diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp index 7445144f1e..534aef2528 100755 --- a/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/Fiberfox/Fiberfox.cpp @@ -1,282 +1,288 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include "mitkCommandLineParser.h" #include #include #include #include #include using namespace mitk; /*! * \brief Command line interface to Fiberfox. * Simulate a diffusion-weighted image from a tractogram using the specified parameter file. */ int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Fiberfox"); parser.setCategory("Diffusion Simulation Tools"); parser.setContributor("MIC"); parser.setDescription("Command line interface to Fiberfox." " Simulate a diffusion-weighted image from a tractogram using the specified parameter file."); parser.setArgumentPrefix("--", "-"); parser.addArgument("", "o", mitkCommandLineParser::String, "Output root:", "output folder and file prefix", us::Any(), false, false, false, mitkCommandLineParser::Output); parser.addArgument("", "i", mitkCommandLineParser::String, "Input:", "input tractogram or diffusion-weighted image", us::Any(), false, false, false, mitkCommandLineParser::Input); parser.addArgument("parameters", "p", mitkCommandLineParser::String, "Parameter file:", "fiberfox parameter file (.ffp)", us::Any(), false, false, false, mitkCommandLineParser::Input); parser.addArgument("template", "t", mitkCommandLineParser::String, "Template image:", "use parameters of the template image", us::Any(), true, false, false, mitkCommandLineParser::Input); parser.addArgument("verbose", "v", mitkCommandLineParser::Bool, "Output additional images:", "output volume fraction images etc.", us::Any()); parser.addArgument("dont_apply_direction_matrix", "", mitkCommandLineParser::Bool, "Don't apply direction matrix:", "don't rotate gradients by image direction matrix", us::Any()); parser.addArgument("fix_seed", "", mitkCommandLineParser::Bool, "Use fix random seed:", "always use same sequence of random numbers", us::Any()); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) { return EXIT_FAILURE; } std::string outName = us::any_cast(parsedArgs["o"]); std::string paramName = us::any_cast(parsedArgs["parameters"]); std::string input=""; if (parsedArgs.count("i")) input = us::any_cast(parsedArgs["i"]); bool fix_seed = false; if (parsedArgs.count("fix_seed")) fix_seed = us::any_cast(parsedArgs["fix_seed"]); bool verbose = false; if (parsedArgs.count("verbose")) verbose = us::any_cast(parsedArgs["verbose"]); bool apply_direction_matrix = true; if (parsedArgs.count("dont_apply_direction_matrix")) apply_direction_matrix = false; FiberfoxParameters parameters; parameters.LoadParameters(paramName, fix_seed); // Test if /path/dir is an existing directory: std::string file_extension = ""; if( itksys::SystemTools::FileIsDirectory( outName ) ) { while( *(--(outName.cend())) == '/') { outName.pop_back(); } outName = outName + '/'; parameters.m_Misc.m_OutputPath = outName; outName = outName + parameters.m_Misc.m_OutputPrefix; // using default m_OutputPrefix as initialized. } else { // outName is NOT an existing directory, so we need to remove all trailing slashes: while( *(--(outName.cend())) == '/') { outName.pop_back(); } // now split up the given outName into directory and (prefix of) filename: if( ! itksys::SystemTools::GetFilenamePath( outName ).empty() && itksys::SystemTools::FileIsDirectory(itksys::SystemTools::GetFilenamePath( outName ) ) ) { parameters.m_Misc.m_OutputPath = itksys::SystemTools::GetFilenamePath( outName ) + '/'; } else { parameters.m_Misc.m_OutputPath = itksys::SystemTools::GetCurrentWorkingDirectory() + '/'; } file_extension = itksys::SystemTools::GetFilenameExtension(outName); if( ! itksys::SystemTools::GetFilenameWithoutExtension( outName ).empty() ) { parameters.m_Misc.m_OutputPrefix = itksys::SystemTools::GetFilenameWithoutExtension( outName ); } else { parameters.m_Misc.m_OutputPrefix = "fiberfox"; } outName = parameters.m_Misc.m_OutputPath + parameters.m_Misc.m_OutputPrefix; } mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images", "Fiberbundles"}, {}); mitk::BaseData::Pointer inputData = mitk::IOUtil::Load(input, &functor)[0]; itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); if ( dynamic_cast(inputData.GetPointer()) ) // simulate dataset from fibers { tractsToDwiFilter->SetFiberBundle(dynamic_cast(inputData.GetPointer())); if (parsedArgs.count("template")) { MITK_INFO << "Loading template image"; typedef itk::VectorImage< short, 3 > ItkDwiType; typedef itk::Image< short, 3 > ItkImageType; mitk::BaseData::Pointer templateData = mitk::IOUtil::Load(us::any_cast(parsedArgs["template"]), &functor)[0]; mitk::Image::Pointer template_image = dynamic_cast(templateData.GetPointer()); if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(template_image)) { ItkDwiType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(template_image); parameters.m_SignalGen.m_ImageRegion = itkVectorImagePointer->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkVectorImagePointer->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkVectorImagePointer->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkVectorImagePointer->GetDirection(); parameters.SetBvalue(mitk::DiffusionPropertyHelper::GetReferenceBValue(template_image)); parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(template_image)); } else { ItkImageType::Pointer itkImagePointer = ItkImageType::New(); mitk::CastToItkImage(template_image, itkImagePointer); parameters.m_SignalGen.m_ImageRegion = itkImagePointer->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkImagePointer->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkImagePointer->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkImagePointer->GetDirection(); } } } else if ( dynamic_cast(inputData.GetPointer()) ) // add artifacts to existing image { typedef itk::VectorImage< short, 3 > ItkDwiType; mitk::Image::Pointer diffImg = dynamic_cast(inputData.GetPointer()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); parameters.m_SignalGen.m_SignalScale = 1; parameters.m_SignalGen.m_ImageRegion = itkVectorImagePointer->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkVectorImagePointer->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkVectorImagePointer->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkVectorImagePointer->GetDirection(); parameters.SetBvalue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(diffImg)); tractsToDwiFilter->SetInputImage(itkVectorImagePointer); } if (verbose) { MITK_DEBUG << outName << ".ffp"; parameters.m_Misc.m_OutputAdditionalImages = true; parameters.SaveParameters(outName+".ffp"); } else parameters.m_Misc.m_OutputAdditionalImages = false; if (apply_direction_matrix) { MITK_INFO << "Applying direction matrix to gradient directions."; parameters.ApplyDirectionMatrix(); } tractsToDwiFilter->SetParameters(parameters); tractsToDwiFilter->SetUseConstantRandSeed(fix_seed); tractsToDwiFilter->Update(); mitk::Image::Pointer image = mitk::GrabItkImageMemory(tractsToDwiFilter->GetOutput()); - if (apply_direction_matrix) - mitk::DiffusionPropertyHelper::SetGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer()); - else - mitk::DiffusionPropertyHelper::SetOriginalGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer()); - mitk::DiffusionPropertyHelper::SetReferenceBValue(image, parameters.m_SignalGen.GetBvalue()); - mitk::DiffusionPropertyHelper::InitializeImage(image); - - if (file_extension=="") - mitk::IOUtil::Save(image, "DWI_NIFTI", outName+".nii.gz"); - else if (file_extension==".nii" || file_extension==".nii.gz") - mitk::IOUtil::Save(image, "DWI_NIFTI", outName+file_extension); + + if (parameters.m_SignalGen.GetNumWeightedVolumes()>0) + { + if (apply_direction_matrix) + mitk::DiffusionPropertyHelper::SetGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer()); + else + mitk::DiffusionPropertyHelper::SetOriginalGradientContainer(image, parameters.m_SignalGen.GetItkGradientContainer()); + mitk::DiffusionPropertyHelper::SetReferenceBValue(image, parameters.m_SignalGen.GetBvalue()); + mitk::DiffusionPropertyHelper::InitializeImage(image); + + if (file_extension=="") + mitk::IOUtil::Save(image, "DWI_NIFTI", outName+".nii.gz"); + else if (file_extension==".nii" || file_extension==".nii.gz") + mitk::IOUtil::Save(image, "DWI_NIFTI", outName+file_extension); + else + mitk::IOUtil::Save(image, outName+file_extension); + } else - mitk::IOUtil::Save(image, outName+file_extension); + mitk::IOUtil::Save(image, outName+".nii.gz"); if (verbose) { if (tractsToDwiFilter->GetTickImage().IsNotNull()) { mitk::Image::Pointer mitkImage = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::Float2DImageType::Pointer itkImage = tractsToDwiFilter->GetTickImage(); mitkImage = mitk::GrabItkImageMemory( itkImage.GetPointer() ); mitk::IOUtil::Save(mitkImage, outName+"_Ticks.nii.gz"); } if (tractsToDwiFilter->GetRfImage().IsNotNull()) { mitk::Image::Pointer mitkImage = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::Float2DImageType::Pointer itkImage = tractsToDwiFilter->GetRfImage(); mitkImage = mitk::GrabItkImageMemory( itkImage.GetPointer() ); mitk::IOUtil::Save(mitkImage, outName+"_TimeFromRf.nii.gz"); } std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = tractsToDwiFilter->GetVolumeFractions(); for (unsigned int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::IOUtil::Save(image, outName+"_Compartment"+boost::lexical_cast(k+1)+".nii.gz"); } if (tractsToDwiFilter->GetPhaseImage().IsNotNull()) { mitk::Image::Pointer image = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkPhase = tractsToDwiFilter->GetPhaseImage(); image = mitk::GrabItkImageMemory( itkPhase.GetPointer() ); mitk::IOUtil::Save(image, outName+"_Phase.nii.gz"); } if (tractsToDwiFilter->GetKspaceImage().IsNotNull()) { mitk::Image::Pointer image = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkImage = tractsToDwiFilter->GetKspaceImage(); image = mitk::GrabItkImageMemory( itkImage.GetPointer() ); mitk::IOUtil::Save(image, outName+"_kSpace.nii.gz"); } int c = 1; std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_real = tractsToDwiFilter->GetOutputImagesReal(); for (auto real : output_real) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(real.GetPointer()); image->SetVolume(real->GetBufferPointer()); mitk::IOUtil::Save(image, outName+"_Coil-"+boost::lexical_cast(c)+"-real.nii.gz"); ++c; } c = 1; std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_imag = tractsToDwiFilter->GetOutputImagesImag(); for (auto imag : output_imag) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(imag.GetPointer()); image->SetVolume(imag->GetBufferPointer()); mitk::IOUtil::Save(image, outName+"_Coil-"+boost::lexical_cast(c)+"-imag.nii.gz"); ++c; } } return EXIT_SUCCESS; } diff --git a/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/StreamlineTractography.cpp b/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/StreamlineTractography.cpp index bf00ae0999..e5f986b2f0 100755 --- a/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/StreamlineTractography.cpp +++ b/Modules/DiffusionImaging/DiffusionCmdApps/Tractography/StreamlineTractography.cpp @@ -1,561 +1,566 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #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[]) { mitkCommandLineParser 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", mitkCommandLineParser::StringList, "Input:", "input image (multiple possible for 'DetTensor' algorithm)", us::Any(), false, false, false, mitkCommandLineParser::Input); parser.addArgument("", "o", mitkCommandLineParser::String, "Output:", "output fiberbundle/probability map", us::Any(), false, false, false, mitkCommandLineParser::Output); parser.addArgument("type", "", mitkCommandLineParser::String, "Type:", "which tracker to use (Peaks; Tensor; ODF; RF)", us::Any(), false); parser.addArgument("probabilistic", "", mitkCommandLineParser::Bool, "Probabilistic:", "Probabilistic tractography", us::Any(false)); parser.endGroup(); parser.beginGroup("2. Seeding:"); parser.addArgument("seeds", "", mitkCommandLineParser::Int, "Seeds per voxel:", "number of seed points per voxel", 1); parser.addArgument("seed_image", "", mitkCommandLineParser::String, "Seed image:", "mask image defining seed voxels", us::Any(), true, false, false, mitkCommandLineParser::Input); parser.addArgument("trials_per_seed", "", mitkCommandLineParser::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", "", mitkCommandLineParser::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", "", mitkCommandLineParser::String, "Mask image:", "streamlines leaving the mask will stop immediately", us::Any(), true, false, false, mitkCommandLineParser::Input); parser.addArgument("stop_image", "", mitkCommandLineParser::String, "Stop ROI image:", "streamlines entering the mask will stop immediately", us::Any(), true, false, false, mitkCommandLineParser::Input); parser.addArgument("exclusion_image", "", mitkCommandLineParser::String, "Exclusion ROI image:", "streamlines entering the mask will be discarded", us::Any(), true, false, false, mitkCommandLineParser::Input); parser.addArgument("ep_constraint", "", mitkCommandLineParser::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", "", mitkCommandLineParser::String, "Target ROI image:", "effact depends on the chosen endpoint constraint (option ep_constraint)", us::Any(), true, false, false, mitkCommandLineParser::Input); parser.endGroup(); parser.beginGroup("4. Streamline integration parameters:"); parser.addArgument("sharpen_odfs", "", mitkCommandLineParser::Bool, "SHarpen ODFs:", "if you are using dODF images as input, it is advisable to sharpen the ODFs (min-max normalize and raise to the power of 4). this is not necessary for CSD fODFs, since they are narurally much sharper."); parser.addArgument("cutoff", "", mitkCommandLineParser::Float, "Cutoff:", "set the FA, GFA or Peak amplitude cutoff for terminating tracks", 0.1); parser.addArgument("odf_cutoff", "", mitkCommandLineParser::Float, "ODF Cutoff:", "threshold on the ODF magnitude. this is useful in case of CSD fODF tractography.", 0.0); parser.addArgument("step_size", "", mitkCommandLineParser::Float, "Step size:", "step size (in voxels)", 0.5); parser.addArgument("min_tract_length", "", mitkCommandLineParser::Float, "Min. tract length:", "minimum fiber length (in mm)", 20); parser.addArgument("angular_threshold", "", mitkCommandLineParser::Float, "Angular threshold:", "angular threshold between two successive steps, (default: 90° * step_size, minimum 15°)"); parser.addArgument("loop_check", "", mitkCommandLineParser::Float, "Check for loops:", "threshold on angular stdev over the last 4 voxel lengths"); + parser.addArgument("peak_jitter", "", mitkCommandLineParser::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.endGroup(); parser.beginGroup("5. Tractography prior:"); parser.addArgument("prior_image", "", mitkCommandLineParser::String, "Peak prior:", "tractography prior in thr for of a peak image", us::Any(), true, false, false, mitkCommandLineParser::Input); parser.addArgument("prior_weight", "", mitkCommandLineParser::Float, "Prior weight", "weighting factor between prior and data.", 0.5); parser.addArgument("dont_restrict_to_prior", "", mitkCommandLineParser::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", "", mitkCommandLineParser::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", "", mitkCommandLineParser::Bool, "Prior Flip X:", "multiply x-coordinate of prior direction by -1"); parser.addArgument("prior_flip_y", "", mitkCommandLineParser::Bool, "Prior Flip Y:", "multiply y-coordinate of prior direction by -1"); parser.addArgument("prior_flip_z", "", mitkCommandLineParser::Bool, "Prior Flip Z:", "multiply z-coordinate of prior direction by -1"); parser.endGroup(); parser.beginGroup("6. Neighborhood sampling:"); parser.addArgument("num_samples", "", mitkCommandLineParser::Int, "Num. neighborhood samples:", "number of neighborhood samples that are use to determine the next progression direction", 0); parser.addArgument("sampling_distance", "", mitkCommandLineParser::Float, "Sampling distance:", "distance of neighborhood sampling points (in voxels)", 0.25); parser.addArgument("use_stop_votes", "", mitkCommandLineParser::Bool, "Use stop votes:", "use stop votes"); parser.addArgument("use_only_forward_samples", "", mitkCommandLineParser::Bool, "Use only forward samples:", "use only forward samples"); parser.endGroup(); parser.beginGroup("7. Tensor tractography specific:"); parser.addArgument("tend_f", "", mitkCommandLineParser::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", "", mitkCommandLineParser::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", "", mitkCommandLineParser::String, "Forest:", "input random forest (HDF5 file)", us::Any(), true, false, false, mitkCommandLineParser::Input); parser.addArgument("use_sh_features", "", mitkCommandLineParser::Bool, "Use SH features:", "use SH features"); parser.endGroup(); parser.beginGroup("9. Additional input:"); parser.addArgument("additional_images", "", mitkCommandLineParser::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, mitkCommandLineParser::Input); parser.endGroup(); parser.beginGroup("10. Misc:"); parser.addArgument("flip_x", "", mitkCommandLineParser::Bool, "Flip X:", "multiply x-coordinate of direction proposal by -1"); parser.addArgument("flip_y", "", mitkCommandLineParser::Bool, "Flip Y:", "multiply y-coordinate of direction proposal by -1"); parser.addArgument("flip_z", "", mitkCommandLineParser::Bool, "Flip Z:", "multiply z-coordinate of direction proposal by -1"); parser.addArgument("no_data_interpolation", "", mitkCommandLineParser::Bool, "Don't interpolate input data:", "don't interpolate input image values"); parser.addArgument("no_mask_interpolation", "", mitkCommandLineParser::Bool, "Don't interpolate masks:", "don't interpolate mask image values"); parser.addArgument("compress", "", mitkCommandLineParser::Float, "Compress:", "compress output fibers using the given error threshold (in mm)"); parser.addArgument("fix_seed", "", mitkCommandLineParser::Bool, "Fix Random Seed:", "always use the same random numbers"); parser.addArgument("parameter_file", "", mitkCommandLineParser::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, mitkCommandLineParser::Input); parser.endGroup(); std::map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; mitkCommandLineParser::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"]); params->m_RestrictToPrior = true; if (parsedArgs.count("dont_restrict_to_prior")) params->m_RestrictToPrior = !us::any_cast(parsedArgs["dont_restrict_to_prior"]); params->m_NewDirectionsFromPrior = true; if (parsedArgs.count("no_new_directions_from_prior")) params->m_NewDirectionsFromPrior = !us::any_cast(parsedArgs["no_new_directions_from_prior"]); params->m_SharpenOdfs = false; if (parsedArgs.count("sharpen_odfs")) params->m_SharpenOdfs = us::any_cast(parsedArgs["sharpen_odfs"]); params->m_InterpolateTractographyData = true; 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"]); params->m_StopVotes = false; if (parsedArgs.count("use_stop_votes")) params->m_StopVotes = us::any_cast(parsedArgs["use_stop_votes"]); params->m_OnlyForwardSamples = false; if (parsedArgs.count("use_only_forward_samples")) params->m_OnlyForwardSamples = us::any_cast(parsedArgs["use_only_forward_samples"]); params->m_FlipX = false; if (parsedArgs.count("flip_x")) params->m_FlipX = us::any_cast(parsedArgs["flip_x"]); params->m_FlipY = false; if (parsedArgs.count("flip_y")) params->m_FlipY = us::any_cast(parsedArgs["flip_y"]); params->m_FlipZ = false; if (parsedArgs.count("flip_z")) params->m_FlipZ = us::any_cast(parsedArgs["flip_z"]); bool prior_flip_x = false; if (parsedArgs.count("prior_flip_x")) prior_flip_x = us::any_cast(parsedArgs["prior_flip_x"]); bool prior_flip_y = false; if (parsedArgs.count("prior_flip_y")) prior_flip_y = us::any_cast(parsedArgs["prior_flip_y"]); bool prior_flip_z = false; if (parsedArgs.count("prior_flip_z")) prior_flip_z = us::any_cast(parsedArgs["prior_flip_z"]); params->m_ApplyDirectionMatrix = false; if (parsedArgs.count("apply_image_rotation")) params->m_ApplyDirectionMatrix = us::any_cast(parsedArgs["apply_image_rotation"]); float compress = -1; if (parsedArgs.count("compress")) compress = us::any_cast(parsedArgs["compress"]); params->m_MinTractLengthMm = 20; if (parsedArgs.count("min_tract_length")) params->m_MinTractLengthMm = us::any_cast(parsedArgs["min_tract_length"]); params->SetLoopCheckDeg(-1); if (parsedArgs.count("loop_check")) params->SetLoopCheckDeg(us::any_cast(parsedArgs["loop_check"])); 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"]); std::string ep_constraint = "NONE"; if (parsedArgs.count("ep_constraint")) ep_constraint = us::any_cast(parsedArgs["ep_constraint"]); params->m_Cutoff = 0.1f; if (parsedArgs.count("cutoff")) params->m_Cutoff = us::any_cast(parsedArgs["cutoff"]); params->m_OdfCutoff = 0.0; if (parsedArgs.count("odf_cutoff")) params->m_OdfCutoff = us::any_cast(parsedArgs["odf_cutoff"]); + params->m_PeakJitter = 0.01; + if (parsedArgs.count("peak_jitter")) + params->m_PeakJitter = us::any_cast(parsedArgs["peak_jitter"]); + params->SetStepSizeVox(-1); if (parsedArgs.count("step_size")) params->SetStepSizeVox(us::any_cast(parsedArgs["step_size"])); params->SetSamplingDistanceVox(-1); if (parsedArgs.count("sampling_distance")) params->SetSamplingDistanceVox(us::any_cast(parsedArgs["sampling_distance"])); params->m_NumSamples = 0; if (parsedArgs.count("num_samples")) params->m_NumSamples = static_cast(us::any_cast(parsedArgs["num_samples"])); params->m_SeedsPerVoxel = 1; if (parsedArgs.count("seeds")) params->m_SeedsPerVoxel = us::any_cast(parsedArgs["seeds"]); params->m_TrialsPerSeed = 10; if (parsedArgs.count("trials_per_seed")) params->m_TrialsPerSeed = static_cast(us::any_cast(parsedArgs["trials_per_seed"])); params->m_F = 1; if (parsedArgs.count("tend_f")) params->m_F = us::any_cast(parsedArgs["tend_f"]); params->m_G = 0; if (parsedArgs.count("tend_g")) params->m_G = us::any_cast(parsedArgs["tend_g"]); params->SetAngularThresholdDeg(-1); if (parsedArgs.count("angular_threshold")) params->SetAngularThresholdDeg(us::any_cast(parsedArgs["angular_threshold"])); params->m_MaxNumFibers = -1; 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 mitkCommandLineParser::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"}, {}); 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 = prior_flip_x; prior_params->m_FlipY = prior_flip_y; prior_params->m_FlipZ = prior_flip_z; prior_params->m_Cutoff = 0.0; dynamic_cast(priorhandler)->SetPeakImage(itkImg); priorhandler->SetParameters(prior_params); tracker->SetTrackingPriorHandler(priorhandler); } mitk::TrackingDataHandler* handler; if (type == "RF") { mitk::TractographyForest::Pointer forest = mitk::IOUtil::Load(forestFile); if (forest.IsNull()) mitkThrow() << "Forest file " << forestFile << " could not be read."; mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"Diffusion Weighted Images"}, {}); auto input = mitk::IOUtil::Load(input_files.at(0), &functor); 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)); 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)); 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 == "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)); itkImg = mitk::convert::GetItkOdfFromTensorImage(input); dynamic_cast(handler)->SetIsOdfFromTensor(true); } else { mitk::PreferenceListReaderOptionsFunctor functor = mitk::PreferenceListReaderOptionsFunctor({"SH Image", "ODF Image"}, {}); auto input = mitk::IOUtil::Load(input_files.at(0), &functor)[0]; if (dynamic_cast(input.GetPointer())) { MITK_INFO << "Converting SH to ODF image"; mitk::Image::Pointer mitkImg = dynamic_cast(input.