInfo.setText("An error occurred during interpolation. Possible cause: Not enough memory!"); errorInfo.exec(); // additional error message on std::cerr std::cerr << "Ill construction in " __FILE__ " l. " << __LINE__ << std::endl; } } void QmitkSlicesInterpolator::OnInterpolationActivated(bool on) { m_2DInterpolationEnabled = on; try { if (m_DataStorage.IsNotNull()) { if (on && !m_DataStorage->Exists(m_FeedbackNode)) { m_DataStorage->Add(m_FeedbackNode); } } } catch (...) { // don't care (double add/remove) } if (m_ToolManager) { mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); mitk::DataNode *referenceNode = m_ToolManager->GetReferenceData(0); QWidget::setEnabled(workingNode != nullptr); m_BtnApply2D->setEnabled(on); m_FeedbackNode->SetVisibility(on); if (!on) { mitk::RenderingManager::GetInstance()->RequestUpdateAll(); return; } if (workingNode) { mitk::Image *segmentation = dynamic_cast(workingNode->GetData()); if (segmentation) { m_Interpolator->SetSegmentationVolume(segmentation); if (referenceNode) { mitk::Image *referenceImage = dynamic_cast(referenceNode->GetData()); m_Interpolator->SetReferenceVolume(referenceImage); // may be nullptr } } } } UpdateVisibleSuggestion(); } void QmitkSlicesInterpolator::Run3DInterpolation() { m_SurfaceInterpolator->Interpolate(); } void QmitkSlicesInterpolator::StartUpdateInterpolationTimer() { m_Timer->start(500); } void QmitkSlicesInterpolator::StopUpdateInterpolationTimer() { m_Timer->stop(); m_InterpolatedSurfaceNode->SetProperty("color", mitk::ColorProperty::New(SURFACE_COLOR_RGB)); mitk::RenderingManager::GetInstance()->RequestUpdate( mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget3"))->GetRenderWindow()); } void QmitkSlicesInterpolator::ChangeSurfaceColor() { float currentColor[3]; m_InterpolatedSurfaceNode->GetColor(currentColor); if (currentColor[2] == SURFACE_COLOR_RGB[2]) { m_InterpolatedSurfaceNode->SetProperty("color", mitk::ColorProperty::New(1.0f, 1.0f, 1.0f)); } else { m_InterpolatedSurfaceNode->SetProperty("color", mitk::ColorProperty::New(SURFACE_COLOR_RGB)); } m_InterpolatedSurfaceNode->Update(); mitk::RenderingManager::GetInstance()->RequestUpdate( mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget3"))->GetRenderWindow()); } void QmitkSlicesInterpolator::On3DInterpolationActivated(bool on) { m_3DInterpolationEnabled = on; this->CheckSupportedImageDimension(); try { if (m_DataStorage.IsNotNull() && m_ToolManager && m_3DInterpolationEnabled) { mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); if (workingNode) { - bool isInterpolationResult(false); - workingNode->GetBoolProperty("3DInterpolationResult", isInterpolationResult); - mitk::NodePredicateAnd::Pointer pred = mitk::NodePredicateAnd::New( - mitk::NodePredicateProperty::New("3DInterpolationResult", mitk::BoolProperty::New(true)), - mitk::NodePredicateDataType::New("Surface")); - mitk::DataStorage::SetOfObjects::ConstPointer interpolationResults = - m_DataStorage->GetDerivations(workingNode, pred); - - for (unsigned int i = 0; i < interpolationResults->Size(); ++i) - { - mitk::DataNode::Pointer currNode = interpolationResults->at(i); - if (currNode.IsNotNull()) - m_DataStorage->Remove(currNode); - } - - if ((workingNode->IsVisible( - mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget2")))) && - !isInterpolationResult && m_3DInterpolationEnabled) + if ((workingNode->IsVisible(mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget2"))))) { int ret = QMessageBox::Yes; if (m_SurfaceInterpolator->EstimatePortionOfNeededMemory() > 0.5) { QMessageBox msgBox; msgBox.setText("Due to short handed system memory the 3D interpolation may be very slow!"); msgBox.setInformativeText("Are you sure you want to activate the 3D interpolation?"); msgBox.setStandardButtons(QMessageBox::No | QMessageBox::Yes); ret = msgBox.exec(); } if (m_Watcher.isRunning()) m_Watcher.waitForFinished(); if (ret == QMessageBox::Yes) { m_Future = QtConcurrent::run(this, &QmitkSlicesInterpolator::Run3DInterpolation); m_Watcher.setFuture(m_Future); } else { m_CmbInterpolation->setCurrentIndex(0); } } - else if (!m_3DInterpolationEnabled) - { - this->Show3DInterpolationResult(false); - m_BtnApply3D->setEnabled(m_3DInterpolationEnabled); - m_BtnSuggestPlane->setEnabled(m_3DInterpolationEnabled); - } } else { QWidget::setEnabled(false); m_ChkShowPositionNodes->setEnabled(m_3DInterpolationEnabled); } } if (!m_3DInterpolationEnabled) { this->Show3DInterpolationResult(false); m_BtnApply3D->setEnabled(m_3DInterpolationEnabled); - m_BtnSuggestPlane->setEnabled(m_3DInterpolationEnabled); + + // T28261 + // m_BtnSuggestPlane->setEnabled(m_3DInterpolationEnabled); } } catch (...) { MITK_ERROR << "Error with 3D surface interpolation!"; } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSlicesInterpolator::EnableInterpolation(bool on) { // only to be called from the outside world // just a redirection to OnInterpolationActivated OnInterpolationActivated(on); } void QmitkSlicesInterpolator::Enable3DInterpolation(bool on) { // only to be called from the outside world // just a redirection to OnInterpolationActivated On3DInterpolationActivated(on); } void QmitkSlicesInterpolator::UpdateVisibleSuggestion() { mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSlicesInterpolator::OnInterpolationInfoChanged(const itk::EventObject & /*e*/) { // something (e.g. undo) changed the interpolation info, we should refresh our display UpdateVisibleSuggestion(); } void QmitkSlicesInterpolator::OnSurfaceInterpolationInfoChanged(const itk::EventObject & /*e*/) { if (m_3DInterpolationEnabled) { if (m_Watcher.isRunning()) m_Watcher.waitForFinished(); m_Future = QtConcurrent::run(this, &QmitkSlicesInterpolator::Run3DInterpolation); m_Watcher.setFuture(m_Future); } } void QmitkSlicesInterpolator::SetCurrentContourListID() { // New ContourList = hide current interpolation Show3DInterpolationResult(false); if (m_DataStorage.IsNotNull() && m_ToolManager && m_LastSNC) { mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); if (workingNode) { - bool isInterpolationResult(false); - workingNode->GetBoolProperty("3DInterpolationResult", isInterpolationResult); + QWidget::setEnabled(true); - if (!isInterpolationResult) + const auto timePoint = m_LastSNC->GetSelectedTimePoint(); + // In case the time is not valid use 0 to access the time geometry of the working node + unsigned int time_position = 0; + if (!workingNode->GetData()->GetTimeGeometry()->IsValidTimePoint(timePoint)) { - QWidget::setEnabled(true); + MITK_WARN << "Cannot accept interpolation. Time point selected by SliceNavigationController is not within the time bounds of WorkingImage. Time point: " << timePoint; + return; + } + time_position = workingNode->GetData()->GetTimeGeometry()->TimePointToTimeStep(timePoint); - const auto timePoint = m_LastSNC->GetSelectedTimePoint(); - // In case the time is not valid use 0 to access the time geometry of the working node - unsigned int time_position = 0; - if (!workingNode->GetData()->GetTimeGeometry()->IsValidTimePoint(timePoint)) + mitk::Vector3D spacing = workingNode->GetData()->GetGeometry(time_position)->GetSpacing(); + double minSpacing(100); + double maxSpacing(0); + for (int i = 0; i < 3; i++) + { + if (spacing[i] < minSpacing) { - MITK_WARN << "Cannot accept interpolation. Time point selected by SliceNavigationController is not within the time bounds of WorkingImage. Time point: " << timePoint; - return; + minSpacing = spacing[i]; } - time_position = workingNode->GetData()->GetTimeGeometry()->TimePointToTimeStep(timePoint); - - mitk::Vector3D spacing = workingNode->GetData()->GetGeometry(time_position)->GetSpacing(); - double minSpacing(100); - double maxSpacing(0); - for (int i = 0; i < 3; i++) + if (spacing[i] > maxSpacing) { - if (spacing[i] < minSpacing) - { - minSpacing = spacing[i]; - } - if (spacing[i] > maxSpacing) - { - maxSpacing = spacing[i]; - } + maxSpacing = spacing[i]; } + } - m_SurfaceInterpolator->SetMaxSpacing(maxSpacing); - m_SurfaceInterpolator->SetMinSpacing(minSpacing); - m_SurfaceInterpolator->SetDistanceImageVolume(50000); + m_SurfaceInterpolator->SetMaxSpacing(maxSpacing); + m_SurfaceInterpolator->SetMinSpacing(minSpacing); + m_SurfaceInterpolator->SetDistanceImageVolume(50000); - mitk::Image *segmentationImage = dynamic_cast(workingNode->GetData()); + mitk::Image *segmentationImage = dynamic_cast(workingNode->GetData()); - m_SurfaceInterpolator->SetCurrentInterpolationSession(segmentationImage); - m_SurfaceInterpolator->SetCurrentTimePoint(timePoint); + m_SurfaceInterpolator->SetCurrentInterpolationSession(segmentationImage); + m_SurfaceInterpolator->SetCurrentTimePoint(timePoint); - if (m_3DInterpolationEnabled) - { - if (m_Watcher.isRunning()) - m_Watcher.waitForFinished(); - m_Future = QtConcurrent::run(this, &QmitkSlicesInterpolator::Run3DInterpolation); - m_Watcher.setFuture(m_Future); - } + if (m_3DInterpolationEnabled) + { + if (m_Watcher.isRunning()) + m_Watcher.waitForFinished(); + m_Future = QtConcurrent::run(this, &QmitkSlicesInterpolator::Run3DInterpolation); + m_Watcher.setFuture(m_Future); } } else { QWidget::setEnabled(false); } } } void QmitkSlicesInterpolator::Show3DInterpolationResult(bool status) { if (m_InterpolatedSurfaceNode.IsNotNull()) m_InterpolatedSurfaceNode->SetVisibility(status); if (m_3DContourNode.IsNotNull()) m_3DContourNode->SetVisibility( status, mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget3"))); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSlicesInterpolator::CheckSupportedImageDimension() { if (m_ToolManager->GetWorkingData(0)) m_Segmentation = dynamic_cast(m_ToolManager->GetWorkingData(0)->GetData()); /*if (m_3DInterpolationEnabled && m_Segmentation && m_Segmentation->GetDimension() != 3) { QMessageBox info; info.setWindowTitle("3D Interpolation Process"); info.setIcon(QMessageBox::Information); info.setText("3D Interpolation is only supported for 3D images at the moment!"); info.exec(); m_CmbInterpolation->setCurrentIndex(0); }*/ } void QmitkSlicesInterpolator::OnSliceNavigationControllerDeleted(const itk::Object *sender, const itk::EventObject & /*e*/) { // Don't know how to avoid const_cast here?! mitk::SliceNavigationController *slicer = dynamic_cast(const_cast(sender)); if (slicer) { m_ControllerToTimeObserverTag.remove(slicer); m_ControllerToSliceObserverTag.remove(slicer); m_ControllerToDeleteObserverTag.remove(slicer); } } void QmitkSlicesInterpolator::WaitForFutures() { if (m_Watcher.isRunning()) { m_Watcher.waitForFinished(); } if (m_PlaneWatcher.isRunning()) { m_PlaneWatcher.waitForFinished(); } } void QmitkSlicesInterpolator::NodeRemoved(const mitk::DataNode* node) { if ((m_ToolManager && m_ToolManager->GetWorkingData(0) == node) || node == m_3DContourNode || node == m_FeedbackNode || node == m_InterpolatedSurfaceNode) { WaitForFutures(); } } diff --git a/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.h b/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.h index a6499b7354..e42072bde1 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.h +++ b/Modules/SegmentationUI/Qmitk/QmitkSlicesInterpolator.h @@ -1,291 +1,292 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 QmitkSlicesInterpolator_h_Included #define QmitkSlicesInterpolator_h_Included #include "mitkDataNode.h" #include "mitkDataStorage.h" #include "mitkSegmentationInterpolationController.h" #include "mitkSliceNavigationController.h" #include "mitkSurfaceInterpolationController.h" #include "mitkToolManager.h" #include #include "mitkFeatureBasedEdgeDetectionFilter.h" #include "mitkPointCloudScoringFilter.h" #include #include #include #include #include #include #include #include "mitkVtkRepresentationProperty.h" #include "vtkProperty.h" // For running 3D interpolation in background #include #include #include #include namespace mitk { class PlaneGeometry; class SliceNavigationController; } class QPushButton; /** \brief GUI for slices interpolation. \ingroup ToolManagerEtAl \ingroup Widgets \sa QmitkInteractiveSegmentation \sa mitk::SegmentationInterpolation While mitk::SegmentationInterpolation does the bookkeeping of interpolation (keeping track of which slices contain how much segmentation) and the algorithmic work, QmitkSlicesInterpolator is responsible to watch the GUI, to notice, which slice is currently visible. It triggers generation of interpolation suggestions and also triggers acception of suggestions. \todo show/hide feedback on demand Last contributor: $Author: maleike $ */ class MITKSEGMENTATIONUI_EXPORT QmitkSlicesInterpolator : public QWidget { Q_OBJECT public: QmitkSlicesInterpolator(QWidget *parent = nullptr, const char *name = nullptr); /** To be called once before real use. */ void Initialize(mitk::ToolManager *toolManager, const QList &controllers); void Uninitialize(); ~QmitkSlicesInterpolator() override; void SetDataStorage(mitk::DataStorage::Pointer storage); mitk::DataStorage *GetDataStorage(); /** Just public because it is called by itk::Commands. You should not need to call this. */ void OnToolManagerWorkingDataModified(); /** Just public because it is called by itk::Commands. You should not need to call this. */ void OnToolManagerReferenceDataModified(); void OnTimeChanged(itk::Object *sender, const itk::EventObject &); void OnSliceChanged(itk::Object *sender, const itk::EventObject &); void OnSliceNavigationControllerDeleted(const itk::Object *sender, const itk::EventObject &); /** Just public because it is called by itk::Commands. You should not need to call this. */ void OnInterpolationInfoChanged(const itk::EventObject &); /** Just public because it is called by itk::Commands. You should not need to call this. */ void OnSurfaceInterpolationInfoChanged(const itk::EventObject &); /** * @brief Set the visibility of the 3d interpolation */ void Show3DInterpolationResult(bool); signals: void SignalRememberContourPositions(bool); void SignalShowMarkerNodes(bool); public slots: virtual void setEnabled(bool); /** Call this from the outside to enable/disable interpolation */ void EnableInterpolation(bool); void Enable3DInterpolation(bool); /** Call this from the outside to accept all interpolations */ void FinishInterpolation(mitk::SliceNavigationController *slicer = nullptr); protected slots: /** Reaction to button clicks. */ void OnAcceptInterpolationClicked(); /* Opens popup to ask about which orientation should be interpolated */ void OnAcceptAllInterpolationsClicked(); /* Reaction to button clicks */ void OnAccept3DInterpolationClicked(); void OnReinit3DInterpolation(); void OnSuggestPlaneClicked(); /* * Will trigger interpolation for all slices in given orientation (called from popup menu of * OnAcceptAllInterpolationsClicked) */ void OnAcceptAllPopupActivated(QAction *action); /** Called on activation/deactivation */ void OnInterpolationActivated(bool); void On3DInterpolationActivated(bool); void OnInterpolationMethodChanged(int index); // Enhancement for 3D interpolation void On2DInterpolationEnabled(bool); void On3DInterpolationEnabled(bool); void OnInterpolationDisabled(bool); void OnShowMarkers(bool); void Run3DInterpolation(); void RunPlaneSuggestion(); void OnSurfaceInterpolationFinished(); void StartUpdateInterpolationTimer(); void StopUpdateInterpolationTimer(); void ChangeSurfaceColor(); protected: const std::map createActionToSliceDimension(); std::map ACTION_TO_SLICEDIMENSION; void AcceptAllInterpolations(mitk::SliceNavigationController *slicer); /** Retrieves the currently selected PlaneGeometry from a SlicedGeometry3D that is generated by a SliceNavigationController and calls Interpolate to further process this PlaneGeometry into an interpolation. \param e is a actually a mitk::SliceNavigationController::GeometrySliceEvent, sent by a SliceNavigationController \param slicer the SliceNavigationController */ bool TranslateAndInterpolateChangedSlice(const itk::EventObject &e, mitk::SliceNavigationController *slicer); /** Given a PlaneGeometry, this method figures out which slice of the first working image (of the associated ToolManager) should be interpolated. The actual work is then done by our SegmentationInterpolation object. */ void Interpolate(mitk::PlaneGeometry *plane, mitk::TimePointType timePoint, mitk::SliceNavigationController *slicer); // void InterpolateSurface(); /** Called internally to update the interpolation suggestion. Finds out about the focused render window and requests an interpolation. */ void UpdateVisibleSuggestion(); void SetCurrentContourListID(); private: void HideAllInterpolationControls(); void Show2DInterpolationControls(bool show); void Show3DInterpolationControls(bool show); void CheckSupportedImageDimension(); void WaitForFutures(); void NodeRemoved(const mitk::DataNode* node); mitk::SegmentationInterpolationController::Pointer m_Interpolator; mitk::SurfaceInterpolationController::Pointer m_SurfaceInterpolator; mitk::FeatureBasedEdgeDetectionFilter::Pointer m_EdgeDetector; mitk::PointCloudScoringFilter::Pointer m_PointScorer; mitk::ToolManager::Pointer m_ToolManager; bool m_Initialized; QHash m_ControllerToTimeObserverTag; QHash m_ControllerToSliceObserverTag; QHash m_ControllerToDeleteObserverTag; unsigned int InterpolationInfoChangedObserverTag; unsigned int SurfaceInterpolationInfoChangedObserverTag; QGroupBox *m_GroupBoxEnableExclusiveInterpolationMode; QComboBox *m_CmbInterpolation; QPushButton *m_BtnApply2D; QPushButton *m_BtnApplyForAllSlices2D; QPushButton *m_BtnApply3D; - QPushButton *m_BtnSuggestPlane; + // T28261 + // QPushButton *m_BtnSuggestPlane; QCheckBox *m_ChkShowPositionNodes; QPushButton *m_BtnReinit3DInterpolation; mitk::DataNode::Pointer m_FeedbackNode; mitk::DataNode::Pointer m_InterpolatedSurfaceNode; mitk::DataNode::Pointer m_3DContourNode; mitk::Image *m_Segmentation; mitk::SliceNavigationController *m_LastSNC; unsigned int m_LastSliceIndex; QHash m_TimePoints; bool m_2DInterpolationEnabled; bool m_3DInterpolationEnabled; // unsigned int m_CurrentListID; mitk::DataStorage::Pointer m_DataStorage; QFuture m_Future; QFutureWatcher m_Watcher; QTimer *m_Timer; QFuture m_PlaneFuture; QFutureWatcher m_PlaneWatcher; bool m_FirstRun; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkToolSelectionBox.cpp b/Modules/SegmentationUI/Qmitk/QmitkToolSelectionBox.cpp index 2036ea6b67..2d42898731 100755 --- a/Modules/SegmentationUI/Qmitk/QmitkToolSelectionBox.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkToolSelectionBox.cpp @@ -1,683 +1,683 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ //#define MBILOG_ENABLE_DEBUG 1 #include #include "QmitkToolSelectionBox.h" #include "QmitkToolGUI.h" #include "mitkBaseRenderer.h" #include #include #include #include #include #include #include #include "usModuleResource.h" #include "usModuleResourceStream.h" #include "mitkToolManagerProvider.h" QmitkToolSelectionBox::QmitkToolSelectionBox(QWidget *parent, mitk::DataStorage *) : QWidget(parent), m_SelfCall(false), m_DisplayedGroups("default"), m_LayoutColumns(2), m_ShowNames(true), m_GenerateAccelerators(false), m_ToolGUIWidget(nullptr), m_LastToolGUI(nullptr), m_ToolButtonGroup(nullptr), m_ButtonLayout(nullptr), m_EnabledMode(EnabledWithReferenceAndWorkingDataVisible) { QFont currentFont = QWidget::font(); currentFont.setBold(true); QWidget::setFont(currentFont); m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); // QButtonGroup m_ToolButtonGroup = new QButtonGroup(this); // some features of QButtonGroup m_ToolButtonGroup->setExclusive(false); // mutually exclusive toggle buttons RecreateButtons(); QWidget::setContentsMargins(0, 0, 0, 0); if (layout() != nullptr) { layout()->setContentsMargins(0, 0, 0, 0); } // reactions to signals connect(m_ToolButtonGroup, SIGNAL(buttonClicked(int)), this, SLOT(toolButtonClicked(int))); // reactions to ToolManager events m_ToolManager->ActiveToolChanged += mitk::MessageDelegate(this, &QmitkToolSelectionBox::OnToolManagerToolModified); m_ToolManager->ReferenceDataChanged += mitk::MessageDelegate(this, &QmitkToolSelectionBox::OnToolManagerReferenceDataModified); m_ToolManager->WorkingDataChanged += mitk::MessageDelegate(this, &QmitkToolSelectionBox::OnToolManagerWorkingDataModified); // show active tool SetOrUnsetButtonForActiveTool(); QWidget::setEnabled(false); } QmitkToolSelectionBox::~QmitkToolSelectionBox() { m_ToolManager->ActiveToolChanged -= mitk::MessageDelegate(this, &QmitkToolSelectionBox::OnToolManagerToolModified); m_ToolManager->ReferenceDataChanged -= mitk::MessageDelegate(this, &QmitkToolSelectionBox::OnToolManagerReferenceDataModified); m_ToolManager->WorkingDataChanged -= mitk::MessageDelegate(this, &QmitkToolSelectionBox::OnToolManagerWorkingDataModified); } void QmitkToolSelectionBox::SetEnabledMode(EnabledMode mode) { m_EnabledMode = mode; SetGUIEnabledAccordingToToolManagerState(); } mitk::ToolManager *QmitkToolSelectionBox::GetToolManager() { return m_ToolManager; } void QmitkToolSelectionBox::SetToolManager( mitk::ToolManager &newManager) // no nullptr pointer allowed here, a manager is required { // say bye to the old manager m_ToolManager->ActiveToolChanged -= mitk::MessageDelegate(this, &QmitkToolSelectionBox::OnToolManagerToolModified); m_ToolManager->ReferenceDataChanged -= mitk::MessageDelegate(this, &QmitkToolSelectionBox::OnToolManagerReferenceDataModified); m_ToolManager->WorkingDataChanged -= mitk::MessageDelegate(this, &QmitkToolSelectionBox::OnToolManagerWorkingDataModified); if (QWidget::isEnabled()) { m_ToolManager->UnregisterClient(); } m_ToolManager = &newManager; RecreateButtons(); // greet the new one m_ToolManager->ActiveToolChanged += mitk::MessageDelegate(this, &QmitkToolSelectionBox::OnToolManagerToolModified); m_ToolManager->ReferenceDataChanged += mitk::MessageDelegate(this, &QmitkToolSelectionBox::OnToolManagerReferenceDataModified); m_ToolManager->WorkingDataChanged += mitk::MessageDelegate(this, &QmitkToolSelectionBox::OnToolManagerWorkingDataModified); if (QWidget::isEnabled()) { m_ToolManager->RegisterClient(); } // ask the new one what the situation is like SetOrUnsetButtonForActiveTool(); } void QmitkToolSelectionBox::toolButtonClicked(int id) { if (!QWidget::isEnabled()) return; // this method could be triggered from the constructor, when we are still disabled MITK_DEBUG << "toolButtonClicked(" << id << "): id translates to tool ID " << m_ToolIDForButtonID[id]; QToolButton *toolButton = dynamic_cast(m_ToolButtonGroup->buttons().at(id)); if (toolButton) { if ((m_ButtonIDForToolID.find(m_ToolManager->GetActiveToolID()) != m_ButtonIDForToolID.end()) // if we have this tool in our box && (m_ButtonIDForToolID[m_ToolManager->GetActiveToolID()] == id)) // the tool corresponding to this button is already active { // disable this button, disable all tools toolButton->setChecked(false); m_ToolManager->ActivateTool(-1); // disable everything } else { // enable the corresponding tool m_SelfCall = true; m_ToolManager->ActivateTool(m_ToolIDForButtonID[id]); m_SelfCall = false; } } } void QmitkToolSelectionBox::OnToolManagerToolModified() { SetOrUnsetButtonForActiveTool(); } void QmitkToolSelectionBox::SetOrUnsetButtonForActiveTool() { // we want to emit a signal in any case, whether we selected ourselves or somebody else changes "our" tool manager. // --> emit before check on m_SelfCall int id = m_ToolManager->GetActiveToolID(); // don't emit signal for shape model tools bool emitSignal = true; mitk::Tool *tool = m_ToolManager->GetActiveTool(); if (tool && std::string(tool->GetGroup()) == "organ_segmentation") emitSignal = false; if (emitSignal) emit ToolSelected(id); // delete old GUI (if any) if (m_LastToolGUI && m_ToolGUIWidget) { if (m_ToolGUIWidget->layout()) { m_ToolGUIWidget->layout()->removeWidget(m_LastToolGUI); } m_LastToolGUI->setParent(nullptr); delete m_LastToolGUI; // will hopefully notify parent and layouts m_LastToolGUI = nullptr; QLayout *layout = m_ToolGUIWidget->layout(); if (layout) { layout->activate(); } } QToolButton *toolButton(nullptr); if (m_ButtonIDForToolID.find(id) != m_ButtonIDForToolID.end()) // if this tool is in our box { toolButton = dynamic_cast(m_ToolButtonGroup->buttons().at(m_ButtonIDForToolID[id])); } if (toolButton) { // mmueller // uncheck all other buttons QAbstractButton *tmpBtn = nullptr; QList::iterator it; for (int i = 0; i < m_ToolButtonGroup->buttons().size(); ++i) { tmpBtn = m_ToolButtonGroup->buttons().at(i); if (tmpBtn != toolButton) dynamic_cast(tmpBtn)->setChecked(false); } toolButton->setChecked(true); if (m_ToolGUIWidget && tool) { // create and reparent new GUI (if any) itk::Object::Pointer possibleGUI = tool->GetGUI("Qmitk", "GUI").GetPointer(); // prefix and postfix if (possibleGUI.IsNull()) possibleGUI = tool->GetGUI("", "GUI").GetPointer(); QmitkToolGUI *gui = dynamic_cast(possibleGUI.GetPointer()); //! m_LastToolGUI = gui; if (gui) { gui->SetTool(tool); gui->setParent(m_ToolGUIWidget); gui->move(gui->geometry().topLeft()); gui->show(); QLayout *layout = m_ToolGUIWidget->layout(); if (!layout) { layout = new QVBoxLayout(m_ToolGUIWidget); } if (layout) { layout->addWidget(gui); layout->activate(); } } } } else { // disable all buttons QToolButton *selectedToolButton = dynamic_cast(m_ToolButtonGroup->checkedButton()); if (selectedToolButton) { selectedToolButton->setChecked(false); } } } void QmitkToolSelectionBox::OnToolManagerReferenceDataModified() { if (m_SelfCall) return; MITK_DEBUG << "OnToolManagerReferenceDataModified()"; this->UpdateButtonsEnabledState(); this->SetGUIEnabledAccordingToToolManagerState(); } void QmitkToolSelectionBox::OnToolManagerWorkingDataModified() { if (m_SelfCall) return; MITK_DEBUG << "OnToolManagerWorkingDataModified()"; this->UpdateButtonsEnabledState(); this->SetGUIEnabledAccordingToToolManagerState(); } /** Implementes the logic, which decides, when tools are activated/deactivated. */ void QmitkToolSelectionBox::SetGUIEnabledAccordingToToolManagerState() { mitk::DataNode *referenceNode = m_ToolManager->GetReferenceData(0); mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); bool enabled = true; switch (m_EnabledMode) { default: case EnabledWithReferenceAndWorkingDataVisible: enabled = referenceNode && workingNode && referenceNode->IsVisible( mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget0"))) && workingNode->IsVisible( mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget0"))) && isVisible(); break; case EnabledWithReferenceData: enabled = referenceNode && isVisible(); break; case EnabledWithWorkingData: enabled = workingNode && isVisible(); break; case AlwaysEnabled: enabled = isVisible(); break; } if (QWidget::isEnabled() == enabled) return; // nothing to change QWidget::setEnabled(enabled); if (enabled) { m_ToolManager->RegisterClient(); int id = m_ToolManager->GetActiveToolID(); emit ToolSelected(id); } else { m_ToolManager->ActivateTool(-1); m_ToolManager->UnregisterClient(); emit ToolSelected(-1); } } /** External enableization... */ void QmitkToolSelectionBox::setEnabled(bool /*enable*/) { SetGUIEnabledAccordingToToolManagerState(); } void QmitkToolSelectionBox::UpdateButtonsEnabledState() { auto buttons = m_ToolButtonGroup->buttons(); const auto refDataNode = m_ToolManager->GetReferenceData(0); const mitk::BaseData* refData = nullptr; if (nullptr != refDataNode) { refData = refDataNode->GetData(); } const auto workingDataNode = m_ToolManager->GetWorkingData(0); const mitk::BaseData* workingData = nullptr; if (nullptr != workingDataNode) { workingData = workingDataNode->GetData(); } - for (const auto& button : buttons) + for (const auto& button : qAsConst(buttons)) { const auto buttonID = m_ToolButtonGroup->id(button); const auto toolID = m_ToolIDForButtonID[buttonID]; const auto tool = m_ToolManager->GetToolById(toolID); button->setEnabled(tool->CanHandle(refData, workingData)); } } void QmitkToolSelectionBox::RecreateButtons() { if (m_ToolManager.IsNull()) return; QList l = m_ToolButtonGroup->buttons(); // remove all buttons that are there QList::iterator it; QAbstractButton *btn; for (it = l.begin(); it != l.end(); ++it) { btn = *it; m_ToolButtonGroup->removeButton(btn); delete btn; } mitk::ToolManager::ToolVectorTypeConst allPossibleTools = m_ToolManager->GetTools(); mitk::ToolManager::ToolVectorTypeConst allTools; typedef std::pair SortPairType; typedef std::priority_queue SortedToolQueueType; SortedToolQueueType toolPositions; // clear and sort all tools // step one: find name/group of all tools in m_DisplayedGroups string. remember these positions for all tools. for (mitk::ToolManager::ToolVectorTypeConst::const_iterator iter = allPossibleTools.begin(); iter != allPossibleTools.end(); ++iter) { const mitk::Tool *tool = *iter; std::string::size_type namePos = m_DisplayedGroups.find(std::string("'") + tool->GetName() + "'"); std::string::size_type groupPos = m_DisplayedGroups.find(std::string("'") + tool->GetGroup() + "'"); if (!m_DisplayedGroups.empty() && namePos == std::string::npos && groupPos == std::string::npos) continue; // skip if (m_DisplayedGroups.empty() && std::string(tool->GetName()).length() > 0) { namePos = static_cast(tool->GetName()[0]); } SortPairType thisPair = std::make_pair(namePos < groupPos ? namePos : groupPos, *iter); toolPositions.push(thisPair); } // step two: sort tools according to previously found positions in m_DisplayedGroups MITK_DEBUG << "Sorting order of tools (lower number --> earlier in button group)"; while (!toolPositions.empty()) { SortPairType thisPair = toolPositions.top(); MITK_DEBUG << "Position " << thisPair.first << " : " << thisPair.second->GetName(); allTools.push_back(thisPair.second); toolPositions.pop(); } std::reverse(allTools.begin(), allTools.end()); MITK_DEBUG << "Sorted tools:"; for (mitk::ToolManager::ToolVectorTypeConst::const_iterator iter = allTools.begin(); iter != allTools.end(); ++iter) { MITK_DEBUG << (*iter)->GetName(); } if (m_ButtonLayout == nullptr) m_ButtonLayout = new QGridLayout; int row(0); int column(-1); int currentButtonID(0); m_ButtonIDForToolID.clear(); m_ToolIDForButtonID.clear(); QToolButton *button = nullptr; MITK_DEBUG << "Creating buttons for tools"; // fill group box with buttons for (mitk::ToolManager::ToolVectorTypeConst::const_iterator iter = allTools.begin(); iter != allTools.end(); ++iter) { const mitk::Tool *tool = *iter; int currentToolID(m_ToolManager->GetToolID(tool)); ++column; // new line if we are at the maximum columns if (column == m_LayoutColumns) { ++row; column = 0; } button = new QToolButton; button->setSizePolicy(QSizePolicy(QSizePolicy::Minimum, QSizePolicy::Minimum)); // add new button to the group MITK_DEBUG << "Adding button with ID " << currentToolID; m_ToolButtonGroup->addButton(button, currentButtonID); // ... and to the layout MITK_DEBUG << "Adding button in row/column " << row << "/" << column; m_ButtonLayout->addWidget(button, row, column); if (m_LayoutColumns == 1) { button->setToolButtonStyle(Qt::ToolButtonTextBesideIcon); } else { button->setToolButtonStyle(Qt::ToolButtonTextUnderIcon); } button->setCheckable(true); if (currentToolID == m_ToolManager->GetActiveToolID()) button->setChecked(true); QString label; if (m_GenerateAccelerators) { label += "&"; } label += tool->GetName(); QString tooltip = tool->GetName(); MITK_DEBUG << tool->GetName() << ", " << label.toLocal8Bit().constData() << ", '" << tooltip.toLocal8Bit().constData(); if (m_ShowNames) { button->setText(label); // a label button->setToolTip(tooltip); QFont currentFont = button->font(); currentFont.setBold(false); button->setFont(currentFont); } us::ModuleResource iconResource = tool->GetIconResource(); if (!iconResource.IsValid()) { button->setIcon(QIcon(QPixmap(tool->GetXPM()))); } else { auto isSVG = "svg" == iconResource.GetSuffix(); auto openmode = isSVG ? std::ios_base::in : std::ios_base::binary; us::ModuleResourceStream resourceStream(iconResource, openmode); resourceStream.seekg(0, std::ios::end); std::ios::pos_type length = resourceStream.tellg(); resourceStream.seekg(0, std::ios::beg); char *data = new char[length]; resourceStream.read(data, length); if (isSVG) { button->setIcon(QmitkStyleManager::ThemeIcon(QByteArray::fromRawData(data, length))); } else { QPixmap pixmap; pixmap.loadFromData(QByteArray::fromRawData(data, length)); button->setIcon(QIcon(pixmap)); } delete[] data; if (m_ShowNames) { if (m_LayoutColumns == 1) button->setToolButtonStyle(Qt::ToolButtonTextBesideIcon); else button->setToolButtonStyle(Qt::ToolButtonTextUnderIcon); button->setIconSize(QSize(24, 24)); } else { button->setToolButtonStyle(Qt::ToolButtonIconOnly); button->setIconSize(QSize(32, 32)); button->setToolTip(tooltip); } } if (m_GenerateAccelerators) { QString firstLetter = QString(tool->GetName()); firstLetter.truncate(1); button->setShortcut( firstLetter); // a keyboard shortcut (just the first letter of the given name w/o any CTRL or something) } m_ButtonIDForToolID[currentToolID] = currentButtonID; m_ToolIDForButtonID[currentButtonID] = currentToolID; MITK_DEBUG << "m_ButtonIDForToolID[" << currentToolID << "] == " << currentButtonID; MITK_DEBUG << "m_ToolIDForButtonID[" << currentButtonID << "] == " << currentToolID; tool->GUIProcessEventsMessage += mitk::MessageDelegate( this, &QmitkToolSelectionBox::OnToolGUIProcessEventsMessage); // will never add a listener twice, so we don't have // to check here tool->ErrorMessage += mitk::MessageDelegate1( this, &QmitkToolSelectionBox::OnToolErrorMessage); // will never add a listener twice, so we don't have to check here tool->GeneralMessage += mitk::MessageDelegate1(this, &QmitkToolSelectionBox::OnGeneralToolMessage); ++currentButtonID; } // setting grid layout for this groupbox this->setLayout(m_ButtonLayout); this->UpdateButtonsEnabledState(); // this->update(); } void QmitkToolSelectionBox::OnToolGUIProcessEventsMessage() { qApp->processEvents(); } void QmitkToolSelectionBox::OnToolErrorMessage(std::string s) { QMessageBox::critical( this, "MITK", QString(s.c_str()), QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); } void QmitkToolSelectionBox::OnGeneralToolMessage(std::string s) { QMessageBox::information( this, "MITK", QString(s.c_str()), QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); } void QmitkToolSelectionBox::SetDisplayedToolGroups(const std::string &toolGroups) { if (m_DisplayedGroups != toolGroups) { QString q_DisplayedGroups = toolGroups.c_str(); // quote all unquoted single words q_DisplayedGroups = q_DisplayedGroups.replace(QRegExp("\\b(\\w+)\\b|'([^']+)'"), "'\\1\\2'"); MITK_DEBUG << "m_DisplayedGroups was \"" << toolGroups << "\""; m_DisplayedGroups = q_DisplayedGroups.toLocal8Bit().constData(); MITK_DEBUG << "m_DisplayedGroups is \"" << m_DisplayedGroups << "\""; RecreateButtons(); SetOrUnsetButtonForActiveTool(); } } void QmitkToolSelectionBox::SetLayoutColumns(int columns) { if (columns > 0 && columns != m_LayoutColumns) { m_LayoutColumns = columns; RecreateButtons(); } } void QmitkToolSelectionBox::SetShowNames(bool show) { if (show != m_ShowNames) { m_ShowNames = show; RecreateButtons(); } } void QmitkToolSelectionBox::SetGenerateAccelerators(bool accel) { if (accel != m_GenerateAccelerators) { m_GenerateAccelerators = accel; RecreateButtons(); } } void QmitkToolSelectionBox::SetToolGUIArea(QWidget *parentWidget) { m_ToolGUIWidget = parentWidget; } void QmitkToolSelectionBox::setTitle(const QString & /*title*/) { } void QmitkToolSelectionBox::showEvent(QShowEvent *e) { QWidget::showEvent(e); SetGUIEnabledAccordingToToolManagerState(); } void QmitkToolSelectionBox::hideEvent(QHideEvent *e) { QWidget::hideEvent(e); SetGUIEnabledAccordingToToolManagerState(); } diff --git a/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.cpp index 41c3151292..fda699f8d4 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.cpp +++ b/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.cpp @@ -1,199 +1,139 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkWatershedToolGUI.h" +#include "mitkWatershedTool.h" #include MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkWatershedToolGUI, "") -QmitkWatershedToolGUI::QmitkWatershedToolGUI() : QmitkToolGUI() +QmitkWatershedToolGUI::QmitkWatershedToolGUI() : QmitkAutoMLSegmentationToolGUIBase() +{ +} + +void QmitkWatershedToolGUI::ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool) +{ + Superclass::ConnectNewTool(newTool); + + auto tool = dynamic_cast(newTool); + if (nullptr != tool) + { + tool->SetLevel(m_Level); + tool->SetThreshold(m_Threshold); + } + + newTool->IsTimePointChangeAwareOff(); +} + +void QmitkWatershedToolGUI::InitializeUI(QBoxLayout* mainLayout) { m_Controls.setupUi(this); m_Controls.thresholdSlider->setMinimum(0); //We set the threshold maximum to 0.5 to avoid crashes in the watershed filter //see T27703 for more details. m_Controls.thresholdSlider->setMaximum(0.5); m_Controls.thresholdSlider->setValue(m_Threshold); m_Controls.thresholdSlider->setPageStep(0.01); m_Controls.thresholdSlider->setSingleStep(0.001); m_Controls.thresholdSlider->setDecimals(4); m_Controls.levelSlider->setMinimum(0); m_Controls.levelSlider->setMaximum(1); m_Controls.levelSlider->setValue(m_Level); m_Controls.levelSlider->setPageStep(0.1); m_Controls.levelSlider->setSingleStep(0.01); connect(m_Controls.previewButton, SIGNAL(clicked()), this, SLOT(OnSettingsAccept())); - connect(m_Controls.m_selectionListWidget, &QmitkSimpleLabelSetListWidget::SelectedLabelsChanged, this, &QmitkWatershedToolGUI::OnRegionSelectionChanged); connect(m_Controls.levelSlider, SIGNAL(valueChanged(double)), this, SLOT(OnLevelChanged(double))); connect(m_Controls.thresholdSlider, SIGNAL(valueChanged(double)), this, SLOT(OnThresholdChanged(double))); - connect(m_Controls.m_ConfSegButton, SIGNAL(clicked()), this, SLOT(OnSegmentationRegionAccept())); - connect(this, SIGNAL(NewToolAssociated(mitk::Tool *)), this, SLOT(OnNewToolAssociated(mitk::Tool *))); -} - -QmitkWatershedToolGUI::~QmitkWatershedToolGUI() -{ - if (m_WatershedTool.IsNotNull()) - { - m_WatershedTool->CurrentlyBusy -= - mitk::MessageDelegate1(this, &QmitkWatershedToolGUI::BusyStateChanged); - } -} - -void QmitkWatershedToolGUI::OnRegionSelectionChanged(const QmitkSimpleLabelSetListWidget::LabelVectorType& selectedLabels) -{ - if (m_WatershedTool.IsNotNull()) - { - mitk::AutoMLSegmentationWithPreviewTool::SelectedLabelVectorType labelIDs; - for (const auto& label : selectedLabels) - { - labelIDs.push_back(label->GetValue()); - } - - m_WatershedTool->SetSelectedLabels(labelIDs); - m_WatershedTool->UpdatePreview(); - - m_Controls.m_ConfSegButton->setEnabled(!labelIDs.empty()); - } -} -void QmitkWatershedToolGUI::OnNewToolAssociated(mitk::Tool *tool) -{ - if (m_WatershedTool.IsNotNull()) - { - m_WatershedTool->CurrentlyBusy -= - mitk::MessageDelegate1(this, &QmitkWatershedToolGUI::BusyStateChanged); - } - - m_WatershedTool = dynamic_cast(tool); - - if (m_WatershedTool.IsNotNull()) - { - m_WatershedTool->CurrentlyBusy += - mitk::MessageDelegate1(this, &QmitkWatershedToolGUI::BusyStateChanged); - - m_WatershedTool->SetLevel(m_Level); - m_WatershedTool->SetThreshold(m_Threshold); + mainLayout->addLayout(m_Controls.verticalLayout); - m_WatershedTool->SetOverwriteExistingSegmentation(true); - m_WatershedTool->IsTimePointChangeAwareOff(); - m_Controls.m_CheckProcessAll->setVisible(m_WatershedTool->GetTargetSegmentationNode()->GetData()->GetTimeSteps() > 1); - } -} - -void QmitkWatershedToolGUI::OnSegmentationRegionAccept() -{ - QString segName = QString::fromStdString(m_WatershedTool->GetCurrentSegmentationName()); - - if (m_WatershedTool.IsNotNull()) - { - if (this->m_Controls.m_CheckCreateNew->isChecked()) - { - m_WatershedTool->SetOverwriteExistingSegmentation(false); - } - else - { - m_WatershedTool->SetOverwriteExistingSegmentation(true); - } - - m_WatershedTool->SetCreateAllTimeSteps(this->m_Controls.m_CheckProcessAll->isChecked()); - - this->m_Controls.m_ConfSegButton->setEnabled(false); - m_WatershedTool->ConfirmSegmentation(); - } + Superclass::InitializeUI(mainLayout); } void QmitkWatershedToolGUI::OnSettingsAccept() { - if (m_WatershedTool.IsNotNull()) + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) { try { m_Threshold = m_Controls.thresholdSlider->value(); m_Level = m_Controls.levelSlider->value(); - m_WatershedTool->SetThreshold(m_Threshold); - m_WatershedTool->SetLevel(m_Level); + tool->SetThreshold(m_Threshold); + tool->SetLevel(m_Level); - m_WatershedTool->UpdatePreview(); + tool->UpdatePreview(); } catch (const std::exception& e) { this->setCursor(Qt::ArrowCursor); std::stringstream stream; stream << "Error while generation watershed segmentation. Reason: " << e.what(); QMessageBox* messageBox = new QMessageBox(QMessageBox::Critical, nullptr, stream.str().c_str()); messageBox->exec(); delete messageBox; MITK_ERROR << stream.str(); return; } catch (...) { this->setCursor(Qt::ArrowCursor); std::stringstream stream; stream << "Unkown error occured while generation watershed segmentation."; QMessageBox* messageBox = new QMessageBox(QMessageBox::Critical, nullptr, stream.str().c_str()); messageBox->exec(); delete messageBox; MITK_ERROR << stream.str(); return; } - m_Controls.m_selectionListWidget->SetLabelSetImage(m_WatershedTool->GetMLPreview()); - m_WatershedTool->IsTimePointChangeAwareOn(); + this->SetLabelSetPreview(tool->GetMLPreview()); + tool->IsTimePointChangeAwareOn(); } } -void QmitkWatershedToolGUI::BusyStateChanged(bool value) +void QmitkWatershedToolGUI::EnableWidgets(bool enabled) { - if (value) - { - QApplication::setOverrideCursor(QCursor(Qt::BusyCursor)); - } - else - { - QApplication::restoreOverrideCursor(); - } - - m_Controls.levelSlider->setEnabled(!value); - m_Controls.thresholdSlider->setEnabled(!value); - m_Controls.m_ConfSegButton->setEnabled(!m_WatershedTool->GetSelectedLabels().empty() && !value); - m_Controls.m_CheckProcessAll->setEnabled(!value); - m_Controls.m_CheckCreateNew->setEnabled(!value); - m_Controls.previewButton->setEnabled(!value); + Superclass::EnableWidgets(enabled); + m_Controls.levelSlider->setEnabled(enabled); + m_Controls.thresholdSlider->setEnabled(enabled); + m_Controls.previewButton->setEnabled(enabled); } void QmitkWatershedToolGUI::OnLevelChanged(double value) { - if (m_WatershedTool.IsNotNull()) + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) { - m_WatershedTool->SetLevel(value); + tool->SetLevel(value); } } void QmitkWatershedToolGUI::OnThresholdChanged(double value) { - if (m_WatershedTool.IsNotNull()) + auto tool = this->GetConnectedToolAs(); + if (nullptr != tool) { - m_WatershedTool->SetThreshold(value); + tool->SetThreshold(value); } } diff --git a/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.h b/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.h index c5b8bbe5f1..193257e01f 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.h +++ b/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUI.h @@ -1,71 +1,66 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkWatershedToolGUI_h_Included #define QmitkWatershedToolGUI_h_Included -#include "QmitkToolGUI.h" -#include "mitkWatershedTool.h" +#include "QmitkAutoMLSegmentationToolGUIBase.h" #include "ui_QmitkWatershedToolGUIControls.h" #include /** \ingroup org_mitk_gui_qt_interactivesegmentation_internal \brief GUI for mitk::WatershedTool. \sa mitk::WatershedTool This GUI shows two sliders to change the watershed parameters. It executes the watershed algorithm by clicking on the button. */ -class MITKSEGMENTATIONUI_EXPORT QmitkWatershedToolGUI : public QmitkToolGUI +class MITKSEGMENTATIONUI_EXPORT QmitkWatershedToolGUI : public QmitkAutoMLSegmentationToolGUIBase { Q_OBJECT public: - mitkClassMacro(QmitkWatershedToolGUI, QmitkToolGUI); + mitkClassMacro(QmitkWatershedToolGUI, QmitkAutoMLSegmentationToolGUIBase); itkFactorylessNewMacro(Self); itkCloneMacro(Self); protected slots : - void OnNewToolAssociated(mitk::Tool *); - void OnSettingsAccept(); - void OnSegmentationRegionAccept(); - - void OnRegionSelectionChanged(const QmitkSimpleLabelSetListWidget::LabelVectorType& selectedLabels); - void OnLevelChanged(double value); void OnThresholdChanged(double value); protected: QmitkWatershedToolGUI(); - ~QmitkWatershedToolGUI() override; + ~QmitkWatershedToolGUI() = default; + + void ConnectNewTool(mitk::AutoSegmentationWithPreviewTool* newTool) override; + void InitializeUI(QBoxLayout* mainLayout) override; - void BusyStateChanged(bool value) override; + void EnableWidgets(bool enabled) override; //Recommendation from ITK is to have a threshold:level ration around 1:100 //we set Level a bit higher. This provokes more oversegmentation, //but produces less objects in the first run and profits form the fact that //decreasing level is quite fast in the filter. double m_Level = 0.6; double m_Threshold = 0.004; Ui_QmitkWatershedToolGUIControls m_Controls; - mitk::WatershedTool::Pointer m_WatershedTool; }; #endif diff --git a/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUIControls.ui b/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUIControls.ui index 4c4931c08a..4ce970d215 100644 --- a/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUIControls.ui +++ b/Modules/SegmentationUI/Qmitk/QmitkWatershedToolGUIControls.ui @@ -1,160 +1,109 @@ QmitkWatershedToolGUIControls 0 0 192 352 0 0 100 0 100000 100000 QmitkOtsuToolWidget + + 0 + + + 0 + + + 0 + + + 0 + Level: 0 0 Threshold: - - - - - 0 - 0 - - - - - 10000000 - 10000000 - - - - 0 0 100000 16777215 Preview - - - - false - - - - 0 - 0 - - - - - 100000 - 16777215 - - - - Confirm Segmentation - - - - - - - Process/overwrite all time steps of the dynamic segmentation and not just the currently visible time step. - - - Process all time steps - - - - - - - Add the confirmed segmentation as a new segmentation instead of overwriting the currently selected. - - - Create as new segmentation - - - - - QmitkSimpleLabelSetListWidget - QWidget -
QmitkSimpleLabelSetListWidget.h
- ctkSliderWidget QWidget
ctkSliderWidget.h
1 diff --git a/Modules/SegmentationUI/files.cmake b/Modules/SegmentationUI/files.cmake index d84231e8a4..fb35d7707a 100644 --- a/Modules/SegmentationUI/files.cmake +++ b/Modules/SegmentationUI/files.cmake @@ -1,84 +1,91 @@ set( CPP_FILES Qmitk/QmitkAdaptiveRegionGrowingToolGUI.cpp +Qmitk/QmitkAutoSegmentationToolGUIBase.cpp +Qmitk/QmitkAutoMLSegmentationToolGUIBase.cpp +Qmitk/QmitkBinaryThresholdToolGUIBase.cpp Qmitk/QmitkBinaryThresholdToolGUI.cpp Qmitk/QmitkBinaryThresholdULToolGUI.cpp Qmitk/QmitkCalculateGrayValueStatisticsToolGUI.cpp Qmitk/QmitkConfirmSegmentationDialog.cpp Qmitk/QmitkCopyToClipBoardDialog.cpp Qmitk/QmitkDrawPaintbrushToolGUI.cpp Qmitk/QmitkErasePaintbrushToolGUI.cpp +Qmitk/QmitkFastMarchingToolGUIBase.cpp Qmitk/QmitkFastMarchingTool3DGUI.cpp Qmitk/QmitkFastMarchingToolGUI.cpp - Qmitk/QmitkLiveWireTool2DGUI.cpp Qmitk/QmitkNewSegmentationDialog.cpp Qmitk/QmitkOtsuTool3DGUI.cpp Qmitk/QmitkPaintbrushToolGUI.cpp Qmitk/QmitkPickingToolGUI.cpp Qmitk/QmitkPixelManipulationToolGUI.cpp Qmitk/QmitkSlicesInterpolator.cpp Qmitk/QmitkToolGUI.cpp Qmitk/QmitkToolGUIArea.cpp Qmitk/QmitkToolSelectionBox.cpp Qmitk/QmitkWatershedToolGUI.cpp #Added from ML Qmitk/QmitkLabelSetWidget.cpp Qmitk/QmitkSurfaceStampWidget.cpp Qmitk/QmitkMaskStampWidget.cpp Qmitk/QmitkSliceBasedInterpolatorWidget.cpp Qmitk/QmitkSurfaceBasedInterpolatorWidget.cpp Qmitk/QmitkSearchLabelDialog.cpp Qmitk/QmitkSimpleLabelSetListWidget.cpp ) set(MOC_H_FILES Qmitk/QmitkAdaptiveRegionGrowingToolGUI.h +Qmitk/QmitkAutoSegmentationToolGUIBase.h +Qmitk/QmitkAutoMLSegmentationToolGUIBase.h +Qmitk/QmitkBinaryThresholdToolGUIBase.h Qmitk/QmitkBinaryThresholdToolGUI.h Qmitk/QmitkBinaryThresholdULToolGUI.h Qmitk/QmitkCalculateGrayValueStatisticsToolGUI.h Qmitk/QmitkConfirmSegmentationDialog.h Qmitk/QmitkCopyToClipBoardDialog.h Qmitk/QmitkDrawPaintbrushToolGUI.h Qmitk/QmitkErasePaintbrushToolGUI.h +Qmitk/QmitkFastMarchingToolGUIBase.h Qmitk/QmitkFastMarchingTool3DGUI.h Qmitk/QmitkFastMarchingToolGUI.h Qmitk/QmitkLiveWireTool2DGUI.h Qmitk/QmitkNewSegmentationDialog.h Qmitk/QmitkOtsuTool3DGUI.h Qmitk/QmitkPaintbrushToolGUI.h Qmitk/QmitkPickingToolGUI.h Qmitk/QmitkPixelManipulationToolGUI.h Qmitk/QmitkSlicesInterpolator.h Qmitk/QmitkToolGUI.h Qmitk/QmitkToolGUIArea.h Qmitk/QmitkToolSelectionBox.h Qmitk/QmitkWatershedToolGUI.h #Added from ML Qmitk/QmitkLabelSetWidget.h Qmitk/QmitkSurfaceStampWidget.h Qmitk/QmitkMaskStampWidget.h Qmitk/QmitkSliceBasedInterpolatorWidget.h Qmitk/QmitkSurfaceBasedInterpolatorWidget.h Qmitk/QmitkSearchLabelDialog.h Qmitk/QmitkSimpleLabelSetListWidget.h ) set(UI_FILES Qmitk/QmitkAdaptiveRegionGrowingToolGUIControls.ui Qmitk/QmitkConfirmSegmentationDialog.ui Qmitk/QmitkOtsuToolWidgetControls.ui Qmitk/QmitkPickingToolGUIControls.ui Qmitk/QmitkLiveWireTool2DGUIControls.ui Qmitk/QmitkWatershedToolGUIControls.ui #Added from ML Qmitk/QmitkLabelSetWidgetControls.ui Qmitk/QmitkSurfaceStampWidgetGUIControls.ui Qmitk/QmitkMaskStampWidgetGUIControls.ui Qmitk/QmitkSliceBasedInterpolatorWidgetGUIControls.ui Qmitk/QmitkSurfaceBasedInterpolatorWidgetGUIControls.ui Qmitk/QmitkSearchLabelDialogGUI.ui ) set(QRC_FILES resources/SegmentationUI.qrc ) diff --git a/Modules/SemanticRelationsUI/src/QmitkLesionTreeModel.cpp b/Modules/SemanticRelationsUI/src/QmitkLesionTreeModel.cpp index c4f1dbb551..c4f2923b2e 100644 --- a/Modules/SemanticRelationsUI/src/QmitkLesionTreeModel.cpp +++ b/Modules/SemanticRelationsUI/src/QmitkLesionTreeModel.cpp @@ -1,298 +1,298 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // semantic relations UI module #include "QmitkLesionTreeModel.h" // semantic relations module #include #include #include #include #include #include // qt #include QmitkLesionTreeModel::QmitkLesionTreeModel(QObject* parent/* = nullptr*/) : QmitkAbstractSemanticRelationsStorageModel(parent) , m_LastSegmentation(nullptr) , m_RootItem(std::make_shared(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(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(lesionPresence.size())) { return "N/A"; } if (lesionPresence.at(index.column() - 1)) { return QString::fromStdString("present"); } return QString::fromStdString("not present"); } } } if (Qt::BackgroundColorRole == 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(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(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) { if (m_DataStorage.IsExpired()) { return; } auto dataStorage = m_DataStorage.Lock(); // 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 newLesionTreeItem = std::make_shared(lesionData); m_RootItem->AddChild(newLesionTreeItem); } void QmitkLesionTreeModel::SetSelectedDataNodesPresence() { m_DataNodePresence.clear(); - for (const auto& dataNode : m_SelectedDataNodes) + for (const auto& dataNode : qAsConst(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::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(index.internalPointer()); if (nullptr != item) { return item; } } return m_RootItem.get(); } diff --git a/Modules/SemanticRelationsUI/src/QmitkPatientTableHeaderView.cpp b/Modules/SemanticRelationsUI/src/QmitkPatientTableHeaderView.cpp index 4c053d9b93..7348ebcfda 100644 --- a/Modules/SemanticRelationsUI/src/QmitkPatientTableHeaderView.cpp +++ b/Modules/SemanticRelationsUI/src/QmitkPatientTableHeaderView.cpp @@ -1,240 +1,240 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include 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()) { m_HeaderModel = variant.value(); } 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 : indexes) + for (const auto& index : qAsConst(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.child(0, i), 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.child(0, i)); } } else { headerList.push_back(currentIndex); } } return headerList; } diff --git a/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp b/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp index c5de38bbee..7555fcef9a 100644 --- a/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp +++ b/Modules/SurfaceInterpolation/mitkSurfaceInterpolationController.cpp @@ -1,719 +1,731 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "mitkSurfaceInterpolationController.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkMemoryUtilities.h" #include "mitkImageToSurfaceFilter.h" //#include "vtkXMLPolyDataWriter.h" #include "vtkPolyDataWriter.h" // Check whether the given contours are coplanar bool ContoursCoplanar(mitk::SurfaceInterpolationController::ContourPositionInformation leftHandSide, mitk::SurfaceInterpolationController::ContourPositionInformation rightHandSide) { // Here we check two things: // 1. Whether the normals of both contours are at least parallel // 2. Whether both contours lie in the same plane // Check for coplanarity: // a. Span a vector between two points one from each contour // b. Calculate dot product for the vector and one of the normals // c. If the dot is zero the two vectors are orthogonal and the contours are coplanar double vec[3]; vec[0] = leftHandSide.contourPoint[0] - rightHandSide.contourPoint[0]; vec[1] = leftHandSide.contourPoint[1] - rightHandSide.contourPoint[1]; vec[2] = leftHandSide.contourPoint[2] - rightHandSide.contourPoint[2]; double n[3]; n[0] = rightHandSide.contourNormal[0]; n[1] = rightHandSide.contourNormal[1]; n[2] = rightHandSide.contourNormal[2]; double dot = vtkMath::Dot(n, vec); double n2[3]; n2[0] = leftHandSide.contourNormal[0]; n2[1] = leftHandSide.contourNormal[1]; n2[2] = leftHandSide.contourNormal[2]; // The normals of both contours have to be parallel but not of the same orientation double lengthLHS = leftHandSide.contourNormal.GetNorm(); double lengthRHS = rightHandSide.contourNormal.GetNorm(); double dot2 = vtkMath::Dot(n, n2); bool contoursParallel = mitk::Equal(fabs(lengthLHS * lengthRHS), fabs(dot2), 0.001); if (mitk::Equal(dot, 0.0, 0.001) && contoursParallel) return true; else return false; } mitk::SurfaceInterpolationController::ContourPositionInformation CreateContourPositionInformation( mitk::Surface::Pointer contour) { mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo; contourInfo.contour = contour; double n[3]; double p[3]; contour->GetVtkPolyData()->GetPoints()->GetPoint(0, p); vtkPolygon::ComputeNormal(contour->GetVtkPolyData()->GetPoints(), n); contourInfo.contourNormal = n; contourInfo.contourPoint = p; return contourInfo; } mitk::SurfaceInterpolationController::SurfaceInterpolationController() : m_SelectedSegmentation(nullptr), m_CurrentTimePoint(0.) { m_DistanceImageSpacing = 0.0; m_ReduceFilter = ReduceContourSetFilter::New(); m_NormalsFilter = ComputeContourSetNormalsFilter::New(); m_InterpolateSurfaceFilter = CreateDistanceImageFromSurfaceFilter::New(); // m_TimeSelector = ImageTimeSelector::New(); m_ReduceFilter->SetUseProgressBar(false); // m_ReduceFilter->SetProgressStepSize(1); m_NormalsFilter->SetUseProgressBar(true); m_NormalsFilter->SetProgressStepSize(1); m_InterpolateSurfaceFilter->SetUseProgressBar(true); m_InterpolateSurfaceFilter->SetProgressStepSize(7); m_Contours = Surface::New(); m_PolyData = vtkSmartPointer::New(); vtkSmartPointer points = vtkSmartPointer::New(); m_PolyData->SetPoints(points); m_InterpolationResult = nullptr; m_CurrentNumberOfReducedContours = 0; } mitk::SurfaceInterpolationController::~SurfaceInterpolationController() { // Removing all observers auto dataIter = m_SegmentationObserverTags.begin(); for (; dataIter != m_SegmentationObserverTags.end(); ++dataIter) { (*dataIter).first->RemoveObserver((*dataIter).second); } m_SegmentationObserverTags.clear(); } mitk::SurfaceInterpolationController *mitk::SurfaceInterpolationController::GetInstance() { static mitk::SurfaceInterpolationController::Pointer m_Instance; if (m_Instance.IsNull()) { m_Instance = SurfaceInterpolationController::New(); } return m_Instance; } void mitk::SurfaceInterpolationController::AddNewContour(mitk::Surface::Pointer newContour) { if (newContour->GetVtkPolyData()->GetNumberOfPoints() > 0) { ContourPositionInformation contourInfo = CreateContourPositionInformation(newContour); this->AddToInterpolationPipeline(contourInfo); this->Modified(); } } void mitk::SurfaceInterpolationController::AddNewContours(std::vector newContours) { for (unsigned int i = 0; i < newContours.size(); ++i) { if (newContours.at(i)->GetVtkPolyData()->GetNumberOfPoints() > 0) { ContourPositionInformation contourInfo = CreateContourPositionInformation(newContours.at(i)); this->AddToInterpolationPipeline(contourInfo); } } this->Modified(); } void mitk::SurfaceInterpolationController::AddToInterpolationPipeline(ContourPositionInformation contourInfo) { if (!m_SelectedSegmentation) { return; } int pos(-1); if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint)) { MITK_ERROR << "Invalid time point requested for interpolation pipeline."; return; } const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint); ContourPositionInformationVec2D currentContours = m_ListOfInterpolationSessions[m_SelectedSegmentation]; ContourPositionInformationList currentContourList = currentContours[currentTimeStep]; mitk::Surface *newContour = contourInfo.contour; for (unsigned int i = 0; i < currentContourList.size(); i++) { ContourPositionInformation contourFromList = currentContourList.at(i); if (ContoursCoplanar(contourInfo, contourFromList)) { pos = i; break; } } // Don't save a new empty contour if (pos == -1 && newContour->GetVtkPolyData()->GetNumberOfPoints() > 0) { m_ReduceFilter->SetInput(m_ListOfInterpolationSessions[m_SelectedSegmentation][currentTimeStep].size(), newContour); m_ListOfInterpolationSessions[m_SelectedSegmentation][currentTimeStep].push_back(contourInfo); } else if (pos != -1 && newContour->GetVtkPolyData()->GetNumberOfPoints() > 0) { m_ListOfInterpolationSessions[m_SelectedSegmentation][currentTimeStep].at(pos) = contourInfo; m_ReduceFilter->SetInput(pos, newContour); } else if (newContour->GetVtkPolyData()->GetNumberOfPoints() == 0) { this->RemoveContour(contourInfo); } } bool mitk::SurfaceInterpolationController::RemoveContour(ContourPositionInformation contourInfo) { if (!m_SelectedSegmentation) { return false; } if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint)) { return false; } const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint); auto it = m_ListOfInterpolationSessions[m_SelectedSegmentation][currentTimeStep].begin(); while (it != m_ListOfInterpolationSessions[m_SelectedSegmentation][currentTimeStep].end()) { ContourPositionInformation currentContour = (*it); if (ContoursCoplanar(currentContour, contourInfo)) { m_ListOfInterpolationSessions[m_SelectedSegmentation][currentTimeStep].erase(it); this->ReinitializeInterpolation(); return true; } ++it; } return false; } const mitk::Surface *mitk::SurfaceInterpolationController::GetContour(ContourPositionInformation contourInfo) { if (!m_SelectedSegmentation) { return nullptr; } if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint)) { return nullptr; } const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint); ContourPositionInformationList contourList = m_ListOfInterpolationSessions[m_SelectedSegmentation][currentTimeStep]; for (unsigned int i = 0; i < contourList.size(); ++i) { ContourPositionInformation currentContour = contourList.at(i); if (ContoursCoplanar(contourInfo, currentContour)) return currentContour.contour; } return nullptr; } unsigned int mitk::SurfaceInterpolationController::GetNumberOfContours() { if (!m_SelectedSegmentation) { return -1; } if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint)) { return -1; } const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint); return m_ListOfInterpolationSessions[m_SelectedSegmentation][currentTimeStep].size(); } void mitk::SurfaceInterpolationController::Interpolate() { if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint)) { MITK_WARN << "No interpolation possible, currently selected timepoint is not in the time bounds of currently selected segmentation. Time point: " << m_CurrentTimePoint; m_InterpolationResult = nullptr; return; } const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint); m_ReduceFilter->Update(); m_CurrentNumberOfReducedContours = m_ReduceFilter->GetNumberOfOutputs(); if (m_CurrentNumberOfReducedContours == 1) { vtkPolyData *tmp = m_ReduceFilter->GetOutput(0)->GetVtkPolyData(); if (tmp == nullptr) { m_CurrentNumberOfReducedContours = 0; } } mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(m_SelectedSegmentation); timeSelector->SetTimeNr(currentTimeStep); timeSelector->SetChannelNr(0); timeSelector->Update(); mitk::Image::Pointer refSegImage = timeSelector->GetOutput(); m_NormalsFilter->SetSegmentationBinaryImage(refSegImage); for (unsigned int i = 0; i < m_CurrentNumberOfReducedContours; i++) { mitk::Surface::Pointer reducedContour = m_ReduceFilter->GetOutput(i); reducedContour->DisconnectPipeline(); m_NormalsFilter->SetInput(i, reducedContour); m_InterpolateSurfaceFilter->SetInput(i, m_NormalsFilter->GetOutput(i)); } if (m_CurrentNumberOfReducedContours < 2) { // If no interpolation is possible reset the interpolation result m_InterpolationResult = nullptr; return; } // Setting up progress bar mitk::ProgressBar::GetInstance()->AddStepsToDo(10); // create a surface from the distance-image mitk::ImageToSurfaceFilter::Pointer imageToSurfaceFilter = mitk::ImageToSurfaceFilter::New(); imageToSurfaceFilter->SetInput(m_InterpolateSurfaceFilter->GetOutput()); imageToSurfaceFilter->SetThreshold(0); imageToSurfaceFilter->SetSmooth(true); imageToSurfaceFilter->SetSmoothIteration(20); imageToSurfaceFilter->Update(); mitk::Surface::Pointer interpolationResult = mitk::Surface::New(); + interpolationResult->Expand(m_SelectedSegmentation->GetTimeSteps()); + + auto geometry = m_SelectedSegmentation->GetTimeGeometry()->Clone(); + geometry->ReplaceTimeStepGeometries(mitk::Geometry3D::New()); + interpolationResult->SetTimeGeometry(geometry); + interpolationResult->SetVtkPolyData(imageToSurfaceFilter->GetOutput()->GetVtkPolyData(), currentTimeStep); + m_InterpolationResult = interpolationResult; m_DistanceImageSpacing = m_InterpolateSurfaceFilter->GetDistanceImageSpacing(); vtkSmartPointer polyDataAppender = vtkSmartPointer::New(); for (unsigned int i = 0; i < m_ListOfInterpolationSessions[m_SelectedSegmentation][currentTimeStep].size(); i++) { polyDataAppender->AddInputData( m_ListOfInterpolationSessions[m_SelectedSegmentation][currentTimeStep].at(i).contour->GetVtkPolyData()); } polyDataAppender->Update(); m_Contours->SetVtkPolyData(polyDataAppender->GetOutput()); + auto* contoursGeometry = static_cast(m_Contours->GetTimeGeometry()); + auto timeBounds = geometry->GetTimeBounds(currentTimeStep); + contoursGeometry->SetFirstTimePoint(timeBounds[0]); + contoursGeometry->SetStepDuration(timeBounds[1] - timeBounds[0]); + // Last progress step mitk::ProgressBar::GetInstance()->Progress(20); m_InterpolationResult->DisconnectPipeline(); } mitk::Surface::Pointer mitk::SurfaceInterpolationController::GetInterpolationResult() { return m_InterpolationResult; } mitk::Surface *mitk::SurfaceInterpolationController::GetContoursAsSurface() { return m_Contours; } void mitk::SurfaceInterpolationController::SetDataStorage(DataStorage::Pointer ds) { m_DataStorage = ds; } void mitk::SurfaceInterpolationController::SetMinSpacing(double minSpacing) { m_ReduceFilter->SetMinSpacing(minSpacing); } void mitk::SurfaceInterpolationController::SetMaxSpacing(double maxSpacing) { m_ReduceFilter->SetMaxSpacing(maxSpacing); m_NormalsFilter->SetMaxSpacing(maxSpacing); } void mitk::SurfaceInterpolationController::SetDistanceImageVolume(unsigned int distImgVolume) { m_InterpolateSurfaceFilter->SetDistanceImageVolume(distImgVolume); } mitk::Image::Pointer mitk::SurfaceInterpolationController::GetCurrentSegmentation() { return m_SelectedSegmentation; } mitk::Image *mitk::SurfaceInterpolationController::GetImage() { return m_InterpolateSurfaceFilter->GetOutput(); } double mitk::SurfaceInterpolationController::EstimatePortionOfNeededMemory() { double numberOfPointsAfterReduction = m_ReduceFilter->GetNumberOfPointsAfterReduction() * 3; double sizeOfPoints = pow(numberOfPointsAfterReduction, 2) * sizeof(double); double totalMem = mitk::MemoryUtilities::GetTotalSizeOfPhysicalRam(); double percentage = sizeOfPoints / totalMem; return percentage; } unsigned int mitk::SurfaceInterpolationController::GetNumberOfInterpolationSessions() { return m_ListOfInterpolationSessions.size(); } template void mitk::SurfaceInterpolationController::GetImageBase(itk::Image *input, itk::ImageBase<3>::Pointer &result) { result->Graft(input); } void mitk::SurfaceInterpolationController::SetCurrentSegmentationInterpolationList(mitk::Image::Pointer segmentation) { this->SetCurrentInterpolationSession(segmentation); } void mitk::SurfaceInterpolationController::SetCurrentInterpolationSession(mitk::Image::Pointer currentSegmentationImage) { if (currentSegmentationImage.GetPointer() == m_SelectedSegmentation) return; if (currentSegmentationImage.IsNull()) { m_SelectedSegmentation = nullptr; return; } m_SelectedSegmentation = currentSegmentationImage.GetPointer(); auto it = m_ListOfInterpolationSessions.find(currentSegmentationImage.GetPointer()); // If the session does not exist yet create a new ContourPositionPairList otherwise reinitialize the interpolation // pipeline if (it == m_ListOfInterpolationSessions.end()) { ContourPositionInformationVec2D newList; m_ListOfInterpolationSessions.insert( std::pair(m_SelectedSegmentation, newList)); m_InterpolationResult = nullptr; m_CurrentNumberOfReducedContours = 0; itk::MemberCommand::Pointer command = itk::MemberCommand::New(); command->SetCallbackFunction(this, &SurfaceInterpolationController::OnSegmentationDeleted); m_SegmentationObserverTags.insert(std::pair( m_SelectedSegmentation, m_SelectedSegmentation->AddObserver(itk::DeleteEvent(), command))); } this->ReinitializeInterpolation(); } bool mitk::SurfaceInterpolationController::ReplaceInterpolationSession(mitk::Image::Pointer oldSession, mitk::Image::Pointer newSession) { if (oldSession.IsNull() || newSession.IsNull()) return false; if (oldSession.GetPointer() == newSession.GetPointer()) return false; if (!mitk::Equal(*(oldSession->GetGeometry()), *(newSession->GetGeometry()), mitk::eps, false)) return false; auto it = m_ListOfInterpolationSessions.find(oldSession.GetPointer()); if (it == m_ListOfInterpolationSessions.end()) return false; if (!newSession->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint)) { MITK_WARN << "Interpolation session cannot be replaced. Currently selected timepoint is not in the time bounds of the new session. Time point: " << m_CurrentTimePoint; return false; } ContourPositionInformationVec2D oldList = (*it).second; m_ListOfInterpolationSessions.insert( std::pair(newSession.GetPointer(), oldList)); itk::MemberCommand::Pointer command = itk::MemberCommand::New(); command->SetCallbackFunction(this, &SurfaceInterpolationController::OnSegmentationDeleted); m_SegmentationObserverTags.insert( std::pair(newSession, newSession->AddObserver(itk::DeleteEvent(), command))); if (m_SelectedSegmentation == oldSession) m_SelectedSegmentation = newSession; const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint); mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(m_SelectedSegmentation); timeSelector->SetTimeNr(currentTimeStep); timeSelector->SetChannelNr(0); timeSelector->Update(); mitk::Image::Pointer refSegImage = timeSelector->GetOutput(); m_NormalsFilter->SetSegmentationBinaryImage(refSegImage); this->RemoveInterpolationSession(oldSession); return true; } void mitk::SurfaceInterpolationController::RemoveSegmentationFromContourList(mitk::Image *segmentation) { this->RemoveInterpolationSession(segmentation); } void mitk::SurfaceInterpolationController::RemoveInterpolationSession(mitk::Image::Pointer segmentationImage) { if (segmentationImage) { if (m_SelectedSegmentation == segmentationImage) { m_NormalsFilter->SetSegmentationBinaryImage(nullptr); m_SelectedSegmentation = nullptr; } m_ListOfInterpolationSessions.erase(segmentationImage); // Remove observer auto pos = m_SegmentationObserverTags.find(segmentationImage); if (pos != m_SegmentationObserverTags.end()) { segmentationImage->RemoveObserver((*pos).second); m_SegmentationObserverTags.erase(pos); } } } void mitk::SurfaceInterpolationController::RemoveAllInterpolationSessions() { // Removing all observers auto dataIter = m_SegmentationObserverTags.begin(); while (dataIter != m_SegmentationObserverTags.end()) { mitk::Image *image = (*dataIter).first; image->RemoveObserver((*dataIter).second); ++dataIter; } m_SegmentationObserverTags.clear(); m_SelectedSegmentation = nullptr; m_ListOfInterpolationSessions.clear(); } void mitk::SurfaceInterpolationController::ReinitializeInterpolation(mitk::Surface::Pointer contours) { // 1. detect coplanar contours // 2. merge coplanar contours into a single surface // 4. add contour to pipeline // Split the surface into separate polygons vtkSmartPointer existingPolys; vtkSmartPointer existingPoints; existingPolys = contours->GetVtkPolyData()->GetPolys(); existingPoints = contours->GetVtkPolyData()->GetPoints(); existingPolys->InitTraversal(); vtkSmartPointer ids = vtkSmartPointer::New(); typedef std::pair PointNormalPair; std::vector list; std::vector> pointsList; int count(0); for (existingPolys->InitTraversal(); existingPolys->GetNextCell(ids);) { // Get the points vtkSmartPointer points = vtkSmartPointer::New(); existingPoints->GetPoints(ids, points); ++count; pointsList.push_back(points); PointNormalPair p_n; double n[3]; vtkPolygon::ComputeNormal(points, n); p_n.first = n; double p[3]; existingPoints->GetPoint(ids->GetId(0), p); p_n.second = p; ContourPositionInformation p_info; p_info.contourNormal = n; p_info.contourPoint = p; list.push_back(p_info); continue; } // Detect and sort coplanar polygons auto outer = list.begin(); std::vector>> relatedPoints; while (outer != list.end()) { auto inner = outer; ++inner; std::vector> rel; auto pointsIter = pointsList.begin(); rel.push_back((*pointsIter)); pointsIter = pointsList.erase(pointsIter); while (inner != list.end()) { if (ContoursCoplanar((*outer), (*inner))) { inner = list.erase(inner); rel.push_back((*pointsIter)); pointsIter = pointsList.erase(pointsIter); } else { ++inner; ++pointsIter; } } relatedPoints.push_back(rel); ++outer; } // Build the separate surfaces again std::vector finalSurfaces; for (unsigned int i = 0; i < relatedPoints.size(); ++i) { vtkSmartPointer contourSurface = vtkSmartPointer::New(); vtkSmartPointer points = vtkSmartPointer::New(); vtkSmartPointer polygons = vtkSmartPointer::New(); unsigned int pointId(0); for (unsigned int j = 0; j < relatedPoints.at(i).size(); ++j) { unsigned int numPoints = relatedPoints.at(i).at(j)->GetNumberOfPoints(); vtkSmartPointer polygon = vtkSmartPointer::New(); polygon->GetPointIds()->SetNumberOfIds(numPoints); polygon->GetPoints()->SetNumberOfPoints(numPoints); vtkSmartPointer currentPoints = relatedPoints.at(i).at(j); for (unsigned k = 0; k < numPoints; ++k) { points->InsertPoint(pointId, currentPoints->GetPoint(k)); polygon->GetPointIds()->SetId(k, pointId); ++pointId; } polygons->InsertNextCell(polygon); } contourSurface->SetPoints(points); contourSurface->SetPolys(polygons); contourSurface->BuildLinks(); mitk::Surface::Pointer surface = mitk::Surface::New(); surface->SetVtkPolyData(contourSurface); finalSurfaces.push_back(surface); } // Add detected contours to interpolation pipeline this->AddNewContours(finalSurfaces); } void mitk::SurfaceInterpolationController::OnSegmentationDeleted(const itk::Object *caller, const itk::EventObject & /*event*/) { auto *tempImage = dynamic_cast(const_cast(caller)); if (tempImage) { if (m_SelectedSegmentation == tempImage) { m_NormalsFilter->SetSegmentationBinaryImage(nullptr); m_SelectedSegmentation = nullptr; } m_SegmentationObserverTags.erase(tempImage); m_ListOfInterpolationSessions.erase(tempImage); } } void mitk::SurfaceInterpolationController::ReinitializeInterpolation() { // If session has changed reset the pipeline m_ReduceFilter->Reset(); m_NormalsFilter->Reset(); m_InterpolateSurfaceFilter->Reset(); itk::ImageBase<3>::Pointer itkImage = itk::ImageBase<3>::New(); if (m_SelectedSegmentation) { if (!m_SelectedSegmentation->GetTimeGeometry()->IsValidTimePoint(m_CurrentTimePoint)) { MITK_WARN << "Interpolation cannot be reinitialized. Currently selected timepoint is not in the time bounds of the currently selected segmentation. Time point: " << m_CurrentTimePoint; return; } const auto currentTimeStep = m_SelectedSegmentation->GetTimeGeometry()->TimePointToTimeStep(m_CurrentTimePoint); mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(m_SelectedSegmentation); timeSelector->SetTimeNr(currentTimeStep); timeSelector->SetChannelNr(0); timeSelector->Update(); mitk::Image::Pointer refSegImage = timeSelector->GetOutput(); AccessFixedDimensionByItk_1(refSegImage, GetImageBase, 3, itkImage); m_InterpolateSurfaceFilter->SetReferenceImage(itkImage.GetPointer()); unsigned int numTimeSteps = m_SelectedSegmentation->GetTimeSteps(); unsigned int size = m_ListOfInterpolationSessions[m_SelectedSegmentation].size(); if (size != numTimeSteps) { m_ListOfInterpolationSessions[m_SelectedSegmentation].resize(numTimeSteps); } if (currentTimeStep < numTimeSteps) { unsigned int numContours = m_ListOfInterpolationSessions[m_SelectedSegmentation][currentTimeStep].size(); for (unsigned int c = 0; c < numContours; ++c) { m_ReduceFilter->SetInput(c, m_ListOfInterpolationSessions[m_SelectedSegmentation][currentTimeStep][c].contour); } m_ReduceFilter->Update(); m_CurrentNumberOfReducedContours = m_ReduceFilter->GetNumberOfOutputs(); if (m_CurrentNumberOfReducedContours == 1) { vtkPolyData *tmp = m_ReduceFilter->GetOutput(0)->GetVtkPolyData(); if (tmp == nullptr) { m_CurrentNumberOfReducedContours = 0; } } for (unsigned int i = 0; i < m_CurrentNumberOfReducedContours; i++) { m_NormalsFilter->SetInput(i, m_ReduceFilter->GetOutput(i)); m_InterpolateSurfaceFilter->SetInput(i, m_NormalsFilter->GetOutput(i)); } } Modified(); } } diff --git a/Modules/ToFHardware/PMD/mitkToFCameraPMDCamBoardController.h b/Modules/ToFHardware/PMD/mitkToFCameraPMDCamBoardController.h index 99902033e7..f8d6258c4b 100644 --- a/Modules/ToFHardware/PMD/mitkToFCameraPMDCamBoardController.h +++ b/Modules/ToFHardware/PMD/mitkToFCameraPMDCamBoardController.h @@ -1,95 +1,94 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 __mitkToFCameraPMDCamBoardController_h #define __mitkToFCameraPMDCamBoardController_h #include "MitkPMDExports.h" #include "mitkCommon.h" #include "mitkToFCameraPMDController.h" #include "itkObject.h" #include "itkObjectFactory.h" namespace mitk { /** * @brief Interface to the Time-of-Flight (ToF) camera PMD CamBoard * * * @ingroup ToFHardware */ class MITKPMD_EXPORT ToFCameraPMDCamBoardController : public ToFCameraPMDController { public: mitkClassMacro( ToFCameraPMDCamBoardController , ToFCameraPMDController ); itkFactorylessNewMacro(Self); itkCloneMacro(Self); /*! \brief opens a connection to the ToF camera and initializes the hardware specific members \return returns whether the connection was successful (true) or not (false) */ virtual bool OpenCameraConnection(); /*! \brief sets an additional distance offset which will be added to all distance values. \param offset offset in m */ bool SetDistanceOffset( float offset ); /*! \brief returns the currently applied distance offset in m - \param offset offset in m */ float GetDistanceOffset(); /*! \brief Setting the region of interest, the camera is configured to only output a certain area of the image. \param leftUpperCornerX x value of left upper corner of region \param leftUpperCornerY y value of left upper corner of region \param width width of region \param height height of region */ bool SetRegionOfInterest( unsigned int leftUpperCornerX, unsigned int leftUpperCornerY, unsigned int width, unsigned int height ); /*! \brief Setting the region of interest, the camera is configured to only output a certain area of the image. \param roi region of interest. roi[0]: x value of left upper corner, roi[1]: y value of left upper corner, roi[2]: width, roi[3]: height */ bool SetRegionOfInterest( unsigned int roi[4] ); /*! \brief returns the region of interest currently set \return currently set region of interest. */ unsigned int* GetRegionOfInterest(); /*! \brief Sets the field of view of the camera lens. \param fov field of view in degrees. The default value is 40 degrees. */ bool SetFieldOfView( float fov ); protected: ToFCameraPMDCamBoardController(); ~ToFCameraPMDCamBoardController(); /* \brief Transform the output of the camera, i.e. cut invalid pixels, and rotate 90 degrees counterclockwise \param input data array of original size (207x204) \param rotated output data array of reduced size (200x200) */ virtual void TransformCameraOutput(float* in, float* out, bool isDist); }; } //END mitk namespace #endif diff --git a/Modules/ToFHardware/PMD/mitkToFCameraPMDCamCubeController.h b/Modules/ToFHardware/PMD/mitkToFCameraPMDCamCubeController.h index b0c00d5d6a..6c83db4255 100644 --- a/Modules/ToFHardware/PMD/mitkToFCameraPMDCamCubeController.h +++ b/Modules/ToFHardware/PMD/mitkToFCameraPMDCamCubeController.h @@ -1,126 +1,125 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef __mitkToFCameraPMDCamCubeController_h #define __mitkToFCameraPMDCamCubeController_h #include #include "mitkCommon.h" #include "mitkToFCameraPMDController.h" #include "itkObject.h" #include "itkObjectFactory.h" namespace mitk { /** * @brief Interface to the Time-of-Flight (ToF) camera PMD CamCube * * * @ingroup ToFHardware */ class MITKPMD_EXPORT ToFCameraPMDCamCubeController : public ToFCameraPMDController { public: mitkClassMacro( ToFCameraPMDCamCubeController , ToFCameraPMDController ); itkFactorylessNewMacro(Self); itkCloneMacro(Self); /*! \brief opens a connection to the ToF camera and initializes the hardware specific members \return returns whether the connection was successful (true) or not (false) */ virtual bool OpenCameraConnection(); /*! \brief sets an additional distance offset which will be added to all distance values. \param offset offset in m \return returns whether set operation was successful (true) or not (false) */ bool SetDistanceOffset( float offset ); /*! \brief returns the currently applied distance offset in m - \param offset offset in m */ float GetDistanceOffset(); /*! \brief Setting the region of interest, the camera is configured to only output a certain area of the image. \param leftUpperCornerX x value of left upper corner of region \param leftUpperCornerY y value of left upper corner of region \param width width of region \param height height of region \return returns whether set operation was successful (true) or not (false) */ bool SetRegionOfInterest( unsigned int leftUpperCornerX, unsigned int leftUpperCornerY, unsigned int width, unsigned int height ); /*! \brief Setting the region of interest, the camera is configured to only output a certain area of the image. \param roi region of interest. roi[0]: x value of left upper corner, roi[1]: y value of left upper corner, roi[2]: width, roi[3]: height \return returns whether set operation was successful (true) or not (false) */ bool SetRegionOfInterest( unsigned int roi[4] ); /*! \brief returns the region of interest currently set \return currently set region of interest. */ unsigned int* GetRegionOfInterest(); /*! \brief sets the exposure mode of the CamCube \param mode exposure mode. 0: normal mode (one exposure), 1: Suppression of motion blur (SMB), minimizes the time needed to capture a distance image from the camera which results in a reduced amount of motion artifact but may lead to increased noise. \return returns whether set operation was successful (true) or not (false) */ bool SetExposureMode( int mode ); /*! \brief Sets the field of view of the camera lens. \param fov field of view in degrees. The default value is 40 degrees. \return returns whether set operation was successful (true) or not (false) */ bool SetFieldOfView( float fov ); /*! \brief Enable/Disable PMD fixed pattern noise (FPN) calibration \param on enabled (true), disabled (false) \return returns whether set operation was successful (true) or not (false) */ bool SetFPNCalibration( bool on ); /*! \brief Enable/Disable PMD fixed pattern phase noise (FPPN) calibration \param on enabled (true), disabled (false) \return returns whether set operation was successful (true) or not (false) */ bool SetFPPNCalibration( bool on ); /*! \brief Enable/Disable PMD linearity calibration \param on enabled (true), disabled (false) \return returns whether set operation was successful (true) or not (false) */ bool SetLinearityCalibration( bool on ); /*! \brief Enable/Disable PMD lens calibration \param on enabled (true), disabled (false) \return returns whether set operation was successful (true) or not (false) */ bool SetLensCalibration( bool on ); protected: virtual void TransformCameraOutput(float* in, float* out, bool isDist); ToFCameraPMDCamCubeController(); ~ToFCameraPMDCamCubeController(); private: }; } //END mitk namespace #endif diff --git a/Plugins/org.blueberry.core.commands/src/berryParameterizedCommand.h b/Plugins/org.blueberry.core.commands/src/berryParameterizedCommand.h index 1b4bc39516..acaf8bf4ff 100755 --- a/Plugins/org.blueberry.core.commands/src/berryParameterizedCommand.h +++ b/Plugins/org.blueberry.core.commands/src/berryParameterizedCommand.h @@ -1,334 +1,334 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef BERRYPARAMETERIZEDCOMMAND_H_ #define BERRYPARAMETERIZEDCOMMAND_H_ #include #include #include "common/berryCommandExceptions.h" #include #include #include namespace berry { struct IParameter; class Command; class Parameterization; /** *

* A command that has had one or more of its parameters specified. This class * serves as a utility class for developers that need to manipulate commands * with parameters. It handles the behaviour of generating a parameter map and a * human-readable name. *

*/ class BERRY_COMMANDS ParameterizedCommand: public Object { //implements Comparable { public: berryObjectMacro(ParameterizedCommand); /** * The index of the parameter id in the parameter values. * * @deprecated no longer used */ static const int INDEX_PARAMETER_ID; // = 0; /** * The index of the human-readable name of the parameter itself, in the * parameter values. * * @deprecated no longer used */ static const int INDEX_PARAMETER_NAME; // = 1; /** * The index of the human-readable name of the value of the parameter for * this command. * * @deprecated no longer used */ static const int INDEX_PARAMETER_VALUE_NAME; // = 2; /** * The index of the value of the parameter that the command can understand. * * @deprecated no longer used */ static const int INDEX_PARAMETER_VALUE_VALUE; // = 3; /** * Constructs a new instance of ParameterizedCommand with * specific values for zero or more of its parameters. * * @param command * The command that is parameterized; must not be * null. * @param parameterizations * An array of parameterizations binding parameters to values for * the command. This value may be null. */ ParameterizedCommand(const SmartPointer& command, const QList& parameterizations); bool operator<(const Object* object) const override; bool operator==(const Object* object) const override; /** * Executes this command with its parameters. This does extra checking to * see if the command is enabled and defined. If it is not both enabled and * defined, then the execution listeners will be notified and an exception * thrown. * * @param trigger * The object that triggered the execution; may be * null. * @param applicationContext * The state of the application at the time the execution was * triggered; may be null. * @return The result of the execution; may be null. * @throws ExecutionException * If the handler has problems executing this command. * @throws NotDefinedException * If the command you are trying to execute is not defined. * @throws NotEnabledException * If the command you are trying to execute is not enabled. * @throws NotHandledException * If there is no handler. */ Object::Pointer ExecuteWithChecks(const Object::ConstPointer& trigger, const Object::Pointer& applicationContext); /** * Returns the base command. It is possible for more than one parameterized * command to have the same identifier. * * @return The command; never null, but may be undefined. */ SmartPointer GetCommand() const; /** * Returns the command's base identifier. It is possible for more than one * parameterized command to have the same identifier. * * @return The command id; never null. */ QString GetId() const; /** * Returns a human-readable representation of this command with all of its * parameterizations. * * @return The human-readable representation of this parameterized command; * never null. * @throws NotDefinedException * If the underlying command is not defined. */ QString GetName() const; /** * Returns the parameter map, as can be used to construct an * ExecutionEvent. * * @return The map of parameter ids (String) to parameter * values (String). This map is never * null, but may be empty. */ QHash GetParameterMap() const; uint HashCode() const override; /** * Returns a \c String containing the command id, parameter ids and * parameter values for this \c ParameterizedCommand . The returned * \c String can be stored by a client and later used to reconstruct an * equivalent {@link ParameterizedCommand} using the * \c CommandManager.deserialize(String) method. *

* The syntax of the returned \c String is as follows: *

* *
- * serialization = commandId [ '(' parameters ')' ]
+ * serialization = commandId [ '(' parameters ')' ]
* parameters = parameter [ ',' parameters ]
- * parameter = parameterId [ '=' parameterValue ] + * parameter = parameterId [ '=' parameterValue ] *
* *

* In the syntax above, sections inside square-brackets are optional. The * characters in single quotes ((, ), * , and =) indicate literal characters. *

*

- * commandId represents the command id encoded with - * separator characters escaped. parameterId and - * parameterValue represent the parameter ids and + * commandId represents the command id encoded with + * separator characters escaped. parameterId and + * parameterValue represent the parameter ids and * values encoded with separator characters escaped. The separator * characters (, ), , and * = are escaped by prepending a %. This * requires % to be escaped, which is also done by prepending * a %. *

*

* The order of the parameters is not defined (and not important). A missing - * parameterValue indicates that the value of the + * parameterValue indicates that the value of the * parameter is null. *

*

* For example, the string shown below represents a serialized parameterized * command that can be used to show the Resource perspective: *

*

* org.eclipse.ui.perspectives.showPerspective(org.eclipse.ui.perspectives.showPerspective.perspectiveId=org.eclipse.ui.resourcePerspective) *

*

* This example shows the more general form with multiple parameters, * null value parameters, and escaped = in the * third parameter value. *

*

* command.id(param1.id=value1,param2.id,param3.id=esc%=val3) *

* * @return A string containing the escaped command id, parameter ids and * parameter values; never null. * @see CommandManager#deserialize(String) */ QString Serialize(); QString ToString() const override; /** *

* Generates all the possible combinations of command parameterizations for * the given command. If the command has no parameters, then this is simply * a parameterized version of that command. If a parameter is optional, both * the included and not included cases are considered. *

*

* If one of the parameters cannot be loaded due to a * ParameterValuesException, then it is simply ignored. *

