diff --git a/CMakeExternals/MITKData.cmake b/CMakeExternals/MITKData.cmake index ca7fee4d86..5271313f53 100644 --- a/CMakeExternals/MITKData.cmake +++ b/CMakeExternals/MITKData.cmake @@ -1,36 +1,36 @@ #----------------------------------------------------------------------------- # MITK Data #----------------------------------------------------------------------------- # Sanity checks if(DEFINED MITK_DATA_DIR AND NOT EXISTS ${MITK_DATA_DIR}) message(FATAL_ERROR "MITK_DATA_DIR variable is defined but corresponds to non-existing directory") endif() set(proj MITK-Data) set(proj_DEPENDENCIES) set(MITK-Data_DEPENDS ${proj}) if(BUILD_TESTING) - set(revision_tag 81f5a871) + set(revision_tag f5b46a38) # ^^^^^^^^ these are just to check correct length of hash part ExternalProject_Add(${proj} URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/MITK-Data_${revision_tag}.tar.gz UPDATE_COMMAND "" CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" DEPENDS ${proj_DEPENDENCIES} ) set(MITK_DATA_DIR ${ep_source_dir}/${proj}) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif(BUILD_TESTING) diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp index a8c4330d70..7a58a8a5be 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkAddArtifactsToDwiImageFilter.cpp @@ -1,336 +1,336 @@ /*=================================================================== 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 __itkAddArtifactsToDwiImageFilter_txx #define __itkAddArtifactsToDwiImageFilter_txx #include #include #include #include "itkAddArtifactsToDwiImageFilter.h" #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include namespace itk { template< class TPixelType > AddArtifactsToDwiImageFilter< TPixelType > ::AddArtifactsToDwiImageFilter() : m_UseConstantRandSeed(false) { this->SetNumberOfRequiredInputs( 1 ); m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); m_RandGen->SetSeed(); } template< class TPixelType > void AddArtifactsToDwiImageFilter< TPixelType > ::GenerateData() { if (m_UseConstantRandSeed) // always generate the same random numbers? m_RandGen->SetSeed(0); else m_RandGen->SetSeed(); m_StartTime = clock(); m_StatusText = "Starting simulation\n"; typename InputImageType::Pointer inputImage = static_cast< InputImageType* >( this->ProcessObject::GetInput(0) ); itk::ImageRegion<3> inputRegion = inputImage->GetLargestPossibleRegion(); typename itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage( inputImage ); duplicator->Update(); typename InputImageType::Pointer outputImage = duplicator->GetOutput(); // is input slize size even? int xMax=inputRegion.GetSize(0); int yMax=inputRegion.GetSize(1); if ( xMax%2 == 1 ) xMax += 1; if ( yMax%2 == 1 ) yMax += 1; // create slice object typename SliceType::Pointer slice = SliceType::New(); ImageRegion<2> sliceRegion; sliceRegion.SetSize(0, xMax); sliceRegion.SetSize(1, yMax); slice->SetLargestPossibleRegion( sliceRegion ); slice->SetBufferedRegion( sliceRegion ); slice->SetRequestedRegion( sliceRegion ); slice->Allocate(); slice->FillBuffer(0.0); ImageRegion<2> upsampledSliceRegion; - if (m_Parameters.m_DoAddGibbsRinging) + if ( m_Parameters.m_SignalGen.m_DoAddGibbsRinging) { upsampledSliceRegion.SetSize(0, xMax*2); upsampledSliceRegion.SetSize(1, yMax*2); } // frequency map slice typename SliceType::Pointer fMapSlice = NULL; - if (m_Parameters.m_FrequencyMap.IsNotNull()) + if ( m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) { fMapSlice = SliceType::New(); fMapSlice->SetLargestPossibleRegion( sliceRegion ); fMapSlice->SetBufferedRegion( sliceRegion ); fMapSlice->SetRequestedRegion( sliceRegion ); fMapSlice->Allocate(); fMapSlice->FillBuffer(0.0); } - m_Parameters.m_SignalScale = 1; - m_Parameters.m_DoSimulateRelaxation = false; + m_Parameters.m_SignalGen.m_SignalScale = 1; + m_Parameters.m_SignalGen.m_DoSimulateRelaxation = false; - if (m_Parameters.m_Spikes>0 || m_Parameters.m_FrequencyMap.IsNotNull() || m_Parameters.m_KspaceLineOffset>0.0 || m_Parameters.m_DoAddGibbsRinging || m_Parameters.m_EddyStrength>0 || m_Parameters.m_CroppingFactor<1.0) + if ( m_Parameters.m_SignalGen.m_Spikes>0 || m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull() || m_Parameters.m_SignalGen.m_KspaceLineOffset>0.0 || m_Parameters.m_SignalGen.m_DoAddGibbsRinging || m_Parameters.m_SignalGen.m_EddyStrength>0 || m_Parameters.m_SignalGen.m_CroppingFactor<1.0) { - ImageRegion<3> croppedRegion = inputRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Parameters.m_CroppingFactor); + ImageRegion<3> croppedRegion = inputRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)* m_Parameters.m_SignalGen.m_CroppingFactor); itk::Point shiftedOrigin = inputImage->GetOrigin(); shiftedOrigin[1] += (inputRegion.GetSize(1)-croppedRegion.GetSize(1))*inputImage->GetSpacing()[1]/2; outputImage = InputImageType::New(); outputImage->SetSpacing( inputImage->GetSpacing() ); outputImage->SetOrigin( shiftedOrigin ); outputImage->SetDirection( inputImage->GetDirection() ); outputImage->SetLargestPossibleRegion( croppedRegion ); outputImage->SetBufferedRegion( croppedRegion ); outputImage->SetRequestedRegion( croppedRegion ); outputImage->SetVectorLength( inputImage->GetVectorLength() ); outputImage->Allocate(); typename InputImageType::PixelType temp; temp.SetSize(inputImage->GetVectorLength()); temp.Fill(0.0); outputImage->FillBuffer(temp); int tempY=croppedRegion.GetSize(1); tempY += tempY%2; croppedRegion.SetSize(1, tempY); m_StatusText += this->GetTime()+" > Adjusting complex signal\n"; - if (m_Parameters.m_FrequencyMap.IsNotNull()) + if ( m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) m_StatusText += "Simulating distortions\n"; - if (m_Parameters.m_DoAddGibbsRinging) + if ( m_Parameters.m_SignalGen.m_DoAddGibbsRinging) m_StatusText += "Simulating ringing artifacts\n"; - if (m_Parameters.m_EddyStrength>0) + if ( m_Parameters.m_SignalGen.m_EddyStrength>0) m_StatusText += "Simulating eddy currents\n"; - if (m_Parameters.m_Spikes>0) + if ( m_Parameters.m_SignalGen.m_Spikes>0) m_StatusText += "Simulating spikes\n"; - if (m_Parameters.m_CroppingFactor<1.0) + if ( m_Parameters.m_SignalGen.m_CroppingFactor<1.0) m_StatusText += "Simulating aliasing artifacts\n"; - if (m_Parameters.m_KspaceLineOffset>0) + if ( m_Parameters.m_SignalGen.m_KspaceLineOffset>0) m_StatusText += "Simulating ghosts\n"; std::vector< unsigned int > spikeVolume; - for (unsigned int i=0; iGetIntegerVariate()%inputImage->GetVectorLength()); std::sort (spikeVolume.begin(), spikeVolume.end()); std::reverse (spikeVolume.begin(), spikeVolume.end()); - FiberfoxParameters doubleParam = m_Parameters.CopyParameters(); + FiberfoxParameters doubleParam = m_Parameters.CopyParameters(); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; boost::progress_display disp(inputImage->GetVectorLength()*inputRegion.GetSize(2)); for (unsigned int g=0; gGetVectorLength(); g++) { std::vector< unsigned int > spikeSlice; while (!spikeVolume.empty() && spikeVolume.back()==g) { spikeSlice.push_back(m_RandGen->GetIntegerVariate()%inputImage->GetLargestPossibleRegion().GetSize(2)); spikeVolume.pop_back(); } std::sort (spikeSlice.begin(), spikeSlice.end()); std::reverse (spikeSlice.begin(), spikeSlice.end()); for (unsigned int z=0; zGetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } std::vector< SliceType::Pointer > compartmentSlices; // extract slice from channel g for (unsigned int y=0; yGetPixel(index3D)[g]; slice->SetPixel(index2D, pix2D); if (fMapSlice.IsNotNull()) - fMapSlice->SetPixel(index2D, m_Parameters.m_FrequencyMap->GetPixel(index3D)); + fMapSlice->SetPixel(index2D, m_Parameters.m_SignalGen.m_FrequencyMap->GetPixel(index3D)); } - if (m_Parameters.m_DoAddGibbsRinging) + if ( m_Parameters.m_SignalGen.m_DoAddGibbsRinging) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(slice); resampler->SetOutputParametersFromImage(slice); resampler->SetSize(upsampledSliceRegion.GetSize()); resampler->SetOutputSpacing(slice->GetSpacing()/2); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); typename SliceType::Pointer upslice = resampler->GetOutput(); compartmentSlices.push_back(upslice); if (fMapSlice.IsNotNull()) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(fMapSlice); resampler->SetOutputParametersFromImage(fMapSlice); resampler->SetSize(upsampledSliceRegion.GetSize()); resampler->SetOutputSpacing(fMapSlice->GetSpacing()/2); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); fMapSlice = resampler->GetOutput(); } } else compartmentSlices.push_back(slice); // fourier transform slice typename ComplexSliceType::Pointer fSlice; itk::Size<2> outSize; outSize.SetElement(0, xMax); outSize.SetElement(1, croppedRegion.GetSize()[1]); typename itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); idft->SetUseConstantRandSeed(m_UseConstantRandSeed); idft->SetParameters(doubleParam); idft->SetCompartmentImages(compartmentSlices); idft->SetFrequencyMapSlice(fMapSlice); - idft->SetDiffusionGradientDirection(m_Parameters.GetGradientDirection(g)); + idft->SetDiffusionGradientDirection( m_Parameters.m_SignalGen.GetGradientDirection(g)); idft->SetZ((double)z-(double)inputRegion.GetSize(2)/2.0); idft->SetOutSize(outSize); int numSpikes = 0; while (!spikeSlice.empty() && spikeSlice.back()==z) { numSpikes++; spikeSlice.pop_back(); } idft->SetSpikesPerSlice(numSpikes); idft->Update(); fSlice = idft->GetOutput(); // inverse fourier transform slice typename SliceType::Pointer newSlice; typename itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New(); dft->SetInput(fSlice); dft->Update(); newSlice = dft->GetOutput(); // put slice back into channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { typename InputImageType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; typename InputImageType::PixelType pix3D = outputImage->GetPixel(index3D); typename SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; double signal = newSlice->GetPixel(index2D); if (signal>0) signal = floor(signal+0.5); else signal = ceil(signal-0.5); pix3D[g] = signal; outputImage->SetPixel(index3D, pix3D); } ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } } m_StatusText += "\n\n"; } - if (m_Parameters.m_NoiseModel!=NULL) + if ( m_Parameters.m_NoiseModel!=NULL) { m_StatusText += this->GetTime()+" > Adding noise\n"; m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; ImageRegionIterator it1 (outputImage, outputImage->GetLargestPossibleRegion()); boost::progress_display disp(outputImage->GetLargestPossibleRegion().GetNumberOfPixels()); while(!it1.IsAtEnd()) { if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; typename InputImageType::PixelType signal = it1.Get(); m_Parameters.m_NoiseModel->AddNoise(signal); it1.Set(signal); ++it1; } m_StatusText += "\n\n"; } this->SetNthOutput(0, outputImage); m_StatusText += "Finished simulation\n"; m_StatusText += "Simulation time: "+GetTime(); } template< class TPixelType > std::string AddArtifactsToDwiImageFilter< TPixelType >::GetTime() { unsigned long total = (double)(clock() - m_StartTime)/CLOCKS_PER_SEC; unsigned long hours = total/3600; unsigned long minutes = (total%3600)/60; unsigned long seconds = total%60; std::string out = ""; out.append(boost::lexical_cast(hours)); out.append(":"); out.append(boost::lexical_cast(minutes)); out.append(":"); out.append(boost::lexical_cast(seconds)); return out; } } #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.cpp index 924e1a7e17..5935ffc6c2 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.cpp @@ -1,249 +1,241 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "itkFibersFromPlanarFiguresFilter.h" #define _USE_MATH_DEFINES #include // MITK #include #include #include #include #include #include #include #include #include // ITK #include #include #include #include // MISC #include namespace itk{ FibersFromPlanarFiguresFilter::FibersFromPlanarFiguresFilter() - : m_FiberDistribution(DISTRIBUTE_UNIFORM) - , m_Density(1000) - , m_FiberSampling(1) - , m_Tension(0) - , m_Continuity(0) - , m_Bias(0) - , m_Variance(0.1) { } FibersFromPlanarFiguresFilter::~FibersFromPlanarFiguresFilter() { } void FibersFromPlanarFiguresFilter::GeneratePoints() { Statistics::MersenneTwisterRandomVariateGenerator::Pointer randGen = Statistics::MersenneTwisterRandomVariateGenerator::New(); randGen->SetSeed((unsigned int)0); m_2DPoints.clear(); int count = 0; - while (count < m_Density) + while (count < m_Parameters.m_Density) { mitk::Vector2D p; - switch (m_FiberDistribution) { - case DISTRIBUTE_GAUSSIAN: - p[0] = randGen->GetNormalVariate(0, m_Variance); - p[1] = randGen->GetNormalVariate(0, m_Variance); + switch (m_Parameters.m_Distribution) { + case FiberGenerationParameters::DISTRIBUTE_GAUSSIAN: + p[0] = randGen->GetNormalVariate(0, m_Parameters.m_Variance); + p[1] = randGen->GetNormalVariate(0, m_Parameters.m_Variance); break; default: p[0] = randGen->GetUniformVariate(-1, 1); p[1] = randGen->GetUniformVariate(-1, 1); } if (sqrt(p[0]*p[0]+p[1]*p[1]) <= 1) { m_2DPoints.push_back(p); count++; } } } -// perform global tracking void FibersFromPlanarFiguresFilter::GenerateData() { // check if enough fiducials are available - for (unsigned int i=0; i m_VtkCellArray = vtkSmartPointer::New(); vtkSmartPointer m_VtkPoints = vtkSmartPointer::New(); - vector< mitk::PlanarEllipse::Pointer > bundle = m_Fiducials.at(i); + vector< mitk::PlanarEllipse::Pointer > bundle = m_Parameters.m_Fiducials.at(i); vector< unsigned int > fliplist; - if (i container = vtkSmartPointer::New(); mitk::PlanarEllipse::Pointer figure = bundle.at(0); mitk::Point2D p0 = figure->GetControlPoint(0); mitk::Point2D p1 = figure->GetControlPoint(1); mitk::Point2D p2 = figure->GetControlPoint(2); mitk::Point2D p3 = figure->GetControlPoint(3); double r1 = p0.EuclideanDistanceTo(p1); double r2 = p0.EuclideanDistanceTo(p2); mitk::Vector2D eDir = p1-p0; eDir.Normalize(); mitk::Vector2D tDir = p3-p0; tDir.Normalize(); // apply twist vnl_matrix_fixed tRot; tRot[0][0] = tDir[0]; tRot[1][1] = tRot[0][0]; tRot[1][0] = sin(acos(tRot[0][0])); tRot[0][1] = -tRot[1][0]; if (tDir[1]<0) tRot.inplace_transpose(); m_2DPoints[j].SetVnlVector(tRot*m_2DPoints[j].GetVnlVector()); // apply new ellipse shape vnl_vector_fixed< double, 2 > newP; newP[0] = m_2DPoints.at(j)[0]; newP[1] = m_2DPoints.at(j)[1]; double alpha = acos(eDir[0]); if (eDir[1]>0) alpha = 2*M_PI-alpha; vnl_matrix_fixed eRot; eRot[0][0] = cos(alpha); eRot[1][1] = eRot[0][0]; eRot[1][0] = sin(alpha); eRot[0][1] = -eRot[1][0]; newP = eRot*newP; newP[0] *= r1; newP[1] *= r2; newP = eRot.transpose()*newP; p0[0] += newP[0]; p0[1] += newP[1]; const mitk::PlaneGeometry* planeGeo = figure->GetPlaneGeometry(); mitk::Point3D w, wc; planeGeo->Map(p0, w); wc = figure->GetWorldControlPoint(0); vtkIdType id = m_VtkPoints->InsertNextPoint(w.GetDataPointer()); container->GetPointIds()->InsertNextId(id); vnl_vector_fixed< double, 3 > n = planeGeo->GetNormalVnl(); for (unsigned int k=1; kGetControlPoint(0); p1 = figure->GetControlPoint(1); p2 = figure->GetControlPoint(2); p3 = figure->GetControlPoint(3); r1 = p0.EuclideanDistanceTo(p1); r2 = p0.EuclideanDistanceTo(p2); eDir = p1-p0; eDir.Normalize(); mitk::Vector2D tDir2 = p3-p0; tDir2.Normalize(); mitk::Vector2D temp; temp.SetVnlVector(tRot.transpose() * tDir2.GetVnlVector()); // apply twist tRot[0][0] = tDir[0]*tDir2[0] + tDir[1]*tDir2[1]; tRot[1][1] = tRot[0][0]; tRot[1][0] = sin(acos(tRot[0][0])); tRot[0][1] = -tRot[1][0]; if (temp[1]<0) tRot.inplace_transpose(); m_2DPoints[j].SetVnlVector(tRot*m_2DPoints[j].GetVnlVector()); tDir = tDir2; // apply new ellipse shape newP[0] = m_2DPoints.at(j)[0]; newP[1] = m_2DPoints.at(j)[1]; // calculate normal mitk::PlaneGeometry* planeGeo = const_cast(figure->GetPlaneGeometry()); mitk::Vector3D perp = wc-planeGeo->ProjectPointOntoPlane(wc); perp.Normalize(); vnl_vector_fixed< double, 3 > n2 = planeGeo->GetNormalVnl(); wc = figure->GetWorldControlPoint(0); // is flip needed? if (dot_product(perp.GetVnlVector(),n2)>0 && dot_product(n,n2)<=0.00001) newP[0] *= -1; if (fliplist.at(k)>0) newP[0] *= -1; n = n2; alpha = acos(eDir[0]); if (eDir[1]>0) alpha = 2*M_PI-alpha; eRot[0][0] = cos(alpha); eRot[1][1] = eRot[0][0]; eRot[1][0] = sin(alpha); eRot[0][1] = -eRot[1][0]; newP = eRot*newP; newP[0] *= r1; newP[1] *= r2; newP = eRot.transpose()*newP; p0[0] += newP[0]; p0[1] += newP[1]; mitk::Point3D w; planeGeo->Map(p0, w); vtkIdType id = m_VtkPoints->InsertNextPoint(w.GetDataPointer()); container->GetPointIds()->InsertNextId(id); } m_VtkCellArray->InsertNextCell(container); } vtkSmartPointer fiberPolyData = vtkSmartPointer::New(); fiberPolyData->SetPoints(m_VtkPoints); fiberPolyData->SetLines(m_VtkCellArray); mitk::FiberBundleX::Pointer mitkFiberBundle = mitk::FiberBundleX::New(fiberPolyData); - mitkFiberBundle->DoFiberSmoothing(m_FiberSampling, m_Tension, m_Continuity, m_Bias); + mitkFiberBundle->DoFiberSmoothing(m_Parameters.m_Sampling, m_Parameters.m_Tension, m_Parameters.m_Continuity, m_Parameters.m_Bias); m_FiberBundles.push_back(mitkFiberBundle); } } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.h index 8d561d7d0b..f7e9451f76 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkFibersFromPlanarFiguresFilter.h @@ -1,106 +1,87 @@ /*=================================================================== 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 itkFibersFromPlanarFiguresFilter_h #define itkFibersFromPlanarFiguresFilter_h // MITK #include #include +#include // ITK #include // VTK #include #include #include #include #include using namespace std; namespace itk{ /** * \brief Generates artificial fibers distributed in and interpolated between the input planar figures. */ class FibersFromPlanarFiguresFilter : public ProcessObject { public: - enum FiberDistribution{ - DISTRIBUTE_UNIFORM, // distribute fibers uniformly in the ROIs - DISTRIBUTE_GAUSSIAN // distribute fibers using a 2D gaussian - }; - typedef FibersFromPlanarFiguresFilter Self; typedef ProcessObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; - typedef vector< vector< mitk::PlanarEllipse::Pointer > > FiducialListType; - typedef vector< vector< unsigned int > > FlipListType; typedef mitk::FiberBundleX::Pointer FiberType; typedef vector< mitk::FiberBundleX::Pointer > FiberContainerType; itkFactorylessNewMacro(Self) itkCloneMacro(Self) itkTypeMacro( FibersFromPlanarFiguresFilter, ProcessObject ) virtual void Update(){ this->GenerateData(); } // input - void SetFlipList(FlipListType fliplist){ m_FlipList = fliplist; } ///< contains flags indicating a flip of the 2D fiber x-coordinates (needed to resolve some unwanted fiber twisting) - void SetFiducials(FiducialListType fiducials){ m_Fiducials = fiducials; } ///< container of the planar ellipses used as fiducials for the fiber generation process - itkSetMacro(Density, int) ///< number of fibers per bundle - itkSetMacro(FiberSampling, double) ///< sampling points of the fibers per cm - itkSetMacro(Tension, double) ///< tension parameter of the Kochanek-Bartels splines - itkSetMacro(Continuity, double) ///< continuity parameter of the Kochanek-Bartels splines - itkSetMacro(Bias, double) ///< bias parameter of the Kochanek-Bartels splines - itkSetMacro(FiberDistribution, FiberDistribution) ///< flag to switch between uniform and gaussian distribution of the fiber waypoints inside of the fiducials - itkSetMacro(Variance, double) ///< variance of the gaussian waypoint distribution + void SetParameters( FiberGenerationParameters param ) ///< Simulation parameters. + { + m_Parameters = param; + } // output FiberContainerType GetFiberBundles(){ return m_FiberBundles; } protected: void GenerateData(); FibersFromPlanarFiguresFilter(); virtual ~FibersFromPlanarFiguresFilter(); void GeneratePoints(); - FiberDistribution m_FiberDistribution; ///< flag to switch between uniform and gaussian distribution of the fiber waypoints inside of the fiducials - 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 - FiberContainerType m_FiberBundles; ///< container for the output fiber bundles - int m_Density; ///< number of fibers per bundle - double m_FiberSampling; ///< sampling points of the fibers per cm - double m_Tension; ///< tension parameter of the Kochanek-Bartels splines - double m_Continuity; ///< continuity parameter of the Kochanek-Bartels splines - double m_Bias; ///< bias parameter of the Kochanek-Bartels splines - double m_Variance; ///< variance of the gaussian waypoint distribution - vector< mitk::Vector2D > m_2DPoints; ///< container for the 2D fiber waypoints + FiberContainerType m_FiberBundles; ///< container for the output fiber bundles + vector< mitk::Vector2D > m_2DPoints; ///< container for the 2D fiber waypoints + FiberGenerationParameters m_Parameters; }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkFibersFromPlanarFiguresFilter.cpp" #endif #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp index 6888736d7e..77448fc7c4 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkKspaceImageFilter.cpp @@ -1,220 +1,220 @@ /*=================================================================== 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 __itkKspaceImageFilter_txx #define __itkKspaceImageFilter_txx #include #include #include #include "itkKspaceImageFilter.h" #include #include #include #include #define _USE_MATH_DEFINES #include namespace itk { template< class TPixelType > KspaceImageFilter< TPixelType > ::KspaceImageFilter() : m_FrequencyMapSlice(NULL) , m_Z(0) , m_UseConstantRandSeed(false) , m_SpikesPerSlice(0) , m_IsBaseline(true) { m_DiffusionGradientDirection.Fill(0.0); m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); m_RandGen->SetSeed(); } template< class TPixelType > void KspaceImageFilter< TPixelType > ::BeforeThreadedGenerateData() { if (m_UseConstantRandSeed) // always generate the same random numbers? m_RandGen->SetSeed(0); else m_RandGen->SetSeed(); typename OutputImageType::Pointer outputImage = OutputImageType::New(); itk::ImageRegion<2> region; region.SetSize(0, m_OutSize[0]); region.SetSize(1, m_OutSize[1]); outputImage->SetLargestPossibleRegion( region ); outputImage->SetBufferedRegion( region ); outputImage->SetRequestedRegion( region ); outputImage->Allocate(); double gamma = 42576000; // Gyromagnetic ratio in Hz/T - if (m_Parameters.m_EddyStrength>0 && m_DiffusionGradientDirection.GetNorm()>0.001) + if ( m_Parameters.m_SignalGen.m_EddyStrength>0 && m_DiffusionGradientDirection.GetNorm()>0.001) { m_DiffusionGradientDirection.Normalize(); - m_DiffusionGradientDirection = m_DiffusionGradientDirection * m_Parameters.m_EddyStrength/1000 * gamma; + m_DiffusionGradientDirection = m_DiffusionGradientDirection * m_Parameters.m_SignalGen.m_EddyStrength/1000 * gamma; m_IsBaseline = false; } this->SetNthOutput(0, outputImage); m_Spike = vcl_complex(0,0); - m_Transform = m_Parameters.m_ImageDirection; + m_Transform = m_Parameters.m_SignalGen.m_ImageDirection; for (int i=0; i<3; i++) for (int j=0; j<3; j++) - m_Transform[i][j] *= m_Parameters.m_ImageSpacing[j]; + m_Transform[i][j] *= m_Parameters.m_SignalGen.m_ImageSpacing[j]; } template< class TPixelType > void KspaceImageFilter< TPixelType > ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType) { typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread); typedef ImageRegionConstIterator< InputImageType > InputIteratorType; double kxMax = outputImage->GetLargestPossibleRegion().GetSize(0); // k-space size in x-direction double kyMax = outputImage->GetLargestPossibleRegion().GetSize(1); // k-space size in y-direction double xMax = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(0); // scanner coverage in x-direction double yMax = m_CompartmentImages.at(0)->GetLargestPossibleRegion().GetSize(1); // scanner coverage in y-direction double numPix = kxMax*kyMax; - double dt = m_Parameters.m_tLine/kxMax; - double fromMaxEcho = - m_Parameters.m_tLine*kyMax/2; + double dt = m_Parameters.m_SignalGen.m_tLine/kxMax; + double fromMaxEcho = - m_Parameters.m_SignalGen.m_tLine*kyMax/2; double upsampling = xMax/kxMax; // discrepany between k-space resolution and image resolution double yMaxFov = kyMax*upsampling; // actual FOV in y-direction (in x-direction xMax==FOV) int xRingingOffset = xMax-kxMax; int yRingingOffset = yMaxFov-kyMax; while( !oit.IsAtEnd() ) { itk::Index< 2 > kIdx; kIdx[0] = oit.GetIndex()[0]; kIdx[1] = oit.GetIndex()[1]; double t = fromMaxEcho + ((double)kIdx[1]*kxMax+(double)kIdx[0])*dt; // dephasing time // rearrange slice if( kIdx[0] < kxMax/2 ) kIdx[0] = kIdx[0] + kxMax/2; else kIdx[0] = kIdx[0] - kxMax/2; if( kIdx[1] < kyMax/2 ) kIdx[1] = kIdx[1] + kyMax/2; else kIdx[1] = kIdx[1] - kyMax/2; // calculate eddy current decay factors double eddyDecay = 0; - if (m_Parameters.m_EddyStrength>0) - eddyDecay = exp(-(m_Parameters.m_tEcho/2 + t)/m_Parameters.m_Tau) * t/1000; + if ( m_Parameters.m_SignalGen.m_EddyStrength>0) + eddyDecay = exp(-( m_Parameters.m_SignalGen.m_tEcho/2 + t)/ m_Parameters.m_SignalGen.m_Tau) * t/1000; // calcualte signal relaxation factors std::vector< double > relaxFactor; - if (m_Parameters.m_DoSimulateRelaxation) + if ( m_Parameters.m_SignalGen.m_DoSimulateRelaxation) for (unsigned int i=0; i=kxMax/2) kx += xRingingOffset; if (ky>=kyMax/2) ky += yRingingOffset; vcl_complex s(0,0); InputIteratorType it(m_CompartmentImages.at(0), m_CompartmentImages.at(0)->GetLargestPossibleRegion() ); while( !it.IsAtEnd() ) { double x = it.GetIndex()[0]-xMax/2; double y = it.GetIndex()[1]-yMax/2; vcl_complex f(0, 0); // sum compartment signals and simulate relaxation for (unsigned int i=0; i( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * relaxFactor.at(i) * m_Parameters.m_SignalScale, 0); + if ( m_Parameters.m_SignalGen.m_DoSimulateRelaxation) + f += std::complex( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * relaxFactor.at(i) * m_Parameters.m_SignalGen.m_SignalScale, 0); else - f += std::complex( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * m_Parameters.m_SignalScale ); + f += std::complex( m_CompartmentImages.at(i)->GetPixel(it.GetIndex()) * m_Parameters.m_SignalGen.m_SignalScale ); // simulate eddy currents and other distortions double omega_t = 0; - if ( m_Parameters.m_EddyStrength>0 && !m_IsBaseline) + if ( m_Parameters.m_SignalGen.m_EddyStrength>0 && !m_IsBaseline) { itk::Vector< double, 3 > pos; pos[0] = x; pos[1] = y; pos[2] = m_Z; pos = m_Transform*pos/1000; // vector from image center to current position (in meter) omega_t += (m_DiffusionGradientDirection[0]*pos[0]+m_DiffusionGradientDirection[1]*pos[1]+m_DiffusionGradientDirection[2]*pos[2])*eddyDecay; } if (m_FrequencyMapSlice.IsNotNull()) // simulate distortions omega_t += m_FrequencyMapSlice->GetPixel(it.GetIndex())*t/1000; if (y<-yMaxFov/2) y += yMaxFov; else if (y>=yMaxFov/2) y -= yMaxFov; // actual DFT term s += f * exp( std::complex(0, 2 * M_PI * (kx*x/xMax + ky*y/yMaxFov + omega_t )) ); ++it; } s /= numPix; if (m_SpikesPerSlice>0 && sqrt(s.imag()*s.imag()+s.real()*s.real()) > sqrt(m_Spike.imag()*m_Spike.imag()+m_Spike.real()*m_Spike.real()) ) m_Spike = s; outputImage->SetPixel(kIdx, s); ++oit; } } template< class TPixelType > void KspaceImageFilter< TPixelType > ::AfterThreadedGenerateData() { typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetOutput(0)); double kxMax = outputImage->GetLargestPossibleRegion().GetSize(0); // k-space size in x-direction double kyMax = outputImage->GetLargestPossibleRegion().GetSize(1); // k-space size in y-direction - m_Spike *= m_Parameters.m_SpikeAmplitude; + m_Spike *= m_Parameters.m_SignalGen.m_SpikeAmplitude; itk::Index< 2 > spikeIdx; for (unsigned int i=0; iGetIntegerVariate()%(int)kxMax; spikeIdx[1] = m_RandGen->GetIntegerVariate()%(int)kyMax; outputImage->SetPixel(spikeIdx, m_Spike); } } } #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp index caef447cf8..d209a3b5df 100755 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.cpp @@ -1,1238 +1,1300 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "itkTractsToDWIImageFilter.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace itk { template< class PixelType > TractsToDWIImageFilter< PixelType >::TractsToDWIImageFilter() : m_FiberBundle(NULL) , m_StatusText("") , m_UseConstantRandSeed(false) , m_RandGen(itk::Statistics::MersenneTwisterRandomVariateGenerator::New()) { m_RandGen->SetSeed(); } template< class PixelType > TractsToDWIImageFilter< PixelType >::~TractsToDWIImageFilter() { } template< class PixelType > TractsToDWIImageFilter< PixelType >::DoubleDwiType::Pointer TractsToDWIImageFilter< PixelType >::DoKspaceStuff( std::vector< DoubleDwiType::Pointer >& images ) { int numFiberCompartments = m_Parameters.m_FiberModelList.size(); // create slice object ImageRegion<2> sliceRegion; sliceRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); sliceRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); Vector< double, 2 > sliceSpacing; sliceSpacing[0] = m_UpsampledSpacing[0]; sliceSpacing[1] = m_UpsampledSpacing[1]; // frequency map slice SliceType::Pointer fMapSlice = NULL; - if (m_Parameters.m_FrequencyMap.IsNotNull()) + if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) { fMapSlice = SliceType::New(); ImageRegion<2> region; region.SetSize(0, m_UpsampledImageRegion.GetSize()[0]); region.SetSize(1, m_UpsampledImageRegion.GetSize()[1]); fMapSlice->SetLargestPossibleRegion( region ); fMapSlice->SetBufferedRegion( region ); fMapSlice->SetRequestedRegion( region ); fMapSlice->Allocate(); fMapSlice->FillBuffer(0.0); } DoubleDwiType::Pointer newImage = DoubleDwiType::New(); - newImage->SetSpacing( m_Parameters.m_ImageSpacing ); - newImage->SetOrigin( m_Parameters.m_ImageOrigin ); - newImage->SetDirection( m_Parameters.m_ImageDirection ); - newImage->SetLargestPossibleRegion( m_Parameters.m_ImageRegion ); - newImage->SetBufferedRegion( m_Parameters.m_ImageRegion ); - newImage->SetRequestedRegion( m_Parameters.m_ImageRegion ); + newImage->SetSpacing( m_Parameters.m_SignalGen.m_ImageSpacing ); + newImage->SetOrigin( m_Parameters.m_SignalGen.m_ImageOrigin ); + newImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); + newImage->SetLargestPossibleRegion( m_Parameters.m_SignalGen.m_ImageRegion ); + newImage->SetBufferedRegion( m_Parameters.m_SignalGen.m_ImageRegion ); + newImage->SetRequestedRegion( m_Parameters.m_SignalGen.m_ImageRegion ); newImage->SetVectorLength( images.at(0)->GetVectorLength() ); newImage->Allocate(); std::vector< unsigned int > spikeVolume; - for (unsigned int i=0; iGetIntegerVariate()%images.at(0)->GetVectorLength()); std::sort (spikeVolume.begin(), spikeVolume.end()); std::reverse (spikeVolume.begin(), spikeVolume.end()); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; unsigned long lastTick = 0; boost::progress_display disp(2*images.at(0)->GetVectorLength()*images.at(0)->GetLargestPossibleRegion().GetSize(2)); for (unsigned int g=0; gGetVectorLength(); g++) { std::vector< unsigned int > spikeSlice; while (!spikeVolume.empty() && spikeVolume.back()==g) { spikeSlice.push_back(m_RandGen->GetIntegerVariate()%images.at(0)->GetLargestPossibleRegion().GetSize(2)); spikeVolume.pop_back(); } std::sort (spikeSlice.begin(), spikeSlice.end()); std::reverse (spikeSlice.begin(), spikeSlice.end()); for (unsigned int z=0; zGetLargestPossibleRegion().GetSize(2); z++) { std::vector< SliceType::Pointer > compartmentSlices; std::vector< double > t2Vector; for (unsigned int i=0; i* signalModel; if (iSetLargestPossibleRegion( sliceRegion ); slice->SetBufferedRegion( sliceRegion ); slice->SetRequestedRegion( sliceRegion ); slice->SetSpacing(sliceSpacing); slice->Allocate(); slice->FillBuffer(0.0); // extract slice from channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; slice->SetPixel(index2D, images.at(i)->GetPixel(index3D)[g]); if (fMapSlice.IsNotNull() && i==0) - fMapSlice->SetPixel(index2D, m_Parameters.m_FrequencyMap->GetPixel(index3D)); + fMapSlice->SetPixel(index2D, m_Parameters.m_SignalGen.m_FrequencyMap->GetPixel(index3D)); } compartmentSlices.push_back(slice); t2Vector.push_back(signalModel->GetT2()); } if (this->GetAbortGenerateData()) return NULL; // create k-sapce (inverse fourier transform slices) - itk::Size<2> outSize; outSize.SetElement(0, m_Parameters.m_ImageRegion.GetSize(0)); outSize.SetElement(1, m_Parameters.m_ImageRegion.GetSize(1)); + itk::Size<2> outSize; outSize.SetElement(0, m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0)); outSize.SetElement(1, m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)); itk::KspaceImageFilter< SliceType::PixelType >::Pointer idft = itk::KspaceImageFilter< SliceType::PixelType >::New(); idft->SetCompartmentImages(compartmentSlices); idft->SetT2(t2Vector); idft->SetUseConstantRandSeed(m_UseConstantRandSeed); idft->SetParameters(m_Parameters); idft->SetZ((double)z-(double)images.at(0)->GetLargestPossibleRegion().GetSize(2)/2.0); - idft->SetDiffusionGradientDirection(m_Parameters.GetGradientDirection(g)); + idft->SetDiffusionGradientDirection(m_Parameters.m_SignalGen.GetGradientDirection(g)); idft->SetFrequencyMapSlice(fMapSlice); idft->SetOutSize(outSize); int numSpikes = 0; while (!spikeSlice.empty() && spikeSlice.back()==z) { numSpikes++; spikeSlice.pop_back(); } idft->SetSpikesPerSlice(numSpikes); idft->Update(); ComplexSliceType::Pointer fSlice; fSlice = idft->GetOutput(); ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; // fourier transform slice SliceType::Pointer newSlice; itk::DftImageFilter< SliceType::PixelType >::Pointer dft = itk::DftImageFilter< SliceType::PixelType >::New(); dft->SetInput(fSlice); dft->Update(); newSlice = dft->GetOutput(); // put slice back into channel g for (unsigned int y=0; yGetLargestPossibleRegion().GetSize(1); y++) for (unsigned int x=0; xGetLargestPossibleRegion().GetSize(0); x++) { DoubleDwiType::IndexType index3D; index3D[0]=x; index3D[1]=y; index3D[2]=z; SliceType::IndexType index2D; index2D[0]=x; index2D[1]=y; DoubleDwiType::PixelType pix3D = newImage->GetPixel(index3D); pix3D[g] = newSlice->GetPixel(index2D); newImage->SetPixel(index3D, pix3D); } ++disp; newTick = 50*disp.count()/disp.