diff --git a/Modules/DiffusionCmdApps/CMakeLists.txt b/Modules/DiffusionCmdApps/CMakeLists.txt index cde5fab..ac0bdff 100644 --- a/Modules/DiffusionCmdApps/CMakeLists.txt +++ b/Modules/DiffusionCmdApps/CMakeLists.txt @@ -1,20 +1,20 @@ MITK_CREATE_MODULE( SUBPROJECTS MITK-Diffusion # INCLUDE_DIRS Helpers - DEPENDS MitkDiffusionCore MitkDiffusionIO MitkFiberTracking MitkMriSimulation MitkConnectomics + DEPENDS MitkDiffusionCore MitkDiffusionIO PACKAGE_DEPENDS PUBLIC ITK ) if(MODULE_IS_ENABLED) add_subdirectory(Connectomics) add_subdirectory(Fiberfox) add_subdirectory(FiberProcessing) add_subdirectory(Tractography) add_subdirectory(TractographyEvaluation) add_subdirectory(Misc) add_subdirectory(Quantification) if(MITK_USE_Python) add_subdirectory(Python) endif() endif() diff --git a/Modules/DiffusionCmdApps/Connectomics/CMakeLists.txt b/Modules/DiffusionCmdApps/Connectomics/CMakeLists.txt index bcfc777..51dc62c 100644 --- a/Modules/DiffusionCmdApps/Connectomics/CMakeLists.txt +++ b/Modules/DiffusionCmdApps/Connectomics/CMakeLists.txt @@ -1,39 +1,39 @@ option(BUILD_DiffusionConnectomicsCmdApps "Build commandline tools for diffusion connectomics" OFF) if(BUILD_DiffusionConnectomicsCmdApps OR MITK_BUILD_ALL_APPS) # needed include directories include_directories( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ) # list of DiffusionConnectomics cmdapps # if an app requires additional dependencies # they are added after a "^^" and separated by "_" set( DiffusionConnectomicscmdapps NetworkCreation^^ NetworkStatistics^^ ) foreach(DiffusionConnectomicscmdapp ${DiffusionConnectomicscmdapps}) # extract cmd app name and dependencies string(REPLACE "^^" "\\;" cmdapp_info ${DiffusionConnectomicscmdapp}) set(cmdapp_info_list ${cmdapp_info}) list(GET cmdapp_info_list 0 appname) list(GET cmdapp_info_list 1 raw_dependencies) string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") set(dependencies_list ${dependencies}) mitkFunctionCreateCommandLineApp( NAME ${appname} - DEPENDS MitkDiffusionCmdApps ${dependencies_list} + DEPENDS MitkDiffusionCmdApps MitkConnectomics ${dependencies_list} PACKAGE_DEPENDS ) endforeach() if(EXECUTABLE_IS_ENABLED) MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) endif() endif() diff --git a/Modules/DiffusionCmdApps/FiberProcessing/CMakeLists.txt b/Modules/DiffusionCmdApps/FiberProcessing/CMakeLists.txt index fdf23fb..5a0544f 100644 --- a/Modules/DiffusionCmdApps/FiberProcessing/CMakeLists.txt +++ b/Modules/DiffusionCmdApps/FiberProcessing/CMakeLists.txt @@ -1,47 +1,47 @@ option(BUILD_DiffusionFiberProcessingCmdApps "Build commandline tools for diffusion fiber processing" OFF) if(BUILD_DiffusionFiberProcessingCmdApps OR MITK_BUILD_ALL_APPS) # needed include directories include_directories( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ) # list of diffusion cmdapps # if an app requires additional dependencies # they are added after a "^^" and separated by "_" set( diffusionFiberProcessingcmdapps TractDensity^^ Sift2WeightCopy^^ FiberExtraction^^ FiberExtractionRoi^^ FiberProcessing^^ FitFibersToImage^^ FiberDirectionExtraction^^ FiberJoin^^ FiberClustering^^ TractDensityFilter^^ ) foreach(diffusionFiberProcessingcmdapp ${diffusionFiberProcessingcmdapps}) # extract cmd app name and dependencies string(REPLACE "^^" "\\;" cmdapp_info ${diffusionFiberProcessingcmdapp}) set(cmdapp_info_list ${cmdapp_info}) list(GET cmdapp_info_list 0 appname) list(GET cmdapp_info_list 1 raw_dependencies) string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") set(dependencies_list ${dependencies}) mitkFunctionCreateCommandLineApp( NAME ${appname} - DEPENDS MitkDiffusionCmdApps ${dependencies_list} + DEPENDS MitkDiffusionCmdApps MitkMriSimulation MitkFiberTracking ${dependencies_list} PACKAGE_DEPENDS ) endforeach() if(EXECUTABLE_IS_ENABLED) MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) endif() endif() diff --git a/Modules/DiffusionCmdApps/Fiberfox/CMakeLists.txt b/Modules/DiffusionCmdApps/Fiberfox/CMakeLists.txt index a2fe4c0..7b1903f 100644 --- a/Modules/DiffusionCmdApps/Fiberfox/CMakeLists.txt +++ b/Modules/DiffusionCmdApps/Fiberfox/CMakeLists.txt @@ -1,39 +1,39 @@ option(BUILD_DiffusionFiberfoxCmdApps "Build commandline tools for diffusion data simulation (Fiberfox)" OFF) if(BUILD_DiffusionFiberfoxCmdApps OR MITK_BUILD_ALL_APPS) # needed include directories include_directories( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ) # list of diffusion cmdapps # if an app requires additional dependencies # they are added after a "^^" and separated by "_" set( diffusionFiberfoxcmdapps Fiberfox^^ RandomFiberPhantom^^ ) foreach(diffusionFiberfoxcmdapp ${diffusionFiberfoxcmdapps}) # extract cmd app name and dependencies string(REPLACE "^^" "\\;" cmdapp_info ${diffusionFiberfoxcmdapp}) set(cmdapp_info_list ${cmdapp_info}) list(GET cmdapp_info_list 0 appname) list(GET cmdapp_info_list 1 raw_dependencies) string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") set(dependencies_list ${dependencies}) mitkFunctionCreateCommandLineApp( NAME ${appname} - DEPENDS MitkDiffusionCmdApps ${dependencies_list} + DEPENDS MitkDiffusionCmdApps MitkMriSimulation ${dependencies_list} PACKAGE_DEPENDS ) endforeach() if(EXECUTABLE_IS_ENABLED) MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) endif() endif() diff --git a/Modules/DiffusionCmdApps/Tractography/CMakeLists.txt b/Modules/DiffusionCmdApps/Tractography/CMakeLists.txt index a14ed6d..8cfdc98 100644 --- a/Modules/DiffusionCmdApps/Tractography/CMakeLists.txt +++ b/Modules/DiffusionCmdApps/Tractography/CMakeLists.txt @@ -1,40 +1,40 @@ option(BUILD_DiffusionTractographyCmdApps "Build commandline tools for diffusion fiber tractography" OFF) if(BUILD_DiffusionTractographyCmdApps OR MITK_BUILD_ALL_APPS) # needed include directories include_directories( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ) # list of diffusion cmdapps # if an app requires additional dependencies # they are added after a "^^" and separated by "_" set( diffusiontractographycmdapps StreamlineTractography^^ GlobalTractography^^ RfTraining^^ ) foreach(diffusiontractographycmdapp ${diffusiontractographycmdapps}) # extract cmd app name and dependencies string(REPLACE "^^" "\\;" cmdapp_info ${diffusiontractographycmdapp}) set(cmdapp_info_list ${cmdapp_info}) list(GET cmdapp_info_list 0 appname) list(GET cmdapp_info_list 1 raw_dependencies) string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") set(dependencies_list ${dependencies}) mitkFunctionCreateCommandLineApp( NAME ${appname} - DEPENDS MitkDiffusionCmdApps ${dependencies_list} + DEPENDS MitkDiffusionCmdApps MitkFiberTracking ${dependencies_list} PACKAGE_DEPENDS ) endforeach() if(EXECUTABLE_IS_ENABLED) MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) endif() endif() diff --git a/Modules/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt b/Modules/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt index 4328bcc..52758e6 100644 --- a/Modules/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt +++ b/Modules/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt @@ -1,46 +1,46 @@ option(BUILD_DiffusionTractographyEvaluationCmdApps "Build commandline tools for diffusion fiber tractography evaluation" OFF) if(BUILD_DiffusionTractographyEvaluationCmdApps OR MITK_BUILD_ALL_APPS) # needed include directories include_directories( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ) # list of diffusion cmdapps # if an app requires additional dependencies # they are added after a "^^" and separated by "_" set( diffusionTractographyEvaluationcmdapps PeaksAngularError^^ MergeOverlappingTracts^^ GetOverlappingTracts^^ ExtractSimilarTracts^^ AnchorConstrainedPlausibility^^ CalculateOverlap^^ CheckEpsAndOverlap^^ ReferenceSimilarity^^ TractDistance^^ ) foreach(diffusionTractographyEvaluationcmdapp ${diffusionTractographyEvaluationcmdapps}) # extract cmd app name and dependencies string(REPLACE "^^" "\\;" cmdapp_info ${diffusionTractographyEvaluationcmdapp}) set(cmdapp_info_list ${cmdapp_info}) list(GET cmdapp_info_list 0 appname) list(GET cmdapp_info_list 1 raw_dependencies) string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") set(dependencies_list ${dependencies}) mitkFunctionCreateCommandLineApp( NAME ${appname} - DEPENDS