* * @param command * The command for which the parameter combinations should be * generated; must not be null. * @return A collection of ParameterizedCommand instances * representing all of the possible combinations. This value is * never empty and it is never null. * @throws NotDefinedException * If the command is not defined. */ static QList GenerateCombinations(const SmartPointer command); /** * Take a command and a map of parameter IDs to values, and generate the * appropriate parameterized command. * * @param command * The command object. Must not be null. * @param parameters * A map of String parameter ids to objects. May be * null. * @return the parameterized command, or null if it could not * be generated */ static ParameterizedCommand::Pointer GenerateCommand(const SmartPointer command, const QHash& parameters); private: /** * The constant integer hash code value meaning the hash code has not yet * been computed. */ static const uint HASH_CODE_NOT_COMPUTED; // = 0; /** * A factor for computing the hash code for all parameterized commands. */ static const uint HASH_FACTOR; // = 89; /** * The seed for the hash code for all parameterized commands. */ static const uint HASH_INITIAL; /** * Escapes special characters in the command id, parameter ids and parameter * values for {@link #serialize()}. The special characters * {@link CommandManager#PARAMETER_START_CHAR}, * {@link CommandManager#PARAMETER_END_CHAR}, * {@link CommandManager#ID_VALUE_CHAR}, * {@link CommandManager#PARAMETER_SEPARATOR_CHAR} and * {@link CommandManager#ESCAPE_CHAR} are escaped by prepending a * {@link CommandManager#ESCAPE_CHAR} character. * * @param rawText * a String to escape special characters in for * serialization. * @return a String representing rawText with * special serialization characters escaped */ static QString Escape(const QString& rawText); /** * Generates every possible combination of parameter values for the given * parameters. Parameters values that cannot be initialized are just * ignored. Optional parameters are considered. * * @param startIndex * The index in the parameters that we should * process. This must be a valid index. * @param parameters * The parameters in to process; must not be null. * @return A collection (Collection) of combinations (List * of Parameterization). */ static QList > ExpandParameters(unsigned int startIndex, const QList >& parameters); /** * The base command which is being parameterized. This value is never * null. */ const SmartPointer command; /** * The hash code for this object. This value is computed lazily, and marked * as invalid when one of the values on which it is based changes. */ mutable uint hashCode; /** * This is an array of parameterization defined for this command. This value * may be null if the command has no parameters. */ QList parameterizations; mutable QString name; }; } #endif /* BERRYPARAMETERIZEDCOMMAND_H_ */ diff --git a/Plugins/org.blueberry.core.runtime/src/berryDebugUtil.cpp b/Plugins/org.blueberry.core.runtime/src/berryDebugUtil.cpp index f0802f513c..7490b5cb8a 100755 --- a/Plugins/org.blueberry.core.runtime/src/berryDebugUtil.cpp +++ b/Plugins/org.blueberry.core.runtime/src/berryDebugUtil.cpp @@ -1,537 +1,537 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "berryIDebugObjectListener.h" #include "berryDebugUtil.h" #include "berryObject.h" #include "berryLog.h" #include "berryPlatform.h" #include "berryDebugBreakpointManager.h" #include "internal/berryCTKPluginActivator.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace berry { static IDebugObjectListener::Events _G_ObjectEvents; const QString DebugUtil::DEBUG_UTIL_XML = "debugutil.xml"; const QString DebugUtil::DEBUGUTIL_TAG = "debugutil"; const QString DebugUtil::TRACEOBJECT_TAG = "traceObject"; const QString DebugUtil::TRACECLASS_TAG = "traceClass"; const QString DebugUtil::ID_ATTR = "id"; const QString DebugUtil::NAME_ATTR = "name"; QHash > DebugUtil::m_TraceIdToSmartPointerMap; QHash DebugUtil::m_TraceIdToObjectMap; QSet DebugUtil::m_TracedObjects; QSet DebugUtil::m_TracedClasses; class NotClassName: public std::unary_function { QString name; public: NotClassName(const QString& s) : name(s) { } bool operator()(const Object* entry) const { return name != entry->GetClassName(); } }; DebugBreakpointManager* DebugUtil::GetBreakpointManager() { static DebugBreakpointManager breakpointManager; return &breakpointManager; } #ifdef BLUEBERRY_DEBUG_SMARTPOINTER void DebugUtil::TraceObject(const Object* object) { BERRY_INFO << "Tracing enabled for: " << object->GetTraceId() << std::endl; m_TracedObjects.insert(object->GetTraceId()); _G_ObjectEvents.objTracingEvent(object->GetTraceId(), true, object); } #else void DebugUtil::TraceObject(const Object* /*object*/) { } #endif #ifdef BLUEBERRY_DEBUG_SMARTPOINTER void DebugUtil::TraceObject(unsigned int traceId) { BERRY_INFO << "Tracing enabled for: " << traceId << std::endl; m_TracedObjects.insert(traceId); TraceIdToObjectType::ConstIterator i = m_TraceIdToObjectMap.find(traceId); if (i != m_TraceIdToObjectMap.end()) _G_ObjectEvents.objTracingEvent(traceId, true, i.value()); else _G_ObjectEvents.objTracingEvent(traceId, true, 0); } #else void DebugUtil::TraceObject(unsigned int /*traceId*/) { } #endif #ifdef BLUEBERRY_DEBUG_SMARTPOINTER void DebugUtil::TraceClass(const QString& className) { BERRY_INFO << "Tracing enabled for: " << className << std::endl; m_TracedClasses.insert(className); //_G_ObjectEvents.objTracingEvent(object->GetTraceId(), true, object); } #else void DebugUtil::TraceClass(const QString& /*className*/) { } #endif #ifdef BLUEBERRY_DEBUG_SMARTPOINTER void DebugUtil::StopTracing(unsigned int traceId) { BERRY_INFO << "Tracing stopped for: " << traceId << std::endl; m_TracedObjects.remove(traceId); TraceIdToObjectType::ConstIterator i = m_TraceIdToObjectMap.find(traceId); if (i != m_TraceIdToObjectMap.end()) _G_ObjectEvents.objTracingEvent(traceId, false, i.value()); else _G_ObjectEvents.objTracingEvent(traceId, false, 0); } #else void DebugUtil::StopTracing(unsigned int /*traceId*/) { } #endif #ifdef BLUEBERRY_DEBUG_SMARTPOINTER void DebugUtil::StopTracing(const Object* obj) { BERRY_INFO << "Tracing stopped for: " << obj->GetTraceId() << std::endl; m_TracedObjects.remove(obj->GetTraceId()); _G_ObjectEvents.objTracingEvent(obj->GetTraceId(), false, obj); } #else void DebugUtil::StopTracing(const Object* /*obj*/) { } #endif #ifdef BLUEBERRY_DEBUG_SMARTPOINTER void DebugUtil::StopTracing(const QString& className) { BERRY_INFO << "Tracing stopped for: " << className << std::endl; m_TracedClasses.remove(className); //_G_ObjectEvents.objTracingEvent(obj->GetTraceId(), false, obj); } #else void DebugUtil::StopTracing(const QString& /*className*/) { } #endif #ifdef BLUEBERRY_DEBUG_SMARTPOINTER bool DebugUtil::IsTraced(const Object* object) { if (m_TracedObjects.find(object->GetTraceId()) != m_TracedObjects.end()) return true; if (m_TracedClasses.find(object->GetClassName()) != m_TracedClasses.end()) return true; return false; } #else bool DebugUtil::IsTraced(const Object* /*object*/) { return false; } #endif #ifdef BLUEBERRY_DEBUG_SMARTPOINTER bool DebugUtil::IsTraced(unsigned int traceId) { if (m_TracedObjects.find(traceId) != m_TracedObjects.end()) return true; TraceIdToObjectType::Iterator it = m_TraceIdToObjectMap.find(traceId); if (it != m_TraceIdToObjectMap.end()) { if (m_TracedClasses.find(it.value()->GetClassName()) != m_TracedClasses.end()) return true; } return false; } #else bool DebugUtil::IsTraced(unsigned int /*traceId*/) { return false; } #endif #ifdef BLUEBERRY_DEBUG_SMARTPOINTER bool DebugUtil::IsTraced(const QString& className) { return m_TracedClasses.find(className) != m_TracedClasses.end(); } #else bool DebugUtil::IsTraced(const QString& /*className*/) { return false; } #endif QSet DebugUtil::GetTracedObjects() { return m_TracedObjects; } const Object* DebugUtil::GetObject(unsigned int traceId) { return m_TraceIdToObjectMap[traceId]; } #ifdef BLUEBERRY_DEBUG_SMARTPOINTER QList DebugUtil::GetSmartPointerIDs( const Object* objectPointer, const QList& excludeList) { Q_ASSERT(objectPointer != 0); QList ids = m_TraceIdToSmartPointerMap[objectPointer->GetTraceId()]; for (QList::const_iterator iter = excludeList.begin(); iter != excludeList.end(); ++iter) ids.removeAll(*iter); return ids; } #else QList DebugUtil::GetSmartPointerIDs( const Object* /*objectPointer*/, const QList& /*excludeList*/) { return QList(); } #endif QList DebugUtil::GetRegisteredObjects() { return m_TraceIdToObjectMap.values(); } void DebugUtil::PrintSmartPointerIDs(const Object* objectPointer, const QList& excludeList) { qDebug() << "SmartPointer IDs [ "; if (IsTraced(objectPointer)) { QList ids = GetSmartPointerIDs(objectPointer, excludeList); for (QList::const_iterator iter = ids.begin(); iter != ids.end(); ++iter) { qDebug() << *iter << " "; } } else { qDebug() << "n/a "; } qDebug() << "]\n"; } void DebugUtil::AddObjectListener(IDebugObjectListener* listener) { _G_ObjectEvents.AddListener(listener); } void DebugUtil::RemoveObjectListener(IDebugObjectListener* listener) { _G_ObjectEvents.RemoveListener(listener); } void DebugUtil::ResetObjectSummary() { m_TraceIdToObjectMap.clear(); m_TraceIdToSmartPointerMap.clear(); m_TracedObjects.clear(); } bool DebugUtil::PrintObjectSummary(bool details) { QSet names; - for (auto object : m_TraceIdToObjectMap) + for (auto object : qAsConst(m_TraceIdToObjectMap)) names.insert(object->GetClassName()); if (!names.isEmpty()) { std::cout << std::endl << std::endl << "#########################################################" << std::endl; std::cout << "######## berry::Object leakage summary: ########" << std::endl << std::endl; for (QSet::const_iterator i = names.begin(); i != names.end(); ++i) { PrintObjectSummary(*i, details); if (details) std::cout << std::endl; } std::cout << std::endl << "#########################################################" << std::endl << std::endl; } return !names.isEmpty(); } bool DebugUtil::PrintObjectSummary(const QString& className, bool details) { TraceIdToObjectType::ConstIterator endIter = std::remove_if(m_TraceIdToObjectMap.begin(), m_TraceIdToObjectMap.end(), NotClassName(className)); qDebug() << "Class:" << className; if (details) std::cout << std::endl; std::size_t count = 0; for (TraceIdToObjectType::ConstIterator iter = m_TraceIdToObjectMap.begin(); iter != endIter; ++iter, ++count) { if (details) { qDebug() << (*(iter.value())); PrintSmartPointerIDs(iter.value()); } } qDebug() << "(" << count << " instances)\n"; return (count!=0); } unsigned int& DebugUtil::GetSmartPointerCounter() { static unsigned int counter = 0; return counter; } #ifdef BLUEBERRY_DEBUG_SMARTPOINTER void DebugUtil::UnregisterSmartPointer(unsigned int smartPointerId, const Object* objectPointer) { poco_assert(objectPointer != 0); m_TraceIdToSmartPointerMap[objectPointer->GetTraceId()].removeAll(smartPointerId); _G_ObjectEvents.spDestroyedEvent(smartPointerId, objectPointer); } #else void DebugUtil::UnregisterSmartPointer(unsigned int /*smartPointerId*/, const Object* /*objectPointer*/) { } #endif #ifdef BLUEBERRY_DEBUG_SMARTPOINTER void DebugUtil::RegisterSmartPointer(unsigned int smartPointerId, const Object* objectPointer, bool /*recordStack*/) { poco_assert(objectPointer != 0); if (m_TracedClasses.find(objectPointer->GetClassName()) != m_TracedClasses.end() || m_TracedObjects.find(objectPointer->GetTraceId()) != m_TracedObjects.end()) { m_TraceIdToSmartPointerMap[objectPointer->GetTraceId()].push_back(smartPointerId); _G_ObjectEvents.spCreatedEvent(smartPointerId, objectPointer); } if (GetBreakpointManager()->BreakAtSmartpointer(smartPointerId)) poco_debugger_msg("SmartPointer Breakpoint reached"); } #else void DebugUtil::RegisterSmartPointer(unsigned int /*smartPointerId*/, const Object* /*objectPointer*/, bool /*recordStack*/) { } #endif #ifdef BLUEBERRY_DEBUG_SMARTPOINTER void DebugUtil::RegisterObject(const Object* objectPointer) { m_TraceIdToObjectMap.insert(objectPointer->GetTraceId(), objectPointer); _G_ObjectEvents.objCreatedEvent(objectPointer); if (GetBreakpointManager()->BreakAtObject(objectPointer->GetTraceId())) { std::string msg = "SmartPointer Breakpoint reached for "; msg += objectPointer->GetClassName().toStdString(); poco_debugger_msg(msg.c_str()); } } #else void DebugUtil::RegisterObject(const Object* /*objectPointer*/) { } #endif #ifdef BLUEBERRY_DEBUG_SMARTPOINTER void DebugUtil::UnregisterObject(const Object* objectPointer) { m_TraceIdToObjectMap.remove(objectPointer->GetTraceId()); _G_ObjectEvents.objDestroyedEvent(objectPointer); } #else void DebugUtil::UnregisterObject(const Object* /*objectPointer*/) { } #endif bool DebugUtil::GetPersistencePath(QDir& path) { QFileInfo statePath = CTKPluginActivator::getPluginContext()->getDataFile(QString()); path = statePath.absoluteFilePath(); return true; } void DebugUtil::SaveState(const QDir& path) { QString saveFile = path.absoluteFilePath(DEBUG_UTIL_XML); auto doc = new Poco::XML::Document(); Poco::XML::Element* debugutil = doc->createElement(DEBUGUTIL_TAG.toStdString()); doc->appendChild(debugutil)->release(); for (QSet::const_iterator i = m_TracedObjects.begin(); i != m_TracedObjects.end(); ++i) { Poco::XML::Element* traceObject = doc->createElement(TRACEOBJECT_TAG.toStdString()); debugutil->appendChild(traceObject)->release(); traceObject->setAttribute(ID_ATTR.toStdString(), QString::number(*i).toStdString()); } for (QSet::const_iterator i = m_TracedClasses.begin(); i != m_TracedClasses.end(); ++i) { Poco::XML::Element* traceClass = doc->createElement(TRACECLASS_TAG.toStdString()); debugutil->appendChild(traceClass)->release(); traceClass->setAttribute(NAME_ATTR.toStdString(), i->toStdString()); } try { Poco::FileOutputStream writer(saveFile.toStdString()); Poco::XML::DOMWriter out; out.setOptions(3); //write declaration and pretty print out.writeNode(writer, doc); doc->release(); // save BreakpointManager QString saveBM = path.absoluteFilePath(QString::fromStdString(DebugBreakpointManager::BREAKPOINTS_XML)); GetBreakpointManager()->SaveState(saveBM); } catch (Poco::FileException& e) { BERRY_WARN << e.displayText(); } } void DebugUtil::RestoreState(const QDir& path) { QString restoreFile = path.absoluteFilePath(DEBUG_UTIL_XML); try { Poco::XML::DOMParser parser; Poco::FileInputStream reader(restoreFile.toStdString()); Poco::XML::InputSource source(reader); //source.setSystemId(baseDir); Poco::XML::Document* doc = parser.parse(&source); Poco::XML::Element* debugutil = doc->documentElement(); if (debugutil) { // restore traced objects Poco::XML::NodeList* elementList = debugutil->getElementsByTagName(TRACEOBJECT_TAG.toStdString()); for (std::size_t i = 0; i < elementList->length(); i++) { Poco::XML::Element* elem = dynamic_cast (elementList->item(static_cast(i))); if (!elem->hasAttribute(ID_ATTR.toStdString())) continue; const std::string& attr = elem->getAttribute(ID_ATTR.toStdString()); int traceId = 0; try { traceId = Poco::NumberParser::parse(attr); } catch (const Poco::SyntaxException& e) { BERRY_WARN << e.displayText(); } DebugUtil::TraceObject(traceId); } elementList->release(); // restore traced classes elementList = debugutil->getElementsByTagName(TRACECLASS_TAG.toStdString()); for (std::size_t i = 0; i < elementList->length(); i++) { Poco::XML::Element* elem = dynamic_cast (elementList->item(static_cast(i))); if (!elem->hasAttribute(NAME_ATTR.toStdString())) continue; const std::string& traceClass = elem->getAttribute(NAME_ATTR.toStdString()); if (!traceClass.empty()) DebugUtil::TraceClass(QString::fromStdString(traceClass)); } elementList->release(); } doc->release(); } catch (Poco::XML::SAXParseException& e) { BERRY_WARN << e.displayText(); } catch (Poco::FileNotFoundException&) { } catch (Poco::FileException& e) { BERRY_WARN << e.displayText(); } // restore BreakpointManager GetBreakpointManager()->RestoreState(path.absoluteFilePath(QString::fromStdString(DebugBreakpointManager::BREAKPOINTS_XML))); } } diff --git a/Plugins/org.blueberry.core.runtime/src/internal/berryApplicationContainer.cpp b/Plugins/org.blueberry.core.runtime/src/internal/berryApplicationContainer.cpp index 62a92d5cf4..3d58e4de79 100644 --- a/Plugins/org.blueberry.core.runtime/src/internal/berryApplicationContainer.cpp +++ b/Plugins/org.blueberry.core.runtime/src/internal/berryApplicationContainer.cpp @@ -1,718 +1,718 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "berryApplicationContainer.h" #include #include #include #include #include #include #include #include "berryApplicationHandle.h" #include "berryApplicationDescriptor.h" #include "berryCoreException.h" #include "berryErrorApplication.h" #include "berryMainApplicationLauncher.h" #include "berryProductExtensionBranding.h" #include "berryProviderExtensionBranding.h" #include #include "berryCTKPluginActivator.h" #include #include namespace berry { static const QString PI_OSGI = "org.blueberry.osgi"; const QString ApplicationContainer::PI_RUNTIME = "org.blueberry.core.runtime"; const QString ApplicationContainer::PT_APPLICATIONS = "applications"; const QString ApplicationContainer::PT_APP_VISIBLE = "visible"; const QString ApplicationContainer::PT_APP_THREAD = "thread"; const QString ApplicationContainer::PT_APP_THREAD_ANY = "any"; const QString ApplicationContainer::PT_APP_CARDINALITY = "cardinality"; const QString ApplicationContainer::PT_APP_CARDINALITY_SINGLETON_GLOBAL = "singleton-global"; const QString ApplicationContainer::PT_APP_CARDINALITY_SINGLETON_SCOPED = "singleton-scoped"; const QString ApplicationContainer::PT_APP_CARDINALITY_UNLIMITED = "*"; const QString ApplicationContainer::PT_APP_ICON = "icon"; const QString ApplicationContainer::PT_PRODUCTS = "products"; const QString ApplicationContainer::EXT_ERROR_APP = "org.blueberry.core.runtime.app.error"; const QString ApplicationContainer::PROP_PRODUCT = "blueberry.product"; const QString ApplicationContainer::PROP_BLUEBERRY_APPLICATION = "blueberry.application"; const QString ApplicationContainer::PROP_BLUEBERRY_APPLICATION_LAUNCH_DEFAULT = "blueberry.application.launchDefault"; const int ApplicationContainer::NOT_LOCKED = 0; const int ApplicationContainer::LOCKED_SINGLETON_GLOBAL_RUNNING = 1; const int ApplicationContainer::LOCKED_SINGLETON_GLOBAL_APPS_RUNNING = 2; const int ApplicationContainer::LOCKED_SINGLETON_SCOPED_RUNNING = 3; const int ApplicationContainer::LOCKED_SINGLETON_LIMITED_RUNNING = 4; const int ApplicationContainer::LOCKED_MAIN_THREAD_RUNNING = 5; ApplicationContainer::ApplicationContainer(ctkPluginContext* context, IExtensionRegistry* extensionRegistry) : context(context) , extensionRegistry(extensionRegistry) , launcherTracker(new ctkServiceTracker(context, this)) , branding(nullptr) , missingProductReported(false) , defaultMainThreadAppHandle(nullptr) , missingApp(false) { } ApplicationContainer::~ApplicationContainer() { } void ApplicationContainer::Start() { launcherTracker->open(); extensionRegistry->AddListener(this, PI_OSGI + '.' + PT_APPLICATIONS); // need to listen for system bundle stopping context->connectPluginListener(this, SLOT(PluginChanged(ctkPluginEvent)), Qt::DirectConnection); // register all the descriptors RegisterAppDescriptors(); QVariant startDefaultProp = context->getProperty(ApplicationContainer::PROP_BLUEBERRY_APPLICATION_LAUNCH_DEFAULT); if (startDefaultProp.isNull() || startDefaultProp.toBool()) { // Start the default application try { StartDefaultApp(true); } catch (const ctkApplicationException& e) { BERRY_ERROR << "An error occurred while starting the application:" << e.message(); } } } void ApplicationContainer::Stop() { // stop all applications StopAllApps(); context->disconnectPluginListener(this); extensionRegistry->RemoveListener(this); // flush the apps apps.clear(); branding.reset(); missingProductReported = false; launcherTracker->close(); } IBranding* ApplicationContainer::GetBranding() const { if (branding) { return branding.data(); } // try pluginContext properties if (context == nullptr) return nullptr; QString productId = context->getProperty(PROP_PRODUCT).toString(); if (productId.isEmpty()) return nullptr; QList entries = extensionRegistry->GetConfigurationElementsFor(PI_RUNTIME, PT_PRODUCTS, productId); if (!entries.isEmpty()) { // There should only be one product with the given id so just take the first element branding.reset(new ProductExtensionBranding(productId, entries[0])); return branding.data(); } QList elements = extensionRegistry->GetConfigurationElementsFor(PI_RUNTIME, PT_PRODUCTS); - for (auto element : elements) + for (const auto &element : qAsConst(elements)) { if (element->GetName().compare("provider", Qt::CaseInsensitive) == 0) { try { IProductProvider* provider = element->CreateExecutableExtension("run"); QList products = provider->GetProducts(); - for (auto product : products) + for (const auto &product : qAsConst(products)) { if (productId.compare(product->GetId(), Qt::CaseInsensitive) == 0) { branding.reset(new ProviderExtensionBranding(product)); return branding.data(); } } } catch (const CoreException&) { BERRY_WARN << "Problem creating the provider registered by " << element->GetParent()->ToString() << "."; } } } if (!missingProductReported) { BERRY_WARN << "Product " << productId << " could not be found."; missingProductReported = true; } return nullptr; } ctkPluginContext* ApplicationContainer::GetContext() const { return context; } ApplicationDescriptor* ApplicationContainer::GetAppDescriptor(const QString& applicationId) { ApplicationDescriptor* result = nullptr; { QMutexLocker l(&lock); auto iter = apps.find(applicationId); result = iter == apps.end() ? nullptr : iter.value(); } if (result == nullptr) { RegisterAppDescriptor(applicationId); // try again just in case we are waiting for an event { QMutexLocker l(&lock); auto iter = apps.find(applicationId); result = iter == apps.end() ? nullptr : iter.value(); } } return result; } ApplicationDescriptor* ApplicationContainer::CreateAppDescriptor(const SmartPointer& appExtension) { if (org_blueberry_core_runtime_Activator::DEBUG) { BERRY_INFO << "Creating application descriptor: " << appExtension->GetUniqueIdentifier(); } QString iconPath; { QMutexLocker l(&lock); auto iter = apps.find(appExtension->GetUniqueIdentifier()); ApplicationDescriptor* appDescriptor = iter == apps.end() ? nullptr : iter.value(); if (appDescriptor != nullptr) { return appDescriptor; } // the appDescriptor does not exist for the app ID; create it QList configs = appExtension->GetConfigurationElements(); ApplicationDescriptor::Flags flags = ApplicationDescriptor::FLAG_CARD_SINGLETON_GLOGAL | ApplicationDescriptor::FLAG_VISIBLE | ApplicationDescriptor::FLAG_TYPE_MAIN_THREAD; int cardinality = 0; if (!configs.isEmpty()) { QString sVisible = configs[0]->GetAttribute(PT_APP_VISIBLE); if (!sVisible.isEmpty() && sVisible.compare("true", Qt::CaseInsensitive) != 0) { flags &= ~(ApplicationDescriptor::FLAG_VISIBLE); } QString sThread = configs[0]->GetAttribute(PT_APP_THREAD); if (PT_APP_THREAD_ANY == sThread) { flags |= ApplicationDescriptor::FLAG_TYPE_ANY_THREAD; flags &= ~(ApplicationDescriptor::FLAG_TYPE_MAIN_THREAD); } QString sCardinality = configs[0]->GetAttribute(PT_APP_CARDINALITY); if (!sCardinality.isEmpty()) { flags &= ~(ApplicationDescriptor::FLAG_CARD_SINGLETON_GLOGAL); // clear the global bit if (PT_APP_CARDINALITY_SINGLETON_SCOPED == sCardinality) { flags |= ApplicationDescriptor::FLAG_CARD_SINGLETON_SCOPED; } else if (PT_APP_CARDINALITY_UNLIMITED == sCardinality) { flags |= ApplicationDescriptor::FLAG_CARD_UNLIMITED; } else if (PT_APP_CARDINALITY_SINGLETON_GLOBAL == sCardinality) { flags |= ApplicationDescriptor::FLAG_CARD_SINGLETON_GLOGAL; } else { bool okay = false; cardinality = sCardinality.toInt(&okay); if (okay) { flags |= ApplicationDescriptor::FLAG_CARD_LIMITED; } else { // TODO should we log this? // just fall back to the default flags |= ApplicationDescriptor::FLAG_CARD_SINGLETON_GLOGAL; } } } QString defaultApp = GetDefaultAppId(); QString appId = appExtension->GetUniqueIdentifier(); if (defaultApp == appId) { flags |= ApplicationDescriptor::FLAG_DEFAULT_APP; } iconPath = configs[0]->GetAttribute(PT_APP_ICON); } appDescriptor = new ApplicationDescriptor(org_blueberry_core_runtime_Activator::GetPlugin(appExtension->GetContributor()), appExtension->GetUniqueIdentifier(), appExtension->GetLabel(), iconPath, flags, cardinality, this); // register the appDescriptor as a service ctkServiceRegistration sr = context->registerService(appDescriptor, appDescriptor->GetServiceProperties()); appDescriptor->SetServiceRegistration(sr); // save the app descriptor in the cache apps.insert(appExtension->GetUniqueIdentifier(), appDescriptor); return appDescriptor; } } ApplicationDescriptor*ApplicationContainer::RemoveAppDescriptor(const QString& applicationId) { if (org_blueberry_core_runtime_Activator::DEBUG) { BERRY_INFO << "Removing application descriptor: " << applicationId; } { QMutexLocker l(&lock); ApplicationDescriptor* appDescriptor = apps.take(applicationId); if (appDescriptor == nullptr) { return nullptr; } appDescriptor->Unregister(); return appDescriptor; } } void ApplicationContainer::StartDefaultApp(bool delayError) { // find the default application QString applicationId = GetDefaultAppId(); ApplicationDescriptor* defaultDesc = nullptr; QHash args; args.insert(ApplicationDescriptor::APP_DEFAULT, true); if (applicationId.isEmpty() && !delayError) { // the application id is not set; use a descriptor that will throw an exception args.insert(ErrorApplication::ERROR_EXCEPTION, QString("No application id has been found.")); defaultDesc = GetAppDescriptor(EXT_ERROR_APP); } else { defaultDesc = GetAppDescriptor(applicationId); if (defaultDesc == nullptr && !delayError) { // the application id is not available in the registry; use a descriptor that will throw an exception args.insert(ErrorApplication::ERROR_EXCEPTION, QString("Application \"%1\" could not be found in the registry. The applications available are: %2.") .arg(applicationId) .arg(GetAvailableAppsMsg())); defaultDesc = GetAppDescriptor(EXT_ERROR_APP); } } if (delayError && defaultDesc == nullptr) { // could not find the application; but we want to delay the error. // another bundle may get installed that provides the application // before we actually try to launch it. missingApp = true; return; } if (defaultDesc != nullptr) { defaultDesc->launch(args); } else { throw ctkApplicationException(ctkApplicationException::APPLICATION_INTERNAL_ERROR, "No application id has been found."); } } void ApplicationContainer::RegisterAppDescriptors() { QList availableApps = GetAvailableAppExtensions(); for (int i = 0; i < availableApps.size(); i++) { CreateAppDescriptor(availableApps[i]); } } void ApplicationContainer::RegisterAppDescriptor(const QString& applicationId) { IExtension::Pointer appExtension = GetAppExtension(applicationId); if (appExtension.IsNotNull()) { CreateAppDescriptor(appExtension); } } QList > ApplicationContainer::GetAvailableAppExtensions() const { IExtensionPoint::Pointer point = extensionRegistry->GetExtensionPoint(PI_OSGI + '.' + PT_APPLICATIONS); if (point.IsNull()) { return QList(); } return point->GetExtensions(); } QString ApplicationContainer::GetAvailableAppsMsg() const { QList availableApps = GetAvailableAppExtensions(); QString availableAppsMsg = ""; if (!availableApps.isEmpty()) { availableAppsMsg = availableApps.front()->GetUniqueIdentifier(); - for (auto availableApp : availableApps) + for (const auto &availableApp : qAsConst(availableApps)) { availableAppsMsg = availableAppsMsg + ", " + availableApp->GetUniqueIdentifier(); } } return availableAppsMsg; } SmartPointer ApplicationContainer::GetAppExtension(const QString& applicationId) const { return extensionRegistry->GetExtension(PI_OSGI, PT_APPLICATIONS, applicationId); } void ApplicationContainer::Launch(ApplicationHandle* appHandle) { bool isDefault = appHandle->IsDefault(); if (appHandle->getApplicationDescriptor()->GetThreadType() == ApplicationDescriptor::FLAG_TYPE_MAIN_THREAD) { // use the ApplicationLauncher provided by the framework to ensure it is launched on the main thread //DefaultApplicationListener curDefaultApplicationListener = null; MainApplicationLauncher* curMissingAppLauncher = nullptr; ctkApplicationLauncher* appLauncher = nullptr; { QMutexLocker l(this); appLauncher = launcherTracker->getService(); if (appLauncher == nullptr) { if (isDefault) { // we need to wait to allow the ApplicationLauncher to get registered; // save the handle to be launched as soon as the ApplicationLauncher is available defaultMainThreadAppHandle = appHandle; return; } throw ctkApplicationException(ctkApplicationException::APPLICATION_INTERNAL_ERROR, QString("The main thread is not available to launch the application: %1").arg(appHandle->getInstanceId())); } //curDefaultApplicationListener = defaultAppListener; curMissingAppLauncher = missingAppLauncher.data(); } //if (curDefaultApplicationListener != nullptr) //{ // curDefaultApplicationListener->launch(appHandle); //} //else if (curMissingAppLauncher != nullptr) { curMissingAppLauncher->Launch(appHandle); } else { appLauncher->launch(appHandle, appHandle->GetArguments()[IApplicationContext::APPLICATION_ARGS]); } } else { if (isDefault) { //DefaultApplicationListener curDefaultApplicationListener = null; MainApplicationLauncher* curMissingAppLauncher = nullptr; ctkApplicationLauncher* appLauncher = nullptr; { QMutexLocker l(this); appLauncher = launcherTracker->getService(); //if (defaultAppListener == nullptr) //{ // defaultAppListener = new DefaultApplicationListener(appHandle); //} //curDefaultApplicationListener = defaultAppListener; if (appLauncher == nullptr) { // we need to wait to allow the ApplicationLauncher to get registered; // save the default app listener to be launched as soon as the ApplicationLauncher is available //defaultMainThreadAppHandle = curDefaultApplicationListener; return; } curMissingAppLauncher = missingAppLauncher.data(); } if (curMissingAppLauncher != nullptr) { //curMissingAppLauncher->Launch(curDefaultApplicationListener); } else { //appLauncher->Launch(curDefaultApplicationListener, QVariant()); } } else { //AnyThreadAppLauncher.launchEclipseApplication(appHandle); } } } void ApplicationContainer::PluginChanged(const ctkPluginEvent& event) { // if this is not the system bundle stopping then ignore the event if ((ctkPluginEvent::STOPPING & event.getType()) == 0 || event.getPlugin()->getPluginId() != 0) { return; } // The system bundle is stopping; better stop all applications and containers now StopAllApps(); } void ApplicationContainer::StopAllApps() { // get a stapshot of running applications QList runningRefs = context->getServiceReferences("(!(application.state=STOPPING))"); - for (auto runningRef : runningRefs) + for (const auto &runningRef : qAsConst(runningRefs)) { ctkApplicationHandle* handle = context->getService(runningRef); try { if (handle != nullptr) { handle->destroy(); } } catch (const std::exception&) { BERRY_WARN << QString("An error occurred while stopping the application: %1").arg(handle->getInstanceId()); } if (handle != nullptr) { context->ungetService(runningRef); } } } QString ApplicationContainer::GetDefaultAppId() const { if (!defaultAppId.isNull()) { return defaultAppId; } // try plugin context properties defaultAppId = context->getProperty(ApplicationContainer::PROP_BLUEBERRY_APPLICATION).toString(); if (!defaultAppId.isEmpty()) { return defaultAppId; } //Derive the application from the product information defaultAppId = GetBranding() == nullptr ? QString("") : GetBranding()->GetApplication(); return defaultAppId; } void ApplicationContainer::Lock(ApplicationHandle* /*appHandle*/) { /* ApplicationDescriptor eclipseApp = (ApplicationDescriptor) appHandle.getApplicationDescriptor(); { QMutexLocker l(&lock); switch (isLocked(eclipseApp)) { case NOT_LOCKED : break; case LOCKED_SINGLETON_GLOBAL_RUNNING : throw new ApplicationException(ApplicationException.APPLICATION_NOT_LAUNCHABLE, NLS.bind(Messages.singleton_running, activeGlobalSingleton.getInstanceId())); case LOCKED_SINGLETON_GLOBAL_APPS_RUNNING : throw new ApplicationException(ApplicationException.APPLICATION_NOT_LAUNCHABLE, Messages.apps_running); case LOCKED_SINGLETON_SCOPED_RUNNING : throw new ApplicationException(ApplicationException.APPLICATION_NOT_LAUNCHABLE, NLS.bind(Messages.singleton_running, activeScopedSingleton.getInstanceId())); case LOCKED_SINGLETON_LIMITED_RUNNING : throw new ApplicationException(ApplicationException.APPLICATION_NOT_LAUNCHABLE, NLS.bind(Messages.max_running, eclipseApp.getApplicationId())); case LOCKED_MAIN_THREAD_RUNNING : throw new ApplicationException(ApplicationException.APPLICATION_NOT_LAUNCHABLE, NLS.bind(Messages.main_running, activeMain.getInstanceId())); default : break; } // ok we can now successfully lock the container switch (eclipseApp.getCardinalityType()) { case ApplicationDescriptor::FLAG_CARD_SINGLETON_GLOGAL : activeGlobalSingleton = appHandle; break; case ApplicationDescriptor::FLAG_CARD_SINGLETON_SCOPED : activeScopedSingleton = appHandle; break; case ApplicationDescriptor::FLAG_CARD_LIMITED : if (activeLimited == null) activeLimited = new HashMap(3); ArrayList limited = (ArrayList) activeLimited.get(eclipseApp.getApplicationId()); if (limited == null) { limited = new ArrayList(eclipseApp.getCardinality()); activeLimited.put(eclipseApp.getApplicationId(), limited); } limited.add(appHandle); break; case ApplicationDescriptor::FLAG_CARD_UNLIMITED : break; default : break; } if (eclipseApp.getThreadType() == ApplicationDescriptor::FLAG_TYPE_MAIN_THREAD) { activeMain = appHandle; } activeHandles.add(appHandle); refreshAppDescriptors(); } */ } void ApplicationContainer::Unlock(ApplicationHandle* /*appHandle*/) { /* QMutexLocker l(&lock); if (activeGlobalSingleton == appHandle) activeGlobalSingleton = null; else if (activeScopedSingleton == appHandle) activeScopedSingleton = null; else if (((ApplicationDescriptor) appHandle.getApplicationDescriptor()).getCardinalityType() == ApplicationDescriptor::FLAG_CARD_LIMITED) { if (activeLimited != null) { ArrayList limited = (ArrayList) activeLimited.get(((ApplicationDescriptor) appHandle.getApplicationDescriptor()).getApplicationId()); if (limited != null) limited.remove(appHandle); } } if (activeMain == appHandle) activeMain = null; if (activeHandles.remove(appHandle)) refreshAppDescriptors(); // only refresh descriptors if we really unlocked something */ } int ApplicationContainer::IsLocked(const ApplicationDescriptor* /*eclipseApp*/) const { /* { QMutexLocker l(&lock); if (activeGlobalSingleton != null) return LOCKED_SINGLETON_GLOBAL_RUNNING; switch (eclipseApp.getCardinalityType()) { case ApplicationDescriptor::FLAG_CARD_SINGLETON_GLOGAL : if (activeHandles.size() > 0) return LOCKED_SINGLETON_GLOBAL_APPS_RUNNING; break; case ApplicationDescriptor::FLAG_CARD_SINGLETON_SCOPED : if (activeScopedSingleton != null) return LOCKED_SINGLETON_SCOPED_RUNNING; break; case ApplicationDescriptor::FLAG_CARD_LIMITED : if (activeLimited != null) { ArrayList limited = (ArrayList) activeLimited.get(eclipseApp.getApplicationId()); if (limited != null && limited.size() >= eclipseApp.getCardinality()) return LOCKED_SINGLETON_LIMITED_RUNNING; } break; case ApplicationDescriptor::FLAG_CARD_UNLIMITED : break; default : break; } if (eclipseApp.getThreadType() == ApplicationDescriptor::FLAG_TYPE_MAIN_THREAD && activeMain != null) return LOCKED_MAIN_THREAD_RUNNING; return NOT_LOCKED; } */ return NOT_LOCKED; } ctkApplicationLauncher* ApplicationContainer::addingService(const ctkServiceReference& reference) { ctkApplicationLauncher* appLauncher = nullptr; ctkApplicationRunnable* appRunnable = nullptr; { QMutexLocker l(this); appLauncher = context->getService(reference); // see if there is a default main threaded application waiting to run appRunnable = defaultMainThreadAppHandle; // null out so we do not attempt to start this handle again defaultMainThreadAppHandle = nullptr; if (appRunnable == nullptr && missingApp) { missingAppLauncher.reset(new MainApplicationLauncher(this)); appRunnable = missingAppLauncher.data(); missingApp = false; } } if (appRunnable != nullptr) { // found a main threaded app; start it now that the app launcher is available ApplicationHandle* handle = dynamic_cast(appRunnable); appLauncher->launch(appRunnable, handle ? handle->GetArguments()[IApplicationContext::APPLICATION_ARGS] : QVariant()); } return appLauncher; } void ApplicationContainer::modifiedService(const ctkServiceReference& /*reference*/, ctkApplicationLauncher* /*service*/) { // Do nothing } void ApplicationContainer::removedService(const ctkServiceReference& /*reference*/, ctkApplicationLauncher* /*service*/) { // Do nothing } void ApplicationContainer::Added(const QList >& extensions) { - for (IExtension::Pointer extension : extensions) + for (const IExtension::Pointer &extension : extensions) { CreateAppDescriptor(extension); } } void ApplicationContainer::Added(const QList >& /*extensionPoints*/) { // nothing } void ApplicationContainer::Removed(const QList >& extensions) { - for (IExtension::Pointer extension : extensions) + for (const IExtension::Pointer &extension : extensions) { RemoveAppDescriptor(extension->GetUniqueIdentifier()); } } void ApplicationContainer::Removed(const QList >& /*extensionPoints*/) { // nothing } void ApplicationContainer::RefreshAppDescriptors() { QMutexLocker l(&lock); for (ApplicationDescriptor* app : apps.values()) { app->RefreshProperties(); } } } diff --git a/Plugins/org.blueberry.core.runtime/src/internal/berryCTKPluginActivator.cpp b/Plugins/org.blueberry.core.runtime/src/internal/berryCTKPluginActivator.cpp index 54b412b2b2..1db15fcebf 100755 --- a/Plugins/org.blueberry.core.runtime/src/internal/berryCTKPluginActivator.cpp +++ b/Plugins/org.blueberry.core.runtime/src/internal/berryCTKPluginActivator.cpp @@ -1,293 +1,293 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 NOMINMAX #define NOMINMAX #endif #include "berryCTKPluginActivator.h" #include #include #include #include "berryApplicationContainer.h" #include "berryPlatform.h" #include "berryInternalPlatform.h" #include "berryErrorApplication.h" #include "berryPreferencesService.h" #include "berryExtensionRegistry.h" #include "berryRegistryConstants.h" #include "berryRegistryProperties.h" #include "berryRegistryStrategy.h" #include "berryRegistryContributor.h" #include #include namespace berry { static const QString XP_APPLICATIONS = "org.blueberry.osgi.applications"; ctkPluginContext* org_blueberry_core_runtime_Activator::context = nullptr; QScopedPointer org_blueberry_core_runtime_Activator::appContainer; const bool org_blueberry_core_runtime_Activator::DEBUG = false; void org_blueberry_core_runtime_Activator::start(ctkPluginContext* context) { this->context = context; BERRY_REGISTER_EXTENSION_CLASS(ErrorApplication, context) RegistryProperties::SetContext(context); //ProcessCommandLine(); this->startRegistry(); preferencesService.reset(new PreferencesService(context->getDataFile("").absolutePath())); prefServiceReg = context->registerService(preferencesService.data()); // // register a listener to catch new plugin installations/resolutions. // pluginListener.reset(new CTKPluginListener(m_ExtensionPointService)); // context->connectPluginListener(pluginListener.data(), SLOT(pluginChanged(ctkPluginEvent)), Qt::DirectConnection); // // populate the registry with all the currently installed plugins. // // There is a small window here while processPlugins is being // // called where the pluginListener may receive a ctkPluginEvent // // to add/remove a plugin from the registry. This is ok since // // the registry is a synchronized object and will not add the // // same bundle twice. // pluginListener->processPlugins(context->getPlugins()); this->startAppContainer(); InternalPlatform::GetInstance()->Start(context); } void org_blueberry_core_runtime_Activator::stop(ctkPluginContext* context) { InternalPlatform::GetInstance()->Stop(context); //pluginListener.reset(); //Platform::GetServiceRegistry().UnRegisterService(IExtensionPointService::SERVICE_ID); prefServiceReg.unregister(); preferencesService->ShutDown(); preferencesService.reset(); prefServiceReg = 0; this->stopRegistry(); RegistryProperties::SetContext(nullptr); stopAppContainer(); this->context = nullptr; } ctkPluginContext* org_blueberry_core_runtime_Activator::getPluginContext() { return context; } ApplicationContainer* org_blueberry_core_runtime_Activator::GetContainer() { return appContainer.data(); } #if defined(Q_OS_LINUX) || defined(Q_OS_DARWIN) #include QString org_blueberry_core_runtime_Activator::getPluginId(void *symbol) { if (symbol == nullptr) return QString(); Dl_info info = {nullptr,nullptr,nullptr,nullptr}; if(dladdr(symbol, &info) == 0) { return QString(); } else if(info.dli_fname) { QFile soPath(info.dli_fname); int index = soPath.fileName().lastIndexOf('.'); QString pluginId = soPath.fileName().left(index); if (pluginId.startsWith("lib")) pluginId = pluginId.mid(3); return pluginId.replace('_', '.'); } return QString(); } #elif defined(Q_CC_MSVC) #include #include #ifdef _MSC_VER # pragma warning(push) # pragma warning(disable: 4091) #endif #include #ifdef _MSC_VER # pragma warning(pop) #endif QString org_blueberry_core_runtime_Activator::getPluginId(void *symbol) { if (symbol == nullptr) return QString(); if (ctk::DebugSymInitialize()) { std::vector moduleBuffer(sizeof(IMAGEHLP_MODULE64)); PIMAGEHLP_MODULE64 pModuleInfo = (PIMAGEHLP_MODULE64)&moduleBuffer.front(); pModuleInfo->SizeOfStruct = sizeof(IMAGEHLP_MODULE64); if (SymGetModuleInfo64(GetCurrentProcess(), (DWORD64)symbol, pModuleInfo)) { QString pluginId = pModuleInfo->ModuleName; return pluginId.replace('_', '.'); } } return QString(); } #endif QSharedPointer org_blueberry_core_runtime_Activator::GetPlugin(const SmartPointer& contributor) { if (RegistryContributor::Pointer regContributor = contributor.Cast()) { bool okay = false; long id = regContributor->GetActualId().toLong(&okay); if (okay) { if (context != nullptr) { return context->getPlugin(id); } } else { // try using the name of the contributor below } } auto plugins = context->getPlugins(); //Return the first plugin that is not installed or uninstalled - for (auto plugin : plugins) + for (auto plugin : qAsConst(plugins)) { if (!(plugin->getState() == ctkPlugin::INSTALLED || plugin->getState() == ctkPlugin::UNINSTALLED)) { return plugin; } } return QSharedPointer(); } org_blueberry_core_runtime_Activator::org_blueberry_core_runtime_Activator() : userRegistryKey(new QObject()) , masterRegistryKey(new QObject()) { } org_blueberry_core_runtime_Activator::~org_blueberry_core_runtime_Activator() { } void org_blueberry_core_runtime_Activator::startRegistry() { // see if the customer suppressed the creation of default registry QString property = context->getProperty(RegistryConstants::PROP_DEFAULT_REGISTRY).toString(); if (property.compare("false", Qt::CaseInsensitive) == 0) return; // check to see if we need to use null as a userToken if (context->getProperty(RegistryConstants::PROP_REGISTRY_nullptr_USER_TOKEN).toString().compare("true", Qt::CaseInsensitive) == 0) { userRegistryKey.reset(nullptr); } // Determine primary and alternative registry locations. BlueBerry extension registry cache // can be found in one of the two locations: // a) in the local configuration area (standard location passed in by the platform) -> priority // b) in the shared configuration area (typically, shared install is used) QList registryLocations; QList readOnlyLocations; RegistryStrategy* strategy = nullptr; //Location configuration = OSGIUtils.getDefault().getConfigurationLocation(); QString configuration = context->getDataFile("").absoluteFilePath(); if (configuration.isEmpty()) { RegistryProperties::SetProperty(RegistryConstants::PROP_NO_REGISTRY_CACHE, "true"); RegistryProperties::SetProperty(RegistryConstants::PROP_NO_LAZY_REGISTRY_CACHE_LOADING, "true"); strategy = new RegistryStrategy(QList(), QList(), masterRegistryKey.data()); } else { //File primaryDir = new File(configuration.getURL().getPath() + '/' + STORAGE_DIR); //bool primaryReadOnly = configuration.isReadOnly(); QString primaryDir = configuration; bool primaryReadOnly = false; //Location parentLocation = configuration.getParentLocation(); QString parentLocation; if (!parentLocation.isEmpty()) { // File secondaryDir = new File(parentLocation.getURL().getFile() + '/' + IRegistryConstants.RUNTIME_NAME); // registryLocations << primaryDir << secondaryDir; // readOnlyLocations << primaryReadOnly << true; // secondary BlueBerry location is always read only } else { registryLocations << primaryDir; readOnlyLocations << primaryReadOnly; } strategy = new RegistryStrategy(registryLocations, readOnlyLocations, masterRegistryKey.data()); } auto registry = new ExtensionRegistry(strategy, masterRegistryKey.data(), userRegistryKey.data()); defaultRegistry.reset(registry); registryServiceReg = context->registerService(registry); //commandRegistration = EquinoxUtils.registerCommandProvider(Activator.getContext()); } void org_blueberry_core_runtime_Activator::stopRegistry() { if (!defaultRegistry.isNull()) { registryServiceReg.unregister(); defaultRegistry->Stop(masterRegistryKey.data()); } // if (!commandRegistration.isNull()) // { // commandRegistration.unregister(); // } } void org_blueberry_core_runtime_Activator::startAppContainer() { appContainer.reset(new ApplicationContainer(context, defaultRegistry.data())); appContainer->Start(); } void org_blueberry_core_runtime_Activator::stopAppContainer() { appContainer->Stop(); } } diff --git a/Plugins/org.blueberry.core.runtime/src/internal/berryProductExtensionBranding.cpp b/Plugins/org.blueberry.core.runtime/src/internal/berryProductExtensionBranding.cpp index d48c39fc52..629c2b1da7 100644 --- a/Plugins/org.blueberry.core.runtime/src/internal/berryProductExtensionBranding.cpp +++ b/Plugins/org.blueberry.core.runtime/src/internal/berryProductExtensionBranding.cpp @@ -1,92 +1,92 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "berryProductExtensionBranding.h" #include #include #include #include "berryCTKPluginActivator.h" namespace berry { const QString ProductExtensionBranding::ATTR_DESCRIPTION = "description"; const QString ProductExtensionBranding::ATTR_NAME = "name"; const QString ProductExtensionBranding::ATTR_APPLICATION = "application"; const QString ProductExtensionBranding::ATTR_VALUE = "value"; ProductExtensionBranding::ProductExtensionBranding(const QString& id, const SmartPointer& element) : id(id) { if (element.IsNull()) return; application = element->GetAttribute(ATTR_APPLICATION); name = element->GetAttribute(ATTR_NAME); description = element->GetAttribute(ATTR_DESCRIPTION); LoadProperties(element); } QSharedPointer ProductExtensionBranding::GetDefiningPlugin() const { return definingPlugin; } QString ProductExtensionBranding::GetApplication() const { return application; } QString ProductExtensionBranding::GetName() const { return name; } QString ProductExtensionBranding::GetDescription() const { return description; } QString ProductExtensionBranding::GetId() const { return id; } QString ProductExtensionBranding::GetProperty(const QString& key) const { auto iter = properties.find(key); return iter != properties.end() ? iter.value() : QString::null; } SmartPointer ProductExtensionBranding::GetProduct() const { return IProduct::Pointer(); } void ProductExtensionBranding::LoadProperties(const SmartPointer& element) { QList children = element->GetChildren(); properties.clear(); - for (auto child : children) + for (const auto &child : qAsConst(children)) { QString key = child->GetAttribute(ATTR_NAME); QString value = child->GetAttribute(ATTR_VALUE); if (!key.isEmpty() && !value.isEmpty()) { properties.insert(key, value); } } definingPlugin = org_blueberry_core_runtime_Activator::GetPlugin(element->GetContributor()); } } diff --git a/Plugins/org.blueberry.ui.qt/src/berryISaveablePart.h b/Plugins/org.blueberry.ui.qt/src/berryISaveablePart.h index 32e813c202..340b20e17a 100644 --- a/Plugins/org.blueberry.ui.qt/src/berryISaveablePart.h +++ b/Plugins/org.blueberry.ui.qt/src/berryISaveablePart.h @@ -1,117 +1,115 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 BERRYISAVEABLEPART_H_ #define BERRYISAVEABLEPART_H_ #include #include #include #include namespace berry { /** * Workbench parts implement or adapt to this interface to participate * in the enablement and execution of the Save and * Save As actions. * * @see IEditorPart */ struct BERRY_UI_QT ISaveablePart : public virtual Object { berryObjectMacro(berry::ISaveablePart); /** * The property id for isDirty. */ static const int PROP_DIRTY; // = IWorkbenchPartConstants.PROP_DIRTY; /** * Saves the contents of this part. *

* If the save is successful, the part should fire a property changed event * reflecting the new dirty state (PROP_DIRTY property). *

*

* If the save is cancelled through user action, or for any other reason, the * part should invoke setCancelled on the IProgressMonitor * to inform the caller. *

*

* This method is long-running; progress and cancellation are provided * by the given progress monitor. *

- * - * @param monitor the progress monitor */ virtual void DoSave(/*IProgressMonitor monitor*/) = 0; /** * Saves the contents of this part to another object. *

* Implementors are expected to open a "Save As" dialog where the user will * be able to select a new name for the contents. After the selection is made, * the contents should be saved to that new name. During this operation a * IProgressMonitor should be used to indicate progress. *

*

* If the save is successful, the part fires a property changed event * reflecting the new dirty state (PROP_DIRTY property). *

*/ virtual void DoSaveAs() = 0; /** * Returns whether the contents of this part have changed since the last save * operation. If this value changes the part must fire a property listener * event with PROP_DIRTY. *

* Note: this method is called often on a part open or part * activation switch, for example by actions to determine their * enabled status. *

* * @return true if the contents have been modified and need * saving, and false if they have not changed since the last * save */ virtual bool IsDirty() const = 0; /** * Returns whether the "Save As" operation is supported by this part. * * @return true if "Save As" is supported, and false * if not supported */ virtual bool IsSaveAsAllowed() const = 0; /** * Returns whether the contents of this part should be saved when the part * is closed. * * @return true if the contents of the part should be saved on * close, and false if the contents are expendable */ virtual bool IsSaveOnCloseNeeded() const = 0; }; } Q_DECLARE_INTERFACE(berry::ISaveablePart, "org.blueberry.ui.ISaveablePart") #endif /* BERRYISAVEABLEPART_H_ */ diff --git a/Plugins/org.blueberry.ui.qt/src/berrySaveable.h b/Plugins/org.blueberry.ui.qt/src/berrySaveable.h index 1657c74af5..33b3627e5a 100644 --- a/Plugins/org.blueberry.ui.qt/src/berrySaveable.h +++ b/Plugins/org.blueberry.ui.qt/src/berrySaveable.h @@ -1,225 +1,223 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 BERRYSAVEABLE_H_ #define BERRYSAVEABLE_H_ #include #include #include #include namespace berry { struct IWorkbenchPage; struct IWorkbenchPart; /** * A Saveable represents a unit of saveability, e.g. an editable * subset of the underlying domain model that may contain unsaved changes. * Different workbench parts (editors and views) may present the same saveables * in different ways. This interface allows the workbench to provide more * appropriate handling of operations such as saving and closing workbench * parts. For example, if two editors sharing the same saveable with unsaved * changes are closed simultaneously, the user is only prompted to save the * changes once for the shared saveable, rather than once for each editor. *

* Workbench parts that work in terms of saveables should implement * {@link ISaveablesSource}. *

* * @see ISaveablesSource */ class BERRY_UI_QT Saveable : /*public InternalSaveable*/ public virtual Object, public IAdaptable { public: berryObjectMacro(Saveable); typedef QSet Set; /** * Attempts to show this saveable in the given page and returns * true on success. The default implementation does nothing * and returns false. * * @param page * the workbench page in which to show this saveable * @return true if this saveable is now visible to the user * @since 3.3 */ virtual bool Show(SmartPointer page); /** * Returns the name of this saveable for display purposes. * * @return the model's name; never null. */ virtual QString GetName() const = 0; /** * Returns the tool tip text for this saveable. This text is used to * differentiate between two inputs with the same name. For instance, * MyClass.java in folder X and MyClass.java in folder Y. The format of the * text varies between input types. * * @return the tool tip text; never null */ virtual QString GetToolTipText() const = 0; /** * Returns the image descriptor for this saveable. * * @return the image descriptor for this model; may be null * if there is no image */ virtual QIcon GetImageDescriptor() const = 0; /** * Saves the contents of this saveable. *

* If the save is cancelled through user action, or for any other reason, * the part should invoke setCancelled on the * IProgressMonitor to inform the caller. *

*

* This method is long-running; progress and cancellation are provided by * the given progress monitor. *

* - * @param monitor - * the progress monitor * @throws CoreException * if the save fails; it is the caller's responsibility to * report the failure to the user */ virtual void DoSave(/*IProgressMonitor monitor*/) = 0; /** * Returns whether the contents of this saveable have changed since the last * save operation. *

* Note: this method is called frequently, for example by actions to * determine their enabled status. *

* * @return true if the contents have been modified and need * saving, and false if they have not changed since * the last save */ virtual bool IsDirty() const = 0; /** * Clients must implement equals and hashCode as defined in * \c Object.equals(Object) and \c Object.hashCode() . Two * saveables should be equal if their dirty state is shared, and saving one * will save the other. If two saveables are equal, their names, tooltips, * and images should be the same because only one of them will be shown when * prompting the user to save. * * @param object * @return true if this Saveable is equal to the given object */ bool operator<(const Object* object) const override = 0; /** * Clients must implement equals and hashCode as defined in * \c Object.equals(Object) and \c Object.hashCode() . Two * saveables should be equal if their dirty state is shared, and saving one * will save the other. If two saveables are equal, their hash codes MUST be * the same, and their names, tooltips, and images should be the same * because only one of them will be shown when prompting the user to save. *

* IMPORTANT: Implementers should ensure that the hashCode returned is * sufficiently unique so as not to collide with hashCodes returned by other * implementations. It is suggested that the defining plug-in's ID be used * as part of the returned hashCode, as in the following example: *

* * 
    *     int PRIME = 31;
    *     int hash = ...; // compute the "normal" hash code, e.g. based on some identifier unique within the defining plug-in
    *     return hash * PRIME + MY_PLUGIN_ID.hashCode();
    *
* * @return a hash code */ uint HashCode() const override = 0; /** * Disables the UI of the given parts containing this saveable if necessary. * This method is not intended to be called by clients. A corresponding call * to *

* Saveables that can be saved in the background should ensure that the user * cannot make changes to their data from the UI, for example by disabling * controls, unless they are prepared to handle this case. This method is * called on the UI thread after a job runnable has been returned from * doSave(IProgressMonitor, IShellProvider) and before * spinning the event loop. The closing flag indicates that * this saveable is currently being saved in response to closing a workbench * part, in which case further changes to this saveable through the UI must * be prevented. *

*

* The default implementation calls setEnabled(false) on the given parts' * composites. *

* * @param parts * the workbench parts containing this saveable * @param closing * a boolean flag indicating whether the save was triggered by a * request to close a workbench part, and all of the given parts * will be closed after the save operation finishes successfully. * * @since 3.3 */ virtual void DisableUI(const QList >& parts, bool closing); /** * Enables the UI of the given parts containing this saveable after a * background save operation has finished. This method is not intended to be * called by clients. *

* The default implementation calls setEnabled(true) on the given parts' * composites. *

* * @param parts * the workbench parts containing this saveable * * @since 3.3 */ virtual void EnableUI(QList >& parts); protected: /** * This implementation of IAdaptable.GetAdapterImpl(const std::type_info&) returns * null. Subclasses may override. This allows two unrelated * subclasses of Saveable to implement \c equals(Object) and * \c hashCode() based on an underlying implementation class that is * shared by both Saveable subclasses. * * @since 3.3 */ Object* GetAdapter(const QString& adapter) const override; }; } #endif /* BERRYSAVEABLE_H_ */ diff --git a/Plugins/org.blueberry.ui.qt/src/berryWorkbenchPlugin.h b/Plugins/org.blueberry.ui.qt/src/berryWorkbenchPlugin.h index 978e3ff5be..2b49a0e0f8 100644 --- a/Plugins/org.blueberry.ui.qt/src/berryWorkbenchPlugin.h +++ b/Plugins/org.blueberry.ui.qt/src/berryWorkbenchPlugin.h @@ -1,470 +1,469 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 BERRYWORKBENCHPLUGIN_H_ #define BERRYWORKBENCHPLUGIN_H_ #include #include #include #include #include #include "berryAbstractUICTKPlugin.h" #include "berryPlatformUI.h" #include "presentations/berryIPresentationFactory.h" #include "internal/berryViewRegistry.h" #include "internal/berryEditorRegistry.h" #include "internal/berryPerspectiveRegistry.h" #include "internal/intro/berryIntroRegistry.h" namespace berry { class QtStyleManager; /** * \ingroup org_blueberry_ui_internal * * This class represents the TOP of the workbench UI world * A plugin class is effectively an application wrapper * for a plugin & its classes. This class should be thought * of as the workbench UI's application class. * * This class is responsible for tracking various registries * font, preference, graphics, dialog store. * * This class is explicitly referenced by the * workbench plugin's "plugin.xml" and places it * into the UI start extension point of the main * overall application harness * * When is this class started? * When the Application * calls createExecutableExtension to create an executable * instance of our workbench class. */ class BERRY_UI_QT WorkbenchPlugin : public AbstractUICTKPlugin { Q_OBJECT Q_PLUGIN_METADATA(IID "org_blueberry_ui_qt") Q_INTERFACES(ctkPluginActivator) private: //static const QString UI_BUNDLE_ACTIVATOR = "org.blueberry.ui.internal.UIPlugin"; //$NON-NLS-1$ // Default instance of the receiver static WorkbenchPlugin* inst; // The presentation factory IPresentationFactory* presentationFactory; // Manager that maps resources to descriptors of editors to use EditorRegistry* editorRegistry; // The context within which this plugin was started. ctkPluginContext* bundleContext; // Other data. //WorkbenchPreferenceManager preferenceManager; ViewRegistry* viewRegistry; PerspectiveRegistry* perspRegistry; IntroRegistry* introRegistry; //SharedImages sharedImages; QScopedPointer styleManager; public: /** * Global workbench ui plugin flag. Only workbench implementation is allowed to use this flag * All other plugins, examples, or test cases must *not* use this flag. */ static bool DEBUG; /** * The character used to separate preference page category ids */ static char PREFERENCE_PAGE_CATEGORY_SEPARATOR; /** * Create an instance of the WorkbenchPlugin. The workbench plugin is * effectively the "application" for the workbench UI. The entire UI * operates as a good plugin citizen. */ WorkbenchPlugin(); ~WorkbenchPlugin() override; /* * Creates an extension. If the extension plugin has not * been loaded a busy cursor will be activated during the duration of * the load. * * @param element the config element defining the extension * @param classAttribute the name of the attribute carrying the class * @return the extension object * @throws CoreException if the extension cannot be created */ // template // static E* CreateExtension(IConfigurationElement::ConstPointer element, // const QString& classAttribute) { // try { // // If plugin has been loaded create extension. // // Otherwise, show busy cursor then create extension. // if (BundleUtility.isActivated(element.getDeclaringExtension() // .getNamespace())) { // return element.createExecutableExtension(classAttribute); // } // final Object[] ret = new Object[1]; // final CoreException[] exc = new CoreException[1]; // BusyIndicator.showWhile(null, new Runnable() { // public void run() { // try { // ret[0] = element // .createExecutableExtension(classAttribute); // } catch (CoreException e) { // exc[0] = e; // } // } // }); // if (exc[0] != null) { // throw exc[0]; // } // return ret[0]; // // } catch (CoreException core) { // throw core; // } catch (Exception e) { // throw new CoreException(new Status(IStatus.ERR, PI_WORKBENCH, // IStatus.ERR, WorkbenchMessages.WorkbenchPlugin_extension,e)); // } // } /** * Answers whether the provided element either has an attribute with the * given name or a child element with the given name with an attribute * called class. * * @param element * the element to test * @param extensionName * the name of the extension to test for * @return whether or not the extension is declared */ static bool HasExecutableExtension(const IConfigurationElement::Pointer& element, const QString& extensionName); /** * Checks to see if the provided element has the syntax for an executable * extension with a given name that resides in a bundle that is already * active. Determining the bundle happens in one of two ways:
*
    *
  • The element has an attribute with the specified name or element text * in the form bundle.id/class.name[:optional attributes]
    • *
  • The element has a child element with the specified name that has a * plugin attribute
    • *
* * @param element * the element to test * @param extensionName * the name of the extension to test for * @return whether or not the bundle expressed by the above criteria is * active. If the bundle cannot be determined then the state of the * bundle that declared the element is returned. */ static bool IsBundleLoadedForExecutableExtension( const IConfigurationElement::Pointer& element, const QString& extensionName); /** * Returns the bundle that contains the class referenced by an executable * extension. Determining the bundle happens in one of two ways:
*
    *
  • The element has an attribute with the specified name or element text * in the form bundle.id/class.name[:optional attributes]
    • *
  • The element has a child element with the specified name that has a * plugin attribute
    • *
* * @param element * the element to test * @param extensionName * the name of the extension to test for * @return the bundle referenced by the extension. If that bundle cannot be * determined the bundle that declared the element is returned. Note * that this may be null. */ static QSharedPointer GetBundleForExecutableExtension( const IConfigurationElement::Pointer& element, const QString& extensionName); /** * Return the default instance of the receiver. This represents the runtime plugin. * @return WorkbenchPlugin * @see AbstractUICTKPlugin for the typical implementation pattern for plugin classes. */ static WorkbenchPlugin* GetDefault(); std::size_t GetBundleCount(); /** * Answer the manager that maps resource types to a the * description of the editor to use * @return IEditorRegistry the editor registry used * by this plug-in. */ IEditorRegistry* GetEditorRegistry(); /** * Answer the element factory for an id, or null. if not found. * @param targetID * @return IElementFactory */ IElementFactory* GetElementFactory(const QString& targetID) const; /** * Returns the presentation factory with the given id, or null if not found. - * @param targetID The id of the presentation factory to use. * @return IPresentationFactory or null * if not factory matches that id. */ IPresentationFactory* GetPresentationFactory(); private: /** * Looks up the configuration element with the given id on the given extension point * and instantiates the class specified by the class attributes. * * @param extensionPointId the extension point id (simple id) * @param elementName the name of the configuration element, or null * to match any element * @param targetID the target id * @return the instantiated extension object, or null if not found */ template C* CreateExtension(const QString& extensionPointId, const QString& elementName, const QString& targetID) { IExtensionPoint::Pointer extensionPoint = Platform::GetExtensionRegistry() ->GetExtensionPoint(PlatformUI::PLUGIN_ID() + "." + extensionPointId); if (extensionPoint == 0) { WorkbenchPlugin::Log("Unable to find extension. Extension point: " + extensionPointId + " not found"); return nullptr; } // Loop through the config elements. IConfigurationElement::Pointer targetElement(nullptr); QList elements( Platform::GetExtensionRegistry()->GetConfigurationElementsFor(PlatformUI::PLUGIN_ID() + "." + extensionPointId)); for (int j = 0; j < elements.size(); j++) { if (elementName == "" || elementName == elements[j]->GetName()) { QString strID = elements[j]->GetAttribute("id"); if (targetID == strID) { targetElement = elements[j]; break; } } } if (targetElement.IsNull()) { // log it since we cannot safely display a dialog. WorkbenchPlugin::Log("Unable to find extension: " + targetID + " in extension point: " + extensionPointId); return nullptr; } // Create the extension. try { return targetElement->CreateExecutableExtension("class"); } catch (const CoreException& /*e*/) { // log it since we cannot safely display a dialog. WorkbenchPlugin::Log("Unable to create extension: " + targetID + " in extension point: " + extensionPointId); } return nullptr; } public: /** * Return the perspective registry. * @return IPerspectiveRegistry. The registry for the receiver. */ IPerspectiveRegistry* GetPerspectiveRegistry(); /** * Returns the introduction registry. * * @return the introduction registry. */ IIntroRegistry* GetIntroRegistry(); /* * Get the preference manager. * @return PreferenceManager the preference manager for * the receiver. */ //PreferenceManager getPreferenceManager(); /** * Answer the view registry. * @return IViewRegistry the view registry for the * receiver. */ IViewRegistry* GetViewRegistry(); /** * Logs the given message to the platform log. * * If you have an exception in hand, call log(String, Throwable) instead. * * If you have a status object in hand call log(String, IStatus) instead. * * This convenience method is for internal use by the Workbench only and * must not be called outside the Workbench. * * @param message * A high level UI message describing when the problem happened. */ static void Log(const QString &message); /** * Log the throwable. * @param exc */ static void Log(const ctkException& exc); /** * Logs the given message and throwable to the platform log. * * If you have a status object in hand call log(String, IStatus) instead. * * This convenience method is for internal use by the Workbench only and * must not be called outside the Workbench. * * @param message * A high level UI message describing when the problem happened. * @param t * The throwable from where the problem actually occurred. */ static void Log(const QString &message, const ctkException& t); /** * Logs the given throwable to the platform log, indicating the class and * method from where it is being logged (this is not necessarily where it * occurred). * * This convenience method is for internal use by the Workbench only and * must not be called outside the Workbench. * * @param clazz * The calling class. * @param methodName * The calling method name. * @param t * The throwable from where the problem actually occurred. */ static void Log(const QString &clazz, const QString &methodName, const ctkException& t); /** * Logs the given message and status to the platform log. * * This convenience method is for internal use by the Workbench only and * must not be called outside the Workbench. * * @param message * A high level UI message describing when the problem happened. * May be null. * @param status * The status describing the problem. Must not be null. */ static void Log(const QString& message, const SmartPointer& status); /** * Log the status to the default log. * @param status */ static void Log(const SmartPointer& status); /* * (non-Javadoc) * @see org.osgi.framework.BundleActivator#start(org.osgi.framework.BundleContext) */ void start(ctkPluginContext* context) override; /* * Return an array of all bundles contained in this workbench. * * @return an array of bundles in the workbench or an empty array if none */ //const QList GetBundles(); /** * Returns the bundle context associated with the workbench plug-in. * * @return the bundle context */ ctkPluginContext* GetPluginContext(); /* (non-Javadoc) * @see org.blueberry.ui.plugin.AbstractUICTKPlugin#stop(org.osgi.framework.BundleContext) */ void stop(ctkPluginContext* context) override; /** * FOR INTERNAL WORKBENCH USE ONLY. * * Returns the path to a location in the file system that can be used * to persist/restore state between workbench invocations. * If the location did not exist prior to this call it will be created. * Returns null if no such location is available. * * @return path to a location in the file system where this plug-in can * persist data between sessions, or null if no such * location is available. */ QString GetDataLocation() const; }; } #endif /*BERRYWORKBENCHPLUGIN_H_*/ diff --git a/Plugins/org.blueberry.ui.qt/src/internal/berryChangeToPerspectiveMenu.cpp b/Plugins/org.blueberry.ui.qt/src/internal/berryChangeToPerspectiveMenu.cpp index ee560fc4bd..6c63eb5ac5 100644 --- a/Plugins/org.blueberry.ui.qt/src/internal/berryChangeToPerspectiveMenu.cpp +++ b/Plugins/org.blueberry.ui.qt/src/internal/berryChangeToPerspectiveMenu.cpp @@ -1,251 +1,251 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "berryChangeToPerspectiveMenu.h" #include #include #include #include #include #include #include #include #include #include #include #include "berryCommandContributionItemParameter.h" #include "berryWorkbenchPlugin.h" #include "berryWorkbenchPreferenceConstants.h" #include "berryPreferenceConstants.h" #include namespace berry { const QString ChangeToPerspectiveMenu::NO_TARGETS_MSG = ""; bool PerspectiveComparator(const IPerspectiveDescriptor::Pointer& d1, const IPerspectiveDescriptor::Pointer& d2) { return d1->GetLabel() < d2->GetLabel(); } ChangeToPerspectiveMenu::ChangeToPerspectiveMenu(IWorkbenchWindow* window, const QString& id) : ContributionItem(id) , window(window) , reg(window->GetWorkbench()->GetPerspectiveRegistry()) , showActive(true) , dirty(true) { CommandContributionItemParameter::Pointer showDlgItemParms( new CommandContributionItemParameter( window, QString::null, IWorkbenchCommandConstants::PERSPECTIVES_SHOW_PERSPECTIVE, CommandContributionItem::STYLE_PUSH)); showDlgItemParms->label = "&Other..."; showDlgItem = new CommandContributionItem(showDlgItemParms); // indicate that a open perspectives submenu has been created /* if (WorkbenchWindow* window = dynamic_cast(window)) { window->AddSubmenu(WorkbenchWindow::OPEN_PERSPECTIVE_SUBMENU); } */ } void ChangeToPerspectiveMenu::Fill(QMenu* menu, QAction* before) { if (MenuManager* mm = dynamic_cast(GetParent())) { this->connect(mm, SIGNAL(AboutToShow(IMenuManager*)), SLOT(AboutToShow(IMenuManager*))); } if (!dirty) { return; } MenuManager::Pointer manager(new MenuManager()); FillMenu(manager.GetPointer()); QList items = manager->GetItems(); if (items.isEmpty()) { auto action = new QAction(NO_TARGETS_MSG, menu); action->setEnabled(false); menu->insertAction(before, action); } else { foreach (IContributionItem::Pointer item, items) { item->Fill(menu, before); } } dirty = false; } bool ChangeToPerspectiveMenu::IsDirty() const { return dirty; } bool ChangeToPerspectiveMenu::IsDynamic() const { return true; } void ChangeToPerspectiveMenu::AboutToShow(IMenuManager* manager) { manager->MarkDirty(); dirty = true; } void ChangeToPerspectiveMenu::FillMenu(IMenuManager* manager) { // Clear out the manager so that we have a blank slate. manager->RemoveAll(); // Collect and sort perspective descriptors. QList persps = GetPerspectiveShortcuts(); qSort(persps.begin(), persps.end(), PerspectiveComparator); /* * Convert the perspective descriptors to command parameters, and filter * using the activity/capability mechanism. */ - for (IPerspectiveDescriptor::Pointer descriptor : persps) + for (const IPerspectiveDescriptor::Pointer &descriptor : qAsConst(persps)) { CommandContributionItemParameter::Pointer ccip = GetItem(descriptor); // if (WorkbenchActivityHelper.filterItem(ccip)) { // continue; // } CommandContributionItem::Pointer item(new CommandContributionItem(ccip)); manager->Add(item); } IPreferences::Pointer prefs = WorkbenchPlugin::GetDefault()->GetPreferences(); bool showOther = true; prefs->GetBool(WorkbenchPreferenceConstants::SHOW_OTHER_IN_PERSPECTIVE_MENU, showOther); if (showOther) { // Add a separator and then "Other..." if (!manager->IsEmpty()) { IContributionItem::Pointer separator(new Separator()); manager->Add(separator); } manager->Add(showDlgItem); } } SmartPointer ChangeToPerspectiveMenu::GetItem(const IPerspectiveDescriptor::Pointer& desc) const { IPreferences::Pointer prefs = WorkbenchPlugin::GetDefault()->GetPreferences(); int mode = prefs->GetInt(PreferenceConstants::OPEN_PERSP_MODE, PreferenceConstants::OPM_ACTIVE_PAGE); IWorkbenchPage::Pointer page = window->GetActivePage(); IPerspectiveDescriptor::Pointer persp; if (page.IsNotNull()) { persp = page->GetPerspective(); } QString perspId = desc->GetId(); class PluginCCIP : public CommandContributionItemParameter, public IPluginContribution { QString localId; QString pluginId; public: typedef PluginCCIP Self; static const char* GetStaticClassName() { return "PluginCCIP"; } berryObjectTypeInfo(CommandContributionItemParameter, IPluginContribution) PluginCCIP(const IPerspectiveDescriptor::Pointer& v, IServiceLocator* serviceLocator, const QString& id, const QString& commandId, CommandContributionItem::Style style) : CommandContributionItemParameter(serviceLocator, id, commandId, style) { PerspectiveDescriptor::Pointer vd = v.Cast(); localId = vd->GetLocalId(); pluginId = vd->GetPluginId(); } QString GetLocalId() const override { return localId; } QString GetPluginId() const override { return pluginId; } }; CommandContributionItemParameter::Pointer parms(new PluginCCIP(desc, window, perspId, IWorkbenchCommandConstants::PERSPECTIVES_SHOW_PERSPECTIVE, CommandContributionItem::STYLE_PUSH)); parms->label = desc->GetLabel(); parms->icon = desc->GetImageDescriptor(); Object::Pointer strId(new ObjectString(perspId)); parms->parameters.insert(IWorkbenchCommandConstants::PERSPECTIVES_SHOW_PERSPECTIVE_PARM_ID, strId); // Only open a new window if user preference is set and the window // has an active perspective. if (PreferenceConstants::OPM_NEW_WINDOW == mode && persp.IsNotNull()) { Object::Pointer bNewWnd(new ObjectBool(true)); parms->parameters.insert(IWorkbenchCommandConstants::PERSPECTIVES_SHOW_PERSPECTIVE_PARM_NEWWINDOW, bNewWnd); } return parms; } QList > ChangeToPerspectiveMenu::GetPerspectiveShortcuts() const { QList list; IWorkbenchPage::Pointer page = window->GetActivePage(); if (page.IsNull()) { return list; } QList ids = page->GetPerspectiveShortcuts(); for (int i = 0; i < ids.size(); i++) { IPerspectiveDescriptor::Pointer desc = reg->FindPerspectiveWithId(ids[i]); if (desc.IsNotNull() && !list.contains(desc)) { /* if (WorkbenchActivityHelper::FilterItem(desc)) { continue; } */ list.push_back(desc); } } return list; } } diff --git a/Plugins/org.blueberry.ui.qt/src/internal/berryKeywordRegistry.cpp b/Plugins/org.blueberry.ui.qt/src/internal/berryKeywordRegistry.cpp index e2d5a3bdd1..bea2f397df 100644 --- a/Plugins/org.blueberry.ui.qt/src/internal/berryKeywordRegistry.cpp +++ b/Plugins/org.blueberry.ui.qt/src/internal/berryKeywordRegistry.cpp @@ -1,88 +1,88 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "berryKeywordRegistry.h" #include "berryIConfigurationElement.h" #include "berryIExtension.h" #include "berryIExtensionPoint.h" #include "berryIExtensionPointFilter.h" #include "berryIExtensionRegistry.h" #include "berryExtensionTracker.h" #include "berryObjectString.h" #include "berryPlatform.h" #include "berryPlatformUI.h" #include "berryWorkbenchRegistryConstants.h" namespace berry { const QString KeywordRegistry::ATT_ID = "id"; const QString KeywordRegistry::ATT_LABEL = "label"; const QString KeywordRegistry::TAG_KEYWORD = "keyword"; KeywordRegistry::KeywordRegistry() { IExtensionTracker* tracker = PlatformUI::GetWorkbench()->GetExtensionTracker(); tracker->RegisterHandler(this, ExtensionTracker::CreateExtensionPointFilter(GetExtensionPointFilter())); QList extensions = GetExtensionPointFilter()->GetExtensions(); for (auto& extension : extensions) { AddExtension(tracker, extension); } } SmartPointer KeywordRegistry::GetExtensionPointFilter() const { return Platform::GetExtensionRegistry()->GetExtensionPoint( PlatformUI::PLUGIN_ID(), WorkbenchRegistryConstants::PL_KEYWORDS); } KeywordRegistry*KeywordRegistry::GetInstance() { static KeywordRegistry instance; return &instance; } void KeywordRegistry::AddExtension(IExtensionTracker* tracker, const SmartPointer& extension) { - for (auto element : extension->GetConfigurationElements()) + for (const auto &element : extension->GetConfigurationElements()) { if (element->GetName() == TAG_KEYWORD) { QString name = element->GetAttribute(ATT_LABEL); QString id = element->GetAttribute(ATT_ID); internalKeywordMap.insert(id, name); Object::Pointer trackedObject(new ObjectString(id)); tracker->RegisterObject(extension, trackedObject, IExtensionTracker::REF_STRONG); } } } QString KeywordRegistry::GetKeywordLabel(const QString& id) { auto it = internalKeywordMap.find(id); return it == internalKeywordMap.end() ? QString::null : *it; } void KeywordRegistry::RemoveExtension(const SmartPointer& /*extension*/, const QList >& objects) { - for (auto object : objects) + for (const auto &object : objects) { if (ObjectString::Pointer objString = object.Cast()) { internalKeywordMap.remove(*objString); } } } } diff --git a/Plugins/org.blueberry.ui.qt/src/internal/berryPreferencePageParameterValues.cpp b/Plugins/org.blueberry.ui.qt/src/internal/berryPreferencePageParameterValues.cpp index d35b99bf88..2c1c25354e 100644 --- a/Plugins/org.blueberry.ui.qt/src/internal/berryPreferencePageParameterValues.cpp +++ b/Plugins/org.blueberry.ui.qt/src/internal/berryPreferencePageParameterValues.cpp @@ -1,74 +1,74 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "berryPreferencePageParameterValues.h" #include "berryPlatform.h" #include "berryPlatformUI.h" #include "berryWorkbenchRegistryConstants.h" #include "berryIConfigurationElement.h" #include "berryIExtensionRegistry.h" #include "berryIWorkbench.h" namespace berry { PreferencePageParameterValues::PreferencePageParameterValues() { QString xpId = PlatformUI::PLUGIN_ID() + "." + WorkbenchRegistryConstants::PL_PREFERENCES; Platform::GetExtensionRegistry()->AddListener(this, xpId); } QHash PreferencePageParameterValues::GetParameterValues() const { if (preferenceMap.empty()) { IExtensionRegistry* registry = Platform::GetExtensionRegistry(); if (registry) { QList configElements = registry->GetConfigurationElementsFor(PlatformUI::PLUGIN_ID(), WorkbenchRegistryConstants::PL_PREFERENCES); - for (auto configElement : configElements) + for (const auto &configElement : qAsConst(configElements)) { if(configElement->GetName() == "page") { preferenceMap.insert(configElement->GetAttribute("name"), configElement->GetAttribute("id")); } } } } return preferenceMap; } void PreferencePageParameterValues::Added(const QList >& /*extensions*/) { preferenceMap.clear(); } void berry::PreferencePageParameterValues::Removed(const QList >& /*extensions*/) { preferenceMap.clear(); } void PreferencePageParameterValues::Added(const QList >& /*extensionPoints*/) { preferenceMap.clear(); } void PreferencePageParameterValues::Removed(const QList >& /*extensionPoints*/) { preferenceMap.clear(); } } diff --git a/Plugins/org.blueberry.ui.qt/src/internal/berryQtShowViewDialog.cpp b/Plugins/org.blueberry.ui.qt/src/internal/berryQtShowViewDialog.cpp index c7e8913037..ae564734bc 100644 --- a/Plugins/org.blueberry.ui.qt/src/internal/berryQtShowViewDialog.cpp +++ b/Plugins/org.blueberry.ui.qt/src/internal/berryQtShowViewDialog.cpp @@ -1,327 +1,327 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "berryQtShowViewDialog.h" #include #include #include #include "berryWorkbenchPlugin.h" #include "berryXMLMemento.h" #include #include namespace berry { static const QString TAG_SHOWVIEWDIALOG = "ShowViewDialog"; static const QString TAG_CATEGORY = "category"; static const QString TAG_SELECTION = "selection"; static const QString TAG_GEOMETRY = "geometry"; class ViewFilterProxyModel : public QSortFilterProxyModel { public: ViewFilterProxyModel(QObject* parent = nullptr) : QSortFilterProxyModel(parent) , m_FilterOnKeywords(true) { this->setFilterCaseSensitivity(Qt::CaseInsensitive); } bool filterOnKeywords() const { return m_FilterOnKeywords; } void setFilterOnKeywords(bool filterOnKeywords) { if (m_FilterOnKeywords != filterOnKeywords) { m_FilterOnKeywords = filterOnKeywords; this->filterChanged(); } } protected: bool filterAcceptsRow(int sourceRow, const QModelIndex& sourceParent) const override { QRegExp regExp = filterRegExp(); if (!regExp.isValid() || regExp.isEmpty()) return true; QModelIndex sourceIndex = sourceModel()->index(sourceRow, 0, sourceParent); QStringList keywords; if (m_FilterOnKeywords) { keywords = sourceModel()->data(sourceIndex, ViewTreeModel::Keywords).toStringList(); } else { if (sourceModel()->hasChildren(sourceIndex)) { // this is a category item int numChildren = sourceModel()->rowCount(sourceIndex); for (int i = 0; i < numChildren; ++i) { keywords.push_back(sourceModel()->data(sourceIndex.child(i, 0)).toString()); } } else { // this is a view item keywords.push_back(sourceModel()->data(sourceIndex).toString()); } } for(auto& keyword : keywords) { if (keyword.contains(regExp)) return true; } return false; } private: bool m_FilterOnKeywords; }; QtShowViewDialog::QtShowViewDialog(const IWorkbenchWindow* window, IViewRegistry* registry, QWidget* parent, Qt::WindowFlags f) : QDialog(parent, f) , m_Window(window) , m_ViewReg(registry) , m_FilterModel(nullptr) { m_UserInterface.setupUi(this); m_UserInterface.m_TreeView->header()->setVisible(false); m_UserInterface.m_TreeView->setSelectionMode(QAbstractItemView::ExtendedSelection); m_FilterModel = new ViewFilterProxyModel(this); auto sourceModel = new ViewTreeModel(window, m_FilterModel); m_FilterModel->setSourceModel(sourceModel); m_UserInterface.m_TreeView->setModel(m_FilterModel); connect(m_UserInterface.m_Filter, SIGNAL(textChanged(QString)), this, SLOT(setFilter(QString))); connect(m_UserInterface.m_TreeView, SIGNAL(clicked(QModelIndex)), this, SLOT(setDescription(QModelIndex))); connect(m_UserInterface.m_TreeView, SIGNAL(collapsed(QModelIndex)), this, SLOT(categoryCollapsed(QModelIndex))); connect(m_UserInterface.m_TreeView, SIGNAL(expanded(QModelIndex)), this, SLOT(categoryExpanded(QModelIndex))); connect(m_UserInterface.m_TreeView, SIGNAL(doubleClicked(QModelIndex)), this, SLOT(accept())); connect(m_UserInterface.m_TreeView, SIGNAL(activated(QModelIndex)), this, SLOT(accept())); connect(m_UserInterface.m_TreeView->selectionModel(), SIGNAL(selectionChanged(QItemSelection,QItemSelection)), this, SLOT(selectionChanged(QItemSelection,QItemSelection))); connect(m_UserInterface.m_KeywordFilter, SIGNAL(clicked(bool)), this, SLOT(enableKeywordFilter(bool))); this->RestoreState(); m_UserInterface.m_Filter->selectAll(); this->UpdateButtons(); } void QtShowViewDialog::setDescription(const QModelIndex& index) { QString description = m_UserInterface.m_TreeView->model()->data(index, Qt::WhatsThisRole).toString(); m_UserInterface.m_Description->setText(description); } void QtShowViewDialog::enableKeywordFilter(bool enable) { m_FilterModel->setFilterOnKeywords(enable); this->RestoreExpandedState(); } void QtShowViewDialog::setFilter(const QString& filter) { m_FilterModel->setFilterWildcard(filter); this->RestoreExpandedState(); } void QtShowViewDialog::categoryCollapsed(const QModelIndex& index) { m_ExpandedCategories.removeAll(m_FilterModel->mapToSource(index)); } void QtShowViewDialog::categoryExpanded(const QModelIndex& index) { m_ExpandedCategories.push_back(m_FilterModel->mapToSource(index)); } void QtShowViewDialog::selectionChanged(const QItemSelection& /*selected*/, const QItemSelection& /*deselected*/) { UpdateButtons(); } void QtShowViewDialog::RestoreExpandedState() { int rowCount = m_FilterModel->rowCount(); for (int i = 0; i < rowCount; ++i) { QModelIndex index = m_FilterModel->index(i, 0); if (m_ExpandedCategories.contains(m_FilterModel->mapToSource(index))) { m_UserInterface.m_TreeView->expand(index); } } } void QtShowViewDialog::UpdateButtons() { QPushButton* okBtn = m_UserInterface.m_ButtonBox->button(QDialogButtonBox::Ok); if (okBtn) { okBtn->setEnabled(!m_UserInterface.m_TreeView->selectionModel()->selection().isEmpty()); } } void QtShowViewDialog::RestoreState() { IPreferences::Pointer prefs = WorkbenchPlugin::GetDefault()->GetPreferences(); QString str = prefs->Get(TAG_SHOWVIEWDIALOG, QString::null); if (str.isEmpty()) return; std::stringstream ss(str.toStdString()); XMLMemento::Pointer memento = XMLMemento::CreateReadRoot(ss); bool keywordFilter = false; if (memento->GetBoolean("keywordFilter", keywordFilter)) { m_UserInterface.m_KeywordFilter->setChecked(keywordFilter); m_FilterModel->setFilterOnKeywords(keywordFilter); } QString filter; if (memento->GetString("filter", filter)) { m_UserInterface.m_Filter->setText(filter); } IMemento::Pointer geomChild = memento->GetChild(TAG_GEOMETRY); if (geomChild.IsNotNull()) { QString geom = geomChild->GetTextData(); if (!geom.isEmpty()) { QByteArray ba = QByteArray::fromBase64(geom.toLatin1()); this->restoreGeometry(ba); } } QHash rootIndices; int rowCount = m_FilterModel->sourceModel()->rowCount(); for (int i = 0; i < rowCount; ++i) { QModelIndex sourceIndex = m_FilterModel->sourceModel()->index(i, 0); QString id = sourceIndex.data(ViewTreeModel::Id).toString(); if (!id.isEmpty()) { rootIndices[id] = sourceIndex; } } - for (IMemento::Pointer categoryChild : memento->GetChildren(TAG_CATEGORY)) + for (const IMemento::Pointer &categoryChild : memento->GetChildren(TAG_CATEGORY)) { QString id = categoryChild->GetID(); if (!id.isEmpty()) { if (rootIndices.contains(id)) { m_ExpandedCategories.push_back(rootIndices[id]); } } } this->RestoreExpandedState(); QItemSelection itemSelection; - for (IMemento::Pointer selectionChild : memento->GetChildren(TAG_SELECTION)) + for (const IMemento::Pointer &selectionChild : memento->GetChildren(TAG_SELECTION)) { QString id = selectionChild->GetID(); if (!id.isEmpty()) { QModelIndexList indexList = m_FilterModel->match(m_FilterModel->index(0, 0), ViewTreeModel::Id, QVariant::fromValue(id), 1, Qt::MatchExactly | Qt::MatchRecursive); if (!indexList.isEmpty()) { QItemSelection subSelection(indexList.front(), indexList.front()); itemSelection.merge(subSelection, QItemSelectionModel::SelectCurrent); } } } m_UserInterface.m_TreeView->selectionModel()->select(itemSelection, QItemSelectionModel::ClearAndSelect); } void QtShowViewDialog::SaveState() { XMLMemento::Pointer memento = XMLMemento::CreateWriteRoot(TAG_SHOWVIEWDIALOG); memento->PutString("filter", m_UserInterface.m_Filter->text()); memento->PutBoolean("keywordFilter", m_UserInterface.m_KeywordFilter->isChecked()); // dialog geometry QByteArray geom = this->saveGeometry(); IMemento::Pointer geomChild = memento->CreateChild(TAG_GEOMETRY); geomChild->PutTextData(geom.toBase64().constData()); // expanded categories - for (QPersistentModelIndex index : m_ExpandedCategories) + for (const QPersistentModelIndex &index : qAsConst(m_ExpandedCategories)) { if (index.isValid()) { QString id = index.data(ViewTreeModel::Id).toString(); if (!id.isEmpty()) { memento->CreateChild(TAG_CATEGORY, id); } } } // we only record a single selected item. restoring a multi-selection might be // confusing for the user QModelIndexList selectedIndices = m_UserInterface.m_TreeView->selectionModel()->selectedIndexes(); if (!selectedIndices.isEmpty()) { QString id = selectedIndices.back().data(ViewTreeModel::Id).toString(); if (!id.isEmpty()) { memento->CreateChild(TAG_SELECTION, id); } } std::stringstream ss; memento->Save(ss); IPreferences::Pointer prefs = WorkbenchPlugin::GetDefault()->GetPreferences(); prefs->Put(TAG_SHOWVIEWDIALOG, QString::fromStdString(ss.str())); prefs->Sync(); } void QtShowViewDialog::done(int r) { this->SaveState(); QDialog::done(r); } QList QtShowViewDialog::GetSelection() const { QList selected; QModelIndexList indices = m_UserInterface.m_TreeView->selectionModel()->selectedIndexes(); - for(QModelIndex index : indices) + for(QModelIndex index : qAsConst(indices)) { QString id = m_FilterModel->data(index, ViewTreeModel::Id).toString(); selected.push_back(id); } return selected; } } diff --git a/Plugins/org.blueberry.ui.qt/src/internal/berryReopenEditorMenu.cpp b/Plugins/org.blueberry.ui.qt/src/internal/berryReopenEditorMenu.cpp index 7ef43c54f0..8309f352a7 100644 --- a/Plugins/org.blueberry.ui.qt/src/internal/berryReopenEditorMenu.cpp +++ b/Plugins/org.blueberry.ui.qt/src/internal/berryReopenEditorMenu.cpp @@ -1,299 +1,299 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "berryReopenEditorMenu.h" #include #include #include #include #include #include "berryEditorHistory.h" #include "berryEditorHistoryItem.h" #include "berryWorkbench.h" #include "berryWorkbenchPlugin.h" #include "berryPreferenceConstants.h" #include #include #include namespace berry { ReopenEditorMenu::ReopenEditorMenu(IWorkbenchWindow* window, const QString& id, bool showSeparator) : ContributionItem(id) , window(window) , history(nullptr) , showSeparator(showSeparator) , dirty(true) { IWorkbench* workbench = window->GetWorkbench(); if (Workbench* w = dynamic_cast(workbench)) { history = w->GetEditorHistory(); } } QString ReopenEditorMenu::CalcText(int index, const QString& name, const QString& toolTip, bool rtl) { QString sb; int mnemonic = index + 1; QString nm = QString::number(mnemonic); if (mnemonic <= MAX_MNEMONIC_SIZE) { nm.prepend('&'); } QString fileName = name; QString pathName = toolTip; if (pathName == fileName) { // tool tip text isn't necessarily a path; // sometimes it's the same as name, so it shouldn't be treated as a path then pathName.clear(); } QFileInfo path(pathName); // if last segment in path is the fileName, remove it if (path.fileName() == fileName) { path.setFile(path.path()); pathName = path.absoluteFilePath(); } if ((fileName.size() + pathName.size()) <= (MAX_TEXT_LENGTH - 4)) { // entire item name fits within maximum length sb += fileName; if (!pathName.isEmpty()) { sb += " [" + pathName + "]"; } } else { // need to shorten the item name int length = fileName.size(); if (length > MAX_TEXT_LENGTH) { // file name does not fit within length, truncate it - sb += fileName.left(MAX_TEXT_LENGTH - 3); + sb += fileName.leftRef(MAX_TEXT_LENGTH - 3); sb += "..."; } else if (length > MAX_TEXT_LENGTH - 7) { sb += fileName; } else { sb += fileName; QStringList pathSegments = path.absoluteFilePath().split('/', QString::SkipEmptyParts); int segmentCount = pathSegments.size(); if (segmentCount > 0) { length += 7; // 7 chars are taken for " [...]" sb += " ["; // Add first n segments that fit int i = 0; while (i < segmentCount && length < MAX_TEXT_LENGTH) { const QString& segment = pathSegments[i]; if (length + segment.size() < MAX_TEXT_LENGTH) { sb += segment + QDir::separator(); length += segment.size() + 1; i++; } else if (i == 0) { // append at least part of the first segment - sb += segment.left(MAX_TEXT_LENGTH - length); + sb += segment.leftRef(MAX_TEXT_LENGTH - length); length = MAX_TEXT_LENGTH; break; } else { break; } } sb += "..."; i = segmentCount - 1; // Add last n segments that fit while (i > 0 && length < MAX_TEXT_LENGTH) { const QString& segment = pathSegments[i]; if (length + segment.size() < MAX_TEXT_LENGTH) { sb += QDir::separator(); sb += segment; length += segment.size() + 1; i--; } else { break; } } sb.append("]"); } } } QString process; if (rtl) { process = sb + " " + nm; } else { process = nm + " " + sb; } //return TextProcessor.process(process, TextProcessor.getDefaultDelimiters() + "[]"); return process; } void ReopenEditorMenu::Fill(QMenu* menu, QAction* before) { if (window->GetActivePage() == nullptr || window->GetActivePage()->GetPerspective().IsNull()) { return; } if (MenuManager* mm = dynamic_cast(this->GetParent())) { mm->connect(mm, SIGNAL(AboutToShow(IMenuManager*)), this, SLOT(MenuAboutToShow(IMenuManager*))); } int itemsToShow = WorkbenchPlugin::GetDefault()->GetPreferences()->GetInt(PreferenceConstants::RECENT_FILES, 6); if (itemsToShow == 0 || history == nullptr) { return; } // Get items. QList historyItems = history->GetItems(); int n = std::min(itemsToShow, historyItems.size()); if (n <= 0) { return; } if (showSeparator) { menu->addSeparator(); } struct _SafeRunnable : public ISafeRunnable { QMenu* menu; QAction* before; EditorHistoryItem::Pointer item; const int historyIndex; _SafeRunnable(QMenu* menu, QAction* before, EditorHistoryItem::Pointer item, int index) : menu(menu), before(before), item(item), historyIndex(index) {} void Run() override { QString text = ReopenEditorMenu::CalcText(historyIndex, item); auto mi = new QAction(text, nullptr); menu->insertAction(before, mi); mi->setData(QVariant::fromValue(item)); } void HandleException(const ctkException& e) override { // just skip the item if there's an error, // e.g. in the calculation of the shortened name WorkbenchPlugin::Log(this->GetClassName(), "Fill", e); } }; for (int i = 0; i < n; i++) { EditorHistoryItem::Pointer item = historyItems[i]; ISafeRunnable::Pointer runnable(new _SafeRunnable(menu, before, item, i)); SafeRunner::Run(runnable); } dirty = false; } bool ReopenEditorMenu::IsDirty() const { return dirty; } bool ReopenEditorMenu::IsDynamic() const { return true; } void ReopenEditorMenu::Open(const EditorHistoryItem::Pointer& item) { IWorkbenchPage::Pointer page = window->GetActivePage(); if (page.IsNotNull()) { try { QString itemName = item->GetName(); if (!item->IsRestored()) { item->RestoreState(); } IEditorInput::Pointer input = item->GetInput(); IEditorDescriptor::Pointer desc = item->GetDescriptor(); if (!input || !desc) { QString title = "Problems opening editor"; QString msg = QString("Unable to open %1.").arg(itemName); QMessageBox::warning(window->GetShell()->GetControl(), title, msg); history->Remove(item); } else { page->OpenEditor(input, desc->GetId()); } } catch (const PartInitException& e2) { QString title = "Problems opening editor"; QMessageBox::warning(window->GetShell()->GetControl(), title, e2.what()); history->Remove(item); } } } QString ReopenEditorMenu::CalcText(int index, const EditorHistoryItem::Pointer& item) { // IMPORTANT: avoid accessing the item's input since // this can require activating plugins. // Instead, ask the item for the info, which can // consult its memento if it is not restored yet. return CalcText(index, item->GetName(), item->GetToolTipText(), false); // Window::GetDefaultOrientation() == SWT.RIGHT_TO_LEFT); } void ReopenEditorMenu::MenuAboutToShow(IMenuManager* manager) { manager->MarkDirty(); dirty = true; } } diff --git a/Plugins/org.blueberry.ui.qt/src/internal/berrySwitchToWindowMenu.cpp b/Plugins/org.blueberry.ui.qt/src/internal/berrySwitchToWindowMenu.cpp index 9622cd5b32..18425006a8 100644 --- a/Plugins/org.blueberry.ui.qt/src/internal/berrySwitchToWindowMenu.cpp +++ b/Plugins/org.blueberry.ui.qt/src/internal/berrySwitchToWindowMenu.cpp @@ -1,155 +1,155 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "berrySwitchToWindowMenu.h" #include #include #include #include #include #include #include #include namespace berry { void SwitchToWindowMenu::AboutToShow(IMenuManager* manager) { manager->MarkDirty(); dirty = true; } void SwitchToWindowMenu::MenuItemTriggered(int index) { if (index < 0 || index >= windows.size()) return; IWorkbenchWindow* window = windows[index]; Shell::Pointer windowShell = window->GetShell(); if (windowShell->GetMinimized()) { windowShell->SetMinimized(false); } windowShell->SetActive(); windowShell->GetControl()->raise(); } QString SwitchToWindowMenu::CalcText(int number, IWorkbenchWindow* window) { QString suffix = window->GetShell()->GetText(); if (suffix.isEmpty()) { return QString::null; } QString sb; if (number < 10) { sb.append('&'); } sb.append(QString::number(number)); sb.append(' '); if (suffix.size() <= MAX_TEXT_LENGTH) { sb.append(suffix); } else { - sb.append(suffix.left(MAX_TEXT_LENGTH)); + sb.append(suffix.leftRef(MAX_TEXT_LENGTH)); sb.append("..."); } return sb; } SwitchToWindowMenu::SwitchToWindowMenu(IWorkbenchWindow* window, const QString& id, bool showSeparator) : ContributionItem(id) , workbenchWindow(window) , showSeparator(showSeparator) , dirty(true) { } void SwitchToWindowMenu::Fill(QMenu* menu, QAction* before) { // Get workbench windows. IWorkbench* workbench = workbenchWindow->GetWorkbench(); windows.clear(); - for (auto window : workbench->GetWorkbenchWindows()) + for (const auto &window : workbench->GetWorkbenchWindows()) { windows.push_back(window.GetPointer()); } // avoid showing the separator and list for 0 or 1 items if (windows.size() < 2) { return; } if (MenuManager* mm = dynamic_cast(GetParent())) { this->connect(mm, SIGNAL(AboutToShow(IMenuManager*)), SLOT(AboutToShow(IMenuManager*))); } if (!dirty) { return; } // Add separator. if (showSeparator) { menu->insertSeparator(before); } // Add one item for each window. auto actionGroup = new QActionGroup(menu); actionGroup->setExclusive(true); auto signalMapper = new QSignalMapper(menu); connect(signalMapper, SIGNAL(mapped(int)), SLOT(MenuItemTriggered(int))); int count = 0; - for (auto window : windows) + for (auto window : qAsConst(windows)) { // can encounter disposed shells if this update is in response to a shell closing //if (!window->GetShell()->IsDisposed()) //{ QString name = CalcText(count, window); if (!name.isEmpty()) { auto mi = new QAction(name, menu); mi->setCheckable(true); mi->setChecked(window == workbenchWindow); actionGroup->addAction(mi); menu->insertAction(before, mi); signalMapper->setMapping(mi, count); connect(mi, SIGNAL(triggered()), signalMapper, SLOT(map())); } ++count; } //} dirty = false; } bool SwitchToWindowMenu::IsDirty() const { return dirty; } bool SwitchToWindowMenu::IsDynamic() const { return true; } } diff --git a/Plugins/org.blueberry.ui.qt/src/internal/dialogs/berryPerspectivesPreferencePage.cpp b/Plugins/org.blueberry.ui.qt/src/internal/dialogs/berryPerspectivesPreferencePage.cpp index ea3d0eabd9..b1050da66d 100644 --- a/Plugins/org.blueberry.ui.qt/src/internal/dialogs/berryPerspectivesPreferencePage.cpp +++ b/Plugins/org.blueberry.ui.qt/src/internal/dialogs/berryPerspectivesPreferencePage.cpp @@ -1,284 +1,284 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "berryPerspectivesPreferencePage.h" #include "ui_berryPerspectivesPreferencePage.h" #include #include #include #include "internal/berryPerspective.h" #include "internal/berryPerspectiveRegistry.h" #include "internal/berryPreferenceConstants.h" #include "internal/berryWorkbenchPage.h" #include "berryWorkbenchPlugin.h" #include #include namespace berry { bool PerspectiveComparator(const PerspectiveDescriptor::Pointer& p1, const PerspectiveDescriptor::Pointer& p2) { return p1->GetLabel() < p2->GetLabel(); } PerspectivesPreferencePage::PerspectivesPreferencePage() : ui(nullptr) , pageWidget(nullptr) , workbench(nullptr) , perspRegistry(nullptr) { } PerspectivesPreferencePage::~PerspectivesPreferencePage() { delete ui; } void PerspectivesPreferencePage::Init(berry::IWorkbench::Pointer workbench) { ui = new Ui::PerspectivesPreferencePage; this->workbench = workbench.GetPointer(); perspRegistry = dynamic_cast(workbench->GetPerspectiveRegistry()); } void PerspectivesPreferencePage::CreateQtControl(QWidget* parent) { pageWidget = new QWidget(parent); ui->setupUi(pageWidget); ui->perspectivesListWidget->setSelectionMode(QAbstractItemView::SingleSelection); ui->perspectivesListWidget->setIconSize(QSize(16, 16)); connect(ui->sameWindowButton, SIGNAL(clicked()), this, SLOT(OpenPerspInSameWindow())); connect(ui->newWindowButton, SIGNAL(clicked()), this, SLOT(OpenPerspInNewWindow())); connect(ui->perspectivesListWidget, SIGNAL(itemSelectionChanged()), this, SLOT(PerspectiveSelectionChanged())); connect(ui->revertButton, SIGNAL(clicked()), this, SLOT(RevertPerspective())); connect(ui->makeDefaultButton, SIGNAL(clicked()), this, SLOT(MakeDefaultPerspective())); connect(ui->deleteButton, SIGNAL(clicked()), this, SLOT(DeletePerspective())); this->Update(); } QWidget* PerspectivesPreferencePage::GetQtControl() const { return pageWidget; } bool PerspectivesPreferencePage::PerformOk() { // Set the default perspective if (defaultPerspectiveId != perspRegistry->GetDefaultPerspective()) { perspRegistry->SetDefaultPerspective(defaultPerspectiveId); } //Delete the perspective if(perspectives.size() < perspRegistry->GetPerspectives().size()) { QList windows = workbench->GetWorkbenchWindows(); // close any perspectives that are about to be deleted for (int i = 0; i < windows.size(); i++) { QList pages = windows[i]->GetPages(); for (int j = 0; j < pages.size(); j++) { WorkbenchPage::Pointer page = pages[j].Cast(); for (int k = 0; k < perspToDelete.size(); k++) { IPerspectiveDescriptor::Pointer desc(perspToDelete[k].GetPointer()); if (page->FindPerspective(desc).IsNotNull()) { page->ClosePerspective(desc, true, true); } } } } perspRegistry->DeletePerspectives(perspToDelete); } // Revert the perspectives perspRegistry->RevertPerspectives(perspToRevert); // store the open perspective mode setting preferences->PutInt(PreferenceConstants::OPEN_PERSP_MODE, openPerspMode); return true; } void PerspectivesPreferencePage::PerformCancel() { } void PerspectivesPreferencePage::Update() { preferences = WorkbenchPlugin::GetDefault()->GetPreferences(); openPerspMode = preferences->GetInt(PreferenceConstants::OPEN_PERSP_MODE, PreferenceConstants::OPM_ACTIVE_PAGE); ui->sameWindowButton->setChecked(openPerspMode == PreferenceConstants::OPM_ACTIVE_PAGE); ui->newWindowButton->setChecked(openPerspMode == PreferenceConstants::OPM_NEW_WINDOW); // Populate the perspectivesTable perspectives.clear(); perspToRevert.clear(); perspToDelete.clear(); QList persps = perspRegistry->GetPerspectives(); for (int i = 0; i < persps.size(); i++) { perspectives.push_back(persps[i].Cast()); } qSort(perspectives.begin(), perspectives.end(), PerspectiveComparator); defaultPerspectiveId = perspRegistry->GetDefaultPerspective(); UpdatePerspectivesTable(); } void PerspectivesPreferencePage::OpenPerspInSameWindow() { openPerspMode = PreferenceConstants::OPM_ACTIVE_PAGE; } void PerspectivesPreferencePage::OpenPerspInNewWindow() { openPerspMode = PreferenceConstants::OPM_NEW_WINDOW; } void PerspectivesPreferencePage::PerspectiveSelectionChanged() { UpdateButtons(); } void PerspectivesPreferencePage::RevertPerspective() { PerspectiveDescriptor::Pointer desc = GetSelectedPerspective(); if (desc.IsNotNull() && !perspToRevert.contains(desc)) { perspToRevert.push_back(desc); } UpdateButtons(); } void PerspectivesPreferencePage::DeletePerspective() { PerspectiveDescriptor::Pointer desc = GetSelectedPerspective(); if (desc.IsNotNull() && !perspToDelete.contains(desc)) { if (!FindOpenInstance(desc)) { perspToDelete.push_back(desc); perspToRevert.removeAll(desc); perspectives.removeAll(desc); UpdatePerspectivesTable(); } } UpdateButtons(); } void PerspectivesPreferencePage::MakeDefaultPerspective() { PerspectiveDescriptor::Pointer desc = GetSelectedPerspective(); if (desc.IsNotNull() && !perspToDelete.contains(desc)) { int row = perspectives.indexOf(desc); defaultPerspectiveId = desc->GetId(); UpdatePerspectivesTable(); ui->perspectivesListWidget->item(row)->setSelected(true); } UpdateButtons(); } void PerspectivesPreferencePage::UpdateButtons() { PerspectiveDescriptor::Pointer desc = GetSelectedPerspective(); if (desc) { ui->revertButton->setEnabled(desc->IsPredefined() && desc->HasCustomDefinition() && !perspToRevert.contains(desc)); ui->deleteButton->setEnabled(!desc->IsPredefined()); ui->makeDefaultButton->setEnabled(true); } else { ui->revertButton->setEnabled(false); ui->deleteButton->setEnabled(false); ui->makeDefaultButton->setEnabled(false); } } void PerspectivesPreferencePage::UpdatePerspectivesTable() { ui->perspectivesListWidget->clear(); - for (PerspectiveDescriptor::Pointer desc : perspectives) + for (const PerspectiveDescriptor::Pointer &desc : qAsConst(perspectives)) { NewPerspectivesTableItem(desc); } } void PerspectivesPreferencePage::NewPerspectivesTableItem(const SmartPointer& desc) { QString label = desc->GetLabel(); if (desc->GetId() == defaultPerspectiveId) { label += " (default)"; } new QListWidgetItem(desc->GetImageDescriptor(), label, ui->perspectivesListWidget); } bool PerspectivesPreferencePage::FindOpenInstance(const PerspectiveDescriptor::Pointer& desc) { QList windows = workbench->GetWorkbenchWindows(); //find all active perspectives currently for (int i = 0; i < windows.size(); i++) { QList pages = windows[i]->GetPages(); for (int j = 0; j < pages.size(); j++) { WorkbenchPage::Pointer page = pages[j].Cast(); if (page->FindPerspective(desc).IsNotNull()) { QMessageBox::StandardButton returnCode = QMessageBox::question(workbench->GetActiveWorkbenchWindow()->GetShell()->GetControl(), "Delete Perspective", QString("Are you sure you want to delete the \"%1\" perspective? It has open instances.").arg(desc->GetLabel()), QMessageBox::Yes | QMessageBox::No, QMessageBox::No); return (returnCode != QMessageBox::Yes); } } } return false; } SmartPointer PerspectivesPreferencePage::GetSelectedPerspective() const { PerspectiveDescriptor::Pointer desc; QList selection = ui->perspectivesListWidget->selectedItems(); if (!selection.isEmpty()) { int row = ui->perspectivesListWidget->row(selection.back()); if (row > -1) { desc = perspectives.at(row); } } return desc; } } diff --git a/Plugins/org.blueberry.ui.qt/src/internal/handlers/berryShowViewHandler.cpp b/Plugins/org.blueberry.ui.qt/src/internal/handlers/berryShowViewHandler.cpp index 3422f36133..bee11dae60 100644 --- a/Plugins/org.blueberry.ui.qt/src/internal/handlers/berryShowViewHandler.cpp +++ b/Plugins/org.blueberry.ui.qt/src/internal/handlers/berryShowViewHandler.cpp @@ -1,112 +1,112 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "berryShowViewHandler.h" #include "berryIWorkbenchCommandConstants.h" #include "berryHandlerUtil.h" #include "berryUIException.h" #include "berryIWorkbenchPage.h" #include "berryIViewDescriptor.h" #include "berryPlatformUI.h" #include "berryWorkbenchPlugin.h" #include "internal/berryQtShowViewDialog.h" #include #include namespace berry { ShowViewHandler::ShowViewHandler() { } Object::Pointer ShowViewHandler::Execute(const ExecutionEvent::ConstPointer& event) { IWorkbenchWindow::Pointer window = HandlerUtil::GetActiveWorkbenchWindowChecked(event); // Get the view identifier, if any. const ExecutionEvent::ParameterMap& parameters = event->GetParameters(); ExecutionEvent::ParameterMap::const_iterator result = parameters.find(IWorkbenchCommandConstants::VIEWS_SHOW_VIEW_PARM_ID); QString viewId = result != parameters.end() ? result.value() : QString::null; result = parameters.find(IWorkbenchCommandConstants::VIEWS_SHOW_VIEW_SECONDARY_ID); QString secondary = result != parameters.end() ? result.value() : QString::null; if (viewId.isEmpty()) { this->OpenOther(window); } else { try { this->OpenView(viewId, secondary, window); } catch (const PartInitException& e) { throw ExecutionException("Part could not be initialized", e); } } return Object::Pointer(nullptr); } void ShowViewHandler::OpenOther(IWorkbenchWindow::Pointer window) { const IWorkbenchPage::Pointer page = window->GetActivePage(); if (page.IsNull()) { return; } QtShowViewDialog dialog(window.GetPointer(), WorkbenchPlugin::GetDefault()->GetViewRegistry()); int returnCode = dialog.exec(); if (returnCode == QDialog::Rejected) { return; } const QList descriptors = dialog.GetSelection(); - for (QString id : descriptors) + for (const QString &id : descriptors) { try { this->OpenView(id, QString(), window); } catch (const PartInitException& e) { BERRY_WARN << e.what(); // StatusUtil.handleStatus(e.getStatus(), // WorkbenchMessages.ShowView_errorTitle // + ": " + e.getMessage(), //$NON-NLS-1$ // StatusManager.SHOW); } } } void ShowViewHandler::OpenView(const QString& viewId, const QString& secondaryId, IWorkbenchWindow::Pointer activeWorkbenchWindow) { const IWorkbenchPage::Pointer activePage = activeWorkbenchWindow->GetActivePage(); if (activePage.IsNull()) { return; } activePage->ShowView(viewId, secondaryId, IWorkbenchPage::VIEW_ACTIVATE); } } diff --git a/Plugins/org.blueberry.ui.qt/src/model/berryViewTreeModel.cpp b/Plugins/org.blueberry.ui.qt/src/model/berryViewTreeModel.cpp index 5911366970..790bb57380 100644 --- a/Plugins/org.blueberry.ui.qt/src/model/berryViewTreeModel.cpp +++ b/Plugins/org.blueberry.ui.qt/src/model/berryViewTreeModel.cpp @@ -1,460 +1,460 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "berryViewTreeModel.h" #include "berryIViewRegistry.h" #include "berryIViewCategory.h" #include "berryIWorkbench.h" #include "berryIWorkbenchWindow.h" #include "berryIWorkbenchPage.h" #include "internal/intro/berryIntroConstants.h" #include "internal/berryKeywordRegistry.h" #include #include namespace berry { // --------------------------- Tree Item Classes --------------------------- struct ViewTreeItem; bool CompareViewTreeItem(ViewTreeItem* item1, ViewTreeItem* item2); struct ViewTreeItem { ViewTreeItem(ViewTreeModel* model) : m_parent(nullptr) , m_model(model) {} virtual ~ViewTreeItem() { QList children = m_children; if (m_parent) m_parent->removeChild(this); qDeleteAll(children); } virtual QVariant data(int role) { if (role == ViewTreeModel::Keywords) { if (m_keywordCache.isEmpty()) { m_keywordCache = QStringList(keywordLabels().toList()); } return m_keywordCache; } return QVariant(); } virtual Qt::ItemFlags flags() const { return Qt::ItemIsEnabled | Qt::ItemIsSelectable; } virtual QSet keywordLabels() const { return QSet(); } void appendChild(ViewTreeItem* child) { m_children.push_back(child); child->m_parent = this; qSort(m_children.begin(), m_children.end(), CompareViewTreeItem); } void removeChild(ViewTreeItem* child) { m_children.removeAll(child); } QList takeChildren() { QList children = m_children; m_children.clear(); return children; } ViewTreeItem* childItem(int row) const { if (row < 0 || row >= m_children.size()) return nullptr; return m_children.at(row); } ViewTreeItem* parentItem() const { return m_parent; } int childCount() const { return m_children.size(); } int row() const { if (m_parent) return m_parent->rowIndex(this); return 0; } int rowIndex(const ViewTreeItem* child) const { return m_children.indexOf(const_cast(child)); } QList m_children; ViewTreeItem* m_parent; ViewTreeModel* m_model; private: QStringList m_keywordCache; }; bool CompareViewTreeItem(ViewTreeItem* item1, ViewTreeItem* item2) { return item1->data(Qt::DisplayRole).toString() < item2->data(Qt::DisplayRole).toString(); } struct RootTreeItem : ViewTreeItem { RootTreeItem(ViewTreeModel* model) : ViewTreeItem(model) {} QVariant data(int /*role*/) override { return QVariant(); } }; struct DescriptorTreeItem : ViewTreeItem { DescriptorTreeItem(ViewTreeModel* model, IViewDescriptor::Pointer descriptor, ViewTreeItem* parent = nullptr); QVariant data(int role) override; protected: QSet keywordLabels() const override; IViewDescriptor::Pointer m_descriptor; }; struct CategoryTreeItem : ViewTreeItem { CategoryTreeItem(ViewTreeModel* model, IViewCategory::Pointer category, ViewTreeItem* parent = nullptr); QVariant data(int role) override; Qt::ItemFlags flags() const override; protected: QSet keywordLabels() const override; /** * Removes the temporary intro view from the list so that it cannot be activated except through * the introduction command. */ void RemoveIntroView(QList& list); private: void CreateChildren(); IViewCategory::Pointer m_category; }; // --------------------------- Tree Model Classes --------------------------- struct ViewTreeModel::Impl { Impl(const IWorkbenchWindow* window) : window(window) , viewRegistry(*window->GetWorkbench()->GetViewRegistry()) { } const IWorkbenchWindow* window; IViewRegistry& viewRegistry; QScopedPointer rootItem; }; ViewTreeModel::ViewTreeModel(const IWorkbenchWindow* window, QObject* parent) : QAbstractItemModel(parent) , d(new Impl(window)) { d->rootItem.reset(new RootTreeItem(this)); QList categoryItems; QList categories = d->viewRegistry.GetCategories(); - for (auto category : categories) + for (const auto &category : qAsConst(categories)) { if (category->GetViews().isEmpty()) continue; CategoryTreeItem* categoryItem = new CategoryTreeItem(this, category); if (categoryItem->childCount() == 0) { delete categoryItem; } else { categoryItems.push_back(categoryItem); } } // if there is only one category, return it's children directly if (categoryItems.size() == 1) { QList items = categoryItems.front()->takeChildren(); - for (auto item : items) + for (auto item : qAsConst(items)) { d->rootItem->appendChild(item); } qDeleteAll(categoryItems); } else { - for (auto category : categoryItems) + for (auto category : qAsConst(categoryItems)) { d->rootItem->appendChild(category); } } } ViewTreeModel::~ViewTreeModel() { } QVariant ViewTreeModel::data(const QModelIndex& index, int role) const { if (!index.isValid()) return QVariant(); return static_cast(index.internalPointer())->data(role); } Qt::ItemFlags ViewTreeModel::flags(const QModelIndex& index) const { if (!index.isValid()) return nullptr; return static_cast(index.internalPointer())->flags(); } QVariant ViewTreeModel::headerData(int section, Qt::Orientation /*orientation*/, int role) const { if (role == Qt::DisplayRole && section == 0) { return "View"; } return QVariant(); } QModelIndex ViewTreeModel::index(int row, int column, const QModelIndex& parent) const { if (!hasIndex(row, column, parent)) { return QModelIndex(); } ViewTreeItem* parentItem = nullptr; if (!parent.isValid()) { parentItem = d->rootItem.data(); } else { parentItem = static_cast(parent.internalPointer()); } ViewTreeItem* childItem = parentItem->childItem(row); if (childItem) { return createIndex(row, column, childItem); } return QModelIndex(); } QModelIndex ViewTreeModel::parent(const QModelIndex& child) const { if (!child.isValid()) { return QModelIndex(); } ViewTreeItem* childItem = static_cast(child.internalPointer()); ViewTreeItem* parentItem = childItem->parentItem(); if (parentItem == d->rootItem.data()) { return QModelIndex(); } return createIndex(parentItem->row(), 0, parentItem); } int ViewTreeModel::rowCount(const QModelIndex& parent) const { ViewTreeItem* parentItem = nullptr; if (parent.column() > 0) return 0; if (!parent.isValid()) { parentItem = d->rootItem.data(); } else { parentItem = static_cast(parent.internalPointer()); } return parentItem->childCount(); } int ViewTreeModel::columnCount(const QModelIndex& /*parent*/) const { return 1; } const IWorkbenchWindow*ViewTreeModel::GetWorkbenchWindow() const { return d->window; } // --------------------------- DescriptorTreeItem --------------------------- DescriptorTreeItem::DescriptorTreeItem(ViewTreeModel* model, IViewDescriptor::Pointer descriptor, ViewTreeItem* parent) : ViewTreeItem(model) , m_descriptor(descriptor) { if (parent) parent->appendChild(this); } QVariant DescriptorTreeItem::data(int role) { if (role == Qt::DisplayRole) { return m_descriptor->GetLabel(); } else if (role == Qt::DecorationRole) { return m_descriptor->GetImageDescriptor(); } else if (role == Qt::ForegroundRole) { IWorkbenchPage::Pointer page = this->m_model->GetWorkbenchWindow()->GetActivePage(); if (page.IsNotNull()) { if (page->FindViewReference(m_descriptor->GetId()).IsNotNull()) { return QBrush(QColor(Qt::gray)); } } } else if (role == ViewTreeModel::Description) { return m_descriptor->GetDescription(); } else if (role == ViewTreeModel::Id) { return m_descriptor->GetId(); } return ViewTreeItem::data(role); } QSet DescriptorTreeItem::keywordLabels() const { KeywordRegistry* registry = KeywordRegistry::GetInstance(); QStringList ids = m_descriptor->GetKeywordReferences(); QSet keywords; keywords.insert(m_descriptor->GetLabel()); - for(auto id : ids) + for(const auto &id : qAsConst(ids)) { QString label = registry->GetKeywordLabel(id); - for (auto keyword : label.split(' ', QString::SkipEmptyParts)) + for (const auto &keyword : label.split(' ', QString::SkipEmptyParts)) { keywords.insert(keyword); } } return keywords; } // --------------------------- CategoryTreeItem --------------------------- CategoryTreeItem::CategoryTreeItem(ViewTreeModel* model, IViewCategory::Pointer category, ViewTreeItem* parent) : ViewTreeItem(model) , m_category(category) { if (parent) parent->appendChild(this); this->CreateChildren(); } QVariant CategoryTreeItem::data(int role) { if (role == Qt::DisplayRole) { return m_category->GetLabel(); } else if (role == Qt::DecorationRole) { return QIcon::fromTheme("folder"); } else if (role == ViewTreeModel::Id) { return m_category->GetId(); } return ViewTreeItem::data(role); } Qt::ItemFlags CategoryTreeItem::flags() const { return Qt::ItemIsEnabled; } QSet CategoryTreeItem::keywordLabels() const { QSet keywords; for(auto child : this->m_children) { - for (auto keyword : child->data(ViewTreeModel::Keywords).toStringList()) + for (const auto &keyword : child->data(ViewTreeModel::Keywords).toStringList()) { keywords.insert(keyword); } } return keywords; } void CategoryTreeItem::CreateChildren() { auto viewDescriptors = m_category->GetViews(); RemoveIntroView(viewDescriptors); - for(auto viewDescriptor : viewDescriptors) + for(const auto &viewDescriptor : qAsConst(viewDescriptors)) { new DescriptorTreeItem(this->m_model, viewDescriptor, this); } } void CategoryTreeItem::RemoveIntroView(QList& list) { for (auto view = list.begin(); view != list.end();) { if ((*view)->GetId() == IntroConstants::INTRO_VIEW_ID) { view = list.erase(view); } else ++view; } } } diff --git a/Plugins/org.blueberry.ui.qt/src/presentations/berryIPresentationFactory.h b/Plugins/org.blueberry.ui.qt/src/presentations/berryIPresentationFactory.h index 710933f8c7..d343d2f512 100755 --- a/Plugins/org.blueberry.ui.qt/src/presentations/berryIPresentationFactory.h +++ b/Plugins/org.blueberry.ui.qt/src/presentations/berryIPresentationFactory.h @@ -1,181 +1,158 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef BERRYIPRESENTATIONFACTORY_H_ #define BERRYIPRESENTATIONFACTORY_H_ #include #include "berryStackPresentation.h" #include namespace berry { /** * This is a factory for presentation objects that control the appearance of * editors, views and other components in the workbench. * * @since 3.0 */ class BERRY_UI_QT IPresentationFactory { public: virtual ~IPresentationFactory(); /** * Bit value for the createSash method's 'style' parameter. * @since 3.4 */ static int SASHTYPE_NORMAL; // = 0; /** * Bit value for the createSash method's 'style' parameter. * @since 3.4 */ static int SASHTYPE_FLOATING; // = 1<<1; /** * Bit value for the createSash method's 'style' parameter. * @since 3.4 */ static int SASHORIENTATION_HORIZONTAL; // = SWT.HORIZONTAL; // 1<<8 /** * Bit value for the createSash method's 'style' parameter. * @since 3.4 */ static int SASHORIENTATION_VERTICAL; // = SWT.VERTICAL; // 1<<9 /** * Creates an editor presentation for presenting editors. *

