diff --git a/CMakeLists.txt b/CMakeLists.txt index e5e1ce68a4..bcce126453 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -1,521 +1,523 @@ cmake_minimum_required(VERSION 2.8.2) project(MITK) #----------------------------------------------------------------------------- # See http://cmake.org/cmake/help/cmake-2-8-docs.html#section_Policies for details #----------------------------------------------------------------------------- set(project_policies CMP0001 # NEW: CMAKE_BACKWARDS_COMPATIBILITY should no longer be used. CMP0002 # NEW: Logical target names must be globally unique. CMP0003 # NEW: Libraries linked via full path no longer produce linker search paths. CMP0004 # NEW: Libraries linked may NOT have leading or trailing whitespace. CMP0005 # NEW: Preprocessor definition values are now escaped automatically. CMP0006 # NEW: Installing MACOSX_BUNDLE targets requires a BUNDLE DESTINATION. CMP0007 # NEW: List command no longer ignores empty elements. CMP0008 # NEW: Libraries linked by full-path must have a valid library file name. CMP0009 # NEW: FILE GLOB_RECURSE calls should not follow symlinks by default. CMP0010 # NEW: Bad variable reference syntax is an error. CMP0011 # NEW: Included scripts do automatic cmake_policy PUSH and POP. CMP0012 # NEW: if() recognizes numbers and boolean constants. CMP0013 # NEW: Duplicate binary directories are not allowed. CMP0014 # NEW: Input directories must have CMakeLists.txt ) foreach(policy ${project_policies}) if(POLICY ${policy}) cmake_policy(SET ${policy} NEW) endif() endforeach() #----------------------------------------------------------------------------- # Update CMake module path #------------------------------------------------------------------------------ set(CMAKE_MODULE_PATH ${MITK_SOURCE_DIR}/CMake ${CMAKE_MODULE_PATH} ) #----------------------------------------------------------------------------- # CMake Function(s) and Macro(s) #----------------------------------------------------------------------------- include(mitkMacroEmptyExternalProject) include(mitkFunctionGenerateProjectXml) #----------------------------------------------------------------------------- # Superbuild Option - Enabled by default #----------------------------------------------------------------------------- option(MITK_USE_SUPERBUILD "Build MITK and the projects it depends on via SuperBuild.cmake." ON) #----------------------------------------------------------------------------- # Output directories. #----------------------------------------------------------------------------- foreach(type LIBRARY RUNTIME ARCHIVE) # Make sure the directory exists if(DEFINED MITK_CMAKE_${type}_OUTPUT_DIRECTORY AND NOT EXISTS ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}) message(FATAL_ERROR "MITK_CMAKE_${type}_OUTPUT_DIRECTORY is set to a non-existing directory [${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}]") endif() if(MITK_USE_SUPERBUILD) set(output_dir ${MITK_BINARY_DIR}/bin) if(NOT DEFINED MITK_CMAKE_${type}_OUTPUT_DIRECTORY) set(MITK_CMAKE_${type}_OUTPUT_DIRECTORY ${MITK_BINARY_DIR}/MITK-build/bin) endif() else() if(NOT DEFINED MITK_CMAKE_${type}_OUTPUT_DIRECTORY) SET(output_dir ${MITK_BINARY_DIR}/bin) else() SET(output_dir ${MITK_CMAKE_${type}_OUTPUT_DIRECTORY}) endif() endif() set(CMAKE_${type}_OUTPUT_DIRECTORY ${output_dir} CACHE INTERNAL "Single output directory for building all libraries.") mark_as_advanced(CMAKE_${type}_OUTPUT_DIRECTORY) endforeach() #----------------------------------------------------------------------------- # Additional MITK Options (also shown during superbuild) #----------------------------------------------------------------------------- option(BUILD_SHARED_LIBS "Build MITK with shared libraries" ON) option(WITH_COVERAGE "Enable/Disable coverage" OFF) option(BUILD_TESTING "Test the project" ON) # some targets in Utilities also depend on Qt. Use this option # to decide if they should be build option(MITK_USE_QT "Use Trolltech's Qt library" ON) if(MITK_USE_QT) # find the package at the very beginning, so that QT4_FOUND is available find_package(Qt4 4.6.0 REQUIRED) endif() option(MITK_INSTALL_RPATH_RELATIVE "Use relative rpath entries for installation packages" OFF) option(MITK_BUILD_ALL_PLUGINS "Build all MITK plugins" OFF) option(MITK_BUILD_TUTORIAL "Build the MITK tutorial" ON) option(MITK_USE_Boost "Use the Boost C++ library" OFF) option(MITK_USE_GDCMIO "Use the GDCMIO class instead of ImageIO2 for DICOM" ON) option(MITK_USE_BLUEBERRY "Build the BlueBerry platform" ON) option(MITK_USE_CTK "EXEPERIMENTAL, superbuild only: Use CTK in MITK" OFF) option(MITK_USE_DCMTK "EXEPERIMENTAL, superbuild only: Use DCMTK in MITK" OFF) mark_as_advanced(MITK_INSTALL_RPATH_RELATIVE MITK_BUILD_ALL_PLUGINS MITK_USE_CTK MITK_USE_DCMTK ) #----------------------------------------------------------------------------- # Additional CXX/C Flags #----------------------------------------------------------------------------- set(ADDITIONAL_C_FLAGS "" CACHE STRING "Additional C Flags") mark_as_advanced(ADDITIONAL_C_FLAGS) set(ADDITIONAL_CXX_FLAGS "" CACHE STRING "Additional CXX Flags") mark_as_advanced(ADDITIONAL_CXX_FLAGS) #----------------------------------------------------------------------------- # Project.xml #----------------------------------------------------------------------------- # A list of topologically ordered targets set(CTEST_PROJECT_SUBPROJECTS) if(MITK_USE_BLUEBERRY) list(APPEND CTEST_PROJECT_SUBPROJECTS BlueBerry) endif() list(APPEND CTEST_PROJECT_SUBPROJECTS MITK-Core MITK-CoreUI MITK-IGT MITK-DTI MITK-Registration MITK-Modules # all modules not contained in a specific subproject MITK-Plugins # all plugins not contained in a specific subproject ) # Configure CTestConfigSubProject.cmake that could be used by CTest scripts configure_file(${MITK_SOURCE_DIR}/CTestConfigSubProject.cmake.in ${MITK_BINARY_DIR}/CTestConfigSubProject.cmake) # Generate Project.xml file expected by the CTest driver script mitkFunctionGenerateProjectXml(${MITK_BINARY_DIR} ${PROJECT_NAME} "${CTEST_PROJECT_SUBPROJECTS}" ${MITK_USE_SUPERBUILD}) #----------------------------------------------------------------------------- # Superbuild script #----------------------------------------------------------------------------- if(MITK_USE_SUPERBUILD) include("${CMAKE_CURRENT_SOURCE_DIR}/SuperBuild.cmake") return() endif() #***************************************************************************** #**************************** END OF SUPERBUILD **************************** #***************************************************************************** #----------------------------------------------------------------------------- # CMake Function(s) and Macro(s) #----------------------------------------------------------------------------- include(mitkFunctionCheckCompilerFlags) include(mitkFunctionGetGccVersion) include(MacroParseArguments) include(mitkFunctionSuppressWarnings) # includes several functions include(mitkFunctionOrganizeSources) include(mitkFunctionGetVersion) include(mitkFunctionCreateWindowsBatchScript) include(mitkMacroCreateModuleConf) include(mitkMacroCreateModule) include(mitkMacroCheckModule) include(mitkMacroCreateModuleTests) include(mitkMacroUseModule) include(mitkMacroMultiplexPicType) include(mitkMacroInstall) include(mitkMacroInstallHelperApp) include(mitkMacroInstallTargets) include(mitkMacroGenerateToolsLibrary) #----------------------------------------------------------------------------- # Prerequesites #----------------------------------------------------------------------------- find_package(ITK REQUIRED) find_package(VTK REQUIRED) #----------------------------------------------------------------------------- # Set MITK specific options and variables (NOT available during superbuild) #----------------------------------------------------------------------------- # ASK THE USER TO SHOW THE CONSOLE WINDOW FOR CoreApp and ExtApp option(MITK_SHOW_CONSOLE_WINDOW "Use this to enable or disable the console window when starting MITK GUI Applications" ON) mark_as_advanced(MITK_SHOW_CONSOLE_WINDOW) # TODO: check if necessary option(USE_ITKZLIB "Use the ITK zlib for pic compression." ON) mark_as_advanced(USE_ITKZLIB) #----------------------------------------------------------------------------- # Get MITK version info #----------------------------------------------------------------------------- mitkFunctionGetVersion(${MITK_SOURCE_DIR} MITK) #----------------------------------------------------------------------------- # Set symbol visibility Flags #----------------------------------------------------------------------------- # MinGW does not export all symbols automatically, so no need to set flags if(CMAKE_COMPILER_IS_GNUCXX AND NOT MINGW) set(VISIBILITY_CXX_FLAGS ) #"-fvisibility=hidden -fvisibility-inlines-hidden") endif() #----------------------------------------------------------------------------- # Set coverage Flags #----------------------------------------------------------------------------- if(WITH_COVERAGE) if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU") set(coverage_flags "-g -fprofile-arcs -ftest-coverage -O0 -DNDEBUG") set(COVERAGE_CXX_FLAGS ${coverage_flags}) set(COVERAGE_C_FLAGS ${coverage_flags}) endif() endif() #----------------------------------------------------------------------------- # MITK C/CXX Flags #----------------------------------------------------------------------------- set(MITK_C_FLAGS "${CMAKE_C_FLAGS} ${COVERAGE_C_FLAGS} ${ADDITIONAL_C_FLAGS}") set(MITK_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${VISIBILITY_CXX_FLAGS} ${COVERAGE_CXX_FLAGS} ${ADDITIONAL_CXX_FLAGS}") if(CMAKE_COMPILER_IS_GNUCXX) set(cflags "-Wall -Wextra -Wpointer-arith -Winvalid-pch -Wcast-align -Wwrite-strings -D_FORTIFY_SOURCE=2") mitkFunctionCheckCompilerFlags("-fdiagnostics-show-option" cflags) mitkFunctionCheckCompilerFlags("-Wl,--no-undefined" cflags) mitkFunctionGetGccVersion(${CMAKE_CXX_COMPILER} GCC_VERSION) # With older version of gcc supporting the flag -fstack-protector-all, an extra dependency to libssp.so # is introduced. If gcc is smaller than 4.4.0 and the build type is Release let's not include the flag. # Doing so should allow to build package made for distribution using older linux distro. if(${GCC_VERSION} VERSION_GREATER "4.4.0" OR (CMAKE_BUILD_TYPE STREQUAL "Debug" AND ${GCC_VERSION} VERSION_LESS "4.4.0")) mitkFunctionCheckCompilerFlags("-fstack-protector-all" cflags) endif() if(MINGW) # suppress warnings about auto imported symbols set(MITK_CXX_FLAGS "-Wl,--enable-auto-import ${MITK_CXX_FLAGS}") # we need to define a Windows version set(MITK_CXX_FLAGS "-D_WIN32_WINNT=0x0500 ${MITK_CXX_FLAGS}") endif() set(MITK_C_FLAGS "${cflags} ${MITK_C_FLAGS}") #set(MITK_CXX_FLAGS "${cflags} -Woverloaded-virtual -Wold-style-cast -Wstrict-null-sentinel -Wsign-promo ${MITK_CXX_FLAGS}") set(MITK_CXX_FLAGS "${cflags} -Woverloaded-virtual -Wstrict-null-sentinel ${MITK_CXX_FLAGS}") endif() #----------------------------------------------------------------------------- # MITK Modules #----------------------------------------------------------------------------- set(MITK_MODULES_CONF_DIR ${MITK_BINARY_DIR}/modulesConf CACHE INTERNAL "Modules Conf") set(MITK_MODULES_PACKAGE_DEPENDS_DIR ${MITK_SOURCE_DIR}/CMake/PackageDepends) set(MODULES_PACKAGE_DEPENDS_DIRS ${MITK_MODULES_PACKAGE_DEPENDS_DIR}) #----------------------------------------------------------------------------- # Testing #----------------------------------------------------------------------------- if(BUILD_TESTING) enable_testing() include(CTest) mark_as_advanced(TCL_TCLSH DART_ROOT) option(MITK_ENABLE_GUI_TESTING OFF "Enable the MITK GUI tests") # Setup file for setting custom ctest vars configure_file( CMake/CTestCustom.cmake.in ${MITK_BINARY_DIR}/CTestCustom.cmake @ONLY ) # Configuration for the CMake-generated test driver set(CMAKE_TESTDRIVER_EXTRA_INCLUDES "#include ") set(CMAKE_TESTDRIVER_BEFORE_TESTMAIN " try {") set(CMAKE_TESTDRIVER_AFTER_TESTMAIN " } catch( std::exception & excp ) { fprintf(stderr,\"%s\\n\",excp.what()); return EXIT_FAILURE; } catch( ... ) { printf(\"Exception caught in the test driver\\n\"); return EXIT_FAILURE; } ") set(MITK_TEST_OUTPUT_DIR "${MITK_BINARY_DIR}/test_output") if(NOT EXISTS ${MITK_TEST_OUTPUT_DIR}) file(MAKE_DIRECTORY ${MITK_TEST_OUTPUT_DIR}) endif() configure_file(mitkTestingConfig.h.in ${MITK_BINARY_DIR}/mitkTestingConfig.h) endif() #----------------------------------------------------------------------------- # MITK_SUPERBUILD_BINARY_DIR #----------------------------------------------------------------------------- # If MITK_SUPERBUILD_BINARY_DIR isn't defined, it means MITK is *NOT* build using Superbuild. # In that specific case, MITK_SUPERBUILD_BINARY_DIR should default to MITK_BINARY_DIR if(NOT DEFINED MITK_SUPERBUILD_BINARY_DIR) set(MITK_SUPERBUILD_BINARY_DIR ${MITK_BINARY_DIR}) endif() #----------------------------------------------------------------------------- # Compile Utilities and set-up MITK variables #----------------------------------------------------------------------------- add_subdirectory(Utilities) include(mitkSetupVariables) if(MITK_USE_BLUEBERRY) include(mitkSetupBlueBerry) endif() #----------------------------------------------------------------------------- # Set C/CXX Flags for MITK code #----------------------------------------------------------------------------- set(CMAKE_CXX_FLAGS ${MITK_CXX_FLAGS}) set(CMAKE_C_FLAGS ${MITK_C_FLAGS}) if(MITK_USE_QT) add_definitions(-DQWT_DLL) endif() #----------------------------------------------------------------------------- # Add custom targets representing CDash subprojects #----------------------------------------------------------------------------- foreach(subproject ${CTEST_PROJECT_SUBPROJECTS}) if(NOT TARGET ${subproject}) add_custom_target(${subproject}) endif() endforeach() #----------------------------------------------------------------------------- # Add subdirectories #----------------------------------------------------------------------------- link_directories(${MITK_LINK_DIRECTORIES}) add_subdirectory(Core) set(MITK_DEFAULT_SUBPROJECTS MITK-CoreUI) if(MITK_USE_QT AND QT4_FOUND) add_subdirectory(CoreUI/Qmitk) endif() add_subdirectory(Modules) if(MITK_USE_BLUEBERRY) set(mitk_core_plugins CoreUI/Bundles/org.mitk.core.services:ON CoreUI/Bundles/org.mitk.gui.common:ON CoreUI/Bundles/org.mitk.gui.qt.common:ON CoreUI/Bundles/org.mitk.gui.qt.application:ON ) set(mitk_ext_plugins Modules/Bundles/org.mitk.core.ext:ON Modules/Bundles/org.mitk.core.jobs:OFF + Modules/Bundles/org.mitk.diffusionimaging:OFF + Modules/Bundles/org.mitk.gui.qt.diffusionimaging:OFF Modules/Bundles/org.mitk.gui.qt.ext:ON Modules/Bundles/org.mitk.gui.qt.extapplication:ON ) ctkMacroSetupExternalPlugins(${mitk_core_plugins} ${mitk_ext_plugins} BUILD_OPTION_PREFIX MITK_BUILD_ BUILD_ALL ${MITK_BUILD_ALL_PLUGINS} COMPACT_OPTIONS) set(MITK_COREAPP_PROVISIONING_FILE "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/CoreApp.provisioning") if(EXISTS "${MITK_COREAPP_PROVISIONING_FILE}") file(REMOVE "${MITK_COREAPP_PROVISIONING_FILE}") endif() file(APPEND "${MITK_COREAPP_PROVISIONING_FILE}" "READ file://${BLUEBERRY_PLUGIN_PROVISIONING_FILE}\n") FunctionCreateProvisioningInfo(prov_info "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/plugins" ${mitk_core_plugins}) file(APPEND "${MITK_COREAPP_PROVISIONING_FILE}" "${prov_info}") set(MITK_EXTAPP_PROVISIONING_FILE "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/ExtApp.provisioning") if(EXISTS "${MITK_EXTAPP_PROVISIONING_FILE}") file(REMOVE "${MITK_EXTAPP_PROVISIONING_FILE}") endif() file(APPEND "${MITK_EXTAPP_PROVISIONING_FILE}" "READ file://${MITK_COREAPP_PROVISIONING_FILE}\n") FunctionCreateProvisioningInfo(prov_info "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/plugins" ${mitk_ext_plugins}) file(APPEND "${MITK_EXTAPP_PROVISIONING_FILE}" "${prov_info}") set(MITK_CORE_PLUGIN_USE_FILE "${MITK_BINARY_DIR}/MitkCorePluginUseFile.cmake") ctkFunctionGeneratePluginUseFile(${MITK_CORE_PLUGIN_USE_FILE}) endif() if(MITK_USE_BLUEBERRY) add_subdirectory(Modules/Bundles) endif() add_subdirectory(Applications) #----------------------------------------------------------------------------- # Python Wrapping #----------------------------------------------------------------------------- set(MITK_WRAPPING_SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Wrapping) set(MITK_WRAPPING_BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/Wrapping) option(MITK_USE_PYTHON "Build cswig Python wrapper support (requires CableSwig)." OFF) if(MITK_USE_PYTHON) add_subdirectory(Wrapping) endif() #----------------------------------------------------------------------------- # Documentation #----------------------------------------------------------------------------- add_subdirectory(Documentation) #----------------------------------------------------------------------------- # Installation #----------------------------------------------------------------------------- if(MITK_INSTALL_RPATH_RELATIVE) set(CMAKE_INSTALL_RPATH ".") else() set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/bin") endif() # on Mac OSX all BlueBerry plugins get copied into every # application bundle (.app directory) specified here if(APPLE) if(MITK_BUILD_org.mitk.gui.qt.extapplication) set(MACOSX_BUNDLE_NAMES ${MACOSX_BUNDLE_NAMES} ExtApp) endif() if(MITK_BUILD_org.mitk.gui.qt.application) set(MACOSX_BUNDLE_NAMES ${MACOSX_BUNDLE_NAMES} CoreApp) endif() endif(APPLE) # set MITK cpack variables include(mitkSetupCPack) if(MITK_BUILD_org.mitk.gui.qt.application) list(APPEND CPACK_CREATE_DESKTOP_LINKS "CoreApp") endif() if(MITK_BUILD_org.mitk.gui.qt.extapplication) list(APPEND CPACK_CREATE_DESKTOP_LINKS "ExtApp") endif() configure_file(${MITK_SOURCE_DIR}/MITKCPackOptions.cmake.in ${MITK_BINARY_DIR}/MITKCPackOptions.cmake @ONLY) set(CPACK_PROJECT_CONFIG_FILE "${MITK_BINARY_DIR}/MITKCPackOptions.cmake") # include CPack model once all variables are set include(CPack) # Additional installation rules include(mitkInstallRules) #----------------------------------------------------------------------------- # Last configuration steps #----------------------------------------------------------------------------- set(MITK_EXPORTS_FILE "${MITK_BINARY_DIR}/MitkExports.cmake") file(REMOVE ${MITK_EXPORTS_FILE}) if(MITK_USE_BLUEBERRY) set(enabled_plugins ${BLUEBERRY_ENABLED_PLUGINS} ${MITK_CORE_ENABLED_PLUGINS} ${MITK_MODULES_ENABLED_PLUGINS} ) # This is for installation support of external projects depending on # MITK plugins. The export file should not be used for linking to MITK # libraries without using LINK_DIRECTORIES, since the exports are incomplete # yet(depending libraries are not exported). foreach(plugin ${enabled_plugins}) string(REPLACE "." "_" plugin_target ${plugin}) export(TARGETS ${plugin_target} APPEND FILE ${MITK_EXPORTS_FILE}) endforeach() endif() configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactory.cpp.in ${MITK_BINARY_DIR}/ToolExtensionITKFactory.cpp.in COPYONLY) configure_file(${MITK_SOURCE_DIR}/CMake/ToolExtensionITKFactoryLoader.cpp.in ${MITK_BINARY_DIR}/ToolExtensionITKFactoryLoader.cpp.in COPYONLY) configure_file(${MITK_SOURCE_DIR}/CMake/ToolGUIExtensionITKFactory.cpp.in ${MITK_BINARY_DIR}/ToolGUIExtensionITKFactory.cpp.in COPYONLY) configure_file(mitkVersion.h.in ${MITK_BINARY_DIR}/mitkVersion.h) configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h) set(VECMATH_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/vecmath) set(IPFUNC_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities/ipFunc) set(UTILITIES_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Utilities) configure_file(mitkConfig.h.in ${MITK_BINARY_DIR}/mitkConfig.h) configure_file(MITKConfig.cmake.in ${MITK_BINARY_DIR}/MITKConfig.cmake @ONLY) diff --git a/Modules/Bundles/CMakeLists.txt b/Modules/Bundles/CMakeLists.txt index 65f518d63c..4d5dcc392f 100644 --- a/Modules/Bundles/CMakeLists.txt +++ b/Modules/Bundles/CMakeLists.txt @@ -1,43 +1,45 @@ IF(MITK_USE_BLUEBERRY) # INCLUDE("${MITK_BINARY_DIR}/mitkExtConfig.cmake") # INCLUDE("${MITK_BINARY_DIR}/QmitkExtConfig.cmake") INCLUDE("${MITK_BINARY_DIR}/Bundles/MITKCoreBundleList.cmake") SET(MITK_DEFAULT_SUBPROJECTS MITK-Plugins) SET(_mitk_bundles_default "org.mitk.planarfigure" ) IF(QT4_FOUND) LIST(APPEND _mitk_bundles_default "org.mitk.gui.qt.ext" "org.mitk.gui.qt.extapplication") # ExtApp required bundles LIST(APPEND _mitk_bundles_default "org.mitk.gui.qt.imagenavigator" "org.mitk.gui.qt.datamanager") # BlueBerry depends on CTK which depends on Qt, so we # need the Qt include direcotries INCLUDE(${QT_USE_FILE}) ENDIF() SET(PLUGIN_EXCLUDE_LIST org.mitk.core.ext org.mitk.gui.qt.volumetry org.mitk.core.jobs + org.mitk.diffusionimaging + org.mitk.gui.qt.diffusionimaging org.mitk.gui.qt.ext org.mitk.gui.qt.extapplication ) MACRO_COLLECT_PLUGINS(OUTPUT_DIR ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/ExtBundles CACHE_PLUGIN_SOURCE_DIRS MITK_MODULES_PLUGIN_SOURCE_DIRS CACHE_PLUGIN_OUTPUT_DIRS MITK_MODULES_PLUGIN_OUTPUT_DIRS CACHE_PLUGIN_TARGETS MITK_MODULES_ENABLED_PLUGINS BUNDLE_LIST_PATH "${MITK_BINARY_DIR}/Bundles/MITKModulesBundleList.cmake" CMAKE_CACHE_PREFIX "MITK" PLUGIN_DEFAULT_ON ${_mitk_bundles_default} PLUGIN_EXCLUDES ${PLUGIN_EXCLUDE_LIST} ${MITK_BUILD_ALL_PLUGINS_OPTION}) ENDIF(MITK_USE_BLUEBERRY) diff --git a/Modules/Bundles/org.mitk.diffusionimaging/CMakeLists.txt b/Modules/Bundles/org.mitk.diffusionimaging/CMakeLists.txt index 4ccff3acb1..3d05bd3950 100644 --- a/Modules/Bundles/org.mitk.diffusionimaging/CMakeLists.txt +++ b/Modules/Bundles/org.mitk.diffusionimaging/CMakeLists.txt @@ -1,2 +1,7 @@ +PROJECT(org_mitk_diffusionimaging) -MACRO_CREATE_MITK_PLUGIN(MitkDiffusionImaging Qmitk QmitkExt) +MACRO_CREATE_MITK_CTK_PLUGIN( + EXPORT_DIRECTIVE ORG_MITK_DIFFUSIONIMAGING_EXPORT + EXPORTED_INCLUDE_SUFFIXES src + MODULE_DEPENDENCIES MitkDiffusionImaging QmitkExt +) diff --git a/Modules/Bundles/org.mitk.diffusionimaging/META-INF/MANIFEST.MF b/Modules/Bundles/org.mitk.diffusionimaging/META-INF/MANIFEST.MF deleted file mode 100644 index a884e68c0e..0000000000 --- a/Modules/Bundles/org.mitk.diffusionimaging/META-INF/MANIFEST.MF +++ /dev/null @@ -1,8 +0,0 @@ -Manifest-Version: 1.0 -Bundle-Name: MBI DiffusionImaging -Bundle-SymbolicName: org.mitk.diffusionimaging -Bundle-Version: 0.1 -Bundle-Vendor: DKFZ, Medical and Biological Informatics -Require-Bundle: org.blueberry.osgi, org.blueberry.ui, org.mitk.gui.common -Bundle-Activator: mitk::DiffusionImagingActivator -Bundle-ActivationPolicy: eager diff --git a/Modules/Bundles/org.mitk.diffusionimaging/files.cmake b/Modules/Bundles/org.mitk.diffusionimaging/files.cmake index fe07714ba8..3b39ed6c21 100644 --- a/Modules/Bundles/org.mitk.diffusionimaging/files.cmake +++ b/Modules/Bundles/org.mitk.diffusionimaging/files.cmake @@ -1,18 +1,22 @@ SET(SRC_CPP_FILES ) SET(INTERNAL_CPP_FILES mitkDiffusionImagingActivator.cpp ) -SET(CPP_FILES manifest.cpp) +SET(MOC_H_FILES + src/internal/mitkDiffusionImagingActivator.h +) + +SET(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) SET(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) SET(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Modules/Bundles/org.mitk.diffusionimaging/manifest.cpp b/Modules/Bundles/org.mitk.diffusionimaging/manifest.cpp deleted file mode 100644 index 4280b3afef..0000000000 --- a/Modules/Bundles/org.mitk.diffusionimaging/manifest.cpp +++ /dev/null @@ -1,25 +0,0 @@ -/*========================================================================= - -Program: Medical Imaging & Interaction Toolkit -Language: C++ -Date: $Date: 2009-07-14 19:11:20 +0200 (Tue, 14 Jul 2009) $ -Version: $Revision: 18127 $ - -Copyright (c) German Cancer Research Center, Division of Medical and -Biological Informatics. All rights reserved. -See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. - -This software is distributed WITHOUT ANY WARRANTY; without even -the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR -PURPOSE. See the above copyright notices for more information. - -=========================================================================*/ - -#include - -#include -#include "src/internal/mitkDiffusionImagingActivator.h" - -POCO_BEGIN_MANIFEST(berry::IBundleActivator) -POCO_EXPORT_CLASS(mitk::DiffusionImagingActivator) -POCO_END_MANIFEST diff --git a/Modules/Bundles/org.mitk.diffusionimaging/manifest_headers.cmake b/Modules/Bundles/org.mitk.diffusionimaging/manifest_headers.cmake new file mode 100644 index 0000000000..e6cfa071fe --- /dev/null +++ b/Modules/Bundles/org.mitk.diffusionimaging/manifest_headers.cmake @@ -0,0 +1,6 @@ +set(Plugin-Name "MBI DiffusionImaging") +set(Plugin-Version "0.1") +set(Plugin-Vendor "DKFZ, Medical and Biological Informatics") +set(Plugin-ContactAddress "http://www.mitk.org") +set(Require-Plugin org.mitk.gui.common) +set(Plugin-ActivationPolicy eager) diff --git a/Modules/Bundles/org.mitk.diffusionimaging/src/internal/mitkDiffusionImagingActivator.cpp b/Modules/Bundles/org.mitk.diffusionimaging/src/internal/mitkDiffusionImagingActivator.cpp index e8db5ee8c2..167af0b088 100644 --- a/Modules/Bundles/org.mitk.diffusionimaging/src/internal/mitkDiffusionImagingActivator.cpp +++ b/Modules/Bundles/org.mitk.diffusionimaging/src/internal/mitkDiffusionImagingActivator.cpp @@ -1,116 +1,54 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date: 2009-07-14 19:11:20 +0200 (Tue, 14 Jul 2009) $ Version: $Revision: 18127 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "mitkDiffusionImagingActivator.h" #include "mitkDiffusionImagingObjectFactory.h" #include "QmitkNodeDescriptorManager.h" #include "mitkNodePredicateDataType.h" -//#include "mitkDataNodeObject.h" -// -//#include "berryISelectionService.h" -//#include "berryIStructuredSelection.h" -//#include "berryPlatformUI.h" -// -//#include -//#include + +#include void -mitk::DiffusionImagingActivator::Start(berry::IBundleContext::Pointer /*context*/) +mitk::DiffusionImagingActivator::start(ctkPluginContext* context) { + Q_UNUSED(context) + RegisterDiffusionImagingObjectFactory(); QmitkNodeDescriptorManager* manager = QmitkNodeDescriptorManager::GetInstance(); mitk::NodePredicateDataType::Pointer isDiffusionImage = mitk::NodePredicateDataType::New("DiffusionImage"); QmitkNodeDescriptor* desc = new QmitkNodeDescriptor(QObject::tr("DiffusionImage"), QString(":/QmitkDiffusionImaging/QBallData24.png"), isDiffusionImage, manager); manager->AddDescriptor(desc); mitk::NodePredicateDataType::Pointer isTensorImage = mitk::NodePredicateDataType::New("TensorImage"); manager->AddDescriptor(new QmitkNodeDescriptor(QObject::tr("TensorImage"), QString(":/QmitkDiffusionImaging/recontensor.png"), isTensorImage, manager)); mitk::NodePredicateDataType::Pointer isQBallImage = mitk::NodePredicateDataType::New("QBallImage"); manager->AddDescriptor(new QmitkNodeDescriptor(QObject::tr("QBallImage"), QString(":/QmitkDiffusionImaging/reconodf.png"), isQBallImage, manager)); - //m_OpacitySlider = new QSlider; - //m_OpacitySlider->setMinimum(0); - //m_OpacitySlider->setMaximum(100); - //m_OpacitySlider->setOrientation(Qt::Horizontal); - //QObject::connect( m_OpacitySlider, SIGNAL( valueChanged(int) ) - // , this, SLOT( OpactiyChanged(int) ) ); - - //QLabel* _OpacityLabel = new QLabel("Channel: "); - //QHBoxLayout* _OpacityWidgetLayout = new QHBoxLayout; - //_OpacityWidgetLayout->addWidget(_OpacityLabel); - //_OpacityWidgetLayout->addWidget(m_OpacitySlider); - //QWidget* _OpacityWidget = new QWidget; - //_OpacityWidget->setLayout(_OpacityWidgetLayout); - - //QWidgetAction* m_OpacityAction = new QWidgetAction(this); - //m_OpacityAction->setDefaultWidget(_OpacityWidget); - //QObject::connect( m_OpacityAction, SIGNAL( changed() ) - // , this, SLOT( OpactiyActionChanged() ) ); - - // desc->AddAction(m_OpacityAction, false); +} +void +mitk::DiffusionImagingActivator::stop(ctkPluginContext* context) +{ + Q_UNUSED(context) } -//void mitk::DiffusionImagingActivator::OpactiyChanged(int value) -//{ -// berry::ISelection::ConstPointer sel( -// berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); -// berry::IStructuredSelection::ConstPointer ssel = sel.Cast(); -// -// if (ssel) -// { -// if (mitk::DataNodeObject::Pointer nodeObj = ssel->Begin()->Cast()) -// { -// mitk::DataNode::Pointer node = nodeObj->GetDataNode(); -// if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) -// { -// node->SetIntProperty("DisplayChannel", value); -// mitk::RenderingManager::GetInstance()->RequestUpdateAll(); -// } -// } -// } -//} -// -//void mitk::DiffusionImagingActivator::OpactiyActionChanged() -//{ -// berry::ISelection::ConstPointer sel( -// berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); -// berry::IStructuredSelection::ConstPointer ssel = sel.Cast(); -// -// if (ssel) -// { -// if (mitk::DataNodeObject::Pointer nodeObj = ssel->Begin()->Cast()) -// { -// mitk::DataNode::Pointer node = nodeObj->GetDataNode(); -// if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) -// { -// int displayChannel = 0.0; -// if(node->GetIntProperty("DisplayChannel", displayChannel)) -// { -// m_OpacitySlider->setValue(displayChannel); -// } -// } -// } -// } -// -// MITK_INFO << "changed"; -//} \ No newline at end of file +Q_EXPORT_PLUGIN2(org_mitk_diffusionimaging, mitk::DiffusionImagingActivator) diff --git a/Modules/Bundles/org.mitk.diffusionimaging/src/internal/mitkDiffusionImagingActivator.h b/Modules/Bundles/org.mitk.diffusionimaging/src/internal/mitkDiffusionImagingActivator.h index 218f3abf82..b0cc568ffa 100644 --- a/Modules/Bundles/org.mitk.diffusionimaging/src/internal/mitkDiffusionImagingActivator.h +++ b/Modules/Bundles/org.mitk.diffusionimaging/src/internal/mitkDiffusionImagingActivator.h @@ -1,65 +1,54 @@ /*========================================================================= Program: MITK Platform Language: C++ Date: $Date: 2009-05-19 15:45:39 +0200 (Di, 19 Mai 2009) $ Version: $Revision: 17020 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITKDIFFUSIONIMAGINGACTIVATOR_H_ #define MITKDIFFUSIONIMAGINGACTIVATOR_H_ -#include - -#include - -//#include -//#include +#include namespace mitk { /** * \ingroup org_mitk_diffusionimaging_internal * * \brief The plug-in activator for the diffusion imaging module * - * When the plug-in is started by the framework, it initialzes sandbox + * When the plug-in is started by the framework, it initialzes diffusion imaging * specific things. */ -class ORG_MITK_DIFFUSIONIMAGING_EXPORT DiffusionImagingActivator : - /*public QObject, */public berry::Plugin +class DiffusionImagingActivator : + public QObject, public ctkPluginActivator { - //Q_OBJECT + Q_OBJECT + Q_INTERFACES(ctkPluginActivator) public: /** - * Registers sandbox core object factories. + * Registers diffusion imaging object factories. */ - void Start(berry::IBundleContext::Pointer context); - - //void OpactiyChanged(int value); - //void OpactiyActionChanged(); - - //void CreateQtPartControl(QWidget *){} - -private: - - //QSlider* m_OpacitySlider; + void start(ctkPluginContext* context); + + void stop(ctkPluginContext* context); }; } #endif /* MITKDIFFUSIONIMAGINGACTIVATOR_H_ */ diff --git a/Modules/Bundles/org.mitk.diffusionimaging/src/mitkDiffusionImagingDll.h b/Modules/Bundles/org.mitk.diffusionimaging/src/mitkDiffusionImagingDll.h deleted file mode 100644 index eae734f38d..0000000000 --- a/Modules/Bundles/org.mitk.diffusionimaging/src/mitkDiffusionImagingDll.h +++ /dev/null @@ -1,43 +0,0 @@ -/*========================================================================= - -Program: Medical Imaging & Interaction Toolkit -Language: C++ -Date: $Date: 2009-05-28 20:03:37 +0200 (Do, 28 Mai 2009) $ -Version: $Revision: 17020 $ - -Copyright (c) German Cancer Research Center, Division of Medical and -Biological Informatics. All rights reserved. -See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. - -This software is distributed WITHOUT ANY WARRANTY; without even -the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR -PURPOSE. See the above copyright notices for more information. - -=========================================================================*/ - -#ifndef _MBI_MITKDIFFUSIONIMAGING_EXPORT_DLL_H_ -#define _MBI_MITKDIFFUSIONIMAGING_EXPORT_DLL_H_ - - -// -// The following block is the standard way of creating macros which make exporting -// from a DLL simpler. All files within this DLL are compiled with the org_mitk_diffusionimaging_EXPORTS -// symbol defined on the command line. this symbol should not be defined on any project -// that uses this DLL. This way any other project whose source files include this file see -// org_mitk_diffusionimaging_EXPORTS functions as being imported from a DLL, wheras this DLL sees symbols -// defined with this macro as being exported. -// -#if defined(_WIN32) && !defined(MITK_STATIC) - #if defined(org_mitk_diffusionimaging_EXPORTS) - #define ORG_MITK_DIFFUSIONIMAGING_EXPORT __declspec(dllexport) - #else - #define ORG_MITK_DIFFUSIONIMAGING_EXPORT __declspec(dllimport) - #endif -#endif - - -#if !defined(ORG_MITK_DIFFUSIONIMAGING_EXPORT) - #define ORG_MITK_DIFFUSIONIMAGING_EXPORT -#endif - -#endif /*_MBI_MITKDIFFUSIONIMAGING_EXPORT_DLL_H_*/ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt index 7c74b94876..775263d718 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/CMakeLists.txt @@ -1,2 +1,7 @@ -INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIR}) -MACRO_CREATE_MITK_PLUGIN(QmitkExt MitkDiffusionImaging) +PROJECT(org_mitk_gui_qt_diffusionimaging) + +MACRO_CREATE_MITK_CTK_PLUGIN( + EXPORT_DIRECTIVE DIFFUSIONIMAGING_EXPORT + EXPORTED_INCLUDE_SUFFIXES src + MODULE_DEPENDENCIES QmitkExt MitkDiffusionImaging +) diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/META-INF/MANIFEST.MF b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/META-INF/MANIFEST.MF deleted file mode 100644 index 98b71130e6..0000000000 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/META-INF/MANIFEST.MF +++ /dev/null @@ -1,7 +0,0 @@ -Manifest-Version: 1.0 -Bundle-Name: Diffusion Imaging -Bundle-SymbolicName: org.mitk.gui.qt.diffusionimaging -Bundle-Version: 0.1 -Bundle-Vendor: DKFZ, Medical and Biological Informatics -Require-Bundle: org.mitk.gui.qt.common, org.mitk.diffusionimaging -Bundle-Activator: diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/files.cmake b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/files.cmake index e14d168c1e..213a109ef8 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/files.cmake +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/files.cmake @@ -1,74 +1,65 @@ SET(SRC_CPP_FILES ) SET(INTERNAL_CPP_FILES + mitkPluginActivator.cpp QmitkQBallReconstructionView.cpp QmitkPreprocessingView.cpp QmitkDiffusionDicomImportView.cpp QmitkDiffusionQuantificationView.cpp QmitkTensorReconstructionView.cpp QmitkDiffusionImagingPublicPerspective.cpp QmitkControlVisualizationPropertiesView.cpp ) SET(UI_FILES src/internal/QmitkQBallReconstructionViewControls.ui src/internal/QmitkPreprocessingViewControls.ui src/internal/QmitkDiffusionDicomImportViewControls.ui src/internal/QmitkDiffusionQuantificationViewControls.ui src/internal/QmitkTensorReconstructionViewControls.ui src/internal/QmitkControlVisualizationPropertiesViewControls.ui ) SET(MOC_H_FILES + src/internal/mitkPluginActivator.h src/internal/QmitkQBallReconstructionView.h src/internal/QmitkPreprocessingView.h src/internal/QmitkDiffusionDicomImportView.h + src/internal/QmitkDiffusionImagingPublicPerspective.h src/internal/QmitkDiffusionQuantificationView.h src/internal/QmitkTensorReconstructionView.h src/internal/QmitkControlVisualizationPropertiesView.h ) -SET(RESOURCE_FILES +SET(CACHED_RESOURCE_FILES # list of resource files which can be used by the plug-in # system without loading the plug-ins shared library, # for example the icon used in the menu and tabs for the # plug-in views in the workbench - resources/dwi.png - resources/tensor.png - resources/qball.png + plugin.xml + resources/preprocessing.png resources/dwiimport.png resources/quantification.png resources/reconodf.png resources/recontensor.png - resources/stats.png - resources/texIntOFFIcon.png - resources/texIntONIcon.png resources/vizControls.png - resources/Refresh_48.png - resources/QBallData24.png - resources/glyphsoff_C.png - resources/glyphsoff_S.png - resources/glyphsoff_T.png - resources/glyphson_C.png - resources/glyphson_S.png - resources/glyphson_T.png ) -SET(RES_FILES +SET(QRC_FILES # uncomment the following line if you want to use Qt resources resources/QmitkDiffusionImaging.qrc ) -SET(CPP_FILES manifest.cpp) +SET(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) SET(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) SET(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/manifest.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/manifest.cpp deleted file mode 100644 index 4dcc09b83f..0000000000 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/manifest.cpp +++ /dev/null @@ -1,42 +0,0 @@ -/*========================================================================= - -Program: Medical Imaging & Interaction Toolkit -Module: $RCSfile$ -Language: C++ -Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ -Version: $Revision: 17495 $ - -Copyright (c) German Cancer Research Center, Division of Medical and -Biological Informatics. All rights reserved. -See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. - -This software is distributed WITHOUT ANY WARRANTY; without even -the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR -PURPOSE. See the above copyright notices for more information. - -=========================================================================*/ - -#include - -#include "src/internal/QmitkQBallReconstructionView.h" -#include "src/internal/QmitkPreprocessingView.h" -#include "src/internal/QmitkDiffusionDicomImportView.h" -#include "src/internal/QmitkDiffusionQuantificationView.h" -#include "src/internal/QmitkTensorReconstructionView.h" -#include "src/internal/QmitkControlVisualizationPropertiesView.h" -//#include "src/internal/QmitkTbssView.h" -#include "src/internal/QmitkDiffusionImagingPublicPerspective.h" - -POCO_BEGIN_NAMED_MANIFEST(berryIPerspectiveFactory, berry::IPerspectiveFactory) - POCO_EXPORT_CLASS(QmitkDiffusionImagingPublicPerspective) -POCO_END_MANIFEST - -POCO_BEGIN_NAMED_MANIFEST(berryIViewPart, berry::IViewPart) - POCO_EXPORT_CLASS(QmitkQBallReconstructionView) - POCO_EXPORT_CLASS(QmitkPreprocessingView) - POCO_EXPORT_CLASS(QmitkDiffusionDicomImport) - POCO_EXPORT_CLASS(QmitkDiffusionQuantificationView) - POCO_EXPORT_CLASS(QmitkTensorReconstructionView) - POCO_EXPORT_CLASS(QmitkControlVisualizationPropertiesView) - //POCO_EXPORT_CLASS(QmitkTbssView) -POCO_END_MANIFEST diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/manifest_headers.cmake b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/manifest_headers.cmake new file mode 100644 index 0000000000..5b8b79e4a1 --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/manifest_headers.cmake @@ -0,0 +1,5 @@ +set(Plugin-Name "Diffusion Imaging") +set(Plugin-Version "0.1") +set(Plugin-Vendor "DKFZ, Medical and Biological Informatics") +set(Plugin-ContactAddress "http://www.mitk.org") +set(Require-Plugin org.mitk.gui.qt.common org.mitk.diffusionimaging) diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/DiffusionimagingDll.