diff --git a/CMake/BuildConfigurations/DiffusionAll.cmake b/CMake/BuildConfigurations/DiffusionAll.cmake index 22fd3320ec..b0b90a6643 100644 --- a/CMake/BuildConfigurations/DiffusionAll.cmake +++ b/CMake/BuildConfigurations/DiffusionAll.cmake @@ -1,39 +1,39 @@ message(STATUS "Configuring MITK Diffusion with all Plugins") # Enable non-optional external dependencies set(MITK_USE_Vigra ON CACHE BOOL "MITK Use Vigra Library" FORCE) set(MITK_USE_HDF5 ON CACHE BOOL "MITK Use HDF5 Library" FORCE) set(MITK_USE_MatchPoint ON CACHE BOOL "" FORCE) set(MITK_USE_DCMTK ON CACHE BOOL "" FORCE) set(MITK_USE_DCMQI OFF CACHE BOOL "" FORCE) set(MITK_USE_PCRE ON CACHE BOOL "" FORCE) set(MITK_USE_SWIG ON CACHE BOOL "" FORCE) set(MITK_USE_Python ON CACHE BOOL "" FORCE) set(MITK_USE_BetData ON CACHE BOOL "" FORCE) # Disable all apps but MITK Diffusion set(MITK_BUILD_ALL_APPS OFF CACHE BOOL "Build all MITK applications" FORCE) set(MITK_BUILD_APP_CoreApp OFF CACHE BOOL "Build the MITK CoreApp" FORCE) set(MITK_BUILD_APP_Diffusion ON CACHE BOOL "Build MITK Diffusion" FORCE) # Activate Diffusion Mini Apps -set(BUILD_DiffusionCoreCmdApps ON CACHE BOOL "Build commandline tools for diffusion" FORCE) set(BUILD_DiffusionFiberProcessingCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber processing" FORCE) set(BUILD_DiffusionFiberfoxCmdApps ON CACHE BOOL "Build commandline tools for diffusion data simulation (Fiberfox)" FORCE) set(BUILD_DiffusionMiscCmdApps ON CACHE BOOL "Build miscellaneous commandline tools for diffusion" FORCE) set(BUILD_DiffusionQuantificationCmdApps ON CACHE BOOL "Build commandline tools for diffusion quantification (IVIM, ADC, ...)" FORCE) set(BUILD_DiffusionTractographyCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography" FORCE) set(BUILD_DiffusionTractographyEvaluationCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography evaluation" FORCE) set(BUILD_DiffusionConnectomicsCmdApps ON CACHE BOOL "Build commandline tools for diffusion connectomics" FORCE) +set(BUILD_DiffusionPythonCmdApps ON CACHE BOOL "Build commandline tools for diffusion with python" FORCE) # Build neither all plugins nor examples set(MITK_BUILD_ALL_PLUGINS OFF CACHE BOOL "Build all MITK plugins" FORCE) set(MITK_BUILD_EXAMPLES OFF CACHE BOOL "Build the MITK examples" FORCE) set(BUILD_TESTING ON CACHE BOOL "Build the MITK tests" FORCE) # Activate in-application help generation set(MITK_DOXYGEN_GENERATE_QCH_FILES ON CACHE BOOL "Use doxygen to generate Qt compressed help files for MITK docs" FORCE) set(BLUEBERRY_USE_QT_HELP ON CACHE BOOL "Enable support for integrating bundle documentation into Qt Help" FORCE) # Disable console window set(MITK_SHOW_CONSOLE_WINDOW ON CACHE BOOL "Use this to enable or disable the console window when starting MITK GUI Applications" FORCE) diff --git a/CMake/BuildConfigurations/DiffusionRelease.cmake b/CMake/BuildConfigurations/DiffusionRelease.cmake index ef55857c2a..7bbb412d7f 100644 --- a/CMake/BuildConfigurations/DiffusionRelease.cmake +++ b/CMake/BuildConfigurations/DiffusionRelease.cmake @@ -1,42 +1,42 @@ message(STATUS "Configuring MITK Diffusion Release Build") # Enable non-optional external dependencies set(MITK_USE_Vigra ON CACHE BOOL "MITK Use Vigra Library" FORCE) set(MITK_USE_HDF5 ON CACHE BOOL "MITK Use HDF5 Library" FORCE) set(MITK_USE_MatchPoint ON CACHE BOOL "" FORCE) set(MITK_USE_DCMTK ON CACHE BOOL "" FORCE) set(MITK_USE_DCMQI OFF CACHE BOOL "" FORCE) set(MITK_USE_PCRE ON CACHE BOOL "" FORCE) set(MITK_USE_SWIG ON CACHE BOOL "" FORCE) set(MITK_USE_Python ON CACHE BOOL "" FORCE) set(MITK_USE_BetData ON CACHE BOOL "" FORCE) # Disable all apps but MITK Diffusion set(MITK_BUILD_ALL_APPS OFF CACHE BOOL "Build all MITK applications" FORCE) set(MITK_BUILD_APP_CoreApp OFF CACHE BOOL "Build the MITK CoreApp" FORCE) set(MITK_BUILD_APP_Workbench OFF CACHE BOOL "Build the MITK Workbench" FORCE) set(MITK_BUILD_APP_Diffusion ON CACHE BOOL "Build MITK Diffusion" FORCE) # Activate Diffusion Mini Apps -set(BUILD_DiffusionCoreCmdApps ON CACHE BOOL "Build commandline tools for diffusion" FORCE) set(BUILD_DiffusionFiberProcessingCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber processing" FORCE) set(BUILD_DiffusionFiberfoxCmdApps ON CACHE BOOL "Build commandline tools for diffusion data simulation (Fiberfox)" FORCE) set(BUILD_DiffusionMiscCmdApps ON CACHE BOOL "Build miscellaneous commandline tools for diffusion" FORCE) set(BUILD_DiffusionQuantificationCmdApps OFF CACHE BOOL "Build commandline tools for diffusion quantification (IVIM, ADC, ...)" FORCE) set(BUILD_DiffusionTractographyCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography" FORCE) set(BUILD_DiffusionTractographyEvaluationCmdApps ON CACHE BOOL "Build commandline tools for diffusion fiber tractography evaluation" FORCE) set(BUILD_DiffusionConnectomicsCmdApps ON CACHE BOOL "Build commandline tools for diffusion connectomics" FORCE) +set(BUILD_DiffusionPythonCmdApps ON CACHE BOOL "Build commandline tools for diffusion with python" FORCE) # Build neither all plugins nor examples set(MITK_BUILD_ALL_PLUGINS OFF CACHE BOOL "Build all MITK plugins" FORCE) set(MITK_BUILD_EXAMPLES OFF CACHE BOOL "Build the MITK examples" FORCE) set(BUILD_TESTING OFF CACHE BOOL "Build the MITK tests" FORCE) # Activate in-application help generation set(MITK_DOXYGEN_GENERATE_QCH_FILES ON CACHE BOOL "Use doxygen to generate Qt compressed help files for MITK docs" FORCE) set(BLUEBERRY_USE_QT_HELP ON CACHE BOOL "Enable support for integrating bundle documentation into Qt Help" FORCE) # Enable console window set(MITK_SHOW_CONSOLE_WINDOW ON CACHE BOOL "Use this to enable or disable the console window when starting MITK GUI Applications" FORCE) set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE) diff --git a/Modules/DiffusionImaging/CMakeLists.txt b/Modules/DiffusionImaging/CMakeLists.txt index bcd76551e5..0be1046bbc 100644 --- a/Modules/DiffusionImaging/CMakeLists.txt +++ b/Modules/DiffusionImaging/CMakeLists.txt @@ -1,13 +1,14 @@ set( diffusion_module_dirs DiffusionCore FiberTracking Connectomics Quantification DiffusionIO + DiffusionCmdApps ) foreach(diffusion_module_dir ${diffusion_module_dirs}) add_subdirectory(${diffusion_module_dir}) endforeach() configure_file(${CMAKE_CURRENT_SOURCE_DIR}/mitkDiffusionImagingConfigure.h.in ${CMAKE_CURRENT_BINARY_DIR}/DiffusionCore/mitkDiffusionImagingConfigure.h) diff --git a/Modules/DiffusionImaging/Connectomics/CMakeLists.txt b/Modules/DiffusionImaging/Connectomics/CMakeLists.txt index ae7887e933..3099bee377 100644 --- a/Modules/DiffusionImaging/Connectomics/CMakeLists.txt +++ b/Modules/DiffusionImaging/Connectomics/CMakeLists.txt @@ -1,9 +1,8 @@ MITK_CREATE_MODULE( SUBPROJECTS MITK-DTI INCLUDE_DIRS Algorithms Algorithms/BrainParcellation IODataStructures Rendering ${CMAKE_CURRENT_BINARY_DIR} DEPENDS MitkDiffusionCore MitkFiberTracking PACKAGE_DEPENDS VTK|vtkInfovisLayout ) add_subdirectory(Testing) -add_subdirectory(cmdapps) diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/CMakeLists.txt new file mode 100644 index 0000000000..ffbde72f1d --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCmdApps/CMakeLists.txt @@ -0,0 +1,20 @@ +MITK_CREATE_MODULE( + SUBPROJECTS MITK-DTI + # INCLUDE_DIRS Helpers + DEPENDS MitkDiffusionCore MitkDiffusionIO MitkFiberTracking MitkQuantification MitkConnectomics + 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/DiffusionImaging/Connectomics/cmdapps/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/CMakeLists.txt similarity index 85% rename from Modules/DiffusionImaging/Connectomics/cmdapps/CMakeLists.txt rename to Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/CMakeLists.txt index c2050ff407..bcfc777262 100755 --- a/Modules/DiffusionImaging/Connectomics/cmdapps/CMakeLists.txt +++ b/Modules/DiffusionImaging/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^^MitkFiberTracking_MitkConnectomics - NetworkStatistics^^MitkConnectomics + 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 MitkCore MitkDiffusionCore ${dependencies_list} - PACKAGE_DEPENDS ITK + DEPENDS MitkDiffusionCmdApps ${dependencies_list} + PACKAGE_DEPENDS ) endforeach() if(EXECUTABLE_IS_ENABLED) MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) endif() endif() diff --git a/Modules/DiffusionImaging/Connectomics/cmdapps/NetworkCreation.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/NetworkCreation.cpp similarity index 100% rename from Modules/DiffusionImaging/Connectomics/cmdapps/NetworkCreation.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/NetworkCreation.cpp diff --git a/Modules/DiffusionImaging/Connectomics/cmdapps/NetworkStatistics.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/NetworkStatistics.cpp similarity index 100% rename from Modules/DiffusionImaging/Connectomics/cmdapps/NetworkStatistics.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Connectomics/NetworkStatistics.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/CMakeLists.txt similarity index 68% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/CMakeLists.txt rename to Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/CMakeLists.txt index 6404d2892b..fdf23fbbd0 100755 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/CMakeLists.txt +++ b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/CMakeLists.txt @@ -1,48 +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^^MitkFiberTracking - Sift2WeightCopy^^MitkFiberTracking - FiberExtraction^^MitkFiberTracking - FiberExtractionRoi^^MitkFiberTracking - FiberProcessing^^MitkFiberTracking - FitFibersToImage^^MitkFiberTracking - FiberDirectionExtraction^^MitkFiberTracking - FiberJoin^^MitkFiberTracking - FiberClustering^^MitkFiberTracking - GetOverlappingTracts^^MitkFiberTracking - TractDensityFilter^^MitkFiberTracking + 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 MitkCore MitkDiffusionCore ${dependencies_list} - PACKAGE_DEPENDS ITK + DEPENDS MitkDiffusionCmdApps ${dependencies_list} + PACKAGE_DEPENDS ) endforeach() if(EXECUTABLE_IS_ENABLED) MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) endif() endif() diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberClustering.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberClustering.cpp similarity index 86% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberClustering.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberClustering.cpp index 61ae8e9bf3..bf5106f096 100644 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberClustering.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberClustering.cpp @@ -1,251 +1,273 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include #include #include #include +#include + +typedef itksys::SystemTools ist; mitk::FiberBundle::Pointer LoadFib(std::string filename) { std::vector fibInfile = mitk::IOUtil::Load(filename); if( fibInfile.empty() ) std::cout << "File " << filename << " could not be read!"; mitk::BaseData::Pointer baseData = fibInfile.at(0); return dynamic_cast(baseData.GetPointer()); } /*! \brief Spatially cluster fibers */ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Fiber Clustering"); parser.setCategory("Fiber Processing"); parser.setContributor("MIC"); parser.setArgumentPrefix("--", "-"); parser.addArgument("", "i", mitkCommandLineParser::InputFile, "Input:", "input fiber bundle (.fib, .trk, .tck)", us::Any(), false); parser.addArgument("", "o", mitkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false); parser.addArgument("cluster_size", "", mitkCommandLineParser::Int, "Cluster size:", "", 10); parser.addArgument("fiber_points", "", mitkCommandLineParser::Int, "Fiber points:", "", 12); parser.addArgument("min_fibers", "", mitkCommandLineParser::Int, "Min. fibers per cluster:", "", 1); parser.addArgument("max_clusters", "", mitkCommandLineParser::Int, "Max. clusters:", ""); parser.addArgument("merge_clusters", "", mitkCommandLineParser::Float, "Merge clusters:", "", -1.0); parser.addArgument("output_centroids", "", mitkCommandLineParser::Bool, "Output centroids:", ""); - parser.addArgument("metrics", "", mitkCommandLineParser::StringList, "Metrics:", "EU_MEAN, EU_STD, EU_MAX, ANAT, MAP, LENGTH"); + parser.addArgument("only_centroids", "", mitkCommandLineParser::Bool, "Output only centroids:", ""); + parser.addArgument("merge_centroids", "", mitkCommandLineParser::Bool, "Merge centroids:", ""); + parser.addArgument("metrics", "", mitkCommandLineParser::StringList, "Metrics:", "EU_MEAN (default), EU_STD, EU_MAX, ANAT, MAP, LENGTH"); parser.addArgument("metric_weights", "", mitkCommandLineParser::StringList, "Metric weights:", "add one float weight for each used metric"); parser.addArgument("input_centroids", "", mitkCommandLineParser::String, "Input centroids:", ""); parser.addArgument("scalar_map", "", mitkCommandLineParser::String, "Scalar map:", ""); parser.addArgument("parcellation", "", mitkCommandLineParser::String, "Parcellation:", ""); parser.addArgument("file_ending", "", mitkCommandLineParser::String, "File ending:", ""); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; std::string inFileName = us::any_cast(parsedArgs["i"]); std::string out_root = us::any_cast(parsedArgs["o"]); + bool only_centroids = false; + if (parsedArgs.count("only_centroids")) + only_centroids = us::any_cast(parsedArgs["only_centroids"]); + + bool merge_centroids = false; + if (parsedArgs.count("merge_centroids")) + merge_centroids = us::any_cast(parsedArgs["merge_centroids"]); + int cluster_size = 10; if (parsedArgs.count("cluster_size")) cluster_size = us::any_cast(parsedArgs["cluster_size"]); int fiber_points = 12; if (parsedArgs.count("fiber_points")) fiber_points = us::any_cast(parsedArgs["fiber_points"]); int min_fibers = 1; if (parsedArgs.count("min_fibers")) min_fibers = us::any_cast(parsedArgs["min_fibers"]); int max_clusters = 0; if (parsedArgs.count("max_clusters")) max_clusters = us::any_cast(parsedArgs["max_clusters"]); float merge_clusters = -1.0; if (parsedArgs.count("merge_clusters")) merge_clusters = us::any_cast(parsedArgs["merge_clusters"]); bool output_centroids = false; if (parsedArgs.count("output_centroids")) output_centroids = us::any_cast(parsedArgs["output_centroids"]); std::vector< std::string > metric_strings = {"EU_MEAN"}; if (parsedArgs.count("metrics")) metric_strings = us::any_cast(parsedArgs["metrics"]); std::vector< std::string > metric_weights = {"1.0"}; if (parsedArgs.count("metric_weights")) metric_weights = us::any_cast(parsedArgs["metric_weights"]); std::string input_centroids = ""; if (parsedArgs.count("input_centroids")) input_centroids = us::any_cast(parsedArgs["input_centroids"]); std::string scalar_map = ""; if (parsedArgs.count("scalar_map")) scalar_map = us::any_cast(parsedArgs["scalar_map"]); std::string parcellation = ""; if (parsedArgs.count("parcellation")) parcellation = us::any_cast(parsedArgs["parcellation"]); std::string file_ending = ".fib"; if (parsedArgs.count("file_ending")) file_ending = us::any_cast(parsedArgs["file_ending"]); if (metric_strings.size()!=metric_weights.size()) { MITK_INFO << "Each metric needs an associated metric weight!"; return EXIT_FAILURE; } try { typedef itk::Image< float, 3 > FloatImageType; typedef itk::Image< short, 3 > ShortImageType; mitk::FiberBundle::Pointer fib = LoadFib(inFileName); float max_d = 0; int i=1; std::vector< float > distances; while (max_d < fib->GetGeometry()->GetDiagonalLength()/2) { distances.push_back(cluster_size*i); max_d = cluster_size*i; ++i; } itk::TractClusteringFilter::Pointer clusterer = itk::TractClusteringFilter::New(); clusterer->SetDistances(distances); clusterer->SetTractogram(fib); if (input_centroids!="") { mitk::FiberBundle::Pointer in_centroids = LoadFib(input_centroids); clusterer->SetInCentroids(in_centroids); } std::vector< mitk::ClusteringMetric* > metrics; int mc = 0; for (auto m : metric_strings) { float w = boost::lexical_cast(metric_weights.at(mc)); MITK_INFO << "Metric: " << m << " (w=" << w << ")"; if (m=="EU_MEAN") metrics.push_back({new mitk::ClusteringMetricEuclideanMean()}); else if (m=="EU_STD") metrics.push_back({new mitk::ClusteringMetricEuclideanStd()}); else if (m=="EU_MAX") metrics.push_back({new mitk::ClusteringMetricEuclideanMax()}); else if (m=="ANGLES") metrics.push_back({new mitk::ClusteringMetricInnerAngles()}); else if (m=="LENGTH") metrics.push_back({new mitk::ClusteringMetricLength()}); else if (m=="MAP" && scalar_map!="") { mitk::Image::Pointer mitk_map = mitk::IOUtil::Load(scalar_map); if (mitk_map->GetDimension()==3) { FloatImageType::Pointer itk_map = FloatImageType::New(); mitk::CastToItkImage(mitk_map, itk_map); mitk::ClusteringMetricScalarMap* metric = new mitk::ClusteringMetricScalarMap(); metric->SetImages({itk_map}); metric->SetScale(distances.at(0)); metrics.push_back(metric); } } else if (m=="ANAT" && parcellation!="") { mitk::Image::Pointer mitk_map = mitk::IOUtil::Load(parcellation); if (mitk_map->GetDimension()==3) { ShortImageType::Pointer itk_map = ShortImageType::New(); mitk::CastToItkImage(mitk_map, itk_map); mitk::ClusteringMetricAnatomic* metric = new mitk::ClusteringMetricAnatomic(); metric->SetParcellations({itk_map}); metrics.push_back(metric); } } metrics.back()->SetScale(w); mc++; } if (metrics.empty()) { MITK_INFO << "No metric selected!"; return EXIT_FAILURE; } clusterer->SetMetrics(metrics); clusterer->SetMergeDuplicateThreshold(merge_clusters); clusterer->SetNumPoints(fiber_points); clusterer->SetMaxClusters(max_clusters); clusterer->SetMinClusterSize(min_fibers); clusterer->Update(); std::vector tracts = clusterer->GetOutTractograms(); std::vector centroids = clusterer->GetOutCentroids(); MITK_INFO << "Saving clusters"; std::streambuf *old = cout.rdbuf(); // <-- save std::stringstream ss; std::cout.rdbuf (ss.rdbuf()); // <-- redirect - unsigned int c = 0; - for (auto f : tracts) - { - mitk::IOUtil::Save(f, out_root + "Cluster_" + boost::lexical_cast(c) + file_ending); - if (output_centroids) - mitk::IOUtil::Save(centroids.at(c), out_root + "Centroid_" + boost::lexical_cast(c) + file_ending); - ++c; + if (!only_centroids) + for (unsigned int i=0; i(i) + file_ending); + + + if (output_centroids && !merge_centroids) + { + for (unsigned int i=0; i(i) + file_ending); } + else if (output_centroids) + { + mitk::FiberBundle::Pointer centroid = mitk::FiberBundle::New(); + centroid = centroid->AddBundles(centroids); + mitk::IOUtil::Save(centroid, out_root + ist::GetFilenameWithoutExtension(inFileName) + "_Centroids" + file_ending); + } + std::cout.rdbuf (old); // <-- restore } catch (itk::ExceptionObject e) { std::cout << e; return EXIT_FAILURE; } catch (std::exception e) { std::cout << e.what(); return EXIT_FAILURE; } catch (...) { std::cout << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberDirectionExtraction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberDirectionExtraction.cpp similarity index 73% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberDirectionExtraction.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberDirectionExtraction.cpp index 69ec445777..5cc08bbf70 100755 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberDirectionExtraction.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberDirectionExtraction.cpp @@ -1,174 +1,181 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include "mitkCommandLineParser.h" #include #include #include #include #include #include #include /*! \brief Extract principal fiber directions from a tractogram */ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Fiber Direction Extraction"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription("Extract principal fiber directions from a tractogram"); parser.setContributor("MIC"); parser.setArgumentPrefix("--", "-"); - parser.addArgument("input", "i", mitkCommandLineParser::InputFile, "Input:", "input tractogram (.fib/.trk)", us::Any(), false); - parser.addArgument("out", "o", mitkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false); - parser.addArgument("mask", "m", mitkCommandLineParser::InputFile, "Mask:", "mask image"); - parser.addArgument("athresh", "a", mitkCommandLineParser::Float, "Angular threshold:", "angular threshold in degrees. closer fiber directions are regarded as one direction and clustered together.", 25, true); - parser.addArgument("peakthresh", "t", mitkCommandLineParser::Float, "Peak size threshold:", "peak size threshold relative to largest peak in voxel", 0.2, true); - parser.addArgument("verbose", "v", mitkCommandLineParser::Bool, "Verbose:", "output optional and intermediate calculation results"); - parser.addArgument("numdirs", "d", mitkCommandLineParser::Int, "Max. num. directions:", "maximum number of fibers per voxel", 3, true); - parser.addArgument("normalization", "n", mitkCommandLineParser::Int, "Normalization method:", "1=global maximum, 2=single vector, 3=voxel-wise maximum", 1); - parser.addArgument("file_ending", "f", mitkCommandLineParser::String, "Image type:", ".nrrd, .nii, .nii.gz"); + parser.addArgument("", "i", mitkCommandLineParser::InputFile, "Input:", "input tractogram (.fib/.trk)", us::Any(), false); + parser.addArgument("", "o", mitkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false); + parser.addArgument("mask", "", mitkCommandLineParser::InputFile, "Mask:", "mask image"); + parser.addArgument("athresh", "", mitkCommandLineParser::Float, "Angular threshold:", "angular threshold in degrees. closer fiber directions are regarded as one direction and clustered together.", 25, true); + parser.addArgument("peakthresh", "", mitkCommandLineParser::Float, "Peak size threshold:", "peak size threshold relative to largest peak in voxel", 0.2, true); + parser.addArgument("only_mask_geometry", "", mitkCommandLineParser::Bool, "Only mask geometry:", "don't use content of mask image, only use it's geometry", false); + parser.addArgument("verbose", "", mitkCommandLineParser::Bool, "Verbose:", "output optional and intermediate calculation results"); + parser.addArgument("numdirs", "", mitkCommandLineParser::Int, "Max. num. directions:", "maximum number of fibers per voxel", 3, true); + parser.addArgument("normalization", "", mitkCommandLineParser::Int, "Normalization method:", "1=global maximum, 2=single vector, 3=voxel-wise maximum", 1); + parser.addArgument("file_ending", "", mitkCommandLineParser::String, "Image type:", ".nrrd, .nii, .nii.gz (default)"); + std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; - std::string fibFile = us::any_cast(parsedArgs["input"]); + std::string fibFile = us::any_cast(parsedArgs["i"]); std::string maskImage(""); if (parsedArgs.count("mask")) maskImage = us::any_cast(parsedArgs["mask"]); float peakThreshold = 0.2; if (parsedArgs.count("peakthresh")) peakThreshold = us::any_cast(parsedArgs["peakthresh"]); float angularThreshold = 25; if (parsedArgs.count("athresh")) angularThreshold = us::any_cast(parsedArgs["athresh"]); - std::string outRoot = us::any_cast(parsedArgs["out"]); + std::string outRoot = us::any_cast(parsedArgs["o"]); bool verbose = false; if (parsedArgs.count("verbose")) verbose = us::any_cast(parsedArgs["verbose"]); + bool only_mask_geometry = false; + if (parsedArgs.count("only_mask_geometry")) + only_mask_geometry = us::any_cast(parsedArgs["only_mask_geometry"]); + int maxNumDirs = 3; if (parsedArgs.count("numdirs")) maxNumDirs = us::any_cast(parsedArgs["numdirs"]); int normalization = 1; if (parsedArgs.count("normalization")) normalization = us::any_cast(parsedArgs["normalization"]); - std::string file_ending = ".nrrd"; + std::string file_ending = ".nii.gz"; if (parsedArgs.count("file_ending")) file_ending = us::any_cast(parsedArgs["file_ending"]); try { typedef itk::Image ItkUcharImgType; // load fiber bundle mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load(fibFile); // load/create mask image ItkUcharImgType::Pointer itkMaskImage = nullptr; if (maskImage.compare("")!=0) { std::cout << "Using mask image"; itkMaskImage = ItkUcharImgType::New(); mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::Load(maskImage); mitk::CastToItkImage(mitkMaskImage, itkMaskImage); } // extract directions from fiber bundle itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); fOdfFilter->SetFiberBundle(inputTractogram); + fOdfFilter->SetOnlyUseMaskGeometry(only_mask_geometry); fOdfFilter->SetMaskImage(itkMaskImage); fOdfFilter->SetAngularThreshold(cos(angularThreshold*itk::Math::pi/180)); switch (normalization) { case 1: fOdfFilter->SetNormalizationMethod(itk::TractsToVectorImageFilter::NormalizationMethods::GLOBAL_MAX); break; case 2: fOdfFilter->SetNormalizationMethod(itk::TractsToVectorImageFilter::NormalizationMethods::SINGLE_VEC_NORM); break; case 3: fOdfFilter->SetNormalizationMethod(itk::TractsToVectorImageFilter::NormalizationMethods::MAX_VEC_NORM); break; } fOdfFilter->SetSizeThreshold(peakThreshold); fOdfFilter->SetMaxNumDirections(maxNumDirs); fOdfFilter->Update(); { itk::TractsToVectorImageFilter::ItkDirectionImageType::Pointer itkImg = fOdfFilter->GetDirectionImage(); typedef itk::ImageFileWriter< itk::TractsToVectorImageFilter::ItkDirectionImageType > WriterType; WriterType::Pointer writer = WriterType::New(); std::string outfilename = outRoot; outfilename.append("_DIRECTIONS"); outfilename.append(file_ending); writer->SetFileName(outfilename.c_str()); writer->SetInput(itkImg); writer->Update(); } if (verbose) { // write num direction image ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage(); typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; WriterType::Pointer writer = WriterType::New(); std::string outfilename = outRoot; outfilename.append("_NUM_DIRECTIONS"); outfilename.append(file_ending); writer->SetFileName(outfilename.c_str()); writer->SetInput(numDirImage); writer->Update(); } } catch (itk::ExceptionObject e) { std::cout << e; return EXIT_FAILURE; } catch (std::exception e) { std::cout << e.what(); return EXIT_FAILURE; } catch (...) { std::cout << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberExtraction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberExtraction.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberExtraction.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberExtraction.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberExtractionRoi.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberExtractionRoi.cpp similarity index 84% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberExtractionRoi.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberExtractionRoi.cpp index 86c7ec8a3f..11be42c254 100755 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberExtractionRoi.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberExtractionRoi.cpp @@ -1,265 +1,276 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include "mitkCommandLineParser.h" #include #include #include #include #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include typedef itksys::SystemTools ist; typedef itk::Image ItkFloatImgType; ItkFloatImgType::Pointer LoadItkImage(const std::string& filename) { mitk::Image::Pointer img = mitk::IOUtil::Load(filename); ItkFloatImgType::Pointer itk_image = ItkFloatImgType::New(); mitk::CastToItkImage(img, itk_image); return itk_image; } /*! \brief Extract fibers from a tractogram using binary image ROIs */ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Fiber Extraction With ROI Image"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setContributor("MIC"); parser.setDescription("Extract fibers from a tractogram using binary image ROIs"); parser.setArgumentPrefix("--", "-"); parser.beginGroup("1. Mandatory arguments:"); parser.addArgument("input", "i", mitkCommandLineParser::String, "Input:", "input tractogram (.fib/.trk/.tck/.dcm)", us::Any(), false); parser.addArgument("out", "o", mitkCommandLineParser::String, "Output:", "output root", us::Any(), false); parser.addArgument("rois", "", mitkCommandLineParser::StringList, "ROI images:", "ROI images", us::Any(), false); parser.endGroup(); parser.beginGroup("2. Label based extraction:"); - parser.addArgument("labels", "", mitkCommandLineParser::StringList, "Labels:", "positive means roi image value in labels vector", us::Any()); parser.addArgument("split_labels", "", mitkCommandLineParser::Bool, "Split labels:", "output a separate tractogram for each label-->label tract", false); parser.addArgument("skip_self_connections", "", mitkCommandLineParser::Bool, "Skip self connections:", "ignore streamlines between two identical labels", false); + parser.addArgument("all_labels", "", mitkCommandLineParser::Bool, "All labels:", "use all labels (0 is excluded)", false); + parser.addArgument("labels", "", mitkCommandLineParser::StringList, "Labels:", "positive means roi image value in labels vector", us::Any()); parser.addArgument("start_labels", "", mitkCommandLineParser::StringList, "Start Labels:", "use separate start and end labels instead of one mixed set", us::Any()); parser.addArgument("end_labels", "", mitkCommandLineParser::StringList, "End Labels:", "use separate start and end labels instead of one mixed set", us::Any()); parser.addArgument("paired", "", mitkCommandLineParser::Bool, "Paired:", "start and end label list are paired", false); parser.endGroup(); parser.beginGroup("3. Misc:"); parser.addArgument("both_ends", "", mitkCommandLineParser::Bool, "Both ends:", "Fibers are extracted if both endpoints are located in the ROI.", false); parser.addArgument("overlap_fraction", "", mitkCommandLineParser::Float, "Overlap fraction:", "Extract by overlap, not by endpoints. Extract fibers that overlap to at least the provided factor (0-1) with the ROI.", -1); parser.addArgument("invert", "", mitkCommandLineParser::Bool, "Invert:", "get streamlines not positive for any of the ROI images", false); parser.addArgument("output_negatives", "", mitkCommandLineParser::Bool, "Negatives:", "output negatives", false); - parser.addArgument("interpolate", "", mitkCommandLineParser::Bool, "Interpolate:", "interpolate ROI images", false); + parser.addArgument("interpolate", "", mitkCommandLineParser::Bool, "Interpolate:", "interpolate ROI images (only for endpoint based extraction)", false); parser.addArgument("threshold", "", mitkCommandLineParser::Float, "Threshold:", "positive means ROI image value threshold", 0.5); parser.addArgument("min_fibers", "", mitkCommandLineParser::Int, "Min. num. fibers:", "discard positive tracts with less fibers", 0); + parser.addArgument("split_rois", "", mitkCommandLineParser::Bool, "Split ROIs:", "output a separate tractogram for each ROI", false); parser.endGroup(); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; std::string inFib = us::any_cast(parsedArgs["input"]); std::string outFib = us::any_cast(parsedArgs["out"]); + mitkCommandLineParser::StringContainerType roi_files = us::any_cast(parsedArgs["rois"]); bool both_ends = false; if (parsedArgs.count("both_ends")) both_ends = us::any_cast(parsedArgs["both_ends"]); bool invert = false; if (parsedArgs.count("invert")) invert = us::any_cast(parsedArgs["invert"]); unsigned int min_fibers = 0; if (parsedArgs.count("min_fibers")) min_fibers = us::any_cast(parsedArgs["min_fibers"]); + bool all_labels = false; + if (parsedArgs.count("all_labels")) + all_labels = us::any_cast(parsedArgs["all_labels"]); + bool split_labels = false; if (parsedArgs.count("split_labels")) split_labels = us::any_cast(parsedArgs["split_labels"]); + bool split_rois = false; + if (parsedArgs.count("split_rois")) + split_rois = us::any_cast(parsedArgs["split_rois"]); + bool skip_self_connections = false; if (parsedArgs.count("skip_self_connections")) skip_self_connections = us::any_cast(parsedArgs["skip_self_connections"]); bool output_negatives = false; if (parsedArgs.count("output_negatives")) output_negatives = us::any_cast(parsedArgs["output_negatives"]); float overlap_fraction = -1; if (parsedArgs.count("overlap_fraction")) overlap_fraction = us::any_cast(parsedArgs["overlap_fraction"]); bool any_point = false; if (overlap_fraction>=0) any_point = true; bool interpolate = false; if (parsedArgs.count("interpolate")) interpolate = us::any_cast(parsedArgs["interpolate"]); float threshold = 0.5; if (parsedArgs.count("threshold")) threshold = us::any_cast(parsedArgs["threshold"]); mitkCommandLineParser::StringContainerType labels; if (parsedArgs.count("labels")) labels = us::any_cast(parsedArgs["labels"]); mitkCommandLineParser::StringContainerType start_labels; if (parsedArgs.count("start_labels")) start_labels = us::any_cast(parsedArgs["start_labels"]); mitkCommandLineParser::StringContainerType end_labels; if (parsedArgs.count("end_labels")) end_labels = us::any_cast(parsedArgs["end_labels"]); bool paired = false; if (parsedArgs.count("paired")) paired = us::any_cast(parsedArgs["paired"]); try { // load fiber bundle mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load(inFib); + std::streambuf *old = cout.rdbuf(); // <-- save + std::stringstream ss; + std::cout.rdbuf (ss.rdbuf()); // <-- redirect std::vector< ItkFloatImgType::Pointer > roi_images; std::vector< std::string > roi_names; for (std::size_t i=0; i roi_images2; for (auto roi : roi_images) roi_images2.push_back(roi); std::vector< unsigned short > short_labels; for (auto l : labels) short_labels.push_back(boost::lexical_cast(l)); std::vector< unsigned short > short_start_labels; for (auto l : start_labels) short_start_labels.push_back(boost::lexical_cast(l)); std::vector< unsigned short > short_end_labels; for (auto l : end_labels) short_end_labels.push_back(boost::lexical_cast(l)); itk::FiberExtractionFilter::Pointer extractor = itk::FiberExtractionFilter::New(); extractor->SetInputFiberBundle(inputTractogram); extractor->SetRoiImages(roi_images2); extractor->SetRoiImageNames(roi_names); extractor->SetOverlapFraction(overlap_fraction); extractor->SetBothEnds(both_ends); extractor->SetInterpolate(interpolate); extractor->SetThreshold(threshold); extractor->SetLabels(short_labels); extractor->SetStartLabels(short_start_labels); extractor->SetEndLabels(short_end_labels); extractor->SetSplitLabels(split_labels); + extractor->SetSplitByRoi(split_rois); extractor->SetMinFibersPerTract(min_fibers); extractor->SetSkipSelfConnections(skip_self_connections); extractor->SetPairedStartEndLabels(paired); if (!any_point) extractor->SetMode(itk::FiberExtractionFilter::MODE::ENDPOINTS); - if (short_labels.size()>0 || short_start_labels.size()>0 || short_end_labels.size()>0) + if (all_labels || short_labels.size()>0 || short_start_labels.size()>0 || short_end_labels.size()>0) extractor->SetInputType(itk::FiberExtractionFilter::INPUT::LABEL_MAP); extractor->Update(); - mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(nullptr); + std::string ext = itksys::SystemTools::GetFilenameExtension(outFib); + if (ext.empty()) + ext = ".trk"; + outFib = itksys::SystemTools::GetFilenamePath(outFib) + '/' + itksys::SystemTools::GetFilenameWithoutExtension(outFib); if (invert) - mitk::IOUtil::Save(extractor->GetNegatives().at(0), outFib + ".trk"); + mitk::IOUtil::Save(extractor->GetNegatives().at(0), outFib + ext); else { - if (!split_labels) + int c = 0; + std::vector< std::string > positive_labels = extractor->GetPositiveLabels(); + for (auto fib : extractor->GetPositives()) { - newFib = newFib->AddBundles(extractor->GetPositives()); - mitk::IOUtil::Save(newFib, outFib + ".trk"); - } - else - { - int c = 0; - std::vector< std::string > positive_labels = extractor->GetPositiveLabels(); - for (auto fib : extractor->GetPositives()) - { - std::string l = positive_labels.at(c); - mitk::IOUtil::Save(fib, outFib + "_" + l + ".trk"); - ++c; - } + std::string l = positive_labels.at(c); + if (l.size()>0) + mitk::IOUtil::Save(fib, outFib + "_" + l + ext); + else + mitk::IOUtil::Save(fib, outFib + ext); + ++c; } } if (output_negatives) { invert = !invert; if (invert) - mitk::IOUtil::Save(extractor->GetNegatives().at(0), outFib + "_negatives.trk"); + mitk::IOUtil::Save(extractor->GetNegatives().at(0), outFib + "_negatives" + ext); else { - if (!split_labels) - { - newFib = newFib->AddBundles(extractor->GetPositives()); - mitk::IOUtil::Save(newFib, outFib + "_negatives.trk"); - } - else + int c = 0; + std::vector< std::string > positive_labels = extractor->GetPositiveLabels(); + for (auto fib : extractor->GetPositives()) { - int c = 0; - std::vector< std::string > positive_labels = extractor->GetPositiveLabels(); - for (auto fib : extractor->GetPositives()) - { - std::string l = positive_labels.at(c); - mitk::IOUtil::Save(fib, outFib + "_" + l + "_negatives.trk"); - ++c; - } + std::string l = positive_labels.at(c); + + if (l.size()>0) + mitk::IOUtil::Save(fib, outFib + "_" + l + "_negatives" + ext); + else + mitk::IOUtil::Save(fib, outFib + "_negatives" + ext); + ++c; } } } } catch (itk::ExceptionObject e) { std::cout << e; return EXIT_FAILURE; } catch (std::exception e) { std::cout << e.what(); return EXIT_FAILURE; } catch (...) { std::cout << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberJoin.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberJoin.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberJoin.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberJoin.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberProcessing.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberProcessing.cpp similarity index 95% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberProcessing.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberProcessing.cpp index 77e5da6ecc..a78860613c 100644 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FiberProcessing.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FiberProcessing.cpp @@ -1,246 +1,254 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include #include "mitkCommandLineParser.h" #include #include #include #include mitk::FiberBundle::Pointer LoadFib(std::string filename) { std::vector fibInfile = mitk::IOUtil::Load(filename); if( fibInfile.empty() ) std::cout << "File " << filename << " could not be read!"; mitk::BaseData::Pointer baseData = fibInfile.at(0); return dynamic_cast(baseData.GetPointer()); } /*! \brief Modify input tractogram: fiber resampling, compression, pruning and transformation. */ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Fiber Processing"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription("Modify input tractogram: fiber resampling, compression, pruning and transformation."); parser.setContributor("MIC"); parser.setArgumentPrefix("--", "-"); parser.beginGroup("1. Mandatory arguments:"); parser.addArgument("input", "i", mitkCommandLineParser::InputFile, "Input:", "Input fiber bundle (.fib, .trk, .tck)", us::Any(), false); parser.addArgument("outFile", "o", mitkCommandLineParser::OutputFile, "Output:", "Output fiber bundle (.fib, .trk)", us::Any(), false); parser.endGroup(); parser.beginGroup("2. Resampling:"); parser.addArgument("spline_resampling", "", mitkCommandLineParser::Float, "Spline resampling:", "Resample fiber using splines with the given point distance (in mm)"); parser.addArgument("linear_resampling", "", mitkCommandLineParser::Float, "Linear resampling:", "Resample fiber linearly with the given point distance (in mm)"); parser.addArgument("num_resampling", "", mitkCommandLineParser::Int, "Num. fiber points resampling:", "Resample all fibers to the given number of points"); parser.addArgument("compress", "", mitkCommandLineParser::Float, "Compress:", "Compress fiber using the given error threshold (in mm)"); parser.endGroup(); parser.beginGroup("3. Filtering:"); parser.addArgument("min_length", "", mitkCommandLineParser::Float, "Minimum length:", "Minimum fiber length (in mm)"); parser.addArgument("max_length", "", mitkCommandLineParser::Float, "Maximum length:", "Maximum fiber length (in mm)"); parser.addArgument("max_angle", "", mitkCommandLineParser::Float, "Maximum angle:", "Maximum angular STDEV over 1cm (in degree)"); parser.addArgument("remove", "", mitkCommandLineParser::Bool, "Remove fibers exceeding curvature threshold:", "If false, only the high curvature parts are removed"); + parser.addArgument("subsample", "", mitkCommandLineParser::Float, "Randomly select fraction of streamlines:", "Randomly select the specified fraction of streamlines from the input tractogram"); parser.endGroup(); parser.beginGroup("4. Transformation:"); parser.addArgument("mirror", "", mitkCommandLineParser::Int, "Invert coordinates:", "Invert fiber coordinates XYZ (e.g. 010 to invert y-coordinate of each fiber point)"); parser.addArgument("rotate_x", "", mitkCommandLineParser::Float, "Rotate x-axis:", "Rotate around x-axis (in deg)"); parser.addArgument("rotate_y", "", mitkCommandLineParser::Float, "Rotate y-axis:", "Rotate around y-axis (in deg)"); parser.addArgument("rotate_z", "", mitkCommandLineParser::Float, "Rotate z-axis:", "Rotate around z-axis (in deg)"); parser.addArgument("scale_x", "", mitkCommandLineParser::Float, "Scale x-axis:", "Scale in direction of x-axis"); parser.addArgument("scale_y", "", mitkCommandLineParser::Float, "Scale y-axis:", "Scale in direction of y-axis"); parser.addArgument("scale_z", "", mitkCommandLineParser::Float, "Scale z-axis", "Scale in direction of z-axis"); parser.addArgument("translate_x", "", mitkCommandLineParser::Float, "Translate x-axis:", "Translate in direction of x-axis (in mm)"); parser.addArgument("translate_y", "", mitkCommandLineParser::Float, "Translate y-axis:", "Translate in direction of y-axis (in mm)"); parser.addArgument("translate_z", "", mitkCommandLineParser::Float, "Translate z-axis:", "Translate in direction of z-axis (in mm)"); parser.endGroup(); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; bool remove = false; if (parsedArgs.count("remove")) remove = us::any_cast(parsedArgs["remove"]); float spline_resampling = -1; if (parsedArgs.count("spline_resampling")) spline_resampling = us::any_cast(parsedArgs["spline_resampling"]); float linear_resampling = -1; if (parsedArgs.count("linear_resampling")) linear_resampling = us::any_cast(parsedArgs["linear_resampling"]); int num_resampling = -1; if (parsedArgs.count("num_resampling")) num_resampling = us::any_cast(parsedArgs["num_resampling"]); + float subsample = -1; + if (parsedArgs.count("subsample")) + subsample = us::any_cast(parsedArgs["subsample"]); + float compress = -1; if (parsedArgs.count("compress")) compress = us::any_cast(parsedArgs["compress"]); float minFiberLength = -1; if (parsedArgs.count("min_length")) minFiberLength = us::any_cast(parsedArgs["min_length"]); float maxFiberLength = -1; if (parsedArgs.count("max_length")) maxFiberLength = us::any_cast(parsedArgs["max_length"]); float maxAngularDev = -1; if (parsedArgs.count("max_angle")) maxAngularDev = us::any_cast(parsedArgs["max_angle"]); int axis = 0; if (parsedArgs.count("mirror")) axis = us::any_cast(parsedArgs["mirror"]); float rotateX = 0; if (parsedArgs.count("rotate_x")) rotateX = us::any_cast(parsedArgs["rotate_x"]); float rotateY = 0; if (parsedArgs.count("rotate_y")) rotateY = us::any_cast(parsedArgs["rotate_y"]); float rotateZ = 0; if (parsedArgs.count("rotate_z")) rotateZ = us::any_cast(parsedArgs["rotate_z"]); float scaleX = 0; if (parsedArgs.count("scale_x")) scaleX = us::any_cast(parsedArgs["scale_x"]); float scaleY = 0; if (parsedArgs.count("scale_y")) scaleY = us::any_cast(parsedArgs["scale_y"]); float scaleZ = 0; if (parsedArgs.count("scale_z")) scaleZ = us::any_cast(parsedArgs["scale_z"]); float translateX = 0; if (parsedArgs.count("translate_x")) translateX = us::any_cast(parsedArgs["translate_x"]); float translateY = 0; if (parsedArgs.count("translate_y")) translateY = us::any_cast(parsedArgs["translate_y"]); float translateZ = 0; if (parsedArgs.count("translate_z")) translateZ = us::any_cast(parsedArgs["translate_z"]); std::string inFileName = us::any_cast(parsedArgs["input"]); std::string outFileName = us::any_cast(parsedArgs["outFile"]); try { mitk::FiberBundle::Pointer fib = LoadFib(inFileName); + if (subsample>0) + fib = fib->SubsampleFibers(subsample); + if (maxAngularDev>0) { auto filter = itk::FiberCurvatureFilter::New(); filter->SetInputFiberBundle(fib); filter->SetAngularDeviation(maxAngularDev); filter->SetDistance(10); filter->SetRemoveFibers(remove); filter->Update(); fib = filter->GetOutputFiberBundle(); } if (minFiberLength>0) fib->RemoveShortFibers(minFiberLength); if (maxFiberLength>0) fib->RemoveLongFibers(maxFiberLength); if (spline_resampling>0) fib->ResampleSpline(spline_resampling); if (linear_resampling>0) fib->ResampleLinear(linear_resampling); if (num_resampling>0) fib->ResampleToNumPoints(num_resampling); if (compress>0) fib->Compress(compress); if (axis/100==1) fib->MirrorFibers(0); if ((axis%100)/10==1) fib->MirrorFibers(1); if (axis%10==1) fib->MirrorFibers(2); if (rotateX > 0 || rotateY > 0 || rotateZ > 0){ std::cout << "Rotate " << rotateX << " " << rotateY << " " << rotateZ; fib->RotateAroundAxis(rotateX, rotateY, rotateZ); } if (translateX > 0 || translateY > 0 || translateZ > 0){ fib->TranslateFibers(translateX, translateY, translateZ); } if (scaleX > 0 || scaleY > 0 || scaleZ > 0) fib->ScaleFibers(scaleX, scaleY, scaleZ); mitk::IOUtil::Save(fib.GetPointer(), outFileName ); } catch (itk::ExceptionObject e) { std::cout << e; return EXIT_FAILURE; } catch (std::exception e) { std::cout << e.what(); return EXIT_FAILURE; } catch (...) { std::cout << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FitFibersToImage.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FitFibersToImage.cpp similarity index 88% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FitFibersToImage.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FitFibersToImage.cpp index ff153e017a..ca8e8e9bbe 100755 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/FitFibersToImage.