diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp index 67cb7166b0..fe7685509e 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp @@ -1,846 +1,855 @@ /*=================================================================== 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. ===================================================================*/ #define RAPIDXML_NO_EXCEPTIONS #include #include #include #include -#include +#include #include template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::FiberfoxParameters() : m_NoiseModel(NULL) { } template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::~FiberfoxParameters() { // if (m_NoiseModel!=NULL) // delete m_NoiseModel; } void mitk::SignalGenerationParameters::GenerateGradientHalfShell() { int NPoints = 2*m_NumGradients; m_GradientDirections.clear(); m_NumBaseline = NPoints/20; if (m_NumBaseline==0) m_NumBaseline=1; GradientType g; g.Fill(0.0); for (unsigned int i=0; i theta; theta.set_size(NPoints); vnl_vector phi; phi.set_size(NPoints); double C = sqrt(4*M_PI); phi(0) = 0.0; phi(NPoints-1) = 0.0; for(int i=0; i0 && i mitk::SignalGenerationParameters::GetBaselineIndices() { std::vector< int > result; for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) result.push_back(i); return result; } unsigned int mitk::SignalGenerationParameters::GetFirstBaselineIndex() { for( unsigned int i=0; im_GradientDirections.size(); i++) if (m_GradientDirections.at(i).GetNorm()<0.0001) return i; return -1; } bool mitk::SignalGenerationParameters::IsBaselineIndex(unsigned int idx) { if (m_GradientDirections.size()>idx && m_GradientDirections.at(idx).GetNorm()<0.0001) return true; return false; } unsigned int mitk::SignalGenerationParameters::GetNumWeightedVolumes() { return m_NumGradients; } unsigned int mitk::SignalGenerationParameters::GetNumBaselineVolumes() { return m_NumBaseline; } unsigned int mitk::SignalGenerationParameters::GetNumVolumes() { return m_GradientDirections.size(); } mitk::SignalGenerationParameters::GradientListType mitk::SignalGenerationParameters::GetGradientDirections() { return m_GradientDirections; } mitk::SignalGenerationParameters::GradientType mitk::SignalGenerationParameters::GetGradientDirection(unsigned int i) { return m_GradientDirections.at(i); } void mitk::SignalGenerationParameters::SetNumWeightedVolumes(int numGradients) { m_NumGradients = numGradients; GenerateGradientHalfShell(); } void mitk::SignalGenerationParameters::SetGradienDirections(GradientListType gradientList) { m_GradientDirections = gradientList; m_NumGradients = 0; m_NumBaseline = 0; for( unsigned int i=0; im_GradientDirections.size(); i++) { if (m_GradientDirections.at(i).GetNorm()>0.0001) m_NumGradients++; else m_NumBaseline++; } } void mitk::SignalGenerationParameters::SetGradienDirections(mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList) { m_NumGradients = 0; m_NumBaseline = 0; m_GradientDirections.clear(); for( unsigned int i=0; iSize(); i++) { GradientType g; g[0] = gradientList->at(i)[0]; g[1] = gradientList->at(i)[1]; g[2] = gradientList->at(i)[2]; m_GradientDirections.push_back(g); if (m_GradientDirections.at(i).GetNorm()>0.0001) m_NumGradients++; else m_NumBaseline++; } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::SaveParameters(string filename) { if(filename.empty()) return; if(".ffp"!=filename.substr(filename.size()-4, 4)) filename += ".ffp"; const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, NULL ); 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; // fiber generation parameters parameters.put("fiberfox.fibers.distribution", m_FiberGen.m_Distribution); parameters.put("fiberfox.fibers.variance", m_FiberGen.m_Variance); parameters.put("fiberfox.fibers.density", m_FiberGen.m_Density); parameters.put("fiberfox.fibers.spline.sampling", m_FiberGen.m_Sampling); parameters.put("fiberfox.fibers.spline.tension", m_FiberGen.m_Tension); parameters.put("fiberfox.fibers.spline.continuity", m_FiberGen.m_Continuity); parameters.put("fiberfox.fibers.spline.bias", m_FiberGen.m_Bias); parameters.put("fiberfox.fibers.rotation.x", m_FiberGen.m_Rotation[0]); parameters.put("fiberfox.fibers.rotation.y", m_FiberGen.m_Rotation[1]); parameters.put("fiberfox.fibers.rotation.z", m_FiberGen.m_Rotation[2]); parameters.put("fiberfox.fibers.translation.x", m_FiberGen.m_Translation[0]); parameters.put("fiberfox.fibers.translation.y", m_FiberGen.m_Translation[1]); parameters.put("fiberfox.fibers.translation.z", m_FiberGen.m_Translation[2]); parameters.put("fiberfox.fibers.scale.x", m_FiberGen.m_Scale[0]); parameters.put("fiberfox.fibers.scale.y", m_FiberGen.m_Scale[1]); parameters.put("fiberfox.fibers.scale.z", m_FiberGen.m_Scale[2]); // image generation parameters parameters.put("fiberfox.image.basic.size.x", m_SignalGen.m_ImageRegion.GetSize(0)); parameters.put("fiberfox.image.basic.size.y", m_SignalGen.m_ImageRegion.GetSize(1)); parameters.put("fiberfox.image.basic.size.z", m_SignalGen.m_ImageRegion.GetSize(2)); parameters.put("fiberfox.image.basic.spacing.x", m_SignalGen.m_ImageSpacing[0]); parameters.put("fiberfox.image.basic.spacing.y", m_SignalGen.m_ImageSpacing[1]); parameters.put("fiberfox.image.basic.spacing.z", m_SignalGen.m_ImageSpacing[2]); parameters.put("fiberfox.image.basic.origin.x", m_SignalGen.m_ImageOrigin[0]); parameters.put("fiberfox.image.basic.origin.y", m_SignalGen.m_ImageOrigin[1]); parameters.put("fiberfox.image.basic.origin.z", m_SignalGen.m_ImageOrigin[2]); parameters.put("fiberfox.image.basic.direction.1", m_SignalGen.m_ImageDirection[0][0]); parameters.put("fiberfox.image.basic.direction.2", m_SignalGen.m_ImageDirection[0][1]); parameters.put("fiberfox.image.basic.direction.3", m_SignalGen.m_ImageDirection[0][2]); parameters.put("fiberfox.image.basic.direction.4", m_SignalGen.m_ImageDirection[1][0]); parameters.put("fiberfox.image.basic.direction.5", m_SignalGen.m_ImageDirection[1][1]); parameters.put("fiberfox.image.basic.direction.6", m_SignalGen.m_ImageDirection[1][2]); parameters.put("fiberfox.image.basic.direction.7", m_SignalGen.m_ImageDirection[2][0]); parameters.put("fiberfox.image.basic.direction.8", m_SignalGen.m_ImageDirection[2][1]); parameters.put("fiberfox.image.basic.direction.9", m_SignalGen.m_ImageDirection[2][2]); parameters.put("fiberfox.image.basic.numgradients", m_SignalGen.GetNumWeightedVolumes()); for( unsigned int i=0; im_SignalGen.GetNumVolumes(); i++) { parameters.put("fiberfox.image.gradients."+boost::lexical_cast(i)+".x", m_SignalGen.GetGradientDirection(i)[0]); parameters.put("fiberfox.image.gradients."+boost::lexical_cast(i)+".y", m_SignalGen.GetGradientDirection(i)[1]); parameters.put("fiberfox.image.gradients."+boost::lexical_cast(i)+".z", m_SignalGen.GetGradientDirection(i)[2]); } parameters.put("fiberfox.image.acquisitiontype", m_SignalGen.m_AcquisitionType); parameters.put("fiberfox.image.coilsensitivityprofile", m_SignalGen.m_CoilSensitivityProfile); parameters.put("fiberfox.image.numberofcoils", m_SignalGen.m_NumberOfCoils); parameters.put("fiberfox.image.reversephase", m_SignalGen.m_ReversePhase); parameters.put("fiberfox.image.partialfourier", m_SignalGen.m_PartialFourier); parameters.put("fiberfox.image.noisevariance", m_SignalGen.m_NoiseVariance); parameters.put("fiberfox.image.trep", m_SignalGen.m_tRep); parameters.put("fiberfox.image.signalScale", m_SignalGen.m_SignalScale); parameters.put("fiberfox.image.tEcho", m_SignalGen.m_tEcho); parameters.put("fiberfox.image.tLine", m_SignalGen.m_tLine); parameters.put("fiberfox.image.tInhom", m_SignalGen.m_tInhom); parameters.put("fiberfox.image.bvalue", m_SignalGen.m_Bvalue); parameters.put("fiberfox.image.simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition); parameters.put("fiberfox.image.axonRadius", m_SignalGen.m_AxonRadius); parameters.put("fiberfox.image.doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation); parameters.put("fiberfox.image.doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume); parameters.put("fiberfox.image.artifacts.spikesnum", m_SignalGen.m_Spikes); parameters.put("fiberfox.image.artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude); parameters.put("fiberfox.image.artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset); parameters.put("fiberfox.image.artifacts.eddyStrength", m_SignalGen.m_EddyStrength); parameters.put("fiberfox.image.artifacts.eddyTau", m_SignalGen.m_Tau); parameters.put("fiberfox.image.artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor); parameters.put("fiberfox.image.artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging); parameters.put("fiberfox.image.artifacts.doAddMotion", m_SignalGen.m_DoAddMotion); parameters.put("fiberfox.image.artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion); parameters.put("fiberfox.image.artifacts.translation0", m_SignalGen.m_Translation[0]); parameters.put("fiberfox.image.artifacts.translation1", m_SignalGen.m_Translation[1]); parameters.put("fiberfox.image.artifacts.translation2", m_SignalGen.m_Translation[2]); parameters.put("fiberfox.image.artifacts.rotation0", m_SignalGen.m_Rotation[0]); parameters.put("fiberfox.image.artifacts.rotation1", m_SignalGen.m_Rotation[1]); parameters.put("fiberfox.image.artifacts.rotation2", m_SignalGen.m_Rotation[2]); parameters.put("fiberfox.image.artifacts.motionvolumes", m_Misc.m_MotionVolumesBox); parameters.put("fiberfox.image.artifacts.addnoise", m_Misc.m_CheckAddNoiseBox); parameters.put("fiberfox.image.artifacts.addghosts", m_Misc.m_CheckAddGhostsBox); parameters.put("fiberfox.image.artifacts.addaliasing", m_Misc.m_CheckAddAliasingBox); parameters.put("fiberfox.image.artifacts.addspikes", m_Misc.m_CheckAddSpikesBox); parameters.put("fiberfox.image.artifacts.addeddycurrents", m_Misc.m_CheckAddEddyCurrentsBox); parameters.put("fiberfox.image.artifacts.doAddDistortions", m_Misc.m_CheckAddDistortionsBox); parameters.put("fiberfox.image.outputvolumefractions", m_Misc.m_CheckOutputVolumeFractionsBox); parameters.put("fiberfox.image.showadvanced", m_Misc.m_CheckAdvancedSignalOptionsBox); parameters.put("fiberfox.image.signalmodelstring", m_Misc.m_SignalModelString); parameters.put("fiberfox.image.artifactmodelstring", m_Misc.m_ArtifactModelString); parameters.put("fiberfox.image.outpath", m_Misc.m_OutputPath); parameters.put("fiberfox.fibers.realtime", m_Misc.m_CheckRealTimeFibersBox); parameters.put("fiberfox.fibers.showadvanced", m_Misc.m_CheckAdvancedFiberOptionsBox); parameters.put("fiberfox.fibers.constantradius", m_Misc.m_CheckConstantRadiusBox); parameters.put("fiberfox.fibers.includeFiducials", m_Misc.m_CheckIncludeFiducialsBox); if (m_NoiseModel!=NULL) { parameters.put("fiberfox.image.artifacts.noisevariance", m_NoiseModel->GetNoiseVariance()); if (dynamic_cast*>(m_NoiseModel.get())) parameters.put("fiberfox.image.artifacts.noisetype", "rice"); else if (dynamic_cast*>(m_NoiseModel.get())) parameters.put("fiberfox.image.artifacts.noisetype", "chisquare"); } for (int i=0; i* signalModel = NULL; if (i(i)+".type", "fiber"); } else { signalModel = m_NonFiberModelList.at(i-m_FiberModelList.size()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".type", "non-fiber"); } if (dynamic_cast*>(signalModel)) { mitk::StickModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "stick"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t1", model->GetT1()); } else if (dynamic_cast*>(signalModel)) { mitk::TensorModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "tensor"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d1", model->GetDiffusivity1()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d2", model->GetDiffusivity2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d3", model->GetDiffusivity3()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t1", model->GetT1()); } else if (dynamic_cast*>(signalModel)) { mitk::RawShModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "prototype"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".minFA", model->GetFaRange().first); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".maxFA", model->GetFaRange().second); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".minADC", model->GetAdcRange().first); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".maxADC", model->GetAdcRange().second); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".maxNumSamples", model->GetMaxNumKernels()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".numSamples", model->GetNumberOfKernels()); int shOrder = model->GetShOrder(); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".numCoeffs", (shOrder*shOrder + shOrder + 2)/2 + shOrder); for (unsigned int j=0; jGetNumberOfKernels(); j++) { vnl_vector< double > coeffs = model->GetCoefficients(j); for (unsigned int k=0; k(i)+".kernels."+boost::lexical_cast(j)+".coeffs."+boost::lexical_cast(k), coeffs[k]); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".kernels."