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } } m_StatusText += "\n\n"; return newImage; } template< class PixelType > void TractsToDWIImageFilter< PixelType >::GenerateData() { m_TimeProbe.Start(); m_StatusText = "Starting simulation\n"; // check input data if (m_FiberBundle.IsNull()) itkExceptionMacro("Input fiber bundle is NULL!"); if (m_Parameters.m_FiberModelList.empty()) itkExceptionMacro("No diffusion model for fiber compartments defined!"); if (m_Parameters.m_NonFiberModelList.empty()) itkExceptionMacro("No diffusion model for non-fiber compartments defined!"); - int baselineIndex = m_Parameters.GetFirstBaselineIndex(); + int baselineIndex = m_Parameters.m_SignalGen.GetFirstBaselineIndex(); if (baselineIndex<0) itkExceptionMacro("No baseline index found!"); - if (!m_Parameters.m_SimulateKspaceAcquisition) - m_Parameters.m_DoAddGibbsRinging = false; + if (!m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition) + m_Parameters.m_SignalGen.m_DoAddGibbsRinging = false; if (m_UseConstantRandSeed) // always generate the same random numbers? m_RandGen->SetSeed(0); else m_RandGen->SetSeed(); // initialize output dwi image - ImageRegion<3> croppedRegion = m_Parameters.m_ImageRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Parameters.m_CroppingFactor); - itk::Point shiftedOrigin = m_Parameters.m_ImageOrigin; shiftedOrigin[1] += (m_Parameters.m_ImageRegion.GetSize(1)-croppedRegion.GetSize(1))*m_Parameters.m_ImageSpacing[1]/2; + ImageRegion<3> croppedRegion = m_Parameters.m_SignalGen.m_ImageRegion; croppedRegion.SetSize(1, croppedRegion.GetSize(1)*m_Parameters.m_SignalGen.m_CroppingFactor); + itk::Point shiftedOrigin = m_Parameters.m_SignalGen.m_ImageOrigin; shiftedOrigin[1] += (m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1)-croppedRegion.GetSize(1))*m_Parameters.m_SignalGen.m_ImageSpacing[1]/2; typename OutputImageType::Pointer outImage = OutputImageType::New(); - outImage->SetSpacing( m_Parameters.m_ImageSpacing ); + outImage->SetSpacing( m_Parameters.m_SignalGen.m_ImageSpacing ); outImage->SetOrigin( shiftedOrigin ); - outImage->SetDirection( m_Parameters.m_ImageDirection ); + outImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); outImage->SetLargestPossibleRegion( croppedRegion ); outImage->SetBufferedRegion( croppedRegion ); outImage->SetRequestedRegion( croppedRegion ); - outImage->SetVectorLength( m_Parameters.GetNumVolumes() ); + outImage->SetVectorLength( m_Parameters.m_SignalGen.GetNumVolumes() ); outImage->Allocate(); typename OutputImageType::PixelType temp; - temp.SetSize(m_Parameters.GetNumVolumes()); + temp.SetSize(m_Parameters.m_SignalGen.GetNumVolumes()); temp.Fill(0.0); outImage->FillBuffer(temp); // ADJUST GEOMETRY FOR FURTHER PROCESSING // is input slize size a power of two? - unsigned int x=m_Parameters.m_ImageRegion.GetSize(0); unsigned int y=m_Parameters.m_ImageRegion.GetSize(1); + unsigned int x=m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0); unsigned int y=m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1); ItkDoubleImgType::SizeType pad; pad[0]=x%2; pad[1]=y%2; pad[2]=0; - m_Parameters.m_ImageRegion.SetSize(0, x+pad[0]); - m_Parameters.m_ImageRegion.SetSize(1, y+pad[1]); - if (m_Parameters.m_FrequencyMap.IsNotNull() && (pad[0]>0 || pad[1]>0)) + m_Parameters.m_SignalGen.m_ImageRegion.SetSize(0, x+pad[0]); + m_Parameters.m_SignalGen.m_ImageRegion.SetSize(1, y+pad[1]); + if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); - zeroPadder->SetInput(m_Parameters.m_FrequencyMap); + zeroPadder->SetInput(m_Parameters.m_SignalGen.m_FrequencyMap); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); - m_Parameters.m_FrequencyMap = zeroPadder->GetOutput(); + m_Parameters.m_SignalGen.m_FrequencyMap = zeroPadder->GetOutput(); } - if (m_Parameters.m_MaskImage.IsNotNull() && (pad[0]>0 || pad[1]>0)) + if (m_Parameters.m_SignalGen.m_MaskImage.IsNotNull() && (pad[0]>0 || pad[1]>0)) { itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); - zeroPadder->SetInput(m_Parameters.m_MaskImage); + zeroPadder->SetInput(m_Parameters.m_SignalGen.m_MaskImage); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); - m_Parameters.m_MaskImage = zeroPadder->GetOutput(); + m_Parameters.m_SignalGen.m_MaskImage = zeroPadder->GetOutput(); } // Apply in-plane upsampling for Gibbs ringing artifact double upsampling = 1; - if (m_Parameters.m_DoAddGibbsRinging) + if (m_Parameters.m_SignalGen.m_DoAddGibbsRinging) upsampling = 2; - m_UpsampledSpacing = m_Parameters.m_ImageSpacing; + m_UpsampledSpacing = m_Parameters.m_SignalGen.m_ImageSpacing; m_UpsampledSpacing[0] /= upsampling; m_UpsampledSpacing[1] /= upsampling; - m_UpsampledImageRegion = m_Parameters.m_ImageRegion; - m_UpsampledImageRegion.SetSize(0, m_Parameters.m_ImageRegion.GetSize()[0]*upsampling); - m_UpsampledImageRegion.SetSize(1, m_Parameters.m_ImageRegion.GetSize()[1]*upsampling); - m_UpsampledOrigin = m_Parameters.m_ImageOrigin; - m_UpsampledOrigin[0] -= m_Parameters.m_ImageSpacing[0]/2; m_UpsampledOrigin[0] += m_UpsampledSpacing[0]/2; - m_UpsampledOrigin[1] -= m_Parameters.m_ImageSpacing[1]/2; m_UpsampledOrigin[1] += m_UpsampledSpacing[1]/2; - m_UpsampledOrigin[2] -= m_Parameters.m_ImageSpacing[2]/2; m_UpsampledOrigin[2] += m_UpsampledSpacing[2]/2; + m_UpsampledImageRegion = m_Parameters.m_SignalGen.m_ImageRegion; + m_UpsampledImageRegion.SetSize(0, m_Parameters.m_SignalGen.m_ImageRegion.GetSize()[0]*upsampling); + m_UpsampledImageRegion.SetSize(1, m_Parameters.m_SignalGen.m_ImageRegion.GetSize()[1]*upsampling); + m_UpsampledOrigin = m_Parameters.m_SignalGen.m_ImageOrigin; + m_UpsampledOrigin[0] -= m_Parameters.m_SignalGen.m_ImageSpacing[0]/2; m_UpsampledOrigin[0] += m_UpsampledSpacing[0]/2; + m_UpsampledOrigin[1] -= m_Parameters.m_SignalGen.m_ImageSpacing[1]/2; m_UpsampledOrigin[1] += m_UpsampledSpacing[1]/2; + m_UpsampledOrigin[2] -= m_Parameters.m_SignalGen.m_ImageSpacing[2]/2; m_UpsampledOrigin[2] += m_UpsampledSpacing[2]/2; // generate double images to store the individual compartment signals m_CompartmentImages.clear(); int numFiberCompartments = m_Parameters.m_FiberModelList.size(); int numNonFiberCompartments = m_Parameters.m_NonFiberModelList.size(); for (int i=0; iSetSpacing( m_UpsampledSpacing ); doubleDwi->SetOrigin( m_UpsampledOrigin ); - doubleDwi->SetDirection( m_Parameters.m_ImageDirection ); + doubleDwi->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); doubleDwi->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleDwi->SetBufferedRegion( m_UpsampledImageRegion ); doubleDwi->SetRequestedRegion( m_UpsampledImageRegion ); - doubleDwi->SetVectorLength( m_Parameters.GetNumVolumes() ); + doubleDwi->SetVectorLength( m_Parameters.m_SignalGen.GetNumVolumes() ); doubleDwi->Allocate(); DoubleDwiType::PixelType pix; - pix.SetSize(m_Parameters.GetNumVolumes()); + pix.SetSize(m_Parameters.m_SignalGen.GetNumVolumes()); pix.Fill(0.0); doubleDwi->FillBuffer(pix); m_CompartmentImages.push_back(doubleDwi); } // initialize output volume fraction images m_VolumeFractions.clear(); for (int i=0; iSetSpacing( m_UpsampledSpacing ); doubleImg->SetOrigin( m_UpsampledOrigin ); - doubleImg->SetDirection( m_Parameters.m_ImageDirection ); + doubleImg->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); doubleImg->SetLargestPossibleRegion( m_UpsampledImageRegion ); doubleImg->SetBufferedRegion( m_UpsampledImageRegion ); doubleImg->SetRequestedRegion( m_UpsampledImageRegion ); doubleImg->Allocate(); doubleImg->FillBuffer(0); m_VolumeFractions.push_back(doubleImg); } // get volume fraction images ItkDoubleImgType::Pointer sumImage = ItkDoubleImgType::New(); bool foundVolumeFractionImage = false; for (int i=0; iGetVolumeFractionImage().IsNotNull()) { foundVolumeFractionImage = true; itk::ConstantPadImageFilter::Pointer zeroPadder = itk::ConstantPadImageFilter::New(); zeroPadder->SetInput(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()); zeroPadder->SetConstant(0); zeroPadder->SetPadUpperBound(pad); zeroPadder->Update(); m_Parameters.m_NonFiberModelList[i]->SetVolumeFractionImage(zeroPadder->GetOutput()); sumImage->SetSpacing( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetSpacing() ); sumImage->SetOrigin( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetOrigin() ); sumImage->SetDirection( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetDirection() ); sumImage->SetLargestPossibleRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->SetBufferedRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->SetRequestedRegion( m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion() ); sumImage->Allocate(); sumImage->FillBuffer(0); break; } } if (!foundVolumeFractionImage) { sumImage->SetSpacing( m_UpsampledSpacing ); sumImage->SetOrigin( m_UpsampledOrigin ); - sumImage->SetDirection( m_Parameters.m_ImageDirection ); + sumImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); sumImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); sumImage->SetBufferedRegion( m_UpsampledImageRegion ); sumImage->SetRequestedRegion( m_UpsampledImageRegion ); sumImage->Allocate(); sumImage->FillBuffer(0.0); } for (int i=0; iGetVolumeFractionImage().IsNull()) { ItkDoubleImgType::Pointer doubleImg = ItkDoubleImgType::New(); doubleImg->SetSpacing( sumImage->GetSpacing() ); doubleImg->SetOrigin( sumImage->GetOrigin() ); doubleImg->SetDirection( sumImage->GetDirection() ); doubleImg->SetLargestPossibleRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->SetBufferedRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->SetRequestedRegion( sumImage->GetLargestPossibleRegion() ); doubleImg->Allocate(); doubleImg->FillBuffer(1.0/numNonFiberCompartments); m_Parameters.m_NonFiberModelList[i]->SetVolumeFractionImage(doubleImg); } ImageRegionIterator it(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage(), m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { sumImage->SetPixel(it.GetIndex(), sumImage->GetPixel(it.GetIndex())+it.Get()); ++it; } } for (int i=0; i it(m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage(), m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { if (sumImage->GetPixel(it.GetIndex())>0) it.Set(it.Get()/sumImage->GetPixel(it.GetIndex())); ++it; } } // resample mask image and frequency map to fit upsampled geometry - if (m_Parameters.m_DoAddGibbsRinging) + if (m_Parameters.m_SignalGen.m_DoAddGibbsRinging) { - if (m_Parameters.m_MaskImage.IsNotNull()) + if (m_Parameters.m_SignalGen.m_MaskImage.IsNotNull()) { // rescale mask image (otherwise there are problems with the resampling) itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); - rescaler->SetInput(0,m_Parameters.m_MaskImage); + rescaler->SetInput(0,m_Parameters.m_SignalGen.m_MaskImage); rescaler->SetOutputMaximum(100); rescaler->SetOutputMinimum(0); rescaler->Update(); // resample mask image itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); resampler->SetInput(rescaler->GetOutput()); - resampler->SetOutputParametersFromImage(m_Parameters.m_MaskImage); + resampler->SetOutputParametersFromImage(m_Parameters.m_SignalGen.m_MaskImage); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); - m_Parameters.m_MaskImage = resampler->GetOutput(); + m_Parameters.m_SignalGen.m_MaskImage = resampler->GetOutput(); itk::ImageFileWriter::Pointer w = itk::ImageFileWriter::New(); w->SetFileName("/local/mask_ups.nrrd"); - w->SetInput(m_Parameters.m_MaskImage); + w->SetInput(m_Parameters.m_SignalGen.m_MaskImage); w->Update(); } // resample frequency map - if (m_Parameters.m_FrequencyMap.IsNotNull()) + if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) { itk::ResampleImageFilter::Pointer resampler = itk::ResampleImageFilter::New(); - resampler->SetInput(m_Parameters.m_FrequencyMap); - resampler->SetOutputParametersFromImage(m_Parameters.m_FrequencyMap); + resampler->SetInput(m_Parameters.m_SignalGen.m_FrequencyMap); + resampler->SetOutputParametersFromImage(m_Parameters.m_SignalGen.m_FrequencyMap); resampler->SetSize(m_UpsampledImageRegion.GetSize()); resampler->SetOutputSpacing(m_UpsampledSpacing); resampler->SetOutputOrigin(m_UpsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); resampler->SetInterpolator(nn_interpolator); resampler->Update(); - m_Parameters.m_FrequencyMap = resampler->GetOutput(); + m_Parameters.m_SignalGen.m_FrequencyMap = resampler->GetOutput(); } } // no input tissue mask is set -> create default - bool maskImageSet = true; - if (m_Parameters.m_MaskImage.IsNull()) + m_MaskImageSet = true; + if (m_Parameters.m_SignalGen.m_MaskImage.IsNull()) { m_StatusText += "No tissue mask set\n"; MITK_INFO << "No tissue mask set"; - m_Parameters.m_MaskImage = ItkUcharImgType::New(); - m_Parameters.m_MaskImage->SetSpacing( m_UpsampledSpacing ); - m_Parameters.m_MaskImage->SetOrigin( m_UpsampledOrigin ); - m_Parameters.m_MaskImage->SetDirection( m_Parameters.m_ImageDirection ); - m_Parameters.m_MaskImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); - m_Parameters.m_MaskImage->SetBufferedRegion( m_UpsampledImageRegion ); - m_Parameters.m_MaskImage->SetRequestedRegion( m_UpsampledImageRegion ); - m_Parameters.m_MaskImage->Allocate(); - m_Parameters.m_MaskImage->FillBuffer(1); - maskImageSet = false; + m_Parameters.m_SignalGen.m_MaskImage = ItkUcharImgType::New(); + m_Parameters.m_SignalGen.m_MaskImage->SetSpacing( m_UpsampledSpacing ); + m_Parameters.m_SignalGen.m_MaskImage->SetOrigin( m_UpsampledOrigin ); + m_Parameters.m_SignalGen.m_MaskImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); + m_Parameters.m_SignalGen.m_MaskImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); + m_Parameters.m_SignalGen.m_MaskImage->SetBufferedRegion( m_UpsampledImageRegion ); + m_Parameters.m_SignalGen.m_MaskImage->SetRequestedRegion( m_UpsampledImageRegion ); + m_Parameters.m_SignalGen.m_MaskImage->Allocate(); + m_Parameters.m_SignalGen.m_MaskImage->FillBuffer(1); + m_MaskImageSet = false; } else { m_StatusText += "Using tissue mask\n"; MITK_INFO << "Using tissue mask"; } - m_Parameters.m_ImageRegion = croppedRegion; - x=m_Parameters.m_ImageRegion.GetSize(0); y=m_Parameters.m_ImageRegion.GetSize(1); + m_Parameters.m_SignalGen.m_ImageRegion = croppedRegion; + x=m_Parameters.m_SignalGen.m_ImageRegion.GetSize(0); y=m_Parameters.m_SignalGen.m_ImageRegion.GetSize(1); if ( x%2 == 1 ) - m_Parameters.m_ImageRegion.SetSize(0, x+1); + m_Parameters.m_SignalGen.m_ImageRegion.SetSize(0, x+1); if ( y%2 == 1 ) - m_Parameters.m_ImageRegion.SetSize(1, y+1); + m_Parameters.m_SignalGen.m_ImageRegion.SetSize(1, y+1); // resample fiber bundle for sufficient voxel coverage m_StatusText += "\n"+this->GetTime()+" > Resampling fibers ...\n"; double segmentVolume = 0.0001; float minSpacing = 1; if(m_UpsampledSpacing[0]GetDeepCopy(); + m_FiberBundleWorkingCopy = m_FiberBundle->GetDeepCopy(); double volumeAccuracy = 10; - fiberBundle->ResampleFibers(minSpacing/volumeAccuracy); - double mmRadius = m_Parameters.m_AxonRadius/1000; + m_FiberBundleWorkingCopy->ResampleFibers(minSpacing/volumeAccuracy); + double mmRadius = m_Parameters.m_SignalGen.m_AxonRadius/1000; if (mmRadius>0) segmentVolume = M_PI*mmRadius*mmRadius*minSpacing/volumeAccuracy; double maxVolume = 0; - double voxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2]; + m_VoxelVolume = m_UpsampledSpacing[0]*m_UpsampledSpacing[1]*m_UpsampledSpacing[2]; - ofstream logFile; - if (m_Parameters.m_DoAddMotion) + if (m_Parameters.m_SignalGen.m_DoAddMotion) { std::string fileName = "fiberfox_motion_0.log"; std::string filePath = mitk::IOUtil::GetTempPath(); - if (m_Parameters.m_OutputPath.size()>0) - filePath = m_Parameters.m_OutputPath; + if (m_Parameters.m_Misc.m_OutputPath.size()>0) + filePath = m_Parameters.m_Misc.m_OutputPath; int c = 1; while (itksys::SystemTools::FileExists((filePath+fileName).c_str())) { fileName = "fiberfox_motion_"; fileName += boost::lexical_cast(c); fileName += ".log"; c++; } - logFile.open((filePath+fileName).c_str()); - logFile << "0 rotation: 0,0,0; translation: 0,0,0\n"; + m_Logfile.open((filePath+fileName).c_str()); + m_Logfile << "0 rotation: 0,0,0; translation: 0,0,0\n"; - if (m_Parameters.m_DoRandomizeMotion) + if (m_Parameters.m_SignalGen.m_DoRandomizeMotion) { m_StatusText += "Adding random motion artifacts:\n"; - m_StatusText += "Maximum rotation: +/-" + boost::lexical_cast(m_Parameters.m_Rotation) + "°\n"; - m_StatusText += "Maximum translation: +/-" + boost::lexical_cast(m_Parameters.m_Translation) + "mm\n"; + m_StatusText += "Maximum rotation: +/-" + boost::lexical_cast(m_Parameters.m_SignalGen.m_Rotation) + "°\n"; + m_StatusText += "Maximum translation: +/-" + boost::lexical_cast(m_Parameters.m_SignalGen.m_Translation) + "mm\n"; } else { m_StatusText += "Adding linear motion artifacts:\n"; - m_StatusText += "Maximum rotation: " + boost::lexical_cast(m_Parameters.m_Rotation) + "°\n"; - m_StatusText += "Maximum translation: " + boost::lexical_cast(m_Parameters.m_Translation) + "mm\n"; + m_StatusText += "Maximum rotation: " + boost::lexical_cast(m_Parameters.m_SignalGen.m_Rotation) + "°\n"; + m_StatusText += "Maximum translation: " + boost::lexical_cast(m_Parameters.m_SignalGen.m_Translation) + "mm\n"; } m_StatusText += "Motion logfile: " + (filePath+fileName) + "\n"; MITK_INFO << "Adding motion artifacts"; - MITK_INFO << "Maximum rotation: " << m_Parameters.m_Rotation; - MITK_INFO << "Maxmimum translation: " << m_Parameters.m_Translation; + MITK_INFO << "Maximum rotation: " << m_Parameters.m_SignalGen.m_Rotation; + MITK_INFO << "Maxmimum translation: " << m_Parameters.m_SignalGen.m_Translation; } maxVolume = 0; m_StatusText += "\n"+this->GetTime()+" > Generating " + boost::lexical_cast(numFiberCompartments+numNonFiberCompartments) + "-compartment diffusion-weighted signal.\n"; int numFibers = m_FiberBundle->GetNumFibers(); - boost::progress_display disp(numFibers*m_Parameters.GetNumVolumes()); + boost::progress_display disp(numFibers*m_Parameters.m_SignalGen.GetNumVolumes()); // get transform for motion artifacts - FiberBundleType fiberBundleTransformed = fiberBundle; - DoubleVectorType rotation = m_Parameters.m_Rotation/m_Parameters.GetNumVolumes(); - DoubleVectorType translation = m_Parameters.m_Translation/m_Parameters.GetNumVolumes(); + m_FiberBundleTransformed = m_FiberBundleWorkingCopy; + m_Rotation = m_Parameters.m_SignalGen.m_Rotation/m_Parameters.m_SignalGen.GetNumVolumes(); + m_Translation = m_Parameters.m_SignalGen.m_Translation/m_Parameters.m_SignalGen.GetNumVolumes(); // creat image to hold transformed mask (motion artifact) - ItkUcharImgType::Pointer tempTissueMask = ItkUcharImgType::New(); + m_MaskImage = ItkUcharImgType::New(); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); - duplicator->SetInputImage(m_Parameters.m_MaskImage); + duplicator->SetInputImage(m_Parameters.m_SignalGen.m_MaskImage); duplicator->Update(); - tempTissueMask = duplicator->GetOutput(); + m_MaskImage = duplicator->GetOutput(); // second upsampling needed for motion artifacts - ImageRegion<3> upsampledImageRegion = m_UpsampledImageRegion; - DoubleVectorType upsampledSpacing = m_UpsampledSpacing; + ImageRegion<3> upsampledImageRegion = m_UpsampledImageRegion; + DoubleVectorType upsampledSpacing = m_UpsampledSpacing; upsampledSpacing[0] /= 4; upsampledSpacing[1] /= 4; upsampledSpacing[2] /= 4; upsampledImageRegion.SetSize(0, m_UpsampledImageRegion.GetSize()[0]*4); upsampledImageRegion.SetSize(1, m_UpsampledImageRegion.GetSize()[1]*4); upsampledImageRegion.SetSize(2, m_UpsampledImageRegion.GetSize()[2]*4); itk::Point upsampledOrigin = m_UpsampledOrigin; upsampledOrigin[0] -= m_UpsampledSpacing[0]/2; upsampledOrigin[0] += upsampledSpacing[0]/2; upsampledOrigin[1] -= m_UpsampledSpacing[1]/2; upsampledOrigin[1] += upsampledSpacing[1]/2; upsampledOrigin[2] -= m_UpsampledSpacing[2]/2; upsampledOrigin[2] += upsampledSpacing[2]/2; - ItkUcharImgType::Pointer upsampledTissueMask = ItkUcharImgType::New(); + m_UpsampledMaskImage = ItkUcharImgType::New(); itk::ResampleImageFilter::Pointer upsampler = itk::ResampleImageFilter::New(); - upsampler->SetInput(m_Parameters.m_MaskImage); - upsampler->SetOutputParametersFromImage(m_Parameters.m_MaskImage); + upsampler->SetInput(m_Parameters.m_SignalGen.m_MaskImage); + upsampler->SetOutputParametersFromImage(m_Parameters.m_SignalGen.m_MaskImage); upsampler->SetSize(upsampledImageRegion.GetSize()); upsampler->SetOutputSpacing(upsampledSpacing); upsampler->SetOutputOrigin(upsampledOrigin); itk::NearestNeighborInterpolateImageFunction::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction::New(); upsampler->SetInterpolator(nn_interpolator); upsampler->Update(); - upsampledTissueMask = upsampler->GetOutput(); + m_UpsampledMaskImage = upsampler->GetOutput(); unsigned long lastTick = 0; - switch (m_Parameters.m_DiffusionDirectionMode) + int signalModelSeed = m_RandGen->GetIntegerVariate(); + switch (m_Parameters.m_SignalGen.m_DiffusionDirectionMode) { - case(FiberfoxParameters<>::FIBER_TANGENT_DIRECTIONS): + case(SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS): // use fiber tangent directions to determine diffusion direction { m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; - for (unsigned int g=0; gSetSeed(signalModelSeed); + for (int i=0; iSetSeed(signalModelSeed); + ItkDoubleImgType::Pointer intraAxonalVolumeImage = ItkDoubleImgType::New(); intraAxonalVolumeImage->SetSpacing( m_UpsampledSpacing ); intraAxonalVolumeImage->SetOrigin( m_UpsampledOrigin ); - intraAxonalVolumeImage->SetDirection( m_Parameters.m_ImageDirection ); + intraAxonalVolumeImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); intraAxonalVolumeImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetBufferedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetRequestedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->Allocate(); intraAxonalVolumeImage->FillBuffer(0); - vtkPolyData* fiberPolyData = fiberBundleTransformed->GetFiberPolyData(); + vtkPolyData* fiberPolyData = m_FiberBundleTransformed->GetFiberPolyData(); // generate fiber signal (if there are any fiber models present) if (!m_Parameters.m_FiberModelList.empty()) for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) continue; for( int j=0; jGetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } double* temp = points->GetPoint(j); itk::Point vertex = GetItkPoint(temp); itk::Vector v = GetItkVector(temp); itk::Vector dir(3); if (jGetPoint(j+1))-v; else dir = v-GetItkVector(points->GetPoint(j-1)); if (dir.GetSquaredNorm()<0.0001 || dir[0]!=dir[0] || dir[1]!=dir[1] || dir[2]!=dir[2]) continue; itk::Index<3> idx; itk::ContinuousIndex contIndex; - tempTissueMask->TransformPhysicalPointToIndex(vertex, idx); - tempTissueMask->TransformPhysicalPointToContinuousIndex(vertex, contIndex); + m_MaskImage->TransformPhysicalPointToIndex(vertex, idx); + m_MaskImage->TransformPhysicalPointToContinuousIndex(vertex, contIndex); - if (!tempTissueMask->GetLargestPossibleRegion().IsInside(idx) || tempTissueMask->GetPixel(idx)<=0) + if (!m_MaskImage->GetLargestPossibleRegion().IsInside(idx) || m_MaskImage->GetPixel(idx)<=0) continue; // generate signal for each fiber compartment for (int k=0; kSetFiberDirection(dir); DoubleDwiType::PixelType pix = m_CompartmentImages.at(k)->GetPixel(idx); pix[g] += segmentVolume*m_Parameters.m_FiberModelList[k]->SimulateMeasurement(g); m_CompartmentImages.at(k)->SetPixel(idx, pix); } // update fiber volume image double vol = intraAxonalVolumeImage->GetPixel(idx) + segmentVolume; intraAxonalVolumeImage->SetPixel(idx, vol); if (g==0 && vol>maxVolume) maxVolume = vol; } // progress report ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; } // generate non-fiber signal - ImageRegionIterator it3(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); + ImageRegionIterator it3(m_MaskImage, m_MaskImage->GetLargestPossibleRegion()); double fact = 1; - if (m_Parameters.m_AxonRadius<0.0001 || maxVolume>voxelVolume) - fact = voxelVolume/maxVolume; + if (m_Parameters.m_SignalGen.m_AxonRadius<0.0001 || maxVolume>m_VoxelVolume) + fact = m_VoxelVolume/maxVolume; while(!it3.IsAtEnd()) { if (it3.Get()>0) { DoubleDwiType::IndexType index = it3.GetIndex(); - // get fiber volume fraction - double intraAxonalVolume = intraAxonalVolumeImage->GetPixel(index)*fact; - - for (int i=0; iGetPixel(index); - pix[g] *= fact; - m_CompartmentImages.at(i)->SetPixel(index, pix); - } - - if (intraAxonalVolume>0.0001 && m_Parameters.m_DoDisablePartialVolume) // only fiber in voxel - { - DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(index); - pix[g] *= voxelVolume/intraAxonalVolume; - m_CompartmentImages.at(0)->SetPixel(index, pix); - m_VolumeFractions.at(0)->SetPixel(index, 1); - for (int i=1; i0.0001) + for (int i=0; iGetPixel(index); - pix[g] = 0; + pix[g] *= fact; m_CompartmentImages.at(i)->SetPixel(index, pix); } - } - else - { - m_VolumeFractions.at(0)->SetPixel(index, intraAxonalVolume/voxelVolume); - - itk::Point point; - tempTissueMask->TransformIndexToPhysicalPoint(index, point); - if (m_Parameters.m_DoAddMotion) - { - if (m_Parameters.m_DoRandomizeMotion && g>0) - point = fiberBundle->TransformPoint(point.GetVnlVector(), -rotation[0],-rotation[1],-rotation[2],-translation[0],-translation[1],-translation[2]); - else - point = fiberBundle->TransformPoint(point.GetVnlVector(), -rotation[0]*g,-rotation[1]*g,-rotation[2]*g,-translation[0]*g,-translation[1]*g,-translation[2]*g); - } - - if (m_Parameters.m_DoDisablePartialVolume) - { - int maxVolumeIndex = 0; - double maxWeight = 0; - for (int i=0; i1) - { - DoubleDwiType::IndexType newIndex; - m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->TransformPhysicalPointToIndex(point, newIndex); - if (!m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion().IsInside(newIndex)) - continue; - weight = m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetPixel(newIndex); - } - - if (weight>maxWeight) - { - maxWeight = weight; - maxVolumeIndex = i; - } - } - DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(maxVolumeIndex+numFiberCompartments); - DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index); - pix[g] += m_Parameters.m_NonFiberModelList[maxVolumeIndex]->SimulateMeasurement(g); - doubleDwi->SetPixel(index, pix); - m_VolumeFractions.at(maxVolumeIndex+numFiberCompartments)->SetPixel(index, 1); - } - else - { - double extraAxonalVolume = voxelVolume-intraAxonalVolume; // non-fiber volume - double interAxonalVolume = 0; - if (numFiberCompartments>1) - interAxonalVolume = extraAxonalVolume * intraAxonalVolume/voxelVolume; // inter-axonal fraction of non fiber compartment scales linearly with f - double other = extraAxonalVolume - interAxonalVolume; // rest of compartment - double singleinter = interAxonalVolume/(numFiberCompartments-1); - - // adjust non-fiber and intra-axonal signal - for (int i=1; iGetPixel(index); - if (intraAxonalVolume>0) // remove scaling by intra-axonal volume from inter-axonal compartment - pix[g] /= intraAxonalVolume; - pix[g] *= singleinter; - m_CompartmentImages.at(i)->SetPixel(index, pix); - m_VolumeFractions.at(i)->SetPixel(index, singleinter/voxelVolume); - } - - for (int i=0; i1) - { - DoubleDwiType::IndexType newIndex; - m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->TransformPhysicalPointToIndex(point, newIndex); - if (!m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion().IsInside(newIndex)) - continue; - weight = m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetPixel(newIndex); - } - - DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(i+numFiberCompartments); - DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index); - - pix[g] += m_Parameters.m_NonFiberModelList[i]->SimulateMeasurement(g)*other*weight; - doubleDwi->SetPixel(index, pix); - m_VolumeFractions.at(i+numFiberCompartments)->SetPixel(index, other/voxelVolume*weight); - } - } - } + // simulate other compartments + SimulateNonFiberSignal(index, intraAxonalVolumeImage->GetPixel(index)*fact, g); } ++it3; } // move fibers - if (m_Parameters.m_DoAddMotion && gGetDeepCopy(); - rotation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Rotation[0]*2)-m_Parameters.m_Rotation[0]; - rotation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Rotation[1]*2)-m_Parameters.m_Rotation[1]; - rotation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Rotation[2]*2)-m_Parameters.m_Rotation[2]; - translation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Translation[0]*2)-m_Parameters.m_Translation[0]; - translation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Translation[1]*2)-m_Parameters.m_Translation[1]; - translation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_Translation[2]*2)-m_Parameters.m_Translation[2]; - } - - // rotate mask image - if (maskImageSet) - { - ImageRegionIterator maskIt(upsampledTissueMask, upsampledTissueMask->GetLargestPossibleRegion()); - tempTissueMask->FillBuffer(0); - - while(!maskIt.IsAtEnd()) - { - if (maskIt.Get()<=0) - { - ++maskIt; - continue; - } - - DoubleDwiType::IndexType index = maskIt.GetIndex(); - itk::Point point; - upsampledTissueMask->TransformIndexToPhysicalPoint(index, point); - if (m_Parameters.m_DoRandomizeMotion) - point = fiberBundle->TransformPoint(point.GetVnlVector(), rotation[0],rotation[1],rotation[2],translation[0],translation[1],translation[2]); - else - point = fiberBundle->TransformPoint(point.GetVnlVector(), rotation[0]*(g+1),rotation[1]*(g+1),rotation[2]*(g+1),translation[0]*(g+1),translation[1]*(g+1),translation[2]*(g+1)); - - tempTissueMask->TransformPhysicalPointToIndex(point, index); - if (tempTissueMask->GetLargestPossibleRegion().IsInside(index)) - tempTissueMask->SetPixel(index,100); - ++maskIt; - } - } - - // rotate fibers - if (logFile.is_open()) - { - logFile << g+1 << " rotation: " << rotation[0] << "," << rotation[1] << "," << rotation[2] << ";"; - logFile << " translation: " << translation[0] << "," << translation[1] << "," << translation[2] << "\n"; - } - fiberBundleTransformed->TransformFibers(rotation[0],rotation[1],rotation[2],translation[0],translation[1],translation[2]); - } + SimulateMotion(g); } break; } - case (FiberfoxParameters<>::MAIN_FIBER_DIRECTIONS): + case (SignalGenerationParameters::MAIN_FIBER_DIRECTIONS): // use main fiber directions to determine voxel-wise diffusion directions { typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; + // calculate main fiber directions itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); - fOdfFilter->SetFiberBundle(fiberBundle); - fOdfFilter->SetMaskImage(tempTissueMask); - fOdfFilter->SetAngularThreshold(cos(45*M_PI/180)); + fOdfFilter->SetFiberBundle(m_FiberBundleTransformed); + fOdfFilter->SetMaskImage(m_MaskImage); + fOdfFilter->SetAngularThreshold(cos(m_Parameters.m_SignalGen.m_FiberSeparationThreshold*M_PI/180.0)); fOdfFilter->SetNormalizeVectors(false); - fOdfFilter->SetUseWorkingCopy(false); + fOdfFilter->SetUseWorkingCopy(true); fOdfFilter->SetSizeThreshold(0); fOdfFilter->SetMaxNumDirections(3); fOdfFilter->Update(); ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); - { - ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage(); - typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; - WriterType::Pointer writer = WriterType::New(); - writer->SetFileName("/local/NumDirections.nrrd"); - writer->SetInput(numDirImage); - writer->Update(); - } - + // allocate image storing intra-axonal volume fraction information ItkDoubleImgType::Pointer intraAxonalVolumeImage = ItkDoubleImgType::New(); intraAxonalVolumeImage->SetSpacing( m_UpsampledSpacing ); intraAxonalVolumeImage->SetOrigin( m_UpsampledOrigin ); - intraAxonalVolumeImage->SetDirection( m_Parameters.m_ImageDirection ); + intraAxonalVolumeImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); intraAxonalVolumeImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetBufferedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->SetRequestedRegion( m_UpsampledImageRegion ); intraAxonalVolumeImage->Allocate(); intraAxonalVolumeImage->FillBuffer(0); - itk::TractDensityImageFilter< ItkDoubleImgType >::Pointer generator = itk::TractDensityImageFilter< ItkDoubleImgType >::New(); - generator->SetFiberBundle(fiberBundle); - generator->SetBinaryOutput(false); - generator->SetOutputAbsoluteValues(false); - generator->SetInputImage(intraAxonalVolumeImage); - generator->SetUseImageGeometry(true); - generator->Update(); - intraAxonalVolumeImage = generator->GetOutput(); + // determine intra-axonal volume fraction using the tract density + itk::TractDensityImageFilter< ItkDoubleImgType >::Pointer tdiFilter = itk::TractDensityImageFilter< ItkDoubleImgType >::New(); + tdiFilter->SetFiberBundle(m_FiberBundleTransformed); + tdiFilter->SetBinaryOutput(false); + tdiFilter->SetOutputAbsoluteValues(false); + tdiFilter->SetInputImage(intraAxonalVolumeImage); + tdiFilter->SetUseImageGeometry(true); + tdiFilter->Update(); + intraAxonalVolumeImage = tdiFilter->GetOutput(); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; - boost::progress_display disp(tempTissueMask->GetLargestPossibleRegion().GetNumberOfPixels()); - ImageRegionIterator< ItkUcharImgType > it(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); - while(!it.IsAtEnd()) + boost::progress_display disp(m_MaskImage->GetLargestPossibleRegion().GetNumberOfPixels()*m_Parameters.m_SignalGen.GetNumVolumes()); + + for (unsigned int g=0; gSetSeed(signalModelSeed); + for (int i=0; iSetSeed(signalModelSeed); - if (this->GetAbortGenerateData()) + if (m_Parameters.m_SignalGen.m_DoAddMotion && g>0) // if fibers have moved we need a new TDI and new directions { - m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; - return; + fOdfFilter->SetFiberBundle(m_FiberBundleTransformed); + fOdfFilter->SetMaskImage(m_MaskImage); + fOdfFilter->Update(); + directionImageContainer = fOdfFilter->GetDirectionImageContainer(); + + tdiFilter->SetFiberBundle(m_FiberBundleTransformed); + tdiFilter->Update(); + intraAxonalVolumeImage = tdiFilter->GetOutput(); } - if (it.Get()>0) + ImageRegionIterator< ItkUcharImgType > it(m_MaskImage, m_MaskImage->GetLargestPossibleRegion()); + while(!it.IsAtEnd()) { - int count = 0; - DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(it.GetIndex()); - for (unsigned int i=0; iSize(); i++) + ++disp; + unsigned long newTick = 50*disp.count()/disp.expected_count(); + for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) + m_StatusText += "*"; + lastTick = newTick; + + if (this->GetAbortGenerateData()) { - itk::Vector< double, 3> dir; - dir.CastFrom(directionImageContainer->GetElement(i)->GetPixel(it.GetIndex())); - double norm = dir.GetNorm(); - if (norm>0.0001) - { - int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_FiberModelList.size()-1); - m_Parameters.m_FiberModelList.at(modelIndex)->SetFiberDirection(dir); - pix += m_Parameters.m_FiberModelList.at(modelIndex)->SimulateMeasurement()*norm; - count++; - } + m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; + return; } - if (count>0) - pix /= count; - pix *= intraAxonalVolumeImage->GetPixel(it.GetIndex()); - // GM/CSF + if (it.Get()>0) { - int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_NonFiberModelList.size()-1); - pix += (1-intraAxonalVolumeImage->GetPixel(it.GetIndex()))*m_Parameters.m_NonFiberModelList.at(modelIndex)->SimulateMeasurement(); - } + // generate fiber signal + for (int c=0; cGetPixel(it.GetIndex()); + for (unsigned int i=0; iSize(); i++) + { + itk::Vector< double, 3> dir; + dir.CastFrom(directionImageContainer->GetElement(i)->GetPixel(it.GetIndex())); + double norm = dir.GetNorm(); + if (norm>0.0001) + { + m_Parameters.m_FiberModelList.at(c)->SetFiberDirection(dir); + pix[g] += m_Parameters.m_FiberModelList.at(c)->SimulateMeasurement(g)*norm; + count++; + } + } + if (count>0) + pix[g] /= count; + pix[g] *= intraAxonalVolumeImage->GetPixel(it.GetIndex())*m_VoxelVolume; + m_CompartmentImages.at(c)->SetPixel(it.GetIndex(), pix); + } - m_CompartmentImages.at(0)->SetPixel(it.GetIndex(), pix); + // simulate other compartments + SimulateNonFiberSignal(it.GetIndex(), intraAxonalVolumeImage->GetPixel(it.GetIndex())*m_VoxelVolume, g); + } + ++it; } - ++it; + + SimulateMotion(g); } + + itk::ImageFileWriter< ItkUcharImgType >::Pointer wr = itk::ImageFileWriter< ItkUcharImgType >::New(); + wr->SetInput(fOdfFilter->GetNumDirectionsImage()); + wr->SetFileName(mitk::IOUtil::GetTempPath()+"/NumDirections_MainFiberDirections.nrrd"); + wr->Update(); break; } - case (FiberfoxParameters<>::RANDOM_DIRECTIONS): + case (SignalGenerationParameters::RANDOM_DIRECTIONS): { ItkUcharImgType::Pointer numDirectionsImage = ItkUcharImgType::New(); numDirectionsImage->SetSpacing( m_UpsampledSpacing ); numDirectionsImage->SetOrigin( m_UpsampledOrigin ); - numDirectionsImage->SetDirection( m_Parameters.m_ImageDirection ); + numDirectionsImage->SetDirection( m_Parameters.m_SignalGen.m_ImageDirection ); numDirectionsImage->SetLargestPossibleRegion( m_UpsampledImageRegion ); numDirectionsImage->SetBufferedRegion( m_UpsampledImageRegion ); numDirectionsImage->SetRequestedRegion( m_UpsampledImageRegion ); numDirectionsImage->Allocate(); numDirectionsImage->FillBuffer(0); + double sepAngle = cos(m_Parameters.m_SignalGen.m_FiberSeparationThreshold*M_PI/180.0); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; - boost::progress_display disp(tempTissueMask->GetLargestPossibleRegion().GetNumberOfPixels()); - ImageRegionIterator it(tempTissueMask, tempTissueMask->GetLargestPossibleRegion()); + boost::progress_display disp(m_MaskImage->GetLargestPossibleRegion().GetNumberOfPixels()); + ImageRegionIterator it(m_MaskImage, m_MaskImage->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { ++disp; unsigned long newTick = 50*disp.count()/disp.expected_count(); for (unsigned int tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } if (it.Get()>0) { int numFibs = m_RandGen->GetIntegerVariate(2)+1; DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(it.GetIndex()); double volume = m_RandGen->GetVariateWithClosedRange(0.3); - double sum = 0; + // double sum = 0; std::vector< double > fractions; for (int i=0; iGetVariateWithClosedRange(0.5)); - sum += fractions.at(i); + // sum += fractions.at(i); } - for (int i=0; i > directions; for (int i=0; iGetVariateWithClosedRange(2)-1.0; fib[1] = m_RandGen->GetVariateWithClosedRange(2)-1.0; fib[2] = m_RandGen->GetVariateWithClosedRange(2)-1.0; fib.Normalize(); double min = 0; for (unsigned int d=0; dmin) min = angle; } - if (min<0.5) + if (minSetFiberDirection(fib); pix += m_Parameters.m_FiberModelList.at(0)->SimulateMeasurement()*fractions[i]; directions.push_back(fib); } else i--; } pix *= (1-volume); + m_CompartmentImages.at(0)->SetPixel(it.GetIndex(), pix); // CSF/GM { - // int modelIndex = m_RandGen->GetIntegerVariate(m_Parameters.m_NonFiberModelList.size()-1); pix += volume*m_Parameters.m_NonFiberModelList.at(0)->SimulateMeasurement(); } - m_CompartmentImages.at(0)->SetPixel(it.GetIndex(), pix); numDirectionsImage->SetPixel(it.GetIndex(), numFibs); } ++it; } itk::ImageFileWriter< ItkUcharImgType >::Pointer wr = itk::ImageFileWriter< ItkUcharImgType >::New(); wr->SetInput(numDirectionsImage); - wr->SetFileName("/local/NumDirections.nrrd"); + wr->SetFileName(mitk::IOUtil::GetTempPath()+"/NumDirections_RandomDirections.nrrd"); wr->Update(); } } - if (logFile.is_open()) + if (m_Logfile.is_open()) { - logFile << "DONE"; - logFile.close(); + m_Logfile << "DONE"; + m_Logfile.close(); } m_StatusText += "\n\n"; if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } - // do k-space stuff DoubleDwiType::Pointer doubleOutImage; - if ( m_Parameters.m_SimulateKspaceAcquisition ) + if ( m_Parameters.m_SignalGen.m_SimulateKspaceAcquisition ) // do k-space stuff { m_StatusText += this->GetTime()+" > Adjusting complex signal\n"; MITK_INFO << "Adjusting complex signal:"; - if (m_Parameters.m_DoSimulateRelaxation) + if (m_Parameters.m_SignalGen.m_DoSimulateRelaxation) m_StatusText += "Simulating signal relaxation\n"; - if (m_Parameters.m_FrequencyMap.IsNotNull()) + if (m_Parameters.m_SignalGen.m_FrequencyMap.IsNotNull()) m_StatusText += "Simulating distortions\n"; - if (m_Parameters.m_DoAddGibbsRinging) + if (m_Parameters.m_SignalGen.m_DoAddGibbsRinging) m_StatusText += "Simulating ringing artifacts\n"; - if (m_Parameters.m_EddyStrength>0) + if (m_Parameters.m_SignalGen.m_EddyStrength>0) m_StatusText += "Simulating eddy currents\n"; - if (m_Parameters.m_Spikes>0) + if (m_Parameters.m_SignalGen.m_Spikes>0) m_StatusText += "Simulating spikes\n"; - if (m_Parameters.m_CroppingFactor<1.0) + if (m_Parameters.m_SignalGen.m_CroppingFactor<1.0) m_StatusText += "Simulating aliasing artifacts\n"; - if (m_Parameters.m_KspaceLineOffset>0) + if (m_Parameters.m_SignalGen.m_KspaceLineOffset>0) m_StatusText += "Simulating ghosts\n"; doubleOutImage = DoKspaceStuff(m_CompartmentImages); - m_Parameters.m_SignalScale = 1; // already scaled in DoKspaceStuff + m_Parameters.m_SignalGen.m_SignalScale = 1; // already scaled in DoKspaceStuff } - else + else // don't do k-space stuff, just sum compartments { m_StatusText += this->GetTime()+" > Summing compartments\n"; MITK_INFO << "Summing compartments"; doubleOutImage = m_CompartmentImages.at(0); for (unsigned int i=1; i::Pointer adder = itk::AddImageFilter< DoubleDwiType, DoubleDwiType, DoubleDwiType>::New(); adder->SetInput1(doubleOutImage); adder->SetInput2(m_CompartmentImages.at(i)); adder->Update(); doubleOutImage = adder->GetOutput(); } } if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } m_StatusText += this->GetTime()+" > Finalizing image\n"; MITK_INFO << "Finalizing image"; - if (m_Parameters.m_SignalScale>1) + if (m_Parameters.m_SignalGen.m_SignalScale>1) m_StatusText += " Scaling signal\n"; if (m_Parameters.m_NoiseModel!=NULL) m_StatusText += " Adding noise\n"; unsigned int window = 0; unsigned int min = itk::NumericTraits::max(); ImageRegionIterator it4 (outImage, outImage->GetLargestPossibleRegion()); - DoubleDwiType::PixelType signal; signal.SetSize(m_Parameters.GetNumVolumes()); + DoubleDwiType::PixelType signal; signal.SetSize(m_Parameters.m_SignalGen.GetNumVolumes()); boost::progress_display disp2(outImage->GetLargestPossibleRegion().GetNumberOfPixels()); m_StatusText += "0% 10 20 30 40 50 60 70 80 90 100%\n"; m_StatusText += "|----|----|----|----|----|----|----|----|----|----|\n*"; lastTick = 0; while(!it4.IsAtEnd()) { if (this->GetAbortGenerateData()) { m_StatusText += "\n"+this->GetTime()+" > Simulation aborted\n"; return; } ++disp2; unsigned long newTick = 50*disp2.count()/disp2.expected_count(); for (unsigned long tick = 0; tick<(newTick-lastTick); tick++) m_StatusText += "*"; lastTick = newTick; typename OutputImageType::IndexType index = it4.GetIndex(); - signal = doubleOutImage->GetPixel(index)*m_Parameters.m_SignalScale; + signal = doubleOutImage->GetPixel(index)*m_Parameters.m_SignalGen.m_SignalScale; if (m_Parameters.m_NoiseModel!=NULL) m_Parameters.m_NoiseModel->AddNoise(signal); for (unsigned int i=0; i0) signal[i] = floor(signal[i]+0.5); else signal[i] = ceil(signal[i]-0.5); - if ( (!m_Parameters.IsBaselineIndex(i) || signal.Size()==1) && signal[i]>window) + if ( (!m_Parameters.m_SignalGen.IsBaselineIndex(i) || signal.Size()==1) && signal[i]>window) window = signal[i]; - if ( (!m_Parameters.IsBaselineIndex(i) || signal.Size()==1) && signal[i]SetNthOutput(0, outImage); m_StatusText += "\n\n"; m_StatusText += "Finished simulation\n"; m_StatusText += "Simulation time: "+GetTime(); m_TimeProbe.Stop(); } +template< class PixelType > +void TractsToDWIImageFilter< PixelType >::SimulateMotion(int g) +{ + if (m_Parameters.m_SignalGen.m_DoAddMotion && gGetDeepCopy(); + m_Rotation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Rotation[0]*2)-m_Parameters.m_SignalGen.m_Rotation[0]; + m_Rotation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Rotation[1]*2)-m_Parameters.m_SignalGen.m_Rotation[1]; + m_Rotation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Rotation[2]*2)-m_Parameters.m_SignalGen.m_Rotation[2]; + m_Translation[0] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Translation[0]*2)-m_Parameters.m_SignalGen.m_Translation[0]; + m_Translation[1] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Translation[1]*2)-m_Parameters.m_SignalGen.m_Translation[1]; + m_Translation[2] = m_RandGen->GetVariateWithClosedRange(m_Parameters.m_SignalGen.m_Translation[2]*2)-m_Parameters.m_SignalGen.m_Translation[2]; + } + + // rotate mask image + if (m_MaskImageSet) + { + ImageRegionIterator maskIt(m_UpsampledMaskImage, m_UpsampledMaskImage->GetLargestPossibleRegion()); + m_MaskImage->FillBuffer(0); + + while(!maskIt.IsAtEnd()) + { + if (maskIt.Get()<=0) + { + ++maskIt; + continue; + } + + DoubleDwiType::IndexType index = maskIt.GetIndex(); + itk::Point point; + m_UpsampledMaskImage->TransformIndexToPhysicalPoint(index, point); + if (m_Parameters.m_SignalGen.m_DoRandomizeMotion) + point = m_FiberBundleWorkingCopy->TransformPoint(point.GetVnlVector(), m_Rotation[0],m_Rotation[1],m_Rotation[2],m_Translation[0],m_Translation[1],m_Translation[2]); + else + point = m_FiberBundleWorkingCopy->TransformPoint(point.GetVnlVector(), m_Rotation[0]*(g+1),m_Rotation[1]*(g+1),m_Rotation[2]*(g+1),m_Translation[0]*(g+1),m_Translation[1]*(g+1),m_Translation[2]*(g+1)); + + m_MaskImage->TransformPhysicalPointToIndex(point, index); + if (m_MaskImage->GetLargestPossibleRegion().IsInside(index)) + m_MaskImage->SetPixel(index,100); + ++maskIt; + } + } + + // rotate fibers + if (m_Logfile.is_open()) + { + m_Logfile << g+1 << " rotation: " << m_Rotation[0] << "," << m_Rotation[1] << "," << m_Rotation[2] << ";"; + m_Logfile << " translation: " << m_Translation[0] << "," << m_Translation[1] << "," << m_Translation[2] << "\n"; + } + m_FiberBundleTransformed->TransformFibers(m_Rotation[0],m_Rotation[1],m_Rotation[2],m_Translation[0],m_Translation[1],m_Translation[2]); + } +} + +template< class PixelType > +void TractsToDWIImageFilter< PixelType >::SimulateNonFiberSignal(ItkUcharImgType::IndexType index, double intraAxonalVolume, int g) +{ + int numFiberCompartments = m_Parameters.m_FiberModelList.size(); + int numNonFiberCompartments = m_Parameters.m_NonFiberModelList.size(); + + if (intraAxonalVolume>0.0001 && m_Parameters.m_SignalGen.m_DoDisablePartialVolume) // only fiber in voxel + { + DoubleDwiType::PixelType pix = m_CompartmentImages.at(0)->GetPixel(index); + if (g>=0) + pix[g] *= m_VoxelVolume/intraAxonalVolume; + else + pix *= m_VoxelVolume/intraAxonalVolume; + m_CompartmentImages.at(0)->SetPixel(index, pix); + m_VolumeFractions.at(0)->SetPixel(index, 1); + for (int i=1; iGetPixel(index); + if (g>=0) + pix[g] = 0.0; + else + pix.Fill(0.0); + m_CompartmentImages.at(i)->SetPixel(index, pix); + } + } + else + { + m_VolumeFractions.at(0)->SetPixel(index, intraAxonalVolume/m_VoxelVolume); + + itk::Point point; + m_MaskImage->TransformIndexToPhysicalPoint(index, point); + if (m_Parameters.m_SignalGen.m_DoAddMotion) + { + if (m_Parameters.m_SignalGen.m_DoRandomizeMotion && g>0) + point = m_FiberBundleWorkingCopy->TransformPoint(point.GetVnlVector(), -m_Rotation[0],-m_Rotation[1],-m_Rotation[2],-m_Translation[0],-m_Translation[1],-m_Translation[2]); + else if (g>=0) + point = m_FiberBundleWorkingCopy->TransformPoint(point.GetVnlVector(), -m_Rotation[0]*g,-m_Rotation[1]*g,-m_Rotation[2]*g,-m_Translation[0]*g,-m_Translation[1]*g,-m_Translation[2]*g); + } + + if (m_Parameters.m_SignalGen.m_DoDisablePartialVolume) + { + int maxVolumeIndex = 0; + double maxWeight = 0; + for (int i=0; i1) + { + DoubleDwiType::IndexType newIndex; + m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->TransformPhysicalPointToIndex(point, newIndex); + if (!m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion().IsInside(newIndex)) + continue; + weight = m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetPixel(newIndex); + } + + if (weight>maxWeight) + { + maxWeight = weight; + maxVolumeIndex = i; + } + } + DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(maxVolumeIndex+numFiberCompartments); + DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index); + + if (g>=0) + pix[g] += m_Parameters.m_NonFiberModelList[maxVolumeIndex]->SimulateMeasurement(g); + else + pix += m_Parameters.m_NonFiberModelList[maxVolumeIndex]->SimulateMeasurement(); + doubleDwi->SetPixel(index, pix); + m_VolumeFractions.at(maxVolumeIndex+numFiberCompartments)->SetPixel(index, 1); + } + else + { + double extraAxonalVolume = m_VoxelVolume-intraAxonalVolume; // non-fiber volume + double interAxonalVolume = 0; + if (numFiberCompartments>1) + interAxonalVolume = extraAxonalVolume * intraAxonalVolume/m_VoxelVolume; // inter-axonal fraction of non fiber compartment scales linearly with f + double other = extraAxonalVolume - interAxonalVolume; // rest of compartment + double singleinter = interAxonalVolume/(numFiberCompartments-1); + + // adjust non-fiber and intra-axonal signal + for (int i=1; iGetPixel(index); + if (intraAxonalVolume>0) // remove scaling by intra-axonal volume from inter-axonal compartment + { + if (g>=0) + pix[g] /= intraAxonalVolume; + else + pix /= intraAxonalVolume; + } + if (g>=0) + pix[g] *= singleinter; + else + pix *= singleinter; + m_CompartmentImages.at(i)->SetPixel(index, pix); + m_VolumeFractions.at(i)->SetPixel(index, singleinter/m_VoxelVolume); + } + + for (int i=0; i1) + { + DoubleDwiType::IndexType newIndex; + m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->TransformPhysicalPointToIndex(point, newIndex); + if (!m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetLargestPossibleRegion().IsInside(newIndex)) + continue; + weight = m_Parameters.m_NonFiberModelList[i]->GetVolumeFractionImage()->GetPixel(newIndex); + } + + DoubleDwiType::Pointer doubleDwi = m_CompartmentImages.at(i+numFiberCompartments); + DoubleDwiType::PixelType pix = doubleDwi->GetPixel(index); + + if (g>=0) + pix[g] += m_Parameters.m_NonFiberModelList[i]->SimulateMeasurement(g)*other*weight; + else + pix += m_Parameters.m_NonFiberModelList[i]->SimulateMeasurement()*other*weight; + doubleDwi->SetPixel(index, pix); + m_VolumeFractions.at(i+numFiberCompartments)->SetPixel(index, other/m_VoxelVolume*weight); + } + } + } +} + template< class PixelType > itk::Point TractsToDWIImageFilter< PixelType >::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } template< class PixelType > itk::Vector TractsToDWIImageFilter< PixelType >::GetItkVector(double point[3]) { itk::Vector itkVector; itkVector[0] = point[0]; itkVector[1] = point[1]; itkVector[2] = point[2]; return itkVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(double point[3]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } template< class PixelType > vnl_vector_fixed TractsToDWIImageFilter< PixelType >::GetVnlVector(Vector& vector) { vnl_vector_fixed vnlVector; vnlVector[0] = vector[0]; vnlVector[1] = vector[1]; vnlVector[2] = vector[2]; return vnlVector; } template< class PixelType > double TractsToDWIImageFilter< PixelType >::RoundToNearest(double num) { return (num > 0.0) ? floor(num + 0.5) : ceil(num - 0.5); } template< class PixelType > std::string TractsToDWIImageFilter< PixelType >::GetTime() { m_TimeProbe.Stop(); unsigned long total = RoundToNearest(m_TimeProbe.GetTotal()); unsigned long hours = total/3600; unsigned long minutes = (total%3600)/60; unsigned long seconds = total%60; std::string out = ""; out.append(boost::lexical_cast(hours)); out.append(":"); out.append(boost::lexical_cast(minutes)); out.append(":"); out.append(boost::lexical_cast(seconds)); m_TimeProbe.Start(); return out; } } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h index dfb640ad23..aa56645ad8 100755 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToDWIImageFilter.h @@ -1,111 +1,132 @@ /*=================================================================== 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 __itkTractsToDWIImageFilter_h__ #define __itkTractsToDWIImageFilter_h__ #include #include #include #include #include #include #include #include #include namespace itk { /** * \brief Generates artificial diffusion weighted image volume from the input fiberbundle using a generic multicompartment model. * See "Fiberfox: Facilitating the creation of realistic white matter software phantoms" (DOI: 10.1002/mrm.25045) for details. */ template< class PixelType > class TractsToDWIImageFilter : public ImageSource< itk::VectorImage< PixelType, 3 > > { public: typedef TractsToDWIImageFilter Self; typedef ImageSource< itk::VectorImage< PixelType, 3 > > Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef typename Superclass::OutputImageType OutputImageType; typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; typedef mitk::FiberBundleX::Pointer FiberBundleType; typedef itk::VectorImage< double, 3 > DoubleDwiType; typedef itk::Matrix MatrixType; typedef itk::Image< double, 2 > SliceType; typedef itk::VnlForwardFFTImageFilter::OutputImageType ComplexSliceType; typedef itk::Vector< double,3> DoubleVectorType; itkFactorylessNewMacro(Self) itkCloneMacro(Self) itkTypeMacro( TractsToDWIImageFilter, ImageSource ) /** Input */ itkSetMacro( FiberBundle, FiberBundleType ) ///< Input fiber bundle itkSetMacro( UseConstantRandSeed, bool ) ///< Seed for random generator. void SetParameters( FiberfoxParameters param ) ///< Simulation parameters. { m_Parameters = param; } /** Output */ FiberfoxParameters GetParameters(){ return m_Parameters; } std::vector< ItkDoubleImgType::Pointer > GetVolumeFractions() ///< one double image for each compartment containing the corresponding volume fraction per voxel { return m_VolumeFractions; } mitk::LevelWindow GetLevelWindow(){ return m_LevelWindow; } itkGetMacro( StatusText, std::string ) void GenerateData(); protected: TractsToDWIImageFilter(); virtual ~TractsToDWIImageFilter(); itk::Point GetItkPoint(double point[3]); itk::Vector GetItkVector(double point[3]); vnl_vector_fixed GetVnlVector(double point[3]); vnl_vector_fixed GetVnlVector(Vector< float, 3 >& vector); double RoundToNearest(double num); std::string GetTime(); /** Transform generated image compartment by compartment, channel by channel and slice by slice using DFT and add k-space artifacts. */ DoubleDwiType::Pointer DoKspaceStuff(std::vector< DoubleDwiType::Pointer >& images); + /** Generate signal of non-fiber compartments. */ + void SimulateNonFiberSignal(ItkUcharImgType::IndexType index, double intraAxonalVolume, int g=-1); + + /** Move fibers to simulate headmotion */ + void SimulateMotion(int g=-1); + + // input mitk::FiberfoxParameters m_Parameters; - itk::Vector m_UpsampledSpacing; - itk::Point m_UpsampledOrigin; - ImageRegion<3> m_UpsampledImageRegion; FiberBundleType m_FiberBundle; + + // output mitk::LevelWindow m_LevelWindow; std::vector< ItkDoubleImgType::Pointer > m_VolumeFractions; std::string m_StatusText; + + // MISC itk::TimeProbe m_TimeProbe; bool m_UseConstantRandSeed; - itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen; + bool m_MaskImageSet; + ofstream m_Logfile; - std::vector< DoubleDwiType::Pointer > m_CompartmentImages; + // signal generation + FiberBundleType m_FiberBundleWorkingCopy; ///< we work on an upsampled version of the input bundle + FiberBundleType m_FiberBundleTransformed; ///< transformed bundle simulating headmotion + itk::Vector m_UpsampledSpacing; + itk::Point m_UpsampledOrigin; + ImageRegion<3> m_UpsampledImageRegion; + double m_VoxelVolume; + std::vector< DoubleDwiType::Pointer > m_CompartmentImages; + ItkUcharImgType::Pointer m_MaskImage; ///< copy of mask image (changes for each motion step) + ItkUcharImgType::Pointer m_UpsampledMaskImage; ///< helper image for motion simulation + DoubleVectorType m_Rotation; + DoubleVectorType m_Translation; + itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen; }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkTractsToDWIImageFilter.cpp" #endif #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp index 9f44d41d0a..975a40f5ec 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.cpp @@ -1,556 +1,563 @@ #include "itkTractsToVectorImageFilter.h" // VTK #include #include #include // ITK #include #include // misc #define _USE_MATH_DEFINES #include #include namespace itk{ static bool CompareVectorLengths(const vnl_vector_fixed< double, 3 >& v1, const vnl_vector_fixed< double, 3 >& v2) { return (v1.magnitude()>v2.magnitude()); } template< class PixelType > TractsToVectorImageFilter< PixelType >::TractsToVectorImageFilter(): m_AngularThreshold(0.7), m_Epsilon(0.999), m_MaskImage(NULL), m_NormalizeVectors(false), m_UseWorkingCopy(true), m_MaxNumDirections(3), m_SizeThreshold(0.2), - m_NumDirectionsImage(NULL) + m_NumDirectionsImage(NULL), + m_CreateDirectionImages(true) { this->SetNumberOfRequiredOutputs(1); } template< class PixelType > TractsToVectorImageFilter< PixelType >::~TractsToVectorImageFilter() { } template< class PixelType > vnl_vector_fixed TractsToVectorImageFilter< PixelType >::GetVnlVector(double point[]) { vnl_vector_fixed vnlVector; vnlVector[0] = point[0]; vnlVector[1] = point[1]; vnlVector[2] = point[2]; return vnlVector; } template< class PixelType > itk::Point TractsToVectorImageFilter< PixelType >::GetItkPoint(double point[]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } template< class PixelType > void TractsToVectorImageFilter< PixelType >::GenerateData() { mitk::BaseGeometry::Pointer geometry = m_FiberBundle->GetGeometry(); // calculate new image parameters itk::Vector spacing; itk::Point origin; itk::Matrix direction; ImageRegion<3> imageRegion; if (!m_MaskImage.IsNull()) { spacing = m_MaskImage->GetSpacing(); imageRegion = m_MaskImage->GetLargestPossibleRegion(); origin = m_MaskImage->GetOrigin(); direction = m_MaskImage->GetDirection(); } else { spacing = geometry->GetSpacing(); origin = geometry->GetOrigin(); mitk::BaseGeometry::BoundsArrayType bounds = geometry->GetBounds(); origin[0] += bounds.GetElement(0); origin[1] += bounds.GetElement(2); origin[2] += bounds.GetElement(4); for (int i=0; i<3; i++) for (int j=0; j<3; j++) direction[j][i] = geometry->GetMatrixColumn(i)[j]; imageRegion.SetSize(0, geometry->GetExtent(0)); imageRegion.SetSize(1, geometry->GetExtent(1)); imageRegion.SetSize(2, geometry->GetExtent(2)); m_MaskImage = ItkUcharImgType::New(); m_MaskImage->SetSpacing( spacing ); m_MaskImage->SetOrigin( origin ); m_MaskImage->SetDirection( direction ); m_MaskImage->SetRegions( imageRegion ); m_MaskImage->Allocate(); m_MaskImage->FillBuffer(1); } OutputImageType::RegionType::SizeType outImageSize = imageRegion.GetSize(); m_OutImageSpacing = m_MaskImage->GetSpacing(); m_ClusteredDirectionsContainer = ContainerType::New(); // initialize num directions image m_NumDirectionsImage = ItkUcharImgType::New(); m_NumDirectionsImage->SetSpacing( spacing ); m_NumDirectionsImage->SetOrigin( origin ); m_NumDirectionsImage->SetDirection( direction ); m_NumDirectionsImage->SetRegions( imageRegion ); m_NumDirectionsImage->Allocate(); m_NumDirectionsImage->FillBuffer(0); // initialize direction images m_DirectionImageContainer = DirectionImageContainerType::New(); // resample fiber bundle double minSpacing = 1; if(m_OutImageSpacing[0]GetDeepCopy(); // resample fiber bundle for sufficient voxel coverage m_FiberBundle->ResampleFibers(minSpacing/10); // iterate over all fibers vtkSmartPointer fiberPolyData = m_FiberBundle->GetFiberPolyData(); int numFibers = m_FiberBundle->GetNumFibers(); m_DirectionsContainer = ContainerType::New(); MITK_INFO << "Generating directions from tractogram"; boost::progress_display disp(numFibers); for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (numPoints<2) continue; vnl_vector_fixed dir; itk::Point worldPos; vnl_vector v; for( int j=0; jGetPoint(j); worldPos = GetItkPoint(temp); itk::Index<3> index; m_MaskImage->TransformPhysicalPointToIndex(worldPos, index); if (!m_MaskImage->GetLargestPossibleRegion().IsInside(index) || m_MaskImage->GetPixel(index)==0) continue; // get fiber tangent direction at this position v = GetVnlVector(temp); dir = GetVnlVector(points->GetPoint(j+1))-v; if (dir.is_zero()) continue; dir.normalize(); // add direction to container unsigned int idx = index[0] + outImageSize[0]*(index[1] + outImageSize[1]*index[2]); DirectionContainerType::Pointer dirCont; if (m_DirectionsContainer->IndexExists(idx)) { dirCont = m_DirectionsContainer->GetElement(idx); if (dirCont.IsNull()) { dirCont = DirectionContainerType::New(); dirCont->push_back(dir); m_DirectionsContainer->InsertElement(idx, dirCont); } else dirCont->push_back(dir); } else { dirCont = DirectionContainerType::New(); dirCont->push_back(dir); m_DirectionsContainer->InsertElement(idx, dirCont); } } } vtkSmartPointer m_VtkCellArray = vtkSmartPointer::New(); vtkSmartPointer m_VtkPoints = vtkSmartPointer::New(); itk::ImageRegionIterator dirIt(m_NumDirectionsImage, m_NumDirectionsImage->GetLargestPossibleRegion()); MITK_INFO << "Clustering directions"; boost::progress_display disp2(outImageSize[0]*outImageSize[1]*outImageSize[2]); while(!dirIt.IsAtEnd()) { ++disp2; OutputImageType::IndexType index = dirIt.GetIndex(); int idx = index[0]+(index[1]+index[2]*outImageSize[1])*outImageSize[0]; if (!m_DirectionsContainer->IndexExists(idx)) { ++dirIt; continue; } DirectionContainerType::Pointer dirCont = m_DirectionsContainer->GetElement(idx); if (dirCont.IsNull() || dirCont->empty()) { ++dirIt; continue; } std::vector< double > lengths; lengths.resize(dirCont->size(), 1); // all peaks have size 1 - DirectionContainerType::Pointer directions = FastClustering(dirCont, lengths); - std::sort( directions->begin(), directions->end(), CompareVectorLengths ); + DirectionContainerType::Pointer directions; + if (m_MaxNumDirections>0) + { + directions = FastClustering(dirCont, lengths); + std::sort( directions->begin(), directions->end(), CompareVectorLengths ); + } + else + directions = dirCont; unsigned int numDir = directions->size(); if (m_MaxNumDirections>0 && numDir>m_MaxNumDirections) numDir = m_MaxNumDirections; int count = 0; for (unsigned int i=0; i container = vtkSmartPointer::New(); itk::ContinuousIndex center; center[0] = index[0]; center[1] = index[1]; center[2] = index[2]; itk::Point worldCenter; m_MaskImage->TransformContinuousIndexToPhysicalPoint( center, worldCenter ); DirectionType dir = directions->at(i); if (dir.magnitude()size()) + if (m_CreateDirectionImages && i<10) { - ItkDirectionImageType::Pointer directionImage = ItkDirectionImageType::New(); - directionImage->SetSpacing( spacing ); - directionImage->SetOrigin( origin ); - directionImage->SetDirection( direction ); - directionImage->SetRegions( imageRegion ); - directionImage->Allocate(); - Vector< float, 3 > nullVec; nullVec.Fill(0.0); - directionImage->FillBuffer(nullVec); - m_DirectionImageContainer->InsertElement(i, directionImage); - } + if (i==m_DirectionImageContainer->size()) + { + ItkDirectionImageType::Pointer directionImage = ItkDirectionImageType::New(); + directionImage->SetSpacing( spacing ); + directionImage->SetOrigin( origin ); + directionImage->SetDirection( direction ); + directionImage->SetRegions( imageRegion ); + directionImage->Allocate(); + Vector< float, 3 > nullVec; nullVec.Fill(0.0); + directionImage->FillBuffer(nullVec); + m_DirectionImageContainer->InsertElement(i, directionImage); + } - // set direction image pixel - ItkDirectionImageType::Pointer directionImage = m_DirectionImageContainer->GetElement(i); - Vector< float, 3 > pixel; - pixel.SetElement(0, dir[0]); - pixel.SetElement(1, dir[1]); - pixel.SetElement(2, dir[2]); - directionImage->SetPixel(index, pixel); + // set direction image pixel + ItkDirectionImageType::Pointer directionImage = m_DirectionImageContainer->GetElement(i); + Vector< float, 3 > pixel; + pixel.SetElement(0, dir[0]); + pixel.SetElement(1, dir[1]); + pixel.SetElement(2, dir[2]); + directionImage->SetPixel(index, pixel); + } // add direction to vector field (with spacing compensation) itk::Point worldStart; worldStart[0] = worldCenter[0]-dir[0]/2*minSpacing; worldStart[1] = worldCenter[1]-dir[1]/2*minSpacing; worldStart[2] = worldCenter[2]-dir[2]/2*minSpacing; vtkIdType id = m_VtkPoints->InsertNextPoint(worldStart.GetDataPointer()); container->GetPointIds()->InsertNextId(id); itk::Point worldEnd; worldEnd[0] = worldCenter[0]+dir[0]/2*minSpacing; worldEnd[1] = worldCenter[1]+dir[1]/2*minSpacing; worldEnd[2] = worldCenter[2]+dir[2]/2*minSpacing; id = m_VtkPoints->InsertNextPoint(worldEnd.GetDataPointer()); container->GetPointIds()->InsertNextId(id); m_VtkCellArray->InsertNextCell(container); } dirIt.Set(count); ++dirIt; } vtkSmartPointer directionsPolyData = vtkSmartPointer::New(); directionsPolyData->SetPoints(m_VtkPoints); directionsPolyData->SetLines(m_VtkCellArray); m_OutputFiberBundle = mitk::FiberBundleX::New(directionsPolyData); } template< class PixelType > TractsToVectorImageFilter< PixelType >::DirectionContainerType::Pointer TractsToVectorImageFilter< PixelType >::FastClustering(DirectionContainerType::Pointer inDirs, std::vector< double > lengths) { DirectionContainerType::Pointer outDirs = DirectionContainerType::New(); if (inDirs->size()<2) return inDirs; DirectionType oldMean, currentMean; std::vector< int > touched; // initialize touched.resize(inDirs->size(), 0); bool free = true; currentMean = inDirs->at(0); // initialize first seed currentMean.normalize(); double length = lengths.at(0); touched[0] = 1; std::vector< double > newLengths; bool meanChanged = false; double max = 0; while (free) { oldMean.fill(0.0); // start mean-shift clustering double angle = 0; while (fabs(dot_product(currentMean, oldMean))<0.99) { oldMean = currentMean; currentMean.fill(0.0); for (unsigned int i=0; isize(); i++) { angle = dot_product(oldMean, inDirs->at(i)); if (angle>=m_AngularThreshold) { currentMean += inDirs->at(i); if (meanChanged) length += lengths.at(i); touched[i] = 1; meanChanged = true; } else if (-angle>=m_AngularThreshold) { currentMean -= inDirs->at(i); if (meanChanged) length += lengths.at(i); touched[i] = 1; meanChanged = true; } } if(!meanChanged) currentMean = oldMean; else currentMean.normalize(); } // found stable mean outDirs->push_back(currentMean); newLengths.push_back(length); if (length>max) max = length; // find next unused seed free = false; for (unsigned int i=0; iat(i); free = true; meanChanged = false; length = lengths.at(i); touched[i] = 1; break; } } if (inDirs->size()==outDirs->size()) { if (!m_NormalizeVectors && max>0) for (unsigned int i=0; isize(); i++) outDirs->SetElement(i, outDirs->at(i)*newLengths.at(i)/max); return outDirs; } else return FastClustering(outDirs, newLengths); } //template< class PixelType > //std::vector< DirectionType > TractsToVectorImageFilter< PixelType >::Clustering(std::vector< DirectionType >& inDirs) //{ // std::vector< DirectionType > outDirs; // if (inDirs.empty()) // return outDirs; // DirectionType oldMean, currentMean, workingMean; // std::vector< DirectionType > normalizedDirs; // std::vector< int > touched; // for (std::size_t i=0; i0.0001) // { // counter = 0; // oldMean = currentMean; // workingMean = oldMean; // workingMean.normalize(); // currentMean.fill(0.0); // for (std::size_t i=0; i=m_AngularThreshold) // { // currentMean += inDirs[i]; // counter++; // } // else if (-angle>=m_AngularThreshold) // { // currentMean -= inDirs[i]; // counter++; // } // } // } // // found stable mean // if (counter>0) // { // bool add = true; // DirectionType normMean = currentMean; // normMean.normalize(); // for (std::size_t i=0; i0) // { // if (mag>max) // max = mag; // outDirs.push_back(currentMean); // } // } // } // } // if (m_NormalizeVectors) // for (std::size_t i=0; i0) // for (std::size_t i=0; i //TractsToVectorImageFilter< PixelType >::DirectionContainerType::Pointer TractsToVectorImageFilter< PixelType >::MeanShiftClustering(DirectionContainerType::Pointer dirCont) //{ // DirectionContainerType::Pointer container = DirectionContainerType::New(); // double max = 0; // for (DirectionContainerType::ConstIterator it = dirCont->Begin(); it!