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/FitFibersToImage.cpp @@ -1,346 +1,299 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include -#include -#include #include #include #include #include #include #include #include +#include -typedef itksys::SystemTools ist; typedef itk::Point PointType4; typedef itk::Image< float, 4 > PeakImgType; -std::vector< std::string > get_file_list(const std::string& path) -{ - std::vector< std::string > file_list; - itk::Directory::Pointer dir = itk::Directory::New(); - - if (dir->Load(path.c_str())) - { - int n = dir->GetNumberOfFiles(); - for (int r = 0; r < n; r++) - { - const char *filename = dir->GetFile(r); - std::string ext = ist::GetFilenameExtension(filename); - if (ext==".fib" || ext==".trk") - file_list.push_back(path + '/' + filename); - } - } - return file_list; -} - /*! \brief Fits the tractogram to the input peak image by assigning a weight to each fiber (similar to https://doi.org/10.1016/j.neuroimage.2015.06.092). */ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Fit Fibers To Image"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription("Assigns a weight to each fiber in order to optimally explain the input peak image"); parser.setContributor("MIC"); parser.setArgumentPrefix("--", "-"); parser.addArgument("", "i1", mitkCommandLineParser::StringList, "Input tractograms:", "input tractograms (.fib, vtk ascii file format)", us::Any(), false); parser.addArgument("", "i2", mitkCommandLineParser::InputFile, "Input image:", "input image", us::Any(), false); parser.addArgument("", "o", mitkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false); parser.addArgument("max_iter", "", mitkCommandLineParser::Int, "Max. iterations:", "maximum number of optimizer iterations", 20); parser.addArgument("bundle_based", "", mitkCommandLineParser::Bool, "Bundle based fit:", "fit one weight per input tractogram/bundle, not for each fiber", false); parser.addArgument("min_g", "", mitkCommandLineParser::Float, "Min. g:", "lower termination threshold for gradient magnitude", 1e-5); parser.addArgument("lambda", "", mitkCommandLineParser::Float, "Lambda:", "modifier for regularization", 0.1); parser.addArgument("save_res", "", mitkCommandLineParser::Bool, "Save Residuals:", "save residual images", false); parser.addArgument("save_weights", "", mitkCommandLineParser::Bool, "Save Weights:", "save fiber weights in a separate text file", false); parser.addArgument("filter_outliers", "", mitkCommandLineParser::Bool, "Filter outliers:", "perform second optimization run with an upper weight bound based on the first weight estimation (99% quantile)", false); parser.addArgument("join_tracts", "", mitkCommandLineParser::Bool, "Join output tracts:", "outout tracts are merged into a single tractogram", false); parser.addArgument("regu", "", mitkCommandLineParser::String, "Regularization:", "MSM, Variance, VoxelVariance (default), Lasso, GroupLasso, GroupVariance, NONE"); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; mitkCommandLineParser::StringContainerType fib_files = us::any_cast(parsedArgs["i1"]); std::string input_image_name = us::any_cast(parsedArgs["i2"]); std::string outRoot = us::any_cast(parsedArgs["o"]); bool single_fib = true; if (parsedArgs.count("bundle_based")) single_fib = !us::any_cast(parsedArgs["bundle_based"]); bool save_residuals = false; if (parsedArgs.count("save_res")) save_residuals = us::any_cast(parsedArgs["save_res"]); bool save_weights = false; if (parsedArgs.count("save_weights")) save_weights = us::any_cast(parsedArgs["save_weights"]); std::string regu = "VoxelVariance"; if (parsedArgs.count("regu")) regu = us::any_cast(parsedArgs["regu"]); bool join_tracts = false; if (parsedArgs.count("join_tracts")) join_tracts = us::any_cast(parsedArgs["join_tracts"]); int max_iter = 20; if (parsedArgs.count("max_iter")) max_iter = us::any_cast(parsedArgs["max_iter"]); float g_tol = 1e-5; if (parsedArgs.count("min_g")) g_tol = us::any_cast(parsedArgs["min_g"]); float lambda = 0.1; if (parsedArgs.count("lambda")) lambda = us::any_cast(parsedArgs["lambda"]); bool filter_outliers = false; if (parsedArgs.count("filter_outliers")) filter_outliers = us::any_cast(parsedArgs["filter_outliers"]); try { MITK_INFO << "Loading data"; -// std::streambuf *old = cout.rdbuf(); // <-- save -// std::stringstream ss; -// std::cout.rdbuf (ss.rdbuf()); // <-- redirect - std::vector< mitk::FiberBundle::Pointer > input_tracts; mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image", "Fiberbundles"}, {}); std::vector< std::string > fib_names; - for (auto item : fib_files) - { - if ( ist::FileIsDirectory(item) ) - { - for ( auto fibFile : get_file_list(item) ) - { - mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load(fibFile); - if (inputTractogram.IsNull()) - continue; - input_tracts.push_back(inputTractogram); - fib_names.push_back(fibFile); - } - } - else - { - mitk::FiberBundle::Pointer inputTractogram = mitk::IOUtil::Load(item); - if (inputTractogram.IsNull()) - continue; - input_tracts.push_back(inputTractogram); - fib_names.push_back(item); - } - } -// std::cout.rdbuf (old); // <-- restore + auto input_tracts = mitk::DiffusionDataIOHelper::load_fibs(fib_files, &fib_names); itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New(); mitk::BaseData::Pointer inputData = mitk::IOUtil::Load(input_image_name, &functor)[0].GetPointer(); mitk::Image::Pointer mitk_image = dynamic_cast(inputData.GetPointer()); mitk::PeakImage::Pointer mitk_peak_image = dynamic_cast(inputData.GetPointer()); if (mitk_peak_image.IsNotNull()) { typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(mitk_peak_image); caster->Update(); mitk::PeakImage::ItkPeakImageType::Pointer peak_image = caster->GetOutput(); fitter->SetPeakImage(peak_image); } else if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image)) { fitter->SetDiffImage(mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk_image)); mitk::TensorModel<>* model = new mitk::TensorModel<>(); model->SetBvalue(1000); model->SetDiffusivity1(0.0010); model->SetDiffusivity2(0.00015); model->SetDiffusivity3(0.00015); model->SetGradientList(mitk::DiffusionPropertyHelper::GetGradientContainer(mitk_image)); fitter->SetSignalModel(model); } else if (mitk_image->GetDimension()==3) { itk::FitFibersToImageFilter::DoubleImgType::Pointer scalar_image = itk::FitFibersToImageFilter::DoubleImgType::New(); mitk::CastToItkImage(mitk_image, scalar_image); fitter->SetScalarImage(scalar_image); } else { MITK_INFO << "Input image invalid. Valid options are peak image, 3D scalar image or raw diffusion-weighted image."; return EXIT_FAILURE; } fitter->SetTractograms(input_tracts); fitter->SetFitIndividualFibers(single_fib); fitter->SetMaxIterations(max_iter); fitter->SetGradientTolerance(g_tol); fitter->SetLambda(lambda); fitter->SetFilterOutliers(filter_outliers); if (regu=="MSM") fitter->SetRegularization(VnlCostFunction::REGU::MSM); else if (regu=="Variance") fitter->SetRegularization(VnlCostFunction::REGU::VARIANCE); else if (regu=="Lasso") fitter->SetRegularization(VnlCostFunction::REGU::LASSO); else if (regu=="VoxelVariance") fitter->SetRegularization(VnlCostFunction::REGU::VOXEL_VARIANCE); else if (regu=="GroupLasso") fitter->SetRegularization(VnlCostFunction::REGU::GROUP_LASSO); else if (regu=="GroupVariance") fitter->SetRegularization(VnlCostFunction::REGU::GROUP_VARIANCE); else if (regu=="NONE") fitter->SetRegularization(VnlCostFunction::REGU::NONE); fitter->Update(); if (save_residuals && mitk_peak_image.IsNotNull()) { itk::ImageFileWriter< PeakImgType >::Pointer writer = itk::ImageFileWriter< PeakImgType >::New(); writer->SetInput(fitter->GetFittedImage()); writer->SetFileName(outRoot + "_fitted.nii.gz"); writer->Update(); writer->SetInput(fitter->GetResidualImage()); writer->SetFileName(outRoot + "_residual.nii.gz"); writer->Update(); writer->SetInput(fitter->GetOverexplainedImage()); writer->SetFileName(outRoot + "_overexplained.nii.gz"); writer->Update(); writer->SetInput(fitter->GetUnderexplainedImage()); writer->SetFileName(outRoot + "_underexplained.nii.gz"); writer->Update(); } else if (save_residuals && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image)) { { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetFittedImageDiff().GetPointer() ); mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true); mitk::DiffusionPropertyHelper::InitializeImage( outImage ); mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_fitted_image.nii.gz"); } { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetResidualImageDiff().GetPointer() ); mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true); mitk::DiffusionPropertyHelper::InitializeImage( outImage ); mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_residual_image.nii.gz"); } { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetOverexplainedImageDiff().GetPointer() ); mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true); mitk::DiffusionPropertyHelper::InitializeImage( outImage ); mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_overexplained_image.nii.gz"); } { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetUnderexplainedImageDiff().GetPointer() ); mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true); mitk::DiffusionPropertyHelper::InitializeImage( outImage ); mitk::IOUtil::Save(outImage, "application/vnd.mitk.nii.gz", outRoot + "_underexplained_image.nii.gz"); } } else if (save_residuals) { itk::ImageFileWriter< itk::FitFibersToImageFilter::DoubleImgType >::Pointer writer = itk::ImageFileWriter< itk::FitFibersToImageFilter::DoubleImgType >::New(); writer->SetInput(fitter->GetFittedImageScalar()); writer->SetFileName(outRoot + "_fitted_image.nii.gz"); writer->Update(); writer->SetInput(fitter->GetResidualImageScalar()); writer->SetFileName(outRoot + "_residual_image.nii.gz"); writer->Update(); writer->SetInput(fitter->GetOverexplainedImageScalar()); writer->SetFileName(outRoot + "_overexplained_image.nii.gz"); writer->Update(); writer->SetInput(fitter->GetUnderexplainedImageScalar()); writer->SetFileName(outRoot + "_underexplained_image.nii.gz"); writer->Update(); } std::vector< mitk::FiberBundle::Pointer > output_tracts = fitter->GetTractograms(); if (!join_tracts) { for (unsigned int bundle=0; bundleGetNumFibers(); ++f) logfile << output_tracts.at(bundle)->GetFiberWeight(f) << "\n"; logfile.close(); } } } else { mitk::FiberBundle::Pointer out = mitk::FiberBundle::New(); out = out->AddBundles(output_tracts); out->ColorFibersByFiberWeights(false, true); mitk::IOUtil::Save(out, outRoot + "_fitted.fib"); if (save_weights) { ofstream logfile; logfile.open (outRoot + "_weights.txt"); for (int f=0; fGetNumFibers(); ++f) logfile << out->GetFiberWeight(f) << "\n"; logfile.close(); } } } catch (itk::ExceptionObject e) { std::cout << e; return EXIT_FAILURE; } catch (std::exception e) { std::cout << e.what(); return EXIT_FAILURE; } catch (...) { std::cout << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/Sift2WeightCopy.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/Sift2WeightCopy.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/Sift2WeightCopy.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/Sift2WeightCopy.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/TractDensity.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/TractDensity.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/TractDensity.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/TractDensity.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/TractDensityFilter.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/TractDensityFilter.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/TractDensityFilter.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/FiberProcessing/TractDensityFilter.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/Fiberfox/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/CMakeLists.txt similarity index 86% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/Fiberfox/CMakeLists.txt rename to Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/CMakeLists.txt index 74361ab3e7..26dc2d25da 100755 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/Fiberfox/CMakeLists.txt +++ b/Modules/DiffusionImaging/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^^MitkFiberTracking - FiberfoxOptimization^^MitkFiberTracking + Fiberfox^^ + FiberfoxOptimization^^ ) 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 MitkCore MitkDiffusionCore ${dependencies_list} - PACKAGE_DEPENDS ITK + DEPENDS MitkDiffusionCmdApps ${dependencies_list} + PACKAGE_DEPENDS ) endforeach() if(EXECUTABLE_IS_ENABLED) MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) endif() endif() diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/Fiberfox/Fiberfox.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/Fiberfox/Fiberfox.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/Fiberfox/FiberfoxOptimization.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/FiberfoxOptimization.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/Fiberfox/FiberfoxOptimization.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/FiberfoxOptimization.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/Misc/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/CMakeLists.txt similarity index 71% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/Misc/CMakeLists.txt rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/CMakeLists.txt index 8342f17ffc..d4746a8381 100644 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/Misc/CMakeLists.txt +++ b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/CMakeLists.txt @@ -1,37 +1,48 @@ option(BUILD_DiffusionMiscCmdApps "Build miscellaneous commandline tools for diffusion" OFF) if(BUILD_DiffusionMiscCmdApps 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( diffusionMisccmdapps - PeakExtraction^^MitkFiberTracking - FileFormatConverter^^MitkFiberTracking - FlipPeaks^^MitkFiberTracking + PeakExtraction^^ + FileFormatConverter^^ + FlipPeaks^^ + ImageResampler^^ + CopyGeometry^^ + Registration^^ + DiffusionDICOMLoader^^ + ResampleGradients^^ + ShToOdfImage^^ + DImp^^ + DReg^^ + HeadMotionCorrection^^ + DmriDenoising^^MitkImageDenoising + RoundBvalues^^ ) foreach(diffusionMisccmdapp ${diffusionMisccmdapps}) # extract cmd app name and dependencies string(REPLACE "^^" "\\;" cmdapp_info ${diffusionMisccmdapp}) 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 MitkCore MitkDiffusionCore ${dependencies_list} - PACKAGE_DEPENDS ITK + DEPENDS MitkDiffusionCmdApps ${dependencies_list} + PACKAGE_DEPENDS ) endforeach() endif() diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/CopyGeometry.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/CopyGeometry.cpp similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps/CopyGeometry.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/CopyGeometry.cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/DICOMLoader.cmake b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DICOMLoader.cmake similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps/DICOMLoader.cmake rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/DICOMLoader.cmake diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/DImp.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DImp.cpp similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps/DImp.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/DImp.cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/DReg.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DReg.cpp similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps/DReg.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/DReg.cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/DiffusionDICOMLoader.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DiffusionDICOMLoader.cpp similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps/DiffusionDICOMLoader.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/DiffusionDICOMLoader.cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/DmriDenoising.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/DmriDenoising.cpp similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps/DmriDenoising.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/DmriDenoising.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/Misc/FileFormatConverter.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/FileFormatConverter.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/Misc/FileFormatConverter.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/FileFormatConverter.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/Misc/FlipPeaks.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/FlipPeaks.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/Misc/FlipPeaks.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/FlipPeaks.cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/HeadMotionCorrection.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/HeadMotionCorrection.cpp similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps/HeadMotionCorrection.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/HeadMotionCorrection.cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/ImageResampler.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/ImageResampler.cpp similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps/ImageResampler.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/ImageResampler.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/Misc/PeakExtraction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/PeakExtraction.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/Misc/PeakExtraction.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/PeakExtraction.cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/Registration.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/Registration.cpp similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps/Registration.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/Registration.cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/ResampleGradients.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/ResampleGradients.cpp similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps/ResampleGradients.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/ResampleGradients.cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/RoundBvalues.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/RoundBvalues.cpp similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps/RoundBvalues.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/RoundBvalues.cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/ShToOdfImage.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Misc/ShToOdfImage.cpp similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps/ShToOdfImage.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Misc/ShToOdfImage.cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps_python/BrainExtraction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Python/BrainExtraction.cpp similarity index 100% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps_python/BrainExtraction.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Python/BrainExtraction.cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps_python/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/Python/CMakeLists.txt similarity index 89% rename from Modules/DiffusionImaging/DiffusionCore/cmdapps_python/CMakeLists.txt rename to Modules/DiffusionImaging/DiffusionCmdApps/Python/CMakeLists.txt index 5cbdd74a2f..8cfbef2cff 100644 --- a/Modules/DiffusionImaging/DiffusionCore/cmdapps_python/CMakeLists.txt +++ b/Modules/DiffusionImaging/DiffusionCmdApps/Python/CMakeLists.txt @@ -1,34 +1,34 @@ option(BUILD_DiffusionPythonCmdApps "Build commandline tools for diffusion with python" OFF) if(BUILD_DiffusionPythonCmdApps 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( diffusionpythoncmdapps BrainExtraction^^ ) foreach(diffusionpythoncmdapp ${diffusionpythoncmdapps}) # extract cmd app name and dependencies string(REPLACE "^^" "\\;" cmdapp_info ${diffusionpythoncmdapp}) 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 CppMicroServices MitkCore MitkDiffusionCore MitkPython ${dependencies_list} - PACKAGE_DEPENDS ITK + DEPENDS CppMicroServices MitkDiffusionCmdApps MitkPython ${dependencies_list} + PACKAGE_DEPENDS ) endforeach() endif() diff --git a/Modules/DiffusionImaging/Quantification/cmdapps/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/CMakeLists.txt similarity index 92% rename from Modules/DiffusionImaging/Quantification/cmdapps/CMakeLists.txt rename to Modules/DiffusionImaging/DiffusionCmdApps/Quantification/CMakeLists.txt index bd65206b21..d21f29655d 100644 --- a/Modules/DiffusionImaging/Quantification/cmdapps/CMakeLists.txt +++ b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/CMakeLists.txt @@ -1,39 +1,39 @@ option(BUILD_DiffusionQuantificationCmdApps "Build commandline tools for diffusion quantification (IVIM, ADC, ...)" OFF) if(BUILD_DiffusionQuantificationCmdApps 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( diffusionQuantificationcmdapps DiffusionIndices^^ QballReconstruction^^ TensorReconstruction^^ TensorDerivedMapsExtraction^^ DiffusionKurtosisFit^^ MultishellMethods^^ ) foreach(diffusionQuantificationcmdapp ${diffusionQuantificationcmdapps}) # extract cmd app name and dependencies string(REPLACE "^^" "\\;" cmdapp_info ${diffusionQuantificationcmdapp}) 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 MitkCore MitkDiffusionCore ${dependencies_list} - PACKAGE_DEPENDS ITK + DEPENDS MitkDiffusionCmdApps ${dependencies_list} + PACKAGE_DEPENDS ) endforeach() endif() diff --git a/Modules/DiffusionImaging/Quantification/cmdapps/DiffusionIndices.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/DiffusionIndices.cpp similarity index 100% rename from Modules/DiffusionImaging/Quantification/cmdapps/DiffusionIndices.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Quantification/DiffusionIndices.cpp diff --git a/Modules/DiffusionImaging/Quantification/cmdapps/DiffusionKurtosisFit.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/DiffusionKurtosisFit.cpp similarity index 100% rename from Modules/DiffusionImaging/Quantification/cmdapps/DiffusionKurtosisFit.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Quantification/DiffusionKurtosisFit.cpp diff --git a/Modules/DiffusionImaging/Quantification/cmdapps/MultishellMethods.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/MultishellMethods.cpp similarity index 100% rename from Modules/DiffusionImaging/Quantification/cmdapps/MultishellMethods.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Quantification/MultishellMethods.cpp diff --git a/Modules/DiffusionImaging/Quantification/cmdapps/QballReconstruction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/QballReconstruction.cpp similarity index 100% rename from Modules/DiffusionImaging/Quantification/cmdapps/QballReconstruction.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Quantification/QballReconstruction.cpp diff --git a/Modules/DiffusionImaging/Quantification/cmdapps/TensorDerivedMapsExtraction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/TensorDerivedMapsExtraction.cpp similarity index 100% rename from Modules/DiffusionImaging/Quantification/cmdapps/TensorDerivedMapsExtraction.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Quantification/TensorDerivedMapsExtraction.cpp diff --git a/Modules/DiffusionImaging/Quantification/cmdapps/TensorReconstruction.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Quantification/TensorReconstruction.cpp similarity index 100% rename from Modules/DiffusionImaging/Quantification/cmdapps/TensorReconstruction.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Quantification/TensorReconstruction.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/Tractography/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/CMakeLists.txt similarity index 83% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/Tractography/CMakeLists.txt rename to Modules/DiffusionImaging/DiffusionCmdApps/Tractography/CMakeLists.txt index f8ab7cfa92..a14ed6d992 100755 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/Tractography/CMakeLists.txt +++ b/Modules/DiffusionImaging/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^^MitkFiberTracking - GlobalTractography^^MitkFiberTracking - RfTraining^^MitkFiberTracking + 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 MitkCore MitkDiffusionCore ${dependencies_list} - PACKAGE_DEPENDS ITK + DEPENDS MitkDiffusionCmdApps ${dependencies_list} + PACKAGE_DEPENDS ) endforeach() if(EXECUTABLE_IS_ENABLED) MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) endif() endif() diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/Tractography/GlobalTractography.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/GlobalTractography.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/Tractography/GlobalTractography.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Tractography/GlobalTractography.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/Tractography/RfTraining.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/RfTraining.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/Tractography/RfTraining.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Tractography/RfTraining.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/Tractography/StreamlineTractography.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/StreamlineTractography.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/Tractography/StreamlineTractography.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/Tractography/StreamlineTractography.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/AnchorConstrainedPlausibility.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/AnchorConstrainedPlausibility.cpp similarity index 61% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/AnchorConstrainedPlausibility.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/AnchorConstrainedPlausibility.cpp index 0a616ad8bf..8198a62615 100755 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/AnchorConstrainedPlausibility.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/AnchorConstrainedPlausibility.cpp @@ -1,558 +1,446 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include +#include +#include -typedef itksys::SystemTools ist; typedef itk::Point PointType4; typedef itk::Image< float, 4 > PeakImgType; typedef itk::Image< unsigned char, 3 > ItkUcharImageType; -std::vector< mitk::FiberBundle::Pointer > CombineTractograms(std::vector< mitk::FiberBundle::Pointer > reference, std::vector< mitk::FiberBundle::Pointer > candidates, int skip=-1) -{ - std::vector< mitk::FiberBundle::Pointer > fib; - for (auto f : reference) - fib.push_back(f); - - int c = 0; - for (auto f : candidates) - { - if (c!=skip) - fib.push_back(f); - ++c; - } - - return fib; -} - -std::vector< std::string > get_file_list(const std::string& path, std::vector< std::string > extensions={".fib", ".trk"}) -{ - std::vector< std::string > file_list; - itk::Directory::Pointer dir = itk::Directory::New(); - - if (dir->Load(path.c_str())) - { - int n = dir->GetNumberOfFiles(); - for (int r = 0; r < n; r++) - { - const char *filename = dir->GetFile(r); - std::string ext = ist::GetFilenameExtension(filename); - for (auto e : extensions) - { - if (ext==e) - { - file_list.push_back(path + '/' + filename); - break; - } - } - } - } - return file_list; -} - /*! \brief Score input candidate tracts using ACP analysis */ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Anchor Constrained Plausibility"); parser.setCategory("Fiber Tracking Evaluation"); parser.setDescription("Score input candidate tracts using ACP analysis"); parser.setContributor("MIC"); parser.setArgumentPrefix("--", "-"); - parser.addArgument("", "a", mitkCommandLineParser::InputFile, "Anchor tractogram:", "anchor tracts in one tractogram file", us::Any(), false); + parser.addArgument("", "a", mitkCommandLineParser::InputFile, "Anchor tractogram:", "anchor tracts in one tractogram file", us::Any()); parser.addArgument("", "p", mitkCommandLineParser::InputFile, "Input peaks:", "input peak image", us::Any(), false); - parser.addArgument("", "c", mitkCommandLineParser::InputDirectory, "Candidates folder:", "folder containing candidate tracts", us::Any(), false); + parser.addArgument("", "c", mitkCommandLineParser::StringList, "Candidates:", "Folder(s) or file list of candidate tracts", us::Any(), false); parser.addArgument("", "o", mitkCommandLineParser::OutputDirectory, "Output folder:", "output folder", us::Any(), false); - parser.addArgument("anchor_masks", "", mitkCommandLineParser::StringList, "Reference Masks:", "reference tract masks for accuracy evaluation"); + parser.addArgument("reference_mask_folders", "", mitkCommandLineParser::StringList, "Reference Mask Folder(s):", "Folder(s) or file list containing reference tract masks for accuracy evaluation"); + parser.addArgument("reference_peaks_folders", "", mitkCommandLineParser::StringList, "Reference Peaks Folder(s):", "Folder(s) or file list containing reference peak images for accuracy evaluation"); + parser.addArgument("mask", "", mitkCommandLineParser::InputFile, "Mask image:", "scoring is only performed inside the mask image"); parser.addArgument("greedy_add", "", mitkCommandLineParser::Bool, "Greedy:", "if enabled, the candidate tracts are not jointly fitted to the residual image but one after the other employing a greedy scheme", false); parser.addArgument("lambda", "", mitkCommandLineParser::Float, "Lambda:", "modifier for regularization", 0.1); parser.addArgument("filter_outliers", "", mitkCommandLineParser::Bool, "Filter outliers:", "perform second optimization run with an upper weight bound based on the first weight estimation (99% quantile)", false); parser.addArgument("regu", "", mitkCommandLineParser::String, "Regularization:", "MSM, Variance, VoxelVariance, Lasso, GroupLasso, GroupVariance, NONE (default)"); parser.addArgument("use_num_streamlines", "", mitkCommandLineParser::Bool, "Use number of streamlines as score:", "Don't fit candidates, simply use number of streamlines per candidate as score", false); parser.addArgument("use_weights", "", mitkCommandLineParser::Bool, "Use input weights as score:", "Don't fit candidates, simply use first input streamline weight per candidate as score", false); parser.addArgument("filter_zero_weights", "", mitkCommandLineParser::Bool, "Filter zero-weights", "Remove streamlines with weight 0 from candidates", false); + parser.addArgument("flipx", "", mitkCommandLineParser::Bool, "Flip x", "flip along x-axis", false); + parser.addArgument("flipy", "", mitkCommandLineParser::Bool, "Flip y", "flip along y-axis", false); + parser.addArgument("flipz", "", mitkCommandLineParser::Bool, "Flip z", "flip along z-axis", false); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; - std::string anchors_file = us::any_cast(parsedArgs["a"]); std::string peak_file_name = us::any_cast(parsedArgs["p"]); - std::string candidate_tract_folder = us::any_cast(parsedArgs["c"]); std::string out_folder = us::any_cast(parsedArgs["o"]); + mitkCommandLineParser::StringContainerType candidate_tract_folders = us::any_cast(parsedArgs["c"]); + + if (!out_folder.empty() && out_folder.back() != '/') + out_folder += "/"; + bool greedy_add = false; if (parsedArgs.count("greedy_add")) greedy_add = us::any_cast(parsedArgs["greedy_add"]); float lambda = 0.1; if (parsedArgs.count("lambda")) lambda = us::any_cast(parsedArgs["lambda"]); bool filter_outliers = false; if (parsedArgs.count("filter_outliers")) filter_outliers = us::any_cast(parsedArgs["filter_outliers"]); bool filter_zero_weights = false; if (parsedArgs.count("filter_zero_weights")) filter_zero_weights = us::any_cast(parsedArgs["filter_zero_weights"]); std::string mask_file = ""; if (parsedArgs.count("mask")) mask_file = us::any_cast(parsedArgs["mask"]); - mitkCommandLineParser::StringContainerType anchor_mask_files_folders; - if (parsedArgs.count("anchor_masks")) - anchor_mask_files_folders = us::any_cast(parsedArgs["anchor_masks"]); + mitkCommandLineParser::StringContainerType reference_mask_files_folders; + if (parsedArgs.count("reference_mask_folders")) + reference_mask_files_folders = us::any_cast(parsedArgs["reference_mask_folders"]); + + mitkCommandLineParser::StringContainerType reference_peaks_files_folders; + if (parsedArgs.count("reference_peaks_folders")) + reference_peaks_files_folders = us::any_cast(parsedArgs["reference_peaks_folders"]); std::string regu = "NONE"; if (parsedArgs.count("regu")) regu = us::any_cast(parsedArgs["regu"]); bool use_weights = false; if (parsedArgs.count("use_weights")) use_weights = us::any_cast(parsedArgs["use_weights"]); bool use_num_streamlines = false; if (parsedArgs.count("use_num_streamlines")) use_num_streamlines = us::any_cast(parsedArgs["use_num_streamlines"]); + + bool flipx = false; + if (parsedArgs.count("flipx")) + flipx = us::any_cast(parsedArgs["flipx"]); + + bool flipy = false; + if (parsedArgs.count("flipy")) + flipy = us::any_cast(parsedArgs["flipy"]); + + bool flipz = false; + if (parsedArgs.count("flipz")) + flipz = us::any_cast(parsedArgs["flipz"]); + try { itk::TimeProbe clock; clock.Start(); if (!ist::PathExists(out_folder)) { MITK_INFO << "Creating output directory"; ist::MakeDirectory(out_folder); } MITK_INFO << "Loading data"; - std::streambuf *old = cout.rdbuf(); // <-- save - std::stringstream ss; - std::cout.rdbuf (ss.rdbuf()); // <-- redirect - - ofstream logfile; - logfile.open (out_folder + "log.txt"); - - itk::ImageFileWriter< PeakImgType >::Pointer peak_image_writer = itk::ImageFileWriter< PeakImgType >::New(); - mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image", "Fiberbundles"}, {}); - mitk::Image::Pointer inputImage = dynamic_cast(mitk::IOUtil::Load(peak_file_name, &functor)[0].GetPointer()); // Load mask file. Fit is only performed inside the mask - itk::FitFibersToImageFilter::UcharImgType::Pointer mask = nullptr; - if (mask_file.compare("")!=0) - { - mitk::Image::Pointer mitk_mask = mitk::IOUtil::Load(mask_file); - mitk::CastToItkImage(mitk_mask, mask); - } + auto mask = mitk::DiffusionDataIOHelper::load_itk_image(mask_file); // Load masks covering the true positives for evaluation purposes - std::vector< itk::FitFibersToImageFilter::UcharImgType::Pointer > reference_masks; std::vector< std::string > anchor_mask_files; - for (auto filename : anchor_mask_files_folders) - { - if (itksys::SystemTools::PathExists(filename)) - { - auto list = get_file_list(filename, {".nrrd",".nii.gz",".nii"}); - for (auto f : list) - { - MITK_INFO << f; - itk::FitFibersToImageFilter::UcharImgType::Pointer ref_mask = nullptr; - mitk::Image::Pointer ref_mitk_mask = mitk::IOUtil::Load(f); - mitk::CastToItkImage(ref_mitk_mask, ref_mask); - reference_masks.push_back(ref_mask); - anchor_mask_files.push_back(f); - } - } - else if (itksys::SystemTools::FileExists(filename)) - { - anchor_mask_files.push_back(filename); - itk::FitFibersToImageFilter::UcharImgType::Pointer ref_mask = nullptr; - mitk::Image::Pointer ref_mitk_mask = mitk::IOUtil::Load(filename); - mitk::CastToItkImage(ref_mitk_mask, ref_mask); - reference_masks.push_back(ref_mask); - } - } + auto reference_masks = mitk::DiffusionDataIOHelper::load_itk_images(reference_mask_files_folders, &anchor_mask_files); + auto reference_peaks = mitk::DiffusionDataIOHelper::load_itk_images(reference_peaks_files_folders); // Load peak image - typedef mitk::ImageToItk< PeakImgType > CasterType; - CasterType::Pointer caster = CasterType::New(); - caster->SetInput(inputImage); - caster->Update(); - PeakImgType::Pointer peak_image = caster->GetOutput(); + auto peak_image = mitk::DiffusionDataIOHelper::load_itk_image(peak_file_name); // Load all candidate tracts - std::vector< std::string > candidate_tract_files = get_file_list(candidate_tract_folder); - std::vector< mitk::FiberBundle::Pointer > input_candidates; - for (std::string f : candidate_tract_files) - { - mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load(f); - if (fib.IsNull()) - continue; - if (fib->GetNumFibers()<=0) - continue; - input_candidates.push_back(fib); - } - std::cout.rdbuf (old); // <-- restore + std::vector< std::string > candidate_tract_files; + auto input_candidates = mitk::DiffusionDataIOHelper::load_fibs(candidate_tract_folders, &candidate_tract_files); + MITK_INFO << "Loaded " << candidate_tract_files.size() << " candidate tracts."; MITK_INFO << "Loaded " << reference_masks.size() << " reference masks."; + MITK_INFO << "Loaded " << reference_peaks.size() << " reference peaks."; + + if (flipx || flipy || flipz) + { + itk::FlipPeaksFilter< float >::Pointer flipper = itk::FlipPeaksFilter< float >::New(); + flipper->SetInput(peak_image); + flipper->SetFlipX(flipx); + flipper->SetFlipY(flipy); + flipper->SetFlipZ(flipz); + flipper->Update(); + peak_image = flipper->GetOutput(); + } + itk::ImageFileWriter< PeakImgType >::Pointer peak_image_writer = itk::ImageFileWriter< PeakImgType >::New(); + ofstream logfile; + logfile.open (out_folder + "scores.txt"); double rmse = 0.0; int iteration = 0; std::string name = "NOANCHOR"; - // Load reference tractogram consisting of all known tracts - std::vector< mitk::FiberBundle::Pointer > input_reference; - mitk::FiberBundle::Pointer anchor_tractogram = mitk::IOUtil::Load(anchors_file); - if ( !(anchor_tractogram.IsNull() || anchor_tractogram->GetNumFibers()==0) ) + + if (parsedArgs.count("a")) { - input_reference.push_back(anchor_tractogram); + // Load reference tractogram consisting of all known tracts + std::string anchors_file = us::any_cast(parsedArgs["a"]); + mitk::FiberBundle::Pointer anchor_tractogram = mitk::IOUtil::Load(anchors_file); + if ( !(anchor_tractogram.IsNull() || anchor_tractogram->GetNumFibers()==0) ) + { + // Fit known tracts to peak image to obtain underexplained image + MITK_INFO << "Fit anchor tracts"; + itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New(); + fitter->SetTractograms({anchor_tractogram}); + fitter->SetLambda(lambda); + fitter->SetFilterOutliers(filter_outliers); + fitter->SetPeakImage(peak_image); + fitter->SetVerbose(true); + fitter->SetMaskImage(mask); + fitter->SetRegularization(VnlCostFunction::REGU::NONE); - // Fit known tracts to peak image to obtain underexplained image - MITK_INFO << "Fit anchor tracts"; - itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New(); - fitter->SetTractograms(input_reference); - fitter->SetLambda(lambda); - fitter->SetFilterOutliers(filter_outliers); - fitter->SetPeakImage(peak_image); - fitter->SetVerbose(true); - fitter->SetMaskImage(mask); - fitter->SetRegularization(VnlCostFunction::REGU::NONE); - fitter->Update(); - rmse = fitter->GetRMSE(); - vnl_vector rms_diff = fitter->GetRmsDiffPerBundle(); - logfile << "RMS_DIFF: " << setprecision(5) << rms_diff[0] << " " << name << " RMSE: " << rmse << "\n"; + fitter->Update(); + rmse = fitter->GetRMSE(); + vnl_vector rms_diff = fitter->GetRmsDiffPerBundle(); - name = ist::GetFilenameWithoutExtension(anchors_file); - mitk::FiberBundle::Pointer anchor_tracts = fitter->GetTractograms().at(0); - anchor_tracts->SetFiberColors(255,255,255); - mitk::IOUtil::Save(anchor_tracts, out_folder + boost::lexical_cast((int)(100000*rms_diff[0])) + "_" + name + ".fib"); + name = ist::GetFilenameWithoutExtension(anchors_file); + mitk::FiberBundle::Pointer anchor_tracts = fitter->GetTractograms().at(0); + anchor_tracts->SetFiberColors(255,255,255); + mitk::IOUtil::Save(anchor_tracts, out_folder + boost::lexical_cast((int)(100000*rms_diff[0])) + "_" + name + ".fib"); - peak_image = fitter->GetUnderexplainedImage(); - peak_image_writer->SetInput(peak_image); - peak_image_writer->SetFileName(out_folder + "Residual_" + name + ".nii.gz"); - peak_image_writer->Update(); + logfile << name << " " << setprecision(5) << rms_diff[0] << "\n"; + + peak_image = fitter->GetUnderexplainedImage(); + peak_image_writer->SetInput(peak_image); + peak_image_writer->SetFileName(out_folder + "Residual_" + name + ".nii.gz"); + peak_image_writer->Update(); + } } if (use_weights || use_num_streamlines) { MITK_INFO << "Using tract weights as scores"; int c = 0; for (auto fib : input_candidates) { int mod = 1; double score = 0; if (use_weights) { score = fib->GetFiberWeight(0); mod = 100000; } else if (use_num_streamlines) score = fib->GetNumFibers(); fib->ColorFibersByOrientation(); std::string bundle_name = ist::GetFilenameWithoutExtension(candidate_tract_files.at(c)); std::streambuf *old = cout.rdbuf(); // <-- save std::stringstream ss; std::cout.rdbuf (ss.rdbuf()); // <-- redirect mitk::IOUtil::Save(fib, out_folder + boost::lexical_cast((int)(mod*score)) + "_" + bundle_name + ".fib"); - float best_overlap = 0; - int best_overlap_index = -1; - int m_idx = 0; - for (auto ref_mask : reference_masks) - { - float overlap = fib->GetOverlap(ref_mask); - if (overlap>best_overlap) - { - best_overlap = overlap; - best_overlap_index = m_idx; - } - ++m_idx; - } - unsigned int num_voxels = 0; { itk::TractDensityImageFilter< ItkUcharImageType >::Pointer masks_filter = itk::TractDensityImageFilter< ItkUcharImageType >::New(); masks_filter->SetInputImage(mask); masks_filter->SetBinaryOutput(true); masks_filter->SetFiberBundle(fib); masks_filter->SetUseImageGeometry(true); masks_filter->Update(); num_voxels = masks_filter->GetNumCoveredVoxels(); } double weight_sum = 0; for (int i=0; iGetNumFibers(); i++) weight_sum += fib->GetFiberWeight(i); std::cout.rdbuf (old); // <-- restore - logfile << "RMS_DIFF: " << setprecision(5) << score << " " << bundle_name << " " << num_voxels << " " << fib->GetNumFibers() << " " << weight_sum << "\n"; - if (best_overlap_index>=0) - logfile << "Best_overlap: " << setprecision(5) << best_overlap << " " << ist::GetFilenameWithoutExtension(anchor_mask_files.at(best_overlap_index)) << "\n"; - else - logfile << "No_overlap\n"; + logfile << bundle_name << " " << setprecision(5) << score << " " << num_voxels << " " << fib->GetNumFibers() << " " << weight_sum << "\n"; ++c; } - } else if (!greedy_add) { MITK_INFO << "Fit candidate tracts"; itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New(); fitter->SetLambda(lambda); fitter->SetFilterOutliers(filter_outliers); fitter->SetVerbose(true); fitter->SetPeakImage(peak_image); fitter->SetMaskImage(mask); fitter->SetTractograms(input_candidates); fitter->SetFitIndividualFibers(true); if (regu=="MSM") fitter->SetRegularization(VnlCostFunction::REGU::MSM); else if (regu=="Variance") fitter->SetRegularization(VnlCostFunction::REGU::VARIANCE); else if (regu=="Lasso") fitter->SetRegularization(VnlCostFunction::REGU::LASSO); else if (regu=="VoxelVariance") fitter->SetRegularization(VnlCostFunction::REGU::VOXEL_VARIANCE); else if (regu=="GroupLasso") fitter->SetRegularization(VnlCostFunction::REGU::GROUP_LASSO); else if (regu=="GroupVariance") fitter->SetRegularization(VnlCostFunction::REGU::GROUP_VARIANCE); else if (regu=="NONE") fitter->SetRegularization(VnlCostFunction::REGU::NONE); fitter->Update(); vnl_vector rms_diff = fitter->GetRmsDiffPerBundle(); -// vnl_vector log_rms_diff = rms_diff-rms_diff.min_value() + 1; -// log_rms_diff = log_rms_diff.apply(std::log); -// log_rms_diff /= log_rms_diff.max_value(); int c = 0; for (auto fib : input_candidates) { -// fib->SetFiberWeights( log_rms_diff[c] ); -// fib->ColorFibersByOrientation(); - std::string bundle_name = ist::GetFilenameWithoutExtension(candidate_tract_files.at(c)); std::streambuf *old = cout.rdbuf(); // <-- save std::stringstream ss; std::cout.rdbuf (ss.rdbuf()); // <-- redirect if (filter_zero_weights) fib = fib->FilterByWeights(0); mitk::IOUtil::Save(fib, out_folder + boost::lexical_cast((int)(100000*rms_diff[c])) + "_" + bundle_name + ".fib"); - float best_overlap = 0; - int best_overlap_index = -1; - int m_idx = 0; - for (auto ref_mask : reference_masks) - { - float overlap = fib->GetOverlap(ref_mask); - if (overlap>best_overlap) - { - best_overlap = overlap; - best_overlap_index = m_idx; - } - ++m_idx; - } - unsigned int num_voxels = 0; { itk::TractDensityImageFilter< ItkUcharImageType >::Pointer masks_filter = itk::TractDensityImageFilter< ItkUcharImageType >::New(); masks_filter->SetInputImage(mask); masks_filter->SetBinaryOutput(true); masks_filter->SetFiberBundle(fib); masks_filter->SetUseImageGeometry(true); masks_filter->Update(); num_voxels = masks_filter->GetNumCoveredVoxels(); } double weight_sum = 0; for (int i=0; iGetNumFibers(); i++) weight_sum += fib->GetFiberWeight(i); std::cout.rdbuf (old); // <-- restore - logfile << "RMS_DIFF: " << setprecision(5) << rms_diff[c] << " " << bundle_name << " " << num_voxels << " " << fib->GetNumFibers() << " " << weight_sum << "\n"; - if (best_overlap_index>=0) - logfile << "Best_overlap: " << setprecision(5) << best_overlap << " " << ist::GetFilenameWithoutExtension(anchor_mask_files.at(best_overlap_index)) << "\n"; - else - logfile << "No_overlap\n"; - + logfile << bundle_name << " " << setprecision(5) << rms_diff[c] << " " << num_voxels << " " << fib->GetNumFibers() << " " << weight_sum << "\n"; ++c; } mitk::FiberBundle::Pointer out_fib = mitk::FiberBundle::New(); out_fib = out_fib->AddBundles(input_candidates); out_fib->ColorFibersByFiberWeights(false, true); mitk::IOUtil::Save(out_fib, out_folder + "AllCandidates.fib"); peak_image = fitter->GetUnderexplainedImage(); peak_image_writer->SetInput(peak_image); peak_image_writer->SetFileName(out_folder + "Residual_AllCandidates.nii.gz"); peak_image_writer->Update(); } else { MITK_INFO << "RMSE: " << setprecision(5) << rmse; // fitter->SetPeakImage(peak_image); // Iteratively add candidate bundles in a greedy manner while (!input_candidates.empty()) { double next_rmse = rmse; - double num_peaks = 0; mitk::FiberBundle::Pointer best_candidate = nullptr; PeakImgType::Pointer best_candidate_peak_image = nullptr; for (int i=0; i<(int)input_candidates.size(); ++i) { // WHY NECESSARY AGAIN?? itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New(); fitter->SetLambda(lambda); fitter->SetFilterOutliers(filter_outliers); fitter->SetVerbose(false); fitter->SetPeakImage(peak_image); fitter->SetMaskImage(mask); // ****************************** fitter->SetTractograms({input_candidates.at(i)}); std::streambuf *old = cout.rdbuf(); // <-- save std::stringstream ss; std::cout.rdbuf (ss.rdbuf()); // <-- redirect fitter->Update(); std::cout.rdbuf (old); // <-- restore double candidate_rmse = fitter->GetRMSE(); if (candidate_rmseGetNumCoveredDirections(); best_candidate = fitter->GetTractograms().at(0); best_candidate_peak_image = fitter->GetUnderexplainedImage(); } } if (best_candidate.IsNull()) break; // fitter->SetPeakImage(peak_image); peak_image = best_candidate_peak_image; int i=0; std::vector< mitk::FiberBundle::Pointer > remaining_candidates; std::vector< std::string > remaining_candidate_files; for (auto fib : input_candidates) { if (fib!