diff --git a/Modules/DiffusionCmdApps/FiberProcessing/FiberClustering.cpp b/Modules/DiffusionCmdApps/FiberProcessing/FiberClustering.cpp index 743207b..a454d3f 100644 --- a/Modules/DiffusionCmdApps/FiberProcessing/FiberClustering.cpp +++ b/Modules/DiffusionCmdApps/FiberProcessing/FiberClustering.cpp @@ -1,273 +1,273 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 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[]) { mitkDiffusionCommandLineParser parser; parser.setTitle("Fiber Clustering"); parser.setCategory("Fiber Processing"); parser.setContributor("MIC"); parser.setArgumentPrefix("--", "-"); parser.addArgument("", "i", mitkDiffusionCommandLineParser::String, "Input:", "input fiber bundle (.fib; .trk; .tck)", us::Any(), false, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("", "o", mitkDiffusionCommandLineParser::String, "Output:", "output root", us::Any(), false, false, false, mitkDiffusionCommandLineParser::Output); parser.addArgument("cluster_size", "", mitkDiffusionCommandLineParser::Int, "Cluster size:", "", 10); parser.addArgument("fiber_points", "", mitkDiffusionCommandLineParser::Int, "Fiber points:", "", 12); parser.addArgument("min_fibers", "", mitkDiffusionCommandLineParser::Int, "Min. fibers per cluster:", "", 1); parser.addArgument("max_clusters", "", mitkDiffusionCommandLineParser::Int, "Max. clusters:", ""); parser.addArgument("merge_clusters", "", mitkDiffusionCommandLineParser::Float, "Merge clusters:", "Set to 0 to avoid merging and to -1 to use the original cluster size", -1.0); parser.addArgument("output_centroids", "", mitkDiffusionCommandLineParser::Bool, "Output centroids:", ""); parser.addArgument("only_centroids", "", mitkDiffusionCommandLineParser::Bool, "Output only centroids:", ""); parser.addArgument("merge_centroids", "", mitkDiffusionCommandLineParser::Bool, "Merge centroids:", ""); parser.addArgument("metrics", "", mitkDiffusionCommandLineParser::StringList, "Metrics:", "EU_MEAN; EU_STD; EU_MAX; ANAT; MAP; LENGTH", std::string("EU_MEAN")); parser.addArgument("metric_weights", "", mitkDiffusionCommandLineParser::StringList, "Metric weights:", "add one float weight for each used metric"); parser.addArgument("input_centroids", "", mitkDiffusionCommandLineParser::String, "Input centroids:", "", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("scalar_map", "", mitkDiffusionCommandLineParser::String, "Scalar map:", "", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("parcellation", "", mitkDiffusionCommandLineParser::String, "Parcellation:", "", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("file_ending", "", mitkDiffusionCommandLineParser::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(); + std::shared_ptr< mitk::TractClusteringFilter > clusterer = std::make_shared(); 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 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 (const itk::ExceptionObject& e) { std::cout << e.what(); 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/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt b/Modules/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt index 52758e6..f80e692 100644 --- a/Modules/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt +++ b/Modules/DiffusionCmdApps/TractographyEvaluation/CMakeLists.txt @@ -1,46 +1,46 @@ option(BUILD_DiffusionTractographyEvaluationCmdApps "Build commandline tools for diffusion fiber tractography evaluation" OFF) if(BUILD_DiffusionTractographyEvaluationCmdApps OR MITK_BUILD_ALL_APPS) # needed include directories include_directories( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ) # list of diffusion cmdapps # if an app requires additional dependencies # they are added after a "^^" and separated by "_" set( diffusionTractographyEvaluationcmdapps PeaksAngularError^^ MergeOverlappingTracts^^ GetOverlappingTracts^^ ExtractSimilarTracts^^ AnchorConstrainedPlausibility^^ CalculateOverlap^^ CheckEpsAndOverlap^^ ReferenceSimilarity^^ TractDistance^^ ) foreach(diffusionTractographyEvaluationcmdapp ${diffusionTractographyEvaluationcmdapps}) # extract cmd app name and dependencies string(REPLACE "^^" "\\;" cmdapp_info ${diffusionTractographyEvaluationcmdapp}) set(cmdapp_info_list ${cmdapp_info}) list(GET cmdapp_info_list 0 appname) list(GET cmdapp_info_list 1 raw_dependencies) string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") set(dependencies_list ${dependencies}) mitkFunctionCreateCommandLineApp( NAME ${appname} - DEPENDS MitkDiffusionCmdApps MitkMriSimulation ${dependencies_list} + DEPENDS MitkDiffusionCmdApps MitkFiberTracking MitkMriSimulation ${dependencies_list} PACKAGE_DEPENDS ) endforeach() if(EXECUTABLE_IS_ENABLED) MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) endif() endif() diff --git a/Modules/DiffusionCmdApps/TractographyEvaluation/ExtractSimilarTracts.cpp b/Modules/DiffusionCmdApps/TractographyEvaluation/ExtractSimilarTracts.cpp index 58a8453..58cac2c 100644 --- a/Modules/DiffusionCmdApps/TractographyEvaluation/ExtractSimilarTracts.cpp +++ b/Modules/DiffusionCmdApps/TractographyEvaluation/ExtractSimilarTracts.cpp @@ -1,199 +1,200 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 itk::Image ItkFloatImgType; /*! \brief Spatially cluster fibers */ int main(int argc, char* argv[]) { mitkDiffusionCommandLineParser parser; parser.setTitle("Extract Similar Tracts"); parser.setCategory("Fiber Tracking Evaluation"); parser.setContributor("MIC"); parser.setArgumentPrefix("--", "-"); parser.addArgument("", "i", mitkDiffusionCommandLineParser::String, "Input:", "input fiber bundle (.fib, .trk, .tck)", us::Any(), false, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("ref_tracts", "", mitkDiffusionCommandLineParser::StringList, "Ref. Tracts:", "reference tracts (.fib, .trk, .tck)", us::Any(), false, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("ref_masks", "", mitkDiffusionCommandLineParser::StringList, "Ref. Masks:", "reference bundle masks", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("", "o", mitkDiffusionCommandLineParser::String, "Output:", "output root", us::Any(), false, false, false, mitkDiffusionCommandLineParser::Output); parser.addArgument("distance", "", mitkDiffusionCommandLineParser::Int, "Distance:", "", 10); parser.addArgument("metric", "", mitkDiffusionCommandLineParser::String, "Metric:", "EU_MEAN (default), EU_STD, EU_MAX"); parser.addArgument("subsample", "", mitkDiffusionCommandLineParser::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"]); mitkDiffusionCommandLineParser::StringContainerType ref_bundle_files = us::any_cast(parsedArgs["ref_tracts"]); mitkDiffusionCommandLineParser::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 = mitk::IOUtil::Load(in_fib); std::srand(0); if (subsample<1.0f) fib = fib->SubsampleFibers(subsample, true); mitk::FiberBundle::Pointer resampled_fib = fib->GetDeepCopy(); resampled_fib->ResampleToNumPoints(12); auto ref_fibs = mitk::DiffusionDataIOHelper::load_fibs(ref_bundle_files); auto ref_masks = mitk::DiffusionDataIOHelper::load_itk_images(ref_mask_files); std::vector< float > distances; distances.push_back(distance); 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(); + std::shared_ptr< mitk::TractClusteringFilter > segmenter = std::make_shared(); // calculate centroids from reference bundle { - itk::TractClusteringFilter::Pointer clusterer = itk::TractClusteringFilter::New(); + std::shared_ptr< mitk::TractClusteringFilter > clusterer = std::make_shared(); 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 if (cSetFilterMask(ref_masks.at(c)); segmenter->SetOverlapThreshold(0.8f); } 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< unsigned int > > 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); 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 << "Extracted streamlines: " << extracted->GetNumFibers(); mitk::IOUtil::Save(extracted, out_root + "extracted_streamlines.trk"); MITK_INFO << "Residual streamlines: " << fib->GetNumFibers(); mitk::IOUtil::Save(fib, out_root + "residual_streamlines.trk"); } catch (const itk::ExceptionObject& e) { std::cout << e.what(); 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/DiffusionCore/IODataStructures/mitkFiberBundle.cpp b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp index 96b7483..74e41d0 100644 --- a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp +++ b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp @@ -1,2792 +1,2840 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 const char* mitk::FiberBundle::FIBER_ID_ARRAY = "Fiber_IDs"; mitk::FiberBundle::FiberBundle( vtkPolyData* fiberPolyData ) : m_NumFibers(0) { m_TrackVisHeader.hdr_size = 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); newFib->SetTrackVisHeader(this->GetTrackVisHeader()); 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>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(); auto num_weights = this->GetNumFibers(); for (auto fib : fibs) num_weights += fib->GetNumFibers(); weights->SetNumberOfValues(num_weights); unsigned int counter = 0; for (unsigned int i=0; iGetNumberOfCells(); ++i) { vtkCell* cell = m_FiberPolyData->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned 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 (unsigned int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned 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 (unsigned int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned 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 (unsigned int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (unsigned 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 (unsigned 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); auto 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)); newFib->SetTrackVisHeader(this->GetTrackVisHeader()); return newFib; } // Only retain a subsample of the fibers mitk::FiberBundle::Pointer mitk::FiberBundle::SubsampleFibers(float factor, bool random_seed) { vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); unsigned int new_num_fibs = static_cast(std::round(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< unsigned int > ids; for (unsigned int i=0; iGetNumFibers(); i++) ids.push_back(i); if (random_seed) std::srand(static_cast(std::time(nullptr))); else std::srand(0); std::random_shuffle(ids.begin(), ids.end()); unsigned int counter = 0; for (unsigned int i=0; iGetCell(ids.at(i)); auto 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); newFib->SetTrackVisHeader(this->GetTrackVisHeader()); 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(unsigned int i=0; iGetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (points==nullptr || numPoints<=0) continue; itk::Point start = mitk::imv::GetItkPoint(points->GetPoint(0)); itk::Point end = mitk::imv::GetItkPoint(points->GetPoint(numPoints-1)); points1.push_back( {start, end} ); } std::vector< std::vector< itk::Point > > points2; for(unsigned int i=0; iGetNumFibers(); i++ ) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (points==nullptr || numPoints<=0) continue; itk::Point start =mitk::imv::GetItkPoint(points->GetPoint(0)); itk::Point end =mitk::imv::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(points1.size()); i++) { bool match = false; for (unsigned int j=0; j(i)); auto v2 = points2.at(j); float dist=0; for (unsigned int c=0; cGetCell(i); auto 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); } /* * 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 = static_cast(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, bool weight_fibers) { if (m_MaxFiberLength<=0) return; auto numOfPoints = this->GetNumberOfPoints(); //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; m_FiberColors = vtkSmartPointer::New(); m_FiberColors->Allocate(numOfPoints * 4); m_FiberColors->SetNumberOfComponents(4); m_FiberColors->SetName("FIBER_COLORS"); auto 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 (unsigned int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); float l = m_FiberLengths.at(i)/m_MaxFiberLength; if (!normalize) { l = m_FiberLengths.at(i)/255.0f; if (l > 1.0f) l = 1.0; } for (int j=0; jGetColor(1.0 - static_cast(l), color); rgba[0] = static_cast(255.0 * color[0]); rgba[1] = static_cast(255.0 * color[1]); rgba[2] = static_cast(255.0 * color[2]); if (opacity) rgba[3] = static_cast(255.0f * l); else rgba[3] = static_cast(255.0); m_FiberColors->InsertTypedTuple(cell->GetPointId(j), rgba); count++; } if (weight_fibers) this->SetFiberWeight(i, m_FiberLengths.at(i)); } m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } +void mitk::FiberBundle::ColorSinglePoint(int f_idx, int p_idx, double rgb[3]) +{ +// vtkPoints* extrPoints = m_FiberPolyData->GetPoints(); +// vtkIdType 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}; +// m_FiberColors = vtkSmartPointer::New(); +// m_FiberColors->Allocate(numOfPoints * 4); +// m_FiberColors->SetNumberOfComponents(4); +// m_FiberColors->SetName("FIBER_COLORS"); + +// auto 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(num_points, idList); +// fiberList->GetCell(f_idx, num_points, idList); + + vtkCell* cell = m_FiberPolyData->GetCell(f_idx); + + +// /* single fiber checkpoints: is number of points valid */ +// if (p_idx < num_points) +// { + rgba[0] = static_cast(255.0 * rgb[0]); + rgba[1] = static_cast(255.0 * rgb[1]); + rgba[2] = static_cast(255.0 * rgb[2]); + rgba[3] = 255; + + m_FiberColors->InsertTypedTuple(cell->GetPointId(p_idx), rgba); +// } +// } + 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 = m_FiberPolyData->GetPoints(); vtkIdType 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}; m_FiberColors = vtkSmartPointer::New(); m_FiberColors->Allocate(numOfPoints * 4); m_FiberColors->SetNumberOfComponents(4); m_FiberColors->SetName("FIBER_COLORS"); auto 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] = static_cast(255.0 * std::fabs(diff[0])); rgba[1] = static_cast(255.0 * std::fabs(diff[1])); rgba[2] = static_cast(255.0 * std::fabs(diff[2])); rgba[3] = static_cast(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] = static_cast(255.0 * std::fabs(diff1[0])); rgba[1] = static_cast(255.0 * std::fabs(diff1[1])); rgba[2] = static_cast(255.0 * std::fabs(diff1[2])); rgba[3] = static_cast(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] = static_cast(255.0 * std::fabs(diff2[0])); rgba[1] = static_cast(255.0 * std::fabs(diff2[1])); rgba[2] = static_cast(255.0 * std::fabs(diff2[2])); rgba[3] = static_cast(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, bool weight_fibers) { double window = 5; //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; 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); std::vector< double > values; double min = 1; double max = 0; MITK_INFO << "Coloring fibers by curvature"; boost::progress_display disp(static_cast(m_FiberPolyData->GetNumberOfCells())); for (int i=0; iGetNumberOfCells(); i++) { ++disp; vtkCell* cell = m_FiberPolyData->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); double mean_curv = 0; // calculate curvatures for (int j=0; j > vectors; vnl_vector_fixed< double, 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< double, 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< double, 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(); if (weight_fibers) mean_curv += dev; dev = 1.0-dev/180.0; values.push_back(dev); if (devmax) max = dev; } if (weight_fibers) this->SetFiberWeight(i, mean_curv/numPoints); } unsigned int count = 0; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); for (int j=0; j1) dev = 1; lookupTable->GetColor(dev, color); rgba[0] = static_cast(255.0 * color[0]); rgba[1] = static_cast(255.0 * color[1]); rgba[2] = static_cast(255.0 * color[2]); rgba[3] = static_cast(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, static_cast(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, bool weight_fibers) { mitkPixelTypeMultiplex4( ColorFibersByScalarMap, FAimage->GetPixelType(), FAimage, opacity, normalize, weight_fibers ); m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } template void mitk::FiberBundle::ColorFibersByScalarMap(const mitk::PixelType, mitk::Image::Pointer image, bool opacity, bool normalize, bool weight_fibers) { 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 = 999999; double max = -999999; for (unsigned int i=0; iGetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); double mean_val = 0; for (int j=0; jGetPoint(j, p); Point3D px; px[0] = p[0]; px[1] = p[1]; px[2] = p[2]; auto pixelValue = static_cast(readimage.GetPixelByWorldCoordinates(px)); if (pixelValue>max) max = pixelValue; if (pixelValueSetFiberWeight(i, mean_val/numPoints); } 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]; auto pixelValue = static_cast(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] = static_cast(255.0 * color[0]); rgba[1] = static_cast(255.0 * color[1]); rgba[2] = static_cast(255.0 * color[2]); if (opacity) rgba[3] = static_cast(255.0 * pixelValue); else rgba[3] = static_cast(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 (unsigned int i=0; iGetFiberWeight(i); if (weight>max) max = weight; if (weightGetCell(i); auto numPoints = cell->GetNumberOfPoints(); auto weight = this->GetFiberWeight(i); for (int j=0; j1) v = 1; double color[3]; lookupTable->GetColor(static_cast(1-v), color); rgba[0] = static_cast(255.0 * color[0]); rgba[1] = static_cast(255.0 * color[1]); rgba[2] = static_cast(255.0 * color[2]); if (opacity) rgba[3] = static_cast(255.0f * v); else rgba[3] = static_cast(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] = static_cast(r); rgba[1] = static_cast(g); rgba[2] = static_cast(b); rgba[3] = static_cast(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 (unsigned int i=0; iGetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); itk::Point startVertex =mitk::imv::GetItkPoint(points->GetPoint(0)); itk::Index<3> startIndex; mask->TransformPhysicalPointToIndex(startVertex, startIndex); itk::Point endVertex =mitk::imv::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 < 0.5f) continue; float v2 = mask->GetPixel(startIndex); if (v2 < 0.5f) continue; if (!different_label) ++in_mask; else if (fabs(v1-v2)>0.00001f) ++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); double length_sum = 0; double in_mask_length = 0; double aligned_length = 0; for (unsigned int i=0; iGetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; j startVertex =mitk::imv::GetItkPoint(points->GetPoint(j)); itk::Index<3> startIndex; itk::ContinuousIndex startIndexCont; mask->TransformPhysicalPointToIndex(startVertex, startIndex); mask->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont); itk::Point endVertex =mitk::imv::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); if (std::isnan(peak[0]) || std::isnan(peak[1]) || std::isnan(peak[2]) || peak.magnitude()<0.0001f) continue; peak.normalize(); double f = 1.0 - std::acos(std::fabs(static_cast(dot_product(fdir, peak)))) * 2.0/itk::Math::pi; aligned_length += segment.second * f; } length_sum += segment.second; } } } if (length_sum<=0.0001) { 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 (unsigned int i=0; iGetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; j startVertex =mitk::imv::GetItkPoint(points->GetPoint(j)); itk::Index<3> startIndex; itk::ContinuousIndex startIndexCont; mask->TransformPhysicalPointToIndex(startVertex, startIndex); mask->TransformPhysicalPointToContinuousIndex(startVertex, startIndexCont); itk::Point endVertex =mitk::imv::GetItkPoint(points->GetPoint(j + 1)); itk::Index<3> endIndex; itk::ContinuousIndex endIndexCont; mask->TransformPhysicalPointToIndex(endVertex, endIndex); mask->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 > segment : segments) { if ( mask->GetLargestPossibleRegion().IsInside(segment.first) && mask->GetPixel(segment.first) > 0 ) in_mask_length += segment.second; length_sum += segment.second; } } } if (length_sum<=0.000001) { MITK_INFO << "Fiber length sum is zero!"; return 0; } return static_cast(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 (unsigned int i=0; iGetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); int newNumPoints = 0; if (numPoints>1) { for (int j=0; j itkP =mitk::imv::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(static_cast(fib_weights.size())); if (vtkNewCells->GetNumberOfCells()<=0) return nullptr; for (unsigned 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); newFib->SetTrackVisHeader(this->GetTrackVisHeader()); 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); fib->SetTrackVisHeader(this->GetTrackVisHeader()); 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( static_cast(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( static_cast(it - result.begin()) ); break; } case 2: // NOT { MITK_INFO << "NOT"; for(unsigned int 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( static_cast(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 (unsigned int i=0; iGetCell(i); auto 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 (unsigned int i=0; iGetCell(i); auto 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 = static_cast(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); auto 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); double 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 += static_cast(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 (unsigned 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); GetTrackVisHeader(); 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; } void mitk::FiberBundle::TransformFibers(itk::ScalableAffineTransform< mitk::ScalarType >::Pointer transform) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (unsigned int i=0; iGetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; j p =mitk::imv::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) { vnl_matrix_fixed< double, 3, 3 > rot = mitk::imv::GetRotationMatrixVnl(rx, ry, rz); mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (unsigned int i=0; iGetCell(i); auto 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 (unsigned int i=0; iGetCell(i); auto 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 (unsigned int i=0; iGetCell(i); auto 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 (unsigned int i=0; iGetCell(i); auto 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 (unsigned int i=0; iGetCell(i); auto 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(static_cast(m_FiberPolyData->GetNumberOfCells())); for (int i=0; iGetNumberOfCells(); i++) { ++disp ; vtkCell* cell = m_FiberPolyData->GetCell(i); auto 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(static_cast(m_FiberPolyData->GetNumberOfCells())); for (int i=0; iGetNumberOfCells(); i++) { ++disp ; vtkCell* cell = m_FiberPolyData->GetCell(i); auto 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] = static_cast(p2[0]-p1[0]); v1[1] = static_cast(p2[1]-p1[1]); v1[2] = static_cast(p2[2]-p1[2]); v2[0] = static_cast(p3[0]-p2[0]); v2[1] = static_cast(p3[1]-p2[1]); v2[2] = static_cast(p3[2]-p2[2]); v3[0] = static_cast(p1[0]-p3[0]); v3[1] = static_cast(p1[1]-p3[1]); v3[2] = static_cast(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 (unsigned int i=0; iGetCell(i); auto 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 (unsigned int i=0; iGetCell(i); auto 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(m_NumFibers); i++) { vtkSmartPointer newPoints = vtkSmartPointer::New(); float length = 0; #pragma omp critical { length = m_FiberLengths.at(static_cast(i)); ++disp; vtkCell* cell = m_FiberPolyData->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); for (int j=0; jInsertNextPoint(points->GetPoint(j)); } int sampling = static_cast(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[static_cast(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 int mitk::FiberBundle::GetNumberOfPoints() const { unsigned int 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 with max. error " << error << "mm"; unsigned int numRemovedPoints = 0; boost::progress_display disp(static_cast(m_FiberPolyData->GetNumberOfCells())); vtkSmartPointer newFiberWeights = vtkSmartPointer::New(); newFiberWeights->SetName("FIBER_WEIGHTS"); newFiberWeights->SetNumberOfValues(m_NumFibers); #pragma omp parallel for for (int i=0; i(m_FiberPolyData->GetNumberOfCells()); 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); auto 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 auto numPoints = vertices.size(); std::vector< int > removedPoints; removedPoints.resize(numPoints, 0); removedPoints[0]=-1; removedPoints[numPoints-1]=-1; vtkSmartPointer container = vtkSmartPointer::New(); unsigned int remCounter = 0; bool pointFound = true; while (pointFound) { pointFound = false; double minError = static_cast(error); unsigned int removeIndex = 0; for (unsigned int j=0; j candV = vertices.at(j); int validP = -1; vnl_vector_fixed< double, 3 > pred; for (int k=static_cast(j)-1; k>=0; k--) if (removedPoints[static_cast(k)]<=0) { pred = vertices.at(static_cast(k)); validP = k; break; } int validS = -1; vnl_vector_fixed< double, 3 > succ; for (unsigned int k=j+1; k(k); break; } if (validP>=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; for (unsigned int i=0; iGetNumberOfCells(); i++) { std::vector< vnl_vector_fixed< double, 3 > > vertices; float weight = 1; double seg_len = 0; { weight = m_FiberWeights->GetValue(i); vtkCell* cell = m_FiberPolyData->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); if (numPoints!=targetPoints) seg_len = static_cast(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); { 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<=0.0000001) { //#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(static_cast(m_FiberPolyData->GetNumberOfCells())); vtkSmartPointer newFiberWeights = vtkSmartPointer::New(); newFiberWeights->SetName("FIBER_WEIGHTS"); newFiberWeights->SetNumberOfValues(m_NumFibers); std::vector< vtkSmartPointer > resampled_streamlines; resampled_streamlines.resize(static_cast(m_FiberPolyData->GetNumberOfCells())); #pragma omp parallel for for (int i=0; i(m_FiberPolyData->GetNumberOfCells()); i++) { std::vector< vnl_vector_fixed< double, 3 > > vertices; #pragma omp critical { ++disp; vtkCell* cell = m_FiberPolyData->GetCell(i); auto 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[static_cast(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 (unsigned int i=0; iGetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkCell* cell2 = fib->GetFiberPolyData()->GetCell(i); auto 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 << 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; os << "\nReference geometry:" << std::endl; os << indent << "Size: [" << std::defaultfloat << m_TrackVisHeader.dim[0] << " " << m_TrackVisHeader.dim[1] << " " << m_TrackVisHeader.dim[2] << "]" << std::endl; os << indent << "Voxel size: [" << m_TrackVisHeader.voxel_size[0] << " " << m_TrackVisHeader.voxel_size[1] << " " << m_TrackVisHeader.voxel_size[2] << "]" << std::endl; os << indent << "Origin: [" << m_TrackVisHeader.origin[0] << " " << m_TrackVisHeader.origin[1] << " " << m_TrackVisHeader.origin[2] << "]" << std::endl; os << indent << "Matrix: " << std::scientific << std::endl; os << indent << "[[" << m_TrackVisHeader.vox_to_ras[0][0] << ", " << m_TrackVisHeader.vox_to_ras[0][1] << ", " << m_TrackVisHeader.vox_to_ras[0][2] << ", " << m_TrackVisHeader.vox_to_ras[0][3] << "]" << std::endl; os << indent << " [" << m_TrackVisHeader.vox_to_ras[1][0] << ", " << m_TrackVisHeader.vox_to_ras[1][1] << ", " << m_TrackVisHeader.vox_to_ras[1][2] << ", " << m_TrackVisHeader.vox_to_ras[1][3] << "]" << std::endl; os << indent << " [" << m_TrackVisHeader.vox_to_ras[2][0] << ", " << m_TrackVisHeader.vox_to_ras[2][1] << ", " << m_TrackVisHeader.vox_to_ras[2][2] << ", " << m_TrackVisHeader.vox_to_ras[2][3] << "]" << std::endl; os << indent << " [" << m_TrackVisHeader.vox_to_ras[3][0] << ", " << m_TrackVisHeader.vox_to_ras[3][1] << ", " << m_TrackVisHeader.vox_to_ras[3][2] << ", " << m_TrackVisHeader.vox_to_ras[3][3] << "]]" << std::defaultfloat << 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 << "\nFiber weight statistics" << std::endl; os << indent << "Min: " << weights.front() << std::endl; os << indent << "1% quantile: " << weights.at(static_cast(weights.size()*0.01)) << std::endl; os << indent << "5% quantile: " << weights.at(static_cast(weights.size()*0.05)) << std::endl; os << indent << "25% quantile: " << weights.at(static_cast(weights.size()*0.25)) << std::endl; os << indent << "Median: " << weights.at(static_cast(weights.size()*0.5)) << std::endl; os << indent << "75% quantile: " << weights.at(static_cast(weights.size()*0.75)) << std::endl; os << indent << "95% quantile: " << weights.at(static_cast(weights.size()*0.95)) << std::endl; os << indent << "99% quantile: " << weights.at(static_cast(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, 0); } mitk::FiberBundle::TrackVis_header mitk::FiberBundle::GetTrackVisHeader() { if (m_TrackVisHeader.hdr_size==0) { mitk::Geometry3D::Pointer geom = dynamic_cast(this->GetGeometry()); SetTrackVisHeader(geom); } return m_TrackVisHeader; } void mitk::FiberBundle::SetTrackVisHeader(const mitk::FiberBundle::TrackVis_header &TrackVisHeader) { m_TrackVisHeader = TrackVisHeader; } void mitk::FiberBundle::SetTrackVisHeader(mitk::BaseGeometry* geometry) { vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New(); matrix->Identity(); if (geometry==nullptr) return; for(int i=0; i<3 ;i++) { m_TrackVisHeader.dim[i] = geometry->GetExtent(i); m_TrackVisHeader.voxel_size[i] = geometry->GetSpacing()[i]; m_TrackVisHeader.origin[i] = geometry->GetOrigin()[i]; matrix = geometry->GetVtkMatrix(); } for (int i=0; i<4; ++i) for (int j=0; j<4; ++j) m_TrackVisHeader.vox_to_ras[i][j] = matrix->GetElement(i, j); m_TrackVisHeader.n_scalars = 0; m_TrackVisHeader.n_properties = 0; sprintf(m_TrackVisHeader.voxel_order,"LPS"); m_TrackVisHeader.image_orientation_patient[0] = 1.0; m_TrackVisHeader.image_orientation_patient[1] = 0.0; m_TrackVisHeader.image_orientation_patient[2] = 0.0; m_TrackVisHeader.image_orientation_patient[3] = 0.0; m_TrackVisHeader.image_orientation_patient[4] = 1.0; m_TrackVisHeader.image_orientation_patient[5] = 0.0; m_TrackVisHeader.pad1[0] = 0; m_TrackVisHeader.pad1[1] = 0; m_TrackVisHeader.pad2[0] = 0; m_TrackVisHeader.pad2[1] = 0; m_TrackVisHeader.invert_x = 0; m_TrackVisHeader.invert_y = 0; m_TrackVisHeader.invert_z = 0; m_TrackVisHeader.swap_xy = 0; m_TrackVisHeader.swap_yz = 0; m_TrackVisHeader.swap_zx = 0; m_TrackVisHeader.n_count = 0; m_TrackVisHeader.version = 2; m_TrackVisHeader.hdr_size = 1000; std::string id = "TRACK"; strcpy(m_TrackVisHeader.id_string, id.c_str()); } /* 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/DiffusionCore/IODataStructures/mitkFiberBundle.h b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.h index 542b91d..71e5b29 100644 --- a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.h +++ b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.h @@ -1,245 +1,246 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 #include namespace mitk { /** * \brief Base Class for Fiber Bundles; */ class MITKDIFFUSIONCORE_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 ColorSinglePoint(int f_idx, int p_idx, double rgb[3]); void ColorFibersByFiberWeights(bool opacity, bool normalize); void ColorFibersByCurvature(bool opacity, bool normalize, bool weight_fibers); void ColorFibersByLength(bool opacity, bool normalize, bool weight_fibers); void ColorFibersByScalarMap(mitk::Image::Pointer, bool opacity, bool normalize, bool weight_fibers); template void ColorFibersByScalarMap(const mitk::PixelType pixelType, mitk::Image::Pointer, bool opacity, bool normalize, bool weight_fibers); 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); template< class TType=float > void TransformPoint(itk::Point& point, itk::Matrix< TType, 3, 3>& rot, TType& tx, TType& ty, TType& tz) { mitk::Point3D center = this->GetGeometry()->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; } template< class TType=float > void TransformPoint(itk::Point& point, TType rx, TType ry, TType rz, TType tx, TType ty, TType tz) { auto rot = mitk::imv::GetRotationMatrixItk(rx, ry, rz); mitk::Point3D center = this->GetGeometry()->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::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, bool random_seed); // get/set data float GetFiberLength(unsigned 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, unsigned 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 int GetNumberOfPoints() const; // copy fiber bundle mitk::FiberBundle::Pointer GetDeepCopy(); // compare fiber bundles bool Equals(FiberBundle* fib, double eps=0.01); vtkSmartPointer GeneratePolyDataByIds(std::vector fiberIds, vtkSmartPointer weights); // Structure to hold metadata of a TrackVis file struct TrackVis_header { char id_string[6]; short int dim[3]; float voxel_size[3]; float origin[3]; short int n_scalars; char scalar_name[10][20]; short int n_properties; char property_name[10][20]; float vox_to_ras[4][4]; char reserved[444]; char voxel_order[4]; char pad2[4]; float image_orientation_patient[6]; char pad1[2]; unsigned char invert_x; unsigned char invert_y; unsigned char invert_z; unsigned char swap_xy; unsigned char swap_yz; unsigned char swap_zx; int n_count; int version; int hdr_size; }; TrackVis_header GetTrackVisHeader(); void SetTrackVisHeader(const TrackVis_header &TrackVisHeader); void SetTrackVisHeader(BaseGeometry *geometry); void PrintSelf(std::ostream &os, itk::Indent indent) const override; protected: FiberBundle( vtkPolyData* fiberPolyData = nullptr ); ~FiberBundle() override; void GenerateFiberIds(); void UpdateFiberGeometry(); private: // actual fiber container vtkSmartPointer m_FiberPolyData; // contains fiber ids vtkSmartPointer m_FiberIdDataSet; unsigned 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; TrackVis_header m_TrackVisHeader; }; } // namespace mitk #endif /* _MITK_FiberBundle_H */ diff --git a/Modules/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetric.h b/Modules/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetric.h index 5fd32ab..7f6f124 100644 --- a/Modules/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetric.h +++ b/Modules/FiberTracking/Algorithms/ClusteringMetrics/mitkClusteringMetric.h @@ -1,61 +1,57 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 _ClusteringMetric #define _ClusteringMetric #include namespace mitk { /** * \brief Base class for fiber clustering metrics */ class ClusteringMetric { public: ClusteringMetric() : m_Scale(1.0) {} virtual ~ClusteringMetric(){} virtual float CalculateDistance(vnl_matrix& s, vnl_matrix& t, bool &flipped) = 0; - float GetScale() const; - void SetScale(float Scale); + float GetScale() const + { + return m_Scale; + } + void SetScale(float Scale) + { + m_Scale = Scale; + } protected: float m_Scale; }; -float ClusteringMetric::GetScale() const -{ - return m_Scale; -} - -void ClusteringMetric::SetScale(float Scale) -{ - m_Scale = Scale; -} - } #endif diff --git a/Modules/FiberTracking/Algorithms/itkTractClusteringFilter.cpp b/Modules/FiberTracking/Algorithms/mitkTractClusteringFilter.cpp similarity index 91% rename from Modules/FiberTracking/Algorithms/itkTractClusteringFilter.cpp rename to Modules/FiberTracking/Algorithms/mitkTractClusteringFilter.cpp index 38318b1..cb1b076 100644 --- a/Modules/FiberTracking/Algorithms/itkTractClusteringFilter.cpp +++ b/Modules/FiberTracking/Algorithms/mitkTractClusteringFilter.cpp @@ -1,558 +1,608 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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" +#include "mitkTractClusteringFilter.h" #define _USE_MATH_DEFINES #include #include #include -namespace itk{ +namespace mitk{ 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< unsigned int > 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); } +unsigned int TractClusteringFilter::GetDiscardedClusters() const +{ + return m_DiscardedClusters; +} + +void TractClusteringFilter::SetDoResampling(bool DoResampling) +{ + m_DoResampling = DoResampling; +} + +void TractClusteringFilter::SetOverlapThreshold(float OverlapThreshold) +{ + m_OverlapThreshold = OverlapThreshold; +} + +void TractClusteringFilter::SetFilterMask(const UcharImageType::Pointer &FilterMask) +{ + m_FilterMask = FilterMask; +} + +void TractClusteringFilter::SetMinClusterSize(unsigned int MinClusterSize) +{ + m_MinClusterSize = MinClusterSize; +} + +void TractClusteringFilter::SetMaxClusters(unsigned int MaxClusters) +{ + m_MaxClusters = MaxClusters; +} + +void TractClusteringFilter::SetNumPoints(unsigned int NumPoints) +{ + m_NumPoints = NumPoints; +} + +void TractClusteringFilter::SetMergeDuplicateThreshold(float MergeDuplicateThreshold) +{ + m_MergeDuplicateThreshold = MergeDuplicateThreshold; +} + +void TractClusteringFilter::SetInCentroids(const mitk::FiberBundle::Pointer &InCentroids) +{ + m_InCentroids = InCentroids; +} + +void TractClusteringFilter::SetTractogram(const mitk::FiberBundle::Pointer &Tractogram) +{ + m_Tractogram = Tractogram; +} + std::vector< TractClusteringFilter::Cluster > TractClusteringFilter::MergeDuplicateClusters2(std::vector< TractClusteringFilter::Cluster >& clusters) { if (m_MergeDuplicateThreshold<0) m_MergeDuplicateThreshold = m_Distances.at(0)/2; else if (m_MergeDuplicateThreshold==0) return clusters; 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 (int k2=0; k2<(int)new_clusters.size(); ++k2) { Cluster c2 = new_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& 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< unsigned int > 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(); 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(); 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; + m_DiscardedClusters = 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++; + m_DiscardedClusters++; } } - MITK_INFO << "Final number of clusters: " << m_OutTractograms.size() << " (discarded " << skipped << " clusters)"; + MITK_INFO << "Final number of clusters: " << m_OutTractograms.size() << " (discarded " << m_DiscardedClusters << " 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/FiberTracking/Algorithms/itkTractClusteringFilter.h b/Modules/FiberTracking/Algorithms/mitkTractClusteringFilter.h similarity index 53% rename from Modules/FiberTracking/Algorithms/itkTractClusteringFilter.h rename to Modules/FiberTracking/Algorithms/mitkTractClusteringFilter.h index b18e2bb..75b574a 100644 --- a/Modules/FiberTracking/Algorithms/itkTractClusteringFilter.h +++ b/Modules/FiberTracking/Algorithms/mitkTractClusteringFilter.h @@ -1,140 +1,131 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 +#ifndef TractClusteringFilter_h +#define TractClusteringFilter_h // MITK +#include #include #include -#include #include // ITK #include // VTK #include #include #include #include #include -namespace itk{ +namespace mitk{ /** * \brief */ -class TractClusteringFilter : public ProcessObject +class MITKFIBERTRACKING_EXPORT TractClusteringFilter { public: struct Cluster { Cluster() : n(0), f_id(-1) {} vnl_matrix h; std::vector< unsigned int > 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; + TractClusteringFilter(); + ~TractClusteringFilter(); + 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{ + void Update(){ 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; + std::vector > GetOutFiberIndices() const; void SetMetrics(const std::vector &Metrics); - std::vector > GetOutFiberIndices() const; + void SetTractogram(const mitk::FiberBundle::Pointer &Tractogram); + + void SetInCentroids(const mitk::FiberBundle::Pointer &InCentroids); + + void SetMergeDuplicateThreshold(float MergeDuplicateThreshold); + + void SetNumPoints(unsigned int NumPoints); + + void SetMaxClusters(unsigned int MaxClusters); + + void SetMinClusterSize(unsigned int MinClusterSize); + + void SetFilterMask(const UcharImageType::Pointer &FilterMask); + + void SetOverlapThreshold(float OverlapThreshold); + + void SetDoResampling(bool DoResampling); + + unsigned int GetDiscardedClusters() const; protected: - void GenerateData() override; + void GenerateData(); std::vector< vnl_matrix > ResampleFibers(FiberBundle::Pointer tractogram); float CalcOverlap(vnl_matrix& t); std::vector< Cluster > ClusterStep(std::vector< unsigned int > 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< unsigned int > 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; + unsigned int m_DiscardedClusters; 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< unsigned int > > m_OutFiberIndices; }; } -#ifndef ITK_MANUAL_INSTANTIATION -#include "itkTractClusteringFilter.cpp" -#endif - #endif diff --git a/Modules/FiberTracking/Testing/mitkStreamlineTractographyTest.cpp b/Modules/FiberTracking/Testing/mitkStreamlineTractographyTest.cpp index 8922705..a5e07f6 100644 --- a/Modules/FiberTracking/Testing/mitkStreamlineTractographyTest.cpp +++ b/Modules/FiberTracking/Testing/mitkStreamlineTractographyTest.cpp @@ -1,438 +1,439 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 class mitkStreamlineTractographyTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkStreamlineTractographyTestSuite); MITK_TEST(Test_Peak1); MITK_TEST(Test_Peak2); MITK_TEST(Test_Tensor1); MITK_TEST(Test_Tensor2); MITK_TEST(Test_Tensor3); MITK_TEST(Test_Odf1); MITK_TEST(Test_Odf2); MITK_TEST(Test_Odf3); MITK_TEST(Test_Odf4); MITK_TEST(Test_Odf5); MITK_TEST(Test_Odf6); CPPUNIT_TEST_SUITE_END(); typedef itk::VectorImage< short, 3> ItkDwiType; private: public: /** Members used inside the different (sub-)tests. All members are initialized via setUp().