=dirCont->End(); ++it) // { // vnl_vector_fixed mean = ClusterStep(dirCont, it.Value()); // if (mean.is_zero()) // continue; // bool addMean = true; // for (DirectionContainerType::ConstIterator it2 = container->Begin(); it2!=container->End(); ++it2) // { // vnl_vector_fixed dir = it2.Value(); // double angle = fabs(dot_product(mean, dir)/(mean.magnitude()*dir.magnitude())); // if (angle>=m_Epsilon) // { // addMean = false; // break; // } // } // if (addMean) // { // if (m_NormalizeVectors) // mean.normalize(); // else if (mean.magnitude()>max) // max = mean.magnitude(); // container->InsertElement(container->Size(), mean); // } // } // // max normalize voxel directions // if (max>0 && !m_NormalizeVectors) // for (std::size_t i=0; iSize(); i++) // container->ElementAt(i) /= max; // if (container->Size()Size()) // return MeanShiftClustering(container); // else // return container; //} //template< class PixelType > //vnl_vector_fixed TractsToVectorImageFilter< PixelType >::ClusterStep(DirectionContainerType::Pointer dirCont, vnl_vector_fixed currentMean) //{ // vnl_vector_fixed newMean; newMean.fill(0); // for (DirectionContainerType::ConstIterator it = dirCont->Begin(); it!=dirCont->End(); ++it) // { // vnl_vector_fixed dir = it.Value(); // double angle = dot_product(currentMean, dir)/(currentMean.magnitude()*dir.magnitude()); // if (angle>=m_AngularThreshold) // newMean += dir; // else if (-angle>=m_AngularThreshold) // newMean -= dir; // } // if (fabs(dot_product(currentMean, newMean)/(currentMean.magnitude()*newMean.magnitude()))>=m_Epsilon || newMean.is_zero()) // return newMean; // else // return ClusterStep(dirCont, newMean); //} } diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.h b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.h index 21d931e14c..3a3eab15be 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.h +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkTractsToVectorImageFilter.h @@ -1,108 +1,110 @@ #ifndef __itkTractsToVectorImageFilter_h__ #define __itkTractsToVectorImageFilter_h__ // MITK #include // ITK #include #include // VTK #include #include #include #include #include using namespace mitk; namespace itk{ /** * \brief Extracts the voxel-wise main directions of the input fiber bundle. */ template< class PixelType > class TractsToVectorImageFilter : public ImageSource< VectorImage< float, 3 > > { public: typedef TractsToVectorImageFilter Self; typedef ProcessObject Superclass; typedef SmartPointer< Self > Pointer; typedef SmartPointer< const Self > ConstPointer; typedef itk::Vector OutputVectorType; typedef itk::Image OutputImageType; typedef std::vector< OutputImageType::Pointer > OutputImageContainerType; typedef vnl_vector_fixed< double, 3 > DirectionType; typedef VectorContainer< unsigned int, DirectionType > DirectionContainerType; typedef VectorContainer< unsigned int, DirectionContainerType::Pointer > ContainerType; typedef Image< Vector< float, 3 >, 3> ItkDirectionImageType; typedef VectorContainer< unsigned int, ItkDirectionImageType::Pointer > DirectionImageContainerType; typedef itk::Image ItkUcharImgType; typedef itk::Image ItkDoubleImgType; itkFactorylessNewMacro(Self) itkCloneMacro(Self) itkTypeMacro( TractsToVectorImageFilter, ImageSource ) itkSetMacro( SizeThreshold, float) itkGetMacro( SizeThreshold, float) itkSetMacro( AngularThreshold, float) ///< cluster directions that are closer together than the specified threshold itkGetMacro( AngularThreshold, float) ///< cluster directions that are closer together than the specified threshold itkSetMacro( NormalizeVectors, bool) ///< Normalize vectors to length 1 itkGetMacro( NormalizeVectors, bool) ///< Normalize vectors to length 1 itkSetMacro( UseWorkingCopy, bool) ///< Do not modify input fiber bundle. Use a copy. itkGetMacro( UseWorkingCopy, bool) ///< Do not modify input fiber bundle. Use a copy. itkSetMacro( MaxNumDirections, unsigned long) ///< If more directions are extracted, only the largest are kept. itkGetMacro( MaxNumDirections, unsigned long) ///< If more directions are extracted, only the largest are kept. itkSetMacro( MaskImage, ItkUcharImgType::Pointer) ///< only process voxels inside mask itkSetMacro( FiberBundle, FiberBundleX::Pointer) ///< input fiber bundle itkGetMacro( ClusteredDirectionsContainer, ContainerType::Pointer) ///< output directions itkGetMacro( NumDirectionsImage, ItkUcharImgType::Pointer) ///< number of directions per voxel itkGetMacro( OutputFiberBundle, FiberBundleX::Pointer) ///< vector field for visualization purposes itkGetMacro( DirectionImageContainer, DirectionImageContainerType::Pointer) ///< output directions + itkSetMacro( CreateDirectionImages, bool) void GenerateData(); protected: DirectionContainerType::Pointer FastClustering(DirectionContainerType::Pointer inDirs, std::vector< double > lengths); ///< cluster fiber directions // std::vector< DirectionType > Clustering(std::vector< DirectionType >& inDirs); // DirectionContainerType::Pointer MeanShiftClustering(DirectionContainerType::Pointer dirCont); // vnl_vector_fixed ClusterStep(DirectionContainerType::Pointer dirCont, vnl_vector_fixed currentMean); vnl_vector_fixed GetVnlVector(double point[3]); itk::Point GetItkPoint(double point[3]); TractsToVectorImageFilter(); virtual ~TractsToVectorImageFilter(); FiberBundleX::Pointer m_FiberBundle; ///< input fiber bundle float m_AngularThreshold; ///< cluster directions that are closer together than the specified threshold float m_Epsilon; ///< epsilon for vector equality check ItkUcharImgType::Pointer m_MaskImage; ///< only voxels inside the binary mask are processed bool m_NormalizeVectors; ///< normalize vectors to length 1 itk::Vector m_OutImageSpacing; ///< spacing of output image ContainerType::Pointer m_DirectionsContainer; ///< container for fiber directions bool m_UseWorkingCopy; ///< do not modify input fiber bundle but work on copy unsigned long m_MaxNumDirections; ///< if more directions per voxel are extracted, only the largest are kept float m_SizeThreshold; + bool m_CreateDirectionImages; // output datastructures ContainerType::Pointer m_ClusteredDirectionsContainer; ///< contains direction vectors for each voxel ItkUcharImgType::Pointer m_NumDirectionsImage; ///< shows number of fibers per voxel DirectionImageContainerType::Pointer m_DirectionImageContainer; ///< contains images that contain the output directions FiberBundleX::Pointer m_OutputFiberBundle; ///< vector field for visualization purposes }; } #ifndef ITK_MANUAL_INSTANTIATION #include "itkTractsToVectorImageFilter.cpp" #endif #endif // __itkTractsToVectorImageFilter_h__ diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp index 41425b0fd2..805447625c 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp @@ -1,471 +1,658 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include +#include -#include -#include -#include -#include -#include +#include +#include template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::FiberfoxParameters() - : m_SignalScale(100) - , m_tEcho(100) - , m_tLine(1) - , m_tInhom(50) - , m_Bvalue(1000) - , m_SimulateKspaceAcquisition(false) - , m_AxonRadius(0) - , m_DiffusionDirectionMode(FIBER_TANGENT_DIRECTIONS) - , m_Spikes(0) - , m_SpikeAmplitude(1) - , m_KspaceLineOffset(0) - , m_EddyStrength(0) - , m_Tau(70) - , m_CroppingFactor(1) - , m_DoAddGibbsRinging(false) - , m_DoSimulateRelaxation(true) - , m_DoDisablePartialVolume(false) - , m_DoAddMotion(false) - , m_DoRandomizeMotion(true) - , m_NoiseModel(NULL) - , m_FrequencyMap(NULL) - , m_MaskImage(NULL) - , m_ResultNode(mitk::DataNode::New()) - , m_ParentNode(NULL) - , m_SignalModelString("") - , m_ArtifactModelString("") - , m_OutputPath("") - , m_NumBaseline(1) - , m_NumGradients(6) + : m_NoiseModel(NULL) { - m_ImageDirection.SetIdentity(); - m_ImageOrigin.Fill(0.0); - m_ImageRegion.SetSize(0, 11); - m_ImageRegion.SetSize(1, 11); - m_ImageRegion.SetSize(2, 3); - m_ImageSpacing.Fill(2.0); - m_Translation.Fill(0.0); - m_Rotation.Fill(0.0); - - GenerateGradientHalfShell(); } template< class ScalarType > mitk::FiberfoxParameters< ScalarType >::~FiberfoxParameters() { // if (m_NoiseModel!=NULL) // delete m_NoiseModel; } -template< class ScalarType > -void mitk::FiberfoxParameters< ScalarType >::GenerateGradientHalfShell() +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 -std::vector< int > mitk::FiberfoxParameters< ScalarType >::GetBaselineIndices() +std::vector< int > 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; } -template< class ScalarType > -unsigned int mitk::FiberfoxParameters< ScalarType >::GetFirstBaselineIndex() +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; } -template< class ScalarType > -bool mitk::FiberfoxParameters< ScalarType >::IsBaselineIndex(unsigned int idx) +bool mitk::SignalGenerationParameters::IsBaselineIndex(unsigned int idx) { if (m_GradientDirections.size()>idx && m_GradientDirections.at(idx).GetNorm()<0.0001) return true; return false; } -template< class ScalarType > -unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumWeightedVolumes() +unsigned int mitk::SignalGenerationParameters::GetNumWeightedVolumes() { return m_NumGradients; } -template< class ScalarType > -unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumBaselineVolumes() +unsigned int mitk::SignalGenerationParameters::GetNumBaselineVolumes() { return m_NumBaseline; } -template< class ScalarType > -unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumVolumes() +unsigned int mitk::SignalGenerationParameters::GetNumVolumes() { return m_GradientDirections.size(); } -template< class ScalarType > -typename mitk::FiberfoxParameters< ScalarType >::GradientListType mitk::FiberfoxParameters< ScalarType >::GetGradientDirections() +typename mitk::SignalGenerationParameters::GradientListType mitk::SignalGenerationParameters::GetGradientDirections() { return m_GradientDirections; } -template< class ScalarType > -typename mitk::FiberfoxParameters< ScalarType >::GradientType mitk::FiberfoxParameters< ScalarType >::GetGradientDirection(unsigned int i) +mitk::SignalGenerationParameters::GradientType mitk::SignalGenerationParameters::GetGradientDirection(unsigned int i) { return m_GradientDirections.at(i); } -template< class ScalarType > -void mitk::FiberfoxParameters< ScalarType >::SetNumWeightedGradients(int numGradients) +void mitk::SignalGenerationParameters::SetNumWeightedVolumes(int numGradients) { m_NumGradients = numGradients; GenerateGradientHalfShell(); } -template< class ScalarType > -void mitk::FiberfoxParameters< ScalarType >::SetGradienDirections(GradientListType gradientList) +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++; } } -template< class ScalarType > -void mitk::FiberfoxParameters< ScalarType >::SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientList) +void mitk::SignalGenerationParameters::SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::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 >::LoadParameters(string filename) +void mitk::FiberfoxParameters< ScalarType >::SaveParameters(string filename) { + if(filename.empty()) + return; + if(".ffp"!=filename.substr(filename.size()-4, 4)) + filename += ".ffp"; + boost::property_tree::ptree parameters; - boost::property_tree::xml_parser::read_xml(filename, 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()); + 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.diffusiondirectionmode", m_SignalGen.m_DiffusionDirectionMode); + parameters.put("fiberfox.image.fiberseparationthreshold", m_SignalGen.m_FiberSeparationThreshold); + 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.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)) + parameters.put("fiberfox.image.artifacts.noisetype", "rice"); + else if (dynamic_cast*>(m_NoiseModel)) + 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)+".stick.d", model->GetDiffusivity()); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".stick.t2", model->GetT2()); + } + else if (dynamic_cast*>(signalModel)) + { + mitk::TensorModel* model = dynamic_cast*>(signalModel); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".tensor.d1", model->GetDiffusivity1()); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".tensor.d2", model->GetDiffusivity2()); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".tensor.d3", model->GetDiffusivity3()); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".tensor.t2", model->GetT2()); + } + else if (dynamic_cast*>(signalModel)) + { + mitk::RawShModel* model = dynamic_cast*>(signalModel); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".prototype.minFA", model->GetFaRange().first); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".prototype.maxFA", model->GetFaRange().second); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".prototype.minADC", model->GetAdcRange().first); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".prototype.maxADC", model->GetAdcRange().second); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".prototype.numSamples", model->GetMaxNumKernels()); + } + else if (dynamic_cast*>(signalModel)) + { + mitk::BallModel* model = dynamic_cast*>(signalModel); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".ball.d", model->GetDiffusivity()); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".ball.t2", model->GetT2()); + } + else if (dynamic_cast*>(signalModel)) + { + mitk::AstroStickModel* model = dynamic_cast*>(signalModel); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".astrosticks.d", model->GetDiffusivity()); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".astrosticks.t2", model->GetT2()); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".astrosticks.randomize", model->GetRandomizeSticks()); + } + else if (dynamic_cast*>(signalModel)) + { + mitk::DotModel* model = dynamic_cast*>(signalModel); + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".dot.t2", model->GetT2()); + } + + 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); + +// if (m_SignalGen.m_DoAddDistortions) +// { +// 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."; +// } +} + +template< class ScalarType > +void mitk::FiberfoxParameters< ScalarType >::LoadParameters(string filename) +{ + if(filename.empty()) + return; + + boost::property_tree::ptree parameterTree; + boost::property_tree::xml_parser::read_xml(filename, parameterTree); m_FiberModelList.clear(); m_NonFiberModelList.clear(); if (m_NoiseModel!=NULL) delete m_NoiseModel; - BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameters.get_child("fiberfox") ) + BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameterTree.get_child("fiberfox") ) { - if( v1.first == "image" ) + if( v1.first == "fibers" ) { - m_ImageRegion.SetSize(0, v1.second.get("basic.size.x")); - m_ImageRegion.SetSize(1, v1.second.get("basic.size.y")); - m_ImageRegion.SetSize(2, v1.second.get("basic.size.z")); - m_ImageSpacing[0] = v1.second.get("basic.spacing.x"); - m_ImageSpacing[1] = v1.second.get("basic.spacing.y"); - m_ImageSpacing[2] = v1.second.get("basic.spacing.z"); - m_NumGradients = v1.second.get("basic.numgradients"); - GenerateGradientHalfShell(); - m_Bvalue = v1.second.get("basic.bvalue"); - m_SignalScale = v1.second.get("signalScale"); - m_tEcho = v1.second.get("tEcho"); - m_tLine = v1.second.get("tLine"); - m_tInhom = v1.second.get("tInhom"); - m_AxonRadius = v1.second.get("axonRadius"); - m_DoSimulateRelaxation = v1.second.get("doSimulateRelaxation"); - m_DoDisablePartialVolume = v1.second.get("doDisablePartialVolume"); - if (v1.second.get("artifacts.addnoise")) - { - switch (v1.second.get("artifacts.noisedistribution")) - { - case 0: - { - m_NoiseModel = new mitk::RicianNoiseModel< ScalarType >(); - break; - } - case 1: - { - m_NoiseModel = new mitk::ChiSquareNoiseModel< ScalarType >(); - break; - } - default: - { - m_NoiseModel = new mitk::RicianNoiseModel< ScalarType >(); - } - } - m_NoiseModel->SetNoiseVariance(v1.second.get("artifacts.noisevariance")); - } + m_Misc.m_CheckRealTimeFibersBox = v1.second.get("realtime", m_Misc.m_CheckRealTimeFibersBox); + m_Misc.m_CheckAdvancedFiberOptionsBox = v1.second.get("showadvanced", m_Misc.m_CheckAdvancedFiberOptionsBox); + m_Misc.m_CheckConstantRadiusBox = v1.second.get("constantradius", m_Misc.m_CheckConstantRadiusBox); + m_Misc.m_CheckIncludeFiducialsBox = v1.second.get("includeFiducials", m_Misc.m_CheckIncludeFiducialsBox); - m_KspaceLineOffset = v1.second.get("artifacts.kspaceLineOffset"); - m_CroppingFactor = (100-v1.second.get("artifacts.aliasingfactor"))/100; - m_Spikes = v1.second.get("artifacts.spikesnum"); - m_SpikeAmplitude = v1.second.get("artifacts.spikesscale"); - m_EddyStrength = v1.second.get("artifacts.eddyStrength"); - m_DoAddGibbsRinging = v1.second.get("artifacts.addringing"); - m_DoAddMotion = v1.second.get("artifacts.doAddMotion"); - m_DoRandomizeMotion = v1.second.get("artifacts.randomMotion"); - m_Translation[0] = v1.second.get("artifacts.translation0"); - m_Translation[1] = v1.second.get("artifacts.translation1"); - m_Translation[2] = v1.second.get("artifacts.translation2"); - m_Rotation[0] = v1.second.get("artifacts.rotation0"); - m_Rotation[1] = v1.second.get("artifacts.rotation1"); - m_Rotation[2] = v1.second.get("artifacts.rotation2"); - - // compartment 1 - switch (v1.second.get("compartment1.index")) + switch (v1.second.get("distribution", 0)) { case 0: - { - mitk::StickModel* stickModel = new mitk::StickModel(); - stickModel->SetGradientList(m_GradientDirections); - stickModel->SetBvalue(m_Bvalue); - stickModel->SetDiffusivity(v1.second.get("compartment1.stick.d")); - stickModel->SetT2(v1.second.get("compartment1.stick.t2")); - m_FiberModelList.push_back(stickModel); + m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; break; - } case 1: - { - mitk::TensorModel* zeppelinModel = new mitk::TensorModel(); - zeppelinModel->SetGradientList(m_GradientDirections); - zeppelinModel->SetBvalue(m_Bvalue); - zeppelinModel->SetDiffusivity1(v1.second.get("compartment1.zeppelin.d1")); - zeppelinModel->SetDiffusivity2(v1.second.get("compartment1.zeppelin.d2")); - zeppelinModel->SetDiffusivity3(v1.second.get("compartment1.zeppelin.d2")); - zeppelinModel->SetT2(v1.second.get("compartment1.zeppelin.t2")); - m_FiberModelList.push_back(zeppelinModel); - break; - } - case 2: - { - mitk::TensorModel* tensorModel = new mitk::TensorModel(); - tensorModel->SetGradientList(m_GradientDirections); - tensorModel->SetBvalue(m_Bvalue); - tensorModel->SetDiffusivity1(v1.second.get("compartment1.tensor.d1")); - tensorModel->SetDiffusivity2(v1.second.get("compartment1.tensor.d2")); - tensorModel->SetDiffusivity3(v1.second.get("compartment1.tensor.d3")); - tensorModel->SetT2(v1.second.get("compartment1.tensor.t2")); - m_FiberModelList.push_back(tensorModel); + m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN; break; + default: + m_FiberGen.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; } - } - - // compartment 2 - switch (v1.second.get("compartment2.index")) + m_FiberGen.m_Variance = v1.second.get("variance", m_FiberGen.m_Variance); + m_FiberGen.m_Density = v1.second.get("density", m_FiberGen.m_Density); + m_FiberGen.m_Sampling = v1.second.get("spline.sampling", m_FiberGen.m_Sampling); + m_FiberGen.m_Tension = v1.second.get("spline.tension", m_FiberGen.m_Tension); + m_FiberGen.m_Continuity = v1.second.get("spline.continuity", m_FiberGen.m_Continuity); + m_FiberGen.m_Bias = v1.second.get("spline.bias", m_FiberGen.m_Bias); + m_FiberGen.m_Rotation[0] = v1.second.get("rotation.x", m_FiberGen.m_Rotation[0]); + m_FiberGen.m_Rotation[1] = v1.second.get("rotation.y", m_FiberGen.m_Rotation[1]); + m_FiberGen.m_Rotation[2] = v1.second.get("rotation.z", m_FiberGen.m_Rotation[2]); + m_FiberGen.m_Translation[0] = v1.second.get("translation.x", m_FiberGen.m_Translation[0]); + m_FiberGen.m_Translation[1] = v1.second.get("translation.y", m_FiberGen.m_Translation[1]); + m_FiberGen.m_Translation[2] = v1.second.get("translation.z", m_FiberGen.m_Translation[2]); + m_FiberGen.m_Scale[0] = v1.second.get("scale.x", m_FiberGen.m_Scale[0]); + m_FiberGen.m_Scale[1] = v1.second.get("scale.y", m_FiberGen.m_Scale[1]); + m_FiberGen.m_Scale[2] = v1.second.get("scale.z", m_FiberGen.m_Scale[2]); + } + else if ( v1.first == "image" ) + { + m_Misc.m_SignalModelString = v1.second.get("signalmodelstring", m_Misc.m_SignalModelString); + m_Misc.m_ArtifactModelString = v1.second.get("artifactmodelstring", m_Misc.m_ArtifactModelString); + m_Misc.m_OutputPath = v1.second.get("outpath", m_Misc.m_OutputPath); + m_Misc.m_CheckOutputVolumeFractionsBox = v1.second.get("outputvolumefractions", m_Misc.m_CheckOutputVolumeFractionsBox); + m_Misc.m_CheckAdvancedSignalOptionsBox = v1.second.get("showadvanced", m_Misc.m_CheckAdvancedSignalOptionsBox); + m_Misc.m_CheckAddDistortionsBox = v1.second.get("artifacts.doAddDistortions", m_Misc.m_CheckAddDistortionsBox); + m_Misc.m_CheckAddNoiseBox = v1.second.get("artifacts.addnoise", m_Misc.m_CheckAddNoiseBox); + m_Misc.m_CheckAddGhostsBox = v1.second.get("artifacts.addghosts", m_Misc.m_CheckAddGhostsBox); + m_Misc.m_CheckAddAliasingBox = v1.second.get("artifacts.addaliasing", m_Misc.m_CheckAddAliasingBox); + m_Misc.m_CheckAddSpikesBox = v1.second.get("artifacts.addspikes", m_Misc.m_CheckAddSpikesBox); + m_Misc.m_CheckAddEddyCurrentsBox = v1.second.get("artifacts.addeddycurrents", m_Misc.m_CheckAddEddyCurrentsBox); + + m_SignalGen.m_ImageRegion.SetSize(0, v1.second.get("basic.size.x",m_SignalGen.m_ImageRegion.GetSize(0))); + m_SignalGen.m_ImageRegion.SetSize(1, v1.second.get("basic.size.y",m_SignalGen.m_ImageRegion.GetSize(1))); + m_SignalGen.m_ImageRegion.SetSize(2, v1.second.get("basic.size.z",m_SignalGen.m_ImageRegion.GetSize(2))); + m_SignalGen.m_ImageSpacing[0] = v1.second.get("basic.spacing.x",m_SignalGen.m_ImageSpacing[0]); + m_SignalGen.m_ImageSpacing[1] = v1.second.get("basic.spacing.y",m_SignalGen.m_ImageSpacing[1]); + m_SignalGen.m_ImageSpacing[2] = v1.second.get("basic.spacing.z",m_SignalGen.m_ImageSpacing[2]); + m_SignalGen.m_ImageOrigin[0] = v1.second.get("basic.origin.x",m_SignalGen.m_ImageOrigin[0]); + m_SignalGen.m_ImageOrigin[1] = v1.second.get("basic.origin.y",m_SignalGen.m_ImageOrigin[1]); + m_SignalGen.m_ImageOrigin[2] = v1.second.get("basic.origin.z",m_SignalGen.m_ImageOrigin[2]); + m_SignalGen.m_ImageDirection[0][0] = v1.second.get("basic.direction.1",m_SignalGen.m_ImageDirection[0][0]); + m_SignalGen.m_ImageDirection[0][1] = v1.second.get("basic.direction.2",m_SignalGen.m_ImageDirection[0][1]); + m_SignalGen.m_ImageDirection[0][2] = v1.second.get("basic.direction.3",m_SignalGen.m_ImageDirection[0][2]); + m_SignalGen.m_ImageDirection[1][0] = v1.second.get("basic.direction.4",m_SignalGen.m_ImageDirection[1][0]); + m_SignalGen.m_ImageDirection[1][1] = v1.second.get("basic.direction.5",m_SignalGen.m_ImageDirection[1][1]); + m_SignalGen.m_ImageDirection[1][2] = v1.second.get("basic.direction.6",m_SignalGen.m_ImageDirection[1][2]); + m_SignalGen.m_ImageDirection[2][0] = v1.second.get("basic.direction.7",m_SignalGen.m_ImageDirection[2][0]); + m_SignalGen.m_ImageDirection[2][1] = v1.second.get("basic.direction.8",m_SignalGen.m_ImageDirection[2][1]); + m_SignalGen.m_ImageDirection[2][2] = v1.second.get("basic.direction.9",m_SignalGen.m_ImageDirection[2][2]); + + m_SignalGen.m_SignalScale = v1.second.get("signalScale", m_SignalGen.m_SignalScale); + m_SignalGen.m_tEcho = v1.second.get("tEcho", m_SignalGen.m_tEcho); + m_SignalGen.m_tLine = v1.second.get("tLine", m_SignalGen.m_tLine); + m_SignalGen.m_tInhom = v1.second.get("tInhom", m_SignalGen.m_tInhom); + m_SignalGen.m_Bvalue = v1.second.get("bvalue", m_SignalGen.m_Bvalue); + m_SignalGen.m_SimulateKspaceAcquisition = v1.second.get("simulatekspace", m_SignalGen.m_SimulateKspaceAcquisition); + + m_SignalGen.m_AxonRadius = v1.second.get("axonRadius", m_SignalGen.m_AxonRadius); + switch (v1.second.get("diffusiondirectionmode", 0)) { case 0: - { - mitk::StickModel* stickModel = new mitk::StickModel(); - stickModel->SetGradientList(m_GradientDirections); - stickModel->SetBvalue(m_Bvalue); - stickModel->SetDiffusivity(v1.second.get("compartment2.stick.d")); - stickModel->SetT2(v1.second.get("compartment2.stick.t2")); - m_FiberModelList.push_back(stickModel); + m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; break; - } case 1: - { - mitk::TensorModel* zeppelinModel = new mitk::TensorModel(); - zeppelinModel->SetGradientList(m_GradientDirections); - zeppelinModel->SetBvalue(m_Bvalue); - zeppelinModel->SetDiffusivity1(v1.second.get("compartment2.zeppelin.d1")); - zeppelinModel->SetDiffusivity2(v1.second.get("compartment2.zeppelin.d2")); - zeppelinModel->SetDiffusivity3(v1.second.get("compartment2.zeppelin.d2")); - zeppelinModel->SetT2(v1.second.get("compartment2.zeppelin.t2")); - m_FiberModelList.push_back(zeppelinModel); + m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::MAIN_FIBER_DIRECTIONS; break; - } case 2: - { - mitk::TensorModel* tensorModel = new mitk::TensorModel(); - tensorModel->SetGradientList(m_GradientDirections); - tensorModel->SetBvalue(m_Bvalue); - tensorModel->SetDiffusivity1(v1.second.get("compartment2.tensor.d1")); - tensorModel->SetDiffusivity2(v1.second.get("compartment2.tensor.d2")); - tensorModel->SetDiffusivity3(v1.second.get("compartment2.tensor.d3")); - tensorModel->SetT2(v1.second.get("compartment2.tensor.t2")); - m_FiberModelList.push_back(tensorModel); + m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::RANDOM_DIRECTIONS; break; + default: + m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; } - } - - // compartment 3 - switch (v1.second.get("compartment3.index")) - { - case 0: - { - mitk::BallModel* ballModel = new mitk::BallModel(); - ballModel->SetGradientList(m_GradientDirections); - ballModel->SetBvalue(m_Bvalue); - ballModel->SetDiffusivity(v1.second.get("compartment3.ball.d")); - ballModel->SetT2(v1.second.get("compartment3.ball.t2")); - m_NonFiberModelList.push_back(ballModel); - break; - } - case 1: + m_SignalGen.m_FiberSeparationThreshold = v1.second.get("fiberseparationthreshold", m_SignalGen.m_FiberSeparationThreshold); + m_SignalGen.m_Spikes = v1.second.get("artifacts.spikesnum", m_SignalGen.m_Spikes); + m_SignalGen.m_SpikeAmplitude = v1.second.get("artifacts.spikesscale", m_SignalGen.m_SpikeAmplitude); + m_SignalGen.m_KspaceLineOffset = v1.second.get("artifacts.kspaceLineOffset", m_SignalGen.m_KspaceLineOffset); + m_SignalGen.m_EddyStrength = v1.second.get("artifacts.eddyStrength", m_SignalGen.m_EddyStrength); + m_SignalGen.m_Tau = v1.second.get("artifacts.eddyTau", m_SignalGen.m_Tau); + m_SignalGen.m_CroppingFactor = v1.second.get("artifacts.aliasingfactor", m_SignalGen.m_CroppingFactor); + m_SignalGen.m_DoAddGibbsRinging = v1.second.get("artifacts.addringing", m_SignalGen.m_DoAddGibbsRinging); + m_SignalGen.m_DoSimulateRelaxation = v1.second.get("doSimulateRelaxation", m_SignalGen.m_DoSimulateRelaxation); + m_SignalGen.m_DoDisablePartialVolume = v1.second.get("doDisablePartialVolume", m_SignalGen.m_DoDisablePartialVolume); + m_SignalGen.m_DoAddMotion = v1.second.get("artifacts.doAddMotion", m_SignalGen.m_DoAddMotion); + m_SignalGen.m_DoRandomizeMotion = v1.second.get("artifacts.randomMotion", m_SignalGen.m_DoRandomizeMotion); + m_SignalGen.m_Translation[0] = v1.second.get("artifacts.translation0", m_SignalGen.m_Translation[0]); + m_SignalGen.m_Translation[1] = v1.second.get("artifacts.translation1", m_SignalGen.m_Translation[1]); + m_SignalGen.m_Translation[2] = v1.second.get("artifacts.translation2", m_SignalGen.m_Translation[2]); + m_SignalGen.m_Rotation[0] = v1.second.get("artifacts.rotation0", m_SignalGen.m_Rotation[0]); + m_SignalGen.m_Rotation[1] = v1.second.get("artifacts.rotation1", m_SignalGen.m_Rotation[1]); + m_SignalGen.m_Rotation[2] = v1.second.get("artifacts.rotation2", m_SignalGen.m_Rotation[2]); + m_SignalGen.SetNumWeightedVolumes(v1.second.get("numgradients", m_SignalGen.GetNumWeightedVolumes())); + + try { - mitk::AstroStickModel* astrosticksModel = new mitk::AstroStickModel(); - astrosticksModel->SetGradientList(m_GradientDirections); - astrosticksModel->SetBvalue(m_Bvalue); - astrosticksModel->SetDiffusivity(v1.second.get("compartment3.astrosticks.d")); - astrosticksModel->SetT2(v1.second.get("compartment3.astrosticks.t2")); - astrosticksModel->SetRandomizeSticks(v1.second.get("compartment3.astrosticks.randomize")); - m_NonFiberModelList.push_back(astrosticksModel); - break; + if (v1.second.get("artifacts.noisetype")=="rice") + { + m_NoiseModel = new mitk::RicianNoiseModel(); + m_NoiseModel->SetNoiseVariance(v1.second.get("artifacts.noisevariance")); + } } - case 2: + catch(...) {} + try { - mitk::DotModel* dotModel = new mitk::DotModel(); - dotModel->SetGradientList(m_GradientDirections); - dotModel->SetT2(v1.second.get("compartment3.dot.t2")); - m_NonFiberModelList.push_back(dotModel); - break; - } + if (v1.second.get("artifacts.noisetype")=="chisquare") + { + m_NoiseModel = new mitk::ChiSquareNoiseModel(); + m_NoiseModel->SetNoiseVariance(v1.second.get("artifacts.noisevariance")); + } } + catch(...){ } - // compartment 4 - switch (v1.second.get("compartment4.index")) - { - case 0: - { - mitk::BallModel* ballModel = new mitk::BallModel(); - ballModel->SetGradientList(m_GradientDirections); - ballModel->SetBvalue(m_Bvalue); - ballModel->SetDiffusivity(v1.second.get("compartment4.ball.d")); - ballModel->SetT2(v1.second.get("compartment4.ball.t2")); - m_NonFiberModelList.push_back(ballModel); - break; - } - case 1: - { - mitk::AstroStickModel* astrosticksModel = new mitk::AstroStickModel(); - astrosticksModel->SetGradientList(m_GradientDirections); - astrosticksModel->SetBvalue(m_Bvalue); - astrosticksModel->SetDiffusivity(v1.second.get("compartment4.astrosticks.d")); - astrosticksModel->SetT2(v1.second.get("compartment4.astrosticks.t2")); - astrosticksModel->SetRandomizeSticks(v1.second.get("compartment4.astrosticks.randomize")); - m_NonFiberModelList.push_back(astrosticksModel); - break; - } - case 2: + + BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("compartments") ) { - mitk::DotModel* dotModel = new mitk::DotModel(); - dotModel->SetGradientList(m_GradientDirections); - dotModel->SetT2(v1.second.get("compartment4.dot.t2")); - m_NonFiberModelList.push_back(dotModel); - break; - } + mitk::DiffusionSignalModel* signalModel = NULL; + try // stick model + { + mitk::StickModel* model = new mitk::StickModel(); + model->SetDiffusivity(v2.second.get("stick.d")); + model->SetT2(v2.second.get("stick.t2")); + model->m_CompartmentId = v2.second.get("ID"); + if (v2.second.get("type")=="fiber") + m_FiberModelList.push_back(model); + else if (v2.second.get("type")=="non-fiber") + m_NonFiberModelList.push_back(model); + signalModel = model; + } + catch (...) { } + + try // tensor model + { + mitk::TensorModel* model = new mitk::TensorModel(); + model->SetDiffusivity1(v2.second.get("tensor.d1")); + model->SetDiffusivity2(v2.second.get("tensor.d2")); + model->SetDiffusivity3(v2.second.get("tensor.d3")); + model->SetT2(v2.second.get("tensor.t2")); + model->m_CompartmentId = v2.second.get("ID"); + if (v2.second.get("type")=="fiber") + m_FiberModelList.push_back(model); + else if (v2.second.get("type")=="non-fiber") + m_NonFiberModelList.push_back(model); + signalModel = model; + } + catch (...) { } + + try // ball model + { + mitk::BallModel* model = new mitk::BallModel(); + model->SetDiffusivity(v2.second.get("ball.d")); + model->SetT2(v2.second.get("ball.t2")); + model->m_CompartmentId = v2.second.get("ID"); + if (v2.second.get("type")=="fiber") + m_FiberModelList.push_back(model); + else if (v2.second.get("type")=="non-fiber") + m_NonFiberModelList.push_back(model); + signalModel = model; + } + catch (...) { } + + try // astrosticks model + { + mitk::AstroStickModel* model = new AstroStickModel(); + model->SetDiffusivity(v2.second.get("astrosticks.d")); + model->SetT2(v2.second.get("astrosticks.t2")); + model->SetRandomizeSticks(v2.second.get("astrosticks.randomize")); + model->m_CompartmentId = v2.second.get("ID"); + if (v2.second.get("type")=="fiber") + m_FiberModelList.push_back(model); + else if (v2.second.get("type")=="non-fiber") + m_NonFiberModelList.push_back(model); + signalModel = model; + } + catch (...) { } + + try // dot model + { + mitk::DotModel* model = new mitk::DotModel(); + model->SetT2(v2.second.get("dot.t2")); + model->m_CompartmentId = v2.second.get("ID"); + if (v2.second.get("type")=="fiber") + m_FiberModelList.push_back(model); + else if (v2.second.get("type")=="non-fiber") + m_NonFiberModelList.push_back(model); + signalModel = model; + } + catch (...) { } + + try // prototype model + { + mitk::RawShModel* model = new mitk::RawShModel(); + model->SetMaxNumKernels(v2.second.get("prototype.numSamples")); + model->SetFaRange(v2.second.get("prototype.minFA"), v2.second.get("prototype.maxFA")); + model->SetAdcRange(v2.second.get("prototype.minADC"), v2.second.get("prototype.maxADC")); + model->m_CompartmentId = v2.second.get("ID"); + if (v2.second.get("type")=="fiber") + m_FiberModelList.push_back(model); + else if (v2.second.get("type")=="non-fiber") + m_NonFiberModelList.push_back(model); + signalModel = model; + } + catch (...) { } + +// if (signalModel!