diff --git a/Applications/Diffusion/CMakeLists.txt b/Applications/Diffusion/CMakeLists.txt index 7115ea0..c4adac9 100644 --- a/Applications/Diffusion/CMakeLists.txt +++ b/Applications/Diffusion/CMakeLists.txt @@ -1,110 +1,107 @@ project(MitkDiffusion) set(DIFFUSIONAPP_NAME MitkDiffusion) set(_app_options) if(MITK_SHOW_CONSOLE_WINDOW) list(APPEND _app_options SHOW_CONSOLE) endif() # Create a cache entry for the provisioning file which is used to export # the file name in the MITKConfig.cmake file. This will keep external projects # which rely on this file happy. set(DIFFUSIONIMAGINGAPP_PROVISIONING_FILE "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${DIFFUSIONAPP_NAME}.provisioning" CACHE INTERNAL "${DIFFUSIONAPP_NAME} provisioning file" FORCE) # should be identical to the list in /CMake/mitkBuildConfigurationmitkDiffusion.cmake # remember to set plugins which should be automatically toggled in target_libraries.cmake set(_plugins org.commontk.configadmin org.commontk.eventadmin org.blueberry.core.runtime org.blueberry.core.expressions org.blueberry.core.commands org.blueberry.ui.qt org.blueberry.ui.qt.log org.blueberry.ui.qt.help org.mitk.core.services org.mitk.gui.common org.mitk.planarfigure org.mitk.core.ext org.mitk.gui.qt.application org.mitk.gui.qt.ext org.mitk.gui.qt.diffusionimagingapp org.mitk.gui.qt.common org.mitk.gui.qt.stdmultiwidgeteditor org.mitk.gui.qt.datamanager org.mitk.gui.qt.measurementtoolbox org.mitk.gui.qt.segmentation org.mitk.gui_qt.multilabelsegmentation org.mitk.gui.qt.python org.mitk.gui.qt.volumevisualization org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.diffusionimaging.connectomics org.mitk.gui.qt.diffusionimaging.fiberfox org.mitk.gui.qt.diffusionimaging.fiberprocessing org.mitk.gui.qt.diffusionimaging.ivim org.mitk.gui.qt.diffusionimaging.odfpeaks org.mitk.gui.qt.diffusionimaging.preprocessing org.mitk.gui.qt.diffusionimaging.reconstruction org.mitk.gui.qt.diffusionimaging.tractography org.mitk.gui.qt.diffusionimaging.registration org.mitk.gui.qt.diffusionimaging.python org.mitk.gui.qt.diffusionimaging.denoising org.mitk.gui.qt.diffusionimaging.partialvolume org.mitk.gui.qt.matchpoint.algorithm.browser org.mitk.gui.qt.matchpoint.algorithm.control org.mitk.gui.qt.matchpoint.mapper org.mitk.gui.qt.imagenavigator org.mitk.gui.qt.moviemaker org.mitk.gui.qt.basicimageprocessing org.mitk.gui.qt.properties org.mitk.gui.qt.viewnavigator org.mitk.gui.qt.renderwindowmanager ) -if(NOT MITK_USE_Python) +if(NOT MITK_USE_Python3) list(REMOVE_ITEM _plugins org.mitk.gui.qt.diffusionimaging.python) list(REMOVE_ITEM _plugins org.mitk.gui.qt.python) endif() - - # Plug-ins listed below will not be # - added as a build-time dependency to the executable # - listed in the provisioning file for the executable # - installed if they are external plug-ins set(_exclude_plugins org.blueberry.test org.blueberry.uitest org.mitk.gui.qt.coreapplication org.mitk.gui.qt.extapplication ) set(_src_files MitkDiffusion.cpp ) qt5_add_resources(_src_files splashscreen.qrc) mitkFunctionCreateBlueBerryApplication( NAME ${DIFFUSIONAPP_NAME} DESCRIPTION "MITK Diffusion" PLUGINS ${_plugins} EXCLUDE_PLUGINS ${_exclude_plugins} SOURCES ${_src_files} ${_app_options} ) mitk_use_modules(TARGET ${DIFFUSIONAPP_NAME} MODULES MitkAppUtil) # Add meta dependencies (e.g. on auto-load modules from depending modules) if(TARGET ${CMAKE_PROJECT_NAME}-autoload) add_dependencies(${DIFFUSIONAPP_NAME} ${CMAKE_PROJECT_NAME}-autoload) endif() # Add