diff --git a/Applications/Diffusion/CMakeLists.txt b/Applications/Diffusion/CMakeLists.txt index c1f4e5175e..0e05791fb0 100644 --- a/Applications/Diffusion/CMakeLists.txt +++ b/Applications/Diffusion/CMakeLists.txt @@ -1,97 +1,102 @@ +if(MITK_USE_Python) + 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.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.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 ) # 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() + +endif() # MITK_USE_PYTHON diff --git a/Applications/Diffusion/target_libraries.cmake b/Applications/Diffusion/target_libraries.cmake index d9241ad619..022c63d39c 100644 --- a/Applications/Diffusion/target_libraries.cmake +++ b/Applications/Diffusion/target_libraries.cmake @@ -1,33 +1,34 @@ # 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_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_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 ) diff --git a/CMake/BuildConfigurations/DiffusionAll.cmake b/CMake/BuildConfigurations/DiffusionAll.cmake index c1ca6adcf2..449fe3c02f 100644 --- a/CMake/BuildConfigurations/DiffusionAll.cmake +++ b/CMake/BuildConfigurations/DiffusionAll.cmake @@ -1,37 +1,38 @@ 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_MatchPoint ON CACHE BOOL "" FORCE) set(MITK_USE_DCMTK ON CACHE BOOL "" FORCE) set(MITK_USE_DCMQI ON CACHE BOOL "" FORCE) set(MITK_USE_Python ON CACHE BOOL "" FORCE) +set(MITK_USE_BetData ON CACHE BOOL "" FORCE) set(MITK_USE_SYSTEM_PYTHON ON 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_Diffusion ON CACHE BOOL "Build MITK Diffusion" FORCE) # Activate Diffusion Mini Apps set(BUILD_DiffusionCoreCmdApps ON CACHE BOOL "Build commandline tools for 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) # 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 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 144f7174dd..4945db9bc6 100644 --- a/CMake/BuildConfigurations/DiffusionRelease.cmake +++ b/CMake/BuildConfigurations/DiffusionRelease.cmake @@ -1,38 +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_Python ON CACHE BOOL "" FORCE) +set(MITK_USE_BetData ON CACHE BOOL "" FORCE) +set(MITK_USE_SYSTEM_PYTHON ON 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_DiffusionCoreCmdApps OFF CACHE BOOL "Build commandline tools for 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 OFF CACHE BOOL "Build miscellaneous commandline tools for diffusion" FORCE) set(BUILD_DiffusionQuantificationCmdApps OFF 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 OFF CACHE BOOL "Build commandline tools for diffusion fiber tractography evaluation" FORCE) set(BUILD_DiffusionConnectomicsCmdApps ON 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(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE) diff --git a/CMake/FindBetData.cmake b/CMake/FindBetData.cmake new file mode 100644 index 0000000000..f15a41f9f2 --- /dev/null +++ b/CMake/FindBetData.cmake @@ -0,0 +1,7 @@ +set(BetData_DIR ${MITK_SUPERBUILD_BINARY_DIR}/ep/src/BetData) + +if(EXISTS ${BetData_DIR}) + set(BetData_FOUND TRUE) +else() + set(BetData_FOUND FALSE) +endif() diff --git a/CMake/PackageDepends/MITK_BetData_Config.cmake b/CMake/PackageDepends/MITK_BetData_Config.cmake new file mode 100644 index 0000000000..e69de29bb2 diff --git a/CMake/mitkInstallRules.cmake b/CMake/mitkInstallRules.cmake index 01d2b71efc..8675299116 100644 --- a/CMake/mitkInstallRules.cmake +++ b/CMake/mitkInstallRules.cmake @@ -1,193 +1,199 @@ MITK_INSTALL(FILES "${MITK_SOURCE_DIR}/mitk.ico") MITK_INSTALL(FILES "${MITK_SOURCE_DIR}/mitk.bmp") # Install CTK Qt (designer) plugins if(MITK_USE_CTK) if(EXISTS ${CTK_QTDESIGNERPLUGINS_DIR}) set(_qtplugin_install_destinations) if(MACOSX_BUNDLE_NAMES) foreach(bundle_name ${MACOSX_BUNDLE_NAMES}) list(APPEND _qtplugin_install_destinations ${bundle_name}.app/Contents/MacOS/${_install_DESTINATION}/plugins/designer) endforeach() else() list(APPEND _qtplugin_install_destinations bin/plugins/designer) endif() set(_ctk_qt_plugin_folder_release) set(_ctk_qt_plugin_folder_debug) if(NOT CMAKE_CFG_INTDIR STREQUAL ".") set(_ctk_qt_plugin_folder_release "Release/") set(_ctk_qt_plugin_folder_debug "Debug/") endif() foreach(_qtplugin_install_dir ${_qtplugin_install_destinations}) install(DIRECTORY "${CTK_QTDESIGNERPLUGINS_DIR}/designer/${_ctk_qt_plugin_folder_release}" DESTINATION ${_qtplugin_install_dir} CONFIGURATIONS Release ) install(DIRECTORY "${CTK_QTDESIGNERPLUGINS_DIR}/designer/${_ctk_qt_plugin_folder_debug}" DESTINATION ${_qtplugin_install_dir} CONFIGURATIONS Debug ) endforeach() endif() endif() # related to MITK:T19679 if(MACOSX_BUNDLE_NAMES) foreach(bundle_name ${MACOSX_BUNDLE_NAMES}) get_property(_qmake_location TARGET ${Qt5Core_QMAKE_EXECUTABLE} PROPERTY IMPORT_LOCATION) get_filename_component(_qmake_path "${_qmake_location}" DIRECTORY) install(FILES "${_qmake_path}/../plugins/platforms/libqcocoa.dylib" DESTINATION "${bundle_name}.app/Contents/MacOS/platforms" CONFIGURATIONS Release) install(FILES "${_qmake_path}/../plugins/sqldrivers/libqsqlite.dylib" DESTINATION "${bundle_name}.app/Contents/MacOS/sqldrivers" CONFIGURATIONS Release) install(FILES "${_qmake_path}/../plugins/iconengines/libqsvgicon.dylib" DESTINATION "${bundle_name}.app/Contents/MacOS/iconengines" CONFIGURATIONS Release) # related to MITK:T19679-InstallQtWebEnginProcess if(MITK_USE_Qt5_WebEngine) get_filename_component(ABS_DIR_HELPERS "${_qmake_path}/../lib/QtWebEngineCore.framework/Helpers" REALPATH) install(DIRECTORY ${ABS_DIR_HELPERS} DESTINATION "${bundle_name}.app/Contents/Frameworks/QtWebEngineCore.framework/" CONFIGURATIONS Release) endif() endforeach() endif() if(WIN32) if(MITK_USE_Qt5) get_property(_qmake_location TARGET ${Qt5Core_QMAKE_EXECUTABLE} PROPERTY IMPORT_LOCATION) get_filename_component(_qmake_path "${_qmake_location}" DIRECTORY) install(FILES "${_qmake_path}/../plugins/platforms/qwindows.dll" DESTINATION "bin/plugins/platforms" CONFIGURATIONS Release) install(FILES "${_qmake_path}/../plugins/sqldrivers/qsqlite.dll" DESTINATION "bin/plugins/sqldrivers" CONFIGURATIONS Release) install(FILES "${_qmake_path}/../plugins/imageformats/qsvg.dll" DESTINATION "bin/plugins/imageformats" CONFIGURATIONS Release) install(FILES "${_qmake_path}/../plugins/iconengines/qsvgicon.dll" DESTINATION "bin/plugins/iconengines" CONFIGURATIONS Release) if(MITK_USE_Qt5_WebEngine) MITK_INSTALL( FILES "${_qmake_path}/QtWebEngineProcess.exe") endif() install(DIRECTORY "${_qmake_path}/../resources/" DESTINATION "bin/resources/" CONFIGURATIONS Release) install(DIRECTORY "${_qmake_path}/../translations/qtwebengine_locales/" DESTINATION "bin/translations/qtwebengine_locales/" CONFIGURATIONS Release) install(FILES "${_qmake_path}/../plugins/platforms/qwindowsd.dll" DESTINATION "bin/plugins/platforms" CONFIGURATIONS Debug) install(FILES "${_qmake_path}/../plugins/sqldrivers/qsqlited.dll" DESTINATION "bin/plugins/sqldrivers" CONFIGURATIONS Debug) install(FILES "${_qmake_path}/../plugins/imageformats/qsvgd.dll" DESTINATION "bin/plugins/imageformats" CONFIGURATIONS Debug) install(FILES "${_qmake_path}/../plugins/iconengines/qsvgicond.dll" DESTINATION "bin/plugins/iconengines" CONFIGURATIONS Debug) install(DIRECTORY "${_qmake_path}/../resources/" DESTINATION "bin/resources/" CONFIGURATIONS Debug) install(DIRECTORY "${_qmake_path}/../translations/qtwebengine_locales/" DESTINATION "bin/translations/qtwebengine_locales/" CONFIGURATIONS Debug) endif() #DCMTK Dlls install target (shared libs on gcc only) if(MINGW AND DCMTK_ofstd_LIBRARY) set(_dcmtk_libs ${DCMTK_dcmdata_LIBRARY} ${DCMTK_dcmimgle_LIBRARY} ${DCMTK_dcmnet_LIBRARY} ${DCMTK_ofstd_LIBRARY} ) foreach(_dcmtk_lib ${_dcmtk_libs}) MITK_INSTALL(FILES ${_dcmtk_lib} ) endforeach() endif() #MinGW dll if(MINGW) find_library(MINGW_RUNTIME_DLL "mingwm10.dll" HINTS ${CMAKE_FIND_ROOT_PATH}/sys-root/mingw/bin) if(MINGW_RUNTIME_DLL) MITK_INSTALL(FILES ${MINGW_RUNTIME_DLL} ) else() message(SEND_ERROR "Could not find mingwm10.dll which is needed for a proper install") endif() find_library(MINGW_GCC_RUNTIME_DLL "libgcc_s_dw2-1.dll" HINTS ${CMAKE_FIND_ROOT_PATH}/sys-root/mingw/bin) if(MINGW_GCC_RUNTIME_DLL) MITK_INSTALL(FILES ${MINGW_GCC_RUNTIME_DLL} ) else() message(SEND_ERROR "Could not find libgcc_s_dw2-1.dll which is needed for a proper install") endif() endif() else() #DCMTK Dlls install target (shared libs on gcc only) if(DCMTK_ofstd_LIBRARY) set(_dcmtk_libs ${DCMTK_dcmdata_LIBRARY} ${DCMTK_dcmimgle_LIBRARY} ${DCMTK_dcmnet_LIBRARY} ${DCMTK_ofstd_LIBRARY} ) foreach(_dcmtk_lib ${_dcmtk_libs}) #MITK_INSTALL(FILES ${_dcmtk_lib} DESTINATION lib) endforeach() endif() # We need to install Webengineprocess and related files on unix as well if(UNIX) if(MITK_USE_Qt5) get_property(_qmake_location TARGET ${Qt5Core_QMAKE_EXECUTABLE} PROPERTY IMPORT_LOCATION) get_filename_component(_qmake_path "${_qmake_location}" DIRECTORY) install(FILES "${_qmake_path}/../plugins/platforms/libqxcb.so" DESTINATION "bin/plugins/platforms") install(FILES "${_qmake_path}/../plugins/sqldrivers/libqsqlite.so" DESTINATION "bin/plugins/sqldrivers") install(FILES "${_qmake_path}/../plugins/imageformats/libqsvg.so" DESTINATION "bin/plugins/imageformats") install(FILES "${_qmake_path}/../plugins/iconengines/libqsvgicon.so" DESTINATION "bin/plugins/iconengines") install(FILES "${_qmake_path}/../plugins/xcbglintegrations/libqxcb-glx-integration.so" DESTINATION "bin/plugins/xcbglintegrations") if(MITK_USE_Qt5_WebEngine) MITK_INSTALL_HELPER_APP( EXECUTABLES "${_qmake_path}/../libexec/QtWebEngineProcess") endif() install(DIRECTORY "${_qmake_path}/../resources/" DESTINATION "bin/resources/") install(DIRECTORY "${_qmake_path}/../translations/qtwebengine_locales/" DESTINATION "bin/translations/qtwebengine_locales/") endif() endif() endif() #install Matchpoint libs that are currently not auto detected if(MITK_USE_MatchPoint) install(DIRECTORY "${MITK_EXTERNAL_PROJECT_PREFIX}/bin/" DESTINATION "bin" FILES_MATCHING PATTERN "MAPUtilities*") install(DIRECTORY "${MITK_EXTERNAL_PROJECT_PREFIX}/bin/" DESTINATION "bin" FILES_MATCHING PATTERN "MAPAlgorithms*") endif() + +if(MITK_USE_BetData) + install(DIRECTORY "${BetData_DIR}" + DESTINATION "bin" + FILES_MATCHING PATTERN "*") +endif() diff --git a/CMakeExternals/BetData.cmake b/CMakeExternals/BetData.cmake new file mode 100644 index 0000000000..9a399c026a --- /dev/null +++ b/CMakeExternals/BetData.cmake @@ -0,0 +1,36 @@ +#----------------------------------------------------------------------------- +# Brain Extraction Data +#----------------------------------------------------------------------------- + +if(MITK_USE_BetData) + + +# Sanity checks +if(DEFINED BetData_DIR AND NOT EXISTS ${BetData_DIR}) + message(FATAL_ERROR "BetData_DIR variable is defined but corresponds to non-existing directory") +endif() + +set(proj BetData) +set(proj_DEPENDENCIES) +set(BetData_DEPENDS ${proj}) + +if(NOT DEFINED BetData_DIR) + + ExternalProject_Add(${proj} + URL http://mitk.org/download/data/MITK-BET-20171220.tar.gz + UPDATE_COMMAND "" + CONFIGURE_COMMAND "" + BUILD_COMMAND "" + INSTALL_COMMAND "" + DEPENDS ${proj_DEPENDENCIES} + ) + + set(BetData_DIR ${ep_prefix}/src/${proj}/) + configure_file(${CMAKE_CURRENT_LIST_DIR}/${proj}.h.in ${CMAKE_BINARY_DIR}/${proj}.h) + +else() + + mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") +endif() + +endif() diff --git a/CMakeExternals/BetData.h.in b/CMakeExternals/BetData.h.in new file mode 100644 index 0000000000..2aa9bba540 --- /dev/null +++ b/CMakeExternals/BetData.h.in @@ -0,0 +1,22 @@ +/*=================================================================== + +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. + +===================================================================*/ + +#ifndef BetData_h +#define BetData_h + +#define BetData_DIR "@BetData_DIR@" + +#endif diff --git a/CMakeExternals/ExternalProjectList.cmake b/CMakeExternals/ExternalProjectList.cmake index 531b51119a..05e6d4c3b6 100644 --- a/CMakeExternals/ExternalProjectList.cmake +++ b/CMakeExternals/ExternalProjectList.cmake @@ -1,44 +1,45 @@ mitkFunctionAddExternalProject(NAME Poco ON COMPONENTS Foundation Net Util XML Zip) mitkFunctionAddExternalProject(NAME DCMTK ON DOC "EXPERIMENTAL, superbuild only: Use DCMTK in MITK") mitkFunctionAddExternalProject(NAME OpenIGTLink OFF) mitkFunctionAddExternalProject(NAME tinyxml ON ADVANCED) mitkFunctionAddExternalProject(NAME GDCM ON ADVANCED) mitkFunctionAddExternalProject(NAME GLUT OFF