diff --git a/Applications/AppList.cmake b/Applications/AppList.cmake index 9d055058c2..96d4a8abb8 100644 --- a/Applications/AppList.cmake +++ b/Applications/AppList.cmake @@ -1,25 +1,23 @@ # This file is included in the top-level MITK CMakeLists.txt file to # allow early dependency checking option(MITK_BUILD_APP_CoreApp "Build the MITK CoreApp" OFF) option(MITK_BUILD_APP_Workbench "Build the MITK Workbench executable" ON) option(MITK_BUILD_APP_Diffusion "Build the MITK Diffusion executable" OFF) -option(MITK_BUILD_APP_Fiberfox "Build the MITK Fiberfox executable" OFF) # This variable is fed to ctkFunctionSetupPlugins() macro in the # top-level MITK CMakeLists.txt file. This allows to automatically # enable required plug-in runtime dependencies for applications using # the CTK DGraph executable and the ctkMacroValidateBuildOptions macro. # For this to work, directories containing executables must contain # a CMakeLists.txt file containing a "project(...)" command and a # target_libraries.cmake file setting a list named "target_libraries" # with required plug-in target names. # Format is "Directory Name^^CMake Option Name^^Executable Name (without file suffix)" set(MITK_APPS CoreApp^^MITK_BUILD_APP_CoreApp^^MitkCoreApp Workbench^^MITK_BUILD_APP_Workbench^^MitkWorkbench Diffusion^^MITK_BUILD_APP_Diffusion^^MitkDiffusion - Fiberfox^^MITK_BUILD_APP_Fiberfox^^MitkFiberfoxGui ) diff --git a/Applications/Diffusion/CMakeLists.txt b/Applications/Diffusion/CMakeLists.txt index c78b58eea6..903b7d2193 100644 --- a/Applications/Diffusion/CMakeLists.txt +++ b/Applications/Diffusion/CMakeLists.txt @@ -1,93 +1,95 @@ 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.common.legacy 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.matchpoint.algorithm.browser + org.mitk.gui.qt.matchpoint.algorithm.control 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} ${MITK_MODULES_ENABLED_PLUGINS}) endif() diff --git a/Applications/Fiberfox/CMakeLists.txt b/Applications/Fiberfox/CMakeLists.txt deleted file mode 100644 index 491c3178f1..0000000000 --- a/Applications/Fiberfox/CMakeLists.txt +++ /dev/null @@ -1,57 +0,0 @@ -project(Fiberfox) - -set(_app_options) -if(MITK_SHOW_CONSOLE_WINDOW) - list(APPEND _app_options SHOW_CONSOLE) -endif() - -# Create a cache entry for the provisioning file which is used to export -# the file name in the MITKConfig.cmake file. This will keep external projects -# which rely on this file happy. -set(MITK_EXTAPP_PROVISIONING_FILE "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/MitkFiberfoxGui.provisioning" CACHE INTERNAL "MitkFiberfoxGui provisioning file" FORCE) - -# 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.diffusionimagingapp - org.mitk.example.gui.customviewer - org.mitk.example.gui.customviewer.views - org.mitk.example.gui.selectionservicemitk - org.mitk.example.gui.selectionservicemitk.views - org.mitk.example.gui.selectionserviceqt - org.mitk.example.gui.extensionpointcontribution - org.mitk.example.gui.extensionpointdefinition - org.mitk.example.gui.minimalapplication - org.mitk.example.gui.multipleperspectives -) - -mitkFunctionCreateBlueBerryApplication( - NAME MitkFiberfoxGui - DESCRIPTION "MITK Fiberfox" - EXCLUDE_PLUGINS ${_exclude_plugins} - ${_app_options} -) -mitk_use_modules(TARGET MitkFiberfoxGui MODULES MitkAppUtil) - -# Add meta dependencies (e.g. on auto-load modules from depending modules) -if(TARGET ${CMAKE_PROJECT_NAME}-autoload) - add_dependencies(MitkFiberfoxGui ${CMAKE_PROJECT_NAME}-autoload) -endif() - -#Setting application icon for mac os x systems -set_target_properties(MitkFiberfoxGui PROPERTIES MACOSX_BUNDLE_ICON_FILE "icon.icns") - -if(APPLE) - install(FILES "icons/icon.icns" DESTINATION "MitkFiberfoxGui.app/Contents/Resources") -endif(APPLE) - -# Add a build time dependency to legacy BlueBerry bundles. -if(MITK_MODULES_ENABLED_PLUGINS) - add_dependencies(MitkFiberfoxGui ${MITK_MODULES_ENABLED_PLUGINS}) -endif() diff --git a/Applications/Fiberfox/MitkFiberfoxGui.cpp b/Applications/Fiberfox/MitkFiberfoxGui.cpp deleted file mode 100644 index 3d1ca39a97..0000000000 --- a/Applications/Fiberfox/MitkFiberfoxGui.cpp +++ /dev/null @@ -1,42 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include - -#include - -int main(int argc, char **argv) -{ - mitk::BaseApplication app(argc, argv); - - app.setSingleMode(false); - app.setApplicationName("MITK Fiberfox"); - app.setOrganizationName("DKFZ"); - - // Preload the org.mitk.gui.qt.ext plug-in (and hence also QmitkExt) to speed - // up a clean-cache start. This also works around bugs in older gcc and glibc implementations, - // which have difficulties with multiple dynamic opening and closing of shared libraries with - // many global static initializers. It also helps if dependent libraries have weird static - // initialization methods and/or missing de-initialization code. - QStringList preloadLibs; - preloadLibs << "liborg_mitk_gui_qt_ext"; - app.setPreloadLibraries(preloadLibs); - - app.setProperty(mitk::BaseApplication::PROP_PRODUCT, "org.mitk.gui.qt.extapplication.fiberfox"); - - // Run Fiberfox. - return app.run(); -} diff --git