a build time dependency to legacy BlueBerry bundles. if(MITK_MODULES_ENABLED_PLUGINS) add_dependencies(${DIFFUSIONAPP_NAME} ${MITK_MODULES_ENABLED_PLUGINS}) endif() - diff --git a/Applications/Diffusion/target_libraries.cmake b/Applications/Diffusion/target_libraries.cmake index 666a884..92557d9 100644 --- a/Applications/Diffusion/target_libraries.cmake +++ b/Applications/Diffusion/target_libraries.cmake @@ -1,43 +1,43 @@ # A list of plug-in targets which should be automatically enabled # (or be available in external projects) for this application set(target_libraries org_blueberry_ui_qt org_blueberry_ui_qt_help org_mitk_planarfigure org_mitk_gui_qt_diffusionimagingapp org_mitk_gui_qt_ext org_mitk_gui_qt_datamanager org_mitk_gui_qt_segmentation org_mitk_gui_qt_multilabelsegmentation org_mitk_gui_qt_python org_mitk_gui_qt_volumevisualization org_mitk_gui_qt_diffusionimaging org_mitk_gui_qt_diffusionimaging_connectomics org_mitk_gui_qt_diffusionimaging_fiberfox org_mitk_gui_qt_diffusionimaging_fiberprocessing org_mitk_gui_qt_diffusionimaging_ivim org_mitk_gui_qt_diffusionimaging_odfpeaks org_mitk_gui_qt_diffusionimaging_preprocessing org_mitk_gui_qt_diffusionimaging_reconstruction org_mitk_gui_qt_diffusionimaging_tractography org_mitk_gui_qt_diffusionimaging_registration org_mitk_gui_qt_diffusionimaging_python org_mitk_gui_qt_diffusionimaging_denoising org_mitk_gui_qt_diffusionimaging_partialvolume org_mitk_gui_qt_matchpoint_algorithm_browser org_mitk_gui_qt_matchpoint_algorithm_control org_mitk_gui_qt_matchpoint_mapper org_mitk_gui_qt_imagenavigator org_mitk_gui_qt_moviemaker org_mitk_gui_qt_measurementtoolbox org_mitk_gui_qt_basicimageprocessing org_mitk_gui_qt_viewnavigator org_mitk_gui_qt_renderwindowmanager ) -if(NOT MITK_USE_Python) +if(NOT MITK_USE_Python3) list(REMOVE_ITEM target_libraries org_mitk_gui_qt_diffusionimaging_python) list(REMOVE_ITEM target_libraries org_mitk_gui_qt_python) endif() diff --git a/CMake/BuildConfigurations/DiffusionAll.cmake b/CMake/BuildConfigurations/DiffusionAll.cmake index 75e57fa..fd0b6f6 100644 --- a/CMake/BuildConfigurations/DiffusionAll.cmake +++ b/CMake/BuildConfigurations/DiffusionAll.cmake @@ -1,32 +1,32 @@ message(STATUS "Configuring MITK Diffusion with all Plugins") # Enable non-optional external dependencies -set(MITK_USE_Vigra ON CACHE BOOL "MITK Use Vigra Library" FORCE) -set(MITK_USE_HDF5 ON CACHE BOOL "MITK Use HDF5 Library" FORCE) +set(MITK_USE_Vigra ON CACHE BOOL "" FORCE) +set(MITK_USE_HDF5 ON CACHE BOOL "" FORCE) set(MITK_USE_MatchPoint ON CACHE BOOL "" FORCE) set(MITK_USE_DCMTK ON CACHE BOOL "" FORCE) set(MITK_USE_DCMQI ON CACHE BOOL "" FORCE) set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE) -set(MITK_USE_Python ON CACHE BOOL "" FORCE) +set(MITK_USE_Python3 ON CACHE BOOL "" FORCE) set(MITK_USE_BetData ON CACHE BOOL "" FORCE) set(MITK_BUILD_APP_Diffusion ON CACHE BOOL "Build MITK Diffusion" FORCE) set(BUILD_DiffusionFiberProcessingCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber processing" FORCE) set(BUILD_DiffusionFiberfoxCmdApps ON CACHE BOOL "Build commandline tools for diffusion data simulation (Fiberfox)" FORCE) set(BUILD_DiffusionMiscCmdApps ON CACHE BOOL "Build miscellaneous commandline tools for diffusion" FORCE) set(BUILD_DiffusionQuantificationCmdApps ON CACHE BOOL "Build commandline tools for diffusion quantification (IVIM, ADC, ...)" FORCE) set(BUILD_DiffusionTractographyCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography" FORCE) set(BUILD_DiffusionTractographyEvaluationCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography evaluation" FORCE) set(BUILD_DiffusionConnectomicsCmdApps ON CACHE BOOL "Build commandline tools for diffusion connectomics" FORCE) set(BUILD_DiffusionPythonCmdApps ON CACHE BOOL "Build commandline tools for diffusion with python" FORCE) # Build neither all plugins nor examples set(BUILD_TESTING ON CACHE BOOL "Build the MITK tests" FORCE) # Activate in-application help generation set(MITK_DOXYGEN_GENERATE_QCH_FILES ON CACHE BOOL "Use doxygen to generate Qt compressed help files for MITK docs" FORCE) set(BLUEBERRY_USE_QT_HELP ON CACHE BOOL "Enable support for integrating bundle documentation into Qt Help" FORCE) # Disable console window set(MITK_SHOW_CONSOLE_WINDOW ON CACHE BOOL "Use this to enable or disable the console window when starting MITK GUI Applications" FORCE) diff --git a/CMake/BuildConfigurations/DiffusionRelease.cmake b/CMake/BuildConfigurations/DiffusionRelease.cmake index 9fac425..0abcf0c 100644 --- a/CMake/BuildConfigurations/DiffusionRelease.cmake +++ b/CMake/BuildConfigurations/DiffusionRelease.cmake @@ -1,42 +1,42 @@ message(STATUS "Configuring MITK Diffusion Release Build") # Enable non-optional external dependencies set(MITK_USE_Vigra ON CACHE BOOL "MITK Use Vigra Library" FORCE) set(MITK_USE_HDF5 ON CACHE BOOL "MITK Use HDF5 Library" FORCE) set(MITK_USE_MatchPoint ON CACHE BOOL "" FORCE) set(MITK_USE_DCMTK ON CACHE BOOL "" FORCE) set(MITK_USE_DCMQI ON CACHE BOOL "" FORCE) set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE) -set(MITK_USE_Python ON CACHE BOOL "" FORCE) +set(MITK_USE_Python3 ON CACHE BOOL "" FORCE) set(MITK_USE_BetData ON CACHE BOOL "" FORCE) set(BUILD_DiffusionPythonCmdApps ON CACHE BOOL "Build commandline tools for diffusion with python" FORCE) # Disable all apps but MITK Diffusion set(MITK_BUILD_ALL_APPS OFF CACHE BOOL "Build all MITK applications" FORCE) set(MITK_BUILD_APP_CoreApp OFF CACHE BOOL "Build the MITK CoreApp" FORCE) set(MITK_BUILD_APP_Workbench OFF CACHE BOOL "Build the MITK Workbench" FORCE) set(MITK_BUILD_APP_Diffusion ON CACHE BOOL "Build MITK Diffusion" FORCE) # Activate Diffusion Mini Apps set(BUILD_DiffusionFiberProcessingCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber processing" FORCE) set(BUILD_DiffusionFiberfoxCmdApps ON CACHE BOOL "Build commandline tools for diffusion data simulation (Fiberfox)" FORCE) set(BUILD_DiffusionMiscCmdApps ON CACHE BOOL "Build miscellaneous commandline tools for diffusion" FORCE) set(BUILD_DiffusionQuantificationCmdApps ON CACHE BOOL "Build commandline tools for diffusion quantification (IVIM, ADC, ...)" FORCE) set(BUILD_DiffusionTractographyCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography" FORCE) set(BUILD_DiffusionTractographyEvaluationCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography evaluation" FORCE) set(BUILD_DiffusionConnectomicsCmdApps OFF CACHE BOOL "Build commandline tools for diffusion connectomics" FORCE) # Build neither all plugins nor examples set(MITK_BUILD_ALL_PLUGINS OFF CACHE BOOL "Build all MITK plugins" FORCE) set(MITK_BUILD_EXAMPLES OFF CACHE BOOL "Build the MITK examples" FORCE) set(BUILD_TESTING OFF CACHE BOOL "Build the MITK tests" FORCE) # Activate in-application help generation set(MITK_DOXYGEN_GENERATE_QCH_FILES ON CACHE BOOL "Use doxygen to generate Qt compressed help files for