diff --git a/Modules/DiffusionCmdApps/Misc/CMakeLists.txt b/Modules/DiffusionCmdApps/Misc/CMakeLists.txt index d4746a8..886bdfa 100644 --- a/Modules/DiffusionCmdApps/Misc/CMakeLists.txt +++ b/Modules/DiffusionCmdApps/Misc/CMakeLists.txt @@ -1,48 +1,49 @@ option(BUILD_DiffusionMiscCmdApps "Build miscellaneous commandline tools for diffusion" OFF) if(BUILD_DiffusionMiscCmdApps OR MITK_BUILD_ALL_APPS) # needed include directories include_directories( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ) # list of diffusion cmdapps # if an app requires additional dependencies # they are added after a "^^" and separated by "_" set( diffusionMisccmdapps PeakExtraction^^ FileFormatConverter^^ FlipPeaks^^ ImageResampler^^ CopyGeometry^^ Registration^^ DiffusionDICOMLoader^^ ResampleGradients^^ ShToOdfImage^^ DImp^^ DReg^^ HeadMotionCorrection^^ DmriDenoising^^MitkImageDenoising RoundBvalues^^ + FiberScreenshot^^ ) foreach(diffusionMisccmdapp ${diffusionMisccmdapps}) # extract cmd app name and dependencies string(REPLACE "^^" "\\;" cmdapp_info ${diffusionMisccmdapp}) set(cmdapp_info_list ${cmdapp_info}) list(GET cmdapp_info_list 0 appname) list(GET cmdapp_info_list 1 raw_dependencies) string(REPLACE "_" "\\;" dependencies "${raw_dependencies}") set(dependencies_list ${dependencies}) mitkFunctionCreateCommandLineApp( NAME ${appname} - DEPENDS MitkDiffusionCmdApps ${dependencies_list} + DEPENDS MitkDiffusionCmdApps MitkTestingHelper ${dependencies_list} PACKAGE_DEPENDS ) endforeach() endif() diff --git a/Modules/DiffusionCmdApps/Misc/FiberScreenshot.cpp b/Modules/DiffusionCmdApps/Misc/FiberScreenshot.cpp new file mode 100644 index 0000000..df5a813 --- /dev/null +++ b/Modules/DiffusionCmdApps/Misc/FiberScreenshot.cpp @@ -0,0 +1,130 @@ +/*=================================================================== + +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 "mitkDiffusionCommandLineParser.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include + + +/*! +\brief Modify input tractogram: fiber resampling, compression, pruning and transformation. +*/ +int main(int argc, char* argv[]) +{ + mitkDiffusionCommandLineParser parser; + + parser.setTitle("Fiber Screenshot"); + parser.setDescription("Take a screenshot of the loaded fiber bundle"); + parser.setContributor("MIC"); + + parser.setArgumentPrefix("--", "-"); + + parser.beginGroup("1. Mandatory arguments:"); + parser.addArgument("", "i", mitkDiffusionCommandLineParser::StringList, "Input:", "input tractograms", us::Any(), false); + parser.addArgument("", "o", mitkDiffusionCommandLineParser::String, "Output:", "Output png", us::Any(), false, false, false, mitkDiffusionCommandLineParser::Output); + parser.addArgument("resample", "", mitkDiffusionCommandLineParser::Float, "", ""); + parser.endGroup(); + + parser.addArgument("rotate_x", "", mitkDiffusionCommandLineParser::Float, "Rotate x-axis:", "Rotate around x-axis (in deg)"); + parser.addArgument("rotate_y", "", mitkDiffusionCommandLineParser::Float, "Rotate y-axis:", "Rotate around y-axis (in deg)"); + parser.addArgument("rotate_z", "", mitkDiffusionCommandLineParser::Float, "Rotate z-axis:", "Rotate around z-axis (in deg)"); + + + std::map parsedArgs = parser.parseArguments(argc, argv); + if (parsedArgs.size()==0) + return EXIT_FAILURE; + + + mitkDiffusionCommandLineParser::StringContainerType inFibs = us::any_cast(parsedArgs["i"]); + std::string outFileName = us::any_cast(parsedArgs["o"]); + + float rotateX = 0; + if (parsedArgs.count("rotate_x")) + rotateX = us::any_cast(parsedArgs["rotate_x"]); + + float rotateY = 0; + if (parsedArgs.count("rotate_y")) + rotateY = us::any_cast(parsedArgs["rotate_y"]); + + float rotateZ = 0; + if (parsedArgs.count("rotate_z")) + rotateZ = us::any_cast(parsedArgs["rotate_z"]); + + try + { + mitk::RenderingTestHelper renderingHelper(640*2, 480*2); + std::vector< mitk::FiberBundle::Pointer > tractograms = mitk::DiffusionDataIOHelper::load_fibs(inFibs); + for (auto fib : tractograms) + { + fib->RotateAroundAxis(rotateX, rotateY, rotateZ); + mitk::DataNode::Pointer node = mitk::DataNode::New(); + node->SetData(fib); + + node->SetFloatProperty("shape.tuberadius", 0.5); + renderingHelper.AddNodeToStorage(node); + } + + renderingHelper.SetMapperIDToRender3D(); + + vtkSmartPointer renderer = renderingHelper.GetVtkRenderer(); + renderer->GetRenderWindow()->DoubleBufferOn(); + + vtkSmartPointer magnifier = vtkSmartPointer::New(); + magnifier->SetInput(renderer); + magnifier->SetMagnification(4); + + vtkSmartPointer fileWriter = vtkSmartPointer::New(); + fileWriter->SetInputConnection(magnifier->GetOutputPort()); + fileWriter->SetFileName(outFileName.c_str()); + + fileWriter->Write(); + + } + 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/Tractography/StreamlineTractography.cpp b/Modules/DiffusionCmdApps/Tractography/StreamlineTractography.cpp index 346123c..ae11ebc 100644 --- a/Modules/DiffusionCmdApps/Tractography/StreamlineTractography.cpp +++ b/Modules/DiffusionCmdApps/Tractography/StreamlineTractography.cpp @@ -1,582 +1,590 @@ /*=================================================================== 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 #include #include #include #include #include #define _USE_MATH_DEFINES #include const int numOdfSamples = 200; typedef itk::Image< itk::Vector< float, numOdfSamples > , 3 > SampledShImageType; /*! \brief */ int main(int argc, char* argv[]) { mitkDiffusionCommandLineParser parser; parser.setTitle("Streamline Tractography"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription("Perform streamline tractography"); parser.setContributor("MIC"); // parameters fo all methods parser.setArgumentPrefix("--", "-"); parser.beginGroup("1. Mandatory arguments:"); parser.addArgument("", "i", mitkDiffusionCommandLineParser::StringList, "Input:", "input image (multiple possible for 'DetTensor' algorithm)", us::Any(), false, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("", "o", mitkDiffusionCommandLineParser::String, "Output:", "output fiberbundle/probability map", us::Any(), false, false, false, mitkDiffusionCommandLineParser::Output); parser.addArgument("type", "", mitkDiffusionCommandLineParser::String, "Type:", "which tracker to use (Peaks; Tensor; ODF; ODF-DIPY/FSL; RF)", us::Any(), false); parser.addArgument("probabilistic", "", mitkDiffusionCommandLineParser::Bool, "Probabilistic:", "Probabilistic tractography", us::Any(false)); parser.endGroup(); parser.beginGroup("2. Seeding:"); parser.addArgument("seeds", "", mitkDiffusionCommandLineParser::Int, "Seeds per voxel:", "number of seed points per voxel", 1); parser.addArgument("seed_image", "", mitkDiffusionCommandLineParser::String, "Seed image:", "mask image defining seed voxels", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("trials_per_seed", "", mitkDiffusionCommandLineParser::Int, "Max. trials per seed:", "try each seed N times until a valid streamline is obtained (only for probabilistic tractography)", 10); parser.addArgument("max_tracts", "", mitkDiffusionCommandLineParser::Int, "Max. number of tracts:", "tractography is stopped if the reconstructed number of tracts is exceeded", -1); parser.endGroup(); parser.beginGroup("3. Tractography constraints:"); parser.addArgument("tracking_mask", "", mitkDiffusionCommandLineParser::String, "Mask image:", "streamlines leaving the mask will stop immediately", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("stop_image", "", mitkDiffusionCommandLineParser::String, "Stop ROI image:", "streamlines entering the mask will stop immediately", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("exclusion_image", "", mitkDiffusionCommandLineParser::String, "Exclusion ROI image:", "streamlines entering the mask will be discarded", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("ep_constraint", "", mitkDiffusionCommandLineParser::String, "Endpoint constraint:", "determines which fibers are accepted based on their endpoint location - options are NONE, EPS_IN_TARGET, EPS_IN_TARGET_LABELDIFF, EPS_IN_SEED_AND_TARGET, MIN_ONE_EP_IN_TARGET, ONE_EP_IN_TARGET and NO_EP_IN_TARGET", us::Any()); parser.addArgument("target_image", "", mitkDiffusionCommandLineParser::String, "Target ROI image:", "effact depends on the chosen endpoint constraint (option ep_constraint)", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.endGroup(); parser.beginGroup("4. Streamline integration parameters:"); parser.addArgument("sharpen_odfs", "", mitkDiffusionCommandLineParser::Int, "Sharpen ODFs:", "if you are using dODF images as input, it is advisable to sharpen the ODFs (power of X). this is not necessary for CSD fODFs, since they are narurally much sharper."); parser.addArgument("cutoff", "", mitkDiffusionCommandLineParser::Float, "Cutoff:", "set the FA, GFA or Peak amplitude cutoff for terminating tracks", 0.1); parser.addArgument("odf_cutoff", "", mitkDiffusionCommandLineParser::Float, "ODF Cutoff:", "threshold on the ODF magnitude. this is useful in case of CSD fODF tractography.", 0.0); parser.addArgument("step_size", "", mitkDiffusionCommandLineParser::Float, "Step size:", "step size (in voxels)", 0.5); parser.addArgument("min_tract_length", "", mitkDiffusionCommandLineParser::Float, "Min. tract length:", "minimum fiber length (in mm)", 20); + parser.addArgument("max_tract_length", "", mitkDiffusionCommandLineParser::Float, "Max. tract length:", "maximum fiber length (in mm)", 400); parser.addArgument("angular_threshold", "", mitkDiffusionCommandLineParser::Float, "Angular threshold:", "angular threshold between two successive steps, (default: 90° * step_size, minimum 15°)"); parser.addArgument("loop_check", "", mitkDiffusionCommandLineParser::Float, "Check for loops:", "threshold on angular stdev over the last 4 voxel lengths"); parser.addArgument("peak_jitter", "", mitkDiffusionCommandLineParser::Float, "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.", 0.01); + parser.addArgument("first_order", "", mitkDiffusionCommandLineParser::Bool, "First order integration:", "use first order integration. default is second order to avoids streamlineovershoot", false); parser.endGroup(); parser.beginGroup("5. Tractography prior:"); parser.addArgument("prior_image", "", mitkDiffusionCommandLineParser::String, "Peak prior:", "tractography prior in thr for of a peak image", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("prior_weight", "", mitkDiffusionCommandLineParser::Float, "Prior weight", "weighting factor between prior and data.", 0.5); parser.addArgument("dont_restrict_to_prior", "", mitkDiffusionCommandLineParser::Bool, "Don't restrict to prior:", "don't restrict tractography to regions where the prior is valid.", us::Any(false)); parser.addArgument("no_new_directions_from_prior", "", mitkDiffusionCommandLineParser::Bool, "No new directios from prior:", "the prior cannot create directions where there are none in the data.", us::Any(false)); parser.addArgument("prior_flip_x", "", mitkDiffusionCommandLineParser::Bool, "Prior Flip X:", "multiply x-coordinate of prior direction by -1"); parser.addArgument("prior_flip_y", "", mitkDiffusionCommandLineParser::Bool, "Prior Flip Y:", "multiply y-coordinate of prior direction by -1"); parser.addArgument("prior_flip_z", "", mitkDiffusionCommandLineParser::Bool, "Prior Flip Z:", "multiply z-coordinate of prior direction by -1"); parser.endGroup(); parser.beginGroup("6. Neighborhood sampling:"); parser.addArgument("num_samples", "", mitkDiffusionCommandLineParser::Int, "Num. neighborhood samples:", "number of neighborhood samples that are use to determine the next progression direction", 0); parser.addArgument("sampling_distance", "", mitkDiffusionCommandLineParser::Float, "Sampling distance:", "distance of neighborhood sampling points (in voxels)", 0.25); parser.addArgument("use_stop_votes", "", mitkDiffusionCommandLineParser::Bool, "Use stop votes:", "use stop votes"); parser.addArgument("use_only_forward_samples", "", mitkDiffusionCommandLineParser::Bool, "Use only forward samples:", "use only forward samples"); parser.endGroup(); parser.beginGroup("7. Tensor tractography specific:"); parser.addArgument("tend_f", "", mitkDiffusionCommandLineParser::Float, "Weight f", "weighting factor between first eigenvector (f=1 equals FACT tracking) and input vector dependent direction (f=0).", 1.0); parser.addArgument("tend_g", "", mitkDiffusionCommandLineParser::Float, "Weight g", "weighting factor between input vector (g=0) and tensor deflection (g=1 equals TEND tracking)", 0.0); parser.endGroup(); parser.beginGroup("8. Random forest tractography specific:"); parser.addArgument("forest", "", mitkDiffusionCommandLineParser::String, "Forest:", "input random forest (HDF5 file)", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.addArgument("use_sh_features", "", mitkDiffusionCommandLineParser::Bool, "Use SH features:", "use SH features"); parser.endGroup(); parser.beginGroup("9. Additional input:"); parser.addArgument("additional_images", "", mitkDiffusionCommandLineParser::StringList, "Additional images:", "specify a list of float images that hold additional information (FA, GFA, additional features for RF tractography)", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.endGroup(); parser.beginGroup("10. Misc:"); parser.addArgument("flip_x", "", mitkDiffusionCommandLineParser::Bool, "Flip X:", "multiply x-coordinate of direction proposal by -1"); parser.addArgument("flip_y", "", mitkDiffusionCommandLineParser::Bool, "Flip Y:", "multiply y-coordinate of direction proposal by -1"); parser.addArgument("flip_z", "", mitkDiffusionCommandLineParser::Bool, "Flip Z:", "multiply z-coordinate of direction proposal by -1"); parser.addArgument("no_data_interpolation", "", mitkDiffusionCommandLineParser::Bool, "Don't interpolate input data:", "don't interpolate input image values"); parser.addArgument("no_mask_interpolation", "", mitkDiffusionCommandLineParser::Bool, "Don't interpolate masks:", "don't interpolate mask image values"); parser.addArgument("compress", "", mitkDiffusionCommandLineParser::Bool, "Compress:", "compress output fibers (lossy)"); parser.addArgument("fix_seed", "", mitkDiffusionCommandLineParser::Bool, "Fix Random Seed:", "always use the same random numbers"); parser.addArgument("parameter_file", "", mitkDiffusionCommandLineParser::String, "Parameter File:", "load parameters from json file (svae using MITK Diffusion GUI). the parameters loaded form this file are overwritten by the manually set parameters.", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input); parser.endGroup(); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; mitkDiffusionCommandLineParser::StringContainerType input_files = us::any_cast(parsedArgs["i"]); std::string outFile = us::any_cast(parsedArgs["o"]); std::string type = us::any_cast(parsedArgs["type"]); std::shared_ptr< mitk::StreamlineTractographyParameters > params = std::make_shared(); if (parsedArgs.count("parameter_file")) { auto parameter_file = us::any_cast(parsedArgs["parameter_file"]); params->LoadParameters(parameter_file); } if (parsedArgs.count("probabilistic")) params->m_Mode = mitk::StreamlineTractographyParameters::MODE::PROBABILISTIC; else { params->m_Mode = mitk::StreamlineTractographyParameters::MODE::DETERMINISTIC; } std::string prior_image = ""; if (parsedArgs.count("prior_image")) prior_image = us::any_cast(parsedArgs["prior_image"]); if (parsedArgs.count("prior_weight")) params->m_Weight = us::any_cast(parsedArgs["prior_weight"]); if (parsedArgs.count("fix_seed")) params->m_FixRandomSeed = us::any_cast(parsedArgs["fix_seed"]); if (parsedArgs.count("dont_restrict_to_prior")) params->m_RestrictToPrior = !us::any_cast(parsedArgs["dont_restrict_to_prior"]); if (parsedArgs.count("no_new_directions_from_prior")) params->m_NewDirectionsFromPrior = !us::any_cast(parsedArgs["no_new_directions_from_prior"]); if (parsedArgs.count("sharpen_odfs")) params->m_SharpenOdfs = us::any_cast(parsedArgs["sharpen_odfs"]); if (parsedArgs.count("no_data_interpolation")) params->m_InterpolateTractographyData = !us::any_cast(parsedArgs["no_data_interpolation"]); params->m_InterpolateRoiImages = true; if (parsedArgs.count("no_mask_interpolation")) params->m_InterpolateRoiImages = !us::any_cast(parsedArgs["no_mask_interpolation"]); bool use_sh_features = false; if (parsedArgs.count("use_sh_features")) use_sh_features = us::any_cast(parsedArgs["use_sh_features"]); if (parsedArgs.count("use_stop_votes")) params->m_StopVotes = us::any_cast(parsedArgs["use_stop_votes"]); if (parsedArgs.count("use_only_forward_samples")) params->m_OnlyForwardSamples = us::any_cast(parsedArgs["use_only_forward_samples"]); if (parsedArgs.count("flip_x")) params->m_FlipX = us::any_cast(parsedArgs["flip_x"]); if (parsedArgs.count("flip_y")) params->m_FlipY = us::any_cast(parsedArgs["flip_y"]); if (parsedArgs.count("flip_z")) params->m_FlipZ = us::any_cast(parsedArgs["flip_z"]); if (parsedArgs.count("prior_flip_x")) params->m_PriorFlipX = us::any_cast(parsedArgs["prior_flip_x"]); if (parsedArgs.count("prior_flip_y")) params->m_PriorFlipY = us::any_cast(parsedArgs["prior_flip_y"]); if (parsedArgs.count("prior_flip_z")) params->m_PriorFlipZ = us::any_cast(parsedArgs["prior_flip_z"]); if (parsedArgs.count("apply_image_rotation")) params->m_ApplyDirectionMatrix = us::any_cast(parsedArgs["apply_image_rotation"]); if (parsedArgs.count("compress")) params->m_CompressFibers = us::any_cast(parsedArgs["compress"]); if (parsedArgs.count("min_tract_length")) params->m_MinTractLengthMm = us::any_cast(parsedArgs["min_tract_length"]); + if (parsedArgs.count("max_tract_length")) + params->m_MaxTractLengthMm = us::any_cast(parsedArgs["max_tract_length"]); + if (parsedArgs.count("loop_check")) params->SetLoopCheckDeg(us::any_cast(parsedArgs["loop_check"])); + if (parsedArgs.count("first_order")) + params->m_SecondOrder = false; + std::string forestFile; if (parsedArgs.count("forest")) forestFile = us::any_cast(parsedArgs["forest"]); std::string maskFile = ""; if (parsedArgs.count("tracking_mask")) maskFile = us::any_cast(parsedArgs["tracking_mask"]); std::string seedFile = ""; if (parsedArgs.count("seed_image")) seedFile = us::any_cast(parsedArgs["seed_image"]); std::string targetFile = ""; if (parsedArgs.count("target_image")) targetFile = us::any_cast(parsedArgs["target_image"]); std::string exclusionFile = ""; if (parsedArgs.count("exclusion_image")) exclusionFile = us::any_cast(parsedArgs["exclusion_image"]); std::string stopFile = ""; if (parsedArgs.count("stop_image")) stopFile = us::any_cast(parsedArgs["stop_image"]); if (parsedArgs.count("ep_constraint")) { if (us::any_cast(parsedArgs["ep_constraint"]) == "NONE") params->m_EpConstraints = mitk::StreamlineTractographyParameters::EndpointConstraints::NONE; else if (us::any_cast(parsedArgs["ep_constraint"]) == "EPS_IN_TARGET") params->m_EpConstraints = mitk::StreamlineTractographyParameters::EndpointConstraints::EPS_IN_TARGET; else if (us::any_cast(parsedArgs["ep_constraint"]) == "EPS_IN_TARGET_LABELDIFF") params->m_EpConstraints = mitk::StreamlineTractographyParameters::EndpointConstraints::EPS_IN_TARGET_LABELDIFF; else if (us::any_cast(parsedArgs["ep_constraint"]) == "EPS_IN_SEED_AND_TARGET") params->m_EpConstraints = mitk::StreamlineTractographyParameters::EndpointConstraints::EPS_IN_SEED_AND_TARGET; else if (us::any_cast(parsedArgs["ep_constraint"]) == "MIN_ONE_EP_IN_TARGET") params->m_EpConstraints = mitk::StreamlineTractographyParameters::EndpointConstraints::MIN_ONE_EP_IN_TARGET; else if (us::any_cast(parsedArgs["ep_constraint"]) == "ONE_EP_IN_TARGET") params->m_EpConstraints = mitk::StreamlineTractographyParameters::EndpointConstraints::ONE_EP_IN_TARGET; else if (us::any_cast(parsedArgs["ep_constraint"]) == "NO_EP_IN_TARGET") params->m_EpConstraints = mitk::StreamlineTractographyParameters::EndpointConstraints::NO_EP_IN_TARGET; } if (parsedArgs.count("cutoff")) params->m_Cutoff = us::any_cast(parsedArgs["cutoff"]); if (parsedArgs.count("odf_cutoff")) params->m_OdfCutoff = us::any_cast(parsedArgs["odf_cutoff"]); if (parsedArgs.count("peak_jitter")) params->m_PeakJitter = us::any_cast(parsedArgs["peak_jitter"]); if (parsedArgs.count("step_size")) params->SetStepSizeVox(us::any_cast(parsedArgs["step_size"])); if (parsedArgs.count("sampling_distance")) params->SetSamplingDistanceVox(us::any_cast(parsedArgs["sampling_distance"])); if (parsedArgs.count("num_samples")) params->m_NumSamples = static_cast(us::any_cast(parsedArgs["num_samples"])); if (parsedArgs.count("seeds")) params->m_SeedsPerVoxel = us::any_cast(parsedArgs["seeds"]); if (parsedArgs.count("trials_per_seed")) params->m_TrialsPerSeed = static_cast(us::any_cast(parsedArgs["trials_per_seed"])); if (parsedArgs.count("tend_f")) params->m_F = us::any_cast(parsedArgs["tend_f"]); if (parsedArgs.count("tend_g")) params->m_G = us::any_cast(parsedArgs["tend_g"]); if (parsedArgs.count("angular_threshold")) params->SetAngularThresholdDeg(us::any_cast(parsedArgs["angular_threshold"])); if (parsedArgs.count("max_tracts")) params->m_MaxNumFibers = us::any_cast(parsedArgs["max_tracts"]); std::string ext = itksys::SystemTools::GetFilenameExtension(outFile); if (ext != ".fib" && ext != ".trk") { MITK_INFO << "Output file format not supported. Use one of .fib, .trk, .nii, .nii.gz, .nrrd"; return EXIT_FAILURE; } // LOAD DATASETS mitkDiffusionCommandLineParser::StringContainerType addFiles; if (parsedArgs.count("additional_images")) addFiles = us::any_cast(parsedArgs["additional_images"]); typedef itk::Image ItkFloatImgType; ItkFloatImgType::Pointer mask = nullptr; if (!maskFile.empty()) { MITK_INFO << "loading mask image"; mitk::Image::Pointer img = mitk::IOUtil::Load(maskFile); mask = ItkFloatImgType::New(); mitk::CastToItkImage(img, mask); } ItkFloatImgType::Pointer seed = nullptr; if (!seedFile.empty()) { MITK_INFO << "loading seed ROI image"; mitk::Image::Pointer img = mitk::IOUtil::Load(seedFile); seed = ItkFloatImgType::New(); mitk::CastToItkImage(img, seed); } ItkFloatImgType::Pointer stop = nullptr; if (!stopFile.empty()) { MITK_INFO << "loading stop ROI image"; mitk::Image::Pointer img = mitk::IOUtil::Load(stopFile); stop = ItkFloatImgType::New(); mitk::CastToItkImage(img, stop); } ItkFloatImgType::Pointer target = nullptr; if (!targetFile.empty()) { MITK_INFO << "loading target ROI image"; mitk::Image::Pointer img = mitk::IOUtil::Load(targetFile); target = ItkFloatImgType::New(); mitk::CastToItkImage(img, target); } ItkFloatImgType::Pointer exclusion = nullptr; if (!exclusionFile.empty()) { MITK_INFO << "loading exclusion ROI image"; mitk::Image::Pointer img = mitk::IOUtil::Load(exclusionFile); exclusion = ItkFloatImgType::New(); mitk::CastToItkImage(img, exclusion); } MITK_INFO << "loading additional images"; std::vector< std::vector< ItkFloatImgType::Pointer > > addImages; addImages.push_back(std::vector< ItkFloatImgType::Pointer >()); for (auto file : addFiles) { mitk::Image::Pointer img = mitk::IOUtil::Load(file); ItkFloatImgType::Pointer itkimg = ItkFloatImgType::New(); mitk::CastToItkImage(img, itkimg); addImages.at(0).push_back(itkimg); } // ////////////////////////////////////////////////////////////////// // omp_set_num_threads(1); typedef itk::StreamlineTrackingFilter TrackerType; TrackerType::Pointer tracker = TrackerType::New(); if (!prior_image.empty()) { mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Peak Image"}, std::vector()); mitk::PeakImage::Pointer priorImage = mitk::IOUtil::Load(prior_image, &functor); if (priorImage.IsNull()) { MITK_INFO << "Only peak images are supported as prior at the moment!"; return EXIT_FAILURE; } mitk::TrackingDataHandler* priorhandler = new mitk::TrackingHandlerPeaks(); typedef mitk::ImageToItk< mitk::TrackingHandlerPeaks::PeakImgType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(priorImage); caster->Update(); mitk::TrackingHandlerPeaks::PeakImgType::Pointer itkImg = caster->GetOutput(); std::shared_ptr< mitk::StreamlineTractographyParameters > prior_params = std::make_shared< mitk::StreamlineTractographyParameters >(*params); prior_params->m_FlipX = params->m_PriorFlipX; prior_params->m_FlipY = params->m_PriorFlipY; prior_params->m_FlipZ = params->m_PriorFlipZ; prior_params->m_Cutoff = 0.0; dynamic_cast(priorhandler)->SetPeakImage(itkImg); priorhandler->SetParameters(prior_params); tracker->SetTrackingPriorHandler(priorhandler); } mitk::TrackingDataHandler* handler; mitk::Image::Pointer reference_image; if (type == "RF") { mitk::TractographyForest::Pointer forest = mitk::IOUtil::Load(forestFile); if (forest.IsNull()) mitkThrow() << "Forest file " << forestFile << " could not be read."; std::vector include = {"Diffusion Weighted Images"}; std::vector exclude = {}; mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor(include, exclude); auto input = mitk::IOUtil::Load(input_files.at(0), &functor); reference_image = input; if (use_sh_features) { handler = new mitk::TrackingHandlerRandomForest<6,28>(); dynamic_cast*>(handler)->SetForest(forest); dynamic_cast*>(handler)->AddDwi(input); dynamic_cast*>(handler)->SetAdditionalFeatureImages(addImages); } else { handler = new mitk::TrackingHandlerRandomForest<6,100>(); dynamic_cast*>(handler)->SetForest(forest); dynamic_cast*>(handler)->AddDwi(input); dynamic_cast*>(handler)->SetAdditionalFeatureImages(addImages); } } else if (type == "Peaks") { handler = new mitk::TrackingHandlerPeaks(); MITK_INFO << "loading input peak image"; mitk::Image::Pointer mitkImage = mitk::IOUtil::Load(input_files.at(0)); reference_image = mitkImage; mitk::TrackingHandlerPeaks::PeakImgType::Pointer itkImg = mitk::convert::GetItkPeakFromPeakImage(mitkImage); dynamic_cast(handler)->SetPeakImage(itkImg); } else if (type == "Tensor" && params->m_Mode == mitk::StreamlineTractographyParameters::MODE::DETERMINISTIC) { handler = new mitk::TrackingHandlerTensor(); MITK_INFO << "loading input tensor images"; std::vector< mitk::Image::Pointer > input_images; for (unsigned int i=0; i(input_files.at(i)); reference_image = mitkImage; mitk::TensorImage::ItkTensorImageType::Pointer itkImg = mitk::convert::GetItkTensorFromTensorImage(mitkImage); dynamic_cast(handler)->AddTensorImage(itkImg.GetPointer()); } if (addImages.at(0).size()>0) dynamic_cast(handler)->SetFaImage(addImages.at(0).at(0)); } else if (type == "ODF" || type == "ODF-DIPY/FSL" || (type == "Tensor" && params->m_Mode == mitk::StreamlineTractographyParameters::MODE::PROBABILISTIC)) { handler = new mitk::TrackingHandlerOdf(); mitk::OdfImage::ItkOdfImageType::Pointer itkImg = nullptr; if (type == "Tensor") { MITK_INFO << "Converting Tensor to ODF image"; auto input = mitk::IOUtil::Load(input_files.at(0)); reference_image = input; itkImg = mitk::convert::GetItkOdfFromTensorImage(input); dynamic_cast(handler)->SetIsOdfFromTensor(true); } else { std::vector include = {"SH Image", "ODF Image"}; std::vector exclude = {}; mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor(include, exclude); auto input = mitk::IOUtil::Load(input_files.at(0), &functor)[0]; reference_image = dynamic_cast(input.GetPointer()); if (dynamic_cast(input.GetPointer())) { MITK_INFO << "Converting SH to ODF image"; mitk::ShImage::Pointer mitkShImage = dynamic_cast(input.GetPointer()); if (type == "ODF-DIPY/FSL") mitkShImage->SetShConvention(mitk::ShImage::SH_CONVENTION::FSL); mitk::Image::Pointer mitkImg = dynamic_cast(mitkShImage.GetPointer()); itkImg = mitk::convert::GetItkOdfFromShImage(mitkImg); } else if (dynamic_cast(input.GetPointer())) { mitk::Image::Pointer mitkImg = dynamic_cast(input.GetPointer()); itkImg = mitk::convert::GetItkOdfFromOdfImage(mitkImg); } else mitkThrow() << ""; } dynamic_cast(handler)->SetOdfImage(itkImg); if (addImages.at(0).size()>0) dynamic_cast(handler)->SetGfaImage(addImages.at(0).at(0)); } else { MITK_INFO << "Unknown tractography algorithm (" + type+"). Known types are Peaks, DetTensor, ProbTensor, DetODF, ProbODF, DetRF, ProbRF."; return EXIT_FAILURE; } float max_size = 0; for (int i=0; i<3; ++i) if (reference_image->GetGeometry()->GetExtentInMM(i)>max_size) max_size = reference_image->GetGeometry()->GetExtentInMM(i); if (params->m_MinTractLengthMm >= max_size) { MITK_INFO << "Max. image size: " << max_size << "mm"; MITK_INFO << "Min. tract length: " << params->m_MinTractLengthMm << "mm"; MITK_ERROR << "Minimum tract length exceeds the maximum image extent! Recommended value is about 1/10 of the image extent."; return EXIT_FAILURE; } else if (params->m_MinTractLengthMm > max_size/10) { MITK_INFO << "Max. image size: " << max_size << "mm"; MITK_INFO << "Min. tract length: " << params->m_MinTractLengthMm << "mm"; MITK_WARN << "Minimum tract length is larger than 1/10 the maximum image extent! Decrease recommended."; } MITK_INFO << "Tractography algorithm: " << type; tracker->SetMaskImage(mask); tracker->SetSeedImage(seed); tracker->SetStoppingRegions(stop); tracker->SetTargetRegions(target); tracker->SetExclusionRegions(exclusion); tracker->SetTrackingHandler(handler); if (ext != ".fib" && ext != ".trk") params->m_OutputProbMap = true; tracker->SetParameters(params); tracker->Update(); if (ext == ".fib" || ext == ".trk") { vtkSmartPointer< vtkPolyData > poly = tracker->GetFiberPolyData(); mitk::FiberBundle::Pointer outFib = mitk::FiberBundle::New(poly); if (params->m_CompressFibers) { float min_sp = 999; auto spacing = handler->GetSpacing(); if (spacing[0] < min_sp) min_sp = spacing[0]; if (spacing[1] < min_sp) min_sp = spacing[1]; if (spacing[2] < min_sp) min_sp = spacing[2]; params->m_Compression = min_sp/10; outFib->Compress(params->m_Compression); } outFib->SetTrackVisHeader(reference_image->GetGeometry()); mitk::IOUtil::Save(outFib, outFile); } else { TrackerType::ItkDoubleImgType::Pointer outImg = tracker->GetOutputProbabilityMap(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); if (ext != ".nii" && ext != ".nii.gz" && ext != ".nrrd") outFile += ".nii.gz"; mitk::IOUtil::Save(img, outFile); } delete handler; return EXIT_SUCCESS; } diff --git a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp index 828d2a6..0059159 100644 --- a/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp +++ b/Modules/DiffusionCore/IODataStructures/mitkFiberBundle.cpp @@ -1,2847 +1,2849 @@ /*=================================================================== 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 #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include const char* mitk::FiberBundle::FIBER_ID_ARRAY = "Fiber_IDs"; mitk::FiberBundle::FiberBundle( vtkPolyData* fiberPolyData ) : m_NumFibers(0) { m_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_device rd; std::mt19937 g(rd()); std::shuffle(ids.begin(), ids.end(), g); 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->CopyStructure(fiberPD); // 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 weight_fibers, mitk::LookupTable::LookupTableType type) { 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(); mitkLookup->SetType(type); if (type!=mitk::LookupTable::MULTILABEL) mitkLookup->GetVtkLookupTable()->SetTableRange(m_MinFiberLength, m_MaxFiberLength); 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; double color[3]; mitkLookup->GetColor(m_FiberLengths.at(i), color); for (int j=0; j(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 opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type) { 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"); std::vector< double > values; double min = 1; double max = 0; MITK_INFO << "Coloring fibers by curvature"; boost::timer::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); } mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New(); mitkLookup->SetType(type); if (type!=mitk::LookupTable::MULTILABEL) mitkLookup->GetVtkLookupTable()->SetTableRange(min, max); unsigned int count = 0; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); auto numPoints = cell->GetNumberOfPoints(); for (int j=0; jGetColor(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]); if (opacity) rgba[3] = static_cast(255.0f * dev/max); else 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 weight_fibers, mitk::LookupTable::LookupTableType type, double max_cap, bool interpolate) { if (FAimage->GetPixelType().GetComponentTypeAsString()=="unsigned char" || FAimage->GetPixelType().GetComponentTypeAsString()=="char" || FAimage->GetPixelType().GetComponentTypeAsString()=="long" || FAimage->GetPixelType().GetComponentTypeAsString()=="unsigned long" || FAimage->GetPixelType().GetComponentTypeAsString()=="short" || FAimage->GetPixelType().GetComponentTypeAsString()=="unsigned short" || FAimage->GetPixelType().GetComponentTypeAsString()=="unsigned int" || FAimage->GetPixelType().GetComponentTypeAsString()=="int") { typedef itk::Image ImageType; ImageType::Pointer itkImage = ImageType::New(); CastToItkImage(FAimage, itkImage); ColorFibersByScalarMap(itkImage, opacity, weight_fibers, type, max_cap, interpolate ); } else { typedef itk::Image ImageType; ImageType::Pointer itkImage = ImageType::New(); CastToItkImage(FAimage, itkImage); ColorFibersByScalarMap(itkImage, opacity, weight_fibers, type, max_cap, interpolate ); } m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } template void mitk::FiberBundle::ColorFibersByScalarMap(typename itk::Image::Pointer image, bool opacity, bool weight_fibers, mitk::LookupTable::LookupTableType type, double max_cap, bool interpolate) { 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}; vtkPoints* pointSet = m_FiberPolyData->GetPoints(); if (type==mitk::LookupTable::MULTILABEL) interpolate = false; auto interpolator = itk::LinearInterpolateImageFunction< itk::Image, float >::New(); interpolator->SetInputImage(image); 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); auto pixelValue = mitk::imv::GetImageValue(mitk::imv::GetItkPoint(p), interpolate, interpolator); if (pixelValue>max) max = pixelValue; if (pixelValueSetFiberWeight(i, mean_val/numPoints); } mitk::LookupTable::Pointer mitkLookup = mitk::LookupTable::New(); mitkLookup->SetType(type); if (type!=mitk::LookupTable::MULTILABEL) mitkLookup->GetVtkLookupTable()->SetTableRange(min, max*max_cap); for(long i=0; iGetNumberOfPoints(); ++i) { itk::Point px; px[0] = pointSet->GetPoint(i)[0]; px[1] = pointSet->GetPoint(i)[1]; px[2] = pointSet->GetPoint(i)[2]; auto pixelValue = mitk::imv::GetImageValue(px, interpolate, interpolator); double color[3]; mitkLookup->GetColor(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, mitk::LookupTable::LookupTableType type) { 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}; unsigned int counter = 0; float max = -999999; float min = 999999; for (unsigned int i=0; iGetFiberWeight(i); if (weight>max) max = weight; if (weightSetType(type); if (type!=mitk::LookupTable::MULTILABEL) mitkLookup->GetVtkLookupTable()->SetTableRange(min, max); for (unsigned int i=0; iGetCell(i); auto numPoints = cell->GetNumberOfPoints(); auto weight = this->GetFiberWeight(i); double color[3]; mitkLookup->GetColor(weight, color); for (int j=0; j(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 * weight/max); 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->SetCellIdsArrayName(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::timer::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::timer::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::timer::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::timer::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::timer::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::timer::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); + auto colors = GetFiberColors(); this->SetFiberPolyData(m_FiberPolyData, true); + SetFiberColors(colors); } void mitk::FiberBundle::ScaleFibers(double x, double y, double z, bool subtractCenter) { MITK_INFO << "Scaling fibers"; boost::timer::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::timer::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::timer::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::timer::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::timer::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::timer::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::timer::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::timer::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::timer::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"); + sprintf(m_TrackVisHeader.voxel_order,"RAS"); 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/mitkTrackvis.cpp b/Modules/DiffusionCore/IODataStructures/mitkTrackvis.cpp index 7058fb7..818ab87 100644 --- a/Modules/DiffusionCore/IODataStructures/mitkTrackvis.cpp +++ b/Modules/DiffusionCore/IODataStructures/mitkTrackvis.cpp @@ -1,310 +1,312 @@ #include #include TrackVisFiberReader::TrackVisFiberReader() { m_Filename = ""; m_FilePointer = nullptr; } TrackVisFiberReader::~TrackVisFiberReader() { if (m_FilePointer) fclose( m_FilePointer ); } // Create a TrackVis file and store standard metadata. The file is ready to append fibers. // --------------------------------------------------------------------------------------- -short TrackVisFiberReader::create(std::string filename , mitk::FiberBundle *fib, bool print_header) +short TrackVisFiberReader::create(std::string filename , mitk::FiberBundle *fib, bool print_header, bool use_lps) { m_Header = fib->GetTrackVisHeader(); + if (use_lps) + sprintf(m_Header.voxel_order,"LPS"); if (print_header) this->print_header(); // write the header to the file m_FilePointer = fopen(filename.c_str(),"w+b"); if (m_FilePointer == nullptr) { printf("[ERROR] Unable to create file '%s'\n",filename.c_str()); return 0; } if (fwrite((char*)&m_Header, 1, 1000, m_FilePointer) != 1000) MITK_ERROR << "TrackVis::create : Error occurding during writing fiber."; this->m_Filename = filename; return 1; } // Open an existing TrackVis file and read metadata information. // The file pointer is positiond at the beginning of fibers data // ------------------------------------------------------------- short TrackVisFiberReader::open( std::string filename ) { m_FilePointer = std::fopen(filename.c_str(), "rb"); if (m_FilePointer == nullptr) { printf("[ERROR] Unable to open file '%s'\n",filename.c_str()); return 0; } this->m_Filename = filename; return fread((char*)(&m_Header), 1, 1000, m_FilePointer); } short TrackVisFiberReader::write(const mitk::FiberBundle *fib) { vtkSmartPointer poly = fib->GetFiberPolyData(); { mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New(); matrix->Identity(); for (int i=0; i<4; ++i) for (int j=0; j<4; ++j) { if (j<3) matrix->SetElement(i, j, m_Header.vox_to_ras[i][j]/m_Header.voxel_size[j]); else matrix->SetElement(i, j, m_Header.vox_to_ras[i][j]); } if (m_Header.voxel_order[0]=='R') { matrix->SetElement(0,0,-matrix->GetElement(0,0)); matrix->SetElement(0,1,-matrix->GetElement(0,1)); matrix->SetElement(0,2,-matrix->GetElement(0,2)); matrix->SetElement(0,3,-matrix->GetElement(0,3)); } if (m_Header.voxel_order[1]=='A') { matrix->SetElement(1,0,-matrix->GetElement(1,0)); matrix->SetElement(1,1,-matrix->GetElement(1,1)); matrix->SetElement(1,2,-matrix->GetElement(1,2)); matrix->SetElement(1,3,-matrix->GetElement(1,3)); } if (m_Header.voxel_order[2]=='I') { matrix->SetElement(2,0,-matrix->GetElement(2,0)); matrix->SetElement(2,1,-matrix->GetElement(2,1)); matrix->SetElement(2,2,-matrix->GetElement(2,2)); matrix->SetElement(2,3,-matrix->GetElement(2,3)); } geometry->SetIndexToWorldTransformByVtkMatrix(matrix); vtkSmartPointer transformFilter = vtkSmartPointer::New(); transformFilter->SetInputData(poly); transformFilter->SetTransform(geometry->GetVtkTransform()->GetInverse()); transformFilter->Update(); poly = transformFilter->GetOutput(); } for (unsigned int i=0; iGetNumFibers(); i++) { vtkCell* cell = poly->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); unsigned int numSaved, pos = 0; //float* tmp = new float[3*maxSteps]; std::vector< float > tmp; tmp.reserve(3*numPoints); numSaved = numPoints; for(unsigned int i=0; iGetPoint(i); // TRK coordinates are corner based, so we have to shift the center based vtk coordinates by half a voxel tmp[pos++] = p[0] + m_Header.voxel_size[0]/2; tmp[pos++] = p[1] + m_Header.voxel_size[1]/2; tmp[pos++] = p[2] + m_Header.voxel_size[2]/2; } // write the coordinates to the file if ( fwrite((char*)&numSaved, 1, 4, m_FilePointer) != 4 ) { printf( "[ERROR] Problems saving the fiber!\n" ); return 1; } if ( fwrite((char*)&(tmp.front()), 1, 4*pos, m_FilePointer) != 4*pos ) { printf( "[ERROR] Problems saving the fiber!\n" ); return 1; } } return 0; } void TrackVisFiberReader::print_header() { std::cout << "--------------------------------------------------------" << std::endl; std::cout << "see http://trackvis.org/docs/?subsect=fileformat" << std::endl; std::cout << "ONLY vox_to_ras AND voxel_order HEADER ENTRIES ARE USED FOR FIBER COORDINATE TRANSFORMATIONS!" << std::endl; std::cout << "\nid_string (should be \"TRACK\"): " << m_Header.id_string << std::endl; std::cout << "dim: [" << std::defaultfloat << m_Header.dim[0] << " " << m_Header.dim[1] << " " << m_Header.dim[2] << "]" << std::endl; std::cout << "voxel_size: [" << m_Header.voxel_size[0] << " " << m_Header.voxel_size[1] << " " << m_Header.voxel_size[2] << "]" << std::endl; std::cout << "origin: [" << m_Header.origin[0] << " " << m_Header.origin[1] << " " << m_Header.origin[2] << "]" << std::endl; std::cout << "vox_to_world: " << std::scientific << std::endl; std::cout << "[[" << m_Header.vox_to_ras[0][0] << ", " << m_Header.vox_to_ras[0][1] << ", " << m_Header.vox_to_ras[0][2] << ", " << m_Header.vox_to_ras[0][3] << "]" << std::endl; std::cout << " [" << m_Header.vox_to_ras[1][0] << ", " << m_Header.vox_to_ras[1][1] << ", " << m_Header.vox_to_ras[1][2] << ", " << m_Header.vox_to_ras[1][3] << "]" << std::endl; std::cout << " [" << m_Header.vox_to_ras[2][0] << ", " << m_Header.vox_to_ras[2][1] << ", " << m_Header.vox_to_ras[2][2] << ", " << m_Header.vox_to_ras[2][3] << "]" << std::endl; std::cout << " [" << m_Header.vox_to_ras[3][0] << ", " << m_Header.vox_to_ras[3][1] << ", " << m_Header.vox_to_ras[3][2] << ", " << m_Header.vox_to_ras[3][3] << "]]" << std::defaultfloat << std::endl; std::cout << "voxel_order: " << m_Header.voxel_order[0] << m_Header.voxel_order[1] << m_Header.voxel_order[2] << std::endl; std::cout << "pad1: " << m_Header.pad1[0] << m_Header.pad1[1] << std::endl; std::cout << "pad2: " << m_Header.pad2[0] << m_Header.pad2[1] << m_Header.pad2[2] << std::endl; std::cout << "image_orientation_patient: [" << m_Header.image_orientation_patient[0] << " " << m_Header.image_orientation_patient[1] << " " << m_Header.image_orientation_patient[2] << " " << m_Header.image_orientation_patient[3] << " " << m_Header.image_orientation_patient[4] << " " << m_Header.image_orientation_patient[5] << "]" << std::endl; std::cout << "invert_x: " << static_cast(m_Header.invert_x) << std::endl; std::cout << "invert_y: " << static_cast(m_Header.invert_y) << std::endl; std::cout << "invert_z: " << static_cast(m_Header.invert_z) << std::endl; std::cout << "swap_xy: " << static_cast(m_Header.swap_xy) << std::endl; std::cout << "swap_yz: " << static_cast(m_Header.swap_yz) << std::endl; std::cout << "swap_zx: " << static_cast(m_Header.swap_zx) << std::endl; std::cout << "n_count: " << m_Header.n_count << std::endl; std::cout << "version: " << m_Header.version << std::endl; std::cout << "hdr_size: " << m_Header.hdr_size << std::endl; std::cout << "\nNot printed: n_scalars, scalar_name, n_properties, property_name, reserved" << std::endl; std::cout << "--------------------------------------------------------" << std::endl; } short TrackVisFiberReader::read( mitk::FiberBundle* fib, bool use_matrix, bool flip_x, bool flip_y, bool flip_z, bool print_header) { int numPoints; vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); if (print_header) this->print_header(); while (fread((char*)&numPoints, 1, 4, m_FilePointer)==4) { if ( numPoints <= 0 ) { printf( "[ERROR] Trying to read a fiber with %d points!\n", numPoints ); return -1; } vtkSmartPointer container = vtkSmartPointer::New(); float tmp[3]; for(int i=0; iInsertNextPoint(tmp); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } vtkSmartPointer fiberPolyData = vtkSmartPointer::New(); fiberPolyData->SetPoints(vtkNewPoints); fiberPolyData->SetLines(vtkNewCells); mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New(); matrix->Identity(); if (use_matrix) for (int i=0; i<4; ++i) for (int j=0; j<4; ++j) { if (j<3) matrix->SetElement(i, j, m_Header.vox_to_ras[i][j]/m_Header.voxel_size[j]); else matrix->SetElement(i, j, m_Header.vox_to_ras[i][j]); } if (m_Header.voxel_order[0]=='R') { matrix->SetElement(0,0,-matrix->GetElement(0,0)); matrix->SetElement(0,1,-matrix->GetElement(0,1)); matrix->SetElement(0,2,-matrix->GetElement(0,2)); matrix->SetElement(0,3,-matrix->GetElement(0,3)); } if (m_Header.voxel_order[1]=='A') { matrix->SetElement(1,0,-matrix->GetElement(1,0)); matrix->SetElement(1,1,-matrix->GetElement(1,1)); matrix->SetElement(1,2,-matrix->GetElement(1,2)); matrix->SetElement(1,3,-matrix->GetElement(1,3)); } if (m_Header.voxel_order[2]=='I') { matrix->SetElement(2,0,-matrix->GetElement(2,0)); matrix->SetElement(2,1,-matrix->GetElement(2,1)); matrix->SetElement(2,2,-matrix->GetElement(2,2)); matrix->SetElement(2,3,-matrix->GetElement(2,3)); } if (flip_x) { matrix->SetElement(0,0,-matrix->GetElement(0,0)); matrix->SetElement(0,1,-matrix->GetElement(0,1)); matrix->SetElement(0,2,-matrix->GetElement(0,2)); matrix->SetElement(0,3,-matrix->GetElement(0,3)); } if (flip_y) { matrix->SetElement(1,0,-matrix->GetElement(1,0)); matrix->SetElement(1,1,-matrix->GetElement(1,1)); matrix->SetElement(1,2,-matrix->GetElement(1,2)); matrix->SetElement(1,3,-matrix->GetElement(1,3)); } if (flip_z) { matrix->SetElement(2,0,-matrix->GetElement(2,0)); matrix->SetElement(2,1,-matrix->GetElement(2,1)); matrix->SetElement(2,2,-matrix->GetElement(2,2)); matrix->SetElement(2,3,-matrix->GetElement(2,3)); } geometry->SetIndexToWorldTransformByVtkMatrix(matrix); vtkSmartPointer transformFilter = vtkSmartPointer::New(); transformFilter->SetInputData(fiberPolyData); transformFilter->SetTransform(geometry->GetVtkTransform()); transformFilter->Update(); fib->SetFiberPolyData(transformFilter->GetOutput()); fib->SetTrackVisHeader(geometry.GetPointer()); fib->SetTrackVisHeader(m_Header); return numPoints; } // Update the field in the header to the new FIBER TOTAL. // ------------------------------------------------------ void TrackVisFiberReader::updateTotal( int totFibers ) { fseek(m_FilePointer, 1000-12, SEEK_SET); if (fwrite((char*)&totFibers, 1, 4, m_FilePointer) != 4) MITK_ERROR << "[ERROR] Problems saving the fiber!"; } void TrackVisFiberReader::writeHdr() { fseek(m_FilePointer, 0, SEEK_SET); if (fwrite((char*)&m_Header, 1, 1000, m_FilePointer) != 1000) MITK_ERROR << "[ERROR] Problems saving the fiber!"; } // Close the TrackVis file, but keep the metadata in the header. // ------------------------------------------------------------- void TrackVisFiberReader::close() { fclose(m_FilePointer); m_FilePointer = nullptr; } bool TrackVisFiberReader::IsTransformValid() { if (fabs(m_Header.image_orientation_patient[0])<=0.001 || fabs(m_Header.image_orientation_patient[3])<=0.001 || fabs(m_Header.image_orientation_patient[5])<=0.001) return false; return true; } diff --git a/Modules/DiffusionCore/IODataStructures/mitkTrackvis.h b/Modules/DiffusionCore/IODataStructures/mitkTrackvis.h index 1a021b6..7c98e3a 100644 --- a/Modules/DiffusionCore/IODataStructures/mitkTrackvis.h +++ b/Modules/DiffusionCore/IODataStructures/mitkTrackvis.h @@ -1,53 +1,53 @@ /*=================================================================== 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 _TRACKVIS #define _TRACKVIS #include #include #include #include #include #include #include #include // Class to handle TrackVis files. // ------------------------------- class MITKDIFFUSIONCORE_EXPORT TrackVisFiberReader { private: std::string m_Filename; FILE* m_FilePointer; mitk::FiberBundle::TrackVis_header m_Header; public: - short create(std::string m_Filename, mitk::FiberBundle *fib, bool print_header); + short create(std::string m_Filename, mitk::FiberBundle *fib, bool print_header, bool use_lps); short open(std::string m_Filename ); short read( mitk::FiberBundle* fib, bool use_matrix, bool flip_x, bool flip_y, bool flip_z, bool print_header); short write(const mitk::FiberBundle* fib ); void writeHdr(); void updateTotal( int totFibers ); void close(); bool IsTransformValid(); void print_header(); TrackVisFiberReader(); ~TrackVisFiberReader(); }; #endif diff --git a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp index dfa927c..1b22f33 100644 --- a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp +++ b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp @@ -1,100 +1,100 @@ /*=================================================================== 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 "mitkFiberBundleTrackVisReader.