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; } if (ep_constraint=="NONE") params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::NONE; else if (ep_constraint=="EPS_IN_TARGET") params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET; else if (ep_constraint=="EPS_IN_TARGET_LABELDIFF") params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_TARGET_LABELDIFF; else if (ep_constraint=="EPS_IN_SEED_AND_TARGET") params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::EPS_IN_SEED_AND_TARGET; else if (ep_constraint=="MIN_ONE_EP_IN_TARGET") params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::MIN_ONE_EP_IN_TARGET; else if (ep_constraint=="ONE_EP_IN_TARGET") params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::ONE_EP_IN_TARGET; else if (ep_constraint=="NO_EP_IN_TARGET") params->m_EpConstraints = itk::StreamlineTrackingFilter::EndpointConstraints::NO_EP_IN_TARGET; 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 (compress > 0) outFib->Compress(compress); 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/DiffusionImaging/DiffusionCore/include/mitkDiffusionFunctionCollection.h b/Modules/DiffusionImaging/DiffusionCore/include/mitkDiffusionFunctionCollection.h index f103c2dee8..37935c9174 100644 --- a/Modules/DiffusionImaging/DiffusionCore/include/mitkDiffusionFunctionCollection.h +++ b/Modules/DiffusionImaging/DiffusionCore/include/mitkDiffusionFunctionCollection.h @@ -1,249 +1,259 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef __mitkDiffusionFunctionCollection_h_ #define __mitkDiffusionFunctionCollection_h_ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace mitk{ class MITKDIFFUSIONCORE_EXPORT imv { public: static std::vector< std::pair< itk::Index<3>, double > > IntersectImage(const itk::Vector& spacing, itk::Index<3>& si, itk::Index<3>& ei, itk::ContinuousIndex& sf, itk::ContinuousIndex& ef); static itk::Point GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = static_cast(point[0]); itkPoint[1] = static_cast(point[1]); itkPoint[2] = static_cast(point[2]); return itkPoint; } template< class TType > static itk::Point GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = static_cast(point[0]); itkPoint[1] = static_cast(point[1]); itkPoint[2] = static_cast(point[2]); return itkPoint; } + template< class TType > + static itk::Vector GetItkVector(double point[3]) + { + itk::Vector itkVector; + itkVector[0] = static_cast(point[0]); + itkVector[1] = static_cast(point[1]); + itkVector[2] = static_cast(point[2]); + return itkVector; + } + template< class TPixelType, class TOutPixelType=TPixelType > static TOutPixelType GetImageValue(const itk::Point& itkP, bool interpolate, typename itk::LinearInterpolateImageFunction< itk::Image< TPixelType, 3 >, float >::Pointer interpolator) { if (interpolator==nullptr) return 0.0; itk::ContinuousIndex< float, 3> cIdx; interpolator->ConvertPointToContinuousIndex(itkP, cIdx); if (interpolator->IsInsideBuffer(cIdx)) { if (interpolate) return interpolator->EvaluateAtContinuousIndex(cIdx); else { itk::Index<3> idx; interpolator->ConvertContinuousIndexToNearestIndex(cIdx, idx); return interpolator->EvaluateAtIndex(idx); } } else return 0.0; } template< class TPixelType=unsigned char > static bool IsInsideMask(const itk::Point& itkP, bool interpolate, typename itk::LinearInterpolateImageFunction< itk::Image< TPixelType, 3 >, float >::Pointer interpolator, float threshold=0.5) { if (interpolator==nullptr) return false; itk::ContinuousIndex< float, 3> cIdx; interpolator->ConvertPointToContinuousIndex(itkP, cIdx); if (interpolator->IsInsideBuffer(cIdx)) { float value = 0.0; if (interpolate) value = interpolator->EvaluateAtContinuousIndex(cIdx); else { itk::Index<3> idx; interpolator->ConvertContinuousIndexToNearestIndex(cIdx, idx); value = interpolator->EvaluateAtIndex(idx); } if (value>=threshold) return true; } return false; } template< class TType=float > static vnl_matrix_fixed< TType, 3, 3 > GetRotationMatrixVnl(TType rx, TType ry, TType rz) { rx = rx*itk::Math::pi/180; ry = ry*itk::Math::pi/180; rz = rz*itk::Math::pi/180; vnl_matrix_fixed< TType, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< TType, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< TType, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; vnl_matrix_fixed< TType, 3, 3 > rot = rotZ*rotY*rotX; return rot; } template< class TType=float > static itk::Matrix< TType, 3, 3 > GetRotationMatrixItk(TType rx, TType ry, TType rz) { rx = rx*itk::Math::pi/180; ry = ry*itk::Math::pi/180; rz = rz*itk::Math::pi/180; itk::Matrix< TType, 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< TType, 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< TType, 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< TType, 3, 3 > rot = rotZ*rotY*rotX; return rot; } }; class MITKDIFFUSIONCORE_EXPORT convert { public: static mitk::OdfImage::ItkOdfImageType::Pointer GetItkOdfFromTensorImage(mitk::Image::Pointer mitkImage); static mitk::OdfImage::Pointer GetOdfFromTensorImage(mitk::Image::Pointer mitkImage); static mitk::TensorImage::ItkTensorImageType::Pointer GetItkTensorFromTensorImage(mitk::Image::Pointer mitkImage); static mitk::PeakImage::ItkPeakImageType::Pointer GetItkPeakFromPeakImage(mitk::Image::Pointer mitkImage); template static typename itk::Image< itk::Vector, 3>::Pointer GetItkShFromShImage(mitk::Image::Pointer mitkImage) { mitk::ShImage::Pointer mitkShImage = dynamic_cast(mitkImage.GetPointer()); if (mitkShImage.IsNull()) mitkThrow() << "Input image is not a SH image!"; typename itk::Image< itk::Vector, 3>::Pointer itkvol; mitk::CastToItkImage(mitkImage, itkvol); return itkvol; } static mitk::OdfImage::ItkOdfImageType::Pointer GetItkOdfFromShImage(mitk::Image::Pointer mitkImage); static mitk::OdfImage::Pointer GetOdfFromShImage(mitk::Image::Pointer mitkImage); static mitk::OdfImage::ItkOdfImageType::Pointer GetItkOdfFromOdfImage(mitk::Image::Pointer mitkImage); }; class MITKDIFFUSIONCORE_EXPORT sh { public: static double factorial(int number); static void Cart2Sph(double x, double y, double z, double* spherical); static vnl_vector_fixed Sph2Cart(const double& theta, const double& phi, const double& rad); static double legendre0(int l); static double spherical_harmonic(int m,int l,double theta,double phi, bool complexPart); static double Yj(int m, int k, float theta, float phi, bool mrtrix=true); static vnl_matrix CalcShBasisForDirections(unsigned int sh_order, vnl_matrix U, bool mrtrix=true); static float GetValue(const vnl_vector& coefficients, const int& sh_order, const vnl_vector_fixed& dir, const bool mrtrix); static float GetValue(const vnl_vector &coefficients, const int &sh_order, const double theta, const double phi, const bool mrtrix); static unsigned int ShOrder(int num_coeffs); template static void SampleOdf(const vnl_vector& coefficients, itk::OrientationDistributionFunction& odf) { auto dirs = odf.GetDirections(); auto basis = CalcShBasisForDirections(ShOrder(coefficients.size()), *dirs); auto odf_vals = basis * coefficients; for (unsigned int i=0; i IndiciesVector; typedef mitk::BValueMapProperty::BValueMap BValueMap; typedef DiffusionPropertyHelper::GradientDirectionsContainerType GradientDirectionContainerType; typedef DiffusionPropertyHelper::GradientDirectionType GradientDirectionType; public: static GradientDirectionContainerType::Pointer ReadBvalsBvecs(std::string bvals_file, std::string bvecs_file, double& reference_bval); static void WriteBvalsBvecs(std::string bvals_file, std::string bvecs_file, GradientDirectionContainerType::Pointer gradients, double reference_bval); static std::vector GetAllUniqueDirections(const BValueMap &bValueMap, GradientDirectionContainerType *refGradientsContainer ); static bool CheckForDifferingShellDirections(const BValueMap &bValueMap, GradientDirectionContainerType::ConstPointer refGradientsContainer); static vnl_matrix ComputeSphericalHarmonicsBasis(const vnl_matrix & QBallReference, const unsigned int & LOrder); static vnl_matrix ComputeSphericalFromCartesian(const IndiciesVector & refShell, const GradientDirectionContainerType * refGradientsContainer); static GradientDirectionContainerType::Pointer CreateNormalizedUniqueGradientDirectionContainer(const BValueMap &bValueMap, const GradientDirectionContainerType * origninalGradentcontainer); }; } #endif //__mitkDiffusionFunctionCollection_h_ diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp index ca809f26e6..efa67a9145 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/TrackingHandlers/mitkTrackingHandlerPeaks.cpp @@ -1,304 +1,306 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkTrackingHandlerPeaks.h" namespace mitk { TrackingHandlerPeaks::TrackingHandlerPeaks() { } TrackingHandlerPeaks::~TrackingHandlerPeaks() { } bool TrackingHandlerPeaks::WorldToIndex(itk::Point& pos, itk::Index<3>& index) { m_DummyImage->TransformPhysicalPointToIndex(pos, index); return m_DummyImage->GetLargestPossibleRegion().IsInside(index); } void TrackingHandlerPeaks::InitForTracking() { MITK_INFO << "Initializing peak tracker."; if (m_NeedsDataInit) { itk::Vector spacing4 = m_PeakImage->GetSpacing(); itk::Point origin4 = m_PeakImage->GetOrigin(); itk::Matrix direction4 = m_PeakImage->GetDirection(); itk::ImageRegion<4> imageRegion4 = m_PeakImage->GetLargestPossibleRegion(); spacing3[0] = spacing4[0]; spacing3[1] = spacing4[1]; spacing3[2] = spacing4[2]; origin3[0] = origin4[0]; origin3[1] = origin4[1]; origin3[2] = origin4[2]; for (int r=0; r<3; r++) for (int c=0; c<3; c++) { direction3[r][c] = direction4[r][c]; m_FloatImageRotation[r][c] = direction4[r][c]; } imageRegion3.SetSize(0, imageRegion4.GetSize()[0]); imageRegion3.SetSize(1, imageRegion4.GetSize()[1]); imageRegion3.SetSize(2, imageRegion4.GetSize()[2]); m_DummyImage = ItkUcharImgType::New(); m_DummyImage->SetSpacing( spacing3 ); m_DummyImage->SetOrigin( origin3 ); m_DummyImage->SetDirection( direction3 ); m_DummyImage->SetRegions( imageRegion3 ); m_DummyImage->Allocate(); m_DummyImage->FillBuffer(0.0); m_NumDirs = imageRegion4.GetSize(3)/3; this->CalculateMinVoxelSize(); m_NeedsDataInit = false; } std::cout << "TrackingHandlerPeaks - Peak threshold: " << m_Parameters->m_Cutoff << std::endl; + if (m_Parameters->m_Mode == MODE::PROBABILISTIC) + std::cout << "TrackingHandlerPeaks - Peak jitter: " << m_Parameters->m_PeakJitter << std::endl; } vnl_vector_fixed TrackingHandlerPeaks::GetMatchingDirection(itk::Index<3> idx3, vnl_vector_fixed& oldDir) { vnl_vector_fixed out_dir; out_dir.fill(0); float angle = 0; float mag = oldDir.magnitude(); if (magm_FixRandomSeed) { // try m_NumDirs times to get a non-zero random direction for (int j=0; jGetIntegerVariate(m_NumDirs-1); out_dir = GetDirection(idx3, i); if (out_dir.magnitude()>mitk::eps) { oldDir[0] = out_dir[0]; oldDir[1] = out_dir[1]; oldDir[2] = out_dir[2]; found = true; break; } } } if (!found) { // if you didn't find a non-zero random direction, take first non-zero direction you find for (int i=0; imitk::eps) { oldDir[0] = out_dir[0]; oldDir[1] = out_dir[1]; oldDir[2] = out_dir[2]; break; } } } } else { for (int i=0; i dir = GetDirection(idx3, i); mag = dir.magnitude(); if (mag>mitk::eps) dir.normalize(); float a = dot_product(dir, oldDir); if (fabs(a)>angle) { angle = fabs(a); if (a<0) out_dir = -dir; else out_dir = dir; out_dir *= mag; out_dir *= angle; // shrink contribution of direction if is less parallel to previous direction } } } return out_dir; } vnl_vector_fixed TrackingHandlerPeaks::GetDirection(itk::Index<3> idx3, int dirIdx) { vnl_vector_fixed dir; dir.fill(0.0); if ( !m_DummyImage->GetLargestPossibleRegion().IsInside(idx3) ) return dir; PeakImgType::IndexType idx4; idx4.SetElement(0,idx3[0]); idx4.SetElement(1,idx3[1]); idx4.SetElement(2,idx3[2]); for (int k=0; k<3; k++) { idx4.SetElement(3, dirIdx*3 + k); dir[k] = m_PeakImage->GetPixel(idx4); } if (m_Parameters->m_FlipX) dir[0] *= -1; if (m_Parameters->m_FlipY) dir[1] *= -1; if (m_Parameters->m_FlipZ) dir[2] *= -1; if (m_Parameters->m_ApplyDirectionMatrix) dir = m_FloatImageRotation*dir; return dir; } vnl_vector_fixed TrackingHandlerPeaks::GetDirection(itk::Point itkP, bool interpolate, vnl_vector_fixed oldDir){ // transform physical point to index coordinates itk::Index<3> idx3; itk::ContinuousIndex< float, 3> cIdx; m_DummyImage->TransformPhysicalPointToIndex(itkP, idx3); m_DummyImage->TransformPhysicalPointToContinuousIndex(itkP, cIdx); vnl_vector_fixed dir; dir.fill(0.0); if ( !m_DummyImage->GetLargestPossibleRegion().IsInside(idx3) ) return dir; if (interpolate) { float frac_x = cIdx[0] - idx3[0]; float frac_y = cIdx[1] - idx3[1]; float frac_z = cIdx[2] - idx3[2]; if (frac_x<0) { idx3[0] -= 1; frac_x += 1; } if (frac_y<0) { idx3[1] -= 1; frac_y += 1; } if (frac_z<0) { idx3[2] -= 1; frac_z += 1; } frac_x = 1-frac_x; frac_y = 1-frac_y; frac_z = 1-frac_z; // int coordinates inside image? if (idx3[0] >= 0 && idx3[0] < static_cast(m_DummyImage->GetLargestPossibleRegion().GetSize(0) - 1) && idx3[1] >= 0 && idx3[1] < static_cast(m_DummyImage->GetLargestPossibleRegion().GetSize(1) - 1) && idx3[2] >= 0 && idx3[2] < static_cast(m_DummyImage->GetLargestPossibleRegion().GetSize(2) - 1)) { // trilinear interpolation vnl_vector_fixed interpWeights; interpWeights[0] = ( frac_x)*( frac_y)*( frac_z); interpWeights[1] = (1-frac_x)*( frac_y)*( frac_z); interpWeights[2] = ( frac_x)*(1-frac_y)*( frac_z); interpWeights[3] = ( frac_x)*( frac_y)*(1-frac_z); interpWeights[4] = (1-frac_x)*(1-frac_y)*( frac_z); interpWeights[5] = ( frac_x)*(1-frac_y)*(1-frac_z); interpWeights[6] = (1-frac_x)*( frac_y)*(1-frac_z); interpWeights[7] = (1-frac_x)*(1-frac_y)*(1-frac_z); dir = GetMatchingDirection(idx3, oldDir) * interpWeights[0]; itk::Index<3> tmpIdx = idx3; tmpIdx[0]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[1]; tmpIdx = idx3; tmpIdx[1]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[2]; tmpIdx = idx3; tmpIdx[2]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[3]; tmpIdx = idx3; tmpIdx[0]++; tmpIdx[1]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[4]; tmpIdx = idx3; tmpIdx[1]++; tmpIdx[2]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[5]; tmpIdx = idx3; tmpIdx[2]++; tmpIdx[0]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[6]; tmpIdx = idx3; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++; dir += GetMatchingDirection(tmpIdx, oldDir) * interpWeights[7]; } } else dir = GetMatchingDirection(idx3, oldDir); return dir; } vnl_vector_fixed TrackingHandlerPeaks::ProposeDirection(const itk::Point& pos, std::deque >& olddirs, itk::Index<3>& oldIndex) { // CHECK: wann wird wo normalisiert vnl_vector_fixed output_direction; output_direction.fill(0); itk::Index<3> index; m_DummyImage->TransformPhysicalPointToIndex(pos, index); vnl_vector_fixed oldDir; oldDir.fill(0.0); if (!olddirs.empty()) oldDir = olddirs.back(); float old_mag = oldDir.magnitude(); if (!m_Parameters->m_InterpolateTractographyData && oldIndex==index) return oldDir; output_direction = GetDirection(pos, m_Parameters->m_InterpolateTractographyData, oldDir); float mag = output_direction.magnitude(); if (mag>=m_Parameters->m_Cutoff) { if (m_Parameters->m_Mode == MODE::PROBABILISTIC) { - output_direction[0] += this->m_RngItk->GetNormalVariate(0, fabs(output_direction[0])*0.01); - output_direction[1] += this->m_RngItk->GetNormalVariate(0, fabs(output_direction[1])*0.01); - output_direction[2] += this->m_RngItk->GetNormalVariate(0, fabs(output_direction[2])*0.01); + output_direction[0] += this->m_RngItk->GetNormalVariate(0, fabs(output_direction[0])*m_Parameters->m_PeakJitter); + output_direction[1] += this->m_RngItk->GetNormalVariate(0, fabs(output_direction[1])*m_Parameters->m_PeakJitter); + output_direction[2] += this->m_RngItk->GetNormalVariate(0, fabs(output_direction[2])*m_Parameters->m_PeakJitter); mag = output_direction.magnitude(); } output_direction.normalize(); float a = 1; if (old_mag>0.5) a = dot_product(output_direction, oldDir); if (a>=m_Parameters->GetAngularThresholdDot()) output_direction *= mag; else output_direction.fill(0); } else output_direction.fill(0); return output_direction; } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp index 0884ca0f39..ae79b0851f 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp @@ -1,976 +1,980 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include "itkStreamlineTrackingFilter.h" #include #include #include #include "itkPointShell.h" #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(); } m_PolyDataContainer.clear(); for (unsigned int i=0; iGetNumberOfThreads(); i++) { PolyDataType poly = PolyDataType::New(); m_PolyDataContainer.push_back(poly); } 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->GetAngularThresholdDot() << "°" << 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; 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); 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_shuffle(m_SeedPoints.begin(), m_SeedPoints.end()); 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; trialsm_TrialsPerSeed; ++trials) + 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) && !m_Parameters->m_InterpolateTractographyData) { algo_code_value = "sup181_ee04"; algo_code_meaning = "FACT"; } 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_code.value", mitk::StringProperty::New(algo_code_value)); fib->SetProperty("DICOM.algo_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/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.cpp index 6ea4e33092..9f704669d5 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.cpp @@ -1,365 +1,367 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include 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.