=NULL) +// { +// try{ +// itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); +// reader->SetFileName(filename+"_VOLUME"+v2.second.get("ID")+".nrrd"); +// reader->Update(); +// signalModel->SetVolumeFractionImage(reader->GetOutput()); +// } +// catch(...) +// { +// } +// } } } } + +// if (m_SignalGen.m_DoAddDistortions) +// { +// try{ +// itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); +// reader->SetFileName(filename+"_FMAP.nrrd"); +// reader->Update(); +// m_SignalGen.m_FrequencyMap = reader->GetOutput(); +// } +// catch(...) +// { +// MITK_INFO << "No frequency map saved."; +// } +// } + +// try{ +// itk::ImageFileReader::Pointer reader = itk::ImageFileReader::New(); +// reader->SetFileName(filename+"_MASK.nrrd"); +// reader->Update(); +// m_SignalGen.m_MaskImage = reader->GetOutput(); +// } +// catch(...) +// { +// MITK_INFO << "No mask image saved."; +// } } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::PrintSelf() { - MITK_INFO << "m_ImageRegion: " << m_ImageRegion; - MITK_INFO << "m_ImageSpacing: " << m_ImageSpacing; - MITK_INFO << "m_ImageOrigin: " << m_ImageOrigin; - MITK_INFO << "m_ImageDirection: " << m_ImageDirection; - MITK_INFO << "m_NumGradients: " << m_NumGradients; - MITK_INFO << "m_Bvalue: " << m_Bvalue; - MITK_INFO << "m_SignalScale: " << m_SignalScale; - MITK_INFO << "m_tEcho: " << m_tEcho; - MITK_INFO << "m_tLine: " << m_tLine; - MITK_INFO << "m_tInhom: " << m_tInhom; - MITK_INFO << "m_AxonRadius: " << m_AxonRadius; - MITK_INFO << "m_KspaceLineOffset: " << m_KspaceLineOffset; - MITK_INFO << "m_AddGibbsRinging: " << m_DoAddGibbsRinging; - MITK_INFO << "m_EddyStrength: " << m_EddyStrength; - MITK_INFO << "m_Spikes: " << m_Spikes; - MITK_INFO << "m_SpikeAmplitude: " << m_SpikeAmplitude; - MITK_INFO << "m_CroppingFactor: " << m_CroppingFactor; - MITK_INFO << "m_DoSimulateRelaxation: " << m_DoSimulateRelaxation; - MITK_INFO << "m_DoDisablePartialVolume: " << m_DoDisablePartialVolume; - MITK_INFO << "m_DoAddMotion: " << m_DoAddMotion; - MITK_INFO << "m_RandomMotion: " << m_DoRandomizeMotion; - MITK_INFO << "m_Translation: " << m_Translation; - MITK_INFO << "m_Rotation: " << m_Rotation; - MITK_INFO << "m_SignalModelString: " << m_SignalModelString; - MITK_INFO << "m_ArtifactModelString: " << m_ArtifactModelString; - MITK_INFO << "m_OutputPath: " << m_OutputPath; + MITK_INFO << "Not implemented :("; } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h index c2a71cd84c..9de94d3c33 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h @@ -1,187 +1,321 @@ /*=================================================================== 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 using namespace std; namespace mitk { -/** - * \brief Datastructure to manage the Fiberfox signal generation parameters. - * - */ - -template< class ScalarType = double > -class FiberfoxParameters +/** Signal generation */ +class SignalGenerationParameters { public: + typedef itk::Image ItkDoubleImgType; + typedef itk::Image ItkUcharImgType; + typedef itk::Vector GradientType; + typedef std::vector GradientListType; enum DiffusionDirectionMode { FIBER_TANGENT_DIRECTIONS, MAIN_FIBER_DIRECTIONS, RANDOM_DIRECTIONS }; - typedef itk::Image ItkDoubleImgType; - typedef itk::Image ItkUcharImgType; - typedef std::vector< DiffusionSignalModel* > DiffusionModelListType; - typedef DiffusionSignalModel::GradientListType GradientListType; - typedef DiffusionSignalModel::GradientType GradientType; - typedef DiffusionNoiseModel NoiseModelType; - typedef DiffusionSignalModel* DiffusionModelType; - - FiberfoxParameters(); - ~FiberfoxParameters(); - - /** Get same parameter object with different template parameter */ - template< class OutType > FiberfoxParameters< OutType > CopyParameters() + SignalGenerationParameters() + : m_FrequencyMap(NULL) + , m_MaskImage(NULL) + , m_SignalScale(100) + , m_tEcho(100) + , m_tLine(1) + , m_tInhom(50) + , m_Bvalue(1000) + , m_SimulateKspaceAcquisition(false) + , m_AxonRadius(0) + , m_DiffusionDirectionMode(SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS) + , m_FiberSeparationThreshold(30) + , m_Spikes(0) + , m_SpikeAmplitude(1) + , m_KspaceLineOffset(0) + , m_EddyStrength(0) + , m_Tau(70) + , m_CroppingFactor(1) + , m_DoAddGibbsRinging(false) + , m_DoSimulateRelaxation(true) + , m_DoDisablePartialVolume(false) + , m_DoAddMotion(false) + , m_DoRandomizeMotion(true) { - FiberfoxParameters< OutType > out; - - out.m_ImageRegion = m_ImageRegion; - out.m_ImageSpacing = m_ImageSpacing; - out.m_ImageOrigin = m_ImageOrigin; - out.m_ImageDirection = m_ImageDirection; - out.SetNumWeightedGradients(m_NumGradients); - out.m_Bvalue = m_Bvalue; - out.m_SignalScale = m_SignalScale; - out.m_tEcho = m_tEcho; - out.m_tLine = m_tLine; - out.m_tInhom = m_tInhom; - out.m_AxonRadius = m_AxonRadius; - out.m_KspaceLineOffset = m_KspaceLineOffset; - out.m_DoAddGibbsRinging = m_DoAddGibbsRinging; - out.m_EddyStrength = m_EddyStrength; - out.m_Spikes = m_Spikes; - out.m_SpikeAmplitude = m_SpikeAmplitude; - out.m_CroppingFactor = m_CroppingFactor; - out.m_DoSimulateRelaxation = m_DoSimulateRelaxation; - out.m_DoDisablePartialVolume = m_DoDisablePartialVolume; - out.m_DoAddMotion = m_DoAddMotion; - out.m_DoRandomizeMotion = m_DoRandomizeMotion; - out.m_Translation = m_Translation; - out.m_Rotation = m_Rotation; - if (m_NoiseModel!=NULL) - { - if (dynamic_cast*>(m_NoiseModel)) - out.m_NoiseModel = new mitk::RicianNoiseModel(); - else if (dynamic_cast*>(m_NoiseModel)) - out.m_NoiseModel = new mitk::ChiSquareNoiseModel(); - out.m_NoiseModel->SetNoiseVariance(m_NoiseModel->GetNoiseVariance()); - } - out.m_FrequencyMap = m_FrequencyMap; - out.m_MaskImage = m_MaskImage; - out.m_ResultNode = m_ResultNode; - out.m_ParentNode = m_ParentNode; - out.m_SignalModelString = m_SignalModelString; - out.m_ArtifactModelString = m_ArtifactModelString; - out.m_OutputPath = m_OutputPath; -// out.m_DiffusionDirectionMode = m_DiffusionDirectionMode; -// out.m_SignalGenerationMode = m_SignalGenerationMode; - out.m_SimulateKspaceAcquisition = m_SimulateKspaceAcquisition; - - // TODO: copy constructor für singalmodelle und rauschen - - return out; + 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); } - /** Output image specifications */ + /** input/output image specifications */ 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 */ double m_SignalScale; ///< Scaling factor for output signal (before noise is added). double m_tEcho; ///< Echo time TE. double m_tLine; ///< k-space line readout time. double m_tInhom; ///< T2' double m_Bvalue; ///< Acquisition b-value - bool m_SimulateKspaceAcquisition;///< - - /** Signal generation */ - DiffusionModelListType m_FiberModelList; ///< Intra- and inter-axonal compartments. - DiffusionModelListType m_NonFiberModelList; ///< Extra-axonal compartments. + 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. DiffusionDirectionMode m_DiffusionDirectionMode; ///< Determines how the main diffusion direction of the signal models is selected + double m_FiberSeparationThreshold; ///< Used for random and and mein fiber deriction DiffusionDirectionMode - /** Artifacts */ + /** 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_DoDisablePartialVolume; ///< Disable partial volume effects. Each voxel is either all fiber or all non-fiber. bool m_DoAddMotion; ///< Enable motion artifacts. bool m_DoRandomizeMotion; ///< Toggles between random and linear motion. itk::Vector m_Translation; ///< Maximum translational motion. itk::Vector m_Rotation; ///< Maximum rotational motion. - NoiseModelType* m_NoiseModel; ///< If != NULL, noise is added to the image. 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. - /** Output parameters (only relevant in GUI application) */ - mitk::DataNode::Pointer m_ResultNode; ///< Stores resulting image. - mitk::DataNode::Pointer m_ParentNode; ///< Parent node or 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. + 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); - void PrintSelf(); ///< Print parameters to stdout. - void LoadParameters(string filename); ///< Load image generation parameters from .ffp file. - void GenerateGradientHalfShell(); ///< Generates half shell of gradient directions (with m_NumGradients non-zero directions) + inline void SetNumWeightedVolumes(int numGradients); ///< Automaticall calls GenerateGradientHalfShell() afterwards. + inline void SetGradienDirections(GradientListType gradientList); + inline void SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientList); - std::vector< int > GetBaselineIndices(); - unsigned int GetFirstBaselineIndex(); - bool IsBaselineIndex(unsigned int idx); +protected: - unsigned int GetNumWeightedVolumes(); - unsigned int GetNumBaselineVolumes(); - unsigned int GetNumVolumes(); - GradientListType GetGradientDirections(); - GradientType GetGradientDirection(unsigned int i); + 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. +}; - void SetNumWeightedGradients(int numGradients); ///< Automaticall calls GenerateGradientHalfShell() afterwards. - void SetGradienDirections(GradientListType gradientList); - void SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientList); +/** Fiber generation */ +class FiberGenerationParameters +{ +public: -protected: + enum FiberDistribution{ + DISTRIBUTE_UNIFORM, // distribute fibers uniformly in the ROIs + DISTRIBUTE_GAUSSIAN // distribute fibers using a 2D gaussian + }; - unsigned int m_NumBaseline; ///< Number of non-diffusion-weighted image volumes. - unsigned int m_NumGradients; ///< Number of diffusion-weighted image volumes. - GradientListType m_GradientDirections; ///< Total number of image volumes. + 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("") + , 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_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. + + /** 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; + // 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)) + out.m_NoiseModel = new mitk::RicianNoiseModel(); + else if (dynamic_cast*>(m_NoiseModel)) + out.m_NoiseModel = new 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 #include #include using namespace mitk; template< class ScalarType > AstroStickModel< ScalarType >::AstroStickModel() : m_BValue(1000) , m_Diffusivity(0.001) , m_NumSticks(42) , m_RandomizeSticks(false) { - m_RandGen = ItkRandGenType::New(); + this->m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); + this->m_RandGen->SetSeed(); - vnl_matrix_fixed* sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell(); + vnl_matrix_fixed* sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell(); for (unsigned int i=0; iget(0,i); stick[1] = sticks->get(1,i); stick[2] = sticks->get(2,i); stick.Normalize(); m_Sticks.push_back(stick); } } template< class ScalarType > AstroStickModel< ScalarType >::~AstroStickModel() { } -template< class ScalarType > -void AstroStickModel< ScalarType >::SetSeed(int s) -{ - m_RandGen->SetSeed(s); -} - template< class ScalarType > ScalarType AstroStickModel< ScalarType >::SimulateMeasurement(unsigned int dir) { ScalarType signal = 0; if (dir>=this->m_GradientList.size()) return signal; ScalarType b = -m_BValue*m_Diffusivity; if (m_RandomizeSticks) // random number of sticks - m_NumSticks = 30 + m_RandGen->GetIntegerVariate()%31; + m_NumSticks = 30 + this->m_RandGen->GetIntegerVariate()%31; GradientType g = this->m_GradientList[dir]; ScalarType bVal = g.GetNorm(); bVal *= bVal; if (bVal>0.0001) // is weighted direction { for (unsigned int j=0; j typename AstroStickModel< ScalarType >::GradientType AstroStickModel< ScalarType >::GetRandomDirection() { GradientType vec; - vec[0] = m_RandGen->GetNormalVariate(); - vec[1] = m_RandGen->GetNormalVariate(); - vec[2] = m_RandGen->GetNormalVariate(); + vec[0] = this->m_RandGen->GetNormalVariate(); + vec[1] = this->m_RandGen->GetNormalVariate(); + vec[2] = this->m_RandGen->GetNormalVariate(); vec.Normalize(); return vec; } template< class ScalarType > typename AstroStickModel< ScalarType >::PixelType AstroStickModel< ScalarType >::SimulateMeasurement() { PixelType signal; signal.SetSize(this->m_GradientList.size()); ScalarType b = -m_BValue*m_Diffusivity; if (m_RandomizeSticks) - m_NumSticks = 30 + m_RandGen->GetIntegerVariate()%31; + m_NumSticks = 30 + this->m_RandGen->GetIntegerVariate()%31; for( unsigned int i=0; im_GradientList.size(); i++) { GradientType g = this->m_GradientList[i]; ScalarType bVal = g.GetNorm(); bVal *= bVal; if (bVal>0.0001) { for (unsigned int j=0; j #include namespace mitk { /** * \brief Generates the diffusion signal using a collection of idealised cylinder with zero radius: e^(-bd(ng)²) * */ -template< class ScalarType > +template< class ScalarType = double > class AstroStickModel : public DiffusionSignalModel< ScalarType > { public: AstroStickModel(); + template< class OtherType >AstroStickModel(AstroStickModel* model) + { + this->m_CompartmentId = model->m_CompartmentId; + this->m_T2 = model->GetT2(); + this->m_FiberDirection = model->GetFiberDirection(); + this->m_GradientList = model->GetGradientList(); + this->m_VolumeFractionImage = model->GetVolumeFractionImage(); + this->m_RandGen = model->GetRandomGenerator(); + + this->m_BValue = model->GetBvalue(); + this->m_Diffusivity = model->GetDiffusivity(); + this->m_Sticks = model->GetSticks(); + this->m_NumSticks = model->GetNumSticks(); + this->m_RandomizeSticks = model->GetRandomizeSticks(); + } ~AstroStickModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; - typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRandGenType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); + void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } - void SetSeed(int s); ///< set seed for random generator that creates the stick orientations - void SetRandomizeSticks(bool randomize=true){ m_RandomizeSticks=randomize; } ///< Random stick configuration in each voxel - void SetBvalue(ScalarType bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal - void SetDiffusivity(ScalarType diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant + bool GetRandomizeSticks() { return m_RandomizeSticks; } + + void SetBvalue(double bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal + double GetBvalue() { return m_BValue; } + + void SetDiffusivity(double diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant + double GetDiffusivity() { return m_Diffusivity; } + void SetNumSticks(unsigned int order) { vnl_matrix sticks; switch (order) { case 1: m_NumSticks = 12; sticks = itk::PointShell<12, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 2: m_NumSticks = 42; sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 3: m_NumSticks = 92; sticks = itk::PointShell<92, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 4: m_NumSticks = 162; sticks = itk::PointShell<162, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; case 5: m_NumSticks = 252; sticks = itk::PointShell<252, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; default: m_NumSticks = 42; sticks = itk::PointShell<42, vnl_matrix_fixed >::DistributePointShell()->as_matrix(); break; } for (int i=0; i namespace mitk { /** * \brief Generates direction independent diffusion measurement employing a scalar diffusion constant d: e^(-bd) * */ -template< class ScalarType > +template< class ScalarType = double > class BallModel : public DiffusionSignalModel< ScalarType > { public: BallModel(); + template< class OtherType >BallModel(BallModel* model) + { + this->m_CompartmentId = model->m_CompartmentId; + this->m_T2 = model->GetT2(); + this->m_FiberDirection = model->GetFiberDirection(); + this->m_GradientList = model->GetGradientList(); + this->m_VolumeFractionImage = model->GetVolumeFractionImage(); + this->m_RandGen = model->GetRandomGenerator(); + + this->m_BValue = model->GetBvalue(); + this->m_Diffusivity = model->GetDiffusivity(); + } ~BallModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); - void SetDiffusivity(ScalarType D) { m_Diffusivity = D; } - void SetBvalue(ScalarType bValue) { m_BValue = bValue; } + void SetDiffusivity(double D) { m_Diffusivity = D; } + double GetDiffusivity() { return m_Diffusivity; } + void SetBvalue(double bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal + double GetBvalue() { return m_BValue; } void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } protected: - ScalarType m_Diffusivity; ///< Scalar diffusion constant - ScalarType m_BValue; ///< b-value used to generate the artificial signal + double m_Diffusivity; ///< Scalar diffusion constant + double m_BValue; ///< b-value used to generate the artificial signal }; } #include "mitkBallModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h index a9a29831aa..4d733a6bec 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h @@ -1,72 +1,91 @@ /*=================================================================== 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_DiffusionSignalModel_H #define _MITK_DiffusionSignalModel_H #include #include #include #include +#include #include namespace mitk { /** * \brief Abstract class for diffusion signal models * */ -template< class ScalarType > +template< class ScalarType = double > class DiffusionSignalModel { public: DiffusionSignalModel() : m_T2(100) {} ~DiffusionSignalModel(){} typedef itk::Image ItkDoubleImgType; typedef itk::VariableLengthVector< ScalarType > PixelType; typedef itk::Vector GradientType; typedef std::vector GradientListType; + typedef itk::Statistics::MersenneTwisterRandomVariateGenerator ItkRandGenType; /** Realizes actual signal generation. Has to be implemented in subclass. **/ virtual PixelType SimulateMeasurement() = 0; virtual ScalarType SimulateMeasurement(unsigned int dir) = 0; virtual void SetFiberDirection(GradientType fiberDirection) = 0; + GradientType GetFiberDirection(){ return m_FiberDirection; } + virtual void SetGradientList(GradientListType gradientList) = 0; + GradientListType GetGradientList(){ return m_GradientList; } + GradientType GetGradientDirection(int i) { return m_GradientList.at(i); } + void SetT2(double T2) { m_T2 = T2; } - void SetVolumeFractionImage(ItkDoubleImgType::Pointer img){ m_VolumeFractionImage = img; } + double GetT2() { return m_T2; } + void SetVolumeFractionImage(ItkDoubleImgType::Pointer img){ m_VolumeFractionImage = img; } ItkDoubleImgType::Pointer GetVolumeFractionImage(){ return m_VolumeFractionImage; } - GradientType GetGradientDirection(int i) { return m_GradientList.at(i); } - double GetT2() { return m_T2; } + + void SetRandomGenerator(ItkRandGenType::Pointer randgen){ m_RandGen = randgen; } + ItkRandGenType::Pointer GetRandomGenerator(){ return m_RandGen; } + + void SetSeed(int s) ///< set seed for random generator + { + if (m_RandGen.IsNull()) + m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); + m_RandGen->SetSeed(s); + } + + unsigned int m_CompartmentId; ///< GUI flag. Which compartment is this model assigned to? protected: GradientType m_FiberDirection; ///< Needed to generate anisotropc signal to determin direction of anisotropy GradientListType m_GradientList; ///< Diffusion gradient direction container double m_T2; ///< Tissue specific relaxation time ItkDoubleImgType::Pointer m_VolumeFractionImage; ///< Tissue specific volume fraction for each voxel (only relevant for non fiber compartments) + ItkRandGenType::Pointer m_RandGen; ///< Random number generator }; } #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h index 3e4a4c9da9..382c2dd903 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h @@ -1,57 +1,66 @@ /*=================================================================== 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_DotModel_H #define _MITK_DotModel_H #include namespace mitk { /** * \brief Generates constant direction independent signal. * */ -template< class ScalarType > +template< class ScalarType = double > class DotModel : public DiffusionSignalModel< ScalarType > { public: DotModel(); + template< class OtherType >DotModel(DotModel* model) + { + this->m_CompartmentId = model->m_CompartmentId; + this->m_T2 = model->GetT2(); + this->m_FiberDirection = model->GetFiberDirection(); + this->m_GradientList = model->GetGradientList(); + this->m_VolumeFractionImage = model->GetVolumeFractionImage(); + this->m_RandGen = model->GetRandomGenerator(); + } ~DotModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } protected: }; } #include "mitkDotModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.cpp b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.cpp index 2fdb8eae50..ebad8020a0 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.cpp +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.cpp @@ -1,257 +1,257 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include using namespace mitk; using namespace boost::math; template< class ScalarType > RawShModel< ScalarType >::RawShModel() : m_ShOrder(0) , m_ModelIndex(-1) , m_MaxNumKernels(1000) { - m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); - m_RandGen->SetSeed(); + this->m_RandGen = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); + this->m_RandGen->SetSeed(); m_AdcRange.first = 0; m_AdcRange.second = 0.004; m_FaRange.first = 0; m_FaRange.second = 1; } template< class ScalarType > RawShModel< ScalarType >::~RawShModel() { } template< class ScalarType > void RawShModel< ScalarType >::Clear() { m_ShCoefficients.clear(); m_PrototypeMaxDirection.clear(); m_B0Signal.clear(); } template< class ScalarType > void RawShModel< ScalarType >::RandomModel() { - m_ModelIndex = m_RandGen->GetIntegerVariate(m_B0Signal.size()-1); + m_ModelIndex = this->m_RandGen->GetIntegerVariate(m_B0Signal.size()-1); } template< class ScalarType > unsigned int RawShModel< ScalarType >::GetNumberOfKernels() { return m_B0Signal.size(); } // convert cartesian to spherical coordinates template< class ScalarType > void RawShModel< ScalarType >::Cart2Sph( GradientListType gradients ) { m_SphCoords.set_size(gradients.size(), 2); m_SphCoords.fill(0.0); for (unsigned int i=0; i 0.0001 ) { gradients[i].Normalize(); m_SphCoords(i,0) = acos(gradients[i][2]); // theta m_SphCoords(i,1) = atan2(gradients[i][1], gradients[i][0]); // phi } } } template< class ScalarType > void RawShModel< ScalarType >::SetFiberDirection(GradientType fiberDirection) { this->m_FiberDirection = fiberDirection; this->m_FiberDirection.Normalize(); RandomModel(); GradientType axis = itk::CrossProduct(this->m_FiberDirection, m_PrototypeMaxDirection.at(m_ModelIndex)); axis.Normalize(); vnl_quaternion rotation(axis.GetVnlVector(), acos(dot_product(this->m_FiberDirection.GetVnlVector(), m_PrototypeMaxDirection.at(m_ModelIndex).GetVnlVector()))); rotation.normalize(); GradientListType gradients; for (unsigned int i=0; im_GradientList.size(); i++) { GradientType dir = this->m_GradientList.at(i); if( dir.GetNorm() > 0.0001 ) { dir.Normalize(); vnl_vector_fixed< double, 3 > vnlDir = rotation.rotate(dir.GetVnlVector()); dir[0] = vnlDir[0]; dir[1] = vnlDir[1]; dir[2] = vnlDir[2]; dir.Normalize(); } gradients.push_back(dir); } Cart2Sph( gradients ); } template< class ScalarType > -bool RawShModel< ScalarType >::SetShCoefficients(vnl_vector< double > shCoefficients, ScalarType b0 ) +bool RawShModel< ScalarType >::SetShCoefficients(vnl_vector< double > shCoefficients, double b0 ) { m_ShOrder = 2; while ( (m_ShOrder*m_ShOrder + m_ShOrder + 2)/2 + m_ShOrder <= shCoefficients.size() ) m_ShOrder += 2; m_ShOrder -= 2; m_ModelIndex = m_B0Signal.size(); m_B0Signal.push_back(b0); m_ShCoefficients.push_back(shCoefficients); // itk::OrientationDistributionFunction odf; // GradientListType gradients; // for (unsigned int i=0; im_GradientList ); // PixelType signal = SimulateMeasurement(); // int minDirIdx = 0; // double min = itk::NumericTraits::max(); // for (unsigned int i=0; ib0 || signal[i]<0) // { // MITK_INFO << "Corrupted signal value detected. Kernel rejected."; // m_B0Signal.pop_back(); // m_ShCoefficients.pop_back(); // return false; // } // if (signal[i]m_GradientList.at(minDirIdx); // maxDir.Normalize(); // m_PrototypeMaxDirection.push_back(maxDir); Cart2Sph( this->m_GradientList ); m_ModelIndex = -1; return true; } template< class ScalarType > ScalarType RawShModel< ScalarType >::SimulateMeasurement(unsigned int dir) { ScalarType signal = 0; if (m_ModelIndex==-1) RandomModel(); if (dir>=this->m_GradientList.size()) return signal; int j, m; double mag, plm; if (this->m_GradientList[dir].GetNorm()>0.001) { j=0; for (int l=0; l<=m_ShOrder; l=l+2) for (m=-l; m<=l; m++) { plm = legendre_p(l,abs(m),cos(m_SphCoords(dir,0))); mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial(l-abs(m))/factorial(l+abs(m)))*plm; double basis; if (m<0) basis = sqrt(2.0)*mag*cos(fabs((double)m)*m_SphCoords(dir,1)); else if (m==0) basis = mag; else basis = pow(-1.0, m)*sqrt(2.0)*mag*sin(m*m_SphCoords(dir,1)); signal += m_ShCoefficients.at(m_ModelIndex)[j]*basis; j++; } } else signal = m_B0Signal.at(m_ModelIndex); m_ModelIndex = -1; return signal; } template< class ScalarType > typename RawShModel< ScalarType >::PixelType RawShModel< ScalarType >::SimulateMeasurement() { if (m_ModelIndex==-1) RandomModel(); PixelType signal; signal.SetSize(this->m_GradientList.size()); int M = this->m_GradientList.size(); int j, m; double mag, plm; vnl_matrix< double > shBasis; shBasis.set_size(M, m_ShCoefficients.at(m_ModelIndex).size()); shBasis.fill(0.0); for (int p=0; pm_GradientList[p].GetNorm()>0.001) { j=0; for (int l=0; l<=m_ShOrder; l=l+2) for (m=-l; m<=l; m++) { plm = legendre_p(l,abs(m),cos(m_SphCoords(p,0))); mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial(l-abs(m))/factorial(l+abs(m)))*plm; if (m<0) shBasis(p,j) = sqrt(2.0)*mag*cos(fabs((double)m)*m_SphCoords(p,1)); else if (m==0) shBasis(p,j) = mag; else shBasis(p,j) = pow(-1.0, m)*sqrt(2.0)*mag*sin(m*m_SphCoords(p,1)); j++; } double val = 0; for (unsigned int cidx=0; cidx namespace mitk { /** * \brief The spherical harmonic representation of a prototype diffusion weighted MR signal is used to obtain the direction dependent signal. * */ -template< class ScalarType > +template< class ScalarType = double > class RawShModel : public DiffusionSignalModel< ScalarType > { public: RawShModel(); + template< class OtherType >RawShModel(RawShModel* model) + { + this->m_CompartmentId = model->m_CompartmentId; + this->m_T2 = model->GetT2(); + this->m_FiberDirection = model->GetFiberDirection(); + this->m_GradientList = model->GetGradientList(); + this->m_VolumeFractionImage = model->GetVolumeFractionImage(); + this->m_RandGen = model->GetRandomGenerator(); + + this->m_AdcRange = model->GetAdcRange(); + this->m_FaRange = model->GetFaRange(); + this->m_ShCoefficients = model->GetShCoefficients(); + this->m_B0Signal = model->GetB0Signals(); + this->m_SphCoords = model->GetSphericalCoordinates(); + this->m_ShOrder = model->GetShOrder(); + this->m_ModelIndex = model->GetModelIndex(); + this->m_MaxNumKernels = model->GetMaxNumKernels(); + } ~RawShModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; typedef itk::Matrix< double, 3, 3 > MatrixType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); - bool SetShCoefficients(vnl_vector< double > shCoefficients, ScalarType b0); + bool SetShCoefficients(vnl_vector< double > shCoefficients, double b0); void SetFiberDirection(GradientType fiberDirection); void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } void SetFaRange(double min, double max){ m_FaRange.first = min; m_FaRange.second = max; } void SetAdcRange(double min, double max){ m_AdcRange.first = min; m_AdcRange.second = max; } void SetMaxNumKernels(unsigned int max){ m_MaxNumKernels = max; } unsigned int GetNumberOfKernels(); std::pair< double, double > GetFaRange(){ return m_FaRange; } std::pair< double, double > GetAdcRange(){ return m_AdcRange; } unsigned int GetMaxNumKernels(){ return m_MaxNumKernels; } void Clear(); - vector< GradientType > m_PrototypeMaxDirection; + std::vector< GradientType > m_PrototypeMaxDirection; + + std::vector< vnl_vector< double > > GetShCoefficients(){ return m_ShCoefficients; } + std::vector< double > GetB0Signals(){ return m_B0Signal; } + vnl_matrix GetSphericalCoordinates(){ return m_SphCoords; } + unsigned int GetShOrder(){ return m_ShOrder; } + int GetModelIndex(){ return m_ModelIndex; } protected: void Cart2Sph( GradientListType gradients ); void RandomModel(); - std::pair< double, double > m_AdcRange; - std::pair< double, double > m_FaRange; - vector< vnl_vector< double > > m_ShCoefficients; - vector< ScalarType > m_B0Signal; - vnl_matrix m_SphCoords; - unsigned int m_ShOrder; - int m_ModelIndex; - unsigned int m_MaxNumKernels; - itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer m_RandGen; + std::pair< double, double > m_AdcRange; + std::pair< double, double > m_FaRange; + std::vector< vnl_vector< double > > m_ShCoefficients; + std::vector< double > m_B0Signal; + vnl_matrix m_SphCoords; + unsigned int m_ShOrder; + int m_ModelIndex; + unsigned int m_MaxNumKernels; }; } #include "mitkRawShModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h index 6af5a320f1..7ecf8635d7 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h @@ -1,62 +1,76 @@ /*=================================================================== 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_StickModel_H #define _MITK_StickModel_H #include namespace mitk { /** * \brief Generates the diffusion signal using an idealised cylinder with zero radius: e^(-bd(ng)²) * */ -template< class ScalarType > +template< class ScalarType = double > class StickModel : public DiffusionSignalModel< ScalarType > { public: StickModel(); + template< class OtherType >StickModel(StickModel* model) + { + this->m_CompartmentId = model->m_CompartmentId; + this->m_T2 = model->GetT2(); + this->m_FiberDirection = model->GetFiberDirection(); + this->m_GradientList = model->GetGradientList(); + this->m_VolumeFractionImage = model->GetVolumeFractionImage(); + this->m_RandGen = model->GetRandomGenerator(); + + this->m_BValue = model->GetBvalue(); + this->m_Diffusivity = model->GetDiffusivity(); + } ~StickModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); - void SetBvalue(ScalarType bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal - void SetDiffusivity(ScalarType diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant + void SetBvalue(double bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal + double GetBvalue() { return m_BValue; } + void SetDiffusivity(double diffusivity) { m_Diffusivity = diffusivity; } ///< Scalar diffusion constant + double GetDiffusivity() { return m_Diffusivity; } void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } protected: - ScalarType m_Diffusivity; ///< Scalar diffusion constant - ScalarType m_BValue; ///< b-value used to generate the artificial signal + double m_Diffusivity; ///< Scalar diffusion constant + double m_BValue; ///< b-value used to generate the artificial signal }; } #include "mitkStickModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h index 4ebe00bc6e..7734ba3cc3 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h @@ -1,69 +1,88 @@ /*=================================================================== 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_TensorModel_H #define _MITK_TensorModel_H #include #include namespace mitk { /** * \brief Generates diffusion measurement employing a second rank tensor model: e^(-bg^TDg) * */ -template< class ScalarType > +template< class ScalarType = double > class TensorModel : public DiffusionSignalModel< ScalarType > { public: TensorModel(); + template< class OtherType >TensorModel(TensorModel* model) + { + this->m_CompartmentId = model->m_CompartmentId; + this->m_T2 = model->GetT2(); + this->m_FiberDirection = model->GetFiberDirection(); + this->m_GradientList = model->GetGradientList(); + this->m_VolumeFractionImage = model->GetVolumeFractionImage(); + this->m_RandGen = model->GetRandomGenerator(); + + this->m_BValue = model->GetBvalue(); + this->m_KernelDirection = model->GetKernelDirection(); + this->m_KernelTensorMatrix = model->GetKernelTensorMatrix(); + } ~TensorModel(); typedef typename DiffusionSignalModel< ScalarType >::PixelType PixelType; typedef itk::DiffusionTensor3D< ScalarType > ItkTensorType; typedef typename DiffusionSignalModel< ScalarType >::GradientType GradientType; typedef typename DiffusionSignalModel< ScalarType >::GradientListType GradientListType; /** Actual signal generation **/ PixelType SimulateMeasurement(); ScalarType SimulateMeasurement(unsigned int dir); - void SetBvalue(ScalarType bValue) { m_BValue = bValue; } - void SetDiffusivity1(ScalarType d1){ m_KernelTensorMatrix[0][0] = d1; } - void SetDiffusivity2(ScalarType d2){ m_KernelTensorMatrix[1][1] = d2; } - void SetDiffusivity3(ScalarType d3){ m_KernelTensorMatrix[2][2] = d3; } + void SetBvalue(double bValue) { m_BValue = bValue; } ///< b-value used to generate the artificial signal + double GetBvalue() { return m_BValue; } + void