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "mitkDiffusionIOMimeTypes.h" mitk::FiberBundleTrackVisReader::FiberBundleTrackVisReader() : mitk::AbstractFileReader( mitk::DiffusionIOMimeTypes::FIBERBUNDLE_TRK_MIMETYPE_NAME(), "TrackVis Fiber Bundle Reader" ) { Options defaultOptions; defaultOptions["Apply index to world transform stored in the TRK header"] = true; defaultOptions["Print header"] = true; - defaultOptions["Flip x"] = true; + defaultOptions["Flip x"] = false; defaultOptions["Flip y"] = false; defaultOptions["Flip z"] = false; this->SetDefaultOptions(defaultOptions); m_ServiceReg = this->RegisterService(); } mitk::FiberBundleTrackVisReader::FiberBundleTrackVisReader(const FiberBundleTrackVisReader &other) :mitk::AbstractFileReader(other) { } mitk::FiberBundleTrackVisReader * mitk::FiberBundleTrackVisReader::Clone() const { return new FiberBundleTrackVisReader(*this); } std::vector > mitk::FiberBundleTrackVisReader::DoRead() { std::vector > result; try { const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, nullptr ); setlocale(LC_ALL, locale.c_str()); std::string filename = this->GetInputLocation(); MITK_INFO << "Loading tractogram (TrackVis format): " << itksys::SystemTools::GetFilenameName(filename); std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename); ext = itksys::SystemTools::LowerCase(ext); if (ext==".trk") { Options options = this->GetOptions(); bool apply_matrix = us::any_cast(options["Apply index to world transform stored in the TRK header"]); bool flip_x = us::any_cast(options["Flip x"]); bool flip_y = us::any_cast(options["Flip y"]); bool flip_z = us::any_cast(options["Flip z"]); bool print_header = us::any_cast(options["Print header"]); FiberBundle::Pointer mitk_fib = FiberBundle::New(); TrackVisFiberReader reader; reader.open(this->GetInputLocation().c_str()); reader.read(mitk_fib.GetPointer(), apply_matrix, flip_x, flip_y, flip_z, print_header); result.push_back(mitk_fib.GetPointer()); return result; } setlocale(LC_ALL, currLocale.c_str()); MITK_INFO << "Fiber bundle read"; } catch(...) { throw; } return result; } diff --git a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisWriter.cpp b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisWriter.cpp index bcd6abb..cf8a924 100644 --- a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisWriter.cpp +++ b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisWriter.cpp @@ -1,108 +1,110 @@ /*=================================================================== 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 "mitkFiberBundleTrackVisWriter.h" #include #include #include #include #include #include #include #include #include #include #include "mitkDiffusionIOMimeTypes.h" mitk::FiberBundleTrackVisWriter::FiberBundleTrackVisWriter() : mitk::AbstractFileWriter(mitk::FiberBundle::GetStaticNameOfClass(), mitk::DiffusionIOMimeTypes::FIBERBUNDLE_TRK_MIMETYPE_NAME(), "TrackVis Fiber Bundle Reader") { Options defaultOptions; defaultOptions["Print header"] = false; + defaultOptions["Use LPS coordinate system (default is RAS)"] = false; this->SetDefaultOptions(defaultOptions); RegisterService(); } mitk::FiberBundleTrackVisWriter::FiberBundleTrackVisWriter(const mitk::FiberBundleTrackVisWriter & other) :mitk::AbstractFileWriter(other) {} mitk::FiberBundleTrackVisWriter::~FiberBundleTrackVisWriter() {} mitk::FiberBundleTrackVisWriter * mitk::FiberBundleTrackVisWriter::Clone() const { return new mitk::FiberBundleTrackVisWriter(*this); } void mitk::FiberBundleTrackVisWriter::Write() { std::ostream* out; std::ofstream outStream; if( this->GetOutputStream() ) { out = this->GetOutputStream(); }else{ outStream.open( this->GetOutputLocation().c_str() ); out = &outStream; } if ( !out->good() ) { mitkThrow() << "Stream not good."; } try { const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, nullptr ); setlocale(LC_ALL, locale.c_str()); std::locale I("C"); out->imbue(I); std::string filename = this->GetOutputLocation().c_str(); mitk::FiberBundle::ConstPointer input = dynamic_cast(this->GetInput()); std::string ext = itksys::SystemTools::GetFilenameLastExtension(this->GetOutputLocation().c_str()); // default extension is .fib if(ext == "") { ext = ".trk"; this->SetOutputLocation(this->GetOutputLocation() + ext); } Options options = this->GetOptions(); bool print_header = us::any_cast(options["Print header"]); + bool use_lps = us::any_cast(options["Use LPS coordinate system (default is RAS)"]); MITK_INFO << "Writing fiber bundle as TRK"; TrackVisFiberReader trk; - trk.create(filename, const_cast(input.GetPointer()), print_header); + trk.create(filename, const_cast(input.GetPointer()), print_header, use_lps); trk.writeHdr(); trk.write(input.GetPointer()); setlocale(LC_ALL, currLocale.c_str()); MITK_INFO << "TrackVis Fiber bundle written to " << filename; } catch(...) { throw; } } diff --git a/Modules/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.cpp b/Modules/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.cpp index 469bb13..8fd9e0d 100644 --- a/Modules/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.cpp +++ b/Modules/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerOdf.cpp @@ -1,300 +1,300 @@ /*=================================================================== 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 "mitkTrackingHandlerOdf.h" #include #include #include #include #include namespace mitk { TrackingHandlerOdf::TrackingHandlerOdf() : m_NumProbSamples(1) , m_OdfFromTensor(false) { m_GfaInterpolator = itk::LinearInterpolateImageFunction< itk::Image< float, 3 >, float >::New(); m_OdfInterpolator = itk::LinearInterpolateImageFunction< itk::Image< ItkOdfImageType::PixelType, 3 >, float >::New(); } TrackingHandlerOdf::~TrackingHandlerOdf() { } bool TrackingHandlerOdf::WorldToIndex(itk::Point& pos, itk::Index<3>& index) { m_OdfImage->TransformPhysicalPointToIndex(pos, index); return m_OdfImage->GetLargestPossibleRegion().IsInside(index); } void TrackingHandlerOdf::InitForTracking() { MITK_INFO << "Initializing ODF tracker."; if (m_NeedsDataInit) { m_OdfHemisphereIndices.clear(); itk::OrientationDistributionFunction< float, ODF_SAMPLING_SIZE > odf; vnl_vector_fixed ref; ref.fill(0); ref[0]=1; for (int i=0; i0) m_OdfHemisphereIndices.push_back(i); m_OdfFloatDirs.set_size(m_OdfHemisphereIndices.size(), 3); auto double_dir = m_OdfImage->GetDirection().GetVnlMatrix(); for (int r=0; r<3; r++) for (int c=0; c<3; c++) { m_FloatImageRotation[r][c] = double_dir[r][c]; } for (unsigned int i=0; i GfaFilterType; GfaFilterType::Pointer gfaFilter = GfaFilterType::New(); gfaFilter->SetInput(m_OdfImage); gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD); gfaFilter->Update(); m_GfaImage = gfaFilter->GetOutput(); } m_NeedsDataInit = false; } if (m_OdfFromTensor) { // m_Parameters->m_OdfCutoff = 0; // m_Parameters->m_SharpenOdfs = false; } m_GfaInterpolator->SetInputImage(m_GfaImage); m_OdfInterpolator->SetInputImage(m_OdfImage); this->CalculateMinVoxelSize(); std::cout << "TrackingHandlerOdf - GFA threshold: " << m_Parameters->m_Cutoff << std::endl; std::cout << "TrackingHandlerOdf - ODF threshold: " << m_Parameters->m_OdfCutoff << std::endl; if (m_Parameters->m_SharpenOdfs > 1) - std::cout << "TrackingHandlerOdf - Raising ODf values to the power of " << m_Parameters->m_SharpenOdfs << std::endl; + std::cout << "TrackingHandlerOdf - Raising ODF values to the power of " << m_Parameters->m_SharpenOdfs << std::endl; } int TrackingHandlerOdf::SampleOdf(vnl_vector< float >& probs, vnl_vector< float >& angles) { boost::random::discrete_distribution dist(probs.begin(), probs.end()); int sampled_idx = 0; int max_sample_idx = -1; float max_prob = 0; int trials = 0; for (int i=0; i> sampler(m_Rng, dist); sampled_idx = sampler(); } if (probs[sampled_idx]>max_prob && probs[sampled_idx]>m_Parameters->m_OdfCutoff && fabs(angles[sampled_idx])>=m_Parameters->GetAngularThresholdDot()) { max_prob = probs[sampled_idx]; max_sample_idx = sampled_idx; } else if ( (probs[sampled_idx]<=m_Parameters->m_OdfCutoff || fabs(angles[sampled_idx])GetAngularThresholdDot()) && trials<50) // we allow 50 trials to exceed the ODF threshold i--; } return max_sample_idx; } void TrackingHandlerOdf::SetIsOdfFromTensor(bool OdfFromTensor) { m_OdfFromTensor = OdfFromTensor; } bool TrackingHandlerOdf::GetIsOdfFromTensor() const { return m_OdfFromTensor; } vnl_vector_fixed TrackingHandlerOdf::ProposeDirection(const itk::Point& pos, std::deque >& olddirs, itk::Index<3>& oldIndex) { vnl_vector_fixed output_direction; output_direction.fill(0); itk::Index<3> idx; m_OdfImage->TransformPhysicalPointToIndex(pos, idx); if ( !m_OdfImage->GetLargestPossibleRegion().IsInside(idx) ) return output_direction; // check GFA threshold for termination float gfa = mitk::imv::GetImageValue(pos, m_Parameters->m_InterpolateTractographyData, m_GfaInterpolator); if (gfam_Cutoff) return output_direction; vnl_vector_fixed last_dir; if (!olddirs.empty()) last_dir = olddirs.back(); if (!m_Parameters->m_InterpolateTractographyData && oldIndex==idx) return last_dir; ItkOdfImageType::PixelType odf_values = mitk::imv::GetImageValue(pos, m_Parameters->m_InterpolateTractographyData, m_OdfInterpolator); vnl_vector< float > probs; probs.set_size(m_OdfHemisphereIndices.size()); vnl_vector< float > angles; angles.set_size(m_OdfHemisphereIndices.size()); angles.fill(1.0); // Find ODF maximum and remove <0 values float max_odf_val = 0; float odf_sum = 0; int max_idx_d = -1; int c = 0; for (int i : m_OdfHemisphereIndices) { if (odf_values[i]<0) probs[c] = 0; else { probs[c] = pow(odf_values[i], m_Parameters->m_SharpenOdfs); if (probs[c]>max_odf_val) { max_odf_val = probs[c]; max_idx_d = c; } odf_sum += probs[c]; } c++; } if (odf_sum>0) { probs /= odf_sum; max_odf_val = max_odf_val/odf_sum; } // no previous direction if (max_odf_val>m_Parameters->m_OdfCutoff && (olddirs.empty() || last_dir.magnitude()<=0.5)) { if (m_Parameters->m_Mode==MODE::DETERMINISTIC) // return maximum peak { output_direction = m_OdfFloatDirs.get_row(max_idx_d); return output_direction * max_odf_val; } else if (m_Parameters->m_Mode==MODE::PROBABILISTIC) // sample from complete ODF { int max_sample_idx = SampleOdf(probs, angles); if (max_sample_idx>=0) output_direction = m_OdfFloatDirs.get_row(max_sample_idx) * probs[max_sample_idx]; return output_direction; } } else if (max_odf_val<=m_Parameters->m_OdfCutoff) // return (0,0,0) { return output_direction; } // correct previous direction if (m_Parameters->m_FlipX) last_dir[0] *= -1; if (m_Parameters->m_FlipY) last_dir[1] *= -1; if (m_Parameters->m_FlipZ) last_dir[2] *= -1; // calculate angles between previous direction and ODF directions angles = m_OdfFloatDirs*last_dir; float probs_sum = 0; float max_prob = 0; for (unsigned int i=0; im_Mode==MODE::DETERMINISTIC && prob>max_prob && prob>m_Parameters->m_OdfCutoff) { // use maximum peak of the ODF weighted with the directional prior max_prob = prob; vnl_vector_fixed d = m_OdfFloatDirs.get_row(i); if (angle<0) d *= -1; output_direction = prob*d; } else if (m_Parameters->m_Mode==MODE::PROBABILISTIC) { probs[i] = prob; probs_sum += probs[i]; } } // do probabilistic sampling if (m_Parameters->m_Mode==MODE::PROBABILISTIC && probs_sum>0.0001) { probs /= probs_sum; // we have to normalize again since the probabilities have been weighted by the directional prior int max_sample_idx = SampleOdf(probs, angles); if (max_sample_idx>=0) { output_direction = m_OdfFloatDirs.get_row(max_sample_idx); if (angles[max_sample_idx]<0) output_direction *= -1; output_direction *= probs[max_sample_idx]; } } // check hard angular threshold float mag = output_direction.magnitude(); if (mag>=0.0001) { output_direction.normalize(); float a = dot_product(output_direction, last_dir); if (aGetAngularThresholdDot()) output_direction.fill(0); } else output_direction.fill(0); if (m_Parameters->m_FlipX) output_direction[0] *= -1; if (m_Parameters->m_FlipY) output_direction[1] *= -1; if (m_Parameters->m_FlipZ) output_direction[2] *= -1; if (m_Parameters->m_ApplyDirectionMatrix) output_direction = m_FloatImageRotation*output_direction; return output_direction; } void TrackingHandlerOdf::SetNumProbSamples(int NumProbSamples) { m_NumProbSamples = NumProbSamples; } } diff --git a/Modules/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp b/Modules/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp index 86abf58..1e8d617 100644 --- a/Modules/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp +++ b/Modules/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp @@ -1,997 +1,1009 @@ /*=================================================================== 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 "itkStreamlineTrackingFilter.h" #include #include #include #include "itkPointShell.h" #include #include #include #include #include #include #include #include #include namespace itk { StreamlineTrackingFilter ::StreamlineTrackingFilter() : m_PauseTracking(false) , m_AbortTracking(false) , m_BuildFibersFinished(false) , m_BuildFibersReady(0) , m_FiberPolyData(nullptr) , m_Points(nullptr) , m_Cells(nullptr) , m_StoppingRegions(nullptr) , m_TargetRegions(nullptr) , m_SeedImage(nullptr) , m_MaskImage(nullptr) , m_ExclusionRegions(nullptr) , m_OutputProbabilityMap(nullptr) , m_Verbose(true) , m_DemoMode(false) , m_CurrentTracts(0) , m_Progress(0) , m_StopTracking(false) , m_TrackingPriorHandler(nullptr) { this->SetNumberOfRequiredInputs(0); } std::string StreamlineTrackingFilter::GetStatusText() { std::string status = "Seedpoints processed: " + boost::lexical_cast(m_Progress) + "/" + boost::lexical_cast(m_SeedPoints.size()); if (m_SeedPoints.size()>0) status += " (" + boost::lexical_cast(100*m_Progress/m_SeedPoints.size()) + "%)"; if (m_Parameters->m_MaxNumFibers>0) status += "\nFibers accepted: " + boost::lexical_cast(m_CurrentTracts) + "/" + boost::lexical_cast(m_Parameters->m_MaxNumFibers); else status += "\nFibers accepted: " + boost::lexical_cast(m_CurrentTracts); return status; } void StreamlineTrackingFilter::BeforeTracking() { m_StopTracking = false; m_TrackingHandler->SetParameters(m_Parameters); m_TrackingHandler->InitForTracking(); m_FiberPolyData = PolyDataType::New(); m_Points = vtkSmartPointer< vtkPoints >::New(); m_Cells = vtkSmartPointer< vtkCellArray >::New(); if (m_TrackingPriorHandler!=nullptr) { m_TrackingPriorHandler->InitForTracking(); } auto imageSpacing = m_TrackingHandler->GetSpacing(); if (m_Parameters->m_OutputProbMap) { m_OutputProbabilityMap = ItkDoubleImgType::New(); m_OutputProbabilityMap->SetSpacing(imageSpacing); m_OutputProbabilityMap->SetOrigin(m_TrackingHandler->GetOrigin()); m_OutputProbabilityMap->SetDirection(m_TrackingHandler->GetDirection()); m_OutputProbabilityMap->SetRegions(m_TrackingHandler->GetLargestPossibleRegion()); m_OutputProbabilityMap->Allocate(); m_OutputProbabilityMap->FillBuffer(0); } m_MaskInterpolator = itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::New(); m_StopInterpolator = itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::New(); m_SeedInterpolator = itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::New(); m_TargetInterpolator = itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::New(); m_ExclusionInterpolator = itk::LinearInterpolateImageFunction< ItkFloatImgType, float >::New(); if (m_StoppingRegions.IsNull()) { m_StoppingRegions = ItkFloatImgType::New(); m_StoppingRegions->SetSpacing( imageSpacing ); m_StoppingRegions->SetOrigin( m_TrackingHandler->GetOrigin() ); m_StoppingRegions->SetDirection( m_TrackingHandler->GetDirection() ); m_StoppingRegions->SetRegions( m_TrackingHandler->GetLargestPossibleRegion() ); m_StoppingRegions->Allocate(); m_StoppingRegions->FillBuffer(0); } else std::cout << "StreamlineTracking - Using stopping region image" << std::endl; m_StopInterpolator->SetInputImage(m_StoppingRegions); if (m_ExclusionRegions.IsNotNull()) { std::cout << "StreamlineTracking - Using exclusion region image" << std::endl; m_ExclusionInterpolator->SetInputImage(m_ExclusionRegions); } if (m_TargetRegions.IsNull()) { m_TargetImageSet = false; m_TargetRegions = ItkFloatImgType::New(); m_TargetRegions->SetSpacing( imageSpacing ); m_TargetRegions->SetOrigin( m_TrackingHandler->GetOrigin() ); m_TargetRegions->SetDirection( m_TrackingHandler->GetDirection() ); m_TargetRegions->SetRegions( m_TrackingHandler->GetLargestPossibleRegion() ); m_TargetRegions->Allocate(); m_TargetRegions->FillBuffer(1); } else { m_TargetImageSet = true; m_TargetInterpolator->SetInputImage(m_TargetRegions); std::cout << "StreamlineTracking - Using target region image" << std::endl; } if (m_SeedImage.IsNull()) { m_SeedImageSet = false; m_SeedImage = ItkFloatImgType::New(); m_SeedImage->SetSpacing( imageSpacing ); m_SeedImage->SetOrigin( m_TrackingHandler->GetOrigin() ); m_SeedImage->SetDirection( m_TrackingHandler->GetDirection() ); m_SeedImage->SetRegions( m_TrackingHandler->GetLargestPossibleRegion() ); m_SeedImage->Allocate(); m_SeedImage->FillBuffer(1); } else { m_SeedImageSet = true; std::cout << "StreamlineTracking - Using seed image" << std::endl; } m_SeedInterpolator->SetInputImage(m_SeedImage); if (m_MaskImage.IsNull()) { // initialize mask image m_MaskImage = ItkFloatImgType::New(); m_MaskImage->SetSpacing( imageSpacing ); m_MaskImage->SetOrigin( m_TrackingHandler->GetOrigin() ); m_MaskImage->SetDirection( m_TrackingHandler->GetDirection() ); m_MaskImage->SetRegions( m_TrackingHandler->GetLargestPossibleRegion() ); m_MaskImage->Allocate(); m_MaskImage->FillBuffer(1); } else std::cout << "StreamlineTracking - Using mask image" << std::endl; m_MaskInterpolator->SetInputImage(m_MaskImage); // Autosettings for endpoint constraints if (m_Parameters->m_EpConstraints==EndpointConstraints::NONE && m_TargetImageSet && m_SeedImageSet) { MITK_INFO << "No endpoint constraint chosen but seed and target image set --> setting constraint to EPS_IN_SEED_AND_TARGET"; m_Parameters->m_EpConstraints = EndpointConstraints::EPS_IN_SEED_AND_TARGET; } else if (m_Parameters->m_EpConstraints==EndpointConstraints::NONE && m_TargetImageSet) { MITK_INFO << "No endpoint constraint chosen but target image set --> setting constraint to EPS_IN_TARGET"; m_Parameters->m_EpConstraints = EndpointConstraints::EPS_IN_TARGET; } // Check if endpoint constraints are valid FiberType test_fib; itk::Point p; p.Fill(0); test_fib.push_back(p); test_fib.push_back(p); IsValidFiber(&test_fib); if (m_SeedPoints.empty()) GetSeedPointsFromSeedImage(); m_BuildFibersReady = 0; m_BuildFibersFinished = false; m_Tractogram.clear(); m_SamplingPointset = mitk::PointSet::New(); m_AlternativePointset = mitk::PointSet::New(); m_StopVotePointset = mitk::PointSet::New(); m_StartTime = std::chrono::system_clock::now(); if (m_DemoMode) omp_set_num_threads(1); if (m_Parameters->m_Mode==mitk::TrackingDataHandler::MODE::DETERMINISTIC) std::cout << "StreamlineTracking - Mode: deterministic" << std::endl; else if(m_Parameters->m_Mode==mitk::TrackingDataHandler::MODE::PROBABILISTIC) { std::cout << "StreamlineTracking - Mode: probabilistic" << std::endl; std::cout << "StreamlineTracking - Trials per seed: " << m_Parameters->m_TrialsPerSeed << std::endl; } else std::cout << "StreamlineTracking - Mode: ???" << std::endl; if (m_Parameters->m_EpConstraints==EndpointConstraints::NONE) std::cout << "StreamlineTracking - Endpoint constraint: NONE" << std::endl; else if (m_Parameters->m_EpConstraints==EndpointConstraints::EPS_IN_TARGET) std::cout << "StreamlineTracking - Endpoint constraint: EPS_IN_TARGET" << std::endl; else if (m_Parameters->m_EpConstraints==EndpointConstraints::EPS_IN_TARGET_LABELDIFF) std::cout << "StreamlineTracking - Endpoint constraint: EPS_IN_TARGET_LABELDIFF" << std::endl; else if (m_Parameters->m_EpConstraints==EndpointConstraints::EPS_IN_SEED_AND_TARGET) std::cout << "StreamlineTracking - Endpoint constraint: EPS_IN_SEED_AND_TARGET" << std::endl; else if (m_Parameters->m_EpConstraints==EndpointConstraints::MIN_ONE_EP_IN_TARGET) std::cout << "StreamlineTracking - Endpoint constraint: MIN_ONE_EP_IN_TARGET" << std::endl; else if (m_Parameters->m_EpConstraints==EndpointConstraints::ONE_EP_IN_TARGET) std::cout << "StreamlineTracking - Endpoint constraint: ONE_EP_IN_TARGET" << std::endl; else if (m_Parameters->m_EpConstraints==EndpointConstraints::NO_EP_IN_TARGET) std::cout << "StreamlineTracking - Endpoint constraint: NO_EP_IN_TARGET" << std::endl; std::cout << "StreamlineTracking - Angular threshold: " << m_Parameters->GetAngularThresholdDeg() << "°" << std::endl; std::cout << "StreamlineTracking - Stepsize: " << m_Parameters->GetStepSizeMm() << "mm (" << m_Parameters->GetStepSizeMm()/m_Parameters->GetMinVoxelSizeMm() << "*vox)" << std::endl; std::cout << "StreamlineTracking - Seeds per voxel: " << m_Parameters->m_SeedsPerVoxel << std::endl; std::cout << "StreamlineTracking - Max. tract length: " << m_Parameters->m_MaxTractLengthMm << "mm" << std::endl; std::cout << "StreamlineTracking - Min. tract length: " << m_Parameters->m_MinTractLengthMm << "mm" << std::endl; std::cout << "StreamlineTracking - Max. num. tracts: " << m_Parameters->m_MaxNumFibers << std::endl; std::cout << "StreamlineTracking - Loop check: " << m_Parameters->GetLoopCheckDeg() << "°" << std::endl; + if (m_Parameters->m_SecondOrder) + std::cout << "StreamlineTracking - Using second order streamline integration" << std::endl; + else + std::cout << "StreamlineTracking - Using first order streamline integration" << std::endl; std::cout << "StreamlineTracking - Num. neighborhood samples: " << m_Parameters->m_NumSamples << std::endl; std::cout << "StreamlineTracking - Max. sampling distance: " << m_Parameters->GetSamplingDistanceMm() << "mm (" << m_Parameters->GetSamplingDistanceMm()/m_Parameters->GetMinVoxelSizeMm() << "*vox)" << std::endl; std::cout << "StreamlineTracking - Deflection modifier: " << m_Parameters->m_DeflectionMod << std::endl; std::cout << "StreamlineTracking - Use stop votes: " << m_Parameters->m_StopVotes << std::endl; std::cout << "StreamlineTracking - Only frontal samples: " << m_Parameters->m_OnlyForwardSamples << std::endl; if (m_TrackingPriorHandler!=nullptr) std::cout << "StreamlineTracking - Using directional prior for tractography (w=" << m_Parameters->m_Weight << ")" << std::endl; if (m_DemoMode) { std::cout << "StreamlineTracking - Running in demo mode"; std::cout << "StreamlineTracking - Starting streamline tracking using 1 thread" << std::endl; } else std::cout << "StreamlineTracking - Starting streamline tracking using " << omp_get_max_threads() << " threads" << std::endl; } void StreamlineTrackingFilter::CalculateNewPosition(itk::Point& pos, vnl_vector_fixed& dir) { pos[0] += dir[0]*m_Parameters->GetStepSizeMm(); pos[1] += dir[1]*m_Parameters->GetStepSizeMm(); pos[2] += dir[2]*m_Parameters->GetStepSizeMm(); } std::vector< vnl_vector_fixed > StreamlineTrackingFilter::CreateDirections(unsigned int NPoints) { std::vector< vnl_vector_fixed > pointshell; if (NPoints<2) return pointshell; std::vector< double > theta; theta.resize(NPoints); std::vector< double > phi; phi.resize(NPoints); auto C = sqrt(4*itk::Math::pi); phi[0] = 0.0; phi[NPoints-1] = 0.0; for(unsigned int i=0; i0 && i d; d[0] = static_cast(cos(theta[i]) * cos(phi[i])); d[1] = static_cast(cos(theta[i]) * sin(phi[i])); d[2] = static_cast(sin(theta[i])); pointshell.push_back(d); } return pointshell; } vnl_vector_fixed StreamlineTrackingFilter::GetNewDirection(const itk::Point &pos, std::deque >& olddirs, itk::Index<3> &oldIndex) { if (m_DemoMode) { m_SamplingPointset->Clear(); m_AlternativePointset->Clear(); m_StopVotePointset->Clear(); } vnl_vector_fixed direction; direction.fill(0); if (mitk::imv::IsInsideMask(pos, m_Parameters->m_InterpolateRoiImages, m_MaskInterpolator) && !mitk::imv::IsInsideMask(pos, m_Parameters->m_InterpolateRoiImages, m_StopInterpolator)) direction = m_TrackingHandler->ProposeDirection(pos, olddirs, oldIndex); // get direction proposal at current streamline position else return direction; int stop_votes = 0; int possible_stop_votes = 0; if (!olddirs.empty()) { vnl_vector_fixed olddir = olddirs.back(); std::vector< vnl_vector_fixed > probeVecs = CreateDirections(m_Parameters->m_NumSamples); itk::Point sample_pos; unsigned int alternatives = 1; for (unsigned int i=0; i d; bool is_stop_voter = false; if (!m_Parameters->m_FixRandomSeed && m_Parameters->m_RandomSampling) { d[0] = static_cast(m_TrackingHandler->GetRandDouble(-0.5, 0.5)); d[1] = static_cast(m_TrackingHandler->GetRandDouble(-0.5, 0.5)); d[2] = static_cast(m_TrackingHandler->GetRandDouble(-0.5, 0.5)); d.normalize(); d *= static_cast(m_TrackingHandler->GetRandDouble(0, static_cast(m_Parameters->GetSamplingDistanceMm()))); } else { d = probeVecs.at(i); float dot = dot_product(d, olddir); if (m_Parameters->m_StopVotes && dot>0.7f) { is_stop_voter = true; possible_stop_votes++; } else if (m_Parameters->m_OnlyForwardSamples && dot<0) continue; d *= m_Parameters->GetSamplingDistanceMm(); } sample_pos[0] = pos[0] + d[0]; sample_pos[1] = pos[1] + d[1]; sample_pos[2] = pos[2] + d[2]; vnl_vector_fixed tempDir; tempDir.fill(0.0); if (mitk::imv::IsInsideMask(sample_pos, m_Parameters->m_InterpolateRoiImages, m_MaskInterpolator)) tempDir = m_TrackingHandler->ProposeDirection(sample_pos, olddirs, oldIndex); // sample neighborhood if (tempDir.magnitude()>static_cast(mitk::eps)) { direction += tempDir; if(m_DemoMode) m_SamplingPointset->InsertPoint(i, sample_pos); } else if (m_Parameters->m_AvoidStop && olddir.magnitude()>0.5f) // out of white matter { if (is_stop_voter) stop_votes++; if (m_DemoMode) m_StopVotePointset->InsertPoint(i, sample_pos); float dot = dot_product(d, olddir); if (dot >= 0.0f) // in front of plane defined by pos and olddir d = -d + 2*dot*olddir; // reflect else d = -d; // invert // look a bit further into the other direction sample_pos[0] = pos[0] + d[0]; sample_pos[1] = pos[1] + d[1]; sample_pos[2] = pos[2] + d[2]; alternatives++; vnl_vector_fixed tempDir; tempDir.fill(0.0); if (mitk::imv::IsInsideMask(sample_pos, m_Parameters->m_InterpolateRoiImages, m_MaskInterpolator)) tempDir = m_TrackingHandler->ProposeDirection(sample_pos, olddirs, oldIndex); // sample neighborhood if (tempDir.magnitude()>static_cast(mitk::eps)) // are we back in the white matter? { direction += d * m_Parameters->m_DeflectionMod; // go into the direction of the white matter direction += tempDir; // go into the direction of the white matter direction at this location if(m_DemoMode) m_AlternativePointset->InsertPoint(alternatives, sample_pos); } else { if (m_DemoMode) m_StopVotePointset->InsertPoint(i, sample_pos); } } else { if (m_DemoMode) m_StopVotePointset->InsertPoint(i, sample_pos); if (is_stop_voter) stop_votes++; } } } bool valid = false; if (direction.magnitude()>0.001f && (possible_stop_votes==0 || static_cast(stop_votes)/possible_stop_votes<0.5f) ) { direction.normalize(); valid = true; } else direction.fill(0); if (m_TrackingPriorHandler!