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_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/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.h index 4b80b27b4e..9a0a818f77 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkStreamlineTractographyParameters.h @@ -1,162 +1,163 @@ #pragma once /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include 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; bool m_SharpenOdfs = false; float m_Cutoff = 0.1; // - fa/gfa image float m_OdfCutoff = 0.00025; float m_MinTractLengthMm = 20; float m_MaxTractLengthMm = 400; float m_F = 1; float m_G = 0; bool m_FixRandomSeed = false; unsigned int m_NumPreviousDirections = 1; + float m_PeakJitter = 0.01; // actual jitter is drawn from a normal distribution with m_PeakJitter*fabs(direction_value) as standard deviation // prior // - peak image float m_Weight = 0.5; bool m_RestrictToPrior = true; bool m_NewDirectionsFromPrior = true; bool m_PriorFlipX = false; bool m_PriorFlipY = false; bool m_PriorFlipZ = false; // neighborhood sampling unsigned int m_NumSamples = 0; bool m_OnlyForwardSamples = false; bool m_StopVotes = false; bool m_AvoidStop = true; bool m_RandomSampling = false; float m_DeflectionMod = 1.0; // data handling bool m_FlipX = false; bool m_FlipY = false; bool m_FlipZ = false; bool m_InterpolateTractographyData = true; bool m_InterpolateRoiImages; bool m_ApplyDirectionMatrix = false; // output and postprocessing bool m_CompressFibers = true; float m_Compression = 0.1; bool m_OutputProbMap = false; float GetAngularThresholdDot() const; float GetAngularThresholdDeg() const; void SetAngularThresholdDeg(float angular_threshold_deg); float GetLoopCheckDeg() const; void SetLoopCheckDeg(float loop_check_deg); float GetStepSizeMm() const; float GetStepSizeVox() const; void SetStepSizeVox(float step_size_vox); float GetSamplingDistanceMm() const; float GetSamplingDistanceVox() const; void SetSamplingDistanceVox(float sampling_distance_vox); void SetMinVoxelSizeMm(float min_voxel_size_mm); float GetMinVoxelSizeMm() const; private: void AutoAdjust(); float m_SamplingDistanceVox = -1; float m_SamplingDistanceMm; float m_AngularThresholdDeg = -1; float m_AngularThresholdDot; float m_LoopCheckDeg = -1; float m_StepSizeVox = -1; float m_StepSizeMm; float m_MinVoxelSizeMm = 1.0; }; } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/files.cmake b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/files.cmake index 21387d0922..2470e9a742 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/files.cmake +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/files.cmake @@ -1,77 +1,73 @@ set(SRC_CPP_FILES QmitkTensorModelParametersWidget.cpp QmitkZeppelinModelParametersWidget.cpp QmitkStickModelParametersWidget.cpp QmitkDotModelParametersWidget.cpp QmitkBallModelParametersWidget.cpp QmitkAstrosticksModelParametersWidget.cpp QmitkPrototypeSignalParametersWidget.cpp ) set(INTERNAL_CPP_FILES QmitkFiberfoxView.cpp QmitkFieldmapGeneratorView.cpp QmitkFiberGenerationView.cpp mitkPluginActivator.cpp Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.cpp ) set(UI_FILES src/internal/QmitkFiberfoxViewControls.ui src/internal/QmitkFieldmapGeneratorViewControls.ui src/internal/QmitkFiberGenerationViewControls.ui src/QmitkTensorModelParametersWidgetControls.ui src/QmitkZeppelinModelParametersWidgetControls.ui src/QmitkStickModelParametersWidgetControls.ui src/QmitkDotModelParametersWidgetControls.ui src/QmitkBallModelParametersWidgetControls.ui src/QmitkAstrosticksModelParametersWidgetControls.ui src/QmitkPrototypeSignalParametersWidgetControls.ui ) set(MOC_H_FILES src/internal/mitkPluginActivator.h src/internal/QmitkFiberfoxView.h src/internal/QmitkFieldmapGeneratorView.h src/internal/QmitkFiberGenerationView.h src/QmitkTensorModelParametersWidget.h src/QmitkZeppelinModelParametersWidget.h src/QmitkStickModelParametersWidget.h src/QmitkDotModelParametersWidget.h src/QmitkBallModelParametersWidget.h src/QmitkAstrosticksModelParametersWidget.h src/QmitkPrototypeSignalParametersWidget.h src/internal/Perspectives/QmitkDIAppSyntheticDataGenerationPerspective.h ) set(CACHED_RESOURCE_FILES plugin.xml resources/phantom.png resources/syntheticdata.png resources/fieldmap.png resources/models.png - resources/upload.ico - resources/download.ico - resources/right.ico - resources/stop.ico ) set(QRC_FILES resources/QmitkFiberfox.qrc ) set(CPP_FILES ) foreach(file ${SRC_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/${file}) endforeach(file ${SRC_CPP_FILES}) foreach(file ${INTERNAL_CPP_FILES}) set(CPP_FILES ${CPP_FILES} src/internal/${file}) endforeach(file ${INTERNAL_CPP_FILES}) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkFiberfox.qrc b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkFiberfox.qrc index eb68645d9b..e369c9cd94 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkFiberfox.qrc +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/QmitkFiberfox.qrc @@ -1,8 +1,10 @@ download.ico right.ico stop.ico upload.ico + circle.png + refresh.xpm diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/refresh.xpm b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/refresh.xpm new file mode 100644 index 0000000000..878265e17a --- /dev/null +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/refresh.xpm @@ -0,0 +1,322 @@ +/* XPM */ +static char * view_refresh_xpm[] = { +"32 32 287 2", +" c None", +". c #396AA9", +"+ c #3D6CA9", +"@ c #3968A8", +"# c #3565A5", +"$ c #3767A6", +"% c #3867A7", +"& c #3A6AA8", +"* c #3567A6", +"= c #3C6BA8", +"- c #4B77B0", +"; 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E+F+G+H+I+J+c+K+L+M+N+O+l+P+Q+R+ ", +" ( S+T+U+V+W+X+Y+Z+`+ @.@$ +@ ", +" @@#@$@%@&@( *@=@-@ ", +" ", +" ", +" ", +" ", +" "}; diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.png b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.png new file mode 100644 index 0000000000..6abef3f7d7 Binary files /dev/null and b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.png differ diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationViewControls.ui index fc21d9ed04..29f96f5379 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberGenerationViewControls.ui @@ -1,2012 +1,2012 @@ QmitkFiberGenerationViewControls 0 0 413 1461 Form Save Parameters - + :/QmitkDiffusionImaging/general_icons/download.ico:/QmitkDiffusionImaging/general_icons/download.ico Load Parameters - + :/QmitkDiffusionImaging/general_icons/upload.ico:/QmitkDiffusionImaging/general_icons/upload.ico Qt::Vertical 20 40 0 0 0 381 731 Manual Fiber Design QFrame::NoFrame QFrame::Raised 0 0 0 0 false 30 30 Draw elliptical fiducial. - - :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png + + :/QmitkFiberfox/circle.png:/QmitkFiberfox/circle.png 32 32 false true false 30 30 Flip fiber waypoints of selcted fiducial around one axis. - - :/QmitkDiffusionImaging/general_icons/refresh.ico:/QmitkDiffusionImaging/general_icons/refresh.ico + + :/QmitkFiberfox/refresh.xpm:/QmitkFiberfox/refresh.xpm 32 32 false true Qt::Horizontal 40 20 color: rgb(255, 0, 0); Please select an image or an existing fiber bundle to draw the fiber fiducials. If you can't provide a suitable image, generate one using the Fiberfox View. Qt::AutoText Qt::AlignJustify|Qt::AlignVCenter true QGroupBox { background-color: transparent; } Fiber Options 6 6 6 6 QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 Tension: false Fiber Sampling: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Bias: false Continuity: false 3 -1.000000000000000 1.000000000000000 0.100000000000000 0.000000000000000 Distance of fiber sampling points (in mm) 1 0.100000000000000 0.100000000000000 1.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 #Fibers: false Specify number of fibers to generate for the selected bundle. 1 1000000 100 100 false QCommandLinkButton:disabled { border: none; } Generate Fibers - + :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 Select fiber distribution inside of the fiducials. Uniform Gaussian Fiber Distribution: false Variance of the gaussian 3 0.001000000000000 10.000000000000000 0.010000000000000 0.100000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 Disable to only generate fibers if "Generate Fibers" button is pressed. Real Time Fibers true Disable to only generate fibers if "Generate Fibers" button is pressed. Advanced Options false QGroupBox { background-color: transparent; } Fiducial Options 6 6 6 6 Fiducial Attributes 6 6 6 6 Length of fiducial axis 2 2 0.000000000000000 9999.000000000000000 0.100000000000000 Axis 1: false Position X: false World Position in mm 2 -99999.000000000000000 99999.000000000000000 0.100000000000000 World Position in mm 2 -360.000000000000000 360.000000000000000 0.100000000000000 World Position in mm 2 -360.000000000000000 360.000000000000000 0.100000000000000 Length of fiducial axis 1 2 0.000000000000000 9999.000000000000000 0.100000000000000 Position Z: false Position Y: false Axis 2: false Twist: false Twist in degree 2 -180.000000000000000 180.000000000000000 0.100000000000000 All fiducials are treated as circles with the same radius as the first fiducial. Use Constant Fiducial Radius false false Align selected fiducials with voxel grid. Shifts selected fiducials to nearest voxel center. QCommandLinkButton:disabled { border: none; } Align With Grid - + :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico 0 0 - 403 + 395 277 Random Phantom Volume Size: false Curvyness: false QFrame::NoFrame QFrame::Raised 0 0 0 0 Specify number of fibers to generate for the selected bundle. 0 90 10 30 Specify number of fibers to generate for the selected bundle. 0 90 10 15 Step Size: false QFrame::NoFrame QFrame::Raised 0 0 0 0 Specify number of fibers to generate for the selected bundle. 1 100 1 15 Specify number of fibers to generate for the selected bundle. 1 100 1 30 Streamline Density: false Specify number of fibers to generate for the selected bundle. 1 1000 1 50 Start Radii: false QFrame::NoFrame QFrame::Raised 0 0 0 0 Specify number of fibers to generate for the selected bundle. 1 90 1 5 Specify number of fibers to generate for the selected bundle. 1 90 1 45 QFrame::NoFrame QFrame::Raised 0 0 0 0 Specify number of fibers to generate for the selected bundle. 1 1000 1 250 Specify number of fibers to generate for the selected bundle. 1 1000 1 250 Specify number of fibers to generate for the selected bundle. 1 1000 1 250 Twist: false #Bundles: false QFrame::NoFrame QFrame::Raised 0 0 0 0 Specify number of fibers to generate for the selected bundle. 1 300 1 5 Specify number of fibers to generate for the selected bundle. 1 300 1 25 QFrame::NoFrame QFrame::Raised 0 0 0 0 Specify number of fibers to generate for the selected bundle. 1 10000 10 200 Specify number of fibers to generate for the selected bundle. 1 10000 10 50 true QCommandLinkButton:disabled { border: none; } Generate - + :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico 0 0 395 283 Operations QFrame::NoFrame QFrame::Raised 0 0 0 0 Y false Rotation angle (in degree) around x-axis. 2 -360.000000000000000 360.000000000000000 0.100000000000000 Axis: false Rotation angle (in degree) around y-axis. 2 -360.000000000000000 360.000000000000000 0.100000000000000 Translation: false Translation (in mm) in direction of the z-axis. 2 -1000.000000000000000 1000.000000000000000 0.100000000000000 Translation (in mm) in direction of the y-axis. 2 -1000.000000000000000 1000.000000000000000 0.100000000000000 X false Rotation: false Z false Rotation angle (in degree) around z-axis. 2 -360.000000000000000 360.000000000000000 0.100000000000000 Translation (in mm) in direction of the x-axis. 2 -1000.000000000000000 1000.000000000000000 0.100000000000000 Scaling: false Scaling factor for selected fiber bundle along the x-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the y-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 Scaling factor for selected fiber bundle along the z-axis. 0.010000000000000 10.000000000000000 0.010000000000000 1.000000000000000 false QCommandLinkButton:disabled { border: none; } Copy Bundles - + :/QmitkDiffusionImaging/general_icons/copy2.ico:/QmitkDiffusionImaging/general_icons/copy2.ico false QCommandLinkButton:disabled { border: none; } Transform Selection - + :/QmitkDiffusionImaging/general_icons/refresh.ico:/QmitkDiffusionImaging/general_icons/refresh.ico false QCommandLinkButton:disabled { border: none; } Join Bundles - + :/QmitkDiffusionImaging/general_icons/plus.ico:/QmitkDiffusionImaging/general_icons/plus.ico If checked, the fiducials belonging to the modified bundle are also modified. Include Fiducials true m_CircleButton m_FlipButton m_RealTimeFibers m_AdvancedOptionsBox m_DistributionBox m_VarianceBox m_FiberDensityBox m_FiberSamplingBox m_TensionBox m_ContinuityBox m_BiasBox m_GenerateFibersButton m_ConstantRadiusBox m_NumBundlesBox m_MinDensityBox m_MaxDensityBox m_MinTwistBox m_MaxTwistBox m_CurvyMinBox m_CurvyMaxBox m_SizeMinBox m_SizeMaxBox m_StepSizeMinBox m_StepSizeMaxBox m_VolumeSizeX m_VolumeSizeY m_VolumeSizeZ m_RandomPhantomButton m_XrotBox m_YrotBox m_ZrotBox m_XtransBox m_YtransBox m_ZtransBox m_XscaleBox m_YscaleBox m_ZscaleBox m_TransformBundlesButton m_CopyBundlesButton m_JoinBundlesButton m_IncludeFiducials m_SaveParametersButton m_LoadParametersButton m_FidAxis1 m_FidPosY m_FidPosZ m_FidAxis2 m_FidTwist m_AlignOnGrid m_FidPosX - + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp index f0266fc553..be3ad8ad0a 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxView.cpp @@ -1,2178 +1,2181 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkFiberfoxView.h" // MITK #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #define RAPIDXML_NO_EXCEPTIONS #include #include #include #include #include "usModuleRegistry.h" #include #include #include #include #include #include #include #include #include #include "mitkNodePredicateDataType.h" #include #include #include #include QmitkFiberfoxWorker::QmitkFiberfoxWorker(QmitkFiberfoxView* view) : m_View(view) { } void QmitkFiberfoxWorker::run() { try{ m_View->m_TractsToDwiFilter->Update(); } catch( ... ) { } m_View->m_Thread.quit(); } const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImageNode( nullptr ) , m_Worker(this) , m_ThreadIsRunning(false) { m_Worker.moveToThread(&m_Thread); connect(&m_Thread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_Thread, SIGNAL(started()), &m_Worker, SLOT(run())); connect(&m_Thread, SIGNAL(finished()), this, SLOT(AfterThread())); // connect(&m_Thread, SIGNAL(terminated()), this, SLOT(AfterThread())); m_SimulationTimer = new QTimer(this); } void QmitkFiberfoxView::KillThread() { MITK_INFO << "Aborting DWI simulation."; m_TractsToDwiFilter->SetAbortGenerateData(true); m_Controls->m_AbortSimulationButton->setEnabled(false); m_Controls->m_AbortSimulationButton->setText("Aborting simulation ..."); } void QmitkFiberfoxView::BeforeThread() { m_SimulationTime = QTime::currentTime(); m_SimulationTimer->start(100); m_Controls->m_AbortSimulationButton->setVisible(true); m_Controls->m_GenerateImageButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(true); m_ThreadIsRunning = true; } void QmitkFiberfoxView::AfterThread() { UpdateSimulationStatus(); m_SimulationTimer->stop(); m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_AbortSimulationButton->setEnabled(true); m_Controls->m_AbortSimulationButton->setText("Abort simulation"); m_Controls->m_GenerateImageButton->setVisible(true); m_ThreadIsRunning = false; QString statusText; FiberfoxParameters parameters; mitk::Image::Pointer mitkImage = mitk::Image::New(); statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); if (m_TractsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_TractsToDwiFilter->GetParameters(); mitkImage = mitk::GrabItkImageMemory( m_TractsToDwiFilter->GetOutput() ); - mitk::DiffusionPropertyHelper::SetGradientContainer(mitkImage, parameters.m_SignalGen.GetItkGradientContainer()); - mitk::DiffusionPropertyHelper::SetReferenceBValue(mitkImage, parameters.m_SignalGen.GetBvalue()); - mitk::DiffusionPropertyHelper::InitializeImage( mitkImage ); + if (parameters.m_SignalGen.GetNumWeightedVolumes() > 0) + { + mitk::DiffusionPropertyHelper::SetGradientContainer(mitkImage, parameters.m_SignalGen.GetItkGradientContainer()); + mitk::DiffusionPropertyHelper::SetReferenceBValue(mitkImage, parameters.m_SignalGen.GetBvalue()); + mitk::DiffusionPropertyHelper::InitializeImage( mitkImage ); + } parameters.m_Misc.m_ResultNode->SetData( mitkImage ); GetDataStorage()->Add(parameters.m_Misc.m_ResultNode, parameters.m_Misc.m_ParentNode); if (m_Controls->m_VolumeFractionsBox->isChecked()) { if (m_TractsToDwiFilter->GetTickImage().IsNotNull()) { mitk::Image::Pointer mitkImage = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::Float2DImageType::Pointer itkImage = m_TractsToDwiFilter->GetTickImage(); mitkImage = mitk::GrabItkImageMemory( itkImage.GetPointer() ); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( mitkImage ); node->SetName("Tick Image"); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); } if (m_TractsToDwiFilter->GetRfImage().IsNotNull()) { mitk::Image::Pointer mitkImage = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::Float2DImageType::Pointer itkImage = m_TractsToDwiFilter->GetRfImage(); mitkImage = mitk::GrabItkImageMemory( itkImage.GetPointer() ); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( mitkImage ); node->SetName("RF Image"); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); } if (m_TractsToDwiFilter->GetPhaseImage().IsNotNull()) { mitk::Image::Pointer phaseImage = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkPhase = m_TractsToDwiFilter->GetPhaseImage(); phaseImage = mitk::GrabItkImageMemory( itkPhase.GetPointer() ); mitk::DataNode::Pointer phaseNode = mitk::DataNode::New(); phaseNode->SetData( phaseImage ); phaseNode->SetName("Phase Image"); GetDataStorage()->Add(phaseNode, parameters.m_Misc.m_ResultNode); } if (m_TractsToDwiFilter->GetKspaceImage().IsNotNull()) { mitk::Image::Pointer image = mitk::Image::New(); itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer itkImage = m_TractsToDwiFilter->GetKspaceImage(); image = mitk::GrabItkImageMemory( itkImage.GetPointer() ); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("k-Space"); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); } { mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(m_TractsToDwiFilter->GetCoilPointset()); node->SetName("Coil Positions"); node->SetProperty("pointsize", mitk::FloatProperty::New(parameters.m_SignalGen.m_ImageSpacing[0]/4)); node->SetProperty("color", mitk::ColorProperty::New(0, 1, 0)); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); } int c = 1; std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_real = m_TractsToDwiFilter->GetOutputImagesReal(); for (auto real : output_real) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(real.GetPointer()); image->SetVolume(real->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Coil-"+QString::number(c).toStdString()+"-real"); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); ++c; } c = 1; std::vector< itk::TractsToDWIImageFilter< short >::DoubleDwiType::Pointer > output_imag = m_TractsToDwiFilter->GetOutputImagesImag(); for (auto imag : output_imag) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(imag.GetPointer()); image->SetVolume(imag->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Coil-"+QString::number(c).toStdString()+"-imag"); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); ++c; } std::vector< itk::TractsToDWIImageFilter< short >::ItkDoubleImgType::Pointer > volumeFractions = m_TractsToDwiFilter->GetVolumeFractions(); for (unsigned int k=0; kInitializeByItk(volumeFractions.at(k).GetPointer()); image->SetVolume(volumeFractions.at(k)->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("CompartmentVolume-"+QString::number(k).toStdString()); GetDataStorage()->Add(node, parameters.m_Misc.m_ResultNode); } } m_TractsToDwiFilter = nullptr; if (parameters.m_Misc.m_AfterSimulationMessage.size()>0) QMessageBox::information( nullptr, "Warning", parameters.m_Misc.m_AfterSimulationMessage.c_str()); mitk::BaseData::Pointer basedata = parameters.m_Misc.m_ResultNode->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } if (!parameters.m_Misc.m_OutputPath.empty()) { try{ QString outputFileName(parameters.m_Misc.m_OutputPath.c_str()); outputFileName += parameters.m_Misc.m_ResultNode->GetName().c_str(); outputFileName.replace(QString("."), QString("_")); SaveParameters(outputFileName+".ffp"); outputFileName += ".dwi"; QString status("Saving output image to "); status += outputFileName; m_Controls->m_SimulationStatusText->append(status); mitk::IOUtil::Save(mitkImage, outputFileName.toStdString()); m_Controls->m_SimulationStatusText->append("File saved successfully."); } catch (itk::ExceptionObject &e) { QString status("Exception during DWI writing: "); status += e.GetDescription(); m_Controls->m_SimulationStatusText->append(status); } catch (...) { m_Controls->m_SimulationStatusText->append("Unknown exception during DWI writing!"); } } parameters.m_SignalGen.m_FrequencyMap = nullptr; } void QmitkFiberfoxView::UpdateSimulationStatus() { QString statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); if (QString::compare(m_SimulationStatusText,statusText)!