a/Applications/Fiberfox/MitkFiberfoxGui.ini b/Applications/Fiberfox/MitkFiberfoxGui.ini deleted file mode 100644 index b73d1ab9b2..0000000000 --- a/Applications/Fiberfox/MitkFiberfoxGui.ini +++ /dev/null @@ -1,4 +0,0 @@ -BlueBerry.home=@BLUEBERRY_BINARY_DIR@ -BlueBerry.plugin_dirs=@MITK_MODULES_PLUGIN_OUTPUT_DIRS@ -BlueBerry.provisioning=@MITK_EXTAPP_PROVISIONING_FILE@ -BlueBerry.qtplugin_path=@BLUEBERRY_QTPLUGIN_PATH@ diff --git a/Applications/Fiberfox/icons/icon.icns b/Applications/Fiberfox/icons/icon.icns deleted file mode 100644 index 5afc942282..0000000000 Binary files a/Applications/Fiberfox/icons/icon.icns and /dev/null differ diff --git a/Applications/Fiberfox/icons/icon.ico b/Applications/Fiberfox/icons/icon.ico deleted file mode 100644 index 27d4c9d1b9..0000000000 Binary files a/Applications/Fiberfox/icons/icon.ico and /dev/null differ diff --git a/Applications/Fiberfox/icons/icon.png b/Applications/Fiberfox/icons/icon.png deleted file mode 100644 index 857e61aef3..0000000000 Binary files a/Applications/Fiberfox/icons/icon.png and /dev/null differ diff --git a/Applications/Fiberfox/icons/mitkFiberfoxGui.rc b/Applications/Fiberfox/icons/mitkFiberfoxGui.rc deleted file mode 100644 index bb10963fb3..0000000000 --- a/Applications/Fiberfox/icons/mitkFiberfoxGui.rc +++ /dev/null @@ -1 +0,0 @@ -IDI_ICON1 ICON DISCARDABLE "icon.ico" \ No newline at end of file diff --git a/Applications/Fiberfox/startMitkFiberfoxGui.bat.in b/Applications/Fiberfox/startMitkFiberfoxGui.bat.in deleted file mode 100644 index 4ef03f3b80..0000000000 --- a/Applications/Fiberfox/startMitkFiberfoxGui.bat.in +++ /dev/null @@ -1,2 +0,0 @@ -PATH=@MITK_RUNTIME_PATH@;%PATH% -@VS_BUILD_TYPE@\MitkFiberfoxGui.exe diff --git a/Applications/Fiberfox/target_libraries.cmake b/Applications/Fiberfox/target_libraries.cmake deleted file mode 100644 index c9bf2b6090..0000000000 --- a/Applications/Fiberfox/target_libraries.cmake +++ /dev/null @@ -1,24 +0,0 @@ - -# 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_extapplication - org_mitk_gui_qt_common_legacy - 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_fiberfox - org_mitk_gui_qt_diffusionimaging_fiberprocessing - org_mitk_gui_qt_diffusionimaging_preprocessing - org_mitk_gui_qt_diffusionimaging_reconstruction - org_mitk_gui_qt_imagenavigator - org_mitk_gui_qt_moviemaker - org_mitk_gui_qt_measurementtoolbox - org_mitk_gui_qt_viewnavigator -) diff --git a/CMake/BuildConfigurations/DiffusionRelease.cmake b/CMake/BuildConfigurations/DiffusionRelease.cmake index e356b9d707..d79a8af152 100644 --- a/CMake/BuildConfigurations/DiffusionRelease.cmake +++ b/CMake/BuildConfigurations/DiffusionRelease.cmake @@ -1,36 +1,37 @@ 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_DCMQI ON CACHE BOOL "" FORCE) +set(MITK_USE_MatchPoint 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_Fiberfox OFF CACHE BOOL "Build MITK Fiberfox" 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/BuildConfigurations/mitkDiffusion.cmake b/CMake/BuildConfigurations/mitkDiffusion.cmake index 5fed539368..5e00e6b54b 100644 --- a/CMake/BuildConfigurations/mitkDiffusion.cmake +++ b/CMake/BuildConfigurations/mitkDiffusion.cmake @@ -1,74 +1,35 @@ 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_DCMQI ON CACHE BOOL "" FORCE) +set(MITK_USE_MatchPoint 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 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 OFF CACHE BOOL "Use this to enable or disable the console window when starting MITK GUI Applications" FORCE) - -# Activate required plugins -# should be identical to the list in /Applications/Diffusion/CMakeLists.txt -set(_plugins - org.commontk.configadmin - org.commontk.eventadmin - org.blueberry.compat - 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.common.legacy - 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.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.connectomics - 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 -) +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/mitkFiberfox.cmake b/CMake/BuildConfigurations/mitkFiberfox.cmake deleted file mode 100644 index 4d1f131af4..0000000000 --- a/CMake/BuildConfigurations/mitkFiberfox.cmake +++ /dev/null @@ -1,49 +0,0 @@ -message(STATUS "Configuring MITK Fiberfox 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) - -# Disable all apps but MITK Fiberfox -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 OFF CACHE BOOL "Build MITK Diffusion" FORCE) -set(MITK_BUILD_APP_Fiberfox ON CACHE BOOL "Build MITK Fiberfox" FORCE) - -# Activate Diffusion Mini Apps -set(BUILD_DiffusionFiberfoxCmdApps ON CACHE BOOL "Build commandline tools for diffusion data simulation (Fiberfox)" 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) - -# 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 OFF CACHE BOOL "Use this to enable or disable the console window when starting MITK GUI Applications" FORCE) - -# Activate required plugins -# should be identical to the list in /Applications/Fiberfox/CMakeLists.txt -set(_plugins - org_blueberry_ui_qt - org_blueberry_ui_qt_help - org_mitk_planarfigure - org_mitk_gui_qt_extapplication - org_mitk_gui_qt_common_legacy - 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_fiberfox - org_mitk_gui_qt_diffusionimaging_fiberprocessing - org_mitk_gui_qt_diffusionimaging_preprocessing - org_mitk_gui_qt_diffusionimaging_reconstruction - org_mitk_gui_qt_imagenavigator - org_mitk_gui_qt_moviemaker - org_mitk_gui_qt_measurementtoolbox - org_mitk_gui_qt_viewnavigator -) diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp index 9add87b441..94b7d103a7 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp @@ -1,867 +1,871 @@ /*=================================================================== 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 RAPIDXML_NO_EXCEPTIONS #include #include #include #include #include #include template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::FiberfoxParameters() : m_NoiseModel(nullptr) { } template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::~FiberfoxParameters() { // if (m_NoiseModel!=nullptr) // delete m_NoiseModel; } void mitk::SignalGenerationParameters::GenerateGradientHalfShell() { int NPoints = 2*m_NumGradients; m_GradientDirections.clear(); m_NumBaseline = NPoints/20; if (m_NumBaseline==0) m_NumBaseline=1; GradientType g; g.Fill(0.0); for (unsigned int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i mitk::SignalGenerationParameters::GetBaselineIndices() { std::vector< int > result; for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) result.push_back(i); return result; } unsigned int mitk::SignalGenerationParameters::GetFirstBaselineIndex() { for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) return i; return -1; } bool mitk::SignalGenerationParameters::IsBaselineIndex(unsigned int idx) { if (m_GradientDirections.size()>idx && m_GradientDirections.at(idx).GetNorm()<0.0001) return true; return false; } unsigned int mitk::SignalGenerationParameters::GetNumWeightedVolumes() { return m_NumGradients; } unsigned int mitk::SignalGenerationParameters::GetNumBaselineVolumes() { return m_NumBaseline; } unsigned int mitk::SignalGenerationParameters::GetNumVolumes() { return m_GradientDirections.size(); } mitk::SignalGenerationParameters::GradientListType mitk::SignalGenerationParameters::GetGradientDirections() { return m_GradientDirections; } mitk::SignalGenerationParameters::GradientType mitk::SignalGenerationParameters::GetGradientDirection(unsigned int i) { return m_GradientDirections.at(i); } void mitk::SignalGenerationParameters::SetNumWeightedVolumes(int numGradients) { m_NumGradients = numGradients; GenerateGradientHalfShell(); } std::vector< int > mitk::SignalGenerationParameters::GetBvalues() { std::vector< int > bVals; for( GradientType g : m_GradientDirections) { float norm = g.GetNorm(); int bVal = std::round(norm*norm*m_Bvalue); if ( std::find(bVals.begin(), bVals.end(), bVal) == bVals.end() ) bVals.push_back(bVal); } return bVals; } void mitk::SignalGenerationParameters::SetGradienDirections(GradientListType gradientList) { m_GradientDirections = gradientList; m_NumGradients = 0; m_NumBaseline = 0; for( unsigned int i=0; im_GradientDirections.size(); i++) { float norm = m_GradientDirections.at(i).GetNorm(); if (norm>0.0001) m_NumGradients++; else m_NumBaseline++; } } void mitk::SignalGenerationParameters::SetGradienDirections(mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList) { m_NumGradients = 0; m_NumBaseline = 0; m_GradientDirections.clear(); for( unsigned int i=0; iSize(); i++) { GradientType g; g[0] = gradientList->at(i)[0]; g[1] = gradientList->at(i)[1]; g[2] = gradientList->at(i)[2]; m_GradientDirections.push_back(g); float norm = m_GradientDirections.at(i).GetNorm(); if (norm>0.0001) m_NumGradients++; else m_NumBaseline++; } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::SaveParameters(string filename) { if(filename.empty()) return; if(".ffp"!=filename.substr(filename.size()-4, 4)) filename += ".ffp"; const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, nullptr ); if ( locale.compare(currLocale)!=0 ) { try { setlocale(LC_ALL, locale.c_str()); } catch(...) { MITK_INFO << "Could not set locale " << locale; } } boost::property_tree::ptree parameters; // fiber generation parameters parameters.put("fiberfox.fibers.distribution", m_FiberGen.m_Distribution); parameters.put("fiberfox.fibers.variance", m_FiberGen.m_Variance); parameters.put("fiberfox.fibers.density", m_FiberGen.m_Density); parameters.put("fiberfox.fibers.spline.sampling", m_FiberGen.m_Sampling); parameters.put("fiberfox.fibers.spline.tension", m_FiberGen.m_Tension); parameters.put("fiberfox.fibers.spline.continuity", m_FiberGen.m_Continuity); parameters.put("fiberfox.fibers.spline.bias", m_FiberGen.m_Bias); parameters.put("fiberfox.fibers.rotation.x", m_FiberGen.m_Rotation[0]); parameters.put("fiberfox.fibers.rotation.y", m_FiberGen.m_Rotation[1]); parameters.put("fiberfox.fibers.rotation.z", m_FiberGen.m_Rotation[2]); parameters.put("fiberfox.fibers.translation.x", m_FiberGen.m_Translation[0]); parameters.put("fiberfox.fibers.translation.y", m_FiberGen.m_Translation[1]); parameters.put("fiberfox.fibers.translation.z", m_FiberGen.m_Translation[2]); parameters.put("fiberfox.fibers.scale.x", m_FiberGen.m_Scale[0]); parameters.put("fiberfox.fibers.scale.y", m_FiberGen.m_Scale[1]); parameters.put("fiberfox.fibers.scale.z", m_FiberGen.m_Scale[2]); // image