=nullptr && (m_Parameters->m_NewDirectionsFromPrior || valid)) { vnl_vector_fixed prior = m_TrackingPriorHandler->ProposeDirection(pos, olddirs, oldIndex); if (prior.magnitude()>0.001f) { prior.normalize(); if (dot_product(prior,direction)<0) prior *= -1; direction = (1.0f-m_Parameters->m_Weight) * direction + m_Parameters->m_Weight * prior; direction.normalize(); } else if (m_Parameters->m_RestrictToPrior) direction.fill(0.0); } return direction; } float StreamlineTrackingFilter::FollowStreamline(itk::Point pos, vnl_vector_fixed dir, FiberType* fib, DirectionContainer* container, float tractLength, bool front, bool &exclude) { vnl_vector_fixed zero_dir; zero_dir.fill(0.0); std::deque< vnl_vector_fixed > last_dirs; for (unsigned int i=0; im_NumPreviousDirections-1; i++) last_dirs.push_back(zero_dir); for (int step=0; step< 5000; step++) { itk::Index<3> oldIndex; m_TrackingHandler->WorldToIndex(pos, oldIndex); // get new position CalculateNewPosition(pos, dir); if (m_ExclusionRegions.IsNotNull() && mitk::imv::IsInsideMask(pos, m_Parameters->m_InterpolateRoiImages, m_ExclusionInterpolator)) { exclude = true; return tractLength; } if (m_AbortTracking) return tractLength; // if yes, add new point to streamline dir.normalize(); if (front) { fib->push_front(pos); container->push_front(dir); } else { fib->push_back(pos); container->push_back(dir); } tractLength += m_Parameters->GetStepSizeMm(); if (m_Parameters->GetLoopCheckDeg()>=0 && CheckCurvature(container, front)>m_Parameters->GetLoopCheckDeg()) return tractLength; if (tractLength>m_Parameters->m_MaxTractLengthMm) return tractLength; if (m_DemoMode && !m_Parameters->m_OutputProbMap) // CHECK: warum sind die samplingpunkte der streamline in der visualisierung immer einen schritt voras? { #pragma omp critical { m_BuildFibersReady++; m_Tractogram.push_back(*fib); BuildFibers(true); m_Stop = true; while (m_Stop){ } } } last_dirs.push_back(dir); if (last_dirs.size()>m_Parameters->m_NumPreviousDirections) last_dirs.pop_front(); dir = GetNewDirection(pos, last_dirs, oldIndex); + if (m_Parameters->m_SecondOrder) + { + itk::Point dpos = pos; + dpos[0] += dir[0]*m_Parameters->GetStepSizeMm()*0.5; + dpos[1] += dir[1]*m_Parameters->GetStepSizeMm()*0.5; + dpos[2] += dir[2]*m_Parameters->GetStepSizeMm()*0.5; + dir = GetNewDirection(dpos, last_dirs, oldIndex); + } while (m_PauseTracking){} if (dir.magnitude()<0.0001f) return tractLength; } return tractLength; } float StreamlineTrackingFilter::CheckCurvature(DirectionContainer* fib, bool front) { if (fib->size()<8) return 0; float m_Distance = std::max(m_Parameters->GetMinVoxelSizeMm()*4, m_Parameters->GetStepSizeMm()*8); float dist = 0; std::vector< vnl_vector_fixed< float, 3 > > vectors; vnl_vector_fixed< float, 3 > meanV; meanV.fill(0); float dev = 0; if (front) { int c = 0; while(dist(fib->size())-1) { dist += m_Parameters->GetStepSizeMm(); vnl_vector_fixed< float, 3 > v = fib->at(static_cast(c)); if (dot_product(v,meanV)<0) v = -v; vectors.push_back(v); meanV += v; c++; } } else { int c = static_cast(fib->size())-1; while(dist=0) { dist += m_Parameters->GetStepSizeMm(); vnl_vector_fixed< float, 3 > v = fib->at(static_cast(c)); if (dot_product(v,meanV)<0) v = -v; vectors.push_back(v); meanV += v; c--; } } meanV.normalize(); for (unsigned int c=0; c1.0f) angle = 1.0; dev += acos(angle)*180.0f/static_cast(itk::Math::pi); } if (vectors.size()>0) dev /= vectors.size(); return dev; } std::shared_ptr StreamlineTrackingFilter::GetParameters() const { return m_Parameters; } void StreamlineTrackingFilter::SetParameters(std::shared_ptr< mitk::StreamlineTractographyParameters > Parameters) { m_Parameters = Parameters; } void StreamlineTrackingFilter::SetTrackingPriorHandler(mitk::TrackingDataHandler *TrackingPriorHandler) { m_TrackingPriorHandler = TrackingPriorHandler; } void StreamlineTrackingFilter::GetSeedPointsFromSeedImage() { MITK_INFO << "StreamlineTracking - Calculating seed points."; m_SeedPoints.clear(); typedef ImageRegionConstIterator< ItkFloatImgType > MaskIteratorType; MaskIteratorType sit(m_SeedImage, m_SeedImage->GetLargestPossibleRegion()); sit.GoToBegin(); while (!sit.IsAtEnd()) { if (sit.Value()>0) { ItkFloatImgType::IndexType index = sit.GetIndex(); itk::ContinuousIndex start; start[0] = index[0]; start[1] = index[1]; start[2] = index[2]; itk::Point worldPos; m_SeedImage->TransformContinuousIndexToPhysicalPoint(start, worldPos); if ( mitk::imv::IsInsideMask(worldPos, m_Parameters->m_InterpolateRoiImages, m_MaskInterpolator) ) { m_SeedPoints.push_back(worldPos); for (unsigned int s = 1; s < m_Parameters->m_SeedsPerVoxel; s++) { start[0] = index[0] + static_cast(m_TrackingHandler->GetRandDouble(-0.5, 0.5)); start[1] = index[1] + static_cast(m_TrackingHandler->GetRandDouble(-0.5, 0.5)); start[2] = index[2] + static_cast(m_TrackingHandler->GetRandDouble(-0.5, 0.5)); itk::Point worldPos; m_SeedImage->TransformContinuousIndexToPhysicalPoint(start, worldPos); m_SeedPoints.push_back(worldPos); } } } ++sit; } if (m_SeedPoints.empty()) mitkThrow() << "No valid seed point in seed image! Is your seed image registered with the image you are tracking on?"; } void StreamlineTrackingFilter::GenerateData() { this->BeforeTracking(); if (!m_Parameters->m_FixRandomSeed) { std::random_device rd; std::mt19937 g(rd()); std::shuffle(m_SeedPoints.begin(), m_SeedPoints.end(), g); } m_CurrentTracts = 0; int num_seeds = static_cast(m_SeedPoints.size()); itk::Index<3> zeroIndex; zeroIndex.Fill(0); m_Progress = 0; int i = 0; int print_interval = num_seeds/100; if (print_interval<100) m_Verbose=false; unsigned int trials_per_seed = 1; if(m_Parameters->m_Mode==mitk::TrackingDataHandler::MODE::PROBABILISTIC) trials_per_seed = m_Parameters->m_TrialsPerSeed; #pragma omp parallel while (i=num_seeds || m_StopTracking) continue; else if (m_Verbose && i%print_interval==0) #pragma omp critical { m_Progress += static_cast(print_interval); std::cout << " \r"; if (m_Parameters->m_MaxNumFibers>0) std::cout << "Tried: " << m_Progress << "/" << num_seeds << " | Accepted: " << m_CurrentTracts << "/" << m_Parameters->m_MaxNumFibers << '\r'; else std::cout << "Tried: " << m_Progress << "/" << num_seeds << " | Accepted: " << m_CurrentTracts << '\r'; cout.flush(); } const itk::Point worldPos = m_SeedPoints.at(static_cast(temp_i)); for (unsigned int trials=0; trials dir; dir.fill(0.0); std::deque< vnl_vector_fixed > olddirs; dir = GetNewDirection(worldPos, olddirs, zeroIndex) * 0.5f; bool exclude = false; if (m_ExclusionRegions.IsNotNull() && mitk::imv::IsInsideMask(worldPos, m_Parameters->m_InterpolateRoiImages, m_ExclusionInterpolator)) exclude = true; bool success = false; if (dir.magnitude()>0.0001f && !exclude) { // forward tracking tractLength = FollowStreamline(worldPos, dir, &fib, &direction_container, 0, false, exclude); fib.push_front(worldPos); // backward tracking if (!exclude) tractLength = FollowStreamline(worldPos, -dir, &fib, &direction_container, tractLength, true, exclude); counter = fib.size(); if (tractLength>=m_Parameters->m_MinTractLengthMm && counter>=2 && !exclude) { #pragma omp critical if ( IsValidFiber(&fib) ) { if (!m_StopTracking) { if (!m_Parameters->m_OutputProbMap) m_Tractogram.push_back(fib); else FiberToProbmap(&fib); m_CurrentTracts++; success = true; } if (m_Parameters->m_MaxNumFibers > 0 && m_CurrentTracts>=static_cast(m_Parameters->m_MaxNumFibers)) { if (!m_StopTracking) { std::cout << " \r"; MITK_INFO << "Reconstructed maximum number of tracts (" << m_CurrentTracts << "). Stopping tractography."; } m_StopTracking = true; } } } } if (success || m_Parameters->m_Mode!=MODE::PROBABILISTIC) break; // we only try one seed point multiple times if we use a probabilistic tracker and have not found a valid streamline yet }// trials per seed }// seed points this->AfterTracking(); } bool StreamlineTrackingFilter::IsValidFiber(FiberType* fib) { if (m_Parameters->m_EpConstraints==EndpointConstraints::NONE) { return true; } else if (m_Parameters->m_EpConstraints==EndpointConstraints::EPS_IN_TARGET) { if (m_TargetImageSet) { if ( mitk::imv::IsInsideMask(fib->front(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) && mitk::imv::IsInsideMask(fib->back(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) ) return true; return false; } else mitkThrow() << "No target image set but endpoint constraint EPS_IN_TARGET chosen!"; } else if (m_Parameters->m_EpConstraints==EndpointConstraints::EPS_IN_TARGET_LABELDIFF) { if (m_TargetImageSet) { float v1 = mitk::imv::GetImageValue(fib->front(), false, m_TargetInterpolator); float v2 = mitk::imv::GetImageValue(fib->back(), false, m_TargetInterpolator); if ( v1>0.0f && v2>0.0f && v1!=v2 ) return true; return false; } else mitkThrow() << "No target image set but endpoint constraint EPS_IN_TARGET_LABELDIFF chosen!"; } else if (m_Parameters->m_EpConstraints==EndpointConstraints::EPS_IN_SEED_AND_TARGET) { if (m_TargetImageSet && m_SeedImageSet) { if ( mitk::imv::IsInsideMask(fib->front(), m_Parameters->m_InterpolateRoiImages, m_SeedInterpolator) && mitk::imv::IsInsideMask(fib->back(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) ) return true; if ( mitk::imv::IsInsideMask(fib->back(), m_Parameters->m_InterpolateRoiImages, m_SeedInterpolator) && mitk::imv::IsInsideMask(fib->front(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) ) return true; return false; } else mitkThrow() << "No target or seed image set but endpoint constraint EPS_IN_SEED_AND_TARGET chosen!"; } else if (m_Parameters->m_EpConstraints==EndpointConstraints::MIN_ONE_EP_IN_TARGET) { if (m_TargetImageSet) { if ( mitk::imv::IsInsideMask(fib->front(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) || mitk::imv::IsInsideMask(fib->back(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) ) return true; return false; } else mitkThrow() << "No target image set but endpoint constraint MIN_ONE_EP_IN_TARGET chosen!"; } else if (m_Parameters->m_EpConstraints==EndpointConstraints::ONE_EP_IN_TARGET) { if (m_TargetImageSet) { if ( mitk::imv::IsInsideMask(fib->front(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) && !mitk::imv::IsInsideMask(fib->back(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) ) return true; if ( !mitk::imv::IsInsideMask(fib->back(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) && mitk::imv::IsInsideMask(fib->front(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) ) return true; return false; } else mitkThrow() << "No target image set but endpoint constraint ONE_EP_IN_TARGET chosen!"; } else if (m_Parameters->m_EpConstraints==EndpointConstraints::NO_EP_IN_TARGET) { if (m_TargetImageSet) { if ( mitk::imv::IsInsideMask(fib->front(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) || mitk::imv::IsInsideMask(fib->back(), m_Parameters->m_InterpolateRoiImages, m_TargetInterpolator) ) return false; return true; } else mitkThrow() << "No target image set but endpoint constraint NO_EP_IN_TARGET chosen!"; } return true; } void StreamlineTrackingFilter::FiberToProbmap(FiberType* fib) { ItkDoubleImgType::IndexType last_idx; last_idx.Fill(0); for (auto p : *fib) { ItkDoubleImgType::IndexType idx; m_OutputProbabilityMap->TransformPhysicalPointToIndex(p, idx); if (idx != last_idx) { if (m_OutputProbabilityMap->GetLargestPossibleRegion().IsInside(idx)) m_OutputProbabilityMap->SetPixel(idx, m_OutputProbabilityMap->GetPixel(idx)+1); last_idx = idx; } } } void StreamlineTrackingFilter::BuildFibers(bool check) { if (m_BuildFibersReady::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); for (unsigned int i=0; i container = vtkSmartPointer::New(); FiberType fib = m_Tractogram.at(i); for (FiberType::iterator it = fib.begin(); it!=fib.end(); ++it) { vtkIdType id = vNewPoints->InsertNextPoint((*it).GetDataPointer()); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } if (check) for (int i=0; iSetPoints(vNewPoints); m_FiberPolyData->SetLines(vNewLines); m_BuildFibersFinished = true; } void StreamlineTrackingFilter::AfterTracking() { if (m_Verbose) std::cout << " \r"; if (!m_Parameters->m_OutputProbMap) { MITK_INFO << "Reconstructed " << m_Tractogram.size() << " fibers."; MITK_INFO << "Generating polydata "; BuildFibers(false); } else { itk::RescaleIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::Pointer filter = itk::RescaleIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); filter->SetInput(m_OutputProbabilityMap); filter->SetOutputMaximum(1.0); filter->SetOutputMinimum(0.0); filter->Update(); m_OutputProbabilityMap = filter->GetOutput(); } MITK_INFO << "done"; m_EndTime = std::chrono::system_clock::now(); std::chrono::hours hh = std::chrono::duration_cast(m_EndTime - m_StartTime); std::chrono::minutes mm = std::chrono::duration_cast(m_EndTime - m_StartTime); std::chrono::seconds ss = std::chrono::duration_cast(m_EndTime - m_StartTime); mm %= 60; ss %= 60; MITK_INFO << "Tracking took " << hh.count() << "h, " << mm.count() << "m and " << ss.count() << "s"; m_SeedPoints.clear(); } void StreamlineTrackingFilter::SetDicomProperties(mitk::FiberBundle::Pointer fib) { std::string model_code_value = "-"; std::string model_code_meaning = "-"; std::string algo_code_value = "-"; std::string algo_code_meaning = "-"; if ( m_Parameters->m_Mode==MODE::DETERMINISTIC && dynamic_cast(m_TrackingHandler)) { algo_code_value = "sup181_ee01"; algo_code_meaning = "Deterministic"; if (m_Parameters->m_F > 0.99 && m_Parameters->m_G < 0.01) { if (m_Parameters->m_InterpolateTractographyData) { algo_code_value = "sup181_ee08"; algo_code_meaning = "Euler"; } else { algo_code_value = "sup181_ee04"; algo_code_meaning = "FACT"; } } else if (m_Parameters->m_G > 0.99 && m_Parameters->m_F < 0.01) { algo_code_value = "sup181_ee06"; algo_code_meaning = "TEND"; } } else if (m_Parameters->m_Mode==MODE::DETERMINISTIC) { algo_code_value = "sup181_ee01"; algo_code_meaning = "Deterministic"; } else if (m_Parameters->m_Mode==MODE::PROBABILISTIC) { algo_code_value = "sup181_ee02"; algo_code_meaning = "Probabilistic"; } if (dynamic_cast(m_TrackingHandler) || (dynamic_cast(m_TrackingHandler) && dynamic_cast(m_TrackingHandler)->GetIsOdfFromTensor() ) ) { if ( dynamic_cast(m_TrackingHandler) && dynamic_cast(m_TrackingHandler)->GetNumTensorImages()>1 ) { model_code_value = "sup181_bb02"; model_code_meaning = "Multi Tensor"; } else { model_code_value = "sup181_bb01"; model_code_meaning = "Single Tensor"; } } else if (dynamic_cast*>(m_TrackingHandler) || dynamic_cast*>(m_TrackingHandler)) { model_code_value = "sup181_bb03"; model_code_meaning = "Model Free"; } else if (dynamic_cast(m_TrackingHandler)) { model_code_value = "-"; model_code_meaning = "ODF"; } else if (dynamic_cast(m_TrackingHandler)) { model_code_value = "-"; model_code_meaning = "Peaks"; } fib->SetProperty("DICOM.anatomy.value", mitk::StringProperty::New("T-A0095")); fib->SetProperty("DICOM.anatomy.meaning", mitk::StringProperty::New("White matter of brain and spinal cord")); fib->SetProperty("DICOM.algo_family_code.value", mitk::StringProperty::New(algo_code_value)); fib->SetProperty("DICOM.algo_family_code.meaning", mitk::StringProperty::New(algo_code_meaning)); fib->SetProperty("DICOM.model_code.value", mitk::StringProperty::New(model_code_value)); fib->SetProperty("DICOM.model_code.meaning", mitk::StringProperty::New(model_code_meaning)); } } diff --git a/Modules/FiberTracking/Testing/mitkStreamlineTractographyTest.cpp b/Modules/FiberTracking/Testing/mitkStreamlineTractographyTest.cpp index cfb7b10..ae7d042 100644 --- a/Modules/FiberTracking/Testing/mitkStreamlineTractographyTest.cpp +++ b/Modules/FiberTracking/Testing/mitkStreamlineTractographyTest.cpp @@ -1,439 +1,440 @@ /*=================================================================== 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_SecondOrder = false; 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 = 1; 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 = 8; 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 = 1; 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 = 1; 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_SeedsPerVoxel = 10; params->m_SharpenOdfs = 8; 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_SeedsPerVoxel = 10; params->m_SharpenOdfs = 8; 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/mitkStreamlineTractographyParameters.cpp b/Modules/FiberTracking/mitkStreamlineTractographyParameters.cpp index 9d059e0..8199e24 100644 --- a/Modules/FiberTracking/mitkStreamlineTractographyParameters.cpp +++ b/Modules/FiberTracking/mitkStreamlineTractographyParameters.cpp @@ -1,367 +1,369 @@ /*=================================================================== 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 mitk::StreamlineTractographyParameters::StreamlineTractographyParameters() { AutoAdjust(); } mitk::StreamlineTractographyParameters::~StreamlineTractographyParameters() { } void mitk::StreamlineTractographyParameters::SaveParameters(std::string filename) { if(filename.empty()) return; if(".stp"!=filename.substr(filename.size()-4, 4)) filename += ".stp"; const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, nullptr ); if ( locale.compare(currLocale)!=0 ) { try { setlocale(LC_ALL, locale.c_str()); } catch(...) { MITK_INFO << "Could not set locale " << locale; } } boost::property_tree::ptree parameters; parameters.put("seeding.seeds_per_voxel", m_SeedsPerVoxel); parameters.put("seeding.trials_per_seed", m_TrialsPerSeed); parameters.put("seeding.max_num_fibers", m_MaxNumFibers); parameters.put("seeding.interactive_radius_mm", m_InteractiveRadiusMm); parameters.put("seeding.num_interactive_seeds", m_NumInteractiveSeeds); parameters.put("seeding.enable_interactive", m_EnableInteractive); parameters.put("roi_constraints.ep_constraints", m_EpConstraints); parameters.put("tractography.mode", m_Mode); parameters.put("tractography.sharpen_odfs", m_SharpenOdfs); parameters.put("tractography.cutoff", m_Cutoff); parameters.put("tractography.odf_cutoff", m_OdfCutoff); parameters.put("tractography.step_size_vox", m_StepSizeVox); parameters.put("tractography.min_tract_length_mm", m_MinTractLengthMm); parameters.put("tractography.max_tract_length_mm", m_MaxTractLengthMm); parameters.put("tractography.angluar_threshold_deg", m_AngularThresholdDeg); parameters.put("tractography.loop_check_deg", m_LoopCheckDeg); parameters.put("tractography.f", m_F); parameters.put("tractography.g", m_G); parameters.put("tractography.fix_seed", m_FixRandomSeed); + parameters.put("tractography.second_order", m_SecondOrder); parameters.put("tractography.peak_jitter", m_PeakJitter); parameters.put("prior.weight", m_Weight); parameters.put("prior.restrict_to_prior", m_RestrictToPrior); parameters.put("prior.new_directions", m_NewDirectionsFromPrior); parameters.put("prior.flip_x", m_PriorFlipX); parameters.put("prior.flip_y", m_PriorFlipY); parameters.put("prior.flip_z", m_PriorFlipZ); parameters.put("nsampling.num_samples", m_NumSamples); parameters.put("nsampling.sampling_distance_vox", m_SamplingDistanceVox); parameters.put("nsampling.only_frontal", m_OnlyForwardSamples); parameters.put("nsampling.stop_votes", m_StopVotes); parameters.put("data_handling.flip_x", m_FlipX); parameters.put("data_handling.flip_y", m_FlipY); parameters.put("data_handling.flip_z", m_FlipZ); parameters.put("data_handling.interpolate_tracto_data", m_InterpolateTractographyData); parameters.put("data_handling.interpolate_roi_images", m_InterpolateRoiImages); parameters.put("output.compress", m_CompressFibers); parameters.put("output.compression", m_Compression); parameters.put("output.prob_map", m_OutputProbMap); boost::property_tree::json_parser::write_json(filename, parameters, std::locale(), true); // try{ // itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); // writer->SetFileName(filename+"_FMAP.nii.gz"); // writer->SetInput(m_SignalGen.m_FrequencyMap); // writer->Update(); // } // catch(...) // { // MITK_INFO << "No frequency map saved."; // } setlocale(LC_ALL, currLocale.c_str()); } template< class ParameterType > ParameterType mitk::StreamlineTractographyParameters::ReadVal(boost::property_tree::ptree::value_type const& v, std::string tag, ParameterType defaultValue, bool essential) { try { return v.second.get(tag); } catch (...) { if (essential) { mitkThrow() << "Parameter file corrupted. Essential tag is missing: '" << tag << "'"; } MITK_INFO << "Tag '" << tag << "' not found. Using default value '" << defaultValue << "'."; return defaultValue; } } void mitk::StreamlineTractographyParameters::LoadParameters(std::string filename) { if(filename.empty()) { return; } const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, nullptr ); if ( locale.compare(currLocale)!=0 ) { try { setlocale(LC_ALL, locale.c_str()); } catch(...) { MITK_INFO << "Could not set locale " << locale; } } boost::property_tree::ptree parameterTree; boost::property_tree::json_parser::read_json( filename, parameterTree ); BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameterTree ) { if( v1.first == "seeding" ) { m_SeedsPerVoxel = ReadVal(v1,"seeds_per_voxel", m_SeedsPerVoxel); m_TrialsPerSeed = ReadVal(v1,"trials_per_seed", m_TrialsPerSeed); m_MaxNumFibers = ReadVal(v1,"max_num_fibers", m_MaxNumFibers); m_InteractiveRadiusMm = ReadVal(v1,"interactive_radius_mm", m_InteractiveRadiusMm); m_NumInteractiveSeeds = ReadVal(v1,"num_interactive_seeds", m_NumInteractiveSeeds); m_EnableInteractive = ReadVal(v1,"enable_interactive", m_EnableInteractive); } else if( v1.first == "roi_constraints" ) { switch( ReadVal(v1,"ep_constraints", 0) ) { default: m_EpConstraints = EndpointConstraints::NONE; break; case 1: m_EpConstraints = EndpointConstraints::EPS_IN_TARGET; break; case 2: m_EpConstraints = EndpointConstraints::EPS_IN_TARGET_LABELDIFF; break; case 3: m_EpConstraints = EndpointConstraints::EPS_IN_SEED_AND_TARGET; break; case 4: m_EpConstraints = EndpointConstraints::MIN_ONE_EP_IN_TARGET; break; case 5: m_EpConstraints = EndpointConstraints::ONE_EP_IN_TARGET; break; case 6: m_EpConstraints = EndpointConstraints::NO_EP_IN_TARGET; break; } } else if( v1.first == "tractography" ) { if(ReadVal(v1,"mode", 0) == 0) m_Mode = MODE::DETERMINISTIC; else m_Mode = MODE::PROBABILISTIC; m_SharpenOdfs = ReadVal(v1,"sharpen_odfs", m_SharpenOdfs); m_Cutoff = ReadVal(v1,"cutoff", m_Cutoff); m_OdfCutoff = ReadVal(v1,"odf_cutoff", m_OdfCutoff); SetStepSizeVox(ReadVal(v1,"step_size_vox", m_StepSizeVox)); m_MinTractLengthMm = ReadVal(v1,"min_tract_length_mm", m_MinTractLengthMm); m_MaxTractLengthMm = ReadVal(v1,"max_tract_length_mm", m_MaxTractLengthMm); SetAngularThresholdDeg(ReadVal(v1,"angluar_threshold_deg", m_AngularThresholdDeg)); SetLoopCheckDeg(ReadVal(v1,"loop_check_deg", m_LoopCheckDeg)); m_F = ReadVal(v1,"f", m_F); m_G = ReadVal(v1,"g", m_G); m_FixRandomSeed = ReadVal(v1,"fix_seed", m_FixRandomSeed); + m_SecondOrder = ReadVal(v1,"second_order", m_SecondOrder); m_PeakJitter = ReadVal(v1,"peak_jitter", m_PeakJitter); } else if( v1.first == "prior" ) { m_Weight = ReadVal(v1,"weight", m_Weight); m_RestrictToPrior = ReadVal(v1,"restrict_to_prior", m_RestrictToPrior); m_NewDirectionsFromPrior = ReadVal(v1,"new_directions", m_NewDirectionsFromPrior); m_PriorFlipX = ReadVal(v1,"flip_x", m_PriorFlipX); m_PriorFlipY = ReadVal(v1,"flip_y", m_PriorFlipY); m_PriorFlipZ = ReadVal(v1,"flip_z", m_PriorFlipZ); } else if( v1.first == "nsampling" ) { m_NumSamples = ReadVal(v1,"num_samples", m_NumSamples); m_SamplingDistanceVox = ReadVal(v1,"sampling_distance_vox", m_SamplingDistanceVox); m_OnlyForwardSamples = ReadVal(v1,"only_frontal", m_OnlyForwardSamples); m_StopVotes = ReadVal(v1,"stop_votes", m_StopVotes); } else if( v1.first == "data_handling" ) { m_FlipX = ReadVal(v1,"flip_x", m_FlipX); m_FlipY = ReadVal(v1,"flip_y", m_FlipY); m_FlipZ = ReadVal(v1,"flip_z", m_FlipZ); m_InterpolateTractographyData = ReadVal(v1,"interpolate_tracto_data", m_InterpolateTractographyData); m_InterpolateRoiImages = ReadVal(v1,"interpolate_roi_images", m_InterpolateRoiImages); } else if( v1.first == "output" ) { m_CompressFibers = ReadVal(v1,"compress", m_CompressFibers); m_Compression = ReadVal(v1,"compression", m_Compression); m_OutputProbMap = ReadVal(v1,"prob_map", m_OutputProbMap); } } // try // { // itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); // reader->SetFileName(filename+"_FMAP.nrrd"); // if ( itksys::SystemTools::FileExists(filename+"_FMAP.nii.gz") ) // reader->SetFileName(filename+"_FMAP.nii.gz"); // else if ( itksys::SystemTools::FileExists(filename+"_FMAP.nii") ) // reader->SetFileName(filename+"_FMAP.nii"); // else // reader->SetFileName(filename+"_FMAP.nrrd"); // reader->Update(); // m_SignalGen.m_FrequencyMap = reader->GetOutput(); // MITK_INFO << "Frequency map loaded."; // } // catch(...) // { // MITK_INFO << "No frequency map found."; // } setlocale(LC_ALL, currLocale.c_str()); } float mitk::StreamlineTractographyParameters::GetSamplingDistanceMm() const { return m_SamplingDistanceMm; } void mitk::StreamlineTractographyParameters::SetSamplingDistanceVox(float sampling_distance_vox) { m_SamplingDistanceVox = sampling_distance_vox; AutoAdjust(); } void mitk::StreamlineTractographyParameters::AutoAdjust() { if (m_StepSizeVox(mitk::eps)) m_StepSizeVox = 0.5; m_StepSizeMm = m_StepSizeVox*m_MinVoxelSizeMm; if (m_AngularThresholdDeg<0) { if (m_StepSizeMm/m_MinVoxelSizeMm<=0.966f) // minimum 15° for automatic estimation m_AngularThresholdDot = static_cast(std::cos( 0.5 * itk::Math::pi * static_cast(m_StepSizeMm/m_MinVoxelSizeMm) )); else m_AngularThresholdDot = static_cast(std::cos( 0.5 * itk::Math::pi * 0.966 )); m_AngularThresholdDeg = std::acos(m_AngularThresholdDot)*180.0/itk::Math::pi; } else m_AngularThresholdDot = static_cast(std::cos( static_cast(m_AngularThresholdDeg)*itk::Math::pi/180.0 )); if (m_SamplingDistanceVox(mitk::eps)) m_SamplingDistanceVox = m_MinVoxelSizeMm*0.25f; m_SamplingDistanceMm = m_SamplingDistanceVox*m_MinVoxelSizeMm; } float mitk::StreamlineTractographyParameters::GetStepSizeVox() const { return m_StepSizeVox; } float mitk::StreamlineTractographyParameters::GetAngularThresholdDeg() const { return m_AngularThresholdDeg; } float mitk::StreamlineTractographyParameters::GetSamplingDistanceVox() const { return m_SamplingDistanceVox; } float mitk::StreamlineTractographyParameters::GetMinVoxelSizeMm() const { return m_MinVoxelSizeMm; } float mitk::StreamlineTractographyParameters::GetStepSizeMm() const { return m_StepSizeMm; } void mitk::StreamlineTractographyParameters::SetMinVoxelSizeMm(float