MitkDiffusionCmdApps ${dependencies_list} + DEPENDS MitkDiffusionCmdApps MitkMriSimulation ${dependencies_list} PACKAGE_DEPENDS ) endforeach() if(EXECUTABLE_IS_ENABLED) MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) endif() endif() diff --git a/Modules/DiffusionCore/CMakeLists.txt b/Modules/DiffusionCore/CMakeLists.txt index c73997b..f633eb1 100644 --- a/Modules/DiffusionCore/CMakeLists.txt +++ b/Modules/DiffusionCore/CMakeLists.txt @@ -1,25 +1,24 @@ # With apple gcc 4.2.1 the following waring leads to an build error if boost is enabled if(APPLE) mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=empty-body" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) endif() MITK_CREATE_MODULE( SUBPROJECTS MITK-Diffusion INCLUDE_DIRS Algorithms Algorithms/Reconstruction Algorithms/Registration Algorithms/Reconstruction/MultishellProcessing Algorithms/Reconstruction/FittingFunctions DicomImport IODataStructures/DiffusionWeightedImages IODataStructures/Properties IODataStructures Rendering ${CMAKE_CURRENT_BINARY_DIR} - DEPENDS MitkMapperExt MitkPlanarFigure MitkImageExtraction MitkSceneSerializationBase MitkDICOMReader MitkMatchPointRegistration + DEPENDS MitkMapperExt MitkPlanarFigure MitkImageExtraction MitkDICOMReader MitkMatchPointRegistration PACKAGE_DEPENDS - PUBLIC ITK|ITKTestKernel+ITKRegistrationCommon+ITKMetricsv4+ITKRegistrationMethodsv4+ITKDistanceMap+ITKLabelVoting+ITKVTK+ITKFFT+ITKDiffusionTensorImage - PUBLIC VTK|vtkFiltersProgrammable OpenMP|OpenMP_CXX Vigra HDF5 + PUBLIC VTK|vtkFiltersProgrammable Vigra HDF5 ) if(MSVC) mitkFunctionCheckCAndCXXCompilerFlags("/wd4005" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) endif() add_subdirectory(Testing) if(MITK_USE_Python) MITK_INSTALL(FILES PythonRequirements.txt) endif() configure_file(${CMAKE_CURRENT_SOURCE_DIR}/mitkDiffusionImagingConfigure.h.in ${CMAKE_CURRENT_BINARY_DIR}/mitkDiffusionImagingConfigure.h) diff --git a/Modules/FiberTracking/CMakeLists.txt b/Modules/FiberTracking/CMakeLists.txt index 37a846f..5f79ccf 100644 --- a/Modules/FiberTracking/CMakeLists.txt +++ b/Modules/FiberTracking/CMakeLists.txt @@ -1,46 +1,46 @@ -set(_module_deps MitkDiffusionCore MitkGraphAlgorithms MitkCLVigraRandomForest) +set(_module_deps MitkDiffusionCore MitkCLVigraRandomForest) mitk_check_module_dependencies( MODULES ${_module_deps} MISSING_DEPENDENCIES_VAR _missing_deps ) if(NOT _missing_deps) set(lut_url http://mitk.org/download/data/FibertrackingLUT.tar.gz) set(lut_tarball ${CMAKE_CURRENT_BINARY_DIR}/FibertrackingLUT.tar.gz) file(DOWNLOAD ${lut_url} ${lut_tarball} EXPECTED_MD5 38ecb6d4a826c9ebb0f4965eb9aeee44 TIMEOUT 60 STATUS status SHOW_PROGRESS ) list(GET status 0 status_code) list(GET status 1 status_msg) if(NOT status_code EQUAL 0) message(SEND_ERROR "${status_msg} (error code ${status_code})") endif() file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Resources) execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ../FibertrackingLUT.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/Resources RESULT_VARIABLE result ERROR_VARIABLE err_msg) if(result) message(SEND_ERROR "Unpacking FibertrackingLUT.tar.gz failed: ${err_msg}") endif() endif() MITK_CREATE_MODULE( SUBPROJECTS MITK-Diffusion - INCLUDE_DIRS Algorithms Algorithms/TrackingHandlers Algorithms/ClusteringMetrics Algorithms/GibbsTracking Algorithms/StochasticTracking IODataStructures ${CMAKE_CURRENT_BINARY_DIR} + INCLUDE_DIRS Algorithms Algorithms/TrackingHandlers Algorithms/ClusteringMetrics Algorithms/GibbsTracking Algorithms/StochasticTracking ${CMAKE_CURRENT_BINARY_DIR} DEPENDS ${_module_deps} ) if(MODULE_IS_ENABLED) add_subdirectory(Testing) endif() diff --git a/Modules/MriSimulation/CMakeLists.txt b/Modules/MriSimulation/CMakeLists.txt index b60e7c5..f8349f8 100644 --- a/Modules/MriSimulation/CMakeLists.txt +++ b/Modules/MriSimulation/CMakeLists.txt @@ -1,11 +1,11 @@ MITK_CREATE_MODULE( SUBPROJECTS MITK-Diffusion INCLUDE_DIRS SignalModels Sequences Algorithms ${CMAKE_CURRENT_BINARY_DIR} - DEPENDS MitkDiffusionCore MitkFiberTracking + DEPENDS MitkFiberTracking ) if(MODULE_IS_ENABLED) add_subdirectory(Testing) endif()