generation parameters parameters.put("fiberfox.image.basic.size.x", m_SignalGen.m_ImageRegion.GetSize(0)); parameters.put("fiberfox.image.basic.size.y", m_SignalGen.m_ImageRegion.GetSize(1)); parameters.put("fiberfox.image.basic.size.z", m_SignalGen.m_ImageRegion.GetSize(2)); parameters.put("fiberfox.image.basic.spacing.x", m_SignalGen.m_ImageSpacing[0]); parameters.put("fiberfox.image.basic.spacing.y", m_SignalGen.m_ImageSpacing[1]); parameters.put("fiberfox.image.basic.spacing.z", m_SignalGen.m_ImageSpacing[2]); parameters.put("fiberfox.image.basic.origin.x", m_SignalGen.m_ImageOrigin[0]); parameters.put("fiberfox.image.basic.origin.y", m_SignalGen.m_ImageOrigin[1]); parameters.put("fiberfox.image.basic.origin.z", m_SignalGen.m_ImageOrigin[2]); parameters.put("fiberfox.image.basic.direction.1", m_SignalGen.m_ImageDirection[0][0]); parameters.put("fiberfox.image.basic.direction.2", m_SignalGen.m_ImageDirection[0][1]); parameters.put("fiberfox.image.basic.direction.3", m_SignalGen.m_ImageDirection[0][2]); parameters.put("fiberfox.image.basic.direction.4", m_SignalGen.m_ImageDirection[1][0]); parameters.put("fiberfox.image.basic.direction.5", m_SignalGen.m_ImageDirection[1][1]); parameters.put("fiberfox.image.basic.direction.6", m_SignalGen.m_ImageDirection[1][2]); parameters.put("fiberfox.image.basic.direction.7", m_SignalGen.m_ImageDirection[2][0]); parameters.put("fiberfox.image.basic.direction.8", m_SignalGen.m_ImageDirection[2][1]); parameters.put("fiberfox.image.basic.direction.9", m_SignalGen.m_ImageDirection[2][2]); parameters.put("fiberfox.image.basic.numgradients", m_SignalGen.GetNumWeightedVolumes()); for( unsigned int i=0; im_SignalGen.GetNumVolumes(); i++) { parameters.put("fiberfox.image.gradients."+boost::lexical_cast(i)+".x", m_SignalGen.GetGradientDirection(i)[0]); parameters.put("fiberfox.image.gradients."+boost::lexical_cast(i)+".y", m_SignalGen.GetGradientDirection(i)[1]); parameters.put("fiberfox.image.gradients."+boost::lexical_cast(i)+".z", m_SignalGen.GetGradientDirection(i)[2]); } parameters.put("fiberfox.image.acquisitiontype", m_SignalGen.m_AcquisitionType); parameters.put("fiberfox.image.coilsensitivityprofile", m_SignalGen.m_CoilSensitivityProfile); parameters.put("fiberfox.image.numberofcoils", m_SignalGen.m_NumberOfCoils); parameters.put("fiberfox.image.reversephase", m_SignalGen.m_ReversePhase); parameters.put("fiberfox.image.partialfourier", m_SignalGen.m_PartialFourier); parameters.put("fiberfox.image.noisevariance", m_SignalGen.m_NoiseVariance); parameters.put("fiberfox.image.trep", m_SignalGen.m_tRep); parameters.put("fiberfox.image.signalScale", m_SignalGen.m_SignalScale); parameters.put("fiberfox.image.tEcho", m_SignalGen.m_tEcho); parameters.put("fiberfox.image.tLine", m_SignalGen.m_tLine); parameters.put("fiberfox.image.tInhom", m_SignalGen.m_tInhom); parameters.put("fiberfox.image.bvalue", m_SignalGen.m_Bvalue); parameters.put("fiberfox.image.simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition); parameters.put("fiberfox.image.axonRadius", m_SignalGen.m_AxonRadius); parameters.put("fiberfox.image.doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation); parameters.put("fiberfox.image.doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume); parameters.put("fiberfox.image.artifacts.spikesnum", m_SignalGen.m_Spikes); parameters.put("fiberfox.image.artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude); parameters.put("fiberfox.image.artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset); parameters.put("fiberfox.image.artifacts.eddyStrength", m_SignalGen.m_EddyStrength); parameters.put("fiberfox.image.artifacts.eddyTau", m_SignalGen.m_Tau); parameters.put("fiberfox.image.artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor); parameters.put("fiberfox.image.artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging); parameters.put("fiberfox.image.artifacts.doAddMotion", m_SignalGen.m_DoAddMotion); parameters.put("fiberfox.image.artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion); parameters.put("fiberfox.image.artifacts.translation0", m_SignalGen.m_Translation[0]); parameters.put("fiberfox.image.artifacts.translation1", m_SignalGen.m_Translation[1]); parameters.put("fiberfox.image.artifacts.translation2", m_SignalGen.m_Translation[2]); parameters.put("fiberfox.image.artifacts.rotation0", m_SignalGen.m_Rotation[0]); parameters.put("fiberfox.image.artifacts.rotation1", m_SignalGen.m_Rotation[1]); parameters.put("fiberfox.image.artifacts.rotation2", m_SignalGen.m_Rotation[2]); parameters.put("fiberfox.image.artifacts.motionvolumes", m_Misc.m_MotionVolumesBox); parameters.put("fiberfox.image.artifacts.addnoise", m_Misc.m_CheckAddNoiseBox); parameters.put("fiberfox.image.artifacts.addghosts", m_Misc.m_CheckAddGhostsBox); parameters.put("fiberfox.image.artifacts.addaliasing", m_Misc.m_CheckAddAliasingBox); parameters.put("fiberfox.image.artifacts.addspikes", m_Misc