ADVANCED) mitkFunctionAddExternalProject(NAME Raptor2 OFF ADVANCED) mitkFunctionAddExternalProject(NAME Eigen ON ADVANCED DOC "Use the Eigen library") mitkFunctionAddExternalProject(NAME ANN ON ADVANCED DOC "Use Approximate Nearest Neighbor Library") mitkFunctionAddExternalProject(NAME CppUnit ON ADVANCED DOC "Use CppUnit for unit tests") mitkFunctionAddExternalProject(NAME PCRE OFF ADVANCED NO_PACKAGE) mitkFunctionAddExternalProject(NAME ZLIB OFF ADVANCED NO_PACKAGE NO_CACHE) mitkFunctionAddExternalProject(NAME HDF5 ON ADVANCED) +mitkFunctionAddExternalProject(NAME BetData OFF ADVANCED) # ----------------------------------------- # The following external projects must be # ordered according to their # inter-dependencies mitkFunctionAddExternalProject(NAME SWIG OFF ADVANCED NO_PACKAGE DEPENDS PCRE) mitkFunctionAddExternalProject(NAME Python OFF NO_PACKAGE DEPENDS SWIG DOC "Use Python wrapping in MITK") mitkFunctionAddExternalProject(NAME Numpy OFF ADVANCED NO_PACKAGE) mitkFunctionAddExternalProject(NAME OpenCV OFF) mitkFunctionAddExternalProject(NAME Vigra OFF DEPENDS HDF5) # These are "hard" dependencies and always set to ON mitkFunctionAddExternalProject(NAME ITK ON NO_CACHE DEPENDS HDF5) mitkFunctionAddExternalProject(NAME VTK ON NO_CACHE) mitkFunctionAddExternalProject(NAME Boost ON NO_CACHE) mitkFunctionAddExternalProject(NAME SimpleITK OFF DEPENDS ITK GDCM SWIG) mitkFunctionAddExternalProject(NAME ACVD OFF DOC "Use Approximated Centroidal Voronoi Diagrams") mitkFunctionAddExternalProject(NAME CTK ON DEPENDS Qt5 DCMTK DOC "Use CTK in MITK") mitkFunctionAddExternalProject(NAME Rasqal OFF DEPENDS Raptor2 PCRE ADVANCED) mitkFunctionAddExternalProject(NAME Redland OFF DEPENDS Rasqal DOC "Use the Redland RDF library") mitkFunctionAddExternalProject(NAME DCMQI OFF DEPENDS DCMTK ITK DOC "Use dcmqi in MITK") mitkFunctionAddExternalProject(NAME MatchPoint OFF ADVANCED DEPENDS ITK DOC "Use the MatchPoint translation image registration library") if(MITK_USE_Qt5) mitkFunctionAddExternalProject(NAME Qwt ON ADVANCED DEPENDS Qt5) endif() diff --git a/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt index 3d2ef66df8..36f9917b3c 100644 --- a/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt +++ b/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt @@ -1,54 +1,52 @@ set(_module_deps MitkDiffusionCore MitkGraphAlgorithms MitkCLVigraRandomForest) mitk_check_module_dependencies( MODULES ${_module_deps} MISSING_DEPENDENCIES_VAR _missing_deps ) if(NOT _missing_deps) set(lut_url http://mitk.org/download/data/FibertrackingLUT.tar.gz) set(lut_tarball ${CMAKE_CURRENT_BINARY_DIR}/FibertrackingLUT.tar.gz) - #message("Downloading FiberTracking LUT ${lut_url}...") file(DOWNLOAD ${lut_url} ${lut_tarball} EXPECTED_MD5 38ecb6d4a826c9ebb0f4965eb9aeee44 TIMEOUT 60 STATUS status SHOW_PROGRESS ) list(GET status 0 status_code) list(GET status 1 status_msg) if(NOT status_code EQUAL 0) message(SEND_ERROR "${status_msg} (error code ${status_code})") endif() file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Resources) - #message("Unpacking FiberTracking LUT tarball...") execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ../FibertrackingLUT.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Resources RESULT_VARIABLE result ERROR_VARIABLE err_msg) if(result) message(SEND_ERROR "Unpacking FibertrackingLUT.tar.gz failed: ${err_msg}") endif() endif() MITK_CREATE_MODULE( SUBPROJECTS MITK-DTI INCLUDE_DIRS Fiberfox Fiberfox/SignalModels Fiberfox/Sequences Algorithms Algorithms/TrackingHandlers Algorithms/ClusteringMetrics Algorithms/GibbsTracking Algorithms/StochasticTracking IODataStructures IODataStructures/FiberBundle IODataStructures/PlanarFigureComposite Rendering ${CMAKE_CURRENT_BINARY_DIR} DEPENDS ${_module_deps} PACKAGE_DEPENDS PUBLIC ITK|ITKFFT ITK|ITKDiffusionTensorImage Vigra HDF5 ) if(MODULE_IS_ENABLED) add_subdirectory(cmdapps/Fiberfox) add_subdirectory(cmdapps/FiberProcessing) add_subdirectory(cmdapps/Tractography) add_subdirectory(cmdapps/TractographyEvaluation) add_subdirectory(cmdapps/Misc) add_subdirectory(Testing) endif() diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/ExtractSimilarTracts.cpp b/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/ExtractSimilarTracts.cpp index a312dd42ac..c3fa02149e 100644 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/ExtractSimilarTracts.cpp +++ b/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/ExtractSimilarTracts.cpp @@ -1,238 +1,236 @@ /*=================================================================== 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 #include #include #include #include #include #include typedef itksys::SystemTools ist; typedef itk::Image ItkFloatImgType; mitk::FiberBundle::Pointer LoadFib(std::string filename) { std::vector fibInfile = mitk::IOUtil::Load(filename); if( fibInfile.empty() ) std::cout << "File " << filename << " could not be read!"; mitk::BaseData::Pointer baseData = fibInfile.at(0); return dynamic_cast(baseData.GetPointer()); } ItkFloatImgType::Pointer LoadItkImage(const std::string& filename) { mitk::Image::Pointer img = dynamic_cast(mitk::IOUtil::Load(filename)[0].GetPointer()); ItkFloatImgType::Pointer itkMask = ItkFloatImgType::New(); mitk::CastToItkImage(img, itkMask); return itkMask; } /*! \brief Spatially cluster fibers */ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Extract Similar Tracts"); parser.setCategory("Fiber Tracking Evaluation"); parser.setContributor("MIC"); parser.setArgumentPrefix("--", "-"); parser.addArgument("", "i", mitkCommandLineParser::InputFile, "Input:", "input fiber bundle (.fib, .trk, .tck)", us::Any(), false); parser.addArgument("ref_tracts", "", mitkCommandLineParser::StringList, "Ref. Tracts:", "reference tracts (.fib, .trk, .tck)", us::Any(), false); parser.addArgument("ref_masks", "", mitkCommandLineParser::StringList, "Ref. Masks:", "reference bundle masks", us::Any()); parser.addArgument("", "o", mitkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false); parser.addArgument("distance", "", mitkCommandLineParser::Int, "Distance:", "", 10); parser.addArgument("metric", "", mitkCommandLineParser::String, "Metric:", ""); parser.addArgument("subsample", "", mitkCommandLineParser::Float, "Subsampling factor:", "Only use specified fraction of input fibers", 1.0); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; std::string in_fib = us::any_cast(parsedArgs["i"]); std::string out_root = us::any_cast(parsedArgs["o"]); mitkCommandLineParser::StringContainerType ref_bundle_files = us::any_cast(parsedArgs["ref_tracts"]); mitkCommandLineParser::StringContainerType ref_mask_files; if (parsedArgs.count("ref_masks")) ref_mask_files = us::any_cast(parsedArgs["ref_masks"]); if (ref_mask_files.size()>0 && ref_mask_files.size()!=ref_bundle_files.size()) { MITK_INFO << "If reference masks are used, there has to be one mask per reference tract."; return EXIT_FAILURE; } int distance = 10; if (parsedArgs.count("distance")) distance = us::any_cast(parsedArgs["distance"]); std::string metric = "EU_MEAN"; if (parsedArgs.count("metric")) metric = us::any_cast(parsedArgs["metric"]); float subsample = 1.0; if (parsedArgs.count("subsample")) subsample = us::any_cast(parsedArgs["subsample"]); try { mitk::FiberBundle::Pointer fib = LoadFib(in_fib); std::srand(0); if (subsample<1.0) fib = fib->SubsampleFibers(subsample); mitk::FiberBundle::Pointer resampled_fib = fib->GetDeepCopy(); resampled_fib->ResampleToNumPoints(12); std::vector< mitk::FiberBundle::Pointer > ref_fibs; std::vector< ItkFloatImgType::Pointer > ref_masks; for (std::size_t i=0; i distances; distances.push_back(distance); mitk::FiberBundle::Pointer anchor_tractogram = mitk::FiberBundle::New(nullptr); unsigned int c = 0; for (auto ref_fib : ref_fibs) { MITK_INFO << "Extracting " << ist::GetFilenameName(ref_bundle_files.at(c)); -// std::streambuf *old = cout.rdbuf(); // <-- save -// std::stringstream ss; -// std::cout.rdbuf (ss.rdbuf()); // <-- redirect + std::streambuf *old = cout.rdbuf(); // <-- save + std::stringstream ss; + std::cout.rdbuf (ss.rdbuf()); // <-- redirect try { itk::TractClusteringFilter::Pointer segmenter = itk::TractClusteringFilter::New(); // calculate centroids from reference bundle { - MITK_INFO << "TEST 1"; itk::TractClusteringFilter::Pointer clusterer = itk::TractClusteringFilter::New(); clusterer->SetDistances({10,20,30}); clusterer->SetTractogram(ref_fib); clusterer->SetMetrics({new mitk::ClusteringMetricEuclideanStd()}); clusterer->SetMergeDuplicateThreshold(0.0); clusterer->Update(); - MITK_INFO << "TEST 2"; std::vector tracts = clusterer->GetOutCentroids(); ref_fib = mitk::FiberBundle::New(nullptr); ref_fib = ref_fib->AddBundles(tracts); mitk::IOUtil::Save(ref_fib, out_root + "centroids_" + ist::GetFilenameName(ref_bundle_files.at(c))); segmenter->SetInCentroids(ref_fib); } // segment tract segmenter->SetFilterMask(ref_masks.at(c)); segmenter->SetOverlapThreshold(0.8); segmenter->SetDistances(distances); segmenter->SetTractogram(resampled_fib); segmenter->SetMergeDuplicateThreshold(0.0); segmenter->SetDoResampling(false); if (metric=="EU_MEAN") segmenter->SetMetrics({new mitk::ClusteringMetricEuclideanMean()}); else if (metric=="EU_STD") segmenter->SetMetrics({new mitk::ClusteringMetricEuclideanStd()}); else if (metric=="EU_MAX") segmenter->SetMetrics({new mitk::ClusteringMetricEuclideanMax()}); segmenter->Update(); std::vector< std::vector< long > > clusters = segmenter->GetOutFiberIndices(); if (clusters.size()>0) { vtkSmartPointer weights = vtkSmartPointer::New(); mitk::FiberBundle::Pointer result = mitk::FiberBundle::New(nullptr); std::vector< mitk::FiberBundle::Pointer > result_fibs; for (unsigned int cluster_index=0; cluster_indexGeneratePolyDataByIds(clusters.at(cluster_index), weights))); result = result->AddBundles(result_fibs); anchor_tractogram = anchor_tractogram->AddBundle(result); mitk::IOUtil::Save(result, out_root + "anchor_" + ist::GetFilenameName(ref_bundle_files.at(c))); fib = mitk::FiberBundle::New(fib->GeneratePolyDataByIds(clusters.back(), weights)); resampled_fib = mitk::FiberBundle::New(resampled_fib->GeneratePolyDataByIds(clusters.back(), weights)); } } catch(itk::ExceptionObject& excpt) { MITK_INFO << "Exception while processing " << ist::GetFilenameName(ref_bundle_files.at(c)); MITK_INFO << excpt.GetDescription(); } catch(std::exception& excpt) { MITK_INFO << "Exception while processing " << ist::GetFilenameName(ref_bundle_files.at(c)); MITK_INFO << excpt.what(); } -// std::cout.rdbuf (old); // <-- restore + std::cout.rdbuf (old); // <-- restore if (fib->GetNumFibers()==0) break; ++c; } MITK_INFO << "Streamlines in anchor tractogram: " << anchor_tractogram->GetNumFibers(); mitk::IOUtil::Save(anchor_tractogram, out_root + "anchor_tractogram.trk"); MITK_INFO << "Streamlines remaining in candidate tractogram: " << fib->GetNumFibers(); mitk::IOUtil::Save(fib, out_root + "candidate_tractogram.trk"); } catch (itk::ExceptionObject e) { std::cout << e; return EXIT_FAILURE; } catch (std::exception e) { std::cout << e.what(); return EXIT_FAILURE; } catch (...) { std::cout << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingViewControls.ui index 72891457e8..35da1a192a 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.denoising/src/internal/QmitkDenoisingViewControls.ui @@ -1,323 +1,329 @@ QmitkDenoisingViewControls 0 0 351 734 0 0 QmitkTemplate 6 9 9 9 9 QFrame::NoFrame QFrame::Raised 0 0 0 0 Input Image: Filter: Parameters 0 0 0 0 Lambda: + + 4 + 0.000000000000000 1.000000000000000 0.100000000000000 0.100000000000000 Iterations: 1 999 1 Parameters 0 0 0 0 Sampling Radius: 1 999 10 1 999 4 1 999 4 Num. Patches: 1 50 1 Iterations: Patch Size: Parameters 0 0 0 0 + + 4 + 1.000000000000000 99999.000000000000000 0.100000000000000 1.000000000000000 Variance: Start Qt::Vertical 20 40 QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp index 26310fa9ab..0fd430d313 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.preprocessing/src/internal/QmitkPreprocessingView.cpp @@ -1,1962 +1,1962 @@ /*=================================================================== 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. ===================================================================*/ //#define MBILOG_ENABLE_DEBUG #include "QmitkPreprocessingView.h" #include "mitkDiffusionImagingConfigure.h" // qt includes #include // itk includes #include "itkTimeProbe.h" #include "itkB0ImageExtractionImageFilter.h" #include "itkB0ImageExtractionToSeparateImageFilter.h" #include "itkBrainMaskExtractionImageFilter.h" #include "itkCastImageFilter.h" #include "itkVectorContainer.h" #include #include #include #include #include #include // Multishell includes #include // Multishell Functors #include #include #include #include // mitk includes #include "QmitkDataStorageComboBox.h" #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkNodePredicateDataType.h" #include "mitkProperties.h" #include "mitkVtkResliceInterpolationProperty.h" #include "mitkLookupTable.h" #include "mitkLookupTableProperty.h" #include "mitkTransferFunction.h" #include "mitkTransferFunctionProperty.h" #include "mitkDataNodeObject.h" #include "mitkOdfNormalizationMethodProperty.h" #include "mitkOdfScaleByProperty.