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/DiffusionimagingDll.h deleted file mode 100644 index 1d59e0f889..0000000000 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/DiffusionimagingDll.h +++ /dev/null @@ -1,44 +0,0 @@ -/*========================================================================= - -Program: Medical Imaging & Interaction Toolkit -Module: $RCSfile$ -Language: C++ -Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ -Version: $Revision: 17495 $ - -Copyright (c) German Cancer Research Center, Division of Medical and -Biological Informatics. All rights reserved. -See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. - -This software is distributed WITHOUT ANY WARRANTY; without even -the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR -PURPOSE. See the above copyright notices for more information. - -=========================================================================*/ - -#ifndef _DIFFUSIONIMAGING_EXPORT_DLL_H_ -#define _DIFFUSIONIMAGING_EXPORT_DLL_H_ - - -// -// The following block is the standard way of creating macros which make exporting -// from a DLL simpler. All files within this DLL are compiled with the org_mitk_gui_qt_diffusionimaging_EXPORTS -// symbol defined on the command line. this symbol should not be defined on any project -// that uses this DLL. This way any other project whose source files include this file see -// org_mitk_gui_qt_diffusionimaging_EXPORTS functions as being imported from a DLL, wheras this DLL sees symbols -// defined with this macro as being exported. -// -#if defined(_WIN32) && !defined(MITK_STATIC) - #if defined(org_mitk_gui_qt_diffusionimaging_EXPORTS) - #define DIFFUSIONIMAGING_EXPORT __declspec(dllexport) - #else - #define DIFFUSIONIMAGING_EXPORT __declspec(dllimport) - #endif -#endif - - -#if !defined(DIFFUSIONIMAGING_EXPORT) - #define DIFFUSIONIMAGING_EXPORT -#endif - -#endif /*_DIFFUSIONIMAGING_EXPORT_DLL_H_*/ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp index e485783c92..2dc89658e7 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp @@ -1,876 +1,882 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkControlVisualizationPropertiesView.h" #include "mitkNodePredicateDataType.h" #include "mitkDataNodeObject.h" #include "mitkOdfNormalizationMethodProperty.h" #include "mitkOdfScaleByProperty.h" #include "mitkDiffusionImage.h" #include "QmitkDataStorageComboBox.h" #include "QmitkStdMultiWidget.h" #include "berryIWorkbenchWindow.h" #include "berryIWorkbenchPage.h" #include "berryISelectionService.h" #include "berryConstants.h" #include "berryPlatformUI.h" #include "itkRGBAPixel.h" const std::string QmitkControlVisualizationPropertiesView::VIEW_ID = "org.mitk.views.controlvisualizationpropertiesview"; using namespace berry; struct CvpSelListener : ISelectionListener { berryObjectMacro(CvpSelListener); CvpSelListener(QmitkControlVisualizationPropertiesView* view) { m_View = view; } void ApplySettings(mitk::DataNode::Pointer node) { bool do_vis; node->GetBoolProperty("VisibleOdfs_T", do_vis); if(do_vis) { m_View->m_Controls->m_VisibleOdfsON_T->setIcon(*m_View->m_IconGlyON_T); m_View->m_Controls->m_VisibleOdfsON_T->setChecked(true); m_View->m_GlyIsOn_T = true; } else { m_View->m_Controls->m_VisibleOdfsON_T->setIcon(*m_View->m_IconGlyOFF_T); m_View->m_Controls->m_VisibleOdfsON_T->setChecked(false); m_View->m_GlyIsOn_T = false; } node->GetBoolProperty("VisibleOdfs_C", do_vis); if(do_vis) { m_View->m_Controls->m_VisibleOdfsON_C->setIcon(*m_View->m_IconGlyON_C); m_View->m_Controls->m_VisibleOdfsON_C->setChecked(true); m_View->m_GlyIsOn_C = true; } else { m_View->m_Controls->m_VisibleOdfsON_C->setIcon(*m_View->m_IconGlyOFF_C); m_View->m_Controls->m_VisibleOdfsON_C->setChecked(false); m_View->m_GlyIsOn_C = false; } node->GetBoolProperty("VisibleOdfs_S", do_vis); if(do_vis) { m_View->m_Controls->m_VisibleOdfsON_S->setIcon(*m_View->m_IconGlyON_S); m_View->m_Controls->m_VisibleOdfsON_S->setChecked(true); m_View->m_GlyIsOn_S = true; } else { m_View->m_Controls->m_VisibleOdfsON_S->setIcon(*m_View->m_IconGlyOFF_S); m_View->m_Controls->m_VisibleOdfsON_S->setChecked(false); m_View->m_GlyIsOn_S = false; } bool tex_int; node->GetBoolProperty("texture interpolation", tex_int); if(tex_int) { m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexON); m_View->m_Controls->m_TextureIntON->setChecked(true); m_View->m_TexIsOn = true; } else { m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexOFF); m_View->m_Controls->m_TextureIntON->setChecked(false); m_View->m_TexIsOn = false; } int val; node->GetIntProperty("ShowMaxNumber", val); m_View->m_Controls->m_ShowMaxNumber->setValue(val); m_View->m_Controls->m_NormalizationDropdown->setCurrentIndex(dynamic_cast(node->GetProperty("Normalization"))->GetValueAsId()); float fval; node->GetFloatProperty("Scaling",fval); m_View->m_Controls->m_ScalingFactor->setValue(fval); m_View->m_Controls->m_AdditionalScaling->setCurrentIndex(dynamic_cast(node->GetProperty("ScaleBy"))->GetValueAsId()); node->GetFloatProperty("IndexParam1",fval); m_View->m_Controls->m_IndexParam1->setValue(fval); node->GetFloatProperty("IndexParam2",fval); m_View->m_Controls->m_IndexParam2->setValue(fval); } void DoSelectionChanged(ISelection::ConstPointer selection) { // save current selection in member variable m_View->m_CurrentSelection = selection.Cast(); m_View->m_Controls->m_VisibleOdfsON_T->setVisible(false); m_View->m_Controls->m_VisibleOdfsON_S->setVisible(false); m_View->m_Controls->m_VisibleOdfsON_C->setVisible(false); m_View->m_Controls->m_TextureIntON->setVisible(false); bool foundDiffusionImage = false; bool foundQBIVolume = false; bool foundTensorVolume = false; bool foundImage = false; bool foundMultipleOdfImages = false; bool foundRGBAImage = false; // do something with the selected items if(m_View->m_CurrentSelection) { // iterate selection for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); i != m_View->m_CurrentSelection->End(); ++i) { // extract datatree node if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); // only look at interesting types if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) { foundDiffusionImage = true; bool tex_int; node->GetBoolProperty("texture interpolation", tex_int); if(tex_int) { m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexON); m_View->m_Controls->m_TextureIntON->setChecked(true); m_View->m_TexIsOn = true; } else { m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexOFF); m_View->m_Controls->m_TextureIntON->setChecked(false); m_View->m_TexIsOn = false; } int val; node->GetIntProperty("DisplayChannel", val); m_View->m_Controls->m_DisplayIndex->setValue(val); QString label = "Channel %1"; label = label.arg(val); m_View->m_Controls->label_channel->setText(label); int maxVal = (dynamic_cast* >(node->GetData()))->GetVectorImage()->GetVectorLength(); m_View->m_Controls->m_DisplayIndex->setMaximum(maxVal-1); } else if(QString("QBallImage").compare(node->GetData()->GetNameOfClass())==0) { foundMultipleOdfImages = foundQBIVolume || foundTensorVolume; foundQBIVolume = true; ApplySettings(node); } else if(QString("TensorImage").compare(node->GetData()->GetNameOfClass())==0) { foundMultipleOdfImages = foundQBIVolume || foundTensorVolume; foundTensorVolume = true; ApplySettings(node); } else if(QString("Image").compare(node->GetData()->GetNameOfClass())==0) { foundImage = true; mitk::Image::Pointer img = dynamic_cast(node->GetData()); if(img.IsNotNull() && img->GetPixelType().GetItkTypeId() == &typeid(itk::RGBAPixel) ) { foundRGBAImage = true; } bool tex_int; node->GetBoolProperty("texture interpolation", tex_int); if(tex_int) { m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexON); m_View->m_Controls->m_TextureIntON->setChecked(true); m_View->m_TexIsOn = true; } else { m_View->m_Controls->m_TextureIntON->setIcon(*m_View->m_IconTexOFF); m_View->m_Controls->m_TextureIntON->setChecked(false); m_View->m_TexIsOn = false; } } } } } m_View->m_Controls->m_DisplayIndex->setVisible(foundDiffusionImage); m_View->m_Controls->label_channel->setVisible(foundDiffusionImage); m_View->m_FoundSingleOdfImage = (foundQBIVolume || foundTensorVolume) && !foundMultipleOdfImages; m_View->m_Controls->m_NumberGlyphsFrame->setVisible(m_View->m_FoundSingleOdfImage); m_View->m_Controls->m_NormalizationDropdown->setVisible(m_View->m_FoundSingleOdfImage); m_View->m_Controls->label->setVisible(m_View->m_FoundSingleOdfImage); m_View->m_Controls->m_ScalingFactor->setVisible(m_View->m_FoundSingleOdfImage); m_View->m_Controls->m_AdditionalScaling->setVisible(m_View->m_FoundSingleOdfImage); m_View->m_Controls->m_NormalizationScalingFrame->setVisible(m_View->m_FoundSingleOdfImage); m_View->m_Controls->OpacMinFrame->setVisible(foundRGBAImage || m_View->m_FoundSingleOdfImage); // changed for SPIE paper, Principle curvature scaling //m_View->m_Controls->params_frame->setVisible(m_View->m_FoundSingleOdfImage); m_View->m_Controls->params_frame->setVisible(false); m_View->m_Controls->m_VisibleOdfsON_T->setVisible(m_View->m_FoundSingleOdfImage); m_View->m_Controls->m_VisibleOdfsON_S->setVisible(m_View->m_FoundSingleOdfImage); m_View->m_Controls->m_VisibleOdfsON_C->setVisible(m_View->m_FoundSingleOdfImage); bool foundAnyImage = foundDiffusionImage || foundQBIVolume || foundTensorVolume || foundImage; m_View->m_Controls->m_Reinit->setVisible(foundAnyImage); m_View->m_Controls->m_TextureIntON->setVisible(foundAnyImage); if(m_View->m_IsInitialized) { //m_View->GetSite()->GetWorkbenchWindow()->GetActivePage() // ->HideView(IViewPart::Pointer(m_View)); //berry::PlatformUI::GetWorkbench()->GetActiveWorkbenchWindow()->GetActivePage() // ->ShowView(QmitkControlVisualizationPropertiesView::VIEW_ID, // "", berry::IWorkbenchPage::VIEW_VISIBLE); } } void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) { // check, if selection comes from datamanager if (part) { QString partname(part->GetPartName().c_str()); if(partname.compare("Datamanager")==0) { // apply selection DoSelectionChanged(selection); } } } QmitkControlVisualizationPropertiesView* m_View; }; QmitkControlVisualizationPropertiesView::QmitkControlVisualizationPropertiesView() : QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL), m_IconTexOFF(new QIcon(":/QmitkDiffusionImaging/texIntOFFIcon.png")), m_IconTexON(new QIcon(":/QmitkDiffusionImaging/texIntONIcon.png")), m_IconGlyOFF_T(new QIcon(":/QmitkDiffusionImaging/glyphsoff_T.png")), m_IconGlyON_T(new QIcon(":/QmitkDiffusionImaging/glyphson_T.png")), m_IconGlyOFF_C(new QIcon(":/QmitkDiffusionImaging/glyphsoff_C.png")), m_IconGlyON_C(new QIcon(":/QmitkDiffusionImaging/glyphson_C.png")), m_IconGlyOFF_S(new QIcon(":/QmitkDiffusionImaging/glyphsoff_S.png")), m_IconGlyON_S(new QIcon(":/QmitkDiffusionImaging/glyphson_S.png")) { } +QmitkControlVisualizationPropertiesView::QmitkControlVisualizationPropertiesView(const QmitkControlVisualizationPropertiesView& other) +{ + Q_UNUSED(other) + throw std::runtime_error("Copy constructor not implemented"); +} + QmitkControlVisualizationPropertiesView::~QmitkControlVisualizationPropertiesView() { this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); } void QmitkControlVisualizationPropertiesView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkControlVisualizationPropertiesViewControls; m_Controls->setupUi(parent); this->CreateConnections(); m_Controls->params_frame->setVisible(false); QIcon icon5(":/QmitkDiffusionImaging/Refresh_48.png"); m_Controls->m_Reinit->setIcon(icon5); m_Controls->m_TextureIntON->setCheckable(true); m_Controls->m_VisibleOdfsON_T->setCheckable(true); m_Controls->m_VisibleOdfsON_S->setCheckable(true); m_Controls->m_VisibleOdfsON_C->setCheckable(true); #ifndef DIFFUSION_IMAGING_EXTENDED int size = m_Controls->m_AdditionalScaling->count(); for(int t=0; tm_AdditionalScaling->itemText(t).toStdString() == "Scale by ASR") { m_Controls->m_AdditionalScaling->removeItem(t); } } #endif m_Controls->m_OpacitySlider->setRange(0.0,1.0); m_Controls->m_OpacitySlider->setLowerValue(0.0); m_Controls->m_OpacitySlider->setUpperValue(0.0); m_Controls->m_ScalingFrame->setVisible(false); m_Controls->m_NormalizationFrame->setVisible(false); } m_IsInitialized = false; m_SelListener = berry::ISelectionListener::Pointer(new CvpSelListener(this)); this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); m_IsInitialized = true; } void QmitkControlVisualizationPropertiesView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkControlVisualizationPropertiesView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkControlVisualizationPropertiesView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_DisplayIndex), SIGNAL(valueChanged(int)), this, SLOT(DisplayIndexChanged(int)) ); connect( (QObject*)(m_Controls->m_TextureIntON), SIGNAL(clicked()), this, SLOT(TextIntON()) ); connect( (QObject*)(m_Controls->m_Reinit), SIGNAL(clicked()), this, SLOT(Reinit()) ); connect( (QObject*)(m_Controls->m_VisibleOdfsON_T), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_T()) ); connect( (QObject*)(m_Controls->m_VisibleOdfsON_S), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_S()) ); connect( (QObject*)(m_Controls->m_VisibleOdfsON_C), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_C()) ); connect( (QObject*)(m_Controls->m_ShowMaxNumber), SIGNAL(editingFinished()), this, SLOT(ShowMaxNumberChanged()) ); connect( (QObject*)(m_Controls->m_NormalizationDropdown), SIGNAL(currentIndexChanged(int)), this, SLOT(NormalizationDropdownChanged(int)) ); connect( (QObject*)(m_Controls->m_ScalingFactor), SIGNAL(valueChanged(double)), this, SLOT(ScalingFactorChanged(double)) ); connect( (QObject*)(m_Controls->m_AdditionalScaling), SIGNAL(currentIndexChanged(int)), this, SLOT(AdditionalScaling(int)) ); connect( (QObject*)(m_Controls->m_IndexParam1), SIGNAL(valueChanged(double)), this, SLOT(IndexParam1Changed(double)) ); connect( (QObject*)(m_Controls->m_IndexParam2), SIGNAL(valueChanged(double)), this, SLOT(IndexParam2Changed(double)) ); connect( (QObject*)(m_Controls->m_NormalizationCheckbox), SIGNAL(clicked()), this, SLOT(NormalizationCheckbox()) ); connect( (QObject*)(m_Controls->m_ScalingCheckbox), SIGNAL(clicked()), this, SLOT(ScalingCheckbox()) ); connect( (QObject*)(m_Controls->m_OpacitySlider), SIGNAL(spanChanged(double,double)), this, SLOT(OpacityChanged(double,double)) ); } } void QmitkControlVisualizationPropertiesView::Activated() { berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); QmitkFunctionality::Activated(); } void QmitkControlVisualizationPropertiesView::Deactivated() { QmitkFunctionality::Deactivated(); } int QmitkControlVisualizationPropertiesView::GetSizeFlags(bool width) { if(!width) { return berry::Constants::MIN | berry::Constants::MAX | berry::Constants::FILL; } else { return 0; } } int QmitkControlVisualizationPropertiesView::ComputePreferredSize(bool width, int /*availableParallel*/, int /*availablePerpendicular*/, int preferredResult) { if(width==false) { return m_FoundSingleOdfImage ? 120 : 80; } else { return preferredResult; } } mitk::DataStorage::SetOfObjects::Pointer QmitkControlVisualizationPropertiesView::ActiveSet(std::string classname) { if (m_CurrentSelection) { mitk::DataStorage::SetOfObjects::Pointer set = mitk::DataStorage::SetOfObjects::New(); int at = 0; for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); i != m_CurrentSelection->End(); ++i) { if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); if(QString(classname.c_str()).compare(node->GetData()->GetNameOfClass())==0) { set->InsertElement(at++, node); } } } return set; } return 0; } void QmitkControlVisualizationPropertiesView::SetBoolProp( mitk::DataStorage::SetOfObjects::Pointer set, std::string name, bool value) { if(set.IsNotNull()) { mitk::DataStorage::SetOfObjects::const_iterator itemiter( set->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( set->end() ); while ( itemiter != itemiterend ) { (*itemiter)->SetBoolProperty(name.c_str(), value); ++itemiter; } } } void QmitkControlVisualizationPropertiesView::SetIntProp( mitk::DataStorage::SetOfObjects::Pointer set, std::string name, int value) { if(set.IsNotNull()) { mitk::DataStorage::SetOfObjects::const_iterator itemiter( set->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( set->end() ); while ( itemiter != itemiterend ) { (*itemiter)->SetIntProperty(name.c_str(), value); ++itemiter; } } } void QmitkControlVisualizationPropertiesView::SetFloatProp( mitk::DataStorage::SetOfObjects::Pointer set, std::string name, float value) { if(set.IsNotNull()) { mitk::DataStorage::SetOfObjects::const_iterator itemiter( set->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( set->end() ); while ( itemiter != itemiterend ) { (*itemiter)->SetFloatProperty(name.c_str(), value); ++itemiter; } } } void QmitkControlVisualizationPropertiesView::SetLevelWindowProp( mitk::DataStorage::SetOfObjects::Pointer set, std::string name, mitk::LevelWindow value) { if(set.IsNotNull()) { mitk::LevelWindowProperty::Pointer prop = mitk::LevelWindowProperty::New(value); mitk::DataStorage::SetOfObjects::const_iterator itemiter( set->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( set->end() ); while ( itemiter != itemiterend ) { (*itemiter)->SetProperty(name.c_str(), prop); ++itemiter; } } } void QmitkControlVisualizationPropertiesView::SetEnumProp( mitk::DataStorage::SetOfObjects::Pointer set, std::string name, mitk::EnumerationProperty::Pointer value) { if(set.IsNotNull()) { mitk::DataStorage::SetOfObjects::const_iterator itemiter( set->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( set->end() ); while ( itemiter != itemiterend ) { (*itemiter)->SetProperty(name.c_str(), value); ++itemiter; } } } void QmitkControlVisualizationPropertiesView::DisplayIndexChanged(int dispIndex) { QString label = "Channel %1"; label = label.arg(dispIndex); m_Controls->label_channel->setText(label); mitk::DataStorage::SetOfObjects::Pointer set = ActiveSet("DiffusionImage"); if(set.IsNotNull()) { mitk::DataStorage::SetOfObjects::const_iterator itemiter( set->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( set->end() ); while ( itemiter != itemiterend ) { (*itemiter)->SetIntProperty("DisplayChannel", dispIndex); ++itemiter; } //m_MultiWidget->RequestUpdate(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkControlVisualizationPropertiesView::Reinit() { if (m_CurrentSelection) { mitk::DataNodeObject::Pointer nodeObj = m_CurrentSelection->Begin()->Cast(); mitk::DataNode::Pointer node = nodeObj->GetDataNode(); mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeSlicedGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } void QmitkControlVisualizationPropertiesView::TextIntON() { if(m_TexIsOn) { m_Controls->m_TextureIntON->setIcon(*m_IconTexOFF); } else { m_Controls->m_TextureIntON->setIcon(*m_IconTexON); } mitk::DataStorage::SetOfObjects::Pointer set = ActiveSet("DiffusionImage"); SetBoolProp(set,"texture interpolation", !m_TexIsOn); set = ActiveSet("TensorImage"); SetBoolProp(set,"texture interpolation", !m_TexIsOn); set = ActiveSet("QBallImage"); SetBoolProp(set,"texture interpolation", !m_TexIsOn); set = ActiveSet("Image"); SetBoolProp(set,"texture interpolation", !m_TexIsOn); m_TexIsOn = !m_TexIsOn; if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } void QmitkControlVisualizationPropertiesView::VisibleOdfsON_S() { if(m_GlyIsOn_S) { m_Controls->m_VisibleOdfsON_S->setIcon(*m_IconGlyOFF_S); } else { m_Controls->m_VisibleOdfsON_S->setIcon(*m_IconGlyON_S); } mitk::DataStorage::SetOfObjects::Pointer set = ActiveSet("QBallImage"); SetBoolProp(set,"VisibleOdfs_S", !m_GlyIsOn_S); set = ActiveSet("TensorImage"); SetBoolProp(set,"VisibleOdfs_S", !m_GlyIsOn_S); m_GlyIsOn_S = !m_GlyIsOn_S; VisibleOdfsON(0); } void QmitkControlVisualizationPropertiesView::VisibleOdfsON_T() { if(m_GlyIsOn_T) { m_Controls->m_VisibleOdfsON_T->setIcon(*m_IconGlyOFF_T); } else { m_Controls->m_VisibleOdfsON_T->setIcon(*m_IconGlyON_T); } mitk::DataStorage::SetOfObjects::Pointer set = ActiveSet("QBallImage"); SetBoolProp(set,"VisibleOdfs_T", !m_GlyIsOn_T); set = ActiveSet("TensorImage"); SetBoolProp(set,"VisibleOdfs_T", !m_GlyIsOn_T); m_GlyIsOn_T = !m_GlyIsOn_T; VisibleOdfsON(1); } void QmitkControlVisualizationPropertiesView::VisibleOdfsON_C() { if(m_GlyIsOn_C) { m_Controls->m_VisibleOdfsON_C->setIcon(*m_IconGlyOFF_C); } else { m_Controls->m_VisibleOdfsON_C->setIcon(*m_IconGlyON_C); } mitk::DataStorage::SetOfObjects::Pointer set = ActiveSet("QBallImage"); SetBoolProp(set,"VisibleOdfs_C", !m_GlyIsOn_C); set = ActiveSet("TensorImage"); SetBoolProp(set,"VisibleOdfs_C", !m_GlyIsOn_C); m_GlyIsOn_C = !m_GlyIsOn_C; VisibleOdfsON(2); } void QmitkControlVisualizationPropertiesView::VisibleOdfsON(int view) { if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } void QmitkControlVisualizationPropertiesView::ShowMaxNumberChanged() { int maxNr = m_Controls->m_ShowMaxNumber->value(); if ( maxNr < 1 ) { m_Controls->m_ShowMaxNumber->setValue( 1 ); maxNr = 1; } mitk::DataStorage::SetOfObjects::Pointer set = ActiveSet("QBallImage"); SetIntProp(set,"ShowMaxNumber", maxNr); set = ActiveSet("TensorImage"); SetIntProp(set,"ShowMaxNumber", maxNr); if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } void QmitkControlVisualizationPropertiesView::NormalizationDropdownChanged(int normDropdown) { typedef mitk::OdfNormalizationMethodProperty PropType; PropType::Pointer normMeth = PropType::New(); switch(normDropdown) { case 0: normMeth->SetNormalizationToMinMax(); break; case 1: normMeth->SetNormalizationToMax(); break; case 2: normMeth->SetNormalizationToNone(); break; case 3: normMeth->SetNormalizationToGlobalMax(); break; default: normMeth->SetNormalizationToMinMax(); } mitk::DataStorage::SetOfObjects::Pointer set = ActiveSet("QBallImage"); SetEnumProp(set,"Normalization", normMeth.GetPointer()); set = ActiveSet("TensorImage"); SetEnumProp(set,"Normalization", normMeth.GetPointer()); if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } void QmitkControlVisualizationPropertiesView::ScalingFactorChanged(double scalingFactor) { mitk::DataStorage::SetOfObjects::Pointer set = ActiveSet("QBallImage"); SetFloatProp(set,"Scaling", scalingFactor); set = ActiveSet("TensorImage"); SetFloatProp(set,"Scaling", scalingFactor); if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } void QmitkControlVisualizationPropertiesView::AdditionalScaling(int additionalScaling) { typedef mitk::OdfScaleByProperty PropType; PropType::Pointer scaleBy = PropType::New(); switch(additionalScaling) { case 0: scaleBy->SetScaleByNothing(); break; case 1: scaleBy->SetScaleByGFA(); //m_Controls->params_frame->setVisible(true); break; #ifdef DIFFUSION_IMAGING_EXTENDED case 2: scaleBy->SetScaleByPrincipalCurvature(); // commented in for SPIE paper, Principle curvature scaling //m_Controls->params_frame->setVisible(true); break; #endif default: scaleBy->SetScaleByNothing(); } mitk::DataStorage::SetOfObjects::Pointer set = ActiveSet("QBallImage"); SetEnumProp(set,"ScaleBy", scaleBy.GetPointer()); set = ActiveSet("TensorImage"); SetEnumProp(set,"ScaleBy", scaleBy.GetPointer()); if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } void QmitkControlVisualizationPropertiesView::IndexParam1Changed(double param1) { mitk::DataStorage::SetOfObjects::Pointer set = ActiveSet("QBallImage"); SetFloatProp(set,"IndexParam1", param1); set = ActiveSet("TensorImage"); SetFloatProp(set,"IndexParam1", param1); if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } void QmitkControlVisualizationPropertiesView::IndexParam2Changed(double param2) { mitk::DataStorage::SetOfObjects::Pointer set = ActiveSet("QBallImage"); SetFloatProp(set,"IndexParam2", param2); set = ActiveSet("TensorImage"); SetFloatProp(set,"IndexParam2", param2); if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } void QmitkControlVisualizationPropertiesView::OpacityChanged(double l, double u) { mitk::LevelWindow olw; olw.SetRangeMinMax(l*255, u*255); mitk::DataStorage::SetOfObjects::Pointer set = ActiveSet("QBallImage"); SetLevelWindowProp(set,"opaclevelwindow", olw); set = ActiveSet("TensorImage"); SetLevelWindowProp(set,"opaclevelwindow", olw); set = ActiveSet("Image"); SetLevelWindowProp(set,"opaclevelwindow", olw); m_Controls->m_OpacityMinFaLabel->setText(QString::number(l,'f',2) + " : " + QString::number(u,'f',2)); if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } void QmitkControlVisualizationPropertiesView::NormalizationCheckbox() { m_Controls->m_NormalizationFrame->setVisible( m_Controls->m_NormalizationCheckbox->isChecked()); } void QmitkControlVisualizationPropertiesView::ScalingCheckbox() { m_Controls->m_ScalingFrame->setVisible( m_Controls->m_ScalingCheckbox->isChecked()); } diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h index e65fa576de..7513535175 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h @@ -1,135 +1,136 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _QMITKControlVisualizationPropertiesView_H_INCLUDED #define _QMITKControlVisualizationPropertiesView_H_INCLUDED #include #include #include "berryISelectionListener.h" #include "berryIStructuredSelection.h" #include "berryISizeProvider.h" #include "ui_QmitkControlVisualizationPropertiesViewControls.h" #include "mitkEnumerationProperty.h" /*! * \ingroup org_mitk_gui_qt_diffusionquantification_internal * * \brief QmitkControlVisualizationPropertiesView * * Document your class here. * * \sa QmitkFunctionality */ -class QmitkControlVisualizationPropertiesView : public QObject, public QmitkFunctionality//, public berry::ISizeProvider +class QmitkControlVisualizationPropertiesView : public QmitkFunctionality//, public berry::ISizeProvider { friend struct CvpSelListener; // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; QmitkControlVisualizationPropertiesView(); + QmitkControlVisualizationPropertiesView(const QmitkControlVisualizationPropertiesView& other); virtual ~QmitkControlVisualizationPropertiesView(); virtual void CreateQtPartControl(QWidget *parent); /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); mitk::DataStorage::SetOfObjects::Pointer ActiveSet(std::string); void SetBoolProp (mitk::DataStorage::SetOfObjects::Pointer,std::string,bool); void SetIntProp (mitk::DataStorage::SetOfObjects::Pointer,std::string,int); void SetFloatProp(mitk::DataStorage::SetOfObjects::Pointer,std::string,float); void SetLevelWindowProp(mitk::DataStorage::SetOfObjects::Pointer,std::string,mitk::LevelWindow); void SetEnumProp (mitk::DataStorage::SetOfObjects::Pointer,std::string,mitk::EnumerationProperty::Pointer); virtual int GetSizeFlags(bool width); virtual int ComputePreferredSize(bool width, int availableParallel, int availablePerpendicular, int preferredResult); protected slots: void DisplayIndexChanged(int); void TextIntON(); void Reinit(); void VisibleOdfsON(int view); void VisibleOdfsON_S(); void VisibleOdfsON_T(); void VisibleOdfsON_C(); void ShowMaxNumberChanged(); void NormalizationDropdownChanged(int); void ScalingFactorChanged(double); void AdditionalScaling(int); void IndexParam1Changed(double); void IndexParam2Changed(double); void OpacityChanged(double,double); void NormalizationCheckbox(); void ScalingCheckbox(); protected: Ui::QmitkControlVisualizationPropertiesViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; berry::ISelectionListener::Pointer m_SelListener; berry::IStructuredSelection::ConstPointer m_CurrentSelection; bool m_FoundSingleOdfImage; bool m_IsInitialized; QIcon* m_IconTexOFF; QIcon* m_IconTexON; QIcon* m_IconGlyOFF_T; QIcon* m_IconGlyON_T; QIcon* m_IconGlyOFF_C; QIcon* m_IconGlyON_C; QIcon* m_IconGlyOFF_S; QIcon* m_IconGlyON_S; bool m_TexIsOn; bool m_GlyIsOn_T; bool m_GlyIsOn_C; bool m_GlyIsOn_S; }; #endif // _QMITKControlVisualizationPropertiesView_H_INCLUDED diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp index 967cc5ed80..732618f934 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.cpp @@ -1,672 +1,678 @@ /*========================================================================= Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkDiffusionDicomImportView.h" // qt includes #include // itk includes #include "itkTimeProbesCollectorBase.h" #include "itkGDCMSeriesFileNames.h" #include "itksys/SystemTools.hxx" // mitk includes #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkProperties.h" #include "mitkRenderingManager.h" #include "mitkMemoryUtilities.h" // diffusion module includes #include "mitkDicomDiffusionImageHeaderReader.h" #include "mitkGroupDiffusionHeadersFilter.h" #include "mitkDicomDiffusionImageReader.h" #include "mitkDiffusionImage.h" #include "mitkNrrdDiffusionImageWriter.h" #if GDCM_MAJOR_VERSION >= 2 #define DGDCM2 #endif #ifdef DGDCM2 #include "gdcmDirectory.h" #include "gdcmScanner.h" #include "gdcmSorter.h" #include "gdcmIPPSorter.h" #include "gdcmAttribute.h" #include "gdcmVersion.h" #endif const std::string QmitkDiffusionDicomImport::VIEW_ID = "org.mitk.views.diffusiondicomimport"; QmitkDiffusionDicomImport::QmitkDiffusionDicomImport(QObject* /*parent*/, const char* /*name*/) : QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL), m_OutputFolderName(""), m_OutputFolderNameSet(false) { } +QmitkDiffusionDicomImport::QmitkDiffusionDicomImport(const QmitkDiffusionDicomImport& other) +{ + Q_UNUSED(other) + throw std::runtime_error("Copy constructor not implemented"); +} + QmitkDiffusionDicomImport::~QmitkDiffusionDicomImport() {} void QmitkDiffusionDicomImport::CreateQtPartControl(QWidget *parent) { m_Parent = parent; if (m_Controls == NULL) { m_Controls = new Ui::QmitkDiffusionDicomImportControls; m_Controls->setupUi(parent); this->CreateConnections(); m_Controls->m_DicomLoadRecursiveCheckbox->setChecked(true); m_Controls->m_DicomLoadAverageDuplicatesCheckbox->setChecked(false); #ifdef DGDCM2 m_Controls->m_DicomLoadRecursiveCheckbox->setVisible(false); #endif AverageClicked(); } } void QmitkDiffusionDicomImport::CreateConnections() { if ( m_Controls ) { connect( m_Controls->m_AddFoldersButton, SIGNAL(clicked()), this, SLOT(DicomLoadAddFolderNames()) ); connect( m_Controls->m_DeleteFoldersButton, SIGNAL(clicked()), this, SLOT(DicomLoadDeleteFolderNames()) ); connect( m_Controls->m_DicomLoadStartLoadButton, SIGNAL(clicked()), this, SLOT(DicomLoadStartLoad()) ); connect( m_Controls->m_DicomLoadAverageDuplicatesCheckbox, SIGNAL(clicked()), this, SLOT(AverageClicked()) ); connect( m_Controls->m_OutputSetButton, SIGNAL(clicked()), this, SLOT(OutputSet()) ); connect( m_Controls->m_OutputClearButton, SIGNAL(clicked()), this, SLOT(OutputClear()) ); } } void QmitkDiffusionDicomImport::OutputSet() { // SELECT FOLDER DIALOG QFileDialog* w = new QFileDialog( m_Parent, QString("Select folders containing DWI data") ); w->setFileMode( QFileDialog::Directory ); // RETRIEVE SELECTION if ( w->exec() != QDialog::Accepted ) return; m_OutputFolderName = w->selectedFiles()[0]; m_OutputFolderNameSet = true; m_Controls->m_OutputLabel->setText(m_OutputFolderName); } void QmitkDiffusionDicomImport::OutputClear() { m_OutputFolderName = ""; m_OutputFolderNameSet = false; m_Controls->m_OutputLabel->setText("... optional out-folder ..."); } void QmitkDiffusionDicomImport::AverageClicked() { m_Controls->m_Blur->setEnabled(m_Controls->m_DicomLoadAverageDuplicatesCheckbox->isChecked()); } void QmitkDiffusionDicomImport::Activated() { QmitkFunctionality::Activated(); } void QmitkDiffusionDicomImport::DicomLoadDeleteFolderNames() { m_Controls->listWidget->clear(); } void QmitkDiffusionDicomImport::DicomLoadAddFolderNames() { // SELECT FOLDER DIALOG QFileDialog* w = new QFileDialog( m_Parent, QString("Select folders containing DWI data") ); w->setFileMode( QFileDialog::Directory ); // RETRIEVE SELECTION if ( w->exec() != QDialog::Accepted ) return; m_Controls->listWidget->addItems(w->selectedFiles()); } #ifdef DGDCM2 bool SortBySeriesUID(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 ) { gdcm::Attribute<0x0020,0x000e> at1; at1.Set( ds1 ); gdcm::Attribute<0x0020,0x000e> at2; at2.Set( ds2 ); return at1 < at2; } bool SortByAcquisitionNumber(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 ) { gdcm::Attribute<0x0020,0x0012> at1; at1.Set( ds1 ); gdcm::Attribute<0x0020,0x0012> at2; at2.Set( ds2 ); return at1 < at2; } bool SortBySeqName(gdcm::DataSet const & ds1, gdcm::DataSet const & ds2 ) { gdcm::Attribute<0x0018, 0x0024> at1; at1.Set( ds1 ); gdcm::Attribute<0x0018, 0x0024> at2; at2.Set( ds2 ); std::string str1 = at1.GetValue(0).Trim(); std::string str2 = at2.GetValue(0).Trim(); return std::lexicographical_compare(str1.begin(), str1.end(), str2.begin(), str2.end() ); } #endif void QmitkDiffusionDicomImport::Status(QString status) { mitk::StatusBar::GetInstance()->DisplayText(status.toAscii()); MITK_INFO << status.toStdString().c_str(); } void QmitkDiffusionDicomImport::Status(std::string status) { mitk::StatusBar::GetInstance()->DisplayText(status.c_str()); MITK_INFO << status.c_str(); } void QmitkDiffusionDicomImport::Status(const char* status) { mitk::StatusBar::GetInstance()->DisplayText(status); MITK_INFO << status; } void QmitkDiffusionDicomImport::Error(QString status) { mitk::StatusBar::GetInstance()->DisplayErrorText(status.toAscii()); MITK_ERROR << status.toStdString().c_str(); } void QmitkDiffusionDicomImport::Error(std::string status) { mitk::StatusBar::GetInstance()->DisplayErrorText(status.c_str()); MITK_ERROR << status.c_str(); } void QmitkDiffusionDicomImport::Error(const char* status) { mitk::StatusBar::GetInstance()->DisplayErrorText(status); MITK_ERROR << status; } void QmitkDiffusionDicomImport::PrintMemoryUsage() { size_t processSize = mitk::MemoryUtilities::GetProcessMemoryUsage(); size_t totalSize = mitk::MemoryUtilities::GetTotalSizeOfPhysicalRam(); float percentage = ( (float) processSize / (float) totalSize ) * 100.0; MITK_INFO << "Current memory usage: " << GetMemoryDescription( processSize, percentage ); } std::string QmitkDiffusionDicomImport::FormatMemorySize( size_t size ) { double val = size; std::string descriptor("B"); if ( val >= 1000.0 ) { val /= 1024.0; descriptor = "KB"; } if ( val >= 1000.0 ) { val /= 1024.0; descriptor = "MB"; } if ( val >= 1000.0 ) { val /= 1024.0; descriptor = "GB"; } std::ostringstream str; str << std::fixed << std::setprecision(2) << val << " " << descriptor; return str.str(); } std::string QmitkDiffusionDicomImport::FormatPercentage( double val ) { std::ostringstream str; str << std::fixed << std::setprecision(2) << val << " " << "%"; return str.str(); } std::string QmitkDiffusionDicomImport::GetMemoryDescription( size_t processSize, float percentage ) { std::ostringstream str; str << FormatMemorySize(processSize) << " (" << FormatPercentage( percentage ) <<")" ; return str.str(); } void QmitkDiffusionDicomImport::DicomLoadStartLoad() { itk::TimeProbesCollectorBase clock; try { int nrFolders = m_Controls->listWidget->count(); if(!nrFolders) { Error(QString("No input folders were selected. ABORTING.")); return; } #ifndef DGDCM2 Status(QString("GDCM 1.x used for DICOM parsing and sorting!")); #else Status(QString("GDCM %1 used for DICOM parsing and sorting!").arg(gdcm::Version::GetVersion())); #endif PrintMemoryUsage(); QString status; mitk::DataNode::Pointer node; mitk::ProgressBar::GetInstance()->AddStepsToDo(3*nrFolders); while(m_Controls->listWidget->count()) { // RETREIVE FOLDERNAME QListWidgetItem * item = m_Controls->listWidget->takeItem(0); QString folderName = item->text(); // PARSING DIRECTORY PrintMemoryUsage(); clock.Start(folderName.toAscii()); std::vector seriesUIDs(0); std::vector > seriesFilenames(0); #ifndef DGDCM2 Status(QString("Parsing directory %1").arg(folderName)); typedef itk::GDCMSeriesFileNames InputNamesType; InputNamesType::Pointer inputNames = InputNamesType::New(); ////////////////////////////////////////////////////// //// //// if you get seg-faults around here, make sure //// to set the itk GDCM_DIR variable in cmake //// correctly when building ITK //// ( e.g. [itk binary dir]/Utilities/gdcm //// if not using system gdcm ) //// ////////////////////////////////////////////////////// inputNames->SetRecursive(m_Controls->m_DicomLoadRecursiveCheckbox->isChecked()); inputNames->SetUseSeriesDetails(true); inputNames->AddSeriesRestriction( "0020|0012" ); inputNames->SetInputDirectory( folderName.toAscii() ); mitk::ProgressBar::GetInstance()->Progress(); seriesUIDs = inputNames->GetSeriesUIDs(); unsigned int size = seriesUIDs.size(); for ( unsigned int i = 0 ; i < size ; ++i ) { seriesFilenames.push_back(inputNames->GetFileNames(seriesUIDs[i])); } #else Status("== Initial Directory Scan =="); gdcm::Directory d; d.Load( folderName.toStdString().c_str(), true ); // recursive ! const gdcm::Directory::FilenamesType &l1 = d.GetFilenames(); const unsigned int ntotalfiles = l1.size(); Status(QString(" ... found %1 different files").arg(ntotalfiles)); Status("Scanning Headers"); gdcm::Scanner s; const gdcm::Tag t1(0x0020,0x000d); // Study Instance UID const gdcm::Tag t2(0x0020,0x000e); // Series Instance UID const gdcm::Tag t5(0x0028, 0x0010); // number rows const gdcm::Tag t6(0x0028, 0x0011); // number cols s.AddTag( t1 ); s.AddTag( t2 ); s.AddTag( t5 ); s.AddTag( t6 ); bool b = s.Scan( d.GetFilenames() ); if( !b ) { Error("Scanner failed"); continue; } // Only get the DICOM files: gdcm::Directory::FilenamesType l2 = s.GetKeys(); const int nfiles = l2.size(); if(nfiles < 1) { Error("No DICOM files found"); continue; } Status(QString(" ... successfully scanned %1 headers.").arg(nfiles)); Status("Sorting"); const gdcm::Scanner::ValuesType &values1 = s.GetValues(t1); int nvalues = values1.size(); if(nvalues>1) { Error("Multiple studies found. Please limit to 1 study per folder"); continue; } const gdcm::Scanner::ValuesType &values5 = s.GetValues(t5); const gdcm::Scanner::ValuesType &values6 = s.GetValues(t6); if(values5.size()>1 || values6.size()>1) { Error("Folder contains images of unequal dimensions that cannot be combined in one 3d volume. ABORTING."); continue; } const gdcm::Scanner::ValuesType &values2 = s.GetValues(t2); int nSeries = values2.size(); gdcm::Directory::FilenamesType files; if(nSeries > 1) { gdcm::Sorter sorter; sorter.SetSortFunction( SortBySeriesUID ); sorter.StableSort( l2 ); files = sorter.GetFilenames(); } else { files = l2; } unsigned int nTotalAcquis = 0; if(nfiles % nSeries != 0) { Error("Number of files in series not equal, ABORTING"); continue; } int filesPerSeries = nfiles / nSeries; gdcm::Scanner::ValuesType::const_iterator it2 = values2.begin(); for(int i=0; i & list = ippsorter.GetFilenames(); seriesFilenames.push_back(list); seriesUIDs.push_back(identifier.c_str()); } ++it2; } if(nfiles % nTotalAcquis != 0) { Error("Number of files per acquisition differs between series, ABORTING"); continue; } int slices = nfiles/nTotalAcquis; Status(QString("Series is composed of %1 different 3D volumes with %2 slices.").arg(nTotalAcquis).arg(slices)); #endif // READING HEADER-INFOS PrintMemoryUsage(); Status(QString("Reading Headers %1").arg(folderName)); mitk::DicomDiffusionImageHeaderReader::Pointer headerReader; mitk::GroupDiffusionHeadersFilter::InputType inHeaders; unsigned int size2 = seriesUIDs.size(); for ( unsigned int i = 0 ; i < size2 ; ++i ) { Status(QString("Reading header image #%1/%2").arg(i+1).arg(size2)); headerReader = mitk::DicomDiffusionImageHeaderReader::New(); headerReader->SetSeriesDicomFilenames(seriesFilenames[i]); headerReader->Update(); inHeaders.push_back(headerReader->GetOutput()); //Status(std::endl; } mitk::ProgressBar::GetInstance()->Progress(); // // GROUP HEADERS // mitk::GroupDiffusionHeadersFilter::Pointer grouper // = mitk::GroupDiffusionHeadersFilter::New(); // mitk::GroupDiffusionHeadersFilter::OutputType outHeaders; // grouper->SetInput(inHeaders); // grouper->Update(); // outHeaders = grouper->GetOutput(); // READ VOLUMES PrintMemoryUsage(); Status(QString("Loading Volumes %1").arg(folderName)); typedef short PixelValueType; typedef mitk::DicomDiffusionImageReader< PixelValueType, 3 > VolumesReader; VolumesReader::Pointer vReader = VolumesReader::New(); VolumesReader::HeaderContainer hc = inHeaders; // hc.insert(hc.end(), outHeaders[1].begin(), outHeaders[1].end() ); // hc.insert(hc.end(), outHeaders[2].begin(), outHeaders[2].end() ); if(hc.size()>1) { vReader->SetHeaders(hc); vReader->Update(); VolumesReader::OutputImageType::Pointer vecImage; vecImage = vReader->GetOutput(); Status(QString("Volumes Loaded (%1)").arg(folderName)); // CONSTRUCT CONTAINER WITH DIRECTIONS typedef vnl_vector_fixed< double, 3 > GradientDirectionType; typedef itk::VectorContainer< unsigned int, GradientDirectionType > GradientDirectionContainerType; GradientDirectionContainerType::Pointer directions = GradientDirectionContainerType::New(); std::vector b_vals; double maxb = 0; for(unsigned int i=0; ibValue; if(maxb vect = hc[i]->DiffusionVector; vect.normalize(); vect *= sqrt(b_vals[i]/maxb); directions->push_back(vect); } // DWI TO DATATREE PrintMemoryUsage(); Status(QString("Initializing Diffusion Image")); typedef mitk::DiffusionImage DiffVolumesType; DiffVolumesType::Pointer diffImage = DiffVolumesType::New(); diffImage->SetDirections(directions); diffImage->SetOriginalDirections(directions); if(m_Controls->m_DicomLoadDKFZ->isChecked()) { diffImage->CorrectDKFZBrokenGradientScheme(m_Controls->m_Blur->value()); } diffImage->SetVectorImage(vecImage); diffImage->SetB_Value(maxb); diffImage->InitializeFromVectorImage(); Status(QString("Diffusion Image initialized")); if(m_Controls->m_DicomLoadAverageDuplicatesCheckbox->isChecked()) { PrintMemoryUsage(); Status(QString("Averaging gradient directions")); diffImage->AverageRedundantGradients(m_Controls->m_Blur->value()); } //if(m_Controls->m_DicomLoadDuplicateIfSingleSliceCheckbox->isChecked()) // diffVolumes->DuplicateIfSingleSlice(); QString descr = QString("%1_%2_%3") .arg(((inHeaders)[0])->seriesDescription.c_str()) .arg(((inHeaders)[0])->seriesNumber) .arg(((inHeaders)[0])->patientName.c_str()); descr = descr.trimmed(); descr = descr.replace(" ", "_"); if(!m_OutputFolderNameSet) { node=mitk::DataNode::New(); node->SetData( diffImage ); GetDefaultDataStorage()->Add(node); SetDwiNodeProperties(node, descr.toStdString().c_str()); Status(QString("Image %1 added to datastorage").arg(descr)); } else { typedef mitk::NrrdDiffusionImageWriter WriterType; WriterType::Pointer writer = WriterType::New(); QString fullpath = QString("%1/%2.dwi") .arg(m_OutputFolderName) .arg(descr); std::string pathstring = itksys::SystemTools::ConvertToOutputPath(fullpath.toStdString().c_str()); writer->SetFileName(pathstring); writer->SetInput(diffImage); try { writer->Update(); } catch (itk::ExceptionObject &ex) { Error(QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription())); continue ; } Status(QString("Image %1 written to disc (%1)").arg(fullpath.toStdString().c_str())); } } else { Status(QString("No diffusion information found (%1)").arg(folderName)); } Status(QString("Finished processing %1 with memory:").arg(folderName)); PrintMemoryUsage(); clock.Stop(folderName.toAscii()); mitk::ProgressBar::GetInstance()->Progress(); } Status("Timing information"); clock.Report(); if(!m_OutputFolderNameSet && node.IsNotNull()) { mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeSlicedGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } catch (itk::ExceptionObject &ex) { Error(QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription())); return ; } Status(QString("Finished import with memory:")); PrintMemoryUsage(); } void QmitkDiffusionDicomImport::SetDwiNodeProperties(mitk::DataNode::Pointer node, std::string name) { node->SetProperty( "IsDWIRawVolume", mitk::BoolProperty::New( true ) ); // set foldername as string property mitk::StringProperty::Pointer nameProp = mitk::StringProperty::New( name ); node->SetProperty( "name", nameProp ); } diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.h index 0c9d7d5971..13aee8814f 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.h +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionDicomImportView.h @@ -1,114 +1,115 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-05 11:31:02 +0200 (Di, 05 Mai 2009) $ Version: $Revision: 10185 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef QmitkDiffusionDicomImportView_H__INCLUDED #define QmitkDiffusionDicomImportView_H__INCLUDED #include "QmitkFunctionality.h" #include "ui_QmitkDiffusionDicomImportViewControls.h" /*! \brief QmitkDiffusionDicomImport \sa QmitkFunctionality \ingroup Functionalities */ -class QmitkDiffusionDicomImport : public QObject, public QmitkFunctionality +class QmitkDiffusionDicomImport : public QmitkFunctionality { Q_OBJECT public: static const std::string VIEW_ID; /*! \ Convenient typedefs */ typedef mitk::DataStorage::SetOfObjects ConstVector; typedef ConstVector::ConstPointer ConstVectorPointer; typedef ConstVector::ConstIterator ConstVectorIterator; /*! \brief default constructor */ QmitkDiffusionDicomImport(QObject *parent=0, const char *name=0); + QmitkDiffusionDicomImport(const QmitkDiffusionDicomImport& other); /*! \brief default destructor */ virtual ~QmitkDiffusionDicomImport(); /*! \brief method for creating the widget containing the application controls, like sliders, buttons etc. */ virtual void CreateQtPartControl(QWidget *parent); /*! \brief method for creating the connections of main and control widget */ virtual void CreateConnections(); virtual void Activated(); void SetDwiNodeProperties(mitk::DataNode::Pointer node, std::string name); protected slots: void DicomLoadAddFolderNames(); void DicomLoadDeleteFolderNames(); void DicomLoadStartLoad() ; void AverageClicked(); void OutputSet(); void OutputClear(); protected: void Status(QString status); void Status(std::string status); void Status(const char* status); void Error(QString status); void Error(std::string status); void Error(const char* status); void PrintMemoryUsage(); std::string FormatMemorySize( size_t size ); std::string FormatPercentage( double val ); std::string GetMemoryDescription( size_t processSize, float percentage ); /*! * controls containing sliders for scrolling through the slices */ Ui::QmitkDiffusionDicomImportControls *m_Controls; QmitkStdMultiWidget* m_MultiWidget; QWidget *m_Parent; QString m_OutputFolderName; bool m_OutputFolderNameSet; }; #endif // !defined(QmitkDiffusionDicomImport_H__INCLUDED) diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionImagingPublicPerspective.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionImagingPublicPerspective.cpp index b897c5b1ca..1fa8ea91ab 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionImagingPublicPerspective.cpp +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionImagingPublicPerspective.cpp @@ -1,68 +1,79 @@ /*========================================================================= Program: BlueBerry Platform Language: C++ Date: $Date: 2009-10-23 02:59:36 +0200 (Fr, 23 Okt 2009) $ Version: $Revision: 19652 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkDiffusionImagingPublicPerspective.h" #include "berryIViewLayout.h" +QmitkDiffusionImagingPublicPerspective::QmitkDiffusionImagingPublicPerspective() +{ + +} + +QmitkDiffusionImagingPublicPerspective::QmitkDiffusionImagingPublicPerspective(const QmitkDiffusionImagingPublicPerspective& other) +{ + Q_UNUSED(other) + throw std::runtime_error("Copy constructor not implemented"); +} + void QmitkDiffusionImagingPublicPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) { std::string editorArea = layout->GetEditorArea(); layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea); layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .2f, "org.mitk.views.datamanager"); berry::IFolderLayout::Pointer left = layout->CreateFolder("org.mitk.leftcontrols", berry::IPageLayout::BOTTOM, 0.125f, "org.mitk.views.controlvisualizationpropertiesview"); layout->AddStandaloneView("org.mitk.views.imagenavigator", false, berry::IPageLayout::BOTTOM, 0.8f, "org.mitk.leftcontrols"); layout->AddStandaloneView("org.mitk.views.perspectiveswitcher", false, berry::IPageLayout::BOTTOM, 0.99f, "org.mitk.views.imagenavigator"); // layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", // berry::IPageLayout::TOP, 0.9f, "org.mitk.views.perspectiveswitcher",false); left->AddView("org.mitk.views.diffusionpreprocessing"); left->AddView("org.mitk.views.tensorreconstruction"); left->AddView("org.mitk.views.qballreconstruction"); left->AddView("org.mitk.views.diffusionquantification"); left->AddView("org.mitk.views.diffusiondicomimport"); berry::IViewLayout::Pointer lo = layout->GetViewLayout("org.mitk.views.diffusionpreprocessing"); lo->SetCloseable(false); lo = layout->GetViewLayout("org.mitk.views.qballreconstruction"); lo->SetCloseable(false); lo = layout->GetViewLayout("org.mitk.views.tensorreconstruction"); lo->SetCloseable(false); lo = layout->GetViewLayout("org.mitk.views.diffusionquantification"); lo->SetCloseable(false); lo = layout->GetViewLayout("org.mitk.views.diffusiondicomimport"); lo->SetCloseable(false); //berry::IFolderLayout::Pointer right2 = // layout->CreateFolder("right2", berry::IPageLayout::BOTTOM, 0.5f, "right"); } diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionImagingPublicPerspective.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionImagingPublicPerspective.h index a5288646e7..12013e5d92 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionImagingPublicPerspective.h +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionImagingPublicPerspective.h @@ -1,31 +1,37 @@ /*========================================================================= Program: BlueBerry Platform Language: C++ Date: $Date: 2009-10-23 02:59:36 +0200 (Fr, 23 Okt 2009) $ Version: $Revision: 19652 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef QMITKDIFFUSIONIMAGINGPUBLICPERSPECTIVE_H_ #define QMITKDIFFUSIONIMAGINGPUBLICPERSPECTIVE_H_ #include -class QmitkDiffusionImagingPublicPerspective : public berry::IPerspectiveFactory +class QmitkDiffusionImagingPublicPerspective : public QObject, public berry::IPerspectiveFactory { + Q_OBJECT + Q_INTERFACES(berry::IPerspectiveFactory) + public: + QmitkDiffusionImagingPublicPerspective(); + QmitkDiffusionImagingPublicPerspective(const QmitkDiffusionImagingPublicPerspective& other); + void CreateInitialLayout(berry::IPageLayout::Pointer layout); }; #endif /* QMITKDIFFUSIONIMAGINGPUBLICPERSPECTIVE_H_ */ diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.cpp index cd056aa261..05fb4de3a3 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.cpp +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.cpp @@ -1,649 +1,655 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkDiffusionQuantificationView.h" #include "mitkDiffusionImagingConfigure.h" #include "itkTimeProbe.h" #include "itkImage.h" #include "mitkNodePredicateDataType.h" #include "mitkDataNodeObject.h" #include "mitkQBallImage.h" #include "mitkImageCast.h" #include "mitkStatusBar.h" #include "itkDiffusionQballGeneralizedFaImageFilter.h" #include "itkShiftScaleImageFilter.h" #include "itkTensorFractionalAnisotropyImageFilter.h" #include "itkTensorRelativeAnisotropyImageFilter.h" #include "itkTensorDerivedMeasurementsFilter.h" #include "QmitkDataStorageComboBox.h" #include "QmitkStdMultiWidget.h" #include #include "berryIWorkbenchWindow.h" #include "berryISelectionService.h" const std::string QmitkDiffusionQuantificationView::VIEW_ID = "org.mitk.views.diffusionquantification"; using namespace berry; const float QmitkDiffusionQuantificationView::m_ScaleDAIValues = 100.0; struct DqSelListener : ISelectionListener { berryObjectMacro(DqSelListener); DqSelListener(QmitkDiffusionQuantificationView* view) { m_View = view; } void DoSelectionChanged(ISelection::ConstPointer selection) { // save current selection in member variable m_View->m_CurrentSelection = selection.Cast(); // do something with the selected items if(m_View->m_CurrentSelection) { bool foundQBIVolume = false; bool foundTensorVolume = false; // iterate selection for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); i != m_View->m_CurrentSelection->End(); ++i) { // extract datatree node if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); // only look at interesting types if(QString("QBallImage").compare(node->GetData()->GetNameOfClass())==0) { foundQBIVolume = true; } if(QString("TensorImage").compare(node->GetData()->GetNameOfClass())==0) { foundTensorVolume = true; } } } m_View->m_Controls->m_GFAButton->setEnabled(foundQBIVolume); m_View->m_Controls->m_CurvatureButton->setEnabled(foundQBIVolume); m_View->m_Controls->m_FAButton->setEnabled(foundTensorVolume); m_View->m_Controls->m_RAButton->setEnabled(foundTensorVolume); m_View->m_Controls->m_ADButton->setEnabled(foundTensorVolume); m_View->m_Controls->m_RDButton->setEnabled(foundTensorVolume); m_View->m_Controls->m_ClusteringAnisotropy->setEnabled(foundTensorVolume); } } void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) { // check, if selection comes from datamanager if (part) { QString partname(part->GetPartName().c_str()); if(partname.compare("Datamanager")==0) { // apply selection DoSelectionChanged(selection); } } } QmitkDiffusionQuantificationView* m_View; }; QmitkDiffusionQuantificationView::QmitkDiffusionQuantificationView() : QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL) { } +QmitkDiffusionQuantificationView::QmitkDiffusionQuantificationView(const QmitkDiffusionQuantificationView& other) +{ + Q_UNUSED(other) + throw std::runtime_error("Copy constructor not implemented"); +} + QmitkDiffusionQuantificationView::~QmitkDiffusionQuantificationView() { this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); } void QmitkDiffusionQuantificationView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkDiffusionQuantificationViewControls; m_Controls->setupUi(parent); this->CreateConnections(); GFACheckboxClicked(); #ifndef DIFFUSION_IMAGING_EXTENDED m_Controls->m_StandardGFACheckbox->setVisible(false); m_Controls->frame_3->setVisible(false); m_Controls->m_CurvatureButton->setVisible(false); #endif } m_SelListener = berry::ISelectionListener::Pointer(new DqSelListener(this)); this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkDiffusionQuantificationView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkDiffusionQuantificationView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkDiffusionQuantificationView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_StandardGFACheckbox), SIGNAL(clicked()), this, SLOT(GFACheckboxClicked()) ); connect( (QObject*)(m_Controls->m_GFAButton), SIGNAL(clicked()), this, SLOT(GFA()) ); connect( (QObject*)(m_Controls->m_CurvatureButton), SIGNAL(clicked()), this, SLOT(Curvature()) ); connect( (QObject*)(m_Controls->m_FAButton), SIGNAL(clicked()), this, SLOT(FA()) ); connect( (QObject*)(m_Controls->m_RAButton), SIGNAL(clicked()), this, SLOT(RA()) ); connect( (QObject*)(m_Controls->m_ADButton), SIGNAL(clicked()), this, SLOT(AD()) ); connect( (QObject*)(m_Controls->m_RDButton), SIGNAL(clicked()), this, SLOT(RD()) ); connect( (QObject*)(m_Controls->m_ClusteringAnisotropy), SIGNAL(clicked()), this, SLOT(ClusterAnisotropy()) ); } } void QmitkDiffusionQuantificationView::Activated() { berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); QmitkFunctionality::Activated(); } void QmitkDiffusionQuantificationView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkDiffusionQuantificationView::GFACheckboxClicked() { m_Controls->frame_2->setVisible(m_Controls-> m_StandardGFACheckbox->isChecked()); } void QmitkDiffusionQuantificationView::GFA() { if(m_Controls->m_StandardGFACheckbox->isChecked()) { QBIQuantify(13); } else { QBIQuantify(0); } } void QmitkDiffusionQuantificationView::Curvature() { QBIQuantify(12); } void QmitkDiffusionQuantificationView::FA() { TensorQuantify(0); } void QmitkDiffusionQuantificationView::RA() { TensorQuantify(1); } void QmitkDiffusionQuantificationView::AD() { TensorQuantify(2); } void QmitkDiffusionQuantificationView::RD() { TensorQuantify(3); } void QmitkDiffusionQuantificationView::ClusterAnisotropy() { TensorQuantify(4); } void QmitkDiffusionQuantificationView::QBIQuantify(int method) { if (m_CurrentSelection) { mitk::DataStorage::SetOfObjects::Pointer set = mitk::DataStorage::SetOfObjects::New(); int at = 0; for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); i != m_CurrentSelection->End(); ++i) { if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); if(QString("QBallImage").compare(node->GetData()->GetNameOfClass())==0) { set->InsertElement(at++, node); } } } QBIQuantification(set, method); } } void QmitkDiffusionQuantificationView::TensorQuantify(int method) { if (m_CurrentSelection) { mitk::DataStorage::SetOfObjects::Pointer set = mitk::DataStorage::SetOfObjects::New(); int at = 0; for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); i != m_CurrentSelection->End(); ++i) { if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); if(QString("TensorImage").compare(node->GetData()->GetNameOfClass())==0) { set->InsertElement(at++, node); } } } TensorQuantification(set, method); } } void QmitkDiffusionQuantificationView::QBIQuantification( mitk::DataStorage::SetOfObjects::Pointer inImages, int method) { itk::TimeProbe clock; QString status; int nrFiles = inImages->size(); if (!nrFiles) return; mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { typedef float TOdfPixelType; const int odfsize = QBALL_ODFSIZE; typedef itk::Vector OdfVectorType; typedef itk::Image OdfVectorImgType; mitk::Image* vol = static_cast((*itemiter)->GetData()); OdfVectorImgType::Pointer itkvol = OdfVectorImgType::New(); mitk::CastToItkImage(vol, itkvol); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); ++itemiter; float p1 = m_Controls->m_ParamKEdit->text().toFloat(); float p2 = m_Controls->m_ParamPEdit->text().toFloat(); // COMPUTE RA clock.Start(); MBI_INFO << "Computing GFA "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( "Computing GFA for %s", nodename.c_str()).toAscii()); typedef OdfVectorType::ValueType RealValueType; typedef itk::Image< RealValueType, 3 > RAImageType; typedef itk::DiffusionQballGeneralizedFaImageFilter GfaFilterType; GfaFilterType::Pointer gfaFilter = GfaFilterType::New(); gfaFilter->SetInput(itkvol); gfaFilter->SetNumberOfThreads(8); double scale = 1; std::string newname; newname.append(nodename); switch(method) { case 0: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD); newname.append("GFA"); scale = m_ScaleDAIValues; break; } case 1: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILES_HIGH_LOW); newname.append("01"); scale = m_ScaleDAIValues; break; } case 2: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILE_HIGH); newname.append("02"); scale = m_ScaleDAIValues; break; } case 3: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_MAX_ODF_VALUE); newname.append("03"); scale = m_ScaleDAIValues; break; } case 4: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_DECONVOLUTION_COEFFS); newname.append("04"); scale = m_ScaleDAIValues; break; } case 5: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_MIN_MAX_NORMALIZED_STANDARD); newname.append("05"); scale = m_ScaleDAIValues; break; } case 6: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_NORMALIZED_ENTROPY); newname.append("06"); break; } case 7: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_NEMATIC_ORDER_PARAMETER); newname.append("07"); scale = m_ScaleDAIValues; break; } case 8: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILES_LOW_HIGH); newname.append("08"); scale = m_ScaleDAIValues; break; } case 9: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_QUANTILE_LOW); newname.append("09"); scale = m_ScaleDAIValues; break; } case 10: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_MIN_ODF_VALUE); newname.append("10"); scale = m_ScaleDAIValues; break; } case 11: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_STD_BY_MAX); newname.append("11"); scale = m_ScaleDAIValues; break; } case 12: { p1 = m_Controls->MinAngle->text().toFloat(); p2 = m_Controls->MaxAngle->text().toFloat(); gfaFilter->SetComputationMethod(GfaFilterType::GFA_PRINCIPLE_CURVATURE); QString paramString; paramString = paramString.append("PC%1-%2").arg(p1).arg(p2); newname.append(paramString.toAscii()); gfaFilter->SetParam1(p1); gfaFilter->SetParam2(p2); scale = m_ScaleDAIValues; break; } case 13: { gfaFilter->SetComputationMethod(GfaFilterType::GFA_GENERALIZED_GFA); QString paramString; paramString = paramString.append("GFAK%1P%2").arg(p1).arg(p2); newname.append(paramString.toAscii()); gfaFilter->SetParam1(p1); gfaFilter->SetParam2(p2); scale = m_ScaleDAIValues; break; } default: { newname.append("0"); gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD); scale = m_ScaleDAIValues; } } gfaFilter->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s."; typedef itk::Image ImgType; ImgType::Pointer img = ImgType::New(); img->SetSpacing( gfaFilter->GetOutput()->GetSpacing() ); // Set the image spacing img->SetOrigin( gfaFilter->GetOutput()->GetOrigin() ); // Set the image origin img->SetDirection( gfaFilter->GetOutput()->GetDirection() ); // Set the image direction img->SetLargestPossibleRegion( gfaFilter->GetOutput()->GetLargestPossibleRegion()); img->SetBufferedRegion( gfaFilter->GetOutput()->GetLargestPossibleRegion() ); img->Allocate(); itk::ImageRegionIterator ot (img, img->GetLargestPossibleRegion() ); ot = ot.Begin(); itk::ImageRegionConstIterator