.m_CheckAddSpikesBox); parameters.put("fiberfox.image.artifacts.addeddycurrents", m_Misc.m_CheckAddEddyCurrentsBox); parameters.put("fiberfox.image.artifacts.doAddDistortions", m_Misc.m_CheckAddDistortionsBox); parameters.put("fiberfox.image.outputvolumefractions", m_Misc.m_CheckOutputVolumeFractionsBox); parameters.put("fiberfox.image.showadvanced", m_Misc.m_CheckAdvancedSignalOptionsBox); parameters.put("fiberfox.image.signalmodelstring", m_Misc.m_SignalModelString); parameters.put("fiberfox.image.artifactmodelstring", m_Misc.m_ArtifactModelString); parameters.put("fiberfox.image.outpath", m_Misc.m_OutputPath); parameters.put("fiberfox.fibers.realtime", m_Misc.m_CheckRealTimeFibersBox); parameters.put("fiberfox.fibers.showadvanced", m_Misc.m_CheckAdvancedFiberOptionsBox); parameters.put("fiberfox.fibers.constantradius", m_Misc.m_CheckConstantRadiusBox); parameters.put("fiberfox.fibers.includeFiducials", m_Misc.m_CheckIncludeFiducialsBox); if (m_NoiseModel!=nullptr) { parameters.put("fiberfox.image.artifacts.noisevariance", m_NoiseModel->GetNoiseVariance()); if (dynamic_cast*>(m_NoiseModel.get())) parameters.put("fiberfox.image.artifacts.noisetype", "rice"); else if (dynamic_cast*>(m_NoiseModel.get())) parameters.put("fiberfox.image.artifacts.noisetype", "chisquare"); } for (std::size_t i=0; i* signalModel = nullptr; if (i(i)+".type", "fiber"); } else { signalModel = m_NonFiberModelList.at(i-m_FiberModelList.size()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".type", "non-fiber"); } if (dynamic_cast*>(signalModel)) { mitk::StickModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "stick"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t1", model->GetT1()); } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "tensor"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d1", model->GetDiffusivity1()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d2", model->GetDiffusivity2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d3", model->GetDiffusivity3()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t1", model->GetT1()); } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "prototype"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".minFA", model->GetFaRange().first); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".maxFA", model->GetFaRange().second); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".minADC", model->GetAdcRange().first); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".maxADC", model->GetAdcRange().second); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".maxNumSamples", model->GetMaxNumKernels()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".numSamples", model->GetNumberOfKernels()); int shOrder = model->GetShOrder(); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".numCoeffs", (shOrder*shOrder + shOrder + 2)/2 + shOrder); for (unsigned int j=0; jGetNumberOfKernels(); j++) { vnl_vector< double > coeffs = model->GetCoefficients(j); for (unsigned int k=0; k(i)+".kernels."+boost::lexical_cast(j)+".coeffs."+boost::lexical_cast(k), coeffs[k]); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".kernels."+boost::lexical_cast(j)+".B0", model->GetBaselineSignal(j)); } } else if (dynamic_cast*>(signalModel)) { mitk::BallModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "ball"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t1", model->GetT1()); } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "astrosticks"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t1", model->GetT1()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".randomize", model->GetRandomizeSticks()); } else if (dynamic_cast*>(signalModel)) { mitk::DotModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "dot"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t1", model->GetT1()); } if (signalModel!=nullptr) { parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".ID", signalModel->m_CompartmentId); if (signalModel->GetVolumeFractionImage().IsNotNull()) { try{ itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); writer->SetFileName(filename+"_VOLUME"+boost::lexical_cast(signalModel->m_CompartmentId)+".nrrd"); writer->SetInput(signalModel->GetVolumeFractionImage()); writer->Update(); MITK_INFO << "Volume fraction image for compartment "+boost::lexical_cast(signalModel->m_CompartmentId)+" saved."; } catch(...) { } } } } boost::property_tree::xml_writer_settings writerSettings(' ', 2); boost::property_tree::xml_parser::write_xml(filename, parameters, std::locale(), writerSettings); try{ itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); writer->SetFileName(filename+"_FMAP.nrrd"); writer->SetInput(m_SignalGen.m_FrequencyMap); writer->Update(); } catch(...) { MITK_INFO << "No frequency map saved."; } try{ itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); writer->SetFileName(filename+"_MASK.nrrd"); writer->SetInput(m_SignalGen.m_MaskImage); writer->Update(); } catch(...) { MITK_INFO << "No mask image saved."; } setlocale(LC_ALL, currLocale.c_str()); } template< class ScalarType > template< class ParameterType > ParameterType mitk::FiberfoxParameters< ScalarType >::ReadVal(boost::property_tree::ptree::value_type const& v, std::string tag, ParameterType defaultValue, bool essential) { try { return v.second.get(tag); } catch (...) { if (essential) { mitkThrow() << "Parameter file corrupted. Essential tag is missing: '" << tag << "'"; } if (tag!