=best_candidate) { remaining_candidates.push_back(fib); remaining_candidate_files.push_back(candidate_tract_files.at(i)); } else name = ist::GetFilenameWithoutExtension(candidate_tract_files.at(i)); ++i; } input_candidates = remaining_candidates; candidate_tract_files = remaining_candidate_files; iteration++; std::streambuf *old = cout.rdbuf(); // <-- save std::stringstream ss; std::cout.rdbuf (ss.rdbuf()); // <-- redirect // Save winning candidate if (filter_zero_weights) best_candidate = best_candidate->FilterByWeights(0); mitk::IOUtil::Save(best_candidate, out_folder + boost::lexical_cast(iteration) + "_" + name + ".fib"); peak_image_writer->SetInput(peak_image); peak_image_writer->SetFileName(out_folder + boost::lexical_cast(iteration) + "_" + name + ".nrrd"); peak_image_writer->Update(); - // Calculate best overlap with reference masks for evaluation purposes - float best_overlap = 0; - int best_overlap_index = -1; - i = 0; - for (auto ref_mask : reference_masks) - { - float overlap = best_candidate->GetOverlap(ref_mask); - if (overlap>best_overlap) - { - best_overlap = overlap; - best_overlap_index = i; - } - ++i; - } std::cout.rdbuf (old); // <-- restore - logfile << "RMSE: " << setprecision(5) << rmse << " " << name << " " << num_peaks << "\n"; - if (best_overlap_index>=0) - logfile << "Best_overlap: " << setprecision(5) << best_overlap << " " << ist::GetFilenameWithoutExtension(anchor_mask_files.at(best_overlap_index)) << "\n"; - else - logfile << "No_overlap\n"; +// logfile << name << " " << setprecision(5) << score << " " << num_voxels << " " << fib->GetNumFibers() << " " << weight_sum << "\n"; } } clock.Stop(); int h = clock.GetTotal()/3600; int m = ((int)clock.GetTotal()%3600)/60; int s = (int)clock.GetTotal()%60; MITK_INFO << "Plausibility estimation took " << h << "h, " << m << "m and " << s << "s"; logfile.close(); } catch (itk::ExceptionObject e) { std::cout << e; return EXIT_FAILURE; } catch (std::exception e) { std::cout << e.what(); return EXIT_FAILURE; } catch (...) { std::cout << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt similarity index 78% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/CMakeLists.txt rename to Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt index fa6a696828..6f3e0156a2 100755 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/CMakeLists.txt +++ b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt @@ -1,43 +1,48 @@ 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^^MitkFiberTracking - TractometerMetrics^^MitkFiberTracking - MergeOverlappingTracts^^MitkFiberTracking - ExtractSimilarTracts^^MitkFiberTracking - AnchorConstrainedPlausibility^^MitkFiberTracking + PeaksAngularError^^ + TractometerMetrics^^ + MergeOverlappingTracts^^ + GetOverlappingTracts^^ + ExtractSimilarTracts^^ + AnchorConstrainedPlausibility^^ + CalculateOverlap^^ + CheckEpsAndOverlap^^ + ReferenceSimilarity^^ + TractDistance^^ # LocalDirectionalFiberPlausibility^^MitkFiberTracking # HAS TO USE NEW PEAK IMAGE FORMAT ) 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 MitkCore MitkDiffusionCore ${dependencies_list} - PACKAGE_DEPENDS ITK + DEPENDS MitkDiffusionCmdApps ${dependencies_list} + PACKAGE_DEPENDS ) endforeach() if(EXECUTABLE_IS_ENABLED) MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) endif() endif() diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CalculateOverlap.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CalculateOverlap.cpp new file mode 100755 index 0000000000..35bdf6a2ad --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CalculateOverlap.cpp @@ -0,0 +1,109 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +typedef itksys::SystemTools ist; +typedef itk::Image ItkFloatImgType; +typedef itk::Image ItkUIntImgType; + +/*! +\brief +*/ +int main(int argc, char* argv[]) +{ + mitkCommandLineParser parser; + + parser.setTitle("Calculate Overlap"); + parser.setCategory("Fiber Tracking Evaluation"); + parser.setDescription(""); + parser.setContributor("MIC"); + + parser.setArgumentPrefix("--", "-"); + parser.addArgument("tractogram", "", mitkCommandLineParser::InputFile, "", "", us::Any(), false); + parser.addArgument("mask", "", mitkCommandLineParser::InputFile, "", "", us::Any(), false); + parser.addArgument("peaks", "", mitkCommandLineParser::InputFile, "", "", us::Any()); + + std::map parsedArgs = parser.parseArguments(argc, argv); + if (parsedArgs.size()==0) + return EXIT_FAILURE; + + std::string input_tractogram = us::any_cast(parsedArgs["tractogram"]); + std::string mask_file = us::any_cast(parsedArgs["mask"]); + + try + { + mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load(input_tractogram); + mitk::Image::Pointer mask = mitk::IOUtil::Load(mask_file); + + ItkFloatImgType::Pointer itk_mask; + mitk::CastToItkImage(mask, itk_mask); + + mitk::PeakImage::ItkPeakImageType::Pointer peaks = nullptr; + if (parsedArgs.count("peaks")) + { + mitk::Image::Pointer mitk_peaks = mitk::IOUtil::Load(us::any_cast(parsedArgs["peaks"])); + + typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType; + CasterType::Pointer caster = CasterType::New(); + caster->SetInput(mitk_peaks); + caster->Update(); + peaks = caster->GetOutput(); + + float overlap = 0; + float directional_overlap = 0; + std::tie(directional_overlap, overlap) = fib->GetDirectionalOverlap(itk_mask, peaks); + MITK_INFO << "Overlap<<" << overlap; + MITK_INFO << "DirectionalOverlap<<" << directional_overlap; + } + else + MITK_INFO << "Overlap<<" << fib->GetOverlap(itk_mask); + } + catch (itk::ExceptionObject e) + { + std::cout << e; + return EXIT_FAILURE; + } + catch (std::exception e) + { + std::cout << e.what(); + return EXIT_FAILURE; + } + catch (...) + { + std::cout << "ERROR!?!"; + return EXIT_FAILURE; + } + return EXIT_SUCCESS; +} diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CheckEpsAndOverlap.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CheckEpsAndOverlap.cpp new file mode 100755 index 0000000000..8740233bf6 --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/CheckEpsAndOverlap.cpp @@ -0,0 +1,99 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +typedef itksys::SystemTools ist; +typedef itk::Image ItkUcharImgType; +typedef itk::Image ItkUIntImgType; + +/*! +\brief +*/ +int main(int argc, char* argv[]) +{ + mitkCommandLineParser parser; + + parser.setTitle("Calculate Overlap"); + parser.setCategory("Fiber Tracking Evaluation"); + parser.setDescription(""); + parser.setContributor("MIC"); + + parser.setArgumentPrefix("--", "-"); + parser.addArgument("tractogram", "", mitkCommandLineParser::InputFile, "", "", us::Any(), false); + parser.addArgument("overlap_image", "", mitkCommandLineParser::InputFile, "", "", us::Any(), false); + parser.addArgument("ep_image", "", mitkCommandLineParser::InputFile, "", "", us::Any(), false); + + std::map parsedArgs = parser.parseArguments(argc, argv); + if (parsedArgs.size()==0) + return EXIT_FAILURE; + + std::string input_tractogram = us::any_cast(parsedArgs["tractogram"]); + std::string mask_file = us::any_cast(parsedArgs["overlap_image"]); + std::string mask_file2 = us::any_cast(parsedArgs["ep_image"]); + + try + { + mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load(input_tractogram); + mitk::Image::Pointer mask = mitk::IOUtil::Load(mask_file); + mitk::Image::Pointer mask2 = mitk::IOUtil::Load(mask_file2); + + ItkUcharImgType::Pointer itk_mask; + mitk::CastToItkImage(mask, itk_mask); + + ItkUcharImgType::Pointer itk_mask2; + mitk::CastToItkImage(mask2, itk_mask2); + + float ol = fib->GetOverlap(itk_mask); + float ep = fib->GetNumEpFractionInMask(itk_mask2, true); + MITK_INFO << "Overlap<<" << ol; + MITK_INFO << "EP-Fraction<<" << ep; + } + catch (itk::ExceptionObject e) + { + std::cout << e; + return EXIT_FAILURE; + } + catch (std::exception e) + { + std::cout << e.what(); + return EXIT_FAILURE; + } + catch (...) + { + std::cout << "ERROR!?!"; + return EXIT_FAILURE; + } + return EXIT_SUCCESS; +} diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/ExtractSimilarTracts.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/ExtractSimilarTracts.cpp similarity index 75% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/ExtractSimilarTracts.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/ExtractSimilarTracts.cpp index 5cefcfc547..125265b2b3 100644 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/ExtractSimilarTracts.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/ExtractSimilarTracts.cpp @@ -1,237 +1,196 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include #include -#include +#include -typedef itksys::SystemTools ist; typedef itk::Image ItkFloatImgType; -mitk::FiberBundle::Pointer LoadFib(std::string filename) -{ - std::vector fibInfile = mitk::IOUtil::Load(filename); - if( fibInfile.empty() ) - std::cout << "File " << filename << " could not be read!"; - mitk::BaseData::Pointer baseData = fibInfile.at(0); - return dynamic_cast(baseData.GetPointer()); -} - -ItkFloatImgType::Pointer LoadItkImage(const std::string& filename) -{ - mitk::Image::Pointer img = mitk::IOUtil::Load(filename); - ItkFloatImgType::Pointer itkMask = ItkFloatImgType::New(); - mitk::CastToItkImage(img, itkMask); - return itkMask; -} - /*! \brief Spatially cluster fibers */ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Extract Similar Tracts"); parser.setCategory("Fiber Tracking Evaluation"); parser.setContributor("MIC"); parser.setArgumentPrefix("--", "-"); parser.addArgument("", "i", mitkCommandLineParser::InputFile, "Input:", "input fiber bundle (.fib, .trk, .tck)", us::Any(), false); parser.addArgument("ref_tracts", "", mitkCommandLineParser::StringList, "Ref. Tracts:", "reference tracts (.fib, .trk, .tck)", us::Any(), false); parser.addArgument("ref_masks", "", mitkCommandLineParser::StringList, "Ref. Masks:", "reference bundle masks", us::Any()); + parser.addArgument("", "o", mitkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false); parser.addArgument("distance", "", mitkCommandLineParser::Int, "Distance:", "", 10); parser.addArgument("metric", "", mitkCommandLineParser::String, "Metric:", "EU_MEAN (default), EU_STD, EU_MAX"); parser.addArgument("subsample", "", mitkCommandLineParser::Float, "Subsampling factor:", "Only use specified fraction of input fibers", 1.0); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; std::string in_fib = us::any_cast(parsedArgs["i"]); std::string out_root = us::any_cast(parsedArgs["o"]); mitkCommandLineParser::StringContainerType ref_bundle_files = us::any_cast(parsedArgs["ref_tracts"]); mitkCommandLineParser::StringContainerType ref_mask_files; if (parsedArgs.count("ref_masks")) ref_mask_files = us::any_cast(parsedArgs["ref_masks"]); if (ref_mask_files.size()>0 && ref_mask_files.size()!=ref_bundle_files.size()) { MITK_INFO << "If reference masks are used, there has to be one mask per reference tract."; return EXIT_FAILURE; } int distance = 10; if (parsedArgs.count("distance")) distance = us::any_cast(parsedArgs["distance"]); std::string metric = "EU_MEAN"; if (parsedArgs.count("metric")) metric = us::any_cast(parsedArgs["metric"]); float subsample = 1.0; if (parsedArgs.count("subsample")) subsample = us::any_cast(parsedArgs["subsample"]); try { - mitk::FiberBundle::Pointer fib = LoadFib(in_fib); + mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load(in_fib); std::srand(0); if (subsample<1.0) fib = fib->SubsampleFibers(subsample); mitk::FiberBundle::Pointer resampled_fib = fib->GetDeepCopy(); resampled_fib->ResampleToNumPoints(12); - std::vector< mitk::FiberBundle::Pointer > ref_fibs; - std::vector< ItkFloatImgType::Pointer > ref_masks; - for (std::size_t i=0; i(ref_mask_files); std::vector< float > distances; distances.push_back(distance); - mitk::FiberBundle::Pointer anchor_tractogram = mitk::FiberBundle::New(nullptr); + mitk::FiberBundle::Pointer extracted = mitk::FiberBundle::New(nullptr); unsigned int c = 0; for (auto ref_fib : ref_fibs) { MITK_INFO << "Extracting " << ist::GetFilenameName(ref_bundle_files.at(c)); std::streambuf *old = cout.rdbuf(); // <-- save std::stringstream ss; std::cout.rdbuf (ss.rdbuf()); // <-- redirect try { itk::TractClusteringFilter::Pointer segmenter = itk::TractClusteringFilter::New(); // calculate centroids from reference bundle { itk::TractClusteringFilter::Pointer clusterer = itk::TractClusteringFilter::New(); clusterer->SetDistances({10,20,30}); clusterer->SetTractogram(ref_fib); clusterer->SetMetrics({new mitk::ClusteringMetricEuclideanStd()}); clusterer->SetMergeDuplicateThreshold(0.0); clusterer->Update(); std::vector tracts = clusterer->GetOutCentroids(); ref_fib = mitk::FiberBundle::New(nullptr); ref_fib = ref_fib->AddBundles(tracts); mitk::IOUtil::Save(ref_fib, out_root + "centroids_" + ist::GetFilenameName(ref_bundle_files.at(c))); segmenter->SetInCentroids(ref_fib); } // segment tract segmenter->SetFilterMask(ref_masks.at(c)); segmenter->SetOverlapThreshold(0.8); segmenter->SetDistances(distances); segmenter->SetTractogram(resampled_fib); segmenter->SetMergeDuplicateThreshold(0.0); segmenter->SetDoResampling(false); if (metric=="EU_MEAN") segmenter->SetMetrics({new mitk::ClusteringMetricEuclideanMean()}); else if (metric=="EU_STD") segmenter->SetMetrics({new mitk::ClusteringMetricEuclideanStd()}); else if (metric=="EU_MAX") segmenter->SetMetrics({new mitk::ClusteringMetricEuclideanMax()}); segmenter->Update(); std::vector< std::vector< long > > clusters = segmenter->GetOutFiberIndices(); if (clusters.size()>0) { vtkSmartPointer weights = vtkSmartPointer::New(); mitk::FiberBundle::Pointer result = mitk::FiberBundle::New(nullptr); std::vector< mitk::FiberBundle::Pointer > result_fibs; for (unsigned int cluster_index=0; cluster_indexGeneratePolyDataByIds(clusters.at(cluster_index), weights))); result = result->AddBundles(result_fibs); - anchor_tractogram = anchor_tractogram->AddBundle(result); - mitk::IOUtil::Save(result, out_root + "anchor_" + ist::GetFilenameName(ref_bundle_files.at(c))); + extracted = extracted->AddBundle(result); + mitk::IOUtil::Save(result, out_root + "extracted_" + ist::GetFilenameName(ref_bundle_files.at(c))); fib = mitk::FiberBundle::New(fib->GeneratePolyDataByIds(clusters.back(), weights)); resampled_fib = mitk::FiberBundle::New(resampled_fib->GeneratePolyDataByIds(clusters.back(), weights)); } } catch(itk::ExceptionObject& excpt) { MITK_INFO << "Exception while processing " << ist::GetFilenameName(ref_bundle_files.at(c)); MITK_INFO << excpt.GetDescription(); } catch(std::exception& excpt) { MITK_INFO << "Exception while processing " << ist::GetFilenameName(ref_bundle_files.at(c)); MITK_INFO << excpt.what(); } std::cout.rdbuf (old); // <-- restore if (fib->GetNumFibers()==0) break; ++c; } - MITK_INFO << "Streamlines in anchor tractogram: " << anchor_tractogram->GetNumFibers(); - mitk::IOUtil::Save(anchor_tractogram, out_root + "anchor_tractogram.trk"); + MITK_INFO << "Extracted streamlines: " << extracted->GetNumFibers(); + mitk::IOUtil::Save(extracted, out_root + "extracted_streamlines.trk"); - MITK_INFO << "Streamlines remaining in candidate tractogram: " << fib->GetNumFibers(); - mitk::IOUtil::Save(fib, out_root + "candidate_tractogram.trk"); + MITK_INFO << "Residual streamlines: " << fib->GetNumFibers(); + mitk::IOUtil::Save(fib, out_root + "residual_streamlines.trk"); } catch (itk::ExceptionObject e) { std::cout << e; return EXIT_FAILURE; } catch (std::exception e) { std::cout << e.what(); return EXIT_FAILURE; } catch (...) { std::cout << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/GetOverlappingTracts.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/GetOverlappingTracts.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/FiberProcessing/GetOverlappingTracts.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/GetOverlappingTracts.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/LocalDirectionalFiberPlausibility.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/LocalDirectionalFiberPlausibility.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/LocalDirectionalFiberPlausibility.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/LocalDirectionalFiberPlausibility.cpp diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/MergeOverlappingTracts.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/MergeOverlappingTracts.cpp similarity index 81% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/MergeOverlappingTracts.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/MergeOverlappingTracts.cpp index 1147856404..f2b12676e4 100755 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/MergeOverlappingTracts.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/MergeOverlappingTracts.cpp @@ -1,250 +1,215 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include -#include -#include #include #include #include #include #include #include #include #include #include +#include -typedef itksys::SystemTools ist; typedef itk::Image ItkFloatImgType; typedef itk::Image ItkUIntImgType; -std::vector< std::string > get_file_list(const std::string& path, std::vector< std::string > extensions={".fib", ".trk"}) -{ - std::vector< std::string > file_list; - itk::Directory::Pointer dir = itk::Directory::New(); - - if (dir->Load(path.c_str())) - { - int n = dir->GetNumberOfFiles(); - for (int r = 0; r < n; r++) - { - const char *filename = dir->GetFile(r); - std::string ext = ist::GetFilenameExtension(filename); - for (auto e : extensions) - { - if (ext==e) - { - file_list.push_back(path + '/' + filename); - break; - } - } - } - } - return file_list; -} /*! \brief */ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Merge Overlapping Tracts"); parser.setCategory("Fiber Tracking Evaluation"); parser.setDescription(""); parser.setContributor("MIC"); parser.setArgumentPrefix("--", "-"); - parser.addArgument("in", "i", mitkCommandLineParser::InputFile, "Input Folder:", "input folder", us::Any(), false); - parser.addArgument("out", "o", mitkCommandLineParser::OutputDirectory, "Output Folder:", "output folder", us::Any(), false); + parser.addArgument("", "i", mitkCommandLineParser::InputFile, "Input Folder:", "input folder", us::Any(), false); + parser.addArgument("", "o", mitkCommandLineParser::OutputDirectory, "Output Folder:", "output folder", us::Any(), false); parser.addArgument("overlap", "", mitkCommandLineParser::Float, "Overlap threshold:", "Tracts with overlap larger than this threshold are merged", 0.8, false); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; - std::string input_folder = us::any_cast(parsedArgs["in"]); - std::string out_folder = us::any_cast(parsedArgs["out"]); + std::string input_folder = us::any_cast(parsedArgs["i"]); + std::string out_folder = us::any_cast(parsedArgs["o"]); float overlap = 0.8; if (parsedArgs.count("overlap")) overlap = us::any_cast(parsedArgs["overlap"]); try { if (!ist::PathExists(out_folder)) ist::MakeDirectory(out_folder); - std::vector< std::string > fib_files = get_file_list(input_folder, {".fib", ".trk", ".tck"}); - if (fib_files.empty()) - return EXIT_FAILURE; + std::vector< mitk::FiberBundle::Pointer > fibs = mitk::DiffusionDataIOHelper::load_fibs({input_folder}); + std::streambuf *old = cout.rdbuf(); // <-- save std::stringstream ss; std::cout.rdbuf (ss.rdbuf()); // <-- redirect - std::vector< mitk::FiberBundle::Pointer > fibs; - for (std::string f : fib_files) - { - mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load(f); - fibs.push_back(fib); - } - mitk::FiberBundle::Pointer combined = mitk::FiberBundle::New(); combined = combined->AddBundles(fibs); itk::TractsToFiberEndingsImageFilter< ItkFloatImgType >::Pointer endings = itk::TractsToFiberEndingsImageFilter< ItkFloatImgType >::New(); endings->SetFiberBundle(combined); endings->SetUpsamplingFactor(0.25); endings->Update(); ItkFloatImgType::Pointer ref_image = endings->GetOutput(); std::cout.rdbuf (old); // <-- restore for (int its = 0; its<3; its++) { std::streambuf *old = cout.rdbuf(); // <-- save std::stringstream ss; std::cout.rdbuf (ss.rdbuf()); // <-- redirect std::vector< ItkFloatImgType::Pointer > mask_images; for (auto fib : fibs) { itk::TractDensityImageFilter< ItkFloatImgType >::Pointer masks = itk::TractDensityImageFilter< ItkFloatImgType >::New(); masks->SetInputImage(ref_image); masks->SetBinaryOutput(true); masks->SetFiberBundle(fib); masks->SetUseImageGeometry(true); masks->Update(); mask_images.push_back(masks->GetOutput()); } int r=0; vnl_matrix< int > mat; mat.set_size(mask_images.size(), mask_images.size()); mat.fill(0); for (auto m1 : mask_images) { float max_overlap = overlap; int c = 0; for (auto m2 : mask_images) { if (c<=r) { ++c; continue; } itk::ImageRegionConstIterator it1(m1, m1->GetLargestPossibleRegion()); itk::ImageRegionConstIterator it2(m2, m2->GetLargestPossibleRegion()); unsigned int c1 = 0; unsigned int c2 = 0; unsigned int intersect = 0; while( !it1.IsAtEnd() ) { if( it1.Get()>0 && it2.Get()>0) ++intersect; if(it1.Get()>0) ++c1; if(it2.Get()>0) ++c2; ++it1; ++it2; } if ( (float)intersect/c1>max_overlap ) { max_overlap = (float)intersect/c1; mat.put(r,c, 1); } if ( (float)intersect/c2>max_overlap ) { max_overlap = (float)intersect/c2; mat.put(r,c, 1); } ++c; } ++r; } std::vector< mitk::FiberBundle::Pointer > out_fibs; std::vector< bool > used; for (unsigned int i=0; i0) { fib = fib->AddBundle(fibs.at(c)); - MITK_INFO << c; used[c] = true; } } out_fibs.push_back(fib); } std::cout.rdbuf (old); // <-- restore MITK_INFO << fibs.size() << " --> " << out_fibs.size(); if (fibs.size()==out_fibs.size()) break; fibs = out_fibs; } int c = 0; for (auto fib : fibs) { std::streambuf *old = cout.rdbuf(); // <-- save std::stringstream ss; std::cout.rdbuf (ss.rdbuf()); // <-- redirect mitk::IOUtil::Save(fib, out_folder + "/bundle_" + boost::lexical_cast(c) + ".trk"); std::cout.rdbuf (old); // <-- restore ++c; } } catch (itk::ExceptionObject e) { std::cout << e; return EXIT_FAILURE; } catch (std::exception e) { std::cout << e.what(); return EXIT_FAILURE; } catch (...) { std::cout << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/PeaksAngularError.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/PeaksAngularError.cpp similarity index 100% rename from Modules/DiffusionImaging/FiberTracking/cmdapps/TractographyEvaluation/PeaksAngularError.cpp rename to Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/PeaksAngularError.cpp diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/ReferenceSimilarity.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/ReferenceSimilarity.cpp new file mode 100644 index 0000000000..28f376323b --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCmdApps/TractographyEvaluation/ReferenceSimilarity.cpp @@ -0,0 +1,149 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +typedef itk::Image< unsigned char, 3 > ItkUcharImageType; +typedef itk::Image< float, 4 > ItkPeakImgType; + +int main(int argc, char* argv[]) +{ + mitkCommandLineParser parser; + + parser.setTitle("Reference Similarity"); + parser.setCategory("Fiber Tracking Evaluation"); + parser.setContributor("MIC"); + + parser.setArgumentPrefix("--", "-"); + parser.addArgument("", "i", mitkCommandLineParser::StringList, "Input Tracts:", "input tracts folder", us::Any(), false); + parser.addArgument("reference_tracts", "", mitkCommandLineParser::StringList, "", "", us::Any(), false); + parser.addArgument("reference_masks", "", mitkCommandLineParser::StringList, "", "", us::Any(), false); + parser.addArgument("reference_peaks", "", mitkCommandLineParser::StringList, "", "", us::Any(), false); + + parser.addArgument("", "o", mitkCommandLineParser::String, "", "", us::Any(), false); + + parser.addArgument("fiber_points", "", mitkCommandLineParser::Int, "Fiber points:", "", 20); + + std::map parsedArgs = parser.parseArguments(argc, argv); + if (parsedArgs.size()==0) + return EXIT_FAILURE; + + std::string out_folder = us::any_cast(parsedArgs["o"]); + mitkCommandLineParser::StringContainerType input_tract_files = us::any_cast(parsedArgs["i"]); + mitkCommandLineParser::StringContainerType reference_tract_files = us::any_cast(parsedArgs["reference_tracts"]); + mitkCommandLineParser::StringContainerType reference_mask_files = us::any_cast(parsedArgs["reference_masks"]); + mitkCommandLineParser::StringContainerType reference_peak_files = us::any_cast(parsedArgs["reference_peaks"]); + + int fiber_points = 20; + if (parsedArgs.count("fiber_points")) + fiber_points = us::any_cast(parsedArgs["fiber_points"]); + + try + { + std::vector input_tract_names; + std::vector ref_tract_names; + std::vector< mitk::FiberBundle::Pointer > input_tracts = mitk::DiffusionDataIOHelper::load_fibs(input_tract_files, &input_tract_names); + std::vector< mitk::FiberBundle::Pointer > reference_tracts = mitk::DiffusionDataIOHelper::load_fibs(reference_tract_files, &ref_tract_names); + std::vector< ItkUcharImageType::Pointer > reference_masks = mitk::DiffusionDataIOHelper::load_itk_images(reference_mask_files); + std::vector< ItkPeakImgType::Pointer > reference_peaks = mitk::DiffusionDataIOHelper::load_itk_images(reference_peak_files); + + MITK_INFO << "Calculating distances"; + itk::TractDistanceFilter::Pointer distance_calculator = itk::TractDistanceFilter::New(); + distance_calculator->SetNumPoints(fiber_points); + distance_calculator->SetTracts1(input_tracts); + distance_calculator->SetTracts2(reference_tracts); + distance_calculator->SetMetrics({new mitk::ClusteringMetricEuclideanMean()}); + distance_calculator->Update(); + auto distances = distance_calculator->GetAllDistances(); + + vnl_matrix voxel_overlap; voxel_overlap.set_size(input_tracts.size(), reference_tracts.size()); + vnl_matrix dir_overlap; dir_overlap.set_size(input_tracts.size(), reference_tracts.size()); + + MITK_INFO << "Calculating overlap"; + boost::progress_display disp(input_tracts.size()*reference_tracts.size()); + int r=0; + for (auto fib : input_tracts) + { + int c=0; + for (auto ref_mask : reference_masks) + { + ++disp; + std::streambuf *old = cout.rdbuf(); // <-- save + std::stringstream ss; + std::cout.rdbuf (ss.rdbuf()); // <-- redirect + float overlap = 0; + float directional_overlap = 0; + std::tie(directional_overlap, overlap) = fib->GetDirectionalOverlap(ref_mask, reference_peaks.at(c)); + voxel_overlap[r][c] = overlap; + dir_overlap[r][c] = directional_overlap; + std::cout.rdbuf (old); // <-- restore + ++c; + } + ++r; + } + + ofstream logfile; + logfile.open(out_folder + "ref_tract_names.txt"); + for (unsigned int i=0; i +#include +#include +#include +#include +#include +#include +#include +#include + + +int main(int argc, char* argv[]) +{ + mitkCommandLineParser parser; + + parser.setTitle("Tract Distance"); + parser.setCategory("Fiber Processing"); + parser.setContributor("MIC"); + + parser.setArgumentPrefix("--", "-"); + parser.addArgument("", "i1", mitkCommandLineParser::String, "Input Folder 1:", "input tracts folder 1", us::Any(), false); + parser.addArgument("", "i2", mitkCommandLineParser::String, "Input Folder 2:", "input tracts folder 2", us::Any(), false); + parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output logfile", us::Any(), false); + + parser.addArgument("fiber_points", "", mitkCommandLineParser::Int, "Fiber points:", "", 12); + parser.addArgument("metrics", "", mitkCommandLineParser::StringList, "Metrics:", "EU_MEAN (default), EU_STD, EU_MAX"); + parser.addArgument("metric_weights", "", mitkCommandLineParser::StringList, "Metric weights:", "add one float weight for each used metric"); + + std::map parsedArgs = parser.parseArguments(argc, argv); + if (parsedArgs.size()==0) + return EXIT_FAILURE; + + std::string t1_folder = us::any_cast(parsedArgs["i1"]); + std::string t2_folder = us::any_cast(parsedArgs["i2"]); + std::string out_file = us::any_cast(parsedArgs["o"]); + + int fiber_points = 12; + if (parsedArgs.count("fiber_points")) + fiber_points = us::any_cast(parsedArgs["fiber_points"]); + + std::vector< std::string > metric_strings = {"EU_MEAN"}; + if (parsedArgs.count("metrics")) + metric_strings = us::any_cast(parsedArgs["metrics"]); + + std::vector< std::string > metric_weights = {"1.0"}; + if (parsedArgs.count("metric_weights")) + metric_weights = us::any_cast(parsedArgs["metric_weights"]); + + if (metric_strings.size()!=metric_weights.size()) + { + MITK_INFO << "Each metric needs an associated metric weight!"; + return EXIT_FAILURE; + } + + try + { + std::vector t1_files; + std::vector< mitk::FiberBundle::Pointer > tractograms1 = mitk::DiffusionDataIOHelper::load_fibs({t1_folder}, &t1_files); + std::vector t2_files; + std::vector< mitk::FiberBundle::Pointer > tractograms2 = mitk::DiffusionDataIOHelper::load_fibs({t2_folder}, &t2_files); + + MITK_INFO << "Loaded " << tractograms1.size() << " source tractograms."; + MITK_INFO << "Loaded " << tractograms2.size() << " target tractograms."; + + itk::TractDistanceFilter::Pointer distance_calculator = itk::TractDistanceFilter::New(); + distance_calculator->SetNumPoints(fiber_points); + distance_calculator->SetTracts1(tractograms1); + distance_calculator->SetTracts2(tractograms2); + + std::vector< mitk::ClusteringMetric* > metrics; + int mc = 0; + for (auto m : metric_strings) + { + float w = boost::lexical_cast(metric_weights.at(mc)); + MITK_INFO << "Metric: " << m << " (w=" << w << ")"; + if (m=="EU_MEAN") + metrics.push_back({new mitk::ClusteringMetricEuclideanMean()}); + else if (m=="EU_STD") + metrics.push_back({new mitk::ClusteringMetricEuclideanStd()}); + else if (m=="EU_MAX") + metrics.push_back({new mitk::ClusteringMetricEuclideanMax()}); + metrics.back()->SetScale(w); + mc++; + } + + if (metrics.empty()) + { + MITK_INFO << "No metric selected!"; + return EXIT_FAILURE; + } + + distance_calculator->SetMetrics(metrics); + distance_calculator->Update(); + MITK_INFO << "Distances:"; + auto distances = distance_calculator->GetMinDistances(); + auto indices = distance_calculator->GetMinIndices(); + + ofstream logfile; + logfile.open (out_file); + for (unsigned int i=0; i mitk::DiffusionDataIOHelper::get_file_list(const std::string& path, const std::vector extensions) +{ + std::vector< std::string > file_list; + itk::Directory::Pointer dir = itk::Directory::New(); + + if (dir->Load(path.c_str())) + { + int n = dir->GetNumberOfFiles(); + for (int r = 0; r < n; r++) + { + const char *filename = dir->GetFile(r); + std::string ext = ist::GetFilenameExtension(filename); + for (auto e : extensions) + { + if (ext==e) + { + file_list.push_back(path + '/' + filename); + break; + } + } + } + } + std::sort(file_list.begin(), file_list.end()); + return file_list; +} + +std::vector< mitk::FiberBundle::Pointer > mitk::DiffusionDataIOHelper::load_fibs(const std::vector files, std::vector* filenames) +{ + std::streambuf *old = cout.rdbuf(); // <-- save + std::stringstream ss; + std::cout.rdbuf (ss.rdbuf()); // <-- redirect + std::vector< mitk::FiberBundle::Pointer > out; + for (auto f : files) + { + if (itksys::SystemTools::PathExists(f)) + { + if (!f.empty() && f.back() != '/') + f += "/"; + + auto list = get_file_list(f, {".fib",".trk",".tck"}); + for (auto file : list) + { + mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load(file); + out.push_back(fib); + if (filenames!=nullptr) + filenames->push_back(file); + } + } + else if (itksys::SystemTools::FileExists(f)) + { + mitk::FiberBundle::Pointer fib = mitk::IOUtil::Load(f); + out.push_back(fib); + if (filenames!=nullptr) + filenames->push_back(f); + } + } + std::cout.rdbuf (old); // <-- restore + MITK_INFO << "Loaded " << out.size() << " tractograms"; + return out; +} diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/mitkDiffusionDataIOHelper.h b/Modules/DiffusionImaging/DiffusionCmdApps/mitkDiffusionDataIOHelper.h new file mode 100644 index 0000000000..4923527fc4 --- /dev/null +++ b/Modules/DiffusionImaging/DiffusionCmdApps/mitkDiffusionDataIOHelper.h @@ -0,0 +1,116 @@ +/*=================================================================== + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center, +Division of Medical and Biological Informatics. +All rights reserved. + +This software is distributed WITHOUT ANY WARRANTY; without +even the implied warranty of MERCHANTABILITY or FITNESS FOR +A PARTICULAR PURPOSE. + +See LICENSE.txt or http://www.mitk.org for details. + +===================================================================*/ + +#ifndef __mitkDiffusionDataIOHelper_h_ +#define __mitkDiffusionDataIOHelper_h_ + +#include +#include +#include +#include +#include +#include + +#include +#include +#include + +typedef itksys::SystemTools ist; + +namespace mitk{ + +class MITKDIFFUSIONCMDAPPS_EXPORT DiffusionDataIOHelper +{ +public: + + static std::vector< std::string > get_file_list(const std::string& path, const std::vector< std::string > extensions={".fib", ".trk"}); + + static std::vector< mitk::FiberBundle::Pointer > load_fibs(const std::vector files, std::vector* filenames=nullptr); + + template< class TYPE > + static typename TYPE::Pointer load_itk_image(const std::string file) + { + if (file.compare("")!=0 && itksys::SystemTools::FileExists(file)) + { + mitk::Image::Pointer image = mitk::IOUtil::Load(file); + + typedef mitk::ImageToItk< TYPE > CasterType; + typename CasterType::Pointer caster = CasterType::New(); + caster->SetInput(image); + caster->Update(); + typename TYPE::Pointer itk_image = caster->GetOutput(); + return itk_image; + } + return nullptr; + } + + template< class TYPE > + static std::vector< typename TYPE::Pointer > load_itk_images(const std::vector files, std::vector* filenames=nullptr) + { + std::streambuf *old = cout.rdbuf(); // <-- save + std::stringstream ss; + std::cout.rdbuf (ss.rdbuf()); // <-- redirect + std::vector< typename TYPE::Pointer > out; + for (auto f : files) + { + if (itksys::SystemTools::PathExists(f)) + { + if (!f.empty() && f.back() != '/') + f += "/"; + + auto list = get_file_list(f, {".nrrd",".nii.gz",".nii"}); + for (auto file : list) + { + mitk::Image::Pointer image = mitk::IOUtil::Load(file); + + typedef mitk::ImageToItk< TYPE > CasterType; + typename CasterType::Pointer caster = CasterType::New(); + caster->SetInput(image); + caster->Update(); + typename TYPE::Pointer itk_image = caster->GetOutput(); + + out.push_back(itk_image); + if (filenames!=nullptr) + filenames->push_back(file); + } + } + else if (itksys::SystemTools::FileExists(f)) + { + mitk::Image::Pointer image = mitk::IOUtil::Load(f); + + typedef mitk::ImageToItk< TYPE > CasterType; + typename CasterType::Pointer caster = CasterType::New(); + caster->SetInput(image); + caster->Update(); + typename TYPE::Pointer itk_image = caster->GetOutput(); + + out.push_back(itk_image); + if (filenames!=nullptr) + filenames->push_back(f); + } + } + + std::cout.rdbuf (old); // <-- restore + MITK_INFO << "Loaded " << out.size() << " images"; + return out; + } + +}; + +} + +#endif //__mitkDiffusionDataIOHelper_h_ + diff --git a/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt index 1b9cedf87a..c2b6ac476b 100644 --- a/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt +++ b/Modules/DiffusionImaging/DiffusionCore/CMakeLists.txt @@ -1,26 +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-DTI INCLUDE_DIRS include/ include/Algorithms include/Algorithms/Reconstruction include/Algorithms/Registration include/Algorithms/Reconstruction/MultishellProcessing include/Algorithms/Reconstruction/FittingFunctions include/DicomImport include/IODataStructures/DiffusionWeightedImages include/IODataStructures/Properties include/IODataStructures/OdfImages include/IODataStructures/TensorImages include/IODataStructures include/Rendering ${CMAKE_CURRENT_BINARY_DIR} DEPENDS MitkMapperExt MitkPlanarFigure MitkImageExtraction MitkSceneSerializationBase MitkDICOMReader MitkMatchPointRegistration PACKAGE_DEPENDS PUBLIC ITK|ITKTestKernel+ITKRegistrationCommon+ITKMetricsv4+ITKRegistrationMethodsv4+ITKDistanceMap+ITKLabelVoting+ITKVTK PUBLIC VTK|vtkFiltersProgrammable ) if(MSVC) mitkFunctionCheckCAndCXXCompilerFlags("/wd4005" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) endif() add_subdirectory(Testing) -add_subdirectory(cmdapps) add_subdirectory(autoload/IO) if(MITK_USE_Python) MITK_INSTALL(FILES PythonRequirements.txt) -add_subdirectory(cmdapps_python) endif() diff --git a/Modules/DiffusionImaging/DiffusionCore/cmdapps/CMakeLists.txt b/Modules/DiffusionImaging/DiffusionCore/cmdapps/CMakeLists.txt deleted file mode 100644 index 19e45bfb5f..0000000000 --- a/Modules/DiffusionImaging/DiffusionCore/cmdapps/CMakeLists.txt +++ /dev/null @@ -1,44 +0,0 @@ -option(BUILD_DiffusionCoreCmdApps "Build commandline tools for diffusion" OFF) - -if(BUILD_DiffusionCoreCmdApps 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( diffusioncorecmdapps - ImageResampler^^ - CopyGeometry^^ - Registration^^ - DiffusionDICOMLoader^^ - ResampleGradients^^ - ShToOdfImage^^ - DImp^^ - DReg^^ - HeadMotionCorrection^^ - DmriDenoising^^ - RoundBvalues^^ - ) - - foreach(diffusioncorecmdapp ${diffusioncorecmdapps}) - # extract cmd app name and dependencies - string(REPLACE "^^" "\\;" cmdapp_info ${diffusioncorecmdapp}) - 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 MitkCore MitkDiffusionCore MitkImageDenoising ${dependencies_list} - PACKAGE_DEPENDS ITK - ) - endforeach() - -endif() diff --git a/Modules/DiffusionImaging/DiffusionCore/include/mitkDiffusionFunctionCollection.h b/Modules/DiffusionImaging/DiffusionCore/include/mitkDiffusionFunctionCollection.h index 4ded475b7c..22261eac41 100644 --- a/Modules/DiffusionImaging/DiffusionCore/include/mitkDiffusionFunctionCollection.h +++ b/Modules/DiffusionImaging/DiffusionCore/include/mitkDiffusionFunctionCollection.h @@ -1,126 +1,135 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __mitkDiffusionFunctionCollection_h_ #define __mitkDiffusionFunctionCollection_h_ #include #include #include #include #include #include #include #include namespace mitk{ class MITKDIFFUSIONCORE_EXPORT imv { public: - static std::vector< std::pair< itk::Index<3>, double > > IntersectImage(itk::Vector& spacing, itk::Index<3>& si, itk::Index<3>& ei, itk::ContinuousIndex& sf, itk::ContinuousIndex& ef); + static std::vector< std::pair< itk::Index<3>, double > > IntersectImage(const itk::Vector& spacing, itk::Index<3>& si, itk::Index<3>& ei, itk::ContinuousIndex& sf, itk::ContinuousIndex& ef); + + static itk::Point GetItkPoint(double point[3]) + { + itk::Point itkPoint; + itkPoint[0] = point[0]; + itkPoint[1] = point[1]; + itkPoint[2] = point[2]; + return itkPoint; + } template< class TPixelType, class TOutPixelType=TPixelType > static TOutPixelType GetImageValue(const itk::Point& itkP, bool interpolate, typename itk::LinearInterpolateImageFunction< itk::Image< TPixelType, 3 >, float >::Pointer interpolator) { if (interpolator==nullptr) return 0.0; itk::ContinuousIndex< float, 3> cIdx; interpolator->ConvertPointToContinuousIndex(itkP, cIdx); if (interpolator->IsInsideBuffer(cIdx)) { if (interpolate) return interpolator->EvaluateAtContinuousIndex(cIdx); else { itk::Index<3> idx; interpolator->ConvertContinuousIndexToNearestIndex(cIdx, idx); return interpolator->EvaluateAtIndex(idx); } } else return 0.0; } template< class TPixelType=unsigned char > static bool IsInsideMask(const itk::Point& itkP, bool interpolate, typename itk::LinearInterpolateImageFunction< itk::Image< TPixelType, 3 >, float >::Pointer interpolator, float threshold=0.5) { if (interpolator==nullptr) return false; itk::ContinuousIndex< float, 3> cIdx; interpolator->ConvertPointToContinuousIndex(itkP, cIdx); if (interpolator->IsInsideBuffer(cIdx)) { double value = 0.0; if (interpolate) value = interpolator->EvaluateAtContinuousIndex(cIdx); else { itk::Index<3> idx; interpolator->ConvertContinuousIndexToNearestIndex(cIdx, idx); value = interpolator->EvaluateAtIndex(idx); } if (value>=threshold) return true; } return false; } }; class MITKDIFFUSIONCORE_EXPORT sh { public: static double factorial(int number); static void Cart2Sph(double x, double y, double z, double* spherical); static double legendre0(int l); static double spherical_harmonic(int m,int l,double theta,double phi, bool complexPart); static double Yj(int m, int k, float theta, float phi, bool mrtrix=true); static vnl_matrix CalcShBasisForDirections(int sh_order, vnl_matrix U, bool mrtrix=true); }; class MITKDIFFUSIONCORE_EXPORT gradients { private: typedef std::vector IndiciesVector; typedef mitk::BValueMapProperty::BValueMap BValueMap; typedef DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType; typedef DiffusionPropertyHelper::GradientDirectionType GradientDirectionType; public: static GradientDirectionContainerType::Pointer ReadBvalsBvecs(std::string bvals_file, std::string bvecs_file, double& reference_bval); static void WriteBvalsBvecs(std::string bvals_file, std::string bvecs_file, GradientDirectionContainerType::Pointer gradients, double reference_bval); static std::vector GetAllUniqueDirections(const BValueMap &bValueMap, GradientDirectionContainerType *refGradientsContainer ); static bool CheckForDifferingShellDirections(const BValueMap &bValueMap, GradientDirectionContainerType::ConstPointer refGradientsContainer); static vnl_matrix ComputeSphericalHarmonicsBasis(const vnl_matrix & QBallReference, const unsigned int & LOrder); static vnl_matrix ComputeSphericalFromCartesian(const IndiciesVector & refShell, const GradientDirectionContainerType * refGradientsContainer); static GradientDirectionContainerType::Pointer CreateNormalizedUniqueGradientDirectionContainer(const BValueMap &bValueMap, const GradientDirectionContainerType * origninalGradentcontainer); }; } #endif //__mitkDiffusionFunctionCollection_h_ diff --git a/Modules/DiffusionImaging/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp b/Modules/DiffusionImaging/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp index cf2f32da62..db526ca271 100644 --- a/Modules/DiffusionImaging/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp +++ b/Modules/DiffusionImaging/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp @@ -1,508 +1,508 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkDiffusionFunctionCollection.h" #include "mitkNumericTypes.h" #include #include #include #include #include "itkVectorContainer.h" #include "vnl/vnl_vector.h" #include #include #include #include // Intersect a finite line (with end points p0 and p1) with all of the // cells of a vtkImageData -std::vector< std::pair< itk::Index<3>, double > > mitk::imv::IntersectImage(itk::Vector& spacing, itk::Index<3>& si, itk::Index<3>& ei, itk::ContinuousIndex& sf, itk::ContinuousIndex& ef) +std::vector< std::pair< itk::Index<3>, double > > mitk::imv::IntersectImage(const itk::Vector& spacing, itk::Index<3>& si, itk::Index<3>& ei, itk::ContinuousIndex& sf, itk::ContinuousIndex& ef) { std::vector< std::pair< itk::Index<3>, double > > out; if (si == ei) { double d[3]; for (int i=0; i<3; ++i) d[i] = (sf[i]-ef[i])*spacing[i]; double len = std::sqrt( d[0]*d[0] + d[1]*d[1] + d[2]*d[2] ); out.push_back( std::pair< itk::Index<3>, double >(si, len) ); return out; } double bounds[6]; double entrancePoint[3]; double exitPoint[3]; double startPoint[3]; double endPoint[3]; double t0, t1; for (int i=0; i<3; ++i) { startPoint[i] = sf[i]; endPoint[i] = ef[i]; if (si[i]>ei[i]) { int t = si[i]; si[i] = ei[i]; ei[i] = t; } } for (int x = si[0]; x<=ei[0]; ++x) for (int y = si[1]; y<=ei[1]; ++y) for (int z = si[2]; z<=ei[2]; ++z) { bounds[0] = (double)x - 0.5; bounds[1] = (double)x + 0.5; bounds[2] = (double)y - 0.5; bounds[3] = (double)y + 0.5; bounds[4] = (double)z - 0.5; bounds[5] = (double)z + 0.5; int entryPlane; int exitPlane; int hit = vtkBox::IntersectWithLine(bounds, startPoint, endPoint, t0, t1, entrancePoint, exitPoint, entryPlane, exitPlane); if (hit) { if (entryPlane>=0 && exitPlane>=0) { double d[3]; for (int i=0; i<3; ++i) d[i] = (exitPoint[i] - entrancePoint[i])*spacing[i]; double len = std::sqrt( d[0]*d[0] + d[1]*d[1] + d[2]*d[2] ); itk::Index<3> idx; idx[0] = x; idx[1] = y; idx[2] = z; out.push_back( std::pair< itk::Index<3>, double >(idx, len) ); } else if (entryPlane>=0) { double d[3]; for (int i=0; i<3; ++i) d[i] = (ef[i] - entrancePoint[i])*spacing[i]; double len = std::sqrt( d[0]*d[0] + d[1]*d[1] + d[2]*d[2] ); itk::Index<3> idx; idx[0] = x; idx[1] = y; idx[2] = z; out.push_back( std::pair< itk::Index<3>, double >(idx, len) ); } else if (exitPlane>=0) { double d[3]; for (int i=0; i<3; ++i) d[i] = (exitPoint[i]-sf[i])*spacing[i]; double len = std::sqrt( d[0]*d[0] + d[1]*d[1] + d[2]*d[2] ); itk::Index<3> idx; idx[0] = x; idx[1] = y; idx[2] = z; out.push_back( std::pair< itk::Index<3>, double >(idx, len) ); } } } return out; } //------------------------- SH-function ------------------------------------ double mitk::sh::factorial(int number) { if(number <= 1) return 1; double result = 1.0; for(int i=1; i<=number; i++) result *= i; return result; } void mitk::sh::Cart2Sph(double x, double y, double z, double *spherical) { double phi, th, rad; rad = sqrt(x*x+y*y+z*z); if( rad < mitk::eps ) { th = itk::Math::pi/2; phi = itk::Math::pi/2; } else { th = acos(z/rad); phi = atan2(y, x); } spherical[0] = phi; spherical[1] = th; spherical[2] = rad; } double mitk::sh::legendre0(int l) { if( l%2 != 0 ) { return 0; } else { double prod1 = 1.0; for(int i=1;i(l,abs(m),-cos(theta)); double mag = sqrt((double)(2*l+1)/(4.0*itk::Math::pi)*::boost::math::factorial(l-abs(m))/::boost::math::factorial(l+abs(m)))*plm; if (m>0) return mag*cos(m*phi); else if (m==0) return mag; else return mag*sin(-m*phi); } return 0; } vnl_matrix mitk::sh::CalcShBasisForDirections(int sh_order, vnl_matrix U, bool mrtrix) { vnl_matrix sh_basis = vnl_matrix(U.cols(), (sh_order*sh_order + sh_order + 2)/2 + sh_order ); for(unsigned int i=0; i bvec_entries; if (!itksys::SystemTools::FileExists(bvecs_file)) mitkThrow() << "bvecs file not existing: " << bvecs_file; else { std::string line; std::ifstream myfile (bvecs_file.c_str()); if (myfile.is_open()) { while (std::getline(myfile, line)) { std::vector strs; boost::split(strs,line,boost::is_any_of("\t \n")); for (auto token : strs) { if (!token.empty()) { try { bvec_entries.push_back(boost::lexical_cast(token)); } catch(...) { mitkThrow() << "Encountered invalid bvecs file entry >" << token << "<"; } } } } myfile.close(); } else { mitkThrow() << "bvecs file could not be opened: " << bvals_file; } } reference_bval = -1; std::vector bval_entries; if (!itksys::SystemTools::FileExists(bvals_file)) mitkThrow() << "bvals file not existing: " << bvals_file; else { std::string line; std::ifstream myfile (bvals_file.c_str()); if (myfile.is_open()) { while (std::getline(myfile, line)) { std::vector strs; boost::split(strs,line,boost::is_any_of("\t \n")); for (auto token : strs) { if (!token.empty()) { try { bval_entries.push_back(boost::lexical_cast(token)); if (bval_entries.back()>reference_bval) reference_bval = bval_entries.back(); } catch(...) { mitkThrow() << "Encountered invalid bvals file entry >" << token << "<"; } } } } myfile.close(); } else { mitkThrow() << "bvals file could not be opened: " << bvals_file; } } for(unsigned int i=0; i 0) { vec.normalize(); vec[0] = sqrt(factor)*vec[0]; vec[1] = sqrt(factor)*vec[1]; vec[2] = sqrt(factor)*vec[2]; } directioncontainer->InsertElement(i,vec); } return directioncontainer; } void mitk::gradients::WriteBvalsBvecs(std::string bvals_file, std::string bvecs_file, GradientDirectionContainerType::Pointer gradients, double reference_bval) { std::ofstream myfile; myfile.open (bvals_file.c_str()); for(unsigned int i=0; iSize(); i++) { double twonorm = gradients->ElementAt(i).two_norm(); myfile << std::round(reference_bval*twonorm*twonorm) << " "; } myfile.close(); std::ofstream myfile2; myfile2.open (bvecs_file.c_str()); for(int j=0; j<3; j++) { for(unsigned int i=0; iSize(); i++) { GradientDirectionType direction = gradients->ElementAt(i); direction.normalize(); myfile2 << direction.get(j) << " "; } myfile2 << std::endl; } } std::vector mitk::gradients::GetAllUniqueDirections(const BValueMap & refBValueMap, GradientDirectionContainerType *refGradientsContainer ) { IndiciesVector directioncontainer; auto mapIterator = refBValueMap.begin(); if(refBValueMap.find(0) != refBValueMap.end() && refBValueMap.size() > 1) mapIterator++; //skip bzero Values for( ; mapIterator != refBValueMap.end(); mapIterator++){ IndiciesVector currentShell = mapIterator->second; while(currentShell.size()>0) { unsigned int wntIndex = currentShell.back(); currentShell.pop_back(); auto containerIt = directioncontainer.begin(); bool directionExist = false; while(containerIt != directioncontainer.end()) { if (fabs(dot_product(refGradientsContainer->ElementAt(*containerIt), refGradientsContainer->ElementAt(wntIndex))) > 0.9998) { directionExist = true; break; } containerIt++; } if(!directionExist) { directioncontainer.push_back(wntIndex); } } } return directioncontainer; } bool mitk::gradients::CheckForDifferingShellDirections(const BValueMap & refBValueMap, GradientDirectionContainerType::ConstPointer refGradientsContainer) { auto mapIterator = refBValueMap.begin(); if(refBValueMap.find(0) != refBValueMap.end() && refBValueMap.size() > 1) mapIterator++; //skip bzero Values for( ; mapIterator != refBValueMap.end(); mapIterator++){ auto mapIterator_2 = refBValueMap.begin(); if(refBValueMap.find(0) != refBValueMap.end() && refBValueMap.size() > 1) mapIterator_2++; //skip bzero Values for( ; mapIterator_2 != refBValueMap.end(); mapIterator_2++){ if(mapIterator_2 == mapIterator) continue; IndiciesVector currentShell = mapIterator->second; IndiciesVector testShell = mapIterator_2->second; for (unsigned int i = 0; i< currentShell.size(); i++) if (fabs(dot_product(refGradientsContainer->ElementAt(currentShell[i]), refGradientsContainer->ElementAt(testShell[i]))) <= 0.9998) { return true; } } } return false; } vnl_matrix mitk::gradients::ComputeSphericalFromCartesian(const IndiciesVector & refShell, const GradientDirectionContainerType * refGradientsContainer) { vnl_matrix Q(3, refShell.size()); Q.fill(0.0); for(unsigned int i = 0; i < refShell.size(); i++) { GradientDirectionType dir = refGradientsContainer->ElementAt(refShell[i]); double x = dir.normalize().get(0); double y = dir.normalize().get(1); double z = dir.normalize().get(2); double cart[3]; mitk::sh::Cart2Sph(x,y,z,cart); Q(0,i) = cart[0]; Q(1,i) = cart[1]; Q(2,i) = cart[2]; } return Q; } vnl_matrix mitk::gradients::ComputeSphericalHarmonicsBasis(const vnl_matrix & QBallReference, const unsigned int & LOrder) { vnl_matrix SHBasisOutput(QBallReference.cols(), (LOrder+1)*(LOrder+2)*0.5); SHBasisOutput.fill(0.0); for(int i=0; i< (int)SHBasisOutput.rows(); i++) for(int k = 0; k <= (int)LOrder; k += 2) for(int m =- k; m <= k; m++) { int j = ( k * k + k + 2 ) / 2.0 + m - 1; double phi = QBallReference(0,i); double th = QBallReference(1,i); double val = mitk::sh::Yj(m,k,th,phi); SHBasisOutput(i,j) = val; } return SHBasisOutput; } mitk::gradients::GradientDirectionContainerType::Pointer mitk::gradients::CreateNormalizedUniqueGradientDirectionContainer(const mitk::gradients::BValueMap & bValueMap, const GradientDirectionContainerType *origninalGradentcontainer) { mitk::gradients::GradientDirectionContainerType::Pointer directioncontainer = mitk::gradients::GradientDirectionContainerType::New(); auto mapIterator = bValueMap.begin(); if(bValueMap.find(0) != bValueMap.end() && bValueMap.size() > 1){ mapIterator++; //skip bzero Values vnl_vector_fixed vec; vec.fill(0.0); directioncontainer->push_back(vec); } for( ; mapIterator != bValueMap.end(); mapIterator++){ IndiciesVector currentShell = mapIterator->second; while(currentShell.size()>0) { unsigned int wntIndex = currentShell.back(); currentShell.pop_back(); mitk::gradients::GradientDirectionContainerType::Iterator containerIt = directioncontainer->Begin(); bool directionExist = false; while(containerIt != directioncontainer->End()) { if (fabs(dot_product(containerIt.Value(), origninalGradentcontainer->ElementAt(wntIndex))) > 0.9998) { directionExist = true; break; } containerIt++; } if(!directionExist) { GradientDirectionType dir(origninalGradentcontainer->ElementAt(wntIndex)); directioncontainer->push_back(dir.normalize()); } } } return directioncontainer; } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.cpp index dc28e08540..18bb94c24b 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.cpp @@ -1,446 +1,504 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __itkFiberExtractionFilter_cpp #define __itkFiberExtractionFilter_cpp #include "itkFiberExtractionFilter.h" #define _USE_MATH_DEFINES #include #include #include #include namespace itk{ template< class PixelType > FiberExtractionFilter< PixelType >::FiberExtractionFilter() : m_DontResampleFibers(false) , m_Mode(MODE::OVERLAP) , m_InputType(INPUT::SCALAR_MAP) , m_BothEnds(true) , m_OverlapFraction(0.8) , m_NoNegatives(false) , m_NoPositives(false) , m_Interpolate(false) , m_Threshold(0.5) - , m_Labels({1}) + , m_Labels() , m_SkipSelfConnections(false) , m_OnlySelfConnections(false) + , m_SplitByRoi(false) , m_SplitLabels(false) , m_MinFibersPerTract(0) , m_PairedStartEndLabels(false) { m_Interpolator = itk::LinearInterpolateImageFunction< itk::Image< PixelType, 3 >, float >::New(); } template< class PixelType > FiberExtractionFilter< PixelType >::~FiberExtractionFilter() { } template< class PixelType > void FiberExtractionFilter< PixelType >::SetRoiImages(const std::vector &rois) { for (auto roi : rois) { if (roi==nullptr) { MITK_INFO << "ROI image is NULL!"; return; } } m_RoiImages = rois; } template< class PixelType > void FiberExtractionFilter< PixelType >::SetRoiImageNames(const std::vector< std::string > roi_names) { m_RoiImageNames = roi_names; } template< class PixelType > mitk::FiberBundle::Pointer FiberExtractionFilter< PixelType >::CreateFib(std::vector< long >& ids) { vtkSmartPointer weights = vtkSmartPointer::New(); vtkSmartPointer pTmp = m_InputFiberBundle->GeneratePolyDataByIds(ids, weights); mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(pTmp); fib->SetFiberWeights(weights); return fib; } template< class PixelType > bool FiberExtractionFilter< PixelType >::IsPositive(const itk::Point& itkP) { if( m_InputType == INPUT::SCALAR_MAP ) return mitk::imv::IsInsideMask(itkP, m_Interpolate, m_Interpolator, m_Threshold); else if( m_InputType == INPUT::LABEL_MAP ) { auto val = mitk::imv::GetImageValue(itkP, m_Interpolate, m_Interpolator); for (auto l : m_Labels) if (l==val) return true; } else mitkThrow() << "No valid input type selected!"; return false; } template< class PixelType > std::vector< std::string > FiberExtractionFilter< PixelType >::GetPositiveLabels() const { return m_PositiveLabels; } template< class PixelType > void FiberExtractionFilter< PixelType >::ExtractOverlap(mitk::FiberBundle::Pointer fib) { MITK_INFO << "Extracting fibers (min. overlap " << m_OverlapFraction << ")"; vtkSmartPointer polydata = fib->GetFiberPolyData(); - std::vector< std::vector< long > > positive_ids; + std::vector< std::vector< long > > positive_ids; // one ID vector per ROI positive_ids.resize(m_RoiImages.size()); std::vector< long > negative_ids; // fibers not overlapping with ANY mask boost::progress_display disp(m_InputFiberBundle->GetNumFibers()); for (int i=0; iGetNumFibers(); i++) { ++disp; vtkCell* cell = polydata->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); - bool positive = false; + float best_ol = 0; + int best_ol_idx = -1; for (unsigned int m=0; mSetInputImage(roi); - int inside = 0; - int outside = 0; - for (int j=0; jGetPoint(j); - - itk::Point itkP; - itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; - - if ( IsPositive(itkP) ) - inside++; - else - outside++; - - if ((float)inside/numPoints > m_OverlapFraction) + itk::Point startVertex = mitk::imv::GetItkPoint(points->GetPoint(j)); + itk::Index<3> startIndex; + itk::ContinuousIndex startIndexCont; + roi->TransformPhysicalPointToIndex(startVertex, startIndex); + roi->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont); + + itk::Point endVertex = mitk::imv::GetItkPoint(points->GetPoint(j + 1)); + itk::Index<3> endIndex; + itk::ContinuousIndex endIndexCont; + roi->TransformPhysicalPointToIndex(endVertex, endIndex); + roi->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont); + + std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(roi->GetSpacing(), startIndex, endIndex, startIndexCont, endIndexCont); + for (std::pair< itk::Index<3>, double > segment : segments) { - positive = true; - positive_ids[m].push_back(i); - break; + if (!roi->GetLargestPossibleRegion().IsInside(segment.first)) + continue; + if (roi->GetPixel(segment.first)>=m_Threshold) + inside += segment.second; + else + outside += segment.second; } } + + float overlap = (float)inside/(inside+outside); + if (overlap > best_ol && overlap >= m_OverlapFraction) + { + best_ol_idx = m; + best_ol = overlap; + } } - if (!positive) + if (best_ol_idx<0) negative_ids.push_back(i); + else + positive_ids.at(best_ol_idx).push_back(i); } if (!m_NoNegatives) m_Negatives.push_back(CreateFib(negative_ids)); if (!m_NoPositives) - for (auto ids : positive_ids) - if (ids.size()>=m_MinFibersPerTract) - m_Positives.push_back(CreateFib(ids)); + { + for (unsigned int i=0; i(i); + + if (positive_ids.at(i).size()>=m_MinFibersPerTract) + { + m_Positives.push_back(CreateFib(positive_ids.at(i))); + m_PositiveLabels.push_back(name); + } + } + if (!m_SplitByRoi) + { + mitk::FiberBundle::Pointer output = mitk::FiberBundle::New(nullptr); + output = output->AddBundles(m_Positives); + m_Positives.clear(); + m_Positives.push_back(output); + m_PositiveLabels.clear(); + m_PositiveLabels.push_back(""); + } + } } template< class PixelType > void FiberExtractionFilter< PixelType >::ExtractEndpoints(mitk::FiberBundle::Pointer fib) { MITK_INFO << "Extracting fibers (endpoints in mask)"; vtkSmartPointer polydata = fib->GetFiberPolyData(); - std::vector< std::vector< long > > positive_ids; + std::vector< std::vector< long > > positive_ids; // one ID vector per ROI positive_ids.resize(m_RoiImages.size()); std::vector< long > negative_ids; // fibers not overlapping with ANY mask boost::progress_display disp(m_InputFiberBundle->GetNumFibers()); for (int i=0; iGetNumFibers(); i++) { ++disp; vtkCell* cell = polydata->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); bool positive = false; if (numPoints>1) for (unsigned int m=0; mSetInputImage(roi); int inside = 0; // check first fiber point { double* p = points->GetPoint(0); itk::Point itkP; itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; if ( IsPositive(itkP) ) inside++; } // check second fiber point { double* p = points->GetPoint(numPoints-1); itk::Point itkP; itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; if ( IsPositive(itkP) ) inside++; } if (inside==2 || (inside==1 && !m_BothEnds)) { positive = true; positive_ids[m].push_back(i); } } if (!positive) negative_ids.push_back(i); } if (!m_NoNegatives) m_Negatives.push_back(CreateFib(negative_ids)); if (!m_NoPositives) - for (auto ids : positive_ids) - if (ids.size()>=m_MinFibersPerTract) - m_Positives.push_back(CreateFib(ids)); + { + for (unsigned int i=0; i(i); + + if (positive_ids.at(i).size()>=m_MinFibersPerTract) + { + m_Positives.push_back(CreateFib(positive_ids.at(i))); + m_PositiveLabels.push_back(name); + } + } + if (!m_SplitByRoi) + { + mitk::FiberBundle::Pointer output = mitk::FiberBundle::New(nullptr); + output = output->AddBundles(m_Positives); + m_Positives.clear(); + m_Positives.push_back(output); + m_PositiveLabels.clear(); + m_PositiveLabels.push_back(""); + } + } } template< class PixelType > void FiberExtractionFilter< PixelType >::ExtractLabels(mitk::FiberBundle::Pointer fib) { MITK_INFO << "Extracting fibers by labels"; vtkSmartPointer polydata = fib->GetFiberPolyData(); - std::vector< std::map< std::string, std::vector< long > > > positive_ids; - positive_ids.resize(m_RoiImages.size()); + std::map< std::string, std::vector< long > > positive_ids; std::vector< long > negative_ids; // fibers not overlapping with ANY label boost::progress_display disp(m_InputFiberBundle->GetNumFibers()); for (int i=0; iGetNumFibers(); i++) { ++disp; vtkCell* cell = polydata->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); bool positive = false; if (numPoints>1) for (unsigned int m=0; mSetInputImage(roi); int inside = 0; double* p1 = points->GetPoint(0); itk::Point itkP1; itkP1[0] = p1[0]; itkP1[1] = p1[1]; itkP1[2] = p1[2]; short label1 = mitk::imv::GetImageValue(itkP1, m_Interpolate, m_Interpolator); double* p2 = points->GetPoint(numPoints-1); itk::Point itkP2; itkP2[0] = p2[0]; itkP2[1] = p2[1]; itkP2[2] = p2[2]; short label2 = mitk::imv::GetImageValue(itkP2, m_Interpolate, m_Interpolator); if (!m_Labels.empty()) // extract fibers from all pairwise label combinations { for (auto l : m_Labels) { if (l==label1) inside++; if (l==label2) inside++; if (inside==2) break; } } - else // extract fibers between start and end labels + else if (!m_StartLabels.empty() || !m_EndLabels.empty()) // extract fibers between start and end labels { - m_BothEnds = true; // if we have start and end labels it does not make sense to not use both endpoints + if (!m_StartLabels.empty() && !m_EndLabels.empty()) + m_BothEnds = true; // if we have start and end labels it does not make sense to not use both endpoints if (m_PairedStartEndLabels) { if (m_StartLabels.size()!=m_EndLabels.size()) mitkThrow() << "Start and end label lists must have same size if paired labels are used"; for (unsigned int ii=0; ii(label1) + "-" + boost::lexical_cast(label2); - else - key = boost::lexical_cast(label2) + "-" + boost::lexical_cast(label1); - if (m(label1) + "-" + boost::lexical_cast(label2); + else + key = boost::lexical_cast(label2) + "-" + boost::lexical_cast(label1); + } + + if (m_SplitByRoi) + { + if (m(m) + "_" + key; + } if (m_BothEnds) { if ( (inside==2 && (!m_SkipSelfConnections || label1!=label2)) || (inside==2 && m_OnlySelfConnections && label1==label2) ) { positive = true; - if ( positive_ids[m].count(key)==0 ) - positive_ids[m].insert( std::pair< std::string, std::vector< long > >( key, {i}) ); + if ( positive_ids.count(key)==0 ) + positive_ids.insert( std::pair< std::string, std::vector< long > >( key, {i}) ); else - positive_ids[m][key].push_back(i); + positive_ids[key].push_back(i); } } else { if ( (inside>=1 && (!m_SkipSelfConnections || label1!=label2)) || (inside==2 && m_OnlySelfConnections && label1==label2) ) { positive = true; - if ( positive_ids[m].count(key)==0 ) - positive_ids[m].insert( std::pair< std::string, std::vector< long > >( key, {i}) ); + if ( positive_ids.count(key)==0 ) + positive_ids.insert( std::pair< std::string, std::vector< long > >( key, {i}) ); else - positive_ids[m][key].push_back(i); + positive_ids[key].push_back(i); } } } if (!positive) negative_ids.push_back(i); } if (!m_NoNegatives) m_Negatives.push_back(CreateFib(negative_ids)); if (!m_NoPositives) { - for (auto labels : positive_ids) - for (auto tuple : labels) + for (auto label : positive_ids) + { + if (label.second.size()>=m_MinFibersPerTract) { - if (tuple.second.size()>=m_MinFibersPerTract) - { - m_Positives.push_back(CreateFib(tuple.second)); - m_PositiveLabels.push_back(tuple.first); - } + m_Positives.push_back(CreateFib(label.second)); + m_PositiveLabels.push_back(label.first); } - if (!m_SplitLabels) - { - mitk::FiberBundle::Pointer output = mitk::FiberBundle::New(nullptr); - output = output->AddBundles(m_Positives); - m_Positives.clear(); - m_Positives.push_back(output); - m_PositiveLabels.clear(); } } } template< class PixelType > void FiberExtractionFilter< PixelType >::SetLabels(const std::vector &Labels) { m_Labels = Labels; } template< class PixelType > void FiberExtractionFilter< PixelType >::SetStartLabels(const std::vector &Labels) { m_StartLabels = Labels; } template< class PixelType > void FiberExtractionFilter< PixelType >::SetEndLabels(const std::vector &Labels) { m_EndLabels = Labels; } template< class PixelType > std::vector FiberExtractionFilter< PixelType >::GetNegatives() const { return m_Negatives; } template< class PixelType > std::vector FiberExtractionFilter< PixelType >::GetPositives() const { return m_Positives; } template< class PixelType > void FiberExtractionFilter< PixelType >::GenerateData() { mitk::FiberBundle::Pointer fib = m_InputFiberBundle; if (fib->GetNumFibers()<=0) { MITK_INFO << "No fibers in tractogram!"; return; } - if (m_Mode==MODE::OVERLAP && !m_DontResampleFibers) - { - float minSpacing = 1; - for (auto mask : m_RoiImages) - { - for (int i=0; i<3; ++i) - if(mask->GetSpacing()[i]GetSpacing()[i]; - } - - fib = m_InputFiberBundle->GetDeepCopy(); - fib->ResampleLinear(minSpacing/5); - } - if (m_Mode == MODE::OVERLAP) ExtractOverlap(fib); else if (m_Mode == MODE::ENDPOINTS) { if (m_InputType==INPUT::LABEL_MAP) ExtractLabels(fib); else ExtractEndpoints(fib); } } } #endif // __itkFiberExtractionFilter_cpp diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.h index 24d2f1bbf2..da31262217 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFiberExtractionFilter.h @@ -1,131 +1,133 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef itkFiberExtractionFilter_h #define itkFiberExtractionFilter_h // MITK #include // ITK #include #include namespace itk{ /** * \brief Extract streamlines from tractograms using ROI images */ template< class PixelType > class FiberExtractionFilter : public ProcessObject { public: enum MODE { OVERLAP, ENDPOINTS }; enum INPUT { SCALAR_MAP, ///< In this case, positive means roi image vlaue > threshold LABEL_MAP ///< In this case, positive means roi image value in labels vector }; typedef FiberExtractionFilter Self; typedef ProcessObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef itk::Image< PixelType , 3> ItkInputImgType; itkFactorylessNewMacro(Self) itkCloneMacro(Self) itkTypeMacro( FiberExtractionFilter, ProcessObject ) void Update() override{ this->GenerateData(); } itkSetMacro( InputFiberBundle, mitk::FiberBundle::Pointer ) itkSetMacro( Mode, MODE ) ///< Overlap or endpoints itkSetMacro( InputType, INPUT ) ///< Scalar map or label image itkSetMacro( BothEnds, bool ) ///< Both streamline ends need to be inside of the ROI for the streamline to be considered positive itkSetMacro( OverlapFraction, float ) ///< Necessary fraction of streamline points inside the ROI for the streamline to be considered positive itkSetMacro( DontResampleFibers, bool ) ///< Don't resample input fibers to ensure coverage itkSetMacro( NoNegatives, bool ) ///< Don't create output tractograms from negative streamlines (save the computation) itkSetMacro( NoPositives, bool ) ///< Don't create output tractograms from positive streamlines (save the computation) - itkSetMacro( Interpolate, bool ) ///< Interpolate input ROI image + itkSetMacro( Interpolate, bool ) ///< Interpolate input ROI image (only relevant for ENDPOINTS mode itkSetMacro( Threshold, float ) ///< Threshold on input ROI image value to determine positives/negatives itkSetMacro( SkipSelfConnections, bool ) ///< Ignore streamlines between two identical labels itkSetMacro( OnlySelfConnections, bool ) ///< Only keep streamlines between two identical labels itkSetMacro( SplitLabels, bool ) ///< Output a separate tractogram for each label-->label tract + itkSetMacro( SplitByRoi, bool ) ///< Output a separate tractogram for each ROI image itkSetMacro( MinFibersPerTract, unsigned int ) ///< Discard positives with less fibers itkSetMacro( PairedStartEndLabels, bool ) void SetRoiImages(const std::vector< ItkInputImgType* > &rois); void SetRoiImageNames(const std::vector< std::string > roi_names); void SetLabels(const std::vector &Labels); void SetStartLabels(const std::vector &Labels); void SetEndLabels(const std::vector &Labels); std::vector GetPositives() const; ///< Get positive tracts (filtered by the input ROIs) std::vector GetNegatives() const; ///< Get negative tracts (not filtered by the ROIs) std::vector< std::string > GetPositiveLabels() const; ///< In case of label extraction, this vector contains the labels corresponding to the positive tracts protected: void GenerateData() override; FiberExtractionFilter(); ~FiberExtractionFilter() override; mitk::FiberBundle::Pointer CreateFib(std::vector< long >& ids); void ExtractOverlap(mitk::FiberBundle::Pointer fib); void ExtractEndpoints(mitk::FiberBundle::Pointer fib); void ExtractLabels(mitk::FiberBundle::Pointer fib); bool IsPositive(const itk::Point& itkP); mitk::FiberBundle::Pointer m_InputFiberBundle; std::vector< mitk::FiberBundle::Pointer > m_Positives; std::vector< mitk::FiberBundle::Pointer > m_Negatives; std::vector< ItkInputImgType* > m_RoiImages; std::vector< std::string > m_RoiImageNames; bool m_DontResampleFibers; MODE m_Mode; INPUT m_InputType; bool m_BothEnds; float m_OverlapFraction; bool m_NoNegatives; bool m_NoPositives; bool m_Interpolate; float m_Threshold; std::vector< unsigned short > m_Labels; bool m_SkipSelfConnections; bool m_OnlySelfConnections; + bool m_SplitByRoi; bool m_SplitLabels; unsigned int m_MinFibersPerTract; std::vector< unsigned short > m_StartLabels; std::vector< unsigned short > m_EndLabels; bool m_PairedStartEndLabels; std::vector< std::string > m_PositiveLabels; typename itk::LinearInterpolateImageFunction< itk::Image< PixelType, 3 >, float >::Pointer m_Interpolator; }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkFiberExtractionFilter.cpp" #endif #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.cpp index 3c7f599a2d..cc815686fe 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFitFibersToImageFilter.cpp @@ -1,997 +1,993 @@ #include "itkFitFibersToImageFilter.h" #include #include namespace itk{ FitFibersToImageFilter::FitFibersToImageFilter() : m_PeakImage(nullptr) , m_DiffImage(nullptr) , m_ScalarImage(nullptr) , m_MaskImage(nullptr) , m_FitIndividualFibers(true) , m_GradientTolerance(1e-5) , m_Lambda(0.1) , m_MaxIterations(20) , m_Coverage(0) , m_Overshoot(0) , m_RMSE(0.0) , m_FilterOutliers(false) , m_MeanWeight(1.0) , m_MedianWeight(1.0) , m_MinWeight(1.0) , m_MaxWeight(1.0) , m_Verbose(true) , m_NumUnknowns(0) , m_NumResiduals(0) , m_NumCoveredDirections(0) , m_SignalModel(nullptr) , sz_x(0) , sz_y(0) , sz_z(0) , m_MeanTractDensity(0) , m_MeanSignal(0) , fiber_count(0) , m_Regularization(VnlCostFunction::REGU::VOXEL_VARIANCE) { this->SetNumberOfRequiredOutputs(3); } FitFibersToImageFilter::~FitFibersToImageFilter() { } itk::Point FitFibersToImageFilter::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } void FitFibersToImageFilter::CreateDiffSystem() { sz_x = m_DiffImage->GetLargestPossibleRegion().GetSize(0); sz_y = m_DiffImage->GetLargestPossibleRegion().GetSize(1); sz_z = m_DiffImage->GetLargestPossibleRegion().GetSize(2); dim_four_size = m_DiffImage->GetVectorLength(); int num_voxels = sz_x*sz_y*sz_z; auto spacing = m_DiffImage->GetSpacing(); m_NumResiduals = num_voxels * dim_four_size; MITK_INFO << "Num. unknowns: " << m_NumUnknowns; MITK_INFO << "Num. residuals: " << m_NumResiduals; MITK_INFO << "Creating system ..."; A.set_size(m_NumResiduals, m_NumUnknowns); b.set_size(m_NumResiduals); b.fill(0.0); m_MeanTractDensity = 0; m_MeanSignal = 0; m_NumCoveredDirections = 0; fiber_count = 0; vnl_vector voxel_indicator; voxel_indicator.set_size(sz_x*sz_y*sz_z); voxel_indicator.fill(0); int numFibers = 0; for (unsigned int bundle=0; bundleGetNumFibers(); boost::progress_display disp(numFibers); m_GroupSizes.clear(); for (unsigned int bundle=0; bundle polydata = m_Tractograms.at(bundle)->GetFiberPolyData(); m_GroupSizes.push_back(m_Tractograms.at(bundle)->GetNumFibers()); for (int i=0; iGetNumFibers(); ++i) { ++disp; vtkCell* cell = polydata->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) MITK_INFO << "FIBER WITH ONLY ONE POINT ENCOUNTERED!"; for (int j=0; jGetPoint(j)); itk::Index<3> startIndex; itk::ContinuousIndex startIndexCont; m_DiffImage->TransformPhysicalPointToIndex(startVertex, startIndex); m_DiffImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont); PointType3 endVertex = GetItkPoint(points->GetPoint(j+1)); itk::Index<3> endIndex; itk::ContinuousIndex endIndexCont; m_DiffImage->TransformPhysicalPointToIndex(endVertex, endIndex); m_DiffImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont); mitk::DiffusionSignalModel<>::GradientType fiber_dir; fiber_dir[0] = endVertex[0]-startVertex[0]; fiber_dir[1] = endVertex[1]-startVertex[1]; fiber_dir[2] = endVertex[2]-startVertex[2]; fiber_dir.Normalize(); std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont); for (std::pair< itk::Index<3>, double > seg : segments) { if (!m_DiffImage->GetLargestPossibleRegion().IsInside(seg.first) || (m_MaskImage.IsNotNull() && m_MaskImage->GetPixel(seg.first)==0)) continue; int x = seg.first[0]; int y = seg.first[1]; int z = seg.first[2]; mitk::DiffusionSignalModel<>::PixelType simulated_pixel = m_SignalModel->SimulateMeasurement(fiber_dir)*seg.second; VectorImgType::PixelType measured_pixel = m_DiffImage->GetPixel(seg.first); double simulated_mean = 0; double measured_mean = 0; int num_nonzero_g = 0; for (int g=0; gGetGradientDirection(g).GetNorm()GetLargestPossibleRegion().GetSize(0); sz_y = m_PeakImage->GetLargestPossibleRegion().GetSize(1); sz_z = m_PeakImage->GetLargestPossibleRegion().GetSize(2); dim_four_size = m_PeakImage->GetLargestPossibleRegion().GetSize(3)/3 + 1; // +1 for zero - peak int num_voxels = sz_x*sz_y*sz_z; itk::Vector< double, 3 > spacing; spacing[0] = m_PeakImage->GetSpacing()[0]; spacing[1] = m_PeakImage->GetSpacing()[1]; spacing[2] = m_PeakImage->GetSpacing()[2]; PointType3 origin; origin[0] = m_PeakImage->GetOrigin()[0]; origin[1] = m_PeakImage->GetOrigin()[1]; origin[2] = m_PeakImage->GetOrigin()[2]; UcharImgType::RegionType::SizeType size; size[0] = m_PeakImage->GetLargestPossibleRegion().GetSize()[0]; size[1] = m_PeakImage->GetLargestPossibleRegion().GetSize()[1]; size[2] = m_PeakImage->GetLargestPossibleRegion().GetSize()[2]; UcharImgType::RegionType imageRegion; imageRegion.SetSize(size); itk::Matrix direction; for (int r=0; r<3; r++) for (int c=0; c<3; c++) direction[r][c] = m_PeakImage->GetDirection()[r][c]; if (m_MaskImage.IsNull()) { m_MaskImage = UcharImgType::New(); m_MaskImage->SetSpacing( spacing ); m_MaskImage->SetOrigin( origin ); m_MaskImage->SetDirection( direction ); m_MaskImage->SetRegions( imageRegion ); m_MaskImage->Allocate(); m_MaskImage->FillBuffer(1); } m_NumResiduals = num_voxels * dim_four_size; MITK_INFO << "Num. unknowns: " << m_NumUnknowns; MITK_INFO << "Num. residuals: " << m_NumResiduals; MITK_INFO << "Creating system ..."; A.set_size(m_NumResiduals, m_NumUnknowns); b.set_size(m_NumResiduals); b.fill(0.0); m_MeanTractDensity = 0; m_MeanSignal = 0; m_NumCoveredDirections = 0; fiber_count = 0; m_GroupSizes.clear(); int numFibers = 0; for (unsigned int bundle=0; bundleGetNumFibers(); boost::progress_display disp(numFibers); for (unsigned int bundle=0; bundle polydata = m_Tractograms.at(bundle)->GetFiberPolyData(); m_GroupSizes.push_back(m_Tractograms.at(bundle)->GetNumFibers()); for (int i=0; iGetNumFibers(); ++i) { ++disp; vtkCell* cell = polydata->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) MITK_INFO << "FIBER WITH ONLY ONE POINT ENCOUNTERED!"; for (int j=0; jGetPoint(j)); itk::Index<3> startIndex; itk::ContinuousIndex startIndexCont; m_MaskImage->TransformPhysicalPointToIndex(startVertex, startIndex); m_MaskImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont); PointType3 endVertex = GetItkPoint(points->GetPoint(j+1)); itk::Index<3> endIndex; itk::ContinuousIndex endIndexCont; m_MaskImage->TransformPhysicalPointToIndex(endVertex, endIndex); m_MaskImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont); vnl_vector_fixed fiber_dir; fiber_dir[0] = endVertex[0]-startVertex[0]; fiber_dir[1] = endVertex[1]-startVertex[1]; fiber_dir[2] = endVertex[2]-startVertex[2]; fiber_dir.normalize(); std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont); for (std::pair< itk::Index<3>, double > seg : segments) { if (!m_MaskImage->GetLargestPossibleRegion().IsInside(seg.first) || m_MaskImage->GetPixel(seg.first)==0) continue; itk::Index<4> idx4; idx4[0]=seg.first[0]; idx4[1]=seg.first[1]; idx4[2]=seg.first[2]; idx4[3]=0; double w = 1; int peak_id = dim_four_size-1; double peak_mag = 0; GetClosestPeak(idx4, m_PeakImage, fiber_dir, peak_id, w, peak_mag); w *= seg.second; int x = idx4[0]; int y = idx4[1]; int z = idx4[2]; unsigned int linear_index = x + sz_x*y + sz_x*sz_y*z + sz_x*sz_y*sz_z*peak_id; if (b[linear_index] == 0 && peak_idGetLargestPossibleRegion().GetSize(0); sz_y = m_ScalarImage->GetLargestPossibleRegion().GetSize(1); sz_z = m_ScalarImage->GetLargestPossibleRegion().GetSize(2); int num_voxels = sz_x*sz_y*sz_z; auto spacing = m_ScalarImage->GetSpacing(); m_NumResiduals = num_voxels; MITK_INFO << "Num. unknowns: " << m_NumUnknowns; MITK_INFO << "Num. residuals: " << m_NumResiduals; MITK_INFO << "Creating system ..."; A.set_size(m_NumResiduals, m_NumUnknowns); b.set_size(m_NumResiduals); b.fill(0.0); m_MeanTractDensity = 0; m_MeanSignal = 0; int numCoveredVoxels = 0; fiber_count = 0; int numFibers = 0; for (unsigned int bundle=0; bundleGetNumFibers(); boost::progress_display disp(numFibers); m_GroupSizes.clear(); for (unsigned int bundle=0; bundle polydata = m_Tractograms.at(bundle)->GetFiberPolyData(); m_GroupSizes.push_back(m_Tractograms.at(bundle)->GetNumFibers()); for (int i=0; iGetNumFibers(); ++i) { ++disp; vtkCell* cell = polydata->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; jGetPoint(j)); itk::Index<3> startIndex; itk::ContinuousIndex startIndexCont; m_ScalarImage->TransformPhysicalPointToIndex(startVertex, startIndex); m_ScalarImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont); PointType3 endVertex = GetItkPoint(points->GetPoint(j+1)); itk::Index<3> endIndex; itk::ContinuousIndex endIndexCont; m_ScalarImage->TransformPhysicalPointToIndex(endVertex, endIndex); m_ScalarImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont); std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont); for (std::pair< itk::Index<3>, double > seg : segments) { if (!m_ScalarImage->GetLargestPossibleRegion().IsInside(seg.first) || (m_MaskImage.IsNotNull() && m_MaskImage->GetPixel(seg.first)==0)) continue; float image_value = m_ScalarImage->GetPixel(seg.first); int x = seg.first[0]; int y = seg.first[1]; int z = seg.first[2]; unsigned int linear_index = x + sz_x*y + sz_x*sz_y*z; if (b[linear_index] == 0) { numCoveredVoxels++; m_MeanSignal += image_value; } m_MeanTractDensity += seg.second; if (m_FitIndividualFibers) { b[linear_index] = image_value; A.put(linear_index, fiber_count, A.get(linear_index, fiber_count) + seg.second); } else { b[linear_index] = image_value; A.put(linear_index, bundle, A.get(linear_index, bundle) + seg.second); } } } ++fiber_count; } } m_MeanTractDensity /= (numCoveredVoxels*fiber_count); m_MeanSignal /= numCoveredVoxels; A /= m_MeanTractDensity; b *= 100.0/m_MeanSignal; // times 100 because we want to avoid too small values for computational reasons // NEW FIT // m_MeanTractDensity /= numCoveredVoxels; // m_MeanSignal /= numCoveredVoxels; // b /= m_MeanSignal; // b *= m_MeanTractDensity; } void FitFibersToImageFilter::GenerateData() { m_NumUnknowns = m_Tractograms.size(); if (m_FitIndividualFibers) { m_NumUnknowns = 0; for (unsigned int bundle=0; bundleGetNumFibers(); } else m_FilterOutliers = false; if (m_NumUnknowns<1) { MITK_INFO << "No fibers in tractogram."; return; } fiber_count = 0; sz_x = 0; sz_y = 0; sz_z = 0; m_MeanTractDensity = 0; m_MeanSignal = 0; if (m_PeakImage.IsNotNull()) CreatePeakSystem(); else if (m_DiffImage.IsNotNull()) CreateDiffSystem(); else if (m_ScalarImage.IsNotNull()) CreateScalarSystem(); else mitkThrow() << "No input image set!"; MITK_INFO << "Initializing optimizer"; double init_lambda = fiber_count; // initialization for lambda estimation itk::TimeProbe clock; clock.Start(); cost = VnlCostFunction(m_NumUnknowns); cost.SetProblem(A, b, init_lambda, m_Regularization); cost.SetGroupSizes(m_GroupSizes); m_Weights.set_size(m_NumUnknowns); m_Weights.fill( 1.0/m_NumUnknowns ); vnl_lbfgsb minimizer(cost); vnl_vector l; l.set_size(m_NumUnknowns); l.fill(0); vnl_vector bound_selection; bound_selection.set_size(m_NumUnknowns); bound_selection.fill(1); minimizer.set_bound_selection(bound_selection); minimizer.set_lower_bound(l); minimizer.set_projected_gradient_tolerance(m_GradientTolerance); if (m_Regularization==VnlCostFunction::REGU::MSM) MITK_INFO << "Regularization type: MSM"; else if (m_Regularization==VnlCostFunction::REGU::VARIANCE) MITK_INFO << "Regularization type: VARIANCE"; else if (m_Regularization==VnlCostFunction::REGU::LASSO) MITK_INFO << "Regularization type: LASSO"; else if (m_Regularization==VnlCostFunction::REGU::VOXEL_VARIANCE) MITK_INFO << "Regularization type: VOXEL_VARIANCE"; else if (m_Regularization==VnlCostFunction::REGU::GROUP_LASSO) MITK_INFO << "Regularization type: GROUP_LASSO"; else if (m_Regularization==VnlCostFunction::REGU::GROUP_VARIANCE) MITK_INFO << "Regularization type: GROUP_VARIANCE"; else if (m_Regularization==VnlCostFunction::REGU::NONE) MITK_INFO << "Regularization type: NONE"; if (m_Regularization!=VnlCostFunction::REGU::NONE) // REMOVE FOR NEW FIT AND SET cost.m_Lambda = m_Lambda { MITK_INFO << "Estimating regularization"; minimizer.set_trace(false); minimizer.set_max_function_evals(2); minimizer.minimize(m_Weights); vnl_vector dx; dx.set_size(m_NumUnknowns); dx.fill(0.0); cost.calc_regularization_gradient(m_Weights, dx); if (m_Weights.magnitude()==0) { MITK_INFO << "Regularization estimation failed. Using default value."; cost.m_Lambda = fiber_count*m_Lambda; } else { double r = dx.magnitude()/m_Weights.magnitude(); // wtf??? cost.m_Lambda *= m_Lambda*55.0/r; MITK_INFO << r << " - " << m_Lambda*55.0/r; if (cost.m_Lambda>10e7) { MITK_INFO << "Regularization estimation failed. Using default value."; cost.m_Lambda = fiber_count*m_Lambda; } } } else cost.m_Lambda = 0; MITK_INFO << "Using regularization factor of " << cost.m_Lambda << " (λ: " << m_Lambda << ")"; MITK_INFO << "Fitting fibers"; minimizer.set_trace(m_Verbose); minimizer.set_max_function_evals(m_MaxIterations); minimizer.minimize(m_Weights); std::vector< double > weights; if (m_FilterOutliers) { for (auto w : m_Weights) weights.push_back(w); std::sort(weights.begin(), weights.end()); MITK_INFO << "Setting upper weight bound to " << weights.at(m_NumUnknowns*0.99); vnl_vector u; u.set_size(m_NumUnknowns); u.fill(weights.at(m_NumUnknowns*0.99)); minimizer.set_upper_bound(u); bound_selection.fill(2); minimizer.set_bound_selection(bound_selection); minimizer.minimize(m_Weights); weights.clear(); } for (auto w : m_Weights) weights.push_back(w); std::sort(weights.begin(), weights.end()); m_MeanWeight = m_Weights.mean(); m_MedianWeight = weights.at(m_NumUnknowns*0.5); m_MinWeight = weights.at(0); m_MaxWeight = weights.at(m_NumUnknowns-1); MITK_INFO << "*************************"; MITK_INFO << "Weight statistics"; MITK_INFO << "Sum: " << m_Weights.sum(); MITK_INFO << "Mean: " << m_MeanWeight; MITK_INFO << "1% quantile: " << weights.at(m_NumUnknowns*0.01); MITK_INFO << "5% quantile: " << weights.at(m_NumUnknowns*0.05); MITK_INFO << "25% quantile: " << weights.at(m_NumUnknowns*0.25); MITK_INFO << "Median: " << m_MedianWeight; MITK_INFO << "75% quantile: " << weights.at(m_NumUnknowns*0.75); MITK_INFO << "95% quantile: " << weights.at(m_NumUnknowns*0.95); MITK_INFO << "99% quantile: " << weights.at(m_NumUnknowns*0.99); MITK_INFO << "Min: " << m_MinWeight; MITK_INFO << "Max: " << m_MaxWeight; MITK_INFO << "*************************"; MITK_INFO << "NumEvals: " << minimizer.get_num_evaluations(); MITK_INFO << "NumIterations: " << minimizer.get_num_iterations(); MITK_INFO << "Residual cost: " << minimizer.get_end_error(); m_RMSE = cost.S->get_rms_error(m_Weights); MITK_INFO << "Final RMSE: " << m_RMSE; clock.Stop(); int h = clock.GetTotal()/3600; int m = ((int)clock.GetTotal()%3600)/60; int s = (int)clock.GetTotal()%60; MITK_INFO << "Optimization took " << h << "h, " << m << "m and " << s << "s"; MITK_INFO << "Weighting fibers"; m_RmsDiffPerBundle.set_size(m_Tractograms.size()); std::streambuf *old = cout.rdbuf(); // <-- save std::stringstream ss; std::cout.rdbuf (ss.rdbuf()); if (m_FitIndividualFibers) { unsigned int fiber_count = 0; for (unsigned int bundle=0; bundle temp_weights; temp_weights.set_size(m_Weights.size()); temp_weights.copy_in(m_Weights.data_block()); for (int i=0; iGetNumFibers(); i++) { m_Tractograms.at(bundle)->SetFiberWeight(i, m_Weights[fiber_count]); temp_weights[fiber_count] = 0; ++fiber_count; } double d_rms = cost.S->get_rms_error(temp_weights) - m_RMSE; m_RmsDiffPerBundle[bundle] = d_rms; - m_Tractograms.at(bundle)->Compress(0.1); - m_Tractograms.at(bundle)->ColorFibersByFiberWeights(false, true); } } else { for (unsigned int i=0; i temp_weights; temp_weights.set_size(m_Weights.size()); temp_weights.copy_in(m_Weights.data_block()); temp_weights[i] = 0; double d_rms = cost.S->get_rms_error(temp_weights) - m_RMSE; m_RmsDiffPerBundle[i] = d_rms; m_Tractograms.at(i)->SetFiberWeights(m_Weights[i]); - m_Tractograms.at(i)->Compress(0.1); - m_Tractograms.at(i)->ColorFibersByFiberWeights(false, true); } } std::cout.rdbuf (old); // transform back A *= m_MeanSignal/100.0; b *= m_MeanSignal/100.0; MITK_INFO << "Generating output images ..."; if (m_PeakImage.IsNotNull()) GenerateOutputPeakImages(); else if (m_DiffImage.IsNotNull()) GenerateOutputDiffImages(); else if (m_ScalarImage.IsNotNull()) GenerateOutputScalarImages(); m_Coverage = m_Coverage/m_MeanSignal; m_Overshoot = m_Overshoot/m_MeanSignal; MITK_INFO << std::fixed << "Coverage: " << setprecision(2) << 100.0*m_Coverage << "%"; MITK_INFO << std::fixed << "Overshoot: " << setprecision(2) << 100.0*m_Overshoot << "%"; } void FitFibersToImageFilter::GenerateOutputDiffImages() { VectorImgType::PixelType pix; pix.SetSize(m_DiffImage->GetVectorLength()); pix.Fill(0); itk::ImageDuplicator< VectorImgType >::Pointer duplicator = itk::ImageDuplicator< VectorImgType >::New(); duplicator->SetInputImage(m_DiffImage); duplicator->Update(); m_UnderexplainedImageDiff = duplicator->GetOutput(); m_UnderexplainedImageDiff->FillBuffer(pix); duplicator->SetInputImage(m_UnderexplainedImageDiff); duplicator->Update(); m_OverexplainedImageDiff = duplicator->GetOutput(); m_OverexplainedImageDiff->FillBuffer(pix); duplicator->SetInputImage(m_OverexplainedImageDiff); duplicator->Update(); m_ResidualImageDiff = duplicator->GetOutput(); m_ResidualImageDiff->FillBuffer(pix); duplicator->SetInputImage(m_ResidualImageDiff); duplicator->Update(); m_FittedImageDiff = duplicator->GetOutput(); m_FittedImageDiff->FillBuffer(pix); vnl_vector fitted_b; fitted_b.set_size(b.size()); cost.S->multiply(m_Weights, fitted_b); itk::ImageRegionIterator it1 = itk::ImageRegionIterator(m_DiffImage, m_DiffImage->GetLargestPossibleRegion()); itk::ImageRegionIterator it2 = itk::ImageRegionIterator(m_FittedImageDiff, m_FittedImageDiff->GetLargestPossibleRegion()); itk::ImageRegionIterator it3 = itk::ImageRegionIterator(m_ResidualImageDiff, m_ResidualImageDiff->GetLargestPossibleRegion()); itk::ImageRegionIterator it4 = itk::ImageRegionIterator(m_UnderexplainedImageDiff, m_UnderexplainedImageDiff->GetLargestPossibleRegion()); itk::ImageRegionIterator it5 = itk::ImageRegionIterator(m_OverexplainedImageDiff, m_OverexplainedImageDiff->GetLargestPossibleRegion()); m_MeanSignal = 0; m_Coverage = 0; m_Overshoot = 0; while( !it2.IsAtEnd() ) { itk::Index<3> idx3 = it2.GetIndex(); VectorImgType::PixelType original_pix =it1.Get(); VectorImgType::PixelType fitted_pix =it2.Get(); VectorImgType::PixelType residual_pix =it3.Get(); VectorImgType::PixelType underexplained_pix =it4.Get(); VectorImgType::PixelType overexplained_pix =it5.Get(); int num_nonzero_g = 0; double original_mean = 0; for (int g=0; gGetGradientDirection(g).GetNorm()>=mitk::eps ) { original_mean += original_pix[g]; ++num_nonzero_g; } } original_mean /= num_nonzero_g; for (int g=0; g=0) { underexplained_pix[g] = residual_pix[g]; m_Coverage += fitted_b[linear_index] + original_mean; } m_MeanSignal += b[linear_index] + original_mean; } it2.Set(fitted_pix); it3.Set(residual_pix); it4.Set(underexplained_pix); it5.Set(overexplained_pix); ++it1; ++it2; ++it3; ++it4; ++it5; } } void FitFibersToImageFilter::GenerateOutputScalarImages() { itk::ImageDuplicator< DoubleImgType >::Pointer duplicator = itk::ImageDuplicator< DoubleImgType >::New(); duplicator->SetInputImage(m_ScalarImage); duplicator->Update(); m_UnderexplainedImageScalar = duplicator->GetOutput(); m_UnderexplainedImageScalar->FillBuffer(0); duplicator->SetInputImage(m_UnderexplainedImageScalar); duplicator->Update(); m_OverexplainedImageScalar = duplicator->GetOutput(); m_OverexplainedImageScalar->FillBuffer(0); duplicator->SetInputImage(m_OverexplainedImageScalar); duplicator->Update(); m_ResidualImageScalar = duplicator->GetOutput(); m_ResidualImageScalar->FillBuffer(0); duplicator->SetInputImage(m_ResidualImageScalar); duplicator->Update(); m_FittedImageScalar = duplicator->GetOutput(); m_FittedImageScalar->FillBuffer(0); vnl_vector fitted_b; fitted_b.set_size(b.size()); cost.S->multiply(m_Weights, fitted_b); itk::ImageRegionIterator it1 = itk::ImageRegionIterator(m_ScalarImage, m_ScalarImage->GetLargestPossibleRegion()); itk::ImageRegionIterator it2 = itk::ImageRegionIterator(m_FittedImageScalar, m_FittedImageScalar->GetLargestPossibleRegion()); itk::ImageRegionIterator it3 = itk::ImageRegionIterator(m_ResidualImageScalar, m_ResidualImageScalar->GetLargestPossibleRegion()); itk::ImageRegionIterator it4 = itk::ImageRegionIterator(m_UnderexplainedImageScalar, m_UnderexplainedImageScalar->GetLargestPossibleRegion()); itk::ImageRegionIterator it5 = itk::ImageRegionIterator(m_OverexplainedImageScalar, m_OverexplainedImageScalar->GetLargestPossibleRegion()); m_MeanSignal = 0; m_Coverage = 0; m_Overshoot = 0; while( !it2.IsAtEnd() ) { itk::Index<3> idx3 = it2.GetIndex(); DoubleImgType::PixelType original_pix =it1.Get(); DoubleImgType::PixelType fitted_pix =it2.Get(); DoubleImgType::PixelType residual_pix =it3.Get(); DoubleImgType::PixelType underexplained_pix =it4.Get(); DoubleImgType::PixelType overexplained_pix =it5.Get(); unsigned int linear_index = idx3[0] + sz_x*idx3[1] + sz_x*sz_y*idx3[2]; fitted_pix = fitted_b[linear_index]; residual_pix = original_pix - fitted_pix; if (residual_pix<0) { overexplained_pix = residual_pix; m_Coverage += b[linear_index]; m_Overshoot -= residual_pix; } else if (residual_pix>=0) { underexplained_pix = residual_pix; m_Coverage += fitted_b[linear_index]; } m_MeanSignal += b[linear_index]; it2.Set(fitted_pix); it3.Set(residual_pix); it4.Set(underexplained_pix); it5.Set(overexplained_pix); ++it1; ++it2; ++it3; ++it4; ++it5; } } VnlCostFunction::REGU FitFibersToImageFilter::GetRegularization() const { return m_Regularization; } void FitFibersToImageFilter::SetRegularization(const VnlCostFunction::REGU &Regularization) { m_Regularization = Regularization; } void FitFibersToImageFilter::GenerateOutputPeakImages() { itk::ImageDuplicator< PeakImgType >::Pointer duplicator = itk::ImageDuplicator< PeakImgType >::New(); duplicator->SetInputImage(m_PeakImage); duplicator->Update(); m_UnderexplainedImage = duplicator->GetOutput(); m_UnderexplainedImage->FillBuffer(0.0); duplicator->SetInputImage(m_UnderexplainedImage); duplicator->Update(); m_OverexplainedImage = duplicator->GetOutput(); m_OverexplainedImage->FillBuffer(0.0); duplicator->SetInputImage(m_OverexplainedImage); duplicator->Update(); m_ResidualImage = duplicator->GetOutput(); m_ResidualImage->FillBuffer(0.0); duplicator->SetInputImage(m_ResidualImage); duplicator->Update(); m_FittedImage = duplicator->GetOutput(); m_FittedImage->FillBuffer(0.0); vnl_vector fitted_b; fitted_b.set_size(b.size()); cost.S->multiply(m_Weights, fitted_b); for (unsigned int r=0; r idx4; unsigned int linear_index = r; idx4[0] = linear_index % sz_x; linear_index /= sz_x; idx4[1] = linear_index % sz_y; linear_index /= sz_y; idx4[2] = linear_index % sz_z; linear_index /= sz_z; int peak_id = linear_index % dim_four_size; if (peak_id