it (gfaFilter->GetOutput(), gfaFilter->GetOutput()->GetLargestPossibleRegion() ); it = it.Begin(); for (it = it.Begin(); !it.IsAtEnd(); ++it) { GfaFilterType::OutputImageType::PixelType val = it.Get(); ot.Set(val * scale); ++ot; } // GFA TO DATATREE mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( img.GetPointer() ); image->SetVolume( img->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); node->SetProperty( "name", mitk::StringProperty::New(newname) ); nodes.push_back(node); mitk::StatusBar::GetInstance()->DisplayText("Computation complete."); } std::vector::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); m_MultiWidget->RequestUpdate(); } void QmitkDiffusionQuantificationView::TensorQuantification( mitk::DataStorage::SetOfObjects::Pointer inImages, int method) { itk::TimeProbe clock; QString status; int nrFiles = inImages->size(); if (!nrFiles) return; mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { typedef float TTensorPixelType; typedef itk::DiffusionTensor3D< TTensorPixelType > TensorPixelType; typedef itk::Image< TensorPixelType, 3 > TensorImageType; mitk::Image* vol = static_cast((*itemiter)->GetData()); TensorImageType::Pointer itkvol = TensorImageType::New(); mitk::CastToItkImage(vol, itkvol); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); ++itemiter; // COMPUTE FA clock.Start(); MBI_INFO << "Computing FA "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( "Computing FA for %s", nodename.c_str()).toAscii()); typedef itk::Image< TTensorPixelType, 3 > FAImageType; typedef itk::ShiftScaleImageFilter ShiftScaleFilterType; ShiftScaleFilterType::Pointer multi = ShiftScaleFilterType::New(); multi->SetShift(0.0); multi->SetScale(m_ScaleDAIValues);//itk::NumericTraits::max() typedef itk::TensorDerivedMeasurementsFilter MeasurementsType; if(method == 0) //FA { /* typedef itk::TensorFractionalAnisotropyImageFilter< TensorImageType, FAImageType > FilterType; FilterType::Pointer anisotropyFilter = FilterType::New(); anisotropyFilter->SetInput( itkvol.GetPointer() ); anisotropyFilter->Update(); multi->SetInput(anisotropyFilter->GetOutput()); nodename = QString(nodename.c_str()).append("_FA").toStdString();*/ MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); measurementsCalculator->SetMeasure(MeasurementsType::FA); measurementsCalculator->Update(); multi->SetInput(measurementsCalculator->GetOutput()); nodename = QString(nodename.c_str()).append("_FA").toStdString(); } else if(method == 1) //RA { /*typedef itk::TensorRelativeAnisotropyImageFilter< TensorImageType, FAImageType > FilterType; FilterType::Pointer anisotropyFilter = FilterType::New(); anisotropyFilter->SetInput( itkvol.GetPointer() ); anisotropyFilter->Update(); multi->SetInput(anisotropyFilter->GetOutput()); nodename = QString(nodename.c_str()).append("_RA").toStdString();*/ MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); measurementsCalculator->SetMeasure(MeasurementsType::RA); measurementsCalculator->Update(); multi->SetInput(measurementsCalculator->GetOutput()); nodename = QString(nodename.c_str()).append("_RA").toStdString(); } else if(method == 2) // AD (Axial diffusivity) { MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); measurementsCalculator->SetMeasure(MeasurementsType::AD); measurementsCalculator->Update(); multi->SetInput(measurementsCalculator->GetOutput()); nodename = QString(nodename.c_str()).append("_AD").toStdString(); } else if(method == 3) // RD (Radial diffusivity, (Lambda2+Lambda3)/2 { MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); measurementsCalculator->SetMeasure(MeasurementsType::RD); measurementsCalculator->Update(); multi->SetInput(measurementsCalculator->GetOutput()); nodename = QString(nodename.c_str()).append("_RD").toStdString(); } else if(method == 4) // 1-(Lambda2+Lambda3)/(2*Lambda1) { MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); measurementsCalculator->SetMeasure(MeasurementsType::CA); measurementsCalculator->Update(); multi->SetInput(measurementsCalculator->GetOutput()); nodename = QString(nodename.c_str()).append("_CA").toStdString(); } multi->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s."; // FA TO DATATREE mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk( multi->GetOutput() ); image->SetVolume( multi->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); node->SetProperty( "name", mitk::StringProperty::New(nodename) ); nodes.push_back(node); mitk::StatusBar::GetInstance()->DisplayText("Computation complete."); } std::vector::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); m_MultiWidget->RequestUpdate(); } diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.h index 96aa65ae8f..b0f2b811fd 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.h +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkDiffusionQuantificationView.h @@ -1,106 +1,107 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _QMITKDIFFUSIONQUANTIFICATIONVIEW_H_INCLUDED #define _QMITKDIFFUSIONQUANTIFICATIONVIEW_H_INCLUDED #include #include #include "berryISelectionListener.h" #include "berryIStructuredSelection.h" #include "ui_QmitkDiffusionQuantificationViewControls.h" /*! * \ingroup org_mitk_gui_qt_diffusionquantification_internal * * \brief QmitkDiffusionQuantificationView * * Document your class here. * * \sa QmitkFunctionality */ -class QmitkDiffusionQuantificationView : public QObject, public QmitkFunctionality +class QmitkDiffusionQuantificationView : public QmitkFunctionality { friend struct DqSelListener; // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; QmitkDiffusionQuantificationView(); + QmitkDiffusionQuantificationView(const QmitkDiffusionQuantificationView& other); virtual ~QmitkDiffusionQuantificationView(); virtual void CreateQtPartControl(QWidget *parent); /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); protected slots: void GFACheckboxClicked(); void GFA(); void Curvature(); void FA(); void RA(); void AD(); void RD(); void ClusterAnisotropy(); void QBIQuantify(int method); void QBIQuantification(mitk::DataStorage::SetOfObjects::Pointer inImages, int method) ; void TensorQuantify(int method); void TensorQuantification(mitk::DataStorage::SetOfObjects::Pointer inImages, int method) ; protected: Ui::QmitkDiffusionQuantificationViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; berry::ISelectionListener::Pointer m_SelListener; berry::IStructuredSelection::ConstPointer m_CurrentSelection; static const float m_ScaleDAIValues; }; #endif // _QMITKDIFFUSIONQUANTIFICATIONVIEW_H_INCLUDED diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp index 5694b60e27..f1d3036cd5 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.cpp @@ -1,401 +1,407 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ //#define MBILOG_ENABLE_DEBUG #include "QmitkPreprocessingView.h" #include "mitkDiffusionImagingConfigure.h" // qt includes #include // itk includes #include "itkTimeProbe.h" // mitk includes #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkNodePredicateDataType.h" #include "QmitkDataStorageComboBox.h" #include "QmitkStdMultiWidget.h" #include "itkVectorContainer.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 "itkB0ImageExtractionImageFilter.h" #include "itkBrainMaskExtractionImageFilter.h" #include "itkCastImageFilter.h" #include "berryIStructuredSelection.h" #include "berryIWorkbenchWindow.h" #include "berryISelectionService.h" const std::string QmitkPreprocessingView::VIEW_ID = "org.mitk.views.preprocessing"; #define DI_INFO MITK_INFO("DiffusionImaging") typedef float TTensorPixelType; using namespace berry; struct PrpSelListener : ISelectionListener { berryObjectMacro(PrpSelListener); PrpSelListener(QmitkPreprocessingView* view) { m_View = view; } void DoSelectionChanged(ISelection::ConstPointer selection) { // save current selection in member variable m_View->m_CurrentSelection = selection.Cast(); // do something with the selected items if(m_View->m_CurrentSelection) { bool foundDwiVolume = false; // iterate selection for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); i != m_View->m_CurrentSelection->End(); ++i) { // extract datatree node if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); // only look at interesting types if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) { foundDwiVolume = true; } } } m_View->m_Controls->m_ButtonBrainMask->setEnabled(foundDwiVolume); m_View->m_Controls->m_ButtonAverageGradients->setEnabled(foundDwiVolume); m_View->m_Controls->m_ButtonExtractB0->setEnabled(foundDwiVolume); } } void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) { // check, if selection comes from datamanager if (part) { QString partname(part->GetPartName().c_str()); if(partname.compare("Datamanager")==0) { // apply selection DoSelectionChanged(selection); } } } QmitkPreprocessingView* m_View; }; QmitkPreprocessingView::QmitkPreprocessingView() : QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL) { } +QmitkPreprocessingView::QmitkPreprocessingView(const QmitkPreprocessingView& other) +{ + Q_UNUSED(other) + throw std::runtime_error("Copy constructor not implemented"); +} + QmitkPreprocessingView::~QmitkPreprocessingView() { this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); } void QmitkPreprocessingView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkPreprocessingViewControls; m_Controls->setupUi(parent); this->CreateConnections(); } m_SelListener = berry::ISelectionListener::Pointer(new PrpSelListener(this)); this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkPreprocessingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkPreprocessingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkPreprocessingView::CreateConnections() { if ( m_Controls ) { 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_ButtonBrainMask), SIGNAL(clicked()), this, SLOT(BrainMask()) ); } } void QmitkPreprocessingView::Activated() { QmitkFunctionality::Activated(); berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkPreprocessingView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkPreprocessingView::ExtractB0() { if (m_CurrentSelection) { mitk::DataStorage::SetOfObjects::Pointer set = mitk::DataStorage::SetOfObjects::New(); int at = 0; for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); i != m_CurrentSelection->End(); ++i) { if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) { set->InsertElement(at++, node); } } } DoExtractB0(set); } } void QmitkPreprocessingView::DoExtractB0 (mitk::DataStorage::SetOfObjects::Pointer inImages) { typedef mitk::DiffusionImage DiffusionImageType; typedef DiffusionImageType::GradientDirectionContainerType GradientContainerType; int nrFiles = inImages->size(); if (!nrFiles) return; mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { DiffusionImageType* vols = static_cast( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); // Extract image using found index typedef itk::B0ImageExtractionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput(vols->GetVectorImage()); filter->SetDirections(vols->GetDirections()); filter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( filter->GetOutput() ); mitkImage->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( mitkImage ); node->SetProperty( "name", mitk::StringProperty::New(nodename + "_B0")); GetDefaultDataStorage()->Add(node); ++itemiter; } } void QmitkPreprocessingView::AverageGradients() { if (m_CurrentSelection) { mitk::DataStorage::SetOfObjects::Pointer set = mitk::DataStorage::SetOfObjects::New(); int at = 0; for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); i != m_CurrentSelection->End(); ++i) { if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) { set->InsertElement(at++, node); } } } DoAverageGradients(set); } } void QmitkPreprocessingView::DoAverageGradients (mitk::DataStorage::SetOfObjects::Pointer inImages) { int nrFiles = inImages->size(); if (!nrFiles) return; mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); vols->AverageRedundantGradients(m_Controls->m_Blur->value()); ++itemiter; } } void QmitkPreprocessingView::BrainMask() { if (m_CurrentSelection) { mitk::DataStorage::SetOfObjects::Pointer set = mitk::DataStorage::SetOfObjects::New(); int at = 0; for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); i != m_CurrentSelection->End(); ++i) { if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) { set->InsertElement(at++, node); } } } DoBrainMask(set); } } void QmitkPreprocessingView::DoBrainMask (mitk::DataStorage::SetOfObjects::Pointer inImages) { int nrFiles = inImages->size(); if (!nrFiles) return; mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); // Extract image using found index typedef itk::B0ImageExtractionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput(vols->GetVectorImage()); filter->SetDirections(vols->GetDirections()); typedef itk::CastImageFilter, itk::Image > CastFilterType; CastFilterType::Pointer castfilter = CastFilterType::New(); castfilter->SetInput(filter->GetOutput()); typedef itk::BrainMaskExtractionImageFilter MaskFilterType; MaskFilterType::Pointer maskfilter = MaskFilterType::New(); maskfilter->SetInput(castfilter->GetOutput()); maskfilter->Update(); mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( maskfilter->GetOutput() ); mitkImage->SetVolume( maskfilter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( mitkImage ); node->SetProperty( "name", mitk::StringProperty::New(nodename + "_Mask")); GetDefaultDataStorage()->Add(node); ++itemiter; } } diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h index 5a695ce5be..a4bf179e07 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkPreprocessingView.h @@ -1,106 +1,107 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _QMITKPREPROCESSINGVIEW_H_INCLUDED #define _QMITKPREPROCESSINGVIEW_H_INCLUDED #include #include #include "ui_QmitkPreprocessingViewControls.h" #include "mitkDiffusionImage.h" #include #include #include typedef short DiffusionPixelType; struct PrpSelListener; /*! * \ingroup org_mitk_gui_qt_preprocessing_internal * * \brief QmitkPreprocessingView * * Document your class here. * * \sa QmitkFunctionality */ -class QmitkPreprocessingView : public QObject, public QmitkFunctionality +class QmitkPreprocessingView : public QmitkFunctionality { friend struct PrpSelListener; // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; QmitkPreprocessingView(); + QmitkPreprocessingView(const QmitkPreprocessingView& other); virtual ~QmitkPreprocessingView(); virtual void CreateQtPartControl(QWidget *parent); /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); static const int nrconvkernels; protected slots: void AverageGradients(); void DoAverageGradients(mitk::DataStorage::SetOfObjects::Pointer inImages); void ExtractB0(); void DoExtractB0(mitk::DataStorage::SetOfObjects::Pointer inImages); void BrainMask(); void DoBrainMask(mitk::DataStorage::SetOfObjects::Pointer inImages); protected: Ui::QmitkPreprocessingViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name); berry::ISelectionListener::Pointer m_SelListener; berry::IStructuredSelection::ConstPointer m_CurrentSelection; }; #endif // _QMITKPREPROCESSINGVIEW_H_INCLUDED diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.cpp index 1533332132..38f37d4ce2 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.cpp +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.cpp @@ -1,768 +1,774 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ //#define MBILOG_ENABLE_DEBUG #include "QmitkQBallReconstructionView.h" #include "mitkDiffusionImagingConfigure.h" // qt includes #include // itk includes #include "itkTimeProbe.h" // mitk includes #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkNodePredicateDataType.h" #include "QmitkDataStorageComboBox.h" #include "QmitkStdMultiWidget.h" #include "itkDiffusionQballReconstructionImageFilter.h" #include "itkAnalyticalDiffusionQballReconstructionImageFilter.h" #include "itkVectorContainer.h" #include "mitkQBallImage.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 "berryIStructuredSelection.h" #include "berryIWorkbenchWindow.h" #include "berryISelectionService.h" #include const std::string QmitkQBallReconstructionView::VIEW_ID = "org.mitk.views.qballreconstruction"; #define DI_INFO MITK_INFO("DiffusionImaging") typedef float TTensorPixelType; const int QmitkQBallReconstructionView::nrconvkernels = 252; using namespace berry; struct QbrSelListener : ISelectionListener { berryObjectMacro(QbrSelListener); QbrSelListener(QmitkQBallReconstructionView* view) { m_View = view; } void DoSelectionChanged(ISelection::ConstPointer selection) { // save current selection in member variable m_View->m_CurrentSelection = selection.Cast(); // do something with the selected items if(m_View->m_CurrentSelection) { bool foundDwiVolume = false; // iterate selection for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); i != m_View->m_CurrentSelection->End(); ++i) { // extract datatree node if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); // only look at interesting types if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) { foundDwiVolume = true; } } } m_View->m_Controls->m_ButtonStandard->setEnabled(foundDwiVolume); } } void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) { // check, if selection comes from datamanager if (part) { QString partname(part->GetPartName().c_str()); if(partname.compare("Datamanager")==0) { // apply selection DoSelectionChanged(selection); } } } QmitkQBallReconstructionView* m_View; }; QmitkQBallReconstructionView::QmitkQBallReconstructionView() : QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL) { } +QmitkQBallReconstructionView::QmitkQBallReconstructionView(const QmitkQBallReconstructionView& other) +{ + Q_UNUSED(other); + throw std::runtime_error("Copy constructor not implemented"); +} + //void QmitkQBallReconstructionView::OpactiyChanged(int value) //{ // if (m_CurrentSelection) // { // if (mitk::DataNodeObject::Pointer nodeObj = m_CurrentSelection->Begin()->Cast()) // { // mitk::DataNode::Pointer node = nodeObj->GetDataNode(); // if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) // { // node->SetIntProperty("DisplayChannel", value); // mitk::RenderingManager::GetInstance()->RequestUpdateAll(); // } // } // } //} // //void QmitkQBallReconstructionView::OpactiyActionChanged() //{ // if (m_CurrentSelection) // { // if (mitk::DataNodeObject::Pointer nodeObj = m_CurrentSelection->Begin()->Cast()) // { // mitk::DataNode::Pointer node = nodeObj->GetDataNode(); // if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) // { // int displayChannel = 0.0; // if(node->GetIntProperty("DisplayChannel", displayChannel)) // { // m_OpacitySlider->setValue(displayChannel); // } // } // } // } // // MITK_INFO << "changed"; //} QmitkQBallReconstructionView::~QmitkQBallReconstructionView() { this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); } void QmitkQBallReconstructionView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkQBallReconstructionViewControls; m_Controls->setupUi(parent); this->CreateConnections(); QStringList items; items << "2" << "4" << "6" << "8"; m_Controls->m_QBallReconstructionMaxLLevelComboBox->addItems(items); m_Controls->m_QBallReconstructionMaxLLevelComboBox->setCurrentIndex(1); m_Controls->m_Description->setText("Spherical harmonics recon. (Desoteaux2007)"); m_Controls->m_QBallReconstructionNumberThreadsSpinbox->setValue(8); #ifndef DIFFUSION_IMAGING_EXTENDED m_Controls->m_QBallReconstructionMethodComboBox->removeItem(3); #endif AdvancedCheckboxClicked(); // define data type for combobox //m_Controls->m_ImageSelector->SetDataStorage( this->GetDefaultDataStorage() ); //m_Controls->m_ImageSelector->SetPredicate( mitk::NodePredicateDataType::New("DiffusionImage") ); } m_SelListener = berry::ISelectionListener::Pointer(new QbrSelListener(this)); this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkQBallReconstructionView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkQBallReconstructionView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkQBallReconstructionView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_ButtonStandard), SIGNAL(clicked()), this, SLOT(ReconstructStandard()) ); connect( (QObject*)(m_Controls->m_AdvancedCheckbox), SIGNAL(clicked()), this, SLOT(AdvancedCheckboxClicked()) ); connect( (QObject*)(m_Controls->m_QBallReconstructionMethodComboBox), SIGNAL(currentIndexChanged(int)), this, SLOT(MethodChoosen(int)) ); } } void