min_voxel_size_mm) { m_MinVoxelSizeMm = min_voxel_size_mm; AutoAdjust(); } float mitk::StreamlineTractographyParameters::GetAngularThresholdDot() const { return m_AngularThresholdDot; } void mitk::StreamlineTractographyParameters::SetStepSizeVox(float step_size_vox) { m_StepSizeVox = step_size_vox; AutoAdjust(); } float mitk::StreamlineTractographyParameters::GetLoopCheckDeg() const { return m_LoopCheckDeg; } void mitk::StreamlineTractographyParameters::SetLoopCheckDeg(float loop_check_deg) { m_LoopCheckDeg = loop_check_deg; } void mitk::StreamlineTractographyParameters::SetAngularThresholdDeg(float angular_threshold_deg) { m_AngularThresholdDeg = angular_threshold_deg; AutoAdjust(); } diff --git a/Modules/FiberTracking/mitkStreamlineTractographyParameters.h b/Modules/FiberTracking/mitkStreamlineTractographyParameters.h index a9b66fd..50985ed 100644 --- a/Modules/FiberTracking/mitkStreamlineTractographyParameters.h +++ b/Modules/FiberTracking/mitkStreamlineTractographyParameters.h @@ -1,163 +1,164 @@ #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; int m_SharpenOdfs = 8; 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 + bool m_SecondOrder = true; // 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 = 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/QmitkFiberQuantificationView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberQuantificationView.cpp index 4738129..4b85564 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 @@ -1,544 +1,575 @@ /*=================================================================== 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->SetOnlyUseMaskGeometry(true); 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, TDI_MODE::DENSITY, true, node->GetName()); name += "_TDI"; break; case 1: newNode = GenerateTractDensityImage(fib, TDI_MODE::DENSITY, false, node->GetName()); name += "_TDI"; break; case 2: newNode = GenerateTractDensityImage(fib, TDI_MODE::BINARY, 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; case 8: newNode = GenerateTractDensityImage(fib, TDI_MODE::VISITATION_COUNT, true, node->GetName()); name += "_visitations"; break; + case 9: + newNode = GenerateFiberPointSet(fib); + name += "_fiber_points"; } 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 pointset displaying the fiber endings +mitk::DataNode::Pointer QmitkFiberQuantificationView::GenerateFiberPointSet(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(); + + for (int j=0; jGetPoint(j); + 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->SetMode(TDI_MODE::BINARY); 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->SetMode(TDI_MODE::BINARY); 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, TDI_MODE mode, bool absolute, std::string name) { mitk::DataNode::Pointer node = mitk::DataNode::New(); if (mode==TDI_MODE::BINARY) { typedef unsigned char OutPixType; typedef itk::Image OutImageType; itk::TractDensityImageFilter< OutImageType >::Pointer generator = itk::TractDensityImageFilter< OutImageType >::New(); generator->SetFiberBundle(fib); generator->SetMode(mode); 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->SetMode(mode); 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 53d0c61..9597ada 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 @@ -1,90 +1,91 @@ /*=================================================================== 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 #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, TDI_MODE mode, 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 GenerateFiberPointSet(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 c2cbb6e..cc451c9 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 @@ -1,435 +1,440 @@ 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 Streamline Visitation Count + + + Fiber Pointset + + 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
 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp index 741505a..09d0d27 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/src/internal/QmitkStreamlineTrackingView.cpp @@ -1,1216 +1,1218 @@ /*=================================================================== 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 // Qmitk #include "QmitkStreamlineTrackingView.h" #include "QmitkStdMultiWidget.h" // Qt #include #include // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include // VTK #include #include #include #include #include #include #include #include #include #include const std::string QmitkStreamlineTrackingView::VIEW_ID = "org.mitk.views.streamlinetracking"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace berry; QmitkStreamlineTrackingWorker::QmitkStreamlineTrackingWorker(QmitkStreamlineTrackingView* view) : m_View(view) { } void QmitkStreamlineTrackingWorker::run() { m_View->m_Tracker->Update(); m_View->m_TrackingThread.quit(); } QmitkStreamlineTrackingView::QmitkStreamlineTrackingView() : m_TrackingWorker(this) , m_Controls(nullptr) , m_FirstTensorProbRun(true) , m_FirstInteractiveRun(true) , m_TrackingHandler(nullptr) , m_ThreadIsRunning(false) , m_DeleteTrackingHandler(false) , m_Visible(false) , m_LastPrior(nullptr) , m_TrackingPriorHandler(nullptr) { m_TrackingWorker.moveToThread(&m_TrackingThread); connect(&m_TrackingThread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_TrackingThread, SIGNAL(started()), &m_TrackingWorker, SLOT(run())); connect(&m_TrackingThread, SIGNAL(finished()), this, SLOT(AfterThread())); m_TrackingTimer = new QTimer(this); } // Destructor QmitkStreamlineTrackingView::~QmitkStreamlineTrackingView() { if (m_Tracker.IsNull()) return; m_Tracker->SetStopTracking(true); m_TrackingThread.wait(); } void QmitkStreamlineTrackingView::CreateQtPartControl( QWidget *parent ) { if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkStreamlineTrackingViewControls; m_Controls->setupUi( parent ); m_Controls->m_FaImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_SeedImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_MaskImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_TargetImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_PriorImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_StopImageSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_ForestSelectionWidget->SetDataStorage(this->GetDataStorage()); m_Controls->m_ExclusionImageSelectionWidget->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isPeakImagePredicate = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isImagePredicate = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isTractographyForest = mitk::TNodePredicateDataType::New(); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateNot::Pointer isNotBinaryPredicate = mitk::NodePredicateNot::New( isBinaryPredicate ); mitk::NodePredicateAnd::Pointer isNotABinaryImagePredicate = mitk::NodePredicateAnd::New( isImagePredicate, isNotBinaryPredicate ); mitk::NodePredicateDimension::Pointer dimensionPredicate = mitk::NodePredicateDimension::New(3); m_Controls->m_ForestSelectionWidget->SetNodePredicate(isTractographyForest); m_Controls->m_FaImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, dimensionPredicate) ); m_Controls->m_FaImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_FaImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_SeedImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_SeedImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_SeedImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_MaskImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_MaskImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_MaskImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_StopImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_StopImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_StopImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_TargetImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_TargetImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_TargetImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_PriorImageSelectionWidget->SetNodePredicate( isPeakImagePredicate ); m_Controls->m_PriorImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_PriorImageSelectionWidget->SetSelectionIsOptional(true); m_Controls->m_ExclusionImageSelectionWidget->SetNodePredicate( mitk::NodePredicateAnd::New(isImagePredicate, dimensionPredicate) ); m_Controls->m_ExclusionImageSelectionWidget->SetEmptyInfo("--"); m_Controls->m_ExclusionImageSelectionWidget->SetSelectionIsOptional(true); connect( m_TrackingTimer, SIGNAL(timeout()), this, SLOT(TimerUpdate()) ); connect( m_Controls->m_SaveParametersButton, SIGNAL(clicked()), this, SLOT(SaveParameters()) ); connect( m_Controls->m_LoadParametersButton, SIGNAL(clicked()), this, SLOT(LoadParameters()) ); connect( m_Controls->commandLinkButton_2, SIGNAL(clicked()), this, SLOT(StopTractography()) ); connect( m_Controls->commandLinkButton, SIGNAL(clicked()), this, SLOT(DoFiberTracking()) ); connect( m_Controls->m_InteractiveBox, SIGNAL(stateChanged(int)), this, SLOT(ToggleInteractive()) ); connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(UpdateGui()) ); connect( m_Controls->m_FaImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::DeleteTrackingHandler ); connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(DeleteTrackingHandler()) ); connect( m_Controls->m_OutputProbMap, SIGNAL(stateChanged(int)), this, SLOT(OutputStyleSwitched()) ); connect( m_Controls->m_SeedImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_StopImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_TargetImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_PriorImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_ExclusionImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_MaskImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_FaImageSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_ForestSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::ForestSwitched ); connect( m_Controls->m_ForestSelectionWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkStreamlineTrackingView::OnParameterChanged ); connect( m_Controls->m_SeedsPerVoxelBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_NumFibersBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_ScalarThresholdBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_OdfCutoffBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_StepSizeBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_SamplingDistanceBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_AngularThresholdBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_MinTractLengthBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_MaxTractLengthBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_fBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_gBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_NumSamplesBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_SeedRadiusBox, SIGNAL(editingFinished()), this, SLOT(InteractiveSeedChanged()) ); connect( m_Controls->m_NumSeedsBox, SIGNAL(editingFinished()), this, SLOT(InteractiveSeedChanged()) ); connect( m_Controls->m_OutputProbMap, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_SharpenOdfsBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_InterpolationBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_MaskInterpolationBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FlipXBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FlipYBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FlipZBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_PriorFlipXBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_PriorFlipYBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_PriorFlipZBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FrontalSamplesBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_StopVotesBox, SIGNAL(stateChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_LoopCheckBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_TrialsPerSeedBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_EpConstraintsBox, SIGNAL(currentIndexChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_PeakJitterBox, SIGNAL(editingFinished()), this, SLOT(OnParameterChanged()) ); m_Controls->m_SharpenOdfsBox->editingFinished(); m_Controls->m_SeedsPerVoxelBox->editingFinished(); m_Controls->m_NumFibersBox->editingFinished(); m_Controls->m_ScalarThresholdBox->editingFinished(); m_Controls->m_OdfCutoffBox->editingFinished(); m_Controls->m_StepSizeBox->editingFinished(); m_Controls->m_SamplingDistanceBox->editingFinished(); m_Controls->m_AngularThresholdBox->editingFinished(); m_Controls->m_MinTractLengthBox->editingFinished(); m_Controls->m_MaxTractLengthBox->editingFinished(); m_Controls->m_fBox->editingFinished(); m_Controls->m_gBox->editingFinished(); m_Controls->m_NumSamplesBox->editingFinished(); m_Controls->m_SeedRadiusBox->editingFinished(); m_Controls->m_NumSeedsBox->editingFinished(); m_Controls->m_LoopCheckBox->editingFinished(); m_Controls->m_TrialsPerSeedBox->editingFinished(); m_Controls->m_PeakJitterBox->editingFinished(); StartStopTrackingGui(false); } m_ParameterFile = QDir::currentPath()+"/param.stp"; UpdateGui(); } void QmitkStreamlineTrackingView::ParametersToGui(mitk::StreamlineTractographyParameters& params) { m_Controls->m_SeedRadiusBox->setValue(params.m_InteractiveRadiusMm); m_Controls->m_NumSeedsBox->setValue(params.m_NumInteractiveSeeds); m_Controls->m_InteractiveBox->setChecked(params.m_EnableInteractive); m_Controls->m_ResampleFibersBox->setChecked(params.m_CompressFibers); m_Controls->m_SeedRadiusBox->setValue(params.m_InteractiveRadiusMm); m_Controls->m_NumFibersBox->setValue(params.m_MaxNumFibers); m_Controls->m_ScalarThresholdBox->setValue(params.m_Cutoff); m_Controls->m_fBox->setValue(params.m_F); m_Controls->m_gBox->setValue(params.m_G); m_Controls->m_OdfCutoffBox->setValue(params.m_OdfCutoff); m_Controls->m_SharpenOdfsBox->setValue(params.m_SharpenOdfs); m_Controls->m_PriorWeightBox->setValue(params.m_Weight); m_Controls->m_PriorAsMaskBox->setChecked(params.m_RestrictToPrior); m_Controls->m_NewDirectionsFromPriorBox->setChecked(params.m_NewDirectionsFromPrior); m_Controls->m_PriorFlipXBox->setChecked(params.m_PriorFlipX); m_Controls->m_PriorFlipYBox->setChecked(params.m_PriorFlipY); m_Controls->m_PriorFlipZBox->setChecked(params.m_PriorFlipZ); m_Controls->m_FlipXBox->setChecked(params.m_FlipX); m_Controls->m_FlipYBox->setChecked(params.m_FlipY); m_Controls->m_FlipZBox->setChecked(params.m_FlipZ); m_Controls->m_InterpolationBox->setChecked(params.m_InterpolateTractographyData); m_Controls->m_MaskInterpolationBox->setChecked(params.m_InterpolateRoiImages); m_Controls->m_SeedsPerVoxelBox->setValue(params.m_SeedsPerVoxel); m_Controls->m_StepSizeBox->setValue(params.GetStepSizeVox()); m_Controls->m_SamplingDistanceBox->setValue(params.GetSamplingDistanceVox()); m_Controls->m_StopVotesBox->setChecked(params.m_StopVotes); m_Controls->m_FrontalSamplesBox->setChecked(params.m_OnlyForwardSamples); m_Controls->m_TrialsPerSeedBox->setValue(params.m_TrialsPerSeed); m_Controls->m_NumSamplesBox->setValue(params.m_NumSamples); m_Controls->m_LoopCheckBox->setValue(params.GetLoopCheckDeg()); m_Controls->m_AngularThresholdBox->setValue(params.GetAngularThresholdDeg()); m_Controls->m_MinTractLengthBox->setValue(params.m_MinTractLengthMm); m_Controls->m_MaxTractLengthBox->setValue(params.m_MaxTractLengthMm); m_Controls->m_OutputProbMap->setChecked(params.m_OutputProbMap); m_Controls->m_FixSeedBox->setChecked(params.m_FixRandomSeed); + m_Controls->m_SecondOrderBox->setChecked(params.m_SecondOrder); m_Controls->m_PeakJitterBox->setValue(params.m_PeakJitter); switch (params.m_Mode) { case mitk::TrackingDataHandler::MODE::DETERMINISTIC: m_Controls->m_ModeBox->setCurrentIndex(0); break; case mitk::TrackingDataHandler::MODE::PROBABILISTIC: m_Controls->m_ModeBox->setCurrentIndex(1); break; } switch (params.m_EpConstraints) { case itk::StreamlineTrackingFilter::EndpointConstraints::NONE: m_Controls->m_EpConstraintsBox->setCurrentIndex(0); break; case itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET: m_Controls->m_EpConstraintsBox->setCurrentIndex(1); break; case itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET_LABELDIFF: m_Controls->m_EpConstraintsBox->setCurrentIndex(2); break; case itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET: m_Controls->m_EpConstraintsBox->setCurrentIndex(3); break; case itk::StreamlineTrackingFilter::EndpointConstraints::MIN_ONE_EP_IN_TARGET: m_Controls->m_EpConstraintsBox->setCurrentIndex(4); break; case itk::StreamlineTrackingFilter::EndpointConstraints::ONE_EP_IN_TARGET: m_Controls->m_EpConstraintsBox->setCurrentIndex(5); break; case itk::StreamlineTrackingFilter::EndpointConstraints::NO_EP_IN_TARGET: m_Controls->m_EpConstraintsBox->setCurrentIndex(6); break; } } std::shared_ptr QmitkStreamlineTrackingView::GetParametersFromGui() { std::shared_ptr params = std::make_shared(); // NOT IN GUI // unsigned int m_NumPreviousDirections = 1; // bool m_AvoidStop = true; // bool m_RandomSampling = false; // float m_DeflectionMod = 1.0; // bool m_ApplyDirectionMatrix = false; // NOT IN GUI BUT AUTOMATICALLY SET if (!m_InputImageNodes.empty()) { float min_sp = 999; auto spacing = dynamic_cast(m_InputImageNodes.at(0)->GetData())->GetGeometry()->GetSpacing(); if (spacing[0] < min_sp) min_sp = spacing[0]; if (spacing[1] < min_sp) min_sp = spacing[1]; if (spacing[2] < min_sp) min_sp = spacing[2]; params->m_Compression = min_sp/10; } params->m_InteractiveRadiusMm = m_Controls->m_SeedRadiusBox->value(); params->m_NumInteractiveSeeds = m_Controls->m_NumSeedsBox->value(); params->m_EnableInteractive = m_Controls->m_InteractiveBox->isChecked(); params->m_CompressFibers = m_Controls->m_ResampleFibersBox->isChecked(); params->m_InteractiveRadiusMm = m_Controls->m_SeedRadiusBox->value(); params->m_MaxNumFibers = m_Controls->m_NumFibersBox->value(); params->m_Cutoff = static_cast(m_Controls->m_ScalarThresholdBox->value()); params->m_F = static_cast(m_Controls->m_fBox->value()); params->m_G = static_cast(m_Controls->m_gBox->value()); params->m_OdfCutoff = static_cast(m_Controls->m_OdfCutoffBox->value()); params->m_SharpenOdfs = m_Controls->m_SharpenOdfsBox->value(); params->m_Weight = static_cast(m_Controls->m_PriorWeightBox->value()); params->m_RestrictToPrior = m_Controls->m_PriorAsMaskBox->isChecked(); params->m_NewDirectionsFromPrior = m_Controls->m_NewDirectionsFromPriorBox->isChecked(); params->m_PriorFlipX = m_Controls->m_PriorFlipXBox->isChecked(); params->m_PriorFlipY = m_Controls->m_PriorFlipYBox->isChecked(); params->m_PriorFlipZ = m_Controls->m_PriorFlipZBox->isChecked(); params->m_FlipX = m_Controls->m_FlipXBox->isChecked(); params->m_FlipY = m_Controls->m_FlipYBox->isChecked(); params->m_FlipZ = m_Controls->m_FlipZBox->isChecked(); params->m_InterpolateTractographyData = m_Controls->m_InterpolationBox->isChecked(); params->m_InterpolateRoiImages = m_Controls->m_MaskInterpolationBox->isChecked(); params->m_SeedsPerVoxel = m_Controls->m_SeedsPerVoxelBox->value(); params->SetStepSizeVox(m_Controls->m_StepSizeBox->value()); params->SetSamplingDistanceVox(m_Controls->m_SamplingDistanceBox->value()); params->m_StopVotes = m_Controls->m_StopVotesBox->isChecked(); params->m_OnlyForwardSamples = m_Controls->m_FrontalSamplesBox->isChecked(); params->m_TrialsPerSeed = m_Controls->m_TrialsPerSeedBox->value(); params->m_NumSamples = m_Controls->m_NumSamplesBox->value(); params->SetLoopCheckDeg(m_Controls->m_LoopCheckBox->value()); params->SetAngularThresholdDeg(m_Controls->m_AngularThresholdBox->value()); params->m_MinTractLengthMm = m_Controls->m_MinTractLengthBox->value(); params->m_MaxTractLengthMm = m_Controls->m_MaxTractLengthBox->value(); params->m_OutputProbMap = m_Controls->m_OutputProbMap->isChecked(); params->m_FixRandomSeed = m_Controls->m_FixSeedBox->isChecked(); + params->m_SecondOrder = m_Controls->m_SecondOrderBox->isChecked(); params->m_PeakJitter = static_cast(m_Controls->m_PeakJitterBox->value()); switch (m_Controls->m_ModeBox->currentIndex()) { case 0: params->m_Mode = mitk::TrackingDataHandler::MODE::DETERMINISTIC; break; case 1: params->m_Mode = mitk::TrackingDataHandler::MODE::PROBABILISTIC; break; default: params->m_Mode = mitk::TrackingDataHandler::MODE::DETERMINISTIC; } switch (m_Controls->m_EpConstraintsBox->currentIndex()) { case 0: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::NONE; break; case 1: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET; break; case 2: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET_LABELDIFF; break; case 3: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET; break; case 4: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::MIN_ONE_EP_IN_TARGET; break; case 5: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::ONE_EP_IN_TARGET; break; case 6: params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::NO_EP_IN_TARGET; break; } return params; } void QmitkStreamlineTrackingView::SaveParameters() { QString filename = QFileDialog::getSaveFileName( 0, tr("Save Tractography Parameters"), m_ParameterFile, tr("Streamline Tractography Parameters (*.stp)") ); if(filename.isEmpty() || filename.isNull()) return; m_ParameterFile = filename; auto params = GetParametersFromGui(); params->SaveParameters(m_ParameterFile.toStdString()); } void QmitkStreamlineTrackingView::LoadParameters() { QString filename = QFileDialog::getOpenFileName( 0, tr("Load Tractography Parameters"), m_ParameterFile, tr("Streamline Tractography Parameters (*.stp)") ); if(filename.isEmpty() || filename.isNull()) return; m_ParameterFile = filename; mitk::StreamlineTractographyParameters params; params.LoadParameters(m_ParameterFile.toStdString()); ParametersToGui(params); } void QmitkStreamlineTrackingView::StopTractography() { if (m_Tracker.IsNull()) return; m_Tracker->SetStopTracking(true); } void QmitkStreamlineTrackingView::TimerUpdate() { if (m_Tracker.IsNull()) return; QString status_text(m_Tracker->GetStatusText().c_str()); m_Controls->m_StatusTextBox->setText(status_text); } void QmitkStreamlineTrackingView::BeforeThread() { m_TrackingTimer->start(1000); } void QmitkStreamlineTrackingView::AfterThread() { auto params = m_Tracker->GetParameters(); m_TrackingTimer->stop(); if (!params->m_OutputProbMap) { vtkSmartPointer fiberBundle = m_Tracker->GetFiberPolyData(); if (!m_Controls->m_InteractiveBox->isChecked() && fiberBundle->GetNumberOfLines() == 0) { QMessageBox warnBox; warnBox.setWindowTitle("Warning"); warnBox.setText("No fiberbundle was generated!"); warnBox.setDetailedText("No fibers were generated using the chosen parameters. Typical reasons are:\n\n- Cutoff too high. Some images feature very low FA/GFA/peak size. Try to lower this parameter.\n- Angular threshold too strict. Try to increase this parameter.\n- A small step sizes also means many steps to go wrong. Especially in the case of probabilistic tractography. Try to adjust the angular threshold.\n- In case of probabilistic tractography, try to increase the parameter for ODF sharpening (for ODF and tensor tractography) or decrease the peak jitter (for peak tracking)."); warnBox.setIcon(QMessageBox::Warning); warnBox.exec(); if (m_InteractivePointSetNode.IsNotNull()) m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); StartStopTrackingGui(false); if (m_DeleteTrackingHandler) DeleteTrackingHandler(); UpdateGui(); return; } mitk::FiberBundle::Pointer fib = mitk::FiberBundle::New(fiberBundle); fib->SetTrackVisHeader(dynamic_cast(m_ParentNode->GetData())->GetGeometry()); if (params->m_CompressFibers && fiberBundle->GetNumberOfLines()>0) fib->Compress(params->m_Compression); fib->ColorFibersByOrientation(); m_Tracker->SetDicomProperties(fib); mitk::DiffusionPropertyHelper::CopyDICOMProperties(m_ParentNode->GetData(), fib); if (m_Controls->m_InteractiveBox->isChecked()) { if (m_InteractiveNode.IsNull()) { m_InteractiveNode = mitk::DataNode::New(); QString name("Interactive"); m_InteractiveNode->SetName(name.toStdString()); GetDataStorage()->Add(m_InteractiveNode); } m_InteractiveNode->SetData(fib); m_InteractiveNode->SetFloatProperty("Fiber2DSliceThickness", params->GetMinVoxelSizeMm()/2); if (auto renderWindowPart = this->GetRenderWindowPart()) renderWindowPart->RequestUpdate(); } else { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(fib); QString name("FiberBundle_"); name += m_ParentNode->GetName().c_str(); name += "_Streamline"; node->SetName(name.toStdString()); node->SetFloatProperty("Fiber2DSliceThickness", params->GetMinVoxelSizeMm()/2); GetDataStorage()->Add(node, m_ParentNode); } } else { TrackerType::ItkDoubleImgType::Pointer outImg = m_Tracker->GetOutputProbabilityMap(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); mitk::DiffusionPropertyHelper::CopyDICOMProperties(m_ParentNode->GetData(), img); if (m_Controls->m_InteractiveBox->isChecked()) { if (m_InteractiveNode.IsNull()) { m_InteractiveNode = mitk::DataNode::New(); QString name("Interactive"); m_InteractiveNode->SetName(name.toStdString()); GetDataStorage()->Add(m_InteractiveNode); } m_InteractiveNode->SetData(img); mitk::LookupTable::Pointer lut = mitk::LookupTable::New(); lut->SetType(mitk::LookupTable::JET_TRANSPARENT); mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New(); lut_prop->SetLookupTable(lut); m_InteractiveNode->SetProperty("LookupTable", lut_prop); m_InteractiveNode->SetProperty("opacity", mitk::FloatProperty::New(0.5)); m_InteractiveNode->SetFloatProperty("Fiber2DSliceThickness", params->GetMinVoxelSizeMm()/2); if (auto renderWindowPart = this->GetRenderWindowPart()) renderWindowPart->RequestUpdate(); } else { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); QString name("ProbabilityMap_"); name += m_ParentNode->GetName().c_str(); node->SetName(name.toStdString()); mitk::LookupTable::Pointer lut = mitk::LookupTable::New(); lut->SetType(mitk::LookupTable::JET_TRANSPARENT); mitk::LookupTableProperty::Pointer lut_prop = mitk::LookupTableProperty::New(); lut_prop->SetLookupTable(lut); node->SetProperty("LookupTable", lut_prop); node->SetProperty("opacity", mitk::FloatProperty::New(0.5)); GetDataStorage()->Add(node, m_ParentNode); } } if (m_InteractivePointSetNode.IsNotNull()) m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); StartStopTrackingGui(false); if (m_DeleteTrackingHandler) DeleteTrackingHandler(); UpdateGui(); } void QmitkStreamlineTrackingView::InteractiveSeedChanged(bool posChanged) { if(!CheckAndStoreLastParams(sender()) && !posChanged) return; if (m_ThreadIsRunning || !m_Visible) return; if (!posChanged && (!m_Controls->m_InteractiveBox->isChecked() || !m_Controls->m_ParamUpdateBox->isChecked()) ) return; std::srand(std::time(0)); m_SeedPoints.clear(); itk::Point world_pos = this->GetRenderWindowPart()->GetSelectedPosition(); m_SeedPoints.push_back(world_pos); float radius = m_Controls->m_SeedRadiusBox->value(); int num = m_Controls->m_NumSeedsBox->value(); mitk::PointSet::Pointer pointset = mitk::PointSet::New(); pointset->InsertPoint(0, world_pos); m_InteractivePointSetNode->SetProperty("pointsize", mitk::FloatProperty::New(radius*2)); m_InteractivePointSetNode->SetProperty("point 2D size", mitk::FloatProperty::New(radius*2)); m_InteractivePointSetNode->SetData(pointset); for (int i=1; i p; p[0] = rand()%1000-500; p[1] = rand()%1000-500; p[2] = rand()%1000-500; p.Normalize(); p *= radius; m_SeedPoints.push_back(world_pos+p); } m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,0,0)); DoFiberTracking(); } bool QmitkStreamlineTrackingView::CheckAndStoreLastParams(QObject* obj) { if (obj!