+boost::lexical_cast(j)+".B0", model->GetBaselineSignal(j)); } } else if (dynamic_cast*>(signalModel)) { mitk::BallModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "ball"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t1", model->GetT1()); } else if (dynamic_cast*>(signalModel)) { mitk::AstroStickModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "astrosticks"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".d", model->GetDiffusivity()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t1", model->GetT1()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".randomize", model->GetRandomizeSticks()); } else if (dynamic_cast*>(signalModel)) { mitk::DotModel* model = dynamic_cast*>(signalModel); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".model", "dot"); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t2", model->GetT2()); parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".t1", model->GetT1()); } if (signalModel!=NULL) { parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".ID", signalModel->m_CompartmentId); if (signalModel->GetVolumeFractionImage().IsNotNull()) { try{ itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); writer->SetFileName(filename+"_VOLUME"+boost::lexical_cast(signalModel->m_CompartmentId)+".nrrd"); writer->SetInput(signalModel->GetVolumeFractionImage()); writer->Update(); MITK_INFO << "Volume fraction image for compartment "+boost::lexical_cast(signalModel->m_CompartmentId)+" saved."; } catch(...) { } } } } boost::property_tree::xml_writer_settings writerSettings(' ', 2); boost::property_tree::xml_parser::write_xml(filename, parameters, std::locale(), writerSettings); try{ itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); writer->SetFileName(filename+"_FMAP.nrrd"); writer->SetInput(m_SignalGen.m_FrequencyMap); writer->Update(); } catch(...) { MITK_INFO << "No frequency map saved."; } try{ itk::ImageFileWriter::Pointer writer = itk::ImageFileWriter::New(); writer->SetFileName(filename+"_MASK.nrrd"); writer->SetInput(m_SignalGen.m_MaskImage); writer->Update(); } catch(...) { MITK_INFO << "No mask image saved."; } setlocale(LC_ALL, currLocale.c_str()); } template< class ScalarType > template< class ParameterType > ParameterType mitk::FiberfoxParameters< ScalarType >::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 << "'"; } if (tag!="artifacts.noisetype") { MITK_INFO << "Tag '" << tag << "' not found. Using default value '" << defaultValue << "'."; m_MissingTags += "\n- "; m_MissingTags += tag; } return defaultValue; } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::LoadParameters(string filename) { m_MissingTags = ""; if(filename.empty()) { return; } const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, NULL ); 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::xml_parser::read_xml( filename, parameterTree ); m_FiberModelList.clear(); m_NonFiberModelList.clear(); if (m_NoiseModel) { m_NoiseModel = nullptr; } BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameterTree.get_child("fiberfox") ) { if( v1.first == "fibers" ) { m_Misc.m_CheckRealTimeFibersBox = ReadVal(v1,"realtime", m_Misc.m_CheckRealTimeFibersBox); m_Misc.m_CheckAdvancedFiberOptionsBox = ReadVal(v1,"showadvanced", m_Misc.m_CheckAdvancedFiberOptionsBox); m_Misc.m_CheckConstantRadiusBox = ReadVal(v1,"constantradius", m_Misc.m_CheckConstantRadiusBox); m_Misc.m_CheckIncludeFiducialsBox = ReadVal(v1,"includeFiducials", m_Misc.m_CheckIncludeFiducialsBox); switch (ReadVal(v1,"distribution", 0)) { case 0: m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; break; case 1: m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN; break; default: m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; } m_FiberGen.m_Variance = ReadVal(v1,"variance", m_FiberGen.m_Variance); m_FiberGen.m_Density = ReadVal(v1,"density", m_FiberGen.m_Density); m_FiberGen.m_Sampling = ReadVal(v1,"spline.sampling", m_FiberGen.m_Sampling); m_FiberGen.m_Tension = ReadVal(v1,"spline.tension", m_FiberGen.m_Tension); m_FiberGen.m_Continuity = ReadVal(v1,"spline.continuity", m_FiberGen.m_Continuity); m_FiberGen.m_Bias = ReadVal(v1,"spline.bias", m_FiberGen.m_Bias); m_FiberGen.m_Rotation[0] = ReadVal(v1,"rotation.x", m_FiberGen.m_Rotation[0]); m_FiberGen.m_Rotation[1] = ReadVal(v1,"rotation.y", m_FiberGen.m_Rotation[1]); m_FiberGen.m_Rotation[2] = ReadVal(v1,"rotation.z", m_FiberGen.m_Rotation[2]); m_FiberGen.m_Translation[0] = ReadVal(v1,"translation.x", m_FiberGen.m_Translation[0]); m_FiberGen.m_Translation[1] = ReadVal(v1,"translation.y", m_FiberGen.m_Translation[1]); m_FiberGen.m_Translation[2] = ReadVal(v1,"translation.z", m_FiberGen.m_Translation[2]); m_FiberGen.m_Scale[0] = ReadVal(v1,"scale.x", m_FiberGen.m_Scale[0]); m_FiberGen.m_Scale[1] = ReadVal(v1,"scale.y", m_FiberGen.m_Scale[1]); m_FiberGen.m_Scale[2] = ReadVal(v1,"scale.z", m_FiberGen.m_Scale[2]); } else if ( v1.first == "image" ) { m_Misc.m_SignalModelString = ReadVal(v1,"signalmodelstring", m_Misc.m_SignalModelString); m_Misc.m_ArtifactModelString = ReadVal(v1,"artifactmodelstring", m_Misc.m_ArtifactModelString); m_Misc.m_OutputPath = ReadVal(v1,"outpath", m_Misc.m_OutputPath); m_Misc.m_CheckOutputVolumeFractionsBox = ReadVal(v1,"outputvolumefractions", m_Misc.m_CheckOutputVolumeFractionsBox); m_Misc.m_CheckAdvancedSignalOptionsBox = ReadVal(v1,"showadvanced", m_Misc.m_CheckAdvancedSignalOptionsBox); m_Misc.m_CheckAddDistortionsBox = ReadVal(v1,"artifacts.doAddDistortions", m_Misc.m_CheckAddDistortionsBox); m_Misc.m_CheckAddNoiseBox = ReadVal(v1,"artifacts.addnoise", m_Misc.m_CheckAddNoiseBox); m_Misc.m_CheckAddGhostsBox = ReadVal(v1,"artifacts.addghosts", m_Misc.m_CheckAddGhostsBox); m_Misc.m_CheckAddAliasingBox = ReadVal(v1,"artifacts.addaliasing", m_Misc.m_CheckAddAliasingBox); m_Misc.m_CheckAddSpikesBox = ReadVal(v1,"artifacts.addspikes", m_Misc.m_CheckAddSpikesBox); m_Misc.m_CheckAddEddyCurrentsBox = ReadVal(v1,"artifacts.addeddycurrents", m_Misc.m_CheckAddEddyCurrentsBox); m_SignalGen.m_ImageRegion.SetSize(0, ReadVal(v1,"basic.size.x",m_SignalGen.m_ImageRegion.GetSize(0))); m_SignalGen.m_ImageRegion.SetSize(1, ReadVal(v1,"basic.size.y",m_SignalGen.m_ImageRegion.GetSize(1))); m_SignalGen.m_ImageRegion.SetSize(2, ReadVal(v1,"basic.size.z",m_SignalGen.m_ImageRegion.GetSize(2))); m_SignalGen.m_ImageSpacing[0] = ReadVal(v1,"basic.spacing.x",m_SignalGen.m_ImageSpacing[0]); m_SignalGen.m_ImageSpacing[1] = ReadVal(v1,"basic.spacing.y",m_SignalGen.m_ImageSpacing[1]); m_SignalGen.m_ImageSpacing[2] = ReadVal(v1,"basic.spacing.z",m_SignalGen.m_ImageSpacing[2]); m_SignalGen.m_ImageOrigin[0] = ReadVal(v1,"basic.origin.x",m_SignalGen.m_ImageOrigin[0]); m_SignalGen.m_ImageOrigin[1] = ReadVal(v1,"basic.origin.y",m_SignalGen.m_ImageOrigin[1]); m_SignalGen.m_ImageOrigin[2] = ReadVal(v1,"basic.origin.z",m_SignalGen.m_ImageOrigin[2]); m_SignalGen.m_ImageDirection[0][0] = ReadVal(v1,"basic.direction.1",m_SignalGen.m_ImageDirection[0][0]); m_SignalGen.m_ImageDirection[0][1] = ReadVal(v1,"basic.direction.2",m_SignalGen.m_ImageDirection[0][1]); m_SignalGen.m_ImageDirection[0][2] = ReadVal(v1,"basic.direction.3",m_SignalGen.m_ImageDirection[0][2]); m_SignalGen.m_ImageDirection[1][0] = ReadVal(v1,"basic.direction.4",m_SignalGen.m_ImageDirection[1][0]); m_SignalGen.m_ImageDirection[1][1] = ReadVal(v1,"basic.direction.5",m_SignalGen.m_ImageDirection[1][1]); m_SignalGen.m_ImageDirection[1][2] = ReadVal(v1,"basic.direction.6",m_SignalGen.m_ImageDirection[1][2]); m_SignalGen.m_ImageDirection[2][0] = ReadVal(v1,"basic.direction.7",m_SignalGen.m_ImageDirection[2][0]); m_SignalGen.m_ImageDirection[2][1] = ReadVal(v1,"basic.direction.8",m_SignalGen.m_ImageDirection[2][1]); m_SignalGen.m_ImageDirection[2][2] = ReadVal(v1,"basic.direction.9",m_SignalGen.m_ImageDirection[2][2]); m_SignalGen.m_AcquisitionType = (SignalGenerationParameters::AcquisitionType) ReadVal(v1,"acquisitiontype", m_SignalGen.m_AcquisitionType); m_SignalGen.m_CoilSensitivityProfile = (SignalGenerationParameters::CoilSensitivityProfile) ReadVal(v1,"coilsensitivityprofile", m_SignalGen.m_CoilSensitivityProfile); m_SignalGen.m_NumberOfCoils = ReadVal(v1,"numberofcoils", m_SignalGen.m_NumberOfCoils); m_SignalGen.m_ReversePhase = ReadVal(v1,"reversephase", m_SignalGen.m_ReversePhase); m_SignalGen.m_PartialFourier = ReadVal(v1,"partialfourier", m_SignalGen.m_PartialFourier); m_SignalGen.m_NoiseVariance = ReadVal(v1,"noisevariance", m_SignalGen.m_NoiseVariance); m_SignalGen.m_tRep = ReadVal(v1,"trep", m_SignalGen.m_tRep); m_SignalGen.m_SignalScale = ReadVal(v1,"signalScale", m_SignalGen.m_SignalScale); m_SignalGen.m_tEcho = ReadVal(v1,"tEcho", m_SignalGen.m_tEcho); m_SignalGen.m_tLine = ReadVal(v1,"tLine", m_SignalGen.m_tLine); m_SignalGen.m_tInhom = ReadVal(v1,"tInhom", m_SignalGen.m_tInhom); m_SignalGen.m_Bvalue = ReadVal(v1,"bvalue", m_SignalGen.m_Bvalue); m_SignalGen.m_SimulateKspaceAcquisition = ReadVal(v1,"simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition); m_SignalGen.m_AxonRadius = ReadVal(v1,"axonRadius", m_SignalGen.m_AxonRadius); m_SignalGen.m_Spikes = ReadVal(v1,"artifacts.spikesnum", m_SignalGen.m_Spikes); m_SignalGen.m_SpikeAmplitude = ReadVal(v1,"artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude); m_SignalGen.m_KspaceLineOffset = ReadVal(v1,"artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset); m_SignalGen.m_EddyStrength = ReadVal(v1,"artifacts.eddyStrength", m_SignalGen.m_EddyStrength); m_SignalGen.m_Tau = ReadVal(v1,"artifacts.eddyTau", m_SignalGen.m_Tau); m_SignalGen.m_CroppingFactor = ReadVal(v1,"artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor); m_SignalGen.m_DoAddGibbsRinging = ReadVal(v1,"artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging); m_SignalGen.m_DoSimulateRelaxation = ReadVal(v1,"doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation); m_SignalGen.m_DoDisablePartialVolume = ReadVal(v1,"doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume); m_SignalGen.m_DoAddMotion = ReadVal(v1,"artifacts.doAddMotion", m_SignalGen.m_DoAddMotion); m_SignalGen.m_DoRandomizeMotion = ReadVal(v1,"artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion); m_SignalGen.m_Translation[0] = ReadVal(v1,"artifacts.translation0", m_SignalGen.m_Translation[0]); m_SignalGen.m_Translation[1] = ReadVal(v1,"artifacts.translation1", m_SignalGen.m_Translation[1]); m_SignalGen.m_Translation[2] = ReadVal(v1,"artifacts.translation2", m_SignalGen.m_Translation[2]); m_SignalGen.m_Rotation[0] = ReadVal(v1,"artifacts.rotation0", m_SignalGen.m_Rotation[0]); m_SignalGen.m_Rotation[1] = ReadVal(v1,"artifacts.rotation1", m_SignalGen.m_Rotation[1]); m_SignalGen.m_Rotation[2] = ReadVal(v1,"artifacts.rotation2", m_SignalGen.m_Rotation[2]); // m_SignalGen.SetNumWeightedVolumes(ReadVal(v1,"numgradients", m_SignalGen.GetNumWeightedVolumes())); SignalGenerationParameters::GradientListType gradients; BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("gradients") ) { SignalGenerationParameters::GradientType g; g[0] = ReadVal(v2,"x",0); g[1] = ReadVal(v2,"y",0); g[2] = ReadVal(v2,"z",0); gradients.push_back(g); } m_SignalGen.SetGradienDirections(gradients); m_Misc.m_MotionVolumesBox = ReadVal(v1,"artifacts.motionvolumes", m_Misc.m_MotionVolumesBox); m_SignalGen.m_MotionVolumes.clear(); + if ( m_Misc.m_MotionVolumesBox == "random" ) { for ( size_t i=0; i < m_SignalGen.GetNumVolumes(); ++i ) { m_SignalGen.m_MotionVolumes.push_back( bool( rand()%2 ) ); } + MITK_DEBUG << "mitkFiberfoxParameters.cpp: Case m_Misc.m_MotionVolumesBox == \"random\"."; } else if ( ! m_Misc.m_MotionVolumesBox.empty() ) { stringstream stream( m_Misc.m_MotionVolumesBox ); std::vector numbers; int nummer = std::numeric_limits::max(); while( stream >> nummer ) { - numbers.push_back( nummer ); + if( nummer < std::numeric_limits::max() ) + { + numbers.push_back( nummer ); + } } // 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 ) + && *(std::max_element( numbers.begin(), numbers.end() )) <= 0 ) // cave: -0 == +0 { for ( size_t i=0; i= 0 ) { - m_SignalGen.m_MotionVolumes.at( *iter ) = false; + m_SignalGen.m_MotionVolumes.at( -(*iter) ) = false; } } + MITK_DEBUG << "mitkFiberfoxParameters.