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 const std::string QmitkPreprocessingView::VIEW_ID = "org.mitk.views.preprocessing"; #define DI_INFO MITK_INFO("DiffusionImaging") typedef float TTensorPixelType; QmitkPreprocessingView::QmitkPreprocessingView() : QmitkAbstractView(), m_Controls(nullptr) { } QmitkPreprocessingView::~QmitkPreprocessingView() { } void QmitkPreprocessingView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkPreprocessingViewControls; m_Controls->setupUi(parent); this->CreateConnections(); m_Controls->m_MeasurementFrameTable->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch); m_Controls->m_MeasurementFrameTable->verticalHeader()->setSectionResizeMode(QHeaderView::Stretch); m_Controls->m_DirectionMatrixTable->horizontalHeader()->setSectionResizeMode(QHeaderView::Stretch); m_Controls->m_DirectionMatrixTable->verticalHeader()->setSectionResizeMode(QHeaderView::Stretch); } } void QmitkPreprocessingView::SetFocus() { m_Controls->m_MirrorGradientToHalfSphereButton->setFocus(); } void QmitkPreprocessingView::CreateConnections() { if ( m_Controls ) { m_Controls->m_NormalizationMaskBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_SelctedImageComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_MergeDwiBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_AlignImageBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isOdf, isDti); mitk::NodePredicateAnd::Pointer noDiffusionImage = mitk::NodePredicateAnd::New(isMitkImage, mitk::NodePredicateNot::New(isDiffusionImage)); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer binaryNoDiffusionImage = mitk::NodePredicateAnd::New(noDiffusionImage, isBinaryPredicate); m_Controls->m_NormalizationMaskBox->SetPredicate(binaryNoDiffusionImage); m_Controls->m_SelctedImageComboBox->SetPredicate(isMitkImage); m_Controls->m_MergeDwiBox->SetPredicate(isMitkImage); m_Controls->m_AlignImageBox->SetPredicate(isMitkImage); m_Controls->m_ExtractBrainMask->setVisible(false); m_Controls->m_BrainMaskIterationsBox->setVisible(false); m_Controls->m_ResampleIntFrame->setVisible(false); connect( (QObject*)(m_Controls->m_ButtonAverageGradients), SIGNAL(clicked()), this, SLOT(AverageGradients()) ); connect( (QObject*)(m_Controls->m_ButtonExtractB0), SIGNAL(clicked()), this, SLOT(ExtractB0()) ); connect( (QObject*)(m_Controls->m_ReduceGradientsButton), SIGNAL(clicked()), this, SLOT(DoReduceGradientDirections()) ); connect( (QObject*)(m_Controls->m_ShowGradientsButton), SIGNAL(clicked()), this, SLOT(DoShowGradientDirections()) ); connect( (QObject*)(m_Controls->m_MirrorGradientToHalfSphereButton), SIGNAL(clicked()), this, SLOT(DoHalfSphereGradientDirections()) ); connect( (QObject*)(m_Controls->m_MergeDwisButton), SIGNAL(clicked()), this, SLOT(MergeDwis()) ); connect( (QObject*)(m_Controls->m_ProjectSignalButton), SIGNAL(clicked()), this, SLOT(DoProjectSignal()) ); connect( (QObject*)(m_Controls->m_B_ValueMap_Rounder_SpinBox), SIGNAL(valueChanged(int)), this, SLOT(UpdateDwiBValueMapRounder(int))); connect( (QObject*)(m_Controls->m_CreateLengthCorrectedDwi), SIGNAL(clicked()), this, SLOT(DoLengthCorrection()) ); connect( (QObject*)(m_Controls->m_NormalizeImageValuesButton), SIGNAL(clicked()), this, SLOT(DoDwiNormalization()) ); connect( (QObject*)(m_Controls->m_ResampleImageButton), SIGNAL(clicked()), this, SLOT(DoResampleImage()) ); connect( (QObject*)(m_Controls->m_ResampleTypeBox), SIGNAL(currentIndexChanged(int)), this, SLOT(DoUpdateInterpolationGui(int)) ); connect( (QObject*)(m_Controls->m_CropImageButton), SIGNAL(clicked()), this, SLOT(DoCropImage()) ); connect( (QObject*)(m_Controls->m_RemoveGradientButton), SIGNAL(clicked()), this, SLOT(DoRemoveGradient()) ); connect( (QObject*)(m_Controls->m_ExtractGradientButton), SIGNAL(clicked()), this, SLOT(DoExtractGradient()) ); connect( (QObject*)(m_Controls->m_FlipAxis), SIGNAL(clicked()), this, SLOT(DoFlipAxis()) ); connect( (QObject*)(m_Controls->m_FlipGradientsButton), SIGNAL(clicked()), this, SLOT(DoFlipGradientDirections()) ); connect( (QObject*)(m_Controls->m_ClearRotationButton), SIGNAL(clicked()), this, SLOT(DoClearRotationOfGradients()) ); connect( (QObject*)(m_Controls->m_ModifyHeader), SIGNAL(clicked()), this, SLOT(DoApplyHeader()) ); connect( (QObject*)(m_Controls->m_AlignImageButton), SIGNAL(clicked()), this, SLOT(DoAlignImages()) ); connect( (QObject*)(m_Controls->m_SelctedImageComboBox), SIGNAL(OnSelectionChanged(const mitk::DataNode*)), this, SLOT(OnImageSelectionChanged()) ); m_Controls->m_NormalizationMaskBox->SetZeroEntryText("--"); } } void QmitkPreprocessingView::DoAlignImages() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } mitk::DataNode::Pointer target_node = m_Controls->m_AlignImageBox->GetSelectedNode(); if (target_node.IsNull()) { return; } mitk::Image::Pointer target_image = dynamic_cast(target_node->GetData()); if ( target_image == nullptr ) { return; } - target_image->SetOrigin(image->GetGeometry()->GetOrigin()); - mitk::RenderingManager::GetInstance()->InitializeViews( target_image->GetTimeGeometry(), + image->SetOrigin(target_image->GetGeometry()->GetOrigin()); + mitk::RenderingManager::GetInstance()->InitializeViews( image->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoFlipAxis() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(node) ); if (isDiffusionImage) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); itk::FixedArray flipAxes; flipAxes[0] = m_Controls->m_FlipX->isChecked(); flipAxes[1] = m_Controls->m_FlipY->isChecked(); flipAxes[2] = m_Controls->m_FlipZ->isChecked(); itk::FlipImageFilter< ItkDwiType >::Pointer flipper = itk::FlipImageFilter< ItkDwiType >::New(); flipper->SetInput(itkVectorImagePointer); flipper->SetFlipAxes(flipAxes); flipper->Update(); GradProp::GradientDirectionsContainerType::Pointer oldGradients = static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); GradProp::GradientDirectionsContainerType::Pointer newGradients = GradProp::GradientDirectionsContainerType::New(); for (unsigned int i=0; iSize(); i++) { GradProp::GradientDirectionType g = oldGradients->GetElement(i); GradProp::GradientDirectionType newG = g; if (flipAxes[0]) { newG[0] *= -1; } if (flipAxes[1]) { newG[1] *= -1; } if (flipAxes[2]) { newG[2] *= -1; } newGradients->InsertElement(i, newG); } mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( flipper->GetOutput() ); PropHelper::CopyProperties(image, newImage, true); newImage->GetPropertyList()->ReplaceProperty( PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( newGradients ) ); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); newImage->GetGeometry()->SetOrigin(image->GetGeometry()->GetOrigin()); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_flipped").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else if( image->GetPixelType().GetNumberOfComponents() == 1 ) { AccessFixedDimensionByItk(image, TemplatedFlipAxis,3); } else { QMessageBox::warning(nullptr,"Warning", QString("Operation not supported in multi-component images") ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedFlipAxis(itk::Image* itkImage) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } itk::FixedArray flipAxes; flipAxes[0] = m_Controls->m_FlipX->isChecked(); flipAxes[1] = m_Controls->m_FlipY->isChecked(); flipAxes[2] = m_Controls->m_FlipZ->isChecked(); typename itk::FlipImageFilter< itk::Image >::Pointer flipper = itk::FlipImageFilter< itk::Image >::New(); flipper->SetInput(itkImage); flipper->SetFlipAxes(flipAxes); flipper->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( flipper->GetOutput() ); newImage->GetGeometry()->SetOrigin(image->GetGeometry()->GetOrigin()); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_flipped").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoRemoveGradient() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } std::vector< unsigned int > channelsToRemove; channelsToRemove.push_back(m_Controls->m_RemoveGradientBox->value()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); itk::RemoveDwiChannelFilter< short >::Pointer filter = itk::RemoveDwiChannelFilter< short >::New(); filter->SetInput(itkVectorImagePointer); filter->SetChannelIndices(channelsToRemove); filter->SetDirections( static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); filter->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::CopyProperties(image, newImage, true); newImage->GetPropertyList()->ReplaceProperty( PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( filter->GetNewDirections() ) ); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_removedgradients").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoExtractGradient() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); unsigned int channel = m_Controls->m_ExtractGradientBox->value(); itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); filter->SetInput( itkVectorImagePointer); filter->SetChannelIndex(channel); filter->Update(); mitk::Image::Pointer newImage = mitk::Image::New(); newImage->InitializeByItk( filter->GetOutput() ); newImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName( (name+"_direction-"+QString::number(channel)).toStdString().c_str() ); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); } void QmitkPreprocessingView::DoCropImage() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( isDiffusionImage ) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); ItkDwiType::SizeType lower; ItkDwiType::SizeType upper; lower[0] = m_Controls->m_XstartBox->value(); lower[1] = m_Controls->m_YstartBox->value(); lower[2] = m_Controls->m_ZstartBox->value(); upper[0] = m_Controls->m_XendBox->value(); upper[1] = m_Controls->m_YendBox->value(); upper[2] = m_Controls->m_ZendBox->value(); itk::CropImageFilter< ItkDwiType, ItkDwiType >::Pointer cropper = itk::CropImageFilter< ItkDwiType, ItkDwiType >::New(); cropper->SetLowerBoundaryCropSize(lower); cropper->SetUpperBoundaryCropSize(upper); cropper->SetInput( itkVectorImagePointer ); cropper->Update(); ItkDwiType::Pointer itkOutImage = cropper->GetOutput(); ItkDwiType::DirectionType dir = itkOutImage->GetDirection(); itk::Point origin = itkOutImage->GetOrigin(); itk::Point t; t[0] = lower[0]*itkOutImage->GetSpacing()[0]; t[1] = lower[1]*itkOutImage->GetSpacing()[1]; t[2] = lower[2]*itkOutImage->GetSpacing()[2]; t= dir*t; origin[0] += t[0]; origin[1] += t[1]; origin[2] += t[2]; itkOutImage->SetOrigin(origin); mitk::Image::Pointer newimage = mitk::GrabItkImageMemory( itkOutImage ); PropHelper::CopyProperties(image, newimage, false); PropHelper propertyHelper( newimage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newimage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_cropped").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } else if( image->GetPixelType().GetNumberOfComponents() ) { AccessFixedDimensionByItk(image, TemplatedCropImage,3); } else { QMessageBox::warning(nullptr,"Warning", QString("Operation not supported in multi-component images") ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedCropImage( itk::Image* itkImage) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } ItkDwiType::SizeType lower; ItkDwiType::SizeType upper; lower[0] = m_Controls->m_XstartBox->value(); lower[1] = m_Controls->m_YstartBox->value(); lower[2] = m_Controls->m_ZstartBox->value(); upper[0] = m_Controls->m_XendBox->value(); upper[1] = m_Controls->m_YendBox->value(); upper[2] = m_Controls->m_ZendBox->value(); typedef itk::Image ImageType; typename itk::CropImageFilter< ImageType, ImageType >::Pointer cropper = itk::CropImageFilter< ImageType, ImageType >::New(); cropper->SetLowerBoundaryCropSize(lower); cropper->SetUpperBoundaryCropSize(upper); cropper->SetInput(itkImage); cropper->Update(); typename ImageType::Pointer itkOutImage = cropper->GetOutput(); typename ImageType::DirectionType dir = itkOutImage->GetDirection(); itk::Point origin = itkOutImage->GetOrigin(); itk::Point t; t[0] = lower[0]*itkOutImage->GetSpacing()[0]; t[1] = lower[1]*itkOutImage->GetSpacing()[1]; t[2] = lower[2]*itkOutImage->GetSpacing()[2]; t= dir*t; origin[0] += t[0]; origin[1] += t[1]; origin[2] += t[2]; itkOutImage->SetOrigin(origin); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( itkOutImage.GetPointer() ); image->SetVolume( itkOutImage->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_cropped").