=nullptr) { std::string new_val = ""; if(qobject_cast(obj)!=nullptr) new_val = boost::lexical_cast(qobject_cast(obj)->value()); else if (qobject_cast(obj)!=nullptr) new_val = boost::lexical_cast(qobject_cast(obj)->value()); else return true; if (m_LastTractoParams.find(obj->objectName())==m_LastTractoParams.end()) { m_LastTractoParams[obj->objectName()] = new_val; return false; } else if (m_LastTractoParams.at(obj->objectName()) != new_val) { m_LastTractoParams[obj->objectName()] = new_val; return true; } else if (m_LastTractoParams.at(obj->objectName()) == new_val) return false; } return true; } void QmitkStreamlineTrackingView::OnParameterChanged() { UpdateGui(); if(!CheckAndStoreLastParams(sender())) return; if (m_Controls->m_InteractiveBox->isChecked() && m_Controls->m_ParamUpdateBox->isChecked()) DoFiberTracking(); } void QmitkStreamlineTrackingView::ToggleInteractive() { UpdateGui(); m_Controls->m_SeedsPerVoxelBox->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); m_Controls->m_SeedsPerVoxelLabel->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); m_Controls->m_SeedImageSelectionWidget->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); m_Controls->label_6->setEnabled(!m_Controls->m_InteractiveBox->isChecked()); if ( m_Controls->m_InteractiveBox->isChecked() ) { if (m_FirstInteractiveRun) { QMessageBox::information(nullptr, "Information", "Place and move a spherical seed region anywhere in the image by left-clicking and dragging. If the seed region is colored red, tracking is in progress. If the seed region is colored white, tracking is finished.\nPlacing the seed region for the first time in a newly selected dataset might cause a short delay, since the tracker needs to be initialized."); m_FirstInteractiveRun = false; } QApplication::setOverrideCursor(Qt::PointingHandCursor); QApplication::processEvents(); m_InteractivePointSetNode = mitk::DataNode::New(); m_InteractivePointSetNode->SetProperty("color", mitk::ColorProperty::New(1,1,1)); m_InteractivePointSetNode->SetName("InteractiveSeedRegion"); mitk::PointSetShapeProperty::Pointer shape_prop = mitk::PointSetShapeProperty::New(); shape_prop->SetValue(mitk::PointSetShapeProperty::PointSetShape::CIRCLE); m_InteractivePointSetNode->SetProperty("Pointset.2D.shape", shape_prop); GetDataStorage()->Add(m_InteractivePointSetNode); m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); } else { QApplication::restoreOverrideCursor(); QApplication::processEvents(); m_InteractiveNode = nullptr; m_InteractivePointSetNode = nullptr; m_SliceChangeListener.RenderWindowPartActivated(this->GetRenderWindowPart()); disconnect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); } } void QmitkStreamlineTrackingView::Activated() { } void QmitkStreamlineTrackingView::Deactivated() { } void QmitkStreamlineTrackingView::Visible() { m_Visible = true; } void QmitkStreamlineTrackingView::Hidden() { m_Visible = false; m_Controls->m_InteractiveBox->setChecked(false); ToggleInteractive(); } void QmitkStreamlineTrackingView::OnSliceChanged() { InteractiveSeedChanged(true); } void QmitkStreamlineTrackingView::SetFocus() { } void QmitkStreamlineTrackingView::DeleteTrackingHandler() { if (!m_ThreadIsRunning && m_TrackingHandler != nullptr) { if (m_TrackingPriorHandler != nullptr) { delete m_TrackingPriorHandler; m_TrackingPriorHandler = nullptr; } delete m_TrackingHandler; m_TrackingHandler = nullptr; m_DeleteTrackingHandler = false; m_LastPrior = nullptr; } else if (m_ThreadIsRunning) { m_DeleteTrackingHandler = true; } } void QmitkStreamlineTrackingView::ForestSwitched() { DeleteTrackingHandler(); } void QmitkStreamlineTrackingView::OutputStyleSwitched() { if (m_InteractiveNode.IsNotNull()) GetDataStorage()->Remove(m_InteractiveNode); m_InteractiveNode = nullptr; } void QmitkStreamlineTrackingView::OnSelectionChanged( berry::IWorkbenchPart::Pointer , const QList& nodes ) { std::vector< mitk::DataNode::Pointer > last_nodes = m_InputImageNodes; m_InputImageNodes.clear(); m_AdditionalInputImages.clear(); bool retrack = false; for( auto node : nodes ) { if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { if( dynamic_cast(node->GetData()) || dynamic_cast(node->GetData()) || dynamic_cast(node->GetData()) || dynamic_cast(node->GetData()) || mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(node->GetData()))) { m_InputImageNodes.push_back(node); retrack = true; } else { mitk::Image* img = dynamic_cast(node->GetData()); if (img!=nullptr && img->GetDimension()==3) m_AdditionalInputImages.push_back(dynamic_cast(node->GetData())); } } } // sometimes the OnSelectionChanged event is sent twice and actually no selection has changed for the first event. We need to catch that. if (last_nodes.size() == m_InputImageNodes.size()) { bool same_nodes = true; for (unsigned int i=0; im_TensorImageLabel->setText("select in data-manager"); m_Controls->m_fBox->setEnabled(false); m_Controls->m_fLabel->setEnabled(false); m_Controls->m_gBox->setEnabled(false); m_Controls->m_gLabel->setEnabled(false); m_Controls->m_FaImageSelectionWidget->setEnabled(true); m_Controls->mFaImageLabel->setEnabled(true); m_Controls->m_OdfCutoffBox->setEnabled(false); m_Controls->m_OdfCutoffLabel->setEnabled(false); m_Controls->m_SharpenOdfsBox->setEnabled(false); m_Controls->m_ForestSelectionWidget->setVisible(false); m_Controls->m_ForestLabel->setVisible(false); m_Controls->commandLinkButton->setEnabled(false); m_Controls->m_TrialsPerSeedBox->setEnabled(false); m_Controls->m_TrialsPerSeedLabel->setEnabled(false); m_Controls->m_TargetImageSelectionWidget->setEnabled(false); m_Controls->m_TargetImageLabel->setEnabled(false); m_Controls->m_PeakJitterBox->setEnabled(false); if (m_Controls->m_InteractiveBox->isChecked()) { m_Controls->m_InteractiveSeedingFrame->setVisible(true); m_Controls->m_StaticSeedingFrame->setVisible(false); m_Controls->commandLinkButton_2->setVisible(false); m_Controls->commandLinkButton->setVisible(false); } else { m_Controls->m_InteractiveSeedingFrame->setVisible(false); m_Controls->m_StaticSeedingFrame->setVisible(true); m_Controls->commandLinkButton_2->setVisible(m_ThreadIsRunning); m_Controls->commandLinkButton->setVisible(!m_ThreadIsRunning); } if (m_Controls->m_EpConstraintsBox->currentIndex()>0) { m_Controls->m_TargetImageSelectionWidget->setEnabled(true); m_Controls->m_TargetImageLabel->setEnabled(true); } // stuff that is only important for probabilistic tractography if (m_Controls->m_ModeBox->currentIndex()==1) { m_Controls->m_TrialsPerSeedBox->setEnabled(true); m_Controls->m_TrialsPerSeedLabel->setEnabled(true); } if(!m_InputImageNodes.empty()) { if (m_InputImageNodes.size()>1) m_Controls->m_TensorImageLabel->setText( ( std::to_string(m_InputImageNodes.size()) + " images selected").c_str() ); else m_Controls->m_TensorImageLabel->setText(m_InputImageNodes.at(0)->GetName().c_str()); m_Controls->commandLinkButton->setEnabled(!m_Controls->m_InteractiveBox->isChecked() && !m_ThreadIsRunning); m_Controls->m_ScalarThresholdBox->setEnabled(true); m_Controls->m_FaThresholdLabel->setEnabled(true); if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) ) { if (m_Controls->m_ModeBox->currentIndex()==1) { m_Controls->m_OdfCutoffBox->setEnabled(true); m_Controls->m_OdfCutoffLabel->setEnabled(true); m_Controls->m_SharpenOdfsBox->setEnabled(true); } else { m_Controls->m_fBox->setEnabled(true); m_Controls->m_fLabel->setEnabled(true); m_Controls->m_gBox->setEnabled(true); m_Controls->m_gLabel->setEnabled(true); } } else if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) || dynamic_cast(m_InputImageNodes.at(0)->GetData())) { m_Controls->m_OdfCutoffBox->setEnabled(true); m_Controls->m_OdfCutoffLabel->setEnabled(true); m_Controls->m_SharpenOdfsBox->setEnabled(true); } else if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_InputImageNodes.at(0)->GetData())) ) { m_Controls->m_ForestSelectionWidget->setVisible(true); m_Controls->m_ForestLabel->setVisible(true); m_Controls->m_ScalarThresholdBox->setEnabled(false); m_Controls->m_FaThresholdLabel->setEnabled(false); } else if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) && m_Controls->m_ModeBox->currentIndex()==1) { m_Controls->m_PeakJitterBox->setEnabled(true); } } } void QmitkStreamlineTrackingView::StartStopTrackingGui(bool start) { m_ThreadIsRunning = start; if (!m_Controls->m_InteractiveBox->isChecked()) { m_Controls->commandLinkButton_2->setVisible(start); m_Controls->commandLinkButton->setVisible(!start); m_Controls->m_InteractiveBox->setEnabled(!start); m_Controls->m_StatusTextBox->setVisible(start); } } void QmitkStreamlineTrackingView::DoFiberTracking() { auto params = GetParametersFromGui(); if (m_InputImageNodes.empty()) { QMessageBox::information(nullptr, "Information", "Please select an input image in the datamaneger (tensor, ODF, peak or dMRI image)!"); return; } if (m_ThreadIsRunning || !m_Visible) return; if (m_Controls->m_InteractiveBox->isChecked() && m_SeedPoints.empty()) return; StartStopTrackingGui(true); m_Tracker = TrackerType::New(); if (params->m_EpConstraints == itk::StreamlineTrackingFilter::EndpointConstraints::NONE) m_Tracker->SetTargetRegions(nullptr); if( dynamic_cast(m_InputImageNodes.at(0)->GetData()) ) { if (m_Controls->m_ModeBox->currentIndex()==1) { if (m_InputImageNodes.size()>1) { QMessageBox::information(nullptr, "Information", "Probabilistic tensor tractography is only implemented for single-tensor mode!"); StartStopTrackingGui(false); return; } if (m_TrackingHandler==nullptr) { m_TrackingHandler = new mitk::TrackingHandlerOdf(); typedef itk::TensorImageToOdfImageFilter< float, float > FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput( mitk::convert::GetItkTensorFromTensorImage(dynamic_cast(m_InputImageNodes.at(0)->GetData())) ); filter->Update(); dynamic_cast(m_TrackingHandler)->SetOdfImage(filter->GetOutput()); if (m_Controls->m_FaImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_FaImageSelectionWidget->GetSelectedNode()->GetData()), itkImg); dynamic_cast(m_TrackingHandler)->SetGfaImage(itkImg); } } dynamic_cast(m_TrackingHandler)->SetIsOdfFromTensor(true); } else { if (m_TrackingHandler==nullptr) { m_TrackingHandler = new mitk::TrackingHandlerTensor(); for (unsigned int i=0; i(m_TrackingHandler)->AddTensorImage(mitk::convert::GetItkTensorFromTensorImage(dynamic_cast(m_InputImageNodes.at(i)->GetData())).GetPointer()); if (m_Controls->m_FaImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_FaImageSelectionWidget->GetSelectedNode()->GetData()), itkImg); dynamic_cast(m_TrackingHandler)->SetFaImage(itkImg); } } } } else if ( dynamic_cast(m_InputImageNodes.at(0)->GetData()) || dynamic_cast(m_InputImageNodes.at(0)->GetData())) { if (m_TrackingHandler==nullptr) { m_TrackingHandler = new mitk::TrackingHandlerOdf(); if (dynamic_cast(m_InputImageNodes.at(0)->GetData())) dynamic_cast(m_TrackingHandler)->SetOdfImage(mitk::convert::GetItkOdfFromShImage(dynamic_cast(m_InputImageNodes.at(0)->GetData()))); else dynamic_cast(m_TrackingHandler)->SetOdfImage(mitk::convert::GetItkOdfFromOdfImage(dynamic_cast(m_InputImageNodes.at(0)->GetData()))); if (m_Controls->m_FaImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer itkImg = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_FaImageSelectionWidget->GetSelectedNode()->GetData()), itkImg); dynamic_cast(m_TrackingHandler)->SetGfaImage(itkImg); } } } else if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_InputImageNodes.at(0)->GetData())) ) { if ( m_Controls->m_ForestSelectionWidget->GetSelectedNode().IsNull() ) { QMessageBox::information(nullptr, "Information", "Not random forest for machine learning based tractography (raw dMRI tractography) selected. Did you accidentally select the raw diffusion-weighted image in the datamanager?"); StartStopTrackingGui(false); return; } if (m_TrackingHandler==nullptr) { mitk::TractographyForest::Pointer forest = dynamic_cast(m_Controls->m_ForestSelectionWidget->GetSelectedNode()->GetData()); mitk::Image::Pointer dwi = dynamic_cast(m_InputImageNodes.at(0)->GetData()); std::vector< std::vector< ItkFloatImageType::Pointer > > additionalFeatureImages; additionalFeatureImages.push_back(std::vector< ItkFloatImageType::Pointer >()); for (auto img : m_AdditionalInputImages) { ItkFloatImageType::Pointer itkimg = ItkFloatImageType::New(); mitk::CastToItkImage(img, itkimg); additionalFeatureImages.at(0).push_back(itkimg); } bool forest_valid = false; if (forest->GetNumFeatures()>=100) { params->m_NumPreviousDirections = static_cast((forest->GetNumFeatures() - (100 + additionalFeatureImages.at(0).size()))/3); m_TrackingHandler = new mitk::TrackingHandlerRandomForest<6, 100>(); dynamic_cast*>(m_TrackingHandler)->AddDwi(dwi); dynamic_cast*>(m_TrackingHandler)->SetAdditionalFeatureImages(additionalFeatureImages); dynamic_cast*>(m_TrackingHandler)->SetForest(forest); forest_valid = dynamic_cast*>(m_TrackingHandler)->IsForestValid(); } else { params->m_NumPreviousDirections = static_cast((forest->GetNumFeatures() - (28 + additionalFeatureImages.at(0).size()))/3); m_TrackingHandler = new mitk::TrackingHandlerRandomForest<6, 28>(); dynamic_cast*>(m_TrackingHandler)->AddDwi(dwi); dynamic_cast*>(m_TrackingHandler)->SetAdditionalFeatureImages(additionalFeatureImages); dynamic_cast*>(m_TrackingHandler)->SetForest(forest); forest_valid = dynamic_cast*>(m_TrackingHandler)->IsForestValid(); } if (!forest_valid) { QMessageBox::information(nullptr, "Information", "Random forest is invalid. The forest signatue does not match the parameters of TrackingHandlerRandomForest."); StartStopTrackingGui(false); return; } } } else { if (m_TrackingHandler==nullptr) { m_TrackingHandler = new mitk::TrackingHandlerPeaks(); dynamic_cast(m_TrackingHandler)->SetPeakImage(mitk::convert::GetItkPeakFromPeakImage(dynamic_cast(m_InputImageNodes.at(0)->GetData()))); } } if (m_Controls->m_InteractiveBox->isChecked()) { m_Tracker->SetSeedPoints(m_SeedPoints); } else if (m_Controls->m_SeedImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_SeedImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetSeedImage(mask); } if (m_Controls->m_MaskImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_MaskImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetMaskImage(mask); } if (m_Controls->m_StopImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_StopImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetStoppingRegions(mask); } if (m_Controls->m_TargetImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_TargetImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetTargetRegions(mask); } if (m_Controls->m_PriorImageSelectionWidget->GetSelectedNode().IsNotNull()) { auto prior_params = GetParametersFromGui(); if (m_LastPrior!=m_Controls->m_PriorImageSelectionWidget->GetSelectedNode() || m_TrackingPriorHandler==nullptr) { typedef mitk::ImageToItk< mitk::TrackingHandlerPeaks::PeakImgType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(dynamic_cast(m_Controls->m_PriorImageSelectionWidget->GetSelectedNode()->GetData())); caster->SetCopyMemFlag(true); caster->Update(); mitk::TrackingHandlerPeaks::PeakImgType::Pointer itkImg = caster->GetOutput(); m_TrackingPriorHandler = new mitk::TrackingHandlerPeaks(); dynamic_cast(m_TrackingPriorHandler)->SetPeakImage(itkImg); m_LastPrior = m_Controls->m_PriorImageSelectionWidget->GetSelectedNode(); } prior_params->m_FlipX = m_Controls->m_PriorFlipXBox->isChecked(); prior_params->m_FlipY = m_Controls->m_PriorFlipYBox->isChecked(); prior_params->m_FlipZ = m_Controls->m_PriorFlipZBox->isChecked(); m_TrackingPriorHandler->SetParameters(prior_params); m_Tracker->SetTrackingPriorHandler(m_TrackingPriorHandler); } else if (m_Controls->m_PriorImageSelectionWidget->GetSelectedNode().IsNull()) m_Tracker->SetTrackingPriorHandler(nullptr); if (m_Controls->m_ExclusionImageSelectionWidget->GetSelectedNode().IsNotNull()) { ItkFloatImageType::Pointer mask = ItkFloatImageType::New(); mitk::CastToItkImage(dynamic_cast(m_Controls->m_ExclusionImageSelectionWidget->GetSelectedNode()->GetData()), mask); m_Tracker->SetExclusionRegions(mask); } if (params->m_EpConstraints!=itk::StreamlineTrackingFilter::EndpointConstraints::NONE && m_Controls->m_TargetImageSelectionWidget->GetSelectedNode().IsNull()) { QMessageBox::information(nullptr, "Error", "Endpoint constraints are used but no target image is set!"); StartStopTrackingGui(false); return; } else if (params->m_EpConstraints==itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET && (m_Controls->m_SeedImageSelectionWidget->GetSelectedNode().IsNull()|| m_Controls->m_TargetImageSelectionWidget->GetSelectedNode().IsNull()) ) { QMessageBox::information(nullptr, "Error", "Endpoint constraint EPS_IN_SEED_AND_TARGET is used but no target or no seed image is set!"); StartStopTrackingGui(false); return; } float min_sp = 999; auto spacing = dynamic_cast(m_InputImageNodes.at(0)->GetData())->GetGeometry()->GetSpacing(); if (spacing[0] < min_sp) min_sp = spacing[0]; if (spacing[1] < min_sp) min_sp = spacing[1]; if (spacing[2] < min_sp) min_sp = spacing[2]; params->m_Compression = min_sp/10; - float max_size = 0; - for (int i=0; i<3; ++i) - if (dynamic_cast(m_InputImageNodes.at(0)->GetData())->GetGeometry()->GetExtentInMM(i)>max_size) - max_size = dynamic_cast(m_InputImageNodes.at(0)->GetData())->GetGeometry()->GetExtentInMM(i); - if (params->m_MinTractLengthMm >= max_size) - { - MITK_INFO << "Max. image size: " << max_size << "mm"; - MITK_INFO << "Min. tract length: " << params->m_MinTractLengthMm << "mm"; - QMessageBox::information(nullptr, "Error", "Minimum tract length exceeds the maximum image extent! Recommended value is about 1/10 of the image extent."); - StartStopTrackingGui(false); - return; - } - else if (params->m_MinTractLengthMm > max_size/10) - { - MITK_INFO << "Max. image size: " << max_size << "mm"; - MITK_INFO << "Min. tract length: " << params->m_MinTractLengthMm << "mm"; - MITK_WARN << "Minimum tract length is larger than 1/10 the maximum image extent! Decrease recommended."; - } +// float max_size = 0; +// for (int i=0; i<3; ++i) +// if (dynamic_cast(m_InputImageNodes.at(0)->GetData())->GetGeometry()->GetExtentInMM(i)>max_size) +// max_size = dynamic_cast(m_InputImageNodes.at(0)->GetData())->GetGeometry()->GetExtentInMM(i); +// if (params->m_MinTractLengthMm >= max_size) +// { +// MITK_INFO << "Max. image size: " << max_size << "mm"; +// MITK_INFO << "Min. tract length: " << params->m_MinTractLengthMm << "mm"; +// QMessageBox::information(nullptr, "Error", "Minimum tract length exceeds the maximum image extent! Recommended value is about 1/10 of the image extent."); +// StartStopTrackingGui(false); +// return; +// } +// else if (params->m_MinTractLengthMm > max_size/10) +// { +// MITK_INFO << "Max. image size: " << max_size << "mm"; +// MITK_INFO << "Min. tract length: " << params->m_MinTractLengthMm << "mm"; +// MITK_WARN << "Minimum tract length is larger than 1/10 the maximum image extent! Decrease recommended."; +// } m_Tracker->SetParameters(params); m_Tracker->SetTrackingHandler(m_TrackingHandler); m_Tracker->SetVerbose(!m_Controls->m_InteractiveBox->isChecked()); m_ParentNode = m_InputImageNodes.at(0); m_TrackingThread.start(QThread::LowestPriority); } 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 65ef468..5e8138d 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 @@ -1,1655 +1,1674 @@ 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: + 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 + 541 + 175 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 - -19 + -270 421 - 436 + 459 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) + 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. - 1 + 5 - 999.000000000000000 + 1.000000000000000 - 1.000000000000000 + 0.100000000000000 - 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: + 0.000250000000000 - - + + - f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!). + 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. - 2 + 3 1.000000000000000 0.100000000000000 - 0.000000000000000 - - - - - - - - - - Sharpen ODFs: + 0.010000000000000 - + Fix Random Seed: - - - - Maximum allowed angular SDTEV over 4 voxel lengths. Default: 30° - - - - - - -1 - - - 180 - - - 30 - - - - - - - + + + + Qt::Vertical - - Angular Threshold: + + + 20 + 40 + - + - - + + - Max. Tract Length: + Mode: Cutoff: - - + + - Angular threshold between two steps (in degree). Default: 90° * step_size + Minimum tract length in mm. Shorter fibers are discarded. - - -1 + + Minimum fiber length (in mm) + + + 1 - 90 + 999.000000000000000 - 1 + 1.000000000000000 - -1 + 20.000000000000000 - - - - Qt::Vertical + + + + - - - 20 - 40 - + + Angular Threshold: - + 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. + Maximum allowed angular SDTEV over 4 voxel lengths. Default: 30° - - - 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 - 1.000000000000000 - - - 0.100000000000000 + 180 - 0.000250000000000 + 30 - - + + - Min. Tract Length: + g: - - + + - + Always produce the same random numbers. - 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: + Sharpen ODFs: - - - 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. + + + + Loop Check: + + + + + + + + + + Step Size: + + + + + + + + + + Max. Tract Length: + + + + + + + + + + FA/GFA Image: + + + + + + + + + + ODF Cutoff: + + + + + + + f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!). - 3 + 2 1.000000000000000 0.100000000000000 - 0.010000000000000 + 0.000000000000000 + + + + + + + Angular threshold between two steps (in degree). Default: 90° * step_size + + + -1 + + + 90 + + + 1 + + + -1 + + + + + + + Toggle between deterministic and probabilistic tractography. Some modes might not be available for all types of tractography. + + + + Deterministic + + + + + Probabilistic + + + + + + + + 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: + + + + + + + + + + Min. Tract Length: Rais ODF to the power of X 1 8 + + + + + + + Second Order: + + + + + + + Always produce the same random numbers. + + + + + + true + + + 0 0 435 - 184 + 189 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 + 189 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 + 189 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 + 189 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 diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp index 9bb2ae0..01cbf65 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp @@ -1,1238 +1,1285 @@ /*=================================================================== 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 "QmitkControlVisualizationPropertiesView.h" #include "mitkNodePredicateDataType.h" #include "mitkDataNodeObject.h" #include "mitkOdfNormalizationMethodProperty.h" #include "mitkOdfScaleByProperty.h" #include "mitkResliceMethodProperty.h" #include "mitkRenderingManager.h" #include "mitkImageCast.h" #include "mitkShImage.h" #include "mitkPlanarFigure.h" #include "mitkFiberBundle.h" #include "QmitkDataStorageComboBox.h" #include "mitkPlanarFigureInteractor.h" #include #include #include #include #include #include "usModuleRegistry.h" #include #include #include "mitkPlaneGeometry.h" #include #include #include #include #include "berryIWorkbenchWindow.h" #include "berryIWorkbenchPage.h" #include "berryISelectionService.h" #include "berryConstants.h" #include "berryPlatformUI.h" #include "itkRGBAPixel.h" #include #include "qwidgetaction.h" #include "qcolordialog.h" #include #include #include #include #define ROUND(a) ((a)>0 ? (int)((a)+0.5) : -(int)(0.5-(a))) const std::string QmitkControlVisualizationPropertiesView::VIEW_ID = "org.mitk.views.controlvisualizationpropertiesview"; using namespace