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= 0 ) { m_SignalGen.m_MotionVolumes.at( *iter ) = true; } } + MITK_DEBUG << "mitkFiberfoxParameters.cpp: Case list of positive numbers."; } else { - MITK_INFO << "mitkFiberfoxParameters.cpp: Inconsistent list of numbers in m_MotionVolumesBox."; + MITK_WARN << "mitkFiberfoxParameters.cpp: Inconsistent list of numbers in m_MotionVolumesBox."; break; } } else { - MITK_INFO << "mitkFiberfoxParameters.cpp: Cannot make sense of string in m_MotionVolumesBox."; + MITK_WARN << "mitkFiberfoxParameters.cpp: Cannot make sense of string in m_MotionVolumesBox."; break; } try { if (ReadVal(v1,"artifacts.noisetype","")=="rice") { m_NoiseModel = std::make_shared< mitk::RicianNoiseModel >(); m_NoiseModel->SetNoiseVariance(ReadVal(v1,"artifacts.noisevariance",m_NoiseModel->GetNoiseVariance())); } } catch(...) { MITK_DEBUG << "mitkFiberfoxParameters.cpp: caught some error while trying m_NoiseModel->SetNoiseVariance()"; // throw; } try { if (ReadVal(v1,"artifacts.noisetype","")=="chisquare") { m_NoiseModel = std::make_shared< mitk::ChiSquareNoiseModel >(); m_NoiseModel->SetNoiseVariance(ReadVal(v1,"artifacts.noisevariance",m_NoiseModel->GetNoiseVariance())); } } catch(...) { MITK_DEBUG << "mitkFiberfoxParameters.cpp: caught some error while trying m_NoiseModel->SetNoiseVariance()"; // throw; } BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("compartments") ) { mitk::DiffusionSignalModel* signalModel = NULL; std::string model = ReadVal(v2,"model","",true); if (model=="stick") { mitk::StickModel* model = new mitk::StickModel(); model->SetDiffusivity(ReadVal(v2,"d",model->GetDiffusivity())); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="tensor") { mitk::TensorModel* model = new mitk::TensorModel(); model->SetDiffusivity1(ReadVal(v2,"d1",model->GetDiffusivity1())); model->SetDiffusivity2(ReadVal(v2,"d2",model->GetDiffusivity2())); model->SetDiffusivity3(ReadVal(v2,"d3",model->GetDiffusivity3())); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="ball") { mitk::BallModel* model = new mitk::BallModel(); model->SetDiffusivity(ReadVal(v2,"d",model->GetDiffusivity())); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="astrosticks") { mitk::AstroStickModel* model = new AstroStickModel(); model->SetDiffusivity(ReadVal(v2,"d",model->GetDiffusivity())); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); model->SetRandomizeSticks(ReadVal(v2,"randomize",model->GetRandomizeSticks())); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="dot") { mitk::DotModel* model = new mitk::DotModel(); model->SetT2(ReadVal(v2,"t2",model->GetT2())); model->SetT1(ReadVal(v2,"t1",model->GetT1())); model->m_CompartmentId = ReadVal(v2,"ID",0,true); if (ReadVal(v2,"type","",true)=="fiber") m_FiberModelList.push_back(model); else if (ReadVal(v2,"type","",true)=="non-fiber") m_NonFiberModelList.push_back(model); signalModel = model; } else if (model=="prototype") { mitk::RawShModel* model = new mitk::RawShModel(); model->SetMaxNumKernels(ReadVal(v2,"maxNumSamples",model->GetMaxNumKernels())); model->SetFaRange(ReadVal(v2,"minFA",model->GetFaRange().first), ReadVal(v2,"maxFA",model->GetFaRange().second)); model->SetAdcRange(ReadVal(v2,"minADC",model->GetAdcRange().first), ReadVal(v2,"maxADC",model->GetAdcRange().second)); model->m_CompartmentId = ReadVal(v2,"ID",0,true); unsigned int numCoeffs = ReadVal(v2,"numCoeffs",0,true); unsigned int numSamples = ReadVal(v2,"numSamples",0,true); for (unsigned int j=0; j coeffs(numCoeffs); for (unsigned int k=0; k(v2,"kernels."+boost::lexical_cast(j)+".coeffs."+boost::lexical_cast(k),0,true); } model->SetShCoefficients( coeffs, ReadVal(v2,"kernels."+boost::lexical_cast(j)+".B0",0,true) ); } if (ReadVal(v2,"type","",true)=="fiber") { m_FiberModelList.push_back(model); } else if (ReadVal(v2,"type","",true)=="non-fiber") { m_NonFiberModelList.push_back(model); } // else ? signalModel = model; } if (signalModel!=NULL) { signalModel->SetGradientList(gradients); try { itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); reader->SetFileName(filename+"_VOLUME"+ReadVal(v2,"ID","")+".nrrd"); reader->Update(); signalModel->SetVolumeFractionImage(reader->GetOutput()); MITK_INFO << "Volume fraction image loaded for compartment " << signalModel->m_CompartmentId; } catch(...) { MITK_INFO << "No volume fraction image found for compartment " << signalModel->m_CompartmentId; } } } } else { } } - try{ + try + { itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); 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."; } - try{ + try + { itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); reader->SetFileName(filename+"_MASK.nrrd"); reader->Update(); m_SignalGen.m_MaskImage = reader->GetOutput(); MITK_INFO << "Mask image loaded."; } catch(...) { MITK_INFO << "No mask image found."; } setlocale(LC_ALL, currLocale.c_str()); } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::PrintSelf() { MITK_INFO << "Not implemented :("; } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h index 16fd4df87b..72f871ed88 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h @@ -1,350 +1,353 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef _MITK_FiberfoxParameters_H #define _MITK_FiberfoxParameters_H #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include using namespace std; -namespace mitk { +namespace mitk +{ /** Signal generation */ class SignalGenerationParameters { public: typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; typedef itk::Vector GradientType; typedef std::vector GradientListType; enum CoilSensitivityProfile : int { COIL_CONSTANT, COIL_LINEAR, COIL_EXPONENTIAL }; - enum AcquisitionType : int { + enum AcquisitionType : int + { SingleShotEpi, SpinEcho }; SignalGenerationParameters() : m_AcquisitionType(SignalGenerationParameters::SingleShotEpi) , m_SignalScale(100) , m_tEcho(100) , m_tRep(4000) , m_tLine(1) , m_tInhom(50) , m_ReversePhase(false) , m_PartialFourier(1.0) , m_NoiseVariance(0.001) , m_NumberOfCoils(1) , m_CoilSensitivityProfile(SignalGenerationParameters::COIL_CONSTANT) , m_Bvalue(1000) , m_SimulateKspaceAcquisition(false) , m_AxonRadius(0) , m_DoDisablePartialVolume(false) , m_Spikes(0) , m_SpikeAmplitude(1) , m_KspaceLineOffset(0) , m_EddyStrength(300) , m_Tau(70) , m_CroppingFactor(1) , m_DoAddGibbsRinging(false) , m_DoSimulateRelaxation(true) , m_DoAddMotion(false) , m_DoRandomizeMotion(true) , m_FrequencyMap(NULL) , m_MaskImage(NULL) { m_ImageRegion.SetSize(0, 12); m_ImageRegion.SetSize(1, 12); m_ImageRegion.SetSize(2, 3); m_ImageSpacing.Fill(2.0); m_ImageOrigin.Fill(0.0); m_ImageDirection.SetIdentity(); m_Translation.Fill(0.0); m_Rotation.Fill(0.0); SetNumWeightedVolumes(6); } /** input/output image specifications */ itk::ImageRegion<3> m_CroppedRegion; ///< Image size with reduced FOV. itk::ImageRegion<3> m_ImageRegion; ///< Image size. itk::Vector m_ImageSpacing; ///< Image voxel size. itk::Point m_ImageOrigin; ///< Image origin. itk::Matrix m_ImageDirection; ///< Image rotation matrix. /** Other acquisitions parameters */ AcquisitionType m_AcquisitionType; ///< determines k-space trajectory and maximum echo position(s) double m_SignalScale; ///< Scaling factor for output signal (before noise is added). double m_tEcho; ///< Echo time TE. double m_tRep; ///< Echo time TR. double m_tLine; ///< k-space line readout time (dwell time). double m_tInhom; ///< T2' bool m_ReversePhase; ///< If true, the phase readout direction will be inverted (-y instead of y) double m_PartialFourier; ///< Partial fourier factor (0.5-1) double m_NoiseVariance; ///< Variance of complex gaussian noise int m_NumberOfCoils; ///< Number of coils in multi-coil acquisition CoilSensitivityProfile m_CoilSensitivityProfile; ///< Choose between constant, linear or exponential sensitivity profile of the used coils double m_Bvalue; ///< Acquisition b-value bool m_SimulateKspaceAcquisition;///< Flag to enable/disable k-space acquisition simulation double m_AxonRadius; ///< Determines compartment volume fractions (0 == automatic axon radius estimation) bool m_DoDisablePartialVolume; ///< Disable partial volume effects. Each voxel is either all fiber or all non-fiber. /** Artifacts and other effects */ unsigned int m_Spikes; ///< Number of spikes randomly appearing in the image double m_SpikeAmplitude; ///< amplitude of spikes relative to the largest signal intensity (magnitude of complex) double m_KspaceLineOffset; ///< Causes N/2 ghosts. Larger offset means stronger ghost. double m_EddyStrength; ///< Strength of eddy current induced gradients in mT/m. double m_Tau; ///< Eddy current decay constant (in ms) double m_CroppingFactor; ///< FOV size in y-direction is multiplied by this factor. Causes aliasing artifacts. bool m_DoAddGibbsRinging; ///< Add Gibbs ringing artifact bool m_DoSimulateRelaxation; ///< Add T2 relaxation effects bool m_DoAddMotion; ///< Enable motion artifacts. bool m_DoRandomizeMotion; ///< Toggles between random and linear motion. std::vector< bool > m_MotionVolumes; ///< Indicates the image volumes that are affected by motion ///< with positive numbers, inverted logic with negative numbers. itk::Vector m_Translation; ///< Maximum translational motion. itk::Vector m_Rotation; ///< Maximum rotational motion. ItkDoubleImgType::Pointer m_FrequencyMap; ///< If != NULL, distortions are added to the image using this frequency map. ItkUcharImgType::Pointer m_MaskImage; ///< Signal is only genrated inside of the mask image. inline void GenerateGradientHalfShell(); ///< Generates half shell of gradient directions (with m_NumGradients non-zero directions) inline std::vector< int > GetBaselineIndices(); ///< Returns list of nun-diffusion-weighted image volume indices inline unsigned int GetFirstBaselineIndex(); ///< Returns index of first non-diffusion-weighted image volume inline bool IsBaselineIndex(unsigned int idx); ///< Checks if image volume with given index is non-diffusion-weighted volume or not. inline unsigned int GetNumWeightedVolumes(); ///< Get number of diffusion-weighted image volumes inline unsigned int GetNumBaselineVolumes(); ///< Get number of non-diffusion-weighted image volumes inline unsigned int GetNumVolumes(); ///< Get number of baseline and diffusion-weighted image volumes inline GradientListType GetGradientDirections(); ///< Return gradient direction container inline GradientType GetGradientDirection(unsigned int i); inline void SetNumWeightedVolumes(int numGradients); ///< Automaticall calls GenerateGradientHalfShell() afterwards. inline void SetGradienDirections(GradientListType gradientList); inline void SetGradienDirections(mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientList); protected: unsigned int m_NumGradients; ///< Number of diffusion-weighted image volumes. unsigned int m_NumBaseline; ///< Number of non-diffusion-weighted image volumes. GradientListType m_GradientDirections; ///< Total number of image volumes. }; /** Fiber generation */ class FiberGenerationParameters { public: - enum FiberDistribution{ + enum FiberDistribution + { DISTRIBUTE_UNIFORM, // distribute fibers uniformly in the ROIs DISTRIBUTE_GAUSSIAN // distribute fibers using a 2D gaussian }; typedef vector< vector< mitk::PlanarEllipse::Pointer > > FiducialListType; typedef vector< vector< unsigned int > > FlipListType; FiberGenerationParameters() : m_Distribution(DISTRIBUTE_UNIFORM) , m_Density(100) , m_Variance(100) , m_Sampling(1) , m_Tension(0) , m_Continuity(0) , m_Bias(0) { m_Rotation.Fill(0.0); m_Translation.Fill(0.0); m_Scale.Fill(1.0); } FiberDistribution m_Distribution; unsigned int m_Density; double m_Variance; double m_Sampling; double m_Tension; double m_Continuity; double m_Bias; mitk::Vector3D m_Rotation; mitk::Vector3D m_Translation; mitk::Vector3D m_Scale; FlipListType m_FlipList; ///< contains flags indicating a flip of the 2D fiber x-coordinates (needed to resolve some unwanted fiber twisting) FiducialListType m_Fiducials; ///< container of the planar ellipses used as fiducials for the fiber generation process }; /** GUI persistence, input, output, ... */ class MiscFiberfoxParameters { public: MiscFiberfoxParameters() : m_ResultNode(DataNode::New()) , m_ParentNode(NULL) , m_SignalModelString("") , m_ArtifactModelString("") , m_OutputPath("/tmp/") , m_OutputPrefix("fiberfox") , m_CheckOutputVolumeFractionsBox(false) , m_CheckAdvancedSignalOptionsBox(false) , m_CheckAddNoiseBox(false) , m_CheckAddGhostsBox(false) , m_CheckAddAliasingBox(false) , m_CheckAddSpikesBox(false) , m_CheckAddEddyCurrentsBox(false) , m_CheckAddDistortionsBox(false) , m_MotionVolumesBox("random") , m_CheckRealTimeFibersBox(true) , m_CheckAdvancedFiberOptionsBox(false) , m_CheckConstantRadiusBox(false) , m_CheckIncludeFiducialsBox(true) {} DataNode::Pointer m_ResultNode; ///< Stores resulting image. DataNode::Pointer m_ParentNode; ///< Parent node of result node. string m_SignalModelString; ///< Appendet to the name of the result node string m_ArtifactModelString; ///< Appendet to the name of the result node string m_OutputPath; ///< Image is automatically saved to the specified folder after simulation is finished. string m_OutputPrefix; /** Prefix for filename of output files and logfile. */ string m_AfterSimulationMessage; ///< Store messages that are displayed after the simulation has finished (e.g. warnings, automatic parameter adjustments etc.) /** member variables that store the check-state of GUI checkboxes */ // image generation bool m_CheckOutputVolumeFractionsBox; bool m_CheckAdvancedSignalOptionsBox; bool m_CheckAddNoiseBox; bool m_CheckAddGhostsBox; bool m_CheckAddAliasingBox; bool m_CheckAddSpikesBox; bool m_CheckAddEddyCurrentsBox; bool m_CheckAddDistortionsBox; string m_MotionVolumesBox; // fiber generation bool m_CheckRealTimeFibersBox; bool m_CheckAdvancedFiberOptionsBox; bool m_CheckConstantRadiusBox; bool m_CheckIncludeFiducialsBox; }; /** * \brief Datastructure to manage the Fiberfox signal generation parameters. * */ template< class ScalarType = double > class FiberfoxParameters { public: typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; typedef DiffusionSignalModel DiffusionModelType; typedef std::vector< DiffusionModelType* > DiffusionModelListType; typedef DiffusionNoiseModel NoiseModelType; FiberfoxParameters(); ~FiberfoxParameters(); /** Get same parameter object with different template parameter */ template< class OutType > FiberfoxParameters< OutType > CopyParameters() { FiberfoxParameters< OutType > out; out.m_FiberGen = m_FiberGen; out.m_SignalGen = m_SignalGen; out.m_Misc = m_Misc; if (m_NoiseModel!