=0) { m_Controls->m_SimulationStatusText->clear(); m_Controls->m_SimulationStatusText->setText(statusText); QScrollBar *vScrollBar = m_Controls->m_SimulationStatusText->verticalScrollBar(); vScrollBar->triggerAction(QScrollBar::SliderToMaximum); } } // Destructor QmitkFiberfoxView::~QmitkFiberfoxView() { delete m_SimulationTimer; } void QmitkFiberfoxView::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::QmitkFiberfoxViewControls; m_Controls->setupUi( parent ); m_Controls->m_StickWidget1->setVisible(true); m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_BallWidget1->setVisible(true); m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_BallWidget2->SetT1(4658); m_Controls->m_BallWidget2->SetT2(2200); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->SetT1(4658); m_Controls->m_AstrosticksWidget2->SetT2(2200); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_DotWidget2->SetT1(4658); m_Controls->m_DotWidget2->SetT2(2200); m_Controls->m_PrototypeWidget1->setVisible(false); m_Controls->m_PrototypeWidget2->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_PrototypeWidget3->SetMinFa(0.0); m_Controls->m_PrototypeWidget3->SetMaxFa(0.15); m_Controls->m_PrototypeWidget4->SetMinFa(0.0); m_Controls->m_PrototypeWidget4->SetMaxFa(0.15); m_Controls->m_PrototypeWidget3->SetMinAdc(0.0); m_Controls->m_PrototypeWidget3->SetMaxAdc(0.001); m_Controls->m_PrototypeWidget4->SetMinAdc(0.003); m_Controls->m_PrototypeWidget4->SetMaxAdc(0.004); m_Controls->m_Comp2FractionFrame->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_NoiseFrame->setVisible(false); m_Controls->m_ZeroRinging->setVisible(false); m_Controls->m_GhostFrame->setVisible(false); m_Controls->m_DistortionsFrame->setVisible(false); m_Controls->m_EddyFrame->setVisible(false); m_Controls->m_SpikeFrame->setVisible(false); m_Controls->m_AliasingFrame->setVisible(false); m_Controls->m_MotionArtifactFrame->setVisible(false); m_Controls->m_DriftFrame->setVisible(false); m_ParameterFile = QDir::currentPath()+"/param.ffp"; m_Controls->m_AbortSimulationButton->setVisible(false); m_Controls->m_SimulationStatusText->setVisible(false); m_Controls->m_FrequencyMapBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp1VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp2VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp3VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp4VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_MaskComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TemplateComboBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_FiberBundleComboBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isFiberBundle = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateIsDWI::Pointer isDwi = mitk::NodePredicateIsDWI::New( ); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer isOdf = mitk::NodePredicateDataType::New("Odfmage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isOdf); mitk::NodePredicateNot::Pointer noDiffusionImage = mitk::NodePredicateNot::New(isDiffusionImage); mitk::NodePredicateAnd::Pointer isNonDiffMitkImage = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer isBinaryMitkImage = mitk::NodePredicateAnd::New( isNonDiffMitkImage, isBinaryPredicate ); m_Controls->m_FrequencyMapBox->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp1VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp1VolumeFraction->SetZeroEntryText("--"); m_Controls->m_Comp2VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp2VolumeFraction->SetZeroEntryText("--"); m_Controls->m_Comp3VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp3VolumeFraction->SetZeroEntryText("--"); m_Controls->m_Comp4VolumeFraction->SetPredicate(isNonDiffMitkImage); m_Controls->m_Comp4VolumeFraction->SetZeroEntryText("--"); m_Controls->m_MaskComboBox->SetPredicate(isBinaryMitkImage); m_Controls->m_MaskComboBox->SetZeroEntryText("--"); m_Controls->m_TemplateComboBox->SetPredicate(isMitkImage); m_Controls->m_TemplateComboBox->SetZeroEntryText("--"); m_Controls->m_FiberBundleComboBox->SetPredicate(isFiberBundle); m_Controls->m_FiberBundleComboBox->SetZeroEntryText("--"); QFont font; font.setFamily("Courier"); font.setStyleHint(QFont::Monospace); font.setFixedPitch(true); font.setPointSize(7); m_Controls->m_SimulationStatusText->setFont(font); connect( m_SimulationTimer, SIGNAL(timeout()), this, SLOT(UpdateSimulationStatus()) ); connect((QObject*) m_Controls->m_AbortSimulationButton, SIGNAL(clicked()), (QObject*) this, SLOT(KillThread())); connect((QObject*) m_Controls->m_GenerateImageButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateImage())); connect((QObject*) m_Controls->m_AddNoise, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddNoise(int))); connect((QObject*) m_Controls->m_AddGhosts, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddGhosts(int))); connect((QObject*) m_Controls->m_AddDistortions, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDistortions(int))); connect((QObject*) m_Controls->m_AddEddy, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddEddy(int))); connect((QObject*) m_Controls->m_AddSpikes, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddSpikes(int))); connect((QObject*) m_Controls->m_AddAliasing, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddAliasing(int))); connect((QObject*) m_Controls->m_AddMotion, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddMotion(int))); connect((QObject*) m_Controls->m_AddDrift, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddDrift(int))); connect((QObject*) m_Controls->m_AddGibbsRinging, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnAddRinging(int))); connect((QObject*) m_Controls->m_Compartment1Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp1ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment2Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp2ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment3Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp3ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_Compartment4Box, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(Comp4ModelFrameVisibility(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_UseBvalsBvecsBox, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(OnBvalsBvecsCheck(int))); connect((QObject*) m_Controls->m_SaveParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(SaveParameters())); connect((QObject*) m_Controls->m_LoadParametersButton, SIGNAL(clicked()), (QObject*) this, SLOT(LoadParameters())); connect((QObject*) m_Controls->m_OutputPathButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetOutputPath())); connect((QObject*) m_Controls->m_LoadBvalsButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetBvalsEdit())); connect((QObject*) m_Controls->m_LoadBvecsButton, SIGNAL(clicked()), (QObject*) this, SLOT(SetBvecsEdit())); connect((QObject*) m_Controls->m_MaskComboBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnMaskSelected(int))); connect((QObject*) m_Controls->m_TemplateComboBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnTemplateSelected(int))); connect((QObject*) m_Controls->m_FiberBundleComboBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnFibSelected(int))); connect((QObject*) m_Controls->m_LineReadoutTimeBox, SIGNAL( valueChanged(double)), (QObject*) this, SLOT(OnTlineChanged())); connect((QObject*) m_Controls->m_SizeX, SIGNAL( valueChanged(int)), (QObject*) this, SLOT(OnTlineChanged())); } OnTlineChanged(); UpdateGui(); } void QmitkFiberfoxView::OnTlineChanged() { double num_pix_line = 0; if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()) // use geometry of selected image { mitk::Image::Pointer img = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); num_pix_line = img->GetDimension(0); } else if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull()) // use geometry of mask image { mitk::Image::Pointer img = dynamic_cast(m_Controls->m_MaskComboBox->GetSelectedNode()->GetData()); num_pix_line = img->GetDimension(0); } else { num_pix_line = m_Controls->m_SizeX->value(); } double value = static_cast(m_Controls->m_LineReadoutTimeBox->value())/1000.0; // line readout time in seconds double dweel_pp = value/num_pix_line; // pixel readout time in seconds double bw = 1/dweel_pp; double bw_pp = bw/num_pix_line; std::string tt = "Bandwidth:\n" + boost::lexical_cast(itk::Math::Round(bw)) + "Hz\n" + boost::lexical_cast(itk::Math::Round(bw_pp)) + "Hz/Px"; m_Controls->m_LineReadoutTimeBox->setToolTip(tt.c_str()); } void QmitkFiberfoxView::OnMaskSelected(int ) { UpdateGui(); } void QmitkFiberfoxView::OnTemplateSelected(int ) { UpdateGui(); } void QmitkFiberfoxView::OnFibSelected(int ) { UpdateGui(); } void QmitkFiberfoxView::OnBvalsBvecsCheck(int ) { UpdateGui(); } void QmitkFiberfoxView::UpdateParametersFromGui() { m_Parameters.ClearSignalParameters(); m_Parameters.m_Misc.m_CheckAdvancedSignalOptionsBox = m_Controls->m_AdvancedOptionsBox_2->isChecked(); m_Parameters.m_Misc.m_OutputAdditionalImages = m_Controls->m_VolumeFractionsBox->isChecked(); std::string outputPath = m_Controls->m_SavePathEdit->text().toStdString(); if (outputPath.compare("-")!=0) { m_Parameters.m_Misc.m_OutputPath = outputPath; m_Parameters.m_Misc.m_OutputPath += "/"; } else { m_Parameters.m_Misc.m_OutputPath = ""; } if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer mitkMaskImage = dynamic_cast(m_Controls->m_MaskComboBox->GetSelectedNode()->GetData()); mitk::CastToItkImage(mitkMaskImage, m_Parameters.m_SignalGen.m_MaskImage); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(m_Parameters.m_SignalGen.m_MaskImage); duplicator->Update(); m_Parameters.m_SignalGen.m_MaskImage = duplicator->GetOutput(); } if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( m_Controls->m_TemplateComboBox->GetSelectedNode())) // use parameters of selected DWI { mitk::Image::Pointer dwi = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(dwi, itkVectorImagePointer); m_Parameters.m_SignalGen.m_ImageRegion = itkVectorImagePointer->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = itkVectorImagePointer->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = itkVectorImagePointer->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = itkVectorImagePointer->GetDirection(); m_Parameters.SetBvalue(mitk::DiffusionPropertyHelper::GetReferenceBValue(dwi)); m_Parameters.SetGradienDirections(mitk::DiffusionPropertyHelper::GetOriginalGradientContainer(dwi)); } else if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()) // use geometry of selected image { mitk::Image::Pointer img = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New(); CastToItkImage< itk::Image< float, 3 > >(img, itkImg); m_Parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); if (m_Controls->m_UseBvalsBvecsBox->isChecked()) { double bval; m_Parameters.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Controls->m_LoadBvalsEdit->text().toStdString(), m_Controls->m_LoadBvecsEdit->text().toStdString(), bval) ); m_Parameters.SetBvalue(bval); } else { m_Parameters.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); m_Parameters.SetBvalue(m_Controls->m_BvalueBox->value()); m_Parameters.GenerateGradientHalfShell(); } } else if (m_Parameters.m_SignalGen.m_MaskImage.IsNotNull()) // use geometry of mask image { ItkUcharImgType::Pointer itkImg = m_Parameters.m_SignalGen.m_MaskImage; m_Parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); if (m_Controls->m_UseBvalsBvecsBox->isChecked()) { double bval; m_Parameters.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Controls->m_LoadBvalsEdit->text().toStdString(), m_Controls->m_LoadBvecsEdit->text().toStdString(), bval) ); m_Parameters.SetBvalue(bval); } else { m_Parameters.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); m_Parameters.SetBvalue(m_Controls->m_BvalueBox->value()); m_Parameters.GenerateGradientHalfShell(); } } else // use GUI parameters { m_Parameters.m_SignalGen.m_ImageRegion.SetSize(0, m_Controls->m_SizeX->value()); m_Parameters.m_SignalGen.m_ImageRegion.SetSize(1, m_Controls->m_SizeY->value()); m_Parameters.m_SignalGen.m_ImageRegion.SetSize(2, m_Controls->m_SizeZ->value()); m_Parameters.m_SignalGen.m_ImageSpacing[0] = m_Controls->m_SpacingX->value(); m_Parameters.m_SignalGen.m_ImageSpacing[1] = m_Controls->m_SpacingY->value(); m_Parameters.m_SignalGen.m_ImageSpacing[2] = m_Controls->m_SpacingZ->value(); m_Parameters.m_SignalGen.m_ImageOrigin[0] = m_Parameters.m_SignalGen.m_ImageSpacing[0]/2; m_Parameters.m_SignalGen.m_ImageOrigin[1] = m_Parameters.m_SignalGen.m_ImageSpacing[1]/2; m_Parameters.m_SignalGen.m_ImageOrigin[2] = m_Parameters.m_SignalGen.m_ImageSpacing[2]/2; m_Parameters.m_SignalGen.m_ImageDirection.SetIdentity(); if (m_Controls->m_UseBvalsBvecsBox->isChecked()) { double bval; m_Parameters.SetGradienDirections( mitk::gradients::ReadBvalsBvecs(m_Controls->m_LoadBvalsEdit->text().toStdString(), m_Controls->m_LoadBvecsEdit->text().toStdString(), bval) ); m_Parameters.SetBvalue(bval); } else { m_Parameters.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); m_Parameters.SetBvalue(m_Controls->m_BvalueBox->value()); m_Parameters.GenerateGradientHalfShell(); } } // signal relaxation m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; if (m_Controls->m_RelaxationBox->isChecked()) { m_Parameters.m_SignalGen.m_DoSimulateRelaxation = true; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(true)); m_Parameters.m_Misc.m_ArtifactModelString += "_RELAX"; } m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = m_Parameters.m_SignalGen.m_DoSimulateRelaxation; // N/2 ghosts m_Parameters.m_Misc.m_DoAddGhosts = m_Controls->m_AddGhosts->isChecked(); m_Parameters.m_SignalGen.m_KspaceLineOffset = m_Controls->m_kOffsetBox->value(); if (m_Controls->m_AddGhosts->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_GHOST"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(m_Parameters.m_SignalGen.m_KspaceLineOffset)); } // Aliasing m_Parameters.m_Misc.m_DoAddAliasing = m_Controls->m_AddAliasing->isChecked(); m_Parameters.m_SignalGen.m_CroppingFactor = (100-m_Controls->m_WrapBox->value())/100; if (m_Controls->m_AddAliasing->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_ALIASING"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value())); } // Spikes m_Parameters.m_Misc.m_DoAddSpikes = m_Controls->m_AddSpikes->isChecked(); m_Parameters.m_SignalGen.m_Spikes = m_Controls->m_SpikeNumBox->value(); m_Parameters.m_SignalGen.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value(); if (m_Controls->m_AddSpikes->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_SPIKES"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(m_Parameters.m_SignalGen.m_Spikes)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(m_Parameters.m_SignalGen.m_SpikeAmplitude)); } // Drift m_Parameters.m_SignalGen.m_DoAddDrift = m_Controls->m_AddDrift->isChecked(); m_Parameters.m_SignalGen.m_Drift = static_cast(m_Controls->m_DriftFactor->value())/100; if (m_Controls->m_AddDrift->isChecked()) { m_Parameters.m_Misc.m_ArtifactModelString += "_DRIFT"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Drift", FloatProperty::New(m_Parameters.m_SignalGen.m_Drift)); } // gibbs ringing m_Parameters.m_SignalGen.m_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); m_Parameters.m_SignalGen.m_ZeroRinging = m_Controls->m_ZeroRinging->value(); if (m_Controls->m_AddGibbsRinging->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true)); m_Parameters.m_Misc.m_ArtifactModelString += "_RINGING"; } // add distortions m_Parameters.m_Misc.m_DoAddDistortions = m_Controls->m_AddDistortions->isChecked(); if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); mitk::Image* img = dynamic_cast(fMapNode->GetData()); ItkFloatImgType::Pointer itkImg = ItkFloatImgType::New(); CastToItkImage< ItkFloatImgType >(img, itkImg); if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNull()) // use geometry of frequency map { m_Parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); m_Parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); m_Parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); m_Parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); } m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(itkImg); duplicator->Update(); m_Parameters.m_SignalGen.m_FrequencyMap = duplicator->GetOutput(); m_Parameters.m_Misc.m_ArtifactModelString += "_DISTORTED"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true)); } m_Parameters.m_SignalGen.m_EddyStrength = m_Controls->m_EddyGradientStrength->value(); m_Parameters.m_Misc.m_DoAddEddyCurrents = m_Controls->m_AddEddy->isChecked(); if (m_Controls->m_AddEddy->isChecked()) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_EDDY"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(m_Parameters.m_SignalGen.m_EddyStrength)); } // Motion m_Parameters.m_SignalGen.m_DoAddMotion = false; m_Parameters.m_SignalGen.m_DoRandomizeMotion = m_Controls->m_RandomMotion->isChecked(); m_Parameters.m_SignalGen.m_Translation[0] = m_Controls->m_MaxTranslationBoxX->value(); m_Parameters.m_SignalGen.m_Translation[1] = m_Controls->m_MaxTranslationBoxY->value(); m_Parameters.m_SignalGen.m_Translation[2] = m_Controls->m_MaxTranslationBoxZ->value(); m_Parameters.m_SignalGen.m_Rotation[0] = m_Controls->m_MaxRotationBoxX->value(); m_Parameters.m_SignalGen.m_Rotation[1] = m_Controls->m_MaxRotationBoxY->value(); m_Parameters.m_SignalGen.m_Rotation[2] = m_Controls->m_MaxRotationBoxZ->value(); m_Parameters.m_SignalGen.m_MotionVolumes.clear(); m_Parameters.m_Misc.m_MotionVolumesBox = m_Controls->m_MotionVolumesBox->text().toStdString(); if ( m_Controls->m_AddMotion->isChecked()) { m_Parameters.m_SignalGen.m_DoAddMotion = true; m_Parameters.m_Misc.m_ArtifactModelString += "_MOTION"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(m_Parameters.m_SignalGen.m_DoRandomizeMotion)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(m_Parameters.m_SignalGen.m_Translation[0])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(m_Parameters.m_SignalGen.m_Translation[1])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(m_Parameters.m_SignalGen.m_Translation[2])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(m_Parameters.m_SignalGen.m_Rotation[0])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(m_Parameters.m_SignalGen.m_Rotation[1])); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(m_Parameters.m_SignalGen.m_Rotation[2])); if ( m_Parameters.m_Misc.m_MotionVolumesBox == "random" ) { for ( size_t i=0; i < m_Parameters.m_SignalGen.GetNumVolumes(); ++i ) { m_Parameters.m_SignalGen.m_MotionVolumes.push_back( bool( rand()%2 ) ); } MITK_DEBUG << "QmitkFiberfoxView.cpp: Case m_Misc.m_MotionVolumesBox == \"random\"."; } else if ( ! m_Parameters.m_Misc.m_MotionVolumesBox.empty() ) { std::stringstream stream( m_Parameters.m_Misc.m_MotionVolumesBox ); std::vector numbers; int number = std::numeric_limits::max(); while( stream >> number ) { if( number < std::numeric_limits::max() ) { numbers.push_back( number ); } } // If a list of negative numbers is given: if( *(std::min_element( numbers.begin(), numbers.end() )) < 0 && *(std::max_element( numbers.begin(), numbers.end() )) <= 0 ) // cave: -0 == +0 { for ( size_t i=0; i < m_Parameters.m_SignalGen.GetNumVolumes(); ++i ) { m_Parameters.m_SignalGen.m_MotionVolumes.push_back( true ); } // set all true except those given. for( auto iter = std::begin( numbers ); iter != std::end( numbers ); ++iter ) { if ( -(*iter) < (int)m_Parameters.m_SignalGen.GetNumVolumes() && -(*iter) >= 0 ) { m_Parameters.m_SignalGen.m_MotionVolumes.at( -(*iter) ) = false; } } MITK_DEBUG << "QmitkFiberfoxView.cpp: Case list of negative numbers."; } // If a list of positive numbers is given: else if( *(std::min_element( numbers.begin(), numbers.end() )) >= 0 && *(std::max_element( numbers.begin(), numbers.end() )) >= 0 ) { for ( size_t i=0; i < m_Parameters.m_SignalGen.GetNumVolumes(); ++i ) { m_Parameters.m_SignalGen.m_MotionVolumes.push_back( false ); } // set all false except those given. for( auto iter = std::begin( numbers ); iter != std::end( numbers ); ++iter ) { if ( *iter < (int)m_Parameters.m_SignalGen.GetNumVolumes() && *iter >= 0 ) { m_Parameters.m_SignalGen.m_MotionVolumes.at( *iter ) = true; } } MITK_DEBUG << "QmitkFiberfoxView.cpp: Case list of positive numbers."; } else { MITK_ERROR << "QmitkFiberfoxView.cpp: Inconsistent list of numbers in m_MotionVolumesBox."; } } else { m_Parameters.m_Misc.m_MotionVolumesBox = ""; // set empty. m_Controls->m_MotionVolumesBox->setText(""); for (unsigned int i=0; im_AcquisitionTypeBox->currentIndex(); m_Parameters.m_SignalGen.m_CoilSensitivityProfile = (SignalGenerationParameters::CoilSensitivityProfile)m_Controls->m_CoilSensBox->currentIndex(); m_Parameters.m_SignalGen.m_NumberOfCoils = m_Controls->m_NumCoilsBox->value(); m_Parameters.m_SignalGen.m_PartialFourier = m_Controls->m_PartialFourier->value(); m_Parameters.m_SignalGen.m_ReversePhase = m_Controls->m_ReversePhaseBox->isChecked(); m_Parameters.m_SignalGen.m_tLine = m_Controls->m_LineReadoutTimeBox->value(); m_Parameters.m_SignalGen.m_tInhom = m_Controls->m_T2starBox->value(); m_Parameters.m_SignalGen.m_EchoTrainLength = m_Controls->m_EtlBox->value(); m_Parameters.m_SignalGen.m_tEcho = m_Controls->m_TEbox->value(); m_Parameters.m_SignalGen.m_tRep = m_Controls->m_TRbox->value(); m_Parameters.m_SignalGen.m_tInv = m_Controls->m_TIbox->value(); m_Parameters.m_SignalGen.m_DoDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked(); m_Parameters.m_SignalGen.m_AxonRadius = m_Controls->m_FiberRadius->value(); m_Parameters.m_SignalGen.m_SignalScale = m_Controls->m_SignalScaleBox->value(); // double voxelVolume = m_Parameters.m_SignalGen.m_ImageSpacing[0] // * m_Parameters.m_SignalGen.m_ImageSpacing[1] // * m_Parameters.m_SignalGen.m_ImageSpacing[2]; // if ( m_Parameters.m_SignalGen.m_SignalScale*voxelVolume > itk::NumericTraits::max()*0.75 ) // { // m_Parameters.m_SignalGen.m_SignalScale = itk::NumericTraits::max()*0.75/voxelVolume; // m_Controls->m_SignalScaleBox->setValue(m_Parameters.m_SignalGen.m_SignalScale); // QMessageBox::information( nullptr, "Warning", // "Maximum signal exceeding data type limits. Automatically adjusted to " // + QString::number(m_Parameters.m_SignalGen.m_SignalScale) // + " to obtain a maximum signal of 75% of the data type maximum." // " Relaxation and other effects that affect the signal intensities are not accounted for."); // } // Noise m_Parameters.m_Misc.m_DoAddNoise = m_Controls->m_AddNoise->isChecked(); m_Parameters.m_SignalGen.m_NoiseVariance = m_Controls->m_NoiseLevel->value(); if (m_Controls->m_AddNoise->isChecked()) { switch (m_Controls->m_NoiseDistributionBox->currentIndex()) { case 0: { if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_COMPLEX-GAUSSIAN-"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Complex Gaussian")); } break; } case 1: { if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_NoiseModel = std::make_shared< mitk::RicianNoiseModel >(); m_Parameters.m_Misc.m_ArtifactModelString += "_RICIAN-"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); m_Parameters.m_NoiseModel->SetNoiseVariance(m_Parameters.m_SignalGen.m_NoiseVariance); } break; } case 2: { if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_NoiseModel = std::make_shared< mitk::ChiSquareNoiseModel >(); m_Parameters.m_Misc.m_ArtifactModelString += "_CHISQUARED-"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared")); m_Parameters.m_NoiseModel->SetNoiseVariance(m_Parameters.m_SignalGen.m_NoiseVariance); } break; } default: { if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; m_Parameters.m_Misc.m_ArtifactModelString += "_COMPLEX-GAUSSIAN-"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Complex Gaussian")); } break; } } if (m_Parameters.m_SignalGen.m_NoiseVariance>0) { m_Parameters.m_Misc.m_ArtifactModelString += QString::number(m_Parameters.m_SignalGen.m_NoiseVariance).toStdString(); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(m_Parameters.m_SignalGen.m_NoiseVariance)); } } // signal models { // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: { mitk::StickModel* model = new mitk::StickModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_StickWidget1->GetD()); model->SetT2(m_Controls->m_StickWidget1->GetT2()); model->SetT1(m_Controls->m_StickWidget1->GetT1()); model->m_CompartmentId = 1; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Stick"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 1: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); model->SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); model->SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); model->SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); model->SetT1(m_Controls->m_ZeppelinWidget1->GetT1()); model->m_CompartmentId = 1; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Zeppelin"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); model->SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); model->SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); model->SetT2(m_Controls->m_TensorWidget1->GetT2()); model->SetT1(m_Controls->m_TensorWidget1->GetT1()); model->m_CompartmentId = 1; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Tensor"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::RawShModel* model = new mitk::RawShModel(); m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetMaxNumKernels(m_Controls->m_PrototypeWidget1->GetNumberOfSamples()); model->SetFaRange(m_Controls->m_PrototypeWidget1->GetMinFa(), m_Controls->m_PrototypeWidget1->GetMaxFa()); model->SetAdcRange(m_Controls->m_PrototypeWidget1->GetMinAdc(), m_Controls->m_PrototypeWidget1->GetMaxAdc()); model->m_CompartmentId = 1; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Prototype"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Prototype") ); break; } } if (m_Controls->m_Comp1VolumeFraction->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp1VolumeFraction->GetSelectedNode(); ItkDoubleImgType::Pointer comp1VolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, comp1VolumeImage); m_Parameters.m_FiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage); } // compartment 2 switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: { mitk::StickModel* model = new mitk::StickModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_StickWidget2->GetD()); model->SetT2(m_Controls->m_StickWidget2->GetT2()); model->SetT1(m_Controls->m_StickWidget2->GetT1()); model->m_CompartmentId = 2; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Stick"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); model->SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); model->SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); model->SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); model->SetT1(m_Controls->m_ZeppelinWidget2->GetT1()); model->m_CompartmentId = 2; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Zeppelin"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); model->SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); model->SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); model->SetT2(m_Controls->m_TensorWidget2->GetT2()); model->SetT1(m_Controls->m_TensorWidget2->GetT1()); model->m_CompartmentId = 2; m_Parameters.m_FiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Tensor"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } } if (m_Controls->m_Comp2VolumeFraction->GetSelectedNode().IsNotNull() && m_Parameters.m_FiberModelList.size()==2) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp2VolumeFraction->GetSelectedNode(); ItkDoubleImgType::Pointer comp1VolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, comp1VolumeImage); m_Parameters.m_FiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage); } // compartment 3 switch (m_Controls->m_Compartment3Box->currentIndex()) { case 0: { mitk::BallModel* model = new mitk::BallModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_BallWidget1->GetD()); model->SetT2(m_Controls->m_BallWidget1->GetT2()); model->SetT1(m_Controls->m_BallWidget1->GetT1()); model->m_CompartmentId = 3; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Ball"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); break; } case 1: { mitk::AstroStickModel* model = new mitk::AstroStickModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); model->SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); model->SetT1(m_Controls->m_AstrosticksWidget1->GetT1()); model->SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); model->m_CompartmentId = 3; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Astrosticks"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); break; } case 2: { mitk::DotModel* model = new mitk::DotModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetT2(m_Controls->m_DotWidget1->GetT2()); model->SetT1(m_Controls->m_DotWidget1->GetT1()); model->m_CompartmentId = 3; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Dot"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::RawShModel* model = new mitk::RawShModel(); m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetMaxNumKernels(m_Controls->m_PrototypeWidget3->GetNumberOfSamples()); model->SetFaRange(m_Controls->m_PrototypeWidget3->GetMinFa(), m_Controls->m_PrototypeWidget3->GetMaxFa()); model->SetAdcRange(m_Controls->m_PrototypeWidget3->GetMinAdc(), m_Controls->m_PrototypeWidget3->GetMaxAdc()); model->m_CompartmentId = 3; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Prototype"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Prototype") ); break; } } if (m_Controls->m_Comp3VolumeFraction->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp3VolumeFraction->GetSelectedNode(); ItkDoubleImgType::Pointer comp1VolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, comp1VolumeImage); m_Parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage); } switch (m_Controls->m_Compartment4Box->currentIndex()) { case 0: break; case 1: { mitk::BallModel* model = new mitk::BallModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_BallWidget2->GetD()); model->SetT2(m_Controls->m_BallWidget2->GetT2()); model->SetT1(m_Controls->m_BallWidget2->GetT1()); model->m_CompartmentId = 4; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Ball"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::AstroStickModel* model = new mitk::AstroStickModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(m_Parameters.m_SignalGen.GetBvalue()); model->SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); model->SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); model->SetT1(m_Controls->m_AstrosticksWidget2->GetT1()); model->SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); model->m_CompartmentId = 4; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Astrosticks"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); break; } case 3: { mitk::DotModel* model = new mitk::DotModel(); model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetT2(m_Controls->m_DotWidget2->GetT2()); model->SetT1(m_Controls->m_DotWidget2->GetT1()); model->m_CompartmentId = 4; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Dot"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); break; } case 4: { mitk::RawShModel* model = new mitk::RawShModel(); m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(m_Parameters.m_SignalGen.GetGradientDirections()); model->SetMaxNumKernels(m_Controls->m_PrototypeWidget4->GetNumberOfSamples()); model->SetFaRange(m_Controls->m_PrototypeWidget4->GetMinFa(), m_Controls->m_PrototypeWidget4->GetMaxFa()); model->SetAdcRange(m_Controls->m_PrototypeWidget4->GetMinAdc(), m_Controls->m_PrototypeWidget4->GetMaxAdc()); model->m_CompartmentId = 4; m_Parameters.m_NonFiberModelList.push_back(model); m_Parameters.m_Misc.m_SignalModelString += "Prototype"; m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Prototype") ); break; } } if (m_Controls->m_Comp4VolumeFraction->GetSelectedNode().IsNotNull() && m_Parameters.m_NonFiberModelList.size()==2) { mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode(); ItkDoubleImgType::Pointer compVolumeImage = ItkDoubleImgType::New(); mitk::Image* img = dynamic_cast(volumeNode->GetData()); CastToItkImage< ItkDoubleImgType >(img, compVolumeImage); m_Parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(compVolumeImage); } } m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(m_Parameters.m_SignalGen.m_SignalScale)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(m_Parameters.m_SignalGen.m_AxonRadius)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(m_Parameters.m_SignalGen.m_tInhom)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.echoTrainLength", IntProperty::New(m_Parameters.m_SignalGen.m_EchoTrainLength)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(m_Parameters.m_SignalGen.m_tLine)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(m_Parameters.m_SignalGen.m_tEcho)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(m_Parameters.m_SignalGen.GetBvalue())); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(m_Parameters.m_SignalGen.m_DoDisablePartialVolume)); m_Parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(m_Parameters.m_SignalGen.m_DoSimulateRelaxation)); m_Parameters.m_Misc.m_ResultNode->AddProperty("binary", BoolProperty::New(false)); } void QmitkFiberfoxView::SaveParameters(QString filename) { UpdateParametersFromGui(); std::vector< int > bVals = m_Parameters.m_SignalGen.GetBvalues(); std::cout << "b-values: "; for (auto v : bVals) std::cout << v << " "; std::cout << std::endl; bool ok = true; bool first = true; bool dosampling = false; mitk::Image::Pointer diffImg = nullptr; itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = nullptr; const int shOrder = 2; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; QballFilterType::CoefficientImageType::Pointer itkFeatureImage = nullptr; ItkDoubleImgType::Pointer adcImage = nullptr; for (unsigned int i=0; i* model = nullptr; if (i* >(m_Parameters.m_FiberModelList.at(i)); } else { model = dynamic_cast< mitk::RawShModel<>* >(m_Parameters.m_NonFiberModelList.at(i-m_Parameters.m_FiberModelList.size())); } if ( model!=nullptr && model->GetNumberOfKernels() <= 0 ) { if (first==true) { if ( QMessageBox::question(nullptr, "Prototype signal sampling", "Do you want to sample prototype signals from the selected diffusion-weighted imag and save them?", QMessageBox::Yes, QMessageBox::No) == QMessageBox::Yes ) dosampling = true; first = false; if ( dosampling && (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNull() || !mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()) ) ) ) { QMessageBox::information(nullptr, "Parameter file not saved", "No diffusion-weighted image selected to sample signal from."); return; } else if (dosampling) { diffImg = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); filter->Update(); tensorImage = filter->GetOutput(); QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput( itkVectorImagePointer ); adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg)); adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); adcFilter->Update(); adcImage = adcFilter->GetOutput(); } } typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); filter->Update(); tensorImage = filter->GetOutput(); QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput( itkVectorImagePointer ); adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg)); adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); adcFilter->Update(); adcImage = adcFilter->GetOutput(); if (dosampling && diffImg.IsNotNull()) { ok = model->SampleKernels(diffImg, m_Parameters.m_SignalGen.m_MaskImage, tensorImage, itkFeatureImage, adcImage); if (!ok) { QMessageBox::information( nullptr, "Parameter file not saved", "No valid prototype signals could be sampled."); return; } } } } m_Parameters.SaveParameters(filename.toStdString()); m_ParameterFile = filename; } void QmitkFiberfoxView::SaveParameters() { QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), m_ParameterFile, tr("Fiberfox Parameters (*.ffp)") ); SaveParameters(filename); } void QmitkFiberfoxView::LoadParameters() { QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QString(itksys::SystemTools::GetFilenamePath(m_ParameterFile.toStdString()).c_str()), tr("Fiberfox Parameters (*.ffp)") ); if(filename.isEmpty() || filename.isNull()) return; m_ParameterFile = filename; m_Parameters.LoadParameters(filename.toStdString()); if (m_Parameters.m_MissingTags.size()>0) { QString missing("Parameter file might be corrupted. The following parameters could not be read: "); missing += QString(m_Parameters.m_MissingTags.c_str()); missing += "\nDefault values have been assigned to the missing parameters."; QMessageBox::information( nullptr, "Warning!", missing); } // image generation parameters m_Controls->m_SizeX->setValue(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0)); m_Controls->m_SizeY->setValue(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)); m_Controls->m_SizeZ->setValue(m_Parameters.m_SignalGen.m_ImageRegion.GetSize(2)); m_Controls->m_SpacingX->setValue(m_Parameters.m_SignalGen.m_ImageSpacing[0]); m_Controls->m_SpacingY->setValue(m_Parameters.m_SignalGen.m_ImageSpacing[1]); m_Controls->m_SpacingZ->setValue(m_Parameters.m_SignalGen.m_ImageSpacing[2]); m_Controls->m_NumGradientsBox->setValue(m_Parameters.m_SignalGen.GetNumWeightedVolumes()); m_Controls->m_BvalueBox->setValue(m_Parameters.m_SignalGen.GetBvalue()); m_Controls->m_SignalScaleBox->setValue(m_Parameters.m_SignalGen.m_SignalScale); m_Controls->m_TEbox->setValue(m_Parameters.m_SignalGen.m_tEcho); m_Controls->m_LineReadoutTimeBox->setValue(m_Parameters.m_SignalGen.m_tLine); m_Controls->m_T2starBox->setValue(m_Parameters.m_SignalGen.m_tInhom); m_Controls->m_EtlBox->setValue(m_Parameters.m_SignalGen.m_EchoTrainLength); m_Controls->m_FiberRadius->setValue(m_Parameters.m_SignalGen.m_AxonRadius); m_Controls->m_RelaxationBox->setChecked(m_Parameters.m_SignalGen.m_DoSimulateRelaxation); m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(m_Parameters.m_SignalGen.m_DoDisablePartialVolume); m_Controls->m_ReversePhaseBox->setChecked(m_Parameters.m_SignalGen.m_ReversePhase); m_Controls->m_PartialFourier->setValue(m_Parameters.m_SignalGen.m_PartialFourier); m_Controls->m_TRbox->setValue(m_Parameters.m_SignalGen.m_tRep); m_Controls->m_TIbox->setValue(m_Parameters.m_SignalGen.m_tInv); m_Controls->m_NumCoilsBox->setValue(m_Parameters.m_SignalGen.m_NumberOfCoils); m_Controls->m_CoilSensBox->setCurrentIndex(m_Parameters.m_SignalGen.m_CoilSensitivityProfile); m_Controls->m_AcquisitionTypeBox->setCurrentIndex(m_Parameters.m_SignalGen.m_AcquisitionType); if (!m_Parameters.m_Misc.m_BvalsFile.empty()) { m_Controls->m_UseBvalsBvecsBox->setChecked(true); m_Controls->m_LoadBvalsEdit->setText(QString(m_Parameters.m_Misc.m_BvalsFile.c_str())); } else m_Controls->m_LoadBvalsEdit->setText("-"); if (!m_Parameters.m_Misc.m_BvecsFile.empty()) { m_Controls->m_UseBvalsBvecsBox->setChecked(true); m_Controls->m_LoadBvecsEdit->setText(QString(m_Parameters.m_Misc.m_BvecsFile.c_str())); } else m_Controls->m_LoadBvecsEdit->setText("-"); if (m_Parameters.m_NoiseModel!=nullptr) { m_Controls->m_AddNoise->setChecked(m_Parameters.m_Misc.m_DoAddNoise); if (dynamic_cast*>(m_Parameters.m_NoiseModel.get())) { m_Controls->m_NoiseDistributionBox->setCurrentIndex(0); } else if (dynamic_cast*>(m_Parameters.m_NoiseModel.get())) { m_Controls->m_NoiseDistributionBox->setCurrentIndex(1); } m_Controls->m_NoiseLevel->setValue(m_Parameters.m_NoiseModel->GetNoiseVariance()); } else { m_Controls->m_AddNoise->setChecked(m_Parameters.m_Misc.m_DoAddNoise); m_Controls->m_NoiseLevel->setValue(m_Parameters.m_SignalGen.m_NoiseVariance); } m_Controls->m_VolumeFractionsBox->setChecked(m_Parameters.m_Misc.m_OutputAdditionalImages); m_Controls->m_AdvancedOptionsBox_2->setChecked(m_Parameters.m_Misc.m_CheckAdvancedSignalOptionsBox); m_Controls->m_AddGhosts->setChecked(m_Parameters.m_Misc.m_DoAddGhosts); m_Controls->m_AddAliasing->setChecked(m_Parameters.m_Misc.m_DoAddAliasing); m_Controls->m_AddDistortions->setChecked(m_Parameters.m_Misc.m_DoAddDistortions); m_Controls->m_AddSpikes->setChecked(m_Parameters.m_Misc.m_DoAddSpikes); m_Controls->m_AddEddy->setChecked(m_Parameters.m_Misc.m_DoAddEddyCurrents); m_Controls->m_AddDrift->setChecked(m_Parameters.m_SignalGen.m_DoAddDrift); m_Controls->m_kOffsetBox->setValue(m_Parameters.m_SignalGen.m_KspaceLineOffset); m_Controls->m_WrapBox->setValue(100*(1-m_Parameters.m_SignalGen.m_CroppingFactor)); m_Controls->m_DriftFactor->setValue(100*m_Parameters.m_SignalGen.m_Drift); m_Controls->m_SpikeNumBox->setValue(m_Parameters.m_SignalGen.m_Spikes); m_Controls->m_SpikeScaleBox->setValue(m_Parameters.m_SignalGen.m_SpikeAmplitude); m_Controls->m_EddyGradientStrength->setValue(m_Parameters.m_SignalGen.m_EddyStrength); m_Controls->m_AddGibbsRinging->setChecked(m_Parameters.m_SignalGen.m_DoAddGibbsRinging); m_Controls->m_ZeroRinging->setValue(m_Parameters.m_SignalGen.m_ZeroRinging); m_Controls->m_AddMotion->setChecked(m_Parameters.m_SignalGen.m_DoAddMotion); m_Controls->m_RandomMotion->setChecked(m_Parameters.m_SignalGen.m_DoRandomizeMotion); m_Controls->m_MotionVolumesBox->setText(QString(m_Parameters.m_Misc.m_MotionVolumesBox.c_str())); m_Controls->m_MaxTranslationBoxX->setValue(m_Parameters.m_SignalGen.m_Translation[0]); m_Controls->m_MaxTranslationBoxY->setValue(m_Parameters.m_SignalGen.m_Translation[1]); m_Controls->m_MaxTranslationBoxZ->setValue(m_Parameters.m_SignalGen.m_Translation[2]); m_Controls->m_MaxRotationBoxX->setValue(m_Parameters.m_SignalGen.m_Rotation[0]); m_Controls->m_MaxRotationBoxY->setValue(m_Parameters.m_SignalGen.m_Rotation[1]); m_Controls->m_MaxRotationBoxZ->setValue(m_Parameters.m_SignalGen.m_Rotation[2]); m_Controls->m_Compartment1Box->setCurrentIndex(0); m_Controls->m_Compartment2Box->setCurrentIndex(0); m_Controls->m_Compartment3Box->setCurrentIndex(0); m_Controls->m_Compartment4Box->setCurrentIndex(0); for (unsigned int i=0; i* signalModel = nullptr; if (iGetVolumeFractionImage().IsNotNull() ) { compVolNode = mitk::DataNode::New(); mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(signalModel->GetVolumeFractionImage().GetPointer()); image->SetVolume(signalModel->GetVolumeFractionImage()->GetBufferPointer()); compVolNode->SetData( image ); compVolNode->SetName("Compartment volume "+QString::number(signalModel->m_CompartmentId).toStdString()); GetDataStorage()->Add(compVolNode); } switch (signalModel->m_CompartmentId) { case 1: { if (compVolNode.IsNotNull()) m_Controls->m_Comp1VolumeFraction->SetSelectedNode(compVolNode); if (dynamic_cast*>(signalModel)) { mitk::StickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_StickWidget1->SetT2(model->GetT2()); m_Controls->m_StickWidget1->SetT1(model->GetT1()); m_Controls->m_StickWidget1->SetD(model->GetDiffusivity()); m_Controls->m_Compartment1Box->setCurrentIndex(0); break; } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_TensorWidget1->SetT2(model->GetT2()); m_Controls->m_TensorWidget1->SetT1(model->GetT1()); m_Controls->m_TensorWidget1->SetD1(model->GetDiffusivity1()); m_Controls->m_TensorWidget1->SetD2(model->GetDiffusivity2()); m_Controls->m_TensorWidget1->SetD3(model->GetDiffusivity3()); m_Controls->m_Compartment1Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget1->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget1->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget1->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget1->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget1->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment1Box->setCurrentIndex(3); break; } break; } case 2: { if (compVolNode.IsNotNull()) m_Controls->m_Comp2VolumeFraction->SetSelectedNode(compVolNode); if (dynamic_cast*>(signalModel)) { mitk::StickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_StickWidget2->SetT2(model->GetT2()); m_Controls->m_StickWidget2->SetT1(model->GetT1()); m_Controls->m_StickWidget2->SetD(model->GetDiffusivity()); m_Controls->m_Compartment2Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_TensorWidget2->SetT2(model->GetT2()); m_Controls->m_TensorWidget2->SetT1(model->GetT1()); m_Controls->m_TensorWidget2->SetD1(model->GetDiffusivity1()); m_Controls->m_TensorWidget2->SetD2(model->GetDiffusivity2()); m_Controls->m_TensorWidget2->SetD3(model->GetDiffusivity3()); m_Controls->m_Compartment2Box->setCurrentIndex(3); break; } break; } case 3: { if (compVolNode.IsNotNull()) m_Controls->m_Comp3VolumeFraction->SetSelectedNode(compVolNode); if (dynamic_cast*>(signalModel)) { mitk::BallModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_BallWidget1->SetT2(model->GetT2()); m_Controls->m_BallWidget1->SetT1(model->GetT1()); m_Controls->m_BallWidget1->SetD(model->GetDiffusivity()); m_Controls->m_Compartment3Box->setCurrentIndex(0); break; } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_AstrosticksWidget1->SetT2(model->GetT2()); m_Controls->m_AstrosticksWidget1->SetT1(model->GetT1()); m_Controls->m_AstrosticksWidget1->SetD(model->GetDiffusivity()); m_Controls->m_AstrosticksWidget1->SetRandomizeSticks(model->GetRandomizeSticks()); m_Controls->m_Compartment3Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::DotModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_DotWidget1->SetT2(model->GetT2()); m_Controls->m_DotWidget1->SetT1(model->GetT1()); m_Controls->m_Compartment3Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget3->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget3->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget3->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget3->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget3->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment3Box->setCurrentIndex(3); break; } break; } case 