QmitkQBallReconstructionView::Activated() { QmitkFunctionality::Activated(); berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkQBallReconstructionView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkQBallReconstructionView::ReconstructStandard() { int index = m_Controls->m_QBallReconstructionMethodComboBox->currentIndex(); #ifndef DIFFUSION_IMAGING_EXTENDED if(index>=3) { index = index + 1; } #endif switch(index) { case 0: { // Numerical Reconstruct(0,0); break; } case 1: { // Standard Reconstruct(1,0); break; } case 2: { // Solid Angle Reconstruct(1,6); break; } case 3: { // Constrained Solid Angle Reconstruct(1,7); break; } case 4: { // ADC Reconstruct(1,4); break; } case 5: { // Raw Signal Reconstruct(1,5); break; } } } void QmitkQBallReconstructionView::MethodChoosen(int method) { switch(method) { case 0: m_Controls->m_Description->setText("Numerical recon. (Tuch2004)"); break; case 1: m_Controls->m_Description->setText("Spherical harmonics recon. (Desoteaux2007)"); break; case 2: m_Controls->m_Description->setText("SH recon. with solid angle consideration (Aganj2009)"); break; case 3: m_Controls->m_Description->setText("SH solid angle with non-neg. constraint (Goh2009)"); break; case 4: m_Controls->m_Description->setText("SH recon. of the plain ADC-profiles"); break; case 5: m_Controls->m_Description->setText("SH recon. of the raw diffusion signal"); break; } } void QmitkQBallReconstructionView::AdvancedCheckboxClicked() { bool check = m_Controls-> m_AdvancedCheckbox->isChecked(); m_Controls->m_QBallReconstructionMaxLLevelTextLabel_2->setVisible(check); m_Controls->m_QBallReconstructionMaxLLevelComboBox->setVisible(check); m_Controls->m_QBallReconstructionLambdaTextLabel_2->setVisible(check); m_Controls->m_QBallReconstructionLambdaLineEdit->setVisible(check); m_Controls->m_QBallReconstructionThresholdLabel_2->setVisible(check); m_Controls->m_QBallReconstructionThreasholdEdit->setVisible(check); m_Controls->m_OutputB0Image->setVisible(check); m_Controls->m_QBallReconstructionNumberThreadsLabel_2->setVisible(check); m_Controls->m_QBallReconstructionNumberThreadsSpinbox->setVisible(check); m_Controls->label_2->setVisible(check); //m_Controls->textLabel1_2->setVisible(check); //m_Controls->m_QBallReconstructionLambdaStepLineEdit->setVisible(check); //m_Controls->textLabel1_3->setVisible(check); m_Controls->frame_2->setVisible(check); } void QmitkQBallReconstructionView::Reconstruct(int method, int normalization) { if (m_CurrentSelection) { mitk::DataStorage::SetOfObjects::Pointer set = mitk::DataStorage::SetOfObjects::New(); int at = 0; for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); i != m_CurrentSelection->End(); ++i) { if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) { set->InsertElement(at++, node); } } } if(method == 0) { NumericalQBallReconstruction(set, normalization); } else { #if BOOST_VERSION / 100000 > 0 #if BOOST_VERSION / 100 % 1000 > 34 if(method == 1) { AnalyticalQBallReconstruction(set, normalization); } #else std::cout << "ERROR: Boost 1.35 minimum required" << std::endl; QMessageBox::warning(NULL,"ERROR","Boost 1.35 minimum required"); #endif #else std::cout << "ERROR: Boost 1.35 minimum required" << std::endl; QMessageBox::warning(NULL,"ERROR","Boost 1.35 minimum required"); #endif } } } void QmitkQBallReconstructionView::NumericalQBallReconstruction (mitk::DataStorage::SetOfObjects::Pointer inImages, int normalization) { try { itk::TimeProbe clock; int nrFiles = inImages->size(); if (!nrFiles) return; QString status; mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); ++itemiter; // QBALL RECONSTRUCTION clock.Start(); MBI_INFO << "QBall reconstruction "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( "QBall reconstruction for %s", nodename.c_str()).toAscii()); typedef itk::DiffusionQballReconstructionImageFilter QballReconstructionImageFilterType; QballReconstructionImageFilterType::Pointer filter = QballReconstructionImageFilterType::New(); filter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() ); filter->SetNumberOfThreads( m_Controls->m_QBallReconstructionNumberThreadsSpinbox->value() ); filter->SetBValue(vols->GetB_Value()); filter->SetThreshold( m_Controls->m_QBallReconstructionThreasholdEdit->text().toFloat() ); switch(normalization) { case 0: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD); break; } case 1: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_B_ZERO_B_VALUE); break; } case 2: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_B_ZERO); break; } case 3: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_NONE); break; } default: { filter->SetNormalizationMethod(QballReconstructionImageFilterType::QBR_STANDARD); } } filter->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s." ; // ODFs TO DATATREE mitk::QBallImage::Pointer image = mitk::QBallImage::New(); image->InitializeByItk( filter->GetOutput() ); //image->SetImportVolume( filter->GetOutput()->GetBufferPointer(), 0, 0, mitk::Image::ImportMemoryManagementType::ManageMemory ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); QString newname; newname = newname.append(nodename.c_str()); newname = newname.append("_QN%1").arg(normalization); SetDefaultNodeProperties(node, newname.toStdString()); nodes.push_back(node); // B-Zero TO DATATREE if(m_Controls->m_OutputB0Image->isChecked()) { mitk::Image::Pointer image4 = mitk::Image::New(); image4->InitializeByItk( filter->GetBZeroImage().GetPointer() ); image4->SetVolume( filter->GetBZeroImage()->GetBufferPointer() ); mitk::DataNode::Pointer node4=mitk::DataNode::New(); node4->SetData( image4 ); node4->SetProperty( "name", mitk::StringProperty::New( QString(nodename.c_str()).append("_b0").toStdString()) ); nodes.push_back(node4); } mitk::ProgressBar::GetInstance()->Progress(); } std::vector::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); m_MultiWidget->RequestUpdate(); } catch (itk::ExceptionObject &ex) { MBI_INFO << ex ; return ; } } void QmitkQBallReconstructionView::AnalyticalQBallReconstruction( mitk::DataStorage::SetOfObjects::Pointer inImages, int normalization) { try { itk::TimeProbe clock; int nrFiles = inImages->size(); if (!nrFiles) return; std::vector lambdas; float minLambda = m_Controls->m_QBallReconstructionLambdaLineEdit->text().toFloat(); lambdas.push_back(minLambda); int nLambdas = lambdas.size(); QString status; mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles*nLambdas); mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector* nodes = new std::vector(); while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name",nodename); itemiter++; // QBALL RECONSTRUCTION clock.Start(); MBI_INFO << "QBall reconstruction "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( "QBall reconstruction for %s", nodename.c_str()).toAscii()); for(int i=0; im_QBallReconstructionMaxLLevelComboBox->currentIndex()) { case 0: { TemplatedAnalyticalQBallReconstruction<2>(vols, currentLambda, nodename, nodes, normalization); break; } case 1: { TemplatedAnalyticalQBallReconstruction<4>(vols, currentLambda, nodename, nodes, normalization); break; } case 2: { TemplatedAnalyticalQBallReconstruction<6>(vols, currentLambda, nodename, nodes, normalization); break; } case 3: { TemplatedAnalyticalQBallReconstruction<8>(vols, currentLambda, nodename, nodes, normalization); break; } } clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s." ; mitk::ProgressBar::GetInstance()->Progress(); } } std::vector::iterator nodeIt; for(nodeIt = nodes->begin(); nodeIt != nodes->end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); m_MultiWidget->RequestUpdate(); mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); } catch (itk::ExceptionObject &ex) { MBI_INFO << ex ; return ; } } template void QmitkQBallReconstructionView::TemplatedAnalyticalQBallReconstruction( mitk::DiffusionImage* vols, float lambda, std::string nodename, std::vector* nodes, int normalization) { typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; typename FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() ); filter->SetNumberOfThreads( m_Controls->m_QBallReconstructionNumberThreadsSpinbox->value() ); filter->SetBValue(vols->GetB_Value()); filter->SetThreshold( m_Controls->m_QBallReconstructionThreasholdEdit->text().toFloat() ); filter->SetLambda(lambda); switch(normalization) { case 0: { filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); break; } case 1: { filter->SetNormalizationMethod(FilterType::QBAR_B_ZERO_B_VALUE); break; } case 2: { filter->SetNormalizationMethod(FilterType::QBAR_B_ZERO); break; } case 3: { filter->SetNormalizationMethod(FilterType::QBAR_NONE); break; } case 4: { filter->SetNormalizationMethod(FilterType::QBAR_ADC_ONLY); break; } case 5: { filter->SetNormalizationMethod(FilterType::QBAR_RAW_SIGNAL); break; } case 6: { filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); break; } case 7: { filter->SetNormalizationMethod(FilterType::QBAR_NONNEG_SOLID_ANGLE); break; } default: { filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); } } filter->Update(); // ODFs TO DATATREE mitk::QBallImage::Pointer image = mitk::QBallImage::New(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); QString newname; newname = newname.append(nodename.c_str()); newname = newname.append("_QA%1").arg(normalization); SetDefaultNodeProperties(node, newname.toStdString()); nodes->push_back(node); // B-Zero TO DATATREE if(m_Controls->m_OutputB0Image->isChecked()) { mitk::Image::Pointer image4 = mitk::Image::New(); image4->InitializeByItk( filter->GetBZeroImage().GetPointer() ); image4->SetVolume( filter->GetBZeroImage()->GetBufferPointer() ); mitk::DataNode::Pointer node4=mitk::DataNode::New(); node4->SetData( image4 ); node4->SetProperty( "name", mitk::StringProperty::New( QString(nodename.c_str()).append("_b0").toStdString()) ); nodes->push_back(node4); } } void QmitkQBallReconstructionView::SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name) { node->SetProperty( "ShowMaxNumber", mitk::IntProperty::New( 500 ) ); node->SetProperty( "Scaling", mitk::FloatProperty::New( 1.0 ) ); node->SetProperty( "Normalization", mitk::OdfNormalizationMethodProperty::New()); node->SetProperty( "ScaleBy", mitk::OdfScaleByProperty::New()); node->SetProperty( "IndexParam1", mitk::FloatProperty::New(2)); node->SetProperty( "IndexParam2", mitk::FloatProperty::New(1)); node->SetProperty( "visible", mitk::BoolProperty::New( true ) ); node->SetProperty( "VisibleOdfs", mitk::BoolProperty::New( false ) ); node->SetProperty ("layer", mitk::IntProperty::New(100)); node->SetProperty( "DoRefresh", mitk::BoolProperty::New( true ) ); //node->SetProperty( "opacity", mitk::FloatProperty::New(1.0f) ); node->SetProperty( "name", mitk::StringProperty::New(name) ); } //node->SetProperty( "volumerendering", mitk::BoolProperty::New( false ) ); //node->SetProperty( "use color", mitk::BoolProperty::New( true ) ); //node->SetProperty( "texture interpolation", mitk::BoolProperty::New( true ) ); //node->SetProperty( "reslice interpolation", mitk::VtkResliceInterpolationProperty::New() ); //node->SetProperty( "layer", mitk::IntProperty::New(0)); //node->SetProperty( "in plane resample extent by geometry", mitk::BoolProperty::New( false ) ); //node->SetOpacity(1.0f); //node->SetColor(1.0,1.0,1.0); //node->SetVisibility(true); //node->SetProperty( "IsQBallVolume", mitk::BoolProperty::New( true ) ); //mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New(); //mitk::LevelWindow levelwindow; //// levelwindow.SetAuto( image ); //levWinProp->SetLevelWindow( levelwindow ); //node->GetPropertyList()->SetProperty( "levelwindow", levWinProp ); //// add a default rainbow lookup table for color mapping //if(!node->GetProperty("LookupTable")) //{ // mitk::LookupTable::Pointer mitkLut = mitk::LookupTable::New(); // vtkLookupTable* vtkLut = mitkLut->GetVtkLookupTable(); // vtkLut->SetHueRange(0.6667, 0.0); // vtkLut->SetTableRange(0.0, 20.0); // vtkLut->Build(); // mitk::LookupTableProperty::Pointer mitkLutProp = mitk::LookupTableProperty::New(); // mitkLutProp->SetLookupTable(mitkLut); // node->SetProperty( "LookupTable", mitkLutProp ); //} //if(!node->GetProperty("binary")) // node->SetProperty( "binary", mitk::BoolProperty::New( false ) ); //// add a default transfer function //mitk::TransferFunction::Pointer tf = mitk::TransferFunction::New(); //node->SetProperty ( "TransferFunction", mitk::TransferFunctionProperty::New ( tf.GetPointer() ) ); //// set foldername as string property //mitk::StringProperty::Pointer nameProp = mitk::StringProperty::New( name ); //node->SetProperty( "name", nameProp ); diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.h index 149a2512fb..bfc262add3 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.h +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkQBallReconstructionView.h @@ -1,118 +1,119 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _QMITKQBALLRECONSTRUCTIONVIEW_H_INCLUDED #define _QMITKQBALLRECONSTRUCTIONVIEW_H_INCLUDED #include #include #include "ui_QmitkQBallReconstructionViewControls.h" #include "mitkDiffusionImage.h" #include #include #include typedef short DiffusionPixelType; struct QbrSelListener; /*! * \ingroup org_mitk_gui_qt_qballreconstruction_internal * * \brief QmitkQBallReconstructionView * * Document your class here. * * \sa QmitkFunctionality */ -class QmitkQBallReconstructionView : public QObject, public QmitkFunctionality +class QmitkQBallReconstructionView : public QmitkFunctionality { friend struct QbrSelListener; // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; QmitkQBallReconstructionView(); + QmitkQBallReconstructionView(const QmitkQBallReconstructionView& other); virtual ~QmitkQBallReconstructionView(); virtual void CreateQtPartControl(QWidget *parent); /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); static const int nrconvkernels; protected slots: void ReconstructStandard(); //void ReconstructNormalized1(); //void ReconstructNormalized2(); //void ReconstructNonNormalized(); //void AnalyticallyReconstructStandard(); //void AnalyticallyReconstructSolidAngle(); //void AnalyticallyReconstructNonNegSolidAngle(); //void AnalyticallyReconstructAdc(); //void AnalyticallyReconstructRaw(); void AdvancedCheckboxClicked(); void MethodChoosen(int method); void Reconstruct(int method, int normalization); void NumericalQBallReconstruction(mitk::DataStorage::SetOfObjects::Pointer inImages, int normalization); void AnalyticalQBallReconstruction(mitk::DataStorage::SetOfObjects::Pointer inImages, int normalization); protected: Ui::QmitkQBallReconstructionViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; template void TemplatedAnalyticalQBallReconstruction(mitk::DiffusionImage* vols, float lambda, std::string nodename, std::vector* nodes, int normalization); void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name); berry::ISelectionListener::Pointer m_SelListener; berry::IStructuredSelection::ConstPointer m_CurrentSelection; }; #endif // _QMITKQBALLRECONSTRUCTIONVIEW_H_INCLUDED diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.cpp index 0f225e9755..21608b7ce9 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.cpp +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.cpp @@ -1,795 +1,801 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkTensorReconstructionView.h" #include "mitkDiffusionImagingConfigure.h" // qt includes #include // itk includes #include "itkTimeProbe.h" //#include "itkTensor.h" // mitk includes #include "mitkProgressBar.h" #include "mitkStatusBar.h" #include "mitkNodePredicateDataType.h" #include "QmitkDataStorageComboBox.h" #include "QmitkStdMultiWidget.h" #include "mitkTeemDiffusionTensor3DReconstructionImageFilter.h" #include "itkDiffusionTensor3DReconstructionImageFilter.h" #include "itkTensorImageToDiffusionImageFilter.h" #include "itkPointShell.h" #include "itkVector.h" #include "mitkTensorImage.h" #include "mitkProperties.h" #include "mitkDataNodeObject.h" #include "mitkOdfNormalizationMethodProperty.h" #include "mitkOdfScaleByProperty.h" #include "mitkDiffusionImageMapper.h" #include "berryIStructuredSelection.h" #include "berryIWorkbenchWindow.h" #include "berryISelectionService.h" const std::string QmitkTensorReconstructionView::VIEW_ID = "org.mitk.views.tensorreconstruction"; #define DI_INFO MITK_INFO("DiffusionImaging") typedef float TTensorPixelType; using namespace berry; struct TrSelListener : ISelectionListener { berryObjectMacro(TrSelListener); TrSelListener(QmitkTensorReconstructionView* view) { m_View = view; } void DoSelectionChanged(ISelection::ConstPointer selection) { // if(!m_View->IsVisible()) // return; // save current selection in member variable m_View->m_CurrentSelection = selection.Cast(); // do something with the selected items if(m_View->m_CurrentSelection) { bool foundDwiVolume = false; bool foundTensorVolume = false; // iterate selection for (IStructuredSelection::iterator i = m_View->m_CurrentSelection->Begin(); i != m_View->m_CurrentSelection->End(); ++i) { // extract datatree node if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); // only look at interesting types if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) { foundDwiVolume = true; } // only look at interesting types if(QString("TensorImage").compare(node->GetData()->GetNameOfClass())==0) { foundTensorVolume = true; } } } m_View->m_Controls->m_ItkReconstruction->setEnabled(foundDwiVolume); m_View->m_Controls->m_TeemReconstruction->setEnabled(foundDwiVolume); m_View->m_Controls->m_TensorsToDWIButton->setEnabled(foundTensorVolume); } } void SelectionChanged(IWorkbenchPart::Pointer part, ISelection::ConstPointer selection) { // check, if selection comes from datamanager if (part) { QString partname(part->GetPartName().c_str()); if(partname.compare("Datamanager")==0) { // apply selection DoSelectionChanged(selection); } } } QmitkTensorReconstructionView* m_View; }; QmitkTensorReconstructionView::QmitkTensorReconstructionView() : QmitkFunctionality(), m_Controls(NULL), m_MultiWidget(NULL) { } +QmitkTensorReconstructionView::QmitkTensorReconstructionView(const QmitkTensorReconstructionView& other) +{ + Q_UNUSED(other) + throw std::runtime_error("Copy constructor not implemented"); +} + QmitkTensorReconstructionView::~QmitkTensorReconstructionView() { this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->RemovePostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); } void QmitkTensorReconstructionView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkTensorReconstructionViewControls; m_Controls->setupUi(parent); this->CreateConnections(); m_Controls->m_TensorReconstructionNumberThreadsSpinbox->setValue(8); QStringList items; items << "LLS (Linear Least Squares)" << "MLE (Maximum Likelihood)" << "NLS (Nonlinear Least Squares)" << "WLS (Weighted Least Squares)"; m_Controls->m_TensorEstimationTeemEstimationMethodCombo->addItems(items); m_Controls->m_TensorEstimationTeemEstimationMethodCombo->setCurrentIndex(0); m_Controls->m_TensorEstimationManualThreashold->setChecked(false); m_Controls->m_TensorEstimationTeemSigmaEdit->setText("NaN"); m_Controls->m_TensorEstimationTeemNumItsSpin->setValue(1); m_Controls->m_TensorEstimationTeemFuzzyEdit->setText("0.0"); m_Controls->m_TensorEstimationTeemMinValEdit->setText("1.0"); m_Controls->m_TensorEstimationTeemNumItsLabel_2->setEnabled(true); m_Controls->m_TensorEstimationTeemNumItsSpin->setEnabled(true); m_Controls->m_TensorsToDWIBValueEdit->setText("1000"); Advanced1CheckboxClicked(); Advanced2CheckboxClicked(); TeemCheckboxClicked(); #ifndef DIFFUSION_IMAGING_EXTENDED m_Controls->m_TeemToggle->setVisible(false); #endif // define data type for combobox //m_Controls->m_ImageSelector->SetDataStorage( this->GetDefaultDataStorage() ); //m_Controls->m_ImageSelector->SetPredicate( mitk::NodePredicateDataType::New("DiffusionImage") ); } m_SelListener = berry::ISelectionListener::Pointer(new