=NULL) { if (dynamic_cast*>(m_NoiseModel.get())) out.m_NoiseModel = std::make_shared< mitk::RicianNoiseModel >(); else if (dynamic_cast*>(m_NoiseModel.get())) out.m_NoiseModel = std::make_shared< mitk::ChiSquareNoiseModel >(); out.m_NoiseModel->SetNoiseVariance(m_NoiseModel->GetNoiseVariance()); } for (unsigned int i=0; i* outModel = NULL; mitk::DiffusionSignalModel* signalModel = NULL; if (i*>(signalModel)) outModel = new mitk::StickModel(dynamic_cast*>(signalModel)); else if (dynamic_cast*>(signalModel)) outModel = new mitk::TensorModel(dynamic_cast*>(signalModel)); else if (dynamic_cast*>(signalModel)) outModel = new mitk::RawShModel(dynamic_cast*>(signalModel)); else if (dynamic_cast*>(signalModel)) outModel = new mitk::BallModel(dynamic_cast*>(signalModel)); else if (dynamic_cast*>(signalModel)) outModel = new mitk::AstroStickModel(dynamic_cast*>(signalModel)); else if (dynamic_cast*>(signalModel)) outModel = new mitk::DotModel(dynamic_cast*>(signalModel)); if (i m_NoiseModel; ///< If != NULL, noise is added to the image. void PrintSelf(); ///< Print parameters to stdout. void SaveParameters(string filename); ///< Save image generation parameters to .ffp file. void LoadParameters(string filename); ///< Load image generation parameters from .ffp file. template< class ParameterType > ParameterType ReadVal(boost::property_tree::ptree::value_type const& v, std::string tag, ParameterType defaultValue, bool essential=false); std::string m_MissingTags; }; } #include "mitkFiberfoxParameters.cpp" #endif diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp index 5a1073066a..471d7d5bb1 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,2856 +1,2898 @@ /*=================================================================== 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. ===================================================================*/ //misc #define _USE_MATH_DEFINES #include // 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 #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 #define _USE_MATH_DEFINES #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( NULL ) , 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() ); mitkImage->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( parameters.m_SignalGen.GetGradientDirections() )); mitkImage->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( parameters.m_SignalGen.m_Bvalue )); mitk::DiffusionPropertyHelper propertyHelper( mitkImage ); propertyHelper.InitializeImage(); parameters.m_Misc.m_ResultNode->SetData( mitkImage ); GetDataStorage()->Add(parameters.m_Misc.m_ResultNode, parameters.m_Misc.m_ParentNode); parameters.m_Misc.m_ResultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(m_TractsToDwiFilter->GetLevelWindow()) ); if (m_Controls->m_VolumeFractionsBox->isChecked()) { 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); } 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); } } m_TractsToDwiFilter = NULL; if (parameters.m_Misc.m_AfterSimulationMessage.size()>0) QMessageBox::information( NULL, "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 = NULL; } 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(4500); m_Controls->m_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_AstrosticksWidget2->SetT1(4500); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); m_Controls->m_DotWidget2->SetT1(4500); 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_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_VarianceBox->setVisible(false); m_Controls->m_NoiseFrame->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_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 isQbi = mitk::NodePredicateDataType::New("QBallImage"); mitk::NodePredicateOr::Pointer isDiffusionImage = mitk::NodePredicateOr::New(isDwi, isDti); isDiffusionImage = mitk::NodePredicateOr::New(isDiffusionImage, isQbi); 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(8); 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_GenerateFibersButton, SIGNAL(clicked()), (QObject*) this, SLOT(GenerateFibers())); connect((QObject*) m_Controls->m_CircleButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnDrawROI())); connect((QObject*) m_Controls->m_FlipButton, SIGNAL(clicked()), (QObject*) this, SLOT(OnFlipButton())); connect((QObject*) m_Controls->m_JoinBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(JoinBundles())); connect((QObject*) m_Controls->m_VarianceBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnVarianceChanged(double))); connect((QObject*) m_Controls->m_DistributionBox, SIGNAL(currentIndexChanged(int)), (QObject*) this, SLOT(OnDistributionChanged(int))); connect((QObject*) m_Controls->m_FiberDensityBox, SIGNAL(valueChanged(int)), (QObject*) this, SLOT(OnFiberDensityChanged(int))); connect((QObject*) m_Controls->m_FiberSamplingBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnFiberSamplingChanged(double))); connect((QObject*) m_Controls->m_TensionBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnTensionChanged(double))); connect((QObject*) m_Controls->m_ContinuityBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnContinuityChanged(double))); connect((QObject*) m_Controls->m_BiasBox, SIGNAL(valueChanged(double)), (QObject*) this, SLOT(OnBiasChanged(double))); 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_ConstantRadiusBox, SIGNAL(stateChanged(int)), (QObject*) this, SLOT(OnConstantRadius(int))); connect((QObject*) m_Controls->m_CopyBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(CopyBundles())); connect((QObject*) m_Controls->m_TransformBundlesButton, SIGNAL(clicked()), (QObject*) this, SLOT(ApplyTransform())); connect((QObject*) m_Controls->m_AlignOnGrid, SIGNAL(clicked()), (QObject*) this, SLOT(AlignOnGrid())); 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, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(int))); connect((QObject*) m_Controls->m_AdvancedOptionsBox_2, SIGNAL( stateChanged(int)), (QObject*) this, SLOT(ShowAdvancedOptions(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_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))); } } void QmitkFiberfoxView::OnMaskSelected(int value) { UpdateGui(); } void QmitkFiberfoxView::OnTemplateSelected(int value) { UpdateGui(); } void QmitkFiberfoxView::OnFibSelected(int value) { UpdateGui(); } template< class ScalarType > FiberfoxParameters< ScalarType > QmitkFiberfoxView::UpdateImageParameters(bool all) { FiberfoxParameters< ScalarType > parameters; parameters.m_Misc.m_OutputPath = ""; parameters.m_Misc.m_CheckAdvancedFiberOptionsBox = m_Controls->m_AdvancedOptionsBox->isChecked(); parameters.m_Misc.m_CheckAdvancedSignalOptionsBox = m_Controls->m_AdvancedOptionsBox_2->isChecked(); parameters.m_Misc.m_CheckOutputVolumeFractionsBox = m_Controls->m_VolumeFractionsBox->isChecked(); parameters.m_Misc.m_AfterSimulationMessage = ""; string outputPath = m_Controls->m_SavePathEdit->text().toStdString(); if (outputPath.compare("-")!=0) { parameters.m_Misc.m_OutputPath = outputPath; parameters.m_Misc.m_OutputPath += "/"; } switch(m_Controls->m_DistributionBox->currentIndex()) { case 0: parameters.m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; break; case 1: parameters.m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN; break; default: parameters.m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; } parameters.m_FiberGen.m_Variance = m_Controls->m_VarianceBox->value(); parameters.m_FiberGen.m_Density = m_Controls->m_FiberDensityBox->value(); parameters.m_FiberGen.m_Sampling = m_Controls->m_FiberSamplingBox->value(); parameters.m_FiberGen.m_Tension = m_Controls->m_TensionBox->value(); parameters.m_FiberGen.m_Continuity = m_Controls->m_ContinuityBox->value(); parameters.m_FiberGen.m_Bias = m_Controls->m_BiasBox->value(); parameters.m_FiberGen.m_Rotation[0] = m_Controls->m_XrotBox->value(); parameters.m_FiberGen.m_Rotation[1] = m_Controls->m_YrotBox->value(); parameters.m_FiberGen.m_Rotation[2] = m_Controls->m_ZrotBox->value(); parameters.m_FiberGen.m_Translation[0] = m_Controls->m_XtransBox->value(); parameters.m_FiberGen.m_Translation[1] = m_Controls->m_YtransBox->value(); parameters.m_FiberGen.m_Translation[2] = m_Controls->m_ZtransBox->value(); parameters.m_FiberGen.m_Scale[0] = m_Controls->m_XscaleBox->value(); parameters.m_FiberGen.m_Scale[1] = m_Controls->m_YscaleBox->value(); parameters.m_FiberGen.m_Scale[2] = m_Controls->m_ZscaleBox->value(); if (!all) return parameters; if (m_Controls->m_MaskComboBox->GetSelectedNode().IsNotNull()) { mitk::Image::Pointer mitkMaskImage = dynamic_cast(m_Controls->m_MaskComboBox->GetSelectedNode()->GetData()); mitk::CastToItkImage(mitkMaskImage, parameters.m_SignalGen.m_MaskImage); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(parameters.m_SignalGen.m_MaskImage); duplicator->Update(); 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); 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.m_SignalGen.m_Bvalue = static_cast(dwi->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() )->GetValue(); parameters.m_SignalGen.SetGradienDirections(static_cast( dwi->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() )->GetGradientDirectionsContainer()); } 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); parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); parameters.m_SignalGen.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); parameters.m_SignalGen.m_Bvalue = m_Controls->m_BvalueBox->value(); } else if (parameters.m_SignalGen.m_MaskImage.IsNotNull()) // use geometry of mask image { ItkUcharImgType::Pointer itkImg = parameters.m_SignalGen.m_MaskImage; parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); parameters.m_SignalGen.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); parameters.m_SignalGen.m_Bvalue = m_Controls->m_BvalueBox->value(); } else // use GUI parameters { parameters.m_SignalGen.m_ImageRegion.SetSize(0, m_Controls->m_SizeX->value()); parameters.m_SignalGen.m_ImageRegion.SetSize(1, m_Controls->m_SizeY->value()); parameters.m_SignalGen.m_ImageRegion.SetSize(2, m_Controls->m_SizeZ->value()); parameters.m_SignalGen.m_ImageSpacing[0] = m_Controls->m_SpacingX->value(); parameters.m_SignalGen.m_ImageSpacing[1] = m_Controls->m_SpacingY->value(); parameters.m_SignalGen.m_ImageSpacing[2] = m_Controls->m_SpacingZ->value(); parameters.m_SignalGen.m_ImageOrigin[0] = parameters.m_SignalGen.m_ImageSpacing[0]/2; parameters.m_SignalGen.m_ImageOrigin[1] = parameters.m_SignalGen.m_ImageSpacing[1]/2; parameters.m_SignalGen.m_ImageOrigin[2] = parameters.m_SignalGen.m_ImageSpacing[2]/2; parameters.m_SignalGen.m_ImageDirection.SetIdentity(); parameters.m_SignalGen.SetNumWeightedVolumes(m_Controls->m_NumGradientsBox->value()); parameters.m_SignalGen.m_Bvalue = m_Controls->m_BvalueBox->value(); parameters.m_SignalGen.GenerateGradientHalfShell(); } // signal relaxation parameters.m_SignalGen.m_DoSimulateRelaxation = false; if (m_Controls->m_RelaxationBox->isChecked() && m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNotNull() ) { parameters.m_SignalGen.m_DoSimulateRelaxation = true; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(true)); parameters.m_Misc.m_ArtifactModelString += "_RELAX"; } parameters.m_SignalGen.m_SimulateKspaceAcquisition = parameters.m_SignalGen.m_DoSimulateRelaxation; // N/2 ghosts parameters.m_Misc.m_CheckAddGhostsBox = m_Controls->m_AddGhosts->isChecked(); if (m_Controls->m_AddGhosts->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_Misc.m_ArtifactModelString += "_GHOST"; parameters.m_SignalGen.m_KspaceLineOffset = m_Controls->m_kOffsetBox->value(); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(parameters.m_SignalGen.m_KspaceLineOffset)); } else parameters.m_SignalGen.m_KspaceLineOffset = 0; // Aliasing parameters.m_Misc.m_CheckAddAliasingBox = m_Controls->m_AddAliasing->isChecked(); if (m_Controls->m_AddAliasing->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_Misc.m_ArtifactModelString += "_ALIASING"; parameters.m_SignalGen.m_CroppingFactor = (100-m_Controls->m_WrapBox->value())/100; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value())); } // Spikes parameters.m_Misc.m_CheckAddSpikesBox = m_Controls->m_AddSpikes->isChecked(); if (m_Controls->m_AddSpikes->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_SignalGen.m_Spikes = m_Controls->m_SpikeNumBox->value(); parameters.m_SignalGen.