="artifacts.noisetype") { MITK_INFO << "Tag '" << tag << "' not found. Using default value '" << defaultValue << "'."; m_MissingTags += "\n- "; m_MissingTags += tag; } return defaultValue; } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::LoadParameters(string filename) { m_MissingTags = ""; if(filename.empty()) { return; } const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, nullptr ); if ( locale.compare(currLocale)!=0 ) { try { setlocale(LC_ALL, locale.c_str()); } catch(...) { MITK_INFO << "Could not set locale " << locale; } } boost::property_tree::ptree parameterTree; boost::property_tree::xml_parser::read_xml( filename, parameterTree ); m_FiberModelList.clear(); m_NonFiberModelList.clear(); if (m_NoiseModel) { m_NoiseModel = nullptr; } BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameterTree.get_child("fiberfox") ) { if( v1.first == "fibers" ) { m_Misc.m_CheckRealTimeFibersBox = ReadVal(v1,"realtime", m_Misc.m_CheckRealTimeFibersBox); m_Misc.m_CheckAdvancedFiberOptionsBox = ReadVal(v1,"showadvanced", m_Misc.m_CheckAdvancedFiberOptionsBox); m_Misc.m_CheckConstantRadiusBox = ReadVal(v1,"constantradius", m_Misc.m_CheckConstantRadiusBox); m_Misc.m_CheckIncludeFiducialsBox = ReadVal(v1,"includeFiducials", m_Misc.m_CheckIncludeFiducialsBox); switch (ReadVal(v1,"distribution", 0)) { case 0: m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; break; case 1: m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN; break; default: m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; } m_FiberGen.m_Variance = ReadVal(v1,"variance", m_FiberGen.m_Variance); m_FiberGen.m_Density = ReadVal(v1,"density", m_FiberGen.m_Density); m_FiberGen.m_Sampling = ReadVal(v1,"spline.sampling", m_FiberGen.m_Sampling); m_FiberGen.m_Tension = ReadVal(v1,"spline.tension", m_FiberGen.m_Tension); m_FiberGen.m_Continuity = ReadVal(v1,"spline.continuity", m_FiberGen.m_Continuity); m_FiberGen.m_Bias = ReadVal(v1,"spline.bias", m_FiberGen.m_Bias); m_FiberGen.m_Rotation[0] = ReadVal(v1,"rotation.x", m_FiberGen.m_Rotation[0]); m_FiberGen.m_Rotation[1] = ReadVal(v1,"rotation.y", m_FiberGen.m_Rotation[1]); m_FiberGen.m_Rotation[2] = ReadVal(v1,"rotation.z", m_FiberGen.m_Rotation[2]); m_FiberGen.m_Translation[0] = ReadVal(v1,"translation.x", m_FiberGen.m_Translation[0]); m_FiberGen.m_Translation[1] = ReadVal(v1,"translation.y", m_FiberGen.m_Translation[1]); m_FiberGen.m_Translation[2] = ReadVal(v1,"translation.z", m_FiberGen.m_Translation[2]); m_FiberGen.m_Scale[0] = ReadVal(v1,"scale.x", m_FiberGen.m_Scale[0]); m_FiberGen.m_Scale[1] = ReadVal(v1,"scale.y", m_FiberGen.m_Scale[1]); m_FiberGen.m_Scale[2] = ReadVal(v1,"scale.z", m_FiberGen.m_Scale[2]); } else if ( v1.first == "image" ) { m_Misc.m_SignalModelString = ReadVal(v1,"signalmodelstring", m_Misc.m_SignalModelString); m_Misc.m_ArtifactModelString = ReadVal(v1,"artifactmodelstring", m_Misc.m_ArtifactModelString); m_Misc.m_OutputPath = ReadVal(v1,"outpath", m_Misc.m_OutputPath); m_Misc.m_CheckOutputVolumeFractionsBox = ReadVal(v1,"outputvolumefractions", m_Misc.m_CheckOutputVolumeFractionsBox); m_Misc.m_CheckAdvancedSignalOptionsBox = ReadVal(v1,"showadvanced", m_Misc.m_CheckAdvancedSignalOptionsBox); m_Misc.m_CheckAddDistortionsBox = ReadVal(v1,"artifacts.doAddDistortions", m_Misc.m_CheckAddDistortionsBox); m_Misc.m_CheckAddNoiseBox = ReadVal(v1,"artifacts.addnoise", m_Misc.m_CheckAddNoiseBox); m_Misc.m_CheckAddGhostsBox = ReadVal(v1,"artifacts.addghosts", m_Misc.m_CheckAddGhostsBox); m_Misc.m_CheckAddAliasingBox = ReadVal(v1,"artifacts.addaliasing", m_Misc.m_CheckAddAliasingBox); m_Misc.m_CheckAddSpikesBox = ReadVal(v1,"artifacts.addspikes", m_Misc.m_CheckAddSpikesBox); m_Misc.m_CheckAddEddyCurrentsBox = ReadVal(v1,"artifacts.addeddycurrents", m_Misc.m_CheckAddEddyCurrentsBox); m_SignalGen.m_ImageRegion.SetSize(0, ReadVal(v1,"basic.size.x",m_SignalGen.m_ImageRegion.GetSize(0))); m_SignalGen.m_ImageRegion.SetSize(1, ReadVal(v1,"basic.size.y",m_SignalGen.m_ImageRegion.GetSize(1))); m_SignalGen.m_ImageRegion.SetSize(2, ReadVal(v1,"basic.size.z",m_SignalGen.m_ImageRegion.GetSize(2))); m_SignalGen.m_ImageSpacing[0] = ReadVal(v1,"basic.spacing.x",m_SignalGen.m_ImageSpacing[0]); m_SignalGen.m_ImageSpacing[1] = ReadVal(v1,"basic.spacing.y",m_SignalGen.m_ImageSpacing[1]); m_SignalGen.m_ImageSpacing[2] = ReadVal(v1,"basic.spacing.z",m_SignalGen.m_ImageSpacing[2]); m_SignalGen.m_ImageOrigin[0] = ReadVal(v1,"basic.origin.x",m_SignalGen.m_ImageOrigin[0]); m_SignalGen.m_ImageOrigin[1] = ReadVal(v1,"basic.origin.y",m_SignalGen.m_ImageOrigin[1]); m_SignalGen.m_ImageOrigin[2] = ReadVal(v1,"basic.origin.z",m_SignalGen.m_ImageOrigin[2]); m_SignalGen.m_ImageDirection[0][0] = ReadVal(v1,"basic.direction.1",m_SignalGen.m_ImageDirection[0][0]); m_SignalGen.m_ImageDirection[0][1] = ReadVal(v1,"basic.direction.2",m_SignalGen.m_ImageDirection[0][1]); m_SignalGen.m_ImageDirection[0][2] = ReadVal(v1,"basic.direction.3",m_SignalGen.m_ImageDirection[0][2]); m_SignalGen.m_ImageDirection[1][0] = ReadVal(v1,"basic.direction.4",m_SignalGen.m_ImageDirection[1][0]); m_SignalGen.m_ImageDirection[1][1] = ReadVal(v1,"basic.direction.5",m_SignalGen.m_ImageDirection[1][1]); m_SignalGen.m_ImageDirection[1][2] = ReadVal(v1,"basic.direction.6",m_SignalGen.m_ImageDirection[1][2]); m_SignalGen.m_ImageDirection[2][0] = ReadVal(v1,"basic.direction.7",m_SignalGen.m_ImageDirection[2][0]); m_SignalGen.m_ImageDirection[2][1] = ReadVal(v1,"basic.direction.8",m_SignalGen.m_ImageDirection[2][1]); m_SignalGen.m_ImageDirection[2][2] = ReadVal(v1,"basic.direction.9",m_SignalGen.m_ImageDirection[2][2]); m_SignalGen.m_AcquisitionType = (SignalGenerationParameters::AcquisitionType) ReadVal(v1,"acquisitiontype", m_SignalGen.m_AcquisitionType); m_SignalGen.m_CoilSensitivityProfile = (SignalGenerationParameters::CoilSensitivityProfile) ReadVal(v1,"coilsensitivityprofile", m_SignalGen.m_CoilSensitivityProfile); m_SignalGen.m_NumberOfCoils = ReadVal(v1,"numberofcoils", m_SignalGen.m_NumberOfCoils); m_SignalGen.m_ReversePhase = ReadVal(v1,"reversephase", m_SignalGen.m_ReversePhase); m_SignalGen.m_PartialFourier = ReadVal(v1,"partialfourier", m_SignalGen.m_PartialFourier); m_SignalGen.m_NoiseVariance = ReadVal(v1,"noisevariance", m_SignalGen.m_NoiseVariance); m_SignalGen.m_tRep = ReadVal(v1,"trep", m_SignalGen.m_tRep); m_SignalGen.m_SignalScale = ReadVal(v1,"signalScale", m_SignalGen.m_SignalScale); m_SignalGen.m_tEcho = ReadVal(v1,"tEcho", m_SignalGen.m_tEcho); m_SignalGen.m_tLine = ReadVal(v1,"tLine", m_SignalGen.m_tLine); m_SignalGen.m_tInhom = ReadVal(v1,"tInhom", m_SignalGen.m_tInhom); m_SignalGen.m_Bvalue = ReadVal(v1,"bvalue", m_SignalGen.m_Bvalue); m_SignalGen.m_SimulateKspaceAcquisition = ReadVal(v1,"simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition); m_SignalGen.m_AxonRadius = ReadVal(v1,"axonRadius", m_SignalGen.m_AxonRadius); m_SignalGen.m_Spikes = ReadVal(v1,"artifacts.spikesnum", m_SignalGen.m_Spikes); m_SignalGen.m_SpikeAmplitude = ReadVal(v1,"artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude); m_SignalGen.m_KspaceLineOffset = ReadVal(v1,"artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset); m_SignalGen.m_EddyStrength = ReadVal(v1,"artifacts.eddyStrength", m_SignalGen.m_EddyStrength); m_SignalGen.m_Tau = ReadVal(v1,"artifacts.eddyTau", m_SignalGen.m_Tau); m_SignalGen.m_CroppingFactor = ReadVal(v1,"artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor); m_SignalGen.m_DoAddGibbsRinging = ReadVal(v1,"artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging); m_SignalGen.m_DoSimulateRelaxation = ReadVal(v1,"doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation); m_SignalGen.m_DoDisablePartialVolume = ReadVal(v1,"doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume); m_SignalGen.m_DoAddMotion = ReadVal(v1,"artifacts.doAddMotion", m_SignalGen.m_DoAddMotion); m_SignalGen.m_DoRandomizeMotion = ReadVal(v1,"artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion); m_SignalGen.m_Translation[0] = ReadVal(v1,"artifacts.translation0", m_SignalGen.m_Translation[0]); m_SignalGen.m_Translation[1] = ReadVal(v1,"artifacts.translation1", m_SignalGen.m_Translation[1]); m_SignalGen.m_Translation[2] = ReadVal(v1,"artifacts.translation2", m_SignalGen.m_Translation[2]); m_SignalGen.m_Rotation[0] = ReadVal(v1,"artifacts.rotation0", m_SignalGen.m_Rotation[0]); m_SignalGen.m_Rotation[1] = ReadVal(v1,"artifacts.rotation1", m_SignalGen.m_Rotation[1]); m_SignalGen.m_Rotation[2] = ReadVal(v1,"artifacts.rotation2", m_SignalGen.m_Rotation[2]); // m_SignalGen.SetNumWeightedVolumes(ReadVal(v1,"numgradients", m_SignalGen.GetNumWeightedVolumes())); SignalGenerationParameters::GradientListType gradients; BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("gradients") ) { SignalGenerationParameters::GradientType g; g[0] = ReadVal(v2,"x",0); g[1] = ReadVal(v2,"y",0); g[2] = ReadVal(v2,"z",0); gradients.push_back(g); } m_SignalGen.SetGradienDirections(gradients); m_Misc.m_MotionVolumesBox = ReadVal(v1,"artifacts.motionvolumes", m_Misc.m_MotionVolumesBox); m_SignalGen.m_MotionVolumes.clear(); if ( m_Misc.m_MotionVolumesBox == "random" ) { for ( size_t i=0; i < m_SignalGen.GetNumVolumes(); ++i ) { m_SignalGen.m_MotionVolumes.push_back( bool( rand()%2 ) ); } MITK_DEBUG << "mitkFiberfoxParameters.cpp: Case m_Misc.m_MotionVolumesBox == \"random\"."; } else if ( ! m_Misc.m_MotionVolumesBox.empty() ) { stringstream stream( m_Misc.m_MotionVolumesBox ); std::vector numbers; int nummer = std::numeric_limits::max(); while( stream >> nummer ) { if( nummer < std::numeric_limits::max() ) { numbers.push_back( nummer ); } } // If a list of negative numbers is given: if( *(std::min_element( numbers.begin(), numbers.end() )) < 0 && *(std::max_element( numbers.begin(), numbers.end() )) <= 0 ) // cave: -0 == +0 { for ( size_t i=0; i(m_SignalGen.GetNumVolumes()) && -number >= 0 ) m_SignalGen.m_MotionVolumes.at(-number) = false; } MITK_DEBUG << "mitkFiberfoxParameters.cpp: Case list of negative