*/ typedef itk::Image ItkFloatImgType; mitk::TrackingHandlerOdf::ItkOdfImageType::Pointer itk_odf_image; mitk::TrackingHandlerTensor::ItkTensorImageType::ConstPointer itk_tensor_image; mitk::TrackingHandlerPeaks::PeakImgType::Pointer itk_peak_image; ItkFloatImgType::Pointer itk_seed_image; ItkFloatImgType::Pointer itk_mask_image; ItkFloatImgType::Pointer itk_gfa_image; float gfa_threshold; float odf_threshold; float peak_threshold; std::shared_ptr params; itk::StreamlineTrackingFilter::Pointer tracker; void setUp() override { omp_set_num_threads(1); gfa_threshold = 0.2f; odf_threshold = 0.1f; peak_threshold = 0.1f; mitk::Image::Pointer odf_image = mitk::IOUtil::Load(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/qball_image.qbi")); mitk::Image::Pointer tensor_image = mitk::IOUtil::Load(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/tensor_image.dti")); mitk::Image::Pointer peak_image = mitk::IOUtil::Load(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/qball_peak_image.nii.gz")); mitk::Image::Pointer seed_image = mitk::IOUtil::Load(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/seed_image.nii.gz")); mitk::Image::Pointer mask_image = mitk::IOUtil::Load(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/mask_image.nii.gz")); mitk::Image::Pointer gfa_image = mitk::IOUtil::Load(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/gfa_image.nii.gz")); params = std::make_shared(); params->m_FixRandomSeed = true; params->m_InterpolateRoiImages = false; + params->SetLoopCheckDeg(-1); // todo: test loop check { typedef mitk::ImageToItk< mitk::TrackingHandlerPeaks::PeakImgType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(peak_image); caster->Update(); itk_peak_image = caster->GetOutput(); } { typedef mitk::ImageToItk< mitk::TrackingHandlerTensor::ItkTensorImageType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(tensor_image); caster->Update(); itk_tensor_image = caster->GetOutput(); } { typedef mitk::ImageToItk< mitk::TrackingHandlerOdf::ItkOdfImageType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(odf_image); caster->Update(); itk_odf_image = caster->GetOutput(); } itk_gfa_image = ItkFloatImgType::New(); mitk::CastToItkImage(gfa_image, itk_gfa_image); itk_seed_image = ItkFloatImgType::New(); mitk::CastToItkImage(seed_image, itk_seed_image); itk_mask_image = ItkFloatImgType::New(); mitk::CastToItkImage(mask_image, itk_mask_image); } mitk::FiberBundle::Pointer LoadReferenceFib(std::string filename) { mitk::FiberBundle::Pointer fib = nullptr; if (itksys::SystemTools::FileExists(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/ReferenceFibs/" + filename))) { mitk::BaseData::Pointer baseData = mitk::IOUtil::Load(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/ReferenceFibs/" + filename)).at(0); fib = dynamic_cast(baseData.GetPointer()); } return fib; } mitk::Image::Pointer LoadReferenceImage(std::string filename) { mitk::Image::Pointer img = nullptr; if (itksys::SystemTools::FileExists(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/ReferenceFibs/" + filename))) { img = mitk::IOUtil::Load(GetTestDataFilePath("DiffusionImaging/StreamlineTractography/ReferenceFibs/" + filename)); } return img; } void SetupTracker(mitk::TrackingDataHandler* handler) { tracker = itk::StreamlineTrackingFilter::New(); // tracker->SetInterpolateMasks(false); // tracker->SetNumberOfSamples(0); // tracker->SetAngularThreshold(-1); tracker->SetMaskImage(itk_mask_image); tracker->SetSeedImage(itk_seed_image); tracker->SetStoppingRegions(nullptr); // tracker->SetSeedsPerVoxel(1); // tracker->SetStepSize(0.5); // tracker->SetSamplingDistance(0.25); // tracker->SetUseStopVotes(true); // tracker->SetOnlyForwardSamples(true); // tracker->SetMinTractLength(20); // tracker->SetMaxNumTracts(-1); tracker->SetTrackingHandler(handler); // tracker->SetUseOutputProbabilityMap(false); tracker->SetParameters(params); } void tearDown() override { } void CheckFibResult(std::string ref_file, mitk::FiberBundle::Pointer test_fib) { mitk::FiberBundle::Pointer ref = LoadReferenceFib(ref_file); if (ref.IsNull()) { mitk::IOUtil::Save(test_fib, mitk::IOUtil::GetTempPath()+ref_file); CPPUNIT_FAIL("Reference file not found. Saving test file to " + mitk::IOUtil::GetTempPath() + ref_file); } else { bool is_equal = ref->Equals(test_fib); if (!is_equal) { mitk::IOUtil::Save(test_fib, mitk::IOUtil::GetTempPath()+ref_file); CPPUNIT_FAIL("Tractograms are not equal! Saving test file to " + mitk::IOUtil::GetTempPath() + ref_file); } } } void CheckImageResult(std::string ref_file, mitk::Image::Pointer test_img) { mitk::Image::Pointer ref = LoadReferenceImage(ref_file); if (ref.IsNull()) { mitk::IOUtil::Save(test_img, mitk::IOUtil::GetTempPath()+ref_file); CPPUNIT_FAIL("Reference file not found. Saving test file to " + mitk::IOUtil::GetTempPath() + ref_file); } else { MITK_ASSERT_EQUAL(test_img, ref, "Images should be equal"); } } void Test_Peak1() { mitk::TrackingHandlerPeaks* handler = new mitk::TrackingHandlerPeaks(); handler->SetPeakImage(itk_peak_image); params->m_Cutoff = peak_threshold; SetupTracker(handler); tracker->Update(); vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); CheckFibResult("Test_Peak1.fib", outFib); delete handler; } void Test_Peak2() { mitk::TrackingHandlerPeaks* handler = new mitk::TrackingHandlerPeaks(); handler->SetPeakImage(itk_peak_image); params->m_Cutoff = peak_threshold; params->m_InterpolateTractographyData = false; SetupTracker(handler); tracker->Update(); vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); CheckFibResult("Test_Peak2.fib", outFib); delete handler; } void Test_Tensor1() { mitk::TrackingHandlerTensor* handler = new mitk::TrackingHandlerTensor(); handler->SetTensorImage(itk_tensor_image); params->m_Cutoff = gfa_threshold; SetupTracker(handler); tracker->Update(); vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); CheckFibResult("Test_Tensor1.fib", outFib); delete handler; } void Test_Tensor2() { mitk::TrackingHandlerTensor* handler = new mitk::TrackingHandlerTensor(); handler->SetTensorImage(itk_tensor_image); params->m_Cutoff = gfa_threshold; params->m_InterpolateTractographyData = false; SetupTracker(handler); tracker->Update(); vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); CheckFibResult("Test_Tensor2.fib", outFib); delete handler; } void Test_Tensor3() { mitk::TrackingHandlerTensor* handler = new mitk::TrackingHandlerTensor(); handler->SetTensorImage(itk_tensor_image); params->m_Cutoff = gfa_threshold; params->m_InterpolateTractographyData = false; params->m_F = 0; params->m_G = 1; SetupTracker(handler); tracker->Update(); vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); CheckFibResult("Test_Tensor3.fib", outFib); delete handler; } void Test_Odf1() { mitk::TrackingHandlerOdf* handler = new mitk::TrackingHandlerOdf(); handler->SetOdfImage(itk_odf_image); params->m_Cutoff = gfa_threshold; params->m_OdfCutoff = 0; params->m_SharpenOdfs = true; SetupTracker(handler); tracker->Update(); vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); CheckFibResult("Test_Odf1.fib", outFib); delete handler; } void Test_Odf2() { mitk::TrackingHandlerOdf* handler = new mitk::TrackingHandlerOdf(); handler->SetOdfImage(itk_odf_image); params->m_Cutoff = gfa_threshold; params->m_OdfCutoff = 0; params->m_SharpenOdfs = false; SetupTracker(handler); tracker->Update(); vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); CheckFibResult("Test_Odf2.fib", outFib); delete handler; } void Test_Odf3() { mitk::TrackingHandlerOdf* handler = new mitk::TrackingHandlerOdf(); handler->SetOdfImage(itk_odf_image); params->m_Cutoff = gfa_threshold; params->m_OdfCutoff = 0; params->m_SharpenOdfs = true; params->m_InterpolateTractographyData = false; SetupTracker(handler); tracker->Update(); vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); CheckFibResult("Test_Odf3.fib", outFib); delete handler; } void Test_Odf4() { mitk::TrackingHandlerOdf* handler = new mitk::TrackingHandlerOdf(); handler->SetOdfImage(itk_odf_image); params->m_Cutoff = gfa_threshold; params->m_OdfCutoff = 0; params->m_SharpenOdfs = true; params->m_SeedsPerVoxel = 3; SetupTracker(handler); tracker->Update(); vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); CheckFibResult("Test_Odf4.fib", outFib); delete handler; } void Test_Odf5() { mitk::TrackingHandlerOdf* handler = new mitk::TrackingHandlerOdf(); handler->SetOdfImage(itk_odf_image); params->m_Cutoff = gfa_threshold; params->m_OdfCutoff = 0; params->m_SharpenOdfs = true; params->m_SeedsPerVoxel = 3; params->m_Mode = mitk::TrackingDataHandler::MODE::PROBABILISTIC; SetupTracker(handler); tracker->Update(); vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); CheckFibResult("Test_Odf5.fib", outFib); delete handler; } void Test_Odf6() { mitk::TrackingHandlerOdf* handler = new mitk::TrackingHandlerOdf(); handler->SetOdfImage(itk_odf_image); params->m_Cutoff = gfa_threshold; params->m_OdfCutoff = 0; params->m_SharpenOdfs = true; params->m_SeedsPerVoxel = 10; params->m_Mode = mitk::TrackingDataHandler::MODE::PROBABILISTIC; params->m_OutputProbMap = true; SetupTracker(handler); tracker->Update(); itk::StreamlineTrackingFilter::ItkDoubleImgType::Pointer outImg = tracker->GetOutputProbabilityMap(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); mitk::IOUtil::Save(img, mitk::IOUtil::GetTempPath()+"Test_Odf6.nrrd"); CheckImageResult("Test_Odf6.nrrd", img); delete handler; } }; MITK_TEST_SUITE_REGISTRATION(mitkStreamlineTractography) diff --git a/Modules/FiberTracking/files.cmake b/Modules/FiberTracking/files.cmake index be71c70..6e5c97c 100644 --- a/Modules/FiberTracking/files.cmake +++ b/Modules/FiberTracking/files.cmake @@ -1,70 +1,71 @@ set(CPP_FILES mitkStreamlineTractographyParameters.cpp # 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/mitkTractClusteringFilter.cpp Algorithms/itkStreamlineTrackingFilter.cpp Algorithms/TrackingHandlers/mitkTrackingDataHandler.cpp Algorithms/TrackingHandlers/mitkTrackingHandlerTensor.cpp Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.cpp ) set(H_FILES mitkStreamlineTractographyParameters.h # Algorithms Algorithms/itkTractDensityImageFilter.h Algorithms/itkTractsToFiberEndingsImageFilter.h Algorithms/itkTractsToRgbaImageFilter.h Algorithms/itkTractsToVectorImageFilter.h Algorithms/itkEvaluateDirectionImagesFilter.h Algorithms/itkEvaluateTractogramDirectionsFilter.h Algorithms/itkFiberCurvatureFilter.h - Algorithms/itkTractClusteringFilter.h + Algorithms/mitkTractClusteringFilter.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 ) set(RESOURCE_FILES # Binary directory resources FiberTrackingLUTBaryCoords.bin FiberTrackingLUTIndices.bin ) diff --git a/Modules/FiberTracking/mitkStreamlineTractographyParameters.h b/Modules/FiberTracking/mitkStreamlineTractographyParameters.h index 96fe4a8..7f35ad4 100644 --- a/Modules/FiberTracking/mitkStreamlineTractographyParameters.h +++ b/Modules/FiberTracking/mitkStreamlineTractographyParameters.h @@ -1,163 +1,163 @@ #pragma once /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 namespace mitk { /** * \brief Datastructure to manage streamline tractography parameters. * */ class MITKFIBERTRACKING_EXPORT StreamlineTractographyParameters { public: enum EndpointConstraints { NONE, ///< No constraints on endpoint locations EPS_IN_TARGET, ///< Both EPs are required to be located in the target image EPS_IN_TARGET_LABELDIFF, ///< Both EPs are required to be located in the target image and the image values at the respective position needs to be distinct EPS_IN_SEED_AND_TARGET, ///< One EP is required to be located in the seed image and one in the target image MIN_ONE_EP_IN_TARGET, ///< At least one EP is required to be located in the target image ONE_EP_IN_TARGET, ///< Exactly one EP is required to be located in the target image NO_EP_IN_TARGET ///< No EP is allowed to be located in the target image }; enum MODE { DETERMINISTIC, PROBABILISTIC }; typedef itk::Image ItkFloatImgType; typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; StreamlineTractographyParameters(); StreamlineTractographyParameters(const StreamlineTractographyParameters ¶ms) = default; ~StreamlineTractographyParameters(); void SaveParameters(std::string filename); ///< Save image generation parameters to .stp file. void LoadParameters(std::string filename); ///< Load image generation parameters from .stp file. template< class ParameterType > ParameterType ReadVal(boost::property_tree::ptree::value_type const& v, std::string tag, ParameterType defaultValue, bool essential=false); // seeding unsigned int m_SeedsPerVoxel = 1; unsigned int m_TrialsPerSeed = 10; int m_MaxNumFibers = -1; // - seed image // interactive float m_InteractiveRadiusMm = 2; unsigned int m_NumInteractiveSeeds = 50; bool m_EnableInteractive = false; // ROI constraints EndpointConstraints m_EpConstraints; // - mask image // - stop image // - exclusion image // - target image // tractography MODE m_Mode= MODE::DETERMINISTIC; bool m_SharpenOdfs = false; float m_Cutoff = 0.1; // - fa/gfa image float m_OdfCutoff = 0.00025; float m_MinTractLengthMm = 20; float m_MaxTractLengthMm = 400; float m_F = 1; float m_G = 0; bool m_FixRandomSeed = false; unsigned int m_NumPreviousDirections = 1; float m_PeakJitter = 0.01; // actual jitter is drawn from a normal distribution with m_PeakJitter*fabs(direction_value) as standard deviation // prior // - peak image float m_Weight = 0.5; bool m_RestrictToPrior = true; bool m_NewDirectionsFromPrior = true; bool m_PriorFlipX = false; bool m_PriorFlipY = false; bool m_PriorFlipZ = false; // neighborhood sampling unsigned int m_NumSamples = 0; bool m_OnlyForwardSamples = false; bool m_StopVotes = false; bool m_AvoidStop = true; bool m_RandomSampling = false; float m_DeflectionMod = 1.0; // data handling bool m_FlipX = false; bool m_FlipY = false; bool m_FlipZ = false; bool m_InterpolateTractographyData = true; bool m_InterpolateRoiImages; bool m_ApplyDirectionMatrix = false; // output and postprocessing bool m_CompressFibers = true; float m_Compression = 0.1; bool m_OutputProbMap = false; float GetAngularThresholdDot() const; float GetAngularThresholdDeg() const; void SetAngularThresholdDeg(float angular_threshold_deg); float GetLoopCheckDeg() const; void SetLoopCheckDeg(float loop_check_deg); float GetStepSizeMm() const; float GetStepSizeVox() const; void SetStepSizeVox(float step_size_vox); float GetSamplingDistanceMm() const; float GetSamplingDistanceVox() const; void SetSamplingDistanceVox(float sampling_distance_vox); void SetMinVoxelSizeMm(float