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoUpdateInterpolationGui(int i) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } switch (i) { case 0: { m_Controls->m_ResampleIntFrame->setVisible(false); m_Controls->m_ResampleDoubleFrame->setVisible(true); break; } case 1: { m_Controls->m_ResampleIntFrame->setVisible(false); m_Controls->m_ResampleDoubleFrame->setVisible(true); mitk::BaseGeometry* geom = image->GetGeometry(); m_Controls->m_ResampleDoubleX->setValue(geom->GetSpacing()[0]); m_Controls->m_ResampleDoubleY->setValue(geom->GetSpacing()[1]); m_Controls->m_ResampleDoubleZ->setValue(geom->GetSpacing()[2]); break; } case 2: { m_Controls->m_ResampleIntFrame->setVisible(true); m_Controls->m_ResampleDoubleFrame->setVisible(false); mitk::BaseGeometry* geom = image->GetGeometry(); m_Controls->m_ResampleIntX->setValue(geom->GetExtent(0)); m_Controls->m_ResampleIntY->setValue(geom->GetExtent(1)); m_Controls->m_ResampleIntZ->setValue(geom->GetExtent(2)); break; } default: { m_Controls->m_ResampleIntFrame->setVisible(false); m_Controls->m_ResampleDoubleFrame->setVisible(true); } } } void QmitkPreprocessingView::DoExtractBrainMask() { } void QmitkPreprocessingView::DoResampleImage() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( isDiffusionImage ) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); typedef itk::ResampleDwiImageFilter< short > ResampleFilter; ResampleFilter::Pointer resampler = ResampleFilter::New(); resampler->SetInput( itkVectorImagePointer ); switch (m_Controls->m_ResampleTypeBox->currentIndex()) { case 0: { itk::Vector< double, 3 > samplingFactor; samplingFactor[0] = m_Controls->m_ResampleDoubleX->value(); samplingFactor[1] = m_Controls->m_ResampleDoubleY->value(); samplingFactor[2] = m_Controls->m_ResampleDoubleZ->value(); resampler->SetSamplingFactor(samplingFactor); break; } case 1: { itk::Vector< double, 3 > newSpacing; newSpacing[0] = m_Controls->m_ResampleDoubleX->value(); newSpacing[1] = m_Controls->m_ResampleDoubleY->value(); newSpacing[2] = m_Controls->m_ResampleDoubleZ->value(); resampler->SetNewSpacing(newSpacing); break; } case 2: { itk::ImageRegion<3> newRegion; newRegion.SetSize(0, m_Controls->m_ResampleIntX->value()); newRegion.SetSize(1, m_Controls->m_ResampleIntY->value()); newRegion.SetSize(2, m_Controls->m_ResampleIntZ->value()); resampler->SetNewImageSize(newRegion); break; } default: { MITK_WARN << "Unknown resampling parameters!"; return; } } QString outAdd; switch (m_Controls->m_InterpolatorBox->currentIndex()) { case 0: { resampler->SetInterpolation(ResampleFilter::Interpolate_NearestNeighbour); outAdd = "NearestNeighbour"; break; } case 1: { resampler->SetInterpolation(ResampleFilter::Interpolate_Linear); outAdd = "Linear"; break; } case 2: { resampler->SetInterpolation(ResampleFilter::Interpolate_BSpline); outAdd = "BSpline"; break; } case 3: { resampler->SetInterpolation(ResampleFilter::Interpolate_WindowedSinc); outAdd = "WindowedSinc"; break; } default: { resampler->SetInterpolation(ResampleFilter::Interpolate_NearestNeighbour); outAdd = "NearestNeighbour"; } } resampler->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( resampler->GetOutput() ); PropHelper::CopyProperties(image, newImage, false); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_resampled_"+outAdd).toStdString().c_str()); imageNode->SetVisibility(false); GetDataStorage()->Add(imageNode, node); } else if( image->GetPixelType().GetNumberOfComponents() ) { AccessFixedDimensionByItk(image, TemplatedResampleImage,3); } else { QMessageBox::warning(nullptr,"Warning", QString("Operation not supported in multi-component images") ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkPreprocessingView::TemplatedResampleImage( itk::Image* itkImage) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } itk::Vector< double, 3 > newSpacing; itk::ImageRegion<3> newRegion; switch (m_Controls->m_ResampleTypeBox->currentIndex()) { case 0: { itk::Vector< double, 3 > sampling; sampling[0] = m_Controls->m_ResampleDoubleX->value(); sampling[1] = m_Controls->m_ResampleDoubleY->value(); sampling[2] = m_Controls->m_ResampleDoubleZ->value(); newSpacing = itkImage->GetSpacing(); newSpacing[0] /= sampling[0]; newSpacing[1] /= sampling[1]; newSpacing[2] /= sampling[2]; newRegion = itkImage->GetLargestPossibleRegion(); newRegion.SetSize(0, newRegion.GetSize(0)*sampling[0]); newRegion.SetSize(1, newRegion.GetSize(1)*sampling[1]); newRegion.SetSize(2, newRegion.GetSize(2)*sampling[2]); break; } case 1: { newSpacing[0] = m_Controls->m_ResampleDoubleX->value(); newSpacing[1] = m_Controls->m_ResampleDoubleY->value(); newSpacing[2] = m_Controls->m_ResampleDoubleZ->value(); itk::Vector< double, 3 > oldSpacing = itkImage->GetSpacing(); itk::Vector< double, 3 > sampling; sampling[0] = oldSpacing[0]/newSpacing[0]; sampling[1] = oldSpacing[1]/newSpacing[1]; sampling[2] = oldSpacing[2]/newSpacing[2]; newRegion = itkImage->GetLargestPossibleRegion(); newRegion.SetSize(0, newRegion.GetSize(0)*sampling[0]); newRegion.SetSize(1, newRegion.GetSize(1)*sampling[1]); newRegion.SetSize(2, newRegion.GetSize(2)*sampling[2]); break; } case 2: { newRegion.SetSize(0, m_Controls->m_ResampleIntX->value()); newRegion.SetSize(1, m_Controls->m_ResampleIntY->value()); newRegion.SetSize(2, m_Controls->m_ResampleIntZ->value()); itk::ImageRegion<3> oldRegion = itkImage->GetLargestPossibleRegion(); itk::Vector< double, 3 > sampling; sampling[0] = (double)newRegion.GetSize(0)/oldRegion.GetSize(0); sampling[1] = (double)newRegion.GetSize(1)/oldRegion.GetSize(1); sampling[2] = (double)newRegion.GetSize(2)/oldRegion.GetSize(2); newSpacing = itkImage->GetSpacing(); newSpacing[0] /= sampling[0]; newSpacing[1] /= sampling[1]; newSpacing[2] /= sampling[2]; break; } default: { MITK_WARN << "Unknown resampling parameters!"; return; } } itk::Point origin = itkImage->GetOrigin(); origin[0] -= itkImage->GetSpacing()[0]/2; origin[1] -= itkImage->GetSpacing()[1]/2; origin[2] -= itkImage->GetSpacing()[2]/2; origin[0] += newSpacing[0]/2; origin[1] += newSpacing[1]/2; origin[2] += newSpacing[2]/2; typedef itk::Image ImageType; typename ImageType::Pointer outImage = ImageType::New(); outImage->SetSpacing( newSpacing ); outImage->SetOrigin( origin ); outImage->SetDirection( itkImage->GetDirection() ); outImage->SetLargestPossibleRegion( newRegion ); outImage->SetBufferedRegion( newRegion ); outImage->SetRequestedRegion( newRegion ); outImage->Allocate(); typedef itk::ResampleImageFilter ResampleFilter; typename ResampleFilter::Pointer resampler = ResampleFilter::New(); resampler->SetInput(itkImage); resampler->SetOutputParametersFromImage(outImage); QString outAdd; switch (m_Controls->m_InterpolatorBox->currentIndex()) { case 0: { typename itk::NearestNeighborInterpolateImageFunction::Pointer interp = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "NearestNeighbour"; break; } case 1: { typename itk::LinearInterpolateImageFunction::Pointer interp = itk::LinearInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "Linear"; break; } case 2: { typename itk::BSplineInterpolateImageFunction::Pointer interp = itk::BSplineInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "BSpline"; break; } case 3: { typename itk::WindowedSincInterpolateImageFunction::Pointer interp = itk::WindowedSincInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "WindowedSinc"; break; } default: { typename itk::NearestNeighborInterpolateImageFunction::Pointer interp = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(interp); outAdd = "NearestNeighbour"; } } resampler->Update(); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( resampler->GetOutput() ); image->SetVolume( resampler->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( image ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_resampled_"+outAdd).toStdString().c_str()); GetDataStorage()->Add(imageNode, node); } void QmitkPreprocessingView::DoApplyHeader() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); bool isDti = false; bool isOdf = false; bool isPeak = false; if (!isDiffusionImage) { if ( dynamic_cast(node->GetData()) ) isDti = true; else if ( dynamic_cast(node->GetData()) ) isOdf = true; else if ( dynamic_cast(node->GetData()) ) isPeak = true; } mitk::Image::Pointer newImage = image->Clone(); mitk::Vector3D spacing; spacing[0] = m_Controls->m_HeaderSpacingX->value(); spacing[1] = m_Controls->m_HeaderSpacingY->value(); spacing[2] = m_Controls->m_HeaderSpacingZ->value(); newImage->GetGeometry()->SetSpacing( spacing ); mitk::Point3D origin; origin[0] = m_Controls->m_HeaderOriginX->value(); origin[1] = m_Controls->m_HeaderOriginY->value(); origin[2] = m_Controls->m_HeaderOriginZ->value(); newImage->GetGeometry()->SetOrigin(origin); vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New(); matrix->SetElement(0,3,newImage->GetGeometry()->GetOrigin()[0]); matrix->SetElement(1,3,newImage->GetGeometry()->GetOrigin()[1]); matrix->SetElement(2,3,newImage->GetGeometry()->GetOrigin()[2]); for (int r=0; r<3; r++) { for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item(r,c); if (!item) continue; matrix->SetElement(r,c,item->text().toDouble()); } } newImage->GetGeometry()->SetIndexToWorldTransformByVtkMatrixWithoutChangingSpacing(matrix); if ( isDiffusionImage ) { vnl_matrix_fixed< double, 3, 3 > mf; for (int r=0; r<3; r++) { for (int c=0; c<3; c++) { QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item(r,c); if (!item) continue; mf[r][c] = item->text().toDouble(); } } newImage->GetPropertyList()->ReplaceProperty( PropHelper::MEASUREMENTFRAMEPROPERTYNAME.c_str(), mitk::MeasurementFrameProperty::New( mf ) ); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); } mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); if (isOdf) { mitk::OdfImage::ItkOdfImageType::Pointer itk_img = mitk::OdfImage::ItkOdfImageType::New(); mitk::CastToItkImage(newImage, itk_img); mitk::Image::Pointer odfImage = dynamic_cast(mitk::OdfImage::New().GetPointer()); mitk::CastToMitkImage(itk_img, odfImage); odfImage->SetVolume(itk_img->GetBufferPointer()); imageNode->SetData( odfImage ); } else if (isDti) { mitk::TensorImage::ItkTensorImageType::Pointer itk_img = mitk::ImageToItkImage(newImage); mitk::Image::Pointer tensorImage = dynamic_cast(mitk::TensorImage::New().GetPointer()); mitk::CastToMitkImage(itk_img, tensorImage); tensorImage->SetVolume(itk_img->GetBufferPointer()); imageNode->SetData( tensorImage ); } else if (isPeak) { mitk::PeakImage::ItkPeakImageType::Pointer itk_img = mitk::ImageToItkImage(newImage); mitk::Image::Pointer peakImage = dynamic_cast(mitk::PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_img, peakImage); peakImage->SetVolume(itk_img->GetBufferPointer()); imageNode->SetData( peakImage ); } else imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_newheader").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); mitk::RenderingManager::GetInstance()->InitializeViews( imageNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkPreprocessingView::DoProjectSignal() { switch(m_Controls->m_ProjectionMethodBox->currentIndex()) { case 0: DoADCAverage(); break; case 1: DoAKCFit(); break; case 2: DoBiExpFit(); break; default: DoADCAverage(); } } void QmitkPreprocessingView::DoDwiNormalization() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) { return; } GradientDirectionContainerType::Pointer gradientContainer = static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); int b0Index = -1; for (unsigned int i=0; isize(); i++) { GradientDirectionType g = gradientContainer->GetElement(i); if (g.magnitude()<0.001) { b0Index = i; break; } } if (b0Index==-1) { return; } typedef itk::DwiNormilzationFilter FilterType; ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkVectorImagePointer ); filter->SetGradientDirections( static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); filter->SetNewMean(m_Controls->m_NewMean->value()); filter->SetNewStdev(m_Controls->m_NewStdev->value()); UcharImageType::Pointer itkImage = nullptr; if (m_Controls->m_NormalizationMaskBox->GetSelectedNode().IsNotNull()) { itkImage = UcharImageType::New(); if ( dynamic_cast(m_Controls->m_NormalizationMaskBox->GetSelectedNode()->GetData()) != nullptr ) { mitk::CastToItkImage( dynamic_cast(m_Controls->m_NormalizationMaskBox->GetSelectedNode()->GetData()), itkImage ); } filter->SetMaskImage(itkImage); } filter->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::CopyProperties(image, newImage, false); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_normalized").