numbers."; } // If a list of positive numbers is given: else if( *(std::min_element( numbers.begin(), numbers.end() )) >= 0 && *(std::max_element( numbers.begin(), numbers.end() )) >= 0 ) { for ( size_t i=0; i(m_SignalGen.GetNumVolumes()) && number >= 0) m_SignalGen.m_MotionVolumes.at(number) = true; } MITK_DEBUG << "mitkFiberfoxParameters.cpp: Case list of positive numbers."; } else { MITK_WARN << "mitkFiberfoxParameters.cpp: Inconsistent list of numbers in m_MotionVolumesBox."; break; } } else { MITK_WARN << "mitkFiberfoxParameters.cpp: Cannot make sense of string in m_MotionVolumesBox."; break; } try { if (ReadVal(v1,"artifacts.noisetype","")=="rice") { m_NoiseModel = std::make_shared< mitk::RicianNoiseModel >(); m_NoiseModel->SetNoiseVariance(ReadVal(v1,"artifacts.noisevariance",m_NoiseModel->GetNoiseVariance())); } } catch(...) { MITK_DEBUG << "mitkFiberfoxParameters.cpp: caught some error while trying m_NoiseModel->SetNoiseVariance()"; // throw; } try { if (ReadVal(v1,"artifacts.noisetype","")=="chisquare") { m_NoiseModel = std::make_shared< mitk::ChiSquareNoiseModel >(); m_NoiseModel->SetNoiseVariance(ReadVal(v1,"artifacts.noisevariance",m_NoiseModel->GetNoiseVariance())); } } catch(...) { MITK_DEBUG << "mitkFiberfoxParameters.cpp: caught some error while trying m_NoiseModel->SetNoiseVariance()"; // throw; } BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("compartments") ) { mitk::DiffusionSignalModel* signalModel = nullptr; std::string model = ReadVal(v2,"model","",true); if (model=="stick") { mitk::StickModel* model = new mitk::StickModel(); model->SetDiffusivity(ReadVal(v2,"d",model->GetDiffusivity())); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); + model->SetBvalue(m_SignalGen.m_Bvalue); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="tensor") { mitk::TensorModel* model = new mitk::TensorModel(); model->SetDiffusivity1(ReadVal(v2,"d1",model->GetDiffusivity1())); model->SetDiffusivity2(ReadVal(v2,"d2",model->GetDiffusivity2())); model->SetDiffusivity3(ReadVal(v2,"d3",model->GetDiffusivity3())); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); + model->SetBvalue(m_SignalGen.m_Bvalue); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="ball") { mitk::BallModel* model = new mitk::BallModel(); model->SetDiffusivity(ReadVal(v2,"d",model->GetDiffusivity())); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); + model->SetBvalue(m_SignalGen.m_Bvalue); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="astrosticks") { mitk::AstroStickModel* model = new AstroStickModel(); model->SetDiffusivity(ReadVal(v2,"d",model->GetDiffusivity())); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); + model->SetBvalue(m_SignalGen.m_Bvalue); model->SetRandomizeSticks(ReadVal(v2,"randomize",model->GetRandomizeSticks())); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="dot") { mitk::DotModel* model = new mitk::DotModel(); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="prototype") { mitk::RawShModel* model = new mitk::RawShModel(); model->SetMaxNumKernels(ReadVal(v2,"maxNumSamples",model->GetMaxNumKernels())); model->SetFaRange(ReadVal(v2,"minFA",model->GetFaRange().first), ReadVal(v2,"maxFA",model->GetFaRange().second)); model->SetAdcRange(ReadVal(v2,"minADC",model->GetAdcRange().first), ReadVal(v2,"maxADC",model->GetAdcRange().second)); model->m_CompartmentId = ReadVal(v2,"ID",0,true); unsigned int numCoeffs = ReadVal(v2,"numCoeffs",0,true); unsigned int numSamples = ReadVal(v2,"numSamples",0,true); for (unsigned int j=0; j coeffs(numCoeffs); for (unsigned int k=0; k(v2,"kernels."+boost::lexical_cast(j)+".coeffs."+boost::lexical_cast(k),0,true); } model->SetShCoefficients( coeffs, ReadVal(v2,"kernels."+boost::lexical_cast(j)+".B0",0,true) ); } if (ReadVal(v2,"type","",true)=="fiber") { m_FiberModelList.push_back(model); } else if (ReadVal(v2,"type","",true)=="non-fiber") { m_NonFiberModelList.push_back(model); } // else ? signalModel = model; } if (signalModel!=nullptr) { signalModel->SetGradientList(gradients); try { itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); reader->SetFileName(filename+"_VOLUME"+ReadVal(v2,"ID","")+".nrrd"); reader->Update(); signalModel->SetVolumeFractionImage(reader->GetOutput()); MITK_INFO << "Volume fraction image loaded for compartment " << signalModel->m_CompartmentId; } catch(...) { MITK_INFO << "No volume fraction image found for compartment " << signalModel->m_CompartmentId; } } } } else { } } try { itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); reader->SetFileName(filename+"_FMAP.nrrd"); reader->Update(); m_SignalGen.m_FrequencyMap = reader->GetOutput(); MITK_INFO << "Frequency map loaded."; } catch(...) { MITK_INFO << "No frequency map found."; } try { itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); reader->SetFileName(filename+"_MASK.nrrd"); reader->Update(); m_SignalGen.m_MaskImage = reader->GetOutput(); MITK_INFO << "Mask image loaded."; } catch(...) { MITK_INFO << "No mask image found."; } setlocale(LC_ALL, currLocale.c_str()); } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::PrintSelf() { MITK_INFO << "Not implemented :("; }