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value(); parameters.m_Misc.m_ArtifactModelString += "_SPIKES"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(parameters.m_SignalGen.m_Spikes)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(parameters.m_SignalGen.m_SpikeAmplitude)); } // gibbs ringing parameters.m_SignalGen.m_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); if (m_Controls->m_AddGibbsRinging->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true)); parameters.m_Misc.m_ArtifactModelString += "_RINGING"; } // add distortions parameters.m_Misc.m_CheckAddDistortionsBox = 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()); ItkDoubleImgType::Pointer itkImg = ItkDoubleImgType::New(); CastToItkImage< ItkDoubleImgType >(img, itkImg); if (m_Controls->m_TemplateComboBox->GetSelectedNode().IsNull()) // use geometry of frequency map { parameters.m_SignalGen.m_ImageRegion = itkImg->GetLargestPossibleRegion(); parameters.m_SignalGen.m_ImageSpacing = itkImg->GetSpacing(); parameters.m_SignalGen.m_ImageOrigin = itkImg->GetOrigin(); parameters.m_SignalGen.m_ImageDirection = itkImg->GetDirection(); } if (parameters.m_SignalGen.m_ImageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && parameters.m_SignalGen.m_ImageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && parameters.m_SignalGen.m_ImageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(itkImg); duplicator->Update(); parameters.m_SignalGen.m_FrequencyMap = duplicator->GetOutput(); parameters.m_Misc.m_ArtifactModelString += "_DISTORTED"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true)); } } parameters.m_SignalGen.m_EddyStrength = 0; parameters.m_Misc.m_CheckAddEddyCurrentsBox = m_Controls->m_AddEddy->isChecked(); if (m_Controls->m_AddEddy->isChecked()) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_SignalGen.m_EddyStrength = m_Controls->m_EddyGradientStrength->value(); parameters.m_Misc.m_ArtifactModelString += "_EDDY"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(parameters.m_SignalGen.m_EddyStrength)); } // Motion parameters.m_SignalGen.m_DoAddMotion = false; parameters.m_SignalGen.m_DoRandomizeMotion = m_Controls->m_RandomMotion->isChecked(); parameters.m_SignalGen.m_Translation[0] = m_Controls->m_MaxTranslationBoxX->value(); parameters.m_SignalGen.m_Translation[1] = m_Controls->m_MaxTranslationBoxY->value(); parameters.m_SignalGen.m_Translation[2] = m_Controls->m_MaxTranslationBoxZ->value(); parameters.m_SignalGen.m_Rotation[0] = m_Controls->m_MaxRotationBoxX->value(); parameters.m_SignalGen.m_Rotation[1] = m_Controls->m_MaxRotationBoxY->value(); parameters.m_SignalGen.m_Rotation[2] = m_Controls->m_MaxRotationBoxZ->value(); parameters.m_SignalGen.m_MotionVolumes.clear(); parameters.m_Misc.m_MotionVolumesBox = m_Controls->m_MotionVolumesBox->text().toStdString(); if ( m_Controls->m_AddMotion->isChecked() && m_Controls->m_FiberBundleComboBox->GetSelectedNode().IsNotNull() ) { parameters.m_SignalGen.m_DoAddMotion = true; parameters.m_Misc.m_ArtifactModelString += "_MOTION"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(parameters.m_SignalGen.m_DoRandomizeMotion)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(parameters.m_SignalGen.m_Translation[0])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(parameters.m_SignalGen.m_Translation[1])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(parameters.m_SignalGen.m_Translation[2])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(parameters.m_SignalGen.m_Rotation[0])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(parameters.m_SignalGen.m_Rotation[1])); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(parameters.m_SignalGen.m_Rotation[2])); - if ( parameters.m_Misc.m_MotionVolumesBox=="random" ) + if ( parameters.m_Misc.m_MotionVolumesBox == "random" ) { - for (int i=0; i numbers; + int nummer = std::numeric_limits::max(); + while( stream >> nummer ) { - parameters.m_SignalGen.m_MotionVolumes.push_back(false); + if( nummer < std::numeric_limits::max() ) + { + numbers.push_back( nummer ); + } } - stringstream stream( parameters.m_Misc.m_MotionVolumesBox ); - int n; - while( stream >> n ) + // 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 { - if ( n < parameters.m_SignalGen.GetNumVolumes() && n >= 0 ) + for ( size_t i=0; i < parameters.m_SignalGen.GetNumVolumes(); ++i ) { - parameters.m_SignalGen.m_MotionVolumes[n] = true; + 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) < parameters.m_SignalGen.GetNumVolumes() && -(*iter) >= 0 ) + { + 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 < parameters.m_SignalGen.GetNumVolumes(); ++i ) + { + 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 < parameters.m_SignalGen.GetNumVolumes() && *iter >= 0 ) + { + 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 { MITK_WARN << "QmitkFiberfoxView.cpp: Unrecognised parameters.m_Misc.m_MotionVolumesBox: " << parameters.m_Misc.m_MotionVolumesBox; parameters.m_Misc.m_MotionVolumesBox = "random"; // set default. for (int i=0; im_AcquisitionTypeBox->currentIndex(); parameters.m_SignalGen.m_CoilSensitivityProfile = (SignalGenerationParameters::CoilSensitivityProfile)m_Controls->m_CoilSensBox->currentIndex(); parameters.m_SignalGen.m_NumberOfCoils = m_Controls->m_NumCoilsBox->value(); parameters.m_SignalGen.m_PartialFourier = m_Controls->m_PartialFourier->value(); parameters.m_SignalGen.m_ReversePhase = m_Controls->m_ReversePhaseBox->isChecked(); parameters.m_SignalGen.m_tLine = m_Controls->m_LineReadoutTimeBox->value(); parameters.m_SignalGen.m_tInhom = m_Controls->m_T2starBox->value(); parameters.m_SignalGen.m_tEcho = m_Controls->m_TEbox->value(); parameters.m_SignalGen.m_tRep = m_Controls->m_TRbox->value(); parameters.m_SignalGen.m_DoDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked(); parameters.m_SignalGen.m_AxonRadius = m_Controls->m_FiberRadius->value(); parameters.m_SignalGen.m_SignalScale = m_Controls->m_SignalScaleBox->value(); double voxelVolume = parameters.m_SignalGen.m_ImageSpacing[0] * parameters.m_SignalGen.m_ImageSpacing[1] * parameters.m_SignalGen.m_ImageSpacing[2]; if ( parameters.m_SignalGen.m_SignalScale*voxelVolume > itk::NumericTraits::max()*0.75 ) { parameters.m_SignalGen.m_SignalScale = itk::NumericTraits::max()*0.75/voxelVolume; m_Controls->m_SignalScaleBox->setValue(parameters.m_SignalGen.m_SignalScale); QMessageBox::information( NULL, "Warning", "Maximum signal exceeding data type limits. Automatically adjusted to " + QString::number(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 parameters.m_Misc.m_CheckAddNoiseBox = m_Controls->m_AddNoise->isChecked(); parameters.m_SignalGen.m_NoiseVariance = 0; if (m_Controls->m_AddNoise->isChecked()) { double noiseVariance = m_Controls->m_NoiseLevel->value(); switch (m_Controls->m_NoiseDistributionBox->currentIndex()) { case 0: { if (noiseVariance>0) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_Misc.m_ArtifactModelString += "_COMPLEX-GAUSSIAN-"; parameters.m_SignalGen.m_NoiseVariance = m_Controls->m_NoiseLevel->value(); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Complex Gaussian")); } break; } case 1: { if (noiseVariance>0) { parameters.m_NoiseModel = std::make_shared< mitk::RicianNoiseModel >(); parameters.m_Misc.m_ArtifactModelString += "_RICIAN-"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); parameters.m_NoiseModel->SetNoiseVariance(noiseVariance); } break; } case 2: { if (noiseVariance>0) { parameters.m_NoiseModel = std::make_shared< mitk::ChiSquareNoiseModel >(); parameters.m_Misc.m_ArtifactModelString += "_CHISQUARED-"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared")); parameters.m_NoiseModel->SetNoiseVariance(noiseVariance); } break; } default: { if (noiseVariance>0) { parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; parameters.m_Misc.m_ArtifactModelString += "_COMPLEX-GAUSSIAN-"; parameters.m_SignalGen.m_NoiseVariance = m_Controls->m_NoiseLevel->value(); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Complex Gaussian")); } break; } } if (noiseVariance>0) { parameters.m_Misc.m_ArtifactModelString += QString::number(noiseVariance).toStdString(); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); } } // signal models { // compartment 1 switch (m_Controls->m_Compartment1Box->currentIndex()) { case 0: { mitk::StickModel* model = new mitk::StickModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); 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; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Stick"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 1: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); 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; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Zeppelin"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); 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; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Tensor"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::RawShModel* model = new mitk::RawShModel(); parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(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; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Prototype"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); 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); 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(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); 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; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Stick"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); 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; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Zeppelin"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::TensorModel* model = new mitk::TensorModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); 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; parameters.m_FiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Tensor"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(model->GetT2()) ); break; } } if (m_Controls->m_Comp2VolumeFraction->GetSelectedNode().IsNotNull() && 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); parameters.m_FiberModelList.back()->SetVolumeFractionImage(comp1VolumeImage); } // compartment 3 switch (m_Controls->m_Compartment3Box->currentIndex()) { case 0: { mitk::BallModel* model = new mitk::BallModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); 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; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Ball"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); break; } case 1: { mitk::AstroStickModel* model = new mitk::AstroStickModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); 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; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Astrosticks"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); 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(parameters.m_SignalGen.GetGradientDirections()); model->SetT2(m_Controls->m_DotWidget1->GetT2()); model->SetT1(m_Controls->m_DotWidget1->GetT1()); model->m_CompartmentId = 3; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Dot"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(model->GetT2()) ); break; } case 3: { mitk::RawShModel* model = new mitk::RawShModel(); parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(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; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Prototype"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); 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); 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(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); 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; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Ball"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); break; } case 2: { mitk::AstroStickModel* model = new mitk::AstroStickModel(); model->SetGradientList(parameters.m_SignalGen.GetGradientDirections()); model->SetBvalue(parameters.m_SignalGen.m_Bvalue); 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; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Astrosticks"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); 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(parameters.m_SignalGen.GetGradientDirections()); model->SetT2(m_Controls->m_DotWidget2->GetT2()); model->SetT1(m_Controls->m_DotWidget2->GetT1()); model->m_CompartmentId = 4; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Dot"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(model->GetT2()) ); break; } case 4: { mitk::RawShModel* model = new mitk::RawShModel(); parameters.m_SignalGen.m_DoSimulateRelaxation = false; model->SetGradientList(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; parameters.m_NonFiberModelList.push_back(model); parameters.m_Misc.m_SignalModelString += "Prototype"; parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Prototype") ); break; } } if (m_Controls->m_Comp4VolumeFraction->GetSelectedNode().IsNotNull() && 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); parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(compVolumeImage); } } parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(parameters.m_SignalGen.m_SignalScale)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(parameters.m_SignalGen.m_AxonRadius)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(parameters.m_SignalGen.m_tInhom)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(parameters.m_SignalGen.m_tLine)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(parameters.m_SignalGen.m_tEcho)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(parameters.m_SignalGen.m_Bvalue)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(parameters.m_SignalGen.m_DoDisablePartialVolume)); parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(parameters.m_SignalGen.m_DoSimulateRelaxation)); parameters.m_Misc.m_ResultNode->AddProperty("binary", BoolProperty::New(false)); parameters.m_Misc.m_CheckRealTimeFibersBox = m_Controls->m_RealTimeFibers->isChecked(); parameters.m_Misc.m_CheckAdvancedFiberOptionsBox = m_Controls->m_AdvancedOptionsBox->isChecked(); parameters.m_Misc.m_CheckIncludeFiducialsBox = m_Controls->m_IncludeFiducials->isChecked(); parameters.m_Misc.m_CheckConstantRadiusBox = m_Controls->m_ConstantRadiusBox->isChecked(); return parameters; } void QmitkFiberfoxView::SaveParameters(QString filename) { FiberfoxParameters<> ffParamaters = UpdateImageParameters(); bool ok = true; bool first = true; bool dosampling = false; mitk::Image::Pointer diffImg = NULL; itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = NULL; const int shOrder = 2; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; QballFilterType::CoefficientImageType::Pointer itkFeatureImage = NULL; ItkDoubleImgType::Pointer adcImage = NULL; for (unsigned int i=0; i* model = nullptr; if (i* >(ffParamaters.m_FiberModelList.at(i)); } else { model = dynamic_cast< mitk::RawShModel<>* >(ffParamaters.m_NonFiberModelList.at(i-ffParamaters.m_FiberModelList.size())); } if ( model!