min_voxel_size_mm); float GetMinVoxelSizeMm() const; private: void AutoAdjust(); float m_SamplingDistanceVox = -1; float m_SamplingDistanceMm; float m_AngularThresholdDeg = -1; float m_AngularThresholdDot; - float m_LoopCheckDeg = -1; + float m_LoopCheckDeg = 30; float m_StepSizeVox = -1; float m_StepSizeMm; float m_MinVoxelSizeMm = 1.0; }; } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp index 5cea14d..038ed58 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/Perspectives/QmitkFiberProcessingPerspective.cpp @@ -1,51 +1,52 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 "QmitkFiberProcessingPerspective.h" #include "berryIViewLayout.h" void QmitkFiberProcessingPerspective::CreateInitialLayout(berry::IPageLayout::Pointer layout) { ///////////////////////////////////////////////////// // all di-app perspectives should have the following: ///////////////////////////////////////////////////// QString editorArea = layout->GetEditorArea(); layout->AddStandaloneViewPlaceholder("org.mitk.views.viewnavigatorview", berry::IPageLayout::LEFT, 0.3f, editorArea, false); layout->AddStandaloneView("org.mitk.views.datamanager", false, berry::IPageLayout::LEFT, 0.3f, editorArea); layout->AddStandaloneView("org.mitk.views.controlvisualizationpropertiesview", false, berry::IPageLayout::BOTTOM, .15f, "org.mitk.views.datamanager"); berry::IFolderLayout::Pointer left = layout->CreateFolder("org.mbi.diffusionimaginginternal.leftcontrols", berry::IPageLayout::BOTTOM, 0.15f, "org.mitk.views.controlvisualizationpropertiesview"); layout->AddStandaloneViewPlaceholder("org.mitk.views.imagenavigator", berry::IPageLayout::BOTTOM, .7f, "org.mbi.diffusionimaginginternal.leftcontrols", false); ///////////////////////////////////////////// // here goes the perspective specific stuff ///////////////////////////////////////////// left->AddView("org.mitk.views.fiberprocessing"); left->AddView("org.mitk.views.fiberquantification"); left->AddView("org.mitk.views.fiberclustering"); left->AddView("org.mitk.views.fiberfit"); + left->AddView("org.mitk.views.tractometry"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringView.cpp index 4a642f2..9d6a150 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberClusteringView.cpp @@ -1,232 +1,233 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 "QmitkFiberClusteringView.h" #include #include #include #include #include -#include +#include #include #include #include #include #include #include #include #include #include +#include const std::string QmitkFiberClusteringView::VIEW_ID = "org.mitk.views.fiberclustering"; using namespace mitk; QmitkFiberClusteringView::QmitkFiberClusteringView() : QmitkAbstractView() , m_Controls( nullptr ) { } // Destructor QmitkFiberClusteringView::~QmitkFiberClusteringView() { } void QmitkFiberClusteringView::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::QmitkFiberClusteringViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(StartClustering()) ); connect( m_Controls->m_TractBox, SIGNAL(currentIndexChanged(int)), this, SLOT(FiberSelectionChanged()) ); mitk::TNodePredicateDataType::Pointer isFib = mitk::TNodePredicateDataType::New(); m_Controls->m_TractBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TractBox->SetPredicate(isFib); m_Controls->m_InCentroidsBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_InCentroidsBox->SetPredicate(isFib); m_Controls->m_InCentroidsBox->SetZeroEntryText("--"); mitk::TNodePredicateDataType::Pointer imageP = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDimension::Pointer dimP = mitk::NodePredicateDimension::New(3); m_Controls->m_MapBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_MapBox->SetPredicate(mitk::NodePredicateAnd::New(imageP, dimP)); m_Controls->m_ParcellationBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_ParcellationBox->SetPredicate(mitk::NodePredicateAnd::New(imageP, dimP)); m_Controls->m_MetricBox6->setVisible(false); m_Controls->m_MetricWeight6->setVisible(false); FiberSelectionChanged(); } } void QmitkFiberClusteringView::SetFocus() { FiberSelectionChanged(); } void QmitkFiberClusteringView::FiberSelectionChanged() { if (m_Controls->m_TractBox->GetSelectedNode().IsNull()) m_Controls->m_StartButton->setEnabled(false); else m_Controls->m_StartButton->setEnabled(true); } void QmitkFiberClusteringView::StartClustering() { if (m_Controls->m_TractBox->GetSelectedNode().IsNull()) return; mitk::DataNode::Pointer node = m_Controls->m_TractBox->GetSelectedNode(); float clusterSize = m_Controls->m_ClusterSizeBox->value(); mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); float max_d = 0; int i=1; std::vector< float > distances; while (max_d < fib->GetGeometry()->GetDiagonalLength()/2) { distances.push_back(clusterSize*i); max_d = clusterSize*i; ++i; } - itk::TractClusteringFilter::Pointer clusterer = itk::TractClusteringFilter::New(); + std::shared_ptr< mitk::TractClusteringFilter > clusterer = std::make_shared(); clusterer->SetDistances(distances); clusterer->SetTractogram(fib); if (m_Controls->m_InCentroidsBox->GetSelectedNode().IsNotNull()) { mitk::FiberBundle::Pointer in_centroids = dynamic_cast(m_Controls->m_InCentroidsBox->GetSelectedNode()->GetData()); clusterer->SetInCentroids(in_centroids); } std::vector< mitk::ClusteringMetric* > metrics; if (m_Controls->m_MetricBox1->isChecked()) { mitk::ClusteringMetricEuclideanMean* metric = new mitk::ClusteringMetricEuclideanMean(); metric->SetScale(m_Controls->m_MetricWeight1->value()); metrics.push_back(metric); } if (m_Controls->m_MetricBox2->isChecked()) { mitk::ClusteringMetricEuclideanStd* metric = new mitk::ClusteringMetricEuclideanStd(); metric->SetScale(m_Controls->m_MetricWeight2->value()); metrics.push_back(metric); } if (m_Controls->m_MetricBox3->isChecked()) { mitk::ClusteringMetricEuclideanMax* metric = new mitk::ClusteringMetricEuclideanMax(); metric->SetScale(m_Controls->m_MetricWeight3->value()); metrics.push_back(metric); } if (m_Controls->m_MetricBox6->isChecked()) { mitk::ClusteringMetricInnerAngles* metric = new mitk::ClusteringMetricInnerAngles(); metric->SetScale(m_Controls->m_MetricWeight6->value()); metrics.push_back(metric); } if (m_Controls->m_MetricBox7->isChecked()) { mitk::ClusteringMetricLength* metric = new mitk::ClusteringMetricLength(); metric->SetScale(m_Controls->m_MetricWeight7->value()); metrics.push_back(metric); } if (m_Controls->m_ParcellationBox->GetSelectedNode().IsNotNull() && m_Controls->m_MetricBox4->isChecked()) { mitk::Image::Pointer mitk_map = dynamic_cast(m_Controls->m_ParcellationBox->GetSelectedNode()->GetData()); ShortImageType::Pointer itk_map = ShortImageType::New(); mitk::CastToItkImage(mitk_map, itk_map); mitk::ClusteringMetricAnatomic* metric = new mitk::ClusteringMetricAnatomic(); metric->SetParcellations({itk_map}); metric->SetScale(m_Controls->m_MetricWeight4->value()); metrics.push_back(metric); } if (m_Controls->m_MapBox->GetSelectedNode().IsNotNull() && m_Controls->m_MetricBox5->isChecked()) { mitk::Image::Pointer mitk_map = dynamic_cast(m_Controls->m_MapBox->GetSelectedNode()->GetData()); FloatImageType::Pointer itk_map = FloatImageType::New(); mitk::CastToItkImage(mitk_map, itk_map); mitk::ClusteringMetricScalarMap* metric = new mitk::ClusteringMetricScalarMap(); metric->SetImages({itk_map}); metric->SetScale(m_Controls->m_MetricWeight5->value()); metrics.push_back(metric); } if (metrics.empty()) { QMessageBox::warning(nullptr, "Warning", "No metric selected!"); return; } clusterer->SetMetrics(metrics); clusterer->SetMergeDuplicateThreshold(m_Controls->m_MergeDuplicatesBox->value()); clusterer->SetNumPoints(m_Controls->m_FiberPointsBox->value()); clusterer->SetMaxClusters(m_Controls->m_MaxClustersBox->value()); clusterer->SetMinClusterSize(m_Controls->m_MinFibersBox->value()); clusterer->Update(); std::vector tracts = clusterer->GetOutTractograms(); std::vector centroids = clusterer->GetOutCentroids(); unsigned int c = 0; for (auto f : tracts) { mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(f); new_node->SetName("Cluster_" + boost::lexical_cast(c)); if (m_Controls->m_InCentroidsBox->GetSelectedNode().IsNotNull()) this->GetDataStorage()->Add(new_node, m_Controls->m_InCentroidsBox->GetSelectedNode()); else this->GetDataStorage()->Add(new_node, node); node->SetVisibility(false); if (m_Controls->m_CentroidsBox->isChecked()) { mitk::DataNode::Pointer new_node2 = mitk::DataNode::New(); new_node2->SetData(centroids.at(c)); new_node2->SetName("Centroid_" + boost::lexical_cast(c)); this->GetDataStorage()->Add(new_node2, new_node); } ++c; } } void QmitkFiberClusteringView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& ) { } 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 787549c..1bd48b6 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 @@ -1,1744 +1,1744 @@ QmitkFiberProcessingViewControls 0 0 385 711 Form QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; } 9 9 9 9 75 true 0 5 0 0 353 503 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 0 0 Extract using planar figures Extract using ROI image QFrame::NoFrame QFrame::Raised 0 0 0 0 6 - Interactive Extraction + 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. :/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/circle.png:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/circle.png 32 32 false true Qt::Horizontal 40 20 30 30 Draw polygonal ROI. Select reference fiber bundle to execute. :/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/polygon.png:/org.mitk.gui.qt.diffusionimaging.fiberprocessing/resources/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 0 353 456 Fiber Removal Remove fibers that satisfy certain criteria from the selected bundle. QFrame::NoFrame QFrame::Raised 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 0 Weight threshold: Only fibers with weight larger than this threshold are kept. 5 99999.000000000000000 0.100000000000000 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 Qt::Vertical 20 40 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 QFrame::NoFrame QFrame::Raised 0 0 0 0 0 6 - + Relative tract density (value between 0.0 and 1.0) 5 0.000000000000000 - 10.000000000000000 + 1.000000000000000 0.100000000000000 - 0.010000000000000 + 0.050000000000000 Density threshold: Min. overlap: Tracts have to spend at least this fraction of their length inside the specified density region. 3 1.000000000000000 0.100000000000000 0.500000000000000 0 0 353 426 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 Scalar map: If checked, the image values are not only used to color the fibers but are also used as opaxity values. Values as opacity false The values used to color the fibers are min-max normalized. If not checked, the values should be between 0 and 1. Normalize color values true If checked, the (mean) unnormalized values per fiber are also used as fiber weights, e.g. the fiber length in mm. Values as weight false 0 0 Resample fibers (spline) Resample fibers (linear) Compress fibers Mirror fibers Weight bundle Color fibers by fiber weights Color & weight fibers by curvature Color & weight fibers by length Color & weight fibers by scalar map (e.g. FA) 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 0 367 182 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
 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.cpp index 1c622f4..88a9f88 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.cpp @@ -1,461 +1,539 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 // Qmitk #include "QmitkFiberQuantificationView.h" // Qt #include // MITK #include #include #include #include #include #include #include #include #include // ITK #include #include #include #include +#include +#include #include const std::string QmitkFiberQuantificationView::VIEW_ID = "org.mitk.views.fiberquantification"; using namespace mitk; QmitkFiberQuantificationView::QmitkFiberQuantificationView() : QmitkAbstractView() , m_Controls( 0 ) , m_UpsamplingFactor(5) , m_Visible(false) { } // Destructor QmitkFiberQuantificationView::~QmitkFiberQuantificationView() { } void QmitkFiberQuantificationView::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::QmitkFiberQuantificationViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_ProcessFiberBundleButton, SIGNAL(clicked()), this, SLOT(ProcessSelectedBundles()) ); connect( m_Controls->m_ExtractFiberPeaks, SIGNAL(clicked()), this, SLOT(CalculateFiberDirections()) ); m_Controls->m_TractBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isFib = mitk::TNodePredicateDataType::New(); m_Controls->m_TractBox->SetPredicate( isFib ); m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_ImageBox->SetZeroEntryText("--"); mitk::TNodePredicateDataType::Pointer isImagePredicate = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDimension::Pointer is3D = mitk::NodePredicateDimension::New(3); m_Controls->m_ImageBox->SetPredicate( mitk::NodePredicateAnd::New(isImagePredicate, is3D) ); connect( (QObject*)(m_Controls->m_TractBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui())); connect( (QObject*)(m_Controls->m_ImageBox), SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui())); } } void QmitkFiberQuantificationView::Activated() { } void QmitkFiberQuantificationView::Deactivated() { } void QmitkFiberQuantificationView::Visible() { m_Visible = true; } void QmitkFiberQuantificationView::Hidden() { m_Visible = false; } void QmitkFiberQuantificationView::SetFocus() { m_Controls->m_ProcessFiberBundleButton->setFocus(); } void QmitkFiberQuantificationView::CalculateFiberDirections() { typedef itk::Image ItkUcharImgType; // load fiber bundle mitk::FiberBundle::Pointer inputTractogram = dynamic_cast(m_SelectedFB.back()->GetData()); itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); if (m_SelectedImage.IsNotNull()) { ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New(); mitk::CastToItkImage(m_SelectedImage, itkMaskImage); fOdfFilter->SetMaskImage(itkMaskImage); } // extract directions from fiber bundle fOdfFilter->SetFiberBundle(inputTractogram); fOdfFilter->SetAngularThreshold(cos(m_Controls->m_AngularThreshold->value()*itk::Math::pi/180)); switch (m_Controls->m_FiberDirNormBox->currentIndex()) { case 0: fOdfFilter->SetNormalizationMethod(itk::TractsToVectorImageFilter::NormalizationMethods::GLOBAL_MAX); break; case 1: fOdfFilter->SetNormalizationMethod(itk::TractsToVectorImageFilter::NormalizationMethods::SINGLE_VEC_NORM); break; case 2: fOdfFilter->SetNormalizationMethod(itk::TractsToVectorImageFilter::NormalizationMethods::MAX_VEC_NORM); break; } fOdfFilter->SetSizeThreshold(m_Controls->m_PeakThreshold->value()); fOdfFilter->SetMaxNumDirections(m_Controls->m_MaxNumDirections->value()); fOdfFilter->Update(); QString name = m_SelectedFB.back()->GetName().c_str(); if (m_Controls->m_NumDirectionsBox->isChecked()) { mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( fOdfFilter->GetNumDirectionsImage().GetPointer() ); mitkImage->SetVolume( fOdfFilter->GetNumDirectionsImage()->GetBufferPointer() ); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(mitkImage); node->SetName((name+"_NUM_DIRECTIONS").toStdString().c_str()); GetDataStorage()->Add(node, m_SelectedFB.back()); } Image::Pointer mitkImage = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(fOdfFilter->GetDirectionImage(), mitkImage); mitkImage->SetVolume(fOdfFilter->GetDirectionImage()->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(mitkImage); node->SetName( (name+"_DIRECTIONS").toStdString().c_str()); GetDataStorage()->Add(node, m_SelectedFB.back()); } void QmitkFiberQuantificationView::UpdateGui() { m_SelectedFB.clear(); if (m_Controls->m_TractBox->GetSelectedNode().IsNotNull()) m_SelectedFB.push_back(m_Controls->m_TractBox->GetSelectedNode()); m_SelectedImage = nullptr; if (m_Controls->m_ImageBox->GetSelectedNode().IsNotNull()) m_SelectedImage = dynamic_cast(m_Controls->m_ImageBox->GetSelectedNode()->GetData()); m_Controls->m_ProcessFiberBundleButton->setEnabled(!m_SelectedFB.empty()); m_Controls->m_ExtractFiberPeaks->setEnabled(!m_SelectedFB.empty()); } void QmitkFiberQuantificationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& ) { UpdateGui(); } void QmitkFiberQuantificationView::ProcessSelectedBundles() { if ( m_SelectedFB.empty() ){ QMessageBox::information( nullptr, "Warning", "No fibe bundle selected!"); MITK_WARN("QmitkFiberQuantificationView") << "no fibe bundle selected"; return; } int generationMethod = m_Controls->m_GenerationBox->currentIndex(); for( unsigned int i=0; i(node->GetData())) { mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); QString name(node->GetName().c_str()); DataNode::Pointer newNode = nullptr; switch(generationMethod){ case 0: newNode = GenerateTractDensityImage(fib, false, true, node->GetName()); name += "_TDI"; break; case 1: newNode = GenerateTractDensityImage(fib, false, false, node->GetName()); name += "_TDI"; break; case 2: newNode = GenerateTractDensityImage(fib, true, false, node->GetName()); name += "_envelope"; break; case 3: newNode = GenerateColorHeatmap(fib); break; case 4: newNode = GenerateFiberEndingsImage(fib); name += "_fiber_endings"; break; case 5: newNode = GenerateFiberEndingsPointSet(fib); name += "_fiber_endings"; break; + case 6: + newNode = GenerateDistanceMap(fib); + name += "_distance_map"; + break; + case 7: + newNode = GenerateBinarySkeleton(fib); + name += "_skeleton"; + break; } if (newNode.IsNotNull()) { newNode->SetName(name.toStdString()); GetDataStorage()->Add(newNode); } } } } // generate pointset displaying the fiber endings mitk::DataNode::Pointer QmitkFiberQuantificationView::GenerateFiberEndingsPointSet(mitk::FiberBundle::Pointer fib) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); vtkSmartPointer fiberPolyData = fib->GetFiberPolyData(); int count = 0; int numFibers = fib->GetNumFibers(); for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints>0) { double* point = points->GetPoint(0); itk::Point itkPoint = mitk::imv::GetItkPoint(point); pointSet->InsertPoint(count, itkPoint); count++; } if (numPoints>2) { double* point = points->GetPoint(numPoints-1); itk::Point itkPoint = mitk::imv::GetItkPoint(point); pointSet->InsertPoint(count, itkPoint); count++; } } mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( pointSet ); return node; } // generate image displaying the fiber endings mitk::DataNode::Pointer QmitkFiberQuantificationView::GenerateFiberEndingsImage(mitk::FiberBundle::Pointer fib) { typedef unsigned int OutPixType; typedef itk::Image OutImageType; typedef itk::TractsToFiberEndingsImageFilter< OutImageType > ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); generator->SetFiberBundle(fib); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { OutImageType::Pointer itkImage = OutImageType::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image OutImageType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } // generate rgba heatmap from fiber bundle mitk::DataNode::Pointer QmitkFiberQuantificationView::GenerateColorHeatmap(mitk::FiberBundle::Pointer fib) { typedef itk::RGBAPixel OutPixType; typedef itk::Image OutImageType; typedef itk::TractsToRgbaImageFilter< OutImageType > ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); generator->SetFiberBundle(fib); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { itk::Image::Pointer itkImage = itk::Image::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } +mitk::DataNode::Pointer QmitkFiberQuantificationView::GenerateBinarySkeleton(mitk::FiberBundle::Pointer fib) +{ + typedef itk::Image UcharImageType; + + itk::TractDensityImageFilter< UcharImageType >::Pointer envelope_generator = itk::TractDensityImageFilter< UcharImageType >::New(); + envelope_generator->SetFiberBundle(fib); + envelope_generator->SetBinaryOutput(true); + envelope_generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); + if (m_SelectedImage.IsNotNull()) + { + UcharImageType::Pointer itkImage = UcharImageType::New(); + CastToItkImage(m_SelectedImage, itkImage); + envelope_generator->SetInputImage(itkImage); + envelope_generator->SetUseImageGeometry(true); + + } + envelope_generator->Update(); + + itk::BinaryThinningImageFilter::Pointer map_generator = itk::BinaryThinningImageFilter::New(); + map_generator->SetInput(envelope_generator->GetOutput()); + map_generator->Update(); + + UcharImageType::Pointer outImg = map_generator->GetOutput(); + mitk::Image::Pointer img = mitk::Image::New(); + img->InitializeByItk(outImg.GetPointer()); + img->SetVolume(outImg->GetBufferPointer()); + + mitk::DataNode::Pointer node = mitk::DataNode::New(); + node->SetData(img); + return node; +} + +mitk::DataNode::Pointer QmitkFiberQuantificationView::GenerateDistanceMap(mitk::FiberBundle::Pointer fib) +{ + typedef itk::Image UcharImageType; + typedef itk::Image FloatImageType; + + itk::TractDensityImageFilter< UcharImageType >::Pointer envelope_generator = itk::TractDensityImageFilter< UcharImageType >::New(); + envelope_generator->SetFiberBundle(fib); + envelope_generator->SetBinaryOutput(true); + envelope_generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); + if (m_SelectedImage.IsNotNull()) + { + UcharImageType::Pointer itkImage = UcharImageType::New(); + CastToItkImage(m_SelectedImage, itkImage); + envelope_generator->SetInputImage(itkImage); + envelope_generator->SetUseImageGeometry(true); + + } + envelope_generator->Update(); + + itk::SignedMaurerDistanceMapImageFilter::Pointer map_generator = itk::SignedMaurerDistanceMapImageFilter::New(); + map_generator->SetInput(envelope_generator->GetOutput()); + map_generator->SetUseImageSpacing(true); + map_generator->SetSquaredDistance(false); + map_generator->SetInsideIsPositive(true); + map_generator->Update(); + + FloatImageType::Pointer outImg = map_generator->GetOutput(); + mitk::Image::Pointer img = mitk::Image::New(); + img->InitializeByItk(outImg.GetPointer()); + img->SetVolume(outImg->GetBufferPointer()); + + mitk::DataNode::Pointer node = mitk::DataNode::New(); + node->SetData(img); + return node; +} + // generate tract density image from fiber bundle mitk::DataNode::Pointer QmitkFiberQuantificationView::GenerateTractDensityImage(mitk::FiberBundle::Pointer fib, bool binary, bool absolute, std::string name) { mitk::DataNode::Pointer node = mitk::DataNode::New(); if (binary) { typedef unsigned char OutPixType; typedef itk::Image OutImageType; itk::TractDensityImageFilter< OutImageType >::Pointer generator = itk::TractDensityImageFilter< OutImageType >::New(); generator->SetFiberBundle(fib); generator->SetBinaryOutput(binary); generator->SetOutputAbsoluteValues(absolute); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { OutImageType::Pointer itkImage = OutImageType::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); if (m_SelectedImage.IsNotNull()) { mitk::LabelSetImage::Pointer multilabelImage = mitk::LabelSetImage::New(); multilabelImage->InitializeByLabeledImage(img); multilabelImage->GetActiveLabelSet()->SetActiveLabel(1); mitk::Label::Pointer label = multilabelImage->GetActiveLabel(); label->SetName("Tractogram"); // Add Segmented Property Category Code Sequence tags (0062, 0003): Sequence defining the general category of this // segment. // (0008,0100) Code Value label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_VALUE_PATH()).c_str(), TemporoSpatialStringProperty::New("T-D000A")); // (0008,0102) Coding Scheme Designator label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_SCHEME_PATH()).c_str(), TemporoSpatialStringProperty::New("SRT")); // (0008,0104) Code Meaning label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_CATEGORY_CODE_MEANING_PATH()).c_str(), TemporoSpatialStringProperty::New("Anatomical Structure")); //------------------------------------------------------------ // Add Segmented Property Type Code Sequence (0062, 000F): Sequence defining the specific property type of this // segment. // (0008,0100) Code Value label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_VALUE_PATH()).c_str(), TemporoSpatialStringProperty::New("DUMMY")); // (0008,0102) Coding Scheme Designator label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_SCHEME_PATH()).c_str(), TemporoSpatialStringProperty::New("SRT")); // (0008,0104) Code Meaning label->SetProperty( DICOMTagPathToPropertyName(DICOMSegmentationConstants::SEGMENT_TYPE_CODE_MEANING_PATH()).c_str(), TemporoSpatialStringProperty::New(name)); //Error: is undeclared// mitk::DICOMQIPropertyHandler::DeriveDICOMSourceProperties(m_SelectedImage, multilabelImage); // init data node node->SetData(multilabelImage); } else { // init data node node->SetData(img); } } else { typedef float OutPixType; typedef itk::Image OutImageType; itk::TractDensityImageFilter< OutImageType >::Pointer generator = itk::TractDensityImageFilter< OutImageType >::New(); generator->SetFiberBundle(fib); generator->SetBinaryOutput(binary); generator->SetOutputAbsoluteValues(absolute); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { OutImageType::Pointer itkImage = OutImageType::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } //generator->SetDoFiberResampling(false); generator->Update(); // get output image typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node node->SetData(img); } return node; } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.h index 5fb5380..bb3d808 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.h @@ -1,86 +1,89 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 QmitkFiberQuantificationView_h #define QmitkFiberQuantificationView_h #include #include "ui_QmitkFiberQuantificationViewControls.h" #include #include #include #include /*! \brief Generation of images from fiber bundles (TDI, envelopes, endpoint distribution) and extraction of principal fiber directions from tractograms. */ class QmitkFiberQuantificationView : public QmitkAbstractView, public mitk::ILifecycleAwarePart { // 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; static const std::string VIEW_ID; QmitkFiberQuantificationView(); virtual ~QmitkFiberQuantificationView(); virtual void CreateQtPartControl(QWidget *parent) override; /// /// Sets the focus to an internal widget. /// virtual void SetFocus() override; virtual void Activated() override; virtual void Deactivated() override; virtual void Visible() override; virtual void Hidden() override; protected slots: void ProcessSelectedBundles(); ///< start selected operation on fiber bundle (e.g. tract density image generation) void CalculateFiberDirections(); ///< Calculate main fiber directions from tractogram void UpdateGui(); ///< update button activity etc. dpending on current datamanager selection protected: /// \brief called by QmitkAbstractView when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; Ui::QmitkFiberQuantificationViewControls* m_Controls; std::vector m_SelectedFB; ///< selected fiber bundle nodes mitk::Image::Pointer m_SelectedImage; float m_UpsamplingFactor; ///< upsampling factor for all image generations mitk::DataNode::Pointer GenerateTractDensityImage(mitk::FiberBundle::Pointer fib, bool binary, bool absolute, std::string name); mitk::DataNode::Pointer GenerateColorHeatmap(mitk::FiberBundle::Pointer fib); mitk::DataNode::Pointer GenerateFiberEndingsImage(mitk::FiberBundle::Pointer fib); mitk::DataNode::Pointer GenerateFiberEndingsPointSet(mitk::FiberBundle::Pointer fib); + mitk::DataNode::Pointer GenerateDistanceMap(mitk::FiberBundle::Pointer fib); + mitk::DataNode::Pointer GenerateBinarySkeleton(mitk::FiberBundle::Pointer fib); + bool m_Visible; }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationViewControls.ui index a2cd044..c427969 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationViewControls.ui @@ -1,420 +1,430 @@ - + QmitkFiberQuantificationViewControls 0 0 365 581 Form QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; } 25 Fiber-derived images 6 6 6 6 false 0 0 200 16777215 11 Perform selected operation on all selected fiber bundles. Generate Image 0 0 Upsampling factor 1 0.100000000000000 10.000000000000000 0.100000000000000 1.000000000000000 0 0 Tract Density Image (TDI) Normalized TDI Binary Envelope Fiber Bundle Image Fiber Endings Image Fiber Endings Pointset + + + Distance Map + + + + + Binary Skeleton + + Principal Fiber Directions 6 6 6 6 QFrame::NoFrame QFrame::Raised 0 0 0 0 0 0 Fiber directions with an angle smaller than the defined threshold are clustered. 