peak_dir; idx4[3] = peak_id*3; peak_dir[0] = m_PeakImage->GetPixel(idx4); idx4[3] += 1; peak_dir[1] = m_PeakImage->GetPixel(idx4); idx4[3] += 1; peak_dir[2] = m_PeakImage->GetPixel(idx4); peak_dir.normalize(); peak_dir *= fitted_b[r]; idx4[3] = peak_id*3; m_FittedImage->SetPixel(idx4, peak_dir[0]); idx4[3] += 1; m_FittedImage->SetPixel(idx4, peak_dir[1]); idx4[3] += 1; m_FittedImage->SetPixel(idx4, peak_dir[2]); } } m_MeanSignal = 0; m_Coverage = 0; m_Overshoot = 0; itk::Index<4> idx4; for (idx4[0]=0; idx4[0] idx3; idx3[0] = idx4[0]; idx3[1] = idx4[1]; idx3[2] = idx4[2]; if (m_MaskImage.IsNotNull() && m_MaskImage->GetPixel(idx3)==0) continue; vnl_vector_fixed peak_dir; vnl_vector_fixed fitted_dir; vnl_vector_fixed overshoot_dir; for (idx4[3]=0; idx4[3]<(itk::IndexValueType)m_PeakImage->GetLargestPossibleRegion().GetSize(3); ++idx4[3]) { peak_dir[idx4[3]%3] = m_PeakImage->GetPixel(idx4); fitted_dir[idx4[3]%3] = m_FittedImage->GetPixel(idx4); m_ResidualImage->SetPixel(idx4, m_PeakImage->GetPixel(idx4) - m_FittedImage->GetPixel(idx4)); if (idx4[3]%3==2) { m_MeanSignal += peak_dir.magnitude(); itk::Index<4> tidx= idx4; if (peak_dir.magnitude()>fitted_dir.magnitude()) { m_Coverage += fitted_dir.magnitude(); m_UnderexplainedImage->SetPixel(tidx, peak_dir[2]-fitted_dir[2]); tidx[3]--; m_UnderexplainedImage->SetPixel(tidx, peak_dir[1]-fitted_dir[1]); tidx[3]--; m_UnderexplainedImage->SetPixel(tidx, peak_dir[0]-fitted_dir[0]); } else { overshoot_dir[0] = fitted_dir[0]-peak_dir[0]; overshoot_dir[1] = fitted_dir[1]-peak_dir[1]; overshoot_dir[2] = fitted_dir[2]-peak_dir[2]; m_Coverage += peak_dir.magnitude(); m_Overshoot += overshoot_dir.magnitude(); m_OverexplainedImage->SetPixel(tidx, overshoot_dir[2]); tidx[3]--; m_OverexplainedImage->SetPixel(tidx, overshoot_dir[1]); tidx[3]--; m_OverexplainedImage->SetPixel(tidx, overshoot_dir[0]); } } } } } void FitFibersToImageFilter::GetClosestPeak(itk::Index<4> idx, PeakImgType::Pointer peak_image , vnl_vector_fixed fiber_dir, int& id, double& w, double& peak_mag ) { int m_NumDirs = peak_image->GetLargestPossibleRegion().GetSize()[3]/3; vnl_vector_fixed out_dir; out_dir.fill(0); float angle = 0.9; for (int i=0; i dir; idx[3] = i*3; dir[0] = peak_image->GetPixel(idx); idx[3] += 1; dir[1] = peak_image->GetPixel(idx); idx[3] += 1; dir[2] = peak_image->GetPixel(idx); float mag = dir.magnitude(); if (magangle) { angle = a; w = angle; peak_mag = mag; id = i; } } } std::vector FitFibersToImageFilter::GetTractograms() const { return m_Tractograms; } void FitFibersToImageFilter::SetTractograms(const std::vector &tractograms) { m_Tractograms = tractograms; } void FitFibersToImageFilter::SetSignalModel(mitk::DiffusionSignalModel<> *SignalModel) { m_SignalModel = SignalModel; } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.cpp index 92f343adc7..3c6a9a446d 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.cpp @@ -1,499 +1,556 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "itkTractClusteringFilter.h" #define _USE_MATH_DEFINES #include #include #include namespace itk{ TractClusteringFilter::TractClusteringFilter() : m_NumPoints(12) , m_InCentroids(nullptr) , m_MinClusterSize(1) , m_MaxClusters(0) , m_MergeDuplicateThreshold(-1) , m_DoResampling(true) , m_FilterMask(nullptr) , m_OverlapThreshold(0.0) { } TractClusteringFilter::~TractClusteringFilter() { for (auto m : m_Metrics) delete m; } std::vector > TractClusteringFilter::GetOutFiberIndices() const { return m_OutFiberIndices; } void TractClusteringFilter::SetMetrics(const std::vector &Metrics) { m_Metrics = Metrics; } std::vector TractClusteringFilter::GetOutClusters() const { return m_OutClusters; } std::vector TractClusteringFilter::GetOutCentroids() const { return m_OutCentroids; } std::vector TractClusteringFilter::GetOutTractograms() const { return m_OutTractograms; } void TractClusteringFilter::SetDistances(const std::vector &Distances) { m_Distances = Distances; } float TractClusteringFilter::CalcOverlap(vnl_matrix& t) { float overlap = 0; if (m_FilterMask.IsNotNull()) { for (unsigned int i=0; i p = t.get_column(i); itk::Point point; point[0] = p[0]; point[1] = p[1]; point[2] = p[2]; itk::Index<3> idx; m_FilterMask->TransformPhysicalPointToIndex(point, idx); if (m_FilterMask->GetLargestPossibleRegion().IsInside(idx) && m_FilterMask->GetPixel(idx)>0) overlap += 1; } overlap /= m_NumPoints; } else return 1.0; return overlap; } std::vector > TractClusteringFilter::ResampleFibers(mitk::FiberBundle::Pointer tractogram) { mitk::FiberBundle::Pointer temp_fib = tractogram->GetDeepCopy(); if (m_DoResampling) temp_fib->ResampleToNumPoints(m_NumPoints); std::vector< vnl_matrix > out_fib; for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = temp_fib->GetFiberPolyData()->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vnl_matrix streamline; streamline.set_size(3, m_NumPoints); streamline.fill(0.0); for (int j=0; jGetPoint(j, cand); vnl_vector_fixed< float, 3 > candV; candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2]; streamline.set_column(j, candV); } out_fib.push_back(streamline); } return out_fib; } std::vector< TractClusteringFilter::Cluster > TractClusteringFilter::ClusterStep(std::vector< long > f_indices, std::vector distances) { float dist_thres = distances.back(); distances.pop_back(); std::vector< Cluster > C; int N = f_indices.size(); Cluster c1; c1.I.push_back(f_indices.at(0)); c1.h = T[f_indices.at(0)]; c1.n = 1; C.push_back(c1); if (f_indices.size()==1) return C; for (int i=1; i t = T.at(f_indices.at(i)); int min_cluster_index = -1; float min_cluster_distance = 99999; bool flip = false; for (unsigned int k=0; k v = C.at(k).h / C.at(k).n; bool f = false; float d = 0; for (auto m : m_Metrics) d += m->CalculateDistance(t, v, f); d /= m_Metrics.size(); if (d=0 && min_cluster_distance outC; #pragma omp parallel for for (int c=0; c<(int)C.size(); c++) { std::vector< Cluster > tempC = ClusterStep(C.at(c).I, distances); #pragma omp critical AppendCluster(outC, tempC); } return outC; } else return C; } void TractClusteringFilter::AppendCluster(std::vector< Cluster >& a, std::vector< Cluster >&b) { for (auto c : b) a.push_back(c); } +std::vector< TractClusteringFilter::Cluster > TractClusteringFilter::MergeDuplicateClusters2(std::vector< TractClusteringFilter::Cluster >& clusters) +{ + if (m_MergeDuplicateThreshold<0) + m_MergeDuplicateThreshold = m_Distances.at(0)/2; + + MITK_INFO << "Merging duplicate clusters with distance threshold " << m_MergeDuplicateThreshold; + + std::vector< TractClusteringFilter::Cluster > new_clusters; + for (Cluster c1 : clusters) + { + vnl_matrix t = c1.h / c1.n; + + int min_idx = -1; + float min_d = 99999; + bool flip = false; + +#pragma omp parallel for + for (unsigned int k2=0; k2 v = c2.h / c2.n; + + bool f = false; + float d = 0; + for (auto m : m_Metrics) + d += m->CalculateDistance(t, v, f); + d /= m_Metrics.size(); + +#pragma omp critical + if (d& clusters) { if (m_MergeDuplicateThreshold<0) m_MergeDuplicateThreshold = m_Distances.at(0)/2; bool found = true; MITK_INFO << "Merging duplicate clusters with distance threshold " << m_MergeDuplicateThreshold; int start = 0; while (found && m_MergeDuplicateThreshold>mitk::eps) { std::cout << " \r"; std::cout << "Number of clusters: " << clusters.size() << '\r'; cout.flush(); found = false; for (int k1=start; k1<(int)clusters.size(); ++k1) { Cluster c1 = clusters.at(k1); vnl_matrix t = c1.h / c1.n; std::vector< int > merge_indices; std::vector< bool > flip_indices; #pragma omp parallel for for (int k2=start+1; k2<(int)clusters.size(); ++k2) { if (k1!=k2) { Cluster c2 = clusters.at(k2); vnl_matrix v = c2.h / c2.n; bool f = false; float d = 0; for (auto m : m_Metrics) d += m->CalculateDistance(t, v, f); d /= m_Metrics.size(); #pragma omp critical if (d TractClusteringFilter::AddToKnownClusters(std::vector< long > f_indices, std::vector >& centroids) { float dist_thres = m_Distances.at(0); int N = f_indices.size(); std::vector< Cluster > C; vnl_matrix zero_h; zero_h.set_size(T.at(0).rows(), T.at(0).cols()); zero_h.fill(0.0); Cluster no_fit; no_fit.h = zero_h; for (unsigned int i=0; i t = T.at(f_indices.at(i)); int min_cluster_index = -1; float min_cluster_distance = 99999; bool flip = false; if (CalcOverlap(t)>=m_OverlapThreshold) { int c_idx = 0; for (vnl_matrix centroid : centroids) { bool f = false; float d = 0; for (auto m : m_Metrics) d += m->CalculateDistance(t, centroid, f); d /= m_Metrics.size(); if (d=0 && min_cluster_distance f_indices; for (unsigned int i=0; i clusters; if (m_InCentroids.IsNull()) { MITK_INFO << "Clustering fibers"; clusters = ClusterStep(f_indices, m_Distances); MITK_INFO << "Number of clusters: " << clusters.size(); - MergeDuplicateClusters(clusters); + clusters = MergeDuplicateClusters2(clusters); std::sort(clusters.begin(),clusters.end()); } else { std::vector > centroids = ResampleFibers(m_InCentroids); if (centroids.empty()) { MITK_INFO << "No fibers in centroid tractogram!"; return; } MITK_INFO << "Clustering with input centroids"; clusters = AddToKnownClusters(f_indices, centroids); no_match = clusters.back(); clusters.pop_back(); MITK_INFO << "Number of clusters: " << clusters.size(); - MergeDuplicateClusters(clusters); + clusters = MergeDuplicateClusters2(clusters); } MITK_INFO << "Clustering finished"; int max = clusters.size()-1; if (m_MaxClusters>0 && clusters.size()-1>m_MaxClusters) max = m_MaxClusters; int skipped = 0; for (int i=clusters.size()-1; i>=0; --i) { Cluster c = clusters.at(i); if ( c.n>=(int)m_MinClusterSize && !(m_MaxClusters>0 && clusters.size()-i>m_MaxClusters) ) { m_OutClusters.push_back(c); vtkSmartPointer weights = vtkSmartPointer::New(); vtkSmartPointer pTmp = m_Tractogram->GeneratePolyDataByIds(c.I, weights); mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(pTmp); if (max>0) fib->SetFiberWeights((float)i/max); m_OutTractograms.push_back(fib); m_OutFiberIndices.push_back(c.I); // create centroid vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); vtkSmartPointer polyData = vtkSmartPointer::New(); vtkSmartPointer container = vtkSmartPointer::New(); vnl_matrix centroid_points = c.h / c.n; for (unsigned int j=0; jInsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); polyData->SetPoints(vtkNewPoints); polyData->SetLines(vtkNewCells); mitk::FiberBundle::Pointer centroid = mitk::FiberBundle::New(polyData); centroid->SetFiberColors(255, 255, 255); m_OutCentroids.push_back(centroid); } else { skipped++; } } MITK_INFO << "Final number of clusters: " << m_OutTractograms.size() << " (discarded " << skipped << " clusters)"; int w = 0; for (auto fib : m_OutTractograms) { if (m_OutTractograms.size()>1) { fib->SetFiberWeights((float)w/(m_OutTractograms.size()-1)); m_OutCentroids.at(w)->SetFiberWeights((float)w/(m_OutTractograms.size()-1)); } else { fib->SetFiberWeights(1); m_OutCentroids.at(w)->SetFiberWeights(1); } fib->ColorFibersByFiberWeights(false, false); ++w; } if (no_match.n>0) { vtkSmartPointer weights = vtkSmartPointer::New(); vtkSmartPointer pTmp = m_Tractogram->GeneratePolyDataByIds(no_match.I, weights); mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(pTmp); fib->SetFiberColors(0, 0, 0); m_OutFiberIndices.push_back(no_match.I); m_OutTractograms.push_back(fib); } } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.h index bf03459e68..116c2f12a1 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractClusteringFilter.h @@ -1,139 +1,140 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef itkTractClusteringFilter_h #define itkTractClusteringFilter_h // MITK #include #include #include #include // ITK #include // VTK #include #include #include #include #include namespace itk{ /** * \brief */ class TractClusteringFilter : public ProcessObject { public: struct Cluster { Cluster() : n(0), f_id(-1) {} vnl_matrix h; std::vector< long > I; int n; int f_id; bool operator <(Cluster const& b) const { return this->n < b.n; } }; typedef TractClusteringFilter Self; typedef ProcessObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef itk::Image< float, 3 > FloatImageType; typedef itk::Image< unsigned char, 3 > UcharImageType; itkFactorylessNewMacro(Self) itkCloneMacro(Self) itkTypeMacro( TractClusteringFilter, ProcessObject ) itkSetMacro(NumPoints, unsigned int) ///< Fibers are resampled to the specified number of points. If scalar maps are used, a larger number of points is recommended. itkGetMacro(NumPoints, unsigned int) ///< Fibers are resampled to the specified number of points. If scalar maps are used, a larger number of points is recommended. itkSetMacro(MinClusterSize, unsigned int) ///< Clusters with too few fibers are discarded itkGetMacro(MinClusterSize, unsigned int) ///< Clusters with too few fibers are discarded itkSetMacro(MaxClusters, unsigned int) ///< Only the N largest clusters are kept itkGetMacro(MaxClusters, unsigned int) ///< Only the N largest clusters are kept itkSetMacro(MergeDuplicateThreshold, float) ///< Clusters with centroids very close to each other are merged. Set to 0 to avoid merging and to -1 to use the original cluster size. itkGetMacro(MergeDuplicateThreshold, float) ///< Clusters with centroids very close to each other are merged. Set to 0 to avoid merging and to -1 to use the original cluster size. itkSetMacro(DoResampling, bool) ///< Resample fibers to equal number of points. This is mandatory, but can be performed outside of the filter if desired. itkGetMacro(DoResampling, bool) ///< Resample fibers to equal number of points. This is mandatory, but can be performed outside of the filter if desired. itkSetMacro(OverlapThreshold, float) ///< Overlap threshold used in conjunction with the filter mask when clustering around known centroids. itkGetMacro(OverlapThreshold, float) ///< Overlap threshold used in conjunction with the filter mask when clustering around known centroids. itkSetMacro(Tractogram, mitk::FiberBundle::Pointer) ///< The streamlines to be clustered itkSetMacro(InCentroids, mitk::FiberBundle::Pointer) ///< If a tractogram containing known tract centroids is set, the input fibers are assigned to the closest centroid. If no centroid is found within the specified smallest clustering distance, the fiber is assigned to the no-fit cluster. itkSetMacro(FilterMask, UcharImageType::Pointer) ///< If fibers are clustered around the nearest input centroids (see SetInCentroids), the complete input tractogram can additionally be pre-filtered with this binary mask and a given overlap threshold (see SetOverlapThreshold). virtual void Update() override{ this->GenerateData(); } void SetDistances(const std::vector &Distances); ///< Set clustering distances that are traversed recoursively. The distances have to be sorted in an ascending manner. The actual cluster size is determined by the smallest entry in the distance-list (index 0). std::vector GetOutTractograms() const; std::vector GetOutCentroids() const; std::vector GetOutClusters() const; void SetMetrics(const std::vector &Metrics); std::vector > GetOutFiberIndices() const; protected: void GenerateData() override; std::vector< vnl_matrix > ResampleFibers(FiberBundle::Pointer tractogram); float CalcOverlap(vnl_matrix& t); std::vector< Cluster > ClusterStep(std::vector< long > f_indices, std::vector< float > distances); + std::vector< TractClusteringFilter::Cluster > MergeDuplicateClusters2(std::vector< TractClusteringFilter::Cluster >& clusters); void MergeDuplicateClusters(std::vector< TractClusteringFilter::Cluster >& clusters); std::vector< Cluster > AddToKnownClusters(std::vector< long > f_indices, std::vector > ¢roids); void AppendCluster(std::vector< Cluster >& a, std::vector< Cluster >&b); TractClusteringFilter(); virtual ~TractClusteringFilter(); unsigned int m_NumPoints; std::vector< float > m_Distances; mitk::FiberBundle::Pointer m_Tractogram; mitk::FiberBundle::Pointer m_InCentroids; std::vector< mitk::FiberBundle::Pointer > m_OutTractograms; std::vector< mitk::FiberBundle::Pointer > m_OutCentroids; std::vector > T; unsigned int m_MinClusterSize; unsigned int m_MaxClusters; float m_MergeDuplicateThreshold; std::vector< Cluster > m_OutClusters; bool m_DoResampling; UcharImageType::Pointer m_FilterMask; float m_OverlapThreshold; std::vector< mitk::ClusteringMetric* > m_Metrics; std::vector< std::vector< long > > m_OutFiberIndices; }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkTractClusteringFilter.cpp" #endif #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp index 254c0a41f9..f009ba8a4d 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractDensityImageFilter.cpp @@ -1,187 +1,189 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Coindex[1]right (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "itkTractDensityImageFilter.h" // VTK #include #include #include #include // misc #include #include #include #include namespace itk{ template< class OutputImageType > TractDensityImageFilter< OutputImageType >::TractDensityImageFilter() : m_UpsamplingFactor(1) , m_InvertImage(false) , m_BinaryOutput(false) , m_UseImageGeometry(false) , m_OutputAbsoluteValues(false) , m_MaxDensity(0) , m_NumCoveredVoxels(0) { } template< class OutputImageType > TractDensityImageFilter< OutputImageType >::~TractDensityImageFilter() { } template< class OutputImageType > itk::Point TractDensityImageFilter< OutputImageType >::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } template< class OutputImageType > void TractDensityImageFilter< OutputImageType >::GenerateData() { // generate upsampled image mitk::BaseGeometry::Pointer geometry = m_FiberBundle->GetGeometry(); typename OutputImageType::Pointer outImage = this->GetOutput(); // calculate new image parameters itk::Vector newSpacing; mitk::Point3D newOrigin; itk::Matrix newDirection; ImageRegion<3> upsampledRegion; if (m_UseImageGeometry && !m_InputImage.IsNull()) { MITK_INFO << "TractDensityImageFilter: using image geometry"; newSpacing = m_InputImage->GetSpacing()/m_UpsamplingFactor; upsampledRegion = m_InputImage->GetLargestPossibleRegion(); newOrigin = m_InputImage->GetOrigin(); typename OutputImageType::RegionType::SizeType size = upsampledRegion.GetSize(); size[0] *= m_UpsamplingFactor; size[1] *= m_UpsamplingFactor; size[2] *= m_UpsamplingFactor; upsampledRegion.SetSize(size); newDirection = m_InputImage->GetDirection(); } else { MITK_INFO << "TractDensityImageFilter: using fiber bundle geometry"; newSpacing = geometry->GetSpacing()/m_UpsamplingFactor; newOrigin = geometry->GetOrigin(); mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds(); // we retrieve the origin from a vtk-polydata (corner-based) and hance have to translate it to an image geometry // i.e. center-based newOrigin[0] += bounds.GetElement(0) + 0.5 * newSpacing[0]; newOrigin[1] += bounds.GetElement(2) + 0.5 * newSpacing[1]; newOrigin[2] += bounds.GetElement(4) + 0.5 * newSpacing[2]; for (int i=0; i<3; i++) for (int j=0; j<3; j++) newDirection[j][i] = geometry->GetMatrixColumn(i)[j]; upsampledRegion.SetSize(0, ceil( geometry->GetExtent(0)*m_UpsamplingFactor ) ); upsampledRegion.SetSize(1, ceil( geometry->GetExtent(1)*m_UpsamplingFactor ) ); upsampledRegion.SetSize(2, ceil( geometry->GetExtent(2)*m_UpsamplingFactor ) ); } typename OutputImageType::RegionType::SizeType upsampledSize = upsampledRegion.GetSize(); // apply new image parameters outImage->SetSpacing( newSpacing ); outImage->SetOrigin( newOrigin ); outImage->SetDirection( newDirection ); outImage->SetLargestPossibleRegion( upsampledRegion ); outImage->SetBufferedRegion( upsampledRegion ); outImage->SetRequestedRegion( upsampledRegion ); outImage->Allocate(); outImage->FillBuffer(0.0); int w = upsampledSize[0]; int h = upsampledSize[1]; int d = upsampledSize[2]; // set/initialize output OutPixelType* outImageBufferPointer = (OutPixelType*)outImage->GetBufferPointer(); MITK_INFO << "TractDensityImageFilter: starting image generation"; vtkSmartPointer fiberPolyData = m_FiberBundle->GetFiberPolyData(); int numFibers = m_FiberBundle->GetNumFibers(); boost::progress_display disp(numFibers); for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); float weight = m_FiberBundle->GetFiberWeight(i); // fill output image for( int j=0; j startVertex = GetItkPoint(points->GetPoint(j)); itk::Index<3> startIndex; itk::ContinuousIndex startIndexCont; outImage->TransformPhysicalPointToIndex(startVertex, startIndex); outImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont); itk::Point endVertex = GetItkPoint(points->GetPoint(j + 1)); itk::Index<3> endIndex; itk::ContinuousIndex endIndexCont; outImage->TransformPhysicalPointToIndex(endVertex, endIndex); outImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont); std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(newSpacing, startIndex, endIndex, startIndexCont, endIndexCont); for (std::pair< itk::Index<3>, double > segment : segments) { + if (!outImage->GetLargestPossibleRegion().IsInside(segment.first)) + continue; if (outImage->GetPixel(segment.first)==0) m_NumCoveredVoxels++; if (m_BinaryOutput) outImage->SetPixel(segment.first, 1); else outImage->SetPixel(segment.first, outImage->GetPixel(segment.first)+segment.second * weight); } } } m_MaxDensity = 0; for (int i=0; i0) for (int i=0; i +#include + +namespace itk{ + +TractDistanceFilter::TractDistanceFilter() + : m_NumPoints(12) + , disp(0) +{ + +} + +TractDistanceFilter::~TractDistanceFilter() +{ + for (auto m : m_Metrics) + delete m; +} + +vnl_matrix TractDistanceFilter::GetAllDistances() const +{ + return m_AllDistances; +} + +vnl_vector TractDistanceFilter::GetMinIndices() const +{ + return m_MinIndices; +} + +vnl_vector TractDistanceFilter::GetMinDistances() const +{ + return m_MinDistances; +} + +void TractDistanceFilter::SetTracts2(const std::vector &Tracts2) +{ + m_Tracts2 = Tracts2; +} + +void TractDistanceFilter::SetTracts1(const std::vector &Tracts1) +{ + m_Tracts1 = Tracts1; +} + +void TractDistanceFilter::SetMetrics(const std::vector &Metrics) +{ + m_Metrics = Metrics; +} + +std::vector > TractDistanceFilter::ResampleFibers(mitk::FiberBundle::Pointer tractogram) +{ + std::streambuf *old = cout.rdbuf(); // <-- save + std::stringstream ss; + std::cout.rdbuf (ss.rdbuf()); // <-- redirect + mitk::FiberBundle::Pointer temp_fib = tractogram->GetDeepCopy(); + temp_fib->ResampleToNumPoints(m_NumPoints); + + std::vector< vnl_matrix > out_fib; + + for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) + { + vtkCell* cell = temp_fib->GetFiberPolyData()->GetCell(i); + int numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + + vnl_matrix streamline; + streamline.set_size(3, m_NumPoints); + streamline.fill(0.0); + + for (int j=0; jGetPoint(j, cand); + + vnl_vector_fixed< float, 3 > candV; + candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2]; + streamline.set_column(j, candV); + } + + out_fib.push_back(streamline); + } + + std::cout.rdbuf (old); // <-- restore + return out_fib; +} + +float TractDistanceFilter::calc_distance(const std::vector >& T1, const std::vector >& T2) +{ + float distance = 0; + for (auto metric : m_Metrics) + { + unsigned int r = 0; + for (auto f1 : T1) + { + unsigned int c = 0; + float min_d = 99999; + for (auto f2 : T2) + { +#pragma omp critical + ++disp; + bool flipped = false; + float d = metric->CalculateDistance(f1, f2, flipped); + if (d < min_d) + min_d = d; + ++c; + } + distance += min_d; + ++r; + } + } + distance /= (T1.size() * m_Metrics.size()); + return distance; +} + +void TractDistanceFilter::GenerateData() +{ + if (m_Metrics.empty()) + { + mitkThrow() << "No metric selected!"; + return; + } + + m_MinIndices.clear(); + m_MinDistances.clear(); + std::vector>> T1; + std::vector>> T2; + + unsigned int num_fibs1 = 0; + unsigned int num_fibs2 = 0; + for (auto t : m_Tracts1) + { + T1.push_back(ResampleFibers(t)); + num_fibs1 += T1.back().size(); + } + for (auto t : m_Tracts2) + { + T2.push_back(ResampleFibers(t)); + num_fibs2 += T2.back().size(); + } + + disp.restart(m_Metrics.size() * num_fibs1 * num_fibs2); + + m_AllDistances.set_size(T1.size(), T2.size()); + + m_MinIndices.set_size(T1.size()); + m_MinDistances.set_size(T1.size()); + +#pragma omp parallel for + for (unsigned int i=0; i +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +namespace itk{ + +/** +* \brief */ + +class TractDistanceFilter : public ProcessObject +{ +public: + + typedef TractDistanceFilter Self; + typedef ProcessObject Superclass; + typedef SmartPointer< Self > Pointer; + typedef SmartPointer< const Self > ConstPointer; + typedef itk::Image< float, 3 > FloatImageType; + typedef itk::Image< unsigned char, 3 > UcharImageType; + + itkFactorylessNewMacro(Self) + itkCloneMacro(Self) + itkTypeMacro( TractDistanceFilter, ProcessObject ) + + itkSetMacro(NumPoints, unsigned int) ///< Fibers are resampled to the specified number of points. If scalar maps are used, a larger number of points is recommended. + + virtual void Update() override{ + this->GenerateData(); + } + + void SetMetrics(const std::vector &Metrics); + + void SetTracts1(const std::vector &Tracts1); + + void SetTracts2(const std::vector &Tracts2); + + vnl_vector GetMinDistances() const; + + vnl_vector GetMinIndices() const; + + vnl_matrix GetAllDistances() const; + +protected: + + void GenerateData() override; + std::vector< vnl_matrix > ResampleFibers(FiberBundle::Pointer tractogram); + float calc_distance(const std::vector > &T1, const std::vector > &T2); + + TractDistanceFilter(); + virtual ~TractDistanceFilter(); + + std::vector m_Tracts1; + std::vector m_Tracts2; + unsigned int m_NumPoints; + std::vector m_Metrics; + vnl_vector m_MinDistances; + vnl_vector m_MinIndices; + vnl_matrix m_AllDistances; + boost::progress_display disp; +}; +} + +#ifndef ITK_MANUAL_INSTANTIATION +#include "itkTractDistanceFilter.cpp" +#endif + +#endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp index b5cf08610f..8d2ae6e9a2 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp @@ -1,406 +1,407 @@ #include "itkTractsToVectorImageFilter.h" // VTK #include #include #include // ITK #include #include // misc #define _USE_MATH_DEFINES #include #include #include namespace itk{ static inline bool CompareVectorLengths(const vnl_vector_fixed< double, 3 >& v1, const vnl_vector_fixed< double, 3 >& v2) { return (v1.magnitude()>v2.magnitude()); } template< class PixelType > TractsToVectorImageFilter< PixelType >::TractsToVectorImageFilter(): m_NormalizationMethod(GLOBAL_MAX), m_AngularThreshold(0.7), m_Epsilon(0.999), m_MaxNumDirections(3), - m_SizeThreshold(0.3) + m_SizeThreshold(0.3), + m_OnlyUseMaskGeometry(false) { this->SetNumberOfRequiredOutputs(1); } template< class PixelType > TractsToVectorImageFilter< PixelType >::~TractsToVectorImageFilter() { } template< class PixelType > vnl_vector_fixed TractsToVectorImageFilter< PixelType >::GetVnlVector(double point[]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } template< class PixelType > itk::Point TractsToVectorImageFilter< PixelType >::GetItkPoint(double point[]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } template< class PixelType > void TractsToVectorImageFilter< PixelType >::GenerateData() { mitk::BaseGeometry::Pointer geometry = m_FiberBundle->GetGeometry(); // calculate new image parameters itk::Vector spacing3; itk::Point origin3; itk::Matrix direction3; ImageRegion<3> imageRegion3; if (!m_MaskImage.IsNull()) { spacing3 = m_MaskImage->GetSpacing(); imageRegion3 = m_MaskImage->GetLargestPossibleRegion(); origin3 = m_MaskImage->GetOrigin(); direction3 = m_MaskImage->GetDirection(); } else { spacing3 = geometry->GetSpacing(); origin3 = geometry->GetOrigin(); mitk::BaseGeometry::BoundsArrayType bounds = geometry->GetBounds(); origin3[0] += bounds.GetElement(0); origin3[1] += bounds.GetElement(2); origin3[2] += bounds.GetElement(4); for (int i=0; i<3; i++) for (int j=0; j<3; j++) direction3[j][i] = geometry->GetMatrixColumn(i)[j]; imageRegion3.SetSize(0, geometry->GetExtent(0)+1); imageRegion3.SetSize(1, geometry->GetExtent(1)+1); imageRegion3.SetSize(2, geometry->GetExtent(2)+1); m_MaskImage = ItkUcharImgType::New(); m_MaskImage->SetSpacing( spacing3 ); m_MaskImage->SetOrigin( origin3 ); m_MaskImage->SetDirection( direction3 ); m_MaskImage->SetRegions( imageRegion3 ); m_MaskImage->Allocate(); m_MaskImage->FillBuffer(1); } OutputImageType::RegionType::SizeType outImageSize = imageRegion3.GetSize(); m_OutImageSpacing = m_MaskImage->GetSpacing(); m_ClusteredDirectionsContainer = ContainerType::New(); // initialize num directions image m_NumDirectionsImage = ItkUcharImgType::New(); m_NumDirectionsImage->SetSpacing( spacing3 ); m_NumDirectionsImage->SetOrigin( origin3 ); m_NumDirectionsImage->SetDirection( direction3 ); m_NumDirectionsImage->SetRegions( imageRegion3 ); m_NumDirectionsImage->Allocate(); m_NumDirectionsImage->FillBuffer(0); itk::Vector spacing4; itk::Point origin4; itk::Matrix direction4; itk::ImageRegion<4> imageRegion4; spacing4[0] = spacing3[0]; spacing4[1] = spacing3[1]; spacing4[2] = spacing3[2]; spacing4[3] = 1; origin4[0] = origin3[0]; origin4[1] = origin3[1]; origin4[2] = origin3[2]; origin3[3] = 0; for (int r=0; r<3; r++) for (int c=0; c<3; c++) direction4[r][c] = direction3[r][c]; direction4[3][3] = 1; imageRegion4.SetSize(0, imageRegion3.GetSize()[0]); imageRegion4.SetSize(1, imageRegion3.GetSize()[1]); imageRegion4.SetSize(2, imageRegion3.GetSize()[2]); imageRegion4.SetSize(3, m_MaxNumDirections*3); m_DirectionImage = ItkDirectionImageType::New(); m_DirectionImage->SetSpacing( spacing4 ); m_DirectionImage->SetOrigin( origin4 ); m_DirectionImage->SetDirection( direction4 ); m_DirectionImage->SetRegions( imageRegion4 ); m_DirectionImage->Allocate(); m_DirectionImage->FillBuffer(0.0); // iterate over all fibers vtkSmartPointer fiberPolyData = m_FiberBundle->GetFiberPolyData(); int numFibers = m_FiberBundle->GetNumFibers(); m_DirectionsContainer = ContainerType::New(); VectorContainer< unsigned int, std::vector< double > >::Pointer peakLengths = VectorContainer< unsigned int, std::vector< double > >::New(); MITK_INFO << "Generating directions from tractogram"; boost::progress_display disp(numFibers); for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) continue; vnl_vector_fixed dir; vnl_vector v; float fiberWeight = m_FiberBundle->GetFiberWeight(i); for( int j=0; j startVertex = GetItkPoint(points->GetPoint(j)); itk::Index<3> startIndex; itk::ContinuousIndex startIndexCont; m_MaskImage->TransformPhysicalPointToIndex(startVertex, startIndex); m_MaskImage->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont); itk::Point endVertex = GetItkPoint(points->GetPoint(j + 1)); itk::Index<3> endIndex; itk::ContinuousIndex endIndexCont; m_MaskImage->TransformPhysicalPointToIndex(endVertex, endIndex); m_MaskImage->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont); dir[0] = endVertex[0]-startVertex[0]; dir[1] = endVertex[1]-startVertex[1]; dir[2] = endVertex[2]-startVertex[2]; if (dir.is_zero()) continue; dir.normalize(); std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing3, startIndex, endIndex, startIndexCont, endIndexCont); for (std::pair< itk::Index<3>, double > segment : segments) { - if (!m_MaskImage->GetLargestPossibleRegion().IsInside(segment.first) || m_MaskImage->GetPixel(segment.first)==0) + if (!m_MaskImage->GetLargestPossibleRegion().IsInside(segment.first) || (!m_OnlyUseMaskGeometry && m_MaskImage->GetPixel(segment.first)==0)) continue; // add direction to container unsigned int idx = segment.first[0] + outImageSize[0]*(segment.first[1] + outImageSize[1]*segment.first[2]); DirectionContainerType::Pointer dirCont; if (m_DirectionsContainer->IndexExists(idx)) { peakLengths->ElementAt(idx).push_back(fiberWeight*segment.second); dirCont = m_DirectionsContainer->GetElement(idx); if (dirCont.IsNull()) { dirCont = DirectionContainerType::New(); dirCont->push_back(dir); m_DirectionsContainer->InsertElement(idx, dirCont); } else dirCont->push_back(dir); } else { dirCont = DirectionContainerType::New(); dirCont->push_back(dir); m_DirectionsContainer->InsertElement(idx, dirCont); std::vector< double > lengths; lengths.push_back(fiberWeight*segment.second); peakLengths->InsertElement(idx, lengths); } } } } itk::ImageRegionIterator dirIt(m_NumDirectionsImage, m_NumDirectionsImage->GetLargestPossibleRegion()); MITK_INFO << "Clustering directions"; float max_dir_mag = 0; boost::progress_display disp2(outImageSize[0]*outImageSize[1]*outImageSize[2]); while(!dirIt.IsAtEnd()) { ++disp2; OutputImageType::IndexType idx3 = dirIt.GetIndex(); int idx_lin = idx3[0]+(idx3[1]+idx3[2]*outImageSize[1])*outImageSize[0]; itk::Index<4> idx4; idx4[0] = idx3[0]; idx4[1] = idx3[1]; idx4[2] = idx3[2]; if (!m_DirectionsContainer->IndexExists(idx_lin)) { ++dirIt; continue; } DirectionContainerType::Pointer dirCont = m_DirectionsContainer->GetElement(idx_lin); if (dirCont.IsNull() || dirCont->empty()) { ++dirIt; continue; } DirectionContainerType::Pointer directions; if (m_MaxNumDirections>0) { directions = FastClustering(dirCont, peakLengths->GetElement(idx_lin)); std::sort( directions->begin(), directions->end(), CompareVectorLengths ); } else directions = dirCont; unsigned int numDir = directions->size(); if (m_MaxNumDirections>0 && numDir>m_MaxNumDirections) numDir = m_MaxNumDirections; float voxel_max_mag = 0; for (unsigned int i=0; iat(i); float mag = dir.magnitude(); if (mag>voxel_max_mag) voxel_max_mag = mag; if (mag>max_dir_mag) max_dir_mag = mag; } int count = 0; for (unsigned int i=0; iat(i); count++; float mag = dir.magnitude(); if (m_NormalizationMethod==MAX_VEC_NORM && voxel_max_mag>mitk::eps) dir /= voxel_max_mag; else if (m_NormalizationMethod==SINGLE_VEC_NORM && mag>mitk::eps) dir.normalize(); for (unsigned int j = 0; j<3; j++) { idx4[3] = i*3 + j; m_DirectionImage->SetPixel(idx4, dir[j]); } } dirIt.Set(count); ++dirIt; } if (m_NormalizationMethod==GLOBAL_MAX && max_dir_mag>0) { itk::ImageRegionIterator dirImgIt(m_DirectionImage, m_DirectionImage->GetLargestPossibleRegion()); while(!dirImgIt.IsAtEnd()) { dirImgIt.Set(dirImgIt.Get()/max_dir_mag); ++dirImgIt; } } } template< class PixelType > TractsToVectorImageFilter< PixelType >::DirectionContainerType::Pointer TractsToVectorImageFilter< PixelType >::FastClustering(DirectionContainerType::Pointer inDirs, std::vector< double > lengths) { DirectionContainerType::Pointer outDirs = DirectionContainerType::New(); if (inDirs->size()<2) { if (inDirs->size()==1) inDirs->SetElement(0, inDirs->at(0)*lengths.at(0)); return inDirs; } DirectionType oldMean, currentMean; std::vector< int > touched; // initialize touched.resize(inDirs->size(), 0); bool free = true; currentMean = inDirs->at(0); // initialize first seed currentMean.normalize(); double length = lengths.at(0); touched[0] = 1; std::vector< double > newLengths; bool meanChanged = false; double max = 0; while (free) { oldMean.fill(0.0); // start mean-shift clustering double angle = 0; while (fabs(dot_product(currentMean, oldMean))<0.99) { oldMean = currentMean; currentMean.fill(0.0); for (unsigned int i=0; isize(); i++) { angle = dot_product(oldMean, inDirs->at(i)); if (angle>=m_AngularThreshold) { currentMean += inDirs->at(i); if (meanChanged) length += lengths.at(i); touched[i] = 1; meanChanged = true; } else if (-angle>=m_AngularThreshold) { currentMean -= inDirs->at(i); if (meanChanged) length += lengths.at(i); touched[i] = 1; meanChanged = true; } } if(!meanChanged) currentMean = oldMean; else currentMean.normalize(); } // found stable mean outDirs->push_back(currentMean); newLengths.push_back(length); if (length>max) max = length; // find next unused seed free = false; for (unsigned int i=0; iat(i); free = true; meanChanged = false; length = lengths.at(i); touched[i] = 1; break; } } if (inDirs->size()==outDirs->size()) { if (max>0) { for (unsigned int i=0; isize(); i++) outDirs->SetElement(i, outDirs->at(i)*newLengths.at(i)); } return outDirs; } else return FastClustering(outDirs, newLengths); } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.h index e8c9f4a0b7..6775611bb3 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.h @@ -1,103 +1,105 @@ #ifndef __itkTractsToVectorImageFilter_h__ #define __itkTractsToVectorImageFilter_h__ // MITK #include // ITK #include #include // VTK #include #include #include #include #include namespace itk{ /** * \brief Extracts the voxel-wise main directions of the input fiber bundle. */ template< class PixelType > class TractsToVectorImageFilter : public ImageSource< Image< PixelType, 4 > > { public: enum NormalizationMethods { GLOBAL_MAX, ///< global maximum normalization SINGLE_VEC_NORM, ///< normalize the single peaks to length 1 MAX_VEC_NORM ///< normalize all peaks according to their length in comparison to the largest peak in the voxel (0-1) }; typedef TractsToVectorImageFilter Self; typedef ProcessObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef itk::Vector OutputVectorType; typedef itk::Image OutputImageType; typedef std::vector< OutputImageType::Pointer > OutputImageContainerType; typedef vnl_vector_fixed< double, 3 > DirectionType; typedef VectorContainer< unsigned int, DirectionType > DirectionContainerType; typedef VectorContainer< unsigned int, DirectionContainerType::Pointer > ContainerType; typedef Image< PixelType, 4 > ItkDirectionImageType; typedef itk::Image ItkUcharImgType; typedef itk::Image ItkDoubleImgType; itkFactorylessNewMacro(Self) itkCloneMacro(Self) itkTypeMacro( TractsToVectorImageFilter, ImageSource ) itkSetMacro( SizeThreshold, float) itkGetMacro( SizeThreshold, float) itkSetMacro( AngularThreshold, float) ///< cluster directions that are closer together than the specified threshold itkGetMacro( AngularThreshold, float) ///< cluster directions that are closer together than the specified threshold itkSetMacro( NormalizationMethod, NormalizationMethods) ///< normalization method of peaks itkSetMacro( MaxNumDirections, unsigned long) ///< If more directions are extracted, only the largest are kept. itkGetMacro( MaxNumDirections, unsigned long) ///< If more directions are extracted, only the largest are kept. itkSetMacro( MaskImage, ItkUcharImgType::Pointer) ///< only process voxels inside mask itkSetMacro( FiberBundle, mitk::FiberBundle::Pointer) ///< input fiber bundle + itkSetMacro( OnlyUseMaskGeometry, bool) ///< don't use content of mask image, only use it's geometry itkGetMacro( ClusteredDirectionsContainer, ContainerType::Pointer) ///< output directions itkGetMacro( NumDirectionsImage, ItkUcharImgType::Pointer) ///< number of directions per voxel itkGetMacro( DirectionImage, typename ItkDirectionImageType::Pointer) ///< output directions void GenerateData() override; protected: DirectionContainerType::Pointer FastClustering(DirectionContainerType::Pointer inDirs, std::vector< double > lengths); ///< cluster fiber directions vnl_vector_fixed GetVnlVector(double point[3]); itk::Point GetItkPoint(double point[3]); TractsToVectorImageFilter(); ~TractsToVectorImageFilter() override; NormalizationMethods m_NormalizationMethod; ///< normalization method of peaks mitk::FiberBundle::Pointer m_FiberBundle; ///< input fiber bundle float m_AngularThreshold; ///< cluster directions that are closer together than the specified threshold float m_Epsilon; ///< epsilon for vector equality check ItkUcharImgType::Pointer m_MaskImage; ///< only voxels inside the binary mask are processed itk::Vector m_OutImageSpacing; ///< spacing of output image ContainerType::Pointer m_DirectionsContainer; ///< container for fiber directions unsigned long m_MaxNumDirections; ///< if more directions per voxel are extracted, only the largest are kept float m_SizeThreshold; + bool m_OnlyUseMaskGeometry; // output datastructures typename ItkDirectionImageType::Pointer m_DirectionImage; ContainerType::Pointer m_ClusteredDirectionsContainer; ///< contains direction vectors for each voxel ItkUcharImgType::Pointer m_NumDirectionsImage; ///< shows number of fibers per voxel }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkTractsToVectorImageFilter.cpp" #endif #endif // __itkTractsToVectorImageFilter_h__ diff --git a/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt b/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt index 36f9917b3c..c0be517ec4 100644 --- a/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt +++ b/Modules/DiffusionImaging/FiberTracking/CMakeLists.txt @@ -1,52 +1,47 @@ set(_module_deps MitkDiffusionCore MitkGraphAlgorithms MitkCLVigraRandomForest) mitk_check_module_dependencies( MODULES ${_module_deps} MISSING_DEPENDENCIES_VAR _missing_deps ) if(NOT _missing_deps) set(lut_url http://mitk.org/download/data/FibertrackingLUT.tar.gz) set(lut_tarball ${CMAKE_CURRENT_BINARY_DIR}/FibertrackingLUT.tar.gz) 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-DTI INCLUDE_DIRS Fiberfox Fiberfox/SignalModels Fiberfox/Sequences Algorithms Algorithms/TrackingHandlers Algorithms/ClusteringMetrics Algorithms/GibbsTracking Algorithms/StochasticTracking IODataStructures IODataStructures/FiberBundle IODataStructures/PlanarFigureComposite Rendering ${CMAKE_CURRENT_BINARY_DIR} DEPENDS ${_module_deps} PACKAGE_DEPENDS PUBLIC ITK|ITKFFT ITK|ITKDiffusionTensorImage Vigra HDF5 ) if(MODULE_IS_ENABLED) - add_subdirectory(cmdapps/Fiberfox) - add_subdirectory(cmdapps/FiberProcessing) - add_subdirectory(cmdapps/Tractography) - add_subdirectory(cmdapps/TractographyEvaluation) - add_subdirectory(cmdapps/Misc) add_subdirectory(Testing) endif() diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.cpp index bc3ff77cdb..b06e860a2a 100755 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.cpp @@ -1,2653 +1,2765 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkFiberBundle.h" #include #include #include #include "mitkImagePixelReadAccessor.