4: { if (compVolNode.IsNotNull()) m_Controls->m_Comp4VolumeFraction->SetSelectedNode(compVolNode); if (dynamic_cast*>(signalModel)) { mitk::BallModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_BallWidget2->SetT2(model->GetT2()); m_Controls->m_BallWidget2->SetT1(model->GetT1()); m_Controls->m_BallWidget2->SetD(model->GetDiffusivity()); m_Controls->m_Compartment4Box->setCurrentIndex(1); break; } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_AstrosticksWidget2->SetT2(model->GetT2()); m_Controls->m_AstrosticksWidget2->SetT1(model->GetT1()); m_Controls->m_AstrosticksWidget2->SetD(model->GetDiffusivity()); m_Controls->m_AstrosticksWidget2->SetRandomizeSticks(model->GetRandomizeSticks()); m_Controls->m_Compartment4Box->setCurrentIndex(2); break; } else if (dynamic_cast*>(signalModel)) { mitk::DotModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_DotWidget2->SetT2(model->GetT2()); m_Controls->m_DotWidget2->SetT1(model->GetT1()); m_Controls->m_Compartment4Box->setCurrentIndex(3); break; } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel<>* model = dynamic_cast*>(signalModel); m_Controls->m_PrototypeWidget4->SetNumberOfSamples(model->GetMaxNumKernels()); m_Controls->m_PrototypeWidget4->SetMinFa(model->GetFaRange().first); m_Controls->m_PrototypeWidget4->SetMaxFa(model->GetFaRange().second); m_Controls->m_PrototypeWidget4->SetMinAdc(model->GetAdcRange().first); m_Controls->m_PrototypeWidget4->SetMaxAdc(model->GetAdcRange().second); m_Controls->m_Compartment4Box->setCurrentIndex(4); break; } break; } } } if ( m_Parameters.m_SignalGen.m_MaskImage ) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(m_Parameters.m_SignalGen.m_MaskImage.GetPointer()); image->SetVolume(m_Parameters.m_SignalGen.m_MaskImage->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Tissue mask"); GetDataStorage()->Add(node); m_Controls->m_MaskComboBox->SetSelectedNode(node); } if ( m_Parameters.m_SignalGen.m_FrequencyMap ) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(m_Parameters.m_SignalGen.m_FrequencyMap.GetPointer()); image->SetVolume(m_Parameters.m_SignalGen.m_FrequencyMap->GetBufferPointer()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Frequency map"); GetDataStorage()->Add(node); m_Controls->m_FrequencyMapBox->SetSelectedNode(node); } } void QmitkFiberfoxView::ShowAdvancedOptions(int state) { if (state) { m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox_2->setChecked(false); } } void QmitkFiberfoxView::Comp1ModelFrameVisibility(int index) { m_Controls->m_StickWidget1->setVisible(false); m_Controls->m_ZeppelinWidget1->setVisible(false); m_Controls->m_TensorWidget1->setVisible(false); m_Controls->m_PrototypeWidget1->setVisible(false); switch (index) { case 0: m_Controls->m_StickWidget1->setVisible(true); break; case 1: m_Controls->m_ZeppelinWidget1->setVisible(true); break; case 2: m_Controls->m_TensorWidget1->setVisible(true); break; case 3: m_Controls->m_PrototypeWidget1->setVisible(true); break; } } void QmitkFiberfoxView::Comp2ModelFrameVisibility(int index) { m_Controls->m_StickWidget2->setVisible(false); m_Controls->m_ZeppelinWidget2->setVisible(false); m_Controls->m_TensorWidget2->setVisible(false); m_Controls->m_Comp2FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); m_Controls->m_Comp2FractionFrame->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); m_Controls->m_Comp2FractionFrame->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->setVisible(true); m_Controls->m_Comp2FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::Comp3ModelFrameVisibility(int index) { m_Controls->m_BallWidget1->setVisible(false); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_PrototypeWidget3->setVisible(false); switch (index) { case 0: m_Controls->m_BallWidget1->setVisible(true); break; case 1: m_Controls->m_AstrosticksWidget1->setVisible(true); break; case 2: m_Controls->m_DotWidget1->setVisible(true); break; case 3: m_Controls->m_PrototypeWidget3->setVisible(true); break; } } void QmitkFiberfoxView::Comp4ModelFrameVisibility(int index) { m_Controls->m_BallWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_PrototypeWidget4->setVisible(false); m_Controls->m_Comp4FractionFrame->setVisible(false); switch (index) { case 0: break; case 1: m_Controls->m_BallWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 2: m_Controls->m_AstrosticksWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 3: m_Controls->m_DotWidget2->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; case 4: m_Controls->m_PrototypeWidget4->setVisible(true); m_Controls->m_Comp4FractionFrame->setVisible(true); break; } } void QmitkFiberfoxView::OnAddMotion(int value) { if (value>0) m_Controls->m_MotionArtifactFrame->setVisible(true); else m_Controls->m_MotionArtifactFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDrift(int value) { if (value>0) m_Controls->m_DriftFrame->setVisible(true); else m_Controls->m_DriftFrame->setVisible(false); } void QmitkFiberfoxView::OnAddAliasing(int value) { if (value>0) m_Controls->m_AliasingFrame->setVisible(true); else m_Controls->m_AliasingFrame->setVisible(false); } void QmitkFiberfoxView::OnAddSpikes(int value) { if (value>0) m_Controls->m_SpikeFrame->setVisible(true); else m_Controls->m_SpikeFrame->setVisible(false); } void QmitkFiberfoxView::OnAddEddy(int value) { if (value>0) m_Controls->m_EddyFrame->setVisible(true); else m_Controls->m_EddyFrame->setVisible(false); } void QmitkFiberfoxView::OnAddDistortions(int value) { if (value>0) m_Controls->m_DistortionsFrame->setVisible(true); else m_Controls->m_DistortionsFrame->setVisible(false); } void QmitkFiberfoxView::OnAddGhosts(int value) { if (value>0) m_Controls->m_GhostFrame->setVisible(true); else m_Controls->m_GhostFrame->setVisible(false); } void QmitkFiberfoxView::OnAddNoise(int value) { if (value>0) m_Controls->m_NoiseFrame->setVisible(true); else m_Controls->m_NoiseFrame->setVisible(false); } void QmitkFiberfoxView::OnAddRinging(int value) { if (value>0) m_Controls->m_ZeroRinging->setVisible(true); else m_Controls->m_ZeroRinging->setVisible(false); } QmitkFiberfoxView::GradientListType QmitkFiberfoxView::GenerateHalfShell(int NPoints) { NPoints *= 2; GradientListType pointshell; int numB0 = NPoints/20; if (numB0==0) numB0=1; GradientType g; g.Fill(0.0); for (int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*itk::Math::pi); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i std::vector > QmitkFiberfoxView::MakeGradientList() { std::vector > retval; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); // Add 0 vector for B0 int numB0 = ndirs/10; if (numB0==0) numB0=1; itk::Vector v; v.Fill(0.0); for (int i=0; i v; v[0] = U->get(0,i); v[1] = U->get(1,i); v[2] = U->get(2,i); retval.push_back(v); } return retval; } void QmitkFiberfoxView::GenerateImage() { if (m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNull() && !mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( m_Controls->m_TemplateComboBox->GetSelectedNode())) { mitk::Image::Pointer image = mitk::ImageGenerator::GenerateGradientImage( m_Controls->m_SizeX->value(), m_Controls->m_SizeY->value(), m_Controls->m_SizeZ->value(), m_Controls->m_SpacingX->value(), m_Controls->m_SpacingY->value(), m_Controls->m_SpacingZ->value()); mitk::Point3D origin; origin[0] = m_Controls->m_SpacingX->value()/2; origin[1] = m_Controls->m_SpacingY->value()/2; origin[2] = m_Controls->m_SpacingZ->value()/2; image->SetOrigin(origin); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); GetDataStorage()->Add(node); m_SelectedImageNode = node; mitk::BaseData::Pointer basedata = node->GetData(); if (basedata.IsNotNull()) { mitk::RenderingManager::GetInstance()->InitializeViews( basedata->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } UpdateGui(); QMessageBox::information(nullptr, "Template image generated", "You have selected no fiber bundle or diffusion-weighted image, which can be used to simulate a new diffusion-weighted image. A template image with the specified geometry has been generated that can be used to draw artificial fibers (see view 'Fiber Generator')."); } else if (m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNotNull()) SimulateImageFromFibers(m_Controls->m_FiberBundleComboBox->GetSelectedNode()); else if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( m_Controls->m_TemplateComboBox->GetSelectedNode()) ) SimulateForExistingDwi(m_Controls->m_TemplateComboBox->GetSelectedNode()); else QMessageBox::information(nullptr, "No image generated", "You have selected no fiber bundle or diffusion-weighted image, which can be used to simulate a new diffusion-weighted image."); } void QmitkFiberfoxView::SetFocus() { } void QmitkFiberfoxView::SimulateForExistingDwi(mitk::DataNode* imageNode) { bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(imageNode->GetData())) ); if ( !isDiffusionImage ) { return; } UpdateParametersFromGui(); mitk::Image::Pointer diffImg = dynamic_cast(imageNode->GetData()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); m_Parameters.m_Misc.m_ParentNode = imageNode; m_Parameters.m_SignalGen.m_SignalScale = 1; m_Parameters.m_Misc.m_ResultNode->SetName("b"+QString::number(m_Parameters.m_SignalGen.GetBvalue()).toStdString() +"_"+m_Parameters.m_Misc.m_SignalModelString +m_Parameters.m_Misc.m_ArtifactModelString); m_Parameters.ApplyDirectionMatrix(); m_TractsToDwiFilter->SetParameters(m_Parameters); m_TractsToDwiFilter->SetInputImage(itkVectorImagePointer); m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::SimulateImageFromFibers(mitk::DataNode* fiberNode) { mitk::FiberBundle::Pointer fiberBundle = dynamic_cast(fiberNode->GetData()); if (fiberBundle->GetNumFibers()<=0) { return; } UpdateParametersFromGui(); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); m_Parameters.m_Misc.m_ParentNode = fiberNode; m_Parameters.m_Misc.m_ResultNode->SetName("b"+QString::number(m_Parameters.m_SignalGen.GetBvalue()).toStdString() +"_"+m_Parameters.m_Misc.m_SignalModelString +m_Parameters.m_Misc.m_ArtifactModelString); if ( m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast (m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()) ) ) { bool first = true; bool ok = true; mitk::Image::Pointer diffImg = dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()); itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = nullptr; const int shOrder = 2; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; QballFilterType::CoefficientImageType::Pointer itkFeatureImage = nullptr; ItkDoubleImgType::Pointer adcImage = nullptr; for (unsigned int i=0; i* model = nullptr; if (i* >(m_Parameters.m_FiberModelList.at(i)); else model = dynamic_cast< mitk::RawShModel<>* >(m_Parameters.m_NonFiberModelList.at(i-m_Parameters.m_FiberModelList.size())); if (model!=0 && model->GetNumberOfKernels()<=0) { if (first==true) { ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); filter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); filter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); filter->Update(); tensorImage = filter->GetOutput(); QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetGradientImage(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg), itkVectorImagePointer ); qballfilter->SetBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput( itkVectorImagePointer ); adcFilter->SetGradientDirections(mitk::DiffusionPropertyHelper::GetGradientContainer(diffImg)); adcFilter->SetB_value(mitk::DiffusionPropertyHelper::GetReferenceBValue(diffImg)); adcFilter->Update(); adcImage = adcFilter->GetOutput(); } ok = model->SampleKernels(diffImg, m_Parameters.m_SignalGen.m_MaskImage, tensorImage, itkFeatureImage, adcImage); if (!ok) break; } } if (!ok) { QMessageBox::information( nullptr, "Simulation cancelled", "No valid prototype signals could be sampled."); return; } } else if ( m_Controls->m_Compartment1Box->currentIndex()==3 || m_Controls->m_Compartment3Box->currentIndex()==3 || m_Controls->m_Compartment4Box->currentIndex()==4 ) { QMessageBox::information( nullptr, "Simulation cancelled", "Prototype signal but no diffusion-weighted image selected to sample signal from."); return; } m_Parameters.ApplyDirectionMatrix(); m_TractsToDwiFilter->SetParameters(m_Parameters); m_TractsToDwiFilter->SetFiberBundle(fiberBundle); m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::SetBvalsEdit() { // SELECT FOLDER DIALOG std::string filename; filename = QFileDialog::getOpenFileName(nullptr, "Select bvals file", QString(filename.c_str())).toStdString(); if (filename.empty()) m_Controls->m_LoadBvalsEdit->setText("-"); else m_Controls->m_LoadBvalsEdit->setText(QString(filename.c_str())); } void QmitkFiberfoxView::SetBvecsEdit() { // SELECT FOLDER DIALOG std::string filename; filename = QFileDialog::getOpenFileName(nullptr, "Select bvecs file", QString(filename.c_str())).toStdString(); if (filename.empty()) m_Controls->m_LoadBvecsEdit->setText("-"); else m_Controls->m_LoadBvecsEdit->setText(QString(filename.c_str())); } void QmitkFiberfoxView::SetOutputPath() { // SELECT FOLDER DIALOG std::string outputPath; outputPath = QFileDialog::getExistingDirectory(nullptr, "Save images to...", QString(outputPath.c_str())).toStdString(); if (outputPath.empty()) m_Controls->m_SavePathEdit->setText("-"); else { outputPath += "/"; m_Controls->m_SavePathEdit->setText(QString(outputPath.c_str())); } } void QmitkFiberfoxView::UpdateGui() { OnTlineChanged(); m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_LoadGradientsFrame->setVisible(false); m_Controls->m_GenerateGradientsFrame->setVisible(false); if (m_Controls->m_UseBvalsBvecsBox->isChecked()) m_Controls->m_LoadGradientsFrame->setVisible(true); else m_Controls->m_GenerateGradientsFrame->setVisible(true); // Signal generation gui if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull() || m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull()) { m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if ( m_Controls->m_TemplateComboBox->GetSelectedNode().IsNotNull() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(m_Controls->m_TemplateComboBox->GetSelectedNode()->GetData()) ) ) { m_Controls->m_DiffusionPropsMessage->setVisible(true); m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); m_Controls->m_LoadGradientsFrame->setVisible(false); m_Controls->m_GenerateGradientsFrame->setVisible(false); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui index b9a2018b76..cb7474b639 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberfox/src/internal/QmitkFiberfoxViewControls.ui @@ -1,2891 +1,2891 @@ QmitkFiberfoxViewControls 0 0 490 2775 Form QGroupBox { background-color: transparent; } Intra-axonal Compartment 6 6 6 6 Select signal model for intra-axonal compartment. Stick Model Zeppelin Model Tensor Model Prototype Signal QFrame::NoFrame QFrame::Raised 0 0 0 0 Volume Fraction: Optional! If no volume fraction map for this compartment is set, the corresponding volume fractions are calculated from the input fibers. QGroupBox { background-color: transparent; } Inter-axonal Compartment 6 6 6 6 Select signal model for intra-axonal compartment. -- Stick Model Zeppelin Model Tensor Model QFrame::NoFrame QFrame::Raised 0 0 0 0 Volume Fraction: Optional! If no volume fraction map for this compartment is set, the corresponding volume fractions are calculated from the input fibers. QGroupBox { background-color: transparent; } Image Settings 6 6 6 6 color: rgb(255, 0, 0); Using geometry of selected image! QFrame::NoFrame QFrame::Raised 0 0 0 0 6 Inversion time (in ms) for inversion recovery sequences. If 0, no inversion pulse is simulated. 0 999999999 1 0 <html><head/><body><p><span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> Relaxation: </p></body></html> false Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). 1 10000 1 50 <html><head/><body><p>Repetition Time <span style=" font-style:italic;">TR</span>: </p></body></html> false TE in milliseconds 1 999999999 1 100 Partial Fourier: false Partial fourier factor (0.5-1) 3 0.500000000000000 1.000000000000000 0.100000000000000 1.000000000000000 Output one image per compartment containing the corresponding volume fractions per voxel. Reverse Phase Encoding Direction false Dwell time (time to read one line in k-space) in ms. 4 100.000000000000000 0.100000000000000 1.000000000000000 Number of coil elements used for the acquisiton. 1 128 1 1 Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. 9999.000000000000000 Dwell Time: false Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. Disable Partial Volume Effects false Acquisition Type: Fiber Radius: Signal Scale: <html><head/><body><p>Number of Channels:</p></body></html> false TR in milliseconds 1 999999999 1 4000 Single Shot EPI Conventional Spin Echo Fast Spin Echo 1 100000 1 100 Constant Linear Exponential <html><head/><body><p><span style=" font-style:italic;">TE</span>, <span style=" font-style:italic;">T</span><span style=" font-style:italic; vertical-align:sub;">inhom</span> and <span style=" font-style:italic;">T2</span> will have no effect if unchecked.</p></body></html> Simulate Signal Relaxation true <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> false <html><head/><body><p>Coil Sensitivity:</p></body></html> false <html><head/><body><p>Inversion Time <span style=" font-style:italic;">TI</span>: </p></body></html> false Output phase image and volume fraction maps. Output Additional Images false <html><head/><body><p>Echo Train Length: </p></body></html> false Only relevant for Fast Spin Echo sequence (number of k-space lines acquired with one RF pulse) 1 999999999 1 8 QFrame::NoFrame QFrame::Raised 0 0 0 0 6 <html><head/><body><p>b-Value<span style=" font-style:italic;"> [s/mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">]</span>:</p></body></html> false b-value in s/mm² 0 10000 100 1000 Gradient Directions: Number of gradient directions distributed over the half sphere. 0 10000 1 30 Advanced Options color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 0 0 0 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Spacing: 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Dimensions: Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 20 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 20 Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 3 Use bvals/bvecs files QFrame::NoFrame QFrame::Raised 0 0 0 0 ... ... - false Bvecs: false Bvals: false - false QGroupBox { background-color: transparent; } Extra-axonal Compartments 6 6 6 6 QFrame::NoFrame QFrame::Raised 0 0 0 0 Volume Fraction: Select signal model for extra-axonal compartment. Ball Model Astrosticks Model Dot Model Prototype Signal Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 0 0 0 Volume Fraction: Optional! If no volume fraction map for this compartment is set, the corresponding volume fractions are calculated from the input fibers. Select signal model for extra-axonal compartment. -- Ball Model Astrosticks Model Dot Model Prototype Signal QGroupBox { background-color: transparent; } Noise and other Artifacts 6 6 6 6 Qt::Horizontal true QFrame::NoFrame QFrame::Raised 0 6 0 0 6 Toggle between random movement and linear movement. Randomize motion true QGroupBox { background-color: transparent; } Rotation 6 9 6 6 Degree: false x false Axis: false Maximum rotation around x-axis. 1 -360.000000000000000 360.000000000000000 1.000000000000000 0.000000000000000 Maximum rotation around z-axis. 1 -360.000000000000000 360.000000000000000 1.000000000000000 15.000000000000000 y false z false Maximum rotation around y-axis. 1 -360.000000000000000 360.000000000000000 1.000000000000000 0.000000000000000 QGroupBox { background-color: transparent; } Translation 6 6 6 Distance: false x false y false Axis: false z false Maximum translation along x-axis. 1 -1000.000000000000000 1000.000000000000000 1.000000000000000 0.000000000000000 Maximum translation along y-axis. 1 -1000.000000000000000 1000.000000000000000 1.000000000000000 0.000000000000000 Maximum translation along z-axis. 1 -1000.000000000000000 1000.000000000000000 1.000000000000000 0.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 Motion volumes: Type in the volume indices that should be affected by motion (e.g. "0 3 7" whithout quotation marks). Leave blank for motion in all volumes. Type in "random" to randomly select volumes for motion. A list of negative numbers (e.g. -1 -2 -3) excludes volumes (e.g. 1 2 3) selects all remaining volumes. random QFrame::NoFrame QFrame::Raised 0 0 0 0 Num. Spikes: The number of randomly occurring signal spikes. 1 Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice. 0.100000000000000 0.100000000000000 Scale: true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Shrink FOV (%): false Shrink FOV by this percentage. 1 0.000000000000000 90.000000000000000 0.100000000000000 40.000000000000000 Qt::Horizontal true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Signal Reduction (%): false Global signal in last simulated volume is specified percentage lower than in the first volume. 1 100.000000000000000 1.000000000000000 6.000000000000000 true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Frequency Map: false Select image specifying the frequency inhomogeneities (in Hz). true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 0 0 0 Gradient: false Eddy current induced magnetic field gradient (in mT/m). 5 1000.000000000000000 0.001000000000000 0.002000000000000 Qt::Horizontal Add Eddy Current Effects false Add Distortions false Add Spikes false Add Signal Drift false QFrame::NoFrame QFrame::Raised 0 0 0 0 Variance: Variance of selected noise distribution. 