* The presentation creates its controls under the given parent composite. *

* * @param parent * the parent composite to use for the presentation's controls * @param site * the site used for communication between the presentation and * the workbench * @return a newly created part presentation */ virtual StackPresentation::Pointer CreateEditorPresentation( QWidget* parent, IStackPresentationSite::Pointer site) = 0; /** * Creates a stack presentation for presenting regular docked views. *

* The presentation creates its controls under the given parent composite. *

* * @param parent * the parent composite to use for the presentation's controls * @param site * the site used for communication between the presentation and * the workbench * @return a newly created part presentation */ virtual StackPresentation::Pointer CreateViewPresentation(QWidget* parent, IStackPresentationSite::Pointer site) = 0; /** * Creates a standalone stack presentation for presenting a standalone view. * A standalone view cannot be docked together with other views. The title * of a standalone view may be hidden. *

* The presentation creates its controls under the given parent composite. *

* * @param parent * the parent composite to use for the presentation's controls * @param site * the site used for communication between the presentation and * the workbench * @param showTitle * true to show the title for the view, * false to hide it * @return a newly created part presentation */ virtual StackPresentation::Pointer CreateStandaloneViewPresentation( QWidget* parent, IStackPresentationSite::Pointer site, bool showTitle) = 0; - /** - * Creates the status line manager for the window. - * Subclasses may override. - * - * @return the window's status line manager - */ -// public IStatusLineManager createStatusLineManager() { -// return new StatusLineManager(); -// } - - /** - * Creates the control for the window's status line. - * Subclasses may override. - * - * @param statusLine the window's status line manager - * @param parent the parent composite - * @return the window's status line control - */ -// public Control createStatusLineControl(IStatusLineManager statusLine, -// Composite parent) { -// return ((StatusLineManager) statusLine).createControl(parent, SWT.NONE); -// } - /** * Returns a globally unique identifier for this type of presentation factory. This is used * to ensure that one presentation is not restored from mementos saved by a different * presentation. * * @return a globally unique identifier for this type of presentation factory. */ virtual QString GetId() = 0; /** * Creates the Sash control that is used to separate view and editor parts. * * @param parent the parent composite * @param style A bit set giving both the 'type' of the desired sash and * its orientation (i.e. one 'SASHTYPE' value and one "SASHORIENTATION" value). * @return the sash control * @since 3.4 */ virtual QWidget* CreateSash(QWidget* parent, int style) = 0; // { // int orientation = style & (SASHORIENTATION_HORIZONTAL // | SASHORIENTATION_VERTICAL); // Sash sash = new Sash(parent, orientation | SWT.SMOOTH); // return sash; // } /** * Returns the size of the Sash control that is used to separate view and editor parts. * * @param style A bit set giving both the 'type' of the desired sash and * its orientation. * @return the sash size * @since 3.4 */ virtual int GetSashSize(int style) = 0; /** * Applies changes of the current theme to the user interface. */ virtual void UpdateTheme() = 0; }; } Q_DECLARE_INTERFACE(berry::IPresentationFactory, "org.blueberry.ui.IPresentationFactory") #endif /* BERRYABSTRACTPRESENTATIONFACTORY_H_ */ diff --git a/Plugins/org.blueberry.ui.qt/src/presentations/berryIStackPresentationSite.h b/Plugins/org.blueberry.ui.qt/src/presentations/berryIStackPresentationSite.h index 089152e7c4..c32e544487 100755 --- a/Plugins/org.blueberry.ui.qt/src/presentations/berryIStackPresentationSite.h +++ b/Plugins/org.blueberry.ui.qt/src/presentations/berryIStackPresentationSite.h @@ -1,187 +1,172 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 BERRYISTACKPRESENTATIONSITE_H_ #define BERRYISTACKPRESENTATIONSITE_H_ #include #include #include "berryIPresentablePart.h" #include namespace berry { /** * Represents the main interface between a StackPresentation and the workbench. * * Not intended to be implemented by clients. * * @since 3.0 */ struct BERRY_UI_QT IStackPresentationSite : public Object { berryObjectMacro(berry::IStackPresentationSite); static int STATE_MINIMIZED; // = 0; static int STATE_MAXIMIZED; // = 1; static int STATE_RESTORED; // = 2; ~IStackPresentationSite() override; /** * Sets the state of the container. Called by the presentation when the * user causes the the container to be minimized, maximized, etc. * * @param newState one of the STATE_* constants */ virtual void SetState(int newState) = 0; /** * Returns the current state of the site (one of the STATE_* constants) * * @return the current state of the site (one of the STATE_* constants) */ virtual int GetState() = 0; /** * Returns true iff the site supports the given state * * @param state one of the STATE_* constants, above * @return true iff the site supports the given state */ virtual bool SupportsState(int state) = 0; /** * Begins dragging the given part * * @param beingDragged the part to drag (not null) * @param initialPosition the mouse position at the time of the initial mousedown * (display coordinates, not null) * @param keyboard true iff the drag was initiated via mouse dragging, * and false if the drag may be using the keyboard */ virtual void DragStart(IPresentablePart::Pointer beingDragged, QPoint& initialPosition, bool keyboard) = 0; /** * Closes the given set of parts. * * @param toClose the set of parts to close (Not null. All of the entries must be non-null) */ virtual void Close(const QList& toClose) = 0; /** * Begins dragging the entire stack of parts * * @param initialPosition the mouse position at the time of the initial mousedown (display coordinates, * not null) * @param keyboard true iff the drag was initiated via mouse dragging, * and false if the drag may be using the keyboard */ virtual void DragStart(QPoint& initialPosition, bool keyboard) = 0; /** * Returns true iff this site will allow the given part to be closed * * @param toClose part to test (not null) * @return true iff the part may be closed */ virtual bool IsCloseable(IPresentablePart::Pointer toClose) = 0; /** * Returns true iff the given part can be dragged. If this * returns false, the given part should not trigger a drag. * * @param toMove part to test (not null) * @return true iff this part is a valid drag source */ virtual bool IsPartMoveable(IPresentablePart::Pointer toMove) = 0; /** * Returns true iff this entire stack can be dragged * * @return true iff the stack can be dragged */ virtual bool IsStackMoveable() = 0; /** * Makes the given part active * * @param toSelect */ virtual void SelectPart(IPresentablePart::Pointer toSelect) = 0; /** * Returns the currently selected part or null if the stack is empty * * @return the currently selected part or null if the stack is empty */ virtual IPresentablePart::Pointer GetSelectedPart() = 0; - /** - * Adds system actions to the given menu manager. The site may - * make use of the following group ids: - *
    - *
  • close, for close actions
    • - *
  • size, for resize actions
    • - *
  • misc, for miscellaneous actions
    • - *
- * The presentation can control the insertion position by creating - * these group IDs where appropriate. - * - * @param menuManager the menu manager to populate - */ - //virtual void AddSystemActions(IMenuManager menuManager); - /** * Notifies the workbench that the preferred size of the presentation has * changed. Hints to the workbench that it should trigger a layout at the * next opportunity. * * @since 3.1 */ virtual void FlushLayout() = 0; /** * Returns the list of presentable parts currently in this site * * @return the list of presentable parts currently in this site * @since 3.1 */ virtual QList GetPartList() = 0; /** * Returns the property with the given id or null. Folder * properties are an extensible mechanism for perspective authors to * customize the appearance of view stacks. The list of customizable * properties is determined by the presentation factory, and set in the * perspective factory. * * @param id * Must not be null. * @return property value, or null if the property is not * set. * @since 3.3 */ virtual QString GetProperty(const QString& id) = 0; }; } #endif /* BERRYISTACKPRESENTATIONSITE_H_ */ diff --git a/Plugins/org.mitk.gui.qt.application/src/QmitkDataNodeContextMenu.cpp b/Plugins/org.mitk.gui.qt.application/src/QmitkDataNodeContextMenu.cpp index de2ccb87e7..a8a7e00ce6 100644 --- a/Plugins/org.mitk.gui.qt.application/src/QmitkDataNodeContextMenu.cpp +++ b/Plugins/org.mitk.gui.qt.application/src/QmitkDataNodeContextMenu.cpp @@ -1,480 +1,480 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include #include #include #include #include #include #include #include #include #include QmitkDataNodeContextMenu::QmitkDataNodeContextMenu(berry::IWorkbenchPartSite::Pointer workbenchPartSite, QWidget* parent) : QMenu(parent), m_Parent(parent), m_WorkbenchPartSite(workbenchPartSite) { this->InitNodeDescriptors(); this->InitDefaultActions(); this->InitExtensionPointActions(); } QmitkDataNodeContextMenu::~QmitkDataNodeContextMenu() { for (auto& descriptorActionPair : m_DescriptorActionList) descriptorActionPair.first->RemoveAction(descriptorActionPair.second); } void QmitkDataNodeContextMenu::SetDataStorage(mitk::DataStorage* dataStorage) { m_DataStorage = dataStorage; for (auto& descriptorActionPair : m_DescriptorActionList) { auto dataNodeAction = dynamic_cast(descriptorActionPair.second); if (nullptr != dataNodeAction) dataNodeAction->SetDataStorage(dataStorage); } } void QmitkDataNodeContextMenu::SetBaseRenderer(mitk::BaseRenderer* baseRenderer) { m_BaseRenderer = baseRenderer; for (auto& descriptorActionPair : m_DescriptorActionList) { auto dataNodeAction = dynamic_cast(descriptorActionPair.second); if (nullptr != dataNodeAction) dataNodeAction->SetBaseRenderer(baseRenderer); } } void QmitkDataNodeContextMenu::SetSurfaceDecimation(bool surfaceDecimation) { m_SurfaceDecimation = surfaceDecimation; } void QmitkDataNodeContextMenu::SetSelectedNodes(const QList& selectedNodes) { m_SelectedNodes = selectedNodes; } void QmitkDataNodeContextMenu::InitNodeDescriptors() { auto nodeDescriptorManager = QmitkNodeDescriptorManager::GetInstance(); m_UnknownDataNodeDescriptor = nodeDescriptorManager->GetUnknownDataNodeDescriptor(); m_ImageDataNodeDescriptor = nodeDescriptorManager->GetDescriptor("Image"); m_MultiComponentImageDataNodeDescriptor = nodeDescriptorManager->GetDescriptor("MultiComponentImage"); m_DiffusionImageDataNodeDescriptor = nodeDescriptorManager->GetDescriptor("DiffusionImage"); m_FiberBundleDataNodeDescriptor = nodeDescriptorManager->GetDescriptor("FiberBundle"); m_PeakImageDataNodeDescriptor = nodeDescriptorManager->GetDescriptor("PeakImage"); m_SegmentDataNodeDescriptor = nodeDescriptorManager->GetDescriptor("Segment"); m_SurfaceDataNodeDescriptor = nodeDescriptorManager->GetDescriptor("Surface"); m_PointSetNodeDescriptor = nodeDescriptorManager->GetDescriptor("PointSet"); m_PlanarLineNodeDescriptor = nodeDescriptorManager->GetDescriptor("PlanarLine"); m_PlanarCircleNodeDescriptor = nodeDescriptorManager->GetDescriptor("PlanarCircle"); m_PlanarEllipseNodeDescriptor = nodeDescriptorManager->GetDescriptor("PlanarEllipse"); m_PlanarAngleNodeDescriptor = nodeDescriptorManager->GetDescriptor("PlanarAngle"); m_PlanarFourPointAngleNodeDescriptor = nodeDescriptorManager->GetDescriptor("PlanarFourPointAngle"); m_PlanarRectangleNodeDescriptor = nodeDescriptorManager->GetDescriptor("PlanarRectangle"); m_PlanarPolygonNodeDescriptor = nodeDescriptorManager->GetDescriptor("PlanarPolygon"); m_PlanarPathNodeDescriptor = nodeDescriptorManager->GetDescriptor("PlanarPath"); m_PlanarDoubleEllipseNodeDescriptor = nodeDescriptorManager->GetDescriptor("PlanarDoubleEllipse"); m_PlanarBezierCurveNodeDescriptor = nodeDescriptorManager->GetDescriptor("PlanarBezierCurve"); m_PlanarSubdivisionPolygonNodeDescriptor = nodeDescriptorManager->GetDescriptor("PlanarSubdivisionPolygon"); } void QmitkDataNodeContextMenu::InitDefaultActions() { auto workbenchPartSite = m_WorkbenchPartSite.Lock(); m_GlobalReinitAction = new QmitkDataNodeGlobalReinitAction(m_Parent, workbenchPartSite); m_GlobalReinitAction->setIcon(QIcon(":/org.mitk.gui.qt.datamanager/Refresh_48.png")); m_UnknownDataNodeDescriptor->AddAction(m_GlobalReinitAction, true); m_DescriptorActionList.push_back(std::make_pair(m_UnknownDataNodeDescriptor, m_GlobalReinitAction)); m_ReinitAction = new QmitkDataNodeReinitAction(m_Parent, workbenchPartSite); m_ReinitAction->setIcon(QIcon(":/org.mitk.gui.qt.datamanager/Refresh_48.png")); m_UnknownDataNodeDescriptor->AddAction(m_ReinitAction, true); m_DescriptorActionList.push_back(std::make_pair(m_UnknownDataNodeDescriptor, m_ReinitAction)); QAction* saveAction = new QmitkFileSaveAction(QIcon(":/org.mitk.gui.qt.datamanager/Save_48.png"), workbenchPartSite->GetWorkbenchWindow()); m_UnknownDataNodeDescriptor->AddAction(saveAction, true); m_DescriptorActionList.push_back(std::make_pair(m_UnknownDataNodeDescriptor, saveAction)); m_RemoveAction = new QmitkDataNodeRemoveAction(m_Parent, workbenchPartSite); m_RemoveAction->setIcon(QIcon(":/org.mitk.gui.qt.datamanager/Remove_48.png")); m_UnknownDataNodeDescriptor->AddAction(m_RemoveAction, true); m_DescriptorActionList.push_back(std::make_pair(m_UnknownDataNodeDescriptor, m_RemoveAction)); m_ShowSelectedNodesAction = new QmitkDataNodeShowSelectedNodesAction(m_Parent, workbenchPartSite); m_RemoveAction->setIcon(QIcon(":/org.mitk.gui.qt.datamanager/ShowSelectedNode_48.png")); m_UnknownDataNodeDescriptor->AddAction(m_ShowSelectedNodesAction, true); m_DescriptorActionList.push_back(std::make_pair(m_UnknownDataNodeDescriptor, m_ShowSelectedNodesAction)); m_ToggleVisibilityAction = new QmitkDataNodeToggleVisibilityAction(m_Parent, workbenchPartSite); m_ToggleVisibilityAction->setIcon(QIcon(":/org.mitk.gui.qt.datamanager/InvertShowSelectedNode_48.png")); m_UnknownDataNodeDescriptor->AddAction(m_ToggleVisibilityAction, true); m_DescriptorActionList.push_back(std::make_pair(m_UnknownDataNodeDescriptor, m_ToggleVisibilityAction)); m_ShowDetailsAction = new QmitkDataNodeShowDetailsAction(m_Parent, workbenchPartSite); m_ShowDetailsAction->setIcon(QIcon(":/org.mitk.gui.qt.datamanager/ShowDataInfo_48.png")); m_UnknownDataNodeDescriptor->AddAction(m_ShowDetailsAction, true); m_DescriptorActionList.push_back(std::make_pair(m_UnknownDataNodeDescriptor, m_ShowDetailsAction)); m_OpacityAction = new QmitkDataNodeOpacityAction(m_Parent, workbenchPartSite); m_UnknownDataNodeDescriptor->AddAction(m_OpacityAction, false); m_DescriptorActionList.push_back(std::make_pair(m_UnknownDataNodeDescriptor, m_OpacityAction)); m_ColorAction = new QmitkDataNodeColorAction(m_Parent, workbenchPartSite); this->AddColorAction(m_ColorAction); m_ColormapAction = new QmitkDataNodeColorMapAction(m_Parent, workbenchPartSite); m_ImageDataNodeDescriptor->AddAction(m_ColormapAction); m_DescriptorActionList.push_back(std::make_pair(m_ImageDataNodeDescriptor, m_ColormapAction)); if (nullptr != m_DiffusionImageDataNodeDescriptor) { m_DiffusionImageDataNodeDescriptor->AddAction(m_ColormapAction, false); m_DescriptorActionList.push_back(std::make_pair(m_DiffusionImageDataNodeDescriptor, m_ColormapAction)); } m_ComponentAction = new QmitkDataNodeComponentAction(m_Parent, workbenchPartSite); m_MultiComponentImageDataNodeDescriptor->AddAction(m_ComponentAction, false); m_DescriptorActionList.push_back(std::make_pair(m_MultiComponentImageDataNodeDescriptor, m_ComponentAction)); if (nullptr != m_DiffusionImageDataNodeDescriptor) { m_DiffusionImageDataNodeDescriptor->AddAction(m_ComponentAction, false); m_DescriptorActionList.push_back(std::make_pair(m_DiffusionImageDataNodeDescriptor, m_ComponentAction)); } m_TextureInterpolationAction = new QmitkDataNodeTextureInterpolationAction(m_Parent, workbenchPartSite); m_ImageDataNodeDescriptor->AddAction(m_TextureInterpolationAction, false); m_DescriptorActionList.push_back(std::make_pair(m_ImageDataNodeDescriptor, m_TextureInterpolationAction)); if (nullptr != m_DiffusionImageDataNodeDescriptor) { m_DiffusionImageDataNodeDescriptor->AddAction(m_TextureInterpolationAction, false); m_DescriptorActionList.push_back(std::make_pair(m_DiffusionImageDataNodeDescriptor, m_TextureInterpolationAction)); } if (nullptr != m_SegmentDataNodeDescriptor) { m_SegmentDataNodeDescriptor->AddAction(m_TextureInterpolationAction, false); m_DescriptorActionList.push_back(std::make_pair(m_SegmentDataNodeDescriptor, m_TextureInterpolationAction)); } m_SurfaceRepresentationAction = new QmitkDataNodeSurfaceRepresentationAction(m_Parent, workbenchPartSite); m_SurfaceDataNodeDescriptor->AddAction(m_SurfaceRepresentationAction, false); m_DescriptorActionList.push_back(std::make_pair(m_SurfaceDataNodeDescriptor, m_SurfaceRepresentationAction)); } void QmitkDataNodeContextMenu::InitExtensionPointActions() { auto extensionPointService = berry::Platform::GetExtensionRegistry(); auto customMenuConfigs = extensionPointService->GetConfigurationElementsFor("org.mitk.gui.qt.datamanager.contextMenuActions"); DescriptorActionListType descriptorActionList; m_ConfigElements.clear(); - for (const auto& customMenuConfig : customMenuConfigs) + for (const auto& customMenuConfig : qAsConst(customMenuConfigs)) { auto descriptorName = customMenuConfig->GetAttribute("nodeDescriptorName"); auto actionLabel = customMenuConfig->GetAttribute("label"); auto actionClass = customMenuConfig->GetAttribute("class"); if (descriptorName.isEmpty() || actionLabel.isEmpty() || actionClass.isEmpty()) continue; auto descriptor = QmitkNodeDescriptorManager::GetInstance()->GetDescriptor(descriptorName); if (nullptr == descriptor) { MITK_WARN << "Cannot add action \"" << actionLabel << "\" to non-existent descriptor \"" << descriptorName << "\"."; continue; } QAction* action = nullptr; auto actionIcon = customMenuConfig->GetAttribute("icon"); if (!actionIcon.isEmpty()) { QIcon icon = !QFile::exists(actionIcon) ? berry::AbstractUICTKPlugin::ImageDescriptorFromPlugin(customMenuConfig->GetContributor()->GetName(), actionIcon) : QIcon(actionIcon); action = new QAction(icon, actionLabel, m_Parent); } else { action = new QAction(actionLabel, m_Parent); } if (nullptr != action) { // See T26938. We do not know why but without the lambda function indirection, the // connection is lost after the content menu was shown for the first time. connect(action, &QAction::triggered, [action, this]() { this->OnExtensionPointActionTriggered(action); }); m_ConfigElements[action] = customMenuConfig; descriptorActionList.push_back(std::make_pair(descriptor, action)); } } this->AddDescriptorActionList(descriptorActionList); } void QmitkDataNodeContextMenu::InitServiceActions() { } void QmitkDataNodeContextMenu::OnContextMenuRequested(const QPoint& /*pos*/) { if (m_WorkbenchPartSite.Expired()) return; auto selection = m_WorkbenchPartSite.Lock()->GetWorkbenchWindow()->GetSelectionService()->GetSelection() .Cast(); if (selection.IsNull() || selection->IsEmpty()) return; m_SelectedNodes = QList::fromStdList(selection->GetSelectedDataNodes()); if (!m_SelectedNodes.isEmpty()) { this->clear(); auto actions = m_SelectedNodes.size() == 1 ? this->GetActions(m_SelectedNodes.front()) : this->GetActions(m_SelectedNodes); for (auto& action : actions) { auto dataNodeAction = dynamic_cast(action); if (nullptr != dataNodeAction) dataNodeAction->SetSelectedNodes(m_SelectedNodes); } this->addActions(actions); this->popup(QCursor::pos()); } } void QmitkDataNodeContextMenu::OnExtensionPointActionTriggered(QAction* action) { auto configElementIter = m_ConfigElements.find(action); if (m_ConfigElements.end() == configElementIter) { MITK_WARN << "Associated configuration element for action \"" << action->text() << "\" not found."; return; } auto configElement = configElementIter->second; auto contextMenuAction = configElement->CreateExecutableExtension("class"); if (!m_DataStorage.IsExpired()) contextMenuAction->SetDataStorage(m_DataStorage.Lock()); if ("QmitkCreatePolygonModelAction" == configElement->GetAttribute("class")) { contextMenuAction->SetSmoothed("true" == configElement->GetAttribute("smoothed")); contextMenuAction->SetDecimated(m_SurfaceDecimation); } contextMenuAction->Run(m_SelectedNodes); } void QmitkDataNodeContextMenu::AddColorAction(QWidgetAction* colorAction) { if (nullptr != m_ImageDataNodeDescriptor) { m_ImageDataNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_ImageDataNodeDescriptor, colorAction)); } if (nullptr != m_MultiComponentImageDataNodeDescriptor) { m_MultiComponentImageDataNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_MultiComponentImageDataNodeDescriptor, colorAction)); } if (nullptr != m_DiffusionImageDataNodeDescriptor) { m_DiffusionImageDataNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_DiffusionImageDataNodeDescriptor, colorAction)); } if (nullptr != m_FiberBundleDataNodeDescriptor) { m_FiberBundleDataNodeDescriptor->AddAction(colorAction, false); m_DescriptorActionList.push_back(std::make_pair(m_FiberBundleDataNodeDescriptor, colorAction)); } if (nullptr != m_PeakImageDataNodeDescriptor) { m_PeakImageDataNodeDescriptor->AddAction(colorAction, false); m_DescriptorActionList.push_back(std::make_pair(m_PeakImageDataNodeDescriptor, colorAction)); } if (nullptr != m_SegmentDataNodeDescriptor) { m_SegmentDataNodeDescriptor->AddAction(colorAction, false); m_DescriptorActionList.push_back(std::make_pair(m_SegmentDataNodeDescriptor, colorAction)); } if (nullptr != m_SurfaceDataNodeDescriptor) { m_SurfaceDataNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_SurfaceDataNodeDescriptor, colorAction)); } if (nullptr != m_PointSetNodeDescriptor) { m_PointSetNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_PointSetNodeDescriptor, colorAction)); } if (nullptr != m_PlanarLineNodeDescriptor) { m_PlanarLineNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_PlanarLineNodeDescriptor, colorAction)); } if (nullptr != m_PlanarCircleNodeDescriptor) { m_PlanarCircleNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_PlanarCircleNodeDescriptor, colorAction)); } if (nullptr != m_PlanarEllipseNodeDescriptor) { m_PlanarEllipseNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_PlanarEllipseNodeDescriptor, colorAction)); } if (nullptr != m_PlanarAngleNodeDescriptor) { m_PlanarAngleNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_PlanarAngleNodeDescriptor, colorAction)); } if (nullptr != m_PlanarFourPointAngleNodeDescriptor) { m_PlanarFourPointAngleNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_PlanarFourPointAngleNodeDescriptor, colorAction)); } if (nullptr != m_PlanarRectangleNodeDescriptor) { m_PlanarRectangleNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_PlanarRectangleNodeDescriptor, colorAction)); } if (nullptr != m_PlanarPolygonNodeDescriptor) { m_PlanarPolygonNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_PlanarPolygonNodeDescriptor, colorAction)); } if (nullptr != m_PlanarPathNodeDescriptor) { m_PlanarPathNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_PlanarPathNodeDescriptor, colorAction)); } if (nullptr != m_PlanarDoubleEllipseNodeDescriptor) { m_PlanarDoubleEllipseNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_PlanarDoubleEllipseNodeDescriptor, colorAction)); } if (nullptr != m_PlanarBezierCurveNodeDescriptor) { m_PlanarBezierCurveNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_PlanarBezierCurveNodeDescriptor, colorAction)); } if (nullptr != m_PlanarSubdivisionPolygonNodeDescriptor) { m_PlanarSubdivisionPolygonNodeDescriptor->AddAction(colorAction, true); m_DescriptorActionList.push_back(std::make_pair(m_PlanarSubdivisionPolygonNodeDescriptor, colorAction)); } } void QmitkDataNodeContextMenu::AddDescriptorActionList(DescriptorActionListType& descriptorActionList) { using ListItem = std::pair; std::sort(descriptorActionList.begin(), descriptorActionList.end(), [](const ListItem& left, const ListItem& right) -> bool { return left.second->text() < right.second->text(); }); for (auto& descriptorActionPair : descriptorActionList) { descriptorActionPair.first->AddAction(descriptorActionPair.second); m_DescriptorActionList.push_back(descriptorActionPair); } } QList QmitkDataNodeContextMenu::GetActions(const mitk::DataNode* node) { QList actions; for(const auto& descriptorActionPair : m_DescriptorActionList) { if (descriptorActionPair.first->CheckNode(node) || "Unknown" == descriptorActionPair.first->GetNameOfClass()) actions.append(descriptorActionPair.second); } return actions; } QList QmitkDataNodeContextMenu::GetActions(const QList& nodes) { QList actions; for (const auto& descriptorActionPair : m_DescriptorActionList) { for (const auto& node : nodes) { if (descriptorActionPair.first->CheckNode(node) || "Unknown" == descriptorActionPair.first->GetNameOfClass()) { auto batchActions = descriptorActionPair.first->GetBatchActions(); if (std::find(batchActions.begin(), batchActions.end(), descriptorActionPair.second) != batchActions.end()) actions.append(descriptorActionPair.second); break; } } } return actions; } diff --git a/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsView.cpp b/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsView.cpp index 5f913cf2a3..904af7f0a7 100644 --- a/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.cest/src/internal/QmitkCESTStatisticsView.cpp @@ -1,815 +1,815 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // itk #include "itksys/SystemTools.hxx" #include #include // Blueberry #include #include // Qmitk #include "QmitkCESTStatisticsView.h" // Qt #include #include // qwt #include // mitk #include #include #include #include #include #include #include #include #include #include #include #include #include // boost #include #include // stl #include #include #include #include #include #include namespace { template void GetSortPermutation(std::vector &out, const std::vector &determiningVector, Compare compare = std::less()) { out.resize(determiningVector.size()); std::iota(out.begin(), out.end(), 0); std::sort(out.begin(), out.end(), [&](unsigned i, unsigned j) { return compare(determiningVector[i], determiningVector[j]); }); } template void ApplyPermutation(const std::vector &order, std::vector &vectorToSort) { assert(order.size() == vectorToSort.size()); std::vector tempVector(vectorToSort.size()); for (unsigned i = 0; i < vectorToSort.size(); i++) { tempVector[i] = vectorToSort[order[i]]; } vectorToSort = tempVector; } template void ApplyPermutation(const std::vector &order, std::vector ¤tVector, std::vector &... remainingVectors) { ApplyPermutation(order, currentVector); ApplyPermutation(order, remainingVectors...); } template void SortVectors(const std::vector &orderDeterminingVector, Compare comparison, std::vector &... vectorsToBeSorted) { std::vector order; GetSortPermutation(order, orderDeterminingVector, comparison); ApplyPermutation(order, vectorsToBeSorted...); } } // namespace const std::string QmitkCESTStatisticsView::VIEW_ID = "org.mitk.views.cest.statistics"; QmitkCESTStatisticsView::QmitkCESTStatisticsView(QObject * /*parent*/, const char * /*name*/) { this->m_CalculatorJob = new QmitkImageStatisticsCalculationJob(); m_currentSelectedPosition.Fill(0.0); m_currentSelectedTimePoint = 0.; m_CrosshairPointSet = mitk::PointSet::New(); } QmitkCESTStatisticsView::~QmitkCESTStatisticsView() { while (this->m_CalculatorJob->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } delete this->m_CalculatorJob; } void QmitkCESTStatisticsView::SetFocus() { m_Controls.threeDimToFourDimPushButton->setFocus(); } void QmitkCESTStatisticsView::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); connect( m_Controls.threeDimToFourDimPushButton, SIGNAL(clicked()), this, SLOT(OnThreeDimToFourDimPushButtonClicked())); connect((QObject *)this->m_CalculatorJob, SIGNAL(finished()), this, SLOT(OnThreadedStatisticsCalculationEnds()), Qt::QueuedConnection); connect((QObject *)(this->m_Controls.fixedRangeCheckBox), SIGNAL(toggled(bool)), (QObject *)this, SLOT(OnFixedRangeCheckBoxToggled(bool))); connect((QObject *)(this->m_Controls.fixedRangeLowerDoubleSpinBox), SIGNAL(editingFinished()), (QObject *)this, SLOT(OnFixedRangeDoubleSpinBoxChanged())); connect((QObject *)(this->m_Controls.fixedRangeUpperDoubleSpinBox), SIGNAL(editingFinished()), (QObject *)this, SLOT(OnFixedRangeDoubleSpinBoxChanged())); m_Controls.threeDimToFourDimPushButton->setEnabled(false); m_Controls.widget_statistics->SetDataStorage(this->GetDataStorage()); this->m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); } void QmitkCESTStatisticsView::RenderWindowPartActivated(mitk::IRenderWindowPart *renderWindowPart) { this->m_SliceChangeListener.RenderWindowPartActivated(renderWindowPart); } void QmitkCESTStatisticsView::RenderWindowPartDeactivated(mitk::IRenderWindowPart *renderWindowPart) { this->m_SliceChangeListener.RenderWindowPartDeactivated(renderWindowPart); } void QmitkCESTStatisticsView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList &nodes) { if (nodes.empty()) { std::stringstream message; message << "Please select an image."; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); this->Clear(); return; } // iterate all selected objects bool atLeastOneWasCESTImage = false; foreach (mitk::DataNode::Pointer node, nodes) { if (node.IsNull()) { continue; } if (dynamic_cast(node->GetData()) != nullptr) { m_Controls.labelWarning->setVisible(false); bool zSpectrumSet = SetZSpectrum(dynamic_cast( node->GetData()->GetProperty(mitk::CEST_PROPERTY_NAME_OFFSETS().c_str()).GetPointer())); atLeastOneWasCESTImage = atLeastOneWasCESTImage || zSpectrumSet; if (zSpectrumSet) { m_ZImage = dynamic_cast(node->GetData()); m_Controls.widget_statistics->SetImageNodes({node.GetPointer()}); } else { m_MaskImage = dynamic_cast(node->GetData()); m_Controls.widget_statistics->SetMaskNodes({node.GetPointer()}); } } if (dynamic_cast(node->GetData()) != nullptr) { m_MaskPlanarFigure = dynamic_cast(node->GetData()); m_Controls.widget_statistics->SetMaskNodes({node.GetPointer()}); } if (dynamic_cast(node->GetData()) != nullptr) { m_PointSet = dynamic_cast(node->GetData()); } } // We only want to offer normalization or timestep copying if one object is selected if (nodes.size() == 1) { if (dynamic_cast(nodes.front()->GetData())) { m_Controls.threeDimToFourDimPushButton->setDisabled(atLeastOneWasCESTImage); } else { m_Controls.threeDimToFourDimPushButton->setEnabled(false); std::stringstream message; message << "The selected node is not an image."; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); } this->Clear(); return; } // we always need a mask, either image or planar figure as well as an image for further processing if (nodes.size() != 2) { this->Clear(); return; } m_Controls.threeDimToFourDimPushButton->setEnabled(false); if (!atLeastOneWasCESTImage) { std::stringstream message; message << "None of the selected data nodes contains required CEST meta information"; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); this->Clear(); return; } bool bothAreImages = (m_ZImage.GetPointer() != nullptr) && (m_MaskImage.GetPointer() != nullptr); if (bothAreImages) { bool geometriesMatch = mitk::Equal(*(m_ZImage->GetTimeGeometry()), *(m_MaskImage->GetTimeGeometry()), mitk::eps, false); if (!geometriesMatch) { std::stringstream message; message << "The selected images have different geometries."; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); this->Clear(); return; } } if (!this->DataSanityCheck()) { this->Clear(); return; } if (m_PointSet.IsNull()) { // initialize thread and trigger it this->m_CalculatorJob->SetIgnoreZeroValueVoxel(false); this->m_CalculatorJob->Initialize(m_ZImage.GetPointer(), m_MaskImage.GetPointer(), m_MaskPlanarFigure.GetPointer()); std::stringstream message; message << "Calculating statistics..."; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); try { // Compute statistics this->m_CalculatorJob->start(); } catch (const mitk::Exception &e) { std::stringstream message; message << "" << e.GetDescription() << ""; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); } catch (const std::runtime_error &e) { // In case of exception, print error message on GUI std::stringstream message; message << "" << e.what() << ""; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); } catch (const std::exception &e) { MITK_ERROR << "Caught exception: " << e.what(); // In case of exception, print error message on GUI std::stringstream message; message << "Error! Unequal Dimensions of Image and Segmentation. No recompute possible "; m_Controls.labelWarning->setText(message.str().c_str()); m_Controls.labelWarning->show(); } while (this->m_CalculatorJob->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } } if (m_PointSet.IsNotNull()) { if (m_ZImage->GetDimension() == 4) { AccessFixedDimensionByItk(m_ZImage, PlotPointSet, 4); } else { MITK_WARN << "Expecting a 4D image."; } } } void QmitkCESTStatisticsView::OnThreadedStatisticsCalculationEnds() { this->m_Controls.m_DataViewWidget->SetAxisTitle(QwtPlot::Axis::xBottom, "delta w"); this->m_Controls.m_DataViewWidget->SetAxisTitle(QwtPlot::Axis::yLeft, "z"); if (this->m_CalculatorJob->GetStatisticsUpdateSuccessFlag()) { auto statistics = this->m_CalculatorJob->GetStatisticsData(); std::string statisticsNodeName = "CEST_statistics"; auto statisticsNode = mitk::CreateImageStatisticsNode(statistics, statisticsNodeName); auto imageRule = mitk::StatisticsToImageRelationRule::New(); imageRule->Connect(statistics, m_CalculatorJob->GetStatisticsImage()); if (m_CalculatorJob->GetMaskImage()) { auto maskRule = mitk::StatisticsToMaskRelationRule::New(); maskRule->Connect(statistics, m_CalculatorJob->GetMaskImage()); } else if (m_CalculatorJob->GetPlanarFigure()) { auto planarFigureRule = mitk::StatisticsToMaskRelationRule::New(); planarFigureRule->Connect(statistics, m_CalculatorJob->GetPlanarFigure()); } this->GetDataStorage()->Add(statisticsNode); QmitkPlotWidget::DataVector::size_type numberOfSpectra = this->m_zSpectrum.size(); QmitkPlotWidget::DataVector means(numberOfSpectra); QmitkPlotWidget::DataVector stdevs(numberOfSpectra); for (unsigned int index = 0; index < numberOfSpectra; ++index) { means[index] = statistics->GetStatisticsForTimeStep(index).GetValueConverted( mitk::ImageStatisticsConstants::MEAN()); stdevs[index] = statistics->GetStatisticsForTimeStep(index).GetValueConverted( mitk::ImageStatisticsConstants::STANDARDDEVIATION()); } QmitkPlotWidget::DataVector xValues = this->m_zSpectrum; RemoveMZeros(xValues, means, stdevs); ::SortVectors(xValues, std::less(), xValues, means, stdevs); unsigned int curveId = this->m_Controls.m_DataViewWidget->InsertCurve("Spectrum"); this->m_Controls.m_DataViewWidget->SetCurveData(curveId, xValues, means, stdevs, stdevs); this->m_Controls.m_DataViewWidget->SetErrorPen(curveId, QPen(Qt::blue)); QwtSymbol *blueSymbol = new QwtSymbol(QwtSymbol::Rect, QColor(Qt::blue), QColor(Qt::blue), QSize(8, 8)); this->m_Controls.m_DataViewWidget->SetCurveSymbol(curveId, blueSymbol); this->m_Controls.m_DataViewWidget->SetLegendAttribute(curveId, QwtPlotCurve::LegendShowSymbol); QwtLegend *legend = new QwtLegend(); legend->setFrameShape(QFrame::Box); legend->setFrameShadow(QFrame::Sunken); legend->setLineWidth(1); this->m_Controls.m_DataViewWidget->SetLegend(legend, QwtPlot::BottomLegend); m_Controls.m_DataViewWidget->GetPlot() ->axisScaleEngine(QwtPlot::Axis::xBottom) ->setAttributes(QwtScaleEngine::Inverted); this->m_Controls.m_DataViewWidget->Replot(); m_Controls.labelWarning->setVisible(false); m_Controls.m_StatisticsGroupBox->setEnabled(true); m_Controls.m_StatisticsGroupBox->setEnabled(true); if (this->m_Controls.fixedRangeCheckBox->isChecked()) { this->m_Controls.m_DataViewWidget->GetPlot()->setAxisAutoScale(2, false); this->m_Controls.m_DataViewWidget->GetPlot()->setAxisScale( 2, this->m_Controls.fixedRangeLowerDoubleSpinBox->value(), this->m_Controls.fixedRangeUpperDoubleSpinBox->value()); } else { this->m_Controls.m_DataViewWidget->GetPlot()->setAxisAutoScale(2, true); } } else { m_Controls.labelWarning->setText(m_CalculatorJob->GetLastErrorMessage().c_str()); m_Controls.labelWarning->setVisible(true); this->Clear(); } } void QmitkCESTStatisticsView::OnFixedRangeDoubleSpinBoxChanged() { if (this->m_Controls.fixedRangeCheckBox->isChecked()) { this->m_Controls.m_DataViewWidget->GetPlot()->setAxisAutoScale(2, false); this->m_Controls.m_DataViewWidget->GetPlot()->setAxisScale(2, this->m_Controls.fixedRangeLowerDoubleSpinBox->value(), this->m_Controls.fixedRangeUpperDoubleSpinBox->value()); } this->m_Controls.m_DataViewWidget->Replot(); } template void QmitkCESTStatisticsView::PlotPointSet(itk::Image *image) { this->m_Controls.m_DataViewWidget->SetAxisTitle(QwtPlot::Axis::xBottom, "delta w"); this->m_Controls.m_DataViewWidget->SetAxisTitle(QwtPlot::Axis::yLeft, "z"); QmitkPlotWidget::DataVector::size_type numberOfSpectra = this->m_zSpectrum.size(); mitk::PointSet::Pointer internalPointset; if (m_PointSet.IsNotNull()) { internalPointset = m_PointSet; } else { internalPointset = m_CrosshairPointSet; } if (internalPointset.IsNull()) { return; } if (!this->DataSanityCheck()) { m_Controls.labelWarning->setText("Data can not be plotted, internally inconsistent."); m_Controls.labelWarning->show(); return; } auto maxIndex = internalPointset->GetMaxId().Index(); for (std::size_t number = 0; number < maxIndex + 1; ++number) { mitk::PointSet::PointType point; if (!internalPointset->GetPointIfExists(number, &point)) { continue; } if (!this->m_ZImage->GetGeometry()->IsInside(point)) { continue; } itk::Index<3> itkIndex; this->m_ZImage->GetGeometry()->WorldToIndex(point, itkIndex); itk::Index itkIndexTime; itkIndexTime[0] = itkIndex[0]; itkIndexTime[1] = itkIndex[1]; itkIndexTime[2] = itkIndex[2]; QmitkPlotWidget::DataVector values(numberOfSpectra); for (std::size_t step = 0; step < numberOfSpectra; ++step) { if (VImageDimension == 4) { itkIndexTime[3] = step; } values[step] = image->GetPixel(itkIndexTime); } std::stringstream name; name << "Point " << number; // Qcolor enums go from 0 to 19, but 19 is transparent and 0,1 are for bitmaps // 3 is white and thus not visible QColor color(static_cast(number % 17 + 4)); QmitkPlotWidget::DataVector xValues = this->m_zSpectrum; RemoveMZeros(xValues, values); ::SortVectors(xValues, std::less(), xValues, values); unsigned int curveId = this->m_Controls.m_DataViewWidget->InsertCurve(name.str().c_str()); this->m_Controls.m_DataViewWidget->SetCurveData(curveId, xValues, values); this->m_Controls.m_DataViewWidget->SetCurvePen(curveId, QPen(color)); QwtSymbol *symbol = new QwtSymbol(QwtSymbol::Rect, color, color, QSize(8, 8)); this->m_Controls.m_DataViewWidget->SetCurveSymbol(curveId, symbol); this->m_Controls.m_DataViewWidget->SetLegendAttribute(curveId, QwtPlotCurve::LegendShowSymbol); } if (this->m_Controls.fixedRangeCheckBox->isChecked()) { this->m_Controls.m_DataViewWidget->GetPlot()->setAxisAutoScale(2, false); this->m_Controls.m_DataViewWidget->GetPlot()->setAxisScale(2, this->m_Controls.fixedRangeLowerDoubleSpinBox->value(), this->m_Controls.fixedRangeUpperDoubleSpinBox->value()); } else { this->m_Controls.m_DataViewWidget->GetPlot()->setAxisAutoScale(2, true); } QwtLegend *legend = new QwtLegend(); legend->setFrameShape(QFrame::Box); legend->setFrameShadow(QFrame::Sunken); legend->setLineWidth(1); this->m_Controls.m_DataViewWidget->SetLegend(legend, QwtPlot::BottomLegend); m_Controls.m_DataViewWidget->GetPlot() ->axisScaleEngine(QwtPlot::Axis::xBottom) ->setAttributes(QwtScaleEngine::Inverted); this->m_Controls.m_DataViewWidget->Replot(); m_Controls.labelWarning->setVisible(false); } void QmitkCESTStatisticsView::OnFixedRangeCheckBoxToggled(bool state) { this->m_Controls.fixedRangeLowerDoubleSpinBox->setEnabled(state); this->m_Controls.fixedRangeUpperDoubleSpinBox->setEnabled(state); } void QmitkCESTStatisticsView::RemoveMZeros(QmitkPlotWidget::DataVector &xValues, QmitkPlotWidget::DataVector &yValues) { QmitkPlotWidget::DataVector tempX; QmitkPlotWidget::DataVector tempY; for (std::size_t index = 0; index < xValues.size(); ++index) { if ((xValues.at(index) < -299) || (xValues.at(index)) > 299) { // do not include } else { tempX.push_back(xValues.at(index)); tempY.push_back(yValues.at(index)); } } xValues = tempX; yValues = tempY; } void QmitkCESTStatisticsView::RemoveMZeros(QmitkPlotWidget::DataVector &xValues, QmitkPlotWidget::DataVector &yValues, QmitkPlotWidget::DataVector &stdDevs) { QmitkPlotWidget::DataVector tempX; QmitkPlotWidget::DataVector tempY; QmitkPlotWidget::DataVector tempDevs; for (std::size_t index = 0; index < xValues.size(); ++index) { if ((xValues.at(index) < -299) || (xValues.at(index)) > 299) { // do not include } else { tempX.push_back(xValues.at(index)); tempY.push_back(yValues.at(index)); tempDevs.push_back(stdDevs.at(index)); } } xValues = tempX; yValues = tempY; stdDevs = tempDevs; } void QmitkCESTStatisticsView::OnThreeDimToFourDimPushButtonClicked() { QList nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataNode *node = nodes.front(); if (!node) { // Nothing selected. Inform the user and return QMessageBox::information(nullptr, "CEST View", "Please load and select an image before starting image processing."); return; } // here we have a valid mitk::DataNode // a node itself is not very useful, we need its data item (the image) mitk::BaseData *data = node->GetData(); if (data) { // test if this data item is an image or not (could also be a surface or something totally different) mitk::Image *image = dynamic_cast(data); if (image) { if (image->GetDimension() == 4) { AccessFixedDimensionByItk(image, CopyTimesteps, 4); } this->Clear(); } } } template void QmitkCESTStatisticsView::CopyTimesteps(itk::Image *image) { typedef itk::Image ImageType; // typedef itk::PasteImageFilter PasteImageFilterType; unsigned int numberOfTimesteps = image->GetLargestPossibleRegion().GetSize(3); typename ImageType::RegionType sourceRegion = image->GetLargestPossibleRegion(); sourceRegion.SetSize(3, 1); typename ImageType::RegionType targetRegion = image->GetLargestPossibleRegion(); targetRegion.SetSize(3, 1); for (unsigned int timestep = 1; timestep < numberOfTimesteps; ++timestep) { targetRegion.SetIndex(3, timestep); itk::ImageRegionConstIterator sourceIterator(image, sourceRegion); itk::ImageRegionIterator targetIterator(image, targetRegion); while (!sourceIterator.IsAtEnd()) { targetIterator.Set(sourceIterator.Get()); ++sourceIterator; ++targetIterator; } } } bool QmitkCESTStatisticsView::SetZSpectrum(mitk::StringProperty *zSpectrumProperty) { if (zSpectrumProperty == nullptr) { return false; } mitk::LocaleSwitch localeSwitch("C"); std::string zSpectrumString = zSpectrumProperty->GetValueAsString(); std::istringstream iss(zSpectrumString); std::vector zSpectra; std::copy( std::istream_iterator(iss), std::istream_iterator(), std::back_inserter(zSpectra)); m_zSpectrum.clear(); m_zSpectrum.resize(0); for (auto const &spectrumString : zSpectra) { m_zSpectrum.push_back(std::stod(spectrumString)); } return (m_zSpectrum.size() > 0); } bool QmitkCESTStatisticsView::DataSanityCheck() { QmitkPlotWidget::DataVector::size_type numberOfSpectra = m_zSpectrum.size(); // if we do not have a spectrum, the data can not be processed if (numberOfSpectra == 0) { return false; } // if we do not have CEST image data, the data can not be processed if (m_ZImage.IsNull()) { return false; } // if the CEST image data and the meta information do not match, the data can not be processed if (numberOfSpectra != m_ZImage->GetTimeSteps()) { MITK_INFO << "CEST meta information and number of volumes does not match."; return false; } // if we have neither a mask image, a point set nor a mask planar figure, we can not do statistics // statistics on the whole image would not make sense if (m_MaskImage.IsNull() && m_MaskPlanarFigure.IsNull() && m_PointSet.IsNull() && m_CrosshairPointSet->IsEmpty()) { return false; } // if we have a mask image and a mask planar figure, we can not do statistics // we do not know which one to use if (m_MaskImage.IsNotNull() && m_MaskPlanarFigure.IsNotNull()) { return false; } return true; } void QmitkCESTStatisticsView::Clear() { this->m_zSpectrum.clear(); this->m_zSpectrum.resize(0); this->m_ZImage = nullptr; this->m_MaskImage = nullptr; this->m_MaskPlanarFigure = nullptr; this->m_PointSet = nullptr; this->m_Controls.m_DataViewWidget->Clear(); this->m_Controls.m_StatisticsGroupBox->setEnabled(false); this->m_Controls.widget_statistics->SetImageNodes({}); this->m_Controls.widget_statistics->SetMaskNodes({}); } void QmitkCESTStatisticsView::OnSliceChanged() { mitk::Point3D currentSelectedPosition = this->GetRenderWindowPart()->GetSelectedPosition(nullptr); mitk::TimePointType currentSelectedTimePoint = this->GetRenderWindowPart()->GetSelectedTimePoint(); - if (m_currentSelectedPosition != currentSelectedPosition || currentSelectedTimePoint != currentSelectedTimePoint) + if (m_currentSelectedPosition != currentSelectedPosition || m_currentSelectedTimePoint != currentSelectedTimePoint) //|| m_selectedNodeTime > m_currentPositionTime) { // the current position has been changed or the selected node has been changed since the last position validation -> // check position m_currentSelectedPosition = currentSelectedPosition; m_currentSelectedTimePoint = currentSelectedTimePoint; m_currentPositionTime.Modified(); m_CrosshairPointSet->Clear(); m_CrosshairPointSet->SetPoint(0, m_currentSelectedPosition); QList nodes = this->GetDataManagerSelection(); if (nodes.empty() || nodes.size() > 1) return; mitk::DataNode *node = nodes.front(); if (!node) { return; } if (dynamic_cast(node->GetData()) != nullptr) { m_Controls.labelWarning->setVisible(false); bool zSpectrumSet = SetZSpectrum(dynamic_cast( node->GetData()->GetProperty(mitk::CEST_PROPERTY_NAME_OFFSETS().c_str()).GetPointer())); if (zSpectrumSet) { m_ZImage = dynamic_cast(node->GetData()); } else { return; } } else { return; } this->m_Controls.m_DataViewWidget->Clear(); AccessFixedDimensionByItk(m_ZImage, PlotPointSet, 4); } } diff --git a/Plugins/org.mitk.gui.qt.common/src/QmitkNodeSelectionDialog.cpp b/Plugins/org.mitk.gui.qt.common/src/QmitkNodeSelectionDialog.cpp index 979715cd2d..07bd9d18be 100644 --- a/Plugins/org.mitk.gui.qt.common/src/QmitkNodeSelectionDialog.cpp +++ b/Plugins/org.mitk.gui.qt.common/src/QmitkNodeSelectionDialog.cpp @@ -1,291 +1,292 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkNodeSelectionDialog.h" #include #include #include #include #include QmitkNodeSelectionDialog::QmitkNodeSelectionDialog(QWidget* parent, QString title, QString hint) : QDialog(parent) , m_NodePredicate(nullptr) , m_SelectOnlyVisibleNodes(false) , m_SelectedNodes(NodeList()) , m_SelectionMode(QAbstractItemView::SingleSelection) { m_Controls.setupUi(this); m_CheckFunction = [](const NodeList &) { return ""; }; auto providers = mitk::DataStorageInspectorGenerator::GetProviders(); auto visibleProviders = mitk::GetVisibleDataStorageInspectors(); auto preferredID = mitk::GetPreferredDataStorageInspector(); if (visibleProviders.empty()) { MITK_DEBUG << "No presets for visible node selection inspectors available. Use fallback (show all available inspectors)"; unsigned int order = 0; - for (auto proIter : providers) + for (const auto &proIter : providers) { visibleProviders.insert(std::make_pair(order, proIter.first)); ++order; } } int preferredIndex = 0; bool preferredFound = false; - for (auto proIter : visibleProviders) + for (const auto &proIter : visibleProviders) { auto finding = providers.find(proIter.second); if (finding != providers.end()) { if (finding->second->GetInspectorID() != QmitkDataStorageFavoriteNodesInspector::INSPECTOR_ID() && finding->second->GetInspectorID() != QmitkDataStorageSelectionHistoryInspector::INSPECTOR_ID()) { auto provider = finding->second; this->AddPanel(provider, preferredID, preferredFound, preferredIndex); } } else { MITK_DEBUG << "No provider registered for inspector that is defined as visible in the preferences. Illegal inspector ID: " << proIter.second; } } if (mitk::GetShowFavoritesInspector()) { auto favoritesPorvider = mitk::DataStorageInspectorGenerator::GetProvider(QmitkDataStorageFavoriteNodesInspector::INSPECTOR_ID()); if (favoritesPorvider != nullptr) { this->AddPanel(favoritesPorvider, preferredID, preferredFound, preferredIndex); } } if (mitk::GetShowHistoryInspector()) { auto historyPorvider = mitk::DataStorageInspectorGenerator::GetProvider(QmitkDataStorageSelectionHistoryInspector::INSPECTOR_ID()); if (historyPorvider != nullptr) { this->AddPanel(historyPorvider, preferredID, preferredFound, preferredIndex); } } m_Controls.tabWidget->setCurrentIndex(preferredIndex); this->setWindowTitle(title); this->setToolTip(hint); m_Controls.hint->setText(hint); m_Controls.hint->setVisible(!hint.isEmpty()); if(hint.isEmpty()) { m_Controls.layoutHint->setContentsMargins(0, 0, 0, 0); } else { m_Controls.layoutHint->setContentsMargins(6, 6, 6, 6); } this->SetErrorText(""); m_Controls.btnAddToFav->setIcon(berry::QtStyleManager::ThemeIcon(QStringLiteral(":/Qmitk/favorite_add.svg"))); connect(m_Controls.btnAddToFav, &QPushButton::clicked, this, &QmitkNodeSelectionDialog::OnFavoriteNodesButtonClicked); connect(m_Controls.buttonBox, &QDialogButtonBox::accepted, this, &QmitkNodeSelectionDialog::OnOK); connect(m_Controls.buttonBox, &QDialogButtonBox::rejected, this, &QmitkNodeSelectionDialog::OnCancel); } void QmitkNodeSelectionDialog::SetDataStorage(mitk::DataStorage* dataStorage) { if (m_DataStorage != dataStorage) { m_DataStorage = dataStorage; if (!m_DataStorage.IsExpired()) { for (auto panel : m_Panels) { panel->SetDataStorage(dataStorage); } } } } void QmitkNodeSelectionDialog::SetNodePredicate(const mitk::NodePredicateBase* nodePredicate) { if (m_NodePredicate != nodePredicate) { m_NodePredicate = nodePredicate; for (auto panel : m_Panels) { panel->SetNodePredicate(m_NodePredicate); } } } const mitk::NodePredicateBase* QmitkNodeSelectionDialog::GetNodePredicate() const { return m_NodePredicate; } QmitkNodeSelectionDialog::NodeList QmitkNodeSelectionDialog::GetSelectedNodes() const { return m_SelectedNodes; } void QmitkNodeSelectionDialog::SetSelectionCheckFunction(const SelectionCheckFunctionType &checkFunction) { m_CheckFunction = checkFunction; auto checkResponse = m_CheckFunction(m_SelectedNodes); SetErrorText(checkResponse); m_Controls.buttonBox->button(QDialogButtonBox::Ok)->setEnabled(checkResponse.empty()); } void QmitkNodeSelectionDialog::SetErrorText(const std::string& checkResponse) { m_Controls.error->setText(QString::fromStdString(checkResponse)); m_Controls.error->setVisible(!checkResponse.empty()); if (checkResponse.empty()) { m_Controls.layoutError->setContentsMargins(0, 0, 0, 0); } else { m_Controls.layoutError->setContentsMargins(6, 6, 6, 6); } } bool QmitkNodeSelectionDialog::GetSelectOnlyVisibleNodes() const { return m_SelectOnlyVisibleNodes; } void QmitkNodeSelectionDialog::SetSelectionMode(SelectionMode mode) { m_SelectionMode = mode; for (auto panel : m_Panels) { panel->SetSelectionMode(mode); } } QmitkNodeSelectionDialog::SelectionMode QmitkNodeSelectionDialog::GetSelectionMode() const { return m_SelectionMode; } void QmitkNodeSelectionDialog::SetSelectOnlyVisibleNodes(bool selectOnlyVisibleNodes) { if (m_SelectOnlyVisibleNodes != selectOnlyVisibleNodes) { m_SelectOnlyVisibleNodes = selectOnlyVisibleNodes; for (auto panel : m_Panels) { panel->SetSelectOnlyVisibleNodes(m_SelectOnlyVisibleNodes); } } } void QmitkNodeSelectionDialog::SetCurrentSelection(NodeList selectedNodes) { m_SelectedNodes = selectedNodes; auto checkResponse = m_CheckFunction(m_SelectedNodes); SetErrorText(checkResponse); m_Controls.buttonBox->button(QDialogButtonBox::Ok)->setEnabled(checkResponse.empty()); for (auto panel : m_Panels) { panel->SetCurrentSelection(selectedNodes); } } void QmitkNodeSelectionDialog::OnSelectionChanged(NodeList selectedNodes) { SetCurrentSelection(selectedNodes); emit CurrentSelectionChanged(selectedNodes); } void QmitkNodeSelectionDialog::OnFavoriteNodesButtonClicked() { - for (auto node : m_SelectedNodes) + for (auto node : qAsConst(m_SelectedNodes)) { node->SetBoolProperty("org.mitk.selection.favorite", true); } } void QmitkNodeSelectionDialog::OnOK() { - for (auto node : m_SelectedNodes) + for (const auto &node : qAsConst(m_SelectedNodes)) { QmitkDataStorageSelectionHistoryInspector::AddNodeToHistory(node); } this->accept(); } void QmitkNodeSelectionDialog::OnCancel() { this->reject(); } void QmitkNodeSelectionDialog::AddPanel(const mitk::IDataStorageInspectorProvider * provider, const mitk::IDataStorageInspectorProvider::InspectorIDType& preferredID, bool &preferredFound, int &preferredIndex) { auto inspector = provider->CreateInspector(); QString name = QString::fromStdString(provider->GetInspectorDisplayName()); QString desc = QString::fromStdString(provider->GetInspectorDescription()); inspector->setParent(this); inspector->SetSelectionMode(m_SelectionMode); auto tabPanel = new QWidget(); tabPanel->setObjectName(QString("tab_") + name); tabPanel->setToolTip(desc); auto verticalLayout = new QVBoxLayout(tabPanel); verticalLayout->setSpacing(0); verticalLayout->setContentsMargins(0, 0, 0, 0); verticalLayout->addWidget(inspector); auto panelPos = m_Controls.tabWidget->insertTab(m_Controls.tabWidget->count(), tabPanel, name); auto icon = provider->GetInspectorIcon(); if (!icon.isNull()) { m_Controls.tabWidget->setTabIcon(panelPos, icon); } m_Panels.push_back(inspector); connect(inspector, &QmitkAbstractDataStorageInspector::CurrentSelectionChanged, this, &QmitkNodeSelectionDialog::OnSelectionChanged); connect(inspector->GetView(), &QAbstractItemView::doubleClicked, this, &QmitkNodeSelectionDialog::OnDoubleClicked); preferredFound = preferredFound || provider->GetInspectorID() == preferredID; if (!preferredFound) { ++preferredIndex; } } void QmitkNodeSelectionDialog::OnDoubleClicked(const QModelIndex& /*index*/) { - if (!m_SelectedNodes.empty()) + const auto isOK = m_Controls.buttonBox->button(QDialogButtonBox::Ok)->isEnabled(); + if (!m_SelectedNodes.empty() && isOK) { this->OnOK(); } } diff --git a/Plugins/org.mitk.gui.qt.common/src/QmitkSliceNavigationListener.cpp b/Plugins/org.mitk.gui.qt.common/src/QmitkSliceNavigationListener.cpp index 4e8df798a0..9c8bf772ba 100644 --- a/Plugins/org.mitk.gui.qt.common/src/QmitkSliceNavigationListener.cpp +++ b/Plugins/org.mitk.gui.qt.common/src/QmitkSliceNavigationListener.cpp @@ -1,172 +1,205 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Qmitk #include "QmitkRenderWindow.h" #include "QmitkSliceNavigationListener.h" #include "mitkIRenderWindowPart.h" // Qt #include #include ///********************************************** -QmitkSliceNavigationListener::QmitkSliceNavigationListener(): m_renderWindowPart(nullptr), +QmitkSliceNavigationListener::QmitkSliceNavigationListener() : m_renderWindowPart(nullptr), m_PendingSliceChangedEvent(false), -m_internalUpdateFlag(false) +m_CurrentSelectedPosition(std::numeric_limits::lowest()), +m_CurrentSelectedTimePoint(std::numeric_limits::lowest()) { } QmitkSliceNavigationListener::~QmitkSliceNavigationListener() { this->RemoveAllObservers(); }; +mitk::TimePointType QmitkSliceNavigationListener::GetCurrentSelectedTimePoint() const +{ + return m_CurrentSelectedTimePoint; +} + +mitk::Point3D QmitkSliceNavigationListener::GetCurrentSelectedPosition() const +{ + return m_CurrentSelectedPosition; +} + void QmitkSliceNavigationListener::OnSliceChangedDelayed() { m_PendingSliceChangedEvent = false; + emit SliceChanged(); + + if (nullptr != m_renderWindowPart) + { + const auto newSelectedPosition = m_renderWindowPart->GetSelectedPosition(); + const auto newSelectedTimePoint = m_renderWindowPart->GetSelectedTimePoint(); + + if (newSelectedPosition != m_CurrentSelectedPosition) + { + m_CurrentSelectedPosition = newSelectedPosition; + emit SelectedPositionChanged(newSelectedPosition); + } + + if (newSelectedTimePoint != m_CurrentSelectedTimePoint) + { + m_CurrentSelectedTimePoint = newSelectedTimePoint; + emit SelectedTimePointChanged(newSelectedTimePoint); + } + } }; void QmitkSliceNavigationListener::OnSliceChangedInternal(const itk::EventObject&) { // Taken from QmitkStdMultiWidget::HandleCrosshairPositionEvent(). // Since there are always 3 events arriving (one for each render window) every time the slice // or time changes, the slot OnSliceChangedDelayed is triggered - and only if it hasn't been // triggered yet - so it is only executed once for every slice/time change. if (!m_PendingSliceChangedEvent) { m_PendingSliceChangedEvent = true; QTimer::singleShot(0, this, SLOT(OnSliceChangedDelayed())); } }; void QmitkSliceNavigationListener::OnSliceNavigationControllerDeleted(const itk::Object* sender, const itk::EventObject& /*e*/) { const mitk::SliceNavigationController* sendingSlicer = dynamic_cast(sender); this->RemoveObservers(sendingSlicer); }; void QmitkSliceNavigationListener::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { if (m_renderWindowPart != renderWindowPart) { m_renderWindowPart = renderWindowPart; if (!InitObservers()) { QMessageBox::information(nullptr, "Error", "Unable to set up the event observers. The " \ "plot will not be triggered on changing the crosshair, " \ "position or time step."); } + + m_CurrentSelectedPosition = m_renderWindowPart->GetSelectedPosition(); + m_CurrentSelectedTimePoint = m_renderWindowPart->GetSelectedTimePoint(); } }; void QmitkSliceNavigationListener::RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) { m_renderWindowPart = nullptr; this->RemoveAllObservers(renderWindowPart); }; bool QmitkSliceNavigationListener::InitObservers() { bool result = true; typedef QHash WindowMapType; WindowMapType windowMap = m_renderWindowPart->GetQmitkRenderWindows(); auto i = windowMap.begin(); while (i != windowMap.end()) { mitk::SliceNavigationController* sliceNavController = i.value()->GetSliceNavigationController(); if (sliceNavController) { itk::ReceptorMemberCommand::Pointer cmdSliceEvent = itk::ReceptorMemberCommand::New(); cmdSliceEvent->SetCallbackFunction(this, &QmitkSliceNavigationListener::OnSliceChangedInternal); int tag = sliceNavController->AddObserver( mitk::SliceNavigationController::GeometrySliceEvent(nullptr, 0), cmdSliceEvent); m_ObserverMap.insert(std::make_pair(sliceNavController, ObserverInfo(sliceNavController, tag, i.key().toStdString(), m_renderWindowPart))); itk::ReceptorMemberCommand::Pointer cmdTimeEvent = itk::ReceptorMemberCommand::New(); cmdTimeEvent->SetCallbackFunction(this, &QmitkSliceNavigationListener::OnSliceChangedInternal); tag = sliceNavController->AddObserver( mitk::SliceNavigationController::GeometryTimeEvent(nullptr, 0), cmdTimeEvent); m_ObserverMap.insert(std::make_pair(sliceNavController, ObserverInfo(sliceNavController, tag, i.key().toStdString(), m_renderWindowPart))); itk::MemberCommand::Pointer cmdDelEvent = itk::MemberCommand::New(); cmdDelEvent->SetCallbackFunction(this, &QmitkSliceNavigationListener::OnSliceNavigationControllerDeleted); tag = sliceNavController->AddObserver( itk::DeleteEvent(), cmdDelEvent); m_ObserverMap.insert(std::make_pair(sliceNavController, ObserverInfo(sliceNavController, tag, i.key().toStdString(), m_renderWindowPart))); } ++i; result = result && sliceNavController; } return result; }; void QmitkSliceNavigationListener::RemoveObservers(const mitk::SliceNavigationController* deletedSlicer) { std::pair < ObserverMapType::const_iterator, ObserverMapType::const_iterator> obsRange = m_ObserverMap.equal_range(deletedSlicer); for (ObserverMapType::const_iterator pos = obsRange.first; pos != obsRange.second; ++pos) { pos->second.controller->RemoveObserver(pos->second.observerTag); } m_ObserverMap.erase(deletedSlicer); }; void QmitkSliceNavigationListener::RemoveAllObservers(mitk::IRenderWindowPart* deletedPart) { for (ObserverMapType::const_iterator pos = m_ObserverMap.begin(); pos != m_ObserverMap.end();) { ObserverMapType::const_iterator delPos = pos++; if (deletedPart == nullptr || deletedPart == delPos->second.renderWindowPart) { delPos->second.controller->RemoveObserver(delPos->second.observerTag); m_ObserverMap.erase(delPos); } } }; QmitkSliceNavigationListener::ObserverInfo::ObserverInfo(mitk::SliceNavigationController* controller, int observerTag, const std::string& renderWindowName, mitk::IRenderWindowPart* part) : controller(controller), observerTag(observerTag), renderWindowName(renderWindowName), renderWindowPart(part) { }; diff --git a/Plugins/org.mitk.gui.qt.common/src/QmitkSliceNavigationListener.h b/Plugins/org.mitk.gui.qt.common/src/QmitkSliceNavigationListener.h index 10ffebfe75..885aa590b1 100644 --- a/Plugins/org.mitk.gui.qt.common/src/QmitkSliceNavigationListener.h +++ b/Plugins/org.mitk.gui.qt.common/src/QmitkSliceNavigationListener.h @@ -1,118 +1,133 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 __Q_MITK_SLICE_NAVIGATION_LISTENER_H #define __Q_MITK_SLICE_NAVIGATION_LISTENER_H +#include +#include + #include #include #include namespace itk { class Object; } namespace mitk { class SliceNavigationController; struct IRenderWindowPart; } /** @brief Helper class to allow QmitkAbstractView and derived classes to react on changes of the slice/time navigation. Purpose of the class to be used in view and to give the respective view class (by composition) the posibility to react on changes of the currently selected timepoint or position in the world geometry.\n + It also offers convinient signals that are only triggered when the selected timepoint or the selected possition of the + active render window have realy changed.\n In order to setup this class properly the following things must be regarded: - View class must also derive public from mitk::IRenderWindowPartListener - View class must implement void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) and pass the renderWindowPart to the listener. void QmitkMyView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { this->m_SliceNavigationListener.RenderWindowPartActivated(renderWindowPart); } - View class must implement void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) and pass the renderWindowPart to the listener. void QmitkMyView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) { this->m_SliceNavigationListener.RenderWindowPartDeactivated(renderWindowPart); } - View class must pass its on render window part in its CreateQtPartControl(QWidget* parent) this->m_SliceNavigationListener.RenderWindowPartActivated(this->GetRenderWindowPart()); - View class must connect the SliceChanged signal of the listener as see fit. */ class MITK_QT_COMMON QmitkSliceNavigationListener : public QObject { Q_OBJECT public: QmitkSliceNavigationListener(); ~QmitkSliceNavigationListener() override; + mitk::TimePointType GetCurrentSelectedTimePoint() const; + mitk::Point3D GetCurrentSelectedPosition() const; + signals: + /** Signal triggered as soon as there is any change. It may be a change in the position/slice or of the selected timepoint.*/ void SliceChanged(); + /** Convinience signal that can be used if you are only interested in changes of the current selected time point. + Changes in spatial position will be ignored.*/ + void SelectedTimePointChanged(const mitk::TimePointType& newTimePoint); + /** Convinience signal that can be used if you are only interested in changes of the current selected position. + Changes in time will be ignored.*/ + void SelectedPositionChanged(const mitk::Point3D& newPoint); public slots: void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart); void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart); protected slots: /** Overwrite function to implement the behavior on slice/time changes. */ void OnSliceChangedDelayed(); protected: /** @brief Calls OnSliceChangedDelayed so the event isn't triggered multiple times. */ void OnSliceChangedInternal(const itk::EventObject& e); void OnSliceNavigationControllerDeleted(const itk::Object* sender, const itk::EventObject& /*e*/); /** Initializes and sets the observers that are used to monitor changes in the selected position or time point in order to actualize the view.h*/ bool InitObservers(); void RemoveObservers(const mitk::SliceNavigationController* deletedSlicer); /** Removes all observers of the deletedPart. If null pointer is passed all observers will be removed.*/ void RemoveAllObservers(mitk::IRenderWindowPart* deletedPart = nullptr); mitk::IRenderWindowPart* m_renderWindowPart; // Needed for observing the events for when a slice or time step is changed. bool m_PendingSliceChangedEvent; /**Helper structure to manage the registered observer events.*/ struct ObserverInfo { mitk::SliceNavigationController* controller; int observerTag; std::string renderWindowName; mitk::IRenderWindowPart* renderWindowPart; ObserverInfo(mitk::SliceNavigationController* controller, int observerTag, const std::string& renderWindowName, mitk::IRenderWindowPart* part); }; typedef std::multimap ObserverMapType; ObserverMapType m_ObserverMap; - /** @brief Is a visualization currently running? */ - bool m_internalUpdateFlag; + mitk::Point3D m_CurrentSelectedPosition; + mitk::TimePointType m_CurrentSelectedTimePoint; }; #endif diff --git a/Plugins/org.mitk.gui.qt.common/src/internal/QmitkNodeSelectionPreferencePage.cpp b/Plugins/org.mitk.gui.qt.common/src/internal/QmitkNodeSelectionPreferencePage.cpp index 9ccc92dc20..0d1d483d1b 100644 --- a/Plugins/org.mitk.gui.qt.common/src/internal/QmitkNodeSelectionPreferencePage.cpp +++ b/Plugins/org.mitk.gui.qt.common/src/internal/QmitkNodeSelectionPreferencePage.cpp @@ -1,215 +1,215 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkNodeSelectionPreferencePage.h" #include "QmitkNodeSelectionPreferenceHelper.h" #include #include //----------------------------------------------------------------------------- QmitkNodeSelectionPreferencePage::QmitkNodeSelectionPreferencePage() : m_MainControl(nullptr), m_Controls(nullptr) { } //----------------------------------------------------------------------------- QmitkNodeSelectionPreferencePage::~QmitkNodeSelectionPreferencePage() { delete m_Controls; } //----------------------------------------------------------------------------- void QmitkNodeSelectionPreferencePage::Init(berry::IWorkbench::Pointer ) { } //----------------------------------------------------------------------------- void QmitkNodeSelectionPreferencePage::CreateQtControl(QWidget* parent) { m_MainControl = new QWidget(parent); m_Controls = new Ui::QmitkNodeSelectionPreferencePage; m_Controls->setupUi( m_MainControl ); connect(m_Controls->comboPreferred, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateWidgets())); connect(m_Controls->btnUp, SIGNAL(clicked(bool)), this, SLOT(MoveUp())); connect(m_Controls->btnDown, SIGNAL(clicked(bool)), this, SLOT(MoveDown())); connect(m_Controls->listInspectors, &QListWidget::itemSelectionChanged, this, &QmitkNodeSelectionPreferencePage::UpdateWidgets); this->Update(); } //----------------------------------------------------------------------------- QWidget* QmitkNodeSelectionPreferencePage::GetQtControl() const { return m_MainControl; } //----------------------------------------------------------------------------- bool QmitkNodeSelectionPreferencePage::PerformOk() { //store preferred auto id = m_Controls->comboPreferred->currentData().toString(); mitk::PutPreferredDataStorageInspector(id.toStdString()); //store visible mitk::VisibleDataStorageInspectorMapType visibles; unsigned int visiblePos = 0; for (int i = 0; i < m_Controls->listInspectors->count(); ++i) { auto item = m_Controls->listInspectors->item(i); if (item->checkState() == Qt::Checked) { visibles.insert(std::make_pair(visiblePos++, item->data(Qt::UserRole).toString().toStdString())); } } mitk::PutVisibleDataStorageInspectors(visibles); mitk::PutShowFavoritesInspector(m_Controls->checkShowFav->isChecked()); mitk::PutShowHistoryInspector(m_Controls->checkShowHistory->isChecked()); return true; } //----------------------------------------------------------------------------- void QmitkNodeSelectionPreferencePage::PerformCancel() { } //----------------------------------------------------------------------------- void QmitkNodeSelectionPreferencePage::Update() { m_Providers = mitk::DataStorageInspectorGenerator::GetProviders(); auto visibleProviders = mitk::GetVisibleDataStorageInspectors(); auto allProviders = mitk::DataStorageInspectorGenerator::GetProviders(); auto preferredInspectorID = mitk::GetPreferredDataStorageInspector(); //fill preferred combo int index = 0; int currentIndex = 0; m_Controls->comboPreferred->clear(); - for (auto iter : m_Providers) + for (const auto &iter : m_Providers) { m_Controls->comboPreferred->addItem(QString::fromStdString(iter.second->GetInspectorDisplayName()), QVariant::fromValue(QString::fromStdString(iter.first))); if (iter.first == preferredInspectorID) { currentIndex = index; }; ++index; } m_Controls->comboPreferred->setCurrentIndex(currentIndex); //fill inspector list m_Controls->listInspectors->clear(); for (const auto& iter : allProviders) { if (iter.first != QmitkDataStorageFavoriteNodesInspector::INSPECTOR_ID() && iter.first != QmitkDataStorageSelectionHistoryInspector::INSPECTOR_ID()) { auto currentID = iter.first; QListWidgetItem* item = new QListWidgetItem; item->setText(QString::fromStdString(iter.second->GetInspectorDisplayName())); item->setData(Qt::UserRole, QVariant::fromValue(QString::fromStdString(currentID))); item->setToolTip(QString::fromStdString(iter.second->GetInspectorDescription())); auto finding = std::find_if(visibleProviders.cbegin(), visibleProviders.cend(), [¤tID](auto v) {return v.second == currentID; }); if (finding == visibleProviders.cend()) { item->setCheckState(Qt::Unchecked); m_Controls->listInspectors->addItem(item); } else { item->setCheckState(Qt::Checked); m_Controls->listInspectors->insertItem(finding->first, item); } } } m_Controls->checkShowFav->setChecked(mitk::GetShowFavoritesInspector()); m_Controls->checkShowHistory->setChecked(mitk::GetShowHistoryInspector()); this->UpdateWidgets(); } void QmitkNodeSelectionPreferencePage::UpdateWidgets() { int currentIndex = m_Controls->listInspectors->currentRow(); m_Controls->btnUp->setEnabled(!m_Controls->listInspectors->selectedItems().empty() && currentIndex > 0); m_Controls->btnDown->setEnabled(!m_Controls->listInspectors->selectedItems().empty() && currentIndex + 1 < m_Controls->listInspectors->count()); for (int i = 0; i < m_Controls->listInspectors->count(); ++i) { auto item = m_Controls->listInspectors->item(i); if (item->data(Qt::UserRole).toString() == m_Controls->comboPreferred->currentData().toString()) { //preferred inspector is always visible. item->setCheckState(Qt::Checked); item->setFlags(Qt::ItemIsSelectable | Qt::ItemIsEnabled | Qt::ItemIsDragEnabled); } else { item->setFlags(Qt::ItemIsSelectable | Qt::ItemIsEnabled | Qt::ItemIsDragEnabled | Qt::ItemIsUserCheckable); } } auto isFavSelected = QmitkDataStorageFavoriteNodesInspector::INSPECTOR_ID() == m_Controls->comboPreferred->currentData().toString(); if (isFavSelected) { m_Controls->checkShowFav->setChecked(true); } m_Controls->checkShowFav->setEnabled(!isFavSelected); auto isHistorySelected = QmitkDataStorageSelectionHistoryInspector::INSPECTOR_ID() == m_Controls->comboPreferred->currentData().toString(); if (isHistorySelected) { m_Controls->checkShowHistory->setChecked(true); } m_Controls->checkShowHistory->setEnabled(!isHistorySelected); } void QmitkNodeSelectionPreferencePage::MoveDown() { int currentIndex = m_Controls->listInspectors->currentRow(); if (currentIndex+1 < m_Controls->listInspectors->count()) { QListWidgetItem *currentItem = m_Controls->listInspectors->takeItem(currentIndex); m_Controls->listInspectors->insertItem(currentIndex + 1, currentItem); m_Controls->listInspectors->setCurrentRow(currentIndex + 1); } this->UpdateWidgets(); } void QmitkNodeSelectionPreferencePage::MoveUp() { int currentIndex = m_Controls->listInspectors->currentRow(); if (currentIndex > 0) { QListWidgetItem *currentItem = m_Controls->listInspectors->takeItem(currentIndex); m_Controls->listInspectors->insertItem(currentIndex - 1, currentItem); m_Controls->listInspectors->setCurrentRow(currentIndex - 1); } this->UpdateWidgets(); } diff --git a/Plugins/org.mitk.gui.qt.common/src/internal/QmitkViewCoordinator.cpp b/Plugins/org.mitk.gui.qt.common/src/internal/QmitkViewCoordinator.cpp index 76604ed003..2a6a403d21 100644 --- a/Plugins/org.mitk.gui.qt.common/src/internal/QmitkViewCoordinator.cpp +++ b/Plugins/org.mitk.gui.qt.common/src/internal/QmitkViewCoordinator.cpp @@ -1,234 +1,234 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkViewCoordinator.h" #include "QmitkAbstractView.h" #include #include #include #include #include QmitkViewCoordinator::QmitkViewCoordinator() : m_ActiveZombieView(nullptr) , m_ActiveRenderWindowPart(nullptr) , m_VisibleRenderWindowPart(nullptr) { } QmitkViewCoordinator::~QmitkViewCoordinator() { } void QmitkViewCoordinator::Start() { berry::PlatformUI::GetWorkbench()->AddWindowListener(this); QList wnds(berry::PlatformUI::GetWorkbench()->GetWorkbenchWindows()); for (QList::iterator i = wnds.begin(); i != wnds.end(); ++i) { (*i)->GetPartService()->AddPartListener(this); } } void QmitkViewCoordinator::Stop() { if (!berry::PlatformUI::IsWorkbenchRunning()) return; berry::PlatformUI::GetWorkbench()->RemoveWindowListener(this); QList wnds(berry::PlatformUI::GetWorkbench()->GetWorkbenchWindows()); for (QList::iterator i = wnds.begin(); i != wnds.end(); ++i) { (*i)->GetPartService()->RemovePartListener(this); } } berry::IPartListener::Events::Types QmitkViewCoordinator::GetPartEventTypes() const { return berry::IPartListener::Events::ACTIVATED | berry::IPartListener::Events::DEACTIVATED | berry::IPartListener::Events::CLOSED | berry::IPartListener::Events::HIDDEN | berry::IPartListener::Events::VISIBLE | berry::IPartListener::Events::OPENED | berry::IPartListener::Events::INPUT_CHANGED; } void QmitkViewCoordinator::PartActivated(const berry::IWorkbenchPartReference::Pointer& partRef) { //MITK_INFO << "*** PartActivated (" << partRef->GetPart(false)->GetPartName() << ")"; berry::IWorkbenchPart* part = partRef->GetPart(false).GetPointer(); // Check for a render window part and inform IRenderWindowPartListener views // that it was activated if (mitk::IRenderWindowPart* renderPart = dynamic_cast(part)) { if (m_VisibleRenderWindowPart != renderPart) { RenderWindowPartActivated(renderPart); m_ActiveRenderWindowPart = renderPart; m_VisibleRenderWindowPart = renderPart; } } // Check if the activated part wants to be notified if (mitk::ILifecycleAwarePart* lifecycleAwarePart = dynamic_cast(part)) { lifecycleAwarePart->Activated(); } // Check if a zombie view has been activated. if (mitk::IZombieViewPart* zombieView = dynamic_cast(part)) { if (m_ActiveZombieView && (m_ActiveZombieView != zombieView)) { // Another zombie view has been activated. Tell the old one about it. m_ActiveZombieView->ActivatedZombieView(partRef); m_ActiveZombieView = zombieView; } } } void QmitkViewCoordinator::PartDeactivated(const berry::IWorkbenchPartReference::Pointer& partRef) { //MITK_INFO << "*** PartDeactivated (" << partRef->GetPart(false)->GetPartName() << ")"; berry::IWorkbenchPart* part = partRef->GetPart(false).GetPointer(); // Check for a render window part and inform IRenderWindowPartListener views // that it was deactivated if (mitk::IRenderWindowPart* renderPart = dynamic_cast(part)) { if (m_ActiveRenderWindowPart == renderPart) { this->RenderWindowPartDeactivated(renderPart); m_ActiveRenderWindowPart = nullptr; m_VisibleRenderWindowPart = nullptr; } } if (mitk::ILifecycleAwarePart* lifecycleAwarePart = dynamic_cast(part)) { lifecycleAwarePart->Deactivated(); } } void QmitkViewCoordinator::PartOpened(const berry::IWorkbenchPartReference::Pointer& partRef) { //MITK_INFO << "*** PartOpened (" << partRef->GetPart(false)->GetPartName() << ")"; berry::IWorkbenchPart* part = partRef->GetPart(false).GetPointer(); if (mitk::IRenderWindowPartListener* renderWindowListener = dynamic_cast(part)) { m_RenderWindowListeners.insert(renderWindowListener); } } void QmitkViewCoordinator::PartClosed(const berry::IWorkbenchPartReference::Pointer& partRef) { //MITK_INFO << "*** PartClosed (" << partRef->GetPart(false)->GetPartName() << ")"; berry::IWorkbenchPart* part = partRef->GetPart(false).GetPointer(); if (mitk::IRenderWindowPartListener* renderWindowListener = dynamic_cast(part)) { m_RenderWindowListeners.remove(renderWindowListener); } } void QmitkViewCoordinator::PartHidden(const berry::IWorkbenchPartReference::Pointer& partRef) { //MITK_INFO << "*** PartHidden (" << partRef->GetPart(false)->GetPartName() << ")"; berry::IWorkbenchPart* part = partRef->GetPart(false).GetPointer(); // Check for a render window part and if it is the currently active on. // Inform IRenderWindowPartListener views that it has been hidden. if (mitk::IRenderWindowPart* renderPart = dynamic_cast(part)) { if (!m_ActiveRenderWindowPart && m_VisibleRenderWindowPart == renderPart) { RenderWindowPartDeactivated(renderPart); m_VisibleRenderWindowPart = nullptr; } } if (mitk::ILifecycleAwarePart* lifecycleAwarePart = dynamic_cast(part)) { lifecycleAwarePart->Hidden(); } } void QmitkViewCoordinator::PartVisible(const berry::IWorkbenchPartReference::Pointer& partRef) { //MITK_INFO << "*** PartVisible (" << partRef->GetPart(false)->GetPartName() << ")"; berry::IWorkbenchPart* part = partRef->GetPart(false).GetPointer(); // Check for a render window part and inform IRenderWindowPartListener views // that it was activated if (mitk::IRenderWindowPart* renderPart = dynamic_cast(part)) { if (!m_ActiveRenderWindowPart) { RenderWindowPartActivated(renderPart); m_VisibleRenderWindowPart = renderPart; } } if (mitk::ILifecycleAwarePart* lifecycleAwarePart = dynamic_cast(part)) { lifecycleAwarePart->Visible(); } } void QmitkViewCoordinator::PartInputChanged(const berry::IWorkbenchPartReference::Pointer& partRef) { berry::IWorkbenchPart* part = partRef->GetPart(false).GetPointer(); // Check for a render window part and inform IRenderWindowPartListener views // that it was changed if (mitk::IRenderWindowPart* renderPart = dynamic_cast(part)) { if (!m_ActiveRenderWindowPart) { RenderWindowPartInputChanged(renderPart); } } } void QmitkViewCoordinator::WindowOpened(const berry::IWorkbenchWindow::Pointer& window) { window->GetPartService()->AddPartListener(this); } void QmitkViewCoordinator::WindowClosed(const berry::IWorkbenchWindow::Pointer& /*window*/) { } void QmitkViewCoordinator::RenderWindowPartActivated(mitk::IRenderWindowPart* renderPart) { - for (auto& listener : m_RenderWindowListeners) + for (auto& listener : qAsConst(m_RenderWindowListeners)) { listener->RenderWindowPartActivated(renderPart); } } void QmitkViewCoordinator::RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderPart) { - for (auto& listener : m_RenderWindowListeners) + for (auto& listener : qAsConst(m_RenderWindowListeners)) { listener->RenderWindowPartDeactivated(renderPart); } } void QmitkViewCoordinator::RenderWindowPartInputChanged(mitk::IRenderWindowPart* renderPart) { - for (auto& listener : m_RenderWindowListeners) + for (auto& listener : qAsConst(m_RenderWindowListeners)) { listener->RenderWindowPartInputChanged(renderPart); } } diff --git a/Plugins/org.mitk.gui.qt.datamanager/src/QmitkDataManagerView.cpp b/Plugins/org.mitk.gui.qt.datamanager/src/QmitkDataManagerView.cpp index d1ac5f23f5..27b424aafd 100644 --- a/Plugins/org.mitk.gui.qt.datamanager/src/QmitkDataManagerView.cpp +++ b/Plugins/org.mitk.gui.qt.datamanager/src/QmitkDataManagerView.cpp @@ -1,272 +1,272 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkDataManagerView.h" // mitk gui qt datamanager #include "internal/QmitkDataManagerItemDelegate.h" #include "internal/QmitkNodeTableViewKeyFilter.h" // mitk core #include #include #include #include #include #include #include #include #include #include #include #include #include #include // qt widgets module #include #include #include #include #include // beery plugins #include #include #include #include #include #include #include #include #include // mitk core services plugin #include #include // mitk gui common plugin #include #include #include // mitk gui qt application plugin #include #include // mitk gui qt common plugin #include // qt #include #include #include #include #include const QString QmitkDataManagerView::VIEW_ID = "org.mitk.views.datamanager"; QmitkDataManagerView::QmitkDataManagerView() : m_ItemDelegate(nullptr) { } QmitkDataManagerView::~QmitkDataManagerView() { // nothing here } void QmitkDataManagerView::CreateQtPartControl(QWidget* parent) { m_CurrentRowCount = 0; m_Parent = parent; berry::IBerryPreferences::Pointer prefs = this->GetPreferences().Cast(); assert(prefs); //# GUI m_NodeTreeModel = new QmitkDataStorageTreeModel(GetDataStorage(), prefs->GetBool("Place new nodes on top", true)); m_NodeTreeModel->setParent(parent); m_NodeTreeModel->SetAllowHierarchyChange(prefs->GetBool("Allow changing of parent node", false)); m_SurfaceDecimation = prefs->GetBool("Use surface decimation", false); // Prepare filters m_HelperObjectFilterPredicate = mitk::NodePredicateOr::New( mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true)), mitk::NodePredicateProperty::New("hidden object", mitk::BoolProperty::New(true))); m_NodeWithNoDataFilterPredicate = mitk::NodePredicateData::New(nullptr); m_FilterModel = new QmitkDataStorageFilterProxyModel(); m_FilterModel->setSourceModel(m_NodeTreeModel); m_FilterModel->AddFilterPredicate(m_HelperObjectFilterPredicate); m_FilterModel->AddFilterPredicate(m_NodeWithNoDataFilterPredicate); m_NodeTreeView = new QTreeView; m_NodeTreeView->setHeaderHidden(true); m_NodeTreeView->setSelectionMode(QAbstractItemView::ExtendedSelection); m_NodeTreeView->setSelectionBehavior(QAbstractItemView::SelectRows); m_NodeTreeView->setAlternatingRowColors(true); m_NodeTreeView->setDragEnabled(true); m_NodeTreeView->setDropIndicatorShown(true); m_NodeTreeView->setAcceptDrops(true); m_NodeTreeView->setContextMenuPolicy(Qt::CustomContextMenu); m_NodeTreeView->setModel(m_FilterModel); m_NodeTreeView->setTextElideMode(Qt::ElideMiddle); m_NodeTreeView->installEventFilter(new QmitkNodeTableViewKeyFilter(this, GetDataStorage())); m_ItemDelegate = new QmitkDataManagerItemDelegate(m_NodeTreeView); m_NodeTreeView->setItemDelegate(m_ItemDelegate); connect(m_NodeTreeModel, SIGNAL(rowsInserted(const QModelIndex&, int, int)), this, SLOT(NodeTreeViewRowsInserted(const QModelIndex&, int, int))); connect(m_NodeTreeModel, SIGNAL(rowsRemoved(const QModelIndex&, int, int)), this, SLOT(NodeTreeViewRowsRemoved(const QModelIndex&, int, int))); connect(m_NodeTreeView->selectionModel(), SIGNAL(selectionChanged(const QItemSelection &, const QItemSelection &)), this, SLOT(NodeSelectionChanged(const QItemSelection &, const QItemSelection &))); connect(m_NodeTreeModel, &QmitkDataStorageTreeModel::nodeVisibilityChanged, this, &QmitkDataManagerView::OnNodeVisibilityChanged); // data node context menu and menu actions m_DataNodeContextMenu = new QmitkDataNodeContextMenu(GetSite(), m_NodeTreeView); m_DataNodeContextMenu->SetDataStorage(GetDataStorage()); m_DataNodeContextMenu->SetSurfaceDecimation(m_SurfaceDecimation); connect(m_NodeTreeView, SIGNAL(customContextMenuRequested(const QPoint&)), m_DataNodeContextMenu, SLOT(OnContextMenuRequested(const QPoint&))); berry::IEditorRegistry* editorRegistry = berry::PlatformUI::GetWorkbench()->GetEditorRegistry(); QList editors = editorRegistry->GetEditors("*.mitk"); if (editors.size() > 1) { m_ShowInMapper = new QSignalMapper(this); foreach(berry::IEditorDescriptor::Pointer descriptor, editors) { QAction* action = new QAction(descriptor->GetLabel(), this); m_ShowInActions << action; m_ShowInMapper->connect(action, SIGNAL(triggered()), m_ShowInMapper, SLOT(map())); m_ShowInMapper->setMapping(action, descriptor->GetId()); } connect(m_ShowInMapper, SIGNAL(mapped(QString)), this, SLOT(ShowIn(QString))); } QGridLayout* dndFrameWidgetLayout = new QGridLayout; dndFrameWidgetLayout->addWidget(m_NodeTreeView, 0, 0); dndFrameWidgetLayout->setContentsMargins(0, 0, 0, 0); m_DnDFrameWidget = new QmitkDnDFrameWidget(m_Parent); m_DnDFrameWidget->setLayout(dndFrameWidgetLayout); QVBoxLayout* layout = new QVBoxLayout(parent); layout->addWidget(m_DnDFrameWidget); layout->setContentsMargins(0, 0, 0, 0); m_Parent->setLayout(layout); } void QmitkDataManagerView::SetFocus() { } ////////////////////////////////////////////////////////////////////////// // Node tree modification ////////////////////////////////////////////////////////////////////////// void QmitkDataManagerView::NodeTreeViewRowsInserted(const QModelIndex& parent, int /*start*/, int /*end*/) { QModelIndex viewIndex = m_FilterModel->mapFromSource(parent); m_NodeTreeView->setExpanded(viewIndex, true); // a new row was inserted if (m_CurrentRowCount == 0 && m_NodeTreeModel->rowCount() == 1) { mitk::WorkbenchUtil::OpenRenderWindowPart(GetSite()->GetPage()); m_CurrentRowCount = m_NodeTreeModel->rowCount(); } } void QmitkDataManagerView::NodeTreeViewRowsRemoved(const QModelIndex& /*parent*/, int /*start*/, int /*end*/) { m_CurrentRowCount = m_NodeTreeModel->rowCount(); } void QmitkDataManagerView::NodeSelectionChanged(const QItemSelection& /*selected*/, const QItemSelection& /*deselected*/) { auto selectedNodes = GetCurrentSelection(); auto nodeSet = m_NodeTreeModel->GetNodeSet(); - for (auto node : nodeSet) + for (auto node : qAsConst(nodeSet)) { if (node.IsNotNull()) { node->SetSelected(selectedNodes.contains(node)); } } m_DataNodeContextMenu->SetSelectedNodes(selectedNodes); } void QmitkDataManagerView::OnNodeVisibilityChanged() { ToggleVisibilityAction::Run(GetSite(), GetDataStorage(), QList()); } void QmitkDataManagerView::ShowIn(const QString& editorId) { berry::IWorkbenchPage::Pointer page = GetSite()->GetPage(); berry::IEditorInput::Pointer input(new mitk::DataStorageEditorInput(GetDataStorageReference())); page->OpenEditor(input, editorId, false, berry::IWorkbenchPage::MATCH_ID); } void QmitkDataManagerView::NodeChanged(const mitk::DataNode* /*node*/) { // m_FilterModel->invalidate(); // fix as proposed by R. Khlebnikov in the mitk-users mail from 02.09.2014 QMetaObject::invokeMethod(m_FilterModel, "invalidate", Qt::QueuedConnection); } void QmitkDataManagerView::OnPreferencesChanged(const berry::IBerryPreferences* prefs) { if (m_NodeTreeModel->GetPlaceNewNodesOnTopFlag() != prefs->GetBool("Place new nodes on top", true)) { m_NodeTreeModel->SetPlaceNewNodesOnTop(!m_NodeTreeModel->GetPlaceNewNodesOnTopFlag()); } bool hideHelperObjects = !prefs->GetBool("Show helper objects", false); if (m_FilterModel->HasFilterPredicate(m_HelperObjectFilterPredicate) != hideHelperObjects) { if (hideHelperObjects) { m_FilterModel->AddFilterPredicate(m_HelperObjectFilterPredicate); } else { m_FilterModel->RemoveFilterPredicate(m_HelperObjectFilterPredicate); } } bool hideNodesWithNoData = !prefs->GetBool("Show nodes containing no data", false); if (m_FilterModel->HasFilterPredicate(m_NodeWithNoDataFilterPredicate) != hideNodesWithNoData) { if (hideNodesWithNoData) { m_FilterModel->AddFilterPredicate(m_NodeWithNoDataFilterPredicate); } else { m_FilterModel->RemoveFilterPredicate(m_NodeWithNoDataFilterPredicate); } } m_NodeTreeView->expandAll(); m_SurfaceDecimation = prefs->GetBool("Use surface decimation", false); m_DataNodeContextMenu->SetSurfaceDecimation(m_SurfaceDecimation); m_NodeTreeModel->SetAllowHierarchyChange(prefs->GetBool("Allow changing of parent node", false)); GlobalReinitAction::Run(GetSite(), GetDataStorage()); } QItemSelectionModel* QmitkDataManagerView::GetDataNodeSelectionModel() const { return m_NodeTreeView->selectionModel(); } diff --git a/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTDoseVisualizer.cpp b/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTDoseVisualizer.cpp index 675f3bdfe6..4b5b2ff5f4 100644 --- a/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTDoseVisualizer.cpp +++ b/Plugins/org.mitk.gui.qt.dosevisualization/src/internal/RTDoseVisualizer.cpp @@ -1,821 +1,821 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Qt #include #include // Blueberry #include #include // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // Qmitk #include "RTDoseVisualizer.h" #include #include #include #include #include #include "QmitkRenderWindow.h" #include "org_mitk_gui_qt_dosevisualization_Activator.h" #include #include "vtkDecimatePro.h" const std::string RTDoseVisualizer::VIEW_ID = "org.mitk.views.rt.dosevisualization"; const std::string RTDoseVisualizer::ISO_LINE_NODE_NAME = "dose iso lines"; namespace mitk { /** @brief Predicate to identify dose nodes. Didn't use NodePredicateeDataProperty, because we want only depend on the property value ('RTDOSE') and not on the property type (e.g. StringProperty or mitkTemperoSpatialStringProperty).