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); } void QmitkPreprocessingView::DoLengthCorrection() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) { return; } typedef itk::DwiGradientLengthCorrectionFilter FilterType; ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); FilterType::Pointer filter = FilterType::New(); filter->SetRoundingValue( m_Controls->m_B_ValueMap_Rounder_SpinBox->value()); filter->SetReferenceBValue( static_cast (image->GetProperty(PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); filter->SetReferenceGradientDirectionContainer( static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); filter->Update(); mitk::Image::Pointer newImage = mitk::Image::New(); newImage->InitializeByItk( itkVectorImagePointer.GetPointer() ); newImage->SetImportVolume( itkVectorImagePointer->GetBufferPointer(), 0, 0, mitk::Image::CopyMemory); itkVectorImagePointer->GetPixelContainer()->ContainerManageMemoryOff(); PropHelper::CopyProperties(image, newImage, true); newImage->GetPropertyList()->ReplaceProperty( PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( filter->GetOutputGradientDirectionContainer() ) ); newImage->GetPropertyList()->ReplaceProperty( PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( filter->GetNewBValue() ) ); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_rounded").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); } void QmitkPreprocessingView::UpdateDwiBValueMapRounder(int i) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(node) ); if ( ! isDiffusionImage ) { return; } UpdateBValueTableWidget(i); } void QmitkPreprocessingView:: CallMultishellToSingleShellFilter( itk::DWIVoxelFunctor * functor, mitk::Image::Pointer image, QString imageName, mitk::DataNode* parent ) { typedef itk::RadialMultishellToSingleshellImageFilter FilterType; // filter input parameter const mitk::BValueMapProperty::BValueMap& originalShellMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); ItkDwiType* vectorImage = itkVectorImagePointer.GetPointer(); const GradProp::GradientDirectionsContainerType::Pointer gradientContainer = static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); const unsigned int& bValue = static_cast (image->GetProperty(PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue(); mitk::DataNode::Pointer imageNode = 0; // filter call FilterType::Pointer filter = FilterType::New(); filter->SetInput(vectorImage); filter->SetOriginalGradientDirections(gradientContainer); filter->SetOriginalBValueMap(originalShellMap); filter->SetOriginalBValue(bValue); filter->SetFunctor(functor); filter->Update(); // create new DWI image mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::CopyProperties(image, outImage, true); outImage->GetPropertyList()->ReplaceProperty( PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( filter->GetTargetGradientDirections() ) ); outImage->GetPropertyList()->ReplaceProperty( PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( m_Controls->m_targetBValueSpinBox->value() ) ); PropHelper propertyHelper( outImage ); propertyHelper.InitializeImage(); imageNode = mitk::DataNode::New(); imageNode->SetData( outImage ); imageNode->SetName(imageName.toStdString().c_str()); GetDataStorage()->Add(imageNode, parent); // if(m_Controls->m_OutputRMSErrorImage->isChecked()){ // // create new Error image // FilterType::ErrorImageType::Pointer errImage = filter->GetErrorImage(); // mitk::Image::Pointer mitkErrImage = mitk::Image::New(); // mitkErrImage->InitializeByItk(errImage); // mitkErrImage->SetVolume(errImage->GetBufferPointer()); // imageNode = mitk::DataNode::New(); // imageNode->SetData( mitkErrImage ); // imageNode->SetName((imageName+"_Error").toStdString().c_str()); // GetDataStorage()->Add(imageNode); // } } void QmitkPreprocessingView::DoBiExpFit() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) { return; } itk::BiExpFitFunctor::Pointer functor = itk::BiExpFitFunctor::New(); QString name(node->GetName().c_str()); const mitk::BValueMapProperty::BValueMap& originalShellMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); mitk::BValueMapProperty::BValueMap::const_iterator it = originalShellMap.begin(); ++it;/* skip b=0*/ unsigned int s = 0; /*shell index */ vnl_vector bValueList(originalShellMap.size()-1); while( it != originalShellMap.end() ) { bValueList.put(s++,(it++)->first); } const double targetBValue = m_Controls->m_targetBValueSpinBox->value(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); CallMultishellToSingleShellFilter(functor,image,name + "_BiExp", node); } void QmitkPreprocessingView::DoAKCFit() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) { return; } itk::KurtosisFitFunctor::Pointer functor = itk::KurtosisFitFunctor::New(); QString name(node->GetName().c_str()); const mitk::BValueMapProperty::BValueMap& originalShellMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); mitk::BValueMapProperty::BValueMap::const_iterator it = originalShellMap.begin(); ++it;/* skip b=0*/ unsigned int s = 0; /*shell index */ vnl_vector bValueList(originalShellMap.size()-1); while(it != originalShellMap.end()) bValueList.put(s++,(it++)->first); const double targetBValue = m_Controls->m_targetBValueSpinBox->value(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); CallMultishellToSingleShellFilter(functor,image,name + "_AKC", node); } void QmitkPreprocessingView::DoADCFit() { // later } void QmitkPreprocessingView::DoADCAverage() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( ! isDiffusionImage ) return; itk::ADCAverageFunctor::Pointer functor = itk::ADCAverageFunctor::New(); QString name(node->GetName().c_str()); const mitk::BValueMapProperty::BValueMap &originalShellMap = static_cast(image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() )->GetBValueMap(); mitk::BValueMapProperty::BValueMap::const_iterator it = originalShellMap.begin(); ++it;/* skip b=0*/ unsigned int s = 0; /*shell index */ vnl_vector bValueList(originalShellMap.size()-1); while(it != originalShellMap.end()) bValueList.put(s++,(it++)->first); const double targetBValue = m_Controls->m_targetBValueSpinBox->value(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); CallMultishellToSingleShellFilter(functor,image,name + "_ADC", node); } void QmitkPreprocessingView::CleanBValueTableWidget() { m_Controls->m_B_ValueMap_TableWidget->clear(); m_Controls->m_B_ValueMap_TableWidget->setRowCount(1); QStringList headerList; headerList << "b-Value" << "Number of gradients"; m_Controls->m_B_ValueMap_TableWidget->setHorizontalHeaderLabels(headerList); m_Controls->m_B_ValueMap_TableWidget->setItem(0,0,new QTableWidgetItem("-")); m_Controls->m_B_ValueMap_TableWidget->setItem(0,1,new QTableWidgetItem("-")); } void QmitkPreprocessingView::UpdateBValueTableWidget(int) { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { CleanBValueTableWidget(); return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage(false); isDiffusionImage = PropHelper::IsDiffusionWeightedImage(image); if ( ! isDiffusionImage ) { CleanBValueTableWidget(); } else { typedef mitk::BValueMapProperty::BValueMap BValueMap; typedef mitk::BValueMapProperty::BValueMap::iterator BValueMapIterator; BValueMapIterator it; BValueMap roundedBValueMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); m_Controls->m_B_ValueMap_TableWidget->clear(); m_Controls->m_B_ValueMap_TableWidget->setRowCount(roundedBValueMap.size() ); QStringList headerList; headerList << "b-Value" << "Number of gradients"; m_Controls->m_B_ValueMap_TableWidget->setHorizontalHeaderLabels(headerList); int i = 0 ; for(it = roundedBValueMap.begin() ;it != roundedBValueMap.end(); it++) { m_Controls->m_B_ValueMap_TableWidget->setItem(i,0,new QTableWidgetItem(QString::number(it->first))); QTableWidgetItem* item = m_Controls->m_B_ValueMap_TableWidget->item(i,0); item->setFlags(item->flags() & ~Qt::ItemIsEditable); m_Controls->m_B_ValueMap_TableWidget->setItem(i,1,new QTableWidgetItem(QString::number(it->second.size()))); i++; } } } void QmitkPreprocessingView::OnSelectionChanged(berry::IWorkbenchPart::Pointer , const QList& nodes) { (void) nodes; this->OnImageSelectionChanged(); } void QmitkPreprocessingView::OnImageSelectionChanged() { for (int r=0; r<3; r++) for (int c=0; c<3; c++) { { QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item( r, c ); delete item; item = new QTableWidgetItem(); m_Controls->m_MeasurementFrameTable->setItem( r, c, item ); } { QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item( r, c ); delete item; item = new QTableWidgetItem(); m_Controls->m_DirectionMatrixTable->setItem( r, c, item ); } } bool foundImageVolume = true; mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } bool foundDwiVolume( PropHelper::IsDiffusionWeightedImage( node ) ); mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool multiComponentVolume = (image->GetPixelType().GetNumberOfComponents() > 1); bool threeDplusTVolume = (image->GetTimeSteps() > 1); m_Controls->m_ButtonAverageGradients->setEnabled(foundDwiVolume); m_Controls->m_ButtonExtractB0->setEnabled(foundDwiVolume); m_Controls->m_CheckExtractAll->setEnabled(foundDwiVolume); m_Controls->m_MeasurementFrameTable->setEnabled(foundDwiVolume); m_Controls->m_ReduceGradientsButton->setEnabled(foundDwiVolume); m_Controls->m_ShowGradientsButton->setEnabled(foundDwiVolume); m_Controls->m_MirrorGradientToHalfSphereButton->setEnabled(foundDwiVolume); m_Controls->m_MergeDwisButton->setEnabled(foundDwiVolume); m_Controls->m_B_ValueMap_Rounder_SpinBox->setEnabled(foundDwiVolume); m_Controls->m_ProjectSignalButton->setEnabled(foundDwiVolume); m_Controls->m_CreateLengthCorrectedDwi->setEnabled(foundDwiVolume); m_Controls->m_targetBValueSpinBox->setEnabled(foundDwiVolume); m_Controls->m_NormalizeImageValuesButton->setEnabled(foundDwiVolume); m_Controls->m_RemoveGradientButton->setEnabled(foundDwiVolume); m_Controls->m_ExtractGradientButton->setEnabled(foundDwiVolume); m_Controls->m_FlipGradientsButton->setEnabled(foundDwiVolume); m_Controls->m_ClearRotationButton->setEnabled(foundDwiVolume); m_Controls->m_DirectionMatrixTable->setEnabled(foundImageVolume); m_Controls->m_ModifyHeader->setEnabled(foundImageVolume); m_Controls->m_AlignImageBox->setEnabled(foundImageVolume); // we do not support multi-component and 3D+t images for certain operations bool foundSingleImageVolume = foundDwiVolume || (foundImageVolume && !