10 0.000000000000000 999999999.000000000000000 0.001000000000000 50.000000000000000 Distribution: Noise distribution Complex Gaussian Rician Qt::Horizontal Qt::Horizontal true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 K-Space Line Offset: false A larger offset increases the inensity of the ghost image. 3 1.000000000000000 0.010000000000000 0.250000000000000 Add Motion Artifacts false Add N/2 Ghosts false Qt::Horizontal Add ringing artifacts occuring at strong edges in the image. Add Gibbs Ringing false Qt::Horizontal Add Noise false Qt::Horizontal Add Aliasing false If > 0, ringing is simulated by by setting the defined percentage of higher frequencies to 0 in k-space. Otherwise, the input to the k-space simulation is generated with twice the resolution and cropped during k-space simulation (much slower). 100 10 Qt::Vertical 20 40 QFrame::NoFrame QFrame::Raised 0 0 0 0 true <html><head/><body><p>Start DWI generation from selected fiber bundle.</p><p>If no fiber bundle but an existing diffusion weighted image is selected, the enabled artifacts are added to this image.</p><p>If neither a fiber bundle nor a diffusion weighted image is selected, a grayscale image containing a simple gradient is generated.</p></body></html> Save Parameters - - :/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.ico:/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/download.ico + + :/QmitkFiberfox/download.ico:/QmitkFiberfox/download.ico true <html><head/><body><p>Start DWI generation from selected fiber bundle.</p><p>If no fiber bundle but an existing diffusion weighted image is selected, the enabled artifacts are added to this image.</p><p>If neither a fiber bundle nor a diffusion weighted image is selected, a grayscale image containing a simple gradient is generated.</p></body></html> Load Parameters - - :/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.ico:/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/upload.ico + + :/QmitkFiberfox/upload.ico:/QmitkFiberfox/upload.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 true <html><head/><body><p>Start DWI generation from selected fiber bundle.</p><p>If no fiber bundle but an existing diffusion weighted image is selected, the enabled artifacts are added to this image.</p><p>If neither a fiber bundle nor a diffusion weighted image is selected, a grayscale image containing a simple gradient is generated.</p></body></html> Start Simulation - - :/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/right.ico:/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/right.ico + + :/QmitkFiberfox/right.ico:/QmitkFiberfox/right.ico QGroupBox { background-color: transparent; } Input Data 6 6 6 6 QFrame::NoFrame QFrame::Raised 0 0 0 0 0 - ... <html><head/><body><p>Select a binary image to define the area of signal generation. Outside of the mask image only noise will be actively generated.</p></body></html> QComboBox::AdjustToMinimumContentsLength Fiber Bundle: false Save path: false Tissue Mask: false <html><head/><body><p>Select a fiber bundle to generate the white matter signal from. You can either use the fiber definition tab to manually define an input fiber bundle or you can also use any existing bundle, e.g. yielded by a tractography algorithm.</p></body></html> QComboBox::AdjustToMinimumContentsLength Template Image: false <html><head/><body><p>The parameters for the simulation (e.g. spacing, size, diffuison-weighted gradients, b-value) are adopted from this image.</p></body></html> QComboBox::AdjustToMinimumContentsLength true Stop current simulation. Abort Simulation - - :/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/stop.ico:/org.mitk.gui.qt.diffusionimaging.fiberfox/resources/stop.ico + + :/QmitkFiberfox/stop.ico:/QmitkFiberfox/stop.ico Courier 7 true QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkDataStorageComboBoxWithSelectNone QComboBox
QmitkDataStorageComboBoxWithSelectNone.h
 QmitkTensorModelParametersWidget QWidget
QmitkTensorModelParametersWidget.h
1 QmitkStickModelParametersWidget QWidget
QmitkStickModelParametersWidget.h
1 QmitkZeppelinModelParametersWidget QWidget
QmitkZeppelinModelParametersWidget.h
1 QmitkBallModelParametersWidget QWidget
QmitkBallModelParametersWidget.h
1 QmitkAstrosticksModelParametersWidget QWidget
QmitkAstrosticksModelParametersWidget.h
1 QmitkDotModelParametersWidget QWidget
QmitkDotModelParametersWidget.h
1 QmitkPrototypeSignalParametersWidget QWidget
QmitkPrototypeSignalParametersWidget.h
1 m_FiberBundleComboBox m_MaskComboBox m_TemplateComboBox m_SavePathEdit m_OutputPathButton m_GenerateImageButton m_AbortSimulationButton m_SimulationStatusText m_LoadParametersButton m_SaveParametersButton m_SizeX m_SizeY m_SizeZ m_SpacingX m_SpacingY m_SpacingZ m_UseBvalsBvecsBox m_LoadBvalsEdit m_LoadBvalsButton m_LoadBvecsEdit m_LoadBvecsButton m_NumGradientsBox m_BvalueBox m_AdvancedOptionsBox_2 m_AcquisitionTypeBox m_SignalScaleBox m_NumCoilsBox m_CoilSensBox m_TEbox m_TRbox m_TIbox m_LineReadoutTimeBox m_PartialFourier m_T2starBox m_FiberRadius m_ReversePhaseBox m_RelaxationBox m_EnforcePureFiberVoxelsBox m_VolumeFractionsBox m_Compartment1Box m_Comp1VolumeFraction m_Compartment2Box m_Comp2VolumeFraction m_Compartment3Box m_Comp3VolumeFraction m_Compartment4Box m_Comp4VolumeFraction m_AddNoise m_NoiseDistributionBox m_NoiseLevel m_AddSpikes m_SpikeNumBox m_SpikeScaleBox m_AddGhosts m_kOffsetBox m_AddAliasing m_WrapBox m_AddDistortions m_FrequencyMapBox m_AddDrift m_DriftFactor m_AddMotion m_RandomMotion m_MotionVolumesBox m_MaxRotationBoxX m_MaxRotationBoxY m_MaxRotationBoxZ m_MaxTranslationBoxX m_MaxTranslationBoxY m_MaxTranslationBoxZ m_AddEddy m_EddyGradientStrength m_AddGibbsRinging m_ZeroRinging - + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp index 1ca7905f97..2374247305 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitView.cpp @@ -1,265 +1,265 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include "QmitkFiberFitView.h" #include #include #include #include #include #include #include #include #include #include #include #include #include const std::string QmitkFiberFitView::VIEW_ID = "org.mitk.views.fiberfit"; using namespace mitk; QmitkFiberFitView::QmitkFiberFitView() : QmitkAbstractView() , m_Controls( nullptr ) { } // Destructor QmitkFiberFitView::~QmitkFiberFitView() { } void QmitkFiberFitView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberFitViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_StartButton, SIGNAL(clicked()), this, SLOT(StartFit()) ); connect( m_Controls->m_ImageBox, SIGNAL(currentIndexChanged(int)), this, SLOT(DataSelectionChanged()) ); connect( m_Controls->m_TractBox, SIGNAL(currentIndexChanged(int)), this, SLOT(DataSelectionChanged()) ); mitk::TNodePredicateDataType::Pointer isFib = mitk::TNodePredicateDataType::New(); mitk::TNodePredicateDataType::Pointer isImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDimension::Pointer is3D = mitk::NodePredicateDimension::New(3); m_Controls->m_TractBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_TractBox->SetPredicate(isFib); m_Controls->m_ImageBox->SetDataStorage(this->GetDataStorage()); m_Controls->m_ImageBox->SetPredicate( mitk::NodePredicateOr::New( mitk::NodePredicateAnd::New(isImage, is3D), mitk::TNodePredicateDataType::New()) ); DataSelectionChanged(); } } void QmitkFiberFitView::DataSelectionChanged() { if (m_Controls->m_TractBox->GetSelectedNode().IsNull() || m_Controls->m_ImageBox->GetSelectedNode().IsNull()) m_Controls->m_StartButton->setEnabled(false); else m_Controls->m_StartButton->setEnabled(true); } void QmitkFiberFitView::SetFocus() { DataSelectionChanged(); } void QmitkFiberFitView::StartFit() { if (m_Controls->m_TractBox->GetSelectedNode().IsNull() || m_Controls->m_ImageBox->GetSelectedNode().IsNull()) return; - mitk::FiberBundle::Pointer input_tracts = dynamic_cast(m_Controls->m_TractBox->GetSelectedNode()->GetData()); + mitk::FiberBundle::Pointer input_tracts = dynamic_cast(m_Controls->m_TractBox->GetSelectedNode()->GetData())->GetDeepCopy(); mitk::DataNode::Pointer node = m_Controls->m_ImageBox->GetSelectedNode(); itk::FitFibersToImageFilter::Pointer fitter = itk::FitFibersToImageFilter::New(); mitk::Image::Pointer mitk_image = dynamic_cast(node->GetData()); mitk::PeakImage::Pointer mitk_peak_image = dynamic_cast(node->GetData()); if (mitk_peak_image.IsNotNull()) { typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(mitk_peak_image); caster->Update(); mitk::PeakImage::ItkPeakImageType::Pointer peak_image = caster->GetOutput(); fitter->SetPeakImage(peak_image); } else { if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image)) { fitter->SetDiffImage(mitk::DiffusionPropertyHelper::GetItkVectorImage(mitk_image)); mitk::TensorModel<>* model = new mitk::TensorModel<>(); model->SetBvalue(1000); model->SetDiffusivity1(0.0010); model->SetDiffusivity2(0.00015); model->SetDiffusivity3(0.00015); model->SetGradientList(mitk::DiffusionPropertyHelper::GetGradientContainer(mitk_image)); fitter->SetSignalModel(model); } else { itk::FitFibersToImageFilter::DoubleImgType::Pointer scalar_image = itk::FitFibersToImageFilter::DoubleImgType::New(); mitk::CastToItkImage(mitk_image, scalar_image); fitter->SetScalarImage(scalar_image); } } if (m_Controls->m_ReguTypeBox->currentIndex()==0) fitter->SetRegularization(VnlCostFunction::REGU::VOXEL_VARIANCE); else if (m_Controls->m_ReguTypeBox->currentIndex()==1) fitter->SetRegularization(VnlCostFunction::REGU::VARIANCE); else if (m_Controls->m_ReguTypeBox->currentIndex()==2) fitter->SetRegularization(VnlCostFunction::REGU::MSM); else if (m_Controls->m_ReguTypeBox->currentIndex()==3) fitter->SetRegularization(VnlCostFunction::REGU::LASSO); else if (m_Controls->m_ReguTypeBox->currentIndex()==4) fitter->SetRegularization(VnlCostFunction::REGU::NONE); fitter->SetTractograms({input_tracts}); fitter->SetFitIndividualFibers(true); fitter->SetMaxIterations(20); fitter->SetVerbose(true); fitter->SetGradientTolerance(1e-5); fitter->SetLambda(m_Controls->m_ReguBox->value()); fitter->SetFilterOutliers(m_Controls->m_OutliersBox->isChecked()); fitter->Update(); mitk::FiberBundle::Pointer output_tracts = fitter->GetTractograms().at(0); output_tracts->ColorFibersByFiberWeights(false, true); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(output_tracts); new_node->SetName("Fitted"); this->GetDataStorage()->Add(new_node, node); m_Controls->m_TractBox->GetSelectedNode()->SetVisibility(false); if (m_Controls->m_ResidualsBox->isChecked() && mitk_peak_image.IsNotNull()) { { mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetFittedImage(); mitk::Image::Pointer mitk_image = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_image, mitk_image); mitk_image->SetVolume(itk_image->GetBufferPointer()); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(mitk_image); new_node->SetName("Fitted"); this->GetDataStorage()->Add(new_node, node); } { mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetResidualImage(); mitk::Image::Pointer mitk_image = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_image, mitk_image); mitk_image->SetVolume(itk_image->GetBufferPointer()); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(mitk_image); new_node->SetName("Residual"); this->GetDataStorage()->Add(new_node, node); } { mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetUnderexplainedImage(); mitk::Image::Pointer mitk_image = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_image, mitk_image); mitk_image->SetVolume(itk_image->GetBufferPointer()); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(mitk_image); new_node->SetName("Underexplained"); this->GetDataStorage()->Add(new_node, node); } { mitk::PeakImage::ItkPeakImageType::Pointer itk_image = fitter->GetOverexplainedImage(); mitk::Image::Pointer mitk_image = dynamic_cast(PeakImage::New().GetPointer()); mitk::CastToMitkImage(itk_image, mitk_image); mitk_image->SetVolume(itk_image->GetBufferPointer()); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(mitk_image); new_node->SetName("Overexplained"); this->GetDataStorage()->Add(new_node, node); } } else if (m_Controls->m_ResidualsBox->isChecked() && mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(mitk_image)) { { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetFittedImageDiff().GetPointer() ); mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true); mitk::DiffusionPropertyHelper::InitializeImage( outImage ); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(outImage); new_node->SetName("Fitted"); this->GetDataStorage()->Add(new_node, node); } { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetResidualImageDiff().GetPointer() ); mitk::DiffusionPropertyHelper::CopyProperties(mitk_image, outImage, true); mitk::DiffusionPropertyHelper::InitializeImage( outImage ); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(outImage); new_node->SetName("Residual"); this->GetDataStorage()->Add(new_node, node); } } else if (m_Controls->m_ResidualsBox->isChecked()) { { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetFittedImageScalar().GetPointer() ); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(outImage); new_node->SetName("Fitted"); this->GetDataStorage()->Add(new_node, node); } { mitk::Image::Pointer outImage = mitk::GrabItkImageMemory( fitter->GetResidualImageScalar().GetPointer() ); mitk::DataNode::Pointer new_node = mitk::DataNode::New(); new_node->SetData(outImage); new_node->SetName("Residual"); this->GetDataStorage()->Add(new_node, node); } } } void QmitkFiberFitView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*part*/, const QList& ) { } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitViewControls.ui index 521636a52e..2b50c5e107 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.fiberprocessing/src/internal/QmitkFiberFitViewControls.ui @@ -1,224 +1,227 @@ - + QmitkFiberFitViewControls 0 0 484 574 Form QCommandLinkButton:disabled { border: none; } QGroupBox { background-color: transparent; } QFrame::NoFrame QFrame::Raised 0 0 0 0 6 - + false Output Residuals: - + Weight for regularization. + + 4 + 999999.000000000000000 0.100000000000000 0.100000000000000 Tractogram: false 0 0 200 16777215 11 - + Start - + λ: Image: - + false Suppress Outliers: Regularization: Voxel-wise Variance Variance Mean Squared Magnitude Lasso None Qt::Vertical 20 40 QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 - - - \ No newline at end of file + + + diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox index f78fb7586c..6cc4616fd8 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox +++ b/Plugins/org.mitk.gui.qt.diffusionimaging.tractography/documentation/UserManual/QmitkStreamlineTrackingViewUserManual.dox @@ -1,104 +1,105 @@ /** \page org_mitk_views_streamlinetracking Streamline Tractography This view enables streamline tractography on various input data. The corresponding command line application is named "MitkStreamlineTractography". Available sections: - \ref StrTrackUserManualInputData - \ref StrTrackUserManualSeeding - \ref StrTrackUserManualConstraints - \ref StrTrackUserManualParameters - \ref StrTrackUserManualNeighbourhoodSampling - \ref StrTrackUserManualDataHandling - \ref StrTrackUserManualPostprocessing - \ref StrTrackUserManualReferences \section StrTrackUserManualInputData Input Data Select the data you want to track on in the datamanager. Supported file types are: - One or multiple DTI images selected in the datamanager. - One ODF image, e.g. obtained using MITK Q-ball reconstruction or MRtrix CSD (tractography similar to [6]). - One peak image (4D float image). - One raw diffusion-weighted image for machine learning based tractography [1]. -- Tractography Forest: Needed for machine learning based tractography [1]. \section StrTrackUserManualSeeding Seeding Specify how, where and how many tractography seed points are placed. This can be either done statically using a seed image or in an interactive fashion. Interactive tractography enables the dynamic placement of spherical seed regions simply by clicking into the image (similar to [5]). Image based seeding: - Seed Image: ROI image used to define the seed voxels. If no seed mask is specified, the whole image volume is seeded. - Seeds per voxel: If set to 1, the seed is defined as the voxel center. If > 1 the seeds are distributet randomly inside the voxel. Interactive seeding: - Update on Parameter Change: When "Update on Parameter Change" is checked, each parameter change causes an instant retracking with the new parameters. This enables an intuitive exploration of the effects that the other tractography parameters have on the resulting tractogram. - Radius: Radius of the manually placed spherical seed region. - Num.Seeds: Number of seeds placed randomly inside the spherical seed region. Parameters for both seeding modes: - Trials Per Seed: Try each seed N times until a valid streamline is obtained (only for probabilistic tractography). - Max. Num. Fibers: Tractography is stopped after the desired number of fibers is reached, even before all seed points are processed. \section StrTrackUserManualConstraints ROI Constraints Specify various ROI and mask images to constrain the tractography process. - Mask Image: ROI image used to constrain the generated streamlines, typically a brain mask. Streamlines that leave the regions defined in this image will stop immediately. - Stop ROI Image: ROI image used to define stopping regions. Streamlines that enter the regions defined in this image will stop immediately. - Exclusion ROI Image: Fibers that enter a region defined in this image will be discarded. - Endpoint Constraints: Determines which fibers are accepted based on their endpoint location. Options are: - No constraints on endpoint locations (command line option NONE) - Both EPs are required to be located in the target image (command line option EPS_IN_TARGET) - Both EPs are required to be located in the target image and the image values at the respective position needs to be distinct (command line option EPS_IN_TARGET_LABELDIFF) - One EP is required to be located in the seed image and one in the target image (command line option EPS_IN_SEED_AND_TARGET) - At least one EP is required to be located in the target image (command line option MIN_ONE_EP_IN_TARGET) - Exactly one EP is required to be located in the target image (command line option ONE_EP_IN_TARGET) - No EP is allowed to be located in the target image (command line option NO_EP_IN_TARGET) - Target Image: ROI image needed for endpoint constraints. \section StrTrackUserManualParameters Tractography Parameters - Mode: Toggle between deterministic and probabilistic tractography (also affects tracking prior proposals). The probabilistic method simply samples the output direction from the discrete probability ditribution provided by the discretized ODF. Probabilistic peak tracking does not derive probabilities from the data but simply adds a normally distributed jitter to the proposed direction. - Sharpen ODFs: If you are using dODF images as input, it is advisable to sharpen the ODFs (min-max normalize and raise to the power of 4). This is not necessary (and not recommended) for CSD fODFs, since they are naturally much sharper. - Cutoff: If the streamline reaches a position with an FA value or peak magnitude lower than the speciefied threshold, tracking is terminated. Typical values are 0.2 for FA/GFA and 0.1 for CSD peaks. - FA/GFA image used to determine streamline termination. If no image is specified, the FA/GFA image is automatically calculated from the input image. If multiple tensor images are used as input, it is recommended to provide such an image since the FA maps calculated from the individual input tensor images can not provide a suitable termination criterion. - ODF Cutoff: 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. - Step Size: The algorithm proceeds along the streamline with a fixed stepsize. Default is 0.5*minSpacing. - Min. Tract Length: Shorter fibers are discarded. - Max. Tract Length: Longer fibers are discarded. -- Angular threshold: Maximum angle between two successive steps (in degree). Default is 90° * step_size. For probabilistic tractography, candidate directions exceeding this threshold have probability 0, i.e. the respective ODF value is set to zero. The probabilities of the valid directions are normalized to sum to 1. +- Angular Threshold: Maximum angle between two successive steps (in degree). Default is 90° * step_size. For probabilistic tractography, candidate directions exceeding this threshold have probability 0, i.e. the respective ODF value is set to zero. The probabilities of the valid directions are normalized to sum to 1. - Loop Check: Stop streamline if the threshold on the angular stdev over the last 4 voxel lengths is exceeded. -1 = no loop check. - f and g values to balance between FACT [2] and TEND [3,4] tracking (only for tensor based tractography). For further information please refer to [2,3] +- Peak Jitter: Used for probabilistic peak tractography. Since no probability are provided by the data, a gausian jitter is added to the peaks. The value influences the standard deviataion of the gaussian (dir[i] += normal(0, peak_jitter*|dir[i]|)). \section StrTrackUserManualTractographyPrior Tractography Prior It is possible to use a peak image as prior for tractography on arbitrary other input images. The local progression direction is determined as the weighted average between the direction obtained from the prior and the input data. - Weight: Weighting factor between prior and input data directions. A weight of zero means that no prior iformation is used. With a weight of one, tractography is performed directly on the prior directions itself. - Restrict to Prior: The prior image is used as tractography mask. Voxels without prior peaks are excluded. - New Directions from Prior: By default, the prior is used even if there is no valid direction found in the data. If unchecked, the prior cannot create directions where there are none in the data. - Flip directions: Internally flips prior directions. This might be necessary depending on the input data. \section StrTrackUserManualDataHandling Data Handling - Flip directions: Internally flips progression directions. This might be necessary depending on the input data. - Interpolate Tractography Data: Trilinearly interpolate the input image used for tractography. - Interpolate ROI Images: Trilinearly interpolate the ROI images used to constrain the tractography. \section StrTrackUserManualNeighbourhoodSampling Neighbourhood Sampling (for details see [1]) - Neighborhood Samples: Number of neighborhood samples that are used to determine the next fiber progression direction. - Sampling Distance: Distance of the sampling positions from the current streamline position (in voxels). - Use Only Frontal Samples: Only neighborhood samples in front of the current streamline position are considered. - Use Stop-Votes: 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. \section StrTrackUserManualPostprocessing Output and Postprocessing - Compress Fibers: Whole brain tractograms obtained with a small step size can contain billions of points. The tractograms can be compressed by removing points that do not really contribute to the fiber shape, such as many points on a straight line. An error threshold (in mm) can be defined to specify which points should be removed and which not. - Output Probability Map: No streamline are generated. Instead, the tractography outputs a visitation-count map that indicates the probability of a fiber to reach a voxel from the selected seed region. For this measure to be sensible, the number of seeds per voxel needs to be rather large. \section StrTrackUserManualReferences References [1] Neher, Peter F., Marc-Alexandre Côté, Jean-Christophe Houde, Maxime Descoteaux, and Klaus H. Maier-Hein. “Fiber Tractography Using Machine Learning.” NeuroImage. Accessed July 19, 2017. doi:10.1016/j.neuroimage.2017.07.028.