=nullptr && model->GetNumberOfKernels() <= 0 ) { if (first==true) { if ( QMessageBox::question(NULL, "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(NULL, "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->SetGradientImage( static_cast ( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(), itkVectorImagePointer ); filter->SetBValue( static_cast ( diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str() ).GetPointer() ) ->GetValue() ); filter->Update(); tensorImage = filter->GetOutput(); QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetGradientImage( static_cast ( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(), itkVectorImagePointer ); qballfilter->SetBValue( static_cast ( diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); 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( static_cast ( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); adcFilter->SetB_value( static_cast (diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); 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->SetGradientImage( static_cast ( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(), itkVectorImagePointer ); filter->SetBValue( static_cast (diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); filter->Update(); tensorImage = filter->GetOutput(); QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetGradientImage( static_cast ( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(), itkVectorImagePointer ); qballfilter->SetBValue( static_cast (diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); 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( static_cast ( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); adcFilter->SetB_value( static_cast (diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); adcFilter->Update(); adcImage = adcFilter->GetOutput(); if (dosampling && diffImg.IsNotNull()) { ok = model->SampleKernels(diffImg, ffParamaters.m_SignalGen.m_MaskImage, tensorImage, itkFeatureImage, adcImage); if (!ok) { QMessageBox::information( NULL, "Parameter file not saved", "No valid prototype signals could be sampled."); return; } } } } ffParamaters.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; FiberfoxParameters<> parameters = UpdateImageParameters(); parameters.LoadParameters(filename.toStdString()); if (parameters.m_MissingTags.size()>0) { QString missing("Parameter file might be corrupted. The following parameters could not be read: "); missing += QString(parameters.m_MissingTags.c_str()); missing += "\nDefault values have been assigned to the missing parameters."; QMessageBox::information( NULL, "Warning!", missing); } m_Controls->m_RealTimeFibers->setChecked(parameters.m_Misc.m_CheckRealTimeFibersBox); m_Controls->m_AdvancedOptionsBox->setChecked(parameters.m_Misc.m_CheckAdvancedFiberOptionsBox); m_Controls->m_IncludeFiducials->setChecked(parameters.m_Misc.m_CheckIncludeFiducialsBox); m_Controls->m_ConstantRadiusBox->setChecked(parameters.m_Misc.m_CheckConstantRadiusBox); m_Controls->m_DistributionBox->setCurrentIndex(parameters.m_FiberGen.m_Distribution); m_Controls->m_VarianceBox->setValue(parameters.m_FiberGen.m_Variance); m_Controls->m_FiberDensityBox->setValue(parameters.m_FiberGen.m_Density); m_Controls->m_FiberSamplingBox->setValue(parameters.m_FiberGen.m_Sampling); m_Controls->m_TensionBox->setValue(parameters.m_FiberGen.m_Tension); m_Controls->m_ContinuityBox->setValue(parameters.m_FiberGen.m_Continuity); m_Controls->m_BiasBox->setValue(parameters.m_FiberGen.m_Bias); m_Controls->m_XrotBox->setValue(parameters.m_FiberGen.m_Rotation[0]); m_Controls->m_YrotBox->setValue(parameters.m_FiberGen.m_Rotation[1]); m_Controls->m_ZrotBox->setValue(parameters.m_FiberGen.m_Rotation[2]); m_Controls->m_XtransBox->setValue(parameters.m_FiberGen.m_Translation[0]); m_Controls->m_YtransBox->setValue(parameters.m_FiberGen.m_Translation[1]); m_Controls->m_ZtransBox->setValue(parameters.m_FiberGen.m_Translation[2]); m_Controls->m_XscaleBox->setValue(parameters.m_FiberGen.m_Scale[0]); m_Controls->m_YscaleBox->setValue(parameters.m_FiberGen.m_Scale[1]); m_Controls->m_ZscaleBox->setValue(parameters.m_FiberGen.m_Scale[2]); // image generation parameters m_Controls->m_SizeX->setValue(parameters.m_SignalGen.m_ImageRegion.GetSize(0)); m_Controls->m_SizeY->setValue(parameters.m_SignalGen.m_ImageRegion.GetSize(1)); m_Controls->m_SizeZ->setValue(parameters.m_SignalGen.m_ImageRegion.GetSize(2)); m_Controls->m_SpacingX->setValue(parameters.m_SignalGen.m_ImageSpacing[0]); m_Controls->m_SpacingY->setValue(parameters.m_SignalGen.m_ImageSpacing[1]); m_Controls->m_SpacingZ->setValue(parameters.m_SignalGen.m_ImageSpacing[2]); m_Controls->m_NumGradientsBox->setValue(parameters.m_SignalGen.GetNumWeightedVolumes()); m_Controls->m_BvalueBox->setValue(parameters.m_SignalGen.m_Bvalue); m_Controls->m_SignalScaleBox->setValue(parameters.m_SignalGen.m_SignalScale); m_Controls->m_TEbox->setValue(parameters.m_SignalGen.m_tEcho); m_Controls->m_LineReadoutTimeBox->setValue(parameters.m_SignalGen.m_tLine); m_Controls->m_T2starBox->setValue(parameters.m_SignalGen.m_tInhom); m_Controls->m_FiberRadius->setValue(parameters.m_SignalGen.m_AxonRadius); m_Controls->m_RelaxationBox->setChecked(parameters.m_SignalGen.m_DoSimulateRelaxation); m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(parameters.m_SignalGen.m_DoDisablePartialVolume); m_Controls->m_ReversePhaseBox->setChecked(parameters.m_SignalGen.m_ReversePhase); m_Controls->m_PartialFourier->setValue(parameters.m_SignalGen.m_PartialFourier); m_Controls->m_TRbox->setValue(parameters.m_SignalGen.m_tRep); m_Controls->m_NumCoilsBox->setValue(parameters.m_SignalGen.m_NumberOfCoils); m_Controls->m_CoilSensBox->setCurrentIndex(parameters.m_SignalGen.m_CoilSensitivityProfile); m_Controls->m_AcquisitionTypeBox->setCurrentIndex(parameters.m_SignalGen.m_AcquisitionType); if (parameters.m_NoiseModel!=NULL) { m_Controls->m_AddNoise->setChecked(parameters.m_Misc.m_CheckAddNoiseBox); if (dynamic_cast*>(parameters.m_NoiseModel.get())) { m_Controls->m_NoiseDistributionBox->setCurrentIndex(0); } else if (dynamic_cast*>(parameters.m_NoiseModel.get())) { m_Controls->m_NoiseDistributionBox->setCurrentIndex(1); } m_Controls->m_NoiseLevel->setValue(parameters.m_NoiseModel->GetNoiseVariance()); } else { m_Controls->m_AddNoise->setChecked(parameters.m_Misc.m_CheckAddNoiseBox); m_Controls->m_NoiseLevel->setValue(parameters.m_SignalGen.m_NoiseVariance); } m_Controls->m_VolumeFractionsBox->setChecked(parameters.m_Misc.m_CheckOutputVolumeFractionsBox); m_Controls->m_AdvancedOptionsBox_2->setChecked(parameters.m_Misc.m_CheckAdvancedSignalOptionsBox); m_Controls->m_AddGhosts->setChecked(parameters.m_Misc.m_CheckAddGhostsBox); m_Controls->m_AddAliasing->setChecked(parameters.m_Misc.m_CheckAddAliasingBox); m_Controls->m_AddDistortions->setChecked(parameters.m_Misc.m_CheckAddDistortionsBox); m_Controls->m_AddSpikes->setChecked(parameters.m_Misc.m_CheckAddSpikesBox); m_Controls->m_AddEddy->setChecked(parameters.m_Misc.m_CheckAddEddyCurrentsBox); m_Controls->m_kOffsetBox->setValue(parameters.m_SignalGen.m_KspaceLineOffset); m_Controls->m_WrapBox->setValue(100*(1-parameters.m_SignalGen.m_CroppingFactor)); m_Controls->m_SpikeNumBox->setValue(parameters.m_SignalGen.m_Spikes); m_Controls->m_SpikeScaleBox->setValue(parameters.m_SignalGen.m_SpikeAmplitude); m_Controls->m_EddyGradientStrength->setValue(parameters.m_SignalGen.m_EddyStrength); m_Controls->m_AddGibbsRinging->setChecked(parameters.m_SignalGen.m_DoAddGibbsRinging); m_Controls->m_AddMotion->setChecked(parameters.m_SignalGen.m_DoAddMotion); m_Controls->m_RandomMotion->setChecked(parameters.m_SignalGen.m_DoRandomizeMotion); m_Controls->m_MotionVolumesBox->setText(QString(parameters.m_Misc.m_MotionVolumesBox.c_str())); m_Controls->m_MaxTranslationBoxX->setValue(parameters.m_SignalGen.m_Translation[0]); m_Controls->m_MaxTranslationBoxY->setValue(parameters.m_SignalGen.m_Translation[1]); m_Controls->m_MaxTranslationBoxZ->setValue(parameters.m_SignalGen.m_Translation[2]); m_Controls->m_MaxRotationBoxX->setValue(parameters.m_SignalGen.m_Rotation[0]); m_Controls->m_MaxRotationBoxY->setValue(parameters.m_SignalGen.m_Rotation[1]); m_Controls->m_MaxRotationBoxZ->setValue(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 = NULL; 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 ( parameters.m_SignalGen.m_MaskImage ) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(parameters.m_SignalGen.m_MaskImage.GetPointer()); image->SetVolume(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 ( parameters.m_SignalGen.m_FrequencyMap ) { mitk::Image::Pointer image = mitk::Image::New(); image->InitializeByItk(parameters.m_SignalGen.m_FrequencyMap.GetPointer()); image->SetVolume(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_AdvancedFiberOptionsFrame->setVisible(true); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(true); m_Controls->m_AdvancedOptionsBox->setChecked(true); m_Controls->m_AdvancedOptionsBox_2->setChecked(true); } else { m_Controls->m_AdvancedFiberOptionsFrame->setVisible(false); m_Controls->m_AdvancedSignalOptionsFrame->setVisible(false); m_Controls->m_AdvancedOptionsBox->setChecked(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::OnConstantRadius(int value) { if (value>0 && m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnAddMotion(int value) { if (value>0) m_Controls->m_MotionArtifactFrame->setVisible(true); else m_Controls->m_MotionArtifactFrame->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::OnDistributionChanged(int value) { if (value==1) m_Controls->m_VarianceBox->setVisible(true); else m_Controls->m_VarianceBox->setVisible(false); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnVarianceChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberDensityChanged(int) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFiberSamplingChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnTensionChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnContinuityChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnBiasChanged(double) { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::AlignOnGrid() { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::DataStorage::SetOfObjects::ConstPointer parentFibs = GetDataStorage()->GetSources(m_SelectedFiducials.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = parentFibs->begin(); it != parentFibs->end(); ++it ) { mitk::DataNode::Pointer pFibNode = *it; if ( pFibNode.IsNotNull() && dynamic_cast(pFibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(pFibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(pImgNode->GetData()); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); break; } } break; } } } for(unsigned int i=0; iGetSources(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it = sources->begin(); it != sources->end(); ++it ) { mitk::DataNode::Pointer imgNode = *it; if ( imgNode.IsNotNull() && dynamic_cast(imgNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::Image::Pointer img = dynamic_cast(imgNode->GetData()); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } break; } } } for(unsigned int i=0; i(m_SelectedImages.at(i)->GetData()); mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) { mitk::DataStorage::SetOfObjects::ConstPointer derivations2 = GetDataStorage()->GetDerivations(fibNode); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations2->begin(); it2 != derivations2->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData()); mitk::Point3D wc0 = pe->GetWorldControlPoint(0); mitk::BaseGeometry::Pointer geom = img->GetGeometry(); itk::Index<3> idx; geom->WorldToIndex(wc0, idx); mitk::Point3D cIdx; cIdx[0]=idx[0]; cIdx[1]=idx[1]; cIdx[2]=idx[2]; mitk::Point3D world; geom->IndexToWorld(cIdx,world); mitk::Vector3D trans = world - wc0; pe->GetGeometry()->Translate(trans); } } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::OnFlipButton() { if (m_SelectedFiducial.IsNull()) return; std::map::iterator it = m_DataNodeToPlanarFigureData.find(m_SelectedFiducial.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; data.m_Flipped += 1; data.m_Flipped %= 2; } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } 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*M_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::OnAddBundle() { if (m_SelectedImageNode.