TrSelListener(this)); this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->AddPostSelectionListener(/*"org.mitk.views.datamanager",*/ m_SelListener); berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); } void QmitkTensorReconstructionView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { berry::ISelection::ConstPointer sel( this->GetSite()->GetWorkbenchWindow()->GetSelectionService()->GetSelection("org.mitk.views.datamanager")); m_CurrentSelection = sel.Cast(); m_SelListener.Cast()->DoSelectionChanged(sel); m_MultiWidget = &stdMultiWidget; } void QmitkTensorReconstructionView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkTensorReconstructionView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_TeemToggle), SIGNAL(clicked()), this, SLOT(TeemCheckboxClicked()) ); connect( (QObject*)(m_Controls->m_ItkReconstruction), SIGNAL(clicked()), this, SLOT(ItkReconstruction()) ); connect( (QObject*)(m_Controls->m_TeemReconstruction), SIGNAL(clicked()), this, SLOT(TeemReconstruction()) ); connect( (QObject*)(m_Controls->m_TensorEstimationTeemEstimationMethodCombo), SIGNAL(currentIndexChanged(int)), this, SLOT(MethodChoosen(int)) ); connect( (QObject*)(m_Controls->m_Advanced1), SIGNAL(clicked()), this, SLOT(Advanced1CheckboxClicked()) ); connect( (QObject*)(m_Controls->m_Advanced2), SIGNAL(clicked()), this, SLOT(Advanced2CheckboxClicked()) ); connect( (QObject*)(m_Controls->m_TensorEstimationManualThreashold), SIGNAL(clicked()), this, SLOT(ManualThresholdClicked()) ); connect( (QObject*)(m_Controls->m_TensorsToDWIButton), SIGNAL(clicked()), this, SLOT(TensorsToDWI()) ); } } void QmitkTensorReconstructionView::TeemCheckboxClicked() { m_Controls->groupBox_3->setVisible(m_Controls-> m_TeemToggle->isChecked()); } void QmitkTensorReconstructionView::Advanced1CheckboxClicked() { bool check = m_Controls-> m_Advanced1->isChecked(); m_Controls->frame->setVisible(check); } void QmitkTensorReconstructionView::Advanced2CheckboxClicked() { bool check = m_Controls-> m_Advanced2->isChecked(); m_Controls->frame_2->setVisible(check); } void QmitkTensorReconstructionView::ManualThresholdClicked() { m_Controls->m_TensorReconstructionThreasholdEdit_2->setEnabled( m_Controls->m_TensorEstimationManualThreashold->isChecked()); } void QmitkTensorReconstructionView::Activated() { QmitkFunctionality::Activated(); } void QmitkTensorReconstructionView::Deactivated() { QmitkFunctionality::Deactivated(); } void QmitkTensorReconstructionView::MethodChoosen(int method) { m_Controls->m_TensorEstimationTeemNumItsLabel_2->setEnabled(method==3); m_Controls->m_TensorEstimationTeemNumItsSpin->setEnabled(method==3); } void QmitkTensorReconstructionView::ItkReconstruction() { Reconstruct(0); } void QmitkTensorReconstructionView::TeemReconstruction() { Reconstruct(1); } void QmitkTensorReconstructionView::Reconstruct(int method) { if (m_CurrentSelection) { mitk::DataStorage::SetOfObjects::Pointer set = mitk::DataStorage::SetOfObjects::New(); int at = 0; for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); i != m_CurrentSelection->End(); ++i) { if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); if(QString("DiffusionImage").compare(node->GetData()->GetNameOfClass())==0) { set->InsertElement(at++, node); } } } if(method == 0) { ItkTensorReconstruction(set); } if(method == 1) { TeemTensorReconstruction(set); } } } void QmitkTensorReconstructionView::ItkTensorReconstruction (mitk::DataStorage::SetOfObjects::Pointer inImages) { try { itk::TimeProbe clock; int nrFiles = inImages->size(); if (!nrFiles) return; QString status; mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); ++itemiter; // TENSOR RECONSTRUCTION clock.Start(); MBI_INFO << "Tensor reconstruction "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( "Tensor reconstruction for %s", nodename.c_str()).toAscii()); typedef itk::DiffusionTensor3DReconstructionImageFilter< DiffusionPixelType, DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter = TensorReconstructionImageFilterType::New(); tensorReconstructionFilter->SetGradientImage( vols->GetDirections(), vols->GetVectorImage() ); tensorReconstructionFilter->SetNumberOfThreads( m_Controls->m_TensorReconstructionNumberThreadsSpinbox->value() ); tensorReconstructionFilter->SetBValue(vols->GetB_Value()); tensorReconstructionFilter->SetThreshold( m_Controls->m_TensorReconstructionThreasholdEdit->text().toFloat() ); tensorReconstructionFilter->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s."; // TENSORS TO DATATREE mitk::TensorImage::Pointer image = mitk::TensorImage::New(); typedef itk::Image, 3> TensorImageType; TensorImageType::Pointer tensorImage; tensorImage = tensorReconstructionFilter->GetOutput(); // Check the tensor for negative eigenvalues if(m_Controls->m_CheckNegativeEigenvalues->isChecked()) { typedef itk::ImageRegionIterator TensorImageIteratorType; TensorImageIteratorType tensorIt(tensorImage, tensorImage->GetRequestedRegion()); tensorIt.GoToBegin(); while(!tensorIt.IsAtEnd()) { typedef itk::DiffusionTensor3D TensorType; //typedef itk::Tensor TensorType2; TensorType tensor = tensorIt.Get(); // TensorType2 tensor2; /* for(int i=0; i SymEigenSystemType; SymEigenSystemType eig (tensor2.GetVnlMatrix()); for(unsigned int i=0; iInitializeByItk( tensorImage.GetPointer() ); image->SetVolume( tensorReconstructionFilter->GetOutput()->GetBufferPointer() ); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); QString newname; newname = newname.append(nodename.c_str()); newname = newname.append("_dti"); SetDefaultNodeProperties(node, newname.toStdString()); nodes.push_back(node); mitk::ProgressBar::GetInstance()->Progress(); } std::vector::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); m_MultiWidget->RequestUpdate(); } catch (itk::ExceptionObject &ex) { MBI_INFO << ex ; return ; } } void QmitkTensorReconstructionView::TeemTensorReconstruction (mitk::DataStorage::SetOfObjects::Pointer inImages) { try { itk::TimeProbe clock; int nrFiles = inImages->size(); if (!nrFiles) return; QString status; mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { mitk::DiffusionImage* vols = static_cast*>( (*itemiter)->GetData()); std::string nodename; (*itemiter)->GetStringProperty("name", nodename); ++itemiter; // TENSOR RECONSTRUCTION clock.Start(); MBI_INFO << "Teem Tensor reconstruction "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( "Teem Tensor reconstruction for %s", nodename.c_str()).toAscii()); typedef mitk::TeemDiffusionTensor3DReconstructionImageFilter< DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter = TensorReconstructionImageFilterType::New(); tensorReconstructionFilter->SetInput( vols ); if(!m_Controls->m_TensorEstimationTeemSigmaEdit->text().contains(QString("NaN"))) tensorReconstructionFilter->SetSigma( m_Controls->m_TensorEstimationTeemSigmaEdit->text().toFloat() ); switch(m_Controls->m_TensorEstimationTeemEstimationMethodCombo->currentIndex()) { // items << "LLS (Linear Least Squares)" //<< "MLE (Maximum Likelihood)" //<< "NLS (Nonlinear Least Squares)" //<< "WLS (Weighted Least Squares)"; case 0: tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsLLS); break; case 1: tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsMLE); break; case 2: tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsNLS); break; case 3: tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsWLS); break; default: tensorReconstructionFilter->SetEstimationMethod(mitk::TeemTensorEstimationMethodsLLS); } tensorReconstructionFilter->SetNumIterations( m_Controls->m_TensorEstimationTeemNumItsSpin->value() ); if(m_Controls->m_TensorEstimationManualThreashold->isChecked()) tensorReconstructionFilter->SetConfidenceThreshold( m_Controls->m_TensorReconstructionThreasholdEdit_2->text().toDouble() ); tensorReconstructionFilter->SetConfidenceFuzzyness( m_Controls->m_TensorEstimationTeemFuzzyEdit->text().toFloat() ); tensorReconstructionFilter->SetMinPlausibleValue( m_Controls->m_TensorEstimationTeemMinValEdit->text().toDouble() ); tensorReconstructionFilter->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s." ; // TENSORS TO DATATREE mitk::DataNode::Pointer node2=mitk::DataNode::New(); node2->SetData( tensorReconstructionFilter->GetOutputItk() ); QString newname; newname = newname.append(nodename.c_str()); newname = newname.append("_dtix"); SetDefaultNodeProperties(node2, newname.toStdString()); nodes.push_back(node2); mitk::ProgressBar::GetInstance()->Progress(); } std::vector::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); m_MultiWidget->RequestUpdate(); } catch (itk::ExceptionObject &ex) { MBI_INFO << ex ; return ; } } void QmitkTensorReconstructionView::SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name) { node->SetProperty( "ShowMaxNumber", mitk::IntProperty::New( 500 ) ); node->SetProperty( "Scaling", mitk::FloatProperty::New( 1.0 ) ); node->SetProperty( "Normalization", mitk::OdfNormalizationMethodProperty::New()); node->SetProperty( "ScaleBy", mitk::OdfScaleByProperty::New()); node->SetProperty( "IndexParam1", mitk::FloatProperty::New(2)); node->SetProperty( "IndexParam2", mitk::FloatProperty::New(1)); node->SetProperty( "visible", mitk::BoolProperty::New( true ) ); node->SetProperty( "VisibleOdfs", mitk::BoolProperty::New( false ) ); node->SetProperty ("layer", mitk::IntProperty::New(100)); node->SetProperty( "DoRefresh", mitk::BoolProperty::New( true ) ); //node->SetProperty( "opacity", mitk::FloatProperty::New(1.0f) ); node->SetProperty( "name", mitk::StringProperty::New(name) ); } //node->SetProperty( "volumerendering", mitk::BoolProperty::New( false ) ); //node->SetProperty( "use color", mitk::BoolProperty::New( true ) ); //node->SetProperty( "texture interpolation", mitk::BoolProperty::New( true ) ); //node->SetProperty( "reslice interpolation", mitk::VtkResliceInterpolationProperty::New() ); //node->SetProperty( "layer", mitk::IntProperty::New(0)); //node->SetProperty( "in plane resample extent by geometry", mitk::BoolProperty::New( false ) ); //node->SetOpacity(1.0f); //node->SetColor(1.0,1.0,1.0); //node->SetVisibility(true); //node->SetProperty( "IsTensorVolume", mitk::BoolProperty::New( true ) ); //mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New(); //mitk::LevelWindow levelwindow; //// levelwindow.SetAuto( image ); //levWinProp->SetLevelWindow( levelwindow ); //node->GetPropertyList()->SetProperty( "levelwindow", levWinProp ); //// add a default rainbow lookup table for color mapping //if(!node->GetProperty("LookupTable")) //{ // mitk::LookupTable::Pointer mitkLut = mitk::LookupTable::New(); // vtkLookupTable* vtkLut = mitkLut->GetVtkLookupTable(); // vtkLut->SetHueRange(0.6667, 0.0); // vtkLut->SetTableRange(0.0, 20.0); // vtkLut->Build(); // mitk::LookupTableProperty::Pointer mitkLutProp = mitk::LookupTableProperty::New(); // mitkLutProp->SetLookupTable(mitkLut); // node->SetProperty( "LookupTable", mitkLutProp ); //} //if(!node->GetProperty("binary")) // node->SetProperty( "binary", mitk::BoolProperty::New( false ) ); //// add a default transfer function //mitk::TransferFunction::Pointer tf = mitk::TransferFunction::New(); //node->SetProperty ( "TransferFunction", mitk::TransferFunctionProperty::New ( tf.GetPointer() ) ); //// set foldername as string property //mitk::StringProperty::Pointer nameProp = mitk::StringProperty::New( name ); //node->SetProperty( "name", nameProp ); void QmitkTensorReconstructionView::TensorsToDWI() { if (m_CurrentSelection) { mitk::DataStorage::SetOfObjects::Pointer set = mitk::DataStorage::SetOfObjects::New(); int at = 0; for (IStructuredSelection::iterator i = m_CurrentSelection->Begin(); i != m_CurrentSelection->End(); ++i) { if (mitk::DataNodeObject::Pointer nodeObj = i->Cast()) { mitk::DataNode::Pointer node = nodeObj->GetDataNode(); if(QString("TensorImage").compare(node->GetData()->GetNameOfClass())==0) { set->InsertElement(at++, node); } } } DoTensorsToDWI(set); } } template std::vector > QmitkTensorReconstructionView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); for(int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } return retval; } void QmitkTensorReconstructionView::DoTensorsToDWI (mitk::DataStorage::SetOfObjects::Pointer inImages) { try { itk::TimeProbe clock; int nrFiles = inImages->size(); if (!nrFiles) return; QString status; mitk::ProgressBar::GetInstance()->AddStepsToDo(nrFiles); mitk::DataStorage::SetOfObjects::const_iterator itemiter( inImages->begin() ); mitk::DataStorage::SetOfObjects::const_iterator itemiterend( inImages->end() ); std::vector nodes; while ( itemiter != itemiterend ) // for all items { std::string nodename; (*itemiter)->GetStringProperty("name", nodename); mitk::TensorImage* vol = static_cast((*itemiter)->GetData()); ++itemiter; typedef float TTensorPixelType; typedef itk::DiffusionTensor3D< TTensorPixelType > TensorPixelType; typedef itk::Image< TensorPixelType, 3 > TensorImageType; TensorImageType::Pointer itkvol = TensorImageType::New(); mitk::CastToItkImage(vol, itkvol); typedef itk::TensorImageToDiffusionImageFilter< TTensorPixelType, DiffusionPixelType > FilterType; FilterType::GradientListType gradientList; switch(m_Controls->m_TensorsToDWINumDirsSelect->currentIndex()) { case 0: gradientList = MakeGradientList<12>(); break; case 1: gradientList = MakeGradientList<42>(); break; case 2: gradientList = MakeGradientList<92>(); break; case 3: gradientList = MakeGradientList<162>(); break; case 4: gradientList = MakeGradientList<252>(); break; case 5: gradientList = MakeGradientList<362>(); break; case 6: gradientList = MakeGradientList<492>(); break; case 7: gradientList = MakeGradientList<642>(); break; case 8: gradientList = MakeGradientList<812>(); break; case 9: gradientList = MakeGradientList<1002>(); break; default: gradientList = MakeGradientList<92>(); } double bVal = m_Controls->m_TensorsToDWIBValueEdit->text().toDouble(); // DWI ESTIMATION clock.Start(); MBI_INFO << "DWI Estimation "; mitk::StatusBar::GetInstance()->DisplayText(status.sprintf( "DWI Estimation for %s", nodename.c_str()).toAscii()); FilterType::Pointer filter = FilterType::New(); filter->SetInput( itkvol ); filter->SetBValue(bVal); filter->SetGradientList(gradientList); filter->SetNumberOfThreads(1); filter->Update(); clock.Stop(); MBI_DEBUG << "took " << clock.GetMeanTime() << "s."; itk::Vector v; v[0] = 0; v[1] = 0; v[2] = 0; gradientList.push_back(v); // TENSORS TO DATATREE mitk::DiffusionImage::Pointer image = mitk::DiffusionImage::New(); image->SetVectorImage( filter->GetOutput() ); image->SetB_Value(bVal); image->SetDirections(gradientList); image->InitializeFromVectorImage(); mitk::DataNode::Pointer node=mitk::DataNode::New(); node->SetData( image ); mitk::DiffusionImageMapper::SetDefaultProperties(node); QString newname; newname = newname.append(nodename.c_str()); newname = newname.append("_dwi"); node->SetName(newname.toAscii()); nodes.push_back(node); mitk::ProgressBar::GetInstance()->Progress(); } std::vector::iterator nodeIt; for(nodeIt = nodes.begin(); nodeIt != nodes.end(); ++nodeIt) GetDefaultDataStorage()->Add(*nodeIt); mitk::StatusBar::GetInstance()->DisplayText(status.sprintf("Finished Processing %d Files", nrFiles).toAscii()); m_MultiWidget->RequestUpdate(); } catch (itk::ExceptionObject &ex) { MBI_INFO << ex ; return ; } -} \ No newline at end of file +} diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.h index 3ecac3b523..c9a8a6bd45 100644 --- a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.h +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkTensorReconstructionView.h @@ -1,119 +1,120 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Module: $RCSfile$ Language: C++ Date: $Date: 2009-05-28 17:19:30 +0200 (Do, 28 Mai 2009) $ Version: $Revision: 17495 $ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef _QMITKTENSORRECONSTRUCTIONVIEW_H_INCLUDED #define _QMITKTENSORRECONSTRUCTIONVIEW_H_INCLUDED #include #include #include "ui_QmitkTensorReconstructionViewControls.h" #include "mitkDiffusionImage.h" #include #include #include typedef short DiffusionPixelType; struct TrSelListener; /*! * \ingroup org_mitk_gui_qt_tensorreconstruction_internal * * \brief QmitkTensorReconstructionView * * Document your class here. * * \sa QmitkFunctionality */ -class QmitkTensorReconstructionView : public QObject, public QmitkFunctionality +class QmitkTensorReconstructionView : public QmitkFunctionality { friend struct TrSelListener; // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; QmitkTensorReconstructionView(); + QmitkTensorReconstructionView(const QmitkTensorReconstructionView& other); virtual ~QmitkTensorReconstructionView(); virtual void CreateQtPartControl(QWidget *parent); /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); /// \brief Called when the functionality is activated virtual void Activated(); virtual void Deactivated(); virtual void StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget); virtual void StdMultiWidgetNotAvailable(); static const int nrconvkernels; protected slots: void TensorsToDWI(); void DoTensorsToDWI(mitk::DataStorage::SetOfObjects::Pointer inImages); void TeemCheckboxClicked(); void Advanced1CheckboxClicked(); void Advanced2CheckboxClicked(); void ManualThresholdClicked(); void MethodChoosen(int method); void Reconstruct(int method); void TeemReconstruction(); void ItkReconstruction(); void ItkTensorReconstruction (mitk::DataStorage::SetOfObjects::Pointer inImages); void TeemTensorReconstruction (mitk::DataStorage::SetOfObjects::Pointer inImages); protected: Ui::QmitkTensorReconstructionViewControls* m_Controls; QmitkStdMultiWidget* m_MultiWidget; template std::vector > MakeGradientList() ; template void TemplatedAnalyticalTensorReconstruction(mitk::DiffusionImage* vols, float lambda, std::string nodename, std::vector* nodes, int normalization); void SetDefaultNodeProperties(mitk::DataNode::Pointer node, std::string name); berry::ISelectionListener::Pointer m_SelListener; berry::IStructuredSelection::ConstPointer m_CurrentSelection; }; #endif // _QMITKTENSORRECONSTRUCTIONVIEW_H_INCLUDED diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp new file mode 100644 index 0000000000..0c6187f534 --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.cpp @@ -0,0 +1,36 @@ +#include "mitkPluginActivator.h" + +#include + + +#include "src/internal/QmitkDiffusionImagingPublicPerspective.h" + +#include "src/internal/QmitkQBallReconstructionView.h" +#include "src/internal/QmitkPreprocessingView.h" +#include "src/internal/QmitkDiffusionDicomImportView.h" +#include "src/internal/QmitkDiffusionQuantificationView.h" +#include "src/internal/QmitkTensorReconstructionView.h" +#include "src/internal/QmitkControlVisualizationPropertiesView.h" + +namespace mitk { + +void PluginActivator::start(ctkPluginContext* context) +{ + BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionImagingPublicPerspective, context) + + BERRY_REGISTER_EXTENSION_CLASS(QmitkQBallReconstructionView, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkPreprocessingView, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionDicomImport, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkDiffusionQuantificationView, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkTensorReconstructionView, context) + BERRY_REGISTER_EXTENSION_CLASS(QmitkControlVisualizationPropertiesView, context) +} + +void PluginActivator::stop(ctkPluginContext* context) +{ + Q_UNUSED(context) +} + +} + +Q_EXPORT_PLUGIN2(org_mitk_gui_qt_diffusionimaging, mitk::PluginActivator) diff --git a/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.h b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.h new file mode 100644 index 0000000000..a34be34be4 --- /dev/null +++ b/Modules/Bundles/org.mitk.gui.qt.diffusionimaging/src/internal/mitkPluginActivator.h @@ -0,0 +1,23 @@ +#ifndef MITKPLUGINACTIVATOR_H +#define MITKPLUGINACTIVATOR_H + +#include + +namespace mitk { + +class PluginActivator : + public QObject, public ctkPluginActivator +{ + Q_OBJECT + Q_INTERFACES(ctkPluginActivator) + +public: + + void start(ctkPluginContext* context); + void stop(ctkPluginContext* context); + +}; // PluginActivator + +} + +#endif // MITKPLUGINACTIVATOR_H