\n [2] Mori, Susumu, Walter E. Kaufmann, Godfrey D. Pearlson, Barbara J. Crain, Bram Stieltjes, Meiyappan Solaiyappan, and Peter C. M. Van Zijl. “In Vivo Visualization of Human Neural Pathways by Magnetic Resonance Imaging.” Annals of Neurology 47 (2000): 412–414.\n [3] Weinstein, David, Gordon Kindlmann, and Eric Lundberg. “Tensorlines: Advection-Diffusion Based Propagation through Diffusion Tensor Fields.” In Proceedings of the Conference on Visualization’99: Celebrating Ten Years, 249–253, n.d.\n [4] Lazar, Mariana, David M. Weinstein, Jay S. Tsuruda, Khader M. Hasan, Konstantinos Arfanakis, M. Elizabeth Meyerand, Benham Badie, et al. “White Matter Tractography Using Diffusion Tensor Deflection.” Human Brain Mapping 18, no. 4 (2003): 306–321.\n [5] Chamberland, M., K. Whittingstall, D. Fortin, D. Mathieu, and M. Descoteaux. “Real-Time Multi-Peak Tractography for Instantaneous Connectivity Display.” Front Neuroinform 8 (2014): 59. doi:10.3389/fninf.2014.00059.\n [6] Tournier, J-Donald, Fernando Calamante, and Alan Connelly. “MRtrix: Diffusion Tractography in Crossing Fiber Regions.” International Journal of Imaging Systems and Technology 22, no. 1 (March 2012): 53–66. doi:10.1002/ima.22005. */ 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 fcf36d578c..3bf1d89ce3 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 @@ -1,1159 +1,1159 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include #include // Qmitk #include "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, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(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, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_ModeBox, SIGNAL(currentIndexChanged(int)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_StopImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_TargetImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_PriorImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_ExclusionImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_MaskImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_FaImageSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(OnParameterChanged()) ); connect( m_Controls->m_ForestSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(ForestSwitched()) ); connect( m_Controls->m_ForestSelectionWidget, SIGNAL(CurrentSelectionChanged(QList)), this, SLOT(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(stateChanged(int)), 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_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_FiberErrorBox->setValue(params.m_Compression); 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->setChecked(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_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() { // 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; std::shared_ptr params = std::make_shared(); 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_Compression = m_Controls->m_FiberErrorBox->value(); 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->isChecked(); 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_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."); 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->SetReferenceGeometry(dynamic_cast(m_ParentNode->GetData())->GetGeometry()); if (m_Controls->m_ResampleFibersBox->isChecked() && fiberBundle->GetNumberOfLines()>0) fib->Compress(m_Controls->m_FiberErrorBox->value()); fib->ColorFibersByOrientation(); m_Tracker->SetDicomProperties(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()); 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); } - // trials per seed are only important for probabilistic tractography + // 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); + m_Controls->m_PeakJitterBox->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()) ) { 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); } } } 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_Controls->m_ModeBox->currentIndex()==1) - { - QMessageBox::information(nullptr, "Information", "Probabilstic tractography is not implemented for peak images."); - StartStopTrackingGui(false); - return; - } 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; } 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 129085a998..82313381e7 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 @@ -1,1669 +1,1698 @@ 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 - - :/org.mitk.gui.qt.diffusionimaging.tractography/resources/download.ico:/org.mitk.gui.qt.diffusionimaging.tractography/resources/download.ico + + :/QmitkTractography/download.ico:/QmitkTractography/download.ico true Load parameters from json file Load Parameters - - :/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.ico:/org.mitk.gui.qt.diffusionimaging.tractography/resources/upload.ico + + :/QmitkTractography/upload.ico:/QmitkTractography/upload.ico false Start Tractography - - :/org.mitk.gui.qt.diffusionimaging.tractography/resources/right.ico:/org.mitk.gui.qt.diffusionimaging.tractography/resources/right.ico + + :/QmitkTractography/right.ico:/QmitkTractography/right.ico true Stop tractography and return all fibers reconstructed until now. Stop Tractography - - :/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.ico:/org.mitk.gui.qt.diffusionimaging.tractography/resources/stop.ico + + :/QmitkTractography/stop.ico:/QmitkTractography/stop.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 Input Image. ODF, tensor and peak images are currently supported. Input Image: Input Image. ODF, tensor, peak, and, in case of ML tractography, raw diffusion-weighted images are currently supported. <html><head/><body><p><span style=" color:#ff0000;">select image in data-manager</span></p></body></html> true Tractography Forest: 0 0 0 0 75 true 0 0 0 421 254 Seeding Specify how, where and how many tractography seed points are placed. QFrame::NoFrame QFrame::Raised 0 0 0 0 QFrame::NoFrame QFrame::Raised 0 0 0 0 Number of seed points equally distributed around selected position. 1 9999999 50 Radius: Seedpoints are equally distributed within a sphere centered at the selected position with the specified radius (in mm). 2 50.000000000000000 0.100000000000000 2.000000000000000 Num. Seeds: true When checked, parameter changes cause instant retracking while in interactive mode. Update on Parameter Change true QFrame::NoFrame QFrame::Raised 0 0 0 0 Try each seed N times until a valid streamline is obtained (only for probabilistic tractography). Minimum fiber length (in mm) 1 999 10 Trials Per Seed: Max. Num. Fibers: Tractography is stopped after the desired number of fibers is reached, even before all seed points are processed (-1 means no limit). -1 999999999 -1 QFrame::NoFrame QFrame::Raised 0 0 0 0 Seeds per Voxel: Seed Image: Number of seed points placed in each voxel. 1 9999999 true Dynamically pick a seed location by click into image. Enable Interactive Tractography Qt::Vertical 20 40 0 0 435 - 184 + 169 ROI Constraints Specify various ROI and mask images to constrain the tractography process. Mask Image: Select which fibers should be accepted or rejected based on the location of their endpoints. QComboBox::AdjustToMinimumContentsLength No Constraints on EP locations Both EPs in Target Image Both EPs in Target Image But Different Label One EP in Seed Image and One EP in Target Image At Least One EP in Target Image Exactly One EP in Target Image No EP in Target Image Endpoint Constraints: Stop ROI Image: Exclusion ROI Image: Target ROI Image: Qt::Vertical 20 40 0 - 0 + -228 421 - 397 + 428 Tractography Parameters Specify the behavior of the tractography at each streamline integration step (step size, deterministic/probabilistic, ...). - - + + - 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 - - - - - - - - - - FA/GFA Image: - - - - - - - - - - ODF Cutoff: + 20.000000000000000 - - + + - Always produce the same random numbers. + 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: - - - - Qt::Vertical - - - - 20 - 40 - - - - f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!). 2 1.000000000000000 0.100000000000000 0.000000000000000 - - + + - Minimum tract length in mm. Shorter fibers are discarded. - - - Minimum fiber length (in mm) - - - 1 - - - 999.000000000000000 - - - 1.000000000000000 + - - 20.000000000000000 + + Sharpen ODFs: - - + + - Sharpen ODFs: + Fix Random Seed: - - + + - Threshold on peak magnitude, FA, GFA, ... + Maximum allowed angular SDTEV over 4 voxel lengths. Default: no loop check. - - 5 + + - - 1.000000000000000 + + -1 - - 0.100000000000000 + + 180 - 0.100000000000000 + -1 - - + + - g: + Angular Threshold: - - + + - Loop Check: + Max. Tract Length: + + + + + + + + + + Cutoff: If you are using dODF images as input, it is advisable to sharpen the ODFs (min-max normalize and raise to the power of 4). This is not necessary for CSD fODFs, since they are naturally much sharper. - - + + + + Angular threshold between two steps (in degree). Default: 90° * step_size + + + -1 + + + 90 + + + 1 + + + -1 + + + + + + + Qt::Vertical + + + + 20 + 40 + + + f=1 + g=0 means FACT (depending on the chosen interpolation). f=0 and g=1 means TEND (disable interpolation for this mode!). 2 1.000000000000000 0.100000000000000 1.000000000000000 - - + + - Maximum allowed angular SDTEV over 4 voxel lengths. Default: no loop check. + Toggle between deterministic and probabilistic tractography. Some modes might not be available for all types of tractography. - + + + Deterministic + + + + + Probabilistic + + + + + + + - - -1 + + 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 - 180 + 1.000000000000000 + + + 0.100000000000000 - -1 + 0.000250000000000 Min. Tract Length: - - + + - 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: + FA/GFA Image: - - + + - Angular Threshold: + Loop Check: - - + + - Step size (in voxels) + Minimum tract length in mm. Shorter fibers are discarded. - - 2 + + Maximum fiber length (in mm) - - 0.010000000000000 + + 1 - 10.000000000000000 + 999.000000000000000 - 0.100000000000000 + 1.000000000000000 - 0.500000000000000 + 400.000000000000000 - - - - Toggle between deterministic and probabilistic tractography. Some modes might not be available for all types of tractography. - - - - Deterministic - - - - - Probabilistic - - - - - - + + - + Always produce the same random numbers. - Mode: + Step Size: - - + + - Cutoff: + ODF Cutoff: - - + + - 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. + Step size (in voxels) - 5 + 2 + + + 0.010000000000000 - 1.000000000000000 + 10.000000000000000 0.100000000000000 - 0.000250000000000 + 0.500000000000000 - - + + - Fix Random Seed: + g: - - + + + + + + + Threshold on peak magnitude, FA, GFA, ... + + + 5 + + + 1.000000000000000 + + + 0.100000000000000 + + + 0.100000000000000 + + + + + - Max. Tract Length: + Peak Jitter: - - + + - Minimum tract length in mm. Shorter fibers are discarded. - - - Maximum fiber length (in mm) + 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. - 1 + 3 - 999.000000000000000 + 1.000000000000000 - 1.000000000000000 + 0.100000000000000 - 400.000000000000000 + 0.010000000000000 0 0 435 - 184 + 169 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 + 169 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 + 169 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 + 169 Output and Postprocessing Specify the tractography output (streamlines or probability maps) and postprocessing steps. QFrame::NoFrame QFrame::Raised 0 0 0 0 Compress fibers using the specified error constraint. Compress Fibers true Qt::StrongFocus Lossy fiber compression. Recommended for large tractograms. Maximum error in mm. 3 10.000000000000000 0.010000000000000 0.100000000000000 Output map with voxel-wise visitation counts instead of streamlines. Output Probability Map false Qt::Vertical 20 40 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 c5f8b976e6..78d2287b87 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkControlVisualizationPropertiesView.cpp @@ -1,1247 +1,1250 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "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::MultiThreader::GetGlobalMaximumNumberOfThreads(); itk::MultiThreader::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(); renderer->GetRenderingManager()->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) { QColor c = QColorDialog::getColor(); - 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); - mitk::RenderingManager::GetInstance()->RequestUpdateAll(); + 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); + 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_FiberThicknessSlider), SIGNAL(sliderReleased()), static_cast(this), SLOT( FiberSlicingThickness2D() ) ); connect(static_cast(m_Controls->m_FiberThicknessSlider), SIGNAL(valueChanged(int)), static_cast(this), SLOT( FiberSlicingUpdateLabel(int) )); 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; m_Controls->m_NumberGlyphsFrame->setVisible(false); m_Controls->m_GlyphFrame->setVisible(false); m_Controls->m_TSMenu->setVisible(false); m_SelectedNode = nullptr; 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); 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); 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_FiberThicknessSlider->setMaximum(max * 10); m_Controls->m_FiberThicknessSlider->setValue(range * 10); } 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); } } 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(); mitk::Image::Pointer image = dynamic_cast(m_SelectedNode->GetData()); typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(image); caster->Update(); mitk::PeakImage::ItkPeakImageType::Pointer itkImg = caster->GetOutput(); 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()); m_SelectedNode->SetData(resultImage); m_SelectedNode->SetName(name); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::Toggle3DPeaks() { if (m_SelectedNode.IsNull() || dynamic_cast(m_SelectedNode->GetData())==nullptr) return; bool enabled = false; m_SelectedNode->GetBoolProperty("Enable3DPeaks", enabled); m_SelectedNode->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; m_SelectedNode->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"); } 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()) ) { m_SelectedNode->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()) ) { m_SelectedNode->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()) ) { m_SelectedNode->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()) ) { m_SelectedNode->SetProperty("ScaleBy", scaleBy.GetPointer()); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkControlVisualizationPropertiesView::Fiber2DfadingEFX() { if (m_SelectedNode && dynamic_cast(m_SelectedNode->GetData()) ) { 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(); } } void QmitkControlVisualizationPropertiesView::FiberSlicingThickness2D() { if (m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) { float fibThickness = m_Controls->m_FiberThicknessSlider->value() * 0.1; 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(); } } void QmitkControlVisualizationPropertiesView::FiberSlicingUpdateLabel(int value) { QString label = "Range %1 mm"; label = label.arg(value * 0.1); m_Controls->label_range->setText(label); FiberSlicingThickness2D(); } 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())) { 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(); } } void QmitkControlVisualizationPropertiesView::ResetColoring() { if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) { 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(); } } void QmitkControlVisualizationPropertiesView::PlanarFigureFocus() { if(m_SelectedNode) { mitk::PlanarFigure* _PlanarFigure = 0; _PlanarFigure = dynamic_cast (m_SelectedNode->GetData()); if (_PlanarFigure && _PlanarFigure->GetPlaneGeometry()) { QmitkRenderWindow* selectedRenderWindow = 0; bool PlanarFigureInitializedWindow = false; auto renderWindowPart = this->GetRenderWindowPart(mitk::WorkbenchUtil::IRenderWindowPartStrategy::OPEN); QmitkRenderWindow* axialRenderWindow = renderWindowPart->GetQmitkRenderWindow("axial"); if (m_SelectedNode->GetBoolProperty("PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, axialRenderWindow->GetRenderer())) { selectedRenderWindow = axialRenderWindow; } QmitkRenderWindow* sagittalRenderWindow = renderWindowPart->GetQmitkRenderWindow("sagittal"); if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, sagittalRenderWindow->GetRenderer())) { selectedRenderWindow = sagittalRenderWindow; } QmitkRenderWindow* coronalRenderWindow = renderWindowPart->GetQmitkRenderWindow("coronal"); if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, coronalRenderWindow->GetRenderer())) { selectedRenderWindow = coronalRenderWindow; } QmitkRenderWindow* _3DRenderWindow = renderWindowPart->GetQmitkRenderWindow("3d"); if (!selectedRenderWindow && m_SelectedNode->GetBoolProperty( "PlanarFigureInitializedWindow", PlanarFigureInitializedWindow, _3DRenderWindow->GetRenderer())) { selectedRenderWindow = _3DRenderWindow; } const mitk::PlaneGeometry* _PlaneGeometry = _PlanarFigure->GetPlaneGeometry(); mitk::VnlVector normal = _PlaneGeometry->GetNormalVnl(); mitk::PlaneGeometry::ConstPointer worldGeometry1 = axialRenderWindow->GetRenderer()->GetCurrentWorldPlaneGeometry(); mitk::PlaneGeometry::ConstPointer _Plane1 = dynamic_cast( worldGeometry1.GetPointer() ); mitk::VnlVector normal1 = _Plane1->GetNormalVnl(); mitk::PlaneGeometry::ConstPointer worldGeometry2 = sagittalRenderWindow->GetRenderer()->GetCurrentWorldPlaneGeometry(); mitk::PlaneGeometry::ConstPointer _Plane2 = dynamic_cast( worldGeometry2.GetPointer() ); mitk::VnlVector normal2 = _Plane2->GetNormalVnl(); mitk::PlaneGeometry::ConstPointer worldGeometry3 = coronalRenderWindow->GetRenderer()->GetCurrentWorldPlaneGeometry(); mitk::PlaneGeometry::ConstPointer _Plane3 = dynamic_cast( worldGeometry3.GetPointer() ); mitk::VnlVector normal3 = _Plane3->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]); double ang1 = angle(normal, normal1); double ang2 = angle(normal, normal2); double ang3 = angle(normal, normal3); if(ang1 < ang2 && ang1 < ang3) { selectedRenderWindow = axialRenderWindow; } else { 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()); } } // 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 ); } 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())) { float newRadius = m_Controls->m_TubeWidth->value(); m_SelectedNode->SetFloatProperty("shape.tuberadius", newRadius); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkControlVisualizationPropertiesView::RibbonWidthChanged() { if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) { float newWidth = m_Controls->m_RibbonWidth->value(); m_SelectedNode->SetFloatProperty("shape.ribbonwidth", newWidth); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } } void QmitkControlVisualizationPropertiesView::LineWidthChanged() { if(m_SelectedNode && dynamic_cast(m_SelectedNode->GetData())) { 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(); } } void QmitkControlVisualizationPropertiesView::Welcome() { berry::PlatformUI::GetWorkbench()->GetIntroManager() ->ShowIntro(GetSite()->GetWorkbenchWindow(), false); } void QmitkControlVisualizationPropertiesView::OnColourisationModeChanged() { if( m_SelectedNode && m_NodeUsedForOdfVisualization.IsNotNull() ) { 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."; } }