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include const char* mitk::FiberBundle::FIBER_ID_ARRAY = "Fiber_IDs"; mitk::FiberBundle::FiberBundle( vtkPolyData* fiberPolyData ) : m_NumFibers(0) { m_FiberWeights = vtkSmartPointer::New(); m_FiberWeights->SetName("FIBER_WEIGHTS"); m_FiberPolyData = vtkSmartPointer::New(); if (fiberPolyData != nullptr) m_FiberPolyData = fiberPolyData; else { this->m_FiberPolyData->SetPoints(vtkSmartPointer::New()); this->m_FiberPolyData->SetLines(vtkSmartPointer::New()); } this->UpdateFiberGeometry(); this->GenerateFiberIds(); this->ColorFibersByOrientation(); } mitk::FiberBundle::~FiberBundle() { } mitk::FiberBundle::Pointer mitk::FiberBundle::GetDeepCopy() { mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(m_FiberPolyData); newFib->SetFiberColors(this->m_FiberColors); newFib->SetFiberWeights(this->m_FiberWeights); return newFib; } vtkSmartPointer mitk::FiberBundle::GeneratePolyDataByIds(std::vector fiberIds, vtkSmartPointer weights) { vtkSmartPointer newFiberPolyData = vtkSmartPointer::New(); vtkSmartPointer newLineSet = vtkSmartPointer::New(); vtkSmartPointer newPointSet = vtkSmartPointer::New(); weights->SetNumberOfValues(fiberIds.size()); int counter = 0; auto finIt = fiberIds.begin(); while ( finIt != fiberIds.end() ) { if (*finIt < 0 || *finIt>GetNumFibers()){ MITK_INFO << "FiberID can not be negative or >NumFibers!!! check id Extraction!" << *finIt; break; } vtkSmartPointer fiber = m_FiberIdDataSet->GetCell(*finIt);//->DeepCopy(fiber); vtkSmartPointer fibPoints = fiber->GetPoints(); vtkSmartPointer newFiber = vtkSmartPointer::New(); newFiber->GetPointIds()->SetNumberOfIds( fibPoints->GetNumberOfPoints() ); for(int i=0; iGetNumberOfPoints(); i++) { newFiber->GetPointIds()->SetId(i, newPointSet->GetNumberOfPoints()); newPointSet->InsertNextPoint(fibPoints->GetPoint(i)[0], fibPoints->GetPoint(i)[1], fibPoints->GetPoint(i)[2]); } weights->InsertValue(counter, this->GetFiberWeight(*finIt)); newLineSet->InsertNextCell(newFiber); ++finIt; ++counter; } newFiberPolyData->SetPoints(newPointSet); newFiberPolyData->SetLines(newLineSet); return newFiberPolyData; } // merge two fiber bundles mitk::FiberBundle::Pointer mitk::FiberBundle::AddBundles(std::vector< mitk::FiberBundle::Pointer > fibs) { vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // add current fiber bundle vtkSmartPointer weights = vtkSmartPointer::New(); int num_weights = this->GetNumFibers(); for (auto fib : fibs) num_weights += fib->GetNumFibers(); weights->SetNumberOfValues(num_weights); unsigned int counter = 0; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, this->GetFiberWeight(i)); vNewLines->InsertNextCell(container); counter++; } for (auto fib : fibs) { // add new fiber bundle for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, fib->GetFiberWeight(i)); vNewLines->InsertNextCell(container); counter++; } } // initialize PolyData vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData); newFib->SetFiberWeights(weights); return newFib; } // merge two fiber bundles mitk::FiberBundle::Pointer mitk::FiberBundle::AddBundle(mitk::FiberBundle* fib) { if (fib==nullptr) return this->GetDeepCopy(); MITK_INFO << "Adding fibers"; vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // add current fiber bundle vtkSmartPointer weights = vtkSmartPointer::New(); weights->SetNumberOfValues(this->GetNumFibers()+fib->GetNumFibers()); unsigned int counter = 0; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, this->GetFiberWeight(i)); vNewLines->InsertNextCell(container); counter++; } // add new fiber bundle for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, fib->GetFiberWeight(i)); vNewLines->InsertNextCell(container); counter++; } // initialize PolyData vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData); newFib->SetFiberWeights(weights); return newFib; } // Only retain fibers with a weight larger than the specified threshold mitk::FiberBundle::Pointer mitk::FiberBundle::FilterByWeights(float weight_thr, bool invert) { vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); std::vector weights; for (int i=0; iGetNumFibers(); i++) { if ( (invert && this->GetFiberWeight(i)>weight_thr) || (!invert && this->GetFiberWeight(i)<=weight_thr)) continue; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); weights.push_back(this->GetFiberWeight(i)); } // initialize PolyData vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData); for (unsigned int i=0; iSetFiberWeight(i, weights.at(i)); return newFib; } // Only retain a subsample of the fibers mitk::FiberBundle::Pointer mitk::FiberBundle::SubsampleFibers(float factor) { vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); int new_num_fibs = this->GetNumFibers()*factor; MITK_INFO << "Subsampling fibers with factor " << factor << "(" << new_num_fibs << "/" << this->GetNumFibers() << ")"; // add current fiber bundle vtkSmartPointer weights = vtkSmartPointer::New(); weights->SetNumberOfValues(new_num_fibs); std::vector< int > ids; for (int i=0; iGetNumFibers(); i++) ids.push_back(i); std::random_shuffle(ids.begin(), ids.end()); unsigned int counter = 0; for (int i=0; iGetCell(ids.at(i)); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } weights->InsertValue(counter, this->GetFiberWeight(ids.at(i))); vNewLines->InsertNextCell(container); counter++; } // initialize PolyData vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(vNewPolyData); newFib->SetFiberWeights(weights); return newFib; } // subtract two fiber bundles mitk::FiberBundle::Pointer mitk::FiberBundle::SubtractBundle(mitk::FiberBundle* fib) { if (fib==nullptr) return this->GetDeepCopy(); MITK_INFO << "Subtracting fibers"; vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); std::vector< std::vector< itk::Point > > points1; for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (points==nullptr || numPoints<=0) continue; itk::Point start = GetItkPoint(points->GetPoint(0)); itk::Point end = GetItkPoint(points->GetPoint(numPoints-1)); points1.push_back( {start, end} ); } std::vector< std::vector< itk::Point > > points2; for( int i=0; iGetNumFibers(); i++ ) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (points==nullptr || numPoints<=0) continue; itk::Point start = GetItkPoint(points->GetPoint(0)); itk::Point end = GetItkPoint(points->GetPoint(numPoints-1)); points2.push_back( {start, end} ); } // int progress = 0; std::vector< int > ids; #pragma omp parallel for for (int i=0; i<(int)points1.size(); i++) { //#pragma omp critical // { // progress++; // std::cout << (int)(100*(float)progress/points1.size()) << "%" << '\r'; // cout.flush(); // } bool match = false; for (unsigned int j=0; jGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (points==nullptr || numPoints<=0) continue; vtkSmartPointer container = vtkSmartPointer::New(); for( int j=0; jInsertNextPoint(points->GetPoint(j)); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } if(vNewLines->GetNumberOfCells()==0) return mitk::FiberBundle::New(); // initialize PolyData vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle return mitk::FiberBundle::New(vNewPolyData); } itk::Point mitk::FiberBundle::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } /* * set PolyData (additional flag to recompute fiber geometry, default = true) */ void mitk::FiberBundle::SetFiberPolyData(vtkSmartPointer fiberPD, bool updateGeometry) { if (fiberPD == nullptr) this->m_FiberPolyData = vtkSmartPointer::New(); else m_FiberPolyData->DeepCopy(fiberPD); m_NumFibers = m_FiberPolyData->GetNumberOfLines(); if (updateGeometry) UpdateFiberGeometry(); GenerateFiberIds(); ColorFibersByOrientation(); } /* * return vtkPolyData */ vtkSmartPointer mitk::FiberBundle::GetFiberPolyData() const { return m_FiberPolyData; } void mitk::FiberBundle::ColorFibersByLength(bool opacity, bool normalize) { if (m_MaxFiberLength<=0) return; int numOfPoints = this->GetNumberOfPoints(); //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; int componentSize = 4; m_FiberColors = vtkSmartPointer::New(); m_FiberColors->Allocate(numOfPoints * componentSize); m_FiberColors->SetNumberOfComponents(componentSize); m_FiberColors->SetName("FIBER_COLORS"); int numOfFibers = m_FiberPolyData->GetNumberOfLines(); if (numOfFibers < 1) return; mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New(); vtkSmartPointer lookupTable = vtkSmartPointer::New(); lookupTable->SetTableRange(0.0, 0.8); lookupTable->Build(); mitkLookup->SetVtkLookupTable(lookupTable); mitkLookup->SetType(mitk::LookupTable::JET); unsigned int count = 0; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); float l = m_FiberLengths.at(i)/m_MaxFiberLength; if (!normalize) { l = m_FiberLengths.at(i)/255.0; if (l > 1.0) l = 1.0; } for (int j=0; jGetColor(1.0 - l, color); rgba[0] = (unsigned char) (255.0 * color[0]); rgba[1] = (unsigned char) (255.0 * color[1]); rgba[2] = (unsigned char) (255.0 * color[2]); if (opacity) rgba[3] = (unsigned char) (255.0 * l); else rgba[3] = (unsigned char) (255.0); m_FiberColors->InsertTypedTuple(cell->GetPointId(j), rgba); count++; } } m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } void mitk::FiberBundle::ColorFibersByOrientation() { //===== FOR WRITING A TEST ======================== // colorT size == tupelComponents * tupelElements // compare color results // to cover this code 100% also PolyData needed, where colorarray already exists // + one fiber with exactly 1 point // + one fiber with 0 points //================================================= vtkPoints* extrPoints = nullptr; extrPoints = m_FiberPolyData->GetPoints(); int numOfPoints = 0; if (extrPoints!=nullptr) numOfPoints = extrPoints->GetNumberOfPoints(); //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; int componentSize = 4; m_FiberColors = vtkSmartPointer::New(); m_FiberColors->Allocate(numOfPoints * componentSize); m_FiberColors->SetNumberOfComponents(componentSize); m_FiberColors->SetName("FIBER_COLORS"); int numOfFibers = m_FiberPolyData->GetNumberOfLines(); if (numOfFibers < 1) return; /* extract single fibers of fiberBundle */ vtkCellArray* fiberList = m_FiberPolyData->GetLines(); fiberList->InitTraversal(); for (int fi=0; fiGetNextCell(pointsPerFiber, idList); /* single fiber checkpoints: is number of points valid */ if (pointsPerFiber > 1) { /* operate on points of single fiber */ for (int i=0; i 0) { /* The color value of the current point is influenced by the previous point and next point. */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); vnl_vector_fixed< double, 3 > diff1; diff1 = currentPntvtk - nextPntvtk; vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; vnl_vector_fixed< double, 3 > diff; diff = (diff1 - diff2) / 2.0; diff.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff[2])); rgba[3] = (unsigned char) (255.0); } else if (i==0) { /* First point has no previous point, therefore only diff1 is taken */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); vnl_vector_fixed< double, 3 > diff1; diff1 = currentPntvtk - nextPntvtk; diff1.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff1[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff1[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff1[2])); rgba[3] = (unsigned char) (255.0); } else if (i==pointsPerFiber-1) { /* Last point has no next point, therefore only diff2 is taken */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; diff2.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff2[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff2[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff2[2])); rgba[3] = (unsigned char) (255.0); } m_FiberColors->InsertTypedTuple(idList[i], rgba); } } else if (pointsPerFiber == 1) { /* a single point does not define a fiber (use vertex mechanisms instead */ continue; } else { MITK_DEBUG << "Fiber with 0 points detected... please check your tractography algorithm!" ; continue; } } m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } void mitk::FiberBundle::ColorFibersByCurvature(bool, bool normalize) { double window = 5; //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; int componentSize = 4; m_FiberColors = vtkSmartPointer::New(); m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * componentSize); m_FiberColors->SetNumberOfComponents(componentSize); m_FiberColors->SetName("FIBER_COLORS"); mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New(); vtkSmartPointer lookupTable = vtkSmartPointer::New(); lookupTable->SetTableRange(0.0, 0.8); lookupTable->Build(); mitkLookup->SetVtkLookupTable(lookupTable); mitkLookup->SetType(mitk::LookupTable::JET); std::vector< double > values; double min = 1; double max = 0; MITK_INFO << "Coloring fibers by curvature"; boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); for (int i=0; iGetNumberOfCells(); i++) { ++disp; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); // calculate curvatures for (int j=0; j > vectors; vnl_vector_fixed< float, 3 > meanV; meanV.fill(0.0); while(dist1) { double p1[3]; points->GetPoint(c-1, p1); double p2[3]; points->GetPoint(c, p2); vnl_vector_fixed< float, 3 > v; v[0] = p2[0]-p1[0]; v[1] = p2[1]-p1[1]; v[2] = p2[2]-p1[2]; dist += v.magnitude(); v.normalize(); vectors.push_back(v); meanV += v; c--; } c = j; dist = 0; while(distGetPoint(c, p1); double p2[3]; points->GetPoint(c+1, p2); vnl_vector_fixed< float, 3 > v; v[0] = p2[0]-p1[0]; v[1] = p2[1]-p1[1]; v[2] = p2[2]-p1[2]; dist += v.magnitude(); v.normalize(); vectors.push_back(v); meanV += v; c++; } meanV.normalize(); double dev = 0; for (unsigned int c=0; c1.0) angle = 1.0; if (angle<-1.0) angle = -1.0; dev += acos(angle)*180/itk::Math::pi; } if (vectors.size()>0) dev /= vectors.size(); dev = 1.0-dev/180.0; values.push_back(dev); if (devmax) max = dev; } } unsigned int count = 0; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); for (int j=0; j1) dev = 1; lookupTable->GetColor(dev, color); rgba[0] = (unsigned char) (255.0 * color[0]); rgba[1] = (unsigned char) (255.0 * color[1]); rgba[2] = (unsigned char) (255.0 * color[2]); rgba[3] = (unsigned char) (255.0); m_FiberColors->InsertTypedTuple(cell->GetPointId(j), rgba); count++; } } m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } void mitk::FiberBundle::SetFiberOpacity(vtkDoubleArray* FAValArray) { for(long i=0; iGetNumberOfTuples(); i++) { double faValue = FAValArray->GetValue(i); faValue = faValue * 255.0; m_FiberColors->SetComponent(i,3, (unsigned char) faValue ); } m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } void mitk::FiberBundle::ResetFiberOpacity() { for(long i=0; iGetNumberOfTuples(); i++) m_FiberColors->SetComponent(i,3, 255.0 ); m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } void mitk::FiberBundle::ColorFibersByScalarMap(mitk::Image::Pointer FAimage, bool opacity, bool normalize) { mitkPixelTypeMultiplex3( ColorFibersByScalarMap, FAimage->GetPixelType(), FAimage, opacity, normalize ); m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } template void mitk::FiberBundle::ColorFibersByScalarMap(const mitk::PixelType, mitk::Image::Pointer image, bool opacity, bool normalize) { m_FiberColors = vtkSmartPointer::New(); m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4); m_FiberColors->SetNumberOfComponents(4); m_FiberColors->SetName("FIBER_COLORS"); mitk::ImagePixelReadAccessor readimage(image, image->GetVolumeData(0)); unsigned char rgba[4] = {0,0,0,0}; vtkPoints* pointSet = m_FiberPolyData->GetPoints(); mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New(); vtkSmartPointer lookupTable = vtkSmartPointer::New(); lookupTable->SetTableRange(0.0, 0.8); lookupTable->Build(); mitkLookup->SetVtkLookupTable(lookupTable); mitkLookup->SetType(mitk::LookupTable::JET); double min = 9999999; double max = -9999999; for(long i=0; iGetNumberOfPoints(); ++i) { Point3D px; px[0] = pointSet->GetPoint(i)[0]; px[1] = pointSet->GetPoint(i)[1]; px[2] = pointSet->GetPoint(i)[2]; double pixelValue = readimage.GetPixelByWorldCoordinates(px); if (pixelValue>max) max = pixelValue; if (pixelValueGetNumberOfPoints(); ++i) { Point3D px; px[0] = pointSet->GetPoint(i)[0]; px[1] = pointSet->GetPoint(i)[1]; px[2] = pointSet->GetPoint(i)[2]; double pixelValue = readimage.GetPixelByWorldCoordinates(px); if (normalize) pixelValue = (pixelValue-min)/(max-min); else if (pixelValue>1) pixelValue = 1; double color[3]; lookupTable->GetColor(1-pixelValue, color); rgba[0] = (unsigned char) (255.0 * color[0]); rgba[1] = (unsigned char) (255.0 * color[1]); rgba[2] = (unsigned char) (255.0 * color[2]); if (opacity) rgba[3] = (unsigned char) (255.0 * pixelValue); else rgba[3] = (unsigned char) (255.0); m_FiberColors->InsertTypedTuple(i, rgba); } m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } void mitk::FiberBundle::ColorFibersByFiberWeights(bool opacity, bool normalize) { m_FiberColors = vtkSmartPointer::New(); m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4); m_FiberColors->SetNumberOfComponents(4); m_FiberColors->SetName("FIBER_COLORS"); mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New(); vtkSmartPointer lookupTable = vtkSmartPointer::New(); lookupTable->SetTableRange(0.0, 0.8); lookupTable->Build(); mitkLookup->SetVtkLookupTable(lookupTable); mitkLookup->SetType(mitk::LookupTable::JET); unsigned char rgba[4] = {0,0,0,0}; unsigned int counter = 0; float max = -999999; float min = 999999; for (int i=0; iGetFiberWeight(i); if (weight>max) max = weight; if (weightGetCell(i); int numPoints = cell->GetNumberOfPoints(); double weight = this->GetFiberWeight(i); for (int j=0; j1) v = 1; double color[3]; lookupTable->GetColor(1-v, color); rgba[0] = (unsigned char) (255.0 * color[0]); rgba[1] = (unsigned char) (255.0 * color[1]); rgba[2] = (unsigned char) (255.0 * color[2]); if (opacity) rgba[3] = (unsigned char) (255.0 * v); else rgba[3] = (unsigned char) (255.0); m_FiberColors->InsertTypedTuple(counter, rgba); counter++; } } m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } void mitk::FiberBundle::SetFiberColors(float r, float g, float b, float alpha) { m_FiberColors = vtkSmartPointer::New(); m_FiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4); m_FiberColors->SetNumberOfComponents(4); m_FiberColors->SetName("FIBER_COLORS"); unsigned char rgba[4] = {0,0,0,0}; for(long i=0; iGetNumberOfPoints(); ++i) { rgba[0] = (unsigned char) r; rgba[1] = (unsigned char) g; rgba[2] = (unsigned char) b; rgba[3] = (unsigned char) alpha; m_FiberColors->InsertTypedTuple(i, rgba); } m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } void mitk::FiberBundle::GenerateFiberIds() { if (m_FiberPolyData == nullptr) return; vtkSmartPointer idFiberFilter = vtkSmartPointer::New(); idFiberFilter->SetInputData(m_FiberPolyData); idFiberFilter->CellIdsOn(); // idFiberFilter->PointIdsOn(); // point id's are not needed idFiberFilter->SetIdsArrayName(FIBER_ID_ARRAY); idFiberFilter->FieldDataOn(); idFiberFilter->Update(); m_FiberIdDataSet = idFiberFilter->GetOutput(); } +float mitk::FiberBundle::GetNumEpFractionInMask(ItkUcharImgType* mask, bool different_label) +{ + vtkSmartPointer PolyData = m_FiberPolyData; + + MITK_INFO << "Calculating EP-Fraction"; + + boost::progress_display disp(m_NumFibers); + unsigned int in_mask = 0; + + for (int i=0; iGetCell(i); + int numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + + itk::Point startVertex = GetItkPoint(points->GetPoint(0)); + itk::Index<3> startIndex; + mask->TransformPhysicalPointToIndex(startVertex, startIndex); + + itk::Point endVertex = GetItkPoint(points->GetPoint(numPoints-1)); + itk::Index<3> endIndex; + mask->TransformPhysicalPointToIndex(endVertex, endIndex); + + if (mask->GetLargestPossibleRegion().IsInside(startIndex) && mask->GetLargestPossibleRegion().IsInside(endIndex)) + { + float v1 = mask->GetPixel(startIndex); + if (v1 < 0.5) + continue; + float v2 = mask->GetPixel(startIndex); + if (v2 < 0.5) + continue; + + if (!different_label) + ++in_mask; + else if (v1 != v2) + ++in_mask; + } + } + return float(in_mask)/m_NumFibers; +} + +std::tuple mitk::FiberBundle::GetDirectionalOverlap(ItkUcharImgType* mask, mitk::PeakImage::ItkPeakImageType* peak_image) +{ + vtkSmartPointer PolyData = m_FiberPolyData; + + MITK_INFO << "Calculating overlap"; + auto spacing = mask->GetSpacing(); + boost::progress_display disp(m_NumFibers); + float length_sum = 0; + float in_mask_length = 0; + float aligned_length = 0; + for (int i=0; iGetCell(i); + int numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + + for (int j=0; j startVertex = GetItkPoint(points->GetPoint(j)); + itk::Index<3> startIndex; + itk::ContinuousIndex startIndexCont; + mask->TransformPhysicalPointToIndex(startVertex, startIndex); + mask->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont); + + itk::Point endVertex = GetItkPoint(points->GetPoint(j + 1)); + itk::Index<3> endIndex; + itk::ContinuousIndex endIndexCont; + mask->TransformPhysicalPointToIndex(endVertex, endIndex); + mask->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont); + + vnl_vector_fixed< float, 3 > fdir; + fdir[0] = endVertex[0] - startVertex[0]; + fdir[1] = endVertex[1] - startVertex[1]; + fdir[2] = endVertex[2] - startVertex[2]; + fdir.normalize(); + + std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont); + for (std::pair< itk::Index<3>, double > segment : segments) + { + if ( mask->GetLargestPossibleRegion().IsInside(segment.first) && mask->GetPixel(segment.first) > 0 ) + { + in_mask_length += segment.second; + + mitk::PeakImage::ItkPeakImageType::IndexType idx4; + idx4[0] = segment.first[0]; + idx4[1] = segment.first[1]; + idx4[2] = segment.first[2]; + + vnl_vector_fixed< float, 3 > peak; + idx4[3] = 0; + peak[0] = peak_image->GetPixel(idx4); + idx4[3] = 1; + peak[1] = peak_image->GetPixel(idx4); + idx4[3] = 2; + peak[2] = peak_image->GetPixel(idx4); + peak.normalize(); + + float f = 1.0 - std::acos(std::fabs(dot_product(fdir, peak))) * 2.0/itk::Math::pi; + aligned_length += segment.second * f; + } + length_sum += segment.second; + } + } + } + + if (length_sum==0) + { + MITK_INFO << "Fiber length sum is zero!"; + return std::make_tuple(0,0); + } + return std::make_tuple(aligned_length/length_sum, in_mask_length/length_sum); +} + float mitk::FiberBundle::GetOverlap(ItkUcharImgType* mask) { vtkSmartPointer PolyData = m_FiberPolyData; MITK_INFO << "Calculating overlap"; auto spacing = mask->GetSpacing(); boost::progress_display disp(m_NumFibers); double length_sum = 0; double in_mask_length = 0; for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; j startVertex = GetItkPoint(points->GetPoint(j)); itk::Index<3> startIndex; itk::ContinuousIndex startIndexCont; mask->TransformPhysicalPointToIndex(startVertex, startIndex); mask->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont); itk::Point endVertex = GetItkPoint(points->GetPoint(j + 1)); itk::Index<3> endIndex; itk::ContinuousIndex endIndexCont; mask->TransformPhysicalPointToIndex(endVertex, endIndex); mask->TransformPhysicalPointToContinuousIndex(endVertex, endIndexCont); - double d[3]; - for (int i=0; i<3; ++i) - d[i] = (endVertex[i]-startVertex[i])*spacing[i]; - length_sum += std::sqrt( d[0]*d[0] + d[1]*d[1] + d[2]*d[2] ); - std::vector< std::pair< itk::Index<3>, double > > segments = mitk::imv::IntersectImage(spacing, startIndex, endIndex, startIndexCont, endIndexCont); for (std::pair< itk::Index<3>, double > segment : segments) { - if ( mask->GetLargestPossibleRegion().IsInside(segment.first) && mask->GetPixel(segment.first) != 0 ) + if ( mask->GetLargestPossibleRegion().IsInside(segment.first) && mask->GetPixel(segment.first) > 0 ) in_mask_length += segment.second; + length_sum += segment.second; } } } if (length_sum==0) { MITK_INFO << "Fiber length sum is zero!"; return length_sum; } return in_mask_length/length_sum; } mitk::FiberBundle::Pointer mitk::FiberBundle::RemoveFibersOutside(ItkUcharImgType* mask, bool invert) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); std::vector< float > fib_weights; MITK_INFO << "Cutting fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); int newNumPoints = 0; if (numPoints>1) { for (int j=0; j itkP = GetItkPoint(points->GetPoint(j)); itk::Index<3> idx; mask->TransformPhysicalPointToIndex(itkP, idx); bool inside = false; if ( mask->GetLargestPossibleRegion().IsInside(idx) && mask->GetPixel(idx)!=0 ) inside = true; if (inside && !invert) { vtkIdType id = vtkNewPoints->InsertNextPoint(itkP.GetDataPointer()); container->GetPointIds()->InsertNextId(id); newNumPoints++; } else if ( !inside && invert ) { vtkIdType id = vtkNewPoints->InsertNextPoint(itkP.GetDataPointer()); container->GetPointIds()->InsertNextId(id); newNumPoints++; } else if (newNumPoints>1) { fib_weights.push_back(this->GetFiberWeight(i)); vtkNewCells->InsertNextCell(container); newNumPoints = 0; container = vtkSmartPointer::New(); } else { newNumPoints = 0; container = vtkSmartPointer::New(); } } if (newNumPoints>1) { fib_weights.push_back(this->GetFiberWeight(i)); vtkNewCells->InsertNextCell(container); } } } vtkSmartPointer newFiberWeights = vtkSmartPointer::New(); newFiberWeights->SetName("FIBER_WEIGHTS"); newFiberWeights->SetNumberOfValues(fib_weights.size()); if (vtkNewCells->GetNumberOfCells()<=0) return nullptr; for (int i=0; iGetNumberOfValues(); i++) newFiberWeights->SetValue(i, fib_weights.at(i)); // vtkSmartPointer newFiberColors = vtkSmartPointer::New(); // newFiberColors->Allocate(m_FiberPolyData->GetNumberOfPoints() * 4); // newFiberColors->SetNumberOfComponents(4); // newFiberColors->SetName("FIBER_COLORS"); // unsigned char rgba[4] = {0,0,0,0}; // for(long i=0; iGetNumberOfPoints(); ++i) // { // rgba[0] = (unsigned char) r; // rgba[1] = (unsigned char) g; // rgba[2] = (unsigned char) b; // rgba[3] = (unsigned char) alpha; // m_FiberColors->InsertTypedTuple(i, rgba); // } vtkSmartPointer newPolyData = vtkSmartPointer::New(); newPolyData->SetPoints(vtkNewPoints); newPolyData->SetLines(vtkNewCells); mitk::FiberBundle::Pointer newFib = mitk::FiberBundle::New(newPolyData); newFib->SetFiberWeights(newFiberWeights); // newFib->Compress(0.1); return newFib; } mitk::FiberBundle::Pointer mitk::FiberBundle::ExtractFiberSubset(DataNode* roi, DataStorage* storage) { if (roi==nullptr || !(dynamic_cast(roi->GetData()) || dynamic_cast(roi->GetData())) ) return nullptr; std::vector tmp = ExtractFiberIdSubset(roi, storage); if (tmp.size()<=0) return mitk::FiberBundle::New(); vtkSmartPointer weights = vtkSmartPointer::New(); vtkSmartPointer pTmp = GeneratePolyDataByIds(tmp, weights); mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(pTmp); fib->SetFiberWeights(weights); return fib; } std::vector mitk::FiberBundle::ExtractFiberIdSubset(DataNode *roi, DataStorage* storage) { std::vector result; if (roi==nullptr || roi->GetData()==nullptr) return result; mitk::PlanarFigureComposite::Pointer pfc = dynamic_cast(roi->GetData()); if (!pfc.IsNull()) // handle composite { DataStorage::SetOfObjects::ConstPointer children = storage->GetDerivations(roi); if (children->size()==0) return result; switch (pfc->getOperationType()) { case 0: // AND { MITK_INFO << "AND"; result = this->ExtractFiberIdSubset(children->ElementAt(0), storage); std::vector::iterator it; for (unsigned int i=1; iSize(); ++i) { std::vector inRoi = this->ExtractFiberIdSubset(children->ElementAt(i), storage); std::vector rest(std::min(result.size(),inRoi.size())); it = std::set_intersection(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() ); rest.resize( it - rest.begin() ); result = rest; } break; } case 1: // OR { MITK_INFO << "OR"; result = ExtractFiberIdSubset(children->ElementAt(0), storage); std::vector::iterator it; for (unsigned int i=1; iSize(); ++i) { it = result.end(); std::vector inRoi = ExtractFiberIdSubset(children->ElementAt(i), storage); result.insert(it, inRoi.begin(), inRoi.end()); } // remove duplicates sort(result.begin(), result.end()); it = unique(result.begin(), result.end()); result.resize( it - result.begin() ); break; } case 2: // NOT { MITK_INFO << "NOT"; for(long i=0; iGetNumFibers(); i++) result.push_back(i); std::vector::iterator it; for (unsigned int i=0; iSize(); ++i) { std::vector inRoi = ExtractFiberIdSubset(children->ElementAt(i), storage); std::vector rest(result.size()-inRoi.size()); it = std::set_difference(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() ); rest.resize( it - rest.begin() ); result = rest; } break; } } } else if ( dynamic_cast(roi->GetData()) ) // actual extraction { if ( dynamic_cast(roi->GetData()) ) { mitk::PlanarFigure::Pointer planarPoly = dynamic_cast(roi->GetData()); //create vtkPolygon using controlpoints from planarFigure polygon vtkSmartPointer polygonVtk = vtkSmartPointer::New(); for (unsigned int i=0; iGetNumberOfControlPoints(); ++i) { itk::Point p = planarPoly->GetWorldControlPoint(i); vtkIdType id = polygonVtk->GetPoints()->InsertNextPoint(p[0], p[1], p[2] ); polygonVtk->GetPointIds()->InsertNextId(id); } MITK_INFO << "Extracting with polygon"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; jGetPoint(j, p1); double p2[3] = {0,0,0}; points->GetPoint(j+1, p2); double tolerance = 0.001; // Outputs double t = 0; // Parametric coordinate of intersection (0 (corresponding to p1) to 1 (corresponding to p2)) double x[3] = {0,0,0}; // The coordinate of the intersection double pcoords[3] = {0,0,0}; int subId = 0; int iD = polygonVtk->IntersectWithLine(p1, p2, tolerance, t, x, pcoords, subId); if (iD!=0) { result.push_back(i); break; } } } } else if ( dynamic_cast(roi->GetData()) ) { mitk::PlanarFigure::Pointer planarFigure = dynamic_cast(roi->GetData()); Vector3D planeNormal = planarFigure->GetPlaneGeometry()->GetNormal(); planeNormal.Normalize(); //calculate circle radius mitk::Point3D V1w = planarFigure->GetWorldControlPoint(0); //centerPoint mitk::Point3D V2w = planarFigure->GetWorldControlPoint(1); //radiusPoint double radius = V1w.EuclideanDistanceTo(V2w); radius *= radius; MITK_INFO << "Extracting with circle"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; jGetPoint(j, p1); double p2[3] = {0,0,0}; points->GetPoint(j+1, p2); // Outputs double t = 0; // Parametric coordinate of intersection (0 (corresponding to p1) to 1 (corresponding to p2)) double x[3] = {0,0,0}; // The coordinate of the intersection int iD = vtkPlane::IntersectWithLine(p1,p2,planeNormal.GetDataPointer(),V1w.GetDataPointer(),t,x); if (iD!=0) { double dist = (x[0]-V1w[0])*(x[0]-V1w[0])+(x[1]-V1w[1])*(x[1]-V1w[1])+(x[2]-V1w[2])*(x[2]-V1w[2]); if( dist <= radius) { result.push_back(i); break; } } } } } return result; } return result; } void mitk::FiberBundle::UpdateFiberGeometry() { vtkSmartPointer cleaner = vtkSmartPointer::New(); cleaner->SetInputData(m_FiberPolyData); cleaner->PointMergingOff(); cleaner->Update(); m_FiberPolyData = cleaner->GetOutput(); m_FiberLengths.clear(); m_MeanFiberLength = 0; m_MedianFiberLength = 0; m_LengthStDev = 0; m_NumFibers = m_FiberPolyData->GetNumberOfCells(); if (m_FiberColors==nullptr || m_FiberColors->GetNumberOfTuples()!=m_FiberPolyData->GetNumberOfPoints()) this->ColorFibersByOrientation(); if (m_FiberWeights->GetNumberOfValues()!=m_NumFibers) { m_FiberWeights = vtkSmartPointer::New(); m_FiberWeights->SetName("FIBER_WEIGHTS"); m_FiberWeights->SetNumberOfValues(m_NumFibers); this->SetFiberWeights(1); } if (m_NumFibers<=0) // no fibers present; apply default geometry { m_MinFiberLength = 0; m_MaxFiberLength = 0; mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); geometry->SetImageGeometry(false); float b[] = {0, 1, 0, 1, 0, 1}; geometry->SetFloatBounds(b); SetGeometry(geometry); return; } double b[6]; m_FiberPolyData->GetBounds(b); // calculate statistics for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int p = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); float length = 0; for (int j=0; jGetPoint(j, p1); double p2[3]; points->GetPoint(j+1, p2); float dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); length += dist; } m_FiberLengths.push_back(length); m_MeanFiberLength += length; if (i==0) { m_MinFiberLength = length; m_MaxFiberLength = length; } else { if (lengthm_MaxFiberLength) m_MaxFiberLength = length; } } m_MeanFiberLength /= m_NumFibers; std::vector< float > sortedLengths = m_FiberLengths; std::sort(sortedLengths.begin(), sortedLengths.end()); for (int i=0; i1) m_LengthStDev /= (m_NumFibers-1); else m_LengthStDev = 0; m_LengthStDev = std::sqrt(m_LengthStDev); m_MedianFiberLength = sortedLengths.at(m_NumFibers/2); mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); geometry->SetFloatBounds(b); this->SetGeometry(geometry); m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } float mitk::FiberBundle::GetFiberWeight(unsigned int fiber) const { return m_FiberWeights->GetValue(fiber); } void mitk::FiberBundle::SetFiberWeights(float newWeight) { for (int i=0; iGetNumberOfValues(); i++) m_FiberWeights->SetValue(i, newWeight); } void mitk::FiberBundle::SetFiberWeights(vtkSmartPointer weights) { if (m_NumFibers!=weights->GetNumberOfValues()) { MITK_INFO << "Weights array not equal to number of fibers! " << weights->GetNumberOfValues() << " vs " << m_NumFibers; return; } for (int i=0; iGetNumberOfValues(); i++) m_FiberWeights->SetValue(i, weights->GetValue(i)); m_FiberWeights->SetName("FIBER_WEIGHTS"); } void mitk::FiberBundle::SetFiberWeight(unsigned int fiber, float weight) { m_FiberWeights->SetValue(fiber, weight); } void mitk::FiberBundle::SetFiberColors(vtkSmartPointer fiberColors) { for(long i=0; iGetNumberOfPoints(); ++i) { unsigned char source[4] = {0,0,0,0}; fiberColors->GetTypedTuple(i, source); unsigned char target[4] = {0,0,0,0}; target[0] = source[0]; target[1] = source[1]; target[2] = source[2]; target[3] = source[3]; m_FiberColors->InsertTypedTuple(i, target); } m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } itk::Matrix< double, 3, 3 > mitk::FiberBundle::TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz) { rx = rx*itk::Math::pi/180; ry = ry*itk::Math::pi/180; rz = rz*itk::Math::pi/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; m = rot*m; return m; } itk::Point mitk::FiberBundle::TransformPoint(vnl_vector_fixed< double, 3 > point, double rx, double ry, double rz, double tx, double ty, double tz) { rx = rx*itk::Math::pi/180; ry = ry*itk::Math::pi/180; rz = rz*itk::Math::pi/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; vnl_matrix_fixed< double, 3, 3 > rot = rotZ*rotY*rotX; mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); point[0] -= center[0]; point[1] -= center[1]; point[2] -= center[2]; point = rot*point; point[0] += center[0]+tx; point[1] += center[1]+ty; point[2] += center[2]+tz; itk::Point out; out[0] = point[0]; out[1] = point[1]; out[2] = point[2]; return out; } void mitk::FiberBundle::TransformFibers(itk::ScalableAffineTransform< mitk::ScalarType >::Pointer transform) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; j p = GetItkPoint(points->GetPoint(j)); p = transform->TransformPoint(p); vtkIdType id = vtkNewPoints->InsertNextPoint(p.GetDataPointer()); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } void mitk::FiberBundle::TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz) { rx = rx*itk::Math::pi/180; ry = ry*itk::Math::pi/180; rz = rz*itk::Math::pi/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; vnl_matrix_fixed< double, 3, 3 > rot = rotZ*rotY*rotX; mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vnl_vector_fixed< double, 3 > dir; dir[0] = p[0]-center[0]; dir[1] = p[1]-center[1]; dir[2] = p[2]-center[2]; dir = rot*dir; dir[0] += center[0]+tx; dir[1] += center[1]+ty; dir[2] += center[2]+tz; vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block()); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } void mitk::FiberBundle::RotateAroundAxis(double x, double y, double z) { x = x*itk::Math::pi/180; y = y*itk::Math::pi/180; z = z*itk::Math::pi/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vnl_vector_fixed< double, 3 > dir; dir[0] = p[0]-center[0]; dir[1] = p[1]-center[1]; dir[2] = p[2]-center[2]; dir = rotZ*rotY*rotX*dir; dir[0] += center[0]; dir[1] += center[1]; dir[2] += center[2]; vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block()); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } void mitk::FiberBundle::ScaleFibers(double x, double y, double z, bool subtractCenter) { MITK_INFO << "Scaling fibers"; boost::progress_display disp(m_NumFibers); mitk::BaseGeometry* geom = this->GetGeometry(); mitk::Point3D c = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); if (subtractCenter) { p[0] -= c[0]; p[1] -= c[1]; p[2] -= c[2]; } p[0] *= x; p[1] *= y; p[2] *= z; if (subtractCenter) { p[0] += c[0]; p[1] += c[1]; p[2] += c[2]; } vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } void mitk::FiberBundle::TranslateFibers(double x, double y, double z) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[0] += x; p[1] += y; p[2] += z; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } void mitk::FiberBundle::MirrorFibers(unsigned int axis) { if (axis>2) return; MITK_INFO << "Mirroring fibers"; boost::progress_display disp(m_NumFibers); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[axis] = -p[axis]; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } void mitk::FiberBundle::RemoveDir(vnl_vector_fixed dir, double threshold) { dir.normalize(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); for (int i=0; iGetNumberOfCells(); i++) { ++disp ; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); // calculate curvatures vtkSmartPointer container = vtkSmartPointer::New(); bool discard = false; for (int j=0; jGetPoint(j, p1); double p2[3]; points->GetPoint(j+1, p2); vnl_vector_fixed< double, 3 > v1; v1[0] = p2[0]-p1[0]; v1[1] = p2[1]-p1[1]; v1[2] = p2[2]-p1[2]; if (v1.magnitude()>0.001) { v1.normalize(); if (fabs(dot_product(v1,dir))>threshold) { discard = true; break; } } } if (!discard) { for (int j=0; jGetPoint(j, p1); vtkIdType id = vtkNewPoints->InsertNextPoint(p1); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); // UpdateColorCoding(); // UpdateFiberGeometry(); } bool mitk::FiberBundle::ApplyCurvatureThreshold(float minRadius, bool deleteFibers) { if (minRadius<0) return true; vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Applying curvature threshold"; boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); for (int i=0; iGetNumberOfCells(); i++) { ++disp ; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); // calculate curvatures vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p1); double p2[3]; points->GetPoint(j+1, p2); double p3[3]; points->GetPoint(j+2, p3); vnl_vector_fixed< float, 3 > v1, v2, v3; v1[0] = p2[0]-p1[0]; v1[1] = p2[1]-p1[1]; v1[2] = p2[2]-p1[2]; v2[0] = p3[0]-p2[0]; v2[1] = p3[1]-p2[1]; v2[2] = p3[2]-p2[2]; v3[0] = p1[0]-p3[0]; v3[1] = p1[1]-p3[1]; v3[2] = p1[2]-p3[2]; float a = v1.magnitude(); float b = v2.magnitude(); float c = v3.magnitude(); float r = a*b*c/std::sqrt((a+b+c)*(a+b-c)*(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle) vtkIdType id = vtkNewPoints->InsertNextPoint(p1); container->GetPointIds()->InsertNextId(id); if (deleteFibers && rInsertNextCell(container); container = vtkSmartPointer::New(); } else if (j==numPoints-3) { id = vtkNewPoints->InsertNextPoint(p2); container->GetPointIds()->InsertNextId(id); id = vtkNewPoints->InsertNextPoint(p3); container->GetPointIds()->InsertNextId(id); vtkNewCells->InsertNextCell(container); } } } if (vtkNewCells->GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); return true; } bool mitk::FiberBundle::RemoveShortFibers(float lengthInMM) { MITK_INFO << "Removing short fibers"; if (lengthInMM<=0 || lengthInMMm_MaxFiberLength) // can't remove all fibers { MITK_WARN << "Process aborted. No fibers would be left!"; return false; } vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); float min = m_MaxFiberLength; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (m_FiberLengths.at(i)>=lengthInMM) { vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); if (m_FiberLengths.at(i)GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); return true; } bool mitk::FiberBundle::RemoveLongFibers(float lengthInMM) { if (lengthInMM<=0 || lengthInMM>m_MaxFiberLength) return true; if (lengthInMM vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Removing long fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (m_FiberLengths.at(i)<=lengthInMM) { vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } } if (vtkNewCells->GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); return true; } void mitk::FiberBundle::ResampleSpline(float pointDistance, double tension, double continuity, double bias ) { if (pointDistance<=0) return; vtkSmartPointer vtkSmoothPoints = vtkSmartPointer::New(); //in smoothpoints the interpolated points representing a fiber are stored. //in vtkcells all polylines are stored, actually all id's of them are stored vtkSmartPointer vtkSmoothCells = vtkSmartPointer::New(); //cellcontainer for smoothed lines MITK_INFO << "Smoothing fibers"; vtkSmartPointer newFiberWeights = vtkSmartPointer::New(); newFiberWeights->SetName("FIBER_WEIGHTS"); newFiberWeights->SetNumberOfValues(m_NumFibers); std::vector< vtkSmartPointer > resampled_streamlines; resampled_streamlines.resize(m_NumFibers); boost::progress_display disp(m_NumFibers); #pragma omp parallel for for (int i=0; i newPoints = vtkSmartPointer::New(); float length = 0; #pragma omp critical { length = m_FiberLengths.at(i); ++disp; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; jInsertNextPoint(points->GetPoint(j)); } int sampling = std::ceil(length/pointDistance); vtkSmartPointer xSpline = vtkSmartPointer::New(); vtkSmartPointer ySpline = vtkSmartPointer::New(); vtkSmartPointer zSpline = vtkSmartPointer::New(); xSpline->SetDefaultBias(bias); xSpline->SetDefaultTension(tension); xSpline->SetDefaultContinuity(continuity); ySpline->SetDefaultBias(bias); ySpline->SetDefaultTension(tension); ySpline->SetDefaultContinuity(continuity); zSpline->SetDefaultBias(bias); zSpline->SetDefaultTension(tension); zSpline->SetDefaultContinuity(continuity); vtkSmartPointer spline = vtkSmartPointer::New(); spline->SetXSpline(xSpline); spline->SetYSpline(ySpline); spline->SetZSpline(zSpline); spline->SetPoints(newPoints); vtkSmartPointer functionSource = vtkSmartPointer::New(); functionSource->SetParametricFunction(spline); functionSource->SetUResolution(sampling); functionSource->SetVResolution(sampling); functionSource->SetWResolution(sampling); functionSource->Update(); vtkPolyData* outputFunction = functionSource->GetOutput(); vtkPoints* tmpSmoothPnts = outputFunction->GetPoints(); //smoothPoints of current fiber vtkSmartPointer smoothLine = vtkSmartPointer::New(); #pragma omp critical { for (int j=0; jGetNumberOfPoints(); j++) { vtkIdType id = vtkSmoothPoints->InsertNextPoint(tmpSmoothPnts->GetPoint(j)); smoothLine->GetPointIds()->InsertNextId(id); } resampled_streamlines[i] = smoothLine; } } for (auto container : resampled_streamlines) { vtkSmoothCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkSmoothPoints); m_FiberPolyData->SetLines(vtkSmoothCells); this->SetFiberPolyData(m_FiberPolyData, true); } void mitk::FiberBundle::ResampleSpline(float pointDistance) { ResampleSpline(pointDistance, 0, 0, 0 ); } unsigned long mitk::FiberBundle::GetNumberOfPoints() const { unsigned long points = 0; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); points += cell->GetNumberOfPoints(); } return points; } void mitk::FiberBundle::Compress(float error) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Compressing fibers"; unsigned long numRemovedPoints = 0; boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); vtkSmartPointer newFiberWeights = vtkSmartPointer::New(); newFiberWeights->SetName("FIBER_WEIGHTS"); newFiberWeights->SetNumberOfValues(m_NumFibers); #pragma omp parallel for for (int i=0; iGetNumberOfCells(); i++) { std::vector< vnl_vector_fixed< double, 3 > > vertices; float weight = 1; #pragma omp critical { ++disp; weight = m_FiberWeights->GetValue(i); vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; jGetPoint(j, cand); vnl_vector_fixed< double, 3 > candV; candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2]; vertices.push_back(candV); } } // calculate curvatures int numPoints = vertices.size(); std::vector< int > removedPoints; removedPoints.resize(numPoints, 0); removedPoints[0]=-1; removedPoints[numPoints-1]=-1; vtkSmartPointer container = vtkSmartPointer::New(); int remCounter = 0; bool pointFound = true; while (pointFound) { pointFound = false; double minError = error; int removeIndex = -1; for (unsigned int j=0; j candV = vertices.at(j); int validP = -1; vnl_vector_fixed< double, 3 > pred; for (int k=j-1; k>=0; k--) if (removedPoints[k]<=0) { pred = vertices.at(k); validP = k; break; } int validS = -1; vnl_vector_fixed< double, 3 > succ; for (int k=j+1; k=0 && validS>=0) { double a = (candV-pred).magnitude(); double b = (candV-succ).magnitude(); double c = (pred-succ).magnitude(); double s=0.5*(a+b+c); double hc=(2.0/c)*sqrt(fabs(s*(s-a)*(s-b)*(s-c))); if (hcInsertNextPoint(vertices.at(j).data_block()); container->GetPointIds()->InsertNextId(id); } } } #pragma omp critical { newFiberWeights->SetValue(vtkNewCells->GetNumberOfCells(), weight); numRemovedPoints += remCounter; vtkNewCells->InsertNextCell(container); } } if (vtkNewCells->GetNumberOfCells()>0) { MITK_INFO << "Removed points: " << numRemovedPoints; SetFiberWeights(newFiberWeights); m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } } void mitk::FiberBundle::ResampleToNumPoints(unsigned int targetPoints) { if (targetPoints<2) mitkThrow() << "Minimum two points required for resampling!"; MITK_INFO << "Resampling fibers (number of points " << targetPoints << ")"; bool unequal_fibs = true; while (unequal_fibs) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); vtkSmartPointer newFiberWeights = vtkSmartPointer::New(); newFiberWeights->SetName("FIBER_WEIGHTS"); newFiberWeights->SetNumberOfValues(m_NumFibers); unequal_fibs = false; //#pragma omp parallel for for (int i=0; iGetNumberOfCells(); i++) { std::vector< vnl_vector_fixed< double, 3 > > vertices; float weight = 1; double seg_len = 0; //#pragma omp critical { weight = m_FiberWeights->GetValue(i); vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); if ((unsigned int)numPoints!=targetPoints) seg_len = this->GetFiberLength(i)/(targetPoints-1);; vtkPoints* points = cell->GetPoints(); for (int j=0; jGetPoint(j, cand); vnl_vector_fixed< double, 3 > candV; candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2]; vertices.push_back(candV); } } vtkSmartPointer container = vtkSmartPointer::New(); vnl_vector_fixed< double, 3 > lastV = vertices.at(0); //#pragma omp critical { vtkIdType id = vtkNewPoints->InsertNextPoint(lastV.data_block()); container->GetPointIds()->InsertNextId(id); } for (unsigned int j=1; j vec = vertices.at(j) - lastV; double new_dist = vec.magnitude(); if (new_dist >= seg_len && seg_len>0) { vnl_vector_fixed< double, 3 > newV = lastV; if ( new_dist-seg_len <= mitk::eps ) { vec.normalize(); newV += vec * seg_len; } else { // intersection between sphere (radius 'pointDistance', center 'lastV') and line (direction 'd' and point 'p') vnl_vector_fixed< double, 3 > p = vertices.at(j-1); vnl_vector_fixed< double, 3 > d = vertices.at(j) - p; double a = d[0]*d[0] + d[1]*d[1] + d[2]*d[2]; double b = 2 * (d[0] * (p[0] - lastV[0]) + d[1] * (p[1] - lastV[1]) + d[2] * (p[2] - lastV[2])); double c = (p[0] - lastV[0])*(p[0] - lastV[0]) + (p[1] - lastV[1])*(p[1] - lastV[1]) + (p[2] - lastV[2])*(p[2] - lastV[2]) - seg_len*seg_len; double v1 =(-b + std::sqrt(b*b-4*a*c))/(2*a); double v2 =(-b - std::sqrt(b*b-4*a*c))/(2*a); if (v1>0) newV = p + d * v1; else if (v2>0) newV = p + d * v2; else MITK_INFO << "ERROR1 - linear resampling"; j--; } //#pragma omp critical { vtkIdType id = vtkNewPoints->InsertNextPoint(newV.data_block()); container->GetPointIds()->InsertNextId(id); } lastV = newV; } else if ( (j==vertices.size()-1 && new_dist>0.0001) || seg_len==0) { //#pragma omp critical { vtkIdType id = vtkNewPoints->InsertNextPoint(vertices.at(j).data_block()); container->GetPointIds()->InsertNextId(id); } } } //#pragma omp critical { newFiberWeights->SetValue(vtkNewCells->GetNumberOfCells(), weight); vtkNewCells->InsertNextCell(container); if (container->GetNumberOfPoints()!=targetPoints) unequal_fibs = true; } } if (vtkNewCells->GetNumberOfCells()>0) { SetFiberWeights(newFiberWeights); m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } } } void mitk::FiberBundle::ResampleLinear(double pointDistance) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Resampling fibers (linear)"; boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); vtkSmartPointer newFiberWeights = vtkSmartPointer::New(); newFiberWeights->SetName("FIBER_WEIGHTS"); newFiberWeights->SetNumberOfValues(m_NumFibers); std::vector< vtkSmartPointer > resampled_streamlines; resampled_streamlines.resize(m_FiberPolyData->GetNumberOfCells()); #pragma omp parallel for for (int i=0; iGetNumberOfCells(); i++) { std::vector< vnl_vector_fixed< double, 3 > > vertices; #pragma omp critical { ++disp; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; jGetPoint(j, cand); vnl_vector_fixed< double, 3 > candV; candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2]; vertices.push_back(candV); } } vtkSmartPointer container = vtkSmartPointer::New(); vnl_vector_fixed< double, 3 > lastV = vertices.at(0); #pragma omp critical { vtkIdType id = vtkNewPoints->InsertNextPoint(lastV.data_block()); container->GetPointIds()->InsertNextId(id); } for (unsigned int j=1; j vec = vertices.at(j) - lastV; double new_dist = vec.magnitude(); if (new_dist >= pointDistance) { vnl_vector_fixed< double, 3 > newV = lastV; if ( new_dist-pointDistance <= mitk::eps ) { vec.normalize(); newV += vec * pointDistance; } else { // intersection between sphere (radius 'pointDistance', center 'lastV') and line (direction 'd' and point 'p') vnl_vector_fixed< double, 3 > p = vertices.at(j-1); vnl_vector_fixed< double, 3 > d = vertices.at(j) - p; double a = d[0]*d[0] + d[1]*d[1] + d[2]*d[2]; double b = 2 * (d[0] * (p[0] - lastV[0]) + d[1] * (p[1] - lastV[1]) + d[2] * (p[2] - lastV[2])); double c = (p[0] - lastV[0])*(p[0] - lastV[0]) + (p[1] - lastV[1])*(p[1] - lastV[1]) + (p[2] - lastV[2])*(p[2] - lastV[2]) - pointDistance*pointDistance; double v1 =(-b + std::sqrt(b*b-4*a*c))/(2*a); double v2 =(-b - std::sqrt(b*b-4*a*c))/(2*a); if (v1>0) newV = p + d * v1; else if (v2>0) newV = p + d * v2; else MITK_INFO << "ERROR1 - linear resampling"; j--; } #pragma omp critical { vtkIdType id = vtkNewPoints->InsertNextPoint(newV.data_block()); container->GetPointIds()->InsertNextId(id); } lastV = newV; } else if (j==vertices.size()-1 && new_dist>0.0001) { #pragma omp critical { vtkIdType id = vtkNewPoints->InsertNextPoint(vertices.at(j).data_block()); container->GetPointIds()->InsertNextId(id); } } } #pragma omp critical { resampled_streamlines[i] = container; } } for (auto container : resampled_streamlines) { vtkNewCells->InsertNextCell(container); } if (vtkNewCells->GetNumberOfCells()>0) { m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); this->SetFiberPolyData(m_FiberPolyData, true); } } // reapply selected colorcoding in case PolyData structure has changed bool mitk::FiberBundle::Equals(mitk::FiberBundle* fib, double eps) { if (fib==nullptr) { MITK_INFO << "Reference bundle is nullptr!"; return false; } if (m_NumFibers!