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImageNode); mitk::FiberBundle::Pointer bundle = mitk::FiberBundle::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( bundle ); QString name = QString("Bundle_%1").arg(children->size()); node->SetName(name.toStdString()); m_SelectedBundles.push_back(node); UpdateGui(); GetDataStorage()->Add(node, m_SelectedImageNode); } void QmitkFiberfoxView::OnDrawROI() { if (m_SelectedBundles.empty()) OnAddBundle(); if (m_SelectedBundles.empty()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedBundles.at(0)); mitk::PlanarEllipse::Pointer figure = mitk::PlanarEllipse::New(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( figure ); node->SetBoolProperty("planarfigure.3drendering", true); node->SetBoolProperty("planarfigure.3drendering.fill", true); QList nodes = this->GetDataManagerSelection(); for( int i=0; iSetSelected(false); m_SelectedFiducial = node; QString name = QString("Fiducial_%1").arg(children->size()); node->SetName(name.toStdString()); node->SetSelected(true); this->DisableCrosshairNavigation(); mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->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( node ); } UpdateGui(); GetDataStorage()->Add(node, m_SelectedBundles.at(0)); } bool CompareLayer(mitk::DataNode::Pointer i,mitk::DataNode::Pointer j) { int li = -1; i->GetPropertyValue("layer", li); int lj = -1; j->GetPropertyValue("layer", lj); return liGetSources(m_SelectedFiducial); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) if(dynamic_cast((*it)->GetData())) m_SelectedBundles.push_back(*it); if (m_SelectedBundles.empty()) return; } FiberfoxParameters parameters = UpdateImageParameters(false); for (unsigned int i=0; iGetDerivations(m_SelectedBundles.at(i)); std::vector< mitk::DataNode::Pointer > childVector; for( mitk::DataStorage::SetOfObjects::const_iterator it = children->begin(); it != children->end(); ++it ) childVector.push_back(*it); sort(childVector.begin(), childVector.end(), CompareLayer); vector< mitk::PlanarEllipse::Pointer > fib; vector< unsigned int > flip; float radius = 1; int count = 0; for( std::vector< mitk::DataNode::Pointer >::const_iterator it = childVector.begin(); it != childVector.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::PlanarEllipse* ellipse = dynamic_cast(node->GetData()); if (m_Controls->m_ConstantRadiusBox->isChecked()) { ellipse->SetTreatAsCircle(true); mitk::Point2D c = ellipse->GetControlPoint(0); mitk::Point2D p = ellipse->GetControlPoint(1); mitk::Vector2D v = p-c; if (count==0) { radius = v.GetVnlVector().magnitude(); ellipse->SetControlPoint(1, p); ellipse->Modified(); } else { v.Normalize(); v *= radius; ellipse->SetControlPoint(1, c+v); ellipse->Modified(); } } fib.push_back(ellipse); std::map::iterator it = m_DataNodeToPlanarFigureData.find(node.GetPointer()); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; flip.push_back(data.m_Flipped); } else flip.push_back(0); } count++; } if (fib.size()>1) { parameters.m_FiberGen.m_Fiducials.push_back(fib); parameters.m_FiberGen.m_FlipList.push_back(flip); } else if (fib.size()>0) m_SelectedBundles.at(i)->SetData( mitk::FiberBundle::New() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); filter->SetParameters(parameters.m_FiberGen); filter->Update(); vector< mitk::FiberBundle::Pointer > fiberBundles = filter->GetFiberBundles(); for (unsigned int i=0; iSetData( fiberBundles.at(i) ); if (fiberBundles.at(i)->GetNumFibers()>50000) m_SelectedBundles.at(i)->SetVisibility(false); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } 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::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( image ); node->SetName("Dummy"); unsigned int window = m_Controls->m_SizeX->value()*m_Controls->m_SizeY->value()*m_Controls->m_SizeZ->value(); unsigned int level = window/2; mitk::LevelWindow lw; lw.SetLevelWindow(level, window); node->SetProperty( "levelwindow", mitk::LevelWindowProperty::New( lw ) ); 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(NULL, "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 tab 'Fiber Definition')."); } 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(NULL, "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::SimulateForExistingDwi(mitk::DataNode* imageNode) { bool isDiffusionImage( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dynamic_cast(imageNode->GetData())) ); if ( !isDiffusionImage ) { return; } FiberfoxParameters parameters = UpdateImageParameters(); mitk::Image::Pointer diffImg = dynamic_cast(imageNode->GetData()); ItkDwiType::Pointer itkVectorImagePointer = ItkDwiType::New(); mitk::CastToItkImage(diffImg, itkVectorImagePointer); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); parameters.m_Misc.m_ParentNode = imageNode; parameters.m_SignalGen.m_SignalScale = 1; parameters.m_Misc.m_ResultNode->SetName(parameters.m_Misc.m_ParentNode->GetName() +"_D"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(0)).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(1)).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(2)).toStdString() +"_S"+QString::number(parameters.m_SignalGen.m_ImageSpacing[0]).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageSpacing[1]).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageSpacing[2]).toStdString() +"_b"+QString::number(parameters.m_SignalGen.m_Bvalue).toStdString() +"_"+parameters.m_Misc.m_SignalModelString +parameters.m_Misc.m_ArtifactModelString); m_TractsToDwiFilter->SetParameters(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; } FiberfoxParameters parameters = UpdateImageParameters(); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); parameters.m_Misc.m_ParentNode = fiberNode; parameters.m_Misc.m_ResultNode->SetName(parameters.m_Misc.m_ParentNode->GetName() +"_D"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(0)).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(1)).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageRegion.GetSize(2)).toStdString() +"_S"+QString::number(parameters.m_SignalGen.m_ImageSpacing[0]).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageSpacing[1]).toStdString() +"-"+QString::number(parameters.m_SignalGen.m_ImageSpacing[2]).toStdString() +"_b"+QString::number(parameters.m_SignalGen.m_Bvalue).toStdString() +"_"+parameters.m_Misc.m_SignalModelString +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 = NULL; const int shOrder = 2; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; QballFilterType::CoefficientImageType::Pointer itkFeatureImage = NULL; ItkDoubleImgType::Pointer adcImage = NULL; for (unsigned int i=0; i* model = NULL; if (i* >(parameters.m_FiberModelList.at(i)); else model = dynamic_cast< mitk::RawShModel<>* >(parameters.m_NonFiberModelList.at(i-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->SetGradientImage( static_cast ( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(), itkVectorImagePointer ); filter->SetBValue( static_cast (diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); filter->Update(); tensorImage = filter->GetOutput(); QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetGradientImage( static_cast ( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer(), itkVectorImagePointer ); qballfilter->SetBValue( static_cast (diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); 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( static_cast ( diffImg->GetProperty(mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str()).GetPointer() ) ->GetGradientDirectionsContainer() ); adcFilter->SetB_value( static_cast (diffImg->GetProperty(mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str()).GetPointer() ) ->GetValue() ); adcFilter->Update(); adcImage = adcFilter->GetOutput(); } ok = model->SampleKernels(diffImg, parameters.m_SignalGen.m_MaskImage, tensorImage, itkFeatureImage, adcImage); if (!ok) break; } } if (!ok) { QMessageBox::information( NULL, "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( NULL, "Simulation cancelled", "Prototype signal but no diffusion-weighted image selected to sample signal from."); return; } m_TractsToDwiFilter->SetParameters(parameters); m_TractsToDwiFilter->SetFiberBundle(fiberBundle); m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::ApplyTransform() { vector< mitk::DataNode::Pointer > selectedBundles; for(unsigned int i=0; iGetDerivations(m_SelectedImages.at(i)); for( mitk::DataStorage::SetOfObjects::const_iterator it = derivations->begin(); it != derivations->end(); ++it ) { mitk::DataNode::Pointer fibNode = *it; if ( fibNode.IsNotNull() && dynamic_cast(fibNode->GetData()) ) selectedBundles.push_back(fibNode); } } if (selectedBundles.empty()) selectedBundles = m_SelectedBundles2; if (!selectedBundles.empty()) { for (std::vector::const_iterator it = selectedBundles.begin(); it!=selectedBundles.end(); ++it) { mitk::FiberBundle::Pointer fib = dynamic_cast((*it)->GetData()); fib->RotateAroundAxis(m_Controls->m_XrotBox->value(), m_Controls->m_YrotBox->value(), m_Controls->m_ZrotBox->value()); fib->TranslateFibers(m_Controls->m_XtransBox->value(), m_Controls->m_YtransBox->value(), m_Controls->m_ZtransBox->value()); fib->ScaleFibers(m_Controls->m_XscaleBox->value(), m_Controls->m_YscaleBox->value(), m_Controls->m_ZscaleBox->value()); // handle child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse* pe = dynamic_cast(fiducialNode->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); // implicit translation mitk::Vector3D trans; trans[0] = geom->GetOrigin()[0]-fib->GetGeometry()->GetCenter()[0]; trans[1] = geom->GetOrigin()[1]-fib->GetGeometry()->GetCenter()[1]; trans[2] = geom->GetOrigin()[2]-fib->GetGeometry()->GetCenter()[2]; mitk::Vector3D newWc = rot*trans; newWc = newWc-trans; geom->Translate(newWc); pe->Modified(); } } } } } else { for (unsigned int i=0; i(m_SelectedFiducials.at(i)->GetData()); mitk::BaseGeometry* geom = pe->GetGeometry(); // translate mitk::Vector3D world; world[0] = m_Controls->m_XtransBox->value(); world[1] = m_Controls->m_YtransBox->value(); world[2] = m_Controls->m_ZtransBox->value(); geom->Translate(world); // calculate rotation matrix double x = m_Controls->m_XrotBox->value()*M_PI/180; double y = m_Controls->m_YrotBox->value()*M_PI/180; double z = m_Controls->m_ZrotBox->value()*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; // transform control point coordinate into geometry translation geom->SetOrigin(pe->GetWorldControlPoint(0)); mitk::Point2D cp; cp.Fill(0.0); pe->SetControlPoint(0, cp); // rotate fiducial geom->GetIndexToWorldTransform()->SetMatrix(rot*geom->GetIndexToWorldTransform()->GetMatrix()); pe->Modified(); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::CopyBundles() { if ( m_SelectedBundles.size()<1 ){ QMessageBox::information( NULL, "Warning", "Select at least one fiber bundle!"); MITK_WARN("QmitkFiberFoxView") << "Select at least one fiber bundle!"; return; } for (std::vector::const_iterator it = m_SelectedBundles.begin(); it!=m_SelectedBundles.end(); ++it) { // find parent image mitk::DataNode::Pointer parentNode; mitk::DataStorage::SetOfObjects::ConstPointer parentImgs = GetDataStorage()->GetSources(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = parentImgs->begin(); it2 != parentImgs->end(); ++it2 ) { mitk::DataNode::Pointer pImgNode = *it2; if ( pImgNode.IsNotNull() && dynamic_cast(pImgNode->GetData()) ) { parentNode = pImgNode; break; } } mitk::FiberBundle::Pointer fib = dynamic_cast((*it)->GetData()); mitk::FiberBundle::Pointer newBundle = fib->GetDeepCopy(); QString name((*it)->GetName().c_str()); name += "_copy"; mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); if (parentNode.IsNotNull()) GetDataStorage()->Add(fbNode, parentNode); else GetDataStorage()->Add(fbNode); // copy child fiducials if (m_Controls->m_IncludeFiducials->isChecked()) { mitk::DataStorage::SetOfObjects::ConstPointer derivations = GetDataStorage()->GetDerivations(*it); for( mitk::DataStorage::SetOfObjects::const_iterator it2 = derivations->begin(); it2 != derivations->end(); ++it2 ) { mitk::DataNode::Pointer fiducialNode = *it2; if ( fiducialNode.IsNotNull() && dynamic_cast(fiducialNode->GetData()) ) { mitk::PlanarEllipse::Pointer pe = dynamic_cast(fiducialNode->GetData())->Clone(); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(pe); newNode->SetName(fiducialNode->GetName()); newNode->SetBoolProperty("planarfigure.3drendering", true); GetDataStorage()->Add(newNode, fbNode); } } } } mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::JoinBundles() { if ( m_SelectedBundles.size()<2 ){ QMessageBox::information( NULL, "Warning", "Select at least two fiber bundles!"); MITK_WARN("QmitkFiberFoxView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); mitk::FiberBundle::Pointer newBundle = dynamic_cast((*it)->GetData()); QString name(""); name += QString((*it)->GetName().c_str()); ++it; for (; it!=m_SelectedBundles.end(); ++it) { newBundle = newBundle->AddBundle(dynamic_cast((*it)->GetData())); name += "+"+QString((*it)->GetName().c_str()); } mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(newBundle); fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberfoxView::UpdateGui() { m_Controls->m_GeometryFrame->setEnabled(true); m_Controls->m_GeometryMessage->setVisible(false); m_Controls->m_DiffusionPropsMessage->setVisible(false); m_Controls->m_FiberGenMessage->setVisible(true); m_Controls->m_TransformBundlesButton->setEnabled(false); m_Controls->m_CopyBundlesButton->setEnabled(false); m_Controls->m_GenerateFibersButton->setEnabled(false); m_Controls->m_FlipButton->setEnabled(false); m_Controls->m_CircleButton->setEnabled(false); m_Controls->m_BvalueBox->setEnabled(true); m_Controls->m_NumGradientsBox->setEnabled(true); m_Controls->m_JoinBundlesButton->setEnabled(false); m_Controls->m_AlignOnGrid->setEnabled(false); // Fiber generation gui if (m_SelectedFiducial.