(multiComponentVolume || threeDplusTVolume)); m_Controls->m_FlipAxis->setEnabled(foundSingleImageVolume); m_Controls->m_CropImageButton->setEnabled(foundSingleImageVolume); m_Controls->m_ExtractBrainMask->setEnabled(foundSingleImageVolume); m_Controls->m_ResampleImageButton->setEnabled(foundSingleImageVolume); // reset sampling frame to 1 and update all ealted components m_Controls->m_B_ValueMap_Rounder_SpinBox->setValue(1); UpdateBValueTableWidget(m_Controls->m_B_ValueMap_Rounder_SpinBox->value()); DoUpdateInterpolationGui(m_Controls->m_ResampleTypeBox->currentIndex()); m_Controls->m_HeaderSpacingX->setValue(image->GetGeometry()->GetSpacing()[0]); m_Controls->m_HeaderSpacingY->setValue(image->GetGeometry()->GetSpacing()[1]); m_Controls->m_HeaderSpacingZ->setValue(image->GetGeometry()->GetSpacing()[2]); m_Controls->m_HeaderOriginX->setValue(image->GetGeometry()->GetOrigin()[0]); m_Controls->m_HeaderOriginY->setValue(image->GetGeometry()->GetOrigin()[1]); m_Controls->m_HeaderOriginZ->setValue(image->GetGeometry()->GetOrigin()[2]); m_Controls->m_XstartBox->setMaximum(image->GetGeometry()->GetExtent(0)-1); m_Controls->m_YstartBox->setMaximum(image->GetGeometry()->GetExtent(1)-1); m_Controls->m_ZstartBox->setMaximum(image->GetGeometry()->GetExtent(2)-1); m_Controls->m_XendBox->setMaximum(image->GetGeometry()->GetExtent(0)-1); m_Controls->m_YendBox->setMaximum(image->GetGeometry()->GetExtent(1)-1); m_Controls->m_ZendBox->setMaximum(image->GetGeometry()->GetExtent(2)-1); for (int r=0; r<3; r++) for (int c=0; c<3; c++) { // Direction matrix QTableWidgetItem* item = m_Controls->m_DirectionMatrixTable->item( r, c ); delete item; item = new QTableWidgetItem(); item->setTextAlignment(Qt::AlignCenter | Qt::AlignVCenter); double val = image->GetGeometry()->GetVtkMatrix()->GetElement(r,c)/image->GetGeometry()->GetSpacing()[c]; item->setText(QString::number(val)); m_Controls->m_DirectionMatrixTable->setItem( r, c, item ); } if (foundDwiVolume) { m_Controls->m_InputData->setTitle("Input Data"); vnl_matrix_fixed< double, 3, 3 > mf = static_cast (image->GetProperty(PropHelper::MEASUREMENTFRAMEPROPERTYNAME.c_str()).GetPointer() ) ->GetMeasurementFrame(); for (int r=0; r<3; r++) for (int c=0; c<3; c++) { // Measurement frame QTableWidgetItem* item = m_Controls->m_MeasurementFrameTable->item( r, c ); delete item; item = new QTableWidgetItem(); item->setTextAlignment(Qt::AlignCenter | Qt::AlignVCenter); item->setText(QString::number(mf.get(r,c))); m_Controls->m_MeasurementFrameTable->setItem( r, c, item ); } //calculate target bValue for MultishellToSingleShellfilter const mitk::BValueMapProperty::BValueMap & bValMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); mitk::BValueMapProperty::BValueMap::const_iterator it = bValMap.begin(); unsigned int targetBVal = 0; while(it != bValMap.end()) { targetBVal += (it++)->first; } targetBVal /= (float)bValMap.size()-1; m_Controls->m_targetBValueSpinBox->setValue(targetBVal); m_Controls->m_RemoveGradientBox->setMaximum(static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer()->Size()-1); m_Controls->m_ExtractGradientBox->setMaximum(static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer()->Size()-1); } } void QmitkPreprocessingView::Activated() { } void QmitkPreprocessingView::Deactivated() { OnImageSelectionChanged(); } void QmitkPreprocessingView::Visible() { OnImageSelectionChanged(); } void QmitkPreprocessingView::Hidden() { } void QmitkPreprocessingView::DoClearRotationOfGradients() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) return; mitk::Image::Pointer image = dynamic_cast(node->GetData()); if (image == nullptr) return; if(!PropHelper::IsDiffusionWeightedImage(image)) return; mitk::Image::Pointer newDwi = image->Clone(); PropHelper propertyHelper( newDwi ); propertyHelper.InitializeImage(); PropHelper::ClearMeasurementFrameAndRotationMatrixFromGradients(newDwi); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = node->GetName().c_str(); imageNode->SetName( (name+"_OriginalGradients").toStdString().c_str() ); GetDataStorage()->Add( imageNode, node ); } void QmitkPreprocessingView::DoFlipGradientDirections() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } mitk::Image::Pointer newDwi = image->Clone(); GradientDirectionContainerType::Pointer gradientContainer = static_cast ( newDwi->GetProperty(PropHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); for (unsigned int j=0; jSize(); j++) { if (m_Controls->m_FlipGradBoxX->isChecked()) { gradientContainer->at(j)[0] *= -1; } if (m_Controls->m_FlipGradBoxY->isChecked()) { gradientContainer->at(j)[1] *= -1; } if (m_Controls->m_FlipGradBoxZ->isChecked()) { gradientContainer->at(j)[2] *= -1; } } PropHelper::CopyProperties(image, newDwi, true); newDwi->GetPropertyList()->ReplaceProperty( PropHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( gradientContainer ) ); PropHelper propertyHelper( newDwi ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = node->GetName().c_str(); imageNode->SetName( (name+"_GradientFlip").toStdString().c_str() ); GetDataStorage()->Add( imageNode, node ); } void QmitkPreprocessingView::DoHalfSphereGradientDirections() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } mitk::Image::Pointer newDwi = image->Clone(); GradientDirectionContainerType::Pointer gradientContainer = static_cast ( newDwi->GetProperty(PropHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); for (unsigned int j=0; jSize(); j++) { if (gradientContainer->at(j)[0]<0) { gradientContainer->at(j) = -gradientContainer->at(j); } } PropHelper::CopyProperties(image, newDwi, true); newDwi->GetPropertyList()->ReplaceProperty( PropHelper::ORIGINALGRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( gradientContainer ) ); PropHelper propertyHelper( newDwi ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = node->GetName().c_str(); imageNode->SetName( (name+"_halfsphere").toStdString().c_str() ); GetDataStorage()->Add( imageNode, node ); } void QmitkPreprocessingView::DoShowGradientDirections() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } int maxIndex = 0; unsigned int maxSize = image->GetDimension(0); if (maxSizeGetDimension(1)) { maxSize = image->GetDimension(1); maxIndex = 1; } if (maxSizeGetDimension(2)) { maxSize = image->GetDimension(2); maxIndex = 2; } mitk::Point3D origin = image->GetGeometry()->GetOrigin(); mitk::PointSet::Pointer originSet = mitk::PointSet::New(); typedef mitk::BValueMapProperty::BValueMap BValueMap; typedef mitk::BValueMapProperty::BValueMap::iterator BValueMapIterator; BValueMap bValMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); GradientDirectionContainerType::Pointer gradientContainer = static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); mitk::BaseGeometry::Pointer geometry = image->GetGeometry(); int shellCount = 1; for(BValueMapIterator it = bValMap.begin(); it!=bValMap.end(); ++it) { mitk::PointSet::Pointer pointset = mitk::PointSet::New(); for (unsigned int j=0; jsecond.size(); j++) { mitk::Point3D ip; vnl_vector_fixed< double, 3 > v = gradientContainer->at(it->second[j]); if (v.magnitude()>mitk::eps) { ip[0] = v[0]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[0]-0.5*geometry->GetSpacing()[0] + geometry->GetSpacing()[0]*image->GetDimension(0)/2; ip[1] = v[1]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[1]-0.5*geometry->GetSpacing()[1] + geometry->GetSpacing()[1]*image->GetDimension(1)/2; ip[2] = v[2]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[2]-0.5*geometry->GetSpacing()[2] + geometry->GetSpacing()[2]*image->GetDimension(2)/2; pointset->InsertPoint(j, ip); } else if (originSet->IsEmpty()) { ip[0] = v[0]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[0]-0.5*geometry->GetSpacing()[0] + geometry->GetSpacing()[0]*image->GetDimension(0)/2; ip[1] = v[1]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[1]-0.5*geometry->GetSpacing()[1] + geometry->GetSpacing()[1]*image->GetDimension(1)/2; ip[2] = v[2]*maxSize*geometry->GetSpacing()[maxIndex]/2 + origin[2]-0.5*geometry->GetSpacing()[2] + geometry->GetSpacing()[2]*image->GetDimension(2)/2; originSet->InsertPoint(j, ip); } } if ( it->first < mitk::eps ) { continue; } // add shell to datastorage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pointset); QString name = node->GetName().c_str(); name += "_Shell_"; name += QString::number( it->first ); newNode->SetName( name.toStdString().c_str() ); newNode->SetProperty( "pointsize", mitk::FloatProperty::New((float)maxSize / 50) ); int b0 = shellCount % 2; int b1 = 0; int b2 = 0; if (shellCount>4) { b2 = 1; } if (shellCount%4 >= 2) { b1 = 1; } newNode->SetProperty("color", mitk::ColorProperty::New( b2, b1, b0 )); GetDataStorage()->Add( newNode, node ); shellCount++; } // add origin to datastorage mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(originSet); QString name = node->GetName().c_str(); name += "_Origin"; newNode->SetName(name.toStdString().c_str()); newNode->SetProperty("pointsize", mitk::FloatProperty::New((float)maxSize/50)); newNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); GetDataStorage()->Add(newNode, node); } void QmitkPreprocessingView::DoReduceGradientDirections() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } typedef itk::ElectrostaticRepulsionDiffusionGradientReductionFilter FilterType; typedef mitk::BValueMapProperty::BValueMap BValueMap; // GetShellSelection from GUI BValueMap shellSlectionMap; BValueMap originalShellMap = static_cast (image->GetProperty(PropHelper::BVALUEMAPPROPERTYNAME.c_str()).GetPointer() ) ->GetBValueMap(); std::vector newNumGradientDirections; int shellCounter = 0; QString name = node->GetName().c_str(); for (int i=0; im_B_ValueMap_TableWidget->rowCount(); i++) { double BValue = m_Controls->m_B_ValueMap_TableWidget->item(i,0)->text().toDouble(); shellSlectionMap[BValue] = originalShellMap[BValue]; unsigned int num = m_Controls->m_B_ValueMap_TableWidget->item(i,1)->text().toUInt(); newNumGradientDirections.push_back(num); name += "_"; name += QString::number(num); shellCounter++; } if (newNumGradientDirections.empty()) { return; } GradientDirectionContainerType::Pointer gradientContainer = static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkVectorImagePointer ); filter->SetOriginalGradientDirections(gradientContainer); filter->SetNumGradientDirections(newNumGradientDirections); filter->SetOriginalBValueMap(originalShellMap); filter->SetShellSelectionBValueMap(shellSlectionMap); filter->Update(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() ); PropHelper::CopyProperties(image, newImage, true); newImage->GetPropertyList()->ReplaceProperty( PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( filter->GetGradientDirections() ) ); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); imageNode->SetName(name.toStdString().c_str()); GetDataStorage()->Add(imageNode, node); // update the b-value widget to remove the modified number of gradients used for extraction this->CleanBValueTableWidget(); this->UpdateBValueTableWidget(0); } void QmitkPreprocessingView::MergeDwis() { typedef GradProp::GradientDirectionsContainerType GradientContainerType; mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } mitk::DataNode::Pointer node2 = m_Controls->m_MergeDwiBox->GetSelectedNode(); if (node2.IsNull()) { return; } mitk::Image::Pointer image2 = dynamic_cast(node2->GetData()); if ( image2 == nullptr ) { return; } typedef itk::VectorImage DwiImageType; typedef std::vector< DwiImageType::Pointer > DwiImageContainerType; typedef std::vector< GradientContainerType::Pointer > GradientListContainerType; DwiImageContainerType imageContainer; GradientListContainerType gradientListContainer; std::vector< double > bValueContainer; QString name = ""; { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); imageContainer.push_back( itkVectorImagePointer ); gradientListContainer.push_back( static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); bValueContainer.push_back( static_cast (image->GetProperty(PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); name += node->GetName().c_str(); } { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image2, itkVectorImagePointer); imageContainer.push_back( itkVectorImagePointer ); gradientListContainer.push_back( static_cast ( image2->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); bValueContainer.push_back( static_cast (image2->GetProperty(PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); name += "+"; name += node2->GetName().c_str(); } typedef itk::MergeDiffusionImagesFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetImageVolumes(imageContainer); filter->SetGradientLists(gradientListContainer); filter->SetBValues(bValueContainer); filter->Update(); vnl_matrix_fixed< double, 3, 3 > mf; mf.set_identity(); mitk::Image::Pointer newImage = mitk::GrabItkImageMemory( filter->GetOutput() ); newImage->GetPropertyList()->ReplaceProperty( PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), GradProp::New( filter->GetOutputGradients() ) ); newImage->GetPropertyList()->ReplaceProperty( PropHelper::MEASUREMENTFRAMEPROPERTYNAME.c_str(), mitk::MeasurementFrameProperty::New( mf ) ); newImage->GetPropertyList()->ReplaceProperty( PropHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( filter->GetB_Value() ) ); PropHelper propertyHelper( newImage ); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newImage ); imageNode->SetName(name.toStdString().c_str()); GetDataStorage()->Add(imageNode); } void QmitkPreprocessingView::ExtractB0() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } // call the extraction withou averaging if the check-box is checked if( this->m_Controls->m_CheckExtractAll->isChecked() ) { DoExtractBOWithoutAveraging(); return; } ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); // Extract image using found index typedef