*/ class NodePredicateDose : public NodePredicateBase { public: mitkClassMacro(NodePredicateDose, NodePredicateBase); itkNewMacro(NodePredicateDose); ~NodePredicateDose() override {}; bool CheckNode(const mitk::DataNode *node) const override { if (!node) return false; auto data = node->GetData(); if (!data) { return false; } auto modalityProperty = data->GetProperty(mitk::GeneratePropertyNameForDICOMTag(0x0008, 0x0060).c_str()); if (modalityProperty.IsNull()) { return false; } std::string modality = modalityProperty->GetValueAsString(); return modality == "RTDOSE"; }; protected: NodePredicateDose() {}; }; } // namespace mitk RTDoseVisualizer::RTDoseVisualizer() { m_selectedNode = nullptr; m_selectedPresetName = ""; m_PrescribedDose_Data = 0.0; m_freeIsoValuesCount = 0; m_internalUpdate = false; m_isDoseOrIsoPredicate = mitk::NodePredicateDose::New(); m_isIsoPredicate = mitk::NodePredicateProperty::New("name", mitk::StringProperty::New(ISO_LINE_NODE_NAME)); m_isDosePredicate = mitk::NodePredicateAnd::New(m_isDoseOrIsoPredicate, mitk::NodePredicateNot::New(m_isIsoPredicate)); } RTDoseVisualizer::~RTDoseVisualizer() { mitk::DataStorage::SetOfObjects::ConstPointer isoNodes = this->GetDataStorage()->GetSubset(m_isIsoPredicate); this->GetDataStorage()->Remove(isoNodes); delete m_LevelSetModel; delete m_DoseColorDelegate; delete m_DoseValueDelegate; delete m_DoseVisualDelegate; } void RTDoseVisualizer::SetFocus(){} void RTDoseVisualizer::CreateQtPartControl( QWidget *parent ) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi( parent ); m_LevelSetModel = new QmitkIsoDoseLevelSetModel(this); m_LevelSetModel->setVisibilityEditOnly(true); m_DoseColorDelegate = new QmitkDoseColorDelegate(this); m_DoseValueDelegate = new QmitkDoseValueDelegate(this); m_DoseVisualDelegate = new QmitkDoseVisualStyleDelegate(this); this->UpdateByPreferences(); auto doseNodes = this->GetDataStorage()->GetSubset(this->m_isDosePredicate); auto doseNodeIter = doseNodes->begin(); while (doseNodeIter != doseNodes->end()) { PrepareDoseNode(*doseNodeIter); ++doseNodeIter; } this->ActualizeIsoLevelsForAllDoseDataNodes(); this->ActualizeReferenceDoseForAllDoseDataNodes(); this->ActualizeDisplayStyleForAllDoseDataNodes(); this->m_Controls.isoLevelSetView->setModel(m_LevelSetModel); this->m_Controls.isoLevelSetView->setItemDelegateForColumn(0,m_DoseColorDelegate); this->m_Controls.isoLevelSetView->setItemDelegateForColumn(1,m_DoseValueDelegate); this->m_Controls.isoLevelSetView->setItemDelegateForColumn(2,m_DoseVisualDelegate); this->m_Controls.isoLevelSetView->setItemDelegateForColumn(3,m_DoseVisualDelegate); this->m_Controls.isoLevelSetView->setContextMenuPolicy(Qt::CustomContextMenu); this->m_Controls.btnRemoveFreeValue->setDisabled(true); this->m_Controls.doseBtn->setVisible(false); connect(m_Controls.spinReferenceDose, SIGNAL(valueChanged(double)), this, SLOT(OnReferenceDoseChanged(double))); connect(m_Controls.spinReferenceDose, SIGNAL(valueChanged(double)), m_LevelSetModel, SLOT(setReferenceDose(double))); connect(m_Controls.radioAbsDose, SIGNAL(toggled(bool)), m_LevelSetModel, SLOT(setShowAbsoluteDose(bool))); connect(m_Controls.radioAbsDose, SIGNAL(toggled(bool)), this, SLOT(OnAbsDoseToggled(bool))); connect(m_Controls.btnAddFreeValue, SIGNAL(clicked()), this, SLOT(OnAddFreeValueClicked())); connect(m_Controls.btnRemoveFreeValue, SIGNAL(clicked()), this, SLOT(OnRemoveFreeValueClicked())); connect(m_Controls.checkGlobalVisColorWash, SIGNAL(toggled(bool)), this, SLOT(OnGlobalVisColorWashToggled(bool))); connect(m_Controls.checkGlobalVisIsoLine, SIGNAL(toggled(bool)), this, SLOT(OnGlobalVisIsoLineToggled(bool))); connect(m_Controls.isoLevelSetView, SIGNAL(customContextMenuRequested(const QPoint&)), this, SLOT(OnShowContextMenuIsoSet(const QPoint&))); connect(m_Controls.comboPresets, SIGNAL(currentIndexChanged ( const QString&)), this, SLOT(OnCurrentPresetChanged(const QString&))); connect(m_Controls.btnUsePrescribedDose, SIGNAL(clicked()), this, SLOT(OnUsePrescribedDoseClicked())); connect(m_Controls.isoLevelSetView->model(), SIGNAL( modelReset()), this, SLOT(OnDataChangedInIsoLevelSetView())); ctkServiceReference ref = mitk::org_mitk_gui_qt_dosevisualization_Activator::GetContext()->getServiceReference(); ctkDictionary propsForSlot; if (ref) { ctkEventAdmin* eventAdmin = mitk::org_mitk_gui_qt_dosevisualization_Activator::GetContext()->getService(ref); propsForSlot[ctkEventConstants::EVENT_TOPIC] = mitk::RTCTKEventConstants::TOPIC_ISO_DOSE_LEVEL_PRESETS_CHANGED.c_str(); eventAdmin->subscribeSlot(this, SLOT(OnHandleCTKEventPresetsChanged(ctkEvent)), propsForSlot); propsForSlot[ctkEventConstants::EVENT_TOPIC] = mitk::RTCTKEventConstants::TOPIC_REFERENCE_DOSE_CHANGED.c_str(); eventAdmin->subscribeSlot(this, SLOT(OnHandleCTKEventReferenceDoseChanged(ctkEvent)), propsForSlot); propsForSlot[ctkEventConstants::EVENT_TOPIC] = mitk::RTCTKEventConstants::TOPIC_GLOBAL_VISIBILITY_CHANGED.c_str(); eventAdmin->subscribeSlot(this, SLOT(OnHandleCTKEventGlobalVisChanged(ctkEvent)), propsForSlot); } this->UpdateBySelectedNode(); } void RTDoseVisualizer::OnReferenceDoseChanged(double value) { if (! m_internalUpdate) { mitk::DoseValueAbs referenceDose = 0.0; bool globalSync = mitk::GetReferenceDoseValue(referenceDose); if (globalSync) { mitk::SetReferenceDoseValue(globalSync, value); this->ActualizeReferenceDoseForAllDoseDataNodes(); } else { if (this->m_selectedNode.IsNotNull()) { this->m_selectedNode->SetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(), value); mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode.IsNotNull()) isoDoseNode->SetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(), value); } } if (this->m_selectedNode.IsNotNull()) { this->UpdateColorWashTransferFunction(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } void RTDoseVisualizer::OnAddFreeValueClicked() { QColor newColor; //Use HSV schema of QColor to calculate a different color depending on the //number of already existing free iso lines. newColor.setHsv((m_freeIsoValuesCount*85)%360,255,255); mitk::IsoDoseLevel::ColorType mColor; mColor[0]=newColor.redF(); mColor[1]=newColor.greenF(); mColor[2]=newColor.blueF(); mitk::IsoDoseLevelVector::Pointer freeIsoDoseVector; mitk::IsoDoseLevelVectorProperty::Pointer propIsoVector; mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode.IsNotNull()) { propIsoVector = dynamic_cast(isoDoseNode->GetProperty(mitk::RTConstants::DOSE_FREE_ISO_VALUES_PROPERTY_NAME.c_str())); freeIsoDoseVector = propIsoVector->GetValue(); if (freeIsoDoseVector.IsNull()) mitk::IsoDoseLevelVector::Pointer freeIsoDoseVector = mitk::IsoDoseLevelVector::New(); mitk::IsoDoseLevel::Pointer newLevel = mitk::IsoDoseLevel::New(0.5, mColor, true, false); freeIsoDoseVector->InsertElement(m_freeIsoValuesCount, newLevel); propIsoVector = mitk::IsoDoseLevelVectorProperty::New(freeIsoDoseVector); isoDoseNode->SetProperty(mitk::RTConstants::DOSE_FREE_ISO_VALUES_PROPERTY_NAME.c_str(), propIsoVector); m_freeIsoValuesCount++; this->m_Controls.btnRemoveFreeValue->setEnabled(true); //Update Widget this->UpdateFreeIsoValues(); //Update Rendering this->ActualizeFreeIsoLine(); } } void RTDoseVisualizer::OnRemoveFreeValueClicked() { int index = this->m_Controls.listFreeValues->currentRow(); if (index > static_cast(m_freeIsoValuesCount) || index < 0) return; mitk::IsoDoseLevelVectorProperty::Pointer propfreeIsoVec; mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); propfreeIsoVec = dynamic_cast(isoDoseNode->GetProperty(mitk::RTConstants::DOSE_FREE_ISO_VALUES_PROPERTY_NAME.c_str())); mitk::IsoDoseLevelVector::Pointer freeIsoDoseLevelVec = propfreeIsoVec->GetValue(); if(freeIsoDoseLevelVec->IndexExists(index)) { //freeIsoDoseLevelVec->DeleteIndex(index); freeIsoDoseLevelVec->erase(freeIsoDoseLevelVec->begin()+index); --m_freeIsoValuesCount; if(m_freeIsoValuesCount == 0) this->m_Controls.btnRemoveFreeValue->setEnabled(true); this->UpdateFreeIsoValues(); this->ActualizeFreeIsoLine(); } } void RTDoseVisualizer::OnUsePrescribedDoseClicked() { m_Controls.spinReferenceDose->setValue(this->m_PrescribedDose_Data); } void RTDoseVisualizer::OnDataChangedInIsoLevelSetView() { //colorwash visibility changed, update the colorwash this->UpdateColorWashTransferFunction(); if(m_selectedNode.IsNotNull()) { //Hack: This is a dirty hack to reinit the isodose contour node. Only if the node (or property) has changed the rendering process register the RequestUpdateAll //Only way to render the isoline by changes without a global reinit mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode.IsNotNull()) isoDoseNode->Modified(); // Reinit if visibility of colorwash or isodoselevel changed mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void RTDoseVisualizer::OnShowContextMenuIsoSet(const QPoint& pos) { QPoint globalPos = m_Controls.isoLevelSetView->viewport()->mapToGlobal(pos); QMenu viewMenu; QAction* invertIsoLineAct = viewMenu.addAction("Invert iso line visibility"); QAction* activateIsoLineAct = viewMenu.addAction("Activate all iso lines"); QAction* deactivateIsoLineAct = viewMenu.addAction("Deactivate all iso lines"); viewMenu.addSeparator(); QAction* invertColorWashAct = viewMenu.addAction("Invert color wash visibility"); QAction* activateColorWashAct = viewMenu.addAction("Activate all color wash levels"); QAction* deactivateColorWashAct = viewMenu.addAction("Deactivate all color wash levels"); viewMenu.addSeparator(); QAction* swapAct = viewMenu.addAction("Swap iso line/color wash visibility"); // ... QAction* selectedItem = viewMenu.exec(globalPos); if (selectedItem == invertIsoLineAct) { this->m_LevelSetModel->invertVisibilityIsoLines(); } else if (selectedItem == activateIsoLineAct) { this->m_LevelSetModel->switchVisibilityIsoLines(true); } else if (selectedItem == deactivateIsoLineAct) { this->m_LevelSetModel->switchVisibilityIsoLines(false); } else if (selectedItem == invertColorWashAct) { this->m_LevelSetModel->invertVisibilityColorWash(); } else if (selectedItem == activateColorWashAct) { this->m_LevelSetModel->switchVisibilityColorWash(true); } else if (selectedItem == deactivateColorWashAct) { this->m_LevelSetModel->switchVisibilityColorWash(false); } else if (selectedItem == swapAct) { this->m_LevelSetModel->swapVisibility(); } } void RTDoseVisualizer::UpdateFreeIsoValues() { this->m_Controls.listFreeValues->clear(); mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode.IsNotNull()) { mitk::IsoDoseLevelVectorProperty::Pointer propfreeIsoVec; propfreeIsoVec = dynamic_cast(isoDoseNode->GetProperty(mitk::RTConstants::DOSE_FREE_ISO_VALUES_PROPERTY_NAME.c_str())); mitk::IsoDoseLevelVector::Pointer freeIsoDoseLevelVec = propfreeIsoVec->GetValue(); for (mitk::IsoDoseLevelVector::Iterator pos = freeIsoDoseLevelVec->Begin(); pos != freeIsoDoseLevelVec->End(); ++pos) { QListWidgetItem* item = new QListWidgetItem; item->setSizeHint(QSize(0, 25)); QmitkFreeIsoDoseLevelWidget* widget = new QmitkFreeIsoDoseLevelWidget; float pref; m_selectedNode->GetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(), pref); widget->setIsoDoseLevel(pos.Value()); widget->setReferenceDose(pref); connect(m_Controls.spinReferenceDose, SIGNAL(valueChanged(double)), widget, SLOT(setReferenceDose(double))); connect(widget, SIGNAL(ColorChanged(mitk::IsoDoseLevel*)), this, SLOT(ActualizeFreeIsoLine())); connect(widget, SIGNAL(ValueChanged(mitk::IsoDoseLevel*, mitk::DoseValueRel)), this, SLOT(ActualizeFreeIsoLine())); connect(widget, SIGNAL(VisualizationStyleChanged(mitk::IsoDoseLevel*)), this, SLOT(ActualizeFreeIsoLine())); this->m_Controls.listFreeValues->addItem(item); this->m_Controls.listFreeValues->setItemWidget(item, widget); } } } void RTDoseVisualizer::ActualizeFreeIsoLine() { if(m_selectedNode.IsNotNull()) { //Hack: This is a dirty hack to reinit the isodose contour node. Only if the node (or property) has changed the rendering process register the RequestUpdateAll //Only way to render the isoline by changes without a global reinit mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode.IsNotNull()) isoDoseNode->Modified(); // Reinit if visibility of colorwash or isodoselevel changed mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void RTDoseVisualizer::OnAbsDoseToggled(bool showAbs) { if (! m_internalUpdate) { mitk::SetDoseDisplayAbsolute(showAbs); this->ActualizeDisplayStyleForAllDoseDataNodes(); } } void RTDoseVisualizer::OnGlobalVisColorWashToggled(bool showColorWash) { if (m_selectedNode.IsNotNull()) { m_selectedNode->SetBoolProperty(mitk::RTConstants::DOSE_SHOW_COLORWASH_PROPERTY_NAME.c_str(), showColorWash); //The rendering mode could be set in the dose mapper: Refactoring! mitk::RenderingModeProperty::Pointer renderingMode = mitk::RenderingModeProperty::New(); if(showColorWash) renderingMode->SetValue(mitk::RenderingModeProperty::COLORTRANSFERFUNCTION_COLOR); else renderingMode->SetValue(mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR); m_selectedNode->SetProperty("Image Rendering.Mode", renderingMode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void RTDoseVisualizer::OnGlobalVisIsoLineToggled(bool showIsoLines) { if (m_selectedNode.IsNotNull()) { mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode.IsNotNull()) { isoDoseNode->SetBoolProperty(mitk::RTConstants::DOSE_SHOW_ISOLINES_PROPERTY_NAME.c_str(), showIsoLines); //toggle the visibility of the free isolevel sliders this->m_Controls.listFreeValues->setEnabled(showIsoLines); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } void RTDoseVisualizer::UpdateColorWashTransferFunction() { //Generating the Colorwash vtkSmartPointer transferFunction = vtkSmartPointer::New(); if(m_selectedNode.IsNotNull()) { mitk::IsoDoseLevelSetProperty::Pointer propIsoSet = dynamic_cast(m_selectedNode->GetProperty(mitk::RTConstants::DOSE_ISO_LEVELS_PROPERTY_NAME.c_str())); mitk::IsoDoseLevelSet::Pointer isoDoseLevelSet = propIsoSet->GetValue(); float referenceDose; m_selectedNode->GetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(),referenceDose); mitk::TransferFunction::ControlPoints scalarOpacityPoints; scalarOpacityPoints.push_back( std::make_pair(0, 1 ) ); //Backgroud transferFunction->AddHSVPoint(((isoDoseLevelSet->Begin())->GetDoseValue()*referenceDose)-0.001,0,0,0,1.0,1.0); for(mitk::IsoDoseLevelSet::ConstIterator itIsoDoseLevel = isoDoseLevelSet->Begin(); itIsoDoseLevel != isoDoseLevelSet->End(); ++itIsoDoseLevel) { float *hsv = new float[3]; //used for transfer rgb to hsv vtkSmartPointer cCalc = vtkSmartPointer::New(); if(itIsoDoseLevel->GetVisibleColorWash()) { cCalc->RGBToHSV(itIsoDoseLevel->GetColor()[0],itIsoDoseLevel->GetColor()[1],itIsoDoseLevel->GetColor()[2],&hsv[0],&hsv[1],&hsv[2]); transferFunction->AddHSVPoint(itIsoDoseLevel->GetDoseValue()*referenceDose,hsv[0],hsv[1],hsv[2],1.0,1.0); } else { scalarOpacityPoints.push_back( std::make_pair(itIsoDoseLevel->GetDoseValue()*referenceDose, 1 ) ); } } mitk::TransferFunction::Pointer mitkTransFunc = mitk::TransferFunction::New(); mitk::TransferFunctionProperty::Pointer mitkTransFuncProp = mitk::TransferFunctionProperty::New(); mitkTransFunc->SetColorTransferFunction(transferFunction); mitkTransFunc->SetScalarOpacityPoints(scalarOpacityPoints); mitkTransFuncProp->SetValue(mitkTransFunc); m_selectedNode->SetProperty("Image Rendering.Transfer Function", mitkTransFuncProp); } } /**Simple check if the passed node has dose visualization properties set.*/ bool hasDoseVisProperties(mitk::DataNode::Pointer doseNode) { return doseNode->GetProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str()) != nullptr; } void RTDoseVisualizer::OnSelectionChanged( berry::IWorkbenchPart::Pointer, const QList&) { QList dataNodes = this->GetDataManagerSelection(); mitk::DataNode* selectedNode = nullptr; if (!dataNodes.empty()) { bool isDoseNode = m_isDosePredicate->CheckNode(dataNodes[0].GetPointer()); if (isDoseNode) { selectedNode = dataNodes[0]; } } if (selectedNode != m_selectedNode.GetPointer()) { m_selectedNode = selectedNode; if (selectedNode) { PrepareDoseNode(m_selectedNode); } } UpdateBySelectedNode(); } void RTDoseVisualizer::PrepareDoseNode( mitk::DataNode* doseNode ) const { mitk::DoseValueAbs dose; mitk::GetReferenceDoseValue(dose); auto presetMap = mitk::LoadPresetsMap(); auto colorPreset = mitk::GenerateIsoLevels_Virtuos(); auto finding = presetMap.find(mitk::GetSelectedPresetName()); if (finding != presetMap.end()) { colorPreset = finding->second; } if (!hasDoseVisProperties(doseNode)) { mitk::ConfigureNodeAsDoseNode(doseNode, colorPreset, dose, true); } mitk::DataNode::Pointer doseOutlineNode = this->GetIsoDoseNode(doseNode); if (doseOutlineNode.IsNull()) { doseOutlineNode = mitk::DataNode::New(); doseOutlineNode->SetData(doseNode->GetData()); doseOutlineNode->SetName(ISO_LINE_NODE_NAME); mitk::ConfigureNodeAsIsoLineNode(doseOutlineNode, colorPreset, dose, true); this->GetDataStorage()->Add(doseOutlineNode, doseNode); } } void RTDoseVisualizer::UpdateBySelectedNode() { m_Controls.groupNodeSpecific->setEnabled(m_selectedNode.IsNotNull()); m_Controls.groupFreeValues->setEnabled(m_selectedNode.IsNotNull()); m_Controls.checkGlobalVisColorWash->setEnabled(m_selectedNode.IsNotNull()); m_Controls.checkGlobalVisIsoLine->setEnabled(m_selectedNode.IsNotNull()); m_Controls.isoLevelSetView->setEnabled(m_selectedNode.IsNotNull()); if(m_selectedNode.IsNull()) { m_Controls.NrOfFractions->setText(QString("N/A. No dose selected")); m_Controls.prescribedDoseSpecific->setText(QString("N/A. No dose selected")); } else { //dose specific information int fracCount = 1; m_selectedNode->GetIntProperty(mitk::RTConstants::DOSE_FRACTION_COUNT_PROPERTY_NAME.c_str(), fracCount); m_Controls.NrOfFractions->setText(QString::number(fracCount)); m_PrescribedDose_Data = 0.0; auto prescibedDoseProperty = m_selectedNode->GetData()->GetProperty(mitk::RTConstants::PRESCRIBED_DOSE_PROPERTY_NAME.c_str()); - auto prescribedDoseGenericProperty = dynamic_cast*>(prescibedDoseProperty.GetPointer()); + auto prescribedDoseGenericProperty = dynamic_cast(prescibedDoseProperty.GetPointer()); m_PrescribedDose_Data = prescribedDoseGenericProperty->GetValue(); m_Controls.prescribedDoseSpecific->setText(QString::number(m_PrescribedDose_Data)); //free iso lines mitk::DataNode::Pointer isoDoseNode = this->GetIsoDoseNode(m_selectedNode); if (isoDoseNode) { mitk::IsoDoseLevelVectorProperty::Pointer propIsoVector; propIsoVector = dynamic_cast(isoDoseNode->GetProperty(mitk::RTConstants::DOSE_FREE_ISO_VALUES_PROPERTY_NAME.c_str())); if (propIsoVector.IsNull()) { mitk::IsoDoseLevelVector::Pointer freeIsoValues = mitk::IsoDoseLevelVector::New(); propIsoVector = mitk::IsoDoseLevelVectorProperty::New(freeIsoValues); isoDoseNode->SetProperty(mitk::RTConstants::DOSE_FREE_ISO_VALUES_PROPERTY_NAME.c_str(), propIsoVector); } UpdateFreeIsoValues(); //global dose issues //ATM the IsoDoseContours have an own (helper) node which is a child of dose node; Will be fixed with the doseMapper refactoring bool showIsoLine = mitk::GetGlobalIsolineVis(); isoDoseNode->GetBoolProperty(mitk::RTConstants::DOSE_SHOW_ISOLINES_PROPERTY_NAME.c_str(), showIsoLine); m_Controls.checkGlobalVisIsoLine->setChecked(showIsoLine); } bool showColorWash = mitk::GetGlobalColorwashVis(); m_selectedNode->GetBoolProperty(mitk::RTConstants::DOSE_SHOW_COLORWASH_PROPERTY_NAME.c_str(),showColorWash); m_Controls.checkGlobalVisColorWash->setChecked(showColorWash); float referenceDose = 0.0; m_selectedNode->GetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(),referenceDose); m_Controls.spinReferenceDose->setValue(referenceDose); mitk::IsoDoseLevelSetProperty::Pointer propIsoSet = dynamic_cast(m_selectedNode->GetProperty(mitk::RTConstants::DOSE_ISO_LEVELS_PROPERTY_NAME.c_str())); if (propIsoSet) { this->m_LevelSetModel->setIsoDoseLevelSet(propIsoSet->GetValue()); } } } void RTDoseVisualizer::NodeRemoved(const mitk::DataNode* node) { /**@TODO This removal seems to be needed because of the current dose rendering approach (additional sub node for iso dose lines). As soon as we have a better and sound single node rendering mechanism for doses. This method should be removed.*/ bool isdose = m_isDosePredicate->CheckNode(node); if (isdose) { mitk::DataStorage::SetOfObjects::ConstPointer childNodes = this->GetDataStorage()->GetDerivations(node, m_isIsoPredicate); auto iterChildNodes = childNodes->begin(); while (iterChildNodes != childNodes->end()) { this->GetDataStorage()->Remove((*iterChildNodes)); ++iterChildNodes; } } } void RTDoseVisualizer::NodeChanged(const mitk::DataNode *node) { /**@TODO This event seems to be needed because of the current dose rendering approach (additional sub node for iso dose lines). As soon as we have a better and sound single node rendering mechanism for doses. This method should be removed.*/ bool isdose = m_isDosePredicate->CheckNode(node); if(isdose) { bool isvisible = true; if(node->GetBoolProperty("visible", isvisible)) { mitk::DataStorage::SetOfObjects::ConstPointer childNodes = this->GetDataStorage()->GetDerivations(node, m_isIsoPredicate); mitk::DataStorage::SetOfObjects::const_iterator iterChildNodes = childNodes->begin(); while (iterChildNodes != childNodes->end()) { (*iterChildNodes)->SetVisibility(isvisible); ++iterChildNodes; } } } } void RTDoseVisualizer::UpdateByPreferences() { m_Presets = mitk::LoadPresetsMap(); m_internalUpdate = true; m_Controls.comboPresets->clear(); this->m_selectedPresetName = mitk::GetSelectedPresetName(); m_Controls.checkGlobalVisIsoLine->setChecked(mitk::GetGlobalIsolineVis()); m_Controls.checkGlobalVisColorWash->setChecked(mitk::GetGlobalColorwashVis()); if(m_Presets.empty()) return; int index = 0; int selectedIndex = -1; for (mitk::PresetMapType::const_iterator pos = m_Presets.begin(); pos != m_Presets.end(); ++pos, ++index) { m_Controls.comboPresets->addItem(QString(pos->first.c_str())); if (this->m_selectedPresetName == pos->first) { selectedIndex = index; } } if (selectedIndex == -1) { selectedIndex = 0; MITK_WARN << "Error. Iso dose level preset specified in preferences does not exist. Preset name: "<m_selectedPresetName; this->m_selectedPresetName = m_Presets.begin()->first; mitk::SetSelectedPresetName(this->m_selectedPresetName); MITK_INFO << "Changed selected iso dose level preset to first existing preset. New preset name: "<m_selectedPresetName; } m_Controls.comboPresets->setCurrentIndex(selectedIndex); this->m_LevelSetModel->setIsoDoseLevelSet(this->m_Presets[this->m_selectedPresetName]); mitk::DoseValueAbs referenceDose = 0.0; bool globalSync = mitk::GetReferenceDoseValue(referenceDose); if (globalSync || this->m_selectedNode.IsNull()) { m_Controls.spinReferenceDose->setValue(referenceDose); } bool displayAbsoluteDose = mitk::GetDoseDisplayAbsolute(); m_Controls.radioAbsDose->setChecked(displayAbsoluteDose); m_Controls.radioRelDose->setChecked(!displayAbsoluteDose); this->m_LevelSetModel->setShowAbsoluteDose(displayAbsoluteDose); m_internalUpdate = false; } void RTDoseVisualizer::OnCurrentPresetChanged(const QString& presetName) { if (! m_internalUpdate) { mitk::SetSelectedPresetName(presetName.toStdString()); this->UpdateByPreferences(); this->ActualizeIsoLevelsForAllDoseDataNodes(); this->UpdateBySelectedNode(); } } void RTDoseVisualizer::ActualizeIsoLevelsForAllDoseDataNodes() { std::string presetName = mitk::GetSelectedPresetName(); mitk::PresetMapType presetMap = mitk::LoadPresetsMap(); mitk::DataStorage::SetOfObjects::ConstPointer nodes = this->GetDataStorage()->GetSubset(m_isDoseOrIsoPredicate); if(presetMap.empty()) return; mitk::IsoDoseLevelSet* selectedPreset = presetMap[presetName]; if (!selectedPreset) { mitkThrow() << "Error. Cannot actualize iso dose level preset. Selected preset does not exist. Preset name: "<begin(); pos != nodes->end(); ++pos) { mitk::IsoDoseLevelSet::Pointer clonedPreset = selectedPreset->Clone(); mitk::IsoDoseLevelSetProperty::Pointer propIsoSet = mitk::IsoDoseLevelSetProperty::New(clonedPreset); (*pos)->SetProperty(mitk::RTConstants::DOSE_ISO_LEVELS_PROPERTY_NAME.c_str(),propIsoSet); } } void RTDoseVisualizer::ActualizeReferenceDoseForAllDoseDataNodes() { mitk::DoseValueAbs value = 0; bool sync = mitk::GetReferenceDoseValue(value); if (sync) { mitk::DataStorage::SetOfObjects::ConstPointer nodes = this->GetDataStorage()->GetSubset(m_isDoseOrIsoPredicate); for(mitk::DataStorage::SetOfObjects::const_iterator pos = nodes->begin(); pos != nodes->end(); ++pos) { (*pos)->SetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(), value); /**@TODO: ATM the IsoDoseContours have an own (helper) node which is a child of dose node; Will be fixed with the doseMapper refactoring*/ mitk::DataStorage::SetOfObjects::ConstPointer childNodes = this->GetDataStorage()->GetDerivations(*pos); mitk::DataStorage::SetOfObjects::const_iterator iterChildNodes = childNodes->begin(); while (iterChildNodes != childNodes->end()) { (*iterChildNodes)->SetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(), value); ++iterChildNodes; } } } } void RTDoseVisualizer::ActualizeDisplayStyleForAllDoseDataNodes() { /** @TODO Klären ob diese präsentations info global oder auch per node gespeichert wird*/ } void RTDoseVisualizer::OnHandleCTKEventReferenceDoseChanged(const ctkEvent&) { mitk::DoseValueAbs referenceDose = 0.0; mitk::GetReferenceDoseValue(referenceDose); this->m_Controls.spinReferenceDose->setValue(referenceDose); } void RTDoseVisualizer::OnHandleCTKEventGlobalVisChanged(const ctkEvent&) { this->m_Controls.checkGlobalVisIsoLine->setChecked(mitk::GetGlobalIsolineVis()); this->m_Controls.checkGlobalVisColorWash->setChecked(mitk::GetGlobalColorwashVis()); } void RTDoseVisualizer::OnHandleCTKEventPresetsChanged(const ctkEvent&) { std::string currentPresetName = mitk::GetSelectedPresetName(); this->OnCurrentPresetChanged(QString::fromStdString(currentPresetName)); } /**@TODO ATM the IsoDoseContours have an own (helper) node which is a child of dose node; Will be fixed with the doseMapper refactoring*/ mitk::DataNode::Pointer RTDoseVisualizer::GetIsoDoseNode(mitk::DataNode::Pointer doseNode) const { mitk::DataStorage::SetOfObjects::ConstPointer childNodes = this->GetDataStorage()->GetDerivations(doseNode, m_isIsoPredicate); if (childNodes->empty()) { return nullptr; } else { return (*childNodes->begin()); } } diff --git a/Plugins/org.mitk.gui.qt.ext/src/QmitkExtWorkbenchWindowAdvisor.cpp b/Plugins/org.mitk.gui.qt.ext/src/QmitkExtWorkbenchWindowAdvisor.cpp index c6fb743873..f3a4196c61 100644 --- a/Plugins/org.mitk.gui.qt.ext/src/QmitkExtWorkbenchWindowAdvisor.cpp +++ b/Plugins/org.mitk.gui.qt.ext/src/QmitkExtWorkbenchWindowAdvisor.cpp @@ -1,1432 +1,1432 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkExtWorkbenchWindowAdvisor.h" #include "QmitkExtActionBarAdvisor.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // UGLYYY #include "internal/QmitkExtWorkbenchWindowAdvisorHack.h" #include "internal/QmitkCommonExtPlugin.h" #include "mitkUndoController.h" #include "mitkVerboseLimitedLinearUndo.h" #include #include #include #include #include #include QmitkExtWorkbenchWindowAdvisorHack* QmitkExtWorkbenchWindowAdvisorHack::undohack = new QmitkExtWorkbenchWindowAdvisorHack(); QString QmitkExtWorkbenchWindowAdvisor::QT_SETTINGS_FILENAME = "QtSettings.ini"; static bool USE_EXPERIMENTAL_COMMAND_CONTRIBUTIONS = false; class PartListenerForTitle: public berry::IPartListener { public: PartListenerForTitle(QmitkExtWorkbenchWindowAdvisor* wa) : windowAdvisor(wa) { } Events::Types GetPartEventTypes() const override { return Events::ACTIVATED | Events::BROUGHT_TO_TOP | Events::CLOSED | Events::HIDDEN | Events::VISIBLE; } void PartActivated(const berry::IWorkbenchPartReference::Pointer& ref) override { if (ref.Cast ()) { windowAdvisor->UpdateTitle(false); } } void PartBroughtToTop(const berry::IWorkbenchPartReference::Pointer& ref) override { if (ref.Cast ()) { windowAdvisor->UpdateTitle(false); } } void PartClosed(const berry::IWorkbenchPartReference::Pointer& /*ref*/) override { windowAdvisor->UpdateTitle(false); } void PartHidden(const berry::IWorkbenchPartReference::Pointer& ref) override { if (!windowAdvisor->lastActiveEditor.Expired() && ref->GetPart(false) == windowAdvisor->lastActiveEditor.Lock()) { windowAdvisor->UpdateTitle(true); } } void PartVisible(const berry::IWorkbenchPartReference::Pointer& ref) override { if (!windowAdvisor->lastActiveEditor.Expired() && ref->GetPart(false) == windowAdvisor->lastActiveEditor.Lock()) { windowAdvisor->UpdateTitle(false); } } private: QmitkExtWorkbenchWindowAdvisor* windowAdvisor; }; class PartListenerForViewNavigator: public berry::IPartListener { public: PartListenerForViewNavigator(QAction* act) : viewNavigatorAction(act) { } Events::Types GetPartEventTypes() const override { return Events::OPENED | Events::CLOSED | Events::HIDDEN | Events::VISIBLE; } void PartOpened(const berry::IWorkbenchPartReference::Pointer& ref) override { if (ref->GetId()=="org.mitk.views.viewnavigatorview") { viewNavigatorAction->setChecked(true); } } void PartClosed(const berry::IWorkbenchPartReference::Pointer& ref) override { if (ref->GetId()=="org.mitk.views.viewnavigatorview") { viewNavigatorAction->setChecked(false); } } void PartVisible(const berry::IWorkbenchPartReference::Pointer& ref) override { if (ref->GetId()=="org.mitk.views.viewnavigatorview") { viewNavigatorAction->setChecked(true); } } void PartHidden(const berry::IWorkbenchPartReference::Pointer& ref) override { if (ref->GetId()=="org.mitk.views.viewnavigatorview") { viewNavigatorAction->setChecked(false); } } private: QAction* viewNavigatorAction; }; class PartListenerForImageNavigator: public berry::IPartListener { public: PartListenerForImageNavigator(QAction* act) : imageNavigatorAction(act) { } Events::Types GetPartEventTypes() const override { return Events::OPENED | Events::CLOSED | Events::HIDDEN | Events::VISIBLE; } void PartOpened(const berry::IWorkbenchPartReference::Pointer& ref) override { if (ref->GetId()=="org.mitk.views.imagenavigator") { imageNavigatorAction->setChecked(true); } } void PartClosed(const berry::IWorkbenchPartReference::Pointer& ref) override { if (ref->GetId()=="org.mitk.views.imagenavigator") { imageNavigatorAction->setChecked(false); } } void PartVisible(const berry::IWorkbenchPartReference::Pointer& ref) override { if (ref->GetId()=="org.mitk.views.imagenavigator") { imageNavigatorAction->setChecked(true); } } void PartHidden(const berry::IWorkbenchPartReference::Pointer& ref) override { if (ref->GetId()=="org.mitk.views.imagenavigator") { imageNavigatorAction->setChecked(false); } } private: QAction* imageNavigatorAction; }; class PerspectiveListenerForTitle: public berry::IPerspectiveListener { public: PerspectiveListenerForTitle(QmitkExtWorkbenchWindowAdvisor* wa) : windowAdvisor(wa) , perspectivesClosed(false) { } Events::Types GetPerspectiveEventTypes() const override { if (USE_EXPERIMENTAL_COMMAND_CONTRIBUTIONS) { return Events::ACTIVATED | Events::SAVED_AS | Events::DEACTIVATED; } else { return Events::ACTIVATED | Events::SAVED_AS | Events::DEACTIVATED | Events::CLOSED | Events::OPENED; } } void PerspectiveActivated(const berry::IWorkbenchPage::Pointer& /*page*/, const berry::IPerspectiveDescriptor::Pointer& /*perspective*/) override { windowAdvisor->UpdateTitle(false); } void PerspectiveSavedAs(const berry::IWorkbenchPage::Pointer& /*page*/, const berry::IPerspectiveDescriptor::Pointer& /*oldPerspective*/, const berry::IPerspectiveDescriptor::Pointer& /*newPerspective*/) override { windowAdvisor->UpdateTitle(false); } void PerspectiveDeactivated(const berry::IWorkbenchPage::Pointer& /*page*/, const berry::IPerspectiveDescriptor::Pointer& /*perspective*/) override { windowAdvisor->UpdateTitle(false); } void PerspectiveOpened(const berry::IWorkbenchPage::Pointer& /*page*/, const berry::IPerspectiveDescriptor::Pointer& /*perspective*/) override { if (perspectivesClosed) { QListIterator i(windowAdvisor->viewActions); while (i.hasNext()) { i.next()->setEnabled(true); } //GetViewRegistry()->Find("org.mitk.views.imagenavigator"); if(windowAdvisor->GetWindowConfigurer()->GetWindow()->GetWorkbench()->GetEditorRegistry()->FindEditor("org.mitk.editors.dicombrowser")) { windowAdvisor->openDicomEditorAction->setEnabled(true); } if (windowAdvisor->GetWindowConfigurer()->GetWindow()->GetWorkbench()->GetEditorRegistry()->FindEditor("org.mitk.editors.stdmultiwidget")) { windowAdvisor->openStdMultiWidgetEditorAction->setEnabled(true); } if (windowAdvisor->GetWindowConfigurer()->GetWindow()->GetWorkbench()->GetEditorRegistry()->FindEditor("org.mitk.editors.mxnmultiwidget")) { windowAdvisor->openMxNMultiWidgetEditorAction->setEnabled(true); } windowAdvisor->fileSaveProjectAction->setEnabled(true); windowAdvisor->closeProjectAction->setEnabled(true); windowAdvisor->undoAction->setEnabled(true); windowAdvisor->redoAction->setEnabled(true); windowAdvisor->imageNavigatorAction->setEnabled(true); windowAdvisor->viewNavigatorAction->setEnabled(true); windowAdvisor->resetPerspAction->setEnabled(true); if( windowAdvisor->GetShowClosePerspectiveMenuItem() ) { windowAdvisor->closePerspAction->setEnabled(true); } } perspectivesClosed = false; } void PerspectiveClosed(const berry::IWorkbenchPage::Pointer& /*page*/, const berry::IPerspectiveDescriptor::Pointer& /*perspective*/) override { berry::IWorkbenchWindow::Pointer wnd = windowAdvisor->GetWindowConfigurer()->GetWindow(); bool allClosed = true; if (wnd->GetActivePage()) { QList perspectives(wnd->GetActivePage()->GetOpenPerspectives()); allClosed = perspectives.empty(); } if (allClosed) { perspectivesClosed = true; QListIterator i(windowAdvisor->viewActions); while (i.hasNext()) { i.next()->setEnabled(false); } if(windowAdvisor->GetWindowConfigurer()->GetWindow()->GetWorkbench()->GetEditorRegistry()->FindEditor("org.mitk.editors.dicombrowser")) { windowAdvisor->openDicomEditorAction->setEnabled(false); } if (windowAdvisor->GetWindowConfigurer()->GetWindow()->GetWorkbench()->GetEditorRegistry()->FindEditor("org.mitk.editors.stdmultiwidget")) { windowAdvisor->openStdMultiWidgetEditorAction->setEnabled(false); } if (windowAdvisor->GetWindowConfigurer()->GetWindow()->GetWorkbench()->GetEditorRegistry()->FindEditor("org.mitk.editors.mxnmultiwidget")) { windowAdvisor->openMxNMultiWidgetEditorAction->setEnabled(false); } windowAdvisor->fileSaveProjectAction->setEnabled(false); windowAdvisor->closeProjectAction->setEnabled(false); windowAdvisor->undoAction->setEnabled(false); windowAdvisor->redoAction->setEnabled(false); windowAdvisor->imageNavigatorAction->setEnabled(false); windowAdvisor->viewNavigatorAction->setEnabled(false); windowAdvisor->resetPerspAction->setEnabled(false); if( windowAdvisor->GetShowClosePerspectiveMenuItem() ) { windowAdvisor->closePerspAction->setEnabled(false); } } } private: QmitkExtWorkbenchWindowAdvisor* windowAdvisor; bool perspectivesClosed; }; class PerspectiveListenerForMenu: public berry::IPerspectiveListener { public: PerspectiveListenerForMenu(QmitkExtWorkbenchWindowAdvisor* wa) : windowAdvisor(wa) { } Events::Types GetPerspectiveEventTypes() const override { return Events::ACTIVATED | Events::DEACTIVATED; } void PerspectiveActivated(const berry::IWorkbenchPage::Pointer& /*page*/, const berry::IPerspectiveDescriptor::Pointer& perspective) override { QAction* action = windowAdvisor->mapPerspIdToAction[perspective->GetId()]; if (action) { action->setChecked(true); } } void PerspectiveDeactivated(const berry::IWorkbenchPage::Pointer& /*page*/, const berry::IPerspectiveDescriptor::Pointer& perspective) override { QAction* action = windowAdvisor->mapPerspIdToAction[perspective->GetId()]; if (action) { action->setChecked(false); } } private: QmitkExtWorkbenchWindowAdvisor* windowAdvisor; }; QmitkExtWorkbenchWindowAdvisor::QmitkExtWorkbenchWindowAdvisor(berry::WorkbenchAdvisor* wbAdvisor, berry::IWorkbenchWindowConfigurer::Pointer configurer) : berry::WorkbenchWindowAdvisor(configurer) , lastInput(nullptr) , wbAdvisor(wbAdvisor) , showViewToolbar(true) , showPerspectiveToolbar(false) , showVersionInfo(true) , showMitkVersionInfo(true) , showViewMenuItem(true) , showNewWindowMenuItem(false) , showClosePerspectiveMenuItem(true) , viewNavigatorFound(false) , showMemoryIndicator(true) , dropTargetListener(new QmitkDefaultDropTargetListener) { productName = QCoreApplication::applicationName(); viewExcludeList.push_back("org.mitk.views.viewnavigatorview"); } QmitkExtWorkbenchWindowAdvisor::~QmitkExtWorkbenchWindowAdvisor() { } berry::ActionBarAdvisor::Pointer QmitkExtWorkbenchWindowAdvisor::CreateActionBarAdvisor(berry::IActionBarConfigurer::Pointer configurer) { if (USE_EXPERIMENTAL_COMMAND_CONTRIBUTIONS) { berry::ActionBarAdvisor::Pointer actionBarAdvisor(new QmitkExtActionBarAdvisor(configurer)); return actionBarAdvisor; } else { return berry::WorkbenchWindowAdvisor::CreateActionBarAdvisor(configurer); } } QWidget* QmitkExtWorkbenchWindowAdvisor::CreateEmptyWindowContents(QWidget* parent) { QWidget* parentWidget = static_cast(parent); auto label = new QLabel(parentWidget); label->setText("No perspectives are open. Open a perspective in the Window->Open Perspective menu."); label->setContentsMargins(10,10,10,10); label->setAlignment(Qt::AlignTop); label->setEnabled(false); parentWidget->layout()->addWidget(label); return label; } void QmitkExtWorkbenchWindowAdvisor::ShowClosePerspectiveMenuItem(bool show) { showClosePerspectiveMenuItem = show; } bool QmitkExtWorkbenchWindowAdvisor::GetShowClosePerspectiveMenuItem() { return showClosePerspectiveMenuItem; } void QmitkExtWorkbenchWindowAdvisor::ShowMemoryIndicator(bool show) { showMemoryIndicator = show; } bool QmitkExtWorkbenchWindowAdvisor::GetShowMemoryIndicator() { return showMemoryIndicator; } void QmitkExtWorkbenchWindowAdvisor::ShowNewWindowMenuItem(bool show) { showNewWindowMenuItem = show; } void QmitkExtWorkbenchWindowAdvisor::ShowViewToolbar(bool show) { showViewToolbar = show; } void QmitkExtWorkbenchWindowAdvisor::ShowViewMenuItem(bool show) { showViewMenuItem = show; } void QmitkExtWorkbenchWindowAdvisor::ShowPerspectiveToolbar(bool show) { showPerspectiveToolbar = show; } void QmitkExtWorkbenchWindowAdvisor::ShowVersionInfo(bool show) { showVersionInfo = show; } void QmitkExtWorkbenchWindowAdvisor::ShowMitkVersionInfo(bool show) { showMitkVersionInfo = show; } void QmitkExtWorkbenchWindowAdvisor::SetProductName(const QString& product) { productName = product; } void QmitkExtWorkbenchWindowAdvisor::SetWindowIcon(const QString& wndIcon) { windowIcon = wndIcon; } void QmitkExtWorkbenchWindowAdvisor::PostWindowCreate() { // very bad hack... berry::IWorkbenchWindow::Pointer window = this->GetWindowConfigurer()->GetWindow(); QMainWindow* mainWindow = qobject_cast (window->GetShell()->GetControl()); if (!windowIcon.isEmpty()) { mainWindow->setWindowIcon(QIcon(windowIcon)); } mainWindow->setContextMenuPolicy(Qt::PreventContextMenu); // Load icon theme QIcon::setThemeSearchPaths(QStringList() << QStringLiteral(":/org_mitk_icons/icons/")); QIcon::setThemeName(QStringLiteral("awesome")); // ==== Application menu ============================ QMenuBar* menuBar = mainWindow->menuBar(); menuBar->setContextMenuPolicy(Qt::PreventContextMenu); #ifdef __APPLE__ menuBar->setNativeMenuBar(true); #else menuBar->setNativeMenuBar(false); #endif auto basePath = QStringLiteral(":/org_mitk_icons/icons/awesome/scalable/actions/"); auto fileOpenAction = new QmitkFileOpenAction(berry::QtStyleManager::ThemeIcon(basePath + "document-open.svg"), window); fileOpenAction->setShortcut(QKeySequence::Open); auto fileSaveAction = new QmitkFileSaveAction(berry::QtStyleManager::ThemeIcon(basePath + "document-save.svg"), window); fileSaveAction->setShortcut(QKeySequence::Save); fileSaveProjectAction = new QmitkExtFileSaveProjectAction(window); fileSaveProjectAction->setIcon(berry::QtStyleManager::ThemeIcon(basePath + "document-save.svg")); closeProjectAction = new QmitkCloseProjectAction(window); closeProjectAction->setIcon(berry::QtStyleManager::ThemeIcon(basePath + "edit-delete.svg")); auto perspGroup = new QActionGroup(menuBar); std::map VDMap; // sort elements (converting vector to map...) QList::const_iterator iter; berry::IViewRegistry* viewRegistry = berry::PlatformUI::GetWorkbench()->GetViewRegistry(); const QList viewDescriptors = viewRegistry->GetViews(); bool skip = false; for (iter = viewDescriptors.begin(); iter != viewDescriptors.end(); ++iter) { // if viewExcludeList is set, it contains the id-strings of view, which // should not appear as an menu-entry in the menu if (viewExcludeList.size() > 0) { for (int i=0; iGetId()) { skip = true; break; } } if (skip) { skip = false; continue; } } if ((*iter)->GetId() == "org.blueberry.ui.internal.introview") continue; if ((*iter)->GetId() == "org.mitk.views.imagenavigator") continue; if ((*iter)->GetId() == "org.mitk.views.viewnavigatorview") continue; std::pair p((*iter)->GetLabel(), (*iter)); VDMap.insert(p); } std::map::const_iterator MapIter; for (MapIter = VDMap.begin(); MapIter != VDMap.end(); ++MapIter) { berry::QtShowViewAction* viewAction = new berry::QtShowViewAction(window, (*MapIter).second); viewActions.push_back(viewAction); } if (!USE_EXPERIMENTAL_COMMAND_CONTRIBUTIONS) { QMenu* fileMenu = menuBar->addMenu("&File"); fileMenu->setObjectName("FileMenu"); fileMenu->addAction(fileOpenAction); fileMenu->addAction(fileSaveAction); fileMenu->addAction(fileSaveProjectAction); fileMenu->addAction(closeProjectAction); fileMenu->addSeparator(); QAction* fileExitAction = new QmitkFileExitAction(window); fileExitAction->setIcon(berry::QtStyleManager::ThemeIcon(basePath + "system-log-out.svg")); fileExitAction->setShortcut(QKeySequence::Quit); fileExitAction->setObjectName("QmitkFileExitAction"); fileMenu->addAction(fileExitAction); // another bad hack to get an edit/undo menu... QMenu* editMenu = menuBar->addMenu("&Edit"); undoAction = editMenu->addAction(berry::QtStyleManager::ThemeIcon(basePath + "edit-undo.svg"), "&Undo", QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onUndo()), QKeySequence("CTRL+Z")); undoAction->setToolTip("Undo the last action (not supported by all modules)"); redoAction = editMenu->addAction(berry::QtStyleManager::ThemeIcon(basePath + "edit-redo.svg"), "&Redo", QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onRedo()), QKeySequence("CTRL+Y")); redoAction->setToolTip("execute the last action that was undone again (not supported by all modules)"); // ==== Window Menu ========================== QMenu* windowMenu = menuBar->addMenu("Window"); if (showNewWindowMenuItem) { windowMenu->addAction("&New Window", QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onNewWindow())); windowMenu->addSeparator(); } QMenu* perspMenu = windowMenu->addMenu("&Open Perspective"); QMenu* viewMenu = nullptr; if (showViewMenuItem) { viewMenu = windowMenu->addMenu("Show &View"); viewMenu->setObjectName("Show View"); } windowMenu->addSeparator(); resetPerspAction = windowMenu->addAction("&Reset Perspective", QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onResetPerspective())); if(showClosePerspectiveMenuItem) closePerspAction = windowMenu->addAction("&Close Perspective", QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onClosePerspective())); windowMenu->addSeparator(); windowMenu->addAction("&Preferences...", QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onEditPreferences()), QKeySequence("CTRL+P")); // fill perspective menu berry::IPerspectiveRegistry* perspRegistry = window->GetWorkbench()->GetPerspectiveRegistry(); QList perspectives( perspRegistry->GetPerspectives()); skip = false; for (QList::iterator perspIt = perspectives.begin(); perspIt != perspectives.end(); ++perspIt) { // if perspectiveExcludeList is set, it contains the id-strings of perspectives, which // should not appear as an menu-entry in the perspective menu if (perspectiveExcludeList.size() > 0) { for (int i=0; iGetId()) { skip = true; break; } } if (skip) { skip = false; continue; } } QAction* perspAction = new berry::QtOpenPerspectiveAction(window, *perspIt, perspGroup); mapPerspIdToAction.insert((*perspIt)->GetId(), perspAction); } perspMenu->addActions(perspGroup->actions()); if (showViewMenuItem) { - for (auto viewAction : viewActions) + for (auto viewAction : qAsConst(viewActions)) { viewMenu->addAction(viewAction); } } // ===== Help menu ==================================== QMenu* helpMenu = menuBar->addMenu("&Help"); helpMenu->addAction("&Welcome",this, SLOT(onIntro())); helpMenu->addAction("&Open Help Perspective", this, SLOT(onHelpOpenHelpPerspective())); helpMenu->addAction("&Context Help",this, SLOT(onHelp()), QKeySequence("F1")); helpMenu->addAction("&About",this, SLOT(onAbout())); // ===================================================== } else { undoAction = new QmitkUndoAction(berry::QtStyleManager::ThemeIcon(basePath + "edit-undo.svg"), nullptr); undoAction->setShortcut(QKeySequence::Undo); redoAction = new QmitkRedoAction(berry::QtStyleManager::ThemeIcon(basePath + "edit-redo.svg"), nullptr); redoAction->setShortcut(QKeySequence::Redo); } // toolbar for showing file open, undo, redo and other main actions auto mainActionsToolBar = new QToolBar; mainActionsToolBar->setObjectName("mainActionsToolBar"); mainActionsToolBar->setContextMenuPolicy(Qt::PreventContextMenu); #ifdef __APPLE__ mainActionsToolBar->setToolButtonStyle ( Qt::ToolButtonTextUnderIcon ); #else mainActionsToolBar->setToolButtonStyle ( Qt::ToolButtonTextBesideIcon ); #endif basePath = QStringLiteral(":/org.mitk.gui.qt.ext/"); imageNavigatorAction = new QAction(berry::QtStyleManager::ThemeIcon(basePath + "image_navigator.svg"), "&Image Navigator", nullptr); bool imageNavigatorViewFound = window->GetWorkbench()->GetViewRegistry()->Find("org.mitk.views.imagenavigator"); if (this->GetWindowConfigurer()->GetWindow()->GetWorkbench()->GetEditorRegistry()->FindEditor("org.mitk.editors.dicombrowser")) { openDicomEditorAction = new QmitkOpenDicomEditorAction(berry::QtStyleManager::ThemeIcon(basePath + "dicom.svg"), window); } if (this->GetWindowConfigurer()->GetWindow()->GetWorkbench()->GetEditorRegistry()->FindEditor("org.mitk.editors.stdmultiwidget")) { openStdMultiWidgetEditorAction = new QmitkOpenStdMultiWidgetEditorAction(QIcon(":/org.mitk.gui.qt.ext/Editor.png"), window); } if (this->GetWindowConfigurer()->GetWindow()->GetWorkbench()->GetEditorRegistry()->FindEditor("org.mitk.editors.mxnmultiwidget")) { openMxNMultiWidgetEditorAction = new QmitkOpenMxNMultiWidgetEditorAction(QIcon(":/org.mitk.gui.qt.ext/Editor.png"), window); } if (imageNavigatorViewFound) { QObject::connect(imageNavigatorAction, SIGNAL(triggered(bool)), QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onImageNavigator())); imageNavigatorAction->setCheckable(true); // add part listener for image navigator imageNavigatorPartListener.reset(new PartListenerForImageNavigator(imageNavigatorAction)); window->GetPartService()->AddPartListener(imageNavigatorPartListener.data()); berry::IViewPart::Pointer imageNavigatorView = window->GetActivePage()->FindView("org.mitk.views.imagenavigator"); imageNavigatorAction->setChecked(false); if (imageNavigatorView) { bool isImageNavigatorVisible = window->GetActivePage()->IsPartVisible(imageNavigatorView); if (isImageNavigatorVisible) imageNavigatorAction->setChecked(true); } imageNavigatorAction->setToolTip("Toggle image navigator for navigating through image"); } viewNavigatorAction = new QAction(berry::QtStyleManager::ThemeIcon(QStringLiteral(":/org.mitk.gui.qt.ext/view-manager.svg")),"&View Navigator", nullptr); viewNavigatorFound = window->GetWorkbench()->GetViewRegistry()->Find("org.mitk.views.viewnavigatorview"); if (viewNavigatorFound) { QObject::connect(viewNavigatorAction, SIGNAL(triggered(bool)), QmitkExtWorkbenchWindowAdvisorHack::undohack, SLOT(onViewNavigator())); viewNavigatorAction->setCheckable(true); // add part listener for view navigator viewNavigatorPartListener.reset(new PartListenerForViewNavigator(viewNavigatorAction)); window->GetPartService()->AddPartListener(viewNavigatorPartListener.data()); berry::IViewPart::Pointer viewnavigatorview = window->GetActivePage()->FindView("org.mitk.views.viewnavigatorview"); viewNavigatorAction->setChecked(false); if (viewnavigatorview) { bool isViewNavigatorVisible = window->GetActivePage()->IsPartVisible(viewnavigatorview); if (isViewNavigatorVisible) viewNavigatorAction->setChecked(true); } viewNavigatorAction->setToolTip("Toggle View Navigator"); } mainActionsToolBar->addAction(fileOpenAction); mainActionsToolBar->addAction(fileSaveProjectAction); mainActionsToolBar->addAction(closeProjectAction); mainActionsToolBar->addAction(undoAction); mainActionsToolBar->addAction(redoAction); if(this->GetWindowConfigurer()->GetWindow()->GetWorkbench()->GetEditorRegistry()->FindEditor("org.mitk.editors.dicombrowser")) { mainActionsToolBar->addAction(openDicomEditorAction); } if (this->GetWindowConfigurer()->GetWindow()->GetWorkbench()->GetEditorRegistry()->FindEditor("org.mitk.editors.stdmultiwidget")) { mainActionsToolBar->addAction(openStdMultiWidgetEditorAction); } if (this->GetWindowConfigurer()->GetWindow()->GetWorkbench()->GetEditorRegistry()->FindEditor("org.mitk.editors.mxnmultiwidget")) { mainActionsToolBar->addAction(openMxNMultiWidgetEditorAction); } if (imageNavigatorViewFound) { mainActionsToolBar->addAction(imageNavigatorAction); } if (viewNavigatorFound) { mainActionsToolBar->addAction(viewNavigatorAction); } mainWindow->addToolBar(mainActionsToolBar); // ==== Perspective Toolbar ================================== auto qPerspectiveToolbar = new QToolBar; qPerspectiveToolbar->setObjectName("perspectiveToolBar"); if (showPerspectiveToolbar) { qPerspectiveToolbar->addActions(perspGroup->actions()); mainWindow->addToolBar(qPerspectiveToolbar); } else delete qPerspectiveToolbar; if (showViewToolbar) { auto prefService = berry::WorkbenchPlugin::GetDefault()->GetPreferencesService(); berry::IPreferences::Pointer stylePrefs = prefService->GetSystemPreferences()->Node(berry::QtPreferences::QT_STYLES_NODE); bool showCategoryNames = stylePrefs->GetBool(berry::QtPreferences::QT_SHOW_TOOLBAR_CATEGORY_NAMES, true); // Order view descriptors by category QMultiMap categoryViewDescriptorMap; - for (auto labelViewDescriptorPair : VDMap) + for (const auto &labelViewDescriptorPair : VDMap) { auto viewDescriptor = labelViewDescriptorPair.second; auto category = !viewDescriptor->GetCategoryPath().isEmpty() ? viewDescriptor->GetCategoryPath().back() : QString(); categoryViewDescriptorMap.insert(category, viewDescriptor); } // Create a separate toolbar for each category - for (auto category : categoryViewDescriptorMap.uniqueKeys()) + for (const auto &category : categoryViewDescriptorMap.uniqueKeys()) { auto viewDescriptorsInCurrentCategory = categoryViewDescriptorMap.values(category); if (!viewDescriptorsInCurrentCategory.isEmpty()) { auto toolbar = new QToolBar; toolbar->setObjectName(category + " View Toolbar"); mainWindow->addToolBar(toolbar); if (showCategoryNames && !category.isEmpty()) { auto categoryButton = new QToolButton; categoryButton->setToolButtonStyle(Qt::ToolButtonTextOnly); categoryButton->setText(category); categoryButton->setStyleSheet("background: transparent; margin: 0; padding: 0;"); toolbar->addWidget(categoryButton); connect(categoryButton, &QToolButton::clicked, [toolbar]() { for (QWidget* widget : toolbar->findChildren()) { if (QStringLiteral("qt_toolbar_ext_button") == widget->objectName() && widget->isVisible()) { QMouseEvent pressEvent(QEvent::MouseButtonPress, QPointF(0.0f, 0.0f), Qt::LeftButton, Qt::LeftButton, Qt::NoModifier); QMouseEvent releaseEvent(QEvent::MouseButtonRelease, QPointF(0.0f, 0.0f), Qt::LeftButton, Qt::LeftButton, Qt::NoModifier); QApplication::sendEvent(widget, &pressEvent); QApplication::sendEvent(widget, &releaseEvent); } } }); } - for (auto viewDescriptor : viewDescriptorsInCurrentCategory) + for (const auto &viewDescriptor : qAsConst(viewDescriptorsInCurrentCategory)) { auto viewAction = new berry::QtShowViewAction(window, viewDescriptor); toolbar->addAction(viewAction); } } } } QSettings settings(GetQSettingsFile(), QSettings::IniFormat); mainWindow->restoreState(settings.value("ToolbarPosition").toByteArray()); auto qStatusBar = new QStatusBar(); //creating a QmitkStatusBar for Output on the QStatusBar and connecting it with the MainStatusBar auto statusBar = new QmitkStatusBar(qStatusBar); //disabling the SizeGrip in the lower right corner statusBar->SetSizeGripEnabled(false); auto progBar = new QmitkProgressBar(); qStatusBar->addPermanentWidget(progBar, 0); progBar->hide(); // progBar->AddStepsToDo(2); // progBar->Progress(1); mainWindow->setStatusBar(qStatusBar); if (showMemoryIndicator) { auto memoryIndicator = new QmitkMemoryUsageIndicatorView(); qStatusBar->addPermanentWidget(memoryIndicator, 0); } } void QmitkExtWorkbenchWindowAdvisor::PreWindowOpen() { berry::IWorkbenchWindowConfigurer::Pointer configurer = GetWindowConfigurer(); // show the shortcut bar and progress indicator, which are hidden by // default //configurer->SetShowPerspectiveBar(true); //configurer->SetShowFastViewBars(true); //configurer->SetShowProgressIndicator(true); // // add the drag and drop support for the editor area // configurer.addEditorAreaTransfer(EditorInputTransfer.getInstance()); // configurer.addEditorAreaTransfer(ResourceTransfer.getInstance()); // configurer.addEditorAreaTransfer(FileTransfer.getInstance()); // configurer.addEditorAreaTransfer(MarkerTransfer.getInstance()); // configurer.configureEditorAreaDropListener(new EditorAreaDropAdapter( // configurer.getWindow())); this->HookTitleUpdateListeners(configurer); menuPerspectiveListener.reset(new PerspectiveListenerForMenu(this)); configurer->GetWindow()->AddPerspectiveListener(menuPerspectiveListener.data()); configurer->AddEditorAreaTransfer(QStringList("text/uri-list")); configurer->ConfigureEditorAreaDropListener(dropTargetListener.data()); } void QmitkExtWorkbenchWindowAdvisor::PostWindowOpen() { berry::WorkbenchWindowAdvisor::PostWindowOpen(); // Force Rendering Window Creation on startup. berry::IWorkbenchWindowConfigurer::Pointer configurer = GetWindowConfigurer(); ctkPluginContext* context = QmitkCommonExtPlugin::getContext(); ctkServiceReference serviceRef = context->getServiceReference(); if (serviceRef) { mitk::IDataStorageService *dsService = context->getService(serviceRef); if (dsService) { mitk::IDataStorageReference::Pointer dsRef = dsService->GetDataStorage(); mitk::DataStorageEditorInput::Pointer dsInput(new mitk::DataStorageEditorInput(dsRef)); mitk::WorkbenchUtil::OpenEditor(configurer->GetWindow()->GetActivePage(),dsInput); } } auto introPart = configurer->GetWindow()->GetWorkbench()->GetIntroManager()->GetIntro(); if (introPart.IsNotNull()) { configurer->GetWindow()->GetWorkbench()->GetIntroManager()->ShowIntro(GetWindowConfigurer()->GetWindow(), false); } } void QmitkExtWorkbenchWindowAdvisor::onIntro() { QmitkExtWorkbenchWindowAdvisorHack::undohack->onIntro(); } void QmitkExtWorkbenchWindowAdvisor::onHelp() { QmitkExtWorkbenchWindowAdvisorHack::undohack->onHelp(); } void QmitkExtWorkbenchWindowAdvisor::onHelpOpenHelpPerspective() { QmitkExtWorkbenchWindowAdvisorHack::undohack->onHelpOpenHelpPerspective(); } void QmitkExtWorkbenchWindowAdvisor::onAbout() { QmitkExtWorkbenchWindowAdvisorHack::undohack->onAbout(); } //-------------------------------------------------------------------------------- // Ugly hack from here on. Feel free to delete when command framework // and undo buttons are done. //-------------------------------------------------------------------------------- QmitkExtWorkbenchWindowAdvisorHack::QmitkExtWorkbenchWindowAdvisorHack() : QObject() { } QmitkExtWorkbenchWindowAdvisorHack::~QmitkExtWorkbenchWindowAdvisorHack() { } void QmitkExtWorkbenchWindowAdvisorHack::onUndo() { mitk::UndoModel* model = mitk::UndoController::GetCurrentUndoModel(); if (model) { if (mitk::VerboseLimitedLinearUndo* verboseundo = dynamic_cast( model )) { mitk::VerboseLimitedLinearUndo::StackDescription descriptions = verboseundo->GetUndoDescriptions(); if (descriptions.size() >= 1) { MITK_INFO << "Undo " << descriptions.front().second; } } model->Undo(); } else { MITK_ERROR << "No undo model instantiated"; } } void QmitkExtWorkbenchWindowAdvisorHack::onRedo() { mitk::UndoModel* model = mitk::UndoController::GetCurrentUndoModel(); if (model) { if (mitk::VerboseLimitedLinearUndo* verboseundo = dynamic_cast( model )) { mitk::VerboseLimitedLinearUndo::StackDescription descriptions = verboseundo->GetRedoDescriptions(); if (descriptions.size() >= 1) { MITK_INFO << "Redo " << descriptions.front().second; } } model->Redo(); } else { MITK_ERROR << "No undo model instantiated"; } } // safe calls to the complete chain // berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetActivePage()->FindView("org.mitk.views.imagenavigator"); // to cover for all possible cases of closed pages etc. static void SafeHandleNavigatorView(QString view_query_name) { berry::IWorkbench* wbench = berry::PlatformUI::GetWorkbench(); if( wbench == nullptr ) return; berry::IWorkbenchWindow::Pointer wbench_window = wbench->GetActiveWorkbenchWindow(); if( wbench_window.IsNull() ) return; berry::IWorkbenchPage::Pointer wbench_page = wbench_window->GetActivePage(); if( wbench_page.IsNull() ) return; auto wbench_view = wbench_page->FindView( view_query_name ); if( wbench_view.IsNotNull() ) { bool isViewVisible = wbench_page->IsPartVisible( wbench_view ); if( isViewVisible ) { wbench_page->HideView( wbench_view ); return; } } wbench_page->ShowView( view_query_name ); } void QmitkExtWorkbenchWindowAdvisorHack::onImageNavigator() { // show/hide ImageNavigatorView SafeHandleNavigatorView("org.mitk.views.imagenavigator"); } void QmitkExtWorkbenchWindowAdvisorHack::onViewNavigator() { // show/hide viewnavigatorView SafeHandleNavigatorView("org.mitk.views.viewnavigatorview"); } void QmitkExtWorkbenchWindowAdvisorHack::onEditPreferences() { QmitkPreferencesDialog _PreferencesDialog(QApplication::activeWindow()); _PreferencesDialog.exec(); } void QmitkExtWorkbenchWindowAdvisorHack::onQuit() { berry::PlatformUI::GetWorkbench()->Close(); } void QmitkExtWorkbenchWindowAdvisorHack::onResetPerspective() { berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetActivePage()->ResetPerspective(); } void QmitkExtWorkbenchWindowAdvisorHack::onClosePerspective() { berry::IWorkbenchPage::Pointer page = berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetActivePage(); page->ClosePerspective(page->GetPerspective(), true, true); } void QmitkExtWorkbenchWindowAdvisorHack::onNewWindow() { berry::PlatformUI::GetWorkbench()->OpenWorkbenchWindow(nullptr); } void QmitkExtWorkbenchWindowAdvisorHack::onIntro() { bool hasIntro = berry::PlatformUI::GetWorkbench()->GetIntroManager()->HasIntro(); if (!hasIntro) { QRegExp reg("(.*)(\\n)*"); QRegExp reg2("(\\n)*(.*)"); QFile file(":/org.mitk.gui.qt.ext/index.html"); file.open(QIODevice::ReadOnly | QIODevice::Text); //text file only for reading QString text = QString(file.readAll()); file.close(); QString title = text; title.replace(reg, ""); title.replace(reg2, ""); std::cout << title.toStdString() << std::endl; QMessageBox::information(nullptr, title, text, "Close"); } else { berry::PlatformUI::GetWorkbench()->GetIntroManager()->ShowIntro( berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow(), false); } } void QmitkExtWorkbenchWindowAdvisorHack::onHelp() { ctkPluginContext* context = QmitkCommonExtPlugin::getContext(); if (context == nullptr) { MITK_WARN << "Plugin context not set, unable to open context help"; return; } // Check if the org.blueberry.ui.qt.help plug-in is installed and started QList > plugins = context->getPlugins(); foreach(QSharedPointer p, plugins) { if (p->getSymbolicName() == "org.blueberry.ui.qt.help") { if (p->getState() != ctkPlugin::ACTIVE) { // try to activate the plug-in explicitly try { p->start(ctkPlugin::START_TRANSIENT); } catch (const ctkPluginException& pe) { MITK_ERROR << "Activating org.blueberry.ui.qt.help failed: " << pe.what(); return; } } } } ctkServiceReference eventAdminRef = context->getServiceReference(); ctkEventAdmin* eventAdmin = nullptr; if (eventAdminRef) { eventAdmin = context->getService(eventAdminRef); } if (eventAdmin == nullptr) { MITK_WARN << "ctkEventAdmin service not found. Unable to open context help"; } else { ctkEvent ev("org/blueberry/ui/help/CONTEXTHELP_REQUESTED"); eventAdmin->postEvent(ev); } } void QmitkExtWorkbenchWindowAdvisorHack::onHelpOpenHelpPerspective() { berry::PlatformUI::GetWorkbench()->ShowPerspective("org.blueberry.perspectives.help", berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()); } void QmitkExtWorkbenchWindowAdvisorHack::onAbout() { auto aboutDialog = new QmitkAboutDialog(QApplication::activeWindow(),nullptr); aboutDialog->open(); } void QmitkExtWorkbenchWindowAdvisor::HookTitleUpdateListeners(berry::IWorkbenchWindowConfigurer::Pointer configurer) { // hook up the listeners to update the window title titlePartListener.reset(new PartListenerForTitle(this)); titlePerspectiveListener.reset(new PerspectiveListenerForTitle(this)); editorPropertyListener.reset(new berry::PropertyChangeIntAdapter< QmitkExtWorkbenchWindowAdvisor>(this, &QmitkExtWorkbenchWindowAdvisor::PropertyChange)); // configurer.getWindow().addPageListener(new IPageListener() { // public void pageActivated(IWorkbenchPage page) { // updateTitle(false); // } // // public void pageClosed(IWorkbenchPage page) { // updateTitle(false); // } // // public void pageOpened(IWorkbenchPage page) { // // do nothing // } // }); configurer->GetWindow()->AddPerspectiveListener(titlePerspectiveListener.data()); configurer->GetWindow()->GetPartService()->AddPartListener(titlePartListener.data()); } QString QmitkExtWorkbenchWindowAdvisor::ComputeTitle() { berry::IWorkbenchWindowConfigurer::Pointer configurer = GetWindowConfigurer(); berry::IWorkbenchPage::Pointer currentPage = configurer->GetWindow()->GetActivePage(); berry::IEditorPart::Pointer activeEditor; if (currentPage) { activeEditor = lastActiveEditor.Lock(); } QString title; berry::IProduct::Pointer product = berry::Platform::GetProduct(); if (product.IsNotNull()) { title = product->GetName(); } if (title.isEmpty()) { // instead of the product name, we use a custom variable for now title = productName; } if(showMitkVersionInfo) { QString mitkVersionInfo = MITK_REVISION_DESC; if(mitkVersionInfo.isEmpty()) mitkVersionInfo = MITK_VERSION_STRING; title += " " + mitkVersionInfo; } if (showVersionInfo) { // add version informatioin QString versions = QString(" (ITK %1.%2.%3 | VTK %4.%5.%6 | Qt %7)") .arg(ITK_VERSION_MAJOR).arg(ITK_VERSION_MINOR).arg(ITK_VERSION_PATCH) .arg(VTK_MAJOR_VERSION).arg(VTK_MINOR_VERSION).arg(VTK_BUILD_VERSION) .arg(QT_VERSION_STR); title += versions; } if (currentPage) { if (activeEditor) { lastEditorTitle = activeEditor->GetTitleToolTip(); if (!lastEditorTitle.isEmpty()) title = lastEditorTitle + " - " + title; } berry::IPerspectiveDescriptor::Pointer persp = currentPage->GetPerspective(); QString label = ""; if (persp) { label = persp->GetLabel(); } berry::IAdaptable* input = currentPage->GetInput(); if (input && input != wbAdvisor->GetDefaultPageInput()) { label = currentPage->GetLabel(); } if (!label.isEmpty()) { title = label + " - " + title; } } title += " (Not for use in diagnosis or treatment of patients)"; return title; } void QmitkExtWorkbenchWindowAdvisor::RecomputeTitle() { berry::IWorkbenchWindowConfigurer::Pointer configurer = GetWindowConfigurer(); QString oldTitle = configurer->GetTitle(); QString newTitle = ComputeTitle(); if (newTitle != oldTitle) { configurer->SetTitle(newTitle); } } void QmitkExtWorkbenchWindowAdvisor::UpdateTitle(bool editorHidden) { berry::IWorkbenchWindowConfigurer::Pointer configurer = GetWindowConfigurer(); berry::IWorkbenchWindow::Pointer window = configurer->GetWindow(); berry::IEditorPart::Pointer activeEditor; berry::IWorkbenchPage::Pointer currentPage = window->GetActivePage(); berry::IPerspectiveDescriptor::Pointer persp; berry::IAdaptable* input = nullptr; if (currentPage) { activeEditor = currentPage->GetActiveEditor(); persp = currentPage->GetPerspective(); input = currentPage->GetInput(); } if (editorHidden) { activeEditor = nullptr; } // Nothing to do if the editor hasn't changed if (activeEditor == lastActiveEditor.Lock() && currentPage == lastActivePage.Lock() && persp == lastPerspective.Lock() && input == lastInput) { return; } if (!lastActiveEditor.Expired()) { lastActiveEditor.Lock()->RemovePropertyListener(editorPropertyListener.data()); } lastActiveEditor = activeEditor; lastActivePage = currentPage; lastPerspective = persp; lastInput = input; if (activeEditor) { activeEditor->AddPropertyListener(editorPropertyListener.data()); } RecomputeTitle(); } void QmitkExtWorkbenchWindowAdvisor::PropertyChange(const berry::Object::Pointer& /*source*/, int propId) { if (propId == berry::IWorkbenchPartConstants::PROP_TITLE) { if (!lastActiveEditor.Expired()) { QString newTitle = lastActiveEditor.Lock()->GetPartName(); if (lastEditorTitle != newTitle) { RecomputeTitle(); } } } } void QmitkExtWorkbenchWindowAdvisor::SetPerspectiveExcludeList(const QList& v) { this->perspectiveExcludeList = v; } QList QmitkExtWorkbenchWindowAdvisor::GetPerspectiveExcludeList() { return this->perspectiveExcludeList; } void QmitkExtWorkbenchWindowAdvisor::SetViewExcludeList(const QList& v) { this->viewExcludeList = v; } QList QmitkExtWorkbenchWindowAdvisor::GetViewExcludeList() { return this->viewExcludeList; } void QmitkExtWorkbenchWindowAdvisor::PostWindowClose() { berry::IWorkbenchWindow::Pointer window = this->GetWindowConfigurer()->GetWindow(); QMainWindow* mainWindow = static_cast (window->GetShell()->GetControl()); QSettings settings(GetQSettingsFile(), QSettings::IniFormat); settings.setValue("ToolbarPosition", mainWindow->saveState()); } QString QmitkExtWorkbenchWindowAdvisor::GetQSettingsFile() const { QFileInfo settingsInfo = QmitkCommonExtPlugin::getContext()->getDataFile(QT_SETTINGS_FILENAME); return settingsInfo.canonicalFilePath(); } diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepCtUsRegistration.cpp b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepCtUsRegistration.cpp index 456093d420..16b5a9a3b8 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepCtUsRegistration.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepCtUsRegistration.cpp @@ -1,2014 +1,2014 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkUSNavigationStepCtUsRegistration.h" #include "ui_QmitkUSNavigationStepCtUsRegistration.h" #include #include "mitkNodeDisplacementFilter.h" #include "../Filter/mitkFloatingImageToUltrasoundRegistrationFilter.h" #include "../QmitkUSNavigationMarkerPlacement.h" #include #include #include #include "mitkProperties.h" #include #include #include #include #include #include #include #include #include #include #include #include static const int NUMBER_FIDUCIALS_NEEDED = 8; QmitkUSNavigationStepCtUsRegistration::QmitkUSNavigationStepCtUsRegistration(QWidget *parent) : QmitkUSAbstractNavigationStep(parent), ui(new Ui::QmitkUSNavigationStepCtUsRegistration), m_PerformingGroundTruthProtocolEvaluation(false), m_FloatingImageToUltrasoundRegistrationFilter(nullptr), m_FreezeCombinedModality(false) { this->UnsetFloatingImageGeometry(); this->DefineDataStorageImageFilter(); this->CreateQtPartControl(this); } QmitkUSNavigationStepCtUsRegistration::~QmitkUSNavigationStepCtUsRegistration() { delete ui; } bool QmitkUSNavigationStepCtUsRegistration::OnStartStep() { MITK_INFO << "OnStartStep()"; return true; } bool QmitkUSNavigationStepCtUsRegistration::OnStopStep() { MITK_INFO << "OnStopStep()"; return true; } bool QmitkUSNavigationStepCtUsRegistration::OnFinishStep() { MITK_INFO << "OnFinishStep()"; return true; } bool QmitkUSNavigationStepCtUsRegistration::OnActivateStep() { MITK_INFO << "OnActivateStep()"; ui->floatingImageComboBox->SetDataStorage(this->GetDataStorage()); ui->ctImagesToChooseComboBox->SetDataStorage(this->GetDataStorage()); ui->segmentationComboBox->SetDataStorage(this->GetDataStorage()); ui->selectedSurfaceComboBox->SetDataStorage(this->GetDataStorage()); ui->pointSetComboBox->SetDataStorage(this->GetDataStorage()); m_FloatingImageToUltrasoundRegistrationFilter = mitk::FloatingImageToUltrasoundRegistrationFilter::New(); return true; } bool QmitkUSNavigationStepCtUsRegistration::OnDeactivateStep() { MITK_INFO << "OnDeactivateStep()"; return true; } void QmitkUSNavigationStepCtUsRegistration::OnUpdate() { if (m_NavigationDataSource.IsNull()) { return; } m_NavigationDataSource->Update(); m_FloatingImageToUltrasoundRegistrationFilter->Update(); } void QmitkUSNavigationStepCtUsRegistration::OnSettingsChanged(const itk::SmartPointer settingsNode) { Q_UNUSED(settingsNode); } QString QmitkUSNavigationStepCtUsRegistration::GetTitle() { return "CT-to-US registration"; } QmitkUSAbstractNavigationStep::FilterVector QmitkUSNavigationStepCtUsRegistration::GetFilter() { return FilterVector(); } void QmitkUSNavigationStepCtUsRegistration::OnSetCombinedModality() { mitk::AbstractUltrasoundTrackerDevice::Pointer combinedModality = this->GetCombinedModality(false); if (combinedModality.IsNotNull()) { m_NavigationDataSource = combinedModality->GetNavigationDataSource(); } } void QmitkUSNavigationStepCtUsRegistration::UnsetFloatingImageGeometry() { m_ImageDimension[0] = 0; m_ImageDimension[1] = 0; m_ImageDimension[2] = 0; m_ImageSpacing[0] = 1; m_ImageSpacing[1] = 1; m_ImageSpacing[2] = 1; } void QmitkUSNavigationStepCtUsRegistration::SetFloatingImageGeometryInformation(mitk::Image * image) { m_ImageDimension[0] = image->GetDimension(0); m_ImageDimension[1] = image->GetDimension(1); m_ImageDimension[2] = image->GetDimension(2); m_ImageSpacing[0] = image->GetGeometry()->GetSpacing()[0]; m_ImageSpacing[1] = image->GetGeometry()->GetSpacing()[1]; m_ImageSpacing[2] = image->GetGeometry()->GetSpacing()[2]; } double QmitkUSNavigationStepCtUsRegistration::GetVoxelVolume() { if (m_FloatingImage.IsNull()) { return 0.0; } MITK_INFO << "ImageSpacing = " << m_ImageSpacing; return m_ImageSpacing[0] * m_ImageSpacing[1] * m_ImageSpacing[2]; } double QmitkUSNavigationStepCtUsRegistration::GetFiducialVolume(double radius) { return 1.333333333 * 3.141592 * (radius * radius * radius); } bool QmitkUSNavigationStepCtUsRegistration::FilterFloatingImage() { if (m_FloatingImage.IsNull()) { return false; } ImageType::Pointer itkImage1 = ImageType::New(); mitk::CastToItkImage(m_FloatingImage, itkImage1); this->InitializeImageFilters(); m_ThresholdFilter->SetInput(itkImage1); m_LaplacianFilter1->SetInput(m_ThresholdFilter->GetOutput()); m_LaplacianFilter2->SetInput(m_LaplacianFilter1->GetOutput()); m_BinaryThresholdFilter->SetInput(m_LaplacianFilter2->GetOutput()); m_HoleFillingFilter->SetInput(m_BinaryThresholdFilter->GetOutput()); m_BinaryImageToShapeLabelMapFilter->SetInput(m_HoleFillingFilter->GetOutput()); m_BinaryImageToShapeLabelMapFilter->Update(); ImageType::Pointer binaryImage = ImageType::New(); binaryImage = m_HoleFillingFilter->GetOutput(); this->EliminateTooSmallLabeledObjects(binaryImage); //mitk::CastToMitkImage(binaryImage, m_FloatingImage); return true; } void QmitkUSNavigationStepCtUsRegistration::InitializeImageFilters() { //Initialize threshold filters m_ThresholdFilter = itk::ThresholdImageFilter::New(); m_ThresholdFilter->SetOutsideValue(0); m_ThresholdFilter->SetLower(500); m_ThresholdFilter->SetUpper(3200); //Initialize binary threshold filter 1 m_BinaryThresholdFilter = BinaryThresholdImageFilterType::New(); m_BinaryThresholdFilter->SetOutsideValue(0); m_BinaryThresholdFilter->SetInsideValue(1); m_BinaryThresholdFilter->SetLowerThreshold(350); m_BinaryThresholdFilter->SetUpperThreshold(10000); //Initialize laplacian recursive gaussian image filter m_LaplacianFilter1 = LaplacianRecursiveGaussianImageFilterType::New(); m_LaplacianFilter2 = LaplacianRecursiveGaussianImageFilterType::New(); //Initialize binary hole filling filter m_HoleFillingFilter = VotingBinaryIterativeHoleFillingImageFilterType::New(); VotingBinaryIterativeHoleFillingImageFilterType::InputSizeType radius; radius.Fill(1); m_HoleFillingFilter->SetRadius(radius); m_HoleFillingFilter->SetBackgroundValue(0); m_HoleFillingFilter->SetForegroundValue(1); m_HoleFillingFilter->SetMaximumNumberOfIterations(5); //Initialize binary image to shape label map filter m_BinaryImageToShapeLabelMapFilter = BinaryImageToShapeLabelMapFilterType::New(); m_BinaryImageToShapeLabelMapFilter->SetInputForegroundValue(1); } double QmitkUSNavigationStepCtUsRegistration::GetCharacteristicDistanceAWithUpperMargin() { switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: return 12.07; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: return 18.105; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: return 24.14; } return 0.0; } double QmitkUSNavigationStepCtUsRegistration::GetCharacteristicDistanceBWithLowerMargin() { switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: return 12.07; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: return 18.105; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: return 24.14; } return 0.0; } double QmitkUSNavigationStepCtUsRegistration::GetCharacteristicDistanceBWithUpperMargin() { switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: return 15.73; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: return 23.595; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: return 31.46; } return 0.0; } double QmitkUSNavigationStepCtUsRegistration::GetMinimalFiducialConfigurationDistance() { switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: return 10.0; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: return 15.0; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: return 20.0; } return 0.0; } void QmitkUSNavigationStepCtUsRegistration::CreateMarkerModelCoordinateSystemPointSet() { if (m_MarkerModelCoordinateSystemPointSet.IsNull()) { m_MarkerModelCoordinateSystemPointSet = mitk::PointSet::New(); } else { m_MarkerModelCoordinateSystemPointSet->Clear(); } mitk::Point3D fiducial1; mitk::Point3D fiducial2; mitk::Point3D fiducial3; mitk::Point3D fiducial4; mitk::Point3D fiducial5; mitk::Point3D fiducial6; mitk::Point3D fiducial7; mitk::Point3D fiducial8; switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: fiducial1[0] = 0; fiducial1[1] = 0; fiducial1[2] = 0; fiducial2[0] = 0; fiducial2[1] = 10; fiducial2[2] = 0; fiducial3[0] = 10; fiducial3[1] = 0; fiducial3[2] = 0; fiducial4[0] = 20; fiducial4[1] = 20; fiducial4[2] = 0; fiducial5[0] = 0; fiducial5[1] = 20; fiducial5[2] = 10; fiducial6[0] = 10; fiducial6[1] = 20; fiducial6[2] = 10; fiducial7[0] = 20; fiducial7[1] = 10; fiducial7[2] = 10; fiducial8[0] = 20; fiducial8[1] = 0; fiducial8[2] = 10; break; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: fiducial1[0] = 0; fiducial1[1] = 0; fiducial1[2] = 0; fiducial2[0] = 0; fiducial2[1] = 15; fiducial2[2] = 0; fiducial3[0] = 15; fiducial3[1] = 0; fiducial3[2] = 0; fiducial4[0] = 30; fiducial4[1] = 30; fiducial4[2] = 0; fiducial5[0] = 0; fiducial5[1] = 30; fiducial5[2] = 15; fiducial6[0] = 15; fiducial6[1] = 30; fiducial6[2] = 15; fiducial7[0] = 30; fiducial7[1] = 15; fiducial7[2] = 15; fiducial8[0] = 30; fiducial8[1] = 0; fiducial8[2] = 15; break; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: fiducial1[0] = 0; fiducial1[1] = 0; fiducial1[2] = 0; fiducial2[0] = 0; fiducial2[1] = 20; fiducial2[2] = 0; fiducial3[0] = 20; fiducial3[1] = 0; fiducial3[2] = 0; fiducial4[0] = 40; fiducial4[1] = 40; fiducial4[2] = 0; fiducial5[0] = 0; fiducial5[1] = 40; fiducial5[2] = 20; fiducial6[0] = 20; fiducial6[1] = 40; fiducial6[2] = 20; fiducial7[0] = 40; fiducial7[1] = 20; fiducial7[2] = 20; fiducial8[0] = 40; fiducial8[1] = 0; fiducial8[2] = 20; break; } m_MarkerModelCoordinateSystemPointSet->InsertPoint(0, fiducial1); m_MarkerModelCoordinateSystemPointSet->InsertPoint(1, fiducial2); m_MarkerModelCoordinateSystemPointSet->InsertPoint(2, fiducial3); m_MarkerModelCoordinateSystemPointSet->InsertPoint(3, fiducial4); m_MarkerModelCoordinateSystemPointSet->InsertPoint(4, fiducial5); m_MarkerModelCoordinateSystemPointSet->InsertPoint(5, fiducial6); m_MarkerModelCoordinateSystemPointSet->InsertPoint(6, fiducial7); m_MarkerModelCoordinateSystemPointSet->InsertPoint(7, fiducial8); /*mitk::DataNode::Pointer node = this->GetDataStorage()->GetNamedNode("Marker Model Coordinate System Point Set"); if (node == nullptr) { node = mitk::DataNode::New(); node->SetName("Marker Model Coordinate System Point Set"); node->SetData(m_MarkerModelCoordinateSystemPointSet); this->GetDataStorage()->Add(node); } else { node->SetData(m_MarkerModelCoordinateSystemPointSet); this->GetDataStorage()->Modified(); }*/ } void QmitkUSNavigationStepCtUsRegistration::InitializePointsToTransformForGroundTruthProtocol() { m_PointsToTransformGroundTruthProtocol.clear(); mitk::Point3D point0mm; mitk::Point3D point20mm; mitk::Point3D point40mm; mitk::Point3D point60mm; mitk::Point3D point80mm; mitk::Point3D point100mm; point0mm[0] = 0.0; point0mm[1] = 0.0; point0mm[2] = 0.0; point20mm[0] = 0.0; point20mm[1] = 0.0; point20mm[2] = 0.0; point40mm[0] = 0.0; point40mm[1] = 0.0; point40mm[2] = 0.0; point60mm[0] = 0.0; point60mm[1] = 0.0; point60mm[2] = 0.0; point80mm[0] = 0.0; point80mm[1] = 0.0; point80mm[2] = 0.0; point100mm[0] = 0.0; point100mm[1] = 0.0; point100mm[2] = 0.0; m_PointsToTransformGroundTruthProtocol.insert(std::pair(0, point0mm)); m_PointsToTransformGroundTruthProtocol.insert(std::pair(20, point20mm)); m_PointsToTransformGroundTruthProtocol.insert(std::pair(40, point40mm)); m_PointsToTransformGroundTruthProtocol.insert(std::pair(60, point60mm)); m_PointsToTransformGroundTruthProtocol.insert(std::pair(80, point80mm)); m_PointsToTransformGroundTruthProtocol.insert(std::pair(100, point100mm)); } void QmitkUSNavigationStepCtUsRegistration::CreatePointsToTransformForGroundTruthProtocol() { this->InitializePointsToTransformForGroundTruthProtocol(); switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: MITK_WARN << "For this marker configuration (10mm) there does not exist a point to transform."; break; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: m_PointsToTransformGroundTruthProtocol.at(0)[0] = 130; // = 30mm to end of clipping plate + 100 mm to middle axis of measurement plate m_PointsToTransformGroundTruthProtocol.at(0)[1] = 15; m_PointsToTransformGroundTruthProtocol.at(0)[2] = -7; // = 5mm distance to clipping plate + 2mm to base m_PointsToTransformGroundTruthProtocol.at(20)[0] = 130; m_PointsToTransformGroundTruthProtocol.at(20)[1] = 15; m_PointsToTransformGroundTruthProtocol.at(20)[2] = -27; // = 5mm distance to clipping plate + 2mm to base + 20mm depth m_PointsToTransformGroundTruthProtocol.at(40)[0] = 130; m_PointsToTransformGroundTruthProtocol.at(40)[1] = 15; m_PointsToTransformGroundTruthProtocol.at(40)[2] = -47; // = 5mm distance to clipping plate + 2mm to base + 40mm depth m_PointsToTransformGroundTruthProtocol.at(60)[0] = 130; m_PointsToTransformGroundTruthProtocol.at(60)[1] = 15; m_PointsToTransformGroundTruthProtocol.at(60)[2] = -67; // = 5mm distance to clipping plate + 2mm to base + 60mm depth m_PointsToTransformGroundTruthProtocol.at(80)[0] = 130; m_PointsToTransformGroundTruthProtocol.at(80)[1] = 15; m_PointsToTransformGroundTruthProtocol.at(80)[2] = -87; // = 5mm distance to clipping plate + 2mm to base + 80mm depth m_PointsToTransformGroundTruthProtocol.at(100)[0] = 130; m_PointsToTransformGroundTruthProtocol.at(100)[1] = 15; m_PointsToTransformGroundTruthProtocol.at(100)[2] = -107; // = 5mm distance to clipping plate + 2mm to base + 100mm depth break; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: m_PointsToTransformGroundTruthProtocol.at(0)[0] = 135; // = 20 + 15mm to end of clipping plate + 100 mm to middle axis of measurement plate m_PointsToTransformGroundTruthProtocol.at(0)[1] = 20; m_PointsToTransformGroundTruthProtocol.at(0)[2] = -9; // = 7mm distance to clipping plate + 2mm to base m_PointsToTransformGroundTruthProtocol.at(20)[0] = 135; m_PointsToTransformGroundTruthProtocol.at(20)[1] = 20; m_PointsToTransformGroundTruthProtocol.at(20)[2] = -29; // = 7mm distance to clipping plate + 2mm to base + 20mm depth m_PointsToTransformGroundTruthProtocol.at(40)[0] = 135; m_PointsToTransformGroundTruthProtocol.at(40)[1] = 20; m_PointsToTransformGroundTruthProtocol.at(40)[2] = -49; // = 7mm distance to clipping plate + 2mm to base + 40mm depth m_PointsToTransformGroundTruthProtocol.at(60)[0] = 135; m_PointsToTransformGroundTruthProtocol.at(60)[1] = 20; m_PointsToTransformGroundTruthProtocol.at(60)[2] = -69; // = 7mm distance to clipping plate + 2mm to base + 60mm depth m_PointsToTransformGroundTruthProtocol.at(80)[0] = 135; m_PointsToTransformGroundTruthProtocol.at(80)[1] = 20; m_PointsToTransformGroundTruthProtocol.at(80)[2] = -89; // = 7mm distance to clipping plate + 2mm to base + 80mm depth m_PointsToTransformGroundTruthProtocol.at(100)[0] = 135; m_PointsToTransformGroundTruthProtocol.at(100)[1] = 20; m_PointsToTransformGroundTruthProtocol.at(100)[2] = -109; // = 7mm distance to clipping plate + 2mm to base + 100mm depth break; } } void QmitkUSNavigationStepCtUsRegistration::TransformPointsGroundTruthProtocol() { if (m_GroundTruthProtocolTransformedPoints.find(0) == m_GroundTruthProtocolTransformedPoints.end()) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(0))); m_GroundTruthProtocolTransformedPoints.insert(std::pair(0, pointSet)); } else { m_GroundTruthProtocolTransformedPoints.at(0)->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(0))); } if (m_GroundTruthProtocolTransformedPoints.find(20) == m_GroundTruthProtocolTransformedPoints.end()) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(20))); m_GroundTruthProtocolTransformedPoints.insert(std::pair(20, pointSet)); } else { m_GroundTruthProtocolTransformedPoints.at(20)->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(20))); } if (m_GroundTruthProtocolTransformedPoints.find(40) == m_GroundTruthProtocolTransformedPoints.end()) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(40))); m_GroundTruthProtocolTransformedPoints.insert(std::pair(40, pointSet)); } else { m_GroundTruthProtocolTransformedPoints.at(40)->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(40))); } if (m_GroundTruthProtocolTransformedPoints.find(60) == m_GroundTruthProtocolTransformedPoints.end()) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(60))); m_GroundTruthProtocolTransformedPoints.insert(std::pair(60, pointSet)); } else { m_GroundTruthProtocolTransformedPoints.at(60)->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(60))); } if (m_GroundTruthProtocolTransformedPoints.find(80) == m_GroundTruthProtocolTransformedPoints.end()) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(80))); m_GroundTruthProtocolTransformedPoints.insert(std::pair(80, pointSet)); } else { m_GroundTruthProtocolTransformedPoints.at(80)->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(80))); } if (m_GroundTruthProtocolTransformedPoints.find(100) == m_GroundTruthProtocolTransformedPoints.end()) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); pointSet->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(100))); m_GroundTruthProtocolTransformedPoints.insert(std::pair(100, pointSet)); } else { m_GroundTruthProtocolTransformedPoints.at(100)->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(m_PointsToTransformGroundTruthProtocol.at(100))); } } void QmitkUSNavigationStepCtUsRegistration::AddTransformedPointsToDataStorage() { if (m_GroundTruthProtocolTransformedPoints.find(0) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(20) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(40) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(60) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(80) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(100) == m_GroundTruthProtocolTransformedPoints.end()) { QMessageBox msgBox; msgBox.setText("Cannot add transformed Points to DataStorage because they do not exist.\ Stopping evaluation the protocol."); msgBox.exec(); return; } std::string nameNode0mm = "GroundTruthProt-Depth0mm"; std::string nameNode20mm = "GroundTruthProt-Depth20mm"; std::string nameNode40mm = "GroundTruthProt-Depth40mm"; std::string nameNode60mm = "GroundTruthProt-Depth60mm"; std::string nameNode80mm = "GroundTruthProt-Depth80mm"; std::string nameNode100mm = "GroundTruthProt-Depth100mm"; //Add transformed points of depth 0mm to the data storage mitk::DataNode::Pointer node0mm = this->GetDataStorage()->GetNamedNode(nameNode0mm); if (node0mm.IsNull()) { node0mm = mitk::DataNode::New(); node0mm->SetName(nameNode0mm); node0mm->SetData(m_GroundTruthProtocolTransformedPoints.at(0)); this->GetDataStorage()->Add(node0mm); } else { node0mm->SetData(m_GroundTruthProtocolTransformedPoints.at(0)); this->GetDataStorage()->Modified(); } if(ui->protocolEvaluationTypeComboBox->currentText().compare("PLANE") == 0 ) { //Add transformed points of depth 20mm to the data storage mitk::DataNode::Pointer node20mm = this->GetDataStorage()->GetNamedNode(nameNode20mm); if (node20mm.IsNull()) { node20mm = mitk::DataNode::New(); node20mm->SetName(nameNode20mm); node20mm->SetData(m_GroundTruthProtocolTransformedPoints.at(20)); this->GetDataStorage()->Add(node20mm); } else { node20mm->SetData(m_GroundTruthProtocolTransformedPoints.at(20)); this->GetDataStorage()->Modified(); } //Add transformed points of depth 40mm to the data storage mitk::DataNode::Pointer node40mm = this->GetDataStorage()->GetNamedNode(nameNode40mm); if (node40mm.IsNull()) { node40mm = mitk::DataNode::New(); node40mm->SetName(nameNode40mm); node40mm->SetData(m_GroundTruthProtocolTransformedPoints.at(40)); this->GetDataStorage()->Add(node40mm); } else { node40mm->SetData(m_GroundTruthProtocolTransformedPoints.at(40)); this->GetDataStorage()->Modified(); } //Add transformed points of depth 60mm to the data storage mitk::DataNode::Pointer node60mm = this->GetDataStorage()->GetNamedNode(nameNode60mm); if (node60mm.IsNull()) { node60mm = mitk::DataNode::New(); node60mm->SetName(nameNode60mm); node60mm->SetData(m_GroundTruthProtocolTransformedPoints.at(60)); this->GetDataStorage()->Add(node60mm); } else { node60mm->SetData(m_GroundTruthProtocolTransformedPoints.at(60)); this->GetDataStorage()->Modified(); } //Add transformed points of depth 80mm to the data storage mitk::DataNode::Pointer node80mm = this->GetDataStorage()->GetNamedNode(nameNode80mm); if (node80mm.IsNull()) { node80mm = mitk::DataNode::New(); node80mm->SetName(nameNode80mm); node80mm->SetData(m_GroundTruthProtocolTransformedPoints.at(80)); this->GetDataStorage()->Add(node80mm); } else { node80mm->SetData(m_GroundTruthProtocolTransformedPoints.at(80)); this->GetDataStorage()->Modified(); } //Add transformed points of depth 100mm to the data storage mitk::DataNode::Pointer node100mm = this->GetDataStorage()->GetNamedNode(nameNode100mm); if (node100mm.IsNull()) { node100mm = mitk::DataNode::New(); node100mm->SetName(nameNode100mm); node100mm->SetData(m_GroundTruthProtocolTransformedPoints.at(100)); this->GetDataStorage()->Add(node100mm); } else { node100mm->SetData(m_GroundTruthProtocolTransformedPoints.at(100)); this->GetDataStorage()->Modified(); } } //Do a global reinit mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); } double QmitkUSNavigationStepCtUsRegistration::CalculateMeanFRE() { double meanFRE = 0.0; for (unsigned int counter = 0; counter < m_GroundTruthProtocolFRE.size(); ++counter) { meanFRE += m_GroundTruthProtocolFRE[counter]; } return meanFRE / m_GroundTruthProtocolFRE.size(); } double QmitkUSNavigationStepCtUsRegistration::CalculateStandardDeviationOfFRE(double meanFRE) { double variance = 0.0; for (unsigned int counter = 0; counter < m_GroundTruthProtocolFRE.size(); ++counter) { variance += ((meanFRE - m_GroundTruthProtocolFRE[counter]) * (meanFRE - m_GroundTruthProtocolFRE[counter])); } variance /= m_GroundTruthProtocolFRE.size(); // calculate the empirical variance (n) and not the sampling variance (n-1) return sqrt(variance); } void QmitkUSNavigationStepCtUsRegistration::CalculateGroundTruthProtocolTRE() { if (m_GroundTruthProtocolTransformedPoints.find(0) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(20) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(40) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(60) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(80) == m_GroundTruthProtocolTransformedPoints.end() || m_GroundTruthProtocolTransformedPoints.find(100) == m_GroundTruthProtocolTransformedPoints.end()) { QMessageBox msgBox; msgBox.setText("Cannot calculate TRE of Ground-Truth-Protocol because points were not transformed."); msgBox.exec(); return; } // clear the std::map containing possibly data of earlier TRE calculations m_GroundTruthProtocolTRE.clear(); // loop through all existing point sets containing the transformed points for (int counter = 0; m_GroundTruthProtocolTransformedPoints.find(counter) != m_GroundTruthProtocolTransformedPoints.end(); counter += 20) { //calculate the middle point of the point set mitk::PointSet::Pointer pointSet = m_GroundTruthProtocolTransformedPoints.at(counter); mitk::Point3D middlePoint; middlePoint[0] = 0.0; middlePoint[1] = 0.0; middlePoint[2] = 0.0; for (int position = 0; position < pointSet->GetSize(); ++position) { middlePoint[0] += pointSet->GetPoint(position)[0]; middlePoint[1] += pointSet->GetPoint(position)[1]; middlePoint[2] += pointSet->GetPoint(position)[2]; } middlePoint[0] /= pointSet->GetSize(); middlePoint[1] /= pointSet->GetSize(); middlePoint[2] /= pointSet->GetSize(); MITK_INFO << "Calculated MiddlePoint: " << middlePoint; //sum up the euclidean distances between the middle point and each transformed point double meanDistance = 0.0; for (int position = 0; position < pointSet->GetSize(); ++position) { meanDistance += middlePoint.SquaredEuclideanDistanceTo(pointSet->GetPoint(position)); MITK_INFO << "SquaredEuclideanDistance: " << middlePoint.SquaredEuclideanDistanceTo(pointSet->GetPoint(position)); } meanDistance /= pointSet->GetSize(); // this can be interpreted as empirical variance // the root of the empirical variance can be interpreted as the protocols registration TRE m_GroundTruthProtocolTRE.insert(std::pair(counter, sqrt(meanDistance))); MITK_INFO << "Ground-Truth-Protocol TRE: " << sqrt(meanDistance); } } void QmitkUSNavigationStepCtUsRegistration::EliminateTooSmallLabeledObjects( ImageType::Pointer binaryImage) { BinaryImageToShapeLabelMapFilterType::OutputImageType::Pointer labelMap = m_BinaryImageToShapeLabelMapFilter->GetOutput(); double voxelVolume = this->GetVoxelVolume(); double fiducialVolume; unsigned int numberOfPixels; if (ui->fiducialDiameter3mmRadioButton->isChecked()) { fiducialVolume = this->GetFiducialVolume(1.5); numberOfPixels = ceil(fiducialVolume / voxelVolume); } else { fiducialVolume = this->GetFiducialVolume(2.5); numberOfPixels = ceil(fiducialVolume / voxelVolume); } MITK_INFO << "Voxel Volume = " << voxelVolume << "; Fiducial Volume = " << fiducialVolume; MITK_INFO << "Number of pixels = " << numberOfPixels; labelMap = m_BinaryImageToShapeLabelMapFilter->GetOutput(); // The output of this filter is an itk::LabelMap, which contains itk::LabelObject's MITK_INFO << "There are " << labelMap->GetNumberOfLabelObjects() << " objects."; // Loop over each region for (int i = labelMap->GetNumberOfLabelObjects() - 1; i >= 0; --i) { // Get the ith region BinaryImageToShapeLabelMapFilterType::OutputImageType::LabelObjectType* labelObject = labelMap->GetNthLabelObject(i); MITK_INFO << "Object " << i << " contains " << labelObject->Size() << " pixel"; //TODO: Threshold-Wert evtl. experimentell besser abstimmen, // um zu verhindern, dass durch Threshold wahre Fiducial-Kandidaten elimiert werden. if (labelObject->Size() < numberOfPixels * 0.8) { for (unsigned int pixelId = 0; pixelId < labelObject->Size(); pixelId++) { binaryImage->SetPixel(labelObject->GetIndex(pixelId), 0); } labelMap->RemoveLabelObject(labelObject); } } } bool QmitkUSNavigationStepCtUsRegistration::EliminateFiducialCandidatesByEuclideanDistances() { if (m_CentroidsOfFiducialCandidates.size() < NUMBER_FIDUCIALS_NEEDED) { return false; } for (unsigned int counter = 0; counter < m_CentroidsOfFiducialCandidates.size(); ++counter) { int amountOfAcceptedFiducials = 0; mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(counter)); //Loop through all fiducial candidates and calculate the distance between the chosen fiducial // candidate and the other candidates. For each candidate with a right distance between // Configuration A: 7.93mm and 31.0mm (10 mm distance between fiducial centers) or // Configuration B: 11.895mm and 45.0mm (15 mm distance between fiducial centers) or // Configuration C: 15.86mm and 59.0mm (20 mm distance between fiducial centers) // // increase the amountOfAcceptedFiducials. for (unsigned int position = 0; position < m_CentroidsOfFiducialCandidates.size(); ++position) { if (position == counter) { continue; } mitk::Point3D otherCentroid(m_CentroidsOfFiducialCandidates.at(position)); double distance = fiducialCentroid.EuclideanDistanceTo(otherCentroid); switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: if (distance > 7.93 && distance < 31.0) { ++amountOfAcceptedFiducials; } break; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: if (distance > 11.895 && distance < 45.0) { ++amountOfAcceptedFiducials; } break; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: if (distance > 15.86 && distance < 59.0) { ++amountOfAcceptedFiducials; } break; } } //The amountOfAcceptedFiducials must be at least 7. Otherwise delete the fiducial candidate // from the list of candidates. if (amountOfAcceptedFiducials < NUMBER_FIDUCIALS_NEEDED - 1) { MITK_INFO << "Deleting fiducial candidate at position: " << m_CentroidsOfFiducialCandidates.at(counter); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + counter); if (m_CentroidsOfFiducialCandidates.size() < NUMBER_FIDUCIALS_NEEDED ) { return false; } counter = -1; } } //Classify the rested fiducial candidates by its characteristic Euclidean distances // between the canidates and remove all candidates with a false distance configuration: this->ClassifyFiducialCandidates(); return true; } void QmitkUSNavigationStepCtUsRegistration::ClassifyFiducialCandidates() { MITK_INFO << "ClassifyFiducialCandidates()"; std::vector fiducialCandidatesToBeRemoved; std::vector> distanceVectorsFiducials; this->CalculateDistancesBetweenFiducials(distanceVectorsFiducials); for (unsigned int counter = 0; counter < distanceVectorsFiducials.size(); ++counter) { int distanceA = 0; // => 10,00mm distance int distanceB = 0; // => 14,14mm distance int distanceC = 0; // => 17,32mm distance int distanceD = 0; // => 22,36mm distance int distanceE = 0; // => 24,49mm distance int distanceF = 0; // => 28,28mm distance std::vector &distances = distanceVectorsFiducials.at(counter); for (unsigned int number = 0; number < distances.size(); ++number) { double &distance = distances.at(number); switch (ui->fiducialMarkerConfigurationComboBox->currentIndex()) { // case 0 is equal to fiducial marker configuration A (10mm distance) case 0: if (distance > 7.93 && distance <= 12.07) { ++distanceA; } else if (distance > 12.07 && distance <= 15.73) { ++distanceB; } else if (distance > 15.73 && distance <= 19.84) { ++distanceC; } else if (distance > 19.84 && distance <= 23.425) { ++distanceD; } else if (distance > 23.425 && distance <= 26.385) { ++distanceE; } else if (distance > 26.385 && distance <= 31.00) { ++distanceF; } break; // case 1 is equal to fiducial marker configuration B (15mm distance) case 1: if (distance > 11.895 && distance <= 18.105) { ++distanceA; } else if (distance > 18.105 && distance <= 23.595) { ++distanceB; } else if (distance > 23.595 && distance <= 29.76) { ++distanceC; } else if (distance > 29.76 && distance <= 35.1375) { ++distanceD; if (distance > 33.54) { ++distanceE; } } else if (distance > 35.1375 && distance <= 39.5775) { ++distanceE; if (distance < 36.735) { ++distanceD; } } else if (distance > 39.5775 && distance <= 45.00) { ++distanceF; } break; // case 2 is equal to fiducial marker configuration C (20mm distance) case 2: if (distance > 15.86 && distance <= 24.14) { ++distanceA; } else if (distance > 24.14 && distance <= 31.46) { ++distanceB; } else if (distance > 31.46 && distance <= 39.68) { ++distanceC; } else if (distance > 39.68 && distance <= 46.85) { ++distanceD; } else if (distance > 46.85 && distance <= 52.77) { ++distanceE; } else if (distance > 52.77 && distance <= 59.00) { ++distanceF; } break; } }// End for-loop distances-vector //Now, having looped through all distances of one fiducial candidate, check // if the combination of different distances is known. The >= is due to the // possible occurrence of other fiducial candidates that have an distance equal to // one of the distances A - E. However, false fiducial candidates outside // the fiducial marker does not have the right distance configuration: if (((distanceA >= 2 && distanceD >= 2 && distanceE >= 2 && distanceF >= 1) || (distanceA >= 1 && distanceB >= 2 && distanceC >= 1 && distanceD >= 2 && distanceE >= 1) || (distanceB >= 2 && distanceD >= 4 && distanceF >= 1) || (distanceA >= 1 && distanceB >= 1 && distanceD >= 3 && distanceE >= 1 && distanceF >= 1)) == false) { MITK_INFO << "Detected fiducial candidate with unknown distance configuration."; fiducialCandidatesToBeRemoved.push_back(counter); } } for (int count = fiducialCandidatesToBeRemoved.size() - 1; count >= 0; --count) { MITK_INFO << "Removing fiducial candidate " << fiducialCandidatesToBeRemoved.at(count); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + fiducialCandidatesToBeRemoved.at(count)); } } void QmitkUSNavigationStepCtUsRegistration::GetCentroidsOfLabeledObjects() { MITK_INFO << "GetCentroidsOfLabeledObjects()"; BinaryImageToShapeLabelMapFilterType::OutputImageType::Pointer labelMap = m_BinaryImageToShapeLabelMapFilter->GetOutput(); for (int i = labelMap->GetNumberOfLabelObjects() - 1; i >= 0; --i) { // Get the ith region BinaryImageToShapeLabelMapFilterType::OutputImageType::LabelObjectType* labelObject = labelMap->GetNthLabelObject(i); MITK_INFO << "Object " << i << " contains " << labelObject->Size() << " pixel"; mitk::Vector3D centroid; centroid[0] = labelObject->GetCentroid()[0]; centroid[1] = labelObject->GetCentroid()[1]; centroid[2] = labelObject->GetCentroid()[2]; m_CentroidsOfFiducialCandidates.push_back(centroid); } //evtl. for later: itk::LabelMapOverlayImageFilter } void QmitkUSNavigationStepCtUsRegistration::NumerateFiducialMarks() { MITK_INFO << "NumerateFiducialMarks()"; bool successFiducialNo1; bool successFiducialNo4; bool successFiducialNo2And3; bool successFiducialNo5; bool successFiducialNo8; bool successFiducialNo6; bool successFiducialNo7; std::vector> distanceVectorsFiducials; this->CalculateDistancesBetweenFiducials(distanceVectorsFiducials); successFiducialNo1 = this->FindFiducialNo1(distanceVectorsFiducials); successFiducialNo4 = this->FindFiducialNo4(distanceVectorsFiducials); successFiducialNo2And3 = this->FindFiducialNo2And3(); successFiducialNo5 = this->FindFiducialNo5(); successFiducialNo8 = this->FindFiducialNo8(); successFiducialNo6 = this->FindFiducialNo6(); successFiducialNo7 = this->FindFiducialNo7(); if (!successFiducialNo1 || !successFiducialNo4 || !successFiducialNo2And3 || !successFiducialNo5 || !successFiducialNo8 || !successFiducialNo6 || !successFiducialNo7) { QMessageBox msgBox; msgBox.setText("Cannot numerate/localize all fiducials successfully."); msgBox.exec(); return; } if (m_MarkerFloatingImageCoordinateSystemPointSet.IsNull()) { m_MarkerFloatingImageCoordinateSystemPointSet = mitk::PointSet::New(); } else if (m_MarkerFloatingImageCoordinateSystemPointSet->GetSize() != 0) { m_MarkerFloatingImageCoordinateSystemPointSet->Clear(); } for (unsigned int counter = 1; counter <= m_FiducialMarkerCentroids.size(); ++counter) { - m_MarkerFloatingImageCoordinateSystemPointSet->InsertPoint(counter - 1, m_FiducialMarkerCentroids.at(counter)); + m_MarkerFloatingImageCoordinateSystemPointSet->InsertPoint(counter - 1, mitk::Point3D(m_FiducialMarkerCentroids.at(counter))); } if( !m_PerformingGroundTruthProtocolEvaluation ) { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_MarkerFloatingImageCoordinateSystemPointSet); node->SetName("MarkerFloatingImageCSPointSet"); //node->SetFloatProperty("pointsize", 5.0); this->GetDataStorage()->Add(node); } } void QmitkUSNavigationStepCtUsRegistration::CalculateDistancesBetweenFiducials(std::vector>& distanceVectorsFiducials) { std::vector distancesBetweenFiducials; for (unsigned int i = 0; i < m_CentroidsOfFiducialCandidates.size(); ++i) { distancesBetweenFiducials.clear(); mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(i)); for (unsigned int n = 0; n < m_CentroidsOfFiducialCandidates.size(); ++n) { mitk::Point3D otherCentroid(m_CentroidsOfFiducialCandidates.at(n)); distancesBetweenFiducials.push_back(fiducialCentroid.EuclideanDistanceTo(otherCentroid)); } //Sort the distances from low to big numbers std::sort(distancesBetweenFiducials.begin(), distancesBetweenFiducials.end()); //First entry of the distance vector must be 0, so erase it if (distancesBetweenFiducials.at(0) == 0.0) { distancesBetweenFiducials.erase(distancesBetweenFiducials.begin()); } //Add the distance vector to the collecting distances vector distanceVectorsFiducials.push_back(distancesBetweenFiducials); } for (unsigned int i = 0; i < distanceVectorsFiducials.size(); ++i) { MITK_INFO << "Vector " << i << ":"; for (unsigned int k = 0; k < distanceVectorsFiducials.at(i).size(); ++k) { MITK_INFO << distanceVectorsFiducials.at(i).at(k); } } } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo1(std::vector>& distanceVectorsFiducials) { for (unsigned int i = 0; i < distanceVectorsFiducials.size(); ++i) { std::vector &distances = distanceVectorsFiducials.at(i); if (distances.size() < NUMBER_FIDUCIALS_NEEDED - 1 ) { MITK_WARN << "Cannot find fiducial 1, there aren't found enough fiducial candidates."; return false; } double characteristicDistanceAWithUpperMargin = this->GetCharacteristicDistanceAWithUpperMargin(); if (distances.at(0) <= characteristicDistanceAWithUpperMargin && distances.at(1) <= characteristicDistanceAWithUpperMargin) { MITK_INFO << "Found Fiducial 1 (PointSet number " << i << ")"; m_FiducialMarkerCentroids.insert( std::pair(1, m_CentroidsOfFiducialCandidates.at(i))); distanceVectorsFiducials.erase(distanceVectorsFiducials.begin() + i); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + i); return true; } } return false; } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo2And3() { if (m_FiducialMarkerCentroids.find(1) == m_FiducialMarkerCentroids.end() ) { MITK_WARN << "Cannot find fiducial No 2 and 3. Before must be found fiducial No 1."; return false; } mitk::Point3D fiducialNo1(m_FiducialMarkerCentroids.at(1)); mitk::Vector3D fiducialVectorA; mitk::Vector3D fiducialVectorB; mitk::Point3D fiducialPointA; mitk::Point3D fiducialPointB; bool foundFiducialA = false; bool foundFiducialB = false; mitk::Vector3D vectorFiducial1ToFiducialA; mitk::Vector3D vectorFiducial1ToFiducialB; for (unsigned int i = 0; i < m_CentroidsOfFiducialCandidates.size(); ++i) { mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(i)); double distance = fiducialNo1.EuclideanDistanceTo(fiducialCentroid); if (distance <= this->GetCharacteristicDistanceAWithUpperMargin()) { fiducialVectorA = m_CentroidsOfFiducialCandidates.at(i); fiducialPointA = fiducialCentroid; m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + i); foundFiducialA = true; break; } } for (unsigned int i = 0; i < m_CentroidsOfFiducialCandidates.size(); ++i) { mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(i)); double distance = fiducialNo1.EuclideanDistanceTo(fiducialCentroid); if (distance <= this->GetCharacteristicDistanceAWithUpperMargin()) { fiducialVectorB = m_CentroidsOfFiducialCandidates.at(i); fiducialPointB = fiducialCentroid; m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + i); foundFiducialB = true; break; } } if (!foundFiducialA || !foundFiducialB) { MITK_WARN << "Cannot identify fiducial candidates 2 and 3"; return false; } else if (m_CentroidsOfFiducialCandidates.size() == 0) { MITK_WARN << "Too less fiducials detected. Cannot identify fiducial candidates 2 and 3"; return false; } vectorFiducial1ToFiducialA = fiducialVectorA - m_FiducialMarkerCentroids.at(1); vectorFiducial1ToFiducialB = fiducialVectorB - m_FiducialMarkerCentroids.at(1); vnl_vector crossProductVnl = vnl_cross_3d(vectorFiducial1ToFiducialA.GetVnlVector(), vectorFiducial1ToFiducialB.GetVnlVector()); mitk::Vector3D crossProduct; crossProduct.SetVnlVector(crossProductVnl); mitk::Vector3D vectorFiducial1ToRandomLeftFiducial = m_CentroidsOfFiducialCandidates.at(0) - m_FiducialMarkerCentroids.at(1); double scalarProduct = (crossProduct * vectorFiducial1ToRandomLeftFiducial) / (crossProduct.GetNorm() * vectorFiducial1ToRandomLeftFiducial.GetNorm()); double alpha = acos(scalarProduct) * 57.29578; //Transform into degree MITK_INFO << "Scalar Product = " << alpha; if (alpha <= 90) { m_FiducialMarkerCentroids[3] = fiducialVectorA; m_FiducialMarkerCentroids[2] = fiducialVectorB; } else { m_FiducialMarkerCentroids[2] = fiducialVectorA; m_FiducialMarkerCentroids[3] = fiducialVectorB; } MITK_INFO << "Found Fiducial 2, PointSet: " << m_FiducialMarkerCentroids.at(2); MITK_INFO << "Found Fiducial 3, PointSet: " << m_FiducialMarkerCentroids.at(3); return true; } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo4(std::vector>& distanceVectorsFiducials) { double characteristicDistanceBWithLowerMargin = this->GetCharacteristicDistanceBWithLowerMargin(); double characteristicDistanceBWithUpperMargin = this->GetCharacteristicDistanceBWithUpperMargin(); for (unsigned int i = 0; i < distanceVectorsFiducials.size(); ++i) { std::vector &distances = distanceVectorsFiducials.at(i); if (distances.size() < NUMBER_FIDUCIALS_NEEDED - 1) { MITK_WARN << "Cannot find fiducial 4, there aren't found enough fiducial candidates."; return false; } if (distances.at(0) > characteristicDistanceBWithLowerMargin && distances.at(0) <= characteristicDistanceBWithUpperMargin && distances.at(1) > characteristicDistanceBWithLowerMargin && distances.at(1) <= characteristicDistanceBWithUpperMargin) { MITK_INFO << "Found Fiducial 4 (PointSet number " << i << ")"; m_FiducialMarkerCentroids.insert(std::pair(4, m_CentroidsOfFiducialCandidates.at(i))); distanceVectorsFiducials.erase(distanceVectorsFiducials.begin() + i); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + i); return true; } } return false; } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo5() { if (m_FiducialMarkerCentroids.find(2) == m_FiducialMarkerCentroids.end()) { MITK_WARN << "To find fiducial No 5, fiducial No 2 has to be found before."; return false; } double characteristicDistanceBWithUpperMargin = this->GetCharacteristicDistanceBWithUpperMargin(); mitk::Point3D fiducialNo2(m_FiducialMarkerCentroids.at(2)); for (unsigned int counter = 0; counter < m_CentroidsOfFiducialCandidates.size(); ++counter) { mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(counter)); double distance = fiducialNo2.EuclideanDistanceTo(fiducialCentroid); if (distance <= characteristicDistanceBWithUpperMargin) { m_FiducialMarkerCentroids[5] = m_CentroidsOfFiducialCandidates.at(counter); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + counter); MITK_INFO << "Found Fiducial No 5, PointSet: " << m_FiducialMarkerCentroids[5]; return true; } } MITK_WARN << "Cannot find fiducial No 5."; return false; } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo6() { if (m_FiducialMarkerCentroids.find(5) == m_FiducialMarkerCentroids.end()) { MITK_WARN << "To find fiducial No 6, fiducial No 5 has to be found before."; return false; } double characteristicDistanceAWithUpperMargin = this->GetCharacteristicDistanceAWithUpperMargin(); mitk::Point3D fiducialNo5(m_FiducialMarkerCentroids.at(5)); for (unsigned int counter = 0; counter < m_CentroidsOfFiducialCandidates.size(); ++counter) { mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(counter)); double distance = fiducialNo5.EuclideanDistanceTo(fiducialCentroid); if (distance <= characteristicDistanceAWithUpperMargin) { m_FiducialMarkerCentroids[6] = m_CentroidsOfFiducialCandidates.at(counter); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + counter); MITK_INFO << "Found Fiducial No 6, PointSet: " << m_FiducialMarkerCentroids[6]; return true; } } MITK_WARN << "Cannot find fiducial No 6."; return false; } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo7() { if (m_FiducialMarkerCentroids.find(8) == m_FiducialMarkerCentroids.end()) { MITK_WARN << "To find fiducial No 7, fiducial No 8 has to be found before."; return false; } double characteristicDistanceAWithUpperMargin = this->GetCharacteristicDistanceAWithUpperMargin(); mitk::Point3D fiducialNo8(m_FiducialMarkerCentroids.at(8)); for (unsigned int counter = 0; counter < m_CentroidsOfFiducialCandidates.size(); ++counter) { mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(counter)); double distance = fiducialNo8.EuclideanDistanceTo(fiducialCentroid); if (distance <= characteristicDistanceAWithUpperMargin) { m_FiducialMarkerCentroids[7] = m_CentroidsOfFiducialCandidates.at(counter); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + counter); MITK_INFO << "Found Fiducial No 7, PointSet: " << m_FiducialMarkerCentroids[7]; return true; } } MITK_WARN << "Cannot find fiducial No 7."; return false; } bool QmitkUSNavigationStepCtUsRegistration::FindFiducialNo8() { if (m_FiducialMarkerCentroids.find(3) == m_FiducialMarkerCentroids.end()) { MITK_WARN << "To find fiducial No 8, fiducial No 3 has to be found before."; return false; } double characteristicDistanceBWithUpperMargin = this->GetCharacteristicDistanceBWithUpperMargin(); mitk::Point3D fiducialNo3(m_FiducialMarkerCentroids.at(3)); for (unsigned int counter = 0; counter < m_CentroidsOfFiducialCandidates.size(); ++counter) { mitk::Point3D fiducialCentroid(m_CentroidsOfFiducialCandidates.at(counter)); double distance = fiducialNo3.EuclideanDistanceTo(fiducialCentroid); if (distance <= characteristicDistanceBWithUpperMargin) { m_FiducialMarkerCentroids[8] = m_CentroidsOfFiducialCandidates.at(counter); m_CentroidsOfFiducialCandidates.erase(m_CentroidsOfFiducialCandidates.begin() + counter); MITK_INFO << "Found Fiducial No 8, PointSet: " << m_FiducialMarkerCentroids[8]; return true; } } MITK_WARN << "Cannot find fiducial No 8."; return false; } void QmitkUSNavigationStepCtUsRegistration::DefineDataStorageImageFilter() { m_IsAPointSetPredicate = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); auto isSegmentation = mitk::NodePredicateDataType::New("Segment"); m_IsASurfacePredicate = mitk::NodePredicateDataType::New("Surface"); mitk::NodePredicateOr::Pointer validImages = mitk::NodePredicateOr::New(); validImages->AddPredicate(mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isSegmentation))); mitk::NodePredicateNot::Pointer isNotAHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true))); m_IsOfTypeImagePredicate = mitk::NodePredicateAnd::New(validImages, isNotAHelperObject); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateNot::Pointer isNotBinaryPredicate = mitk::NodePredicateNot::New(isBinaryPredicate); mitk::NodePredicateAnd::Pointer isABinaryImagePredicate = mitk::NodePredicateAnd::New(m_IsOfTypeImagePredicate, isBinaryPredicate); mitk::NodePredicateAnd::Pointer isNotABinaryImagePredicate = mitk::NodePredicateAnd::New(m_IsOfTypeImagePredicate, isNotBinaryPredicate); m_IsASegmentationImagePredicate = mitk::NodePredicateOr::New(isABinaryImagePredicate, mitk::TNodePredicateDataType::New()); m_IsAPatientImagePredicate = mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, mitk::NodePredicateNot::New(mitk::TNodePredicateDataType::New())); } void QmitkUSNavigationStepCtUsRegistration::CreateQtPartControl(QWidget *parent) { ui->setupUi(parent); ui->floatingImageComboBox->SetPredicate(m_IsAPatientImagePredicate); ui->ctImagesToChooseComboBox->SetPredicate(m_IsAPatientImagePredicate); ui->segmentationComboBox->SetPredicate(m_IsASegmentationImagePredicate); ui->selectedSurfaceComboBox->SetPredicate(m_IsASurfacePredicate); ui->pointSetComboBox->SetPredicate(m_IsAPointSetPredicate); // create signal/slot connections connect(ui->floatingImageComboBox, SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnFloatingImageComboBoxSelectionChanged(const mitk::DataNode*))); connect(ui->doRegistrationMarkerToImagePushButton, SIGNAL(clicked()), this, SLOT(OnRegisterMarkerToFloatingImageCS())); connect(ui->localizeFiducialMarkerPushButton, SIGNAL(clicked()), this, SLOT(OnLocalizeFiducials())); connect(ui->visualizeCTtoUSregistrationPushButton, SIGNAL(clicked()), this, SLOT(OnVisualizeCTtoUSregistration())); connect(ui->freezeUnfreezePushButton, SIGNAL(clicked()), this, SLOT(OnFreeze())); connect(ui->addCtImagePushButton, SIGNAL(clicked()), this, SLOT(OnAddCtImageClicked())); connect(ui->removeCtImagePushButton, SIGNAL(clicked()), this, SLOT(OnRemoveCtImageClicked())); connect(ui->evaluateProtocolPushButton, SIGNAL(clicked()), this, SLOT(OnEvaluateGroundTruthFiducialLocalizationProtocol())); connect(ui->actualizeSegmentationSurfacePSetDataPushButton, SIGNAL(clicked()), this, SLOT(OnActualizeSegmentationSurfacePointSetData())); connect(ui->calculateTREPushButton, SIGNAL(clicked()), this, SLOT(OnGetCursorPosition())); connect(ui->calculateCenterPushButton, SIGNAL(clicked()), this, SLOT(OnCalculateCenter())); } void QmitkUSNavigationStepCtUsRegistration::OnFloatingImageComboBoxSelectionChanged(const mitk::DataNode* node) { MITK_INFO << "OnFloatingImageComboBoxSelectionChanged()"; if (m_FloatingImage.IsNotNull()) { //TODO: Define, what will happen if the imageCT is not null... } if (node == nullptr) { this->UnsetFloatingImageGeometry(); m_FloatingImage = nullptr; return; } mitk::DataNode* selectedFloatingImage = ui->floatingImageComboBox->GetSelectedNode(); if (selectedFloatingImage == nullptr) { this->UnsetFloatingImageGeometry(); m_FloatingImage = nullptr; return; } mitk::Image::Pointer floatingImage = dynamic_cast(selectedFloatingImage->GetData()); if (floatingImage.IsNull()) { MITK_WARN << "Failed to cast selected segmentation node to mitk::Image*"; this->UnsetFloatingImageGeometry(); m_FloatingImage = nullptr; return; } m_FloatingImage = floatingImage; this->SetFloatingImageGeometryInformation(floatingImage.GetPointer()); } void QmitkUSNavigationStepCtUsRegistration::OnRegisterMarkerToFloatingImageCS() { this->CreateMarkerModelCoordinateSystemPointSet(); //Check for initialization if( m_MarkerModelCoordinateSystemPointSet.IsNull() || m_MarkerFloatingImageCoordinateSystemPointSet.IsNull() ) { MITK_WARN << "Fiducial Landmarks are not initialized yet, cannot register"; return; } //Retrieve fiducials if (m_MarkerFloatingImageCoordinateSystemPointSet->GetSize() != m_MarkerModelCoordinateSystemPointSet->GetSize()) { MITK_WARN << "Not the same number of fiducials, cannot register"; return; } else if (m_MarkerFloatingImageCoordinateSystemPointSet->GetSize() < 3) { MITK_WARN << "Need at least 3 fiducials, cannot register"; return; } //############### conversion to vtk data types (we will use the vtk landmark based transform) ########################## //convert point sets to vtk poly data vtkSmartPointer sourcePoints = vtkSmartPointer::New(); vtkSmartPointer targetPoints = vtkSmartPointer::New(); for (int i = 0; iGetSize(); i++) { double point[3] = { m_MarkerModelCoordinateSystemPointSet->GetPoint(i)[0], m_MarkerModelCoordinateSystemPointSet->GetPoint(i)[1], m_MarkerModelCoordinateSystemPointSet->GetPoint(i)[2] }; sourcePoints->InsertNextPoint(point); double point_targets[3] = { m_MarkerFloatingImageCoordinateSystemPointSet->GetPoint(i)[0], m_MarkerFloatingImageCoordinateSystemPointSet->GetPoint(i)[1], m_MarkerFloatingImageCoordinateSystemPointSet->GetPoint(i)[2] }; targetPoints->InsertNextPoint(point_targets); } //########################### here, the actual transform is computed ########################## //compute transform vtkSmartPointer transform = vtkSmartPointer::New(); transform->SetSourceLandmarks(sourcePoints); transform->SetTargetLandmarks(targetPoints); transform->SetModeToRigidBody(); transform->Modified(); transform->Update(); //compute FRE of transform double FRE = mitk::StaticIGTHelperFunctions::ComputeFRE(m_MarkerModelCoordinateSystemPointSet, m_MarkerFloatingImageCoordinateSystemPointSet, transform); MITK_INFO << "FRE: " << FRE << " mm"; if (m_PerformingGroundTruthProtocolEvaluation) { m_GroundTruthProtocolFRE.push_back(FRE); } //############################################################################################# //############### conversion back to itk/mitk data types ########################## //convert from vtk to itk data types itk::Matrix rotationFloat = itk::Matrix(); itk::Vector translationFloat = itk::Vector(); itk::Matrix rotationDouble = itk::Matrix(); itk::Vector translationDouble = itk::Vector(); vtkSmartPointer m = transform->GetMatrix(); for (int k = 0; k<3; k++) for (int l = 0; l<3; l++) { rotationFloat[k][l] = m->GetElement(k, l); rotationDouble[k][l] = m->GetElement(k, l); } for (int k = 0; k<3; k++) { translationFloat[k] = m->GetElement(k, 3); translationDouble[k] = m->GetElement(k, 3); } //create mitk affine transform 3D and save it to the class member m_TransformMarkerCSToFloatingImageCS = mitk::AffineTransform3D::New(); m_TransformMarkerCSToFloatingImageCS->SetMatrix(rotationDouble); m_TransformMarkerCSToFloatingImageCS->SetOffset(translationDouble); MITK_INFO << m_TransformMarkerCSToFloatingImageCS; //################################################################ //############### object is transformed ########################## //transform surface/image //only move image if we have one. Sometimes, this widget is used just to register point sets without images. /*if (m_ImageNode.IsNotNull()) { //first we have to store the original ct image transform to compose it with the new transform later mitk::AffineTransform3D::Pointer imageTransform = m_ImageNode->GetData()->GetGeometry()->GetIndexToWorldTransform(); imageTransform->Compose(mitkTransform); mitk::AffineTransform3D::Pointer newImageTransform = mitk::AffineTransform3D::New(); //create new image transform... setting the composed directly leads to an error itk::Matrix rotationFloatNew = imageTransform->GetMatrix(); itk::Vector translationFloatNew = imageTransform->GetOffset(); newImageTransform->SetMatrix(rotationFloatNew); newImageTransform->SetOffset(translationFloatNew); m_ImageNode->GetData()->GetGeometry()->SetIndexToWorldTransform(newImageTransform); }*/ //If this option is set, each point will be transformed and the acutal coordinates of the points change. if( !m_PerformingGroundTruthProtocolEvaluation ) { mitk::PointSet* pointSet_orig = m_MarkerModelCoordinateSystemPointSet; mitk::PointSet::Pointer pointSet_moved = mitk::PointSet::New(); for (int i = 0; i < pointSet_orig->GetSize(); i++) { pointSet_moved->InsertPoint(m_TransformMarkerCSToFloatingImageCS->TransformPoint(pointSet_orig->GetPoint(i))); } pointSet_orig->Clear(); for (int i = 0; i < pointSet_moved->GetSize(); i++) pointSet_orig->InsertPoint(pointSet_moved->GetPoint(i)); //Do a global reinit mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); } } void QmitkUSNavigationStepCtUsRegistration::OnLocalizeFiducials() { m_FiducialMarkerCentroids.clear(); m_CentroidsOfFiducialCandidates.clear(); if (m_MarkerFloatingImageCoordinateSystemPointSet.IsNotNull()) { m_MarkerFloatingImageCoordinateSystemPointSet->Clear(); } if (!this->FilterFloatingImage()) { QMessageBox msgBox; msgBox.setText("Cannot perform filtering of the image. The floating image = nullptr."); msgBox.exec(); return; } mitk::AffineTransform3D::Pointer transform = m_FloatingImage->GetGeometry()->GetIndexToWorldTransform(); MITK_WARN << "IndexToWorldTransform_CTimage = " << transform; this->GetCentroidsOfLabeledObjects(); if (!this->EliminateFiducialCandidatesByEuclideanDistances() || m_CentroidsOfFiducialCandidates.size() != NUMBER_FIDUCIALS_NEEDED) { QMessageBox msgBox; QString text = QString("Have found %1 instead of 8 fiducial candidates.\ Cannot perform fiducial localization procedure.").arg(m_CentroidsOfFiducialCandidates.size()); msgBox.setText(text); msgBox.exec(); return; } //Before calling NumerateFiducialMarks it must be sure, // that there rested only 8 fiducial candidates. this->NumerateFiducialMarks(); } void QmitkUSNavigationStepCtUsRegistration::OnVisualizeCTtoUSregistration() { emit this->ActualizeCtToUsRegistrationWidget(); mitk::DataNode* segmentationNode = ui->segmentationComboBox->GetSelectedNode(); if (segmentationNode == nullptr) { QMessageBox msgBox; msgBox.setText("Cannot visualize CT-to-US registration. There is no segmentation selected."); msgBox.exec(); return; } mitk::AffineTransform3D::Pointer transform = segmentationNode->GetData()->GetGeometry()->GetIndexToWorldTransform(); MITK_WARN << "IndexToWorldTransform_segmentation = " << transform; mitk::DataNode* surfaceNode = ui->selectedSurfaceComboBox->GetSelectedNode(); if (surfaceNode == nullptr) { QMessageBox msgBox; msgBox.setText("Cannot visualize CT-to-US registration. There is no surface selected."); msgBox.exec(); return; } mitk::DataNode* pointSetNode = ui->pointSetComboBox->GetSelectedNode(); if (pointSetNode == nullptr) { QMessageBox msgBox; msgBox.setText("Cannot visualize CT-to-US registration. There is no pointSet selected."); msgBox.exec(); return; } if (this->GetCombinedModality(false).IsNull()) { QMessageBox msgBox; msgBox.setText("CombinedModality not yet set.\nPlease try again and click on the button."); msgBox.exec(); return; } if (m_FloatingImageToUltrasoundRegistrationFilter.IsNull()) { QMessageBox msgBox; msgBox.setText("Cannot visualize CT-to-US registration.\ The FloatingImageToUltrasoundRegistrationFilter is not initialized."); msgBox.exec(); return; } //Set the transformation from marker-CS to the sensor-CS accordingly to the chosen user-option m_FloatingImageToUltrasoundRegistrationFilter ->InitializeTransformationMarkerCSToSensorCS(ui->useNdiTrackerCheckBox->isChecked()); m_FloatingImageToUltrasoundRegistrationFilter->SetPointSet(pointSetNode); m_FloatingImageToUltrasoundRegistrationFilter->SetSegmentation(segmentationNode, m_FloatingImage); m_FloatingImageToUltrasoundRegistrationFilter->SetSurface(surfaceNode); m_FloatingImageToUltrasoundRegistrationFilter ->SetTransformMarkerCSToFloatingImageCS(m_TransformMarkerCSToFloatingImageCS); m_FloatingImageToUltrasoundRegistrationFilter ->SetTransformUSimageCSToTrackingCS(this->GetCombinedModality()->GetCalibration()); m_FloatingImageToUltrasoundRegistrationFilter ->ConnectTo(this->GetCombinedModality()->GetNavigationDataSource()); } void QmitkUSNavigationStepCtUsRegistration::OnFreeze() { if (this->GetCombinedModality(false).IsNull()) { return; } if (!m_FreezeCombinedModality) { m_FreezeCombinedModality = true; ui->freezeUnfreezePushButton->setText("Unfreeze"); this->GetCombinedModality()->SetIsFreezed(true); } else { m_FreezeCombinedModality = false; ui->freezeUnfreezePushButton->setText("Freeze"); this->GetCombinedModality()->SetIsFreezed(false); } } void QmitkUSNavigationStepCtUsRegistration::OnActualizeSegmentationSurfacePointSetData() { mitk::DataNode* segmentationNode = ui->segmentationComboBox->GetSelectedNode(); if (segmentationNode == nullptr) { QMessageBox msgBox; msgBox.setText("Cannot actualize segmentation + surface + pointset data. There is no segmentation selected."); msgBox.exec(); return; } mitk::DataNode* surfaceNode = ui->selectedSurfaceComboBox->GetSelectedNode(); if (surfaceNode == nullptr) { QMessageBox msgBox; msgBox.setText("Cannot actualize segmentation + surface + pointset data. There is no surface selected."); msgBox.exec(); return; } mitk::DataNode* pointSetNode = ui->pointSetComboBox->GetSelectedNode(); if (pointSetNode == nullptr) { QMessageBox msgBox; msgBox.setText("Cannot actualize segmentation + surface + pointset data. There is no pointSet selected."); msgBox.exec(); return; } m_FloatingImageToUltrasoundRegistrationFilter->SetPointSet(pointSetNode); m_FloatingImageToUltrasoundRegistrationFilter->SetSegmentation(segmentationNode, m_FloatingImage); m_FloatingImageToUltrasoundRegistrationFilter->SetSurface(surfaceNode); } void QmitkUSNavigationStepCtUsRegistration::OnGetCursorPosition() { emit GetCursorPosition(); } void QmitkUSNavigationStepCtUsRegistration::OnCalculateTRE(mitk::Point3D centroidOfTargetInUSImage) { mitk::DataNode::Pointer pointSetNode = ui->pointSetComboBox->GetSelectedNode(); if (pointSetNode.IsNull()) { QMessageBox msgBox; msgBox.setText("Cannot calculate TRE. The pointSetComboBox node returned a nullptr."); msgBox.exec(); return; } mitk::PointSet::Pointer pointSet = dynamic_cast(pointSetNode->GetData()); if (pointSet.IsNull()) { ui->distanceTREValue->setText(QString("Unknown")); return; } double distance = pointSet->GetPoint(0).EuclideanDistanceTo(centroidOfTargetInUSImage); ui->distanceTREValue->setText(QString("%1").arg(distance)); } void QmitkUSNavigationStepCtUsRegistration::OnCalculateCenter() { mitk::DataNode::Pointer node = ui->segmentationComboBox->GetSelectedNode(); if (node.IsNull()) { QMessageBox msgBox; msgBox.setText("Cannot calculate the centroid of the segmentation."\ "The segmentationComboBox node returned a nullptr."); msgBox.exec(); return; } mitk::LabelSetImage::Pointer image = dynamic_cast(node->GetData()); if (image.IsNull()) { MITK_WARN << "Cannot CalculateCenter - the segmentation cannot be converted to mitk::Image"; return; } ImageType::Pointer itkImage = ImageType::New(); mitk::CastToItkImage(image, itkImage); //Initialize binary image to shape label map filter BinaryImageToShapeLabelMapFilterType::Pointer shapeLabelMapFilter = BinaryImageToShapeLabelMapFilterType::New(); shapeLabelMapFilter->SetInputForegroundValue(1); shapeLabelMapFilter->SetInput(itkImage); shapeLabelMapFilter->Update(); BinaryImageToShapeLabelMapFilterType::OutputImageType::Pointer labelMap = shapeLabelMapFilter->GetOutput(); for (int i = labelMap->GetNumberOfLabelObjects() - 1; i >= 0; --i) { // Get the ith region BinaryImageToShapeLabelMapFilterType::OutputImageType::LabelObjectType* labelObject = labelMap->GetNthLabelObject(i); mitk::Vector3D centroid; centroid[0] = labelObject->GetCentroid()[0]; centroid[1] = labelObject->GetCentroid()[1]; centroid[2] = labelObject->GetCentroid()[2]; MITK_INFO << "Centroid of segmentation = " << centroid; } } void QmitkUSNavigationStepCtUsRegistration::OnAddCtImageClicked() { mitk::DataNode* selectedCtImage = ui->ctImagesToChooseComboBox->GetSelectedNode(); if (selectedCtImage == nullptr) { return; } mitk::Image::Pointer ctImage = dynamic_cast(selectedCtImage->GetData()); if (ctImage.IsNull()) { MITK_WARN << "Failed to cast selected segmentation node to mitk::Image*"; return; } QString name = QString::fromStdString(selectedCtImage->GetName()); for( int counter = 0; counter < ui->chosenCtImagesListWidget->count(); ++counter) { MITK_INFO << ui->chosenCtImagesListWidget->item(counter)->text() << " - " << counter; MITK_INFO << m_ImagesGroundTruthProtocol.at(counter).GetPointer(); if (ui->chosenCtImagesListWidget->item(counter)->text().compare(name) == 0) { MITK_INFO << "CT image already exist in list of chosen CT images. Do not add the image."; return; } } ui->chosenCtImagesListWidget->addItem(name); m_ImagesGroundTruthProtocol.push_back(ctImage); } void QmitkUSNavigationStepCtUsRegistration::OnRemoveCtImageClicked() { int position = ui->chosenCtImagesListWidget->currentRow(); if (ui->chosenCtImagesListWidget->count() == 0 || position < 0) { return; } m_ImagesGroundTruthProtocol.erase(m_ImagesGroundTruthProtocol.begin() + position); QListWidgetItem *item = ui->chosenCtImagesListWidget->currentItem(); ui->chosenCtImagesListWidget->removeItemWidget(item); delete item; } void QmitkUSNavigationStepCtUsRegistration::OnEvaluateGroundTruthFiducialLocalizationProtocol() { m_GroundTruthProtocolFRE.clear(); if (m_ImagesGroundTruthProtocol.size() != 6) { QMessageBox msgBox; msgBox.setText("For evaluating the Ground-Truth-Fiducial-Localization-Protocol there must be loaded 6 different CT images."); msgBox.exec(); return; } m_PerformingGroundTruthProtocolEvaluation = true; this->CreatePointsToTransformForGroundTruthProtocol(); m_GroundTruthProtocolTransformedPoints.clear(); for (unsigned int cycleNo = 0; cycleNo < m_ImagesGroundTruthProtocol.size(); ++cycleNo) { m_FloatingImage = m_ImagesGroundTruthProtocol.at(cycleNo); this->SetFloatingImageGeometryInformation(m_FloatingImage.GetPointer()); this->OnLocalizeFiducials(); this->OnRegisterMarkerToFloatingImageCS(); this->TransformPointsGroundTruthProtocol(); } this->AddTransformedPointsToDataStorage(); double meanFRE = this->CalculateMeanFRE(); double sdOfFRE = this->CalculateStandardDeviationOfFRE(meanFRE); this->CalculateGroundTruthProtocolTRE(); ui->meanFREValue->setText(QString("%1").arg(meanFRE)); ui->sdFREValue->setText(QString("%1").arg(sdOfFRE)); if (ui->protocolEvaluationTypeComboBox->currentText().compare("ANGLE") == 0) { if (m_GroundTruthProtocolTRE.find(0) != m_GroundTruthProtocolTRE.end()) { ui->TREValue->setText(QString("%1").arg(m_GroundTruthProtocolTRE.at(0))); } } else if (ui->protocolEvaluationTypeComboBox->currentText().compare("PLANE") == 0) { if (m_GroundTruthProtocolTRE.find(0) != m_GroundTruthProtocolTRE.end() && m_GroundTruthProtocolTRE.find(20) != m_GroundTruthProtocolTRE.end() && m_GroundTruthProtocolTRE.find(40) != m_GroundTruthProtocolTRE.end() && m_GroundTruthProtocolTRE.find(60) != m_GroundTruthProtocolTRE.end() && m_GroundTruthProtocolTRE.find(80) != m_GroundTruthProtocolTRE.end() && m_GroundTruthProtocolTRE.find(100) != m_GroundTruthProtocolTRE.end()) { ui->TREValue->setText(QString("Depth 0mm: %1\nDepth 20mm: %2\nDepth 40mm: %3\ \nDepth 60mm: %4\nDepth 80mm: %5\nDepth 100mm: %6") .arg(m_GroundTruthProtocolTRE.at(0)) .arg(m_GroundTruthProtocolTRE.at(20)) .arg(m_GroundTruthProtocolTRE.at(40)) .arg(m_GroundTruthProtocolTRE.at(60)) .arg(m_GroundTruthProtocolTRE.at(80)) .arg(m_GroundTruthProtocolTRE.at(100))); } } m_PerformingGroundTruthProtocolEvaluation = false; } diff --git a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.cpp b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.cpp index 14450e93af..7fd7430f85 100644 --- a/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.cpp +++ b/Plugins/org.mitk.gui.qt.igt.app.ultrasoundtrackingnavigation/src/internal/NavigationStepWidgets/QmitkUSNavigationStepPunctuationIntervention.cpp @@ -1,290 +1,290 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkUSNavigationStepPunctuationIntervention.h" #include "ui_QmitkUSNavigationStepPunctuationIntervention.h" #include "mitkNeedleProjectionFilter.h" #include "../Widgets/QmitkZoneProgressBar.h" #include "../QmitkUSNavigationMarkerPlacement.h" #include "usModuleRegistry.h" #include QmitkUSNavigationStepPunctuationIntervention::QmitkUSNavigationStepPunctuationIntervention(QWidget *parent) : QmitkUSAbstractNavigationStep(parent), m_Ui(new Ui::QmitkUSNavigationStepPunctuationIntervention), m_ZoneNodes(nullptr), m_NeedleProjectionFilter(mitk::NeedleProjectionFilter::New()), m_NeedleNavigationTool(mitk::NavigationTool::New()), m_OldColors(), m_SphereSource(vtkSmartPointer::New()), m_OBBTree(vtkSmartPointer::New()), m_IntersectPoints(vtkSmartPointer::New()) { m_Ui->setupUi(this); connect(m_Ui->m_AddNewAblationZone, SIGNAL(clicked()), this, SLOT(OnAddAblationZoneClicked())); connect(m_Ui->m_ShowToolAxisN, SIGNAL(stateChanged(int)), this, SLOT(OnShowToolAxisEnabled(int))); connect(m_Ui->m_EnableAblationMarking, SIGNAL(clicked()), this, SLOT(OnEnableAblationZoneMarkingClicked())); connect(m_Ui->m_AblationZoneSizeSlider, SIGNAL(valueChanged(int)), this, SLOT(OnAblationZoneSizeSliderChanged(int))); m_Ui->m_AblationZonesBox->setVisible(false); } void QmitkUSNavigationStepPunctuationIntervention::SetNeedleMetaData(mitk::NavigationTool::Pointer needleNavigationTool) { this->m_NeedleNavigationTool = needleNavigationTool; } void QmitkUSNavigationStepPunctuationIntervention::OnEnableAblationZoneMarkingClicked() { if(m_Ui->m_EnableAblationMarking->isChecked()) m_Ui->m_AblationZonesBox->setVisible(true); else m_Ui->m_AblationZonesBox->setVisible(false); } void QmitkUSNavigationStepPunctuationIntervention::OnAblationZoneSizeSliderChanged(int size) { int id = m_Ui->m_AblationZonesList->currentRow(); if (id!=-1) {emit AblationZoneChanged(id,size);} }// void QmitkUSNavigationStepPunctuationIntervention::OnAddAblationZoneClicked() { QListWidgetItem* newItem = new QListWidgetItem("Ablation Zone (initial size: " + QString::number(m_Ui->m_AblationZoneSizeSlider->value()) + " mm)", m_Ui->m_AblationZonesList); newItem->setSelected(true); emit AddAblationZoneClicked(m_Ui->m_AblationZoneSizeSlider->value()); } QmitkUSNavigationStepPunctuationIntervention::~QmitkUSNavigationStepPunctuationIntervention() { mitk::DataStorage::Pointer dataStorage = this->GetDataStorage(false); if ( dataStorage.IsNotNull() ) { // remove needle path from data storage if it is there mitk::DataNode::Pointer node = this->GetNamedDerivedNode ("Needle Path", QmitkUSAbstractNavigationStep::DATANAME_BASENODE); if ( node.IsNotNull() ) { dataStorage->Remove(node); } } delete m_Ui; } bool QmitkUSNavigationStepPunctuationIntervention::OnStartStep() { // create node for Needle Projection mitk::DataNode::Pointer node = this->GetNamedDerivedNodeAndCreate ("Needle Path", QmitkUSAbstractNavigationStep::DATANAME_BASENODE); node->SetData(m_NeedleProjectionFilter->GetProjection()); node->SetBoolProperty("show contour", true); //m_NeedleProjectionFilter->SetToolAxisForFilter(m_NeedleNavigationTool->GetToolAxis()); return true; } bool QmitkUSNavigationStepPunctuationIntervention::OnRestartStep() { return this->OnActivateStep(); } bool QmitkUSNavigationStepPunctuationIntervention::OnFinishStep() { mitk::DataNode::Pointer finishPunctionResult = mitk::DataNode::New(); finishPunctionResult->SetName("PunctionResult"); mitk::Point3D needlePos = m_NeedleProjectionFilter->GetOutput(0)->GetPosition(); mitk::Quaternion needleRot = m_NeedleProjectionFilter->GetOutput(0)->GetOrientation(); finishPunctionResult->SetProperty("USNavigation::TipPositionEnd", mitk::Point3dProperty::New(needlePos)); MITK_INFO("USNavigationLogging") << "Instrument tip at end: " <ClearZones(); mitk::DataStorage::Pointer dataStorage = this->GetDataStorage(); // add progress bars for risk zone nodes m_ZoneNodes = dataStorage->GetDerivations(dataStorage->GetNamedNode(QmitkUSNavigationMarkerPlacement::DATANAME_ZONES)); // add zones to the widgets for risk structures for (mitk::DataStorage::SetOfObjects::ConstIterator it = m_ZoneNodes->Begin(); it != m_ZoneNodes->End(); ++it) { m_Ui->riskStructuresRangeWidget->AddZone(it->Value()); float rgb[3]; it->Value()->GetColor(rgb); mitk::Color color; color.SetRed(rgb[0]); color.SetGreen(rgb[1]); color.SetBlue(rgb[2]); m_OldColors[it->Value()] = color; } m_NeedleProjectionFilter->SelectInput(0); return true; } void QmitkUSNavigationStepPunctuationIntervention::OnShowToolAxisEnabled(int enabled) { if (enabled == 0) { m_NeedleProjectionFilter->ShowToolAxis(false); } else { m_NeedleProjectionFilter->ShowToolAxis(true); } } void QmitkUSNavigationStepPunctuationIntervention::OnUpdate() { if (this->GetCombinedModality(false).IsNull()) return; // get navigation data source and make sure that it is not null mitk::NavigationDataSource::Pointer navigationDataSource = this->GetCombinedModality()->GetNavigationDataSource(); if ( navigationDataSource.IsNull() ) { MITK_ERROR("QmitkUSAbstractNavigationStep")("QmitkUSNavigationStepPunctuationIntervention") << "Navigation Data Source of Combined Modality must not be null."; mitkThrow() << "Navigation Data Source of Combined Modality must not be null."; } // update body marker this->UpdateBodyMarkerStatus(navigationDataSource->GetOutput(1)); // update critical structures this->UpdateCriticalStructures(navigationDataSource->GetOutput(0),m_NeedleProjectionFilter->GetProjection()); m_NeedleProjectionFilter->Update(); //Update Distance to US image mitk::Point3D point1 = m_NeedleProjectionFilter->GetProjection()->GetPoint(0); mitk::Point3D point2 = m_NeedleProjectionFilter->GetProjection()->GetPoint(1); double distance = point1.EuclideanDistanceTo(point2); m_Ui->m_DistanceToUSPlane->setText(QString::number(distance) + " mm"); } void QmitkUSNavigationStepPunctuationIntervention::OnSettingsChanged(const itk::SmartPointer settingsNode) { if ( settingsNode.IsNull() ) { return; } } QString QmitkUSNavigationStepPunctuationIntervention::GetTitle() { return "Computer-assisted Intervention"; } bool QmitkUSNavigationStepPunctuationIntervention::GetIsRestartable() { return false; } QmitkUSNavigationStepPunctuationIntervention::FilterVector QmitkUSNavigationStepPunctuationIntervention::GetFilter() { return FilterVector(1, m_NeedleProjectionFilter.GetPointer()); } void QmitkUSNavigationStepPunctuationIntervention::OnSetCombinedModality() { mitk::AbstractUltrasoundTrackerDevice::Pointer combinedModality = this->GetCombinedModality(false); if ( combinedModality.IsNotNull() ) { m_NeedleProjectionFilter->ConnectTo(combinedModality->GetNavigationDataSource()); // set calibration of the combined modality to the needle projection filter mitk::AffineTransform3D::Pointer usPlaneTransform = combinedModality->GetUSPlaneTransform(); if (usPlaneTransform.IsNotNull()) { m_NeedleProjectionFilter->SetTargetPlane(usPlaneTransform); } } else { MITK_WARN << "CombinedModality is null!"; } } void QmitkUSNavigationStepPunctuationIntervention::ClearZones() { m_Ui->riskStructuresRangeWidget->ClearZones(); } void QmitkUSNavigationStepPunctuationIntervention::UpdateBodyMarkerStatus(mitk::NavigationData::Pointer bodyMarker) { if ( bodyMarker.IsNull() ) { MITK_ERROR("QmitkUSAbstractNavigationStep")("QmitkUSNavigationStepPunctuationIntervention") << "Current Navigation Data for body marker of Combined Modality must not be null."; mitkThrow() << "Current Navigation Data for body marker of Combined Modality must not be null."; } bool valid = bodyMarker->IsDataValid(); // update body marker status label if (valid) { m_Ui->bodyMarkerTrackingStatusLabel->setStyleSheet( "background-color: #8bff8b; margin-right: 1em; margin-left: 1em; border: 1px solid grey"); m_Ui->bodyMarkerTrackingStatusLabel->setText("Body marker is inside the tracking volume."); } else { m_Ui->bodyMarkerTrackingStatusLabel->setStyleSheet( "background-color: #ff7878; margin-right: 1em; margin-left: 1em; border: 1px solid grey"); m_Ui->bodyMarkerTrackingStatusLabel->setText("Body marker is not inside the tracking volume."); } m_Ui->riskStructuresRangeGroupBox->setEnabled(valid); } void QmitkUSNavigationStepPunctuationIntervention::UpdateCriticalStructures(mitk::NavigationData::Pointer needle, mitk::PointSet::Pointer path) { // update the distances for the risk structures widget m_Ui->riskStructuresRangeWidget->UpdateDistancesToNeedlePosition(needle); //iterate through all zones for (mitk::DataStorage::SetOfObjects::ConstIterator it = m_ZoneNodes->Begin(); it != m_ZoneNodes->End(); ++it) { mitk::DataNode::Pointer currentNode = it->Value(); //get center point and radius float radius = -1; mitk::Point3D center; currentNode->GetFloatProperty("zone.size", radius); - center = currentNode->GetData()->GetGeometry()->GetIndexToWorldTransform()->GetTranslation(); + center = mitk::Point3D(currentNode->GetData()->GetGeometry()->GetIndexToWorldTransform()->GetTranslation()); mitk::Point3D point0 = path->GetPoint(0); mitk::Point3D point1 = path->GetPoint(1); if (CheckSphereLineIntersection(center,radius,point0,point1)) {currentNode->SetColor(mitk::IGTColor_WARNING);} else {currentNode->SetColor(m_OldColors[currentNode]);} } } bool QmitkUSNavigationStepPunctuationIntervention::CheckSphereLineIntersection(mitk::Point3D& sphereOrigin, float& sphereRadius, mitk::Point3D& lineStart, mitk::Point3D& lineEnd) { double center[3] = {sphereOrigin[0],sphereOrigin[1],sphereOrigin[2]}; m_SphereSource->SetCenter(center); m_SphereSource->SetRadius(sphereRadius); m_SphereSource->Update(); m_OBBTree->SetDataSet(m_SphereSource->GetOutput()); m_OBBTree->BuildLocator(); double lineP0[3] = {lineStart[0], lineStart[1], lineStart[2]}; double lineP1[3] = {lineEnd[0], lineEnd[1], lineEnd[2]}; m_OBBTree->IntersectWithLine(lineP0, lineP1, m_IntersectPoints, nullptr); if (m_IntersectPoints->GetNumberOfPoints() > 0) {return true;} else {return false;} } diff --git a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkIGTNavigationToolCalibration.cpp b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkIGTNavigationToolCalibration.cpp index 9b73b74a67..74ac043b7c 100644 --- a/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkIGTNavigationToolCalibration.cpp +++ b/Plugins/org.mitk.gui.qt.igttracking/src/internal/QmitkIGTNavigationToolCalibration.cpp @@ -1,756 +1,756 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 // Blueberry #include #include // Qmitk #include "QmitkIGTNavigationToolCalibration.h" // mitk #include #include #include #include #include #include #include // Qt #include #include #include // vtk #include const std::string QmitkIGTNavigationToolCalibration::VIEW_ID = "org.mitk.views.igtnavigationtoolcalibration"; QmitkIGTNavigationToolCalibration::QmitkIGTNavigationToolCalibration() { m_ToolTransformationWidget = new QmitkInteractiveTransformationWidget(); } QmitkIGTNavigationToolCalibration::~QmitkIGTNavigationToolCalibration() { //The following code is required due to a bug in the point list widget. //If this is removed, MITK crashes when closing the view: m_Controls.m_RegistrationLandmarkWidget->SetPointSetNode(nullptr); m_Controls.m_CalibrationLandmarkWidget->SetPointSetNode(nullptr); //clean up data storage this->GetDataStorage()->Remove(m_ToolTipPointPreview); delete m_ToolTransformationWidget; } void QmitkIGTNavigationToolCalibration::SetFocus() { } void QmitkIGTNavigationToolCalibration::OnToolCalibrationMethodChanged(int index) { //if pivot calibration (3) or manual(0) is chosen only calibration pointer is needed if (index == 0 || index == 3) { if (!CheckInitialization(false)) { return; } } else{ if (!CheckInitialization()) { return; } } UpdateManualToolTipCalibrationView(); m_Controls.m_CalibrationMethodsWidget->setCurrentIndex(index); m_IndexCurrentCalibrationMethod = index; } void QmitkIGTNavigationToolCalibration::CreateQtPartControl(QWidget *parent) { m_TrackingTimer = new QTimer(this); // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); connect(m_Controls.m_SetToolToCalibrate, SIGNAL(clicked()), this, SLOT(SetToolToCalibrate())); connect(m_Controls.m_SetPointer, SIGNAL(clicked()), this, SLOT(SetCalibrationPointer())); connect(m_TrackingTimer, SIGNAL(timeout()), this, SLOT(UpdateTrackingTimer())); connect(m_Controls.m_AddLandmark, SIGNAL(clicked()), this, SLOT(AddLandmark())); connect(m_Controls.m_SaveCalibratedTool, SIGNAL(clicked()), this, SLOT(SaveCalibratedTool())); connect(m_Controls.m_AddPivotPose, SIGNAL(clicked()), this, SLOT(OnAddPivotPose())); connect(m_Controls.m_ComputePivot, SIGNAL(clicked()), this, SLOT(OnComputePivot())); connect(m_Controls.m_UseComputedPivotPoint, SIGNAL(clicked()), this, SLOT(OnUseComputedPivotPoint())); connect(m_Controls.m_StartEditTooltipManually, SIGNAL(clicked()), this, SLOT(OnStartManualToolTipCalibration())); connect(m_Controls.m_GetPositions, SIGNAL(clicked()), this, SLOT(OnGetPositions())); connect(m_Controls.m_ToolAxis_X, SIGNAL(valueChanged(double)), this, SLOT(OnToolAxisSpinboxChanged())); connect(m_Controls.m_ToolAxis_Y, SIGNAL(valueChanged(double)), this, SLOT(OnToolAxisSpinboxChanged())); connect(m_Controls.m_ToolAxis_Z, SIGNAL(valueChanged(double)), this, SLOT(OnToolAxisSpinboxChanged())); connect(m_Controls.m_CalibrateToolAxis, SIGNAL(clicked()), this, SLOT(OnCalibrateToolAxis())); connect((QObject*)(m_ToolTransformationWidget), SIGNAL(EditToolTipFinished(mitk::AffineTransform3D::Pointer)), this, SLOT(OnManualEditToolTipFinished(mitk::AffineTransform3D::Pointer))); connect(m_Controls.m_CalibrationMethodComboBox, SIGNAL(currentIndexChanged(int)), this, SLOT(OnToolCalibrationMethodChanged(int))); connect((QObject*)(m_Controls.m_RunCalibrationButton), SIGNAL(clicked()), (QObject*) this, SLOT(OnRunSingleRefToolCalibrationClicked())); connect((QObject*)(m_Controls.m_CollectNavigationDataButton), SIGNAL(clicked()), (QObject*) this, SLOT(OnLoginSingleRefToolNavigationDataClicked())); connect((QObject*)(m_Controls.m_SetNewToolTipPosButton), SIGNAL(clicked()), (QObject*) this, SLOT(OnSetNewToolTipPosButtonClicked())); m_IDToolToCalibrate = -1; m_IDCalibrationPointer = -1; m_IndexCurrentCalibrationMethod = -1; m_OnLoginSingleRefToolNavigationDataClicked = false; m_NumberOfNavigationDataCounter = 0; m_NumberOfNavigationData = -1; //for pivot calibration m_OnAddPivotPoseClicked = false; PivotCount = 0; m_PivotPoses = std::vector(); m_CalibrationLandmarks = mitk::PointSet::New(); m_CalibrationLandmarksNode = mitk::DataNode::New(); m_CalibrationLandmarksNode->SetData(m_CalibrationLandmarks); m_Controls.m_CalibrationLandmarkWidget->SetPointSetNode(m_CalibrationLandmarksNode); m_RegistrationLandmarks = mitk::PointSet::New(); m_RegistrationLandmarksNode = mitk::DataNode::New(); m_RegistrationLandmarksNode->SetData(m_RegistrationLandmarks); m_Controls.m_RegistrationLandmarkWidget->SetPointSetNode(m_RegistrationLandmarksNode); m_ToolSurfaceInToolCoordinatesDataNode = mitk::DataNode::New(); m_ToolSurfaceInToolCoordinatesDataNode->SetName("ToolSurface(ToolCoordinates)"); m_LoggedNavigationDataDifferences = std::vector< mitk::NavigationData::Pointer >(); } void QmitkIGTNavigationToolCalibration::OnRunSingleRefToolCalibrationClicked() { if (!CheckInitialization()) { return; } mitk::NavigationData::Pointer ToolTipTransform = mitk::NavigationData::New(); if (m_Controls.m_CalibratePosition->isChecked()) { //1: Compute mean translational offset vector m_ResultOffsetVector.Fill(0); for (std::vector::iterator vecIter = m_LoggedNavigationDataOffsets.begin(); vecIter != m_LoggedNavigationDataOffsets.end(); vecIter++) { m_ResultOffsetVector[0] = m_ResultOffsetVector[0] + (*vecIter)[0]; m_ResultOffsetVector[1] = m_ResultOffsetVector[1] + (*vecIter)[1]; m_ResultOffsetVector[2] = m_ResultOffsetVector[2] + (*vecIter)[2]; } m_ResultOffsetVector[0] = m_ResultOffsetVector[0] / m_LoggedNavigationDataOffsets.size(); m_ResultOffsetVector[1] = m_ResultOffsetVector[1] / m_LoggedNavigationDataOffsets.size(); m_ResultOffsetVector[2] = m_ResultOffsetVector[2] / m_LoggedNavigationDataOffsets.size(); this->m_Controls.m_ResultOfCalibration->setText( QString("x: ") + QString(QString::number(m_ResultOffsetVector[0], 103, 3)) + QString("; y: ") + (QString::number(m_ResultOffsetVector[1], 103, 3)) + QString("; z: ") + (QString::number(m_ResultOffsetVector[2], 103, 3))); ToolTipTransform->SetPosition(m_ResultOffsetVector); } if (m_Controls.m_CalibrateOrientation->isChecked()) { //2: Compute mean orientation mitk::Quaternion meanOrientation; std::vector allOrientations = std::vector (); for (std::size_t i = 0; i < m_LoggedNavigationDataDifferences.size(); i++) { allOrientations.push_back(m_LoggedNavigationDataDifferences.at(i)->GetOrientation()); } meanOrientation = mitk::QuaternionAveraging::CalcAverage(allOrientations); this->m_Controls.m_ResultOfCalibrationOrientation->setText( QString("qx: ") + QString(QString::number(meanOrientation.x(), 103, 3)) + QString("; qy: ") + (QString::number(meanOrientation.y(), 103, 3)) + QString("; qz: ") + (QString::number(meanOrientation.z(), 103, 3)) + QString("; qr: ") + (QString::number(meanOrientation.r(), 103, 3))); ToolTipTransform->SetOrientation(meanOrientation); } MITK_INFO << "Computed calibration: "; MITK_INFO << "Translation Vector: " << ToolTipTransform->GetPosition(); MITK_INFO << "Quaternion: (" << ToolTipTransform->GetOrientation() << ")"; MITK_INFO << "Euler Angles [rad]: (" << ToolTipTransform->GetOrientation().rotation_euler_angles() << ")"; MITK_INFO << "Matrix:"; vnl_matrix_fixed rotMatrix = ToolTipTransform->GetOrientation().rotation_matrix_transpose(); MITK_INFO << rotMatrix[0][0] << " " << rotMatrix[0][1] << " " << rotMatrix[0][2] << std::endl; MITK_INFO << rotMatrix[1][0] << " " << rotMatrix[1][1] << " " << rotMatrix[1][2] << std::endl; MITK_INFO << rotMatrix[2][0] << " " << rotMatrix[2][1] << " " << rotMatrix[2][2] << std::endl; //3: write everything into the final tool tip transform and save it as member (it will be written to the tool later on) mitk::NavigationData::Pointer ToolTipInTrackingCoordinates = mitk::NavigationData::New(); ToolTipInTrackingCoordinates->Compose(ToolTipTransform); ToolTipInTrackingCoordinates->Compose(m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate)); ShowToolTipPreview(ToolTipInTrackingCoordinates); m_Controls.m_SetNewToolTipPosButton->setEnabled(true); m_ComputedToolTipTransformation = ToolTipTransform; } void QmitkIGTNavigationToolCalibration::OnLoginSingleRefToolNavigationDataClicked() { if (!CheckInitialization()) { return; } //reset old data m_LoggedNavigationDataOffsets.clear(); m_LoggedNavigationDataDifferences.clear(); m_OnLoginSingleRefToolNavigationDataClicked = true; m_Controls.m_CollectNavigationDataButton->setEnabled(false); m_NumberOfNavigationData = m_Controls.m_NumberOfNavigationDataToCollect->value(); MITK_INFO << "Collecting " << m_NumberOfNavigationData << " NavigationData ... " << endl; } void QmitkIGTNavigationToolCalibration::LoginSingleRefToolNavigationData() { if (!CheckInitialization()) { return; } if (m_NumberOfNavigationDataCounter < m_NumberOfNavigationData) { //update label text QString labelText = "Collecting Data: " + QString::number(m_NumberOfNavigationDataCounter); m_Controls.m_CollectionStatus->setText(labelText); mitk::NavigationData::Pointer referenceTool = m_NavigationDataSourceOfCalibrationPointer->GetOutput(m_IDCalibrationPointer); mitk::NavigationData::Pointer toolToCalibrate = m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate); //compute difference: // differenceND = toolToCalibrate^-1 * referenceTool mitk::NavigationData::Pointer differenceND = mitk::NavigationData::New(); differenceND->Compose(referenceTool); differenceND->Compose(toolToCalibrate->GetInverse()); //inverse mode... if (m_Controls.m_InvertQuaternions->isChecked()) { // negate identity matrix to directly show parameters that will set up in NDI 6D Software Architect differenceND = differenceND->GetInverse(); } //save difference in member m_LoggedNavigationDataOffsets.push_back(differenceND->GetPosition()); m_LoggedNavigationDataDifferences.push_back(differenceND); m_NumberOfNavigationDataCounter++; } if (m_NumberOfNavigationDataCounter == m_NumberOfNavigationData) { m_NumberOfNavigationDataCounter = 0; m_OnLoginSingleRefToolNavigationDataClicked = false; m_Controls.m_CollectNavigationDataButton->setEnabled(true); m_Controls.m_RunCalibrationButton->setEnabled(true); MITK_INFO << "Collecting " << m_NumberOfNavigationData << " NavigationData ... Finished" << endl; QString labelText = "Collected " + QString::number(m_NumberOfNavigationData) + " data samples!"; m_Controls.m_CollectionStatus->setText(labelText); } } void QmitkIGTNavigationToolCalibration::OnSetNewToolTipPosButtonClicked() { ApplyToolTipTransform(m_ComputedToolTipTransformation); RemoveToolTipPreview(); } void QmitkIGTNavigationToolCalibration::ClearOldPivot() { mitk::NavigationData::Pointer tempND = mitk::NavigationData::New(); this->ApplyToolTipTransform(tempND); UpdateManualToolTipCalibrationView(); //m_ManualToolTipEditWidget->hide(); //TODO this->GetDataStorage()->Remove(m_ToolSurfaceInToolCoordinatesDataNode); } void QmitkIGTNavigationToolCalibration::OnAddPivotPose() { ClearOldPivot(); //When the collect Poses Button is Clicked m_OnAddPivotPoseClicked = true; m_NumberOfNavigationData = m_Controls.m_PosesToCollect->value(); } void QmitkIGTNavigationToolCalibration::AddPivotPose() { //Save the poses to be used in computation if (PivotCount < m_NumberOfNavigationData) { mitk::NavigationData::Pointer currentPose = mitk::NavigationData::New(); currentPose->Graft(m_Controls.m_SelectionWidget->GetSelectedNavigationDataSource()->GetOutput(m_IDToolToCalibrate)); m_PivotPoses.push_back(currentPose); m_Controls.m_PoseNumber->setText(QString::number(m_PivotPoses.size())); PivotCount++; } if (PivotCount == m_NumberOfNavigationData) { m_OnAddPivotPoseClicked = false; } } void QmitkIGTNavigationToolCalibration::OnComputePivot() { mitk::PivotCalibration::Pointer myPivotCalibration = mitk::PivotCalibration::New(); for (std::size_t i = 0; i < this->m_PivotPoses.size(); i++) { myPivotCalibration->AddNavigationData(m_PivotPoses.at(i)); } QString resultString; if (myPivotCalibration->ComputePivotResult()) { mitk::NavigationData::Pointer markerTransformationTrackingCoordinates = m_PivotPoses.at(0); //Get computed pivot transfromation in tool coordinates mitk::NavigationData::Pointer ToolTipToTool = mitk::NavigationData::New(); ToolTipToTool->SetPosition(myPivotCalibration->GetResultPivotPoint()); ToolTipToTool->SetOrientation(mitk::Quaternion(0,0,0,1)); mitk::NavigationData::Pointer TrackerToTool = mitk::NavigationData::New(); TrackerToTool->SetOrientation(markerTransformationTrackingCoordinates->GetOrientation()); TrackerToTool->SetPosition(markerTransformationTrackingCoordinates->GetPosition()); TrackerToTool->Compose(ToolTipToTool); // Compute pivot point in relation to marker transformation for preview mitk::NavigationData::Pointer ToolTipToTracker = mitk::NavigationData::New(); ToolTipToTracker->Compose(ToolTipToTool); ToolTipToTracker->Compose(markerTransformationTrackingCoordinates); //add the preview node to the data storage ShowToolTipPreview(ToolTipToTracker); //parse result string resultString = QString("Pivot computation succeeded!