berry; QmitkControlVisualizationPropertiesView::QmitkControlVisualizationPropertiesView() : QmitkAbstractView(), m_Controls(nullptr), m_CurrentSelection(nullptr), m_IconTexOFF(new QIcon(":/QmitkDiffusionImaging/texIntOFFIcon.png")), m_IconTexON(new QIcon(":/QmitkDiffusionImaging/texIntONIcon.png")), m_IconGlyOFF_T(new QIcon(":/QmitkDiffusionImaging/glyphsoff_T.png")), m_IconGlyON_T(new QIcon(":/QmitkDiffusionImaging/glyphson_T.png")), m_IconGlyOFF_C(new QIcon(":/QmitkDiffusionImaging/glyphsoff_C.png")), m_IconGlyON_C(new QIcon(":/QmitkDiffusionImaging/glyphson_C.png")), m_IconGlyOFF_S(new QIcon(":/QmitkDiffusionImaging/glyphsoff_S.png")), m_IconGlyON_S(new QIcon(":/QmitkDiffusionImaging/glyphson_S.png")), m_GlyIsOn_T(false), m_GlyIsOn_C(false), m_GlyIsOn_S(false), m_CurrentThickSlicesMode(1), m_CurrentThickSlicesNum(0), m_CurrentPickingNode(nullptr), m_ColorPropertyObserverTag(0), m_OpacityPropertyObserverTag(0) { m_MyMenu = nullptr; auto numThread = itk::MultiThreaderBase::GetGlobalMaximumNumberOfThreads(); itk::MultiThreaderBase::SetGlobalDefaultNumberOfThreads(numThread); } QmitkControlVisualizationPropertiesView::~QmitkControlVisualizationPropertiesView() { } void QmitkControlVisualizationPropertiesView::SetTs(int currentThickSlicesMode, int num, std::string render_window) { if (auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN)) { mitk::BaseRenderer::Pointer renderer = renderWindowPart->GetQmitkRenderWindow(QString(render_window.c_str()))->GetRenderer(); renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices.num", mitk::IntProperty::New(num)); if(num>0) { renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices", mitk::ResliceMethodProperty::New(currentThickSlicesMode)); renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices.showarea", mitk::BoolProperty::New(true)); } else { renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices", mitk::ResliceMethodProperty::New(0)); renderer->GetCurrentWorldPlaneGeometryNode()->SetProperty("reslice.thickslices.showarea", mitk::BoolProperty::New(false)); } renderer->SendUpdateSlice(); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkControlVisualizationPropertiesView::OnThickSlicesModeSelected( QAction* action ) { m_CurrentThickSlicesMode = action->data().toInt(); switch( m_CurrentThickSlicesMode ) { case 0: return; case 1: this->m_Controls->m_TSMenu->setText("MIP"); break; case 2: this->m_Controls->m_TSMenu->setText("SUM"); break; case 3: this->m_Controls->m_TSMenu->setText("WEIGH"); break; default: return; } SetTs(m_CurrentThickSlicesMode, m_CurrentThickSlicesNum, "axial"); SetTs(m_CurrentThickSlicesMode, m_CurrentThickSlicesNum, "sagittal"); SetTs(m_CurrentThickSlicesMode, m_CurrentThickSlicesNum, "coronal"); } void QmitkControlVisualizationPropertiesView::OnTSNumChanged( int num ) { m_CurrentThickSlicesNum = num; SetTs(m_CurrentThickSlicesMode, m_CurrentThickSlicesNum, "axial"); SetTs(m_CurrentThickSlicesMode, m_CurrentThickSlicesNum, "sagittal"); SetTs(m_CurrentThickSlicesMode, m_CurrentThickSlicesNum, "coronal"); m_TSLabel->setText(QString::number( num*2 + 1 )); } void QmitkControlVisualizationPropertiesView::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets m_Controls = new Ui::QmitkControlVisualizationPropertiesViewControls; m_Controls->setupUi(parent); this->CreateConnections(); // hide warning (ODFs in rotated planes) m_Controls->m_lblRotatedPlanesWarning->hide(); m_MyMenu = new QMenu(parent); m_Controls->m_TSMenu->setMenu( m_MyMenu ); QIcon iconFiberFade(":/QmitkDiffusionImaging/MapperEfx2D.png"); m_Controls->m_FiberFading2D->setIcon(iconFiberFade); m_Controls->m_NormalizationFrame->setVisible(false); m_Controls->m_Crosshair->setVisible(false); mitk::IRenderWindowPart* renderWindow = this->GetRenderWindowPart(); if (renderWindow) { m_SliceChangeListener.RenderWindowPartActivated(renderWindow); connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); } connect(m_Controls->m_SetColor1, SIGNAL(clicked()), this, SLOT(SetColor())); connect(m_Controls->m_SetColor2, SIGNAL(clicked()), this, SLOT(SetColor())); } } void QmitkControlVisualizationPropertiesView::SetColor() { - if(m_SelectedNode) + for (auto node : m_SelectedNodes) { QColor c = QColorDialog::getColor(); if (c.isValid()) { float rgb[3]; rgb[0] = static_cast(c.redF()); rgb[1] = static_cast(c.greenF()); rgb[2] = static_cast(c.blueF()); - m_SelectedNode->SetColor(rgb); + node->SetColor(rgb); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } } void QmitkControlVisualizationPropertiesView::SetFocus() { m_Controls->m_TSMenu->setFocus(); } void QmitkControlVisualizationPropertiesView::SliceRotation(const itk::EventObject&) { // test if plane rotated if( m_GlyIsOn_T || m_GlyIsOn_C || m_GlyIsOn_S ) { if( this->IsPlaneRotated() ) { // show label m_Controls->m_lblRotatedPlanesWarning->show(); } else { //hide label m_Controls->m_lblRotatedPlanesWarning->hide(); } } } void QmitkControlVisualizationPropertiesView::NodeRemoved(const mitk::DataNode* /*node*/) { } #include void QmitkControlVisualizationPropertiesView::CreateConnections() { if ( m_Controls ) { connect( static_cast(m_Controls->m_VisibleOdfsON_T), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_T()) ); connect( static_cast(m_Controls->m_VisibleOdfsON_S), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_S()) ); connect( static_cast(m_Controls->m_VisibleOdfsON_C), SIGNAL(clicked()), this, SLOT(VisibleOdfsON_C()) ); connect( static_cast(m_Controls->m_ShowMaxNumber), SIGNAL(editingFinished()), this, SLOT(ShowMaxNumberChanged()) ); connect( static_cast(m_Controls->m_NormalizationDropdown), SIGNAL(currentIndexChanged(int)), this, SLOT(NormalizationDropdownChanged(int)) ); connect( static_cast(m_Controls->m_ScalingFactor), SIGNAL(valueChanged(double)), this, SLOT(ScalingFactorChanged(double)) ); connect( static_cast(m_Controls->m_AdditionalScaling), SIGNAL(currentIndexChanged(int)), this, SLOT(AdditionalScaling(int)) ); connect(static_cast(m_Controls->m_ResetColoring), SIGNAL(clicked()), static_cast(this), SLOT(ResetColoring())); connect(static_cast(m_Controls->m_ResetColoring2), SIGNAL(clicked()), static_cast(this), SLOT(ResetColoring())); connect(static_cast(m_Controls->m_FiberFading2D), SIGNAL(clicked()), static_cast(this), SLOT( Fiber2DfadingEFX() ) ); connect(static_cast(m_Controls->m_FiberClippingBox), SIGNAL(editingFinished()), static_cast(this), SLOT( FiberSlicingThickness2D() ) ); connect(static_cast(m_Controls->m_Crosshair), SIGNAL(clicked()), static_cast(this), SLOT(SetInteractor())); connect(static_cast(m_Controls->m_LineWidth), SIGNAL(editingFinished()), static_cast(this), SLOT(LineWidthChanged())); connect(static_cast(m_Controls->m_TubeWidth), SIGNAL(editingFinished()), static_cast(this), SLOT(TubeRadiusChanged())); connect(static_cast(m_Controls->m_RibbonWidth), SIGNAL(editingFinished()), static_cast(this), SLOT(RibbonWidthChanged())); connect( static_cast(m_Controls->m_OdfColorBox), SIGNAL(currentIndexChanged(int)), static_cast(this), SLOT(OnColourisationModeChanged() ) ); connect(static_cast(m_Controls->m_Clip0), SIGNAL(toggled(bool)), static_cast(this), SLOT(Toggle3DClipping(bool))); connect(static_cast(m_Controls->m_Clip1), SIGNAL(toggled(bool)), static_cast(this), SLOT(Toggle3DClipping(bool))); connect(static_cast(m_Controls->m_Clip2), SIGNAL(toggled(bool)), static_cast(this), SLOT(Toggle3DClipping(bool))); connect(static_cast(m_Controls->m_Clip3), SIGNAL(toggled(bool)), static_cast(this), SLOT(Toggle3DClipping(bool))); connect(static_cast(m_Controls->m_FlipClipBox), SIGNAL(stateChanged(int)), static_cast(this), SLOT(Toggle3DClipping())); connect(static_cast(m_Controls->m_Enable3dPeaks), SIGNAL(stateChanged(int)), static_cast(this), SLOT(Toggle3DPeaks())); connect(static_cast(m_Controls->m_FlipPeaksButton), SIGNAL(clicked()), static_cast(this), SLOT(FlipPeaks())); m_Controls->m_BundleControlsFrame->setVisible(false); m_Controls->m_ImageControlsFrame->setVisible(false); m_Controls->m_PeakImageFrame->setVisible(false); m_Controls->m_lblRotatedPlanesWarning->setVisible(false); m_Controls->m_3DClippingBox->setVisible(false); } } // set diffusion image channel to b0 volume void QmitkControlVisualizationPropertiesView::NodeAdded(const mitk::DataNode *node) { mitk::DataNode* notConst = const_cast(node); bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(node->GetData())) ); if (isDiffusionImage) { mitk::Image::Pointer dimg = dynamic_cast(notConst->GetData()); // if there is no b0 image in the dataset, the GetB0Indices() returns a vector of size 0 // and hence we cannot set the Property directly to .front() int displayChannelPropertyValue = 0; mitk::DiffusionPropertyHelper::BValueMapType map = mitk::DiffusionPropertyHelper::GetBValueMap(dimg); if( map[0].size() > 0) { displayChannelPropertyValue = map[0].front(); } notConst->SetIntProperty("DisplayChannel", displayChannelPropertyValue ); } } /* OnSelectionChanged is registered to SelectionService, therefore no need to implement SelectionService Listener explicitly */ void QmitkControlVisualizationPropertiesView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& nodes) { m_Controls->m_BundleControlsFrame->setVisible(false); m_Controls->m_ImageControlsFrame->setVisible(false); m_Controls->m_PeakImageFrame->setVisible(false); m_Controls->m_3DClippingBox->setVisible(false); m_Controls->m_FlipClipBox->setVisible(false); m_Controls->m_Enable3dPeaks->setVisible(false); - if (nodes.size()>1) // only do stuff if one node is selected - return; +// if (nodes.size()>1) // only do stuff if one node is selected +// return; m_Controls->m_NumberGlyphsFrame->setVisible(false); m_Controls->m_GlyphFrame->setVisible(false); m_Controls->m_TSMenu->setVisible(false); - m_SelectedNode = nullptr; + m_SelectedNodes.clear(); int numOdfImages = 0; for (mitk::DataNode::Pointer node: nodes) { if(node.IsNull()) continue; mitk::BaseData* nodeData = node->GetData(); if(nodeData == nullptr) continue; - m_SelectedNode = node; - if (dynamic_cast(nodeData)) { m_Controls->m_PeakImageFrame->setVisible(true); if (m_Color.IsNotNull()) m_Color->RemoveObserver(m_ColorPropertyObserverTag); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkControlVisualizationPropertiesView::SetCustomColor ); m_Color = dynamic_cast(node->GetProperty("color", nullptr)); if (m_Color.IsNotNull()) m_ColorPropertyObserverTag = m_Color->AddObserver( itk::ModifiedEvent(), command ); int ClippingPlaneId = -1; - m_SelectedNode->GetPropertyValue("3DClippingPlaneId",ClippingPlaneId); + node->GetPropertyValue("3DClippingPlaneId",ClippingPlaneId); switch(ClippingPlaneId) { case 0: m_Controls->m_Clip0->setChecked(1); break; case 1: m_Controls->m_Clip1->setChecked(1); break; case 2: m_Controls->m_Clip2->setChecked(1); break; case 3: m_Controls->m_Clip3->setChecked(1); break; default : m_Controls->m_Clip0->setChecked(1); } m_Controls->m_Enable3dPeaks->setVisible(true); m_Controls->m_3DClippingBox->setVisible(true); } else if (dynamic_cast(nodeData)) { int ClippingPlaneId = -1; - m_SelectedNode->GetPropertyValue("3DClippingPlaneId",ClippingPlaneId); + node->GetPropertyValue("3DClippingPlaneId",ClippingPlaneId); switch(ClippingPlaneId) { case 0: m_Controls->m_Clip0->setChecked(1); break; case 1: m_Controls->m_Clip1->setChecked(1); break; case 2: m_Controls->m_Clip2->setChecked(1); break; case 3: m_Controls->m_Clip3->setChecked(1); break; default : m_Controls->m_Clip0->setChecked(1); } // handle fiber property observers if (m_Color.IsNotNull()) m_Color->RemoveObserver(m_ColorPropertyObserverTag); itk::ReceptorMemberCommand::Pointer command = itk::ReceptorMemberCommand::New(); command->SetCallbackFunction( this, &QmitkControlVisualizationPropertiesView::SetCustomColor ); m_Color = dynamic_cast(node->GetProperty("color", nullptr)); if (m_Color.IsNotNull()) m_ColorPropertyObserverTag = m_Color->AddObserver( itk::ModifiedEvent(), command ); m_Controls->m_FlipClipBox->setVisible(true); m_Controls->m_3DClippingBox->setVisible(true); m_Controls->m_BundleControlsFrame->setVisible(true); if(m_CurrentPickingNode != 0 && node.GetPointer() != m_CurrentPickingNode) { m_Controls->m_Crosshair->setEnabled(false); } else { m_Controls->m_Crosshair->setEnabled(true); } int width; node->GetIntProperty("shape.linewidth", width); m_Controls->m_LineWidth->setValue(width); float radius; node->GetFloatProperty("shape.tuberadius", radius); m_Controls->m_TubeWidth->setValue(radius); float range; node->GetFloatProperty("Fiber2DSliceThickness",range); mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); mitk::BaseGeometry::Pointer geo = fib->GetGeometry(); mitk::ScalarType max = geo->GetExtentInMM(0); max = std::max(max, geo->GetExtentInMM(1)); max = std::max(max, geo->GetExtentInMM(2)); m_Controls->m_FiberClippingBox->setMaximum(max); m_Controls->m_FiberClippingBox->setValue(range); } else if(dynamic_cast(nodeData) || dynamic_cast(nodeData) || dynamic_cast(nodeData)) { m_Controls->m_ImageControlsFrame->setVisible(true); m_Controls->m_NumberGlyphsFrame->setVisible(true); m_Controls->m_GlyphFrame->setVisible(true); m_Controls->m_NormalizationFrame->setVisible(true); if(m_NodeUsedForOdfVisualization.IsNotNull()) { m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_S", false); m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_C", false); m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_T", false); } m_NodeUsedForOdfVisualization = node; m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_S", m_GlyIsOn_S); m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_C", m_GlyIsOn_C); m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_T", m_GlyIsOn_T); if (dynamic_cast(nodeData)) { m_Controls->m_NormalizationDropdown->setVisible(false); m_Controls->m_NormalizationLabel->setVisible(false); } else { m_Controls->m_NormalizationDropdown->setVisible(true); m_Controls->m_NormalizationLabel->setVisible(true); } int val; node->GetIntProperty("ShowMaxNumber", val); m_Controls->m_ShowMaxNumber->setValue(val); m_Controls->m_NormalizationDropdown->setCurrentIndex(dynamic_cast(node->GetProperty("Normalization"))->GetValueAsId()); float fval; node->GetFloatProperty("Scaling",fval); m_Controls->m_ScalingFactor->setValue(fval); m_Controls->m_AdditionalScaling->setCurrentIndex(dynamic_cast(node->GetProperty("ScaleBy"))->GetValueAsId()); bool switchTensorViewValue = false; node->GetBoolProperty( "DiffusionCore.Rendering.OdfVtkMapper.SwitchTensorView", switchTensorViewValue ); bool colourisationModeBit = false; node->GetBoolProperty("DiffusionCore.Rendering.OdfVtkMapper.ColourisationModeBit", colourisationModeBit ); m_Controls->m_OdfColorBox->setCurrentIndex(colourisationModeBit); numOdfImages++; } else if(dynamic_cast(nodeData)) { PlanarFigureFocus(); } else if( dynamic_cast(nodeData) ) { m_Controls->m_ImageControlsFrame->setVisible(true); m_Controls->m_TSMenu->setVisible(true); } + + m_SelectedNodes.push_back(node); } if( nodes.empty() ) { return; } mitk::DataNode::Pointer node = nodes.at(0); if( node.IsNull() ) { return; } QMenu *myMenu = m_MyMenu; myMenu->clear(); QActionGroup* thickSlicesActionGroup = new QActionGroup(myMenu); thickSlicesActionGroup->setExclusive(true); int currentTSMode = 0; { mitk::ResliceMethodProperty::Pointer m = dynamic_cast(node->GetProperty( "reslice.thickslices" )); if( m.IsNotNull() ) currentTSMode = m->GetValueAsId(); } int maxTS = 30; for (auto node: nodes) { mitk::Image* image = dynamic_cast(node->GetData()); if (image) { int size = std::max(image->GetDimension(0), std::max(image->GetDimension(1), image->GetDimension(2))); if (size>maxTS) { maxTS=size; } } } maxTS /= 2; int currentNum = 0; { mitk::IntProperty::Pointer m = dynamic_cast(node->GetProperty( "reslice.thickslices.num" )); if( m.IsNotNull() ) { currentNum = m->GetValue(); if(currentNum < 0) { currentNum = 0; } if(currentNum > maxTS) { currentNum = maxTS; } } } if(currentTSMode==0) { currentNum=0; } QSlider *m_TSSlider = new QSlider(myMenu); m_TSSlider->setMinimum(0); m_TSSlider->setMaximum(maxTS-1); m_TSSlider->setValue(currentNum); m_TSSlider->setOrientation(Qt::Horizontal); connect( m_TSSlider, SIGNAL( valueChanged(int) ), this, SLOT( OnTSNumChanged(int) ) ); QHBoxLayout* _TSLayout = new QHBoxLayout; _TSLayout->setContentsMargins(4,4,4,4); _TSLayout->addWidget(m_TSSlider); _TSLayout->addWidget(m_TSLabel=new QLabel(QString::number(currentNum*2+1),myMenu)); QWidget* _TSWidget = new QWidget; _TSWidget->setLayout(_TSLayout); QActionGroup* thickSliceModeActionGroup = new QActionGroup(myMenu); thickSliceModeActionGroup->setExclusive(true); QWidgetAction *m_TSSliderAction = new QWidgetAction(myMenu); m_TSSliderAction->setDefaultWidget(_TSWidget); myMenu->addAction(m_TSSliderAction); QAction* mipThickSlicesAction = new QAction(myMenu); mipThickSlicesAction->setActionGroup(thickSliceModeActionGroup); mipThickSlicesAction->setText("MIP (max. intensity proj.)"); mipThickSlicesAction->setCheckable(true); mipThickSlicesAction->setChecked(m_CurrentThickSlicesMode==1); mipThickSlicesAction->setData(1); myMenu->addAction( mipThickSlicesAction ); QAction* sumThickSlicesAction = new QAction(myMenu); sumThickSlicesAction->setActionGroup(thickSliceModeActionGroup); sumThickSlicesAction->setText("SUM (sum intensity proj.)"); sumThickSlicesAction->setCheckable(true); sumThickSlicesAction->setChecked(m_CurrentThickSlicesMode==2); sumThickSlicesAction->setData(2); myMenu->addAction( sumThickSlicesAction ); QAction* weightedThickSlicesAction = new QAction(myMenu); weightedThickSlicesAction->setActionGroup(thickSliceModeActionGroup); weightedThickSlicesAction->setText("WEIGHTED (gaussian proj.)"); weightedThickSlicesAction->setCheckable(true); weightedThickSlicesAction->setChecked(m_CurrentThickSlicesMode==3); weightedThickSlicesAction->setData(3); myMenu->addAction( weightedThickSlicesAction ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); connect( thickSliceModeActionGroup, SIGNAL(triggered(QAction*)), this, SLOT(OnThickSlicesModeSelected(QAction*)) ); } void QmitkControlVisualizationPropertiesView::VisibleOdfsON_S() { m_GlyIsOn_S = m_Controls->m_VisibleOdfsON_S->isChecked(); if (m_NodeUsedForOdfVisualization.IsNull()) { MITK_WARN << "ODF visualization activated but m_NodeUsedForOdfVisualization is nullptr"; return; } m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_S", m_GlyIsOn_S); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::Visible() { mitk::IRenderWindowPart* renderWindow = this->GetRenderWindowPart(); if (renderWindow) { m_SliceChangeListener.RenderWindowPartActivated(renderWindow); connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); } } void QmitkControlVisualizationPropertiesView::Hidden() { } void QmitkControlVisualizationPropertiesView::Activated() { mitk::IRenderWindowPart* renderWindow = this->GetRenderWindowPart(); if (renderWindow) { m_SliceChangeListener.RenderWindowPartActivated(renderWindow); connect(&m_SliceChangeListener, SIGNAL(SliceChanged()), this, SLOT(OnSliceChanged())); } } void QmitkControlVisualizationPropertiesView::Deactivated() { } void QmitkControlVisualizationPropertiesView::FlipPeaks() { - if (m_SelectedNode.IsNull() || dynamic_cast(m_SelectedNode->GetData())==nullptr) - return; - std::string name = m_SelectedNode->GetName(); + for (auto node : m_SelectedNodes) + { + if (dynamic_cast(node->GetData())==nullptr) + continue; - mitk::Image::Pointer image = dynamic_cast(m_SelectedNode->GetData()); + std::string name = node->GetName(); - typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType; - CasterType::Pointer caster = CasterType::New(); - caster->SetInput(image); - caster->Update(); - mitk::PeakImage::ItkPeakImageType::Pointer itkImg = caster->GetOutput(); + mitk::Image::Pointer image = dynamic_cast(node->GetData()); - itk::FlipPeaksFilter< float >::Pointer flipper = itk::FlipPeaksFilter< float >::New(); - flipper->SetInput(itkImg); - flipper->SetFlipX(m_Controls->m_FlipPeaksX->isChecked()); - flipper->SetFlipY(m_Controls->m_FlipPeaksY->isChecked()); - flipper->SetFlipZ(m_Controls->m_FlipPeaksZ->isChecked()); - flipper->Update(); + typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType; + CasterType::Pointer caster = CasterType::New(); + caster->SetInput(image); + caster->Update(); + mitk::PeakImage::ItkPeakImageType::Pointer itkImg = caster->GetOutput(); - mitk::Image::Pointer resultImage = dynamic_cast(mitk::PeakImage::New().GetPointer()); - mitk::CastToMitkImage(flipper->GetOutput(), resultImage); - resultImage->SetVolume(flipper->GetOutput()->GetBufferPointer()); - m_SelectedNode->SetData(resultImage); - m_SelectedNode->SetName(name); + itk::FlipPeaksFilter< float >::Pointer flipper = itk::FlipPeaksFilter< float >::New(); + flipper->SetInput(itkImg); + flipper->SetFlipX(m_Controls->m_FlipPeaksX->isChecked()); + flipper->SetFlipY(m_Controls->m_FlipPeaksY->isChecked()); + flipper->SetFlipZ(m_Controls->m_FlipPeaksZ->isChecked()); + flipper->Update(); + + mitk::Image::Pointer resultImage = dynamic_cast(mitk::PeakImage::New().GetPointer()); + mitk::CastToMitkImage(flipper->GetOutput(), resultImage); + resultImage->SetVolume(flipper->GetOutput()->GetBufferPointer()); + node->SetData(resultImage); + node->SetName(name); + } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::Toggle3DPeaks() { - if (m_SelectedNode.IsNull() || dynamic_cast(m_SelectedNode->GetData())==nullptr) - return; + for (auto node : m_SelectedNodes) + { + if (dynamic_cast(node->GetData())==nullptr) + continue; - bool enabled = false; - m_SelectedNode->GetBoolProperty("Enable3DPeaks", enabled); - m_SelectedNode->SetBoolProperty( "Enable3DPeaks", !enabled ); + bool enabled = false; + node->GetBoolProperty("Enable3DPeaks", enabled); + node->SetBoolProperty( "Enable3DPeaks", !enabled ); + } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::Toggle3DClipping(bool enabled) { - if (!enabled || m_SelectedNode.IsNull() || (dynamic_cast(m_SelectedNode->GetData())==nullptr && dynamic_cast(m_SelectedNode->GetData())==nullptr)) - return; + for (auto node : m_SelectedNodes) + { + if (!enabled || node.IsNull() || (dynamic_cast(node->GetData())==nullptr && dynamic_cast(node->GetData())==nullptr)) + continue; - m_SelectedNode->SetBoolProperty( "3DClippingPlaneFlip", m_Controls->m_FlipClipBox->isChecked() ); + node->SetBoolProperty( "3DClippingPlaneFlip", m_Controls->m_FlipClipBox->isChecked() ); - if (m_Controls->m_Clip0->isChecked()) - { - m_SelectedNode->SetIntProperty( "3DClippingPlaneId", 0 ); - Set3DClippingPlane(true, m_SelectedNode, ""); - } - else if (m_Controls->m_Clip1->isChecked()) - { - m_SelectedNode->SetIntProperty( "3DClippingPlaneId", 1 ); - Set3DClippingPlane(false, m_SelectedNode, "axial"); - } - else if (m_Controls->m_Clip2->isChecked()) - { - m_SelectedNode->SetIntProperty( "3DClippingPlaneId", 2 ); - Set3DClippingPlane(false, m_SelectedNode, "sagittal"); - } - else if (m_Controls->m_Clip3->isChecked()) - { - m_SelectedNode->SetIntProperty( "3DClippingPlaneId", 3 ); - Set3DClippingPlane(false, m_SelectedNode, "coronal"); + if (m_Controls->m_Clip0->isChecked()) + { + node->SetIntProperty( "3DClippingPlaneId", 0 ); + Set3DClippingPlane(true, node, ""); + } + else if (m_Controls->m_Clip1->isChecked()) + { + node->SetIntProperty( "3DClippingPlaneId", 1 ); + Set3DClippingPlane(false, node, "axial"); + } + else if (m_Controls->m_Clip2->isChecked()) + { + node->SetIntProperty( "3DClippingPlaneId", 2 ); + Set3DClippingPlane(false, node, "sagittal"); + } + else if (m_Controls->m_Clip3->isChecked()) + { + node->SetIntProperty( "3DClippingPlaneId", 3 ); + Set3DClippingPlane(false, node, "coronal"); + } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::OnSliceChanged() { mitk::DataStorage::SetOfObjects::ConstPointer nodes = this->GetDataStorage()->GetAll(); for (unsigned int i=0; iSize(); ++i) { mitk::DataNode::Pointer node = nodes->GetElement(i); int plane_id = -1; node->GetIntProperty("3DClippingPlaneId", plane_id); if (plane_id==1) Set3DClippingPlane(false, node, "axial"); else if (plane_id==2) Set3DClippingPlane(false, node, "sagittal"); else if (plane_id==3) Set3DClippingPlane(false, node, "coronal"); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::Set3DClippingPlane(bool disable, mitk::DataNode* node, std::string plane) { mitk::IRenderWindowPart* renderWindow = this->GetRenderWindowPart(); if (renderWindow && node && (dynamic_cast(node->GetData()) || dynamic_cast(node->GetData()))) { mitk::Vector3D planeNormal; planeNormal.Fill(0.0); mitk::Point3D planeOrigin; planeOrigin.Fill(0.0); if (!disable) { mitk::SliceNavigationController* slicer = renderWindow->GetQmitkRenderWindow(QString(plane.c_str()))->GetSliceNavigationController(); mitk::PlaneGeometry::ConstPointer planeGeo = slicer->GetCurrentPlaneGeometry(); planeOrigin = this->GetRenderWindowPart()->GetSelectedPosition(); planeNormal = planeGeo->GetNormal(); } node->SetProperty( "3DClipping", mitk::ClippingProperty::New( planeOrigin, planeNormal ) ); if (dynamic_cast(node->GetData())) dynamic_cast(node->GetData())->RequestUpdate(); else mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkControlVisualizationPropertiesView::VisibleOdfsON_T() { m_GlyIsOn_T = m_Controls->m_VisibleOdfsON_T->isChecked(); if (m_NodeUsedForOdfVisualization.IsNull()) { MITK_WARN << "ODF visualization activated but m_NodeUsedForOdfVisualization is nullptr"; return; } m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_T", m_GlyIsOn_T); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::VisibleOdfsON_C() { m_GlyIsOn_C = m_Controls->m_VisibleOdfsON_C->isChecked(); if (m_NodeUsedForOdfVisualization.IsNull()) { MITK_WARN << "ODF visualization activated but m_NodeUsedForOdfVisualization is