itk::B0ImageExtractionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkVectorImagePointer ); filter->SetDirections( static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); filter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( filter->GetOutput() ); mitkImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer newNode=mitk::DataNode::New(); newNode->SetData( mitkImage ); newNode->SetProperty( "name", mitk::StringProperty::New(node->GetName() + "_B0")); GetDataStorage()->Add(newNode, node); } void QmitkPreprocessingView::DoExtractBOWithoutAveraging() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) { return; } // typedefs typedef itk::B0ImageExtractionToSeparateImageFilter< short, short> FilterType; ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(image, itkVectorImagePointer); // Extract image using found index FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkVectorImagePointer ); filter->SetDirections( static_cast ( image->GetProperty(PropHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); filter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( filter->GetOutput() ); mitkImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer newNode=mitk::DataNode::New(); newNode->SetData( mitkImage ); newNode->SetProperty( "name", mitk::StringProperty::New(node->GetName() + "_B0_ALL")); GetDataStorage()->Add(newNode, node); /*A reinitialization is needed to access the time channels via the ImageNavigationController The Global-Geometry can not recognize the time channel without a re-init. (for a new selection in datamanger a automatically updated of the Global-Geometry should be done - if it contains the time channel)*/ mitk::RenderingManager::GetInstance()->InitializeViews( newNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); } void QmitkPreprocessingView::AverageGradients() { mitk::DataNode::Pointer node = m_Controls->m_SelctedImageComboBox->GetSelectedNode(); if (node.IsNull()) { return; } mitk::Image::Pointer image = dynamic_cast(node->GetData()); if ( image == nullptr ) { return; } bool isDiffusionImage( PropHelper::IsDiffusionWeightedImage(image) ); if ( !isDiffusionImage ) return; mitk::Image::Pointer newDwi = image->Clone(); PropHelper propertyHelper(newDwi); propertyHelper.AverageRedundantGradients(m_Controls->m_Blur->value()); propertyHelper.InitializeImage(); mitk::DataNode::Pointer imageNode = mitk::DataNode::New(); imageNode->SetData( newDwi ); QString name = node->GetName().c_str(); imageNode->SetName((name+"_averaged").toStdString().c_str()); GetDataStorage()->Add(imageNode, node); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt b/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt index a0feafa1d4..67809aa513 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/CMakeLists.txt @@ -1,14 +1,14 @@ if(MITK_USE_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( EXPORT_DIRECTIVE DIFFUSIONIMAGING_PREPROCESSING_EXPORT EXPORTED_INCLUDE_SUFFIXES src MODULE_DEPENDS MitkDiffusionCore MitkPython MitkQtPython - PACKAGE_DEPENDS Qt5|Network + PACKAGE_DEPENDS Qt5|Network BetData ) endif() diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.cpp index a0f5da805b..e527f6dcc7 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.cpp @@ -1,229 +1,218 @@ /*=================================================================== 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. ===================================================================*/ //misc #define _USE_MATH_DEFINES #include // Blueberry #include #include // Qmitk #include "QmitkBrainExtractionView.h" // MITK #include // Qt #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include -#define _USE_MATH_DEFINES -#include - - -FileDownloader::FileDownloader(QObject *parent) : QObject(parent) -{ - -} - -void FileDownloader::download(QUrl url) -{ - connect(&m_WebCtrl, SIGNAL (finished(QNetworkReply*)), SLOT (Downloaded(QNetworkReply*))); - - QNetworkRequest request(url); - m_WebCtrl.get(request); -} - -void FileDownloader::Downloaded(QNetworkReply *reply) -{ - MITK_INFO << "FileDownloader::Downloaded TESTTEST"; - QFile localFile("/home/neher/test_download.tar.gz"); - if (!localFile.open(QIODevice::WriteOnly)) - return; - localFile.write(reply->readAll()); - localFile.close(); - delete reply; +#include +#include +#include +#include +#include - QMessageBox::information(nullptr, "FILE DOWNLOADED", "BLABL"); -} +#include -FileDownloader::~FileDownloader() -{ +#define _USE_MATH_DEFINES +#include -} +typedef itksys::SystemTools ist; const std::string QmitkBrainExtractionView::VIEW_ID = "org.mitk.views.brainextraction"; QmitkBrainExtractionView::QmitkBrainExtractionView() : QmitkAbstractView() , m_Controls( 0 ) , m_DiffusionImage( nullptr ) { } // Destructor QmitkBrainExtractionView::~QmitkBrainExtractionView() { } void QmitkBrainExtractionView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkBrainExtractionViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_ImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGUI()) ); connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(StartBrainExtraction()) ); this->m_Parent = parent; m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage()); mitk::NodePredicateDimension::Pointer dimPred = mitk::NodePredicateDimension::New(3); mitk::TNodePredicateDataType::Pointer isImagePredicate = mitk::TNodePredicateDataType::New(); -// m_Controls->m_ImageBox->SetPredicate(mitk::NodePredicateAnd::New(isImagePredicate,dimPred)); m_Controls->m_ImageBox->SetPredicate(isImagePredicate); UpdateGUI(); - - std::string module_library_full_path = us::GetModuleContext()->GetModule()->GetLocation(); - std::string library_file; - itksys::SystemTools::SplitProgramPath(module_library_full_path, m_ModulePath, library_file); - m_ModulePath += "/BET"; } } void QmitkBrainExtractionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList& ) { } void QmitkBrainExtractionView::UpdateGUI() { if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull()) m_Controls->m_StartButton->setEnabled(true); else m_Controls->m_StartButton->setEnabled(false); } void QmitkBrainExtractionView::SetFocus() { UpdateGUI(); m_Controls->m_StartButton->setFocus(); } -void QmitkBrainExtractionView::StartBrainExtraction() +std::string QmitkBrainExtractionView::GetPythonFile(std::string filename) { -// FileDownloader dl; -// dl.download(QUrl("http://mitk.org/download/releases/MITK-2012.06/MITK-2012.06.0-src.tar.gz")); + std::string out = ""; + std::string bet_dir = std::string(BetData_DIR); + + if ( ist::FileExists(bet_dir + filename) ) + out = bet_dir + filename; + else if ( ist::FileExists( ist::GetCurrentWorkingDirectory() + filename) ) + out = ist::GetCurrentWorkingDirectory() + filename; + else if ( ist::FileExists( ist::GetCurrentWorkingDirectory() + "BetData/" + filename) ) + out = ist::GetCurrentWorkingDirectory() + "BetData/" + filename; + + return out; +} + +void QmitkBrainExtractionView::StartBrainExtraction() +{ mitk::DataNode::Pointer node = m_Controls->m_ImageBox->GetSelectedNode(); mitk::Image::Pointer mitk_image = dynamic_cast(node->GetData()); bool missing_file = false; std::string missing_file_string = ""; - if ( !itksys::SystemTools::FileExists(m_ModulePath + "/brain_extraction_script.py") ) + if ( GetPythonFile("brain_extraction_script.py").empty() ) { - missing_file_string += "Brain extraction script file missing:\n" + m_ModulePath + "/brain_extraction_script.py\n\n"; + missing_file_string += "Brain extraction script file missing: brain_extraction_script.py\n\n"; missing_file = true; } - if ( !itksys::SystemTools::FileExists(m_ModulePath + "/brain_extraction_model.model") ) + if ( GetPythonFile("brain_extraction_model.model").empty() ) { - missing_file_string += "Brain extraction model file missing:\n" + m_ModulePath + "/brain_extraction_model.model\n\n"; + missing_file_string += "Brain extraction model file missing: brain_extraction_model.model\n\n"; missing_file = true; } - if ( !itksys::SystemTools::FileExists(m_ModulePath + "/basic_config_just_like_braintumor.py") ) + if ( GetPythonFile("basic_config_just_like_braintumor.py").empty() ) { - missing_file_string += "Config file missing:\n" + m_ModulePath + "/basic_config_just_like_braintumor.py\n\n"; + missing_file_string += "Config file missing: basic_config_just_like_braintumor.py\n\n"; missing_file = true; } if (missing_file) { QMessageBox::warning(nullptr, "Error", (missing_file_string).c_str(), QMessageBox::Ok); return; } try { us::ModuleContext* context = us::GetModuleContext(); us::ServiceReference m_PythonServiceRef = context->GetServiceReference(); mitk::IPythonService* m_PythonService = dynamic_cast ( context->GetService(m_PythonServiceRef) ); mitk::IPythonService::ForceLoadModule(); m_PythonService->Execute("import SimpleITK as sitk"); m_PythonService->Execute("import SimpleITK._SimpleITK as _SimpleITK"); m_PythonService->Execute("import numpy"); m_PythonService->CopyToPythonAsSimpleItkImage( mitk_image, "in_image"); - m_PythonService->Execute("model_file=\""+m_ModulePath+"/brain_extraction_model.model\""); - m_PythonService->Execute("config_file=\""+m_ModulePath+"/basic_config_just_like_braintumor.py\""); - m_PythonService->ExecuteScript(m_ModulePath + "/brain_extraction_script.py"); + m_PythonService->Execute("model_file=\""+GetPythonFile("brain_extraction_model.model")+"\""); + m_PythonService->Execute("config_file=\""+GetPythonFile("basic_config_just_like_braintumor.py")+"\""); + m_PythonService->ExecuteScript( GetPythonFile("brain_extraction_script.py") ); { mitk::Image::Pointer image = m_PythonService->CopySimpleItkImageFromPython("brain_mask"); mitk::DataNode::Pointer corrected_node = mitk::DataNode::New(); corrected_node->SetData( image ); QString name(node->GetName().c_str()); name += "_BrainMask"; corrected_node->SetName(name.toStdString()); GetDataStorage()->Add(corrected_node, node); } { mitk::Image::Pointer image = m_PythonService->CopySimpleItkImageFromPython("brain_extracted"); if(mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image)) { mitk::DiffusionPropertyHelper propertyHelper(image); mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, image, true); propertyHelper.InitializeImage(); } mitk::DataNode::Pointer corrected_node = mitk::DataNode::New(); corrected_node->SetData( image ); QString name(node->GetName().c_str()); name += "_SkullStripped"; corrected_node->SetName(name.toStdString()); GetDataStorage()->Add(corrected_node, node); + + mitk::RenderingManager::GetInstance()->InitializeViews( corrected_node->GetData()->GetTimeGeometry(), + mitk::RenderingManager::REQUEST_UPDATE_ALL, + true); } } catch(...) { QMessageBox::warning(nullptr, "Error", "File could not be processed.\nIs pytorch installed on your system?