=fib->GetNumFibers()) { MITK_INFO << "Unequal number of fibers!"; MITK_INFO << m_NumFibers << " vs. " << fib->GetNumFibers(); return false; } for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkCell* cell2 = fib->GetFiberPolyData()->GetCell(i); int numPoints2 = cell2->GetNumberOfPoints(); vtkPoints* points2 = cell2->GetPoints(); if (numPoints2!=numPoints) { MITK_INFO << "Unequal number of points in fiber " << i << "!"; MITK_INFO << numPoints2 << " vs. " << numPoints; return false; } for (int j=0; jGetPoint(j); double* p2 = points2->GetPoint(j); if (fabs(p1[0]-p2[0])>eps || fabs(p1[1]-p2[1])>eps || fabs(p1[2]-p2[2])>eps) { MITK_INFO << "Unequal points in fiber " << i << " at position " << j << "!"; MITK_INFO << "p1: " << p1[0] << ", " << p1[1] << ", " << p1[2]; MITK_INFO << "p2: " << p2[0] << ", " << p2[1] << ", " << p2[2]; return false; } } } return true; } void mitk::FiberBundle::PrintSelf(std::ostream &os, itk::Indent indent) const { os << this->GetNameOfClass() << ":\n"; os << indent << "Number of fibers: " << this->GetNumFibers() << std::endl; os << indent << "Min. fiber length: " << this->GetMinFiberLength() << std::endl; os << indent << "Max. fiber length: " << this->GetMaxFiberLength() << std::endl; os << indent << "Mean fiber length: " << this->GetMeanFiberLength() << std::endl; os << indent << "Median fiber length: " << this->GetMedianFiberLength() << std::endl; os << indent << "STDEV fiber length: " << this->GetLengthStDev() << std::endl; os << indent << "Number of points: " << this->GetNumberOfPoints() << std::endl; os << indent << "Extent x: " << this->GetGeometry()->GetExtentInMM(0) << "mm" << std::endl; os << indent << "Extent y: " << this->GetGeometry()->GetExtentInMM(1) << "mm" << std::endl; os << indent << "Extent z: " << this->GetGeometry()->GetExtentInMM(2) << "mm" << std::endl; os << indent << "Diagonal: " << this->GetGeometry()->GetDiagonalLength() << "mm" << std::endl; if (m_FiberWeights!=nullptr) { std::vector< float > weights; for (int i=0; iGetSize(); i++) weights.push_back(m_FiberWeights->GetValue(i)); std::sort(weights.begin(), weights.end()); os << indent << "\nFiber weight statistics" << std::endl; os << indent << "Min: " << weights.front() << std::endl; os << indent << "1% quantile: " << weights.at(weights.size()*0.01) << std::endl; os << indent << "5% quantile: " << weights.at(weights.size()*0.05) << std::endl; os << indent << "25% quantile: " << weights.at(weights.size()*0.25) << std::endl; os << indent << "Median: " << weights.at(weights.size()*0.5) << std::endl; os << indent << "75% quantile: " << weights.at(weights.size()*0.75) << std::endl; os << indent << "95% quantile: " << weights.at(weights.size()*0.95) << std::endl; os << indent << "99% quantile: " << weights.at(weights.size()*0.99) << std::endl; os << indent << "Max: " << weights.back() << std::endl; } else os << indent << "\n\nNo fiber weight array found." << std::endl; Superclass::PrintSelf(os, indent); } /* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */ void mitk::FiberBundle::UpdateOutputInformation() { } void mitk::FiberBundle::SetRequestedRegionToLargestPossibleRegion() { } bool mitk::FiberBundle::RequestedRegionIsOutsideOfTheBufferedRegion() { return false; } bool mitk::FiberBundle::VerifyRequestedRegion() { return true; } void mitk::FiberBundle::SetRequestedRegion(const itk::DataObject* ) { } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.h index 01d7525c3c..b6ae5896c5 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundle/mitkFiberBundle.h @@ -1,183 +1,185 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef _MITK_FiberBundle_H #define _MITK_FiberBundle_H //includes for MITK datastructure #include #include #include #include #include #include #include - +#include //includes storing fiberdata #include #include #include #include #include #include #include namespace mitk { /** * \brief Base Class for Fiber Bundles; */ class MITKFIBERTRACKING_EXPORT FiberBundle : public BaseData { public: typedef itk::Image ItkUcharImgType; // fiber colorcodings static const char* FIBER_ID_ARRAY; void UpdateOutputInformation() override; void SetRequestedRegionToLargestPossibleRegion() override; bool RequestedRegionIsOutsideOfTheBufferedRegion() override; bool VerifyRequestedRegion() override; void SetRequestedRegion(const itk::DataObject*) override; mitkClassMacro( FiberBundle, BaseData ) itkFactorylessNewMacro(Self) itkCloneMacro(Self) mitkNewMacro1Param(Self, vtkSmartPointer) // custom constructor // colorcoding related methods void ColorFibersByFiberWeights(bool opacity, bool normalize); void ColorFibersByCurvature(bool opacity, bool normalize); void ColorFibersByLength(bool opacity, bool normalize); void ColorFibersByScalarMap(mitk::Image::Pointer, bool opacity, bool normalize); template void ColorFibersByScalarMap(const mitk::PixelType pixelType, mitk::Image::Pointer, bool opacity, bool normalize); void ColorFibersByOrientation(); void SetFiberOpacity(vtkDoubleArray *FAValArray); void ResetFiberOpacity(); void SetFiberColors(vtkSmartPointer fiberColors); void SetFiberColors(float r, float g, float b, float alpha=255); vtkSmartPointer GetFiberColors() const { return m_FiberColors; } // fiber compression void Compress(float error = 0.0); // fiber resampling void ResampleSpline(float pointDistance=1); void ResampleSpline(float pointDistance, double tension, double continuity, double bias ); void ResampleLinear(double pointDistance=1); void ResampleToNumPoints(unsigned int targetPoints); mitk::FiberBundle::Pointer FilterByWeights(float weight_thr, bool invert=false); bool RemoveShortFibers(float lengthInMM); bool RemoveLongFibers(float lengthInMM); bool ApplyCurvatureThreshold(float minRadius, bool deleteFibers); void MirrorFibers(unsigned int axis); void RotateAroundAxis(double x, double y, double z); void TranslateFibers(double x, double y, double z); void ScaleFibers(double x, double y, double z, bool subtractCenter=true); void TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz); void TransformFibers(itk::ScalableAffineTransform< mitk::ScalarType >::Pointer transform); void RemoveDir(vnl_vector_fixed dir, double threshold); itk::Point TransformPoint(vnl_vector_fixed< double, 3 > point, double rx, double ry, double rz, double tx, double ty, double tz); itk::Matrix< double, 3, 3 > TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz); // add/subtract fibers FiberBundle::Pointer AddBundle(FiberBundle* fib); mitk::FiberBundle::Pointer AddBundles(std::vector< mitk::FiberBundle::Pointer > fibs); FiberBundle::Pointer SubtractBundle(FiberBundle* fib); // fiber subset extraction FiberBundle::Pointer ExtractFiberSubset(DataNode *roi, DataStorage* storage); std::vector ExtractFiberIdSubset(DataNode* roi, DataStorage* storage); FiberBundle::Pointer RemoveFibersOutside(ItkUcharImgType* mask, bool invert=false); float GetOverlap(ItkUcharImgType* mask); + std::tuple GetDirectionalOverlap(ItkUcharImgType* mask, mitk::PeakImage::ItkPeakImageType* peak_image); + float GetNumEpFractionInMask(ItkUcharImgType* mask, bool different_label); mitk::FiberBundle::Pointer SubsampleFibers(float factor); // get/set data float GetFiberLength(int index) const { return m_FiberLengths.at(index); } vtkSmartPointer GetFiberWeights() const { return m_FiberWeights; } float GetFiberWeight(unsigned int fiber) const; void SetFiberWeights(float newWeight); void SetFiberWeight(unsigned int fiber, float weight); void SetFiberWeights(vtkSmartPointer weights); void SetFiberPolyData(vtkSmartPointer, bool updateGeometry = true); vtkSmartPointer GetFiberPolyData() const; itkGetConstMacro( NumFibers, int) //itkGetMacro( FiberSampling, int) itkGetConstMacro( MinFiberLength, float ) itkGetConstMacro( MaxFiberLength, float ) itkGetConstMacro( MeanFiberLength, float ) itkGetConstMacro( MedianFiberLength, float ) itkGetConstMacro( LengthStDev, float ) itkGetConstMacro( UpdateTime2D, itk::TimeStamp ) itkGetConstMacro( UpdateTime3D, itk::TimeStamp ) void RequestUpdate2D(){ m_UpdateTime2D.Modified(); } void RequestUpdate3D(){ m_UpdateTime3D.Modified(); } void RequestUpdate(){ m_UpdateTime2D.Modified(); m_UpdateTime3D.Modified(); } unsigned long GetNumberOfPoints() const; // copy fiber bundle mitk::FiberBundle::Pointer GetDeepCopy(); // compare fiber bundles bool Equals(FiberBundle* fib, double eps=0.01); itkSetMacro( ReferenceGeometry, mitk::BaseGeometry::Pointer ) itkGetConstMacro( ReferenceGeometry, mitk::BaseGeometry::Pointer ) vtkSmartPointer GeneratePolyDataByIds(std::vector fiberIds, vtkSmartPointer weights); protected: FiberBundle( vtkPolyData* fiberPolyData = nullptr ); ~FiberBundle() override; void GenerateFiberIds(); itk::Point GetItkPoint(double point[3]); void UpdateFiberGeometry(); void PrintSelf(std::ostream &os, itk::Indent indent) const override; private: // actual fiber container vtkSmartPointer m_FiberPolyData; // contains fiber ids vtkSmartPointer m_FiberIdDataSet; int m_NumFibers; vtkSmartPointer m_FiberColors; vtkSmartPointer m_FiberWeights; std::vector< float > m_FiberLengths; float m_MinFiberLength; float m_MaxFiberLength; float m_MeanFiberLength; float m_MedianFiberLength; float m_LengthStDev; itk::TimeStamp m_UpdateTime2D; itk::TimeStamp m_UpdateTime3D; mitk::BaseGeometry::Pointer m_ReferenceGeometry; }; } // namespace mitk #endif /* _MITK_FiberBundle_H */ diff --git a/Modules/DiffusionImaging/FiberTracking/cmdapps/Misc/PythonTest.cpp b/Modules/DiffusionImaging/FiberTracking/cmdapps/Misc/PythonTest.cpp deleted file mode 100755 index b5c21e3952..0000000000 --- a/Modules/DiffusionImaging/FiberTracking/cmdapps/Misc/PythonTest.cpp +++ /dev/null @@ -1,80 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include -#include - -#include -#include -#include - -#include -#include - -#include -#include -#include -#include - -typedef itk::Image< float, 3 > ItkImageType; - -/*! -\brief -*/ -int main(int argc, char* argv[]) -{ - mitkCommandLineParser parser; - parser.setArgumentPrefix("--", "-"); - parser.addArgument("image", "i", mitkCommandLineParser::InputFile, "Input image", "sh coefficient image", us::Any(), false); - parser.addArgument("script", "s", mitkCommandLineParser::InputFile, "", "", us::Any(), false); - parser.addArgument("params", "p", mitkCommandLineParser::InputFile, "", "", us::Any(), false); - parser.addArgument("out_file", "o", mitkCommandLineParser::OutputDirectory, "Output image", "output image", us::Any(), false); - - parser.setCategory("TEST"); - parser.setTitle("TEST"); - parser.setDescription("TEST"); - parser.setContributor("MIC"); - - std::map parsedArgs = parser.parseArguments(argc, argv); - if (parsedArgs.size()==0) - return EXIT_FAILURE; - - std::string image_file = us::any_cast(parsedArgs["image"]); - std::string script = us::any_cast(parsedArgs["script"]); - std::string params = us::any_cast(parsedArgs["params"]); - std::string out_file = us::any_cast(parsedArgs["out_file"]); - - mitk::Image::Pointer mitk_image = mitk::IOUtil::Load(image_file); - us::ModuleContext* context = us::GetModuleContext(); - - us::ServiceReference m_PythonServiceRef = context->GetServiceReference(); - mitk::IPythonService* m_PythonService = dynamic_cast ( context->GetService(m_PythonServiceRef) ); - - mitk::IPythonService::ForceLoadModule(); - - m_PythonService->Execute("import SimpleITK as sitk"); - m_PythonService->Execute("import SimpleITK._SimpleITK as _SimpleITK"); - m_PythonService->Execute("import numpy"); - - m_PythonService->CopyToPythonAsSimpleItkImage( mitk_image, "myvar"); - m_PythonService->Execute("myparams=\""+params+"\""); - m_PythonService->ExecuteScript(script); - - mitk::Image::Pointer out_seg = m_PythonService->CopySimpleItkImageFromPython("out_image"); - mitk::IOUtil::Save(out_seg, out_file); - - return EXIT_FAILURE; -} diff --git a/Modules/DiffusionImaging/FiberTracking/files.cmake b/Modules/DiffusionImaging/FiberTracking/files.cmake index 9d63278f86..765654b61e 100644 --- a/Modules/DiffusionImaging/FiberTracking/files.cmake +++ b/Modules/DiffusionImaging/FiberTracking/files.cmake @@ -1,106 +1,107 @@ set(CPP_FILES mitkFiberTrackingModuleActivator.cpp ## IO datastructures IODataStructures/FiberBundle/mitkFiberBundle.cpp IODataStructures/FiberBundle/mitkTrackvis.cpp IODataStructures/PlanarFigureComposite/mitkPlanarFigureComposite.cpp IODataStructures/mitkTractographyForest.cpp IODataStructures/mitkFiberfoxParameters.cpp # Interactions # Tractography Algorithms/GibbsTracking/mitkParticleGrid.cpp Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.cpp Algorithms/GibbsTracking/mitkEnergyComputer.cpp Algorithms/GibbsTracking/mitkGibbsEnergyComputer.cpp Algorithms/GibbsTracking/mitkFiberBuilder.cpp Algorithms/GibbsTracking/mitkSphereInterpolator.cpp Algorithms/itkStreamlineTrackingFilter.cpp Algorithms/TrackingHandlers/mitkTrackingDataHandler.cpp Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.cpp Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.cpp ) set(H_FILES # DataStructures -> FiberBundle IODataStructures/FiberBundle/mitkFiberBundle.h IODataStructures/FiberBundle/mitkTrackvis.h IODataStructures/mitkFiberfoxParameters.h IODataStructures/mitkTractographyForest.h # Algorithms Algorithms/itkTractDensityImageFilter.h Algorithms/itkTractsToFiberEndingsImageFilter.h Algorithms/itkTractsToRgbaImageFilter.h Algorithms/itkTractsToVectorImageFilter.h Algorithms/itkEvaluateDirectionImagesFilter.h Algorithms/itkEvaluateTractogramDirectionsFilter.h Algorithms/itkFiberCurvatureFilter.h Algorithms/itkFitFibersToImageFilter.h Algorithms/itkTractClusteringFilter.h + Algorithms/itkTractDistanceFilter.h Algorithms/itkFiberExtractionFilter.h Algorithms/itkTdiToVolumeFractionFilter.h # Tractography Algorithms/TrackingHandlers/mitkTrackingDataHandler.h Algorithms/TrackingHandlers/mitkTrackingHandlerRandomForest.h Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.h Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.h Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.h Algorithms/itkGibbsTrackingFilter.h Algorithms/itkStochasticTractographyFilter.h Algorithms/GibbsTracking/mitkParticle.h Algorithms/GibbsTracking/mitkParticleGrid.h Algorithms/GibbsTracking/mitkMetropolisHastingsSampler.h Algorithms/GibbsTracking/mitkSimpSamp.h Algorithms/GibbsTracking/mitkEnergyComputer.h Algorithms/GibbsTracking/mitkGibbsEnergyComputer.h Algorithms/GibbsTracking/mitkSphereInterpolator.h Algorithms/GibbsTracking/mitkFiberBuilder.h Algorithms/itkStreamlineTrackingFilter.h # Clustering Algorithms/ClusteringMetrics/mitkClusteringMetric.h Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanMean.h Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanMax.h Algorithms/ClusteringMetrics/mitkClusteringMetricEuclideanStd.h Algorithms/ClusteringMetrics/mitkClusteringMetricAnatomic.h Algorithms/ClusteringMetrics/mitkClusteringMetricScalarMap.h Algorithms/ClusteringMetrics/mitkClusteringMetricInnerAngles.h Algorithms/ClusteringMetrics/mitkClusteringMetricLength.h # Fiberfox Fiberfox/itkFibersFromPlanarFiguresFilter.h Fiberfox/itkTractsToDWIImageFilter.h Fiberfox/itkKspaceImageFilter.h Fiberfox/itkDftImageFilter.h Fiberfox/itkFieldmapGeneratorFilter.h Fiberfox/SignalModels/mitkDiffusionSignalModel.h Fiberfox/SignalModels/mitkTensorModel.h Fiberfox/SignalModels/mitkBallModel.h Fiberfox/SignalModels/mitkDotModel.h Fiberfox/SignalModels/mitkAstroStickModel.h Fiberfox/SignalModels/mitkStickModel.h Fiberfox/SignalModels/mitkRawShModel.h Fiberfox/SignalModels/mitkDiffusionNoiseModel.h Fiberfox/SignalModels/mitkRicianNoiseModel.h Fiberfox/SignalModels/mitkChiSquareNoiseModel.h Fiberfox/Sequences/mitkAcquisitionType.h Fiberfox/Sequences/mitkSingleShotEpi.h Fiberfox/Sequences/mitkCartesianReadout.h ) set(RESOURCE_FILES # Binary directory resources FiberTrackingLUTBaryCoords.bin FiberTrackingLUTIndices.bin ) diff --git a/Modules/DiffusionImaging/MiniApps/ExtractAllGradients.cpp b/Modules/DiffusionImaging/MiniApps/ExtractAllGradients.cpp deleted file mode 100644 index 848d857171..0000000000 --- a/Modules/DiffusionImaging/MiniApps/ExtractAllGradients.cpp +++ /dev/null @@ -1,86 +0,0 @@ -/*=================================================================== - -The Medical Imaging Interaction Toolkit (MITK) - -Copyright (c) German Cancer Research Center, -Division of Medical and Biological Informatics. -All rights reserved. - -This software is distributed WITHOUT ANY WARRANTY; without -even the implied warranty of MERCHANTABILITY or FITNESS FOR -A PARTICULAR PURPOSE. - -See LICENSE.txt or http://www.mitk.org for details. - -===================================================================*/ - -#include -#include -#include -#include "mitkCommandLineParser.h" -#include - -using namespace mitk; -using namespace std; - -/*! -\brief Copies transformation matrix of one image to another -*/ -int main(int argc, char* argv[]) -{ - typedef itk::VectorImage< short, 3 > ItkDwiType; - - mitkCommandLineParser parser; - - parser.setTitle("Extract all gradients"); - parser.setCategory("Preprocessing Tools"); - parser.setDescription("Extract all gradients from an diffusion image"); - parser.setContributor("MBI"); - - parser.setArgumentPrefix("--", "-"); - parser.addArgument("in", "i", mitkCommandLineParser::InputFile, "Input:", "input image", us::Any(), false); - //parser.addArgument("extension", "e", mitkCommandLineParser::String, "File Extension:", "Extension of the output file", us::Any(), false); - //parser.addArgument("out", "o", mitkCommandLineParser::OutputFile, "Output:", "output image", us::Any(), false); - - map parsedArgs = parser.parseArguments(argc, argv); - if (parsedArgs.size() == 0) - return EXIT_FAILURE; - - MITK_INFO << "Extract parameter"; - // mandatory arguments - /*string inputName = us::any_cast(parsedArgs["in"]); - string extensionName = us::any_cast(parsedArgs["extension"]); - string ouputName = us::any_cast(parsedArgs["out"]);*/ - string in = us::any_cast(parsedArgs["in"]); - string inputName = "E:\\Kollektive\\R02-Lebertumore-Diffusion\\01-Extrahierte-Daten\\" + in + "\\" + in + "-DWI.dwi"; - string extensionName = ".nrrd"; - string ouputName = "E:\\Kollektive\\R02-Lebertumore-Diffusion\\01-Extrahierte-Daten\\" + in + "\\" + in + "-"; - - MITK_INFO << "Load Image: "; - mitk::Image::Pointer image = mitk::IOUtil::Load(inputName); - - //bool isDiffusionImage(mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image)); - //if (!isDiffusionImage) - //{ - // MITK_INFO << "Input file is not of type diffusion image"; - // return; - //} - - ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); - mitk::CastToItkImage(image, itkVectorImagePointer); - - unsigned int channel = 0; - for (unsigned int channel = 0; channel < itkVectorImagePointer->GetVectorLength(); ++channel) - { - itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); - filter->SetInput(itkVectorImagePointer); - filter->SetChannelIndex(channel); - filter->Update(); - - mitk::Image::Pointer newImage = mitk::Image::New(); - newImage->InitializeByItk(filter->GetOutput()); - newImage->SetImportChannel(filter->GetOutput()->GetBufferPointer()); - mitk::IOUtil::SaveImage(newImage, ouputName + to_string(channel) + extensionName); - } - return EXIT_SUCCESS; -} diff --git a/Modules/DiffusionImaging/Quantification/CMakeLists.txt b/Modules/DiffusionImaging/Quantification/CMakeLists.txt index 4f465c02c4..d3b6e845cc 100644 --- a/Modules/DiffusionImaging/Quantification/CMakeLists.txt +++ b/Modules/DiffusionImaging/Quantification/CMakeLists.txt @@ -1,15 +1,14 @@ # 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() #DiffusionImaging/Quantification MITK_CREATE_MODULE( SUBPROJECTS MITK-DTI INCLUDE_DIRS Algorithms IODataStructures IODataStructures/TbssImages Rendering ${CMAKE_CURRENT_BINARY_DIR} DEPENDS MitkDiffusionCore MitkFiberTracking MitkGraphAlgorithms PACKAGE_DEPENDS ITK|ITKThresholding ) add_subdirectory(Testing) -add_subdirectory(cmdapps) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringViewControls.ui index 22d11ae3eb..b9edec8bfc 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringViewControls.ui @@ -1,524 +1,524 @@ - + QmitkFiberClusteringViewControls 0 0 474 - 683 + 695 Form QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; } 25 Qt::Vertical 20 40 Metrics 6 6 6 6 Weighting factor for metric values. 1 999.000000000000000 1.000000000000000 Euclidean true Weighting factor for metric values. 1 999.000000000000000 1.000000000000000 Euclidean STDEV Weighting factor for metric values. 1 999.000000000000000 1.000000000000000 Euclidean Maximum Weighting factor for metric values. 1 999.000000000000000 1.000000000000000 Weighting factor for metric values. 1 999.000000000000000 1.000000000000000 Inner Angles Weighting factor for metric values. 1 999.000000000000000 1.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 Distance is based on the selected parcellation. Anatomical Distance is based on the selected parcellation. Weighting factor for metric values. 1 999.000000000000000 30.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 Distance is based on the scalar map values along the tract. Scalar Map Distance is based on the scalar map values along the tract. Streamline Length Input Data 6 6 6 6 Input Centroids: If set, the input tractogram is clustered around the input centroids and no new clusters are created. false 0 0 200 16777215 11 - + Start Tractogram: - + Parameters Only output clusters with ate least the specified number of fibers. 1 9999999 50 Only output the N largest clusters. Zero means no limit. 99999999 10 Min. Fibers per Cluster: Max. Clusters: Fiber Points: Merge duplicate clusters withthe specified distance threshold. If threshold is < 0, the threshold is set to half of the specified cluster size. -1.000000000000000 99999.000000000000000 - 0.000000000000000 + -1.000000000000000 Cluster Size: Cluster size in mm. 1 9999999 20 Fibers are resampled to the desired number of points for clustering. Smaller is faster but less accurate. 2 9999999 12 Merge Duplicate Clusters: Output Centroids: - + QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkDataStorageComboBoxWithSelectNone QComboBox
QmitkDataStorageComboBoxWithSelectNone.h
 - - - \ No newline at end of file + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp index aa1703963f..1ca7905f97 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp @@ -1,264 +1,265 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include "QmitkFiberFitView.h" #include #include #include #include #include #include #include #include #include #include #include #include #include const std::string QmitkFiberFitView::VIEW_ID = "org.mitk.views.fiberfit"; using namespace mitk; QmitkFiberFitView::QmitkFiberFitView() : QmitkAbstractView() , m_Controls( nullptr ) { } // Destructor QmitkFiberFitView::~QmitkFiberFitView() { } void QmitkFiberFitView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberFitViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(StartFit()) ); connect( m_Controls->m_ImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(DataSelectionChanged()) ); connect( m_Controls->m_TractBox, SIGNAL(currentIndexChanged(int)), this, SLOT(DataSelectionChanged()) ); mitk::TNodePredicateDataType::Pointer isFib = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDimension::Pointer is3D = mitk::NodePredicateDimension::New(3); m_Controls->m_TractBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TractBox->SetPredicate(isFib); m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_ImageBox->SetPredicate( mitk::NodePredicateOr::New( mitk::NodePredicateAnd::New(isImage, is3D), mitk::TNodePredicateDataType::New()) ); DataSelectionChanged(); } } void QmitkFiberFitView::DataSelectionChanged() { if (m_Controls->m_TractBox->GetSelectedNode().IsNull() || m_Controls->m_ImageBox->GetSelectedNode().IsNull()) m_Controls->m_StartButton->setEnabled(false); else m_Controls->m_StartButton->setEnabled(true); } void QmitkFiberFitView::SetFocus() { DataSelectionChanged(); } void QmitkFiberFitView::StartFit() { if (m_Controls->m_TractBox->GetSelectedNode().IsNull() || m_Controls->m_ImageBox->GetSelectedNode().IsNull()) return; mitk::FiberBundle::Pointer input_tracts = dynamic_cast(m_Controls->m_TractBox->GetSelectedNode()->GetData()); mitk::DataNode::Pointer node = m_Controls->m_ImageBox->GetSelectedNode(); itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New(); mitk::Image::Pointer mitk_image = dynamic_cast(node->GetData()); mitk::PeakImage::Pointer mitk_peak_image = dynamic_cast(node->GetData()); if (mitk_peak_image.IsNotNull()) { typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(mitk_peak_image); caster->Update(); mitk::PeakImage::ItkPeakImageType::Pointer peak_image = caster->GetOutput(); fitter->SetPeakImage(peak_image); } else { if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image)) { fitter->SetDiffImage(mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk_image)); mitk::TensorModel<>* model = new mitk::TensorModel<>(); model->SetBvalue(1000); model->SetDiffusivity1(0.0010); model->SetDiffusivity2(0.00015); model->SetDiffusivity3(0.00015); model->SetGradientList(mitk::DiffusionPropertyHelper::GetGradientContainer(mitk_image)); fitter->SetSignalModel(model); } else { itk::FitFibersToImageFilter::DoubleImgType::Pointer scalar_image = itk::FitFibersToImageFilter::DoubleImgType::New(); mitk::CastToItkImage(mitk_image, scalar_image); fitter->SetScalarImage(scalar_image); } } if (m_Controls->m_ReguTypeBox->currentIndex()==0) fitter->SetRegularization(VnlCostFunction::REGU::VOXEL_VARIANCE); else if (m_Controls->m_ReguTypeBox->currentIndex()==1) fitter->SetRegularization(VnlCostFunction::REGU::VARIANCE); else if (m_Controls->m_ReguTypeBox->currentIndex()==2) fitter->SetRegularization(VnlCostFunction::REGU::MSM); else if (m_Controls->m_ReguTypeBox->currentIndex()==3) fitter->SetRegularization(VnlCostFunction::REGU::LASSO); else if (m_Controls->m_ReguTypeBox->currentIndex()==4) fitter->SetRegularization(VnlCostFunction::REGU::NONE); fitter->SetTractograms({input_tracts}); fitter->SetFitIndividualFibers(true); fitter->SetMaxIterations(20); fitter->SetVerbose(true); fitter->SetGradientTolerance(1e-5); fitter->SetLambda(m_Controls->m_ReguBox->value()); fitter->SetFilterOutliers(m_Controls->m_OutliersBox->isChecked()); fitter->Update(); mitk::FiberBundle::Pointer output_tracts = fitter->GetTractograms().at(0); + output_tracts->ColorFibersByFiberWeights(false, true); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(output_tracts); new_node->SetName("Fitted"); this->GetDataStorage()->Add(new_node, node); m_Controls->m_TractBox->GetSelectedNode()->SetVisibility(false); if (m_Controls->m_ResidualsBox->isChecked() && mitk_peak_image.IsNotNull()) { { mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetFittedImage(); mitk::Image::Pointer mitk_image = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_image, mitk_image); mitk_image->SetVolume(itk_image->GetBufferPointer()); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(mitk_image); new_node->SetName("Fitted"); this->GetDataStorage()->Add(new_node, node); } { mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetResidualImage(); mitk::Image::Pointer mitk_image = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_image, mitk_image); mitk_image->SetVolume(itk_image->GetBufferPointer()); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(mitk_image); new_node->SetName("Residual"); this->GetDataStorage()->Add(new_node, node); } { mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetUnderexplainedImage(); mitk::Image::Pointer mitk_image = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_image, mitk_image); mitk_image->SetVolume(itk_image->GetBufferPointer()); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(mitk_image); new_node->SetName("Underexplained"); this->GetDataStorage()->Add(new_node, node); } { mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetOverexplainedImage(); mitk::Image::Pointer mitk_image = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_image, mitk_image); mitk_image->SetVolume(itk_image->GetBufferPointer()); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(mitk_image); new_node->SetName("Overexplained"); this->GetDataStorage()->Add(new_node, node); } } else if (m_Controls->m_ResidualsBox->isChecked() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image)) { { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetFittedImageDiff().GetPointer() ); mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true); mitk::DiffusionPropertyHelper::InitializeImage( outImage ); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(outImage); new_node->SetName("Fitted"); this->GetDataStorage()->Add(new_node, node); } { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetResidualImageDiff().GetPointer() ); mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true); mitk::DiffusionPropertyHelper::InitializeImage( outImage ); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(outImage); new_node->SetName("Residual"); this->GetDataStorage()->Add(new_node, node); } } else if (m_Controls->m_ResidualsBox->isChecked()) { { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetFittedImageScalar().GetPointer() ); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(outImage); new_node->SetName("Fitted"); this->GetDataStorage()->Add(new_node, node); } { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetResidualImageScalar().GetPointer() ); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(outImage); new_node->SetName("Residual"); this->GetDataStorage()->Add(new_node, node); } } } void QmitkFiberFitView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& ) { } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp index 86635c518d..6098c451b7 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.cpp @@ -1,1614 +1,1733 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include #include // Qmitk #include "QmitkFiberProcessingView.h" -// Qt #include -// MITK #include #include #include #include #include #include #include #include #include #include #include "usModuleRegistry.h" #include #include "mitkNodePredicateDataType.h" #include #include #include #include -// ITK #include #include #include #include #include #include #include #include +#include +#include + const std::string QmitkFiberProcessingView::VIEW_ID = "org.mitk.views.fiberprocessing"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace mitk; QmitkFiberProcessingView::QmitkFiberProcessingView() : QmitkAbstractView() , m_Controls( 0 ) , m_CircleCounter(0) , m_PolygonCounter(0) , m_UpsamplingFactor(1) { } // Destructor QmitkFiberProcessingView::~QmitkFiberProcessingView() { RemoveObservers(); } void QmitkFiberProcessingView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberProcessingViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_CircleButton, SIGNAL( clicked() ), this, SLOT( OnDrawCircle() ) ); connect( m_Controls->m_PolygonButton, SIGNAL( clicked() ), this, SLOT( OnDrawPolygon() ) ); connect(m_Controls->PFCompoANDButton, SIGNAL(clicked()), this, SLOT(GenerateAndComposite()) ); connect(m_Controls->PFCompoORButton, SIGNAL(clicked()), this, SLOT(GenerateOrComposite()) ); connect(m_Controls->PFCompoNOTButton, SIGNAL(clicked()), this, SLOT(GenerateNotComposite()) ); connect(m_Controls->m_GenerateRoiImage, SIGNAL(clicked()), this, SLOT(GenerateRoiImage()) ); connect(m_Controls->m_JoinBundles, SIGNAL(clicked()), this, SLOT(JoinBundles()) ); connect(m_Controls->m_SubstractBundles, SIGNAL(clicked()), this, SLOT(SubstractBundles()) ); connect(m_Controls->m_CopyBundle, SIGNAL(clicked()), this, SLOT(CopyBundles()) ); connect(m_Controls->m_ExtractFibersButton, SIGNAL(clicked()), this, SLOT(Extract())); connect(m_Controls->m_RemoveButton, SIGNAL(clicked()), this, SLOT(Remove())); connect(m_Controls->m_ModifyButton, SIGNAL(clicked()), this, SLOT(Modify())); connect(m_Controls->m_ExtractionMethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui())); connect(m_Controls->m_RemovalMethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui())); connect(m_Controls->m_ModificationMethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui())); connect(m_Controls->m_ExtractionBoxMask, SIGNAL(currentIndexChanged(int)), this, SLOT(OnMaskExtractionChanged())); m_Controls->m_ColorMapBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("OdfImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isOdf); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); m_Controls->m_ColorMapBox->SetPredicate(finalPredicate); - - m_Controls->label_17->setVisible(false); - m_Controls->m_FiberExtractionFractionBox->setVisible(false); } UpdateGui(); + OnMaskExtractionChanged(); } void QmitkFiberProcessingView::OnMaskExtractionChanged() { + m_Controls->m_FiberExtractionFractionLabel->setVisible(false); + m_Controls->m_FiberExtractionFractionBox->setVisible(false); + + m_Controls->m_FiberExtractionThresholdLabel->setVisible(false); + m_Controls->m_FiberExtractionThresholdBox->setVisible(false); + + m_Controls->m_InterpolateRoiBox->setVisible(false); + m_Controls->m_BothEnds->setVisible(false); + + m_Controls->m_LabelsBox->setVisible(false); + m_Controls->m_LabelsLabel->setVisible(false); + if (m_Controls->m_ExtractionBoxMask->currentIndex() == 2 || m_Controls->m_ExtractionBoxMask->currentIndex() == 3) { - m_Controls->label_17->setVisible(true); + m_Controls->m_FiberExtractionFractionLabel->setVisible(true); m_Controls->m_FiberExtractionFractionBox->setVisible(true); - m_Controls->m_BothEnds->setVisible(false); + + m_Controls->m_FiberExtractionThresholdLabel->setVisible(true); + m_Controls->m_FiberExtractionThresholdBox->setVisible(true); + + m_Controls->m_InterpolateRoiBox->setVisible(true); } - else + else if (m_Controls->m_ExtractionBoxMask->currentIndex() == 0 || m_Controls->m_ExtractionBoxMask->currentIndex() == 1) { - m_Controls->label_17->setVisible(false); - m_Controls->m_FiberExtractionFractionBox->setVisible(false); if (m_Controls->m_ExtractionBoxMask->currentIndex() != 3) m_Controls->m_BothEnds->setVisible(true); + m_Controls->m_InterpolateRoiBox->setVisible(true); + + m_Controls->m_FiberExtractionThresholdLabel->setVisible(true); + m_Controls->m_FiberExtractionThresholdBox->setVisible(true); + } + else if (m_Controls->m_ExtractionBoxMask->currentIndex() == 4) + { + m_Controls->m_BothEnds->setVisible(true); + + m_Controls->m_LabelsBox->setVisible(true); + m_Controls->m_LabelsLabel->setVisible(true); } } void QmitkFiberProcessingView::SetFocus() { m_Controls->toolBoxx->setFocus(); } void QmitkFiberProcessingView::Modify() { switch (m_Controls->m_ModificationMethodBox->currentIndex()) { case 0: { ResampleSelectedBundlesSpline(); break; } case 1: { ResampleSelectedBundlesLinear(); break; } case 2: { CompressSelectedBundles(); break; } case 3: { DoImageColorCoding(); break; } case 4: { MirrorFibers(); break; } case 5: { WeightFibers(); break; } case 6: { DoCurvatureColorCoding(); break; } case 7: { DoWeightColorCoding(); break; } case 8: { DoLengthColorCoding(); break; } } } void QmitkFiberProcessingView::WeightFibers() { float weight = this->m_Controls->m_BundleWeightBox->value(); for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); fib->SetFiberWeights(weight); } } void QmitkFiberProcessingView::Remove() { switch (m_Controls->m_RemovalMethodBox->currentIndex()) { case 0: { RemoveDir(); break; } case 1: { PruneBundle(); break; } case 2: { ApplyCurvatureThreshold(); break; } case 3: { RemoveWithMask(false); break; } case 4: { RemoveWithMask(true); break; } case 5: { ApplyWeightThreshold(); break; } + case 6: + { + ApplyDensityThreshold(); + break; + } } } void QmitkFiberProcessingView::Extract() { switch (m_Controls->m_ExtractionMethodBox->currentIndex()) { case 0: { ExtractWithPlanarFigure(); break; } case 1: { switch (m_Controls->m_ExtractionBoxMask->currentIndex()) { { case 0: - ExtractWithMask(true, false); + ExtractWithMask(true, false, false); break; } { case 1: - ExtractWithMask(true, true); + ExtractWithMask(true, true, false); break; } { case 2: - ExtractWithMask(false, false); + ExtractWithMask(false, false, false); break; } { case 3: - ExtractWithMask(false, true); + ExtractWithMask(false, true, false); + break; + } + { + case 4: + ExtractWithMask(true, false, true); break; } } break; } } } void QmitkFiberProcessingView::PruneBundle() { int minLength = this->m_Controls->m_PruneFibersMinBox->value(); int maxLength = this->m_Controls->m_PruneFibersMaxBox->value(); for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); if (!fib->RemoveShortFibers(minLength)) QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers."); else if (!fib->RemoveLongFibers(maxLength)) QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers."); } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::ApplyWeightThreshold() { float thr = this->m_Controls->m_WeightThresholdBox->value(); std::vector< DataNode::Pointer > nodes = m_SelectedFB; for (auto node : nodes) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); mitk::FiberBundle::Pointer newFib = fib->FilterByWeights(thr); if (newFib->GetNumFibers()>0) { newFib->ColorFibersByFiberWeights(false, true); node->SetData(newFib); } else QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers."); } RenderingManager::GetInstance()->RequestUpdateAll(); } +void QmitkFiberProcessingView::ApplyDensityThreshold() +{ + float thr = this->m_Controls->m_DensityThresholdBox->value(); + float ol = this->m_Controls->m_DensityOverlapBox->value(); + std::vector< DataNode::Pointer > nodes = m_SelectedFB; + for (auto node : nodes) + { + mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); + + itk::TractDensityImageFilter< ItkFloatImageType >::Pointer generator = itk::TractDensityImageFilter< ItkFloatImageType >::New(); + generator->SetFiberBundle(fib); + generator->SetBinaryOutput(false); + generator->SetOutputAbsoluteValues(false); + generator->Update(); + + itk::FiberExtractionFilter::Pointer extractor = itk::FiberExtractionFilter::New(); + extractor->SetRoiImages({generator->GetOutput()}); + extractor->SetInputFiberBundle(fib); + extractor->SetOverlapFraction(ol); + extractor->SetInterpolate(true); + extractor->SetThreshold(thr); + extractor->SetNoNegatives(true); + extractor->Update(); + + if (extractor->GetPositives().empty()) + { + QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers."); + continue; + } + + mitk::FiberBundle::Pointer newFib = extractor->GetPositives().at(0); + if (newFib->GetNumFibers()>0) + node->SetData(newFib); + else + QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers."); + } + RenderingManager::GetInstance()->RequestUpdateAll(); +} + void QmitkFiberProcessingView::ApplyCurvatureThreshold() { int angle = this->m_Controls->m_CurvSpinBox->value(); int dist = this->m_Controls->m_CurvDistanceSpinBox->value(); std::vector< DataNode::Pointer > nodes = m_SelectedFB; for (auto node : nodes) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); itk::FiberCurvatureFilter::Pointer filter = itk::FiberCurvatureFilter::New(); filter->SetInputFiberBundle(fib); filter->SetAngularDeviation(angle); filter->SetDistance(dist); filter->SetRemoveFibers(m_Controls->m_RemoveCurvedFibersBox->isChecked()); filter->Update(); mitk::FiberBundle::Pointer newFib = filter->GetOutputFiberBundle(); if (newFib->GetNumFibers()>0) { newFib->ColorFibersByOrientation(); node->SetData(newFib); } else QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers."); } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::RemoveDir() { for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); vnl_vector_fixed dir; dir[0] = m_Controls->m_ExtractDirX->value(); dir[1] = m_Controls->m_ExtractDirY->value(); dir[2] = m_Controls->m_ExtractDirZ->value(); fib->RemoveDir(dir,cos((float)m_Controls->m_ExtractAngle->value()*itk::Math::pi/180)); } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::RemoveWithMask(bool removeInside) { if (m_RoiImageNode.IsNull()) return; mitk::Image::Pointer mitkMask = dynamic_cast(m_RoiImageNode->GetData()); for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(mitkMask, mask); mitk::FiberBundle::Pointer newFib = fib->RemoveFibersOutside(mask, removeInside); if (newFib->GetNumFibers()<=0) { QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers."); continue; } node->SetData(newFib); } RenderingManager::GetInstance()->RequestUpdateAll(); } -void QmitkFiberProcessingView::ExtractWithMask(bool onlyEnds, bool invert) +void QmitkFiberProcessingView::ExtractWithMask(bool onlyEnds, bool invert, bool labelmap) { if (m_RoiImageNode.IsNull()) return; mitk::Image::Pointer mitkMask = dynamic_cast(m_RoiImageNode->GetData()); for (auto node : m_SelectedFB) { + std::string roi_name = m_RoiImageNode->GetName(); mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); - QString name(node->GetName().c_str()); - ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(mitkMask, mask); itk::FiberExtractionFilter::Pointer extractor = itk::FiberExtractionFilter::New(); extractor->SetInputFiberBundle(fib); extractor->SetRoiImages({mask}); + extractor->SetRoiImageNames({roi_name}); extractor->SetThreshold(m_Controls->m_FiberExtractionThresholdBox->value()); extractor->SetOverlapFraction(m_Controls->m_FiberExtractionFractionBox->value()); extractor->SetBothEnds(m_Controls->m_BothEnds->isChecked()); extractor->SetInterpolate(m_Controls->m_InterpolateRoiBox->isChecked()); + extractor->SetMinFibersPerTract(m_Controls->m_MinExtractedFibersBox->value()); + extractor->SetSplitByRoi(true); if (invert) extractor->SetNoPositives(true); else extractor->SetNoNegatives(true); + + if (labelmap) + { + std::string labels_string = m_Controls->m_LabelsBox->text().toStdString(); + if (labels_string!