nullptr"; return; } m_NodeUsedForOdfVisualization->SetBoolProperty("VisibleOdfs_C", m_GlyIsOn_C); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } bool QmitkControlVisualizationPropertiesView::IsPlaneRotated() { mitk::Image* currentImage = dynamic_cast( m_NodeUsedForOdfVisualization->GetData() ); if( currentImage == nullptr ) { MITK_ERROR << " Casting problems. Returning false"; return false; } mitk::Vector3D imageNormal0 = currentImage->GetSlicedGeometry()->GetAxisVector(0); mitk::Vector3D imageNormal1 = currentImage->GetSlicedGeometry()->GetAxisVector(1); mitk::Vector3D imageNormal2 = currentImage->GetSlicedGeometry()->GetAxisVector(2); imageNormal0.Normalize(); imageNormal1.Normalize(); imageNormal2.Normalize(); auto renderWindowPart = this->GetRenderWindowPart(); double eps = 0.000001; // for all 2D renderwindows of the render window part check alignment { mitk::PlaneGeometry::ConstPointer displayPlane = dynamic_cast ( renderWindowPart->GetQmitkRenderWindow("axial")->GetRenderer()->GetCurrentWorldPlaneGeometry() ); if (displayPlane.IsNull()) { return false; } mitk::Vector3D normal = displayPlane->GetNormal(); normal.Normalize(); int test = 0; if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal0.GetVnlVector()))-1) > eps ) { test++; } if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal1.GetVnlVector()))-1) > eps ) { test++; } if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal2.GetVnlVector()))-1) > eps ) { test++; } if (test==3) { return true; } } { mitk::PlaneGeometry::ConstPointer displayPlane = dynamic_cast ( renderWindowPart->GetQmitkRenderWindow("sagittal")->GetRenderer()->GetCurrentWorldPlaneGeometry() ); if (displayPlane.IsNull()) { return false; } mitk::Vector3D normal = displayPlane->GetNormal(); normal.Normalize(); int test = 0; if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal0.GetVnlVector()))-1) > eps ) { test++; } if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal1.GetVnlVector()))-1) > eps ) { test++; } if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal2.GetVnlVector()))-1) > eps ) { test++; } if (test==3) { return true; } } { mitk::PlaneGeometry::ConstPointer displayPlane = dynamic_cast ( renderWindowPart->GetQmitkRenderWindow("coronal")->GetRenderer()->GetCurrentWorldPlaneGeometry() ); if (displayPlane.IsNull()) { return false; } mitk::Vector3D normal = displayPlane->GetNormal(); normal.Normalize(); int test = 0; if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal0.GetVnlVector()))-1) > eps ) { test++; } if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal1.GetVnlVector()))-1) > eps ) { test++; } if( fabs(fabs(dot_product(normal.GetVnlVector(),imageNormal2.GetVnlVector()))-1) > eps ) { test++; } if (test==3) { return true; } } return false; } void QmitkControlVisualizationPropertiesView::ShowMaxNumberChanged() { int maxNr = m_Controls->m_ShowMaxNumber->value(); if ( maxNr < 1 ) { m_Controls->m_ShowMaxNumber->setValue( 1 ); maxNr = 1; } - if ( dynamic_cast(m_SelectedNode->GetData()) - || dynamic_cast(m_SelectedNode->GetData()) - || dynamic_cast(m_SelectedNode->GetData()) ) + for (auto node : m_SelectedNodes) { - m_SelectedNode->SetIntProperty("ShowMaxNumber", maxNr); + if ( dynamic_cast(node->GetData()) + || dynamic_cast(node->GetData()) + || dynamic_cast(node->GetData()) ) + { + node->SetIntProperty("ShowMaxNumber", maxNr); + } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::NormalizationDropdownChanged(int normDropdown) { typedef mitk::OdfNormalizationMethodProperty PropType; PropType::Pointer normMeth = PropType::New(); switch(normDropdown) { case 0: normMeth->SetNormalizationToMinMax(); break; case 1: normMeth->SetNormalizationToMax(); break; case 2: normMeth->SetNormalizationToNone(); break; case 3: normMeth->SetNormalizationToGlobalMax(); break; default: normMeth->SetNormalizationToMinMax(); } - if ( dynamic_cast(m_SelectedNode->GetData()) - || dynamic_cast(m_SelectedNode->GetData()) - || dynamic_cast(m_SelectedNode->GetData()) ) + for (auto node : m_SelectedNodes) { - m_SelectedNode->SetProperty("Normalization", normMeth.GetPointer()); + if ( dynamic_cast(node->GetData()) + || dynamic_cast(node->GetData()) + || dynamic_cast(node->GetData()) ) + { + node->SetProperty("Normalization", normMeth.GetPointer()); + } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::ScalingFactorChanged(double scalingFactor) { - if ( dynamic_cast(m_SelectedNode->GetData()) - || dynamic_cast(m_SelectedNode->GetData()) - || dynamic_cast(m_SelectedNode->GetData()) ) + for (auto node : m_SelectedNodes) { - m_SelectedNode->SetFloatProperty("Scaling", scalingFactor); + if ( dynamic_cast(node->GetData()) + || dynamic_cast(node->GetData()) + || dynamic_cast(node->GetData()) ) + { + node->SetFloatProperty("Scaling", scalingFactor); + } } if (auto renderWindowPart = this->GetRenderWindowPart()) { renderWindowPart->RequestUpdate(); } } void QmitkControlVisualizationPropertiesView::AdditionalScaling(int additionalScaling) { typedef mitk::OdfScaleByProperty PropType; PropType::Pointer scaleBy = PropType::New(); switch(additionalScaling) { case 0: scaleBy->SetScaleByNothing(); break; case 1: scaleBy->SetScaleByGFA(); //m_Controls->params_frame->setVisible(true); break; default: scaleBy->SetScaleByNothing(); } - if ( dynamic_cast(m_SelectedNode->GetData()) - || dynamic_cast(m_SelectedNode->GetData()) - || dynamic_cast(m_SelectedNode->GetData()) ) + for (auto node : m_SelectedNodes) { - m_SelectedNode->SetProperty("ScaleBy", scaleBy.GetPointer()); + if ( dynamic_cast(node->GetData()) + || dynamic_cast(node->GetData()) + || dynamic_cast(node->GetData()) ) + { + node->SetProperty("ScaleBy", scaleBy.GetPointer()); + } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::Fiber2DfadingEFX() { - if (m_SelectedNode && dynamic_cast(m_SelectedNode->GetData()) ) + for (auto node : m_SelectedNodes) { - bool currentMode; - m_SelectedNode->GetBoolProperty("Fiber2DfadeEFX", currentMode); - m_SelectedNode->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(!currentMode)); - dynamic_cast(m_SelectedNode->GetData())->RequestUpdate2D(); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + if (node && dynamic_cast(node->GetData()) ) + { + bool currentMode; + node->GetBoolProperty("Fiber2DfadeEFX", currentMode); + node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(!currentMode)); + dynamic_cast(node->GetData())->RequestUpdate2D(); + } } + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::FiberSlicingThickness2D() { - if (m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) + for (auto node : m_SelectedNodes) { - float fibThickness = m_Controls->m_FiberClippingBox->value(); - float currentThickness = 0; - m_SelectedNode->GetFloatProperty("Fiber2DSliceThickness", currentThickness); - if ( fabs(fibThickness-currentThickness) < 0.001 ) - return; - - m_SelectedNode->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(fibThickness)); - dynamic_cast(m_SelectedNode->GetData())->RequestUpdate2D(); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + if (node && dynamic_cast(node->GetData())) + { + float fibThickness = m_Controls->m_FiberClippingBox->value(); + float currentThickness = 0; + node->GetFloatProperty("Fiber2DSliceThickness", currentThickness); + if ( fabs(fibThickness-currentThickness) < 0.001 ) + continue; + + node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(fibThickness)); + dynamic_cast(node->GetData())->RequestUpdate2D(); + } } + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::SetCustomColor(const itk::EventObject& /*e*/) { - if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) - { - float color[3]; - m_SelectedNode->GetColor(color); - mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedNode->GetData()); - fib->SetFiberColors(color[0]*255, color[1]*255, color[2]*255); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - } - else if (m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) + for (auto node : m_SelectedNodes) { - float color[3]; - m_SelectedNode->GetColor(color); - mitk::PeakImage::Pointer img = dynamic_cast(m_SelectedNode->GetData()); - img->SetCustomColor(color[0]*255, color[1]*255, color[2]*255); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + if(node && dynamic_cast(node->GetData())) + { + float color[3]; + node->GetColor(color); + mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); + fib->SetFiberColors(color[0]*255, color[1]*255, color[2]*255); + } + else if (node && dynamic_cast(node->GetData())) + { + float color[3]; + node->GetColor(color); + mitk::PeakImage::Pointer img = dynamic_cast(node->GetData()); + img->SetCustomColor(color[0]*255, color[1]*255, color[2]*255); + } } + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::ResetColoring() { - if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) + for (auto node : m_SelectedNodes) { - mitk::FiberBundle::Pointer fib = dynamic_cast(m_SelectedNode->GetData()); - fib->ColorFibersByOrientation(); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - } - else if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) - { - mitk::PeakImage::Pointer fib = dynamic_cast(m_SelectedNode->GetData()); - fib->ColorByOrientation(); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + if(node && dynamic_cast(node->GetData())) + { + mitk::FiberBundle::Pointer fib = dynamic_cast(node->GetData()); + fib->ColorFibersByOrientation(); + } + else if(node && dynamic_cast(node->GetData())) + { + mitk::PeakImage::Pointer fib = dynamic_cast(node->GetData()); + fib->ColorByOrientation(); + } } + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::PlanarFigureFocus() { - if(m_SelectedNode) + for (auto node : m_SelectedNodes) { - mitk::PlanarFigure* _PlanarFigure = 0; - _PlanarFigure = dynamic_cast (m_SelectedNode->GetData()); - - if (_PlanarFigure && _PlanarFigure->GetPlaneGeometry()) + if(node) { + mitk::PlanarFigure* _PlanarFigure = 0; + _PlanarFigure = dynamic_cast (node->GetData()); - QmitkRenderWindow* selectedRenderWindow = 0; - bool PlanarFigureInitializedWindow = false; + if (_PlanarFigure && _PlanarFigure->GetPlaneGeometry()) + { - auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN); + QmitkRenderWindow* selectedRenderWindow = 0; + bool PlanarFigureInitializedWindow = false; - QmitkRenderWindow* axialRenderWindow = - renderWindowPart->GetQmitkRenderWindow("axial"); + auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN); - if (m_SelectedNode->GetBoolProperty("PlanarFigureInitializedWindow", - PlanarFigureInitializedWindow, axialRenderWindow->GetRenderer())) - { - selectedRenderWindow = axialRenderWindow; - } + QmitkRenderWindow* axialRenderWindow = + renderWindowPart->GetQmitkRenderWindow("axial"); - QmitkRenderWindow* sagittalRenderWindow = - renderWindowPart->GetQmitkRenderWindow("sagittal"); + if (node->GetBoolProperty("PlanarFigureInitializedWindow", + PlanarFigureInitializedWindow, axialRenderWindow->GetRenderer())) + { + selectedRenderWindow = axialRenderWindow; + } - if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty( - "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, - sagittalRenderWindow->GetRenderer())) - { - selectedRenderWindow = sagittalRenderWindow; - } + QmitkRenderWindow* sagittalRenderWindow = + renderWindowPart->GetQmitkRenderWindow("sagittal"); - QmitkRenderWindow* coronalRenderWindow = - renderWindowPart->GetQmitkRenderWindow("coronal"); + if (!selectedRenderWindow && node->GetBoolProperty( + "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, + sagittalRenderWindow->GetRenderer())) + { + selectedRenderWindow = sagittalRenderWindow; + } - if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty( - "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, - coronalRenderWindow->GetRenderer())) - { - selectedRenderWindow = coronalRenderWindow; - } + QmitkRenderWindow* coronalRenderWindow = + renderWindowPart->GetQmitkRenderWindow("coronal"); - QmitkRenderWindow* _3DRenderWindow = - renderWindowPart->GetQmitkRenderWindow("3d"); + if (!selectedRenderWindow && node->GetBoolProperty( + "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, + coronalRenderWindow->GetRenderer())) + { + selectedRenderWindow = coronalRenderWindow; + } - if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty( - "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, - _3DRenderWindow->GetRenderer())) - { - selectedRenderWindow = _3DRenderWindow; - } + QmitkRenderWindow* _3DRenderWindow = + renderWindowPart->GetQmitkRenderWindow("3d"); - const mitk::PlaneGeometry* _PlaneGeometry = _PlanarFigure->GetPlaneGeometry(); + if (!selectedRenderWindow && node->GetBoolProperty( + "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, + _3DRenderWindow->GetRenderer())) + { + selectedRenderWindow = _3DRenderWindow; + } - mitk::VnlVector normal = _PlaneGeometry->GetNormalVnl(); + const mitk::PlaneGeometry* _PlaneGeometry = _PlanarFigure->GetPlaneGeometry(); - mitk::PlaneGeometry::ConstPointer worldGeometry1 = - axialRenderWindow->GetRenderer()->GetCurrentWorldPlaneGeometry(); - mitk::PlaneGeometry::ConstPointer _Plane1 = - dynamic_cast( worldGeometry1.GetPointer() ); - mitk::VnlVector normal1 = _Plane1->GetNormalVnl(); + mitk::VnlVector normal = _PlaneGeometry->GetNormalVnl(); - mitk::PlaneGeometry::ConstPointer worldGeometry2 = - sagittalRenderWindow->GetRenderer()->GetCurrentWorldPlaneGeometry(); - mitk::PlaneGeometry::ConstPointer _Plane2 = - dynamic_cast( worldGeometry2.GetPointer() ); - mitk::VnlVector normal2 = _Plane2->GetNormalVnl(); + mitk::PlaneGeometry::ConstPointer worldGeometry1 = + axialRenderWindow->GetRenderer()->GetCurrentWorldPlaneGeometry(); + mitk::PlaneGeometry::ConstPointer _Plane1 = + dynamic_cast( worldGeometry1.GetPointer() ); + mitk::VnlVector normal1 = _Plane1->GetNormalVnl(); - mitk::PlaneGeometry::ConstPointer worldGeometry3 = - coronalRenderWindow->GetRenderer()->GetCurrentWorldPlaneGeometry(); - mitk::PlaneGeometry::ConstPointer _Plane3 = - dynamic_cast( worldGeometry3.GetPointer() ); - mitk::VnlVector normal3 = _Plane3->GetNormalVnl(); + mitk::PlaneGeometry::ConstPointer worldGeometry2 = + sagittalRenderWindow->GetRenderer()->GetCurrentWorldPlaneGeometry(); + mitk::PlaneGeometry::ConstPointer _Plane2 = + dynamic_cast( worldGeometry2.GetPointer() ); + mitk::VnlVector normal2 = _Plane2->GetNormalVnl(); - normal[0] = fabs(normal[0]); normal[1] = fabs(normal[1]); normal[2] = fabs(normal[2]); - normal1[0] = fabs(normal1[0]); normal1[1] = fabs(normal1[1]); normal1[2] = fabs(normal1[2]); - normal2[0] = fabs(normal2[0]); normal2[1] = fabs(normal2[1]); normal2[2] = fabs(normal2[2]); - normal3[0] = fabs(normal3[0]); normal3[1] = fabs(normal3[1]); normal3[2] = fabs(normal3[2]); + mitk::PlaneGeometry::ConstPointer worldGeometry3 = + coronalRenderWindow->GetRenderer()->GetCurrentWorldPlaneGeometry(); + mitk::PlaneGeometry::ConstPointer _Plane3 = + dynamic_cast( worldGeometry3.GetPointer() ); + mitk::VnlVector normal3 = _Plane3->GetNormalVnl(); - double ang1 = angle(normal, normal1); - double ang2 = angle(normal, normal2); - double ang3 = angle(normal, normal3); + normal[0] = fabs(normal[0]); normal[1] = fabs(normal[1]); normal[2] = fabs(normal[2]); + normal1[0] = fabs(normal1[0]); normal1[1] = fabs(normal1[1]); normal1[2] = fabs(normal1[2]); + normal2[0] = fabs(normal2[0]); normal2[1] = fabs(normal2[1]); normal2[2] = fabs(normal2[2]); + normal3[0] = fabs(normal3[0]); normal3[1] = fabs(normal3[1]); normal3[2] = fabs(normal3[2]); - if(ang1 < ang2 && ang1 < ang3) - { - selectedRenderWindow = axialRenderWindow; - } - else - { - if(ang2 < ang3) + double ang1 = angle(normal, normal1); + double ang2 = angle(normal, normal2); + double ang3 = angle(normal, normal3); + + if(ang1 < ang2 && ang1 < ang3) { - selectedRenderWindow = sagittalRenderWindow; + selectedRenderWindow = axialRenderWindow; } else { - selectedRenderWindow = coronalRenderWindow; + if(ang2 < ang3) + { + selectedRenderWindow = sagittalRenderWindow; + } + else + { + selectedRenderWindow = coronalRenderWindow; + } + } + + // make node visible + if (selectedRenderWindow) + { + const mitk::Point3D& centerP = _PlaneGeometry->GetOrigin(); + selectedRenderWindow->GetSliceNavigationController()->ReorientSlices( + centerP, _PlaneGeometry->GetNormal()); } } - // make node visible - if (selectedRenderWindow) + // set interactor for new node (if not already set) + mitk::PlanarFigureInteractor::Pointer figureInteractor + = dynamic_cast(node->GetDataInteractor().GetPointer()); + + if(figureInteractor.IsNull()) { - const mitk::Point3D& centerP = _PlaneGeometry->GetOrigin(); - selectedRenderWindow->GetSliceNavigationController()->ReorientSlices( - centerP, _PlaneGeometry->GetNormal()); + figureInteractor = mitk::PlanarFigureInteractor::New(); + us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); + figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); + figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); + figureInteractor->SetDataNode( node ); } - } - - // set interactor for new node (if not already set) - mitk::PlanarFigureInteractor::Pointer figureInteractor - = dynamic_cast(m_SelectedNode->GetDataInteractor().GetPointer()); - if(figureInteractor.IsNull()) - { - figureInteractor = mitk::PlanarFigureInteractor::New(); - us::Module* planarFigureModule = us::ModuleRegistry::GetModule( "MitkPlanarFigure" ); - figureInteractor->LoadStateMachine("PlanarFigureInteraction.xml", planarFigureModule ); - figureInteractor->SetEventConfig( "PlanarFigureConfig.xml", planarFigureModule ); - figureInteractor->SetDataNode( m_SelectedNode ); + node->SetProperty("planarfigure.iseditable",mitk::BoolProperty::New(true)); } - - m_SelectedNode->SetProperty("planarfigure.iseditable",mitk::BoolProperty::New(true)); } } void QmitkControlVisualizationPropertiesView::SetInteractor() { // BUG 19179 // typedef std::vector Container; // Container _NodeSet = this->GetDataManagerSelection(); // mitk::DataNode* node = 0; // mitk::FiberBundle* bundle = 0; // mitk::FiberBundleInteractor::Pointer bundleInteractor = 0; // // finally add all nodes to the model // for(Container::const_iterator it=_NodeSet.begin(); it!=_NodeSet.end() // ; it++) // { // node = const_cast(*it); // bundle = dynamic_cast(node->GetData()); // if(bundle) // { // bundleInteractor = dynamic_cast(node->GetInteractor()); // if(bundleInteractor.IsNotNull()) // mitk::GlobalInteraction::GetInstance()->RemoveInteractor(bundleInteractor); // if(!m_Controls->m_Crosshair->isChecked()) // { // m_Controls->m_Crosshair->setChecked(false); // this->GetActiveStdMultiWidget()->GetRenderWindow4()->setCursor(Qt::ArrowCursor); // m_CurrentPickingNode = 0; // } // else // { // m_Controls->m_Crosshair->setChecked(true); // bundleInteractor = mitk::FiberBundleInteractor::New("FiberBundleInteractor", node); // mitk::GlobalInteraction::GetInstance()->AddInteractor(bundleInteractor); // this->GetActiveStdMultiWidget()->GetRenderWindow4()->setCursor(Qt::CrossCursor); // m_CurrentPickingNode = node; // } // } // } } void QmitkControlVisualizationPropertiesView::TubeRadiusChanged() { - if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) + for (auto node : m_SelectedNodes) { - float newRadius = m_Controls->m_TubeWidth->value(); - m_SelectedNode->SetFloatProperty("shape.tuberadius", newRadius); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + if(node && dynamic_cast(node->GetData())) + { + float newRadius = m_Controls->m_TubeWidth->value(); + node->SetFloatProperty("shape.tuberadius", newRadius); + } } + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::RibbonWidthChanged() { - if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) + for (auto node : m_SelectedNodes) { - float newWidth = m_Controls->m_RibbonWidth->value(); - m_SelectedNode->SetFloatProperty("shape.ribbonwidth", newWidth); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + if(node && dynamic_cast(node->GetData())) + { + float newWidth = m_Controls->m_RibbonWidth->value(); + node->SetFloatProperty("shape.ribbonwidth", newWidth); + } } + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::LineWidthChanged() { - if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) + for (auto node : m_SelectedNodes) { - auto newWidth = m_Controls->m_LineWidth->value(); - float currentWidth = 0; - m_SelectedNode->SetFloatProperty("shape.linewidth", currentWidth); - if (currentWidth==newWidth) - return; - m_SelectedNode->SetFloatProperty("shape.linewidth", newWidth); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + if(node && dynamic_cast(node->GetData())) + { + auto newWidth = m_Controls->m_LineWidth->value(); + float currentWidth = 0; + node->SetFloatProperty("shape.linewidth", currentWidth); + if (currentWidth==newWidth) + continue; + node->SetFloatProperty("shape.linewidth", newWidth); + } } + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::Welcome() { berry::PlatformUI::GetWorkbench()->GetIntroManager() ->ShowIntro(GetSite()->GetWorkbenchWindow(), false); } void QmitkControlVisualizationPropertiesView::OnColourisationModeChanged() { - if( m_SelectedNode && m_NodeUsedForOdfVisualization.IsNotNull() ) + for (auto node : m_SelectedNodes) { - m_SelectedNode->SetProperty( "DiffusionCore.Rendering.OdfVtkMapper.ColourisationModeBit", mitk::BoolProperty::New( m_Controls->m_OdfColorBox->currentIndex() ) ); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); - } - else - { - MITK_DEBUG << "QmitkControlVisualizationPropertiesView::OnColourisationModeChanged() was called but m_NodeUsedForOdfVisualization was Null."; + if( node && m_NodeUsedForOdfVisualization.IsNotNull() ) + { + node->SetProperty( "DiffusionCore.Rendering.OdfVtkMapper.ColourisationModeBit", mitk::BoolProperty::New( m_Controls->m_OdfColorBox->currentIndex() ) ); + } + else + { + MITK_DEBUG << "QmitkControlVisualizationPropertiesView::OnColourisationModeChanged() was called but m_NodeUsedForOdfVisualization was Null."; + } } + mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h index e75ffd3..6c2bcbe 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.h @@ -1,154 +1,154 @@ /*=================================================================== 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 _QMITKControlVisualizationPropertiesView_H_INCLUDED #define _QMITKControlVisualizationPropertiesView_H_INCLUDED #include #include #include "berryISelectionListener.h" #include "berryIStructuredSelection.h" #include "berryISizeProvider.h" #include "ui_QmitkControlVisualizationPropertiesViewControls.h" #include "mitkEnumerationProperty.h" #include #include /*! * \ingroup org_mitk_gui_qt_diffusionquantification_internal * * \brief QmitkControlVisualizationPropertiesView * * Document your class here. */ class QmitkControlVisualizationPropertiesView : public QmitkAbstractView, public mitk::ILifecycleAwarePart { friend struct CvpSelListener; // this is needed for all Qt objects that should have a MOC object (everything that derives from QObject) Q_OBJECT public: static const std::string VIEW_ID; QmitkControlVisualizationPropertiesView(); virtual ~QmitkControlVisualizationPropertiesView(); virtual void CreateQtPartControl(QWidget *parent) override; /// \brief Creation of the connections of main and control widget virtual void CreateConnections(); protected slots: void VisibleOdfsON_S(); void VisibleOdfsON_T(); void VisibleOdfsON_C(); void ShowMaxNumberChanged(); void NormalizationDropdownChanged(int); void ScalingFactorChanged(double); void AdditionalScaling(int); void OnThickSlicesModeSelected( QAction* action ); void OnTSNumChanged(int num); void ResetColoring(); void PlanarFigureFocus(); void Fiber2DfadingEFX(); void FiberSlicingThickness2D(); void LineWidthChanged(); void TubeRadiusChanged(); void RibbonWidthChanged(); void SetInteractor(); void Toggle3DClipping(bool enabled=true); void FlipPeaks(); void Welcome(); void OnSliceChanged(); void SetColor(); void Toggle3DPeaks(); /// \brief Slot function for switching colourisation mode of glyphs. void OnColourisationModeChanged(); protected: virtual void SetFocus() override; virtual void Activated() override; virtual void Deactivated() override; virtual void Visible() override; virtual void Hidden() override; virtual void NodeRemoved(const mitk::DataNode* node) override; /// \brief called by QmitkAbstractView when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList& nodes) override; virtual void NodeAdded(const mitk::DataNode *node) override; void SetCustomColor(const itk::EventObject& /*e*/); bool IsPlaneRotated(); void SliceRotation(const itk::EventObject&); void Set3DClippingPlane(bool disable, mitk::DataNode *node, std::string plane); void SetTs(int m_CurrentThickSlicesMode, int num, std::string render_window); Ui::QmitkControlVisualizationPropertiesViewControls* m_Controls; QScopedPointer m_SelListener; berry::IStructuredSelection::ConstPointer m_CurrentSelection; mitk::DataNode::Pointer m_NodeUsedForOdfVisualization; QIcon* m_IconTexOFF; QIcon* m_IconTexON; QIcon* m_IconGlyOFF_T; QIcon* m_IconGlyON_T; QIcon* m_IconGlyOFF_C; QIcon* m_IconGlyON_C; QIcon* m_IconGlyOFF_S; QIcon* m_IconGlyON_S; bool m_TexIsOn; bool m_GlyIsOn_T; bool m_GlyIsOn_C; bool m_GlyIsOn_S; int m_CurrentThickSlicesMode; int m_CurrentThickSlicesNum; QLabel* m_TSLabel; QMenu* m_MyMenu; // for planarfigure and bundle handling: - mitk::DataNode::Pointer m_SelectedNode; + std::vector< mitk::DataNode::Pointer > m_SelectedNodes; mitk::DataNode* m_CurrentPickingNode; unsigned long m_ColorPropertyObserverTag; unsigned long m_OpacityPropertyObserverTag; mitk::ColorProperty::Pointer m_Color; mitk::FloatProperty::Pointer m_Opacity; QmitkSliceNavigationListener m_SliceChangeListener; }; #endif // _QMITKControlVisualizationPropertiesView_H_INCLUDED