MITK docs" FORCE) set(BLUEBERRY_USE_QT_HELP ON CACHE BOOL "Enable support for integrating bundle documentation into Qt Help" FORCE) # Enable console window set(MITK_SHOW_CONSOLE_WINDOW ON CACHE BOOL "Use this to enable or disable the console window when starting MITK GUI Applications" FORCE) set(MITK_VTK_DEBUG_LEAKS OFF CACHE BOOL "" FORCE) set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE) diff --git a/CMake/BuildConfigurations/DiffusionRelease_NoPython.cmake b/CMake/BuildConfigurations/DiffusionRelease_NoPython.cmake index 0fb51db..04ba3f7 100644 --- a/CMake/BuildConfigurations/DiffusionRelease_NoPython.cmake +++ b/CMake/BuildConfigurations/DiffusionRelease_NoPython.cmake @@ -1,41 +1,41 @@ message(STATUS "Configuring MITK Diffusion Release Build") # Enable non-optional external dependencies set(MITK_USE_Vigra ON CACHE BOOL "MITK Use Vigra Library" FORCE) set(MITK_USE_HDF5 ON CACHE BOOL "MITK Use HDF5 Library" FORCE) set(MITK_USE_MatchPoint ON CACHE BOOL "" FORCE) set(MITK_USE_DCMTK ON CACHE BOOL "" FORCE) set(MITK_USE_DCMQI ON CACHE BOOL "" FORCE) set(MITK_USE_OpenMP ON CACHE BOOL "" FORCE) -set(MITK_USE_Python OFF CACHE BOOL "" FORCE) +set(MITK_USE_Python3 OFF CACHE BOOL "" FORCE) # Disable all apps but MITK Diffusion set(MITK_BUILD_ALL_APPS OFF CACHE BOOL "Build all MITK applications" FORCE) set(MITK_BUILD_APP_CoreApp OFF CACHE BOOL "Build the MITK CoreApp" FORCE) set(MITK_BUILD_APP_Workbench OFF CACHE BOOL "Build the MITK Workbench" FORCE) set(MITK_BUILD_APP_Diffusion ON CACHE BOOL "Build MITK Diffusion" FORCE) # Activate Diffusion Mini Apps set(BUILD_DiffusionFiberProcessingCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber processing" FORCE) set(BUILD_DiffusionFiberfoxCmdApps ON CACHE BOOL "Build commandline tools for diffusion data simulation (Fiberfox)" FORCE) set(BUILD_DiffusionMiscCmdApps ON CACHE BOOL "Build miscellaneous commandline tools for diffusion" FORCE) set(BUILD_DiffusionQuantificationCmdApps ON CACHE BOOL "Build commandline tools for diffusion quantification (IVIM, ADC, ...)" FORCE) set(BUILD_DiffusionTractographyCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography" FORCE) set(BUILD_DiffusionTractographyEvaluationCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography evaluation" FORCE) set(BUILD_DiffusionConnectomicsCmdApps OFF CACHE BOOL "Build commandline tools for diffusion connectomics" FORCE) set(BUILD_DiffusionPythonCmdApps OFF CACHE BOOL "Build commandline tools for diffusion with python" FORCE) # Build neither all plugins nor examples set(MITK_BUILD_ALL_PLUGINS OFF CACHE BOOL "Build all MITK plugins" FORCE) set(MITK_BUILD_EXAMPLES OFF CACHE BOOL "Build the MITK examples" FORCE) set(BUILD_TESTING OFF CACHE BOOL "Build the MITK tests" FORCE) # Activate in-application help generation set(MITK_DOXYGEN_GENERATE_QCH_FILES ON CACHE BOOL "Use doxygen to generate Qt compressed help files for MITK docs" FORCE) set(BLUEBERRY_USE_QT_HELP ON CACHE BOOL "Enable support for integrating bundle documentation into Qt Help" FORCE) # Enable console window set(MITK_SHOW_CONSOLE_WINDOW ON CACHE BOOL "Use this to enable or disable the console window when starting MITK GUI Applications" FORCE) set(MITK_VTK_DEBUG_LEAKS OFF CACHE BOOL "" FORCE) set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE) diff --git a/Modules/DiffusionCmdApps/CMakeLists.txt b/Modules/DiffusionCmdApps/CMakeLists.txt index e4616a0..203fd92 100644 --- a/Modules/DiffusionCmdApps/CMakeLists.txt +++ b/Modules/DiffusionCmdApps/CMakeLists.txt @@ -1,20 +1,20 @@ -MITK_CREATE_MODULE( +mitk_create_module( SUBPROJECTS MITK-Diffusion # INCLUDE_DIRS Helpers DEPENDS MitkDiffusionCore MitkDiffusionIO MitkCommandLine PACKAGE_DEPENDS PUBLIC ITK ) if(MODULE_IS_ENABLED) add_subdirectory(Connectomics) add_subdirectory(Fiberfox) add_subdirectory(FiberProcessing) add_subdirectory(Tractography) add_subdirectory(TractographyEvaluation) add_subdirectory(Misc) add_subdirectory(Quantification) -if(MITK_USE_Python) +if(MITK_USE_Python3) add_subdirectory(Python) endif() endif() diff --git a/Modules/DiffusionCore/CMakeLists.txt b/Modules/DiffusionCore/CMakeLists.txt index 0115980..393a1dc 100644 --- a/Modules/DiffusionCore/CMakeLists.txt +++ b/Modules/DiffusionCore/CMakeLists.txt @@ -1,32 +1,32 @@ # With apple gcc 4.2.1 the following waring leads to an build error if boost is enabled if(APPLE) mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=empty-body" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) endif() -MITK_CREATE_MODULE( +mitk_create_module( SUBPROJECTS MITK-Diffusion INCLUDE_DIRS Algorithms Algorithms/Reconstruction Algorithms/Registration Algorithms/Reconstruction/MultishellProcessing Algorithms/Reconstruction/FittingFunctions DicomImport IODataStructures/DiffusionWeightedImages IODataStructures/Properties IODataStructures Rendering ${CMAKE_CURRENT_BINARY_DIR} DEPENDS MitkMapperExt MitkPlanarFigure MitkImageExtraction MitkDICOMReader MitkMatchPointRegistration PACKAGE_DEPENDS PUBLIC VTK|vtkFiltersProgrammable Vigra HDF5 ) if(TARGET ${MODULE_TARGET} AND MITK_USE_OpenMP) target_link_libraries(${MODULE_TARGET} PUBLIC OpenMP::OpenMP_CXX) endif() if(MSVC) mitkFunctionCheckCAndCXXCompilerFlags("/wd4005" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) endif() add_subdirectory(Testing) -if(MITK_USE_Python) -MITK_INSTALL(FILES PythonRequirements.txt) +if(MITK_USE_Python3) + mitk_install(FILES PythonRequirements.txt) endif() configure_file(${CMAKE_CURRENT_SOURCE_DIR}/mitkDiffusionImagingConfigure.h.in ${CMAKE_CURRENT_BINARY_DIR}/mitkDiffusionImagingConfigure.h) mitkFunctionGetVersion(${CMAKE_CURRENT_SOURCE_DIR} MITKDIFFUSION) mitkFunctionGetVersionDescription(${CMAKE_CURRENT_SOURCE_DIR} MITKDIFFUSION) configure_file(mitkDiffusionVersion.h.in ${MITK_BINARY_DIR}/mitkDiffusionVersion.h) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt index 7c3281f..0f86e2c 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt @@ -1,18 +1,18 @@ -if(MITK_USE_Python) +if(MITK_USE_Python3) -# The project name must correspond to the directory name of your plug-in -# and must not contain periods. -project(org_mitk_gui_qt_diffusionimaging_python) + # The project name must correspond to the directory name of your plug-in + # and must not contain periods. + project(org_mitk_gui_qt_diffusionimaging_python) -mitk_create_plugin( - SUBPROJECTS MITK-Diffusion - EXPORT_DIRECTIVE DIFFUSIONIMAGING_PREPROCESSING_EXPORT - EXPORTED_INCLUDE_SUFFIXES src - MODULE_DEPENDS MitkDiffusionCore MitkPython - PACKAGE_DEPENDS Qt5|Network BetData -) + mitk_create_plugin( + SUBPROJECTS MITK-Diffusion + EXPORT_DIRECTIVE DIFFUSIONIMAGING_PREPROCESSING_EXPORT + EXPORTED_INCLUDE_SUFFIXES src + MODULE_DEPENDS MitkDiffusionCore MitkPython + PACKAGE_DEPENDS Qt5|Network BetData + ) -#set(_install_DESTINATION "BetData") -MITK_INSTALL(DIRECTORY ${BetData_DIR}/) + #set(_install_DESTINATION "BetData") + mitk_install(DIRECTORY ${BetData_DIR}/) endif()