\nDoes your script use the correct input and output variable names (in: in_image & model, out: brain_mask & brain_extracted)?", QMessageBox::Ok); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.h index 6ffc91add7..a60a588042 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.python/src/internal/QmitkBrainExtractionView.h @@ -1,104 +1,79 @@ /*=================================================================== 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 "ui_QmitkBrainExtractionViewControls.h" #include #include #include -#include -#include -#include -#include #include -class QmitkBrainExtractionView; - -class FileDownloader : public QObject -{ - Q_OBJECT -public: - explicit FileDownloader(QObject *parent = 0); - - virtual ~FileDownloader(); - - QByteArray downloadedData() const; - void download(QUrl url); - -protected slots: - - void Downloaded(QNetworkReply* reply); - -private: - - QNetworkAccessManager m_WebCtrl; - -}; /*! \brief View for diffusion image registration / head motion correction */ class QmitkBrainExtractionView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; typedef itk::VectorImage< short, 3 > ItkDwiType; typedef mitk::GradientDirectionsProperty GradProp; QmitkBrainExtractionView(); virtual ~QmitkBrainExtractionView(); virtual void CreateQtPartControl(QWidget *parent) override; void SetFocus() override; protected slots: void StartBrainExtraction(); void UpdateGUI(); ///< update button activity etc. dpending on current datamanager selection + std::string GetPythonFile(std::string filename); + protected: /// \brief called by QmitkAbstractView when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; Ui::QmitkBrainExtractionViewControls* m_Controls; mitk::Image::Pointer m_DiffusionImage; std::vector< mitk::DataNode::Pointer > m_SelectedDiffusionNodes; private: void UpdateRegistrationStatus(); ///< update textual status display of the Registration process // the Qt parent of our GUI (NOT of this object) QWidget* m_Parent; - std::string m_ModulePath; }; diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.cpp index c13e1f5199..7905469296 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.registration/src/internal/QmitkSimpleRegistrationView.cpp @@ -1,388 +1,392 @@ /*=================================================================== 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. ===================================================================*/ //misc #define _USE_MATH_DEFINES #include // Blueberry #include #include // Qmitk #include "QmitkSimpleRegistrationView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include // Qt #include #define _USE_MATH_DEFINES #include const std::string QmitkSimpleRegistrationView::VIEW_ID = "org.mitk.views.simpleregistrationview"; QmitkSimpleRegistrationView::QmitkSimpleRegistrationView() : QmitkAbstractView() , m_Controls( 0 ) , m_RegistrationType(0) { } // Destructor QmitkSimpleRegistrationView::~QmitkSimpleRegistrationView() { } void QmitkSimpleRegistrationView::StartRegistration() { QmitkRegistrationJob* pJob; if (m_Controls->m_RegBox->currentIndex()==0) { mitk::MultiModalRigidDefaultRegistrationAlgorithm< ItkFloatImageType >::Pointer algo = mitk::MultiModalRigidDefaultRegistrationAlgorithm< ItkFloatImageType >::New(); pJob = new QmitkRegistrationJob(algo); m_RegistrationType = 0; } else { mitk::MultiModalAffineDefaultRegistrationAlgorithm< ItkFloatImageType >::Pointer algo = mitk::MultiModalAffineDefaultRegistrationAlgorithm< ItkFloatImageType >::New(); pJob = new QmitkRegistrationJob(algo); m_RegistrationType = 1; } pJob->setAutoDelete(true); m_MovingImageNode = m_Controls->m_MovingImageBox->GetSelectedNode(); mitk::Image::Pointer movingImage = dynamic_cast(m_MovingImageNode->GetData()); if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(movingImage)) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(movingImage, itkVectorImagePointer); itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); filter->SetInput( itkVectorImagePointer); filter->SetChannelIndex(m_Controls->m_MovingChannelBox->value()); filter->Update(); mitk::Image::Pointer newImage = mitk::Image::New(); newImage->InitializeByItk( filter->GetOutput() ); newImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); pJob->m_spMovingData = newImage; } else pJob->m_spMovingData = movingImage; mitk::Image::Pointer fixedImage = dynamic_cast(m_Controls->m_FixedImageBox->GetSelectedNode()->GetData()); if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(fixedImage)) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(fixedImage, itkVectorImagePointer); itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); filter->SetInput( itkVectorImagePointer); filter->SetChannelIndex(m_Controls->m_MovingChannelBox->value()); filter->Update(); mitk::Image::Pointer newImage = mitk::Image::New(); newImage->InitializeByItk( filter->GetOutput() ); newImage->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); pJob->m_spTargetData = newImage; } else pJob->m_spTargetData = fixedImage; pJob->m_TargetDataUID = mitk::EnsureUID(m_Controls->m_FixedImageBox->GetSelectedNode()->GetData()); pJob->m_MovingDataUID = mitk::EnsureUID(m_Controls->m_MovingImageBox->GetSelectedNode()->GetData()); connect(pJob, SIGNAL(RegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer, const QmitkRegistrationJob*)), this, SLOT(OnRegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer, const QmitkRegistrationJob*)), Qt::BlockingQueuedConnection); QThreadPool* threadPool = QThreadPool::globalInstance(); threadPool->start(pJob); m_Controls->m_RegistrationStartButton->setEnabled(false); m_Controls->m_RegistrationStartButton->setText("Registration in progress ..."); } void QmitkSimpleRegistrationView::OnRegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer spResultRegistration, const QmitkRegistrationJob* job) { mitk::Image::Pointer movingImage = dynamic_cast(m_MovingImageNode->GetData()); mitk::Image::Pointer image; if (m_RegistrationType==0) { image = mitk::ImageMappingHelper::refineGeometry(movingImage, spResultRegistration, true); } else { if (!mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(movingImage)) { image = mitk::ImageMappingHelper::map(movingImage, spResultRegistration, false, 0, job->m_spTargetData->GetGeometry(), false, 0, mitk::ImageMappingInterpolator::BSpline_3); } else { typedef itk::ComposeImageFilter < ITKDiffusionVolumeType > ComposeFilterType; ComposeFilterType::Pointer composer = ComposeFilterType::New(); ItkDwiType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(movingImage); for (unsigned int i=0; iGetVectorLength(); ++i) { itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); filter->SetInput( itkVectorImagePointer); filter->SetChannelIndex(i); filter->Update(); mitk::Image::Pointer gradientVolume = mitk::Image::New(); gradientVolume->InitializeByItk( filter->GetOutput() ); gradientVolume->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); mitk::Image::Pointer registered_mitk_image = mitk::ImageMappingHelper::map(gradientVolume, spResultRegistration, false, 0, job->m_spTargetData->GetGeometry(), false, 0, mitk::ImageMappingInterpolator::BSpline_3); ITKDiffusionVolumeType::Pointer registered_itk_image = ITKDiffusionVolumeType::New(); mitk::CastToItkImage(registered_mitk_image, registered_itk_image); composer->SetInput(i, registered_itk_image); } composer->Update(); image = mitk::GrabItkImageMemory( composer->GetOutput() ); mitk::DiffusionPropertyHelper::CopyProperties(movingImage, image, true); } } if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image)) { mitk::DiffusionPropertyHelper propertyHelper( image ); propertyHelper.InitializeImage(); } mitk::DataNode::Pointer resultNode = mitk::DataNode::New(); resultNode->SetData(image); if (m_MovingImageNode.IsNotNull()) { m_MovingImageNode->SetVisibility(false); QString name = m_MovingImageNode->GetName().c_str(); if (m_RegistrationType==0) resultNode->SetName((name+"_registered (rigid)").toStdString().c_str()); else resultNode->SetName((name+"_registered (affine)").toStdString().c_str()); } else { if (m_RegistrationType==0) resultNode->SetName("Registered (rigid)"); else resultNode->SetName("Registered (affine)"); } resultNode->SetOpacity(0.6); resultNode->SetColor(0.0, 0.0, 1.0); GetDataStorage()->Add(resultNode); + mitk::RenderingManager::GetInstance()->InitializeViews( resultNode->GetData()->GetTimeGeometry(), + mitk::RenderingManager::REQUEST_UPDATE_ALL, + true); + if (m_Controls->m_RegOutputBox->isChecked()) { mitk::DataNode::Pointer registration_node = mitk::DataNode::New(); registration_node->SetData(spResultRegistration); if (m_RegistrationType==0) registration_node->SetName("Registration Object (rigid)"); else registration_node->SetName("Registration Object (affine)"); GetDataStorage()->Add(registration_node, resultNode); } this->GetRenderWindowPart()->RequestUpdate(); m_Controls->m_RegistrationStartButton->setEnabled(true); m_Controls->m_RegistrationStartButton->setText("Start Registration"); m_MovingImageNode = nullptr; TractoChanged(); } void QmitkSimpleRegistrationView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkSimpleRegistrationViewControls; m_Controls->setupUi( parent ); m_Controls->m_FixedImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_MovingImageBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isImagePredicate = mitk::TNodePredicateDataType::New(); m_Controls->m_FixedImageBox->SetPredicate(isImagePredicate); m_Controls->m_MovingImageBox->SetPredicate(isImagePredicate); mitk::TNodePredicateDataType::Pointer isFib = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isReg = mitk::TNodePredicateDataType::New(); m_Controls->m_TractoBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_RegObjectBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TractoBox->SetPredicate(isFib); m_Controls->m_RegObjectBox->SetPredicate(isReg); connect( m_Controls->m_FixedImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(FixedImageChanged()) ); connect( m_Controls->m_MovingImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(MovingImageChanged()) ); connect( m_Controls->m_TractoBox, SIGNAL(currentIndexChanged(int)), this, SLOT(TractoChanged()) ); connect( m_Controls->m_RegObjectBox, SIGNAL(currentIndexChanged(int)), this, SLOT(TractoChanged()) ); connect( m_Controls->m_RegistrationStartButton, SIGNAL(clicked()), this, SLOT(StartRegistration()) ); connect( m_Controls->m_TractoRegistrationStartButton, SIGNAL(clicked()), this, SLOT(StartTractoRegistration()) ); FixedImageChanged(); MovingImageChanged(); TractoChanged(); } } void QmitkSimpleRegistrationView::StartTractoRegistration() { mitk::FiberBundle::Pointer fib = dynamic_cast(m_Controls->m_TractoBox->GetSelectedNode()->GetData()); mitk::MAPRegistrationWrapper::Pointer reg = dynamic_cast(m_Controls->m_RegObjectBox->GetSelectedNode()->GetData()); mitk::MITKRegistrationHelper::Affine3DTransformType::Pointer affine = mitk::MITKRegistrationHelper::getAffineMatrix(reg, false); mitk::FiberBundle::Pointer fib_copy = fib->GetDeepCopy(); fib_copy->TransformFibers(affine); mitk::DataNode::Pointer registration_node = mitk::DataNode::New(); registration_node->SetData(fib_copy); QString name = m_Controls->m_TractoBox->GetSelectedNode()->GetName().c_str(); registration_node->SetName((name+"_registered").toStdString().c_str()); GetDataStorage()->Add(registration_node, m_Controls->m_TractoBox->GetSelectedNode()); } void QmitkSimpleRegistrationView::TractoChanged() { if (m_Controls->m_RegObjectBox->GetSelectedNode().IsNotNull() && m_Controls->m_TractoBox->GetSelectedNode().IsNotNull()) m_Controls->m_TractoRegistrationStartButton->setEnabled(true); else m_Controls->m_TractoRegistrationStartButton->setEnabled(false); } void QmitkSimpleRegistrationView::FixedImageChanged() { if (m_Controls->m_FixedImageBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer image = dynamic_cast(m_Controls->m_FixedImageBox->GetSelectedNode()->GetData()); int channels = image->GetNumberOfChannels(); int dims = image->GetDimension(); int fourth_dim_size = image->GetTimeSteps(); bool isdiff = mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image); if (dims==4 || channels>1) { m_Controls->m_FixedChannelBox->setEnabled(false); m_Controls->m_RegistrationStartButton->setEnabled(false); } if (isdiff) { m_Controls->m_FixedChannelBox->setEnabled(true); if (fourth_dim_size>1) m_Controls->m_FixedChannelBox->setMaximum(fourth_dim_size-1); else if (isdiff) m_Controls->m_FixedChannelBox->setMaximum(mitk::DiffusionPropertyHelper::GetGradientContainer(image)->Size()-1); } else { m_Controls->m_FixedChannelBox->setEnabled(false); } m_Controls->m_RegistrationStartButton->setEnabled(true); } else { m_Controls->m_FixedChannelBox->setEnabled(false); m_Controls->m_RegistrationStartButton->setEnabled(false); } } void QmitkSimpleRegistrationView::MovingImageChanged() { if (m_Controls->m_MovingImageBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer image = dynamic_cast(m_Controls->m_MovingImageBox->GetSelectedNode()->GetData()); int channels = image->GetNumberOfChannels(); int dims = image->GetDimension(); int fourth_dim_size = image->GetTimeSteps(); bool isdiff = mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image); if (dims==4 || channels>1) { m_Controls->m_MovingChannelBox->setEnabled(false); m_Controls->m_RegistrationStartButton->setEnabled(false); } if (isdiff) { m_Controls->m_MovingChannelBox->setEnabled(true); if (fourth_dim_size>1) m_Controls->m_MovingChannelBox->setMaximum(fourth_dim_size-1); else if (isdiff) m_Controls->m_MovingChannelBox->setMaximum(mitk::DiffusionPropertyHelper::GetGradientContainer(image)->Size()-1); } else { m_Controls->m_MovingChannelBox->setEnabled(false); } m_Controls->m_RegistrationStartButton->setEnabled(true); } else { m_Controls->m_MovingChannelBox->setEnabled(false); m_Controls->m_RegistrationStartButton->setEnabled(false); } } void QmitkSimpleRegistrationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList& ) { FixedImageChanged(); MovingImageChanged(); TractoChanged(); } void QmitkSimpleRegistrationView::SetFocus() { m_Controls->m_RegistrationStartButton->setFocus(); FixedImageChanged(); MovingImageChanged(); }