\n") + QString("RMS Error: ") + QString::number(myPivotCalibration->GetResultRMSError()) + QString("\n") + QString("Pivot Point: ") + QString::number(myPivotCalibration->GetResultPivotPoint()[0]) + ";" + QString::number(myPivotCalibration->GetResultPivotPoint()[1]) + ";" + QString::number(myPivotCalibration->GetResultPivotPoint()[2]) + QString("\n"); //finally: save results to member variable m_ComputedToolTipTransformation = ToolTipToTool; //enable button to use the computed point with the tool m_Controls.m_UseComputedPivotPoint->setEnabled(true); } else { resultString = "Pivot computation failed!"; } MITK_INFO << resultString.toStdString().c_str(); m_Controls.m_ResultText->setText(resultString); } void QmitkIGTNavigationToolCalibration::UpdatePivotCount() { PivotCount = 0; while (!m_PivotPoses.empty()) { m_PivotPoses.pop_back(); } m_Controls.m_PoseNumber->setText(QString::number(PivotCount)); } void QmitkIGTNavigationToolCalibration::OnUseComputedPivotPoint() { RemoveToolTipPreview(); QString resultString = QString("Pivoted tool tip transformation was written to the tool ") + m_ToolToCalibrate->GetToolName().c_str(); ApplyToolTipTransform(m_ComputedToolTipTransformation, resultString.toStdString()); m_Controls.m_ResultText->setText(resultString); UpdatePivotCount(); } void QmitkIGTNavigationToolCalibration::ApplyToolTipTransform(mitk::NavigationData::Pointer ToolTipTransformInToolCoordinates, std::string message) { if (!CheckInitialization(false)) { return; } //Update tool in tool storage m_ToolToCalibrate->SetToolTipPosition(ToolTipTransformInToolCoordinates->GetPosition()); m_ToolToCalibrate->SetToolAxisOrientation(ToolTipTransformInToolCoordinates->GetOrientation()); //And also update tracking device, so the transform is directly used mitk::TrackingDeviceSource::Pointer trackingDeviceSource; try { trackingDeviceSource = dynamic_cast(m_NavigationDataSourceOfToolToCalibrate.GetPointer()); mitk::TrackingTool::Pointer TrackingToolToCalibrate = trackingDeviceSource->GetTrackingDevice()->GetTool(m_IDToolToCalibrate); TrackingToolToCalibrate->SetToolTipPosition(ToolTipTransformInToolCoordinates->GetPosition(), ToolTipTransformInToolCoordinates->GetOrientation()); } catch (std::exception& e) { MITK_ERROR << "Error while trying to set the tool tip to the running tracking device. Aborting! (" << e.what() << ")"; } MITK_INFO << message; } void QmitkIGTNavigationToolCalibration::ShowToolTipPreview(mitk::NavigationData::Pointer ToolTipInTrackingCoordinates) { if(m_ToolTipPointPreview.IsNull()) { m_ToolTipPointPreview = mitk::DataNode::New(); m_ToolTipPointPreview->SetName("Modified Tool Tip Preview"); mitk::Color blue; blue.SetBlue(1); m_ToolTipPointPreview->SetColor(blue); mitk::Surface::Pointer mySphere = mitk::Surface::New(); vtkSmartPointer vtkData = vtkSmartPointer::New(); vtkData->SetRadius(3.0f); vtkData->SetCenter(0.0, 0.0, 0.0); vtkData->Update(); mySphere->SetVtkPolyData(vtkData->GetOutput()); m_ToolTipPointPreview->SetData(mySphere); this->GetDataStorage()->Add(m_ToolTipPointPreview); } m_ToolTipPointPreview->GetData()->GetGeometry()->SetIndexToWorldTransform(ToolTipInTrackingCoordinates->GetAffineTransform3D()); } void QmitkIGTNavigationToolCalibration::RemoveToolTipPreview() { this->GetDataStorage()->Remove(m_ToolTipPointPreview.GetPointer()); } void QmitkIGTNavigationToolCalibration::UpdateManualToolTipCalibrationView() { if (m_ToolToCalibrate.IsNull()) { return; } //parse human readable transformation data and display it std::stringstream translation; std::stringstream orientation; translation << m_ToolToCalibrate->GetToolTipPosition(); orientation << "Quaternion: (" << m_ToolToCalibrate->GetToolAxisOrientation() << ")" << std::endl; orientation << std::endl; orientation << "Euler Angles [rad]: (" << m_ToolToCalibrate->GetToolAxisOrientation().rotation_euler_angles() << ")" << std::endl; orientation << std::endl; orientation << "Matrix:" << std::endl; vnl_matrix_fixed rotMatrix = m_ToolToCalibrate->GetToolAxisOrientation().rotation_matrix_transpose(); orientation << rotMatrix[0][0] << " " << rotMatrix[0][1] << " " << rotMatrix[0][2] << std::endl; orientation << rotMatrix[1][0] << " " << rotMatrix[1][1] << " " << rotMatrix[1][2] << std::endl; orientation << rotMatrix[2][0] << " " << rotMatrix[2][1] << " " << rotMatrix[2][2] << std::endl; m_Controls.m_ManualCurrentTranslation->setText(translation.str().c_str()); m_Controls.m_ManualCurrentOrientation->setPlainText(orientation.str().c_str()); } void QmitkIGTNavigationToolCalibration::OnStartManualToolTipCalibration() { if (!CheckInitialization(false)) { return; } m_ToolTransformationWidget->SetToolToEdit(m_ToolToCalibrate); m_ToolTransformationWidget->SetDefaultOffset(m_ToolToCalibrate->GetToolTipPosition()); m_ToolTransformationWidget->SetDefaultRotation(m_ToolToCalibrate->GetToolAxisOrientation()); m_ToolTransformationWidget->open(); } void QmitkIGTNavigationToolCalibration::OnManualEditToolTipFinished(mitk::AffineTransform3D::Pointer toolTip) { //This function is called, when the toolTipEdit view is closed. //if user pressed cancle, nullptr is returned. Do nothing. Else, set values. if (toolTip) { mitk::NavigationData::Pointer tempND = mitk::NavigationData::New(toolTip);//Convert to Navigation data for simple transversion to quaternion QString resultString = QString("Manual edited values are written to ") + m_ToolToCalibrate->GetToolName().c_str(); ApplyToolTipTransform(tempND, resultString.toStdString()); m_Controls.m_ResultText->setText(resultString); m_ComputedToolTipTransformation = tempND; } UpdateManualToolTipCalibrationView(); } void QmitkIGTNavigationToolCalibration::OnGetPositions() { if (!CheckInitialization(true)) { return; } //Navigation Data from Tool which should be calibrated if (!m_AxisCalibration_ToolToCalibrate) m_AxisCalibration_ToolToCalibrate = mitk::NavigationData::New(); m_AxisCalibration_ToolToCalibrate->Graft(m_Controls.m_SelectionWidget->GetSelectedNavigationDataSource()->GetOutput(m_IDToolToCalibrate)); //Navigation Data from calibration pointer tool if (!m_AxisCalibration_NavDataCalibratingTool) m_AxisCalibration_NavDataCalibratingTool = mitk::NavigationData::New(); m_AxisCalibration_NavDataCalibratingTool->Graft(m_Controls.m_SelectionWidget->GetSelectedNavigationDataSource()->GetOutput(m_IDCalibrationPointer)); MITK_DEBUG << "Positions for tool axis calibration:"; MITK_DEBUG << " ToolTip: " << m_AxisCalibration_ToolToCalibrate->GetPosition() << ","; MITK_DEBUG << " Rotation: \n" << m_AxisCalibration_ToolToCalibrate->GetRotationMatrix(); MITK_DEBUG << " End of the tool: " << m_AxisCalibration_NavDataCalibratingTool->GetPosition(); QString _label = "Position recorded: " + QString::number(m_AxisCalibration_NavDataCalibratingTool->GetPosition()[0], 'f', 1) + ", " + QString::number(m_AxisCalibration_NavDataCalibratingTool->GetPosition()[1], 'f', 1) + ", " + QString::number(m_AxisCalibration_NavDataCalibratingTool->GetPosition()[2], 'f', 1); m_Controls.m_ToolAxisPositionLabel->setText(_label); } void QmitkIGTNavigationToolCalibration::OnCalibrateToolAxis() { if (!m_ComputedToolTipTransformation) { MITK_ERROR << "Please compute tool tip first."; QMessageBox::information(nullptr, "Error", "Please compute / specifiy tool tip first"); return; } if (!m_AxisCalibration_ToolToCalibrate || !m_AxisCalibration_NavDataCalibratingTool) { MITK_ERROR << "Please record position first."; QMessageBox::information(nullptr, "Error", "Please record position first"); return; } //Calculate the tool tip //here is an explanation, what is happening here: /* The axis is equal to the (tool tip) minus the (end of the tool) in tool coordinates of the tool which should be calibrated. The tool tip is defined as the origin of the tool coordinate system. The end of the tool is recorded by the calibration pointer's position and is transformed into the coordinate system of the tool to be calibrated Normalize it. */ //m_CalibratedToolAxis = -m_AxisCalibration_ToolToCalibrate->TransformPoint(m_AxisCalibration_NavDataCalibratingTool->GetPosition()).GetVectorFromOrigin(); m_CalibratedToolAxis = -m_AxisCalibration_ToolToCalibrate->GetInverse()->TransformPoint(m_AxisCalibration_NavDataCalibratingTool->GetPosition()).GetVectorFromOrigin(); MITK_DEBUG << "Tool Endpoint in Tool coordinates: " << m_CalibratedToolAxis; m_CalibratedToolAxis.Normalize(); MITK_DEBUG << "Tool Axis: " << m_CalibratedToolAxis; - m_ToolToCalibrate->SetToolAxis(m_CalibratedToolAxis); + m_ToolToCalibrate->SetToolAxis(mitk::Point3D(m_CalibratedToolAxis)); // Update TrackingTool m_ComputedToolTipTransformation->SetPosition(m_ToolToCalibrate->GetToolTipPosition()); m_ComputedToolTipTransformation->SetOrientation(m_ToolToCalibrate->GetToolAxisOrientation()); ApplyToolTipTransform(m_ComputedToolTipTransformation); //Update GUI QString calibratedToolAxisString = "Tool Axis: " + QString::number(m_CalibratedToolAxis.GetElement(0), 'f', 3) + ", " + QString::number(m_CalibratedToolAxis.GetElement(1), 'f', 3) + ", " + QString::number(m_CalibratedToolAxis.GetElement(2), 'f', 3); m_Controls.m_ToolAxisCalibrationLabel->setText(calibratedToolAxisString); //Block QT signals, we don't want to emit SpinboxChanged on the first value to overwrite the next ones m_Controls.m_ToolAxis_X->blockSignals(true); m_Controls.m_ToolAxis_Y->blockSignals(true); m_Controls.m_ToolAxis_Z->blockSignals(true); m_Controls.m_ToolAxis_X->setValue(m_CalibratedToolAxis[0]); m_Controls.m_ToolAxis_Y->setValue(m_CalibratedToolAxis[1]); m_Controls.m_ToolAxis_Z->setValue(m_CalibratedToolAxis[2]); m_Controls.m_ToolAxis_X->blockSignals(false); m_Controls.m_ToolAxis_Y->blockSignals(false); m_Controls.m_ToolAxis_Z->blockSignals(false); } void QmitkIGTNavigationToolCalibration::OnToolAxisSpinboxChanged() { m_CalibratedToolAxis.SetElement(0, m_Controls.m_ToolAxis_X->value()); m_CalibratedToolAxis.SetElement(1, m_Controls.m_ToolAxis_Y->value()); m_CalibratedToolAxis.SetElement(2, m_Controls.m_ToolAxis_Z->value()); - m_ToolToCalibrate->SetToolAxis(m_CalibratedToolAxis); + m_ToolToCalibrate->SetToolAxis(mitk::Point3D(m_CalibratedToolAxis)); // Update TrackingTool if (m_ComputedToolTipTransformation.IsNull()) { m_ComputedToolTipTransformation = mitk::NavigationData::New(); } m_ComputedToolTipTransformation->SetPosition(m_ToolToCalibrate->GetToolTipPosition()); m_ComputedToolTipTransformation->SetOrientation(m_ToolToCalibrate->GetToolAxisOrientation()); ApplyToolTipTransform(m_ComputedToolTipTransformation); MITK_INFO << "Tool axis changed to " << m_CalibratedToolAxis; } void QmitkIGTNavigationToolCalibration::SetToolToCalibrate() { m_IDToolToCalibrate = m_Controls.m_SelectionWidget->GetSelectedToolID(); if (m_IDToolToCalibrate == -1) //no valid tool to calibrate { m_Controls.m_CalToolLabel->setText(""); m_Controls.m_StatusWidgetToolToCalibrate->RemoveStatusLabels(); m_TrackingTimer->stop(); } else { m_ToolToCalibrate = m_Controls.m_SelectionWidget->GetSelectedNavigationTool(); m_NavigationDataSourceOfToolToCalibrate = m_Controls.m_SelectionWidget->GetSelectedNavigationDataSource(); m_Controls.m_CalToolLabel->setText(m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate)->GetName()); //initialize widget m_Controls.m_StatusWidgetToolToCalibrate->RemoveStatusLabels(); m_Controls.m_StatusWidgetToolToCalibrate->SetShowPositions(true); m_Controls.m_StatusWidgetToolToCalibrate->SetTextAlignment(Qt::AlignLeft); m_Controls.m_StatusWidgetToolToCalibrate->AddNavigationData(m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate)); m_Controls.m_StatusWidgetToolToCalibrate->ShowStatusLabels(); //initialize manual tool tip calibration view UpdateManualToolTipCalibrationView(); //save tool surface in tool coordinates for further editing mitk::Surface::Pointer ToolSurface = dynamic_cast(m_ToolToCalibrate->GetDataNode()->GetData())->Clone(); m_ToolSurfaceInToolCoordinatesDataNode->SetData(ToolSurface); m_ToolSurfaceInToolCoordinatesDataNode->GetData()->GetGeometry()->SetIdentity(); // update tool tip and rotation information for tool tip calibration tab UpdateManualToolTipCalibrationView(); // update tool axis information for tool axis calibration tab mitk::Point3D toolAxis = m_ToolToCalibrate->GetToolAxis(); m_CalibratedToolAxis[0] = toolAxis[0]; m_CalibratedToolAxis[1] = toolAxis[1]; m_CalibratedToolAxis[2] = toolAxis[2]; m_Controls.m_ToolAxis_X->blockSignals(true); m_Controls.m_ToolAxis_Y->blockSignals(true); m_Controls.m_ToolAxis_Z->blockSignals(true); m_Controls.m_ToolAxis_X->setValue(m_CalibratedToolAxis[0]); m_Controls.m_ToolAxis_Y->setValue(m_CalibratedToolAxis[1]); m_Controls.m_ToolAxis_Z->setValue(m_CalibratedToolAxis[2]); m_Controls.m_ToolAxis_X->blockSignals(false); m_Controls.m_ToolAxis_Y->blockSignals(false); m_Controls.m_ToolAxis_Z->blockSignals(false); //start updating timer for status widgets, etc. if (!m_TrackingTimer->isActive()) m_TrackingTimer->start(100); } } void QmitkIGTNavigationToolCalibration::SetCalibrationPointer() { m_IDCalibrationPointer = m_Controls.m_SelectionWidget->GetSelectedToolID(); if (m_IDCalibrationPointer == -1) { m_Controls.m_PointerLabel->setText(""); m_Controls.m_StatusWidgetCalibrationPointer->RemoveStatusLabels(); m_TrackingTimer->stop(); } else { m_NavigationDataSourceOfCalibrationPointer = m_Controls.m_SelectionWidget->GetSelectedNavigationDataSource(); m_Controls.m_PointerLabel->setText(m_NavigationDataSourceOfCalibrationPointer->GetOutput(m_IDCalibrationPointer)->GetName()); //initialize widget m_Controls.m_StatusWidgetCalibrationPointer->RemoveStatusLabels(); m_Controls.m_StatusWidgetCalibrationPointer->SetShowPositions(true); m_Controls.m_StatusWidgetCalibrationPointer->SetTextAlignment(Qt::AlignLeft); m_Controls.m_StatusWidgetCalibrationPointer->AddNavigationData(m_NavigationDataSourceOfCalibrationPointer->GetOutput(m_IDCalibrationPointer)); m_Controls.m_StatusWidgetCalibrationPointer->ShowStatusLabels(); if (!m_TrackingTimer->isActive()) m_TrackingTimer->start(100); } } void QmitkIGTNavigationToolCalibration::UpdateOffsetCoordinates() { if (m_NavigationDataSourceOfCalibrationPointer.IsNull() || m_NavigationDataSourceOfToolToCalibrate.IsNull()) { return; } mitk::NavigationData::Pointer referenceToolND = m_NavigationDataSourceOfCalibrationPointer->GetOutput(m_IDCalibrationPointer); mitk::NavigationData::Pointer toolToCalibrateND = m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate); if (referenceToolND->IsDataValid() && toolToCalibrateND->IsDataValid()) { //computation: difference between both tools (in tool coordinates) //differenceND = toolToCalibrateND^-1 * referenceToolND mitk::NavigationData::Pointer differenceND = mitk::NavigationData::New(); differenceND->Compose(referenceToolND); differenceND->Compose(toolToCalibrateND->GetInverse()); //display this orientation in the UI m_Controls.m_OffsetCoordinates->setText( QString("x: ") + QString(QString::number(differenceND->GetPosition()[0], 103, 3)) + QString("; y: ") + (QString::number(differenceND->GetPosition()[1], 103, 3)) + QString("; z: ") + (QString::number(differenceND->GetPosition()[2], 103, 3))); m_Controls.m_OrientationOffsetCoordinates->setText( QString("qx: ") + QString(QString::number(differenceND->GetOrientation().x(), 103, 3)) + QString("; qy: ") + (QString::number(differenceND->GetOrientation().y(), 103, 3)) + QString("; qz: ") + (QString::number(differenceND->GetOrientation().z(), 103, 3)) + QString("; qr: ") + (QString::number(differenceND->GetOrientation().r(), 103, 3))); //also update preview if active if (m_ToolTipPointPreview.IsNotNull()) //NOT WORKING! TODO: fix or remove! { mitk::NavigationData::Pointer ToolTipTransform = mitk::NavigationData::New(); ToolTipTransform->SetPosition(m_ResultOffsetVector); mitk::NavigationData::Pointer ToolTipInTrackingCoordinates = mitk::NavigationData::New(); //maybe store as for better peformance... ToolTipInTrackingCoordinates->Compose(m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate)); ToolTipInTrackingCoordinates->Compose(ToolTipTransform); m_ToolTipPointPreview->GetData()->GetGeometry()->SetIndexToWorldTransform(ToolTipInTrackingCoordinates->GetAffineTransform3D()); } } } void QmitkIGTNavigationToolCalibration::UpdateTrackingTimer() { m_Controls.m_StatusWidgetToolToCalibrate->Refresh(); m_Controls.m_StatusWidgetCalibrationPointer->Refresh(); if (m_OnLoginSingleRefToolNavigationDataClicked) LoginSingleRefToolNavigationData(); if (m_OnAddPivotPoseClicked) AddPivotPose(); // 1 == Single Reference Calibration Method if (m_IndexCurrentCalibrationMethod == 1) UpdateOffsetCoordinates(); } void QmitkIGTNavigationToolCalibration::AddLandmark() { if (!CheckInitialization()) { return; } mitk::NavigationData::Pointer navDataTool = m_NavigationDataSourceOfToolToCalibrate->GetOutput(m_IDToolToCalibrate); mitk::Point3D landmark = m_NavigationDataSourceOfCalibrationPointer->GetOutput(m_IDCalibrationPointer)->GetPosition(); //convert to itk transform itk::Vector translation; for (int k = 0; k < 3; k++) translation[k] = navDataTool->GetPosition()[k]; itk::Matrix rotation; for (int k = 0; k < 3; k++) for (int l = 0; l < 3; l++) rotation[k][l] = navDataTool->GetOrientation().rotation_matrix_transpose()[k][l]; rotation = rotation.GetTranspose(); itk::Vector landmarkItk; landmarkItk[0] = landmark[0]; landmarkItk[1] = landmark[1]; landmarkItk[2] = landmark[2]; //compute landmark in tool coordinates itk::Matrix rotationInverse; for (int k = 0; k < 3; k++) for (int l = 0; l < 3; l++) rotationInverse[k][l] = rotation.GetInverse()[k][l]; landmarkItk = rotationInverse * (landmarkItk - translation); //convert back and add landmark to pointset landmark[0] = landmarkItk[0]; landmark[1] = landmarkItk[1]; landmark[2] = landmarkItk[2]; m_RegistrationLandmarks->InsertPoint(m_RegistrationLandmarks->GetSize(), landmark); } void QmitkIGTNavigationToolCalibration::SaveCalibratedTool() { if (m_ToolToCalibrate.IsNotNull()) { mitk::NavigationTool::Pointer calibratedTool = m_ToolToCalibrate; calibratedTool->SetToolControlPoints(this->m_CalibrationLandmarks); calibratedTool->SetToolLandmarks(this->m_RegistrationLandmarks); mitk::NavigationToolWriter::Pointer myWriter = mitk::NavigationToolWriter::New(); QString filename = QFileDialog::getSaveFileName(nullptr,tr("Save Navigation Tool"), "/", "*.IGTTool"); if (filename.isEmpty()) return; // ensure that file suffix is set QFileInfo file(filename); if (file.suffix().isEmpty()) { filename += ".IGTTool"; } if (myWriter->DoWrite(filename.toStdString(), calibratedTool)) MITK_INFO << "Saved calibrated tool to file " << filename; else MITK_WARN << "Can't write tool to file " << filename; } else { MITK_ERROR << "Did not find navigation tool storage of calibrated tool, aborting!"; } } bool QmitkIGTNavigationToolCalibration::CheckInitialization(bool CalibrationPointerRequired) { if ((m_IDToolToCalibrate == -1) || ((CalibrationPointerRequired) && (m_IDCalibrationPointer == -1) ) ) { QMessageBox msgBox; msgBox.setText("Tool to calibrate and/or calibration pointer not initialized, cannot proceed!"); msgBox.exec(); return false; } else { return true; } } diff --git a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropperView.cpp b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropperView.cpp index 3594ac014f..bab702db82 100644 --- a/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropperView.cpp +++ b/Plugins/org.mitk.gui.qt.imagecropper/src/internal/QmitkImageCropperView.cpp @@ -1,496 +1,506 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkImageCropperView.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include const std::string QmitkImageCropperView::VIEW_ID = "org.mitk.views.qmitkimagecropper"; QmitkImageCropperView::QmitkImageCropperView(QObject *) : m_ParentWidget(nullptr) , m_BoundingShapeInteractor(nullptr) , m_CropOutsideValue(0) { CreateBoundingShapeInteractor(false); } QmitkImageCropperView::~QmitkImageCropperView() { //disable interactor if (m_BoundingShapeInteractor != nullptr) { m_BoundingShapeInteractor->SetDataNode(nullptr); m_BoundingShapeInteractor->EnableInteraction(false); } } void QmitkImageCropperView::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Controls.imageSelectionWidget->SetDataStorage(GetDataStorage()); m_Controls.imageSelectionWidget->SetNodePredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); m_Controls.imageSelectionWidget->SetSelectionIsOptional(true); m_Controls.imageSelectionWidget->SetAutoSelectNewNodes(true); m_Controls.imageSelectionWidget->SetEmptyInfo(QString("Please select an image node")); m_Controls.imageSelectionWidget->SetPopUpTitel(QString("Select image node")); connect(m_Controls.imageSelectionWidget, &QmitkSingleNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkImageCropperView::OnImageSelectionChanged); m_Controls.boundingBoxSelectionWidget->SetDataStorage(GetDataStorage()); m_Controls.boundingBoxSelectionWidget->SetNodePredicate(mitk::NodePredicateAnd::New( mitk::TNodePredicateDataType::New(), mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")))); m_Controls.boundingBoxSelectionWidget->SetSelectionIsOptional(true); m_Controls.boundingBoxSelectionWidget->SetAutoSelectNewNodes(true); m_Controls.boundingBoxSelectionWidget->SetEmptyInfo(QString("Please select a bounding box")); m_Controls.boundingBoxSelectionWidget->SetPopUpTitel(QString("Select bounding box node")); connect(m_Controls.boundingBoxSelectionWidget, &QmitkSingleNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkImageCropperView::OnBoundingBoxSelectionChanged); connect(m_Controls.buttonCreateNewBoundingBox, SIGNAL(clicked()), this, SLOT(OnCreateNewBoundingBox())); connect(m_Controls.buttonCropping, SIGNAL(clicked()), this, SLOT(OnCropping())); connect(m_Controls.buttonMasking, SIGNAL(clicked()), this, SLOT(OnMasking())); auto lambda = [this]() { m_Controls.groupImageSettings->setVisible(!m_Controls.groupImageSettings->isVisible()); }; connect(m_Controls.buttonAdvancedSettings, &ctkExpandButton::clicked, this, lambda); connect(m_Controls.spinBoxOutsidePixelValue, SIGNAL(valueChanged(int)), this, SLOT(OnSliderValueChanged(int))); SetDefaultGUI(); m_ParentWidget = parent; + + this->OnImageSelectionChanged(m_Controls.imageSelectionWidget->GetSelectedNodes()); + this->OnBoundingBoxSelectionChanged(m_Controls.boundingBoxSelectionWidget->GetSelectedNodes()); } void QmitkImageCropperView::OnImageSelectionChanged(QList) { bool rotationEnabled = false; auto imageNode = m_Controls.imageSelectionWidget->GetSelectedNode(); if (imageNode.IsNull()) { SetDefaultGUI(); return; } auto image = dynamic_cast(imageNode->GetData()); if (nullptr != image) { if (image->GetDimension() < 3) { QMessageBox::warning(nullptr, tr("Invalid image selected"), tr("ImageCropper only works with 3 or more dimensions."), QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); SetDefaultGUI(); return; } m_ParentWidget->setEnabled(true); m_Controls.buttonCreateNewBoundingBox->setEnabled(true); vtkSmartPointer imageMat = image->GetGeometry()->GetVtkMatrix(); // check whether the image geometry is rotated; if so, no pixel aligned cropping or masking can be performed if ((imageMat->GetElement(1, 0) == 0.0) && (imageMat->GetElement(0, 1) == 0.0) && (imageMat->GetElement(1, 2) == 0.0) && (imageMat->GetElement(2, 1) == 0.0) && (imageMat->GetElement(2, 0) == 0.0) && (imageMat->GetElement(0, 2) == 0.0)) { rotationEnabled = false; m_Controls.labelWarningRotation->setVisible(false); } else { rotationEnabled = true; m_Controls.labelWarningRotation->setStyleSheet(" QLabel { color: rgb(255, 0, 0) }"); m_Controls.labelWarningRotation->setVisible(true); } this->CreateBoundingShapeInteractor(rotationEnabled); if (itk::ImageIOBase::SCALAR == image->GetPixelType().GetPixelType()) { // Might be changed with the upcoming new image statistics plugin //(recomputation might be very expensive for large images ;) ) auto statistics = image->GetStatistics(); auto minPixelValue = statistics->GetScalarValueMin(); auto maxPixelValue = statistics->GetScalarValueMax(); if (minPixelValue < std::numeric_limits::min()) { minPixelValue = std::numeric_limits::min(); } if (maxPixelValue > std::numeric_limits::max()) { maxPixelValue = std::numeric_limits::max(); } m_Controls.spinBoxOutsidePixelValue->setEnabled(true); m_Controls.spinBoxOutsidePixelValue->setMaximum(static_cast(maxPixelValue)); m_Controls.spinBoxOutsidePixelValue->setMinimum(static_cast(minPixelValue)); m_Controls.spinBoxOutsidePixelValue->setValue(static_cast(minPixelValue)); } else { m_Controls.spinBoxOutsidePixelValue->setEnabled(false); } unsigned int dim = image->GetDimension(); if (dim < 2 || dim > 4) { m_ParentWidget->setEnabled(false); } if (m_Controls.boundingBoxSelectionWidget->GetSelectedNode().IsNotNull()) { m_Controls.buttonCropping->setEnabled(true); m_Controls.buttonMasking->setEnabled(true); m_Controls.buttonAdvancedSettings->setEnabled(true); m_Controls.groupImageSettings->setEnabled(true); } } } void QmitkImageCropperView::OnBoundingBoxSelectionChanged(QList) { auto boundingBoxNode = m_Controls.boundingBoxSelectionWidget->GetSelectedNode(); if (boundingBoxNode.IsNull()) { SetDefaultGUI(); m_BoundingShapeInteractor->EnableInteraction(false); m_BoundingShapeInteractor->SetDataNode(nullptr); if (m_Controls.imageSelectionWidget->GetSelectedNode().IsNotNull()) { m_Controls.buttonCreateNewBoundingBox->setEnabled(true); } return; } auto boundingBox = dynamic_cast(boundingBoxNode->GetData()); if (nullptr != boundingBox) { // node newly selected boundingBoxNode->SetVisibility(true); m_BoundingShapeInteractor->EnableInteraction(true); m_BoundingShapeInteractor->SetDataNode(boundingBoxNode); mitk::RenderingManager::GetInstance()->InitializeViews(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls.imageSelectionWidget->GetSelectedNode().IsNotNull()) { m_Controls.buttonCropping->setEnabled(true); m_Controls.buttonMasking->setEnabled(true); m_Controls.buttonAdvancedSettings->setEnabled(true); m_Controls.groupImageSettings->setEnabled(true); } } } void QmitkImageCropperView::OnCreateNewBoundingBox() { auto imageNode = m_Controls.imageSelectionWidget->GetSelectedNode(); if (imageNode.IsNull()) { return; } if (nullptr == imageNode->GetData()) { return; } QString name = QString::fromStdString(imageNode->GetName() + " Bounding Shape"); auto boundingShape = this->GetDataStorage()->GetNode(mitk::NodePredicateFunction::New([&name](const mitk::DataNode *node) { return 0 == node->GetName().compare(name.toStdString()); })); if (nullptr != boundingShape) { name = this->AdaptBoundingObjectName(name); } // get current timestep to support 3d+t images auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN); const auto timePoint = renderWindowPart->GetSelectedTimePoint(); const auto imageGeometry = imageNode->GetData()->GetTimeGeometry()->GetGeometryForTimePoint(timePoint); auto boundingBox = mitk::GeometryData::New(); boundingBox->SetGeometry(static_cast(this->InitializeWithImageGeometry(imageGeometry))); auto boundingBoxNode = mitk::DataNode::New(); boundingBoxNode->SetData(boundingBox); boundingBoxNode->SetProperty("name", mitk::StringProperty::New(name.toStdString())); boundingBoxNode->SetProperty("color", mitk::ColorProperty::New(1.0, 1.0, 1.0)); boundingBoxNode->SetProperty("opacity", mitk::FloatProperty::New(0.6)); boundingBoxNode->SetProperty("layer", mitk::IntProperty::New(99)); boundingBoxNode->AddProperty("handle size factor", mitk::DoubleProperty::New(1.0 / 40.0)); boundingBoxNode->SetBoolProperty("pickable", true); if (!this->GetDataStorage()->Exists(boundingBoxNode)) { GetDataStorage()->Add(boundingBoxNode, imageNode); } m_Controls.boundingBoxSelectionWidget->SetCurrentSelectedNode(boundingBoxNode); } void QmitkImageCropperView::OnCropping() { this->ProcessImage(false); } void QmitkImageCropperView::OnMasking() { this->ProcessImage(true); } void QmitkImageCropperView::OnSliderValueChanged(int slidervalue) { m_CropOutsideValue = slidervalue; } void QmitkImageCropperView::CreateBoundingShapeInteractor(bool rotationEnabled) { if (m_BoundingShapeInteractor.IsNull()) { m_BoundingShapeInteractor = mitk::BoundingShapeInteractor::New(); m_BoundingShapeInteractor->LoadStateMachine("BoundingShapeInteraction.xml", us::ModuleRegistry::GetModule("MitkBoundingShape")); m_BoundingShapeInteractor->SetEventConfig("BoundingShapeMouseConfig.xml", us::ModuleRegistry::GetModule("MitkBoundingShape")); } m_BoundingShapeInteractor->SetRotationEnabled(rotationEnabled); } mitk::Geometry3D::Pointer QmitkImageCropperView::InitializeWithImageGeometry(const mitk::BaseGeometry* geometry) const { // convert a BaseGeometry into a Geometry3D (otherwise IO is not working properly) if (geometry == nullptr) mitkThrow() << "Geometry is not valid."; auto boundingGeometry = mitk::Geometry3D::New(); boundingGeometry->SetBounds(geometry->GetBounds()); boundingGeometry->SetImageGeometry(geometry->GetImageGeometry()); boundingGeometry->SetOrigin(geometry->GetOrigin()); boundingGeometry->SetSpacing(geometry->GetSpacing()); boundingGeometry->SetIndexToWorldTransform(geometry->GetIndexToWorldTransform()->Clone()); boundingGeometry->Modified(); return boundingGeometry; } void QmitkImageCropperView::ProcessImage(bool mask) { auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN); const auto timePoint = renderWindowPart->GetSelectedTimePoint(); auto imageNode = m_Controls.imageSelectionWidget->GetSelectedNode(); if (imageNode.IsNull()) { QMessageBox::information(nullptr, "Warning", "Please load and select an image before starting image processing."); return; } auto boundingBoxNode = m_Controls.boundingBoxSelectionWidget->GetSelectedNode(); if (boundingBoxNode.IsNull()) { QMessageBox::information(nullptr, "Warning", "Please load and select a cropping object before starting image processing."); return; } if (!imageNode->GetData()->GetTimeGeometry()->IsValidTimePoint(timePoint)) { QMessageBox::information(nullptr, "Warning", "Please select a time point that is within the time bounds of the selected image."); return; } const auto timeStep = imageNode->GetData()->GetTimeGeometry()->TimePointToTimeStep(timePoint); auto image = dynamic_cast(imageNode->GetData()); auto boundingBox = dynamic_cast(boundingBoxNode->GetData()); if (nullptr != image && nullptr != boundingBox) { QString imageName; if (mask) { imageName = QString::fromStdString(imageNode->GetName() + "_" + boundingBoxNode->GetName() + "_masked"); } else { imageName = QString::fromStdString(imageNode->GetName() + "_" + boundingBoxNode->GetName() + "_cropped"); } if (m_Controls.checkBoxCropTimeStepOnly->isChecked()) { imageName = imageName + "_T" + QString::number(timeStep); } // image and bounding shape ok, set as input auto croppedImageNode = mitk::DataNode::New(); auto cutter = mitk::BoundingShapeCropper::New(); cutter->SetGeometry(boundingBox); // adjustable in advanced settings cutter->SetUseWholeInputRegion(mask); //either mask (mask=true) or crop (mask=false) cutter->SetOutsideValue(m_CropOutsideValue); cutter->SetUseCropTimeStepOnly(m_Controls.checkBoxCropTimeStepOnly->isChecked()); cutter->SetCurrentTimeStep(timeStep); // TODO: Add support for MultiLayer (right now only Mulitlabel support) auto labelsetImageInput = dynamic_cast(image); if (nullptr != labelsetImageInput) { cutter->SetInput(labelsetImageInput); // do the actual cutting try { cutter->Update(); } catch (const itk::ExceptionObject& e) { std::string message = std::string("The Cropping filter could not process because of: \n ") + e.GetDescription(); QMessageBox::warning(nullptr, tr("Cropping not possible!"), tr(message.c_str()), QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); return; } auto labelSetImage = mitk::LabelSetImage::New(); labelSetImage->InitializeByLabeledImage(cutter->GetOutput()); for (unsigned int i = 0; i < labelsetImageInput->GetNumberOfLayers(); i++) { labelSetImage->AddLabelSetToLayer(i, labelsetImageInput->GetLabelSet(i)); } croppedImageNode->SetData(labelSetImage); croppedImageNode->SetProperty("name", mitk::StringProperty::New(imageName.toStdString())); //add cropping result to the current data storage as child node to the image node if (!m_Controls.checkOverwriteImage->isChecked()) { if (!this->GetDataStorage()->Exists(croppedImageNode)) { this->GetDataStorage()->Add(croppedImageNode, imageNode); } } else // original image will be overwritten by the result image and the bounding box of the result is adjusted { imageNode->SetData(labelSetImage); imageNode->Modified(); // Adjust coordinate system by doing a reinit on auto tempDataStorage = mitk::DataStorage::SetOfObjects::New(); tempDataStorage->InsertElement(0, imageNode); // initialize the views to the bounding geometry auto bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(tempDataStorage); mitk::RenderingManager::GetInstance()->InitializeViews(bounds); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } else { cutter->SetInput(image); // do the actual cutting try { cutter->Update(); } catch (const itk::ExceptionObject& e) { std::string message = std::string("The Cropping filter could not process because of: \n ") + e.GetDescription(); QMessageBox::warning(nullptr, tr("Cropping not possible!"), tr(message.c_str()), QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton); return; } //add cropping result to the current data storage as child node to the image node if (!m_Controls.checkOverwriteImage->isChecked()) { croppedImageNode->SetData(cutter->GetOutput()); croppedImageNode->SetProperty("name", mitk::StringProperty::New(imageName.toStdString())); croppedImageNode->SetProperty("color", mitk::ColorProperty::New(1.0, 1.0, 1.0)); - croppedImageNode->SetProperty("layer", mitk::IntProperty::New(99)); // arbitrary, copied from segmentation functionality + + mitk::LevelWindow levelWindow; + imageNode->GetLevelWindow(levelWindow); + croppedImageNode->SetLevelWindow(levelWindow); + if (!this->GetDataStorage()->Exists(croppedImageNode)) { this->GetDataStorage()->Add(croppedImageNode, imageNode); + imageNode->SetVisibility(mask); // Give the user a visual clue that something happened when image was cropped } } else // original image will be overwritten by the result image and the bounding box of the result is adjusted { + mitk::LevelWindow levelWindow; + imageNode->GetLevelWindow(levelWindow); imageNode->SetData(cutter->GetOutput()); - imageNode->Modified(); + imageNode->SetLevelWindow(levelWindow); // Adjust coordinate system by doing a reinit on auto tempDataStorage = mitk::DataStorage::SetOfObjects::New(); tempDataStorage->InsertElement(0, imageNode); // initialize the views to the bounding geometry auto bounds = this->GetDataStorage()->ComputeBoundingGeometry3D(tempDataStorage); mitk::RenderingManager::GetInstance()->InitializeViews(bounds); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } else { QMessageBox::information(nullptr, "Warning", "Please load and select an image before starting image processing."); } } void QmitkImageCropperView::SetDefaultGUI() { m_Controls.labelWarningRotation->setVisible(false); m_Controls.buttonCreateNewBoundingBox->setEnabled(false); m_Controls.buttonCropping->setEnabled(false); m_Controls.buttonMasking->setEnabled(false); m_Controls.buttonAdvancedSettings->setEnabled(false); m_Controls.groupImageSettings->setEnabled(false); m_Controls.groupImageSettings->setVisible(false); m_Controls.checkOverwriteImage->setChecked(false); m_Controls.checkBoxCropTimeStepOnly->setChecked(false); } QString QmitkImageCropperView::AdaptBoundingObjectName(const QString& name) const { unsigned int counter = 2; QString newName = QString("%1 %2").arg(name).arg(counter); while (nullptr != this->GetDataStorage()->GetNode(mitk::NodePredicateFunction::New([&newName](const mitk::DataNode *node) { return 0 == node->GetName().compare(newName.toStdString()); }))) { newName = QString("%1 %2").arg(name).arg(++counter); } return newName; } diff --git a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/src/internal/QmitkMatchPointRegistrationEvaluator.cpp b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/src/internal/QmitkMatchPointRegistrationEvaluator.cpp index 5da7f6c349..46c3272a68 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.evaluator/src/internal/QmitkMatchPointRegistrationEvaluator.cpp +++ b/Plugins/org.mitk.gui.qt.matchpoint.evaluator/src/internal/QmitkMatchPointRegistrationEvaluator.cpp @@ -1,309 +1,310 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include // Mitk #include #include #include #include "mitkRegVisPropertyTags.h" #include "mitkMatchPointPropertyTags.h" #include "mitkRegEvaluationObject.h" #include "mitkRegistrationHelper.h" #include "mitkRegEvaluationMapper2D.h" #include +#include "mitkProperties.h" // Qmitk #include "QmitkRenderWindow.h" #include "QmitkMatchPointRegistrationEvaluator.h" // Qt #include #include #include const std::string QmitkMatchPointRegistrationEvaluator::VIEW_ID = "org.mitk.views.matchpoint.registration.evaluator"; const std::string QmitkMatchPointRegistrationEvaluator::HelperNodeName = "RegistrationEvaluationHelper"; QmitkMatchPointRegistrationEvaluator::QmitkMatchPointRegistrationEvaluator() : m_Parent(nullptr), m_activeEvaluation(false), m_currentSelectedTimePoint(0.) { m_currentSelectedPosition.Fill(0.0); } QmitkMatchPointRegistrationEvaluator::~QmitkMatchPointRegistrationEvaluator() { if (this->m_selectedEvalNode.IsNotNull() && this->GetDataStorage().IsNotNull()) { this->GetDataStorage()->Remove(this->m_selectedEvalNode); } } void QmitkMatchPointRegistrationEvaluator::SetFocus() { } void QmitkMatchPointRegistrationEvaluator::Error(QString msg) { mitk::StatusBar::GetInstance()->DisplayErrorText(msg.toLatin1()); MITK_ERROR << msg.toStdString().c_str(); } void QmitkMatchPointRegistrationEvaluator::CreateQtPartControl(QWidget* parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Parent = parent; this->m_Controls.registrationNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls.registrationNodeSelector->SetSelectionIsOptional(true); this->m_Controls.movingNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls.movingNodeSelector->SetSelectionIsOptional(false); this->m_Controls.targetNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls.targetNodeSelector->SetSelectionIsOptional(false); this->m_Controls.registrationNodeSelector->SetInvalidInfo("Select valid registration."); this->m_Controls.registrationNodeSelector->SetEmptyInfo("Assuming identity. Select registration to change."); this->m_Controls.registrationNodeSelector->SetPopUpTitel("Select registration."); this->m_Controls.registrationNodeSelector->SetPopUpHint("Select a registration object that should be evaluated. If no registration is selected, identity will be assumed for evaluation."); this->m_Controls.movingNodeSelector->SetInvalidInfo("Select moving image."); this->m_Controls.movingNodeSelector->SetPopUpTitel("Select moving image."); this->m_Controls.movingNodeSelector->SetPopUpHint("Select the moving image for the evaluation. This is the image that will be mapped by the registration."); this->m_Controls.targetNodeSelector->SetInvalidInfo("Select target image."); this->m_Controls.targetNodeSelector->SetPopUpTitel("Select target image."); this->m_Controls.targetNodeSelector->SetPopUpHint("Select the target image for the evaluation."); this->m_Controls.checkAutoSelect->setChecked(true); this->ConfigureNodePredicates(); connect(m_Controls.pbEval, SIGNAL(clicked()), this, SLOT(OnEvalBtnPushed())); connect(m_Controls.pbStop, SIGNAL(clicked()), this, SLOT(OnStopBtnPushed())); connect(m_Controls.evalSettings, SIGNAL(SettingsChanged(mitk::DataNode*)), this, SLOT(OnSettingsChanged(mitk::DataNode*))); connect(m_Controls.registrationNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointRegistrationEvaluator::OnNodeSelectionChanged); connect(m_Controls.movingNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointRegistrationEvaluator::OnNodeSelectionChanged); connect(m_Controls.targetNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointRegistrationEvaluator::OnNodeSelectionChanged); this->m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); m_selectedEvalNode = this->GetDataStorage()->GetNamedNode(HelperNodeName); this->CheckInputs(); this->ConfigureControls(); } void QmitkMatchPointRegistrationEvaluator::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { this->m_SliceChangeListener.RenderWindowPartActivated(renderWindowPart); } void QmitkMatchPointRegistrationEvaluator::RenderWindowPartDeactivated( mitk::IRenderWindowPart* renderWindowPart) { this->m_SliceChangeListener.RenderWindowPartDeactivated(renderWindowPart); } void QmitkMatchPointRegistrationEvaluator::ConfigureNodePredicates() { this->m_Controls.registrationNodeSelector->SetNodePredicate(mitk::MITKRegistrationHelper::RegNodePredicate()); this->m_Controls.movingNodeSelector->SetNodePredicate(mitk::MITKRegistrationHelper::ImageNodePredicate()); this->m_Controls.targetNodeSelector->SetNodePredicate(mitk::MITKRegistrationHelper::ImageNodePredicate()); } void QmitkMatchPointRegistrationEvaluator::CheckInputs() { if (!m_activeEvaluation) { bool autoSelectInput = m_Controls.checkAutoSelect->isChecked() && this->m_spSelectedRegNode != this->m_Controls.registrationNodeSelector->GetSelectedNode(); this->m_spSelectedRegNode = this->m_Controls.registrationNodeSelector->GetSelectedNode(); this->m_spSelectedMovingNode = this->m_Controls.movingNodeSelector->GetSelectedNode(); this->m_spSelectedTargetNode = this->m_Controls.targetNodeSelector->GetSelectedNode(); if (this->m_spSelectedRegNode.IsNotNull() && (this->m_spSelectedMovingNode.IsNull() || autoSelectInput)) { mitk::BaseProperty* uidProp = m_spSelectedRegNode->GetData()->GetProperty(mitk::Prop_RegAlgMovingData); if (uidProp) { //search for the moving node mitk::NodePredicateDataProperty::Pointer predicate = mitk::NodePredicateDataProperty::New(mitk::Prop_UID, uidProp); mitk::DataNode::Pointer movingNode = this->GetDataStorage()->GetNode(predicate); if (movingNode.IsNotNull()) { this->m_spSelectedMovingNode = movingNode; QmitkSingleNodeSelectionWidget::NodeList selection({ movingNode }); this->m_Controls.movingNodeSelector->SetCurrentSelection(selection); } } } if (this->m_spSelectedRegNode.IsNotNull() && (this->m_spSelectedTargetNode.IsNull() || autoSelectInput)) { mitk::BaseProperty* uidProp = m_spSelectedRegNode->GetData()->GetProperty(mitk::Prop_RegAlgTargetData); if (uidProp) { //search for the target node mitk::NodePredicateDataProperty::Pointer predicate = mitk::NodePredicateDataProperty::New(mitk::Prop_UID, uidProp); mitk::DataNode::Pointer targetNode = this->GetDataStorage()->GetNode(predicate); if (targetNode.IsNotNull()) { this->m_spSelectedTargetNode = targetNode; QmitkSingleNodeSelectionWidget::NodeList selection({ targetNode }); this->m_Controls.targetNodeSelector->SetCurrentSelection(selection); } } } } } void QmitkMatchPointRegistrationEvaluator::OnNodeSelectionChanged(QList /*nodes*/) { this->CheckInputs(); this->ConfigureControls(); } void QmitkMatchPointRegistrationEvaluator::NodeRemoved(const mitk::DataNode* node) { if (node == this->m_spSelectedMovingNode || node == this->m_spSelectedRegNode || node == this->m_spSelectedTargetNode || node == this->m_selectedEvalNode) { if (node == this->m_selectedEvalNode) { this->m_selectedEvalNode = nullptr; } this->OnStopBtnPushed(); MITK_INFO << "Stopped current MatchPoint evaluation session, because at least one relevant node was removed from storage."; } } void QmitkMatchPointRegistrationEvaluator::ConfigureControls() { //config settings widget this->m_Controls.evalSettings->setVisible(m_activeEvaluation); this->m_Controls.pbEval->setEnabled(this->m_spSelectedMovingNode.IsNotNull() && this->m_spSelectedTargetNode.IsNotNull()); this->m_Controls.pbEval->setVisible(!m_activeEvaluation); this->m_Controls.pbStop->setVisible(m_activeEvaluation); this->m_Controls.registrationNodeSelector->setEnabled(!m_activeEvaluation); this->m_Controls.movingNodeSelector->setEnabled(!m_activeEvaluation); this->m_Controls.targetNodeSelector->setEnabled(!m_activeEvaluation); } void QmitkMatchPointRegistrationEvaluator::OnSliceChanged() { mitk::Point3D currentSelectedPosition = GetRenderWindowPart()->GetSelectedPosition(nullptr); auto currentTimePoint = GetRenderWindowPart()->GetSelectedTimePoint(); if (m_currentSelectedPosition != currentSelectedPosition || m_currentSelectedTimePoint != currentTimePoint || m_selectedNodeTime > m_currentPositionTime) { //the current position has been changed or the selected node has been changed since the last position validation -> check position m_currentSelectedPosition = currentSelectedPosition; m_currentSelectedTimePoint = currentTimePoint; m_currentPositionTime.Modified(); if (this->m_selectedEvalNode.IsNotNull()) { - this->m_selectedEvalNode->SetProperty(mitk::nodeProp_RegEvalCurrentPosition, mitk::GenericProperty::New(currentSelectedPosition)); + this->m_selectedEvalNode->SetProperty(mitk::nodeProp_RegEvalCurrentPosition, mitk::Point3dProperty::New(currentSelectedPosition)); } } } void QmitkMatchPointRegistrationEvaluator::OnSettingsChanged(mitk::DataNode*) { this->GetRenderWindowPart()->RequestUpdate(); } void QmitkMatchPointRegistrationEvaluator::OnEvalBtnPushed() { //reinit view mitk::RenderingManager::GetInstance()->InitializeViews(m_spSelectedTargetNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); mitk::RegEvaluationObject::Pointer regEval = mitk::RegEvaluationObject::New(); mitk::MAPRegistrationWrapper::Pointer reg; if (m_spSelectedRegNode.IsNotNull()) { reg = dynamic_cast(this->m_spSelectedRegNode->GetData()); } else { //generate a dymme reg to use reg = mitk::GenerateIdentityRegistration3D(); } regEval->SetRegistration(reg); regEval->SetTargetNode(this->m_spSelectedTargetNode); regEval->SetMovingNode(this->m_spSelectedMovingNode); if (this->m_selectedEvalNode.IsNotNull()) { this->GetDataStorage()->Remove(this->m_selectedEvalNode); } this->m_selectedEvalNode = mitk::DataNode::New(); this->m_selectedEvalNode->SetData(regEval); mitk::RegEvaluationMapper2D::SetDefaultProperties(this->m_selectedEvalNode); this->m_selectedEvalNode->SetName(HelperNodeName); this->m_selectedEvalNode->SetBoolProperty("helper object", true); this->GetDataStorage()->Add(this->m_selectedEvalNode); this->m_Controls.evalSettings->SetNode(this->m_selectedEvalNode); this->OnSliceChanged(); this->GetRenderWindowPart()->RequestUpdate(); this->m_activeEvaluation = true; this->CheckInputs(); this->ConfigureControls(); } void QmitkMatchPointRegistrationEvaluator::OnStopBtnPushed() { this->m_activeEvaluation = false; if (this->m_selectedEvalNode.IsNotNull()) { this->GetDataStorage()->Remove(this->m_selectedEvalNode); } this->m_selectedEvalNode = nullptr; this->m_Controls.evalSettings->SetNode(this->m_selectedEvalNode); this->CheckInputs(); this->ConfigureControls(); if (nullptr != this->GetRenderWindowPart()) { this->GetRenderWindowPart()->RequestUpdate(); } } diff --git a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/src/internal/QmitkMatchPointRegistrationManipulator.cpp b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/src/internal/QmitkMatchPointRegistrationManipulator.cpp index 1205c3929e..ac29f25c5d 100644 --- a/Plugins/org.mitk.gui.qt.matchpoint.manipulator/src/internal/QmitkMatchPointRegistrationManipulator.cpp +++ b/Plugins/org.mitk.gui.qt.matchpoint.manipulator/src/internal/QmitkMatchPointRegistrationManipulator.cpp @@ -1,495 +1,496 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include // Mitk #include #include #include #include "mitkRegVisPropertyTags.h" #include "mitkMatchPointPropertyTags.h" #include "mitkRegEvaluationObject.h" #include "mitkRegistrationHelper.h" #include "mitkRegEvaluationMapper2D.h" #include #include #include +#include "mitkProperties.h" // Qmitk #include "QmitkRenderWindow.h" #include "QmitkMatchPointRegistrationManipulator.h" #include // Qt #include #include #include #include //MatchPoint #include #include #include #include #include #include #include const std::string QmitkMatchPointRegistrationManipulator::VIEW_ID = "org.mitk.views.matchpoint.registration.manipulator"; const std::string QmitkMatchPointRegistrationManipulator::HelperNodeName = "RegistrationManipulationEvaluationHelper"; QmitkMatchPointRegistrationManipulator::QmitkMatchPointRegistrationManipulator() : m_Parent(nullptr), m_activeManipulation(false), m_currentSelectedTimePoint(0.), m_internalUpdate(false) { m_currentSelectedPosition.Fill(0.0); } QmitkMatchPointRegistrationManipulator::~QmitkMatchPointRegistrationManipulator() { if (this->m_EvalNode.IsNotNull() && this->GetDataStorage().IsNotNull()) { this->GetDataStorage()->Remove(this->m_EvalNode); } } void QmitkMatchPointRegistrationManipulator::SetFocus() { } void QmitkMatchPointRegistrationManipulator::Error(QString msg) { mitk::StatusBar::GetInstance()->DisplayErrorText(msg.toLatin1()); MITK_ERROR << msg.toStdString().c_str(); } void QmitkMatchPointRegistrationManipulator::CreateQtPartControl(QWidget* parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); m_Parent = parent; this->m_Controls.registrationNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls.registrationNodeSelector->SetSelectionIsOptional(false); this->m_Controls.movingNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls.movingNodeSelector->SetSelectionIsOptional(false); this->m_Controls.targetNodeSelector->SetDataStorage(this->GetDataStorage()); this->m_Controls.targetNodeSelector->SetSelectionIsOptional(false); this->m_Controls.registrationNodeSelector->SetInvalidInfo("Select base registration."); this->m_Controls.registrationNodeSelector->SetPopUpTitel("Select registration."); this->m_Controls.registrationNodeSelector->SetPopUpHint("Select a registration object that should be used as starting point for the manual manipulation."); this->m_Controls.movingNodeSelector->SetInvalidInfo("Select moving image."); this->m_Controls.movingNodeSelector->SetPopUpTitel("Select moving image."); this->m_Controls.movingNodeSelector->SetPopUpHint("Select the moving image for the evaluation. This is the image that will be mapped by the registration."); this->m_Controls.targetNodeSelector->SetInvalidInfo("Select target image."); this->m_Controls.targetNodeSelector->SetPopUpTitel("Select target image."); this->m_Controls.targetNodeSelector->SetPopUpHint("Select the target image for the evaluation."); this->m_Controls.checkAutoSelect->setChecked(true); this->ConfigureNodePredicates(); connect(m_Controls.pbStart, SIGNAL(clicked()), this, SLOT(OnStartBtnPushed())); connect(m_Controls.pbCancel, SIGNAL(clicked()), this, SLOT(OnCancelBtnPushed())); connect(m_Controls.pbStore, SIGNAL(clicked()), this, SLOT(OnStoreBtnPushed())); connect(m_Controls.evalSettings, SIGNAL(SettingsChanged(mitk::DataNode*)), this, SLOT(OnSettingsChanged(mitk::DataNode*))); connect(m_Controls.radioSelectedReg, SIGNAL(toggled(bool)), this, SLOT(OnRegSourceChanged())); connect(m_Controls.comboCenter, SIGNAL(currentIndexChanged(int)), this, SLOT(OnCenterTypeChanged(int))); connect(m_Controls.manipulationWidget, SIGNAL(RegistrationChanged(map::core::RegistrationBase*)), this, SLOT(OnRegistrationChanged())); connect(m_Controls.registrationNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointRegistrationManipulator::OnNodeSelectionChanged); connect(m_Controls.movingNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointRegistrationManipulator::OnNodeSelectionChanged); connect(m_Controls.targetNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkMatchPointRegistrationManipulator::OnNodeSelectionChanged); this->m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); m_Controls.radioNewReg->setChecked(true); m_EvalNode = this->GetDataStorage()->GetNamedNode(HelperNodeName); this->CheckInputs(); this->StopSession(); this->ConfigureControls(); } void QmitkMatchPointRegistrationManipulator::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { this->m_SliceChangeListener.RenderWindowPartActivated(renderWindowPart); } void QmitkMatchPointRegistrationManipulator::RenderWindowPartDeactivated( mitk::IRenderWindowPart* renderWindowPart) { this->m_SliceChangeListener.RenderWindowPartDeactivated(renderWindowPart); } void QmitkMatchPointRegistrationManipulator::ConfigureNodePredicates() { this->m_Controls.registrationNodeSelector->SetNodePredicate(mitk::MITKRegistrationHelper::RegNodePredicate()); this->m_Controls.movingNodeSelector->SetNodePredicate(mitk::MITKRegistrationHelper::ImageNodePredicate()); this->m_Controls.targetNodeSelector->SetNodePredicate(mitk::MITKRegistrationHelper::ImageNodePredicate()); } void QmitkMatchPointRegistrationManipulator::CheckInputs() { if (!m_activeManipulation) { bool autoSelectInput = m_Controls.checkAutoSelect->isChecked() && this->m_SelectedPreRegNode != this->m_Controls.registrationNodeSelector->GetSelectedNode(); this->m_SelectedPreRegNode = this->m_Controls.registrationNodeSelector->GetSelectedNode(); this->m_SelectedMovingNode = this->m_Controls.movingNodeSelector->GetSelectedNode(); this->m_SelectedTargetNode = this->m_Controls.targetNodeSelector->GetSelectedNode(); if (this->m_SelectedPreRegNode.IsNotNull()) { mitk::MAPRegistrationWrapper* regWrapper = dynamic_cast(m_SelectedPreRegNode->GetData()); if (regWrapper) { this->m_SelectedPreReg = dynamic_cast(regWrapper->GetRegistration()); } } if (this->m_SelectedPreRegNode.IsNotNull() && (this->m_SelectedMovingNode.IsNull() || autoSelectInput)) { mitk::BaseProperty* uidProp = m_SelectedPreRegNode->GetData()->GetProperty(mitk::Prop_RegAlgMovingData); if (uidProp) { //search for the moving node mitk::NodePredicateDataProperty::Pointer predicate = mitk::NodePredicateDataProperty::New(mitk::Prop_UID, uidProp); mitk::DataNode::Pointer movingNode = this->GetDataStorage()->GetNode(predicate); if (movingNode.IsNotNull()) { this->m_SelectedMovingNode = movingNode; QmitkSingleNodeSelectionWidget::NodeList selection({ movingNode }); this->m_Controls.movingNodeSelector->SetCurrentSelection(selection); } } } if (this->m_SelectedPreRegNode.IsNotNull() && (this->m_SelectedTargetNode.IsNull() || autoSelectInput)) { mitk::BaseProperty* uidProp = m_SelectedPreRegNode->GetData()->GetProperty(mitk::Prop_RegAlgTargetData); if (uidProp) { //search for the target node mitk::NodePredicateDataProperty::Pointer predicate = mitk::NodePredicateDataProperty::New(mitk::Prop_UID, uidProp); mitk::DataNode::Pointer targetNode = this->GetDataStorage()->GetNode(predicate); if (targetNode.IsNotNull()) { this->m_SelectedTargetNode = targetNode; QmitkSingleNodeSelectionWidget::NodeList selection({ targetNode }); this->m_Controls.targetNodeSelector->SetCurrentSelection(selection); } } } } } void QmitkMatchPointRegistrationManipulator::OnRegSourceChanged() { this->CheckInputs(); this->ConfigureControls(); } void QmitkMatchPointRegistrationManipulator::OnNodeSelectionChanged(QList /*nodes*/) { this->CheckInputs(); this->ConfigureControls(); } void QmitkMatchPointRegistrationManipulator::NodeRemoved(const mitk::DataNode* node) { if (node == this->m_SelectedMovingNode || node == this->m_SelectedTargetNode || node == this->m_EvalNode) { if (node == this->m_EvalNode) { this->m_EvalNode = nullptr; } if (this->m_activeManipulation) { MITK_INFO << "Stopped current MatchPoint manual registration session, because at least one relevant node was removed from storage."; } this->OnCancelBtnPushed(); } } void QmitkMatchPointRegistrationManipulator::ConfigureControls() { if (!m_activeManipulation) { QString name = "ManuelRegistration"; if (m_SelectedPreRegNode.IsNotNull()) { name = QString::fromStdString(m_SelectedPreRegNode->GetName()) + " manual refined"; } this->m_Controls.lbNewRegName->setText(name); } //config settings widget this->m_Controls.groupReg->setEnabled(!m_activeManipulation); this->m_Controls.pbStart->setEnabled(this->m_SelectedMovingNode.IsNotNull() && this->m_SelectedTargetNode.IsNotNull() && !m_activeManipulation && (this->m_Controls.radioNewReg->isChecked() || this->m_SelectedPreReg.IsNotNull())); this->m_Controls.lbNewRegName->setEnabled(m_activeManipulation); this->m_Controls.checkMapEntity->setEnabled(m_activeManipulation); this->m_Controls.tabWidget->setEnabled(m_activeManipulation); this->m_Controls.pbCancel->setEnabled(m_activeManipulation); this->m_Controls.pbStore->setEnabled(m_activeManipulation); this->m_Controls.registrationNodeSelector->setEnabled(!m_activeManipulation && this->m_Controls.radioSelectedReg->isChecked()); this->m_Controls.checkAutoSelect->setEnabled(!m_activeManipulation && this->m_Controls.radioSelectedReg->isChecked()); this->m_Controls.movingNodeSelector->setEnabled(!m_activeManipulation); this->m_Controls.targetNodeSelector->setEnabled(!m_activeManipulation); } void QmitkMatchPointRegistrationManipulator::InitSession() { if (this->m_Controls.radioNewReg->isChecked()) { //init to map the image centers auto movingCenter = m_SelectedMovingNode->GetData()->GetTimeGeometry()->GetCenterInWorld(); auto targetCenter = m_SelectedTargetNode->GetData()->GetTimeGeometry()->GetCenterInWorld(); this->m_Controls.manipulationWidget->Initialize(movingCenter, targetCenter); } else { //use selected pre registration as baseline m_Controls.manipulationWidget->Initialize(m_SelectedPreReg); } this->m_CurrentRegistration = m_Controls.manipulationWidget->GetInterimRegistration(); this->m_CurrentRegistrationWrapper = mitk::MAPRegistrationWrapper::New(m_CurrentRegistration); this->m_Controls.comboCenter->setCurrentIndex(0); this->OnCenterTypeChanged(0); //reinit view mitk::RenderingManager::GetInstance()->InitializeViews(m_SelectedTargetNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); //generate evaluation node mitk::RegEvaluationObject::Pointer regEval = mitk::RegEvaluationObject::New(); regEval->SetRegistration(this->m_CurrentRegistrationWrapper); regEval->SetTargetNode(this->m_SelectedTargetNode); regEval->SetMovingNode(this->m_SelectedMovingNode); this->m_EvalNode = mitk::DataNode::New(); this->m_EvalNode->SetData(regEval); mitk::RegEvaluationMapper2D::SetDefaultProperties(this->m_EvalNode); this->m_EvalNode->SetName(HelperNodeName); this->m_EvalNode->SetBoolProperty("helper object", true); this->GetDataStorage()->Add(this->m_EvalNode); this->m_Controls.evalSettings->SetNode(this->m_EvalNode); this->m_activeManipulation = true; } void QmitkMatchPointRegistrationManipulator::StopSession() { this->m_activeManipulation = false; if (this->m_EvalNode.IsNotNull()) { this->GetDataStorage()->Remove(this->m_EvalNode); } this->m_EvalNode = nullptr; this->m_CurrentRegistration = nullptr; this->m_CurrentRegistrationWrapper = nullptr; m_Controls.manipulationWidget->Initialize(); } void QmitkMatchPointRegistrationManipulator::OnRegistrationChanged() { if (this->m_EvalNode.IsNotNull()) { this->m_EvalNode->Modified(); } if (this->m_CurrentRegistrationWrapper.IsNotNull()) { this->m_CurrentRegistrationWrapper->Modified(); } this->GetRenderWindowPart()->RequestUpdate(); } void QmitkMatchPointRegistrationManipulator::OnSliceChanged() { mitk::Point3D currentSelectedPosition = GetRenderWindowPart()->GetSelectedPosition(nullptr); auto currentTimePoint = GetRenderWindowPart()->GetSelectedTimePoint(); if (m_currentSelectedPosition != currentSelectedPosition || m_currentSelectedTimePoint != currentTimePoint || m_selectedNodeTime > m_currentPositionTime) { //the current position has been changed or the selected node has been changed since the last position validation -> check position m_currentSelectedPosition = currentSelectedPosition; m_currentSelectedTimePoint = currentTimePoint; m_currentPositionTime.Modified(); if (this->m_EvalNode.IsNotNull()) { - this->m_EvalNode->SetProperty(mitk::nodeProp_RegEvalCurrentPosition, mitk::GenericProperty::New(currentSelectedPosition)); + this->m_EvalNode->SetProperty(mitk::nodeProp_RegEvalCurrentPosition, mitk::Point3dProperty::New(currentSelectedPosition)); } if (m_activeManipulation && m_Controls.comboCenter->currentIndex() == 2) { //update transform with the current position. m_Controls.manipulationWidget->SetCenterOfRotation(m_currentSelectedPosition); } } } void QmitkMatchPointRegistrationManipulator::OnSettingsChanged(mitk::DataNode*) { this->GetRenderWindowPart()->RequestUpdate(); } void QmitkMatchPointRegistrationManipulator::OnStartBtnPushed() { this->InitSession(); this->OnSliceChanged(); this->GetRenderWindowPart()->RequestUpdate(); this->CheckInputs(); this->ConfigureControls(); } void QmitkMatchPointRegistrationManipulator::OnCancelBtnPushed() { this->StopSession(); this->CheckInputs(); this->ConfigureControls(); if (this->GetRenderWindowPart()) { this->GetRenderWindowPart()->RequestUpdate(); } } void QmitkMatchPointRegistrationManipulator::OnStoreBtnPushed() { map::core::RegistrationBase::Pointer newReg = this->m_Controls.manipulationWidget->GenerateRegistration(); auto newRegWrapper = mitk::MAPRegistrationWrapper::New(newReg); mitk::DataNode::Pointer spResultRegistrationNode = mitk::generateRegistrationResultNode( this->m_Controls.lbNewRegName->text().toStdString(), newRegWrapper, "org.mitk::manual_registration", mitk::EnsureUID(m_SelectedMovingNode->GetData()), mitk::EnsureUID(m_SelectedTargetNode->GetData())); this->GetDataStorage()->Add(spResultRegistrationNode); if (m_Controls.checkMapEntity->checkState() == Qt::Checked) { QmitkMappingJob* pMapJob = new QmitkMappingJob(); pMapJob->setAutoDelete(true); pMapJob->m_spInputData = this->m_SelectedMovingNode->GetData(); pMapJob->m_InputDataUID = mitk::EnsureUID(m_SelectedMovingNode->GetData()); pMapJob->m_spRegNode = spResultRegistrationNode; pMapJob->m_doGeometryRefinement = false; pMapJob->m_spRefGeometry = this->m_SelectedTargetNode->GetData()->GetGeometry()->Clone().GetPointer(); pMapJob->m_MappedName = this->m_Controls.lbNewRegName->text().toStdString() + std::string(" mapped moving data"); pMapJob->m_allowUndefPixels = true; pMapJob->m_paddingValue = 100; pMapJob->m_allowUnregPixels = true; pMapJob->m_errorValue = 200; pMapJob->m_InterpolatorLabel = "Linear Interpolation"; pMapJob->m_InterpolatorType = mitk::ImageMappingInterpolator::Linear; connect(pMapJob, SIGNAL(Error(QString)), this, SLOT(Error(QString))); connect(pMapJob, SIGNAL(MapResultIsAvailable(mitk::BaseData::Pointer, const QmitkMappingJob*)), this, SLOT(OnMapResultIsAvailable(mitk::BaseData::Pointer, const QmitkMappingJob*)), Qt::BlockingQueuedConnection); QThreadPool* threadPool = QThreadPool::globalInstance(); threadPool->start(pMapJob); } this->StopSession(); this->CheckInputs(); this->ConfigureControls(); this->GetRenderWindowPart()->RequestUpdate(); } void QmitkMatchPointRegistrationManipulator::OnMapResultIsAvailable(mitk::BaseData::Pointer spMappedData, const QmitkMappingJob* job) { mitk::DataNode::Pointer spMappedNode = mitk::generateMappedResultNode(job->m_MappedName, spMappedData, job->GetRegistration()->getRegistrationUID(), job->m_InputDataUID, job->m_doGeometryRefinement, job->m_InterpolatorLabel); this->GetDataStorage()->Add(spMappedNode); this->GetRenderWindowPart()->RequestUpdate(); } void QmitkMatchPointRegistrationManipulator::OnCenterTypeChanged(int index) { ConfigureTransformCenter(index); if (this->m_EvalNode.IsNotNull()) { this->m_EvalNode->Modified(); } if (this->m_CurrentRegistrationWrapper.IsNotNull()) { this->m_CurrentRegistrationWrapper->Modified(); } this->GetRenderWindowPart()->RequestUpdate(); } void QmitkMatchPointRegistrationManipulator::ConfigureTransformCenter(int centerType) { if (centerType == 0) { //image center auto center = m_SelectedMovingNode->GetData()->GetTimeGeometry()->GetCenterInWorld(); m_Controls.manipulationWidget->SetCenterOfRotationIsRelativeToTarget(false); m_Controls.manipulationWidget->SetCenterOfRotation(center); } else if (centerType == 1) { //world origin mitk::Point3D center; center.Fill(0.0); m_Controls.manipulationWidget->SetCenterOfRotationIsRelativeToTarget(false); m_Controls.manipulationWidget->SetCenterOfRotation(center); } else { //current selected point m_Controls.manipulationWidget->SetCenterOfRotationIsRelativeToTarget(true); m_Controls.manipulationWidget->SetCenterOfRotation(m_currentSelectedPosition); } } diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp index 5a2bfebebd..60f918782e 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp @@ -1,444 +1,473 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkImageStatisticsView.h" #include // berry includes #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "mitkPlanarFigureMaskGenerator.h" #include "QmitkImageStatisticsDataGenerator.h" #include "mitkImageStatisticsContainerManager.h" #include const std::string QmitkImageStatisticsView::VIEW_ID = "org.mitk.views.imagestatistics"; QmitkImageStatisticsView::~QmitkImageStatisticsView() { } void QmitkImageStatisticsView::CreateQtPartControl(QWidget *parent) { m_Controls.setupUi(parent); - m_Controls.widget_histogram->SetTheme(GetColorTheme()); m_Controls.widget_intensityProfile->SetTheme(GetColorTheme()); m_Controls.groupBox_histogram->setVisible(true); m_Controls.groupBox_intensityProfile->setVisible(false); m_Controls.label_currentlyComputingStatistics->setVisible(false); m_Controls.sliderWidget_histogram->setPrefix("Time: "); m_Controls.sliderWidget_histogram->setDecimals(0); m_Controls.sliderWidget_histogram->setVisible(false); m_Controls.sliderWidget_intensityProfile->setPrefix("Time: "); m_Controls.sliderWidget_intensityProfile->setDecimals(0); m_Controls.sliderWidget_intensityProfile->setVisible(false); ResetGUI(); m_DataGenerator = new QmitkImageStatisticsDataGenerator(parent); m_DataGenerator->SetDataStorage(this->GetDataStorage()); m_DataGenerator->SetAutoUpdate(true); m_Controls.widget_statistics->SetDataStorage(this->GetDataStorage()); - m_Controls.widget_histogram->SetTheme(GetColorTheme()); m_Controls.imageNodesSelector->SetDataStorage(this->GetDataStorage()); m_Controls.imageNodesSelector->SetNodePredicate(mitk::GetImageStatisticsImagePredicate()); m_Controls.imageNodesSelector->SetSelectionCheckFunction(this->CheckForSameGeometry()); m_Controls.imageNodesSelector->SetSelectionIsOptional(false); m_Controls.imageNodesSelector->SetInvalidInfo(QStringLiteral("Please select images for statistics")); m_Controls.imageNodesSelector->SetPopUpTitel(QStringLiteral("Select input images")); m_Controls.roiNodesSelector->SetPopUpHint(QStringLiteral("You may select multiple images for the statistics computation. But all selected images must have the same geometry.")); m_Controls.roiNodesSelector->SetDataStorage(this->GetDataStorage()); m_Controls.roiNodesSelector->SetNodePredicate(this->GenerateROIPredicate()); m_Controls.roiNodesSelector->SetSelectionIsOptional(true); m_Controls.roiNodesSelector->SetEmptyInfo(QStringLiteral("Please select ROIs")); m_Controls.roiNodesSelector->SetPopUpTitel(QStringLiteral("Select ROIs for statistics computation")); m_Controls.roiNodesSelector->SetPopUpHint(QStringLiteral("You may select ROIs (e.g. planar figures, segmentations) that should be used for the statistics computation. The statistics will only computed for the image parts defined by the ROIs.")); - CreateConnections(); + + this->m_TimePointChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); + connect(&m_TimePointChangeListener, &QmitkSliceNavigationListener::SelectedTimePointChanged, this, & QmitkImageStatisticsView::OnSelectedTimePointChanged); +} + +void QmitkImageStatisticsView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) +{ + this->m_TimePointChangeListener.RenderWindowPartActivated(renderWindowPart); +} + +void QmitkImageStatisticsView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) +{ + this->m_TimePointChangeListener.RenderWindowPartDeactivated(renderWindowPart); } void QmitkImageStatisticsView::CreateConnections() { connect(m_Controls.checkBox_ignoreZero, &QCheckBox::stateChanged, this, &QmitkImageStatisticsView::OnCheckBoxIgnoreZeroStateChanged); connect(m_Controls.buttonSelection, &QAbstractButton::clicked, this, &QmitkImageStatisticsView::OnButtonSelectionPressed); connect(m_Controls.widget_histogram, &QmitkHistogramVisualizationWidget::RequestHistogramUpdate, this, &QmitkImageStatisticsView::OnRequestHistogramUpdate); connect(m_DataGenerator, &QmitkImageStatisticsDataGenerator::DataGenerationStarted, this, &QmitkImageStatisticsView::OnGenerationStarted); connect(m_DataGenerator, &QmitkImageStatisticsDataGenerator::GenerationFinished, this, &QmitkImageStatisticsView::OnGenerationFinished); connect(m_DataGenerator, &QmitkImageStatisticsDataGenerator::JobError, this, &QmitkImageStatisticsView::OnJobError); connect(m_Controls.imageNodesSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkImageStatisticsView::OnImageSelectionChanged); connect(m_Controls.roiNodesSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkImageStatisticsView::OnROISelectionChanged); connect(m_Controls.sliderWidget_intensityProfile, &ctkSliderWidget::valueChanged, this, &QmitkImageStatisticsView::UpdateIntensityProfile); } void QmitkImageStatisticsView::UpdateIntensityProfile() { m_Controls.groupBox_intensityProfile->setVisible(false); const auto selectedImageNodes = m_Controls.imageNodesSelector->GetSelectedNodes(); const auto selectedROINodes = m_Controls.roiNodesSelector->GetSelectedNodes(); if (selectedImageNodes.size()==1 && selectedROINodes.size()==1) { //only supported for one image and roi currently auto image = dynamic_cast(selectedImageNodes.front()->GetData()); auto maskPlanarFigure = dynamic_cast(selectedROINodes.front()->GetData()); if (maskPlanarFigure != nullptr) { if (!maskPlanarFigure->IsClosed()) { mitk::Image::Pointer inputImage; if (image->GetDimension() == 4) { m_Controls.sliderWidget_intensityProfile->setVisible(true); unsigned int maxTimestep = image->GetTimeSteps(); m_Controls.sliderWidget_intensityProfile->setMaximum(maxTimestep - 1); // Intensity profile can only be calculated on 3D, so extract if 4D mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); int currentTimestep = static_cast(m_Controls.sliderWidget_intensityProfile->value()); timeSelector->SetInput(image); timeSelector->SetTimeNr(currentTimestep); timeSelector->Update(); inputImage = timeSelector->GetOutput(); } else { m_Controls.sliderWidget_intensityProfile->setVisible(false); inputImage = image; } auto intensityProfile = mitk::ComputeIntensityProfile(inputImage, maskPlanarFigure); m_Controls.groupBox_intensityProfile->setVisible(true); m_Controls.widget_intensityProfile->Reset(); m_Controls.widget_intensityProfile->SetIntensityProfile(intensityProfile.GetPointer(), "Intensity Profile of " + selectedImageNodes.front()->GetName()); } } } } void QmitkImageStatisticsView::UpdateHistogramWidget() { - m_Controls.groupBox_histogram->setVisible(false); + bool visibility = false; const auto selectedImageNodes = m_Controls.imageNodesSelector->GetSelectedNodes(); const auto selectedMaskNodes = m_Controls.roiNodesSelector->GetSelectedNodes(); if (selectedImageNodes.size() == 1 && selectedMaskNodes.size()<=1) { //currently only supported for one image and roi due to histogram widget limitations. auto imageNode = selectedImageNodes.front(); const mitk::DataNode* roiNode = nullptr; const mitk::PlanarFigure* planarFigure = nullptr; if (!selectedMaskNodes.empty()) { roiNode = selectedMaskNodes.front(); planarFigure = dynamic_cast(roiNode->GetData()); } - if (planarFigure == nullptr || planarFigure->IsClosed()) + if ((planarFigure == nullptr || planarFigure->IsClosed()) + && imageNode->GetData()->GetTimeGeometry()->IsValidTimePoint(m_TimePointChangeListener.GetCurrentSelectedTimePoint())) { //if a planar figure is not closed, we show the intensity profile instead of the histogram. auto statisticsNode = m_DataGenerator->GetLatestResult(imageNode, roiNode, true); if (statisticsNode.IsNotNull()) { auto statistics = dynamic_cast(statisticsNode->GetData()); if (statistics) { + const auto timeStep = imageNode->GetData()->GetTimeGeometry()->TimePointToTimeStep(m_TimePointChangeListener.GetCurrentSelectedTimePoint()); + std::stringstream label; - label << "Histogram " << imageNode->GetName(); + label << imageNode->GetName(); if (imageNode->GetData()->GetTimeSteps() > 1) { - label << "[0]"; + label << "["<< timeStep <<"]"; } if (roiNode) { label << " with " << roiNode->GetName(); } - m_Controls.widget_histogram->SetHistogram(statistics->GetHistogramForTimeStep(0), label.str()); + //Hardcoded labels are currently needed because the current histogram widget (and ChartWidget) + //do not allow correct removal or sound update/insertion of serveral charts. + //only thing that works for now is always to update/overwrite the same data label + //This is a quick fix for T28223 and T28221 + m_Controls.widget_histogram->SetHistogram(statistics->GetHistogramForTimeStep(timeStep), "histogram"); + + visibility = true; } - m_Controls.groupBox_histogram->setVisible(statisticsNode.IsNotNull()); } } } + + if (visibility != m_Controls.groupBox_histogram->isVisible()) + { + m_Controls.groupBox_histogram->setVisible(visibility); + } + } QmitkChartWidget::ColorTheme QmitkImageStatisticsView::GetColorTheme() const { ctkPluginContext *context = berry::WorkbenchPlugin::GetDefault()->GetPluginContext(); ctkServiceReference styleManagerRef = context->getServiceReference(); if (styleManagerRef) { auto styleManager = context->getService(styleManagerRef); if (styleManager->GetStyle().name == "Dark") { return QmitkChartWidget::ColorTheme::darkstyle; } else { return QmitkChartWidget::ColorTheme::lightstyle; } } return QmitkChartWidget::ColorTheme::darkstyle; } void QmitkImageStatisticsView::ResetGUI() { m_Controls.widget_statistics->Reset(); m_Controls.widget_statistics->setEnabled(false); m_Controls.widget_histogram->Reset(); m_Controls.widget_histogram->setEnabled(false); m_Controls.widget_histogram->SetTheme(GetColorTheme()); } void QmitkImageStatisticsView::OnGenerationStarted(const mitk::DataNode* /*imageNode*/, const mitk::DataNode* /*roiNode*/, const QmitkDataGenerationJobBase* /*job*/) { m_Controls.label_currentlyComputingStatistics->setVisible(true); } void QmitkImageStatisticsView::OnGenerationFinished() { m_Controls.label_currentlyComputingStatistics->setVisible(false); mitk::StatusBar::GetInstance()->Clear(); this->UpdateIntensityProfile(); this->UpdateHistogramWidget(); } +void QmitkImageStatisticsView::OnSelectedTimePointChanged(const mitk::TimePointType& /*newTimePoint*/) +{ + this->UpdateHistogramWidget(); +} + void QmitkImageStatisticsView::OnJobError(QString error, const QmitkDataGenerationJobBase* /*failedJob*/) { mitk::StatusBar::GetInstance()->DisplayErrorText(error.toStdString().c_str()); MITK_WARN << "Error when calculating statistics: " << error; } void QmitkImageStatisticsView::OnRequestHistogramUpdate(unsigned int nbins) { m_Controls.widget_statistics->SetHistogramNBins(nbins); m_DataGenerator->SetHistogramNBins(nbins); this->UpdateIntensityProfile(); this->UpdateHistogramWidget(); } void QmitkImageStatisticsView::OnCheckBoxIgnoreZeroStateChanged(int state) { auto ignoreZeroValueVoxel = (state == Qt::Unchecked) ? false : true; m_Controls.widget_statistics->SetIgnoreZeroValueVoxel(ignoreZeroValueVoxel); m_DataGenerator->SetIgnoreZeroValueVoxel(ignoreZeroValueVoxel); this->UpdateIntensityProfile(); this->UpdateHistogramWidget(); } void QmitkImageStatisticsView::OnImageSelectionChanged(QmitkAbstractNodeSelectionWidget::NodeList /*nodes*/) { auto images = m_Controls.imageNodesSelector->GetSelectedNodesStdVector(); m_Controls.widget_statistics->SetImageNodes(images); m_Controls.widget_statistics->setEnabled(!images.empty()); m_Controls.roiNodesSelector->SetNodePredicate(this->GenerateROIPredicate()); m_DataGenerator->SetAutoUpdate(false); m_DataGenerator->SetImageNodes(images); m_DataGenerator->Generate(); m_DataGenerator->SetAutoUpdate(true); this->UpdateHistogramWidget(); this->UpdateIntensityProfile(); } void QmitkImageStatisticsView::OnROISelectionChanged(QmitkAbstractNodeSelectionWidget::NodeList /*nodes*/) { auto rois = m_Controls.roiNodesSelector->GetSelectedNodesStdVector(); m_Controls.widget_statistics->SetMaskNodes(rois); m_DataGenerator->SetAutoUpdate(false); m_DataGenerator->SetROINodes(rois); m_DataGenerator->Generate(); m_DataGenerator->SetAutoUpdate(true); this->UpdateHistogramWidget(); this->UpdateIntensityProfile(); } void QmitkImageStatisticsView::OnButtonSelectionPressed() { QmitkNodeSelectionDialog* dialog = new QmitkNodeSelectionDialog(nullptr, "Select input for the statistic","You may select images and ROIs to compute their statistic. ROIs may be segmentations or planar figures."); dialog->SetDataStorage(GetDataStorage()); dialog->SetSelectionCheckFunction(CheckForSameGeometry()); // set predicates auto isPlanarFigurePredicate = mitk::GetImageStatisticsPlanarFigurePredicate(); auto isMaskPredicate = mitk::GetImageStatisticsMaskPredicate(); auto isImagePredicate = mitk::GetImageStatisticsImagePredicate(); auto isMaskOrPlanarFigurePredicate = mitk::NodePredicateOr::New(isPlanarFigurePredicate, isMaskPredicate); auto isImageOrMaskOrPlanarFigurePredicate = mitk::NodePredicateOr::New(isMaskOrPlanarFigurePredicate, isImagePredicate); dialog->SetNodePredicate(isImageOrMaskOrPlanarFigurePredicate); dialog->SetSelectionMode(QAbstractItemView::MultiSelection); dialog->SetCurrentSelection(m_Controls.imageNodesSelector->GetSelectedNodes()+m_Controls.roiNodesSelector->GetSelectedNodes()); if (dialog->exec()) { auto selectedNodeList = dialog->GetSelectedNodes(); m_Controls.imageNodesSelector->SetCurrentSelection(selectedNodeList); m_Controls.roiNodesSelector->SetCurrentSelection(selectedNodeList); } delete dialog; } QmitkNodeSelectionDialog::SelectionCheckFunctionType QmitkImageStatisticsView::CheckForSameGeometry() const { auto isMaskPredicate = mitk::GetImageStatisticsMaskPredicate(); auto lambda = [isMaskPredicate](const QmitkNodeSelectionDialog::NodeList& nodes) { if (nodes.empty()) { return std::string(); } const mitk::Image* imageNodeData = nullptr; for (auto& node : nodes) { auto castedData = dynamic_cast(node->GetData()); if (castedData != nullptr && !isMaskPredicate->CheckNode(node)) { imageNodeData = castedData; break; } } if (imageNodeData == nullptr) { std::stringstream ss; ss << "