="ALL") + { + std::vector strs; + boost::split(strs,labels_string,boost::is_any_of(" ,;\t")); + + std::vector< unsigned short > labels_vector; + for (auto v : strs) + { + try{ + unsigned short l = boost::lexical_cast(v); + labels_vector.push_back(l); + } + catch(...) + { + + } + } + extractor->SetLabels(labels_vector); + } + + extractor->SetInterpolate(false); + extractor->SetInputType(itk::FiberExtractionFilter::INPUT::LABEL_MAP); + extractor->SetSplitLabels(true); + onlyEnds = true; + } + if (onlyEnds) extractor->SetMode(itk::FiberExtractionFilter::MODE::ENDPOINTS); extractor->Update(); - mitk::FiberBundle::Pointer newFib; + std::vector< mitk::FiberBundle::Pointer > newFibs; if (invert) - newFib = extractor->GetNegatives().at(0); + newFibs = extractor->GetNegatives(); else - newFib = extractor->GetPositives().at(0); + newFibs = extractor->GetPositives(); - if (newFib.IsNull() || newFib->GetNumFibers()<=0) + if (newFibs.empty()) { - QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers."); + QMessageBox::information(nullptr, "No output generated:", "No fibers could be extracted."); continue; } - DataNode::Pointer newNode = DataNode::New(); - newNode->SetData(newFib); + auto labels = extractor->GetPositiveLabels(); + MITK_INFO << labels.size(); - if (invert) + for (unsigned int i=0; iSetData(fib); + std::string name = roi_name; + if (iSetName(name.toStdString()); - GetDataStorage()->Add(newNode); + newNode->SetName(name); + GetDataStorage()->Add(newNode, node); + } node->SetVisibility(false); } } void QmitkFiberProcessingView::GenerateRoiImage() { if (m_SelectedPF.empty()) return; mitk::BaseGeometry::Pointer geometry; if (!m_SelectedFB.empty()) { mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedFB.front()->GetData()); geometry = fib->GetGeometry(); } else if (m_SelectedImage) geometry = m_SelectedImage->GetGeometry(); else return; itk::Vector spacing = geometry->GetSpacing(); spacing /= m_UpsamplingFactor; mitk::Point3D newOrigin = geometry->GetOrigin(); mitk::Geometry3D::BoundsArrayType bounds = geometry->GetBounds(); newOrigin[0] += bounds.GetElement(0); newOrigin[1] += bounds.GetElement(2); newOrigin[2] += bounds.GetElement(4); itk::Matrix direction; itk::ImageRegion<3> imageRegion; for (int i=0; i<3; i++) for (int j=0; j<3; j++) direction[j][i] = geometry->GetMatrixColumn(i)[j]/spacing[j]; imageRegion.SetSize(0, geometry->GetExtent(0)*m_UpsamplingFactor); imageRegion.SetSize(1, geometry->GetExtent(1)*m_UpsamplingFactor); imageRegion.SetSize(2, geometry->GetExtent(2)*m_UpsamplingFactor); m_PlanarFigureImage = ItkUCharImageType::New(); m_PlanarFigureImage->SetSpacing( spacing ); // Set the image spacing m_PlanarFigureImage->SetOrigin( newOrigin ); // Set the image origin m_PlanarFigureImage->SetDirection( direction ); // Set the image direction m_PlanarFigureImage->SetRegions( imageRegion ); m_PlanarFigureImage->Allocate(); m_PlanarFigureImage->FillBuffer( 0 ); Image::Pointer tmpImage = Image::New(); tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer()); tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer()); std::string name = m_SelectedPF.at(0)->GetName(); WritePfToImage(m_SelectedPF.at(0), tmpImage); for (unsigned int i=1; iGetName(); WritePfToImage(m_SelectedPF.at(i), tmpImage); } DataNode::Pointer node = DataNode::New(); tmpImage = Image::New(); tmpImage->InitializeByItk(m_PlanarFigureImage.GetPointer()); tmpImage->SetVolume(m_PlanarFigureImage->GetBufferPointer()); node->SetData(tmpImage); node->SetName(name); this->GetDataStorage()->Add(node); } void QmitkFiberProcessingView::WritePfToImage(mitk::DataNode::Pointer node, mitk::Image* image) { if (dynamic_cast(node->GetData())) { m_PlanarFigure = dynamic_cast(node->GetData()); AccessFixedDimensionByItk_2( image, InternalReorientImagePlane, 3, m_PlanarFigure->GetGeometry(), -1); AccessFixedDimensionByItk_2( m_InternalImage, InternalCalculateMaskFromPlanarFigure, 3, 2, node->GetName() ); } else if (dynamic_cast(node->GetData())) { DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(node); for (unsigned int i=0; iSize(); i++) { WritePfToImage(children->at(i), image); } } } template < typename TPixel, unsigned int VImageDimension > void QmitkFiberProcessingView::InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > *image, mitk::BaseGeometry* planegeo3D, int additionalIndex ) { typedef itk::Image< TPixel, VImageDimension > ImageType; typedef itk::Image< float, VImageDimension > FloatImageType; typedef itk::ResampleImageFilter ResamplerType; typename ResamplerType::Pointer resampler = ResamplerType::New(); mitk::PlaneGeometry* planegeo = dynamic_cast(planegeo3D); float upsamp = m_UpsamplingFactor; float gausssigma = 0.5; // Spacing typename ResamplerType::SpacingType spacing = planegeo->GetSpacing(); spacing[0] = image->GetSpacing()[0] / upsamp; spacing[1] = image->GetSpacing()[1] / upsamp; spacing[2] = image->GetSpacing()[2]; resampler->SetOutputSpacing( spacing ); // Size typename ResamplerType::SizeType size; size[0] = planegeo->GetExtentInMM(0) / spacing[0]; size[1] = planegeo->GetExtentInMM(1) / spacing[1]; size[2] = 1; resampler->SetSize( size ); // Origin typename mitk::Point3D orig = planegeo->GetOrigin(); typename mitk::Point3D corrorig; planegeo3D->WorldToIndex(orig,corrorig); corrorig[0] += 0.5/upsamp; corrorig[1] += 0.5/upsamp; corrorig[2] += 0; planegeo3D->IndexToWorld(corrorig,corrorig); resampler->SetOutputOrigin(corrorig ); // Direction typename ResamplerType::DirectionType direction; typename mitk::AffineTransform3D::MatrixType matrix = planegeo->GetIndexToWorldTransform()->GetMatrix(); for(unsigned int c=0; cSetOutputDirection( direction ); // Gaussian interpolation if(gausssigma != 0) { double sigma[3]; for( unsigned int d = 0; d < 3; d++ ) sigma[d] = gausssigma * image->GetSpacing()[d]; double alpha = 2.0; typedef itk::GaussianInterpolateImageFunction GaussianInterpolatorType; typename GaussianInterpolatorType::Pointer interpolator = GaussianInterpolatorType::New(); interpolator->SetInputImage( image ); interpolator->SetParameters( sigma, alpha ); resampler->SetInterpolator( interpolator ); } else { typedef typename itk::LinearInterpolateImageFunction InterpolatorType; typename InterpolatorType::Pointer interpolator = InterpolatorType::New(); interpolator->SetInputImage( image ); resampler->SetInterpolator( interpolator ); } resampler->SetInput( image ); resampler->SetDefaultPixelValue(0); resampler->Update(); if(additionalIndex < 0) { this->m_InternalImage = mitk::Image::New(); this->m_InternalImage->InitializeByItk( resampler->GetOutput() ); this->m_InternalImage->SetVolume( resampler->GetOutput()->GetBufferPointer() ); } } template < typename TPixel, unsigned int VImageDimension > void QmitkFiberProcessingView::InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string ) { typedef itk::Image< TPixel, VImageDimension > ImageType; // Generate mask image as new image with same header as input image and // initialize with "1". ItkUCharImageType::Pointer newMaskImage = ItkUCharImageType::New(); newMaskImage->SetSpacing( image->GetSpacing() ); // Set the image spacing newMaskImage->SetOrigin( image->GetOrigin() ); // Set the image origin newMaskImage->SetDirection( image->GetDirection() ); // Set the image direction newMaskImage->SetRegions( image->GetLargestPossibleRegion() ); newMaskImage->Allocate(); newMaskImage->FillBuffer( 1 ); // Generate VTK polygon from (closed) PlanarFigure polyline // (The polyline points are shifted by -0.5 in z-direction to make sure // that the extrusion filter, which afterwards elevates all points by +0.5 // in z-direction, creates a 3D object which is cut by the the plane z=0) const PlaneGeometry *planarFigurePlaneGeometry = m_PlanarFigure->GetPlaneGeometry(); const PlanarFigure::PolyLineType planarFigurePolyline = m_PlanarFigure->GetPolyLine( 0 ); const BaseGeometry *imageGeometry3D = m_InternalImage->GetGeometry( 0 ); vtkPolyData *polyline = vtkPolyData::New(); polyline->Allocate( 1, 1 ); // Determine x- and y-dimensions depending on principal axis int i0, i1; switch ( axis ) { case 0: i0 = 1; i1 = 2; break; case 1: i0 = 0; i1 = 2; break; case 2: default: i0 = 0; i1 = 1; break; } // Create VTK polydata object of polyline contour vtkPoints *points = vtkPoints::New(); PlanarFigure::PolyLineType::const_iterator it; unsigned int numberOfPoints = 0; for ( it = planarFigurePolyline.begin(); it != planarFigurePolyline.end(); ++it ) { Point3D point3D; // Convert 2D point back to the local index coordinates of the selected image Point2D point2D = *it; planarFigurePlaneGeometry->WorldToIndex(point2D, point2D); point2D[0] -= 0.5/m_UpsamplingFactor; point2D[1] -= 0.5/m_UpsamplingFactor; planarFigurePlaneGeometry->IndexToWorld(point2D, point2D); planarFigurePlaneGeometry->Map( point2D, point3D ); // Polygons (partially) outside of the image bounds can not be processed further due to a bug in vtkPolyDataToImageStencil if ( !imageGeometry3D->IsInside( point3D ) ) { float bounds[2] = {0,0}; bounds[0] = this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i0); bounds[1] = this->m_InternalImage->GetLargestPossibleRegion().GetSize().GetElement(i1); imageGeometry3D->WorldToIndex( point3D, point3D ); if (point3D[i0]<0) point3D[i0] = 0.0; else if (point3D[i0]>bounds[0]) point3D[i0] = bounds[0]-0.001; if (point3D[i1]<0) point3D[i1] = 0.0; else if (point3D[i1]>bounds[1]) point3D[i1] = bounds[1]-0.001; points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 ); numberOfPoints++; } else { imageGeometry3D->WorldToIndex( point3D, point3D ); // Add point to polyline array points->InsertNextPoint( point3D[i0], point3D[i1], -0.5 ); numberOfPoints++; } } polyline->SetPoints( points ); points->Delete(); vtkIdType *ptIds = new vtkIdType[numberOfPoints]; for ( vtkIdType i = 0; i < numberOfPoints; ++i ) ptIds[i] = i; polyline->InsertNextCell( VTK_POLY_LINE, numberOfPoints, ptIds ); // Extrude the generated contour polygon vtkLinearExtrusionFilter *extrudeFilter = vtkLinearExtrusionFilter::New(); extrudeFilter->SetInputData( polyline ); extrudeFilter->SetScaleFactor( 1 ); extrudeFilter->SetExtrusionTypeToNormalExtrusion(); extrudeFilter->SetVector( 0.0, 0.0, 1.0 ); // Make a stencil from the extruded polygon vtkPolyDataToImageStencil *polyDataToImageStencil = vtkPolyDataToImageStencil::New(); polyDataToImageStencil->SetInputConnection( extrudeFilter->GetOutputPort() ); // Export from ITK to VTK (to use a VTK filter) typedef itk::VTKImageImport< ItkUCharImageType > ImageImportType; typedef itk::VTKImageExport< ItkUCharImageType > ImageExportType; typename ImageExportType::Pointer itkExporter = ImageExportType::New(); itkExporter->SetInput( newMaskImage ); vtkImageImport *vtkImporter = vtkImageImport::New(); this->ConnectPipelines( itkExporter, vtkImporter ); vtkImporter->Update(); // Apply the generated image stencil to the input image vtkImageStencil *imageStencilFilter = vtkImageStencil::New(); imageStencilFilter->SetInputConnection( vtkImporter->GetOutputPort() ); imageStencilFilter->SetStencilConnection(polyDataToImageStencil->GetOutputPort() ); imageStencilFilter->ReverseStencilOff(); imageStencilFilter->SetBackgroundValue( 0 ); imageStencilFilter->Update(); // Export from VTK back to ITK vtkImageExport *vtkExporter = vtkImageExport::New(); vtkExporter->SetInputConnection( imageStencilFilter->GetOutputPort() ); vtkExporter->Update(); typename ImageImportType::Pointer itkImporter = ImageImportType::New(); this->ConnectPipelines( vtkExporter, itkImporter ); itkImporter->Update(); // calculate cropping bounding box m_InternalImageMask3D = itkImporter->GetOutput(); m_InternalImageMask3D->SetDirection(image->GetDirection()); itk::ImageRegionConstIterator itmask(m_InternalImageMask3D, m_InternalImageMask3D->GetLargestPossibleRegion()); itk::ImageRegionIterator itimage(image, image->GetLargestPossibleRegion()); itmask.GoToBegin(); itimage.GoToBegin(); typename ImageType::SizeType lowersize = {{itk::NumericTraits::max(),itk::NumericTraits::max(),itk::NumericTraits::max()}}; typename ImageType::SizeType uppersize = {{0,0,0}}; while( !itmask.IsAtEnd() ) { if(itmask.Get() == 0) itimage.Set(0); else { typename ImageType::IndexType index = itimage.GetIndex(); typename ImageType::SizeType signedindex; signedindex[0] = index[0]; signedindex[1] = index[1]; signedindex[2] = index[2]; lowersize[0] = signedindex[0] < lowersize[0] ? signedindex[0] : lowersize[0]; lowersize[1] = signedindex[1] < lowersize[1] ? signedindex[1] : lowersize[1]; lowersize[2] = signedindex[2] < lowersize[2] ? signedindex[2] : lowersize[2]; uppersize[0] = signedindex[0] > uppersize[0] ? signedindex[0] : uppersize[0]; uppersize[1] = signedindex[1] > uppersize[1] ? signedindex[1] : uppersize[1]; uppersize[2] = signedindex[2] > uppersize[2] ? signedindex[2] : uppersize[2]; } ++itmask; ++itimage; } typename ImageType::IndexType index; index[0] = lowersize[0]; index[1] = lowersize[1]; index[2] = lowersize[2]; typename ImageType::SizeType size; size[0] = uppersize[0] - lowersize[0] + 1; size[1] = uppersize[1] - lowersize[1] + 1; size[2] = uppersize[2] - lowersize[2] + 1; itk::ImageRegion<3> cropRegion = itk::ImageRegion<3>(index, size); // crop internal mask typedef itk::RegionOfInterestImageFilter< ItkUCharImageType, ItkUCharImageType > ROIMaskFilterType; typename ROIMaskFilterType::Pointer roi2 = ROIMaskFilterType::New(); roi2->SetRegionOfInterest(cropRegion); roi2->SetInput(m_InternalImageMask3D); roi2->Update(); m_InternalImageMask3D = roi2->GetOutput(); Image::Pointer tmpImage = Image::New(); tmpImage->InitializeByItk(m_InternalImageMask3D.GetPointer()); tmpImage->SetVolume(m_InternalImageMask3D->GetBufferPointer()); Image::Pointer tmpImage2 = Image::New(); tmpImage2->InitializeByItk(m_PlanarFigureImage.GetPointer()); const BaseGeometry *pfImageGeometry3D = tmpImage2->GetGeometry( 0 ); const BaseGeometry *intImageGeometry3D = tmpImage->GetGeometry( 0 ); typedef itk::ImageRegionIteratorWithIndex IteratorType; IteratorType imageIterator (m_InternalImageMask3D, m_InternalImageMask3D->GetRequestedRegion()); imageIterator.GoToBegin(); while ( !imageIterator.IsAtEnd() ) { unsigned char val = imageIterator.Value(); if (val>0) { itk::Index<3> index = imageIterator.GetIndex(); Point3D point; point[0] = index[0]; point[1] = index[1]; point[2] = index[2]; intImageGeometry3D->IndexToWorld(point, point); pfImageGeometry3D->WorldToIndex(point, point); point[i0] += 0.5; point[i1] += 0.5; index[0] = point[0]; index[1] = point[1]; index[2] = point[2]; if (pfImageGeometry3D->IsIndexInside(index)) m_PlanarFigureImage->SetPixel(index, 1); } ++imageIterator; } // Clean up VTK objects polyline->Delete(); extrudeFilter->Delete(); polyDataToImageStencil->Delete(); vtkImporter->Delete(); imageStencilFilter->Delete(); //vtkExporter->Delete(); // TODO: crashes when outcommented; memory leak?? delete[] ptIds; } void QmitkFiberProcessingView::UpdateGui() { m_Controls->m_FibLabel->setText("mandatory"); m_Controls->m_PfLabel->setText("needed for extraction"); m_Controls->m_InputData->setTitle("Please Select Input Data"); m_Controls->m_RemoveButton->setEnabled(false); m_Controls->m_PlanarFigureButtonsFrame->setEnabled(false); m_Controls->PFCompoANDButton->setEnabled(false); m_Controls->PFCompoORButton->setEnabled(false); m_Controls->PFCompoNOTButton->setEnabled(false); m_Controls->m_GenerateRoiImage->setEnabled(false); m_Controls->m_ExtractFibersButton->setEnabled(false); m_Controls->m_ModifyButton->setEnabled(false); m_Controls->m_CopyBundle->setEnabled(false); m_Controls->m_JoinBundles->setEnabled(false); m_Controls->m_SubstractBundles->setEnabled(false); // disable alle frames m_Controls->m_BundleWeightFrame->setVisible(false); m_Controls->m_ExtactionFramePF->setVisible(false); m_Controls->m_RemoveDirectionFrame->setVisible(false); m_Controls->m_RemoveLengthFrame->setVisible(false); m_Controls->m_RemoveCurvatureFrame->setVisible(false); m_Controls->m_RemoveByWeightFrame->setVisible(false); + m_Controls->m_RemoveByDensityFrame->setVisible(false); m_Controls->m_SmoothFibersFrame->setVisible(false); m_Controls->m_CompressFibersFrame->setVisible(false); m_Controls->m_ColorFibersFrame->setVisible(false); m_Controls->m_MirrorFibersFrame->setVisible(false); m_Controls->m_MaskExtractionFrame->setVisible(false); m_Controls->m_ColorMapBox->setVisible(false); bool pfSelected = !m_SelectedPF.empty(); bool fibSelected = !m_SelectedFB.empty(); bool multipleFibsSelected = (m_SelectedFB.size()>1); bool maskSelected = m_RoiImageNode.IsNotNull(); bool imageSelected = m_SelectedImage.IsNotNull(); // toggle visibility of elements according to selected method switch ( m_Controls->m_ExtractionMethodBox->currentIndex() ) { case 0: m_Controls->m_ExtactionFramePF->setVisible(true); break; case 1: m_Controls->m_MaskExtractionFrame->setVisible(true); break; } switch ( m_Controls->m_RemovalMethodBox->currentIndex() ) { case 0: m_Controls->m_RemoveDirectionFrame->setVisible(true); if ( fibSelected ) m_Controls->m_RemoveButton->setEnabled(true); break; case 1: m_Controls->m_RemoveLengthFrame->setVisible(true); if ( fibSelected ) m_Controls->m_RemoveButton->setEnabled(true); break; case 2: m_Controls->m_RemoveCurvatureFrame->setVisible(true); if ( fibSelected ) m_Controls->m_RemoveButton->setEnabled(true); break; case 3: break; case 4: break; case 5: m_Controls->m_RemoveByWeightFrame->setVisible(true); if ( fibSelected ) m_Controls->m_RemoveButton->setEnabled(true); break; + case 6: + m_Controls->m_RemoveByDensityFrame->setVisible(true); + if ( fibSelected ) + m_Controls->m_RemoveButton->setEnabled(true); + break; } switch ( m_Controls->m_ModificationMethodBox->currentIndex() ) { case 0: m_Controls->m_SmoothFibersFrame->setVisible(true); break; case 1: m_Controls->m_SmoothFibersFrame->setVisible(true); break; case 2: m_Controls->m_CompressFibersFrame->setVisible(true); break; case 3: m_Controls->m_ColorFibersFrame->setVisible(true); m_Controls->m_ColorMapBox->setVisible(true); break; case 4: m_Controls->m_MirrorFibersFrame->setVisible(true); if (m_SelectedSurfaces.size()>0) m_Controls->m_ModifyButton->setEnabled(true); break; case 5: m_Controls->m_BundleWeightFrame->setVisible(true); break; case 6: m_Controls->m_ColorFibersFrame->setVisible(true); break; case 7: m_Controls->m_ColorFibersFrame->setVisible(true); break; case 8: m_Controls->m_ColorFibersFrame->setVisible(true); break; } // are fiber bundles selected? if ( fibSelected ) { m_Controls->m_CopyBundle->setEnabled(true); m_Controls->m_ModifyButton->setEnabled(true); m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true); m_Controls->m_FibLabel->setText(QString(m_SelectedFB.at(0)->GetName().c_str())); // one bundle and one planar figure needed to extract fibers if (pfSelected && m_Controls->m_ExtractionMethodBox->currentIndex()==0) { m_Controls->m_InputData->setTitle("Input Data"); m_Controls->m_PfLabel->setText(QString(m_SelectedPF.at(0)->GetName().c_str())); m_Controls->m_ExtractFibersButton->setEnabled(true); } // more than two bundles needed to join/subtract if (multipleFibsSelected) { m_Controls->m_FibLabel->setText("multiple bundles selected"); m_Controls->m_JoinBundles->setEnabled(true); m_Controls->m_SubstractBundles->setEnabled(true); } if (maskSelected && m_Controls->m_ExtractionMethodBox->currentIndex()==1) { m_Controls->m_InputData->setTitle("Input Data"); m_Controls->m_PfLabel->setText(QString(m_RoiImageNode->GetName().c_str())); m_Controls->m_ExtractFibersButton->setEnabled(true); } if (maskSelected && (m_Controls->m_RemovalMethodBox->currentIndex()==3 || m_Controls->m_RemovalMethodBox->currentIndex()==4) ) { m_Controls->m_InputData->setTitle("Input Data"); m_Controls->m_PfLabel->setText(QString(m_RoiImageNode->GetName().c_str())); m_Controls->m_RemoveButton->setEnabled(true); } } // are planar figures selected? if (pfSelected) { if ( fibSelected || m_SelectedImage.IsNotNull()) m_Controls->m_GenerateRoiImage->setEnabled(true); if (m_SelectedPF.size() > 1) { m_Controls->PFCompoANDButton->setEnabled(true); m_Controls->PFCompoORButton->setEnabled(true); } else m_Controls->PFCompoNOTButton->setEnabled(true); } // is image selected if (imageSelected || maskSelected) { m_Controls->m_PlanarFigureButtonsFrame->setEnabled(true); } } void QmitkFiberProcessingView::NodeRemoved(const mitk::DataNode* node ) { for (auto fnode: m_SelectedFB) if (node == fnode) { m_SelectedFB.clear(); break; } berry::IWorkbenchPart::Pointer nullPart; QList nodes; OnSelectionChanged(nullPart, nodes); } void QmitkFiberProcessingView::NodeAdded(const mitk::DataNode* ) { if (!m_Controls->m_InteractiveBox->isChecked()) { berry::IWorkbenchPart::Pointer nullPart; QList nodes; OnSelectionChanged(nullPart, nodes); } } void QmitkFiberProcessingView::OnEndInteraction() { if (m_Controls->m_InteractiveBox->isChecked()) ExtractWithPlanarFigure(true); } void QmitkFiberProcessingView::AddObservers() { typedef itk::SimpleMemberCommand< QmitkFiberProcessingView > SimpleCommandType; for (auto node : m_SelectedPF) { mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); if (figure!=nullptr) { figure->RemoveAllObservers(); // add observer for event when interaction with figure starts SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New(); endInteractionCommand->SetCallbackFunction( this, &QmitkFiberProcessingView::OnEndInteraction); m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand ); } } } void QmitkFiberProcessingView::RemoveObservers() { for (auto node : m_SelectedPF) { mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); if (figure!=nullptr) figure->RemoveAllObservers(); } } void QmitkFiberProcessingView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& nodes) { RemoveObservers(); //reset existing Vectors containing FiberBundles and PlanarFigures from a previous selection std::vector lastSelectedFB = m_SelectedFB; m_SelectedFB.clear(); m_SelectedPF.clear(); m_SelectedSurfaces.clear(); m_SelectedImage = nullptr; m_RoiImageNode = nullptr; for (auto node: nodes) { if ( dynamic_cast(node->GetData()) ) m_SelectedFB.push_back(node); else if (dynamic_cast(node->GetData()) || dynamic_cast(node->GetData()) || dynamic_cast(node->GetData())) m_SelectedPF.push_back(node); else if (dynamic_cast(node->GetData())) { m_SelectedImage = dynamic_cast(node->GetData()); if (m_SelectedImage->GetDimension()==3) m_RoiImageNode = node; } else if (dynamic_cast(node->GetData())) m_SelectedSurfaces.push_back(dynamic_cast(node->GetData())); } // if we perform interactive fiber extraction, we want to avoid auto-selection of the extracted bundle if (m_SelectedFB.empty() && m_Controls->m_InteractiveBox->isChecked()) m_SelectedFB = lastSelectedFB; // if no fibers or surfaces are selected, select topmost if (m_SelectedFB.empty() && m_SelectedSurfaces.empty()) { int maxLayer = 0; itk::VectorContainer::ConstPointer nodes = this->GetDataStorage()->GetAll(); for (unsigned int i=0; iSize(); i++) if (dynamic_cast(nodes->at(i)->GetData())) { mitk::DataStorage::SetOfObjects::ConstPointer sources = GetDataStorage()->GetSources(nodes->at(i)); if (sources->Size()>0) continue; int layer = 0; nodes->at(i)->GetPropertyValue("layer", layer); if (layer>=maxLayer) { maxLayer = layer; m_SelectedFB.clear(); m_SelectedFB.push_back(nodes->at(i)); } } } // if no plar figure is selected, select topmost if (m_SelectedPF.empty()) { int maxLayer = 0; itk::VectorContainer::ConstPointer nodes = this->GetDataStorage()->GetAll(); for (unsigned int i=0; iSize(); i++) if (dynamic_cast(nodes->at(i)->GetData()) || dynamic_cast(nodes->at(i)->GetData()) || dynamic_cast(nodes->at(i)->GetData())) { mitk::DataStorage::SetOfObjects::ConstPointer sources = GetDataStorage()->GetSources(nodes->at(i)); if (sources->Size()>0) continue; int layer = 0; nodes->at(i)->GetPropertyValue("layer", layer); if (layer>=maxLayer) { maxLayer = layer; m_SelectedPF.clear(); m_SelectedPF.push_back(nodes->at(i)); } } } AddObservers(); UpdateGui(); } void QmitkFiberProcessingView::OnDrawPolygon() { mitk::PlanarPolygon::Pointer figure = mitk::PlanarPolygon::New(); figure->ClosedOn(); this->AddFigureToDataStorage(figure, QString("Polygon%1").arg(++m_PolygonCounter)); } void QmitkFiberProcessingView::OnDrawCircle() { mitk::PlanarCircle::Pointer figure = mitk::PlanarCircle::New(); this->AddFigureToDataStorage(figure, QString("Circle%1").arg(++m_CircleCounter)); } void QmitkFiberProcessingView::AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char *, mitk::BaseProperty* ) { // initialize figure's geometry with empty geometry mitk::PlaneGeometry::Pointer emptygeometry = mitk::PlaneGeometry::New(); figure->SetPlaneGeometry( emptygeometry ); //set desired data to DataNode where Planarfigure is stored mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetName(name.toStdString()); newNode->SetData(figure); newNode->SetBoolProperty("planarfigure.3drendering", true); newNode->SetBoolProperty("planarfigure.3drendering.fill", true); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(newNode->GetDataInteractor().GetPointer()); if(figureInteractor.IsNull()) { figureInteractor = mitk::PlanarFigureInteractor::New(); us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); figureInteractor->SetDataNode(newNode); } // figure drawn on the topmost layer / image GetDataStorage()->Add(newNode ); RemoveObservers(); for(unsigned int i = 0; i < m_SelectedPF.size(); i++) m_SelectedPF[i]->SetSelected(false); newNode->SetSelected(true); m_SelectedPF.clear(); m_SelectedPF.push_back(newNode); AddObservers(); UpdateGui(); } void QmitkFiberProcessingView::ExtractWithPlanarFigure(bool interactive) { if ( m_SelectedFB.empty() || m_SelectedPF.empty() ){ QMessageBox::information( nullptr, "Warning", "No fibe bundle selected!"); return; } try { std::vector fiberBundles = m_SelectedFB; mitk::DataNode::Pointer planarFigure = m_SelectedPF.at(0); for (unsigned int i=0; i(fiberBundles.at(i)->GetData()); mitk::FiberBundle::Pointer extFB = fib->ExtractFiberSubset(planarFigure, GetDataStorage()); if (interactive && m_Controls->m_InteractiveBox->isChecked()) { if (m_InteractiveNode.IsNull()) { m_InteractiveNode = mitk::DataNode::New(); QString name("Interactive"); m_InteractiveNode->SetName(name.toStdString()); GetDataStorage()->Add(m_InteractiveNode); } float op = 5.0/sqrt(fib->GetNumFibers()); float currentOp = 0; fiberBundles.at(i)->GetFloatProperty("opacity", currentOp); if (currentOp!=op) { fib->SetFiberColors(255, 255, 255); fiberBundles.at(i)->SetFloatProperty("opacity", op); fiberBundles.at(i)->SetBoolProperty("Fiber2DfadeEFX", false); } m_InteractiveNode->SetData(extFB); } else { if (extFB->GetNumFibers()<=0) { QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers."); continue; } mitk::DataNode::Pointer node; node = mitk::DataNode::New(); node->SetData(extFB); QString name(fiberBundles.at(i)->GetName().c_str()); name += "*"; node->SetName(name.toStdString()); fiberBundles.at(i)->SetVisibility(false); GetDataStorage()->Add(node); } } } catch(const std::out_of_range& ) { QMessageBox::warning( nullptr, "Fiber extraction failed", "Did you only create the planar figure, using the circle or polygon button, but forgot to actually place it in the image afterwards? \nAfter creating a planar figure, simply left-click at the desired position in the image or on the tractogram to place it."); } } void QmitkFiberProcessingView::GenerateAndComposite() { mitk::PlanarFigureComposite::Pointer PFCAnd = mitk::PlanarFigureComposite::New(); PFCAnd->setOperationType(mitk::PlanarFigureComposite::AND); mitk::DataNode::Pointer newPFCNode; newPFCNode = mitk::DataNode::New(); newPFCNode->SetName("AND"); newPFCNode->SetData(PFCAnd); AddCompositeToDatastorage(newPFCNode, m_SelectedPF); RemoveObservers(); m_SelectedPF.clear(); m_SelectedPF.push_back(newPFCNode); AddObservers(); UpdateGui(); } void QmitkFiberProcessingView::GenerateOrComposite() { mitk::PlanarFigureComposite::Pointer PFCOr = mitk::PlanarFigureComposite::New(); PFCOr->setOperationType(mitk::PlanarFigureComposite::OR); mitk::DataNode::Pointer newPFCNode; newPFCNode = mitk::DataNode::New(); newPFCNode->SetName("OR"); newPFCNode->SetData(PFCOr); RemoveObservers(); AddCompositeToDatastorage(newPFCNode, m_SelectedPF); m_SelectedPF.clear(); m_SelectedPF.push_back(newPFCNode); UpdateGui(); } void QmitkFiberProcessingView::GenerateNotComposite() { mitk::PlanarFigureComposite::Pointer PFCNot = mitk::PlanarFigureComposite::New(); PFCNot->setOperationType(mitk::PlanarFigureComposite::NOT); mitk::DataNode::Pointer newPFCNode; newPFCNode = mitk::DataNode::New(); newPFCNode->SetName("NOT"); newPFCNode->SetData(PFCNot); RemoveObservers(); AddCompositeToDatastorage(newPFCNode, m_SelectedPF); m_SelectedPF.clear(); m_SelectedPF.push_back(newPFCNode); AddObservers(); UpdateGui(); } void QmitkFiberProcessingView::AddCompositeToDatastorage(mitk::DataNode::Pointer pfc, std::vector children, mitk::DataNode::Pointer parentNode ) { pfc->SetSelected(true); if (parentNode.IsNotNull()) GetDataStorage()->Add(pfc, parentNode); else GetDataStorage()->Add(pfc); for (auto child : children) { if (dynamic_cast(child->GetData())) { mitk::DataNode::Pointer newChild; newChild = mitk::DataNode::New(); newChild->SetData(dynamic_cast(child->GetData())); newChild->SetName( child->GetName() ); newChild->SetBoolProperty("planarfigure.3drendering", true); newChild->SetBoolProperty("planarfigure.3drendering.fill", true); GetDataStorage()->Add(newChild, pfc); GetDataStorage()->Remove(child); } else if (dynamic_cast(child->GetData())) { mitk::DataNode::Pointer newChild; newChild = mitk::DataNode::New(); newChild->SetData(dynamic_cast(child->GetData())); newChild->SetName( child->GetName() ); std::vector< mitk::DataNode::Pointer > grandChildVector; mitk::DataStorage::SetOfObjects::ConstPointer grandchildren = GetDataStorage()->GetDerivations(child); for( mitk::DataStorage::SetOfObjects::const_iterator it = grandchildren->begin(); it != grandchildren->end(); ++it ) grandChildVector.push_back(*it); AddCompositeToDatastorage(newChild, grandChildVector, pfc); GetDataStorage()->Remove(child); } } UpdateGui(); } void QmitkFiberProcessingView::CopyBundles() { if ( m_SelectedFB.empty() ){ QMessageBox::information( nullptr, "Warning", "Select at least one fiber bundle!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least one fiber bundle!"; return; } for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); mitk::FiberBundle::Pointer newFib = fib->GetDeepCopy(); node->SetVisibility(false); QString name(""); name += QString(m_SelectedFB.at(0)->GetName().c_str()); name += "_copy"; mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newFib); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); } UpdateGui(); } void QmitkFiberProcessingView::JoinBundles() { if ( m_SelectedFB.size()<2 ){ QMessageBox::information( nullptr, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } m_SelectedFB.at(0)->SetVisibility(false); mitk::FiberBundle::Pointer newBundle = dynamic_cast(m_SelectedFB.at(0)->GetData()); std::vector< mitk::FiberBundle::Pointer > tractograms; for (unsigned int i=1; iSetVisibility(false); tractograms.push_back(dynamic_cast(m_SelectedFB.at(i)->GetData())); } newBundle = newBundle->AddBundles(tractograms); mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName("Joined_Tractograms"); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); UpdateGui(); } void QmitkFiberProcessingView::SubstractBundles() { if ( m_SelectedFB.size()<2 ){ QMessageBox::information( nullptr, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } mitk::FiberBundle::Pointer newBundle = dynamic_cast(m_SelectedFB.at(0)->GetData()); m_SelectedFB.at(0)->SetVisibility(false); QString name(""); name += QString(m_SelectedFB.at(0)->GetName().c_str()); for (unsigned int i=1; iSubtractBundle(dynamic_cast(m_SelectedFB.at(i)->GetData())); if (newBundle.IsNull()) break; name += "-"+QString(m_SelectedFB.at(i)->GetName().c_str()); m_SelectedFB.at(i)->SetVisibility(false); } if (newBundle.IsNull()) { QMessageBox::information(nullptr, "No output generated:", "The resulting fiber bundle contains no fibers. Did you select the fiber bundles in the correct order? X-Y is not equal to Y-X!"); return; } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); UpdateGui(); } void QmitkFiberProcessingView::ResampleSelectedBundlesSpline() { double factor = this->m_Controls->m_SmoothFibersBox->value(); for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); fib->ResampleSpline(factor); } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::ResampleSelectedBundlesLinear() { double factor = this->m_Controls->m_SmoothFibersBox->value(); for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); fib->ResampleLinear(factor); } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::CompressSelectedBundles() { double factor = this->m_Controls->m_ErrorThresholdBox->value(); for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); fib->Compress(factor); fib->ColorFibersByOrientation(); } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::DoImageColorCoding() { if (m_Controls->m_ColorMapBox->GetSelectedNode().IsNull()) { QMessageBox::information(nullptr, "Bundle coloring aborted:", "No image providing the scalar values for coloring the selected bundle available."); return; } for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); fib->ColorFibersByScalarMap(dynamic_cast(m_Controls->m_ColorMapBox->GetSelectedNode()->GetData()), m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_NormalizeColorValues->isChecked()); } if (auto renderWindowPart = this->GetRenderWindowPart()) { renderWindowPart->RequestUpdate(); } } void QmitkFiberProcessingView::DoCurvatureColorCoding() { for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); fib->ColorFibersByCurvature(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_NormalizeColorValues->isChecked()); } if (auto renderWindowPart = this->GetRenderWindowPart()) { renderWindowPart->RequestUpdate(); } } void QmitkFiberProcessingView::DoLengthColorCoding() { for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); fib->ColorFibersByLength(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_NormalizeColorValues->isChecked()); } if (auto renderWindowPart = this->GetRenderWindowPart()) { renderWindowPart->RequestUpdate(); } } void QmitkFiberProcessingView::DoWeightColorCoding() { for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); fib->ColorFibersByFiberWeights(m_Controls->m_FiberOpacityBox->isChecked(), m_Controls->m_NormalizeColorValues->isChecked()); } if (auto renderWindowPart = this->GetRenderWindowPart()) { renderWindowPart->RequestUpdate(); } } void QmitkFiberProcessingView::MirrorFibers() { unsigned int axis = this->m_Controls->m_MirrorFibersBox->currentIndex(); for (auto node : m_SelectedFB) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); if (m_SelectedImage.IsNotNull()) fib->SetReferenceGeometry(m_SelectedImage->GetGeometry()); fib->MirrorFibers(axis); } for (auto surf : m_SelectedSurfaces) { vtkSmartPointer poly = surf->GetVtkPolyData(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); for (int i=0; iGetNumberOfPoints(); i++) { double* point = poly->GetPoint(i); point[axis] *= -1; vtkNewPoints->InsertNextPoint(point); } poly->SetPoints(vtkNewPoints); surf->CalculateBoundingBox(); } if (auto renderWindowPart = this->GetRenderWindowPart()) { renderWindowPart->RequestUpdate(); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.h index 07e9b8660b..50e7649deb 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingView.h @@ -1,202 +1,203 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QmitkFiberProcessingView_h #define QmitkFiberProcessingView_h #include #include "ui_QmitkFiberProcessingViewControls.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /*! \brief View to process fiber bundles. Supplies methods to extract fibers from the bundle, fiber resampling, mirroring, join and subtract bundles and much more. */ class QmitkFiberProcessingView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: typedef itk::Image< unsigned char, 3 > ItkUCharImageType; typedef itk::Image< float, 3 > ItkFloatImageType; static const std::string VIEW_ID; QmitkFiberProcessingView(); virtual ~QmitkFiberProcessingView(); virtual void CreateQtPartControl(QWidget *parent) override; /// /// Sets the focus to an internal widget. /// virtual void SetFocus() override; protected slots: void OnDrawCircle(); ///< add circle interactors etc. void OnDrawPolygon(); ///< add circle interactors etc. void GenerateAndComposite(); void GenerateOrComposite(); void GenerateNotComposite(); void CopyBundles(); ///< add copies of selected bundles to data storage void JoinBundles(); ///< merge selected fiber bundles void SubstractBundles(); ///< subtract bundle A from bundle B. Not commutative! Defined by order of selection. void GenerateRoiImage(); ///< generate binary image of selected planar figures. void Remove(); void Extract(); void Modify(); void UpdateGui(); ///< update button activity etc. dpending on current datamanager selection void OnMaskExtractionChanged(); virtual void AddFigureToDataStorage(mitk::PlanarFigure* figure, const QString& name, const char *propertyKey = nullptr, mitk::BaseProperty *property = nullptr ); protected: void MirrorFibers(); ///< mirror bundle on the specified plane void ResampleSelectedBundlesSpline(); ///< void ResampleSelectedBundlesLinear(); ///< void DoImageColorCoding(); ///< color fibers by selected scalar image void DoWeightColorCoding(); ///< color fibers by their respective weights void DoLengthColorCoding(); ///< color fibers by length void DoCurvatureColorCoding(); ///< color fibers by curvature void CompressSelectedBundles(); ///< remove points below certain error threshold void WeightFibers(); void ApplyWeightThreshold(); + void ApplyDensityThreshold(); void RemoveWithMask(bool removeInside); void RemoveDir(); void ApplyCurvatureThreshold(); ///< remove/split fibers with a too high curvature threshold void PruneBundle(); ///< remove too short/too long fibers - void ExtractWithMask(bool onlyEnds, bool invert); + void ExtractWithMask(bool onlyEnds, bool invert, bool labelmap); void ExtractWithPlanarFigure(bool interactive=false); void OnEndInteraction(); /// \brief called by QmitkAbstractView when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; Ui::QmitkFiberProcessingViewControls* m_Controls; /** Connection from VTK to ITK */ template void ConnectPipelines(VTK_Exporter* exporter, ITK_Importer importer) { importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback()); importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback()); importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback()); importer->SetSpacingCallback(exporter->GetSpacingCallback()); importer->SetOriginCallback(exporter->GetOriginCallback()); importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback()); importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback()); importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback()); importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback()); importer->SetDataExtentCallback(exporter->GetDataExtentCallback()); importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()); importer->SetCallbackUserData(exporter->GetCallbackUserData()); } template void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer) { importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback()); importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback()); importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback()); importer->SetSpacingCallback(exporter->GetSpacingCallback()); importer->SetOriginCallback(exporter->GetOriginCallback()); importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback()); importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback()); importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback()); importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback()); importer->SetDataExtentCallback(exporter->GetDataExtentCallback()); importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()); importer->SetCallbackUserData(exporter->GetCallbackUserData()); } template < typename TPixel, unsigned int VImageDimension > void InternalCalculateMaskFromPlanarFigure( itk::Image< TPixel, VImageDimension > *image, unsigned int axis, std::string nodeName ); template < typename TPixel, unsigned int VImageDimension > void InternalReorientImagePlane( const itk::Image< TPixel, VImageDimension > *image, mitk::BaseGeometry* planegeo3D, int additionalIndex ); int m_CircleCounter; ///< used for data node naming int m_PolygonCounter; ///< used for data node naming std::vector m_SelectedFB; ///< selected fiber bundle nodes std::vector m_SelectedPF; ///< selected planar figure nodes std::vector m_SelectedSurfaces; mitk::Image::Pointer m_SelectedImage; mitk::Image::Pointer m_InternalImage; mitk::PlanarFigure::Pointer m_PlanarFigure; ItkUCharImageType::Pointer m_InternalImageMask3D; ItkUCharImageType::Pointer m_PlanarFigureImage; float m_UpsamplingFactor; ///< upsampling factor for all image generations mitk::DataNode::Pointer m_RoiImageNode; unsigned int m_StartInteractionObserverTag; unsigned int m_EndInteractionObserverTag; mitk::DataNode::Pointer m_InteractiveNode; void AddCompositeToDatastorage(mitk::DataNode::Pointer pfc, std::vector children, mitk::DataNode::Pointer parentNode=nullptr); void debugPFComposition(mitk::PlanarFigureComposite::Pointer , int ); void WritePfToImage(mitk::DataNode::Pointer node, mitk::Image* image); mitk::DataNode::Pointer GenerateTractDensityImage(mitk::FiberBundle::Pointer fib, bool binary, bool absolute); mitk::DataNode::Pointer GenerateColorHeatmap(mitk::FiberBundle::Pointer fib); mitk::DataNode::Pointer GenerateFiberEndingsImage(mitk::FiberBundle::Pointer fib); mitk::DataNode::Pointer GenerateFiberEndingsPointSet(mitk::FiberBundle::Pointer fib); void NodeAdded( const mitk::DataNode* node ) override; void NodeRemoved(const mitk::DataNode* node) override; void RemoveObservers(); void AddObservers(); }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui index 8a38651dfc..e56f21b27a 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberProcessingViewControls.ui @@ -1,1603 +1,1732 @@ QmitkFiberProcessingViewControls 0 0 385 - 684 + 711 Form QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; } 9 9 9 9 75 true 0 5 0 - 0 + -18 353 - 441 + 503 Fiber Extraction Extract a fiber subset from the selected fiber bundle using manually placed planar figures as waypoints or binary regions of interest. - + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + 0 + + + 0 + + + + + Min. overlap: + + + + + + + Threshold: + + + + + + + Min. num. fibers: + + + + + + + Threshold on ROI image for positions to be considered as positive. + + + 3 + + + 9999.000000000000000 + + + 0.100000000000000 + + + 0.500000000000000 + + + + + + + + 0 + 0 + + + + + Ending in ROI + + + + + Not ending in ROI + + + + + Passing ROI + + + + + Not passing ROI + + + + + Labelmap + + + + + + + + Both ends + + + true + + + + + + + Interpolate ROI + + + true + + + + + + + 1 + + + 999999999 + + + + + + + Extract fibers: + + + + + + + Minimum overlap of streamlines and ROI in terms of streamline length. Zero means that one streamline point inside the ROI is enough to be considered as "overlapping". + + + 3 + + + 1.000000000000000 + + + 0.100000000000000 + + + + + + + Labels: + + + + + + + Label values seperated by whitespace. + + + ALL + + + + + + + false 0 0 200 16777215 11 Extract fibers passing through selected ROI or composite ROI. Select ROI and fiber bundle to execute. Extract - - - - Qt::Vertical - - - - 20 - 40 - + + + + + 0 + 0 + - + + + Extract using planar figures + + + + + Extract using ROI image + + + QFrame::NoFrame QFrame::Raised 0 0 0 0 6 Interactive Extraction 0 0 200 0 16777215 60 QFrame::NoFrame QFrame::Raised 0 0 0 0 30 30 Draw circular ROI. Select reference fiber bundle to execute. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true Qt::Horizontal 40 20 30 30 Draw polygonal ROI. Select reference fiber bundle to execute. :/QmitkDiffusionImaging/polygon.png:/QmitkDiffusionImaging/polygon.png 32 32 true true 0 0 200 0 16777215 60 QFrame::NoFrame QFrame::Raised 0 0 0 0 false 60 16777215 Create NOT composition from selected ROI. NOT false 60 16777215 Create OR composition with selected ROIs. OR Qt::Horizontal 40 20 false 60 16777215 Create AND composition with selected ROIs. AND false 0 0 16777215 16777215 11 Generate a binary image containing all selected ROIs. Select at least one ROI (planar figure) and a reference fiber bundle or image. Generate ROI Image - - - - - 0 - 0 - - - - - Extract using planar figures - - - - - Extract using ROI image - - - - - - + + + + + + 0 + -34 + 353 + 456 + + + + Fiber Removal + + + Remove fibers that satisfy certain criteria from the selected bundle. + + + + QFrame::NoFrame QFrame::Raised - + 0 0 0 0 - - + + 0 + + + - Min. overlap: + X: - - + + - Extract fibers: + Y: - - + + + + + + + + - Both ends + Z: - - true + + + + + + + + + Angle: - - + + - Minimum overlap of streamlines and ROI in terms of streamline length. Zero means that one streamline point inside the ROI is enough to be considered as "overlapping". + Angular deviation threshold in degree - 3 + 1 - 1.000000000000000 + 90.000000000000000 - 0.100000000000000 - - - - - - - - 0 - 0 - - - - - Ending in ROI - - - - - Not ending in ROI - - - - - Passing ROI - - - - - Not passing ROI - - - - - - - - Interpolate ROI + 1.000000000000000 - - true + + 25.000000000000000 - - + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + - Threshold: + Weight threshold: - - + + - Threshold on ROI image for positions to be considered as positive. + Only fibers with weight larger than this threshold are kept. - 3 + 5 - 9999.000000000000000 + 99999.000000000000000 0.100000000000000 - - 0.500000000000000 - - - - - - - 0 - 0 - 367 - 408 - - - - Fiber Removal - - - Remove fibers that satisfy certain criteria from the selected bundle. - - + + + + false + + + + 0 + 0 + + + + + 200 + 16777215 + + + + + 11 + + + + + + + Remove + + + + + + + + 0 + 0 + + + + + Remove fibers in direction + + + + + Remove fibers by length + + + + + Remove fibers by curvature + + + + + Remove fiber parts outside mask + + + + + Remove fiber parts inside mask + + + + + Remove fibers by weight + + + + + Remove fibers by tract density + + + + QFrame::NoFrame QFrame::Raised 0 0 0 0 If unchecked, the fiber exceeding the threshold will be split in two instead of removed. Remove Fiber false QFrame::NoFrame QFrame::Raised 0 0 0 0 0 Max. Angular Deviation: Qt::Horizontal 40 20 Maximum angular deviation in degree 180.000000000000000 0.100000000000000 30.000000000000000 Distance: Distance in mm 1 999.000000000000000 1.000000000000000 10.000000000000000 - - - - QFrame::NoFrame + + + + Qt::Vertical - - QFrame::Raised + + + 20 + 40 + - - - 0 - - - 0 - - - 0 - - - 0 - - - 0 - - - - - X: - - - - - - - Y: - - - - - - - - - - - - - Z: - - - - - - - - - - Angle: - - - - - - - Angular deviation threshold in degree - - - 1 - - - 90.000000000000000 - - - 1.000000000000000 - - - 25.000000000000000 - - - - - + QFrame::NoFrame QFrame::Raised 0 0 0 0 Qt::Horizontal 40 20 Minimum fiber length in mm 0 999999999 20 Max. Length: Min. Length: Maximum fiber length in mm 0 999999999 300 - - - false - - - - 0 - 0 - - - - - 200 - 16777215 - - - - - 11 - - - - - - - Remove - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - 0 - 0 - - - - - Remove fibers in direction - - - - - Remove fibers by length - - - - - Remove fibers by curvature - - - - - Remove fiber parts outside mask - - - - - Remove fiber parts inside mask - - - - - Remove fibers by weight - - - - - - + QFrame::NoFrame QFrame::Raised - + 0 0 0 0 - + 0 + + 6 + + + + + + + + 5 + + + 0.000000000000000 + + + 10.000000000000000 + + + 0.100000000000000 + + + 0.010000000000000 + + + - + - Weight threshold: + Density threshold: - - + + + + Min. overlap: + + + + + - Only fibers with weight larger than this threshold are kept. + Tracts have to spend at least this fraction of their length inside the specified density region. - 5 + 3 - 99999.000000000000000 + 1.000000000000000 0.100000000000000 + + 0.500000000000000 + 0 0 367 408 Bundle Modification Modify the selected bundle with operations such as fiber resampling, FA coloring, etc. QFrame::NoFrame QFrame::Raised 0 0 0 0 0 6 Error threshold in mm: 999999999.000000000000000 0.100000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 0 6 Sagittal Coronal Axial Select direction: QFrame::NoFrame QFrame::Raised 0 0 0 0 0 6 If checked, the image values are not only used to color the fibers but are also used as opaxity values. Values as opacity false Scalar map: The values used to color the fibers are min-max normalized. If not checked, the values should be between 0 and 1. Normalize values true 0 0 Resample fibers (spline) Resample fibers (linear) Compress fibers Color fibers by scalar map (e.g. FA) Mirror fibers Weight bundle Color fibers by curvature Color fibers by fiber weights Color fibers by length QFrame::NoFrame QFrame::Raised 0 0 0 0 0 6 0.010000000000000 999999999.000000000000000 0.100000000000000 1.000000000000000 Point distance in mm: Qt::Vertical 20 40 false 0 0 200 16777215 11 Execute QFrame::NoFrame QFrame::Raised 0 0 0 0 0 Weight: 7 999999999.000000000000000 0.100000000000000 1.000000000000000 0 0 367 - 168 + 182 Bundle Operations Join, subtract or copy bundles. false 0 0 200 16777215 11 Returns all fibers contained in bundle X that are not contained in bundle Y (not commutative!). Select at least two fiber bundles to execute. Substract Qt::Vertical 20 40 false 0 0 200 16777215 11 Merge selected fiber bundles. Select at least two fiber bundles to execute. Join false 0 0 200 16777215 11 Merge selected fiber bundles. Select at least two fiber bundles to execute. Copy Please Select Input Data 6 6 6 6 <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true <html><head/><body><p><span style=" color:#969696;">needed for extraction</span></p></body></html> true Input DTI Fiber Bundle: Binary seed ROI. If not specified, the whole image area is seeded. ROI: Qt::Vertical 20 40 QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h