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_FlipButton->setEnabled(true); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_SelectedImageNode.IsNotNull() || !m_SelectedBundles.empty()) { m_Controls->m_CircleButton->setEnabled(true); m_Controls->m_FiberGenMessage->setVisible(false); } if (m_SelectedImageNode.IsNotNull() && !m_SelectedBundles.empty()) m_Controls->m_AlignOnGrid->setEnabled(true); if (!m_SelectedBundles.empty()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_CopyBundlesButton->setEnabled(true); m_Controls->m_GenerateFibersButton->setEnabled(true); if (m_SelectedBundles.size()>1) m_Controls->m_JoinBundlesButton->setEnabled(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_BvalueBox->setEnabled(false); m_Controls->m_NumGradientsBox->setEnabled(false); m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } } void QmitkFiberfoxView::OnSelectionChanged( berry::IWorkbenchPart::Pointer, const QList& nodes ) { m_SelectedBundles2.clear(); m_SelectedImages.clear(); m_SelectedFiducials.clear(); m_SelectedFiducial = NULL; m_SelectedBundles.clear(); m_SelectedImageNode = NULL; // iterate all selected objects, adjust warning visibility for( int i=0; i(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImageNode = node; } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedBundles2.push_back(node); if (m_Controls->m_RealTimeFibers->isChecked()) { m_SelectedBundles.push_back(node); mitk::FiberBundle::Pointer newFib = dynamic_cast(node->GetData()); if (newFib->GetNumFibers()!=m_Controls->m_FiberDensityBox->value()) GenerateFibers(); } else m_SelectedBundles.push_back(node); } else if ( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedFiducials.push_back(node); m_SelectedFiducial = node; m_SelectedBundles.clear(); mitk::DataStorage::SetOfObjects::ConstPointer parents = GetDataStorage()->GetSources(node); for( mitk::DataStorage::SetOfObjects::const_iterator it = parents->begin(); it != parents->end(); ++it ) { mitk::DataNode::Pointer pNode = *it; if ( pNode.IsNotNull() && dynamic_cast(pNode->GetData()) ) m_SelectedBundles.push_back(pNode); } } } UpdateGui(); } void QmitkFiberfoxView::EnableCrosshairNavigation() { if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::DisableCrosshairNavigation() { } void QmitkFiberfoxView::NodeRemoved(const mitk::DataNode* node) { mitk::DataNode* nonConstNode = const_cast(node); std::map::iterator it = m_DataNodeToPlanarFigureData.find(nonConstNode); if (dynamic_cast(node->GetData())) { m_SelectedBundles.clear(); m_SelectedBundles2.clear(); } else if (dynamic_cast(node->GetData())) m_SelectedImages.clear(); if( it != m_DataNodeToPlanarFigureData.end() ) { QmitkPlanarFigureData& data = it->second; // remove observers data.m_Figure->RemoveObserver( data.m_EndPlacementObserverTag ); data.m_Figure->RemoveObserver( data.m_SelectObserverTag ); data.m_Figure->RemoveObserver( data.m_StartInteractionObserverTag ); data.m_Figure->RemoveObserver( data.m_EndInteractionObserverTag ); m_DataNodeToPlanarFigureData.erase( it ); } } void QmitkFiberfoxView::NodeAdded( const mitk::DataNode* node ) { // add observer for selection in renderwindow mitk::PlanarFigure* figure = dynamic_cast(node->GetData()); bool isPositionMarker (false); node->GetBoolProperty("isContourMarker", isPositionMarker); if( figure && !isPositionMarker ) { MITK_DEBUG << "figure added. will add interactor if needed."; mitk::PlanarFigureInteractor::Pointer figureInteractor = dynamic_cast(node->GetDataInteractor().GetPointer()); mitk::DataNode* nonConstNode = const_cast( node ); 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( nonConstNode ); } MITK_DEBUG << "will now add observers for planarfigure"; QmitkPlanarFigureData data; data.m_Figure = figure; // // add observer for event when figure has been placed typedef itk::SimpleMemberCommand< QmitkFiberfoxView > SimpleCommandType; // SimpleCommandType::Pointer initializationCommand = SimpleCommandType::New(); // initializationCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureInitialized ); // data.m_EndPlacementObserverTag = figure->AddObserver( mitk::EndPlacementPlanarFigureEvent(), initializationCommand ); // add observer for event when figure is picked (selected) typedef itk::MemberCommand< QmitkFiberfoxView > MemberCommandType; MemberCommandType::Pointer selectCommand = MemberCommandType::New(); selectCommand->SetCallbackFunction( this, &QmitkFiberfoxView::PlanarFigureSelected ); data.m_SelectObserverTag = figure->AddObserver( mitk::SelectPlanarFigureEvent(), selectCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer startInteractionCommand = SimpleCommandType::New(); startInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::DisableCrosshairNavigation); data.m_StartInteractionObserverTag = figure->AddObserver( mitk::StartInteractionPlanarFigureEvent(), startInteractionCommand ); // add observer for event when interaction with figure starts SimpleCommandType::Pointer endInteractionCommand = SimpleCommandType::New(); endInteractionCommand->SetCallbackFunction( this, &QmitkFiberfoxView::EnableCrosshairNavigation); data.m_EndInteractionObserverTag = figure->AddObserver( mitk::EndInteractionPlanarFigureEvent(), endInteractionCommand ); m_DataNodeToPlanarFigureData[nonConstNode] = data; } } void QmitkFiberfoxView::PlanarFigureSelected( itk::Object* object, const itk::EventObject& ) { mitk::TNodePredicateDataType::Pointer isPf = mitk::TNodePredicateDataType::New(); mitk::DataStorage::SetOfObjects::ConstPointer allPfs = this->GetDataStorage()->GetSubset( isPf ); for ( mitk::DataStorage::SetOfObjects::const_iterator it = allPfs->begin(); it!=allPfs->end(); ++it) { mitk::DataNode* node = *it; if( node->GetData() == object ) { node->SetSelected(true); m_SelectedFiducial = node; } else node->SetSelected(false); } UpdateGui(); this->RequestRenderWindowUpdate(); } void QmitkFiberfoxView::SetFocus() { m_Controls->m_CircleButton->setFocus(); } void QmitkFiberfoxView::SetOutputPath() { // SELECT FOLDER DIALOG string outputPath = QFileDialog::getExistingDirectory(NULL, "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())); } } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui index 02384bac87..80ef2c1f12 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui @@ -1,3453 +1,3453 @@ QmitkFiberfoxViewControls 0 0 524 2652 Form Load Parameters :/QmitkDiffusionImaging/general_icons/upload.ico:/QmitkDiffusionImaging/general_icons/upload.ico 0 Fiber Definition Qt::Vertical 20 40 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 "Signal Generation" tab. Qt::AutoText Qt::AlignJustify|Qt::AlignVCenter true Fiducial Options 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. Align With Grid :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico Operations false Join Bundles :/QmitkDiffusionImaging/general_icons/plus.ico:/QmitkDiffusionImaging/general_icons/plus.ico QFrame::NoFrame QFrame::Raised 0 0 0 0 Y false Rotation angle (in degree) around x-axis. 3 -360.000000000000000 360.000000000000000 0.100000000000000 Axis: false Rotation angle (in degree) around y-axis. 3 -360.000000000000000 360.000000000000000 0.100000000000000 Translation: false Translation (in mm) in direction of the z-axis. 3 -1000.000000000000000 1000.000000000000000 0.100000000000000 Translation (in mm) in direction of the y-axis. 3 -1000.000000000000000 1000.000000000000000 0.100000000000000 X false Rotation: false Z false Rotation angle (in degree) around z-axis. 3 -360.000000000000000 360.000000000000000 0.100000000000000 Translation (in mm) in direction of the x-axis. 3 -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 Copy Bundles :/QmitkDiffusionImaging/general_icons/copy2.ico:/QmitkDiffusionImaging/general_icons/copy2.ico false Transform Selection :/QmitkDiffusionImaging/general_icons/refresh.ico:/QmitkDiffusionImaging/general_icons/refresh.ico If checked, the fiducials belonging to the modified bundle are also modified. Include Fiducials true Fiber Options 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 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 QFrame::NoFrame QFrame::Raised 0 0 0 0 false 30 30 Draw elliptical fiducial. :/QmitkDiffusionImaging/circle.png:/QmitkDiffusionImaging/circle.png 32 32 false true false 30 30 Flip fiber waypoints of selcted fiducial around one axis. :/QmitkDiffusionImaging/refresh.xpm:/QmitkDiffusionImaging/refresh.xpm 32 32 false true Qt::Horizontal 40 20 Signal Generation Extra-axonal Compartments 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 Qt::Vertical 20 40 Image Settings Advanced Options QFrame::NoFrame QFrame::Raised 0 0 0 0 6 Gradient Directions: Number of gradient directions distributed over the half sphere. 0 10000 1 30 <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 color: rgb(255, 0, 0); Using geometry of selected image! color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 0 0 0 6 <html><head/><body><p>Number of Channels:</p></body></html> false TR in milliseconds 1 999999999 1 4000 Output one image per compartment containing the corresponding volume fractions per voxel. Reverse Phase Encoding Direction false Signal Scale: Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. 0 1000 0 Dwell time (time to read one line in k-space) in ms. 100.000000000000000 0.100000000000000 1.000000000000000 TE in milliseconds 1 999999999 1 100 Fiber Radius: Partial Fourier: false Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. Disable Partial Volume Effects false <html><head/><body><p>Coil Sensitivity:</p></body></html> false Partial fourier factor (0.5-1) 3 0.500000000000000 1.000000000000000 0.100000000000000 1.000000000000000 Output phase image and volume fraction maps. Output Additional Images 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 Constant Linear Exponential Dwell Time: false <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 <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 TE in milliseconds 1 10000 1 100 Number of coil elements used for the acquisiton. 1 128 1 1 Acquisition Type: Single Shot EPI Spin Echo 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 Inter-axonal Compartment 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. true Stop current simulation. Abort Simulation :/QmitkDiffusionImaging/general_icons/abort.ico:/QmitkDiffusionImaging/general_icons/abort.ico Data 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 8 true Noise and other Artifacts Add Distortions false Add Spikes false true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 0 0 0 Gradient: false Eddy current induced magnetic field gradient (in mT/m). 4 1000.000000000000000 0.001000000000000 0.010000000000000 Add Motion Artifacts false 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 Noise false 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 0 6 0 0 6 Toggle between random movement and linear movement. Randomize motion true Rotation 0 9 0 0 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 Translation 0 0 0 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. + 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 Add ringing artifacts occuring at strong edges in the image. Add Gibbs Ringing false Qt::Horizontal Qt::Horizontal Qt::Horizontal Qt::Horizontal Add N/2 Ghosts false Add Aliasing false Qt::Horizontal Qt::Horizontal Add Eddy Current Effects false 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 25.000000000000000 true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Frequency Map: false Select image specifying the frequency inhomogeneities (in Hz). 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 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 :/QmitkDiffusionImaging/general_icons/right.ico:/QmitkDiffusionImaging/general_icons/right.ico Intra-axonal Compartment 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. Save Parameters :/QmitkDiffusionImaging/general_icons/download.ico:/QmitkDiffusionImaging/general_icons/download.ico QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.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 QmitkDataStorageComboBoxWithSelectNone QComboBox
QmitkDataStorageComboBoxWithSelectNone.h
 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_AlignOnGrid 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_FiberBundleComboBox m_MaskComboBox m_TemplateComboBox m_SavePathEdit m_OutputPathButton m_GenerateImageButton m_AbortSimulationButton m_SimulationStatusText m_SizeX m_SizeY m_SizeZ m_SpacingX m_SpacingY m_SpacingZ m_NumGradientsBox m_BvalueBox m_AdvancedOptionsBox_2 m_SignalScaleBox m_TEbox m_TRbox 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_AddMotion m_RandomMotion m_MaxRotationBoxX m_MaxRotationBoxY m_MaxRotationBoxZ m_MaxTranslationBoxX m_MaxTranslationBoxY m_MaxTranslationBoxZ m_AddEddy m_EddyGradientStrength m_AddGibbsRinging m_SaveParametersButton m_LoadParametersButton tabWidget