Select at least one image.

"; return ss.str(); } auto imageGeoPredicate = mitk::NodePredicateGeometry::New(imageNodeData->GetGeometry()); auto maskGeoPredicate = mitk::NodePredicateSubGeometry::New(imageNodeData->GetGeometry()); for (auto& rightNode : nodes) { if (imageNodeData != rightNode->GetData()) { bool validGeometry = true; if (isMaskPredicate->CheckNode(rightNode)) { validGeometry = maskGeoPredicate->CheckNode(rightNode); } else if (dynamic_cast(rightNode->GetData())) { validGeometry = imageGeoPredicate->CheckNode(rightNode); } else { const mitk::PlanarFigure* planar2 = dynamic_cast(rightNode->GetData()); if (planar2) { validGeometry = mitk::PlanarFigureMaskGenerator::CheckPlanarFigureIsNotTilted(planar2->GetPlaneGeometry(), imageNodeData->GetGeometry()); } } if (!validGeometry) { std::stringstream ss; ss << "

Invalid selection: All selected nodes must have the same geometry.

Differing node i.a.: \""; ss << rightNode->GetName() <<"\"

"; return ss.str(); } } } return std::string(); }; return lambda; } mitk::NodePredicateBase::Pointer QmitkImageStatisticsView::GenerateROIPredicate() const { auto isPlanarFigurePredicate = mitk::GetImageStatisticsPlanarFigurePredicate(); auto isMaskPredicate = mitk::GetImageStatisticsMaskPredicate(); auto isMaskOrPlanarFigurePredicate = mitk::NodePredicateOr::New(isPlanarFigurePredicate, isMaskPredicate); mitk::NodePredicateBase::Pointer result = isMaskOrPlanarFigurePredicate.GetPointer(); if(!m_Controls.imageNodesSelector->GetSelectedNodes().empty()) { auto image = m_Controls.imageNodesSelector->GetSelectedNodes().front()->GetData(); auto imageGeoPredicate = mitk::NodePredicateSubGeometry::New(image->GetGeometry()); auto lambda = [image, imageGeoPredicate](const mitk::DataNode* node) { bool sameGeometry = true; if (dynamic_cast(node->GetData()) != nullptr) { sameGeometry = imageGeoPredicate->CheckNode(node); } else { const auto planar2 = dynamic_cast(node->GetData()); if (planar2) { sameGeometry = mitk::PlanarFigureMaskGenerator::CheckPlanarFigureIsNotTilted(planar2->GetPlaneGeometry(), image->GetGeometry()); } } return sameGeometry; }; result = mitk::NodePredicateAnd::New(isMaskOrPlanarFigurePredicate, mitk::NodePredicateFunction::New(lambda)).GetPointer(); } return result; } diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h index c9f8dd618b..3d5e633e39 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h @@ -1,85 +1,95 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 QMITKIMAGESTATISTICSVIEW_H #define QMITKIMAGESTATISTICSVIEW_H #include "ui_QmitkImageStatisticsViewControls.h" #include #include #include +#include #include +#include + class QmitkImageStatisticsDataGenerator; class QmitkDataGenerationJobBase; /*! \brief QmitkImageStatisticsView is a bundle that allows statistics calculation from images. Three modes are supported: 1. Statistics of one image, 2. Statistics of an image and a segmentation, 3. Statistics of an image and a Planar Figure. The statistics calculation is realized in a separate thread to keep the gui accessible during calculation. \ingroup Plugins/org.mitk.gui.qt.measurementtoolbox */ -class QmitkImageStatisticsView : public QmitkAbstractView +class QmitkImageStatisticsView : public QmitkAbstractView, public mitk::IRenderWindowPartListener { Q_OBJECT public: static const std::string VIEW_ID; /*! \brief default destructor */ ~QmitkImageStatisticsView() override; + +protected: /*! \brief Creates the widget containing the application controls, like sliders, buttons etc.*/ - void CreateQtPartControl(QWidget *parent) override; + void CreateQtPartControl(QWidget* parent) override; -protected: + void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) override; + void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) override; using HistogramType = mitk::ImageStatisticsContainer::HistogramType; void SetFocus() override { }; virtual void CreateConnections(); void UpdateIntensityProfile(); void UpdateHistogramWidget(); QmitkChartWidget::ColorTheme GetColorTheme() const; void ResetGUI(); void OnGenerationStarted(const mitk::DataNode* imageNode, const mitk::DataNode* roiNode, const QmitkDataGenerationJobBase* job); void OnGenerationFinished(); void OnJobError(QString error, const QmitkDataGenerationJobBase* failedJob); void OnRequestHistogramUpdate(unsigned int); void OnCheckBoxIgnoreZeroStateChanged(int state); void OnButtonSelectionPressed(); void OnImageSelectionChanged(QmitkAbstractNodeSelectionWidget::NodeList nodes); void OnROISelectionChanged(QmitkAbstractNodeSelectionWidget::NodeList nodes); + void OnSelectedTimePointChanged(const mitk::TimePointType& newTimePoint); // member variable Ui::QmitkImageStatisticsViewControls m_Controls; private: QmitkNodeSelectionDialog::SelectionCheckFunctionType CheckForSameGeometry() const; mitk::NodePredicateBase::Pointer GenerateROIPredicate() const; std::vector m_StatisticsForSelection; QmitkImageStatisticsDataGenerator* m_DataGenerator = nullptr; + + QmitkSliceNavigationListener m_TimePointChangeListener; + }; #endif // QMITKIMAGESTATISTICSVIEW_H diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentationUtilities.dox b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentationUtilities.dox index 86c557c429..7a44044261 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentationUtilities.dox +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentationUtilities.dox @@ -1,82 +1,91 @@ /** \page org_mitk_views_multilabelsegmentationutilities The Multilabel Segmentation Utilities \imageMacro{multilabelsegmentation_utilities.svg,"Icon of the Multilabel Segmentation Utilities Plugin",5.00} \imageMacro{QmitkMultiLabelSegmentationUtilities_Overview.png, "The Multilabel Segmentation Utilities View",16.00} \tableofcontents \section org_mitk_views_multilabelSegmentationUtilitiesOverview Overview The Multilabel Segmentation Utilities Plugin allows to postprocess existing segmentations. Currently five different operations exist:
  • \ref org_mitk_views_multilabelSegmentationUtilitiesBooleanOperations +
  • \ref org_mitk_views_multilabelSegmentationUtilitiesContourToImage +
  • \ref org_mitk_views_multilabelSegmentationUtilitiesImageMasking
  • \ref org_mitk_views_multilabelSegmentationUtilitiesMorphologicalOperations
  • \ref org_mitk_views_multilabelSegmentationUtilitiesSurfaceToImage -
  • \ref org_mitk_views_multilabelSegmentationUtilitiesImageMasking
  • \ref org_mitk_views_multilabelSegmentationUtilitiesConvertToMultiLabel
\section org_mitk_views_multilabelSegmentationUtilitiesDataSelection Data Selection All postprocessing operations provide one or more selection widgets, which allow to select the data for the operation. \section org_mitk_views_multilabelSegmentationUtilitiesBooleanOperations Boolean operations Boolean operations allows to perform the following fundamental operations on two segmentations:
  • Difference: Subtracts the second segmentation from the first segmentation.
  • Intersection: Extracts the overlapping areas of the two selected segmentations.
  • Union: Combines the two existing segmentations.
The selected segmentations must have the same geometry (size, spacing, ...) in order for the operations to work correctly. The result will be stored in a new data node as a child node of the first selected segmentation. \imageMacro{QmitkMultiLabelSegmentationUtilities_BooleanOperations.png,"Boolean operations",6.00} +\section org_mitk_views_multilabelSegmentationUtilitiesContourToImage Contour to image + +Contour to image allows to create a segmentation out of a given contour-model. +The operation requires a contour model set and a reference image. +The created segmentation image will have the same geometrical properties like the reference image (dimension, size and Geometry3D). + +\imageMacro{QmitkMultiLabelSegmentationUtilities_ContourToImage.png,"Contour to image",6.00} + +\section org_mitk_views_multilabelSegmentationUtilitiesImageMasking Image masking + +Image masking allows to mask an image with either an existing segmentation or a surface. +The operation requires an image and a binary image mask or a surface. +The result will be an image containing only the pixels that are covered by the respective mask. +Depending on the selected mode ("make output binary" or "overwrite foreground" / "overwrite background") +the result will be a simple image or a binary image. + +\imageMacro{QmitkMultiLabelSegmentationUtilities_ImageMasking.png,"Image masking",6.00} + \section org_mitk_views_multilabelSegmentationUtilitiesMorphologicalOperations Morphological operations Morphological operations are applied to a single segmentation image. Based on a given structuring element the underlying segmentation will be modfied. The plugin provides a ball and a cross as structuring elements. The follow operations are available:
  • Dilation: Each labeled pixel within the segmentation will be dilated based on the selected structuring element.
  • Erosion: Each labeled pixel within the segmentation will be eroded based on the selected structuring element.
  • Closing: An erosion followed by a dilation, used for filling small holes.
  • Opening: A dilation followed by an erosion, used for smoothing edges or eliminating small objects.
  • Fill Holes: Fills bigger holes within a segmentation.
\imageMacro{QmitkMultiLabelSegmentationUtilities_MorphologicalOperations.png,"Morphological operations",6.00} \section org_mitk_views_multilabelSegmentationUtilitiesSurfaceToImage Surface to image Surface to image allows to create a segmentation out of a given surface. The operation requires a surface and a reference image. The created segmentation image will have the same geometrical properties like the reference image (dimension, size and Geometry3D). Depending on the selected mode ("make output binary" or "overwrite background") the result will be a simple image or a binary image. \imageMacro{QmitkMultiLabelSegmentationUtilities_SurfaceToImage.png,"Surface to image",6.00} -\section org_mitk_views_multilabelSegmentationUtilitiesImageMasking Image masking - -Image masking allows to mask an image with either an existing segmentation or a surface. -The operation requires an image and a binary image mask or a surface. -The result will be an image containing only the pixels that are covered by the respective mask. -Depending on the selected mode ("make output binary" or "overwrite foreground" / "overwrite background") -the result will be a simple image or a binary image. - -\imageMacro{QmitkMultiLabelSegmentationUtilities_ImageMasking.png,"Image masking",6.00} - \section org_mitk_views_multilabelSegmentationUtilitiesConvertToMultiLabel Convert to Multilabel Convert to multilabel allows to interpret the pixel values of a given image as label IDs and convert the image content into the respective Multilabel image. The new segmentation will contain one layer with as many labels as the original image contains different pixel values. \imageMacro{QmitkMultiLabelSegmentationUtilities_ConvertToMultilabel.png,"Convert to Multilabel",6.00} **/ diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentationUtilities_ContourToImage.png b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentationUtilities_ContourToImage.png new file mode 100644 index 0000000000..3d1bd4b980 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.multilabelsegmentation/documentation/UserManual/QmitkMultiLabelSegmentationUtilities_ContourToImage.png differ diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/files.cmake b/Plugins/org.mitk.gui.qt.multilabelsegmentation/files.cmake index d1857f2cda..7906c490d9 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/files.cmake +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/files.cmake @@ -1,103 +1,106 @@ set(SRC_CPP_FILES QmitkMultiLabelSegmentationPreferencePage.cpp ) set(INTERNAL_CPP_FILES mitkPluginActivator.cpp QmitkMultiLabelSegmentationView.cpp QmitkThresholdAction.cpp QmitkConvertSurfaceToLabelAction.cpp QmitkConvertMaskToLabelAction.cpp QmitkConvertToMultiLabelSegmentationAction.cpp QmitkCreateMultiLabelSegmentationAction.cpp QmitkLoadMultiLabelPresetAction.cpp QmitkCreateMultiLabelPresetAction.cpp Common/QmitkDataSelectionWidget.cpp SegmentationUtilities/QmitkMultiLabelSegmentationUtilitiesView.cpp SegmentationUtilities/QmitkSegmentationUtilityWidget.cpp SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.cpp + SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidget.cpp SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.cpp SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp SegmentationUtilities/ConvertToMl/QmitkConvertToMlWidget.cpp ) set(UI_FILES src/internal/QmitkMultiLabelSegmentationControls.ui src/internal/Common/QmitkDataSelectionWidgetControls.ui src/internal/SegmentationUtilities/QmitkMultiLabelSegmentationUtilitiesViewControls.ui src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidgetControls.ui + src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidgetControls.ui src/internal/SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidgetControls.ui src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidgetControls.ui src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui src/internal/SegmentationUtilities/ConvertToMl/QmitkConvertToMlWidgetControls.ui ) set(MOC_H_FILES src/QmitkMultiLabelSegmentationPreferencePage.h src/internal/mitkPluginActivator.h src/internal/QmitkMultiLabelSegmentationView.h src/internal/QmitkThresholdAction.h src/internal/QmitkConvertSurfaceToLabelAction.h src/internal/QmitkLoadMultiLabelPresetAction.h src/internal/QmitkCreateMultiLabelPresetAction.h src/internal/QmitkConvertMaskToLabelAction.h src/internal/QmitkConvertToMultiLabelSegmentationAction.h src/internal/QmitkCreateMultiLabelSegmentationAction.h src/internal/Common/QmitkDataSelectionWidget.h src/internal/SegmentationUtilities/QmitkMultiLabelSegmentationUtilitiesView.h src/internal/SegmentationUtilities/QmitkSegmentationUtilityWidget.h src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.h + src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.h src/internal/SegmentationUtilities/MorphologicalOperations/QmitkMorphologicalOperationsWidget.h src/internal/SegmentationUtilities/SurfaceToImage/QmitkSurfaceToImageWidget.h src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h src/internal/SegmentationUtilities/ConvertToMl/QmitkConvertToMlWidget.h ) set(CACHED_RESOURCE_FILES resources/BooleanDifference_48x48.png resources/BooleanIntersection_48x48.png resources/BooleanOperations_48x48.png resources/BooleanUnion_48x48.png resources/Closing_48x48.png resources/CTKWidgets_48x48.png resources/deformablePlane.png resources/Dilate_48x48.png resources/Erode_48x48.png resources/FillHoles_48x48.png resources/Icons.svg resources/ImageMasking_48x48.png resources/MorphologicalOperations_48x48.png resources/multilabelsegmentation.svg resources/multilabelsegmentation_utilities.svg resources/NewLabel_48x48.png resources/NewSegmentationSession_48x48.png resources/Opening_48x48.png resources/SurfaceToImage_48x48.png plugin.xml ) set(QRC_FILES resources/multilabelsegmentation.qrc resources/MultiLabelSegmentationUtilities.qrc resources/MorphologicalOperationsWidget.qrc resources/BooleanOperationsWidget.qrc ) set(CPP_FILES) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) #usFunctionEmbedResources( #CPP_FILES # LIBRARY_NAME "liborg_mitk_gui_qt_multilabelsegmentation" #ROOT_DIR resources #FILES Interactions/SegmentationInteraction.xml # Interactions/ConfigSegmentation.xml #) 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.multilabelsegmentation/resources/ContourModelSetToImage_48x48.png b/Plugins/org.mitk.gui.qt.multilabelsegmentation/resources/ContourModelSetToImage_48x48.png new file mode 100644 index 0000000000..43b53ece52 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.multilabelsegmentation/resources/ContourModelSetToImage_48x48.png differ diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/resources/MultiLabelSegmentationUtilities.qrc b/Plugins/org.mitk.gui.qt.multilabelsegmentation/resources/MultiLabelSegmentationUtilities.qrc index 44a56f1ae5..f1f88d9114 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/resources/MultiLabelSegmentationUtilities.qrc +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/resources/MultiLabelSegmentationUtilities.qrc @@ -1,11 +1,12 @@ BooleanOperations_48x48.png + ContourModelSetToImage_48x48.png ImageMasking_48x48.png MorphologicalOperations_48x48.png SurfaceToImage_48x48.png multilabelsegmentation_utilities.svg CTKWidgets_48x48.png multilabelsegmentation.svg diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/QmitkMultiLabelSegmentationPreferencePage.cpp b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/QmitkMultiLabelSegmentationPreferencePage.cpp index 305d5fd4a9..ae6433cdce 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/QmitkMultiLabelSegmentationPreferencePage.cpp +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/QmitkMultiLabelSegmentationPreferencePage.cpp @@ -1,166 +1,151 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkMultiLabelSegmentationPreferencePage.h" #include #include #include #include #include #include #include #include #include #include QmitkMultiLabelSegmentationPreferencePage::QmitkMultiLabelSegmentationPreferencePage() -: m_MainControl(nullptr) -, m_Initializing(false) + : m_MainControl(nullptr), + m_RadioOutline(nullptr), + m_RadioOverlay(nullptr), + m_SmoothingSpinBox(nullptr), + m_DecimationSpinBox(nullptr), + m_SelectionModeCheckBox(nullptr), + m_Initializing(false) { } QmitkMultiLabelSegmentationPreferencePage::~QmitkMultiLabelSegmentationPreferencePage() { } void QmitkMultiLabelSegmentationPreferencePage::Init(berry::IWorkbench::Pointer ) { } void QmitkMultiLabelSegmentationPreferencePage::CreateQtControl(QWidget* parent) { m_Initializing = true; berry::IPreferencesService* prefService = berry::Platform::GetPreferencesService(); m_SegmentationPreferencesNode = prefService->GetSystemPreferences()->Node("/org.mitk.views.multilabelsegmentation"); m_MainControl = new QWidget(parent); QVBoxLayout* displayOptionsLayout = new QVBoxLayout; m_RadioOutline = new QRadioButton( "Draw as outline", m_MainControl); displayOptionsLayout->addWidget( m_RadioOutline ); m_RadioOverlay = new QRadioButton( "Draw as transparent overlay", m_MainControl); displayOptionsLayout->addWidget( m_RadioOverlay ); QFormLayout *formLayout = new QFormLayout; formLayout->setHorizontalSpacing(8); formLayout->setVerticalSpacing(24); formLayout->addRow( "2D display", displayOptionsLayout ); - m_VolumeRenderingCheckBox = new QCheckBox( "Show as volume rendering", m_MainControl ); - formLayout->addRow( "3D display", m_VolumeRenderingCheckBox ); - connect( m_VolumeRenderingCheckBox, SIGNAL(stateChanged(int)), this, SLOT(OnVolumeRenderingCheckboxChecked(int)) ); - QFormLayout* surfaceLayout = new QFormLayout; surfaceLayout->setSpacing(8); m_SmoothingSpinBox = new QDoubleSpinBox(m_MainControl); m_SmoothingSpinBox->setMinimum(0.0); m_SmoothingSpinBox->setSingleStep(0.5); m_SmoothingSpinBox->setValue(0.1); m_SmoothingSpinBox->setToolTip("The Smoothing value is used as Sigma for a gaussian blur."); surfaceLayout->addRow("Smoothing value (mm)", m_SmoothingSpinBox); m_DecimationSpinBox = new QDoubleSpinBox(m_MainControl); m_DecimationSpinBox->setMinimum(0.0); m_DecimationSpinBox->setMaximum(0.99); m_DecimationSpinBox->setSingleStep(0.1); m_DecimationSpinBox->setValue(0.5); m_DecimationSpinBox->setToolTip("Valid range is [0, 1). High values increase decimation, especially when very close to 1. A value of 0 disables decimation."); surfaceLayout->addRow("Decimation rate", m_DecimationSpinBox); m_SelectionModeCheckBox = new QCheckBox("Enable auto-selection mode", m_MainControl); m_SelectionModeCheckBox->setToolTip("If checked the segmentation plugin ensures that only one segmentation and the according greyvalue image are visible at one time."); formLayout->addRow("Data node selection mode",m_SelectionModeCheckBox); formLayout->addRow("Smoothed surface creation", surfaceLayout); m_MainControl->setLayout(formLayout); this->Update(); m_Initializing = false; } QWidget* QmitkMultiLabelSegmentationPreferencePage::GetQtControl() const { return m_MainControl; } bool QmitkMultiLabelSegmentationPreferencePage::PerformOk() { m_SegmentationPreferencesNode->PutBool("draw outline", m_RadioOutline->isChecked()); - m_SegmentationPreferencesNode->PutBool("volume rendering", m_VolumeRenderingCheckBox->isChecked()); m_SegmentationPreferencesNode->PutDouble("smoothing value", m_SmoothingSpinBox->value()); m_SegmentationPreferencesNode->PutDouble("decimation rate", m_DecimationSpinBox->value()); m_SegmentationPreferencesNode->PutBool("auto selection", m_SelectionModeCheckBox->isChecked()); return true; } void QmitkMultiLabelSegmentationPreferencePage::PerformCancel() { } void QmitkMultiLabelSegmentationPreferencePage::Update() { //m_EnableSingleEditing->setChecked(m_SegmentationPreferencesNode->GetBool("Single click property editing", true)); if (m_SegmentationPreferencesNode->GetBool("draw outline", true) ) { m_RadioOutline->setChecked( true ); } else { m_RadioOverlay->setChecked( true ); } - m_VolumeRenderingCheckBox->setChecked( m_SegmentationPreferencesNode->GetBool("volume rendering", false) ); - if (m_SegmentationPreferencesNode->GetBool("smoothing hint", true)) { m_SmoothingSpinBox->setDisabled(true); } else { m_SmoothingSpinBox->setEnabled(true); } m_SelectionModeCheckBox->setChecked( m_SegmentationPreferencesNode->GetBool("auto selection", false) ); m_SmoothingSpinBox->setValue(m_SegmentationPreferencesNode->GetDouble("smoothing value", 0.1)); m_DecimationSpinBox->setValue(m_SegmentationPreferencesNode->GetDouble("decimation rate", 0.5)); } -void QmitkMultiLabelSegmentationPreferencePage::OnVolumeRenderingCheckboxChecked(int state) -{ - if (m_Initializing) return; - - if ( state != Qt::Unchecked ) - { - QMessageBox::information(nullptr, - "Memory warning", - "Turning on volume rendering of segmentations will make the application more memory intensive (and potentially prone to crashes).\n\n" - "If you encounter out-of-memory problems, try turning off volume rendering again."); - } -} - void QmitkMultiLabelSegmentationPreferencePage::OnSmoothingCheckboxChecked(int state) { if (state != Qt::Unchecked) m_SmoothingSpinBox->setDisabled(true); else m_SmoothingSpinBox->setEnabled(true); } diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/QmitkMultiLabelSegmentationPreferencePage.h b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/QmitkMultiLabelSegmentationPreferencePage.h index b020541197..6eb6075a4e 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/QmitkMultiLabelSegmentationPreferencePage.h +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/QmitkMultiLabelSegmentationPreferencePage.h @@ -1,77 +1,75 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkMultiLabelSegmentationPreferencePage_h_included #define QmitkMultiLabelSegmentationPreferencePage_h_included #include "berryIQtPreferencePage.h" #include "org_mitk_gui_qt_multilabelsegmentation_Export.h" #include class QWidget; class QCheckBox; class QRadioButton; class QDoubleSpinBox; class MITK_QT_SEGMENTATION QmitkMultiLabelSegmentationPreferencePage : public QObject, public berry::IQtPreferencePage { Q_OBJECT Q_INTERFACES(berry::IPreferencePage) public: QmitkMultiLabelSegmentationPreferencePage(); ~QmitkMultiLabelSegmentationPreferencePage() override; void Init(berry::IWorkbench::Pointer workbench) override; void CreateQtControl(QWidget* widget) override; QWidget* GetQtControl() const override; /// /// \see IPreferencePage::PerformOk() /// bool PerformOk() override; /// /// \see IPreferencePage::PerformCancel() /// void PerformCancel() override; /// /// \see IPreferencePage::Update() /// void Update() override; protected slots: - void OnVolumeRenderingCheckboxChecked(int); void OnSmoothingCheckboxChecked(int); protected: QWidget* m_MainControl; QRadioButton* m_RadioOutline; QRadioButton* m_RadioOverlay; - QCheckBox* m_VolumeRenderingCheckBox; QDoubleSpinBox* m_SmoothingSpinBox; QDoubleSpinBox* m_DecimationSpinBox; QCheckBox* m_SelectionModeCheckBox; bool m_Initializing; berry::IPreferences::Pointer m_SegmentationPreferencesNode; }; #endif /* QMITKDATAMANAGERPREFERENCEPAGE_H_ */ diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/Common/QmitkDataSelectionWidget.cpp b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/Common/QmitkDataSelectionWidget.cpp index 1dc33be279..4e32b042d5 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/Common/QmitkDataSelectionWidget.cpp +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/Common/QmitkDataSelectionWidget.cpp @@ -1,225 +1,249 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkDataSelectionWidget.h" #include "internal/mitkPluginActivator.h" #include + +#include +#include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include static mitk::NodePredicateBase::Pointer CreatePredicate(QmitkDataSelectionWidget::PredicateType predicateType) { + auto nonHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateOr::New( + mitk::NodePredicateProperty::New("helper object"), + mitk::NodePredicateProperty::New("hidden object"))); + + auto imageType = mitk::TNodePredicateDataType::New(); + auto contourModelType = mitk::TNodePredicateDataType::New(); + auto contourModelSetType = mitk::TNodePredicateDataType::New(); - mitk::NodePredicateAnd::Pointer segmentationPredicate = mitk::NodePredicateAnd::New(); - segmentationPredicate->AddPredicate(mitk::TNodePredicateDataType::New()); - segmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); + auto segmentationPredicate = mitk::TNodePredicateDataType::New(); - mitk::NodePredicateAnd::Pointer maskPredicate = mitk::NodePredicateAnd::New(); - maskPredicate->AddPredicate(mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true))); - maskPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true)))); + auto maskPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); - mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); - mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); - mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage"); - mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); + auto isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); + auto isDti = mitk::NodePredicateDataType::New("TensorImage"); + auto isOdf = mitk::NodePredicateDataType::New("OdfImage"); + auto isImage = mitk::TNodePredicateDataType::New(); - mitk::NodePredicateOr::Pointer validImages = mitk::NodePredicateOr::New(); + auto validImages = mitk::NodePredicateOr::New(); validImages->AddPredicate(isImage); validImages->AddPredicate(isDwi); validImages->AddPredicate(isDti); validImages->AddPredicate(isOdf); - mitk::NodePredicateAnd::Pointer imagePredicate = mitk::NodePredicateAnd::New(); + auto imagePredicate = mitk::NodePredicateAnd::New(); imagePredicate->AddPredicate(validImages); imagePredicate->AddPredicate(mitk::NodePredicateNot::New(segmentationPredicate)); imagePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)))); - imagePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true)))); - mitk::NodePredicateAnd::Pointer surfacePredicate = mitk::NodePredicateAnd::New(); - surfacePredicate->AddPredicate(mitk::TNodePredicateDataType::New()); - surfacePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true)))); + auto surfacePredicate = mitk::TNodePredicateDataType::New(); + + mitk::NodePredicateBase::Pointer result; switch(predicateType) { case QmitkDataSelectionWidget::ImagePredicate: - return imagePredicate.GetPointer(); - - case QmitkDataSelectionWidget::MaskPredicate: - return maskPredicate.GetPointer(); + result = imagePredicate.GetPointer(); + break; case QmitkDataSelectionWidget::SegmentationPredicate: - return segmentationPredicate.GetPointer(); + result = segmentationPredicate.GetPointer(); + break; case QmitkDataSelectionWidget::SurfacePredicate: - return surfacePredicate.GetPointer(); + result = surfacePredicate.GetPointer(); + break; + + case QmitkDataSelectionWidget::ImageAndSegmentationPredicate: + result = imageType.GetPointer(); + break; + + case QmitkDataSelectionWidget::ContourModelPredicate: + result = mitk::NodePredicateOr::New( + contourModelSetType, + contourModelSetType).GetPointer(); + break; + + case QmitkDataSelectionWidget::MaskPredicate: + result = maskPredicate.GetPointer(); + break; default: assert(false && "Unknown predefined predicate!"); return nullptr; } + + return mitk::NodePredicateAnd::New(result, nonHelperObject).GetPointer(); } QmitkDataSelectionWidget::QmitkDataSelectionWidget(QWidget* parent) : QWidget(parent) { m_Controls.setupUi(this); m_Controls.helpLabel->hide(); } QmitkDataSelectionWidget::~QmitkDataSelectionWidget() { } unsigned int QmitkDataSelectionWidget::AddDataSelection(QmitkDataSelectionWidget::PredicateType predicate) { QString hint = "Select node"; - QString popupTitel = "Select node"; switch (predicate) { case QmitkDataSelectionWidget::ImagePredicate: hint = "Select an image"; - popupTitel = "Select an image"; break; case QmitkDataSelectionWidget::MaskPredicate: hint = "Select a binary mask"; - popupTitel = "Select a binary mask"; break; case QmitkDataSelectionWidget::SegmentationPredicate: hint = "Select an ML segmentation"; - popupTitel = "Select an ML segmentation"; break; case QmitkDataSelectionWidget::SurfacePredicate: hint = "Select a surface"; - popupTitel = "Select a surface"; + break; + + case QmitkDataSelectionWidget::ImageAndSegmentationPredicate: + hint = "Select an image or segmentation"; + break; + + case QmitkDataSelectionWidget::ContourModelPredicate: + hint = "Select a contour model"; break; } - return this->AddDataSelection("", hint, popupTitel, "", predicate); + return this->AddDataSelection("", hint, hint, "", predicate); } unsigned int QmitkDataSelectionWidget::AddDataSelection(mitk::NodePredicateBase* predicate) { return this->AddDataSelection("", "Select a node", "Select a node", "", predicate); } unsigned int QmitkDataSelectionWidget::AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, QmitkDataSelectionWidget::PredicateType predicate) { return this->AddDataSelection(labelText, info, popupHint, popupTitel, CreatePredicate(predicate)); } unsigned int QmitkDataSelectionWidget::AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, mitk::NodePredicateBase* predicate) { int row = m_Controls.gridLayout->rowCount(); if (!labelText.isEmpty()) { QLabel* label = new QLabel(labelText, m_Controls.dataSelectionWidget); label->setSizePolicy(QSizePolicy::Maximum, QSizePolicy::Preferred); m_Controls.gridLayout->addWidget(label, row, 0); } QmitkSingleNodeSelectionWidget* nodeSelection = new QmitkSingleNodeSelectionWidget(m_Controls.dataSelectionWidget); nodeSelection->SetSelectionIsOptional(false); nodeSelection->SetAutoSelectNewNodes(false); nodeSelection->SetInvalidInfo(info); nodeSelection->SetPopUpTitel(popupTitel); nodeSelection->SetPopUpHint(popupHint); nodeSelection->SetDataStorage(this->GetDataStorage()); nodeSelection->SetNodePredicate(predicate); nodeSelection->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Minimum); nodeSelection->setMinimumSize(0, 40); connect(nodeSelection, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkDataSelectionWidget::OnSelectionChanged); m_Controls.gridLayout->addWidget(nodeSelection, row, 1); m_NodeSelectionWidgets.push_back(nodeSelection); return static_cast(m_NodeSelectionWidgets.size() - 1); } mitk::DataStorage::Pointer QmitkDataSelectionWidget::GetDataStorage() const { ctkServiceReference ref = mitk::PluginActivator::getContext()->getServiceReference(); assert(ref == true); mitk::IDataStorageService* service = mitk::PluginActivator::getContext()->getService(ref); assert(service); return service->GetDefaultDataStorage()->GetDataStorage(); } mitk::DataNode::Pointer QmitkDataSelectionWidget::GetSelection(unsigned int index) { assert(index < m_NodeSelectionWidgets.size()); return m_NodeSelectionWidgets[index]->GetSelectedNode(); } void QmitkDataSelectionWidget::SetPredicate(unsigned int index, PredicateType predicate) { this->SetPredicate(index, CreatePredicate(predicate)); } void QmitkDataSelectionWidget::SetPredicate(unsigned int index, mitk::NodePredicateBase* predicate) { assert(index < m_NodeSelectionWidgets.size()); m_NodeSelectionWidgets[index]->SetNodePredicate(predicate); } void QmitkDataSelectionWidget::SetHelpText(const QString& text) { if (!text.isEmpty()) { m_Controls.helpLabel->setText(text); if (!m_Controls.helpLabel->isVisible()) m_Controls.helpLabel->show(); } else { m_Controls.helpLabel->hide(); } } void QmitkDataSelectionWidget::OnSelectionChanged(QList selection) { std::vector::iterator it = std::find(m_NodeSelectionWidgets.begin(), m_NodeSelectionWidgets.end(), sender()); assert(it != m_NodeSelectionWidgets.end()); const mitk::DataNode* result = nullptr; if (!selection.empty()) { result = selection.front(); } emit SelectionChanged(std::distance(m_NodeSelectionWidgets.begin(), it), result); } diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/Common/QmitkDataSelectionWidget.h b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/Common/QmitkDataSelectionWidget.h index 2b485e207e..021ec73920 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/Common/QmitkDataSelectionWidget.h +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/Common/QmitkDataSelectionWidget.h @@ -1,66 +1,68 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 QmitkDataSelectionWidget_h #define QmitkDataSelectionWidget_h #include #include #include #include namespace mitk { class NodePredicateBase; } class QmitkSingleNodeSelectionWidget; class QmitkDataSelectionWidget : public QWidget { Q_OBJECT public: enum PredicateType { ImagePredicate, - MaskPredicate, SegmentationPredicate, - SurfacePredicate + SurfacePredicate, + ImageAndSegmentationPredicate, + ContourModelPredicate, + MaskPredicate }; explicit QmitkDataSelectionWidget(QWidget* parent = nullptr); ~QmitkDataSelectionWidget() override; unsigned int AddDataSelection(PredicateType predicate); unsigned int AddDataSelection(mitk::NodePredicateBase* predicate = nullptr); unsigned int AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, PredicateType predicate); unsigned int AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, mitk::NodePredicateBase* predicate = nullptr); mitk::DataStorage::Pointer GetDataStorage() const; mitk::DataNode::Pointer GetSelection(unsigned int index); void SetPredicate(unsigned int index, PredicateType predicate); void SetPredicate(unsigned int index, mitk::NodePredicateBase* predicate); void SetHelpText(const QString& text); signals: void SelectionChanged(unsigned int index, const mitk::DataNode* selection); private slots: void OnSelectionChanged(QList selection); private: Ui::QmitkDataSelectionWidgetControls m_Controls; std::vector m_NodeSelectionWidgets; }; #endif diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkConvertToMultiLabelSegmentationAction.cpp b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkConvertToMultiLabelSegmentationAction.cpp index 4cb6bfe1ce..2e334747df 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkConvertToMultiLabelSegmentationAction.cpp +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkConvertToMultiLabelSegmentationAction.cpp @@ -1,83 +1,83 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkConvertToMultiLabelSegmentationAction.h" #include "mitkLabelSetImage.h" #include "mitkRenderingManager.h" //needed for qApp #include QmitkConvertToMultiLabelSegmentationAction::QmitkConvertToMultiLabelSegmentationAction() { } QmitkConvertToMultiLabelSegmentationAction::~QmitkConvertToMultiLabelSegmentationAction() { } void QmitkConvertToMultiLabelSegmentationAction::Run( const QList &selectedNodes ) { - for (auto referenceNode : selectedNodes) + for (const auto &referenceNode : selectedNodes) { if (referenceNode.IsNotNull()) { mitk::Image* referenceImage = dynamic_cast(referenceNode->GetData()); if (nullptr == referenceImage) { MITK_WARN << "Could not convert to multi label segmentation for non-image node - skipping action."; continue; } mitk::LabelSetImage::Pointer lsImage = mitk::LabelSetImage::New(); try { lsImage->InitializeByLabeledImage(referenceImage); } catch (mitk::Exception &e) { MITK_ERROR << "Exception caught: " << e.GetDescription(); return; } if (m_DataStorage.IsNotNull()) { mitk::DataNode::Pointer newNode = mitk::DataNode::New(); std::string newName = referenceNode->GetName(); newName += "-labels"; newNode->SetName(newName); newNode->SetData(lsImage); m_DataStorage->Add(newNode,referenceNode); } lsImage->Modified(); } } } void QmitkConvertToMultiLabelSegmentationAction::SetDataStorage(mitk::DataStorage* dataStorage) { m_DataStorage = dataStorage; } void QmitkConvertToMultiLabelSegmentationAction::SetFunctionality(berry::QtViewPart* /*functionality*/) { //not needed } void QmitkConvertToMultiLabelSegmentationAction::SetSmoothed(bool) { //not needed } void QmitkConvertToMultiLabelSegmentationAction::SetDecimated(bool) { //not needed } diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkCreateMultiLabelPresetAction.cpp b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkCreateMultiLabelPresetAction.cpp index 37facd0558..5c245ed824 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkCreateMultiLabelPresetAction.cpp +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkCreateMultiLabelPresetAction.cpp @@ -1,63 +1,63 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkCreateMultiLabelPresetAction.h" #include #include #include #include void QmitkCreateMultiLabelPresetAction::Run(const QList &selectedNodes) { - for (auto node : selectedNodes) + for (const auto &node : selectedNodes) { if (node.IsNull()) continue; mitk::LabelSetImage::Pointer image = dynamic_cast(node->GetData()); if (image.IsNull()) continue; const auto filename = QFileDialog::getSaveFileName(nullptr, QStringLiteral("Save LabelSet Preset"), QString(), QStringLiteral("LabelSet Preset (*.lsetp)")).toStdString(); if (filename.empty()) continue; if(!mitk::LabelSetIOHelper::SaveLabelSetImagePreset(filename, image)) { QMessageBox::critical(nullptr, QStringLiteral("Save LabelSetImage Preset"), QString("Could not save \"%1\" as preset.").arg(QString::fromStdString(node->GetName()))); continue; } } } void QmitkCreateMultiLabelPresetAction::SetDataStorage(mitk::DataStorage*) { } void QmitkCreateMultiLabelPresetAction::SetFunctionality(berry::QtViewPart*) { } void QmitkCreateMultiLabelPresetAction::SetSmoothed(bool) { } void QmitkCreateMultiLabelPresetAction::SetDecimated(bool) { } diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkCreateMultiLabelSegmentationAction.cpp b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkCreateMultiLabelSegmentationAction.cpp index 723f3b00eb..d476aa0b44 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkCreateMultiLabelSegmentationAction.cpp +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkCreateMultiLabelSegmentationAction.cpp @@ -1,120 +1,120 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkCreateMultiLabelSegmentationAction.h" #include "mitkLabelSetImage.h" #include "mitkRenderingManager.h" #include "QInputDialog" #include "QMessageBox" #include "QmitkNewSegmentationDialog.h" #include "QmitkMultiLabelSegmentationView.h" #include "QmitkSegmentationOrganNamesHandling.cpp" //needed for qApp #include QmitkCreateMultiLabelSegmentationAction::QmitkCreateMultiLabelSegmentationAction() { } QmitkCreateMultiLabelSegmentationAction::~QmitkCreateMultiLabelSegmentationAction() { } void QmitkCreateMultiLabelSegmentationAction::Run( const QList &selectedNodes ) { if (m_DataStorage.IsNull()) { auto message = tr("Data storage not set."); MITK_ERROR << message; QMessageBox::warning(nullptr, "New Segmentation Session", message); return; } - for ( auto referenceNode : selectedNodes ) + for ( const auto &referenceNode : selectedNodes ) { if (referenceNode.IsNotNull()) { mitk::Image* referenceImage = dynamic_cast( referenceNode->GetData() ); if (nullptr == referenceImage) { MITK_WARN << "Could not create multi label segmentation for non-image node - skipping action."; continue; } QString newName = QString::fromStdString(referenceNode->GetName()); newName.append("-labels"); bool ok = false; newName = QInputDialog::getText(nullptr, "New Segmentation Session", "New name:", QLineEdit::Normal, newName, &ok); if(!ok) return; mitk::LabelSetImage::Pointer workingImage = mitk::LabelSetImage::New(); try { workingImage->Initialize(referenceImage); } catch ( mitk::Exception& e ) { MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::warning(nullptr, "New Segmentation Session", "Could not create a new segmentation session."); return; } mitk::DataNode::Pointer workingNode = mitk::DataNode::New(); workingNode->SetData(workingImage); workingNode->SetName(newName.toStdString()); // set additional image information workingImage->GetExteriorLabel()->SetProperty("name.parent",mitk::StringProperty::New(referenceNode->GetName().c_str())); workingImage->GetExteriorLabel()->SetProperty("name.image",mitk::StringProperty::New(newName.toStdString().c_str())); if (!m_DataStorage->Exists(workingNode)) m_DataStorage->Add(workingNode, referenceNode); QmitkNewSegmentationDialog* dialog = new QmitkNewSegmentationDialog( ); dialog->SetSuggestionList( mitk::OrganNamesHandling::GetDefaultOrganColorString()); dialog->setWindowTitle("New Label"); int dialogReturnValue = dialog->exec(); if ( dialogReturnValue == QDialog::Rejected ) return; QString segName = dialog->GetSegmentationName(); if(segName.isEmpty()) segName = "Unnamed"; workingImage->GetActiveLabelSet()->AddLabel(segName.toStdString(), dialog->GetColor()); } } } void QmitkCreateMultiLabelSegmentationAction::SetDataStorage(mitk::DataStorage* dataStorage) { m_DataStorage = dataStorage; } void QmitkCreateMultiLabelSegmentationAction::SetFunctionality(berry::QtViewPart*) { //not needed } void QmitkCreateMultiLabelSegmentationAction::SetSmoothed(bool) { //not needed } void QmitkCreateMultiLabelSegmentationAction::SetDecimated(bool) { //not needed } diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkLoadMultiLabelPresetAction.cpp b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkLoadMultiLabelPresetAction.cpp index b5ab7769e2..b013a31949 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkLoadMultiLabelPresetAction.cpp +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkLoadMultiLabelPresetAction.cpp @@ -1,56 +1,56 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkLoadMultiLabelPresetAction.h" #include #include #include void QmitkLoadMultiLabelPresetAction::Run(const QList &selectedNodes) { const auto filename = QFileDialog::getOpenFileName(nullptr, QStringLiteral("Load LabelSet Preset"), QString(), QStringLiteral("LabelSet Preset (*.lsetp)")).toStdString(); if (filename.empty()) return; - for (auto node : selectedNodes) + for (const auto &node : selectedNodes) { if (node.IsNull()) continue; mitk::LabelSetImage::Pointer image = dynamic_cast(node->GetData()); if (image.IsNull()) continue; mitk::LabelSetIOHelper::LoadLabelSetImagePreset(filename, image); } } void QmitkLoadMultiLabelPresetAction::SetDataStorage(mitk::DataStorage*) { } void QmitkLoadMultiLabelPresetAction::SetFunctionality(berry::QtViewPart*) { } void QmitkLoadMultiLabelPresetAction::SetSmoothed(bool) { } void QmitkLoadMultiLabelPresetAction::SetDecimated(bool) { } diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkMultiLabelSegmentationView.cpp b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkMultiLabelSegmentationView.cpp index 7af75c5031..83489b5ac7 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkMultiLabelSegmentationView.cpp +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/QmitkMultiLabelSegmentationView.cpp @@ -1,1102 +1,1093 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkMultiLabelSegmentationView.h" // blueberry #include #include // mitk #include "mitkApplicationCursor.h" #include "mitkLabelSetImage.h" #include "mitkStatusBar.h" #include "mitkToolManagerProvider.h" #include "mitkInteractionEventObserver.h" #include "mitkPlanePositionManager.h" #include "mitkPluginActivator.h" #include "mitkSegTool2D.h" #include "mitkImageTimeSelector.h" #include "mitkNodePredicateSubGeometry.h" // Qmitk #include #include "QmitkNewSegmentationDialog.h" #include "QmitkRenderWindow.h" #include "QmitkSegmentationOrganNamesHandling.cpp" #include "QmitkCreateMultiLabelPresetAction.h" #include "QmitkLoadMultiLabelPresetAction.h" // us #include #include #include #include #include // Qt #include #include #include #include #include #include #include const std::string QmitkMultiLabelSegmentationView::VIEW_ID = "org.mitk.views.multilabelsegmentation"; QmitkMultiLabelSegmentationView::QmitkMultiLabelSegmentationView() : m_Parent(nullptr), m_IRenderWindowPart(nullptr), m_ToolManager(nullptr), m_ReferenceNode(nullptr), m_WorkingNode(nullptr), m_AutoSelectionEnabled(false), m_MouseCursorSet(false) { m_SegmentationPredicate = mitk::NodePredicateAnd::New(); m_SegmentationPredicate->AddPredicate(mitk::TNodePredicateDataType::New()); m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); + m_SegmentationPredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("hidden object"))); mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateProperty::Pointer isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer isMask = mitk::NodePredicateAnd::New(isBinary, isImage); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage"); auto isSegment = mitk::NodePredicateDataType::New("Segment"); mitk::NodePredicateOr::Pointer validImages = mitk::NodePredicateOr::New(); validImages->AddPredicate(mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isSegment))); validImages->AddPredicate(isDwi); validImages->AddPredicate(isDti); validImages->AddPredicate(isOdf); m_ReferencePredicate = mitk::NodePredicateAnd::New(); m_ReferencePredicate->AddPredicate(validImages); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(m_SegmentationPredicate)); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(isMask)); m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))); + m_ReferencePredicate->AddPredicate(mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("hidden object"))); } QmitkMultiLabelSegmentationView::~QmitkMultiLabelSegmentationView() { // Loose LabelSetConnections OnLooseLabelSetConnection(); } void QmitkMultiLabelSegmentationView::CreateQtPartControl(QWidget *parent) { // setup the basic GUI of this view m_Parent = parent; m_Controls.setupUi(parent); m_Controls.m_tbSavePreset->setIcon(QmitkStyleManager::ThemeIcon(QStringLiteral(":/org_mitk_icons/icons/awesome/scalable/actions/document-save.svg"))); m_Controls.m_tbLoadPreset->setIcon(QmitkStyleManager::ThemeIcon(QStringLiteral(":/org_mitk_icons/icons/awesome/scalable/actions/document-open.svg"))); // *------------------------ // * Shortcuts // *------------------------ QShortcut* visibilityShortcut = new QShortcut(QKeySequence("CTRL+H"), parent); connect(visibilityShortcut, &QShortcut::activated, this, &QmitkMultiLabelSegmentationView::OnVisibilityShortcutActivated); QShortcut* labelToggleShortcut = new QShortcut(QKeySequence("CTRL+L"), parent); connect(labelToggleShortcut, &QShortcut::activated, this, &QmitkMultiLabelSegmentationView::OnLabelToggleShortcutActivated); // *------------------------ // * DATA SELECTION WIDGETS // *------------------------ m_Controls.m_ReferenceNodeSelector->SetNodePredicate(m_ReferencePredicate); m_Controls.m_ReferenceNodeSelector->SetDataStorage(this->GetDataStorage()); m_Controls.m_ReferenceNodeSelector->SetInvalidInfo("Select an image"); m_Controls.m_ReferenceNodeSelector->SetPopUpTitel("Select an image"); m_Controls.m_ReferenceNodeSelector->SetPopUpHint("Select an image that should be used to define the geometry and bounds of the segmentation."); m_Controls.m_WorkingNodeSelector->SetNodePredicate(m_SegmentationPredicate); m_Controls.m_WorkingNodeSelector->SetDataStorage(this->GetDataStorage()); m_Controls.m_WorkingNodeSelector->SetInvalidInfo("Select a segmentation"); m_Controls.m_WorkingNodeSelector->SetPopUpTitel("Select a segmentation"); m_Controls.m_WorkingNodeSelector->SetPopUpHint("Select a segmentation that should be modified. Only segmentation with the same geometry and within the bounds of the reference image are selected."); connect(m_Controls.m_ReferenceNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this,&QmitkMultiLabelSegmentationView::OnReferenceSelectionChanged); connect(m_Controls.m_WorkingNodeSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this,&QmitkMultiLabelSegmentationView::OnSegmentationSelectionChanged); // *------------------------ // * ToolManager // *------------------------ m_ToolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(mitk::ToolManagerProvider::MULTILABEL_SEGMENTATION); m_ToolManager->SetDataStorage(*(this->GetDataStorage())); m_ToolManager->InitializeTools(); m_Controls.m_ManualToolSelectionBox2D->SetToolManager(*m_ToolManager); m_Controls.m_ManualToolSelectionBox3D->SetToolManager(*m_ToolManager); // *------------------------ // * LabelSetWidget // *------------------------ m_Controls.m_LabelSetWidget->SetDataStorage(this->GetDataStorage()); m_Controls.m_LabelSetWidget->SetOrganColors(mitk::OrganNamesHandling::GetDefaultOrganColorString()); m_Controls.m_LabelSetWidget->hide(); // *------------------------ // * Interpolation // *------------------------ m_Controls.m_SurfaceBasedInterpolatorWidget->SetDataStorage(*(this->GetDataStorage())); m_Controls.m_SliceBasedInterpolatorWidget->SetDataStorage(*(this->GetDataStorage())); connect(m_Controls.m_cbInterpolation, SIGNAL(activated(int)), this, SLOT(OnInterpolationSelectionChanged(int))); m_Controls.m_cbInterpolation->setCurrentIndex(0); m_Controls.m_swInterpolation->hide(); m_Controls.m_gbInterpolation->hide(); // See T27436 - QString segTools2D = tr("Add Subtract Fill Erase Paint Wipe 'Region Growing' FastMarching2D Correction 'Live Wire'"); + QString segTools2D = tr("Add Subtract Fill Erase Paint Wipe 'Region Growing' FastMarching2D 'Live Wire'"); QString segTools3D = tr("Threshold 'Two Thresholds' 'Auto Threshold' 'Multiple Otsu'"); std::regex extSegTool2DRegEx("SegTool2D$"); std::regex extSegTool3DRegEx("SegTool3D$"); auto tools = m_ToolManager->GetTools(); for (const auto &tool : tools) { if (std::regex_search(tool->GetNameOfClass(), extSegTool2DRegEx)) { segTools2D.append(QString(" '%1'").arg(tool->GetName())); } else if (std::regex_search(tool->GetNameOfClass(), extSegTool3DRegEx)) { segTools3D.append(QString(" '%1'").arg(tool->GetName())); } } // *------------------------ // * ToolSelection 2D // *------------------------ m_Controls.m_ManualToolSelectionBox2D->SetGenerateAccelerators(true); m_Controls.m_ManualToolSelectionBox2D->SetToolGUIArea(m_Controls.m_ManualToolGUIContainer2D); m_Controls.m_ManualToolSelectionBox2D->SetDisplayedToolGroups(segTools2D.toStdString()); // todo: "Correction // 'Live Wire'" m_Controls.m_ManualToolSelectionBox2D->SetEnabledMode( QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible); connect(m_Controls.m_ManualToolSelectionBox2D, SIGNAL(ToolSelected(int)), this, SLOT(OnManualTool2DSelected(int))); // *------------------------ // * ToolSelection 3D // *------------------------ m_Controls.m_ManualToolSelectionBox3D->SetGenerateAccelerators(true); m_Controls.m_ManualToolSelectionBox3D->SetToolGUIArea(m_Controls.m_ManualToolGUIContainer3D); m_Controls.m_ManualToolSelectionBox3D->SetDisplayedToolGroups(segTools3D.toStdString()); // todo add : FastMarching3D RegionGrowing Watershed m_Controls.m_ManualToolSelectionBox3D->SetLayoutColumns(2); m_Controls.m_ManualToolSelectionBox3D->SetEnabledMode( QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible); // *------------------------* // * Connect PushButtons (pb) // *------------------------* connect(m_Controls.m_pbNewLabel, SIGNAL(clicked()), this, SLOT(OnNewLabel())); connect(m_Controls.m_tbSavePreset, SIGNAL(clicked()), this, SLOT(OnSavePreset())); connect(m_Controls.m_tbLoadPreset, SIGNAL(clicked()), this, SLOT(OnLoadPreset())); connect(m_Controls.m_pbNewSegmentationSession, SIGNAL(clicked()), this, SLOT(OnNewSegmentationSession())); connect(m_Controls.m_pbShowLabelTable, SIGNAL(toggled(bool)), this, SLOT(OnShowLabelTable(bool))); // *------------------------* // * Connect LabelSetWidget // *------------------------* connect(m_Controls.m_LabelSetWidget, SIGNAL(goToLabel(const mitk::Point3D &)), this, SLOT(OnGoToLabel(const mitk::Point3D &))); connect(m_Controls.m_LabelSetWidget, SIGNAL(resetView()), this, SLOT(OnResetView())); // *------------------------* // * DATA SLECTION WIDGET // *------------------------* m_IRenderWindowPart = this->GetRenderWindowPart(); if (m_IRenderWindowPart) { QList controllers; controllers.push_back(m_IRenderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); controllers.push_back(m_IRenderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); controllers.push_back(m_IRenderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); m_Controls.m_SliceBasedInterpolatorWidget->SetSliceNavigationControllers(controllers); } // this->InitializeListeners(); connect(m_Controls.m_btAddLayer, SIGNAL(clicked()), this, SLOT(OnAddLayer())); connect(m_Controls.m_btDeleteLayer, SIGNAL(clicked()), this, SLOT(OnDeleteLayer())); connect(m_Controls.m_btPreviousLayer, SIGNAL(clicked()), this, SLOT(OnPreviousLayer())); connect(m_Controls.m_btNextLayer, SIGNAL(clicked()), this, SLOT(OnNextLayer())); connect(m_Controls.m_btLockExterior, SIGNAL(toggled(bool)), this, SLOT(OnLockExteriorToggled(bool))); connect(m_Controls.m_cbActiveLayer, SIGNAL(currentIndexChanged(int)), this, SLOT(OnChangeLayer(int))); m_Controls.m_btAddLayer->setEnabled(false); m_Controls.m_btDeleteLayer->setEnabled(false); m_Controls.m_btNextLayer->setEnabled(false); m_Controls.m_btPreviousLayer->setEnabled(false); m_Controls.m_cbActiveLayer->setEnabled(false); m_Controls.m_pbNewLabel->setEnabled(false); m_Controls.m_btLockExterior->setEnabled(false); m_Controls.m_tbSavePreset->setEnabled(false); m_Controls.m_tbLoadPreset->setEnabled(false); m_Controls.m_pbShowLabelTable->setEnabled(false); // Make sure the GUI notices if appropriate data is already present on creation m_Controls.m_ReferenceNodeSelector->SetAutoSelectNewNodes(true); m_Controls.m_WorkingNodeSelector->SetAutoSelectNewNodes(true); } void QmitkMultiLabelSegmentationView::Activated() { m_ToolManager->SetReferenceData(m_Controls.m_ReferenceNodeSelector->GetSelectedNode()); m_ToolManager->SetWorkingData(m_Controls.m_WorkingNodeSelector->GetSelectedNode()); } void QmitkMultiLabelSegmentationView::Deactivated() { // Not yet implemented } void QmitkMultiLabelSegmentationView::Visible() { // Not yet implemented } void QmitkMultiLabelSegmentationView::Hidden() { // Not yet implemented } int QmitkMultiLabelSegmentationView::GetSizeFlags(bool width) { if (!width) { return berry::Constants::MIN | berry::Constants::MAX | berry::Constants::FILL; } else { return 0; } } int QmitkMultiLabelSegmentationView::ComputePreferredSize(bool width, int /*availableParallel*/, int /*availablePerpendicular*/, int preferredResult) { if (width == false) { return 100; } else { return preferredResult; } } /************************************************************************/ /* protected slots */ /************************************************************************/ void QmitkMultiLabelSegmentationView::OnVisibilityShortcutActivated() { mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0); assert(workingNode); bool isVisible = false; workingNode->GetBoolProperty("visible", isVisible); workingNode->SetVisibility(!isVisible); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkMultiLabelSegmentationView::OnLabelToggleShortcutActivated() { mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0); assert(workingNode); mitk::LabelSetImage* workingImage = dynamic_cast(workingNode->GetData()); assert(workingImage); WaitCursorOn(); workingImage->GetActiveLabelSet()->SetNextActiveLabel(); workingImage->Modified(); WaitCursorOff(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkMultiLabelSegmentationView::OnManualTool2DSelected(int id) { this->ResetMouseCursor(); mitk::StatusBar::GetInstance()->DisplayText(""); if (id >= 0) { std::string text = "Active Tool: \""; text += m_ToolManager->GetToolById(id)->GetName(); text += "\""; mitk::StatusBar::GetInstance()->DisplayText(text.c_str()); us::ModuleResource resource = m_ToolManager->GetToolById(id)->GetCursorIconResource(); this->SetMouseCursor(resource, 0, 0); } } void QmitkMultiLabelSegmentationView::OnNewLabel() { m_ToolManager->ActivateTool(-1); if (m_ReferenceNode.IsNull()) { QMessageBox::information( m_Parent, "New Segmentation Session", "Please load and select a patient image before starting some action."); return; } if (nullptr == m_ReferenceNode->GetData()) { QMessageBox::information( m_Parent, "New Segmentation Session", "Please load and select a patient image before starting some action."); return; } mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0); if (!workingNode) { QMessageBox::information( m_Parent, "New Segmentation Session", "Please load and select a patient image before starting some action."); return; } mitk::LabelSetImage* workingImage = dynamic_cast(workingNode->GetData()); if (!workingImage) { QMessageBox::information( m_Parent, "New Segmentation Session", "Please load and select a patient image before starting some action."); return; } QmitkNewSegmentationDialog* dialog = new QmitkNewSegmentationDialog(m_Parent); dialog->SetSuggestionList(mitk::OrganNamesHandling::GetDefaultOrganColorString()); dialog->setWindowTitle("New Label"); int dialogReturnValue = dialog->exec(); if (dialogReturnValue == QDialog::Rejected) { return; } QString segName = dialog->GetSegmentationName(); if (segName.isEmpty()) { segName = "Unnamed"; } workingImage->GetActiveLabelSet()->AddLabel(segName.toStdString(), dialog->GetColor()); UpdateControls(); m_Controls.m_LabelSetWidget->ResetAllTableWidgetItems(); this->ReinitializeViews(); } void QmitkMultiLabelSegmentationView::OnSavePreset() { QmitkAbstractNodeSelectionWidget::NodeList nodes; nodes.append(m_WorkingNode); QmitkCreateMultiLabelPresetAction action; action.Run(nodes); } void QmitkMultiLabelSegmentationView::OnLoadPreset() { QmitkAbstractNodeSelectionWidget::NodeList nodes; nodes.append(m_WorkingNode); QmitkLoadMultiLabelPresetAction action; action.Run(nodes); } void QmitkMultiLabelSegmentationView::OnShowLabelTable(bool value) { if (value) m_Controls.m_LabelSetWidget->show(); else m_Controls.m_LabelSetWidget->hide(); } void QmitkMultiLabelSegmentationView::OnNewSegmentationSession() { mitk::DataNode *referenceNode = m_Controls.m_ReferenceNodeSelector->GetSelectedNode(); if (!referenceNode) { QMessageBox::information( m_Parent, "New Segmentation Session", "Please load and select a patient image before starting some action."); return; } m_ToolManager->ActivateTool(-1); mitk::Image::ConstPointer referenceImage = dynamic_cast(referenceNode->GetData()); assert(referenceImage); const auto currentTimePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); unsigned int imageTimeStep = 0; if (referenceImage->GetTimeGeometry()->IsValidTimePoint(currentTimePoint)) { imageTimeStep = referenceImage->GetTimeGeometry()->TimePointToTimeStep(currentTimePoint); } auto segTemplateImage = referenceImage; if (referenceImage->GetDimension() > 3) { - auto result = QMessageBox::question(m_Parent, tr("Generate a static mask?"), tr("The selected image has multiple time steps. You can either generate a simple/static masks resembling the geometry of the first timestep of the image. Or you can generate a dynamic mask that equals the selected image in geometry and number of timesteps; thus a dynamic mask can change over time (e.g. according to the image)."), tr("Yes, generate a static mask"), tr("No, generate a dynamic mask"), QString(), 0, 0); + auto result = QMessageBox::question(m_Parent, tr("Create a static or dynamic segmentation?"), tr("The patient image has multiple time steps.\n\nDo you want to create a static segmentation that is identical for all time steps or do you want to create a dynamic segmentation to segment individual time steps?"), tr("Create static segmentation"), tr("Create dynamic segmentation"), QString(), 0, 0); if (result == 0) { auto selector = mitk::ImageTimeSelector::New(); selector->SetInput(referenceImage); selector->SetTimeNr(0); selector->Update(); const auto refTimeGeometry = referenceImage->GetTimeGeometry(); auto newTimeGeometry = mitk::ProportionalTimeGeometry::New(); newTimeGeometry->SetFirstTimePoint(refTimeGeometry->GetMinimumTimePoint()); newTimeGeometry->SetStepDuration(refTimeGeometry->GetMaximumTimePoint() - refTimeGeometry->GetMinimumTimePoint()); mitk::Image::Pointer newImage = selector->GetOutput(); newTimeGeometry->SetTimeStepGeometry(referenceImage->GetGeometry(imageTimeStep), 0); newImage->SetTimeGeometry(newTimeGeometry); segTemplateImage = newImage; } } QString newName = QString::fromStdString(referenceNode->GetName()); newName.append("-labels"); bool ok = false; newName = QInputDialog::getText(m_Parent, "New Segmentation Session", "New name:", QLineEdit::Normal, newName, &ok); if (!ok) { return; } this->WaitCursorOn(); mitk::LabelSetImage::Pointer workingImage = mitk::LabelSetImage::New(); try { workingImage->Initialize(segTemplateImage); } catch (mitk::Exception& e) { this->WaitCursorOff(); MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::information(m_Parent, "New Segmentation Session", "Could not create a new segmentation session.\n"); return; } this->WaitCursorOff(); mitk::DataNode::Pointer workingNode = mitk::DataNode::New(); workingNode->SetData(workingImage); workingNode->SetName(newName.toStdString()); workingImage->GetExteriorLabel()->SetProperty("name.parent", mitk::StringProperty::New(referenceNode->GetName().c_str())); workingImage->GetExteriorLabel()->SetProperty("name.image", mitk::StringProperty::New(newName.toStdString().c_str())); if (!GetDataStorage()->Exists(workingNode)) { GetDataStorage()->Add(workingNode, referenceNode); } m_Controls.m_WorkingNodeSelector->SetCurrentSelectedNode(workingNode); OnNewLabel(); } void QmitkMultiLabelSegmentationView::OnGoToLabel(const mitk::Point3D& pos) { if (m_IRenderWindowPart) m_IRenderWindowPart->SetSelectedPosition(pos); } void QmitkMultiLabelSegmentationView::OnResetView() { if (m_IRenderWindowPart) m_IRenderWindowPart->ForceImmediateUpdate(); } void QmitkMultiLabelSegmentationView::OnAddLayer() { m_ToolManager->ActivateTool(-1); mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0); assert(workingNode); mitk::LabelSetImage* workingImage = dynamic_cast(workingNode->GetData()); assert(workingImage); QString question = "Do you really want to add a layer to the current segmentation session?"; QMessageBox::StandardButton answerButton = QMessageBox::question( m_Controls.m_LabelSetWidget, "Add layer", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answerButton != QMessageBox::Yes) return; try { WaitCursorOn(); workingImage->AddLayer(); WaitCursorOff(); } catch ( mitk::Exception& e ) { WaitCursorOff(); MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::information( m_Controls.m_LabelSetWidget, "Add Layer", "Could not add a new layer. See error log for details.\n"); return; } OnNewLabel(); } void QmitkMultiLabelSegmentationView::OnDeleteLayer() { m_ToolManager->ActivateTool(-1); mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0); assert(workingNode); mitk::LabelSetImage* workingImage = dynamic_cast(workingNode->GetData()); assert(workingImage); if (workingImage->GetNumberOfLayers() < 2) return; QString question = "Do you really want to delete the current layer?"; QMessageBox::StandardButton answerButton = QMessageBox::question( m_Controls.m_LabelSetWidget, "Delete layer", question, QMessageBox::Yes | QMessageBox::Cancel, QMessageBox::Yes); if (answerButton != QMessageBox::Yes) { return; } try { this->WaitCursorOn(); workingImage->RemoveLayer(); this->WaitCursorOff(); } catch (mitk::Exception& e) { this->WaitCursorOff(); MITK_ERROR << "Exception caught: " << e.GetDescription(); QMessageBox::information(m_Controls.m_LabelSetWidget, "Delete Layer", "Could not delete the currently active layer. See error log for details.\n"); return; } UpdateControls(); m_Controls.m_LabelSetWidget->ResetAllTableWidgetItems(); } void QmitkMultiLabelSegmentationView::OnPreviousLayer() { m_ToolManager->ActivateTool(-1); mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); assert(workingNode); mitk::LabelSetImage *workingImage = dynamic_cast(workingNode->GetData()); assert(workingImage); OnChangeLayer(workingImage->GetActiveLayer() - 1); } void QmitkMultiLabelSegmentationView::OnNextLayer() { m_ToolManager->ActivateTool(-1); mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); assert(workingNode); mitk::LabelSetImage *workingImage = dynamic_cast(workingNode->GetData()); assert(workingImage); OnChangeLayer(workingImage->GetActiveLayer() + 1); } void QmitkMultiLabelSegmentationView::OnChangeLayer(int layer) { m_ToolManager->ActivateTool(-1); mitk::DataNode *workingNode = m_ToolManager->GetWorkingData(0); assert(workingNode); mitk::LabelSetImage *workingImage = dynamic_cast(workingNode->GetData()); assert(workingImage); this->WaitCursorOn(); workingImage->SetActiveLayer(layer); this->WaitCursorOff(); UpdateControls(); m_Controls.m_LabelSetWidget->ResetAllTableWidgetItems(); } void QmitkMultiLabelSegmentationView::OnDeactivateActiveTool() { m_ToolManager->ActivateTool(-1); } void QmitkMultiLabelSegmentationView::OnLockExteriorToggled(bool checked) { mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0); assert(workingNode); mitk::LabelSetImage* workingImage = dynamic_cast(workingNode->GetData()); assert(workingImage); workingImage->GetLabel(0)->SetLocked(checked); } void QmitkMultiLabelSegmentationView::OnReferenceSelectionChanged(QList /*nodes*/) { m_ToolManager->ActivateTool(-1); auto refNode = m_Controls.m_ReferenceNodeSelector->GetSelectedNode(); m_ReferenceNode = refNode; m_ToolManager->SetReferenceData(m_ReferenceNode); if (m_ReferenceNode.IsNotNull()) { auto segPredicate = mitk::NodePredicateAnd::New(m_SegmentationPredicate.GetPointer(), mitk::NodePredicateSubGeometry::New(refNode->GetData()->GetGeometry())); m_Controls.m_WorkingNodeSelector->SetNodePredicate(segPredicate); if (m_AutoSelectionEnabled) { // hide all image nodes to later show only the automatically selected ones mitk::DataStorage::SetOfObjects::ConstPointer patientNodes = GetDataStorage()->GetSubset(m_ReferencePredicate); for (mitk::DataStorage::SetOfObjects::const_iterator iter = patientNodes->begin(); iter != patientNodes->end(); ++iter) { (*iter)->SetVisibility(false); } } m_ReferenceNode->SetVisibility(true); } UpdateControls(); } void QmitkMultiLabelSegmentationView::OnSegmentationSelectionChanged(QList /*nodes*/) { m_ToolManager->ActivateTool(-1); if (m_WorkingNode.IsNotNull()) OnLooseLabelSetConnection(); m_WorkingNode = m_Controls.m_WorkingNodeSelector->GetSelectedNode(); m_ToolManager->SetWorkingData(m_WorkingNode); if (m_WorkingNode.IsNotNull()) { OnEstablishLabelSetConnection(); if (m_AutoSelectionEnabled) { // hide all segmentation nodes to later show only the automatically selected ones mitk::DataStorage::SetOfObjects::ConstPointer segmentationNodes = GetDataStorage()->GetSubset(m_SegmentationPredicate); for (mitk::DataStorage::SetOfObjects::const_iterator iter = segmentationNodes->begin(); iter != segmentationNodes->end(); ++iter) { (*iter)->SetVisibility(false); } } m_WorkingNode->SetVisibility(true); } UpdateControls(); if (m_WorkingNode.IsNotNull()) { m_Controls.m_LabelSetWidget->ResetAllTableWidgetItems(); this->ReinitializeViews(); } } void QmitkMultiLabelSegmentationView::OnInterpolationSelectionChanged(int index) { if (index == 1) { m_Controls.m_SurfaceBasedInterpolatorWidget->m_Controls.m_btStart->setChecked(false);//OnToggleWidgetActivation(false); m_Controls.m_swInterpolation->setCurrentIndex(0); m_Controls.m_swInterpolation->show(); } else if (index == 2) { m_Controls.m_SliceBasedInterpolatorWidget->m_Controls.m_btStart->setChecked(false); m_Controls.m_swInterpolation->setCurrentIndex(1); m_Controls.m_swInterpolation->show(); } else { m_Controls.m_SurfaceBasedInterpolatorWidget->m_Controls.m_btStart->setChecked(false); m_Controls.m_SliceBasedInterpolatorWidget->m_Controls.m_btStart->setChecked(false); m_Controls.m_swInterpolation->setCurrentIndex(2); m_Controls.m_swInterpolation->hide(); } } /************************************************************************/ /* protected */ /************************************************************************/ void QmitkMultiLabelSegmentationView::OnPreferencesChanged(const berry::IBerryPreferences* prefs) { - if (m_Parent && m_WorkingNode.IsNotNull()) - { - m_AutoSelectionEnabled = prefs->GetBool("auto selection", false); + m_AutoSelectionEnabled = prefs->GetBool("auto selection", false); - mitk::BoolProperty::Pointer drawOutline = mitk::BoolProperty::New(prefs->GetBool("draw outline", true)); - mitk::BoolProperty::Pointer volumeRendering = mitk::BoolProperty::New(prefs->GetBool("volume rendering", false)); - mitk::LabelSetImage* labelSetImage; - mitk::DataNode* segmentation; + mitk::BoolProperty::Pointer drawOutline = mitk::BoolProperty::New(prefs->GetBool("draw outline", true)); + mitk::LabelSetImage* labelSetImage; + mitk::DataNode* segmentation; - // iterate all segmentations (binary (single label) and LabelSetImages) - mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); - mitk::NodePredicateOr::Pointer allSegmentationsPredicate = mitk::NodePredicateOr::New(isBinaryPredicate, m_SegmentationPredicate); - mitk::DataStorage::SetOfObjects::ConstPointer allSegmentations = GetDataStorage()->GetSubset(allSegmentationsPredicate); + // iterate all segmentations (binary (single label) and LabelSetImages) + mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); + mitk::NodePredicateOr::Pointer allSegmentationsPredicate = mitk::NodePredicateOr::New(isBinaryPredicate, m_SegmentationPredicate); + mitk::DataStorage::SetOfObjects::ConstPointer allSegmentations = GetDataStorage()->GetSubset(allSegmentationsPredicate); - for (mitk::DataStorage::SetOfObjects::const_iterator it = allSegmentations->begin(); it != allSegmentations->end(); ++it) + for (mitk::DataStorage::SetOfObjects::const_iterator it = allSegmentations->begin(); it != allSegmentations->end(); ++it) + { + segmentation = *it; + labelSetImage = dynamic_cast(segmentation->GetData()); + if (nullptr != labelSetImage) + { + // segmentation node is a multi label segmentation + segmentation->SetProperty("labelset.contour.active", drawOutline); + //segmentation->SetProperty("opacity", mitk::FloatProperty::New(drawOutline->GetValue() ? 1.0f : 0.3f)); + // force render window update to show outline + segmentation->GetData()->Modified(); + } + else if (nullptr != segmentation->GetData()) { - segmentation = *it; - labelSetImage = dynamic_cast(segmentation->GetData()); - if (nullptr != labelSetImage) + // node is actually a 'single label' segmentation, + // but its outline property can be set in the 'multi label' segmentation preference page as well + bool isBinary = false; + segmentation->GetBoolProperty("binary", isBinary); + if (isBinary) { - // segmentation node is a multi label segmentation - segmentation->SetProperty("labelset.contour.active", drawOutline); + segmentation->SetProperty("outline binary", drawOutline); + segmentation->SetProperty("outline width", mitk::FloatProperty::New(2.0)); //segmentation->SetProperty("opacity", mitk::FloatProperty::New(drawOutline->GetValue() ? 1.0f : 0.3f)); - segmentation->SetProperty("volumerendering", volumeRendering); // force render window update to show outline segmentation->GetData()->Modified(); } - else if (nullptr != segmentation->GetData()) - { - // node is actually a 'single label' segmentation, - // but its outline property can be set in the 'multi label' segmentation preference page as well - bool isBinary = false; - segmentation->GetBoolProperty("binary", isBinary); - if (isBinary) - { - segmentation->SetProperty("outline binary", drawOutline); - segmentation->SetProperty("outline width", mitk::FloatProperty::New(2.0)); - //segmentation->SetProperty("opacity", mitk::FloatProperty::New(drawOutline->GetValue() ? 1.0f : 0.3f)); - segmentation->SetProperty("volumerendering", volumeRendering); - // force render window update to show outline - segmentation->GetData()->Modified(); - } - } - else - { - // "interpolation feedback" data nodes have binary flag but don't have a data set. So skip them for now. - MITK_INFO << "DataNode " << segmentation->GetName() << " doesn't contain a base data."; - } } } } void QmitkMultiLabelSegmentationView::NodeRemoved(const mitk::DataNode *node) { bool isHelperObject(false); node->GetBoolProperty("helper object", isHelperObject); if (isHelperObject) { return; } if (m_ReferenceNode.IsNotNull() && dynamic_cast(node->GetData())) { // remove all possible contour markers of the segmentation mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = this->GetDataStorage()->GetDerivations( node, mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true))); ctkPluginContext *context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService *service = context->getService(ppmRef); for (mitk::DataStorage::SetOfObjects::ConstIterator it = allContourMarkers->Begin(); it != allContourMarkers->End(); ++it) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1; service->RemovePlanePosition(id); this->GetDataStorage()->Remove(it->Value()); } context->ungetService(ppmRef); service = nullptr; } } void QmitkMultiLabelSegmentationView::OnEstablishLabelSetConnection() { if (m_WorkingNode.IsNull()) { return; } mitk::LabelSetImage *workingImage = dynamic_cast(m_WorkingNode->GetData()); assert(workingImage); workingImage->GetActiveLabelSet()->AddLabelEvent += mitk::MessageDelegate( m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->RemoveLabelEvent += mitk::MessageDelegate( m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->ModifyLabelEvent += mitk::MessageDelegate( m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->AllLabelsModifiedEvent += mitk::MessageDelegate( m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->ActiveLabelEvent += mitk::MessageDelegate1(m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::SelectLabelByPixelValue); // Removed in T27851 to have a chance to react to AfterChangeLayerEvent. Did it brake something? // workingImage->BeforeChangeLayerEvent += mitk::MessageDelegate( // this, &QmitkMultiLabelSegmentationView::OnLooseLabelSetConnection); workingImage->AfterChangeLayerEvent += mitk::MessageDelegate( this, &QmitkMultiLabelSegmentationView::UpdateControls); } void QmitkMultiLabelSegmentationView::OnLooseLabelSetConnection() { if (m_WorkingNode.IsNull()) return; auto* workingImage = dynamic_cast(m_WorkingNode->GetData()); if (nullptr == workingImage) return; // data (type) was changed in-place, e.g. LabelSetImage -> Image // Reset LabelSetWidget Events workingImage->GetActiveLabelSet()->AddLabelEvent -= mitk::MessageDelegate( m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->RemoveLabelEvent -= mitk::MessageDelegate( m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::ResetAllTableWidgetItems); workingImage->GetActiveLabelSet()->ModifyLabelEvent -= mitk::MessageDelegate( m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->AllLabelsModifiedEvent -= mitk::MessageDelegate( m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::UpdateAllTableWidgetItems); workingImage->GetActiveLabelSet()->ActiveLabelEvent -= mitk::MessageDelegate1(m_Controls.m_LabelSetWidget, &QmitkLabelSetWidget::SelectLabelByPixelValue); // Removed in T27851 to have a chance to react to AfterChangeLayerEvent. Did it brake something? // workingImage->BeforeChangeLayerEvent -= mitk::MessageDelegate( // this, &QmitkMultiLabelSegmentationView::OnLooseLabelSetConnection); workingImage->AfterChangeLayerEvent -= mitk::MessageDelegate( this, &QmitkMultiLabelSegmentationView::UpdateControls); } void QmitkMultiLabelSegmentationView::SetFocus() { } void QmitkMultiLabelSegmentationView::UpdateControls() { mitk::DataNode* referenceNode = m_ToolManager->GetReferenceData(0); bool hasReferenceNode = referenceNode != nullptr; mitk::DataNode* workingNode = m_ToolManager->GetWorkingData(0); bool hasValidWorkingNode = workingNode != nullptr; m_Controls.m_pbNewLabel->setEnabled(false); m_Controls.m_gbInterpolation->setEnabled(false); m_Controls.m_SliceBasedInterpolatorWidget->setEnabled(false); m_Controls.m_SurfaceBasedInterpolatorWidget->setEnabled(false); m_Controls.m_LabelSetWidget->setEnabled(false); m_Controls.m_btAddLayer->setEnabled(false); m_Controls.m_btDeleteLayer->setEnabled(false); m_Controls.m_cbActiveLayer->setEnabled(false); m_Controls.m_btPreviousLayer->setEnabled(false); m_Controls.m_btNextLayer->setEnabled(false); m_Controls.m_btLockExterior->setChecked(false); m_Controls.m_btLockExterior->setEnabled(false); m_Controls.m_tbSavePreset->setEnabled(false); m_Controls.m_tbLoadPreset->setEnabled(false); m_Controls.m_pbShowLabelTable->setChecked(false); m_Controls.m_pbShowLabelTable->setEnabled(false); m_Controls.m_ManualToolSelectionBox3D->SetEnabledMode(QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible); m_Controls.m_ManualToolSelectionBox2D->SetEnabledMode(QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible); if (hasValidWorkingNode) { // TODO adapt tool manager so that this check is done there, e.g. convenience function mitk::LabelSetImage* workingImage = dynamic_cast(workingNode->GetData()); hasValidWorkingNode = workingImage != nullptr; if (hasValidWorkingNode) { m_Controls.m_pbNewLabel->setEnabled(true); m_Controls.m_btLockExterior->setEnabled(true); m_Controls.m_tbSavePreset->setEnabled(true); m_Controls.m_tbLoadPreset->setEnabled(true); m_Controls.m_pbShowLabelTable->setEnabled(true); m_Controls.m_gbInterpolation->setEnabled(true); m_Controls.m_SliceBasedInterpolatorWidget->setEnabled(true); m_Controls.m_SurfaceBasedInterpolatorWidget->setEnabled(true); m_Controls.m_LabelSetWidget->setEnabled(true); m_Controls.m_btAddLayer->setEnabled(true); int activeLayer = workingImage->GetActiveLayer(); int numberOfLayers = workingImage->GetNumberOfLayers(); m_Controls.m_cbActiveLayer->blockSignals(true); m_Controls.m_cbActiveLayer->clear(); for (unsigned int lidx = 0; lidx < workingImage->GetNumberOfLayers(); ++lidx) { m_Controls.m_cbActiveLayer->addItem(QString::number(lidx)); } m_Controls.m_cbActiveLayer->setCurrentIndex(activeLayer); m_Controls.m_cbActiveLayer->blockSignals(false); m_Controls.m_cbActiveLayer->setEnabled(numberOfLayers > 1); m_Controls.m_btDeleteLayer->setEnabled(numberOfLayers > 1); m_Controls.m_btPreviousLayer->setEnabled(activeLayer > 0); m_Controls.m_btNextLayer->setEnabled(activeLayer != numberOfLayers - 1); m_Controls.m_btLockExterior->setChecked(workingImage->GetLabel(0, activeLayer)->GetLocked()); m_Controls.m_pbShowLabelTable->setChecked(workingImage->GetNumberOfLabels() > 1 /*1st is exterior*/); //MLI TODO //m_Controls.m_ManualToolSelectionBox2D->SetEnabledMode(QmitkToolSelectionBox::EnabledWithWorkingDataVisible); } } if (hasValidWorkingNode && hasReferenceNode) { int layer = -1; referenceNode->GetIntProperty("layer", layer); workingNode->SetIntProperty("layer", layer + 1); } this->RequestRenderWindowUpdate(mitk::RenderingManager::REQUEST_UPDATE_ALL); } void QmitkMultiLabelSegmentationView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { if (m_IRenderWindowPart != renderWindowPart) { m_IRenderWindowPart = renderWindowPart; m_Parent->setEnabled(true); QList controllers; controllers.push_back(m_IRenderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); controllers.push_back(m_IRenderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); controllers.push_back(m_IRenderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); m_Controls.m_SliceBasedInterpolatorWidget->SetSliceNavigationControllers(controllers); } } void QmitkMultiLabelSegmentationView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* /*renderWindowPart*/) { m_ToolManager->ActivateTool(-1); m_IRenderWindowPart = nullptr; m_Parent->setEnabled(false); } void QmitkMultiLabelSegmentationView::ResetMouseCursor() { if (m_MouseCursorSet) { mitk::ApplicationCursor::GetInstance()->PopCursor(); m_MouseCursorSet = false; } } void QmitkMultiLabelSegmentationView::SetMouseCursor(const us::ModuleResource resource, int hotspotX, int hotspotY) { // Remove previously set mouse cursor if (m_MouseCursorSet) this->ResetMouseCursor(); if (resource) { us::ModuleResourceStream cursor(resource, std::ios::binary); mitk::ApplicationCursor::GetInstance()->PushCursor(cursor, hotspotX, hotspotY); m_MouseCursorSet = true; } } void QmitkMultiLabelSegmentationView::InitializeListeners() { if (m_Interactor.IsNull()) { us::Module* module = us::GetModuleContext()->GetModule(); std::vector resources = module->FindResources("/", "*", true); for (std::vector::iterator iter = resources.begin(); iter != resources.end(); ++iter) { MITK_INFO << iter->GetResourcePath(); } m_Interactor = mitk::SegmentationInteractor::New(); if (!m_Interactor->LoadStateMachine("SegmentationInteraction.xml", module)) { MITK_WARN << "Error loading state machine"; } if (!m_Interactor->SetEventConfig("ConfigSegmentation.xml", module)) { MITK_WARN << "Error loading state machine configuration"; } // Register as listener via micro services us::ServiceProperties props; props["name"] = std::string("SegmentationInteraction"); m_ServiceRegistration = us::GetModuleContext()->RegisterService(m_Interactor.GetPointer(), props); } } void QmitkMultiLabelSegmentationView::ReinitializeViews() const { if (m_ReferenceNode.IsNotNull() && nullptr != m_ReferenceNode->GetData()) { const auto currentTimePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); unsigned int imageTimeStep = 0; if (m_ReferenceNode->GetData()->GetTimeGeometry()->IsValidTimePoint(currentTimePoint)) { imageTimeStep = m_ReferenceNode->GetData()->GetTimeGeometry()->TimePointToTimeStep(currentTimePoint); } mitk::RenderingManager::GetInstance()->InitializeViews(m_ReferenceNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetTime()->SetPos(imageTimeStep); } } diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.cpp b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.cpp index 87c10cacf2..874d15aefb 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.cpp +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.cpp @@ -1,140 +1,143 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkBooleanOperationsWidget.h" #include "../../Common/QmitkDataSelectionWidget.h" #include #include #include static const char* const HelpText = "Select two different masks above"; -std::string GetPrefix(mitk::BooleanOperation::Type type) +namespace { - switch (type) + std::string GetPrefix(mitk::BooleanOperation::Type type) { - case mitk::BooleanOperation::Difference: - return "DifferenceFrom_"; + switch (type) + { + case mitk::BooleanOperation::Difference: + return "DifferenceFrom_"; - case mitk::BooleanOperation::Intersection: - return "IntersectionWith_"; + case mitk::BooleanOperation::Intersection: + return "IntersectionWith_"; - case mitk::BooleanOperation::Union: - return "UnionWith_"; + case mitk::BooleanOperation::Union: + return "UnionWith_"; - default: - assert(false && "Unknown boolean operation type"); - return "UNKNOWN_BOOLEAN_OPERATION_WITH_"; + default: + assert(false && "Unknown boolean operation type"); + return "UNKNOWN_BOOLEAN_OPERATION_WITH_"; + } } -} -void AddToDataStorage(mitk::DataStorage::Pointer dataStorage, mitk::Image::Pointer segmentation, const std::string& name, mitk::DataNode::Pointer parent = nullptr) -{ - mitk::DataNode::Pointer dataNode = mitk::DataNode::New(); + void AddToDataStorage(mitk::DataStorage::Pointer dataStorage, mitk::Image::Pointer segmentation, const std::string& name, mitk::DataNode::Pointer parent = nullptr) + { + mitk::DataNode::Pointer dataNode = mitk::DataNode::New(); - dataNode->SetBoolProperty("binary", true); - dataNode->SetName(name); - dataNode->SetData(segmentation); + dataNode->SetBoolProperty("binary", true); + dataNode->SetName(name); + dataNode->SetData(segmentation); - dataStorage->Add(dataNode, parent); + dataStorage->Add(dataNode, parent); + } } QmitkBooleanOperationsWidget::QmitkBooleanOperationsWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent) { m_Controls.setupUi(this); m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::MaskPredicate); m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::MaskPredicate); m_Controls.dataSelectionWidget->SetHelpText(HelpText); connect(m_Controls.dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); connect(m_Controls.differenceButton, SIGNAL(clicked()), this, SLOT(OnDifferenceButtonClicked())); connect(m_Controls.intersectionButton, SIGNAL(clicked()), this, SLOT(OnIntersectionButtonClicked())); connect(m_Controls.unionButton, SIGNAL(clicked()), this, SLOT(OnUnionButtonClicked())); } QmitkBooleanOperationsWidget::~QmitkBooleanOperationsWidget() { } void QmitkBooleanOperationsWidget::OnSelectionChanged(unsigned int, const mitk::DataNode*) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; mitk::DataNode::Pointer node0 = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer node1 = dataSelectionWidget->GetSelection(1); if (node0.IsNotNull() && node1.IsNotNull() && node0 != node1) { dataSelectionWidget->SetHelpText(""); this->EnableButtons(); } else { dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); } } void QmitkBooleanOperationsWidget::EnableButtons(bool enable) { m_Controls.differenceButton->setEnabled(enable); m_Controls.intersectionButton->setEnabled(enable); m_Controls.unionButton->setEnabled(enable); } void QmitkBooleanOperationsWidget::OnDifferenceButtonClicked() { this->DoBooleanOperation(mitk::BooleanOperation::Difference); } void QmitkBooleanOperationsWidget::OnIntersectionButtonClicked() { this->DoBooleanOperation(mitk::BooleanOperation::Intersection); } void QmitkBooleanOperationsWidget::OnUnionButtonClicked() { this->DoBooleanOperation(mitk::BooleanOperation::Union); } void QmitkBooleanOperationsWidget::DoBooleanOperation(mitk::BooleanOperation::Type type) { mitk::SliceNavigationController* timeNavigationController = this->GetTimeNavigationController(); assert(timeNavigationController != nullptr); mitk::Image::Pointer segmentation0 = static_cast(m_Controls.dataSelectionWidget->GetSelection(0)->GetData()); mitk::Image::Pointer segmentation1 = static_cast(m_Controls.dataSelectionWidget->GetSelection(1)->GetData()); mitk::Image::Pointer result; try { mitk::BooleanOperation booleanOperation(type, segmentation0, segmentation1, timeNavigationController->GetSelectedTimePoint()); result = booleanOperation.GetResult(); } catch (const mitk::Exception &exception) { MITK_ERROR << "Boolean operation failed: " << exception.GetDescription(); } assert(result.IsNotNull()); QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; AddToDataStorage( dataSelectionWidget->GetDataStorage(), result, GetPrefix(type) + dataSelectionWidget->GetSelection(1)->GetName(), dataSelectionWidget->GetSelection(0)); } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp similarity index 90% copy from Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp copy to Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp index 59ff902954..90e41d7aea 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp @@ -1,245 +1,246 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkContourModelToImageWidget.h" #include "mitkImage.h" #include "../../Common/QmitkDataSelectionWidget.h" #include #include +#include #include #include #include #include #include static const char* const HelpText = "Select a image and a contour(set)"; class QmitkContourModelToImageWidgetPrivate { public: QmitkContourModelToImageWidgetPrivate(); ~QmitkContourModelToImageWidgetPrivate(); /** @brief Check if selections is valid. */ void SelectionControl( unsigned int index, const mitk::DataNode* selection); /** @brief Enable buttons if data selction is valid. */ void EnableButtons(bool enable = true); /** @brief Does the actual contour filling */ - mitk::Image::Pointer FillContourModelSetIntoImage(mitk::Image *image, mitk::ContourModelSet *contourSet, mitk::TimePointType timePoint); + mitk::LabelSetImage::Pointer FillContourModelSetIntoImage(mitk::Image *image, mitk::ContourModelSet *contourSet, mitk::TimePointType timePoint); Ui::QmitkContourModelToImageWidgetControls m_Controls; - QFutureWatcher m_Watcher; + QFutureWatcher m_Watcher; }; QmitkContourModelToImageWidgetPrivate::QmitkContourModelToImageWidgetPrivate() { } QmitkContourModelToImageWidgetPrivate::~QmitkContourModelToImageWidgetPrivate() { } void QmitkContourModelToImageWidgetPrivate::EnableButtons(bool enable) { m_Controls.btnProcess->setEnabled(enable); } void QmitkContourModelToImageWidgetPrivate::SelectionControl(unsigned int index, const mitk::DataNode* /*selection*/) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(index); dataSelectionWidget->SetHelpText(""); this->EnableButtons(); } -mitk::Image::Pointer QmitkContourModelToImageWidgetPrivate::FillContourModelSetIntoImage(mitk::Image* image, mitk::ContourModelSet* contourSet, mitk::TimePointType timePoint) +mitk::LabelSetImage::Pointer QmitkContourModelToImageWidgetPrivate::FillContourModelSetIntoImage(mitk::Image* image, mitk::ContourModelSet* contourSet, mitk::TimePointType timePoint) { // Use mitk::ContourModelSetToImageFilter to fill the ContourModelSet into the image mitk::ContourModelSetToImageFilter::Pointer contourFiller = mitk::ContourModelSetToImageFilter::New(); auto timeStep = image->GetTimeGeometry()->TimePointToTimeStep(timePoint); contourFiller->SetTimeStep(timeStep); contourFiller->SetImage(image); contourFiller->SetInput(contourSet); contourFiller->MakeOutputBinaryOn(); - mitk::Image::Pointer result = nullptr; try { contourFiller->Update(); - result = contourFiller->GetOutput(); } catch (const std::exception & e) { MITK_ERROR << "Error while converting contour model. "<< e.what(); } catch (...) { MITK_ERROR << "Unknown error while converting contour model."; } - if (result.IsNull()) + if (nullptr == contourFiller->GetOutput()) { MITK_ERROR<<"Could not write the selected contours into the image!"; } - result->DisconnectPipeline(); + auto result = mitk::LabelSetImage::New(); + result->InitializeByLabeledImage(contourFiller->GetOutput()); + return result; } void QmitkContourModelToImageWidget::OnSelectionChanged(unsigned int index, const mitk::DataNode* selection) { Q_D(QmitkContourModelToImageWidget); QmitkDataSelectionWidget* dataSelectionWidget = d->m_Controls.dataSelectionWidget; mitk::DataNode::Pointer node0 = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer node1 = dataSelectionWidget->GetSelection(1); if (node0.IsNull() || node1.IsNull() ) { d->EnableButtons(false); dataSelectionWidget->SetHelpText(HelpText); } else { d->SelectionControl(index, selection); } } void QmitkContourModelToImageWidget::OnProcessingFinished() { // Called when processing finished // Adding the result to the data storage Q_D(QmitkContourModelToImageWidget); // Adding the result to the data storage - mitk::Image::Pointer result = d->m_Watcher.result(); + auto result = d->m_Watcher.result(); if (result.IsNotNull()) { QmitkDataSelectionWidget* dataSelectionWidget = d->m_Controls.dataSelectionWidget; mitk::DataNode::Pointer imageNode = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer contourNode = dataSelectionWidget->GetSelection(1); mitk::DataNode::Pointer filled = mitk::DataNode::New(); std::stringstream stream; stream << imageNode->GetName(); stream << "_"; stream << contourNode->GetName(); filled->SetName(stream.str()); filled->SetData(result); dataSelectionWidget->GetDataStorage()->Add(filled, imageNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else { MITK_ERROR<<"Error filling contours into an image!"; } d->EnableButtons(); } void QmitkContourModelToImageWidget::OnProcessPressed() { Q_D(QmitkContourModelToImageWidget); QmitkDataSelectionWidget* dataSelectionWidget = d->m_Controls.dataSelectionWidget; mitk::DataNode::Pointer imageNode = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer contourNode = dataSelectionWidget->GetSelection(1); // Check if data nodes are valid if(imageNode.IsNull() || contourNode.IsNull() ) { MITK_ERROR << "Selection does not contain valid data"; QMessageBox::information( this, "Contour To Image", "Selection does not contain valid data, please select a binary image and a contour(set)", QMessageBox::Ok ); d->m_Controls.btnProcess->setEnabled(false); return; } mitk::Image::Pointer image = static_cast(imageNode->GetData()); // Check if the image is valid if (image.IsNull()) { MITK_ERROR<<"Error writing contours into image! Invalid image data selected!"; return; } const auto timePoint = this->GetTimeNavigationController()->GetSelectedTimePoint(); if (!image->GetTimeGeometry()->IsValidTimePoint(timePoint)) { MITK_ERROR << "Error writing contours into image! Currently selected time point is not supported by selected image data."; return; } // Check if the selected contours are valid mitk::ContourModelSet::Pointer contourSet; mitk::ContourModel::Pointer contour = dynamic_cast(contourNode->GetData()); if (contour.IsNotNull()) { contourSet = mitk::ContourModelSet::New(); contourSet->AddContourModel(contour); } else { contourSet = static_cast(contourNode->GetData()); if (contourSet.IsNull()) { MITK_ERROR<<"Error writing contours into binary image! Invalid contour data selected!"; return; } } //Disable Buttons during calculation and initialize Progressbar d->EnableButtons(false); // Start the computation in a background thread - QFuture< mitk::Image::Pointer > future = QtConcurrent::run(d, &QmitkContourModelToImageWidgetPrivate::FillContourModelSetIntoImage, image, contourSet, timePoint); + QFuture< mitk::LabelSetImage::Pointer > future = QtConcurrent::run(d, &QmitkContourModelToImageWidgetPrivate::FillContourModelSetIntoImage, image, contourSet, timePoint); d->m_Watcher.setFuture(future); } QmitkContourModelToImageWidget::QmitkContourModelToImageWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent), d_ptr(new QmitkContourModelToImageWidgetPrivate()) { Q_D(QmitkContourModelToImageWidget); // Set up UI d->m_Controls.setupUi(this); d->m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::ImageAndSegmentationPredicate); d->m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::ContourModelPredicate); d->m_Controls.dataSelectionWidget->SetHelpText(HelpText); d->EnableButtons(false); // Create connections connect (d->m_Controls.btnProcess, SIGNAL(pressed()), this, SLOT(OnProcessPressed())); connect(d->m_Controls.dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); connect(&d->m_Watcher, SIGNAL(finished()), this, SLOT(OnProcessingFinished())); if( d->m_Controls.dataSelectionWidget->GetSelection(0).IsNotNull() && d->m_Controls.dataSelectionWidget->GetSelection(1).IsNotNull() ) { OnSelectionChanged(0, d->m_Controls.dataSelectionWidget->GetSelection(0)); } } QmitkContourModelToImageWidget::~QmitkContourModelToImageWidget() { } diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.h b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.h new file mode 100644 index 0000000000..c31fb9f4dc --- /dev/null +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.h @@ -0,0 +1,70 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#ifndef QmitkContourModelToImageWidget_h +#define QmitkContourModelToImageWidget_h + +#include "../QmitkSegmentationUtilityWidget.h" +#include + +#include + +class QmitkContourModelToImageWidgetPrivate; + +namespace mitk { + class Image; + class ContourModelSet; + class ContourModel; + class Geometry3D; + class PlaneGeometry; +} + +/*! + \brief QmitkContourModelToImageWidget + + Tool masks an image with a binary image or a surface. The Method requires + an image and a binary image mask or a surface. The input image and the binary + image mask must be of the same size. Masking with a surface creates first a + binary image of the surface and then use this for the masking of the input image. +*/ +class QmitkContourModelToImageWidget : public QmitkSegmentationUtilityWidget +{ + Q_OBJECT + +public: + + /** @brief Default constructor, including creation of GUI elements and signals/slots connections. */ + explicit QmitkContourModelToImageWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent = nullptr); + + /** @brief Defaul destructor. */ + ~QmitkContourModelToImageWidget() override; + +private slots: + + /** @brief This slot is called if the selection in the workbench is changed. */ + void OnSelectionChanged(unsigned int index, const mitk::DataNode* selection); + + /** @brief This slot is called if user activates the button to mask an image. */ + void OnProcessPressed(); + + /** @brief This slot is called after processing is finished */ + void OnProcessingFinished(); + +private: + + QScopedPointer d_ptr; + + Q_DECLARE_PRIVATE(QmitkContourModelToImageWidget) + Q_DISABLE_COPY(QmitkContourModelToImageWidget) +}; + +#endif diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidgetControls.ui similarity index 55% copy from Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui copy to Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidgetControls.ui index 1882ccdfbf..4f9be6b5bf 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidgetControls.ui @@ -1,82 +1,56 @@ - QmitkImageMaskingWidgetControls - + QmitkContourModelToImageWidgetControls + 0 0 - 147 - 155 + 98 + 62 0 0 - - - Masking Mode - - - - - - Image Masking - - - true - - - - - - - Surface Masking - - - - - - - - + - Mask + Process Qt::Vertical 20 40 QmitkDataSelectionWidget QWidget
internal/Common/QmitkDataSelectionWidget.h
1 diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/QmitkMultiLabelSegmentationUtilitiesView.cpp b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/QmitkMultiLabelSegmentationUtilitiesView.cpp index 41370bc597..3ccaa49638 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/QmitkMultiLabelSegmentationUtilitiesView.cpp +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/QmitkMultiLabelSegmentationUtilitiesView.cpp @@ -1,94 +1,93 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // #define ENABLE_CTK_WIDGETS_WIDGET +#include #include "QmitkMultiLabelSegmentationUtilitiesView.h" #include "BooleanOperations/QmitkBooleanOperationsWidget.h" +#include "ContourModelToImage/QmitkContourModelToImageWidget.h" #include "MorphologicalOperations/QmitkMorphologicalOperationsWidget.h" #include "SurfaceToImage/QmitkSurfaceToImageWidget.h" #include "ImageMasking/QmitkImageMaskingWidget.h" #include "ConvertToMl/QmitkConvertToMlWidget.h" QmitkMultiLabelSegmentationUtilitiesView::QmitkMultiLabelSegmentationUtilitiesView() : m_BooleanOperationsWidget(nullptr), + m_ContourModelToImageWidget(nullptr), m_MorphologicalOperationsWidget(nullptr), m_SurfaceToImageWidget(nullptr), m_ImageMaskingWidget(nullptr), m_ConvertToMlWidget(nullptr) { } QmitkMultiLabelSegmentationUtilitiesView::~QmitkMultiLabelSegmentationUtilitiesView() { } void QmitkMultiLabelSegmentationUtilitiesView::CreateQtPartControl(QWidget* parent) { m_Controls.setupUi(parent); mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart(); mitk::SliceNavigationController* timeNavigationController = renderWindowPart != nullptr ? renderWindowPart->GetTimeNavigationController() : nullptr; m_BooleanOperationsWidget = new QmitkBooleanOperationsWidget(timeNavigationController, parent); - + m_ContourModelToImageWidget = new QmitkContourModelToImageWidget(timeNavigationController, parent); m_MorphologicalOperationsWidget = new QmitkMorphologicalOperationsWidget(timeNavigationController, parent); - m_SurfaceToImageWidget = new QmitkSurfaceToImageWidget(timeNavigationController, parent); - m_ImageMaskingWidget = new QmitkImageMaskingWidget(timeNavigationController, parent); - m_ConvertToMlWidget = new QmitkConvertToMlWidget(timeNavigationController, parent); this->AddUtilityWidget(m_BooleanOperationsWidget, QIcon(":/MultiLabelSegmentationUtilities/BooleanOperations_48x48.png"), "Boolean Operations"); - + this->AddUtilityWidget(m_ContourModelToImageWidget, QIcon(":/MultiLabelSegmentationUtilities/ContourModelSetToImage_48x48.png"), "Contour to Image"); + this->AddUtilityWidget(m_ImageMaskingWidget, QIcon(":/MultiLabelSegmentationUtilities/ImageMasking_48x48.png"), "Image Masking"); this->AddUtilityWidget(m_MorphologicalOperationsWidget, QIcon(":/MultiLabelSegmentationUtilities/MorphologicalOperations_48x48.png"), "Morphological Operations"); - this->AddUtilityWidget(m_SurfaceToImageWidget, QIcon(":/MultiLabelSegmentationUtilities/SurfaceToImage_48x48.png"), "Surface To Image"); - - this->AddUtilityWidget(m_ImageMaskingWidget, QIcon(":/MultiLabelSegmentationUtilities/ImageMasking_48x48.png"), "Image Masking"); - - this->AddUtilityWidget(m_ConvertToMlWidget, QIcon(":/MultiLabelSegmentationUtilities/multilabelsegmentation.svg"), "Convert To MultiLabel"); + this->AddUtilityWidget(m_ConvertToMlWidget, QmitkStyleManager::ThemeIcon(QStringLiteral(":/MultiLabelSegmentationUtilities/multilabelsegmentation.svg")), "Convert to MultiLabel"); } void QmitkMultiLabelSegmentationUtilitiesView::AddUtilityWidget(QWidget* widget, const QIcon& icon, const QString& text) { m_Controls.toolBox->addItem(widget, icon, text); } void QmitkMultiLabelSegmentationUtilitiesView::SetFocus() { m_Controls.toolBox->setFocus(); } void QmitkMultiLabelSegmentationUtilitiesView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { mitk::SliceNavigationController* timeNavigationController = renderWindowPart->GetTimeNavigationController(); m_BooleanOperationsWidget->SetTimeNavigationController(timeNavigationController); + m_ContourModelToImageWidget->SetTimeNavigationController(timeNavigationController); + m_ImageMaskingWidget->SetTimeNavigationController(timeNavigationController); m_MorphologicalOperationsWidget->SetTimeNavigationController(timeNavigationController); m_SurfaceToImageWidget->SetTimeNavigationController(timeNavigationController); - m_ImageMaskingWidget->SetTimeNavigationController(timeNavigationController); m_ConvertToMlWidget->SetTimeNavigationController(timeNavigationController); } void QmitkMultiLabelSegmentationUtilitiesView::RenderWindowPartDeactivated(mitk::IRenderWindowPart*) { m_BooleanOperationsWidget->SetTimeNavigationController(nullptr); + m_ContourModelToImageWidget->SetTimeNavigationController(nullptr); + m_ImageMaskingWidget->SetTimeNavigationController(nullptr); m_MorphologicalOperationsWidget->SetTimeNavigationController(nullptr); m_SurfaceToImageWidget->SetTimeNavigationController(nullptr); - m_ImageMaskingWidget->SetTimeNavigationController(nullptr); m_ConvertToMlWidget->SetTimeNavigationController(nullptr); } diff --git a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/QmitkMultiLabelSegmentationUtilitiesView.h b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/QmitkMultiLabelSegmentationUtilitiesView.h index 128d3ccc95..31ae381d04 100644 --- a/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/QmitkMultiLabelSegmentationUtilitiesView.h +++ b/Plugins/org.mitk.gui.qt.multilabelsegmentation/src/internal/SegmentationUtilities/QmitkMultiLabelSegmentationUtilitiesView.h @@ -1,57 +1,59 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkMultiLabelSegmentationUtilitiesView_h #define QmitkMultiLabelSegmentationUtilitiesView_h #include #include #include class QmitkBooleanOperationsWidget; +class QmitkContourModelToImageWidget; class QmitkSurfaceToImageWidget; class QmitkImageMaskingWidget; class QmitkMorphologicalOperationsWidget; -class QmitkMorphologicalOperationsWidget; class QmitkConvertToMlWidget; class QmitkMultiLabelSegmentationUtilitiesView : public QmitkAbstractView, public mitk::IRenderWindowPartListener { Q_OBJECT public: QmitkMultiLabelSegmentationUtilitiesView(); ~QmitkMultiLabelSegmentationUtilitiesView() override; void CreateQtPartControl(QWidget* parent) override; void SetFocus() override; void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) override; void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) override; private: void AddUtilityWidget(QWidget* widget, const QIcon& icon, const QString& text); QmitkBooleanOperationsWidget* m_BooleanOperationsWidget; + QmitkContourModelToImageWidget* m_ContourModelToImageWidget; + QmitkMorphologicalOperationsWidget* m_MorphologicalOperationsWidget; QmitkSurfaceToImageWidget* m_SurfaceToImageWidget; QmitkImageMaskingWidget* m_ImageMaskingWidget; QmitkConvertToMlWidget* m_ConvertToMlWidget; Ui::QmitkMultiLabelSegmentationUtilitiesViewControls m_Controls; }; #endif diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/src/internal/QmitkPointSetInteractionView.cpp b/Plugins/org.mitk.gui.qt.pointsetinteraction/src/internal/QmitkPointSetInteractionView.cpp index d63cf1e9d6..dfbd27ae6a 100755 --- a/Plugins/org.mitk.gui.qt.pointsetinteraction/src/internal/QmitkPointSetInteractionView.cpp +++ b/Plugins/org.mitk.gui.qt.pointsetinteraction/src/internal/QmitkPointSetInteractionView.cpp @@ -1,127 +1,118 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkPointSetInteractionView.h" #include -#include -#include #include +#include #include +#include #include #include #include const std::string QmitkPointSetInteractionView::VIEW_ID = "org.mitk.views.pointsetinteraction"; QmitkPointSetInteractionView::QmitkPointSetInteractionView() : m_Controls(nullptr) { } QmitkPointSetInteractionView::~QmitkPointSetInteractionView() { } void QmitkPointSetInteractionView::CreateQtPartControl(QWidget *parent) { m_Controls = new Ui::QmitkPointSetInteractionViewControls; m_Controls->setupUi(parent); m_Controls->selectedPointSetWidget->SetDataStorage(GetDataStorage()); m_Controls->selectedPointSetWidget->SetNodePredicate(mitk::NodePredicateAnd::New( mitk::TNodePredicateDataType::New(), - mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")))); + mitk::NodePredicateNot::New(mitk::NodePredicateOr::New( + mitk::NodePredicateProperty::New("helper object"), + mitk::NodePredicateProperty::New("hidden object"))))); m_Controls->selectedPointSetWidget->SetSelectionIsOptional(true); m_Controls->selectedPointSetWidget->SetAutoSelectNewNodes(true); m_Controls->selectedPointSetWidget->SetEmptyInfo(QString("Please select a point set")); m_Controls->selectedPointSetWidget->SetPopUpTitel(QString("Select point set")); connect(m_Controls->selectedPointSetWidget, &QmitkSingleNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkPointSetInteractionView::OnCurrentSelectionChanged); connect(m_Controls->addPointSetPushButton, &QPushButton::clicked, this, &QmitkPointSetInteractionView::OnAddPointSetClicked); - if (mitk::IRenderWindowPart* renderWindowPart = GetRenderWindowPart()) - { - RenderWindowPartActivated(renderWindowPart); - } + auto renderWindowPart = this->GetRenderWindowPart(); + + if (nullptr != renderWindowPart) + this->RenderWindowPartActivated(renderWindowPart); + + this->OnCurrentSelectionChanged(m_Controls->selectedPointSetWidget->GetSelectedNodes()); } void QmitkPointSetInteractionView::SetFocus() { m_Controls->addPointSetPushButton->setFocus(); } -void QmitkPointSetInteractionView::OnCurrentSelectionChanged(QList nodes) +void QmitkPointSetInteractionView::OnCurrentSelectionChanged(QmitkSingleNodeSelectionWidget::NodeList /*nodes*/) { - if (nodes.empty() || nodes.front().IsNull()) - { - m_Controls->poinSetListWidget->SetPointSetNode(nullptr); - return; - } - - auto selectedPointSet = dynamic_cast(nodes.front()->GetData()); - if (nullptr == selectedPointSet) - { - m_Controls->poinSetListWidget->SetPointSetNode(nullptr); - return; - } - - m_Controls->poinSetListWidget->SetPointSetNode(nodes.front()); + m_Controls->poinSetListWidget->SetPointSetNode(m_Controls->selectedPointSetWidget->GetSelectedNode()); } void QmitkPointSetInteractionView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { if (nullptr != m_Controls) { m_Controls->poinSetListWidget->AddSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); m_Controls->poinSetListWidget->AddSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); m_Controls->poinSetListWidget->AddSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); } } void QmitkPointSetInteractionView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) { if (nullptr != m_Controls) { m_Controls->poinSetListWidget->RemoveSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); m_Controls->poinSetListWidget->RemoveSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); m_Controls->poinSetListWidget->RemoveSliceNavigationController(renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); } } void QmitkPointSetInteractionView::OnAddPointSetClicked() { // ask for the name of the point set bool ok = false; QString name = QInputDialog::getText(QApplication::activeWindow(), tr("Add point set..."), tr("Enter name for the new point set"), QLineEdit::Normal, tr("PointSet"), &ok); if (!ok || name.isEmpty()) { return; } mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); mitk::DataNode::Pointer pointSetNode = mitk::DataNode::New(); pointSetNode->SetData(pointSet); pointSetNode->SetProperty("name", mitk::StringProperty::New(name.toStdString())); pointSetNode->SetProperty("opacity", mitk::FloatProperty::New(1)); pointSetNode->SetColor(1.0, 1.0, 0.0); this->GetDataStorage()->Add(pointSetNode); m_Controls->selectedPointSetWidget->SetCurrentSelectedNode(pointSetNode); } diff --git a/Plugins/org.mitk.gui.qt.pointsetinteraction/src/internal/QmitkPointSetInteractionView.h b/Plugins/org.mitk.gui.qt.pointsetinteraction/src/internal/QmitkPointSetInteractionView.h index 769d6dc3ab..c7bc89fc2e 100755 --- a/Plugins/org.mitk.gui.qt.pointsetinteraction/src/internal/QmitkPointSetInteractionView.h +++ b/Plugins/org.mitk.gui.qt.pointsetinteraction/src/internal/QmitkPointSetInteractionView.h @@ -1,61 +1,53 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QMITKPOINTSETINTERACTIONVIEW_H #define QMITKPOINTSETINTERACTIONVIEW_H #include "ui_QmitkPointSetInteractionViewControls.h" -// mitk core #include - -// org mitk gui common plugin #include -// org mitk gui qt common plugin #include +#include -/** -* @brief -* -* -*/ class QmitkPointSetInteractionView : public QmitkAbstractView, public mitk::IRenderWindowPartListener { Q_OBJECT public: static const std::string VIEW_ID; QmitkPointSetInteractionView(); ~QmitkPointSetInteractionView() override; void SetFocus() override; void RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) override; void RenderWindowPartDeactivated(mitk::IRenderWindowPart* renderWindowPart) override; private Q_SLOT: - void OnCurrentSelectionChanged(QList nodes); + void OnCurrentSelectionChanged(QmitkSingleNodeSelectionWidget::NodeList nodes); void OnAddPointSetClicked(); private: void CreateQtPartControl(QWidget *parent) override; Ui::QmitkPointSetInteractionViewControls* m_Controls; }; -#endif // QMITKPOINTSETINTERACTIONVIEW_H +#endif diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox index ea04956862..efcc12808f 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation.dox @@ -1,299 +1,285 @@ /** \page org_mitk_views_segmentation The Segmentation View \imageMacro{segmentation-dox.svg,"Icon of the segmentation view",2.00} Some of the features described below are closed source additions to the open source toolkit MITK and are not available in every application. \tableofcontents \section org_mitk_views_segmentationUserManualOverview Overview Segmentation is the act of partitioning an image into subsets by either manual or automated delineation to create i.e. a distinction between foreground and background. The MITK segmentation plugin allows you to create segmentations of anatomical and pathological structures in medical images. The plugin consists of a number of views:
  • Segmentation View: Manual and (semi-)automatic segmentation
  • \subpage org_mitk_views_segmentationutilities : Segmentation post-processing
In this documentation, the features and usage of the segmentation view will be described. For an introduction to the segmentation utilities and clipping plane views, please be referred to the respective documentation pages. \imageMacro{QmitkSegmentationPlugin_Overview.png,"Segmentation plugin overview", 16.00} \section org_mitk_views_segmentationPreferences Preferences The segmentation plugin offers a number of preferences which can be set via the MITK Workbench application preferences: \imageMacro{QmitkSegmentationPreferences.png,"Segmentation preferences", 10.00}
  • Slim view: Allows you to show or hide the tool button description of the segmentation view
  • 2D display: Specify whether the segmentation is drawn as outline or as a transparent overlay
  • 3D display: Activate 3D volume rendering for your segmentation
  • Data node selection mode: If activated the segmentation image is automatically chosen from the data manager selection.
  • Smoothed surface creation: Set certain smoothing parameters for surface creation
\section org_mitk_views_segmentationUserManualTechnical Technical Issues The segmentation plugin makes a number of assumptions:
  • Images must be 2D, 3D, or 3D+t.
  • Images must be single-values, i.e. CT, MRI or "normal" ultrasound. Images from color doppler or photographic (RGB) images are only partially supported (please be aware that some tools might not be compatible with this image type).
  • Segmentations are handled as binary images of the same extent as the original image.
\section org_mitk_views_segmentationUserManualImageSelection Data Selection & Creating New Segmentations To select a reference image for the segmentation, click on the Patient Image selection widget and choose a suitable image from the selection available in the data manager. By default the auto selection mode is enabled (see \ref org_mitk_views_segmentationPreferences).\n Once a patient image is selected, a new segmentation can be created on this reference image by clicking the New... button to the right of the Segmentation selection widget. An input field will appear which allows you to set the name and display color of the segmentation. Notice that the input field suggests names once you start typing and that it also suggests colors for known organ names. Once generated the segmentation will be added with "binary mask" icon to the data manager as sub-node of the reference image. This item is automatically selected for you, allowing you to start editing the new segmentation right away. \subsection org_mitk_views_segmentationUserManualManualKringeling2 Selecting Segmentations for Editing Alternatively to creating a new segmentation, an existing one can be edited as well. As you might have segmented multiple structures within a single image, the application needs to know which of them to use for editing. For that you click the segmentation selection widget and a selection field will open, containing all suitable segmentations for the parent dataset available in the data manager. \section org_mitk_views_segmentationUserManualToolOverview Segmentation Tool Overview MITK offers a comprehensive set of slice-based 2D and (semi-)automated 3D segmentation tools. The manual 2D tools require some user interaction and can only be applied to a single image slice whereas the 3D tools operate on the whole image. The 3D tools usually only require a small amount of user interaction, i.e. placing seed points or setting/adjusting parameters. You can switch between the different toolsets by selecting the 2D or 3D tab in the segmentation view. \imageMacro{QmitkSegmentation_ToolOverview.png,"An overview of the existing 2D and 3D tools in MITK.",5.50} \section org_mitk_views_segmentationUserManualManualKringeling 2D Segmentation Tools With 2D manual contouring you define which voxels are part of the segmentation and which ones are not. This allows you to create segmentations of any structures of interest in an image. You can also use manual contouring to correct segmentations that result from sub-optimal automatic methods. The drawback of manual contouring is that you might need to define contours on many 2D slices. However, this is mitigated by the interpolation feature, which will make suggestions for a segmentation. \subsection org_mitk_views_segmentationUserManualManualKringeling3 Selecting Editing Tools To start using one of the editing tools, click its button from the displayed toolbox. The selected editing tool will be active and its corresponding button will stay pressed until you click the button again. Selecting a different tool also deactivates the previous one.\n If you have to delineate a lot of images, shortcuts to switch between tools becomes convenient. For that, just hit the first letter of each tool to activate it (A for Add, S for Subtract, etc.). \subsection org_mitk_views_segmentationUserManualManualKringeling4 Using Editing Tools All of the editing tools work by the same principle: you use the mouse (left button) to click anywhere in a 2D window (any of the orientations axial, sagittal, or coronal), move the mouse while holding the mouse button and release to finish the editing action. Multi-step undo and redo is fully supported by all editing tools. Use the application-wide undo button in the toolbar to revert erroneous %actions. Remark: If you are familiar with the MITK Workbench, you know that clicking and moving the mouse in any of the 2D render windows will move around the crosshair that defines what part of the image is displayed. This behavior is disabled whilst any of the manual segmentation tools are active- otherwise you might have a hard time concentrating on the contour you are drawing. \subsection org_mitk_views_segmentationUserManualAddSubtractTools Add and Subtract Tools \imageMacro{QmitkSegmentation_IMGIconAddSubtract.png,"Add and Subtract Tools",7.70} Use the left mouse button to draw a closed contour. When releasing the mouse button, the contour will be added (Add tool) to or removed (Subtract tool) from the current segmentation. Adding and subtracting voxels can be iteratively repeated for the same segmentation. Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of adding voxels, they will be subtracted). \subsection org_mitk_views_segmentationUserManualPaintWipeTools Paint and Wipe Tools \imageMacro{QmitkSegmentation_IMGIconPaintWipe.png,"Paint and Wipe Tools",7.68} Use the Size slider to change the radius of the round paintbrush tool. Move the mouse in any 2D window and press the left button to draw or erase pixels. Holding CTRL / CMD while drawing will invert the current tool's behavior (i.e. instead of painting voxels, they will be wiped). \subsection org_mitk_views_segmentationUserManualRegionGrowingTool Region Growing Tool \imageMacro{QmitkSegmentation_IMGIconRegionGrowing.png,"Region Growing Tool",3.81} Click at one point in a 2D slice widget to add an image region to the segmentation with the region growing tool. Region Growing selects all pixels around the mouse cursor that have a similar gray value as the pixel below the mouse cursor. This enables you to quickly create segmentations of structures that have a good contrast to surrounding tissue. The tool operates based on the current level window, so changing the level window to optimize the contrast for the ROI is encouraged. Moving the mouse up/down is different from left/right: Moving up the cursor while holding the left mouse button widens the range for the included grey values; moving it down narrows it. Moving the mouse left and right will shift the range. The tool will select more or less pixels, corresponding to the changing gray value range. - \if THISISNOTIMPLEMENTEDATTHEMOMENT A common issue with region growing is the so called "leakage" which happens when the structure of interest is connected to other pixels, of similar gray values, through a narrow "bridge" at the border of the structure. The Region Growing tool comes with a "leakage detection/removal" feature. If leakage happens, you can left-click into the leakage region and the tool will try to automatically remove this region (see illustration below). \imageMacro{QmitkSegmentation_IMGLeakage.png,"Leakage correction feature of the Region Growing tool",11.28} \endif -\subsection org_mitk_views_segmentationUserManualCorrectionTool Correction Tool -
-\imageMacro{QmitkSegmentation_IMGIconCorrection.png,"Correction Tool",3.77} - -You do not have to draw a closed contour to use the Correction tool and do not need to switch between the Add and Substract tool to perform -small corrective changes. The following figure shows the usage of this tool: -
    -
  • a) If the user draws a line which %starts and ends outside the segmenation a part of it is cut off. -
  • b) If the line is drawn fully inside the segmentation the marked region is added to the segmentation. -
- -\imageMacro{QmitkSegmentation_IMGCorrectionActions.png,"Usage of the Correction tool.",13.50} -
\subsection org_mitk_views_segmentationUserManualFillTool Fill Tool \imageMacro{QmitkSegmentation_IMGIconFill.png,"Fill Tool",3.81} Left-click inside a segmentation with holes to completely fill all holes. Left-click inside a hole to fill only this specific hole. \subsection org_mitk_views_segmentationUserManualEraseTool Erase Tool \imageMacro{QmitkSegmentation_IMGIconErase.png,"Erase Tool",3.79} This tool removes a connected part of pixels that form a segmentation. You may use it to remove single segmentations (left-click on specific segmentation) or to clear a whole slice at once (left-click outside a segmentation). \subsection org_mitk_views_segmentationUserManualLiveWireTool Live Wire Tool \imageMacro{QmitkSegmentation_IMGIconLiveWire.png,"Live Wire Tool",3.01} The Live Wire Tool acts as a magnetic lasso with a contour snapping to edges of objects. \imageMacro{QmitkSegmentation_IMGLiveWireUsage.PNG,"Steps for using the Live Wire Tool",16.00}
  • (1) To start the tool you have to double-click near the edge of the object you want to segment. The initial anchor point will snap to the edge within a 3x3 region.
  • (2) Move the mouse. You don't have trace the edge of the object. The contour will automatically snap to it.
  • (3) To fix a segment you can set anchor points by single left mouse button click.
  • (4) Go on with moving the mouse and setting anchor points.
  • (5) To close the contour double-click on the initial anchor point.
  • (6) After closing, the contour can be edited by moving, inserting and deleting anchor points.
The contour will be transferred to its binary image representation by deactivating the tool. \subsection org_mitk_views_segmentationUserManual2DFastMarchingTool 2D Fast Marching Tool \imageMacro{QmitkSegmentation_IMG2DFastMarchingUsage.png,"2D Fast Marching Tool",3.01} Provides a fast marching based 2D interaction segmentation tool. You start with setting seed points in an image slice. Via several sliders you can adapt parameters and see the fast marching result instantly. \subsection org_mitk_views_segmentationUserManualManualKringeling5 2D and 3D Interpolation Creating segmentations using 2D manual contouring for large image volumes may be very time-consuming, because structures of interest may cover a large range of slices. The segmentation view offers two helpful features to mitigate this drawback:
  • 2D Interpolation
  • 3D Interpolation
The 2D Interpolation creates suggestions for a segmentation whenever you have a slice that
  • has got neighboring slices with segmentations (these do not need to be direct neighbors but could also be a couple of slices away) AND
  • is completely clear of a manual segmentation, i.e. there will be no suggestion if there is even only a single pixel of segmentation in the current slice.
\imageMacro{QmitkSegmentation_2DInterpolation.png,"2D Interpolation Usage",3.01} Interpolated suggestions are displayed as outlines, until you confirm them as part of the segmentation. To confirm single slices, click the Confirm for single slice button below the toolbox. You may also review the interpolations visually and then accept all of them at once by selecting Confirm for all slices. The 3D interpolation creates suggestions for 3D segmentations. That means if you start contouring, from the second contour onwards, the surface of the segmented area will be interpolated based on the given contour information. The interpolation works with all available manual tools. Please note that this is currently a pure mathematical interpolation, i.e. image intensity information is not taken into account. With each further contour the interpolation result will be improved, but the more contours you provide the longer the recalculation will take. To achieve an optimal interpolation result and in this way a most accurate segmentation you should try to describe the surface with sparse contours by segmenting in arbitrary oriented planes. The 3D interpolation is not meant to be used for parallel slice-wise segmentation, but rather segmentations in i.e. the axial, coronal and sagittal plane. \imageMacro{QmitkSegmentation_3DInterpolationWrongRight.png,"3D Interpolation Usage",16.00} You can accept the interpolation result by clicking the Confirm-button below the tool buttons. In this case the 3D interpolation will be deactivated automatically so that the result can be post-processed without any interpolation running in the background. Additional to the surface, black contours are shown in the 3D render window, which mark all the drawn contours used for the interpolation. You can navigate between the drawn contours by clicking on the corresponding position nodes in the data manager which are stored as sub-nodes of the selected segmentation. If you do not want to see these nodes just uncheck the Show Position Nodes checkbox and these nodes will be hidden. If you want to delete a drawn contour we recommend to use the Erase-Tool since Redo/Undo is not yet working for 3D interpolation. The current state of the 3D interpolation can be saved across application restart. For that, just click on save project during the interpolation is active. After restarting the application and load your project you can click on "Reinit Interpolation" within the 3D interpolation GUI area. \section org_mitk_views_segmentationUserManual3DSegmentationTools 3D Segmentation Tools The 3D tools operate on the whole image and require usually a small amount of interaction like placing seed-points or specifying certain parameters. All 3D tools provide an immediate segmentation feedback, which is displayed as a transparent green overlay. For accepting a preview you have to press the Confirm button of the selected tool. The following 3D tools are available: \subsection org_mitk_views_segmentationUserManual3DThresholdTool 3D Threshold Tool The thresholding tool simply applies a 3D threshold to the patient image. All pixels with values equal or above the selected threshold are labeled as part of the segmentation. You can change the threshold by either moving the slider of setting a certain value in the spinbox. \imageMacro{QmitkSegmentation_3DThresholdTool.png,"3D Threshold tool",10.00} \subsection org_mitk_views_segmentationUserManual3DULTool 3D Upper/Lower Threshold Tool The Upper/Lower Thresholding tool works similar to the simple 3D threshold tool but allows you to define an upper and lower threshold. All pixels with values within this threshold interval will be labeled as part of the segmentation. \imageMacro{QmitkSegmentation_3DULThresholdTool.png,"3D Upper/Lower Threshold tool",10.00} \subsection org_mitk_views_segmentationUserManual3DOtsuTool 3D Otsu Tool The 3D Otsu tool provides a more sophisticated thresholding algorithm. It allows you to define a number of regions. Based on the image histogram the pixels will then be divided into different regions. The more regions you define the longer the calculation will take. You can select afterwards which of these regions you want to confirm as segmentation. \imageMacro{QmitkSegmentation_3DOtsuTool.png,"3D Otsu tool",10.00} \subsection org_mitk_views_segmentationUserManual3DFMTool 3D Fast Marching Tool The 3D Fast Marching tool works similar to the 2D pendant but on the whole image. Depending on your image size the calculation might take some time. You can interactively set the parameters of the algorithm via the GUI. The resulting segmentation will be automatically updated. \imageMacro{QmitkSegmentation_3DFMTool.png,"3D Fast Marching tool",10.00} \subsection org_mitk_views_segmentationUserManual3DRGTool 3D Region Growing Tool The 3D Region Growing tool works similar to the 2D pendant. At the beginning you have to place a seedpoint and define a threshold interval. If you press Run Segmentation a preview is calculated. By moving the Adapt region growing slider you can interactively adapt the segmentation result. \imageMacro{QmitkSegmentation_3DRGTool.png,"3D Region Growing tool",10.00} \subsection org_mitk_views_segmentationUserManual3DWatershedTool 3D Watershed Tool This tool provides a watershed based segmentation algorithm. For a detailed explanation of the parameters level and threshold, please be referred to https://itk.org/Doxygen/html/classitk_1_1WatershedImageFilter.html . Remark: The tool is (due to its implementation) faster if you use lower levels. So in doubt you should start with high levels (supposed to undersegment) and then lower the levels until you are happy. \imageMacro{QmitkSegmentation_3DWatershedTool.png,"3D Watershed tool",10.00} \subsection org_mitk_views_segmentationUserManualPickingTool Picking Tool The Picking tool allows you to select islands within your segmentation. This is especially useful if e.g. a thresholding provided you with several areas within your image but you are just interested in one special region. \imageMacro{QmitkSegmentation_PickingTool.png,"Picking tool",10.00} \section org_mitk_views_segmentationUserManualPostprocessing Additional things you can do with segmentations Segmentations are never an end in themselves. Consequently, the segmentation view adds a couple of "post-processing" actions, accessible through the context-menu of the data manager. \imageMacro{QmitkSegmentation_IMGDataManagerContextMenu.png,"Context menu items for segmentations.",10.58}
  • Create polygon %model applies the marching cubes algorithm to the segmentation. This polygon %model can be used for visualization in 3D or other applications such as stereolithography (3D printing).
  • Create smoothed polygon %model uses smoothing in addition to the marching cubes algorithm, which creates models that do not follow the exact outlines of the segmentation, but look smoother.
  • Autocrop can save memory. Manual segmentations have the same extent as the patient image, even if the segmentation comprises only a small sub-volume. This invisible and meaningless margin is removed by autocropping.
\section org_mitk_views_segmentationof3DTImages Segmentation of 3D+t images For segmentation of 3D+t images, some tools give you the option to choose between creating dynamic and static masks.
  • Dynamic masks can be created on each time frame individually.
  • Static masks will be defined on one time frame and will be the same for all other time frames.
In general, segmentation is applied on the time frame that is selected when execution is performed. If you alter the time frame, the segmentation preview is adapted. \section org_mitk_views_segmentationUserManualTechnicalDetail Technical Information for Developers For technical specifications see \subpage QmitkSegmentationTechnicalPage and for information on the extensions of the tools system \subpage toolextensions . */ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities.dox b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities.dox index 0d9b10b310..623bfb4c2b 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities.dox +++ b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities.dox @@ -1,80 +1,80 @@ /** \page org_mitk_views_segmentationutilities The Segmentation Utilities View \imageMacro{segmentation_utilities-dox.svg,"Icon of the Segmentation Utilities View",5.00} \imageMacro{QmitkSegmentationUtilities_Overview.png,"The Segmentation Utilities View",16.00} \tableofcontents \section org_mitk_views_segmentationUtilitiesManualOverview Overview The Segmentation Utilities View allows to postprocess existing segmentations. Currently five different operations exist:
  • \ref org_mitk_views_segmentationUtilitiesBooleanOperations
  • \ref org_mitk_views_segmentationUtilitiesContourToImage
  • \ref org_mitk_views_segmentationUtilitiesImageMasking
  • \ref org_mitk_views_segmentationUtilitiesMorphologicalOperations
  • \ref org_mitk_views_segmentationUtilitiesSurfaceToImage
\section org_mitk_views_segmentationUtilitiesDataSelection Data Selection All postprocessing operations provide one or more selection widgets, which allow to select the data for the operation. \section org_mitk_views_segmentationUtilitiesBooleanOperations Boolean operations Boolean operations allows to perform the following fundamental operations on two segmentations:
  • Difference: Subtracts the second segmentation from the first segmentation.
  • Intersection: Extracts the overlapping areas of the two selected segmentations.
  • Union: Combines the two existing segmentations.
The selected segmentations must have the same geometry (size, spacing, ...) in order for the operations to work correctly. The result will be stored in a new data node as a child node of the first selected segmentation. \imageMacro{QmitkSegmentationUtilities_BooleanOperations.png,"Boolean operations",6.00} \section org_mitk_views_segmentationUtilitiesContourToImage Contour to image Contour to image allows to create a segmentation out of a given contour-model. The operation requires a contour model set and a reference image. The created segmentation image will have the same geometrical properties like the reference image (dimension, size and Geometry3D). \imageMacro{QmitkSegmentationUtilities_ContourToImage.png,"Contour to image",6.00} \section org_mitk_views_segmentationUtilitiesImageMasking Image masking Image masking allows to mask an image with either an existing segmentation or a surface. -The operation requires an image and a binary image mask or a surface. +The operation requires an image and a segmentation or a surface. The result will be an image containing only the pixels that are covered by the respective mask. \imageMacro{QmitkSegmentationUtilities_ImageMasking.png,"Image masking",6.00} \section org_mitk_views_segmentationUtilitiesMorphologicalOperations Morphological operations Morphological operations are applied to a single segmentation image. Based on a given structuring element the underlying segmentation will be modfied. The plugin provides a ball and a cross as structuring elements. The follow operations are available:
  • Dilation: Each labeled pixel within the segmentation will be dilated based on the selected structuring element.
  • Erosion: Each labeled pixel within the segmentation will be eroded based on the selected structuring element.
  • Opening: A dilation followed by an erosion, used for smoothing edges or eliminating small objects.
  • Closing: An erosion followed by an dilation, used for filling small holes.
  • Fill Holes: Fills bigger holes within a segmentation.
\imageMacro{QmitkSegmentationUtilities_MorphologicalOperations.png,"Morphological operations",6.00} \section org_mitk_views_segmentationUtilitiesSurfaceToImage Surface to image Surface to image allows to create a segmentation out of a given surface. The operation requires a surface and a reference image. The created segmentation image will have the same geometrical properties like the reference image (dimension, size and Geometry3D). \imageMacro{QmitkSegmentationUtilities_SurfaceToImage.png,"Surface to image",6.00} **/ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities_ImageMasking.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities_ImageMasking.png index ae33391505..5664184a23 100644 Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities_ImageMasking.png and b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentationUtilities_ImageMasking.png differ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGCorrectionActions.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGCorrectionActions.png deleted file mode 100644 index 52a07f399a..0000000000 Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGCorrectionActions.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGIconCorrection.png b/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGIconCorrection.png deleted file mode 100644 index dbd9ce37f1..0000000000 Binary files a/Plugins/org.mitk.gui.qt.segmentation/documentation/UserManual/QmitkSegmentation_IMGIconCorrection.png and /dev/null differ diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.cpp index a7a049c890..057e60feec 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.cpp @@ -1,189 +1,176 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkSegmentationPreferencePage.h" #include #include #include #include #include #include #include #include #include #include QmitkSegmentationPreferencePage::QmitkSegmentationPreferencePage() -: m_MainControl(nullptr) -, m_Initializing(false) + : m_MainControl(nullptr), + m_SlimViewCheckBox(nullptr), + m_RadioOutline(nullptr), + m_RadioOverlay(nullptr), + m_SmoothingCheckBox(nullptr), + m_SmoothingSpinBox(nullptr), + m_DecimationSpinBox(nullptr), + m_ClosingSpinBox(nullptr), + m_SelectionModeCheckBox(nullptr), + m_Initializing(false) { - } QmitkSegmentationPreferencePage::~QmitkSegmentationPreferencePage() { } void QmitkSegmentationPreferencePage::Init(berry::IWorkbench::Pointer ) { } void QmitkSegmentationPreferencePage::CreateQtControl(QWidget* parent) { m_Initializing = true; berry::IPreferencesService* prefService = berry::Platform::GetPreferencesService(); m_SegmentationPreferencesNode = prefService->GetSystemPreferences()->Node("/org.mitk.views.segmentation"); m_MainControl = new QWidget(parent); auto formLayout = new QFormLayout; formLayout->setHorizontalSpacing(8); formLayout->setVerticalSpacing(24); m_SlimViewCheckBox = new QCheckBox("Hide tool button texts and increase icon size", m_MainControl); formLayout->addRow("Slim view", m_SlimViewCheckBox); auto displayOptionsLayout = new QVBoxLayout; m_RadioOutline = new QRadioButton( "Draw as outline", m_MainControl); displayOptionsLayout->addWidget( m_RadioOutline ); m_RadioOverlay = new QRadioButton( "Draw as transparent overlay", m_MainControl); displayOptionsLayout->addWidget( m_RadioOverlay ); formLayout->addRow( "2D display", displayOptionsLayout ); - m_VolumeRenderingCheckBox = new QCheckBox( "Show as volume rendering", m_MainControl ); - formLayout->addRow( "3D display", m_VolumeRenderingCheckBox ); - connect( m_VolumeRenderingCheckBox, SIGNAL(stateChanged(int)), this, SLOT(OnVolumeRenderingCheckboxChecked(int)) ); - auto surfaceLayout = new QFormLayout; surfaceLayout->setSpacing(8); m_SmoothingCheckBox = new QCheckBox("Use image spacing as smoothing value hint", m_MainControl); surfaceLayout->addRow(m_SmoothingCheckBox); connect(m_SmoothingCheckBox, SIGNAL(stateChanged(int)), this, SLOT(OnSmoothingCheckboxChecked(int))); m_SmoothingSpinBox = new QDoubleSpinBox(m_MainControl); m_SmoothingSpinBox->setMinimum(0.0); m_SmoothingSpinBox->setSingleStep(0.5); m_SmoothingSpinBox->setValue(1.0); m_SmoothingSpinBox->setToolTip("The Smoothing value is used as variance for a gaussian blur."); surfaceLayout->addRow("Smoothing value (mm)", m_SmoothingSpinBox); m_DecimationSpinBox = new QDoubleSpinBox(m_MainControl); m_DecimationSpinBox->setMinimum(0.0); m_DecimationSpinBox->setMaximum(0.99); m_DecimationSpinBox->setSingleStep(0.1); m_DecimationSpinBox->setValue(0.5); m_DecimationSpinBox->setToolTip("Valid range is [0, 1). High values increase decimation, especially when very close to 1. A value of 0 disables decimation."); surfaceLayout->addRow("Decimation rate", m_DecimationSpinBox); m_ClosingSpinBox = new QDoubleSpinBox(m_MainControl); m_ClosingSpinBox->setMinimum(0.0); m_ClosingSpinBox->setMaximum(1.0); m_ClosingSpinBox->setSingleStep(0.1); m_ClosingSpinBox->setValue(0.0); m_ClosingSpinBox->setToolTip("Valid range is [0, 1]. Higher values increase closing. A value of 0 disables closing."); surfaceLayout->addRow("Closing Ratio", m_ClosingSpinBox); m_SelectionModeCheckBox = new QCheckBox("Enable auto-selection mode", m_MainControl); - m_SelectionModeCheckBox->setToolTip("If checked the segmentation plugin ensures that only one segmentation and the according greyvalue image are visible at one time."); + m_SelectionModeCheckBox->setToolTip("Automatically select a patient image and a segmentation if available"); formLayout->addRow("Data node selection mode",m_SelectionModeCheckBox); formLayout->addRow("Smoothed surface creation", surfaceLayout); m_MainControl->setLayout(formLayout); this->Update(); m_Initializing = false; } QWidget* QmitkSegmentationPreferencePage::GetQtControl() const { return m_MainControl; } bool QmitkSegmentationPreferencePage::PerformOk() { m_SegmentationPreferencesNode->PutBool("slim view", m_SlimViewCheckBox->isChecked()); m_SegmentationPreferencesNode->PutBool("draw outline", m_RadioOutline->isChecked()); - m_SegmentationPreferencesNode->PutBool("volume rendering", m_VolumeRenderingCheckBox->isChecked()); m_SegmentationPreferencesNode->PutBool("smoothing hint", m_SmoothingCheckBox->isChecked()); m_SegmentationPreferencesNode->PutDouble("smoothing value", m_SmoothingSpinBox->value()); m_SegmentationPreferencesNode->PutDouble("decimation rate", m_DecimationSpinBox->value()); m_SegmentationPreferencesNode->PutDouble("closing ratio", m_ClosingSpinBox->value()); m_SegmentationPreferencesNode->PutBool("auto selection", m_SelectionModeCheckBox->isChecked()); return true; } void QmitkSegmentationPreferencePage::PerformCancel() { } void QmitkSegmentationPreferencePage::Update() { //m_EnableSingleEditing->setChecked(m_SegmentationPreferencesNode->GetBool("Single click property editing", true)); m_SlimViewCheckBox->setChecked(m_SegmentationPreferencesNode->GetBool("slim view", false)); if (m_SegmentationPreferencesNode->GetBool("draw outline", true) ) { m_RadioOutline->setChecked( true ); } else { m_RadioOverlay->setChecked( true ); } - m_VolumeRenderingCheckBox->setChecked( m_SegmentationPreferencesNode->GetBool("volume rendering", false) ); - if (m_SegmentationPreferencesNode->GetBool("smoothing hint", true)) { m_SmoothingCheckBox->setChecked(true); m_SmoothingSpinBox->setDisabled(true); } else { m_SmoothingCheckBox->setChecked(false); m_SmoothingSpinBox->setEnabled(true); } m_SelectionModeCheckBox->setChecked( m_SegmentationPreferencesNode->GetBool("auto selection", true) ); m_SmoothingSpinBox->setValue(m_SegmentationPreferencesNode->GetDouble("smoothing value", 1.0)); m_DecimationSpinBox->setValue(m_SegmentationPreferencesNode->GetDouble("decimation rate", 0.5)); m_ClosingSpinBox->setValue(m_SegmentationPreferencesNode->GetDouble("closing ratio", 0.0)); } -void QmitkSegmentationPreferencePage::OnVolumeRenderingCheckboxChecked(int state) -{ - if (m_Initializing) return; - - if ( state != Qt::Unchecked ) - { - QMessageBox::information(nullptr, - "Memory warning", - "Turning on volume rendering of segmentations will make the application more memory intensive (and potentially prone to crashes).\n\n" - "If you encounter out-of-memory problems, try turning off volume rendering again."); - } -} - void QmitkSegmentationPreferencePage::OnSmoothingCheckboxChecked(int state) { if (state != Qt::Unchecked) m_SmoothingSpinBox->setDisabled(true); else m_SmoothingSpinBox->setEnabled(true); } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.h b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.h index 3a34f4c8fa..9d7e1100e9 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.h +++ b/Plugins/org.mitk.gui.qt.segmentation/src/QmitkSegmentationPreferencePage.h @@ -1,81 +1,79 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkSegmentationPreferencePage_h_included #define QmitkSegmentationPreferencePage_h_included #include "org_mitk_gui_qt_segmentation_Export.h" #include #include "berryIQtPreferencePage.h" class QWidget; class QCheckBox; class QRadioButton; class QDoubleSpinBox; class MITK_QT_SEGMENTATION QmitkSegmentationPreferencePage : public QObject, public berry::IQtPreferencePage { Q_OBJECT Q_INTERFACES(berry::IPreferencePage) public: QmitkSegmentationPreferencePage(); ~QmitkSegmentationPreferencePage() override; void Init(berry::IWorkbench::Pointer workbench) override; void CreateQtControl(QWidget* widget) override; QWidget* GetQtControl() const override; /// /// \see IPreferencePage::PerformOk() /// bool PerformOk() override; /// /// \see IPreferencePage::PerformCancel() /// void PerformCancel() override; /// /// \see IPreferencePage::Update() /// void Update() override; protected slots: - void OnVolumeRenderingCheckboxChecked(int); void OnSmoothingCheckboxChecked(int); protected: QWidget* m_MainControl; QCheckBox* m_SlimViewCheckBox; QRadioButton* m_RadioOutline; QRadioButton* m_RadioOverlay; - QCheckBox* m_VolumeRenderingCheckBox; QCheckBox* m_SmoothingCheckBox; QDoubleSpinBox* m_SmoothingSpinBox; QDoubleSpinBox* m_DecimationSpinBox; QDoubleSpinBox* m_ClosingSpinBox; QCheckBox* m_SelectionModeCheckBox; bool m_Initializing; berry::IPreferences::Pointer m_SegmentationPreferencesNode; }; #endif /* QMITKDATAMANAGERPREFERENCEPAGE_H_ */ diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.cpp index 183ee609a3..5ca2bbd0d5 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.cpp @@ -1,229 +1,236 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkDataSelectionWidget.h" #include "../mitkPluginActivator.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include static mitk::NodePredicateBase::Pointer CreatePredicate(QmitkDataSelectionWidget::Predicate predicate) { auto imageType = mitk::TNodePredicateDataType::New(); auto labelSetImageType = mitk::TNodePredicateDataType::New(); auto surfaceType = mitk::TNodePredicateDataType::New(); auto contourModelType = mitk::TNodePredicateDataType::New(); auto contourModelSetType = mitk::TNodePredicateDataType::New(); auto nonLabelSetImageType = mitk::NodePredicateAnd::New(imageType, mitk::NodePredicateNot::New(labelSetImageType)); - auto nonHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object")); + auto nonHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateOr::New( + mitk::NodePredicateProperty::New("helper object"), + mitk::NodePredicateProperty::New("hidden object"))); auto isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); auto isSegmentation = mitk::NodePredicateProperty::New("segmentation", mitk::BoolProperty::New(true)); auto isBinaryOrSegmentation = mitk::NodePredicateOr::New(isBinary, isSegmentation); mitk::NodePredicateBase::Pointer returnValue; switch(predicate) { case QmitkDataSelectionWidget::ImagePredicate: returnValue = mitk::NodePredicateAnd::New( mitk::NodePredicateNot::New(isBinaryOrSegmentation), nonLabelSetImageType).GetPointer(); break; case QmitkDataSelectionWidget::SegmentationPredicate: returnValue = mitk::NodePredicateOr::New( mitk::NodePredicateAnd::New(imageType, isBinaryOrSegmentation), labelSetImageType).GetPointer(); break; case QmitkDataSelectionWidget::SurfacePredicate: returnValue = surfaceType.GetPointer(); break; case QmitkDataSelectionWidget::ImageAndSegmentationPredicate: returnValue = imageType.GetPointer(); break; case QmitkDataSelectionWidget::ContourModelPredicate: returnValue = mitk::NodePredicateOr::New( contourModelSetType, contourModelSetType).GetPointer(); break; + case QmitkDataSelectionWidget::SegmentationOrSurfacePredicate: + returnValue = mitk::NodePredicateOr::New( + mitk::NodePredicateAnd::New(imageType, isBinaryOrSegmentation), + labelSetImageType).GetPointer(); + returnValue = mitk::NodePredicateOr::New(returnValue, surfaceType).GetPointer(); + break; + default: assert(false && "Unknown predefined predicate!"); return nullptr; } return mitk::NodePredicateAnd::New(returnValue, nonHelperObject).GetPointer(); } QmitkDataSelectionWidget::QmitkDataSelectionWidget(QWidget* parent) : QWidget(parent) { m_Controls.setupUi(this); m_Controls.helpLabel->hide(); } QmitkDataSelectionWidget::~QmitkDataSelectionWidget() { } unsigned int QmitkDataSelectionWidget::AddDataSelection(QmitkDataSelectionWidget::Predicate predicate) { QString hint = "Select node"; - QString popupTitel = "Select node"; switch (predicate) { - case QmitkDataSelectionWidget::ImagePredicate: + case QmitkDataSelectionWidget::ImagePredicate: hint = "Select an image"; - popupTitel = "Select an image"; - break; + break; - case QmitkDataSelectionWidget::SegmentationPredicate: + case QmitkDataSelectionWidget::SegmentationPredicate: hint = "Select a segmentation"; - popupTitel = "Select a segmentation"; - break; - - case QmitkDataSelectionWidget::SurfacePredicate: - hint = "Select a surface"; - popupTitel = "Select a surface"; - break; - - case QmitkDataSelectionWidget::ImageAndSegmentationPredicate: - hint = "Select an image or segmentation"; - popupTitel = "Select an image or segmentation"; - break; - - case QmitkDataSelectionWidget::ContourModelPredicate: - hint = "Select a contour model"; - popupTitel = "Select a contour model"; - break; + break; + + case QmitkDataSelectionWidget::SurfacePredicate: + hint = "Select a surface"; + break; + + case QmitkDataSelectionWidget::ImageAndSegmentationPredicate: + hint = "Select an image or segmentation"; + break; + + case QmitkDataSelectionWidget::ContourModelPredicate: + hint = "Select a contour model"; + break; + + case QmitkDataSelectionWidget::SegmentationOrSurfacePredicate: + hint = "Select a segmentation or surface"; + break; } - return this->AddDataSelection("", hint, popupTitel, "", predicate); + return this->AddDataSelection("", hint, hint, "", predicate); } unsigned int QmitkDataSelectionWidget::AddDataSelection(mitk::NodePredicateBase* predicate) { return this->AddDataSelection("", "Select a node", "Select a node", "", predicate); } unsigned int QmitkDataSelectionWidget::AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, QmitkDataSelectionWidget::Predicate predicate) { return this->AddDataSelection(labelText, info, popupHint, popupTitel, CreatePredicate(predicate)); } unsigned int QmitkDataSelectionWidget::AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, mitk::NodePredicateBase* predicate) { int row = m_Controls.gridLayout->rowCount(); if (!labelText.isEmpty()) { QLabel* label = new QLabel(labelText, m_Controls.dataSelectionWidget); label->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Minimum); m_Controls.gridLayout->addWidget(label, row, 0); } QmitkSingleNodeSelectionWidget* nodeSelection = new QmitkSingleNodeSelectionWidget(m_Controls.dataSelectionWidget); nodeSelection->SetSelectionIsOptional(false); nodeSelection->SetAutoSelectNewNodes(false); nodeSelection->SetInvalidInfo(info); nodeSelection->SetPopUpTitel(popupTitel); nodeSelection->SetPopUpHint(popupHint); nodeSelection->SetDataStorage(this->GetDataStorage()); nodeSelection->SetNodePredicate(predicate); nodeSelection->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Minimum); nodeSelection->setMinimumSize(0, 40); connect(nodeSelection, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkDataSelectionWidget::OnSelectionChanged); m_Controls.gridLayout->addWidget(nodeSelection, row, 1); m_NodeSelectionWidgets.push_back(nodeSelection); return static_cast(m_NodeSelectionWidgets.size() - 1); } mitk::DataStorage::Pointer QmitkDataSelectionWidget::GetDataStorage() const { ctkServiceReference ref = mitk::PluginActivator::getContext()->getServiceReference(); assert(ref == true); mitk::IDataStorageService* service = mitk::PluginActivator::getContext()->getService(ref); assert(service); return service->GetDefaultDataStorage()->GetDataStorage(); } mitk::DataNode::Pointer QmitkDataSelectionWidget::GetSelection(unsigned int index) { assert(index < m_NodeSelectionWidgets.size()); return m_NodeSelectionWidgets[index]->GetSelectedNode(); } void QmitkDataSelectionWidget::SetPredicate(unsigned int index, Predicate predicate) { this->SetPredicate(index, CreatePredicate(predicate)); } void QmitkDataSelectionWidget::SetPredicate(unsigned int index, mitk::NodePredicateBase* predicate) { assert(index < m_NodeSelectionWidgets.size()); m_NodeSelectionWidgets[index]->SetNodePredicate(predicate); } void QmitkDataSelectionWidget::SetHelpText(const QString& text) { if (!text.isEmpty()) { m_Controls.helpLabel->setText(text); if (!m_Controls.helpLabel->isVisible()) m_Controls.helpLabel->show(); } else { m_Controls.helpLabel->hide(); } } void QmitkDataSelectionWidget::OnSelectionChanged(QList selection) { std::vector::iterator it = std::find(m_NodeSelectionWidgets.begin(), m_NodeSelectionWidgets.end(), sender()); assert(it != m_NodeSelectionWidgets.end()); const mitk::DataNode* result = nullptr; if (!selection.empty()) { result = selection.front(); } emit SelectionChanged(std::distance(m_NodeSelectionWidgets.begin(), it), result); } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.h b/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.h index 48cbcdeab7..f702654857 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.h +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/Common/QmitkDataSelectionWidget.h @@ -1,67 +1,68 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 QmitkDataSelectionWidget_h #define QmitkDataSelectionWidget_h #include #include #include #include namespace mitk { class NodePredicateBase; } class QmitkSingleNodeSelectionWidget; class QmitkDataSelectionWidget : public QWidget { Q_OBJECT public: enum Predicate { ImagePredicate, SegmentationPredicate, SurfacePredicate, ImageAndSegmentationPredicate, - ContourModelPredicate + ContourModelPredicate, + SegmentationOrSurfacePredicate }; explicit QmitkDataSelectionWidget(QWidget* parent = nullptr); ~QmitkDataSelectionWidget() override; unsigned int AddDataSelection(Predicate predicate); unsigned int AddDataSelection(mitk::NodePredicateBase* predicate = nullptr); unsigned int AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, Predicate predicate); unsigned int AddDataSelection(const QString &labelText, const QString &info, const QString &popupTitel, const QString &popupHint, mitk::NodePredicateBase* predicate = nullptr); mitk::DataStorage::Pointer GetDataStorage() const; mitk::DataNode::Pointer GetSelection(unsigned int index); void SetPredicate(unsigned int index, Predicate predicate); void SetPredicate(unsigned int index, mitk::NodePredicateBase* predicate); void SetHelpText(const QString& text); signals: void SelectionChanged(unsigned int index, const mitk::DataNode* selection); private slots: void OnSelectionChanged(QList selection); private: Ui::QmitkDataSelectionWidgetControls m_Controls; std::vector m_NodeSelectionWidgets; }; #endif diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp index d608a7078f..117e144453 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/QmitkSegmentationView.cpp @@ -1,907 +1,904 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 #include "mitkProperties.h" #include "mitkSegTool2D.h" #include "mitkStatusBar.h" #include "QmitkNewSegmentationDialog.h" #include #include #include #include "QmitkSegmentationView.h" #include #include "mitkVtkResliceInterpolationProperty.h" #include "mitkApplicationCursor.h" #include "mitkSegmentationObjectFactory.h" #include "mitkPluginActivator.h" #include "mitkCameraController.h" #include "mitkLabelSetImage.h" #include "mitkImageTimeSelector.h" #include "mitkNodePredicateSubGeometry.h" #include #include "usModuleResource.h" #include "usModuleResourceStream.h" //micro service to get the ToolManager instance #include "mitkToolManagerProvider.h" #include #include const std::string QmitkSegmentationView::VIEW_ID = "org.mitk.views.segmentation"; QmitkSegmentationView::QmitkSegmentationView() : m_Parent(nullptr) , m_Controls(nullptr) , m_RenderWindowPart(nullptr) , m_MouseCursorSet(false) , m_DataSelectionChanged(false) { mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage"); auto isSegment = mitk::NodePredicateDataType::New("Segment"); mitk::NodePredicateOr::Pointer validImages = mitk::NodePredicateOr::New(); validImages->AddPredicate(mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isSegment))); validImages->AddPredicate(isDwi); validImages->AddPredicate(isDti); validImages->AddPredicate(isOdf); m_IsNotAHelperObject = mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true))); m_IsOfTypeImagePredicate = mitk::NodePredicateAnd::New(validImages, m_IsNotAHelperObject); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateNot::Pointer isNotBinaryPredicate = mitk::NodePredicateNot::New(isBinaryPredicate); mitk::NodePredicateAnd::Pointer isABinaryImagePredicate = mitk::NodePredicateAnd::New(m_IsOfTypeImagePredicate, isBinaryPredicate); mitk::NodePredicateAnd::Pointer isNotABinaryImagePredicate = mitk::NodePredicateAnd::New(m_IsOfTypeImagePredicate, isNotBinaryPredicate); auto isMLImageType = mitk::TNodePredicateDataType::New(); mitk::NodePredicateAnd::Pointer isAMLImagePredicate = mitk::NodePredicateAnd::New(isMLImageType, m_IsNotAHelperObject); mitk::NodePredicateAnd::Pointer isNotAMLImagePredicate = mitk::NodePredicateAnd::New(mitk::NodePredicateNot::New(isMLImageType), m_IsNotAHelperObject); m_IsASegmentationImagePredicate = mitk::NodePredicateOr::New(isABinaryImagePredicate, isAMLImagePredicate); m_IsAPatientImagePredicate = mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, isNotAMLImagePredicate); } QmitkSegmentationView::~QmitkSegmentationView() { if (m_Controls) { SetToolSelectionBoxesEnabled(false); // deactivate all tools mitk::ToolManagerProvider::GetInstance()->GetToolManager()->ActivateTool(-1); // removing all observers for (NodeTagMapType::iterator dataIter = m_WorkingDataObserverTags.begin(); dataIter != m_WorkingDataObserverTags.end(); ++dataIter) { (*dataIter).first->GetProperty("visible")->RemoveObserver((*dataIter).second); } m_WorkingDataObserverTags.clear(); mitk::RenderingManager::GetInstance()->RemoveObserver(m_RenderingManagerObserverTag); ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); service->RemoveAllPlanePositions(); context->ungetService(ppmRef); SetToolManagerSelection(nullptr, nullptr); } delete m_Controls; } void QmitkSegmentationView::NewNodeObjectsGenerated(mitk::ToolManager::DataVectorType* nodes) { if (!nodes) return; mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); if (!toolManager) return; for (mitk::ToolManager::DataVectorType::iterator iter = nodes->begin(); iter != nodes->end(); ++iter) { this->FireNodeSelected( *iter ); // only last iteration meaningful, multiple generated objects are not taken into account here } } void QmitkSegmentationView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { if (m_RenderWindowPart != renderWindowPart) { m_RenderWindowPart = renderWindowPart; } if (m_Parent) { m_Parent->setEnabled(true); } // tell the interpolation about tool manager, data storage and render window part if (m_Controls) { mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); m_Controls->m_SlicesInterpolator->SetDataStorage(this->GetDataStorage()); QList controllers; controllers.push_back(renderWindowPart->GetQmitkRenderWindow("axial")->GetSliceNavigationController()); controllers.push_back(renderWindowPart->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()); controllers.push_back(renderWindowPart->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()); m_Controls->m_SlicesInterpolator->Initialize(toolManager, controllers); } } void QmitkSegmentationView::RenderWindowPartDeactivated(mitk::IRenderWindowPart* /*renderWindowPart*/) { m_RenderWindowPart = nullptr; if (m_Parent) { m_Parent->setEnabled(false); } } void QmitkSegmentationView::OnPreferencesChanged(const berry::IBerryPreferences* prefs) { if (m_Controls != nullptr) { bool slimView = prefs->GetBool("slim view", false); m_Controls->m_ManualToolSelectionBox2D->SetShowNames(!slimView); m_Controls->m_ManualToolSelectionBox3D->SetShowNames(!slimView); m_Controls->btnNewSegmentation->setToolButtonStyle(slimView ? Qt::ToolButtonIconOnly : Qt::ToolButtonTextOnly); } auto autoSelectionEnabled = prefs->GetBool("auto selection", true); m_Controls->patImageSelector->SetAutoSelectNewNodes(autoSelectionEnabled); m_Controls->segImageSelector->SetAutoSelectNewNodes(autoSelectionEnabled); this->ForceDisplayPreferencesUponAllImages(); } void QmitkSegmentationView::CreateNewSegmentation() { mitk::DataNode::Pointer node = mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetReferenceData(0); if (node.IsNotNull()) { mitk::Image::ConstPointer referenceImage = dynamic_cast(node->GetData()); if (referenceImage.IsNotNull()) { if (referenceImage->GetDimension() > 1) { // ask about the name and organ type of the new segmentation QmitkNewSegmentationDialog* dialog = new QmitkNewSegmentationDialog(m_Parent); // needs a QWidget as parent, "this" is not QWidget QStringList organColors = mitk::OrganNamesHandling::GetDefaultOrganColorString();; dialog->SetSuggestionList(organColors); int dialogReturnValue = dialog->exec(); if (dialogReturnValue == QDialog::Rejected) { // user clicked cancel or pressed Esc or something similar return; } const auto currentTimePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint(); unsigned int imageTimeStep = 0; if (referenceImage->GetTimeGeometry()->IsValidTimePoint(currentTimePoint)) { imageTimeStep = referenceImage->GetTimeGeometry()->TimePointToTimeStep(currentTimePoint); } auto segTemplateImage = referenceImage; if (referenceImage->GetDimension() > 3) { - auto result = QMessageBox::question(m_Parent, tr("Generate a static mask?"),tr("The selected image has multiple time steps. You can either generate a simple/static masks resembling the geometry of the first timestep of the image. Or you can generate a dynamic mask that equals the selected image in geometry and number of timesteps; thus a dynamic mask can change over time (e.g. according to the image)."), tr("Yes, generate a static mask"), tr("No, generate a dynamic mask"), QString(), 0,0); + auto result = QMessageBox::question(m_Parent, tr("Create a static or dynamic segmentation?"), tr("The patient image has multiple time steps.\n\nDo you want to create a static segmentation that is identical for all time steps or do you want to create a dynamic segmentation to segment individual time steps?"), tr("Create static segmentation"), tr("Create dynamic segmentation"), QString(), 0,0); if (result == 0) { auto selector = mitk::ImageTimeSelector::New(); selector->SetInput(referenceImage); selector->SetTimeNr(0); selector->Update(); const auto refTimeGeometry = referenceImage->GetTimeGeometry(); auto newTimeGeometry = mitk::ProportionalTimeGeometry::New(); newTimeGeometry->SetFirstTimePoint(refTimeGeometry->GetMinimumTimePoint()); newTimeGeometry->SetStepDuration(refTimeGeometry->GetMaximumTimePoint() - refTimeGeometry->GetMinimumTimePoint()); mitk::Image::Pointer newImage = selector->GetOutput(); newTimeGeometry->SetTimeStepGeometry(referenceImage->GetGeometry(imageTimeStep), 0); newImage->SetTimeGeometry(newTimeGeometry); segTemplateImage = newImage; } } // ask the user about an organ type and name, add this information to the image's (!) propertylist // create a new image of the same dimensions and smallest possible pixel type mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); mitk::Tool* firstTool = toolManager->GetToolById(0); if (firstTool) { try { std::string newNodeName = dialog->GetSegmentationName().toStdString(); if (newNodeName.empty()) { newNodeName = "no_name"; } mitk::DataNode::Pointer emptySegmentation = firstTool->CreateEmptySegmentationNode(segTemplateImage, newNodeName, dialog->GetColor()); // initialize showVolume to false to prevent recalculating the volume while working on the segmentation emptySegmentation->SetProperty("showVolume", mitk::BoolProperty::New(false)); if (!emptySegmentation) { return; // could be aborted by user } mitk::OrganNamesHandling::UpdateOrganList(organColors, dialog->GetSegmentationName(), dialog->GetColor()); // escape ';' here (replace by '\;'), see longer comment above QString stringForStorage = organColors.replaceInStrings(";", "\\;").join(";"); MITK_DEBUG << "Will store: " << stringForStorage; this->GetPreferences()->Put("Organ-Color-List", stringForStorage); this->GetPreferences()->Flush(); if (mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0)) { mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0)->SetSelected(false); } emptySegmentation->SetSelected(true); this->GetDataStorage()->Add(emptySegmentation, node); // add as a child, because the segmentation "derives" from the original m_Controls->segImageSelector->SetCurrentSelectedNode(emptySegmentation); mitk::RenderingManager::GetInstance()->InitializeViews(referenceImage->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetTime()->SetPos(imageTimeStep); } catch (const std::bad_alloc&) { QMessageBox::warning(nullptr, tr("Create new segmentation"), tr("Could not allocate memory for new segmentation")); } } } else { QMessageBox::information(nullptr, tr("Segmentation"), tr("Segmentation is currently not supported for 2D images")); } } } else { MITK_ERROR << "'Create new segmentation' button should never be clickable unless a patient image is selected..."; } } void QmitkSegmentationView::OnVisiblePropertyChanged() { this->CheckRenderingState(); } void QmitkSegmentationView::NodeAdded(const mitk::DataNode *node) { if (!m_IsASegmentationImagePredicate->CheckNode(node)) { return; } itk::SimpleMemberCommand::Pointer command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::OnVisiblePropertyChanged); m_WorkingDataObserverTags.insert(std::pair(const_cast(node), node->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command))); ApplyDisplayOptions(const_cast(node)); } void QmitkSegmentationView::NodeRemoved(const mitk::DataNode* node) { if (m_IsASegmentationImagePredicate->CheckNode(node)) { //First of all remove all possible contour markers of the segmentation mitk::DataStorage::SetOfObjects::ConstPointer allContourMarkers = this->GetDataStorage()->GetDerivations(node, mitk::NodePredicateProperty::New("isContourMarker", mitk::BoolProperty::New(true))); ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); for (mitk::DataStorage::SetOfObjects::ConstIterator it = allContourMarkers->Begin(); it != allContourMarkers->End(); ++it) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t + 1).c_str()) - 1; service->RemovePlanePosition(id); this->GetDataStorage()->Remove(it->Value()); } context->ungetService(ppmRef); service = nullptr; if ((mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetWorkingData(0) == node) && m_Controls->patImageSelector->GetSelectedNode().IsNotNull()) { this->SetToolManagerSelection(mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetReferenceData(0), nullptr); this->UpdateWarningLabel(tr("Select or create a segmentation")); } mitk::Image* image = dynamic_cast(node->GetData()); mitk::SurfaceInterpolationController::GetInstance()->RemoveInterpolationSession(image); } mitk::DataNode* tempNode = const_cast(node); //Remove observer if one was registered auto finding = m_WorkingDataObserverTags.find(tempNode); if (finding != m_WorkingDataObserverTags.end()) { node->GetProperty("visible")->RemoveObserver(m_WorkingDataObserverTags[tempNode]); m_WorkingDataObserverTags.erase(tempNode); } } void QmitkSegmentationView::OnPatientSelectionChanged(QList nodes) { if(! nodes.empty()) { this->UpdateWarningLabel(""); auto node = nodes.first(); auto segPredicate = mitk::NodePredicateAnd::New(m_IsASegmentationImagePredicate.GetPointer(), mitk::NodePredicateSubGeometry::New(node->GetData()->GetGeometry())); m_Controls->segImageSelector->SetNodePredicate(segPredicate); mitk::DataNode* segNode = m_Controls->segImageSelector->GetSelectedNode(); this->SetToolManagerSelection(node, segNode); if (segNode) { //Doing this we can assure that the segmentation is always visible if the segmentation and the patient image are //loaded separately int layer(10); node->GetIntProperty("layer", layer); layer++; segNode->SetProperty("layer", mitk::IntProperty::New(layer)); this->CheckRenderingState(); } else { this->SetToolSelectionBoxesEnabled( false ); this->UpdateWarningLabel(tr("Select or create a segmentation")); } } else { m_Controls->segImageSelector->SetNodePredicate(m_IsASegmentationImagePredicate); this->UpdateWarningLabel(tr("Please select an image!")); this->SetToolSelectionBoxesEnabled( false ); } } void QmitkSegmentationView::OnSegmentationSelectionChanged(QList nodes) { if (nodes.empty()) { this->UpdateWarningLabel(tr("Select or create a segmentation")); this->SetToolSelectionBoxesEnabled( false ); return; } auto refNode = m_Controls->patImageSelector->GetSelectedNode(); auto segNode = nodes.front(); if (!refNode) { this->UpdateWarningLabel(tr("Please select the matching patient image!")); this->SetToolSelectionBoxesEnabled(false); this->SetToolManagerSelection(nullptr, segNode); return; } this->CheckRenderingState(); if ( m_Controls->lblSegmentationWarnings->isVisible()) // "this->CheckRenderingState()" caused a warning. we do not need to go any further return; this->SetToolManagerSelection(refNode, segNode); if (segNode) { //Doing this we can assure that the segmenation is always visible if the segmentation and the patient image are //loaded separately int layer(10); refNode->GetIntProperty("layer", layer); layer++; segNode->SetProperty("layer", mitk::IntProperty::New(layer)); } else { this->SetToolSelectionBoxesEnabled(false); this->UpdateWarningLabel(tr("Select or create a segmentation")); } mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart(); if (!renderWindowPart || !segNode->IsVisible(renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderer())) { this->UpdateWarningLabel(tr("The selected segmentation is currently not visible!")); this->SetToolSelectionBoxesEnabled( false ); } } void QmitkSegmentationView::OnShowMarkerNodes (bool state) { mitk::SegTool2D::Pointer manualSegmentationTool; unsigned int numberOfExistingTools = mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetTools().size(); for(unsigned int i = 0; i < numberOfExistingTools; i++) { manualSegmentationTool = dynamic_cast(mitk::ToolManagerProvider::GetInstance()->GetToolManager()->GetToolById(i)); if (manualSegmentationTool) { if(state == true) { manualSegmentationTool->SetShowMarkerNodes( true ); } else { manualSegmentationTool->SetShowMarkerNodes( false ); } } } } void QmitkSegmentationView::OnContourMarkerSelected(const mitk::DataNode *node) { QmitkRenderWindow* selectedRenderWindow = nullptr; QmitkRenderWindow* axialRenderWindow = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("axial"); QmitkRenderWindow* sagittalRenderWindow = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("sagittal"); QmitkRenderWindow* coronalRenderWindow = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("coronal"); QmitkRenderWindow* _3DRenderWindow = GetRenderWindowPart(mitk::WorkbenchUtil::OPEN)->GetQmitkRenderWindow("3d"); bool PlanarFigureInitializedWindow = false; // find initialized renderwindow if (node->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, axialRenderWindow->GetRenderer())) { selectedRenderWindow = axialRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, sagittalRenderWindow->GetRenderer())) { selectedRenderWindow = sagittalRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, coronalRenderWindow->GetRenderer())) { selectedRenderWindow = coronalRenderWindow; } if (!selectedRenderWindow && node->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, _3DRenderWindow->GetRenderer())) { selectedRenderWindow = _3DRenderWindow; } // make node visible if (selectedRenderWindow) { std::string nodeName = node->GetName(); unsigned int t = nodeName.find_last_of(" "); unsigned int id = atof(nodeName.substr(t+1).c_str())-1; { ctkPluginContext* context = mitk::PluginActivator::getContext(); ctkServiceReference ppmRef = context->getServiceReference(); mitk::PlanePositionManagerService* service = context->getService(ppmRef); selectedRenderWindow->GetSliceNavigationController()->ExecuteOperation(service->GetPlanePosition(id)); context->ungetService(ppmRef); } selectedRenderWindow->GetRenderer()->GetCameraController()->Fit(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkSegmentationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList &nodes) { if (nodes.size() != 0) { std::string markerName = "Position"; unsigned int numberOfNodes = nodes.size(); std::string nodeName = nodes.at(0)->GetName(); if ((numberOfNodes == 1) && (nodeName.find(markerName) == 0)) { this->OnContourMarkerSelected(nodes.at(0)); return; } } } void QmitkSegmentationView::OnTabWidgetChanged(int id) { //always disable tools on tab changed mitk::ToolManagerProvider::GetInstance()->GetToolManager()->ActivateTool(-1); //2D Tab ID = 0 //3D Tab ID = 1 if (id == 0) { //Hide 3D selection box, show 2D selection box m_Controls->m_ManualToolSelectionBox3D->hide(); m_Controls->m_ManualToolSelectionBox2D->show(); //Deactivate possible active tool //TODO Remove possible visible interpolations -> Maybe changes in SlicesInterpolator } else { //Hide 3D selection box, show 2D selection box m_Controls->m_ManualToolSelectionBox2D->hide(); m_Controls->m_ManualToolSelectionBox3D->show(); //Deactivate possible active tool } } void QmitkSegmentationView::SetToolManagerSelection(mitk::DataNode* referenceData, mitk::DataNode* workingData) { // called as a result of new BlueBerry selections // tells the ToolManager for manual segmentation about new selections // updates GUI information about what the user should select mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); toolManager->SetReferenceData(const_cast(referenceData)); toolManager->SetWorkingData(const_cast(workingData)); m_Controls->btnNewSegmentation->setEnabled(referenceData != nullptr); } void QmitkSegmentationView::ForceDisplayPreferencesUponAllImages() { if (!m_Parent) { return; } // check all images and segmentations in DataStorage: // (items in brackets are implicitly done by previous steps) // 1. // if a reference image is selected, // show the reference image // and hide all other images (orignal and segmentation), // (and hide all segmentations of the other original images) // and show all the reference's segmentations // if no reference image is selected, do do nothing // // 2. // if a segmentation is selected, // show it // (and hide all all its siblings (childs of the same parent, incl, nullptr parent)) // if no segmentation is selected, do nothing if (!m_Controls) { return; // might happen on initialization (preferences loaded) } mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); mitk::DataNode::Pointer referenceData = toolManager->GetReferenceData(0); mitk::DataNode::Pointer workingData = toolManager->GetWorkingData(0); // 1. if (referenceData.IsNotNull()) { // iterate all images mitk::DataStorage::SetOfObjects::ConstPointer allImages = this->GetDataStorage()->GetSubset(m_IsASegmentationImagePredicate); for ( mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter) { mitk::DataNode* node = *iter; // apply display preferences ApplyDisplayOptions(node); // set visibility node->SetVisibility(node == referenceData); } } // 2. if (workingData.IsNotNull()) workingData->SetVisibility(true); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkSegmentationView::ApplyDisplayOptions(mitk::DataNode* node) { if (!node) { return; } mitk::BoolProperty::Pointer drawOutline = mitk::BoolProperty::New(GetPreferences()->GetBool("draw outline", true)); - mitk::BoolProperty::Pointer volumeRendering = mitk::BoolProperty::New(GetPreferences()->GetBool("volume rendering", false)); mitk::LabelSetImage* labelSetImage = dynamic_cast(node->GetData()); if (nullptr != labelSetImage) { // node is actually a multi label segmentation, // but its outline property can be set in the 'single label' segmentation preference page as well node->SetProperty("labelset.contour.active", drawOutline); //node->SetProperty("opacity", mitk::FloatProperty::New(drawOutline->GetValue() ? 1.0f : 0.3f)); - node->SetProperty("volumerendering", volumeRendering); // force render window update to show outline node->GetData()->Modified(); } else { // node is a 'single label' segmentation bool isBinary = false; node->GetBoolProperty("binary", isBinary); if (isBinary) { node->SetProperty("outline binary", drawOutline); node->SetProperty("outline width", mitk::FloatProperty::New(2.0)); //node->SetProperty("opacity", mitk::FloatProperty::New(drawOutline->GetValue() ? 1.0f : 0.3f)); - node->SetProperty("volumerendering", volumeRendering); // force render window update to show outline node->GetData()->Modified(); } } } void QmitkSegmentationView::CheckRenderingState() { mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart(); mitk::DataNode* workingNode = m_Controls->segImageSelector->GetSelectedNode(); if (!workingNode) { this->SetToolSelectionBoxesEnabled(false); this->UpdateWarningLabel(tr("Select or create a segmentation")); return; } bool selectedNodeIsVisible = renderWindowPart && workingNode->IsVisible(renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderer()); if (!selectedNodeIsVisible) { this->SetToolSelectionBoxesEnabled(false); this->UpdateWarningLabel(tr("The selected segmentation is currently not visible!")); return; } /* * Here we check whether the geometry of the selected segmentation image if aligned with the worldgeometry * At the moment it is not supported to use a geometry different from the selected image for reslicing. * For further information see Bug 16063 */ const mitk::BaseGeometry* worldGeo = this->GetRenderWindowPart()->GetQmitkRenderWindow("3d")->GetSliceNavigationController()->GetCurrentGeometry3D(); if (workingNode && worldGeo) { const mitk::BaseGeometry* workingNodeGeo = workingNode->GetData()->GetGeometry(); const mitk::BaseGeometry* worldGeo = this->GetRenderWindowPart()->GetQmitkRenderWindow("3d")->GetSliceNavigationController()->GetCurrentGeometry3D(); if (mitk::Equal(*workingNodeGeo->GetBoundingBox(), *worldGeo->GetBoundingBox(), mitk::eps, true)) { this->SetToolManagerSelection(m_Controls->patImageSelector->GetSelectedNode(), workingNode); this->SetToolSelectionBoxesEnabled(true); this->UpdateWarningLabel(""); return; } } this->SetToolManagerSelection(m_Controls->patImageSelector->GetSelectedNode(), nullptr); this->SetToolSelectionBoxesEnabled(false); this->UpdateWarningLabel(tr("Please perform a reinit on the segmentation image!")); } void QmitkSegmentationView::UpdateWarningLabel(QString text) { if (text.size() == 0) m_Controls->lblSegmentationWarnings->hide(); else m_Controls->lblSegmentationWarnings->show(); m_Controls->lblSegmentationWarnings->setText("" + text + ""); } void QmitkSegmentationView::CreateQtPartControl(QWidget* parent) { // setup the basic GUI of this view m_Parent = parent; m_Controls = new Ui::QmitkSegmentationControls; m_Controls->setupUi(parent); m_Controls->patImageSelector->SetDataStorage(GetDataStorage()); m_Controls->patImageSelector->SetNodePredicate(m_IsAPatientImagePredicate); m_Controls->patImageSelector->SetSelectionIsOptional(false); m_Controls->patImageSelector->SetInvalidInfo("Select an image."); m_Controls->patImageSelector->SetPopUpTitel("Select an image."); m_Controls->patImageSelector->SetPopUpHint("Select an image that should be used to define the geometry and bounds of the segmentation."); UpdateWarningLabel(tr("Please select an image")); if (m_Controls->patImageSelector->GetSelectedNode().IsNotNull()) { UpdateWarningLabel(tr("Select or create a new segmentation")); } m_Controls->segImageSelector->SetDataStorage(GetDataStorage()); m_Controls->segImageSelector->SetNodePredicate(m_IsASegmentationImagePredicate); m_Controls->segImageSelector->SetSelectionIsOptional(false); m_Controls->segImageSelector->SetInvalidInfo("Select a segmentation."); m_Controls->segImageSelector->SetPopUpTitel("Select a segmentation."); m_Controls->segImageSelector->SetPopUpHint("Select a segmentation that should be modified. Only segmentation with the same geometry and within the bounds of the reference image are selected."); if (m_Controls->segImageSelector->GetSelectedNode().IsNotNull()) { UpdateWarningLabel(""); } mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); assert(toolManager); toolManager->SetDataStorage(*(GetDataStorage())); toolManager->InitializeTools(); - QString segTools2D = tr("Add Subtract Correction Paint Wipe 'Region Growing' Fill Erase 'Live Wire' '2D Fast Marching'"); + QString segTools2D = tr("Add Subtract Paint Wipe 'Region Growing' Fill Erase 'Live Wire' '2D Fast Marching'"); QString segTools3D = tr("Threshold 'UL Threshold' Otsu 'Fast Marching 3D' 'Region Growing 3D' Watershed Picking"); std::regex extSegTool2DRegEx("SegTool2D$"); std::regex extSegTool3DRegEx("SegTool3D$"); auto tools = toolManager->GetTools(); for (const auto &tool : tools) { if (std::regex_search(tool->GetNameOfClass(), extSegTool2DRegEx)) { segTools2D.append(QString(" '%1'").arg(tool->GetName())); } else if (std::regex_search(tool->GetNameOfClass(), extSegTool3DRegEx)) { segTools3D.append(QString(" '%1'").arg(tool->GetName())); } } // all part of open source MITK m_Controls->m_ManualToolSelectionBox2D->setEnabled(true); m_Controls->m_ManualToolSelectionBox2D->SetGenerateAccelerators(true); m_Controls->m_ManualToolSelectionBox2D->SetToolGUIArea(m_Controls->m_ManualToolGUIContainer2D); m_Controls->m_ManualToolSelectionBox2D->SetDisplayedToolGroups(segTools2D.toStdString()); m_Controls->m_ManualToolSelectionBox2D->SetLayoutColumns(3); m_Controls->m_ManualToolSelectionBox2D->SetEnabledMode(QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible); connect(m_Controls->m_ManualToolSelectionBox2D, &QmitkToolSelectionBox::ToolSelected, this, &QmitkSegmentationView::OnManualTool2DSelected); //setup 3D Tools m_Controls->m_ManualToolSelectionBox3D->setEnabled(true); m_Controls->m_ManualToolSelectionBox3D->SetGenerateAccelerators(true); m_Controls->m_ManualToolSelectionBox3D->SetToolGUIArea(m_Controls->m_ManualToolGUIContainer3D); //specify tools to be added to 3D Tool area m_Controls->m_ManualToolSelectionBox3D->SetDisplayedToolGroups(segTools3D.toStdString()); m_Controls->m_ManualToolSelectionBox3D->SetLayoutColumns(3); m_Controls->m_ManualToolSelectionBox3D->SetEnabledMode(QmitkToolSelectionBox::EnabledWithReferenceAndWorkingDataVisible); //Hide 3D selection box, show 2D selection box m_Controls->m_ManualToolSelectionBox3D->hide(); m_Controls->m_ManualToolSelectionBox2D->show(); // update the list of segmentations toolManager->NewNodeObjectsGenerated += mitk::MessageDelegate1(this, &QmitkSegmentationView::NewNodeObjectsGenerated); // create signal/slot connections connect(m_Controls->patImageSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkSegmentationView::OnPatientSelectionChanged); connect(m_Controls->segImageSelector, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkSegmentationView::OnSegmentationSelectionChanged); connect(m_Controls->btnNewSegmentation, &QToolButton::clicked, this, &QmitkSegmentationView::CreateNewSegmentation); connect(m_Controls->tabWidgetSegmentationTools, &QTabWidget::currentChanged, this, &QmitkSegmentationView::OnTabWidgetChanged); connect(m_Controls->m_SlicesInterpolator, &QmitkSlicesInterpolator::SignalShowMarkerNodes, this, &QmitkSegmentationView::OnShowMarkerNodes); // set callback function for already existing nodes (images & segmentations) mitk::DataStorage::SetOfObjects::ConstPointer allImages = GetDataStorage()->GetSubset(m_IsOfTypeImagePredicate); for (mitk::DataStorage::SetOfObjects::const_iterator iter = allImages->begin(); iter != allImages->end(); ++iter) { mitk::DataNode* node = *iter; itk::SimpleMemberCommand::Pointer command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::OnVisiblePropertyChanged); m_WorkingDataObserverTags.insert(std::pair(node, node->GetProperty("visible")->AddObserver(itk::ModifiedEvent(), command))); } itk::SimpleMemberCommand::Pointer command = itk::SimpleMemberCommand::New(); command->SetCallbackFunction(this, &QmitkSegmentationView::CheckRenderingState); m_RenderingManagerObserverTag = mitk::RenderingManager::GetInstance()->AddObserver(mitk::RenderingManagerViewsInitializedEvent(), command); SetToolManagerSelection(m_Controls->patImageSelector->GetSelectedNode(), m_Controls->segImageSelector->GetSelectedNode()); m_RenderWindowPart = GetRenderWindowPart(); if (m_RenderWindowPart) { RenderWindowPartActivated(m_RenderWindowPart); } //Should be done last, if everything else is configured because it triggers the autoselection of data. m_Controls->patImageSelector->SetAutoSelectNewNodes(true); m_Controls->segImageSelector->SetAutoSelectNewNodes(true); } void QmitkSegmentationView::SetFocus() { m_Controls->btnNewSegmentation->setFocus(); } void QmitkSegmentationView::OnManualTool2DSelected(int id) { if (id >= 0) { std::string text = "Active Tool: \""; mitk::ToolManager* toolManager = mitk::ToolManagerProvider::GetInstance()->GetToolManager(); text += toolManager->GetToolById(id)->GetName(); text += "\""; mitk::StatusBar::GetInstance()->DisplayText(text.c_str()); us::ModuleResource resource = toolManager->GetToolById(id)->GetCursorIconResource(); this->SetMouseCursor(resource, 0, 0); } else { this->ResetMouseCursor(); mitk::StatusBar::GetInstance()->DisplayText(""); } } void QmitkSegmentationView::ResetMouseCursor() { if ( m_MouseCursorSet ) { mitk::ApplicationCursor::GetInstance()->PopCursor(); m_MouseCursorSet = false; } } void QmitkSegmentationView::SetMouseCursor( const us::ModuleResource& resource, int hotspotX, int hotspotY ) { // Remove previously set mouse cursor if (m_MouseCursorSet) this->ResetMouseCursor(); if (resource) { us::ModuleResourceStream cursor(resource, std::ios::binary); mitk::ApplicationCursor::GetInstance()->PushCursor(cursor, hotspotX, hotspotY); m_MouseCursorSet = true; } } void QmitkSegmentationView::SetToolSelectionBoxesEnabled(bool status) { if (status) { m_Controls->m_ManualToolSelectionBox2D->RecreateButtons(); m_Controls->m_ManualToolSelectionBox3D->RecreateButtons(); } m_Controls->m_ManualToolSelectionBox2D->setEnabled(status); m_Controls->m_ManualToolSelectionBox3D->setEnabled(status); m_Controls->m_SlicesInterpolator->setEnabled(status); } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.cpp index abb337ba5b..10322cfe9d 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/BooleanOperations/QmitkBooleanOperationsWidget.cpp @@ -1,141 +1,144 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkBooleanOperationsWidget.h" #include "../../Common/QmitkDataSelectionWidget.h" #include #include #include #include static const char* const HelpText = "Select two different segmentations above"; -static std::string GetPrefix(mitk::BooleanOperation::Type type) +namespace { - switch (type) + static std::string GetPrefix(mitk::BooleanOperation::Type type) { - case mitk::BooleanOperation::Difference: - return "DifferenceFrom_"; + switch (type) + { + case mitk::BooleanOperation::Difference: + return "DifferenceFrom_"; - case mitk::BooleanOperation::Intersection: - return "IntersectionWith_"; + case mitk::BooleanOperation::Intersection: + return "IntersectionWith_"; - case mitk::BooleanOperation::Union: - return "UnionWith_"; + case mitk::BooleanOperation::Union: + return "UnionWith_"; - default: - assert(false && "Unknown boolean operation type"); - return "UNKNOWN_BOOLEAN_OPERATION_WITH_"; + default: + assert(false && "Unknown boolean operation type"); + return "UNKNOWN_BOOLEAN_OPERATION_WITH_"; + } } -} -static void AddToDataStorage(mitk::DataStorage::Pointer dataStorage, mitk::Image::Pointer segmentation, const std::string& name, mitk::DataNode::Pointer parent = nullptr) -{ - auto dataNode = mitk::DataNode::New(); + static void AddToDataStorage(mitk::DataStorage::Pointer dataStorage, mitk::Image::Pointer segmentation, const std::string& name, mitk::DataNode::Pointer parent = nullptr) + { + auto dataNode = mitk::DataNode::New(); - dataNode->SetName(name); - dataNode->SetData(segmentation); + dataNode->SetName(name); + dataNode->SetData(segmentation); - dataStorage->Add(dataNode, parent); + dataStorage->Add(dataNode, parent); + } } QmitkBooleanOperationsWidget::QmitkBooleanOperationsWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent) { m_Controls.setupUi(this); m_Controls.dataSelectionWidget->AddDataSelection("", "Select 1st segmentation", "Select 1st segmentation", "", QmitkDataSelectionWidget::SegmentationPredicate); m_Controls.dataSelectionWidget->AddDataSelection("", "Select 2nd segmentation", "Select 2nd segmentation", "", QmitkDataSelectionWidget::SegmentationPredicate); m_Controls.dataSelectionWidget->SetHelpText(HelpText); connect(m_Controls.dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); connect(m_Controls.differenceButton, SIGNAL(clicked()), this, SLOT(OnDifferenceButtonClicked())); connect(m_Controls.intersectionButton, SIGNAL(clicked()), this, SLOT(OnIntersectionButtonClicked())); connect(m_Controls.unionButton, SIGNAL(clicked()), this, SLOT(OnUnionButtonClicked())); } QmitkBooleanOperationsWidget::~QmitkBooleanOperationsWidget() { } void QmitkBooleanOperationsWidget::OnSelectionChanged(unsigned int, const mitk::DataNode*) { auto dataSelectionWidget = m_Controls.dataSelectionWidget; auto nodeA = dataSelectionWidget->GetSelection(0); auto nodeB = dataSelectionWidget->GetSelection(1); if (nodeA.IsNotNull() && nodeB.IsNotNull() && nodeA != nodeB) { dataSelectionWidget->SetHelpText(""); this->EnableButtons(); } else { dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); } } void QmitkBooleanOperationsWidget::EnableButtons(bool enable) { m_Controls.differenceButton->setEnabled(enable); m_Controls.intersectionButton->setEnabled(enable); m_Controls.unionButton->setEnabled(enable); } void QmitkBooleanOperationsWidget::OnDifferenceButtonClicked() { this->DoBooleanOperation(mitk::BooleanOperation::Difference); } void QmitkBooleanOperationsWidget::OnIntersectionButtonClicked() { this->DoBooleanOperation(mitk::BooleanOperation::Intersection); } void QmitkBooleanOperationsWidget::OnUnionButtonClicked() { this->DoBooleanOperation(mitk::BooleanOperation::Union); } void QmitkBooleanOperationsWidget::DoBooleanOperation(mitk::BooleanOperation::Type type) { auto timeNavigationController = this->GetTimeNavigationController(); assert(timeNavigationController != nullptr); mitk::Image::Pointer segmentationA = dynamic_cast(m_Controls.dataSelectionWidget->GetSelection(0)->GetData()); mitk::Image::Pointer segmentationB = dynamic_cast(m_Controls.dataSelectionWidget->GetSelection(1)->GetData()); mitk::Image::Pointer result; try { mitk::BooleanOperation booleanOperation(type, segmentationA, segmentationB, timeNavigationController->GetSelectedTimePoint()); result = booleanOperation.GetResult(); assert(result.IsNotNull()); auto dataSelectionWidget = m_Controls.dataSelectionWidget; AddToDataStorage( dataSelectionWidget->GetDataStorage(), result, GetPrefix(type) + dataSelectionWidget->GetSelection(1)->GetName(), dataSelectionWidget->GetSelection(0)); } catch (const mitk::Exception& exception) { MITK_ERROR << "Boolean operation failed: " << exception.GetDescription(); QMessageBox::information(nullptr, "Boolean operation failed", exception.GetDescription()); } } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp index 59ff902954..90e41d7aea 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ContourModelToImage/QmitkContourModelToImageWidget.cpp @@ -1,245 +1,246 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkContourModelToImageWidget.h" #include "mitkImage.h" #include "../../Common/QmitkDataSelectionWidget.h" #include #include +#include #include #include #include #include #include static const char* const HelpText = "Select a image and a contour(set)"; class QmitkContourModelToImageWidgetPrivate { public: QmitkContourModelToImageWidgetPrivate(); ~QmitkContourModelToImageWidgetPrivate(); /** @brief Check if selections is valid. */ void SelectionControl( unsigned int index, const mitk::DataNode* selection); /** @brief Enable buttons if data selction is valid. */ void EnableButtons(bool enable = true); /** @brief Does the actual contour filling */ - mitk::Image::Pointer FillContourModelSetIntoImage(mitk::Image *image, mitk::ContourModelSet *contourSet, mitk::TimePointType timePoint); + mitk::LabelSetImage::Pointer FillContourModelSetIntoImage(mitk::Image *image, mitk::ContourModelSet *contourSet, mitk::TimePointType timePoint); Ui::QmitkContourModelToImageWidgetControls m_Controls; - QFutureWatcher m_Watcher; + QFutureWatcher m_Watcher; }; QmitkContourModelToImageWidgetPrivate::QmitkContourModelToImageWidgetPrivate() { } QmitkContourModelToImageWidgetPrivate::~QmitkContourModelToImageWidgetPrivate() { } void QmitkContourModelToImageWidgetPrivate::EnableButtons(bool enable) { m_Controls.btnProcess->setEnabled(enable); } void QmitkContourModelToImageWidgetPrivate::SelectionControl(unsigned int index, const mitk::DataNode* /*selection*/) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(index); dataSelectionWidget->SetHelpText(""); this->EnableButtons(); } -mitk::Image::Pointer QmitkContourModelToImageWidgetPrivate::FillContourModelSetIntoImage(mitk::Image* image, mitk::ContourModelSet* contourSet, mitk::TimePointType timePoint) +mitk::LabelSetImage::Pointer QmitkContourModelToImageWidgetPrivate::FillContourModelSetIntoImage(mitk::Image* image, mitk::ContourModelSet* contourSet, mitk::TimePointType timePoint) { // Use mitk::ContourModelSetToImageFilter to fill the ContourModelSet into the image mitk::ContourModelSetToImageFilter::Pointer contourFiller = mitk::ContourModelSetToImageFilter::New(); auto timeStep = image->GetTimeGeometry()->TimePointToTimeStep(timePoint); contourFiller->SetTimeStep(timeStep); contourFiller->SetImage(image); contourFiller->SetInput(contourSet); contourFiller->MakeOutputBinaryOn(); - mitk::Image::Pointer result = nullptr; try { contourFiller->Update(); - result = contourFiller->GetOutput(); } catch (const std::exception & e) { MITK_ERROR << "Error while converting contour model. "<< e.what(); } catch (...) { MITK_ERROR << "Unknown error while converting contour model."; } - if (result.IsNull()) + if (nullptr == contourFiller->GetOutput()) { MITK_ERROR<<"Could not write the selected contours into the image!"; } - result->DisconnectPipeline(); + auto result = mitk::LabelSetImage::New(); + result->InitializeByLabeledImage(contourFiller->GetOutput()); + return result; } void QmitkContourModelToImageWidget::OnSelectionChanged(unsigned int index, const mitk::DataNode* selection) { Q_D(QmitkContourModelToImageWidget); QmitkDataSelectionWidget* dataSelectionWidget = d->m_Controls.dataSelectionWidget; mitk::DataNode::Pointer node0 = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer node1 = dataSelectionWidget->GetSelection(1); if (node0.IsNull() || node1.IsNull() ) { d->EnableButtons(false); dataSelectionWidget->SetHelpText(HelpText); } else { d->SelectionControl(index, selection); } } void QmitkContourModelToImageWidget::OnProcessingFinished() { // Called when processing finished // Adding the result to the data storage Q_D(QmitkContourModelToImageWidget); // Adding the result to the data storage - mitk::Image::Pointer result = d->m_Watcher.result(); + auto result = d->m_Watcher.result(); if (result.IsNotNull()) { QmitkDataSelectionWidget* dataSelectionWidget = d->m_Controls.dataSelectionWidget; mitk::DataNode::Pointer imageNode = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer contourNode = dataSelectionWidget->GetSelection(1); mitk::DataNode::Pointer filled = mitk::DataNode::New(); std::stringstream stream; stream << imageNode->GetName(); stream << "_"; stream << contourNode->GetName(); filled->SetName(stream.str()); filled->SetData(result); dataSelectionWidget->GetDataStorage()->Add(filled, imageNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else { MITK_ERROR<<"Error filling contours into an image!"; } d->EnableButtons(); } void QmitkContourModelToImageWidget::OnProcessPressed() { Q_D(QmitkContourModelToImageWidget); QmitkDataSelectionWidget* dataSelectionWidget = d->m_Controls.dataSelectionWidget; mitk::DataNode::Pointer imageNode = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer contourNode = dataSelectionWidget->GetSelection(1); // Check if data nodes are valid if(imageNode.IsNull() || contourNode.IsNull() ) { MITK_ERROR << "Selection does not contain valid data"; QMessageBox::information( this, "Contour To Image", "Selection does not contain valid data, please select a binary image and a contour(set)", QMessageBox::Ok ); d->m_Controls.btnProcess->setEnabled(false); return; } mitk::Image::Pointer image = static_cast(imageNode->GetData()); // Check if the image is valid if (image.IsNull()) { MITK_ERROR<<"Error writing contours into image! Invalid image data selected!"; return; } const auto timePoint = this->GetTimeNavigationController()->GetSelectedTimePoint(); if (!image->GetTimeGeometry()->IsValidTimePoint(timePoint)) { MITK_ERROR << "Error writing contours into image! Currently selected time point is not supported by selected image data."; return; } // Check if the selected contours are valid mitk::ContourModelSet::Pointer contourSet; mitk::ContourModel::Pointer contour = dynamic_cast(contourNode->GetData()); if (contour.IsNotNull()) { contourSet = mitk::ContourModelSet::New(); contourSet->AddContourModel(contour); } else { contourSet = static_cast(contourNode->GetData()); if (contourSet.IsNull()) { MITK_ERROR<<"Error writing contours into binary image! Invalid contour data selected!"; return; } } //Disable Buttons during calculation and initialize Progressbar d->EnableButtons(false); // Start the computation in a background thread - QFuture< mitk::Image::Pointer > future = QtConcurrent::run(d, &QmitkContourModelToImageWidgetPrivate::FillContourModelSetIntoImage, image, contourSet, timePoint); + QFuture< mitk::LabelSetImage::Pointer > future = QtConcurrent::run(d, &QmitkContourModelToImageWidgetPrivate::FillContourModelSetIntoImage, image, contourSet, timePoint); d->m_Watcher.setFuture(future); } QmitkContourModelToImageWidget::QmitkContourModelToImageWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent), d_ptr(new QmitkContourModelToImageWidgetPrivate()) { Q_D(QmitkContourModelToImageWidget); // Set up UI d->m_Controls.setupUi(this); d->m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::ImageAndSegmentationPredicate); d->m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::ContourModelPredicate); d->m_Controls.dataSelectionWidget->SetHelpText(HelpText); d->EnableButtons(false); // Create connections connect (d->m_Controls.btnProcess, SIGNAL(pressed()), this, SLOT(OnProcessPressed())); connect(d->m_Controls.dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); connect(&d->m_Watcher, SIGNAL(finished()), this, SLOT(OnProcessingFinished())); if( d->m_Controls.dataSelectionWidget->GetSelection(0).IsNotNull() && d->m_Controls.dataSelectionWidget->GetSelection(1).IsNotNull() ) { OnSelectionChanged(0, d->m_Controls.dataSelectionWidget->GetSelection(0)); } } QmitkContourModelToImageWidget::~QmitkContourModelToImageWidget() { } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp index 033d760819..e1818bc9b9 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.cpp @@ -1,298 +1,291 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkImageMaskingWidget.h" #include "mitkImage.h" #include "../../Common/QmitkDataSelectionWidget.h" #include #include #include #include #include #include #include #include -static const char* const HelpText = "Select a regular image and a binary image"; +namespace +{ + bool IsSurface(const mitk::DataNode* dataNode) + { + if (nullptr != dataNode) + { + if (nullptr != dynamic_cast(dataNode->GetData())) + return true; + } + + return false; + } +} + +static const char* const HelpText = "Select an image and a segmentation or surface"; QmitkImageMaskingWidget::QmitkImageMaskingWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent) : QmitkSegmentationUtilityWidget(timeNavigationController, parent) { m_Controls.setupUi(this); m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::ImagePredicate); - m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::SegmentationPredicate); + m_Controls.dataSelectionWidget->AddDataSelection(QmitkDataSelectionWidget::SegmentationOrSurfacePredicate); m_Controls.dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); - connect (m_Controls.rbMaskImage, SIGNAL(toggled(bool)), this, SLOT(OnImageMaskingToggled(bool))); - connect (m_Controls.rbMaskSurface, SIGNAL(toggled(bool)), this, SLOT(OnSurfaceMaskingToggled(bool))); connect (m_Controls.btnMaskImage, SIGNAL(clicked()), this, SLOT(OnMaskImagePressed())); connect(m_Controls.dataSelectionWidget, SIGNAL(SelectionChanged(unsigned int, const mitk::DataNode*)), this, SLOT(OnSelectionChanged(unsigned int, const mitk::DataNode*))); if( m_Controls.dataSelectionWidget->GetSelection(0).IsNotNull() && m_Controls.dataSelectionWidget->GetSelection(1).IsNotNull() ) { this->OnSelectionChanged(0, m_Controls.dataSelectionWidget->GetSelection(0)); } } QmitkImageMaskingWidget::~QmitkImageMaskingWidget() { } void QmitkImageMaskingWidget::OnSelectionChanged(unsigned int index, const mitk::DataNode* selection) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; mitk::DataNode::Pointer node0 = dataSelectionWidget->GetSelection(0); mitk::DataNode::Pointer node1 = dataSelectionWidget->GetSelection(1); if (node0.IsNull() || node1.IsNull() ) { - if( m_Controls.rbMaskImage->isChecked() ) - { - dataSelectionWidget->SetHelpText(HelpText); - } - else - { - dataSelectionWidget->SetHelpText("Select a regular image and a surface"); - } + dataSelectionWidget->SetHelpText(HelpText); this->EnableButtons(false); } else { this->SelectionControl(index, selection); } } void QmitkImageMaskingWidget::SelectionControl(unsigned int index, const mitk::DataNode* selection) { QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; mitk::DataNode::Pointer node = dataSelectionWidget->GetSelection(index); //if Image-Masking is enabled, check if image-dimension of reference and binary image is identical - if( m_Controls.rbMaskImage->isChecked() ) + if( !IsSurface(dataSelectionWidget->GetSelection(1)) ) { if( dataSelectionWidget->GetSelection(0) == dataSelectionWidget->GetSelection(1) ) { dataSelectionWidget->SetHelpText("Select two different images above"); this->EnableButtons(false); return; } else if( node.IsNotNull() && selection ) { mitk::Image::Pointer referenceImage = dynamic_cast ( dataSelectionWidget->GetSelection(0)->GetData() ); mitk::Image::Pointer maskImage = dynamic_cast ( dataSelectionWidget->GetSelection(1)->GetData() ); if( maskImage.IsNull() || referenceImage->GetLargestPossibleRegion().GetSize() != maskImage->GetLargestPossibleRegion().GetSize() ) { dataSelectionWidget->SetHelpText("Different image sizes cannot be masked"); this->EnableButtons(false); return; } } else { dataSelectionWidget->SetHelpText(HelpText); return; } } dataSelectionWidget->SetHelpText(""); this->EnableButtons(); } void QmitkImageMaskingWidget::EnableButtons(bool enable) { m_Controls.btnMaskImage->setEnabled(enable); } -void QmitkImageMaskingWidget::OnImageMaskingToggled(bool status) -{ - if (status) - { - m_Controls.dataSelectionWidget->SetHelpText("Select a regular image and a binary image"); - m_Controls.dataSelectionWidget->SetPredicate(1, QmitkDataSelectionWidget::SegmentationPredicate); - } -} - -void QmitkImageMaskingWidget::OnSurfaceMaskingToggled(bool status) -{ - if (status) - { - m_Controls.dataSelectionWidget->SetHelpText("Select a regular image and a surface"); - m_Controls.dataSelectionWidget->SetPredicate(1, QmitkDataSelectionWidget::SurfacePredicate); - } -} - - void QmitkImageMaskingWidget::OnMaskImagePressed() { //Disable Buttons during calculation and initialize Progressbar this->EnableButtons(false); mitk::ProgressBar::GetInstance()->AddStepsToDo(4); mitk::ProgressBar::GetInstance()->Progress(); QmitkDataSelectionWidget* dataSelectionWidget = m_Controls.dataSelectionWidget; //create result image, get mask node and reference image mitk::Image::Pointer resultImage(nullptr); mitk::DataNode::Pointer maskingNode = dataSelectionWidget->GetSelection(1); mitk::Image::Pointer referenceImage = static_cast(dataSelectionWidget->GetSelection(0)->GetData()); if(referenceImage.IsNull() || maskingNode.IsNull() ) { MITK_ERROR << "Selection does not contain an image"; QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain an image", QMessageBox::Ok ); m_Controls.btnMaskImage->setEnabled(true); return; } //Do Image-Masking - if (m_Controls.rbMaskImage->isChecked()) + if (!IsSurface(maskingNode)) { mitk::ProgressBar::GetInstance()->Progress(); mitk::Image::Pointer maskImage = dynamic_cast ( maskingNode->GetData() ); if(maskImage.IsNull() ) { - MITK_ERROR << "Selection does not contain a binary image"; - QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain a binary image", QMessageBox::Ok ); + MITK_ERROR << "Selection does not contain a segmentation"; + QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain a segmentation", QMessageBox::Ok ); this->EnableButtons(); return; } if( referenceImage->GetLargestPossibleRegion().GetSize() == maskImage->GetLargestPossibleRegion().GetSize() ) { resultImage = this->MaskImage( referenceImage, maskImage ); } } //Do Surface-Masking else { mitk::ProgressBar::GetInstance()->Progress(); //1. convert surface to image mitk::Surface::Pointer surface = dynamic_cast ( maskingNode->GetData() ); //TODO Get 3D Surface of current time step if(surface.IsNull()) { MITK_ERROR << "Selection does not contain a surface"; QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain a surface", QMessageBox::Ok ); this->EnableButtons(); return; } mitk::Image::Pointer maskImage = this->ConvertSurfaceToImage( referenceImage, surface ); //2. mask reference image with mask image if(maskImage.IsNotNull() && referenceImage->GetLargestPossibleRegion().GetSize() == maskImage->GetLargestPossibleRegion().GetSize() ) { resultImage = this->MaskImage( referenceImage, maskImage ); } } mitk::ProgressBar::GetInstance()->Progress(); if( resultImage.IsNull() ) { MITK_ERROR << "Masking failed"; QMessageBox::information( this, "Image and Surface Masking", "Masking failed. For more information please see logging window.", QMessageBox::Ok ); this->EnableButtons(); mitk::ProgressBar::GetInstance()->Progress(4); return; } //Add result to data storage this->AddToDataStorage( dataSelectionWidget->GetDataStorage(), resultImage, dataSelectionWidget->GetSelection(0)->GetName() + "_" + dataSelectionWidget->GetSelection(1)->GetName(), dataSelectionWidget->GetSelection(0)); this->EnableButtons(); mitk::ProgressBar::GetInstance()->Progress(); } mitk::Image::Pointer QmitkImageMaskingWidget::MaskImage(mitk::Image::Pointer referenceImage, mitk::Image::Pointer maskImage ) { mitk::Image::Pointer resultImage(nullptr); mitk::MaskImageFilter::Pointer maskFilter = mitk::MaskImageFilter::New(); maskFilter->SetInput( referenceImage ); maskFilter->SetMask( maskImage ); maskFilter->OverrideOutsideValueOn(); maskFilter->SetOutsideValue( referenceImage->GetStatistics()->GetScalarValueMin() ); try { maskFilter->Update(); } catch(itk::ExceptionObject& excpt) { MITK_ERROR << excpt.GetDescription(); return nullptr; } resultImage = maskFilter->GetOutput(); return resultImage; } mitk::Image::Pointer QmitkImageMaskingWidget::ConvertSurfaceToImage( mitk::Image::Pointer image, mitk::Surface::Pointer surface ) { mitk::ProgressBar::GetInstance()->AddStepsToDo(2); mitk::ProgressBar::GetInstance()->Progress(); mitk::SurfaceToImageFilter::Pointer surfaceToImageFilter = mitk::SurfaceToImageFilter::New(); surfaceToImageFilter->MakeOutputBinaryOn(); surfaceToImageFilter->SetInput(surface); surfaceToImageFilter->SetImage(image); try { surfaceToImageFilter->Update(); } catch(itk::ExceptionObject& excpt) { MITK_ERROR << excpt.GetDescription(); return nullptr; } mitk::ProgressBar::GetInstance()->Progress(); mitk::Image::Pointer resultImage = mitk::Image::New(); resultImage = surfaceToImageFilter->GetOutput(); return resultImage; } void QmitkImageMaskingWidget::AddToDataStorage(mitk::DataStorage::Pointer dataStorage, mitk::Image::Pointer segmentation, const std::string& name, mitk::DataNode::Pointer parent ) { - mitk::DataNode::Pointer dataNode = mitk::DataNode::New(); + auto dataNode = mitk::DataNode::New(); dataNode->SetName(name); dataNode->SetData(segmentation); + if (parent.IsNotNull()) + { + mitk::LevelWindow levelWindow; + parent->GetLevelWindow(levelWindow); + dataNode->SetLevelWindow(levelWindow); + } + dataStorage->Add(dataNode, parent); } diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h index 374d9bc5c2..37a5711983 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h @@ -1,80 +1,74 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef QmitkImageMaskingWidget_h #define QmitkImageMaskingWidget_h #include "../QmitkSegmentationUtilityWidget.h" #include #include namespace mitk { class Image; } /*! \brief QmitkImageMaskingWidget Tool masks an image with a binary image or a surface. The Method requires an image and a binary image mask or a surface. The input image and the binary image mask must be of the same size. Masking with a surface creates first a binary image of the surface and then use this for the masking of the input image. */ class QmitkImageMaskingWidget : public QmitkSegmentationUtilityWidget { Q_OBJECT public: /** @brief Default constructor, including creation of GUI elements and signals/slots connections. */ explicit QmitkImageMaskingWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent = nullptr); /** @brief Defaul destructor. */ ~QmitkImageMaskingWidget() override; private slots: /** @brief This slot is called if the selection in the workbench is changed. */ void OnSelectionChanged(unsigned int index, const mitk::DataNode* selection); - /** @brief This slot is called if user activates the radio button for masking an image with a binary image mask. */ - void OnImageMaskingToggled(bool); - - /** @brief This slot is called if user activates the radio button for masking an image with a surface. */ - void OnSurfaceMaskingToggled(bool); - /** @brief This slot is called if user activates the button to mask an image. */ void OnMaskImagePressed(); private: /** @brief Check if selections is valid. */ void SelectionControl( unsigned int index, const mitk::DataNode* selection); /** @brief Enable buttons if data selction is valid. */ void EnableButtons(bool enable = true); /** @brief Mask an image with a given binary mask. Note that the input image and the mask image must be of the same size. */ itk::SmartPointer MaskImage(itk::SmartPointer referenceImage, itk::SmartPointer maskImage ); /** @brief Convert a surface into an binary image. */ itk::SmartPointer ConvertSurfaceToImage( itk::SmartPointer image, mitk::Surface::Pointer surface ); /** @brief Adds a new data object to the DataStorage.*/ void AddToDataStorage(mitk::DataStorage::Pointer dataStorage, itk::SmartPointer segmentation, const std::string& name, mitk::DataNode::Pointer parent = nullptr); Ui::QmitkImageMaskingWidgetControls m_Controls; }; #endif diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui index 1882ccdfbf..7ff3b3184c 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui @@ -1,82 +1,56 @@ QmitkImageMaskingWidgetControls 0 0 147 155 0 0 - - - - Masking Mode - - - - - - Image Masking - - - true - - - - - - - Surface Masking - - - - - - Mask Qt::Vertical 20 40 QmitkDataSelectionWidget QWidget
internal/Common/QmitkDataSelectionWidget.h
1 diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/QmitkSegmentationUtilitiesView.cpp b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/QmitkSegmentationUtilitiesView.cpp index c170fcac65..b0afb7cfd2 100644 --- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/QmitkSegmentationUtilitiesView.cpp +++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/QmitkSegmentationUtilitiesView.cpp @@ -1,84 +1,84 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) 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 "QmitkSegmentationUtilitiesView.h" #include "BooleanOperations/QmitkBooleanOperationsWidget.h" #include "ContourModelToImage/QmitkContourModelToImageWidget.h" #include "ImageMasking/QmitkImageMaskingWidget.h" #include "MorphologicalOperations/QmitkMorphologicalOperationsWidget.h" #include "SurfaceToImage/QmitkSurfaceToImageWidget.h" QmitkSegmentationUtilitiesView::QmitkSegmentationUtilitiesView() : m_BooleanOperationsWidget(nullptr), m_ContourModelToImageWidget(nullptr), m_ImageMaskingWidget(nullptr), m_MorphologicalOperationsWidget(nullptr), m_SurfaceToImageWidget(nullptr) { } QmitkSegmentationUtilitiesView::~QmitkSegmentationUtilitiesView() { } void QmitkSegmentationUtilitiesView::CreateQtPartControl(QWidget* parent) { m_Controls.setupUi(parent); mitk::IRenderWindowPart* renderWindowPart = this->GetRenderWindowPart(); mitk::SliceNavigationController* timeNavigationController = renderWindowPart != nullptr ? renderWindowPart->GetTimeNavigationController() : nullptr; m_BooleanOperationsWidget = new QmitkBooleanOperationsWidget(timeNavigationController, parent); m_ContourModelToImageWidget = new QmitkContourModelToImageWidget(timeNavigationController, parent); m_ImageMaskingWidget = new QmitkImageMaskingWidget(timeNavigationController, parent); m_MorphologicalOperationsWidget = new QmitkMorphologicalOperationsWidget(timeNavigationController, parent); m_SurfaceToImageWidget = new QmitkSurfaceToImageWidget(timeNavigationController, parent); this->AddUtilityWidget(m_BooleanOperationsWidget, QIcon(":/SegmentationUtilities/BooleanOperations_48x48.png"), "Boolean Operations"); - this->AddUtilityWidget(m_ContourModelToImageWidget, QIcon(":/SegmentationUtilities/ContourModelSetToImage_48x48.png"), "Contour To Image"); + this->AddUtilityWidget(m_ContourModelToImageWidget, QIcon(":/SegmentationUtilities/ContourModelSetToImage_48x48.png"), "Contour to Image"); this->AddUtilityWidget(m_ImageMaskingWidget, QIcon(":/SegmentationUtilities/ImageMasking_48x48.png"), "Image Masking"); this->AddUtilityWidget(m_MorphologicalOperationsWidget, QIcon(":/SegmentationUtilities/MorphologicalOperations_48x48.png"), "Morphological Operations"); - this->AddUtilityWidget(m_SurfaceToImageWidget, QIcon(":/SegmentationUtilities/SurfaceToImage_48x48.png"), "Surface To Image"); + this->AddUtilityWidget(m_SurfaceToImageWidget, QIcon(":/SegmentationUtilities/SurfaceToImage_48x48.png"), "Surface to Image"); } void QmitkSegmentationUtilitiesView::AddUtilityWidget(QWidget* widget, const QIcon& icon, const QString& text) { m_Controls.toolBox->addItem(widget, icon, text); } void QmitkSegmentationUtilitiesView::SetFocus() { m_Controls.toolBox->setFocus(); } void QmitkSegmentationUtilitiesView::RenderWindowPartActivated(mitk::IRenderWindowPart* renderWindowPart) { mitk::SliceNavigationController* timeNavigationController = renderWindowPart->GetTimeNavigationController(); m_BooleanOperationsWidget->SetTimeNavigationController(timeNavigationController); m_ContourModelToImageWidget->SetTimeNavigationController(timeNavigationController); m_ImageMaskingWidget->SetTimeNavigationController(timeNavigationController); m_MorphologicalOperationsWidget->SetTimeNavigationController(timeNavigationController); m_SurfaceToImageWidget->SetTimeNavigationController(timeNavigationController); } void QmitkSegmentationUtilitiesView::RenderWindowPartDeactivated(mitk::IRenderWindowPart*) { m_BooleanOperationsWidget->SetTimeNavigationController(nullptr); m_ContourModelToImageWidget->SetTimeNavigationController(nullptr); m_ImageMaskingWidget->SetTimeNavigationController(nullptr); m_MorphologicalOperationsWidget->SetTimeNavigationController(nullptr); m_SurfaceToImageWidget->SetTimeNavigationController(nullptr); } diff --git a/Plugins/org.mitk.gui.qt.xnat/CMakeLists.txt b/Plugins/org.mitk.gui.qt.xnat/CMakeLists.txt index 480138e063..8a4a4fa2db 100644 --- a/Plugins/org.mitk.gui.qt.xnat/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.xnat/CMakeLists.txt @@ -1,26 +1,8 @@ project(org_mitk_gui_qt_xnat) -if(WIN32) - set(MITK_OPENSSL_SSL_DLL "" CACHE FILEPATH "") - set(MITK_OPENSSL_CRYPTO_DLL "" CACHE FILEPATH "") - - 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() - mitk_create_plugin( PACKAGE_DEPENDS Poco|Zip MODULE_DEPENDS MitkXNAT EXPORT_DIRECTIVE XNAT_EXPORT EXPORTED_INCLUDE_SUFFIXES src ) diff --git a/README.md b/README.md index ff95bb0ea0..8e65813fa5 100644 --- a/README.md +++ b/README.md @@ -1,93 +1,108 @@ ![MITK Logo][logo] The [Medical Imaging Interaction Toolkit][mitk] (MITK) is a free open-source software system for development of interactive medical image processing software. MITK combines the [Insight Toolkit][itk] (ITK) and the [Visualization Toolkit][vtk] (VTK) with an application framework. The links below provide high-level and reference documentation targeting different usage scenarios: - Get a [high-level overview][mitk-overview] about MITK with pointers to further documentation - End-users looking for help with MITK applications should read the [MITK User Manual][mitk-usermanual] - Developers contributing to or using MITK, please see the [MITK Developer Manual][mitk-devmanual] as well as the [MITK API Reference][mitk-apiref] See the [MITK homepage][mitk] for details. -Supported Platforms +Supported platforms ------------------- MITK is a cross-platform C++ toolkit and officially supports: - Windows - Linux - macOS For details, please read the [Supported Platforms][platforms] page. +### Build status of develop branch + +[![Windows][windows-build-status]][cdash] +[![Ubuntu 18.04][ubuntu-18.04-build-status]][cdash] +[![Ubuntu 20.04][ubuntu-20.04-build-status]][cdash] +[![macOS 10.14 Mojave][macos-10.14-build-status]][cdash] + +We highly recommend to use the stable **master** branch instead. It is updated 1-2 times per month accompanied by curated [changelogs][changelog] and [snapshot installers][snapshot-installers]. + License ------- Copyright (c) [German Cancer Research Center (DKFZ)][dkfz]. All rights reserved. MITK is available as free open-source software under a [3-clause BSD license][license]. Download -------- The MITK source code and binaries for the *MitkWorkbench* application are released regularly according to the [MITK release cycle][release-cycle]. See the [Download][download] page for a list of releases. The official MITK source code is available in the [MITK Git repository][phab_repo]. The Git clone command is git clone https://phabricator.mitk.org/source/mitk.git MITK -Active development takes place in the MITK master branch and its usage is advised for advanced users only. +Active development takes place in the MITK develop branch and its usage is advised for advanced users only. -How to Contribute +How to contribute ----------------- Contributions of all kind are happily accepted. However, to make the contribution process as smooth as possible, please read the [How to contribute to MITK][contribute] page if you plan to contribute to MITK. - -Build Instructions +Build instructions ------------------ MITK uses [CMake][cmake] to configure a build tree. The following is a crash course about cloning, configuring, and building MITK on a Linux/Unix system: git clone https://phabricator.mitk.org/source/mitk.git MITK mkdir MITK-build cd MITK-build cmake ../MITK make -j4 Read the comprehensive [build instructions][build] page for details. -Useful Links +Useful links ------------ - [Homepage][mitk] - [Download][download] - [Mailing list][mailinglist] - [Issue tracker][bugs] [logo]: https://github.com/MITK/MITK/raw/master/mitk.png [mitk]: http://mitk.org [itk]: https://itk.org [vtk]: https://vtk.org [mitk-overview]: http://docs.mitk.org/nightly/Overview.html [mitk-usermanual]: http://docs.mitk.org/nightly/UserManualPortal.html [mitk-devmanual]: http://docs.mitk.org/nightly/DeveloperManualPortal.html [mitk-apiref]: http://docs.mitk.org/nightly/usergroup0.html [platforms]: http://docs.mitk.org/nightly/SupportedPlatformsPage.html [dkfz]: https://www.dkfz.de [license]: https://github.com/MITK/MITK/blob/master/LICENSE [release-cycle]: http://mitk.org/MitkReleaseCycle [download]: http://mitk.org/Download [phab_repo]: https://phabricator.mitk.org/source/mitk/ [contribute]: http://mitk.org/How_to_contribute [cmake]: https://www.cmake.org [build]: http://docs.mitk.org/nightly/BuildInstructionsPage.html [mailinglist]: http://mitk.org/Mailinglist [bugs]: https://phabricator.mitk.org/maniphest/ +[cdash]: https://cdash.mitk.org/index.php?project=MITK +[changelog]: https://phabricator.mitk.org/w/mitk/changelog/ +[snapshot-installers]: https://www.mitk.org/download/ci/snapshots/ +[windows-build-status]: https://ci.mitk.org/buildStatus/icon?job=MITK%2FContinuous%2FWindows&subject=Windows +[ubuntu-18.04-build-status]: https://ci.mitk.org/buildStatus/icon?job=MITK%2FContinuous%2FUbuntu+18.04&subject=Ubuntu+18.04 +[ubuntu-20.04-build-status]: https://ci.mitk.org/buildStatus/icon?job=MITK%2FContinuous%2FUbuntu+20.04&subject=Ubuntu+20.04 +[macOS-10.14-build-status]: https://ci.mitk.org/buildStatus/icon?job=MITK%2FContinuous%2FmacOS+Mojave&subject=macOS+10.14+Mojave