2 0.000000000000000 90.000000000000000 1.000000000000000 30.000000000000000 0 0 <html><head/><body><p>Directions shorter than the defined threshold are discarded.</p></body></html> 3 1.000000000000000 0.100000000000000 0.300000000000000 Angular Threshold: Max. Peaks: Size Threshold: 0 0 Maximum number of fiber directions per voxel. 100 3 Normalization: 0 0 0 Global maximum Single vector Voxel-wise maximum 0 0 Image containing the number of distinct fiber clusters per voxel. Output #Directions per Voxel false false Generate Directions Input Data 6 6 6 6 - + - + Tractogram: Reference Image: Qt::Vertical 20 40 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/QmitkTractometryView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.cpp index 7b5988e..ff92686 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.cpp @@ -1,352 +1,598 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 "QmitkTractometryView.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include +#include +#include +#include const std::string QmitkTractometryView::VIEW_ID = "org.mitk.views.tractometry"; using namespace mitk; QmitkTractometryView::QmitkTractometryView() : QmitkAbstractView() , m_Controls( nullptr ) , m_Visible(false) { } // Destructor QmitkTractometryView::~QmitkTractometryView() { } void QmitkTractometryView::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::QmitkTractometryViewControls; m_Controls->setupUi( parent ); - connect( m_Controls->m_SamplingPointsBox, SIGNAL(valueChanged(int)), this, SLOT(UpdateGui()) ); - connect( m_Controls->m_StDevBox, SIGNAL(stateChanged(int)), this, SLOT(UpdateGui()) ); + connect( m_Controls->m_MethodBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()) ); + connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(StartTractometry()) ); mitk::TNodePredicateDataType::Pointer imageP = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDimension::Pointer dimP = mitk::NodePredicateDimension::New(3); m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_ImageBox->SetPredicate(mitk::NodePredicateAnd::New(imageP, dimP)); m_Controls->m_ChartWidget->SetTheme(GetColorTheme()); m_Controls->m_ChartWidget->SetXAxisLabel("Tract position"); m_Controls->m_ChartWidget->SetYAxisLabel("Image Value"); } } ::QmitkChartWidget::ColorTheme QmitkTractometryView::GetColorTheme() { berry::IPreferencesService* prefService = berry::WorkbenchPlugin::GetDefault()->GetPreferencesService(); berry::IPreferences::Pointer m_StylePref = prefService->GetSystemPreferences()->Node(berry::QtPreferences::QT_STYLES_NODE); QString styleName = m_StylePref->Get(berry::QtPreferences::QT_STYLE_NAME, ""); if (styleName == ":/org.blueberry.ui.qt/darkstyle.qss") { return QmitkChartWidget::ColorTheme::darkstyle; } else { return QmitkChartWidget::ColorTheme::lightstyle; } } void QmitkTractometryView::SetFocus() { } void QmitkTractometryView::UpdateGui() { berry::IWorkbenchPart::Pointer nullPart; OnSelectionChanged(nullPart, QList(m_CurrentSelection)); } bool QmitkTractometryView::Flip(vtkSmartPointer< vtkPolyData > polydata1, int i, vtkSmartPointer< vtkPolyData > ref_poly) { double d_direct = 0; double d_flipped = 0; vtkCell* cell1 = polydata1->GetCell(0); if (ref_poly!=nullptr) cell1 = ref_poly->GetCell(0); auto numPoints1 = cell1->GetNumberOfPoints(); vtkPoints* points1 = cell1->GetPoints(); std::vector> ref_points; for (int j=0; jGetPoint(j); itk::Point itk_p; itk_p[0] = p1[0]; itk_p[1] = p1[1]; itk_p[2] = p1[2]; ref_points.push_back(itk_p); } vtkCell* cell2 = polydata1->GetCell(i); vtkPoints* points2 = cell2->GetPoints(); for (int j=0; jGetPoint(j); d_direct = (p1[0]-p2[0])*(p1[0]-p2[0]) + (p1[1]-p2[1])*(p1[1]-p2[1]) + (p1[2]-p2[2])*(p1[2]-p2[2]); double* p3 = points2->GetPoint(numPoints1-j-1); d_flipped = (p1[0]-p3[0])*(p1[0]-p3[0]) + (p1[1]-p3[1])*(p1[1]-p3[1]) + (p1[2]-p3[2])*(p1[2]-p3[2]); } if (d_direct>d_flipped) return true; return false; } template -void QmitkTractometryView::ImageValuesAlongTract(const mitk::PixelType, mitk::Image::Pointer image, mitk::FiberBundle::Pointer fib, std::vector > &data, std::string& clipboard_string) +void QmitkTractometryView::StaticResamplingTractometry(const mitk::PixelType, mitk::Image::Pointer image, mitk::DataNode::Pointer node, std::vector > &data, std::string& clipboard_string) { + mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); + unsigned int num_points = m_Controls->m_SamplingPointsBox->value(); mitk::ImagePixelReadAccessor readimage(image, image->GetVolumeData(0)); mitk::FiberBundle::Pointer working_fib = fib->GetDeepCopy(); working_fib->ResampleToNumPoints(num_points); vtkSmartPointer< vtkPolyData > polydata = working_fib->GetFiberPolyData(); + double rgb[3] = {0,0,0}; + + mitk::LookupTable::Pointer lookupTable = mitk::LookupTable::New(); + lookupTable->SetType(mitk::LookupTable::MULTILABEL); + std::vector > all_values; std::vector< double > mean_values; for (unsigned int i=0; iGetNumFibers(); ++i) { vtkCell* cell = polydata->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); std::vector< double > fib_vals; bool flip = false; if (i>0) flip = Flip(polydata, i); else if (m_ReferencePolyData!=nullptr) flip = Flip(polydata, 0, m_ReferencePolyData); for (int j=0; jGetTableValue(j, rgb); + double* p; if (flip) - p = points->GetPoint(numPoints - j - 1); + { + auto p_idx = numPoints - j - 1; + p = points->GetPoint(p_idx); + + working_fib->ColorSinglePoint(i, p_idx, rgb); + } else + { p = points->GetPoint(j); + working_fib->ColorSinglePoint(i, j, rgb); + } + Point3D px; px[0] = p[0]; px[1] = p[1]; px[2] = p[2]; double pixelValue = static_cast(readimage.GetPixelByWorldCoordinates(px)); fib_vals.push_back(pixelValue); mean += pixelValue; if (pixelValuemax) max = pixelValue; mean_values.at(j) += pixelValue; + } all_values.push_back(fib_vals); } if (m_ReferencePolyData==nullptr) m_ReferencePolyData = polydata; std::vector< double > std_values1; std::vector< double > std_values2; for (unsigned int i=0; iGetNumFibers(); double stdev = 0; for (unsigned int j=0; j(mean_values.at(i)); clipboard_string += " "; clipboard_string += boost::lexical_cast(stdev); clipboard_string += "\n"; } clipboard_string += "\n"; data.push_back(mean_values); data.push_back(std_values1); data.push_back(std_values2); MITK_INFO << "Min: " << min; MITK_INFO << "Max: " << max; MITK_INFO << "Mean: " << mean/working_fib->GetNumberOfPoints(); + + if (m_Controls->m_ShowBinned->isChecked()) + { + mitk::DataNode::Pointer new_node = mitk::DataNode::New(); + auto children = GetDataStorage()->GetDerivations(node); + for (unsigned int i=0; isize(); ++i) + { + if (children->at(i)->GetName() == "binned_static") + { + new_node = children->at(i); + new_node->SetData(working_fib); + new_node->SetVisibility(true); + node->SetVisibility(false); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + return; + } + } + + new_node->SetData(working_fib); + new_node->SetName("binned_static"); + new_node->SetVisibility(true); + node->SetVisibility(false); + GetDataStorage()->Add(new_node, node); + } +} + +template +void QmitkTractometryView::NearestCentroidPointTractometry(const mitk::PixelType, mitk::Image::Pointer image, mitk::DataNode::Pointer node, std::vector< std::vector< double > >& data, std::string& clipboard_string) +{ + mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); + + unsigned int num_points = m_Controls->m_SamplingPointsBox->value(); + mitk::ImagePixelReadAccessor readimage(image, image->GetVolumeData(0)); + mitk::FiberBundle::Pointer working_fib = fib->GetDeepCopy(); + working_fib->ResampleSpline(1.0); + vtkSmartPointer< vtkPolyData > working_polydata = working_fib->GetFiberPolyData(); + + // clustering + std::vector< mitk::ClusteringMetric* > metrics; + metrics.push_back({new mitk::ClusteringMetricEuclideanStd()}); + + mitk::FiberBundle::Pointer fib_static_resampled = fib->GetDeepCopy(); + fib_static_resampled->ResampleToNumPoints(num_points); + vtkSmartPointer< vtkPolyData > polydata_static_resampled = fib_static_resampled->GetFiberPolyData(); + + std::vector centroids; + std::shared_ptr< mitk::TractClusteringFilter > clusterer = std::make_shared(); + int c=0; + while (c<30 && (centroids.empty() || centroids.size()>static_cast(m_Controls->m_MaxCentroids->value()))) + { + float cluster_size = m_Controls->m_ClusterSize->value() + m_Controls->m_ClusterSize->value()*c*0.2; + float max_d = 0; + int i=1; + std::vector< float > distances; + while (max_d < working_fib->GetGeometry()->GetDiagonalLength()/2) + { + distances.push_back(cluster_size*i); + max_d = cluster_size*i; + ++i; + } + + clusterer->SetDistances(distances); + clusterer->SetTractogram(fib_static_resampled); + clusterer->SetMetrics(metrics); + clusterer->SetMergeDuplicateThreshold(cluster_size); + clusterer->SetDoResampling(false); + clusterer->SetNumPoints(num_points); + // clusterer->SetMaxClusters(m_Controls->m_MaxCentroids->value()); + clusterer->SetMinClusterSize(1); + clusterer->Update(); + centroids = clusterer->GetOutCentroids(); + ++c; + } + + double rgb[3] = {0,0,0}; + mitk::LookupTable::Pointer lookupTable = mitk::LookupTable::New(); + lookupTable->SetType(mitk::LookupTable::MULTILABEL); + + std::vector > all_values; + std::vector< double > mean_values; + std::vector< unsigned int > value_count; + for (unsigned int i=0; iGetNumFibers(); ++i) + { + vtkCell* cell = working_polydata->GetCell(i); + auto numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + + std::vector< double > fib_vals; + for (int j=0; jGetPoint(j); + + int min_bin = 0; + float d=999999; + for (auto centroid : centroids) + { + auto centroid_polydata = centroid->GetFiberPolyData(); + + vtkCell* centroid_cell = centroid_polydata->GetCell(0); + auto centroid_numPoints = centroid_cell->GetNumberOfPoints(); + vtkPoints* centroid_points = centroid_cell->GetPoints(); + + bool centroid_flip = Flip(centroid_polydata, 0, centroids.at(0)->GetFiberPolyData()); + + for (int bin=0; binGetPoint(bin); + float temp_d = std::sqrt((p[0]-centroid_p[0])*(p[0]-centroid_p[0]) + (p[1]-centroid_p[1])*(p[1]-centroid_p[1]) + (p[2]-centroid_p[2])*(p[2]-centroid_p[2])); + if (temp_dGetTableValue(min_bin, rgb); + working_fib->ColorSinglePoint(i, j, rgb); + + Point3D px; + px[0] = p[0]; + px[1] = p[1]; + px[2] = p[2]; + double pixelValue = static_cast(readimage.GetPixelByWorldCoordinates(px)); + fib_vals.push_back(pixelValue); + mean += pixelValue; + if (pixelValuemax) + max = pixelValue; + + mean_values.at(min_bin) += pixelValue; + value_count.at(min_bin) += 1; + } + + all_values.push_back(fib_vals); + } + + if (m_ReferencePolyData==nullptr) + m_ReferencePolyData = working_polydata; + + std::vector< double > std_values1; + std::vector< double > std_values2; + for (unsigned int i=0; i(mean_values.at(i)); + clipboard_string += " "; + clipboard_string += boost::lexical_cast(stdev); + clipboard_string += "\n"; + } + clipboard_string += "\n"; + + data.push_back(mean_values); + data.push_back(std_values1); + data.push_back(std_values2); + + MITK_INFO << "Min: " << min; + MITK_INFO << "Max: " << max; + MITK_INFO << "Mean: " << mean/working_fib->GetNumberOfPoints(); + + if (m_Controls->m_ShowBinned->isChecked()) + { + mitk::DataNode::Pointer new_node = mitk::DataNode::New(); +// mitk::DataNode::Pointer new_node2; + auto children = GetDataStorage()->GetDerivations(node); + for (unsigned int i=0; isize(); ++i) + { + if (children->at(i)->GetName() == "binned_centroid") + { + new_node = children->at(i); + new_node->SetData(working_fib); + new_node->SetVisibility(true); + node->SetVisibility(false); + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + return; + } + } + new_node->SetData(working_fib); + new_node->SetName("binned_centroid"); + new_node->SetVisibility(true); + node->SetVisibility(false); + GetDataStorage()->Add(new_node, node); + } } void QmitkTractometryView::Activated() { } void QmitkTractometryView::Deactivated() { } void QmitkTractometryView::Visible() { m_Visible = true; QList selection = GetDataManagerSelection(); berry::IWorkbenchPart::Pointer nullPart; OnSelectionChanged(nullPart, selection); } void QmitkTractometryView::Hidden() { m_Visible = false; } std::string QmitkTractometryView::RGBToHexString(double *rgb) { std::ostringstream os; for (int i = 0; i < 3; ++i) { os << std::setw(2) << std::setfill('0') << std::hex << static_cast(rgb[i] * 255); } return os.str(); } -void QmitkTractometryView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& nodes) +void QmitkTractometryView::StartTractometry() { - if (!m_Visible) - return; - - m_CurrentSelection.clear(); - if(m_Controls->m_ImageBox->GetSelectedNode().IsNull()) - return; - - std::string clipboardString = ""; m_ReferencePolyData = nullptr; - mitk::Image::Pointer image = dynamic_cast(m_Controls->m_ImageBox->GetSelectedNode()->GetData()); vtkSmartPointer lookupTable = vtkSmartPointer::New(); lookupTable->SetTableRange(0.0, 1.0); lookupTable->Build(); - int num_tracts = 0; - for (auto node: nodes) - if ( dynamic_cast(node->GetData()) ) - num_tracts++; + mitk::Image::Pointer image = dynamic_cast(m_Controls->m_ImageBox->GetSelectedNode()->GetData()); - int c = 1; this->m_Controls->m_ChartWidget->Clear(); - for (auto node: nodes) + std::string clipboardString = ""; + int c = 1; + for (auto node : m_CurrentSelection) { - if ( dynamic_cast(node->GetData()) ) - { - clipboardString += node->GetName() + "\n"; - clipboardString += "mean stdev\n"; - mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); - m_CurrentSelection.push_back(node); + clipboardString += node->GetName() + "\n"; + clipboardString += "mean stdev\n"; - std::vector< std::vector< double > > data; - mitkPixelTypeMultiplex4( ImageValuesAlongTract, image->GetPixelType(), image, fib, data, clipboardString ); - - m_Controls->m_ChartWidget->AddData1D(data.at(0), node->GetName() + " Mean", QmitkChartWidget::ChartType::line); - if (m_Controls->m_StDevBox->isChecked()) - { - this->m_Controls->m_ChartWidget->AddData1D(data.at(1), node->GetName() + " +STDEV", QmitkChartWidget::ChartType::line); - this->m_Controls->m_ChartWidget->AddData1D(data.at(2), node->GetName() + " -STDEV", QmitkChartWidget::ChartType::line); - } + std::vector< std::vector< double > > data; + if (m_Controls->m_MethodBox->currentIndex()==0) + { + mitkPixelTypeMultiplex4( StaticResamplingTractometry, image->GetPixelType(), image, node, data, clipboardString ); + } + else + { + mitkPixelTypeMultiplex4( NearestCentroidPointTractometry, image->GetPixelType(), image, node, data, clipboardString ); + } - double color[3]; - if (num_tracts>1) - { - float scalar_color = ( (float)c/num_tracts - 1.0/num_tracts )/(1.0-1.0/num_tracts); - lookupTable->GetColor(1.0 - scalar_color, color); - } - else - lookupTable->GetColor(0, color); + m_Controls->m_ChartWidget->AddData1D(data.at(0), node->GetName() + " Mean", QmitkChartWidget::ChartType::line); + if (m_Controls->m_StDevBox->isChecked()) + { + this->m_Controls->m_ChartWidget->AddData1D(data.at(1), node->GetName() + " +STDEV", QmitkChartWidget::ChartType::line); + this->m_Controls->m_ChartWidget->AddData1D(data.at(2), node->GetName() + " -STDEV", QmitkChartWidget::ChartType::line); + } - this->m_Controls->m_ChartWidget->SetColor(node->GetName() + " Mean", RGBToHexString(color)); + double color[3]; + if (m_CurrentSelection.size()>1) + { + float scalar_color = ( (float)c/m_CurrentSelection.size() - 1.0/m_CurrentSelection.size() )/(1.0-1.0/m_CurrentSelection.size()); + lookupTable->GetColor(1.0 - scalar_color, color); + } + else + lookupTable->GetColor(0, color); - if (m_Controls->m_StDevBox->isChecked()) - { - color[0] *= 0.5; - color[1] *= 0.5; - color[2] *= 0.5; - this->m_Controls->m_ChartWidget->SetColor(node->GetName() + " +STDEV", RGBToHexString(color)); - this->m_Controls->m_ChartWidget->SetColor(node->GetName() + " -STDEV", RGBToHexString(color)); - } + this->m_Controls->m_ChartWidget->SetColor(node->GetName() + " Mean", RGBToHexString(color)); - this->m_Controls->m_ChartWidget->Show(true); - this->m_Controls->m_ChartWidget->SetShowDataPoints(false); - ++c; + if (m_Controls->m_StDevBox->isChecked()) + { + color[0] *= 0.5; + color[1] *= 0.5; + color[2] *= 0.5; + this->m_Controls->m_ChartWidget->SetColor(node->GetName() + " +STDEV", RGBToHexString(color)); + this->m_Controls->m_ChartWidget->SetColor(node->GetName() + " -STDEV", RGBToHexString(color)); } + + this->m_Controls->m_ChartWidget->Show(true); + this->m_Controls->m_ChartWidget->SetShowDataPoints(false); + ++c; } QApplication::clipboard()->setText(clipboardString.c_str(), QClipboard::Clipboard); +} +void QmitkTractometryView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& nodes) +{ + m_Controls->m_StartButton->setEnabled(false); + + if (!m_Visible) + return; + + if (m_Controls->m_MethodBox->currentIndex()==0) + m_Controls->m_ClusterFrame->setVisible(false); + else + m_Controls->m_ClusterFrame->setVisible(true); + + m_CurrentSelection.clear(); + if(m_Controls->m_ImageBox->GetSelectedNode().IsNull()) + return; + + for (auto node: nodes) + if ( dynamic_cast(node->GetData()) ) + m_CurrentSelection.push_back(node); + if (!m_CurrentSelection.empty()) + m_Controls->m_StartButton->setEnabled(true); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.h b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.h index 27ac1a0..d8939fb 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryView.h @@ -1,81 +1,85 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center. 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 QmitkTractometryView_h #define QmitkTractometryView_h #include #include "ui_QmitkTractometryViewControls.h" #include #include #include #include #include #include /*! \brief Weight fibers by linearly fitting them to the image data. */ class QmitkTractometryView : public QmitkAbstractView, public mitk::ILifecycleAwarePart { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; QmitkTractometryView(); virtual ~QmitkTractometryView(); virtual void CreateQtPartControl(QWidget *parent) override; template - void ImageValuesAlongTract(const mitk::PixelType, mitk::Image::Pointer image, mitk::FiberBundle::Pointer fib, std::vector< std::vector< double > >& data, std::string& clipboard_string); + void StaticResamplingTractometry(const mitk::PixelType, mitk::Image::Pointer image, mitk::DataNode::Pointer node, std::vector< std::vector< double > >& data, std::string& clipboard_string); + + template + void NearestCentroidPointTractometry(const mitk::PixelType, mitk::Image::Pointer image, mitk::DataNode::Pointer node, std::vector< std::vector< double > >& data, std::string& clipboard_string); virtual void SetFocus() override; virtual void Activated() override; virtual void Deactivated() override; virtual void Visible() override; virtual void Hidden() override; protected slots: void UpdateGui(); + void StartTractometry(); protected: /// \brief called by QmitkAbstractView when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; QmitkChartWidget::ColorTheme GetColorTheme(); Ui::QmitkTractometryViewControls* m_Controls; bool Flip(vtkSmartPointer< vtkPolyData > polydata1, int i, vtkSmartPointer ref_poly=nullptr); std::string RGBToHexString(double *rgb); vtkSmartPointer< vtkPolyData > m_ReferencePolyData; QList m_CurrentSelection; bool m_Visible; }; #endif // _QMITKFIBERTRACKINGVIEW_H_INCLUDED diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryViewControls.ui index ed26c90..5123bbe 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkTractometryViewControls.ui @@ -1,136 +1,217 @@ QmitkTractometryViewControls 0 0 484 - 574 + 744 Form QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; } + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + Show STDEV + + + true + + + + + + + Show binned tract + + + true + + + + + + + + 0 + 600 + + + + + + + + Centroid Options + + + + + + Cluster Size: + + + + + + + Max. Number of Centroids: + + + + + + + 1 + + + 99 + + + 1 + + + + + + + 15.000000000000000 + + + + + + QFrame::NoFrame QFrame::Raised 0 0 0 0 6 - - - - Input Image: - - - - + 3 99999 20 - + + + + Input Image: + + + + Sampling Points: + + + + + Static Resampling + + + + + Centroid Based + + + + + + + + Binning Method: + + + - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - - 0 - 600 - - - - - + - Show STDEV - - - true + Start Tractometry QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkChartWidget QWidget
QmitkChartWidget.h
 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui index 66f5d48..89eedb8 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingViewControls.ui @@ -1,1652 +1,1652 @@ QmitkStreamlineTrackingViewControls 0 0 453 859 0 0 QmitkTemplate QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; } 3 3 0 40 QFrame::NoFrame QFrame::Raised 0 15 0 0 6 15 true 0 0 true QFrame::NoFrame QFrame::Raised 0 0 0 0 0 true Save parameters to json file Save Parameters :/QmitkTractography/download.png:/QmitkTractography/download.png true Load parameters from json file Load Parameters :/QmitkTractography/upload.png:/QmitkTractography/upload.png false Start Tractography :/QmitkTractography/right.png:/QmitkTractography/right.png true Stop tractography and return all fibers reconstructed until now. Stop Tractography :/QmitkTractography/stop.png:/QmitkTractography/stop.png QFrame::NoFrame QFrame::Raised 0 0 0 0 Input Image. ODF, tensor and peak images are currently supported. Input Image: Input Image. ODF, tensor, peak, and, in case of ML tractography, raw diffusion-weighted images are currently supported. <html><head/><body><p><span style=" color:#ff0000;">select image in data-manager</span></p></body></html> true Tractography Forest: 0 0 0 0 75 true 0 0 0 421 254 Seeding Specify how, where and how many tractography seed points are placed. QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 Number of seed points equally distributed around selected position. 1 9999999 50 Radius: Seedpoints are equally distributed within a sphere centered at the selected position with the specified radius (in mm). 2 50.000000000000000 0.100000000000000 2.000000000000000 Num. Seeds: true When checked, parameter changes cause instant retracking while in interactive mode. Update on Parameter Change true QFrame::NoFrame QFrame::Raised 0 0 0 0 Try each seed N times until a valid streamline is obtained (only for probabilistic tractography). Minimum fiber length (in mm) 1 999 10 Trials Per Seed: Max. Num. Fibers: Tractography is stopped after the desired number of fibers is reached, even before all seed points are processed (-1 means no limit). -1 999999999 -1 QFrame::NoFrame QFrame::Raised 0 0 0 0 Seeds per Voxel: Seed Image: Number of seed points placed in each voxel. 1 9999999 true Dynamically pick a seed location by click into image. Enable Interactive Tractography Qt::Vertical 20 40 0 0 435 - 184 + 181 ROI Constraints Specify various ROI and mask images to constrain the tractography process. Mask Image: Select which fibers should be accepted or rejected based on the location of their endpoints. QComboBox::AdjustToMinimumContentsLength No Constraints on EP locations Both EPs in Target Image Both EPs in Target Image But Different Label One EP in Seed Image and One EP in Target Image At Least One EP in Target Image Exactly One EP in Target Image No EP in Target Image Endpoint Constraints: Stop ROI Image: Exclusion ROI Image: Target ROI Image: Qt::Vertical 20 40 0 - 0 + -191 421 428 Tractography Parameters Specify the behavior of the tractography at each streamline integration step (step size, deterministic/probabilistic, ...). Minimum tract length in mm. Shorter fibers are discarded. Minimum fiber length (in mm) 1 999.000000000000000 1.000000000000000 20.000000000000000 f parameter of tensor tractography. f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!). f: f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!). 2 1.000000000000000 0.100000000000000 0.000000000000000 Sharpen ODFs: Fix Random Seed: - Maximum allowed angular SDTEV over 4 voxel lengths. Default: no loop check. + Maximum allowed angular SDTEV over 4 voxel lengths. Default: 30° -1 180 - -1 + 30 Angular Threshold: Max. Tract Length: Cutoff: If you are using dODF images as input, it is advisable to sharpen the ODFs (min-max normalize and raise to the power of 4). This is not necessary for CSD fODFs, since they are naturally much sharper. Angular threshold between two steps (in degree). Default: 90° * step_size -1 90 1 -1 Qt::Vertical 20 40 f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!). 2 1.000000000000000 0.100000000000000 1.000000000000000 Toggle between deterministic and probabilistic tractography. Some modes might not be available for all types of tractography. Deterministic Probabilistic Mode: Additional threshold on the ODF magnitude. This is useful in case of CSD fODF tractography. For fODFs a good default value is 0.1, for normalized dODFs, e.g. Q-ball ODFs, this threshold should be very low (0.00025) or 0. 5 1.000000000000000 0.100000000000000 0.000250000000000 Min. Tract Length: FA/GFA Image: Loop Check: Minimum tract length in mm. Shorter fibers are discarded. Maximum fiber length (in mm) 1 999.000000000000000 1.000000000000000 400.000000000000000 Always produce the same random numbers. Step Size: ODF Cutoff: Step size (in voxels) 2 0.010000000000000 10.000000000000000 0.100000000000000 0.500000000000000 g: Threshold on peak magnitude, FA, GFA, ... 5 1.000000000000000 0.100000000000000 0.100000000000000 Peak Jitter: Important for probabilistic peak tractography and peak prior. Actual jitter is drawn from a normal distribution with peak_jitter*fabs(direction_value) as standard deviation. 3 1.000000000000000 0.100000000000000 0.010000000000000 0 0 435 - 184 + 181 Tractography Prior Weight: Weighting factor between prior and data. 1.000000000000000 0.100000000000000 0.500000000000000 Peak Image: Qt::Vertical 20 40 If unchecked, the prior cannot create directions where there are none in the data. true New Directions from Prior: Restrict to Prior: Restrict tractography to regions where the prior is valid. true QFrame::NoFrame QFrame::Raised 0 0 0 0 0 y x z Flip Directions: 0 0 435 - 184 + 181 Neighborhood Sampling Specify if and how information about the current streamline neighborhood should be used. Only neighborhood samples in front of the current streamline position are considered. Use Only Frontal Samples false If checked, the majority of sampling points has to place a stop-vote for the streamline to terminate. If not checked, all sampling positions have to vote for a streamline termination. Use Stop-Votes false QFrame::NoFrame QFrame::Raised 0 0 0 0 Num. Samples: Number of neighborhood samples that are used to determine the next fiber progression direction. 50 Sampling Distance: Sampling distance (in voxels) 2 10.000000000000000 0.100000000000000 0.250000000000000 Qt::Vertical 20 40 0 0 435 - 184 + 181 Data Handling Specify interpolation and direction flips. QFrame::NoFrame QFrame::Raised 0 0 0 0 Trilinearly interpolate the input image used for tractography. Interpolate Tractography Data true Trilinearly interpolate the ROI images used to constrain the tractography. Interpolate ROI Images true QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 Internally flips progression directions. This might be necessary depending on the input data. x Internally flips progression directions. This might be necessary depending on the input data. y Internally flips progression directions. This might be necessary depending on the input data. z Flip directions: Qt::Vertical 20 40 0 0 435 - 184 + 181 Output and Postprocessing Specify the tractography output (streamlines or probability maps) and postprocessing steps. Qt::Vertical 20 40 Compress fibers using the specified error constraint. Compress Fibers true Output map with voxel-wise visitation counts instead of streamlines. Output Probability Map false QmitkSingleNodeSelectionWidget QWidget
QmitkSingleNodeSelectionWidget.h
1