SetDiffusivity1(double d1){ m_KernelTensorMatrix[0][0] = d1; } + void SetDiffusivity2(double d2){ m_KernelTensorMatrix[1][1] = d2; } + void SetDiffusivity3(double d3){ m_KernelTensorMatrix[2][2] = d3; } + double GetDiffusivity1() { return m_KernelTensorMatrix[0][0]; } + double GetDiffusivity2() { return m_KernelTensorMatrix[1][1]; } + double GetDiffusivity3() { return m_KernelTensorMatrix[2][2]; } void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } + GradientType GetKernelDirection(){ return m_KernelDirection; } + vnl_matrix_fixed GetKernelTensorMatrix(){ return m_KernelTensorMatrix; } protected: /** Calculates tensor matrix from FA and ADC **/ void UpdateKernelTensor(); GradientType m_KernelDirection; ///< Direction of the kernel tensors principal eigenvector - vnl_matrix_fixed m_KernelTensorMatrix; ///< 3x3 matrix containing the kernel tensor values - ScalarType m_BValue; ///< b-value used to generate the artificial signal + vnl_matrix_fixed m_KernelTensorMatrix; ///< 3x3 matrix containing the kernel tensor values + double m_BValue; ///< b-value used to generate the artificial signal }; } #include "mitkTensorModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp index 643b9da551..2e06ab9d38 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberGenerationTest.cpp @@ -1,86 +1,78 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include /**Documentation * Test if fiber transfortaiom methods work correctly */ int mitkFiberGenerationTest(int argc, char* argv[]) { MITK_TEST_BEGIN("mitkFiberGenerationTest"); MITK_TEST_CONDITION_REQUIRED(argc==6,"check for input data") try{ mitk::PlanarEllipse::Pointer pf1 = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[1])->GetData()); mitk::PlanarEllipse::Pointer pf2 = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[2])->GetData()); mitk::PlanarEllipse::Pointer pf3 = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[3])->GetData()); mitk::FiberBundleX::Pointer uniform = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[4])->GetData()); mitk::FiberBundleX::Pointer gaussian = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[5])->GetData()); - + FiberGenerationParameters parameters; vector< mitk::PlanarEllipse::Pointer > fid; fid.push_back(pf1); fid.push_back(pf2); fid.push_back(pf3); vector< unsigned int > flip; flip.push_back(0); flip.push_back(0); flip.push_back(0); - vector< vector< mitk::PlanarEllipse::Pointer > > fiducials; - vector< vector< unsigned int > > fliplist; - fiducials.push_back(fid); fliplist.push_back(flip); + parameters.m_Fiducials.push_back(fid); parameters.m_FlipList.push_back(flip); + parameters.m_Density = 50; + parameters.m_Tension = 0; + parameters.m_Continuity = 0; + parameters.m_Bias = 0; + parameters.m_Sampling = 1; + parameters.m_Variance = 0.1; // check uniform fiber distribution { itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); - filter->SetFiducials(fiducials); - filter->SetFlipList(fliplist); - filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_UNIFORM); - filter->SetDensity(50); - filter->SetTension(0); - filter->SetContinuity(0); - filter->SetBias(0); - filter->SetFiberSampling(1); + parameters.m_Distribution = FiberGenerationParameters::DISTRIBUTE_UNIFORM; + filter->SetParameters(parameters); filter->Update(); vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles(); MITK_TEST_CONDITION_REQUIRED(uniform->Equals(fiberBundles.at(0)),"check uniform bundle") } // check gaussian fiber distribution { itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); - filter->SetFiducials(fiducials); - filter->SetFlipList(fliplist); - filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_GAUSSIAN); - filter->SetVariance(0.1); - filter->SetDensity(50); - filter->SetTension(0); - filter->SetContinuity(0); - filter->SetBias(0); - filter->SetFiberSampling(1); + parameters.m_Distribution = FiberGenerationParameters::DISTRIBUTE_GAUSSIAN; + filter->SetParameters(parameters); + filter->SetParameters(parameters); filter->Update(); vector< mitk::FiberBundleX::Pointer > fiberBundles = filter->GetFiberBundles(); MITK_TEST_CONDITION_REQUIRED(gaussian->Equals(fiberBundles.at(0)),"check gaussian bundle") } } catch(...) { return EXIT_FAILURE; } // always end with this! MITK_TEST_END(); } diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp index bcb759106d..bef3714322 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxAddArtifactsToDwiTest.cpp @@ -1,181 +1,181 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /**Documentation * Test the Fiberfox simulation functions (diffusion weighted image -> diffusion weighted image) */ class mitkFiberfoxAddArtifactsToDwiTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkFiberfoxAddArtifactsToDwiTestSuite); MITK_TEST(Spikes); MITK_TEST(GibbsRinging); MITK_TEST(Ghost); MITK_TEST(Aliasing); MITK_TEST(Eddy); MITK_TEST(RicianNoise); MITK_TEST(ChiSquareNoise); MITK_TEST(Distortions); CPPUNIT_TEST_SUITE_END(); private: mitk::DiffusionImage::Pointer m_InputDwi; FiberfoxParameters m_Parameters; public: void setUp() { // reference files m_InputDwi = dynamic_cast*>(mitk::IOUtil::LoadDataNode(GetTestDataFilePath("DiffusionImaging/Fiberfox/StickBall_RELAX.dwi"))->GetData()); // parameter setup m_Parameters = FiberfoxParameters(); - m_Parameters.m_ImageRegion = m_InputDwi->GetVectorImage()->GetLargestPossibleRegion(); - m_Parameters.m_ImageSpacing = m_InputDwi->GetVectorImage()->GetSpacing(); - m_Parameters.m_ImageOrigin = m_InputDwi->GetVectorImage()->GetOrigin(); - m_Parameters.m_ImageDirection = m_InputDwi->GetVectorImage()->GetDirection(); - m_Parameters.m_Bvalue = m_InputDwi->GetReferenceBValue(); - m_Parameters.SetGradienDirections(m_InputDwi->GetDirections()); + m_Parameters.m_SignalGen.m_ImageRegion = m_InputDwi->GetVectorImage()->GetLargestPossibleRegion(); + m_Parameters.m_SignalGen.m_ImageSpacing = m_InputDwi->GetVectorImage()->GetSpacing(); + m_Parameters.m_SignalGen.m_ImageOrigin = m_InputDwi->GetVectorImage()->GetOrigin(); + m_Parameters.m_SignalGen.m_ImageDirection = m_InputDwi->GetVectorImage()->GetDirection(); + m_Parameters.m_SignalGen.m_Bvalue = m_InputDwi->GetReferenceBValue(); + m_Parameters.m_SignalGen.SetGradienDirections(m_InputDwi->GetDirections()); } bool CompareDwi(itk::VectorImage< short, 3 >* dwi1, itk::VectorImage< short, 3 >* dwi2) { typedef itk::VectorImage< short, 3 > DwiImageType; try{ itk::ImageRegionIterator< DwiImageType > it1(dwi1, dwi1->GetLargestPossibleRegion()); itk::ImageRegionIterator< DwiImageType > it2(dwi2, dwi2->GetLargestPossibleRegion()); while(!it1.IsAtEnd()) { if (it1.Get()!=it2.Get()) return false; ++it1; ++it2; } } catch(...) { return false; } return true; } void StartSimulation(string testFileName) { mitk::DiffusionImage::Pointer refImage = NULL; if (!testFileName.empty()) CPPUNIT_ASSERT(refImage = dynamic_cast*>(mitk::IOUtil::LoadDataNode(testFileName)->GetData())); itk::AddArtifactsToDwiImageFilter< short >::Pointer artifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New(); artifactsToDwiFilter->SetUseConstantRandSeed(true); artifactsToDwiFilter->SetInput(m_InputDwi->GetVectorImage()); artifactsToDwiFilter->SetParameters(m_Parameters); CPPUNIT_ASSERT_NO_THROW(artifactsToDwiFilter->Update()); mitk::DiffusionImage::Pointer testImage = mitk::DiffusionImage::New(); testImage->SetVectorImage( artifactsToDwiFilter->GetOutput() ); - testImage->SetReferenceBValue(m_Parameters.m_Bvalue); - testImage->SetDirections(m_Parameters.GetGradientDirections()); + testImage->SetReferenceBValue( m_Parameters.m_SignalGen.m_Bvalue); + testImage->SetDirections( m_Parameters.m_SignalGen.GetGradientDirections()); testImage->InitializeFromVectorImage(); if (refImage.IsNotNull()) { CPPUNIT_ASSERT_MESSAGE(testFileName, CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage())); } } void Spikes() { - m_Parameters.m_Spikes = 5; - m_Parameters.m_SpikeAmplitude = 1; + m_Parameters.m_SignalGen.m_Spikes = 5; + m_Parameters.m_SignalGen.m_SpikeAmplitude = 1; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/spikes2.dwi") ); } void GibbsRinging() { - m_Parameters.m_DoAddGibbsRinging = true; + m_Parameters.m_SignalGen.m_DoAddGibbsRinging = true; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/gibbsringing2.dwi") ); } void Ghost() { - m_Parameters.m_KspaceLineOffset = 0.25; + m_Parameters.m_SignalGen.m_KspaceLineOffset = 0.25; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/ghost2.dwi") ); } void Aliasing() { - m_Parameters.m_CroppingFactor = 0.4; + m_Parameters.m_SignalGen.m_CroppingFactor = 0.4; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/aliasing2.dwi") ); } void Eddy() { - m_Parameters.m_EddyStrength = 0.05; + m_Parameters.m_SignalGen.m_EddyStrength = 0.05; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/eddy2.dwi") ); } void RicianNoise() { mitk::RicianNoiseModel* ricianNoiseModel = new mitk::RicianNoiseModel(); ricianNoiseModel->SetNoiseVariance(1000000); ricianNoiseModel->SetSeed(0); m_Parameters.m_NoiseModel = ricianNoiseModel; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/riciannoise2.dwi") ); - delete m_Parameters.m_NoiseModel; + delete m_Parameters.m_NoiseModel; } void ChiSquareNoise() { mitk::ChiSquareNoiseModel* chiSquareNoiseModel = new mitk::ChiSquareNoiseModel(); chiSquareNoiseModel->SetNoiseVariance(1000000); chiSquareNoiseModel->SetSeed(0); m_Parameters.m_NoiseModel = chiSquareNoiseModel; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/chisquarenoise2.dwi") ); - delete m_Parameters.m_NoiseModel; + delete m_Parameters.m_NoiseModel; } void Distortions() { mitk::Image::Pointer mitkFMap = dynamic_cast(mitk::IOUtil::LoadDataNode( GetTestDataFilePath("DiffusionImaging/Fiberfox/Fieldmap.nrrd") )->GetData()); typedef itk::Image ItkDoubleImgType; ItkDoubleImgType::Pointer fMap = ItkDoubleImgType::New(); mitk::CastToItkImage(mitkFMap, fMap); - m_Parameters.m_FrequencyMap = fMap; + m_Parameters.m_SignalGen.m_FrequencyMap = fMap; StartSimulation( GetTestDataFilePath("DiffusionImaging/Fiberfox/distortions2.dwi") ); } }; MITK_TEST_SUITE_REGISTRATION(mitkFiberfoxAddArtifactsToDwi) diff --git a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp index f67c4bc20c..1f28408a0a 100644 --- a/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Testing/mitkFiberfoxSignalGenerationTest.cpp @@ -1,276 +1,276 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /**Documentation * Test the Fiberfox simulation functions (fiberBundle -> diffusion weighted image) */ bool CompareDwi(itk::VectorImage< short, 3 >* dwi1, itk::VectorImage< short, 3 >* dwi2) { typedef itk::VectorImage< short, 3 > DwiImageType; try{ itk::ImageRegionIterator< DwiImageType > it1(dwi1, dwi1->GetLargestPossibleRegion()); itk::ImageRegionIterator< DwiImageType > it2(dwi2, dwi2->GetLargestPossibleRegion()); while(!it1.IsAtEnd()) { if (it1.Get()!=it2.Get()) return false; ++it1; ++it2; } } catch(...) { return false; } return true; } void StartSimulation(FiberfoxParameters parameters, FiberBundleX::Pointer fiberBundle, mitk::DiffusionImage::Pointer refImage, string message) { itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); tractsToDwiFilter->SetUseConstantRandSeed(true); tractsToDwiFilter->SetParameters(parameters); tractsToDwiFilter->SetFiberBundle(fiberBundle); tractsToDwiFilter->Update(); mitk::DiffusionImage::Pointer testImage = mitk::DiffusionImage::New(); testImage->SetVectorImage( tractsToDwiFilter->GetOutput() ); - testImage->SetReferenceBValue(parameters.m_Bvalue); - testImage->SetDirections(parameters.GetGradientDirections()); + testImage->SetReferenceBValue(parameters.m_SignalGen.m_Bvalue); + testImage->SetDirections(parameters.m_SignalGen.GetGradientDirections()); testImage->InitializeFromVectorImage(); if (refImage.IsNotNull()) { bool cond = CompareDwi(testImage->GetVectorImage(), refImage->GetVectorImage()); if (!cond) { MITK_INFO << "Saving test and rference image to " << mitk::IOUtil::GetTempPath(); mitk::IOUtil::SaveBaseData(testImage, mitk::IOUtil::GetTempPath()+"testImage.dwi"); mitk::IOUtil::SaveBaseData(refImage, mitk::IOUtil::GetTempPath()+"refImage.dwi"); } MITK_TEST_CONDITION_REQUIRED(cond, message); } } int mitkFiberfoxSignalGenerationTest(int argc, char* argv[]) { MITK_TEST_BEGIN("mitkFiberfoxSignalGenerationTest"); MITK_TEST_CONDITION_REQUIRED(argc>=19,"check for input data"); // input fiber bundle FiberBundleXReader::Pointer fibReader = FiberBundleXReader::New(); fibReader->SetFileName(argv[1]); fibReader->Update(); FiberBundleX::Pointer fiberBundle = dynamic_cast(fibReader->GetOutput()); // reference diffusion weighted images mitk::DiffusionImage::Pointer stickBall = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[2])->GetData()); mitk::DiffusionImage::Pointer stickAstrosticks = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[3])->GetData()); mitk::DiffusionImage::Pointer stickDot = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[4])->GetData()); mitk::DiffusionImage::Pointer tensorBall = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[5])->GetData()); mitk::DiffusionImage::Pointer stickTensorBall = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[6])->GetData()); mitk::DiffusionImage::Pointer stickTensorBallAstrosticks = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[7])->GetData()); mitk::DiffusionImage::Pointer gibbsringing = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[8])->GetData()); mitk::DiffusionImage::Pointer ghost = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[9])->GetData()); mitk::DiffusionImage::Pointer aliasing = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[10])->GetData()); mitk::DiffusionImage::Pointer eddy = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[11])->GetData()); mitk::DiffusionImage::Pointer linearmotion = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[12])->GetData()); mitk::DiffusionImage::Pointer randommotion = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[13])->GetData()); mitk::DiffusionImage::Pointer spikes = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[14])->GetData()); mitk::DiffusionImage::Pointer riciannoise = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[15])->GetData()); mitk::DiffusionImage::Pointer chisquarenoise = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[16])->GetData()); mitk::DiffusionImage::Pointer distortions = dynamic_cast*>(mitk::IOUtil::LoadDataNode(argv[17])->GetData()); mitk::Image::Pointer mitkFMap = dynamic_cast(mitk::IOUtil::LoadDataNode(argv[18])->GetData()); typedef itk::Image ItkDoubleImgType; ItkDoubleImgType::Pointer fMap = ItkDoubleImgType::New(); mitk::CastToItkImage(mitkFMap, fMap); FiberfoxParameters parameters; - parameters.m_SimulateKspaceAcquisition = true; - parameters.m_SignalScale = 10000; - parameters.m_ImageRegion = stickBall->GetVectorImage()->GetLargestPossibleRegion(); - parameters.m_ImageSpacing = stickBall->GetVectorImage()->GetSpacing(); - parameters.m_ImageOrigin = stickBall->GetVectorImage()->GetOrigin(); - parameters.m_ImageDirection = stickBall->GetVectorImage()->GetDirection(); - parameters.m_Bvalue = stickBall->GetReferenceBValue(); - parameters.SetGradienDirections(stickBall->GetDirections()); + parameters.m_SignalGen.m_SimulateKspaceAcquisition = true; + parameters.m_SignalGen.m_SignalScale = 10000; + parameters.m_SignalGen.m_ImageRegion = stickBall->GetVectorImage()->GetLargestPossibleRegion(); + parameters.m_SignalGen.m_ImageSpacing = stickBall->GetVectorImage()->GetSpacing(); + parameters.m_SignalGen.m_ImageOrigin = stickBall->GetVectorImage()->GetOrigin(); + parameters.m_SignalGen.m_ImageDirection = stickBall->GetVectorImage()->GetDirection(); + parameters.m_SignalGen.m_Bvalue = stickBall->GetReferenceBValue(); + parameters.m_SignalGen.SetGradienDirections(stickBall->GetDirections()); // intra and inter axonal compartments mitk::StickModel stickModel; - stickModel.SetBvalue(parameters.m_Bvalue); + stickModel.SetBvalue(parameters.m_SignalGen.m_Bvalue); stickModel.SetT2(110); stickModel.SetDiffusivity(0.001); - stickModel.SetGradientList(parameters.GetGradientDirections()); + stickModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); mitk::TensorModel tensorModel; tensorModel.SetT2(110); - stickModel.SetBvalue(parameters.m_Bvalue); + stickModel.SetBvalue(parameters.m_SignalGen.m_Bvalue); tensorModel.SetDiffusivity1(0.001); tensorModel.SetDiffusivity2(0.00025); tensorModel.SetDiffusivity3(0.00025); - tensorModel.SetGradientList(parameters.GetGradientDirections()); + tensorModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); // extra axonal compartment models mitk::BallModel ballModel; ballModel.SetT2(80); - ballModel.SetBvalue(parameters.m_Bvalue); + ballModel.SetBvalue(parameters.m_SignalGen.m_Bvalue); ballModel.SetDiffusivity(0.001); - ballModel.SetGradientList(parameters.GetGradientDirections()); + ballModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); mitk::AstroStickModel astrosticksModel; astrosticksModel.SetT2(80); - astrosticksModel.SetBvalue(parameters.m_Bvalue); + astrosticksModel.SetBvalue(parameters.m_SignalGen.m_Bvalue); astrosticksModel.SetDiffusivity(0.001); astrosticksModel.SetRandomizeSticks(true); astrosticksModel.SetSeed(0); - astrosticksModel.SetGradientList(parameters.GetGradientDirections()); + astrosticksModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); mitk::DotModel dotModel; dotModel.SetT2(80); - dotModel.SetGradientList(parameters.GetGradientDirections()); + dotModel.SetGradientList(parameters.m_SignalGen.GetGradientDirections()); // noise models mitk::RicianNoiseModel* ricianNoiseModel = new mitk::RicianNoiseModel(); ricianNoiseModel->SetNoiseVariance(1000000); ricianNoiseModel->SetSeed(0); // Rician noise mitk::ChiSquareNoiseModel* chiSquareNoiseModel = new mitk::ChiSquareNoiseModel(); chiSquareNoiseModel->SetNoiseVariance(1000000); chiSquareNoiseModel->SetSeed(0); try{ // Stick-Ball parameters.m_FiberModelList.push_back(&stickModel); parameters.m_NonFiberModelList.push_back(&ballModel); StartSimulation(parameters, fiberBundle, stickBall, argv[2]); // Srick-Astrosticks parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&astrosticksModel); StartSimulation(parameters, fiberBundle, stickAstrosticks, argv[3]); // Stick-Dot parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&dotModel); StartSimulation(parameters, fiberBundle, stickDot, argv[4]); // Tensor-Ball parameters.m_FiberModelList.clear(); parameters.m_FiberModelList.push_back(&tensorModel); parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&ballModel); StartSimulation(parameters, fiberBundle, tensorBall, argv[5]); // Stick-Tensor-Ball parameters.m_FiberModelList.clear(); parameters.m_FiberModelList.push_back(&stickModel); parameters.m_FiberModelList.push_back(&tensorModel); parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&ballModel); StartSimulation(parameters, fiberBundle, stickTensorBall, argv[6]); // Stick-Tensor-Ball-Astrosticks parameters.m_NonFiberModelList.push_back(&astrosticksModel); StartSimulation(parameters, fiberBundle, stickTensorBallAstrosticks, argv[7]); // Gibbs ringing parameters.m_FiberModelList.clear(); parameters.m_FiberModelList.push_back(&stickModel); parameters.m_NonFiberModelList.clear(); parameters.m_NonFiberModelList.push_back(&ballModel); - parameters.m_DoAddGibbsRinging = true; + parameters.m_SignalGen.m_DoAddGibbsRinging = true; StartSimulation(parameters, fiberBundle, gibbsringing, argv[8]); // Ghost - parameters.m_DoAddGibbsRinging = false; - parameters.m_KspaceLineOffset = 0.25; + parameters.m_SignalGen.m_DoAddGibbsRinging = false; + parameters.m_SignalGen.m_KspaceLineOffset = 0.25; StartSimulation(parameters, fiberBundle, ghost, argv[9]); // Aliasing - parameters.m_KspaceLineOffset = 0; - parameters.m_CroppingFactor = 0.4; - parameters.m_SignalScale = 1000; + parameters.m_SignalGen.m_KspaceLineOffset = 0; + parameters.m_SignalGen.m_CroppingFactor = 0.4; + parameters.m_SignalGen.m_SignalScale = 1000; StartSimulation(parameters, fiberBundle, aliasing, argv[10]); // Eddy currents - parameters.m_CroppingFactor = 1; - parameters.m_SignalScale = 10000; - parameters.m_EddyStrength = 0.05; + parameters.m_SignalGen.m_CroppingFactor = 1; + parameters.m_SignalGen.m_SignalScale = 10000; + parameters.m_SignalGen.m_EddyStrength = 0.05; StartSimulation(parameters, fiberBundle, eddy, argv[11]); // Motion (linear) - parameters.m_EddyStrength = 0.0; - parameters.m_DoAddMotion = true; - parameters.m_DoRandomizeMotion = false; - parameters.m_Translation[1] = 10; - parameters.m_Rotation[2] = 90; + parameters.m_SignalGen.m_EddyStrength = 0.0; + parameters.m_SignalGen.m_DoAddMotion = true; + parameters.m_SignalGen.m_DoRandomizeMotion = false; + parameters.m_SignalGen.m_Translation[1] = 10; + parameters.m_SignalGen.m_Rotation[2] = 90; StartSimulation(parameters, fiberBundle, linearmotion, argv[12]); // Motion (random) - parameters.m_DoRandomizeMotion = true; - parameters.m_Translation[1] = 5; - parameters.m_Rotation[2] = 45; + parameters.m_SignalGen.m_DoRandomizeMotion = true; + parameters.m_SignalGen.m_Translation[1] = 5; + parameters.m_SignalGen.m_Rotation[2] = 45; StartSimulation(parameters, fiberBundle, randommotion, argv[13]); // Spikes - parameters.m_DoAddMotion = false; - parameters.m_Spikes = 5; - parameters.m_SpikeAmplitude = 1; + parameters.m_SignalGen.m_DoAddMotion = false; + parameters.m_SignalGen.m_Spikes = 5; + parameters.m_SignalGen.m_SpikeAmplitude = 1; StartSimulation(parameters, fiberBundle, spikes, argv[14]); // Rician noise - parameters.m_Spikes = 0; + parameters.m_SignalGen.m_Spikes = 0; parameters.m_NoiseModel = ricianNoiseModel; StartSimulation(parameters, fiberBundle, riciannoise, argv[15]); delete parameters.m_NoiseModel; // Chi-square noise parameters.m_NoiseModel = chiSquareNoiseModel; StartSimulation(parameters, fiberBundle, chisquarenoise, argv[16]); delete parameters.m_NoiseModel; // Distortions parameters.m_NoiseModel = NULL; - parameters.m_FrequencyMap = fMap; + parameters.m_SignalGen.m_FrequencyMap = fMap; StartSimulation(parameters, fiberBundle, distortions, argv[17]); } catch (std::exception &e) { MITK_TEST_CONDITION_REQUIRED(false, e.what()); } // always end with this! MITK_TEST_END(); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp index cb8521e316..abf9af0b68 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberProcessingView.cpp @@ -1,559 +1,572 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkFiberProcessingView.h" #include // Qt #include // MITK #include #include #include #include #include #include #include #include #include #include #include #include // ITK #include #include #include #include #include #include #include #include #include #include const std::string QmitkFiberProcessingView::VIEW_ID = "org.mitk.views.fiberprocessing"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace mitk; QmitkFiberProcessingView::QmitkFiberProcessingView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_UpsamplingFactor(5) { } // Destructor QmitkFiberProcessingView::~QmitkFiberProcessingView() { } void QmitkFiberProcessingView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkFiberProcessingViewControls; m_Controls->setupUi( parent ); connect( m_Controls->m_ProcessFiberBundleButton, SIGNAL(clicked()), this, SLOT(ProcessSelectedBundles()) ); connect( m_Controls->m_ResampleFibersButton, SIGNAL(clicked()), this, SLOT(ResampleSelectedBundles()) ); connect(m_Controls->m_FaColorFibersButton, SIGNAL(clicked()), this, SLOT(DoImageColorCoding())); connect( m_Controls->m_PruneFibersButton, SIGNAL(clicked()), this, SLOT(PruneBundle()) ); connect( m_Controls->m_CurvatureThresholdButton, SIGNAL(clicked()), this, SLOT(ApplyCurvatureThreshold()) ); connect( m_Controls->m_MirrorFibersButton, SIGNAL(clicked()), this, SLOT(MirrorFibers()) ); connect( m_Controls->m_CompressFibersButton, SIGNAL(clicked()), this, SLOT(CompressSelectedBundles()) ); connect( m_Controls->m_ExtractFiberPeaks, SIGNAL(clicked()), this, SLOT(CalculateFiberDirections()) ); } } void QmitkFiberProcessingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkFiberProcessingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkFiberProcessingView::CalculateFiberDirections() { typedef itk::Image ItkUcharImgType; typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; // load fiber bundle mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast(m_SelectedFB.back()->GetData()); itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); - // load/create mask image if (m_SelectedImage.IsNotNull()) { ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New(); mitk::CastToItkImage(m_SelectedImage, itkMaskImage); fOdfFilter->SetMaskImage(itkMaskImage); } // extract directions from fiber bundle fOdfFilter->SetFiberBundle(inputTractogram); fOdfFilter->SetAngularThreshold(cos(m_Controls->m_AngularThreshold->value()*M_PI/180)); fOdfFilter->SetNormalizeVectors(true); fOdfFilter->SetUseWorkingCopy(true); + fOdfFilter->SetCreateDirectionImages(m_Controls->m_DirectionImagesBox->isChecked()); fOdfFilter->SetSizeThreshold(m_Controls->m_PeakThreshold->value()); fOdfFilter->SetMaxNumDirections(m_Controls->m_MaxNumDirections->value()); fOdfFilter->Update(); QString name = m_SelectedFB.back()->GetName().c_str(); if (m_Controls->m_VectorFieldBox->isChecked()) { + float minSpacing = 1; + if (m_SelectedImage.IsNotNull()) + { + mitk::Vector3D outImageSpacing = m_SelectedImage->GetGeometry()->GetSpacing(); + + if(outImageSpacing[0]GetOutputFiberBundle(); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(directions); node->SetName((name+"_vectorfield").toStdString().c_str()); -// node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(minSpacing)); + node->SetProperty("Fiber2DSliceThickness", mitk::FloatProperty::New(minSpacing)); node->SetProperty("Fiber2DfadeEFX", mitk::BoolProperty::New(false)); node->SetProperty("color", mitk::ColorProperty::New(1.0f, 1.0f, 1.0f)); GetDefaultDataStorage()->Add(node, m_SelectedFB.back()); } if (m_Controls->m_NumDirectionsBox->isChecked()) { mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( fOdfFilter->GetNumDirectionsImage().GetPointer() ); mitkImage->SetVolume( fOdfFilter->GetNumDirectionsImage()->GetBufferPointer() ); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(mitkImage); node->SetName((name+"_numdirections").toStdString().c_str()); GetDefaultDataStorage()->Add(node, m_SelectedFB.back()); } if (m_Controls->m_DirectionImagesBox->isChecked()) { ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); for (unsigned int i=0; iSize(); i++) { itk::TractsToVectorImageFilter::ItkDirectionImageType::Pointer itkImg = directionImageContainer->GetElement(i); if (itkImg.IsNull()) return; mitk::Image::Pointer mitkImage = mitk::Image::New(); mitkImage->InitializeByItk( itkImg.GetPointer() ); mitkImage->SetVolume( itkImg->GetBufferPointer() ); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(mitkImage); node->SetName( (name+"_direction_"+boost::lexical_cast(i).c_str()).toStdString().c_str()); node->SetVisibility(false); GetDefaultDataStorage()->Add(node, m_SelectedFB.back()); } } } void QmitkFiberProcessingView::UpdateGui() { m_Controls->m_CompressFibersButton->setEnabled(!m_SelectedFB.empty()); m_Controls->m_ProcessFiberBundleButton->setEnabled(!m_SelectedFB.empty()); m_Controls->m_ResampleFibersButton->setEnabled(!m_SelectedFB.empty()); m_Controls->m_FaColorFibersButton->setEnabled(!m_SelectedFB.empty()); m_Controls->m_PruneFibersButton->setEnabled(!m_SelectedFB.empty()); m_Controls->m_CurvatureThresholdButton->setEnabled(!m_SelectedFB.empty()); m_Controls->m_ExtractFiberPeaks->setEnabled(!m_SelectedFB.empty()); // are fiber bundles selected? if ( m_SelectedFB.empty() ) { if (m_SelectedSurfaces.size()>0) m_Controls->m_MirrorFibersButton->setEnabled(true); else m_Controls->m_MirrorFibersButton->setEnabled(false); } else { if (m_SelectedImage.IsNotNull()) m_Controls->m_FaColorFibersButton->setEnabled(true); } } void QmitkFiberProcessingView::OnSelectionChanged( std::vector nodes ) { //reset existing Vectors containing FiberBundles and PlanarFigures from a previous selection m_SelectedFB.clear(); m_SelectedSurfaces.clear(); m_SelectedImage = NULL; for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if ( dynamic_cast(node->GetData()) ) { m_SelectedFB.push_back(node); } else if (dynamic_cast(node->GetData())) m_SelectedImage = dynamic_cast(node->GetData()); else if (dynamic_cast(node->GetData())) { m_SelectedSurfaces.push_back(dynamic_cast(node->GetData())); } } UpdateGui(); GenerateStats(); } void QmitkFiberProcessingView::Activated() { } void QmitkFiberProcessingView::PruneBundle() { int minLength = this->m_Controls->m_PruneFibersSpinBox->value(); int maxLength = this->m_Controls->m_MaxPruneFibersSpinBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); if (!fib->RemoveShortFibers(minLength)) QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); else if (!fib->RemoveLongFibers(maxLength)) QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); } GenerateStats(); RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::ApplyCurvatureThreshold() { int mm = this->m_Controls->m_MinCurvatureRadiusBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); if (!fib->ApplyCurvatureThreshold(mm, this->m_Controls->m_RemoveFiberDueToCurvatureCheckbox->isChecked())) QMessageBox::information(NULL, "No output generated:", "The resulting fiber bundle contains no fibers."); } GenerateStats(); RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::GenerateStats() { if ( m_SelectedFB.empty() ) return; QString stats(""); for( int i=0; i(node->GetData())) { if (i>0) stats += "\n-----------------------------\n"; stats += QString(node->GetName().c_str()) + "\n"; mitk::FiberBundleX::Pointer fib = dynamic_cast(node->GetData()); stats += "Number of fibers: "+ QString::number(fib->GetNumFibers()) + "\n"; stats += "Number of points: "+ QString::number(fib->GetNumberOfPoints()) + "\n"; stats += "Min. length: "+ QString::number(fib->GetMinFiberLength(),'f',1) + " mm\n"; stats += "Max. length: "+ QString::number(fib->GetMaxFiberLength(),'f',1) + " mm\n"; stats += "Mean length: "+ QString::number(fib->GetMeanFiberLength(),'f',1) + " mm\n"; stats += "Median length: "+ QString::number(fib->GetMedianFiberLength(),'f',1) + " mm\n"; stats += "Standard deviation: "+ QString::number(fib->GetLengthStDev(),'f',1) + " mm\n"; } } this->m_Controls->m_StatsTextEdit->setText(stats); } void QmitkFiberProcessingView::ProcessSelectedBundles() { if ( m_SelectedFB.empty() ){ QMessageBox::information( NULL, "Warning", "No fibe bundle selected!"); MITK_WARN("QmitkFiberProcessingView") << "no fibe bundle selected"; return; } int generationMethod = m_Controls->m_GenerationBox->currentIndex(); for( int i=0; i(node->GetData())) { mitk::FiberBundleX::Pointer fib = dynamic_cast(node->GetData()); QString name(node->GetName().c_str()); DataNode::Pointer newNode = NULL; switch(generationMethod){ case 0: newNode = GenerateTractDensityImage(fib, false, true); name += "_TDI"; break; case 1: newNode = GenerateTractDensityImage(fib, false, false); name += "_TDI"; break; case 2: newNode = GenerateTractDensityImage(fib, true, false); name += "_envelope"; break; case 3: newNode = GenerateColorHeatmap(fib); break; case 4: newNode = GenerateFiberEndingsImage(fib); name += "_fiber_endings"; break; case 5: newNode = GenerateFiberEndingsPointSet(fib); name += "_fiber_endings"; break; } if (newNode.IsNotNull()) { newNode->SetName(name.toStdString()); GetDataStorage()->Add(newNode); } } } } // generate pointset displaying the fiber endings mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateFiberEndingsPointSet(mitk::FiberBundleX::Pointer fib) { mitk::PointSet::Pointer pointSet = mitk::PointSet::New(); vtkSmartPointer fiberPolyData = fib->GetFiberPolyData(); vtkSmartPointer vLines = fiberPolyData->GetLines(); vLines->InitTraversal(); int count = 0; int numFibers = fib->GetNumFibers(); for( int i=0; iGetNextCell ( numPoints, points ); if (numPoints>0) { double* point = fiberPolyData->GetPoint(points[0]); itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; pointSet->InsertPoint(count, itkPoint); count++; } if (numPoints>2) { double* point = fiberPolyData->GetPoint(points[numPoints-1]); itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; pointSet->InsertPoint(count, itkPoint); count++; } } mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData( pointSet ); return node; } // generate image displaying the fiber endings mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateFiberEndingsImage(mitk::FiberBundleX::Pointer fib) { typedef unsigned char OutPixType; typedef itk::Image OutImageType; typedef itk::TractsToFiberEndingsImageFilter< OutImageType > ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); generator->SetFiberBundle(fib); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { OutImageType::Pointer itkImage = OutImageType::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image OutImageType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } // generate rgba heatmap from fiber bundle mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateColorHeatmap(mitk::FiberBundleX::Pointer fib) { typedef itk::RGBAPixel OutPixType; typedef itk::Image OutImageType; typedef itk::TractsToRgbaImageFilter< OutImageType > ImageGeneratorType; ImageGeneratorType::Pointer generator = ImageGeneratorType::New(); generator->SetFiberBundle(fib); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { itk::Image::Pointer itkImage = itk::Image::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } // generate tract density image from fiber bundle mitk::DataNode::Pointer QmitkFiberProcessingView::GenerateTractDensityImage(mitk::FiberBundleX::Pointer fib, bool binary, bool absolute) { typedef float OutPixType; typedef itk::Image OutImageType; itk::TractDensityImageFilter< OutImageType >::Pointer generator = itk::TractDensityImageFilter< OutImageType >::New(); generator->SetFiberBundle(fib); generator->SetBinaryOutput(binary); generator->SetOutputAbsoluteValues(absolute); generator->SetUpsamplingFactor(m_Controls->m_UpsamplingSpinBox->value()); if (m_SelectedImage.IsNotNull()) { OutImageType::Pointer itkImage = OutImageType::New(); CastToItkImage(m_SelectedImage, itkImage); generator->SetInputImage(itkImage); generator->SetUseImageGeometry(true); } generator->Update(); // get output image typedef itk::Image OutType; OutType::Pointer outImg = generator->GetOutput(); mitk::Image::Pointer img = mitk::Image::New(); img->InitializeByItk(outImg.GetPointer()); img->SetVolume(outImg->GetBufferPointer()); // init data node mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(img); return node; } void QmitkFiberProcessingView::ResampleSelectedBundles() { double factor = this->m_Controls->m_ResampleFibersSpinBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); fib->DoFiberSmoothing(factor); } GenerateStats(); RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::CompressSelectedBundles() { double factor = this->m_Controls->m_FiberErrorSpinBox->value(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); fib->CompressFibers(factor); } GenerateStats(); RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::MirrorFibers() { unsigned int axis = this->m_Controls->m_AxisSelectionBox->currentIndex(); for (int i=0; i(m_SelectedFB.at(i)->GetData()); fib->MirrorFibers(axis); } if (m_SelectedFB.size()>0) GenerateStats(); if (m_SelectedSurfaces.size()>0) { for (int i=0; i poly = surf->GetVtkPolyData(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); for (int i=0; iGetNumberOfPoints(); i++) { double* point = poly->GetPoint(i); point[axis] *= -1; vtkNewPoints->InsertNextPoint(point); } poly->SetPoints(vtkNewPoints); surf->CalculateBoundingBox(); } } RenderingManager::GetInstance()->RequestUpdateAll(); } void QmitkFiberProcessingView::DoImageColorCoding() { if (m_SelectedImage.IsNull()) return; for( int i=0; i(m_SelectedFB.at(i)->GetData()); fib->SetFAMap(m_SelectedImage); fib->SetColorCoding(mitk::FiberBundleX::COLORCODING_FA_BASED); fib->DoColorCodingFaBased(); } if(m_MultiWidget) m_MultiWidget->RequestUpdate(); } 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 2c85f47582..f15fc8c968 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,2579 +1,2643 @@ /*=================================================================== 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 #include #include #include #include #include "usModuleRegistry.h" #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include QmitkFiberfoxWorker::QmitkFiberfoxWorker(QmitkFiberfoxView* view) : m_View(view) { } void QmitkFiberfoxWorker::run() { try{ switch (m_FilterType) { case 0: m_View->m_TractsToDwiFilter->Update(); break; case 1: m_View->m_ArtifactsToDwiFilter->Update(); break; } } catch( ... ) { } m_View->m_Thread.quit(); } const std::string QmitkFiberfoxView::VIEW_ID = "org.mitk.views.fiberfoxview"; QmitkFiberfoxView::QmitkFiberfoxView() : QmitkAbstractView() , m_Controls( 0 ) , m_SelectedImage( 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."; switch (m_Worker.m_FilterType) { case 0: m_TractsToDwiFilter->SetAbortGenerateData(true); break; case 1: m_ArtifactsToDwiFilter->SetAbortGenerateData(true); break; } 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::DiffusionImage::Pointer mitkImage = mitk::DiffusionImage::New(); switch (m_Worker.m_FilterType) { case 0: { statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); if (m_TractsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_TractsToDwiFilter->GetParameters(); mitkImage->SetVectorImage( m_TractsToDwiFilter->GetOutput() ); - mitkImage->SetReferenceBValue(parameters.m_Bvalue); - mitkImage->SetDirections(parameters.GetGradientDirections()); + mitkImage->SetReferenceBValue(parameters.m_SignalGen.m_Bvalue); + mitkImage->SetDirections(parameters.m_SignalGen.GetGradientDirections()); mitkImage->InitializeFromVectorImage(); - parameters.m_ResultNode->SetData( mitkImage ); + parameters.m_Misc.m_ResultNode->SetData( mitkImage ); - parameters.m_ResultNode->SetName(parameters.m_ParentNode->GetName() - +"_D"+QString::number(parameters.m_ImageRegion.GetSize(0)).toStdString() - +"-"+QString::number(parameters.m_ImageRegion.GetSize(1)).toStdString() - +"-"+QString::number(parameters.m_ImageRegion.GetSize(2)).toStdString() - +"_S"+QString::number(parameters.m_ImageSpacing[0]).toStdString() - +"-"+QString::number(parameters.m_ImageSpacing[1]).toStdString() - +"-"+QString::number(parameters.m_ImageSpacing[2]).toStdString() - +"_b"+QString::number(parameters.m_Bvalue).toStdString() - +"_"+parameters.m_SignalModelString - +parameters.m_ArtifactModelString); + 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); - GetDataStorage()->Add(parameters.m_ResultNode, parameters.m_ParentNode); + GetDataStorage()->Add(parameters.m_Misc.m_ResultNode, parameters.m_Misc.m_ParentNode); - parameters.m_ResultNode->SetProperty( "levelwindow", mitk::LevelWindowProperty::New(m_TractsToDwiFilter->GetLevelWindow()) ); + 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(parameters.m_ParentNode->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString()); - GetDataStorage()->Add(node, parameters.m_ParentNode); + node->SetName(parameters.m_Misc.m_ParentNode->GetName()+"_CompartmentVolume-"+QString::number(k).toStdString()); + GetDataStorage()->Add(node, parameters.m_Misc.m_ParentNode); } } m_TractsToDwiFilter = NULL; break; } case 1: { statusText = QString(m_ArtifactsToDwiFilter->GetStatusText().c_str()); if (m_ArtifactsToDwiFilter->GetAbortGenerateData()) { MITK_INFO << "Simulation aborted."; return; } parameters = m_ArtifactsToDwiFilter->GetParameters().CopyParameters(); - mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(parameters.m_ParentNode->GetData()); + mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(parameters.m_Misc.m_ParentNode->GetData()); mitkImage = mitk::DiffusionImage::New(); mitkImage->SetVectorImage( m_ArtifactsToDwiFilter->GetOutput() ); mitkImage->SetReferenceBValue(diffImg->GetReferenceBValue()); mitkImage->SetDirections(diffImg->GetDirections()); mitkImage->InitializeFromVectorImage(); - parameters.m_ResultNode->SetData( mitkImage ); - parameters.m_ResultNode->SetName(parameters.m_ParentNode->GetName()+parameters.m_ArtifactModelString); - GetDataStorage()->Add(parameters.m_ResultNode, parameters.m_ParentNode); + parameters.m_Misc.m_ResultNode->SetData( mitkImage ); + parameters.m_Misc.m_ResultNode->SetName(parameters.m_Misc.m_ParentNode->GetName()+parameters.m_Misc.m_ArtifactModelString); + GetDataStorage()->Add(parameters.m_Misc.m_ResultNode, parameters.m_Misc.m_ParentNode); m_ArtifactsToDwiFilter = NULL; break; } } - mitk::BaseData::Pointer basedata = parameters.m_ResultNode->GetData(); + 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_OutputPath.empty()) + if (!parameters.m_Misc.m_OutputPath.empty()) { try{ - QString outputFileName(parameters.m_OutputPath.c_str()); - outputFileName += parameters.m_ResultNode->GetName().c_str(); + QString outputFileName(parameters.m_Misc.m_OutputPath.c_str()); + outputFileName += parameters.m_Misc.m_ResultNode->GetName().c_str(); outputFileName.replace(QString("."), QString("_")); outputFileName += ".dwi"; QString status("Saving output image to "); status += outputFileName; m_Controls->m_SimulationStatusText->append(status); mitk::IOUtil::SaveBaseData(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_FrequencyMap = NULL; + parameters.m_SignalGen.m_FrequencyMap = NULL; } void QmitkFiberfoxView::UpdateSimulationStatus() { QString statusText; switch (m_Worker.m_FilterType) { case 0: statusText = QString(m_TractsToDwiFilter->GetStatusText().c_str()); break; case 1: statusText = QString(m_ArtifactsToDwiFilter->GetStatusText().c_str()); break; } if (QString::compare(m_SimulationStatusText,statusText)!=0) { m_Controls->m_SimulationStatusText->clear(); statusText = "
"+statusText+"
"; 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_AstrosticksWidget1->setVisible(false); m_Controls->m_AstrosticksWidget2->setVisible(false); m_Controls->m_DotWidget1->setVisible(false); m_Controls->m_DotWidget2->setVisible(false); 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_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()); mitk::TNodePredicateDataType::Pointer isMitkImage = mitk::TNodePredicateDataType::New(); mitk::NodePredicateDataType::Pointer isDwi = mitk::NodePredicateDataType::New("DiffusionImage"); mitk::NodePredicateDataType::Pointer isDti = mitk::NodePredicateDataType::New("TensorImage"); mitk::NodePredicateDataType::Pointer 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 finalPredicate = mitk::NodePredicateAnd::New(isMitkImage, noDiffusionImage); m_Controls->m_FrequencyMapBox->SetPredicate(finalPredicate); m_Controls->m_Comp4VolumeFraction->SetDataStorage(this->GetDataStorage()); m_Controls->m_Comp4VolumeFraction->SetPredicate(finalPredicate); 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())); } } template< class ScalarType > FiberfoxParameters< ScalarType > QmitkFiberfoxView::UpdateImageParameters() { FiberfoxParameters< ScalarType > parameters; - parameters.m_OutputPath = ""; + 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(); string outputPath = m_Controls->m_SavePathEdit->text().toStdString(); if (outputPath.compare("-")!=0) { - parameters.m_OutputPath = outputPath; - parameters.m_OutputPath += "/"; + parameters.m_Misc.m_OutputPath = outputPath; + parameters.m_Misc.m_OutputPath += "/"; } if (m_MaskImageNode.IsNotNull()) { mitk::Image::Pointer mitkMaskImage = dynamic_cast(m_MaskImageNode->GetData()); - mitk::CastToItkImage(mitkMaskImage, parameters.m_MaskImage); + mitk::CastToItkImage(mitkMaskImage, parameters.m_SignalGen.m_MaskImage); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); - duplicator->SetInputImage(parameters.m_MaskImage); + duplicator->SetInputImage(parameters.m_SignalGen.m_MaskImage); duplicator->Update(); - parameters.m_MaskImage = duplicator->GetOutput(); + parameters.m_SignalGen.m_MaskImage = duplicator->GetOutput(); } if (m_SelectedDWI.IsNotNull()) // use parameters of selected DWI { mitk::DiffusionImage::Pointer dwi = dynamic_cast*>(m_SelectedDWI->GetData()); - parameters.m_ImageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion(); - parameters.m_ImageSpacing = dwi->GetVectorImage()->GetSpacing(); - parameters.m_ImageOrigin = dwi->GetVectorImage()->GetOrigin(); - parameters.m_ImageDirection = dwi->GetVectorImage()->GetDirection(); - parameters.m_Bvalue = dwi->GetReferenceBValue(); - parameters.SetGradienDirections(dwi->GetDirections()); + parameters.m_SignalGen.m_ImageRegion = dwi->GetVectorImage()->GetLargestPossibleRegion(); + parameters.m_SignalGen.m_ImageSpacing = dwi->GetVectorImage()->GetSpacing(); + parameters.m_SignalGen.m_ImageOrigin = dwi->GetVectorImage()->GetOrigin(); + parameters.m_SignalGen.m_ImageDirection = dwi->GetVectorImage()->GetDirection(); + parameters.m_SignalGen.m_Bvalue = dwi->GetReferenceBValue(); + parameters.m_SignalGen.SetGradienDirections(dwi->GetDirections()); } else if (m_SelectedImage.IsNotNull()) // use geometry of selected image { mitk::Image::Pointer img = dynamic_cast(m_SelectedImage->GetData()); itk::Image< float, 3 >::Pointer itkImg = itk::Image< float, 3 >::New(); CastToItkImage< itk::Image< float, 3 > >(img, itkImg); - parameters.m_ImageRegion = itkImg->GetLargestPossibleRegion(); - parameters.m_ImageSpacing = itkImg->GetSpacing(); - parameters.m_ImageOrigin = itkImg->GetOrigin(); - parameters.m_ImageDirection = itkImg->GetDirection(); - parameters.SetNumWeightedGradients(m_Controls->m_NumGradientsBox->value()); - parameters.m_Bvalue = m_Controls->m_BvalueBox->value(); + 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_ImageRegion.SetSize(0, m_Controls->m_SizeX->value()); - parameters.m_ImageRegion.SetSize(1, m_Controls->m_SizeY->value()); - parameters.m_ImageRegion.SetSize(2, m_Controls->m_SizeZ->value()); - parameters.m_ImageSpacing[0] = m_Controls->m_SpacingX->value(); - parameters.m_ImageSpacing[1] = m_Controls->m_SpacingY->value(); - parameters.m_ImageSpacing[2] = m_Controls->m_SpacingZ->value(); - parameters.m_ImageOrigin[0] = parameters.m_ImageSpacing[0]/2; - parameters.m_ImageOrigin[1] = parameters.m_ImageSpacing[1]/2; - parameters.m_ImageOrigin[2] = parameters.m_ImageSpacing[2]/2; - parameters.m_ImageDirection.SetIdentity(); - parameters.SetNumWeightedGradients(m_Controls->m_NumGradientsBox->value()); - parameters.m_Bvalue = m_Controls->m_BvalueBox->value(); - parameters.GenerateGradientHalfShell(); + 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_DoSimulateRelaxation = m_Controls->m_RelaxationBox->isChecked(); - parameters.m_SimulateKspaceAcquisition = parameters.m_DoSimulateRelaxation; - if (parameters.m_DoSimulateRelaxation && m_SelectedBundles.size()>0 ) - parameters.m_ArtifactModelString += "_RELAX"; + parameters.m_SignalGen.m_DoSimulateRelaxation = m_Controls->m_RelaxationBox->isChecked(); + parameters.m_SignalGen.m_SimulateKspaceAcquisition = parameters.m_SignalGen.m_DoSimulateRelaxation; + if (parameters.m_SignalGen.m_DoSimulateRelaxation && m_SelectedBundles.size()>0 ) + parameters.m_Misc.m_ArtifactModelString += "_RELAX"; // N/2 ghosts + parameters.m_Misc.m_CheckAddGhostsBox = m_Controls->m_AddGhosts->isChecked(); if (m_Controls->m_AddGhosts->isChecked()) { - parameters.m_SimulateKspaceAcquisition = true; - parameters.m_ArtifactModelString += "_GHOST"; - parameters.m_KspaceLineOffset = m_Controls->m_kOffsetBox->value(); - parameters.m_ResultNode->AddProperty("Fiberfox.Ghost", DoubleProperty::New(parameters.m_KspaceLineOffset)); + 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_KspaceLineOffset = 0; + 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_SimulateKspaceAcquisition = true; - parameters.m_ArtifactModelString += "_ALIASING"; - parameters.m_CroppingFactor = (100-m_Controls->m_WrapBox->value())/100; - parameters.m_ResultNode->AddProperty("Fiberfox.Aliasing", DoubleProperty::New(m_Controls->m_WrapBox->value())); + 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_SimulateKspaceAcquisition = true; - parameters.m_Spikes = m_Controls->m_SpikeNumBox->value(); - parameters.m_SpikeAmplitude = m_Controls->m_SpikeScaleBox->value(); - parameters.m_ArtifactModelString += "_SPIKES"; - parameters.m_ResultNode->AddProperty("Fiberfox.Spikes.Number", IntProperty::New(parameters.m_Spikes)); - parameters.m_ResultNode->AddProperty("Fiberfox.Spikes.Amplitude", DoubleProperty::New(parameters.m_SpikeAmplitude)); + 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_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); + parameters.m_SignalGen.m_DoAddGibbsRinging = m_Controls->m_AddGibbsRinging->isChecked(); if (m_Controls->m_AddGibbsRinging->isChecked()) { - parameters.m_SimulateKspaceAcquisition = true; - parameters.m_ResultNode->AddProperty("Fiberfox.Ringing", BoolProperty::New(true)); - parameters.m_ArtifactModelString += "_RINGING"; + 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 (parameters.m_ImageRegion.GetSize(0)==itkImg->GetLargestPossibleRegion().GetSize(0) && - parameters.m_ImageRegion.GetSize(1)==itkImg->GetLargestPossibleRegion().GetSize(1) && - parameters.m_ImageRegion.GetSize(2)==itkImg->GetLargestPossibleRegion().GetSize(2)) + if (m_SelectedImage.IsNull()) // use geometry of frequency map { - parameters.m_SimulateKspaceAcquisition = true; + 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_FrequencyMap = duplicator->GetOutput(); - parameters.m_ArtifactModelString += "_DISTORTED"; - parameters.m_ResultNode->AddProperty("Fiberfox.Distortions", BoolProperty::New(true)); + 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_EddyStrength = 0; + parameters.m_SignalGen.m_EddyStrength = 0; + parameters.m_Misc.m_CheckAddEddyCurrentsBox = m_Controls->m_AddEddy->isChecked(); if (m_Controls->m_AddEddy->isChecked()) { - parameters.m_EddyStrength = m_Controls->m_EddyGradientStrength->value(); - parameters.m_ArtifactModelString += "_EDDY"; - parameters.m_ResultNode->AddProperty("Fiberfox.Eddy-strength", DoubleProperty::New(parameters.m_EddyStrength)); + 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_DoAddMotion = m_Controls->m_AddMotion->isChecked(); - parameters.m_DoRandomizeMotion = m_Controls->m_RandomMotion->isChecked(); - parameters.m_Translation[0] = m_Controls->m_MaxTranslationBoxX->value(); - parameters.m_Translation[1] = m_Controls->m_MaxTranslationBoxY->value(); - parameters.m_Translation[2] = m_Controls->m_MaxTranslationBoxZ->value(); - parameters.m_Rotation[0] = m_Controls->m_MaxRotationBoxX->value(); - parameters.m_Rotation[1] = m_Controls->m_MaxRotationBoxY->value(); - parameters.m_Rotation[2] = m_Controls->m_MaxRotationBoxZ->value(); + parameters.m_SignalGen.m_DoAddMotion = m_Controls->m_AddMotion->isChecked(); + 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(); if ( m_Controls->m_AddMotion->isChecked() && m_SelectedBundles.size()>0 ) { - parameters.m_ArtifactModelString += "_MOTION"; - parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Random", BoolProperty::New(parameters.m_DoRandomizeMotion)); - parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-x", DoubleProperty::New(parameters.m_Translation[0])); - parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-y", DoubleProperty::New(parameters.m_Translation[1])); - parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Translation-z", DoubleProperty::New(parameters.m_Translation[2])); - parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-x", DoubleProperty::New(parameters.m_Rotation[0])); - parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-y", DoubleProperty::New(parameters.m_Rotation[1])); - parameters.m_ResultNode->AddProperty("Fiberfox.Motion.Rotation-z", DoubleProperty::New(parameters.m_Rotation[2])); + 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])); } // other imaging parameters - parameters.m_tLine = m_Controls->m_LineReadoutTimeBox->value(); - parameters.m_tInhom = m_Controls->m_T2starBox->value(); - parameters.m_tEcho = m_Controls->m_TEbox->value(); - parameters.m_DoDisablePartialVolume = m_Controls->m_EnforcePureFiberVoxelsBox->isChecked(); - parameters.m_AxonRadius = m_Controls->m_FiberRadius->value(); - parameters.m_SignalScale = m_Controls->m_SignalScaleBox->value(); + 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_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(); // adjust echo time if needed - if ( parameters.m_tEcho < parameters.m_ImageRegion.GetSize(1)*parameters.m_tLine ) + if ( parameters.m_SignalGen.m_tEcho < parameters.m_SignalGen.m_ImageRegion.GetSize(1)*parameters.m_SignalGen.m_tLine ) { - this->m_Controls->m_TEbox->setValue( parameters.m_ImageRegion.GetSize(1)*parameters.m_tLine ); - parameters.m_tEcho = m_Controls->m_TEbox->value(); - QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(parameters.m_tEcho)+" ms"); + this->m_Controls->m_TEbox->setValue( parameters.m_SignalGen.m_ImageRegion.GetSize(1)*parameters.m_SignalGen.m_tLine ); + parameters.m_SignalGen.m_tEcho = m_Controls->m_TEbox->value(); + QMessageBox::information( NULL, "Warning", "Echo time is too short! Time not sufficient to read slice. Automaticall adjusted to "+QString::number(parameters.m_SignalGen.m_tEcho)+" ms"); } // Noise + parameters.m_Misc.m_CheckAddNoiseBox = m_Controls->m_AddNoise->isChecked(); if (m_Controls->m_AddNoise->isChecked()) { double noiseVariance = m_Controls->m_NoiseLevel->value(); { switch (m_Controls->m_NoiseDistributionBox->currentIndex()) { case 0: { parameters.m_NoiseModel = new mitk::RicianNoiseModel(); - parameters.m_ArtifactModelString += "_RICIAN-"; - parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); + parameters.m_Misc.m_ArtifactModelString += "_RICIAN-"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); break; } case 1: { parameters.m_NoiseModel = new mitk::ChiSquareNoiseModel(); - parameters.m_ArtifactModelString += "_CHISQUARED-"; - parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared")); + parameters.m_Misc.m_ArtifactModelString += "_CHISQUARED-"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Chi-squared")); break; } default: { parameters.m_NoiseModel = new mitk::RicianNoiseModel(); - parameters.m_ArtifactModelString += "_RICIAN-"; - parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); + parameters.m_Misc.m_ArtifactModelString += "_RICIAN-"; + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Distribution", StringProperty::New("Rician")); } } } parameters.m_NoiseModel->SetNoiseVariance(noiseVariance); - parameters.m_ArtifactModelString += QString::number(noiseVariance).toStdString(); - parameters.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); + parameters.m_Misc.m_ArtifactModelString += QString::number(noiseVariance).toStdString(); + parameters.m_Misc.m_ResultNode->AddProperty("Fiberfox.Noise-Variance", DoubleProperty::New(noiseVariance)); } // adjusting line readout time to the adapted image size needed for the DFT - unsigned int y = parameters.m_ImageRegion.GetSize(1); + unsigned int y = parameters.m_SignalGen.m_ImageRegion.GetSize(1); y += y%2; - if ( y>parameters.m_ImageRegion.GetSize(1) ) - parameters.m_tLine *= (double)parameters.m_ImageRegion.GetSize(1)/y; + if ( y>parameters.m_SignalGen.m_ImageRegion.GetSize(1) ) + parameters.m_SignalGen.m_tLine *= (double)parameters.m_SignalGen.m_ImageRegion.GetSize(1)/y; // signal models - m_PrototypeModel1.Clear(); - m_PrototypeModel3.Clear(); - m_PrototypeModel4.Clear(); - - // compartment 1 - switch (m_Controls->m_Compartment1Box->currentIndex()) - { - case 0: - m_StickModel1.SetGradientList(parameters.GetGradientDirections()); - m_StickModel1.SetBvalue(parameters.m_Bvalue); - m_StickModel1.SetDiffusivity(m_Controls->m_StickWidget1->GetD()); - m_StickModel1.SetT2(m_Controls->m_StickWidget1->GetT2()); - parameters.m_FiberModelList.push_back(&m_StickModel1); - parameters.m_SignalModelString += "Stick"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Stick") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D", DoubleProperty::New(m_Controls->m_StickWidget1->GetD()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_StickModel1.GetT2()) ); - break; - case 1: - m_ZeppelinModel1.SetGradientList(parameters.GetGradientDirections()); - m_ZeppelinModel1.SetBvalue(parameters.m_Bvalue); - m_ZeppelinModel1.SetDiffusivity1(m_Controls->m_ZeppelinWidget1->GetD1()); - m_ZeppelinModel1.SetDiffusivity2(m_Controls->m_ZeppelinWidget1->GetD2()); - m_ZeppelinModel1.SetDiffusivity3(m_Controls->m_ZeppelinWidget1->GetD2()); - m_ZeppelinModel1.SetT2(m_Controls->m_ZeppelinWidget1->GetT2()); - parameters.m_FiberModelList.push_back(&m_ZeppelinModel1); - parameters.m_SignalModelString += "Zeppelin"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Zeppelin") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD1()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget1->GetD2()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) ); - break; - case 2: - m_TensorModel1.SetGradientList(parameters.GetGradientDirections()); - m_TensorModel1.SetBvalue(parameters.m_Bvalue); - m_TensorModel1.SetDiffusivity1(m_Controls->m_TensorWidget1->GetD1()); - m_TensorModel1.SetDiffusivity2(m_Controls->m_TensorWidget1->GetD2()); - m_TensorModel1.SetDiffusivity3(m_Controls->m_TensorWidget1->GetD3()); - m_TensorModel1.SetT2(m_Controls->m_TensorWidget1->GetT2()); - parameters.m_FiberModelList.push_back(&m_TensorModel1); - parameters.m_SignalModelString += "Tensor"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Tensor") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D1", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD1()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D2", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD2()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.D3", DoubleProperty::New(m_Controls->m_TensorWidget1->GetD3()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.T2", DoubleProperty::New(m_ZeppelinModel1.GetT2()) ); - break; - case 3: - parameters.m_SimulateKspaceAcquisition = false; - m_PrototypeModel1.SetGradientList(parameters.GetGradientDirections()); - m_PrototypeModel1.SetMaxNumKernels(m_Controls->m_PrototypeWidget1->GetNumberOfSamples()); - m_PrototypeModel1.SetFaRange(m_Controls->m_PrototypeWidget1->GetMinFa(), m_Controls->m_PrototypeWidget1->GetMaxFa()); - m_PrototypeModel1.SetAdcRange(m_Controls->m_PrototypeWidget1->GetMinAdc(), m_Controls->m_PrototypeWidget1->GetMaxAdc()); - parameters.m_FiberModelList.push_back(&m_PrototypeModel1); - parameters.m_SignalModelString += "Prototype"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Description", StringProperty::New("Intra-axonal compartment") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment1.Model", StringProperty::New("Prototype") ); - break; - } - - // compartment 2 - switch (m_Controls->m_Compartment2Box->currentIndex()) - { - case 0: - break; - case 1: - m_StickModel2.SetGradientList(parameters.GetGradientDirections()); - m_StickModel2.SetBvalue(parameters.m_Bvalue); - m_StickModel2.SetDiffusivity(m_Controls->m_StickWidget2->GetD()); - m_StickModel2.SetT2(m_Controls->m_StickWidget2->GetT2()); - parameters.m_FiberModelList.push_back(&m_StickModel2); - parameters.m_SignalModelString += "Stick"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Stick") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D", DoubleProperty::New(m_Controls->m_StickWidget2->GetD()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_StickModel2.GetT2()) ); - break; - case 2: - m_ZeppelinModel2.SetGradientList(parameters.GetGradientDirections()); - m_ZeppelinModel2.SetBvalue(parameters.m_Bvalue); - m_ZeppelinModel2.SetDiffusivity1(m_Controls->m_ZeppelinWidget2->GetD1()); - m_ZeppelinModel2.SetDiffusivity2(m_Controls->m_ZeppelinWidget2->GetD2()); - m_ZeppelinModel2.SetDiffusivity3(m_Controls->m_ZeppelinWidget2->GetD2()); - m_ZeppelinModel2.SetT2(m_Controls->m_ZeppelinWidget2->GetT2()); - parameters.m_FiberModelList.push_back(&m_ZeppelinModel2); - parameters.m_SignalModelString += "Zeppelin"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Zeppelin") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD1()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_ZeppelinWidget2->GetD2()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) ); - break; - case 3: - m_TensorModel2.SetGradientList(parameters.GetGradientDirections()); - m_TensorModel2.SetBvalue(parameters.m_Bvalue); - m_TensorModel2.SetDiffusivity1(m_Controls->m_TensorWidget2->GetD1()); - m_TensorModel2.SetDiffusivity2(m_Controls->m_TensorWidget2->GetD2()); - m_TensorModel2.SetDiffusivity3(m_Controls->m_TensorWidget2->GetD3()); - m_TensorModel2.SetT2(m_Controls->m_TensorWidget2->GetT2()); - parameters.m_FiberModelList.push_back(&m_TensorModel2); - parameters.m_SignalModelString += "Tensor"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Description", StringProperty::New("Inter-axonal compartment") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.Model", StringProperty::New("Tensor") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D1", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD1()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D2", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD2()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.D3", DoubleProperty::New(m_Controls->m_TensorWidget2->GetD3()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment2.T2", DoubleProperty::New(m_ZeppelinModel2.GetT2()) ); - break; - } - - // compartment 3 - switch (m_Controls->m_Compartment3Box->currentIndex()) - { - case 0: - m_BallModel1.SetGradientList(parameters.GetGradientDirections()); - m_BallModel1.SetBvalue(parameters.m_Bvalue); - m_BallModel1.SetDiffusivity(m_Controls->m_BallWidget1->GetD()); - m_BallModel1.SetT2(m_Controls->m_BallWidget1->GetT2()); - parameters.m_NonFiberModelList.push_back(&m_BallModel1); - parameters.m_SignalModelString += "Ball"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Ball") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_BallWidget1->GetD()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_BallModel1.GetT2()) ); - break; - case 1: - m_AstrosticksModel1.SetGradientList(parameters.GetGradientDirections()); - m_AstrosticksModel1.SetBvalue(parameters.m_Bvalue); - m_AstrosticksModel1.SetDiffusivity(m_Controls->m_AstrosticksWidget1->GetD()); - m_AstrosticksModel1.SetT2(m_Controls->m_AstrosticksWidget1->GetT2()); - m_AstrosticksModel1.SetRandomizeSticks(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); - parameters.m_NonFiberModelList.push_back(&m_AstrosticksModel1); - parameters.m_SignalModelString += "Astrosticks"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Astrosticks") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget1->GetD()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_AstrosticksModel1.GetT2()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()) ); - break; - case 2: - m_DotModel1.SetGradientList(parameters.GetGradientDirections()); - m_DotModel1.SetT2(m_Controls->m_DotWidget1->GetT2()); - parameters.m_NonFiberModelList.push_back(&m_DotModel1); - parameters.m_SignalModelString += "Dot"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Dot") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.T2", DoubleProperty::New(m_DotModel1.GetT2()) ); - break; - case 3: - parameters.m_SimulateKspaceAcquisition = false; - m_PrototypeModel3.SetGradientList(parameters.GetGradientDirections()); - m_PrototypeModel3.SetMaxNumKernels(m_Controls->m_PrototypeWidget3->GetNumberOfSamples()); - m_PrototypeModel3.SetFaRange(m_Controls->m_PrototypeWidget3->GetMinFa(), m_Controls->m_PrototypeWidget3->GetMaxFa()); - m_PrototypeModel3.SetAdcRange(m_Controls->m_PrototypeWidget3->GetMinAdc(), m_Controls->m_PrototypeWidget3->GetMaxAdc()); - parameters.m_NonFiberModelList.push_back(&m_PrototypeModel3); - parameters.m_SignalModelString += "Prototype"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Description", StringProperty::New("Extra-axonal compartment 1") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment3.Model", StringProperty::New("Prototype") ); - break; - } - - // compartment 4 - ItkDoubleImgType::Pointer comp4VolumeImage = NULL; - ItkDoubleImgType::Pointer comp3VolumeImage = NULL; - if (m_Controls->m_Compartment4Box->currentIndex()>0) { - mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode(); - if (volumeNode.IsNull()) + // compartment 1 + switch (m_Controls->m_Compartment1Box->currentIndex()) { - MITK_WARN << "No volume fraction image selected! Second extra-axonal compartment has been disabled."; + 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->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; } - else + case 1: { - MITK_INFO << "Rescaling volume fraction image..."; - comp4VolumeImage = ItkDoubleImgType::New(); - mitk::Image* img = dynamic_cast(volumeNode->GetData()); - CastToItkImage< ItkDoubleImgType >(img, comp4VolumeImage); - - double max = itk::NumericTraits::min(); - double min = itk::NumericTraits::max(); - - itk::ImageRegionIterator< ItkDoubleImgType > it(comp4VolumeImage, comp4VolumeImage->GetLargestPossibleRegion()); - while(!it.IsAtEnd()) - { - if (parameters.m_MaskImage.IsNotNull() && parameters.m_MaskImage->GetPixel(it.GetIndex())<=0) - { - it.Set(0.0); - ++it; - continue; - } - - if (it.Get()>max) - max = it.Get(); - if (it.Get()::Pointer scaler = itk::ShiftScaleImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); - scaler->SetInput(comp4VolumeImage); - scaler->SetShift(-min); - scaler->SetScale(1/(max-min)); - scaler->Update(); - comp4VolumeImage = scaler->GetOutput(); - - itk::ImageFileWriter< ItkDoubleImgType >::Pointer wr = itk::ImageFileWriter< ItkDoubleImgType >::New(); - wr->SetInput(comp4VolumeImage); - wr->SetFileName("/local/comp4.nrrd"); - wr->Update(); - -// if (max>1 || min<0) // are volume fractions between 0 and 1? -// { -// itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); -// rescaler->SetInput(0, comp4VolumeImage); -// rescaler->SetOutputMaximum(1); -// rescaler->SetOutputMinimum(0); -// rescaler->Update(); -// comp4VolumeImage = rescaler->GetOutput(); -// } - - itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::Pointer inverter = itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); - inverter->SetMaximum(1.0); - inverter->SetInput(comp4VolumeImage); - inverter->Update(); - comp3VolumeImage = inverter->GetOutput(); + 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->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->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_SimulateKspaceAcquisition = 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 (comp4VolumeImage.IsNotNull()) - switch (m_Controls->m_Compartment4Box->currentIndex()) + // compartment 2 + switch (m_Controls->m_Compartment2Box->currentIndex()) { case 0: break; case 1: { - m_BallModel2.SetGradientList(parameters.GetGradientDirections()); - m_BallModel2.SetBvalue(parameters.m_Bvalue); - m_BallModel2.SetDiffusivity(m_Controls->m_BallWidget2->GetD()); - m_BallModel2.SetT2(m_Controls->m_BallWidget2->GetT2()); - m_BallModel2.SetVolumeFractionImage(comp4VolumeImage); - parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); - parameters.m_NonFiberModelList.push_back(&m_BallModel2); - parameters.m_SignalModelString += "Ball"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Ball") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_BallWidget2->GetD()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_BallModel2.GetT2()) ); + 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->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: { - m_AstrosticksModel2.SetGradientList(parameters.GetGradientDirections()); - m_AstrosticksModel2.SetBvalue(parameters.m_Bvalue); - m_AstrosticksModel2.SetDiffusivity(m_Controls->m_AstrosticksWidget2->GetD()); - m_AstrosticksModel2.SetT2(m_Controls->m_AstrosticksWidget2->GetT2()); - m_AstrosticksModel2.SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); - parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); - m_AstrosticksModel2.SetVolumeFractionImage(comp4VolumeImage); - parameters.m_NonFiberModelList.push_back(&m_AstrosticksModel2); - parameters.m_SignalModelString += "Astrosticks"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Astrosticks") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.D", DoubleProperty::New(m_Controls->m_AstrosticksWidget2->GetD()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_AstrosticksModel2.GetT2()) ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.RandomSticks", BoolProperty::New(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()) ); + 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->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: { - m_DotModel2.SetGradientList(parameters.GetGradientDirections()); - m_DotModel2.SetT2(m_Controls->m_DotWidget2->GetT2()); - m_DotModel2.SetVolumeFractionImage(comp4VolumeImage); - parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); - parameters.m_NonFiberModelList.push_back(&m_DotModel2); - parameters.m_SignalModelString += "Dot"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Dot") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.T2", DoubleProperty::New(m_DotModel2.GetT2()) ); + 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->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; } - case 4: + } + + // 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->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->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->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: { - parameters.m_SimulateKspaceAcquisition = false; - m_PrototypeModel4.SetGradientList(parameters.GetGradientDirections()); - m_PrototypeModel4.SetMaxNumKernels(m_Controls->m_PrototypeWidget4->GetNumberOfSamples()); - m_PrototypeModel4.SetFaRange(m_Controls->m_PrototypeWidget4->GetMinFa(), m_Controls->m_PrototypeWidget4->GetMaxFa()); - m_PrototypeModel4.SetAdcRange(m_Controls->m_PrototypeWidget4->GetMinAdc(), m_Controls->m_PrototypeWidget4->GetMaxAdc()); - m_PrototypeModel4.SetVolumeFractionImage(comp4VolumeImage); - parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); - parameters.m_NonFiberModelList.push_back(&m_PrototypeModel4); - parameters.m_SignalModelString += "Prototype"; - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Description", StringProperty::New("Extra-axonal compartment 2") ); - parameters.m_ResultNode->AddProperty("Fiberfox.Compartment4.Model", StringProperty::New("Prototype") ); + mitk::RawShModel* model = new mitk::RawShModel(); + parameters.m_SignalGen.m_SimulateKspaceAcquisition = 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; } } - parameters.m_DiffusionDirectionMode = FiberfoxParameters::FIBER_TANGENT_DIRECTIONS; + // compartment 4 + ItkDoubleImgType::Pointer comp4VolumeImage = NULL; + ItkDoubleImgType::Pointer comp3VolumeImage = NULL; + if (m_Controls->m_Compartment4Box->currentIndex()>0) + { + mitk::DataNode::Pointer volumeNode = m_Controls->m_Comp4VolumeFraction->GetSelectedNode(); + if (volumeNode.IsNull()) + { + QMessageBox::information( NULL, "Information", "No volume fraction image selected! Second extra-axonal compartment has been disabled for this simultation."); + MITK_WARN << "No volume fraction image selected! Second extra-axonal compartment has been disabled."; + } + else + { + MITK_INFO << "Rescaling volume fraction image..."; + comp4VolumeImage = ItkDoubleImgType::New(); + mitk::Image* img = dynamic_cast(volumeNode->GetData()); + CastToItkImage< ItkDoubleImgType >(img, comp4VolumeImage); + + double max = itk::NumericTraits::min(); + double min = itk::NumericTraits::max(); + + itk::ImageRegionIterator< ItkDoubleImgType > it(comp4VolumeImage, comp4VolumeImage->GetLargestPossibleRegion()); + while(!it.IsAtEnd()) + { + if (parameters.m_SignalGen.m_MaskImage.IsNotNull() && parameters.m_SignalGen.m_MaskImage->GetPixel(it.GetIndex())<=0) + { + it.Set(0.0); + ++it; + continue; + } + + if (it.Get()>max) + max = it.Get(); + if (it.Get()::Pointer scaler = itk::ShiftScaleImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); + scaler->SetInput(comp4VolumeImage); + scaler->SetShift(-min); + scaler->SetScale(1.0/(max-min)); + scaler->Update(); + comp4VolumeImage = scaler->GetOutput(); + + // itk::ImageFileWriter< ItkDoubleImgType >::Pointer wr = itk::ImageFileWriter< ItkDoubleImgType >::New(); + // wr->SetInput(comp4VolumeImage); + // wr->SetFileName("/local/comp4.nrrd"); + // wr->Update(); + + // if (max>1 || min<0) // are volume fractions between 0 and 1? + // { + // itk::RescaleIntensityImageFilter::Pointer rescaler = itk::RescaleIntensityImageFilter::New(); + // rescaler->SetInput(0, comp4VolumeImage); + // rescaler->SetOutputMaximum(1); + // rescaler->SetOutputMinimum(0); + // rescaler->Update(); + // comp4VolumeImage = rescaler->GetOutput(); + // } + + itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::Pointer inverter = itk::InvertIntensityImageFilter< ItkDoubleImgType, ItkDoubleImgType >::New(); + inverter->SetMaximum(1.0); + inverter->SetInput(comp4VolumeImage); + inverter->Update(); + comp3VolumeImage = inverter->GetOutput(); + } + } + + if (comp4VolumeImage.IsNotNull()) + { + 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->SetVolumeFractionImage(comp4VolumeImage); + model->m_CompartmentId = 4; + parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); + 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->SetRandomizeSticks(m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); + parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); + model->SetVolumeFractionImage(comp4VolumeImage); + 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->SetVolumeFractionImage(comp4VolumeImage); + model->m_CompartmentId = 4; + parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); + 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_SimulateKspaceAcquisition = 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->SetVolumeFractionImage(comp4VolumeImage); + model->m_CompartmentId = 4; + parameters.m_NonFiberModelList.back()->SetVolumeFractionImage(comp3VolumeImage); + 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; + } + } + } + } + + parameters.m_SignalGen.m_FiberSeparationThreshold = m_Controls->m_SeparationAngleBox->value(); + switch (m_Controls->m_DiffusionDirectionBox->currentIndex()) + { + case 0: + parameters.m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; + break; + case 1: + parameters.m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::MAIN_FIBER_DIRECTIONS; + break; + case 2: + parameters.m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::RANDOM_DIRECTIONS; + parameters.m_SignalGen.m_DoAddMotion = false; + parameters.m_SignalGen.m_DoAddGibbsRinging = false; + parameters.m_SignalGen.m_KspaceLineOffset = 0.0; + parameters.m_SignalGen.m_FrequencyMap = NULL; + parameters.m_SignalGen.m_CroppingFactor = 1.0; + parameters.m_SignalGen.m_EddyStrength = 0; + break; + default: + parameters.m_SignalGen.m_DiffusionDirectionMode = SignalGenerationParameters::FIBER_TANGENT_DIRECTIONS; + } - parameters.m_ResultNode->AddProperty("Fiberfox.SignalScale", IntProperty::New(parameters.m_SignalScale)); - parameters.m_ResultNode->AddProperty("Fiberfox.FiberRadius", IntProperty::New(parameters.m_AxonRadius)); - parameters.m_ResultNode->AddProperty("Fiberfox.Tinhom", DoubleProperty::New(parameters.m_tInhom)); - parameters.m_ResultNode->AddProperty("Fiberfox.Tline", DoubleProperty::New(parameters.m_tLine)); - parameters.m_ResultNode->AddProperty("Fiberfox.TE", DoubleProperty::New(parameters.m_tEcho)); - parameters.m_ResultNode->AddProperty("Fiberfox.b-value", DoubleProperty::New(parameters.m_Bvalue)); - parameters.m_ResultNode->AddProperty("Fiberfox.NoPartialVolume", BoolProperty::New(parameters.m_DoDisablePartialVolume)); - parameters.m_ResultNode->AddProperty("Fiberfox.Relaxation", BoolProperty::New(parameters.m_DoSimulateRelaxation)); - parameters.m_ResultNode->AddProperty("binary", BoolProperty::New(false)); + 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(); + + 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(); return parameters; } void QmitkFiberfoxView::SaveParameters() { - FiberfoxParameters ffParamaters = UpdateImageParameters(); + FiberfoxParameters<> ffParamaters = UpdateImageParameters(); QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), m_ParameterFile, tr("Fiberfox Parameters (*.ffp)") ); - if(filename.isEmpty() || filename.isNull()) - return; - if(!filename.endsWith(".ffp")) - filename += ".ffp"; - + ffParamaters.SaveParameters(filename.toStdString()); m_ParameterFile = filename; - - boost::property_tree::ptree parameters; - - // fiber generation parameters - parameters.put("fiberfox.fibers.realtime", m_Controls->m_RealTimeFibers->isChecked()); - parameters.put("fiberfox.fibers.showadvanced", m_Controls->m_AdvancedOptionsBox->isChecked()); - parameters.put("fiberfox.fibers.distribution", m_Controls->m_DistributionBox->currentIndex()); - parameters.put("fiberfox.fibers.variance", m_Controls->m_VarianceBox->value()); - parameters.put("fiberfox.fibers.density", m_Controls->m_FiberDensityBox->value()); - parameters.put("fiberfox.fibers.spline.sampling", m_Controls->m_FiberSamplingBox->value()); - parameters.put("fiberfox.fibers.spline.tension", m_Controls->m_TensionBox->value()); - parameters.put("fiberfox.fibers.spline.continuity", m_Controls->m_ContinuityBox->value()); - parameters.put("fiberfox.fibers.spline.bias", m_Controls->m_BiasBox->value()); - parameters.put("fiberfox.fibers.constantradius", m_Controls->m_ConstantRadiusBox->isChecked()); - parameters.put("fiberfox.fibers.rotation.x", m_Controls->m_XrotBox->value()); - parameters.put("fiberfox.fibers.rotation.y", m_Controls->m_YrotBox->value()); - parameters.put("fiberfox.fibers.rotation.z", m_Controls->m_ZrotBox->value()); - parameters.put("fiberfox.fibers.translation.x", m_Controls->m_XtransBox->value()); - parameters.put("fiberfox.fibers.translation.y", m_Controls->m_YtransBox->value()); - parameters.put("fiberfox.fibers.translation.z", m_Controls->m_ZtransBox->value()); - parameters.put("fiberfox.fibers.scale.x", m_Controls->m_XscaleBox->value()); - parameters.put("fiberfox.fibers.scale.y", m_Controls->m_YscaleBox->value()); - parameters.put("fiberfox.fibers.scale.z", m_Controls->m_ZscaleBox->value()); - parameters.put("fiberfox.fibers.includeFiducials", m_Controls->m_IncludeFiducials->isChecked()); - parameters.put("fiberfox.fibers.includeFiducials", m_Controls->m_IncludeFiducials->isChecked()); - - // image generation parameters - parameters.put("fiberfox.image.basic.size.x", ffParamaters.m_ImageRegion.GetSize(0)); - parameters.put("fiberfox.image.basic.size.y", ffParamaters.m_ImageRegion.GetSize(1)); - parameters.put("fiberfox.image.basic.size.z", ffParamaters.m_ImageRegion.GetSize(2)); - parameters.put("fiberfox.image.basic.spacing.x", ffParamaters.m_ImageSpacing[0]); - parameters.put("fiberfox.image.basic.spacing.y", ffParamaters.m_ImageSpacing[1]); - parameters.put("fiberfox.image.basic.spacing.z", ffParamaters.m_ImageSpacing[2]); - parameters.put("fiberfox.image.basic.numgradients", ffParamaters.GetNumWeightedVolumes()); - parameters.put("fiberfox.image.basic.bvalue", ffParamaters.m_Bvalue); - parameters.put("fiberfox.image.showadvanced", m_Controls->m_AdvancedOptionsBox_2->isChecked()); - parameters.put("fiberfox.image.signalScale", ffParamaters.m_SignalScale); - parameters.put("fiberfox.image.tEcho", ffParamaters.m_tEcho); - parameters.put("fiberfox.image.tLine", m_Controls->m_LineReadoutTimeBox->value()); - parameters.put("fiberfox.image.tInhom", ffParamaters.m_tInhom); - parameters.put("fiberfox.image.axonRadius", ffParamaters.m_AxonRadius); - parameters.put("fiberfox.image.doSimulateRelaxation", ffParamaters.m_DoSimulateRelaxation); - parameters.put("fiberfox.image.doDisablePartialVolume", ffParamaters.m_DoDisablePartialVolume); - parameters.put("fiberfox.image.outputvolumefractions", m_Controls->m_VolumeFractionsBox->isChecked()); - - parameters.put("fiberfox.image.artifacts.addnoise", m_Controls->m_AddNoise->isChecked()); - parameters.put("fiberfox.image.artifacts.noisedistribution", m_Controls->m_NoiseDistributionBox->currentIndex()); - parameters.put("fiberfox.image.artifacts.noisevariance", m_Controls->m_NoiseLevel->value()); - parameters.put("fiberfox.image.artifacts.addghost", m_Controls->m_AddGhosts->isChecked()); - parameters.put("fiberfox.image.artifacts.kspaceLineOffset", m_Controls->m_kOffsetBox->value()); - parameters.put("fiberfox.image.artifacts.distortions", m_Controls->m_AddDistortions->isChecked()); - parameters.put("fiberfox.image.artifacts.addeddy", m_Controls->m_AddEddy->isChecked()); - parameters.put("fiberfox.image.artifacts.eddyStrength", m_Controls->m_EddyGradientStrength->value()); - parameters.put("fiberfox.image.artifacts.addringing", m_Controls->m_AddGibbsRinging->isChecked()); - parameters.put("fiberfox.image.artifacts.addspikes", m_Controls->m_AddSpikes->isChecked()); - parameters.put("fiberfox.image.artifacts.spikesnum", m_Controls->m_SpikeNumBox->value()); - parameters.put("fiberfox.image.artifacts.spikesscale", m_Controls->m_SpikeScaleBox->value()); - parameters.put("fiberfox.image.artifacts.addaliasing", m_Controls->m_AddAliasing->isChecked()); - parameters.put("fiberfox.image.artifacts.aliasingfactor", m_Controls->m_WrapBox->value()); - parameters.put("fiberfox.image.artifacts.doAddMotion", m_Controls->m_AddMotion->isChecked()); - parameters.put("fiberfox.image.artifacts.randomMotion", m_Controls->m_RandomMotion->isChecked()); - parameters.put("fiberfox.image.artifacts.translation0", m_Controls->m_MaxTranslationBoxX->value()); - parameters.put("fiberfox.image.artifacts.translation1", m_Controls->m_MaxTranslationBoxY->value()); - parameters.put("fiberfox.image.artifacts.translation2", m_Controls->m_MaxTranslationBoxZ->value()); - parameters.put("fiberfox.image.artifacts.rotation0", m_Controls->m_MaxRotationBoxX->value()); - parameters.put("fiberfox.image.artifacts.rotation1", m_Controls->m_MaxRotationBoxY->value()); - parameters.put("fiberfox.image.artifacts.rotation2", m_Controls->m_MaxRotationBoxZ->value()); - - parameters.put("fiberfox.image.compartment1.index", m_Controls->m_Compartment1Box->currentIndex()); - parameters.put("fiberfox.image.compartment2.index", m_Controls->m_Compartment2Box->currentIndex()); - parameters.put("fiberfox.image.compartment3.index", m_Controls->m_Compartment3Box->currentIndex()); - parameters.put("fiberfox.image.compartment4.index", m_Controls->m_Compartment4Box->currentIndex()); - - parameters.put("fiberfox.image.compartment1.stick.d", m_Controls->m_StickWidget1->GetD()); - parameters.put("fiberfox.image.compartment1.stick.t2", m_Controls->m_StickWidget1->GetT2()); - parameters.put("fiberfox.image.compartment1.zeppelin.d1", m_Controls->m_ZeppelinWidget1->GetD1()); - parameters.put("fiberfox.image.compartment1.zeppelin.d2", m_Controls->m_ZeppelinWidget1->GetD2()); - parameters.put("fiberfox.image.compartment1.zeppelin.t2", m_Controls->m_ZeppelinWidget1->GetT2()); - parameters.put("fiberfox.image.compartment1.tensor.d1", m_Controls->m_TensorWidget1->GetD1()); - parameters.put("fiberfox.image.compartment1.tensor.d2", m_Controls->m_TensorWidget1->GetD2()); - parameters.put("fiberfox.image.compartment1.tensor.d3", m_Controls->m_TensorWidget1->GetD3()); - parameters.put("fiberfox.image.compartment1.tensor.t2", m_Controls->m_TensorWidget1->GetT2()); - parameters.put("fiberfox.image.compartment1.prototype.minFA", m_Controls->m_PrototypeWidget1->GetMinFa()); - parameters.put("fiberfox.image.compartment1.prototype.maxFA", m_Controls->m_PrototypeWidget1->GetMaxFa()); - parameters.put("fiberfox.image.compartment1.prototype.minADC", m_Controls->m_PrototypeWidget1->GetMinAdc()); - parameters.put("fiberfox.image.compartment1.prototype.maxADC", m_Controls->m_PrototypeWidget1->GetMaxAdc()); - parameters.put("fiberfox.image.compartment1.prototype.numSamples", m_Controls->m_PrototypeWidget1->GetNumberOfSamples()); - - parameters.put("fiberfox.image.compartment2.stick.d", m_Controls->m_StickWidget2->GetD()); - parameters.put("fiberfox.image.compartment2.stick.t2", m_Controls->m_StickWidget2->GetT2()); - parameters.put("fiberfox.image.compartment2.zeppelin.d1", m_Controls->m_ZeppelinWidget2->GetD1()); - parameters.put("fiberfox.image.compartment2.zeppelin.d2", m_Controls->m_ZeppelinWidget2->GetD2()); - parameters.put("fiberfox.image.compartment2.zeppelin.t2", m_Controls->m_ZeppelinWidget2->GetT2()); - parameters.put("fiberfox.image.compartment2.tensor.d1", m_Controls->m_TensorWidget2->GetD1()); - parameters.put("fiberfox.image.compartment2.tensor.d2", m_Controls->m_TensorWidget2->GetD2()); - parameters.put("fiberfox.image.compartment2.tensor.d3", m_Controls->m_TensorWidget2->GetD3()); - parameters.put("fiberfox.image.compartment2.tensor.t2", m_Controls->m_TensorWidget2->GetT2()); - - parameters.put("fiberfox.image.compartment3.ball.d", m_Controls->m_BallWidget1->GetD()); - parameters.put("fiberfox.image.compartment3.ball.t2", m_Controls->m_BallWidget1->GetT2()); - parameters.put("fiberfox.image.compartment3.astrosticks.d", m_Controls->m_AstrosticksWidget1->GetD()); - parameters.put("fiberfox.image.compartment3.astrosticks.t2", m_Controls->m_AstrosticksWidget1->GetT2()); - parameters.put("fiberfox.image.compartment3.astrosticks.randomize", m_Controls->m_AstrosticksWidget1->GetRandomizeSticks()); - parameters.put("fiberfox.image.compartment3.dot.t2", m_Controls->m_DotWidget1->GetT2()); - parameters.put("fiberfox.image.compartment3.prototype.minFA", m_Controls->m_PrototypeWidget3->GetMinFa()); - parameters.put("fiberfox.image.compartment3.prototype.maxFA", m_Controls->m_PrototypeWidget3->GetMaxFa()); - parameters.put("fiberfox.image.compartment3.prototype.minADC", m_Controls->m_PrototypeWidget3->GetMinAdc()); - parameters.put("fiberfox.image.compartment3.prototype.maxADC", m_Controls->m_PrototypeWidget3->GetMaxAdc()); - parameters.put("fiberfox.image.compartment3.prototype.numSamples", m_Controls->m_PrototypeWidget3->GetNumberOfSamples()); - - parameters.put("fiberfox.image.compartment4.ball.d", m_Controls->m_BallWidget2->GetD()); - parameters.put("fiberfox.image.compartment4.ball.t2", m_Controls->m_BallWidget2->GetT2()); - parameters.put("fiberfox.image.compartment4.astrosticks.d", m_Controls->m_AstrosticksWidget2->GetD()); - parameters.put("fiberfox.image.compartment4.astrosticks.t2", m_Controls->m_AstrosticksWidget2->GetT2()); - parameters.put("fiberfox.image.compartment4.astrosticks.randomize", m_Controls->m_AstrosticksWidget2->GetRandomizeSticks()); - parameters.put("fiberfox.image.compartment4.dot.t2", m_Controls->m_DotWidget2->GetT2()); - parameters.put("fiberfox.image.compartment4.prototype.minFA", m_Controls->m_PrototypeWidget4->GetMinFa()); - parameters.put("fiberfox.image.compartment4.prototype.maxFA", m_Controls->m_PrototypeWidget4->GetMaxFa()); - parameters.put("fiberfox.image.compartment4.prototype.minADC", m_Controls->m_PrototypeWidget4->GetMinAdc()); - parameters.put("fiberfox.image.compartment4.prototype.maxADC", m_Controls->m_PrototypeWidget4->GetMaxAdc()); - parameters.put("fiberfox.image.compartment4.prototype.numSamples", m_Controls->m_PrototypeWidget4->GetNumberOfSamples()); - - boost::property_tree::xml_parser::write_xml(filename.toStdString(), parameters); } 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; - boost::property_tree::ptree parameters; - boost::property_tree::xml_parser::read_xml(filename.toStdString(), parameters); + FiberfoxParameters<> parameters; + parameters.LoadParameters(filename.toStdString()); + + 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]); - BOOST_FOREACH( boost::property_tree::ptree::value_type const& v1, parameters.get_child("fiberfox") ) - { - if( v1.first == "fibers" ) + // 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); + + if (parameters.m_NoiseModel!=NULL) + { + m_Controls->m_AddNoise->setChecked(parameters.m_Misc.m_CheckAddNoiseBox); + if (dynamic_cast*>(parameters.m_NoiseModel)) + m_Controls->m_NoiseDistributionBox->setCurrentIndex(0); + else if (dynamic_cast*>(parameters.m_NoiseModel)) + m_Controls->m_NoiseDistributionBox->setCurrentIndex(1); + m_Controls->m_NoiseLevel->setValue(parameters.m_NoiseModel->GetNoiseVariance()); + } + else + m_Controls->m_AddNoise->setChecked(false); + + 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_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_DiffusionDirectionBox->setCurrentIndex(parameters.m_SignalGen.m_DiffusionDirectionMode); + m_Controls->m_SeparationAngleBox->setValue(parameters.m_SignalGen.m_FiberSeparationThreshold); + + 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 (im_CompartmentId) { - m_Controls->m_RealTimeFibers->setChecked(v1.second.get("realtime")); - m_Controls->m_AdvancedOptionsBox->setChecked(v1.second.get("showadvanced")); - m_Controls->m_DistributionBox->setCurrentIndex(v1.second.get("distribution")); - m_Controls->m_VarianceBox->setValue(v1.second.get("variance")); - m_Controls->m_FiberDensityBox->setValue(v1.second.get("density")); - m_Controls->m_IncludeFiducials->setChecked(v1.second.get("includeFiducials")); - m_Controls->m_ConstantRadiusBox->setChecked(v1.second.get("constantradius")); - - BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second ) + case 1: + { + if (dynamic_cast*>(signalModel)) { - if( v2.first == "spline" ) - { - m_Controls->m_FiberSamplingBox->setValue(v2.second.get("sampling")); - m_Controls->m_TensionBox->setValue(v2.second.get("tension")); - m_Controls->m_ContinuityBox->setValue(v2.second.get("continuity")); - m_Controls->m_BiasBox->setValue(v2.second.get("bias")); - } - if( v2.first == "rotation" ) - { - m_Controls->m_XrotBox->setValue(v2.second.get("x")); - m_Controls->m_YrotBox->setValue(v2.second.get("y")); - m_Controls->m_ZrotBox->setValue(v2.second.get("z")); - } - if( v2.first == "translation" ) - { - m_Controls->m_XtransBox->setValue(v2.second.get("x")); - m_Controls->m_YtransBox->setValue(v2.second.get("y")); - m_Controls->m_ZtransBox->setValue(v2.second.get("z")); - } - if( v2.first == "scale" ) - { - m_Controls->m_XscaleBox->setValue(v2.second.get("x")); - m_Controls->m_YscaleBox->setValue(v2.second.get("y")); - m_Controls->m_ZscaleBox->setValue(v2.second.get("z")); - } + mitk::StickModel<>* model = dynamic_cast*>(signalModel); + m_Controls->m_StickWidget1->SetT2(model->GetT2()); + 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->SetD1(model->GetDiffusivity1()); + m_Controls->m_TensorWidget1->SetD2(model->GetDiffusivity1()); + m_Controls->m_TensorWidget1->SetD3(model->GetDiffusivity1()); + 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 (dynamic_cast*>(signalModel)) + { + mitk::StickModel<>* model = dynamic_cast*>(signalModel); + m_Controls->m_StickWidget2->SetT2(model->GetT2()); + 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->SetD1(model->GetDiffusivity1()); + m_Controls->m_TensorWidget2->SetD2(model->GetDiffusivity1()); + m_Controls->m_TensorWidget2->SetD3(model->GetDiffusivity1()); + m_Controls->m_Compartment2Box->setCurrentIndex(3); + break; + } + break; + } + case 3: + { + if (dynamic_cast*>(signalModel)) + { + mitk::BallModel<>* model = dynamic_cast*>(signalModel); + m_Controls->m_BallWidget1->SetT2(model->GetT2()); + 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->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_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; } - if( v1.first == "image" ) + case 4: { - m_Controls->m_SizeX->setValue(v1.second.get("basic.size.x")); - m_Controls->m_SizeY->setValue(v1.second.get("basic.size.y")); - m_Controls->m_SizeZ->setValue(v1.second.get("basic.size.z")); - m_Controls->m_SpacingX->setValue(v1.second.get("basic.spacing.x")); - m_Controls->m_SpacingY->setValue(v1.second.get("basic.spacing.y")); - m_Controls->m_SpacingZ->setValue(v1.second.get("basic.spacing.z")); - m_Controls->m_NumGradientsBox->setValue(v1.second.get("basic.numgradients")); - m_Controls->m_BvalueBox->setValue(v1.second.get("basic.bvalue")); - m_Controls->m_AdvancedOptionsBox_2->setChecked(v1.second.get("showadvanced")); - m_Controls->m_SignalScaleBox->setValue(v1.second.get("signalScale")); - m_Controls->m_TEbox->setValue(v1.second.get("tEcho")); - m_Controls->m_LineReadoutTimeBox->setValue(v1.second.get("tLine")); - m_Controls->m_T2starBox->setValue(v1.second.get("tInhom")); - m_Controls->m_FiberRadius->setValue(v1.second.get("axonRadius")); - m_Controls->m_RelaxationBox->setChecked(v1.second.get("doSimulateRelaxation")); - m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(v1.second.get("doDisablePartialVolume")); - m_Controls->m_VolumeFractionsBox->setChecked(v1.second.get("outputvolumefractions")); - - m_Controls->m_AddNoise->setChecked(v1.second.get("artifacts.addnoise")); - m_Controls->m_NoiseDistributionBox->setCurrentIndex(v1.second.get("artifacts.noisedistribution")); - m_Controls->m_NoiseLevel->setValue(v1.second.get("artifacts.noisevariance")); - m_Controls->m_AddGhosts->setChecked(v1.second.get("artifacts.addghost")); - m_Controls->m_kOffsetBox->setValue(v1.second.get("artifacts.kspaceLineOffset")); - m_Controls->m_AddAliasing->setChecked(v1.second.get("artifacts.addaliasing")); - m_Controls->m_WrapBox->setValue(v1.second.get("artifacts.aliasingfactor")); - m_Controls->m_AddDistortions->setChecked(v1.second.get("artifacts.distortions")); - m_Controls->m_AddSpikes->setChecked(v1.second.get("artifacts.addspikes")); - m_Controls->m_SpikeNumBox->setValue(v1.second.get("artifacts.spikesnum")); - m_Controls->m_SpikeScaleBox->setValue(v1.second.get("artifacts.spikesscale")); - m_Controls->m_AddEddy->setChecked(v1.second.get("artifacts.addeddy")); - m_Controls->m_EddyGradientStrength->setValue(v1.second.get("artifacts.eddyStrength")); - m_Controls->m_AddGibbsRinging->setChecked(v1.second.get("artifacts.addringing")); - m_Controls->m_AddMotion->setChecked(v1.second.get("artifacts.doAddMotion")); - m_Controls->m_RandomMotion->setChecked(v1.second.get("artifacts.randomMotion")); - m_Controls->m_MaxTranslationBoxX->setValue(v1.second.get("artifacts.translation0")); - m_Controls->m_MaxTranslationBoxY->setValue(v1.second.get("artifacts.translation1")); - m_Controls->m_MaxTranslationBoxZ->setValue(v1.second.get("artifacts.translation2")); - m_Controls->m_MaxRotationBoxX->setValue(v1.second.get("artifacts.rotation0")); - m_Controls->m_MaxRotationBoxY->setValue(v1.second.get("artifacts.rotation1")); - m_Controls->m_MaxRotationBoxZ->setValue(v1.second.get("artifacts.rotation2")); - - m_Controls->m_Compartment1Box->setCurrentIndex(v1.second.get("compartment1.index")); - m_Controls->m_Compartment2Box->setCurrentIndex(v1.second.get("compartment2.index")); - m_Controls->m_Compartment3Box->setCurrentIndex(v1.second.get("compartment3.index")); - m_Controls->m_Compartment4Box->setCurrentIndex(v1.second.get("compartment4.index")); - - m_Controls->m_StickWidget1->SetD(v1.second.get("compartment1.stick.d")); - m_Controls->m_StickWidget1->SetT2(v1.second.get("compartment1.stick.t2")); - m_Controls->m_ZeppelinWidget1->SetD1(v1.second.get("compartment1.zeppelin.d1")); - m_Controls->m_ZeppelinWidget1->SetD2(v1.second.get("compartment1.zeppelin.d2")); - m_Controls->m_ZeppelinWidget1->SetT2(v1.second.get("compartment1.zeppelin.t2")); - m_Controls->m_TensorWidget1->SetD1(v1.second.get("compartment1.tensor.d1")); - m_Controls->m_TensorWidget1->SetD2(v1.second.get("compartment1.tensor.d2")); - m_Controls->m_TensorWidget1->SetD3(v1.second.get("compartment1.tensor.d3")); - m_Controls->m_TensorWidget1->SetT2(v1.second.get("compartment1.tensor.t2")); - m_Controls->m_PrototypeWidget1->SetMinFa(v1.second.get("compartment1.prototype.minFA")); - m_Controls->m_PrototypeWidget1->SetMaxFa(v1.second.get("compartment1.prototype.maxFA")); - m_Controls->m_PrototypeWidget1->SetMinAdc(v1.second.get("compartment1.prototype.minADC")); - m_Controls->m_PrototypeWidget1->SetMaxAdc(v1.second.get("compartment1.prototype.maxADC")); - m_Controls->m_PrototypeWidget1->SetNumberOfSamples(v1.second.get("compartment1.prototype.numSamples")); - - m_Controls->m_StickWidget2->SetD(v1.second.get("compartment2.stick.d")); - m_Controls->m_StickWidget2->SetT2(v1.second.get("compartment2.stick.t2")); - m_Controls->m_ZeppelinWidget2->SetD1(v1.second.get("compartment2.zeppelin.d1")); - m_Controls->m_ZeppelinWidget2->SetD2(v1.second.get("compartment2.zeppelin.d2")); - m_Controls->m_ZeppelinWidget2->SetT2(v1.second.get("compartment2.zeppelin.t2")); - m_Controls->m_TensorWidget2->SetD1(v1.second.get("compartment2.tensor.d1")); - m_Controls->m_TensorWidget2->SetD2(v1.second.get("compartment2.tensor.d2")); - m_Controls->m_TensorWidget2->SetD3(v1.second.get("compartment2.tensor.d3")); - m_Controls->m_TensorWidget2->SetT2(v1.second.get("compartment2.tensor.t2")); - - m_Controls->m_BallWidget1->SetD(v1.second.get("compartment3.ball.d")); - m_Controls->m_BallWidget1->SetT2(v1.second.get("compartment3.ball.t2")); - m_Controls->m_AstrosticksWidget1->SetD(v1.second.get("compartment3.astrosticks.d")); - m_Controls->m_AstrosticksWidget1->SetT2(v1.second.get("compartment3.astrosticks.t2")); - m_Controls->m_AstrosticksWidget1->SetRandomizeSticks(v1.second.get("compartment3.astrosticks.randomize")); - m_Controls->m_DotWidget1->SetT2(v1.second.get("compartment3.dot.t2")); - m_Controls->m_PrototypeWidget3->SetMinFa(v1.second.get("compartment3.prototype.minFA")); - m_Controls->m_PrototypeWidget3->SetMaxFa(v1.second.get("compartment3.prototype.maxFA")); - m_Controls->m_PrototypeWidget3->SetMinAdc(v1.second.get("compartment3.prototype.minADC")); - m_Controls->m_PrototypeWidget3->SetMaxAdc(v1.second.get("compartment3.prototype.maxADC")); - m_Controls->m_PrototypeWidget3->SetNumberOfSamples(v1.second.get("compartment3.prototype.numSamples")); - - m_Controls->m_BallWidget2->SetD(v1.second.get("compartment4.ball.d")); - m_Controls->m_BallWidget2->SetT2(v1.second.get("compartment4.ball.t2")); - m_Controls->m_AstrosticksWidget2->SetD(v1.second.get("compartment4.astrosticks.d")); - m_Controls->m_AstrosticksWidget2->SetT2(v1.second.get("compartment4.astrosticks.t2")); - m_Controls->m_AstrosticksWidget2->SetRandomizeSticks(v1.second.get("compartment4.astrosticks.randomize")); - m_Controls->m_DotWidget2->SetT2(v1.second.get("compartment4.dot.t2")); - m_Controls->m_PrototypeWidget4->SetMinFa(v1.second.get("compartment4.prototype.minFA")); - m_Controls->m_PrototypeWidget4->SetMaxFa(v1.second.get("compartment4.prototype.maxFA")); - m_Controls->m_PrototypeWidget4->SetMinAdc(v1.second.get("compartment4.prototype.minADC")); - m_Controls->m_PrototypeWidget4->SetMaxAdc(v1.second.get("compartment4.prototype.maxADC")); - m_Controls->m_PrototypeWidget4->SetNumberOfSamples(v1.second.get("compartment4.prototype.numSamples")); + if (dynamic_cast*>(signalModel)) + { + mitk::BallModel<>* model = dynamic_cast*>(signalModel); + m_Controls->m_BallWidget2->SetT2(model->GetT2()); + 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->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_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; + } } } } 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); switch (index) { case 0: break; case 1: m_Controls->m_StickWidget2->setVisible(true); break; case 2: m_Controls->m_ZeppelinWidget2->setVisible(true); break; case 3: m_Controls->m_TensorWidget2->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_SelectedImage.IsNull()) return; mitk::DataStorage::SetOfObjects::ConstPointer children = GetDataStorage()->GetDerivations(m_SelectedImage); mitk::FiberBundleX::Pointer bundle = mitk::FiberBundleX::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_SelectedImage); } 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); 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; } - vector< vector< mitk::PlanarEllipse::Pointer > > fiducials; - vector< vector< unsigned int > > fliplist; + FiberfoxParameters parameters = UpdateImageParameters(); + 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); } else { v.Normalize(); v *= radius; ellipse->SetControlPoint(1, c+v); } } 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) { - fiducials.push_back(fib); - fliplist.push_back(flip); + 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::FiberBundleX::New() ); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); } itk::FibersFromPlanarFiguresFilter::Pointer filter = itk::FibersFromPlanarFiguresFilter::New(); - filter->SetFiducials(fiducials); - filter->SetFlipList(fliplist); - - switch(m_Controls->m_DistributionBox->currentIndex()){ - case 0: - filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_UNIFORM); - break; - case 1: - filter->SetFiberDistribution(itk::FibersFromPlanarFiguresFilter::DISTRIBUTE_GAUSSIAN); - filter->SetVariance(m_Controls->m_VarianceBox->value()); - break; - } - - filter->SetDensity(m_Controls->m_FiberDensityBox->value()); - filter->SetTension(m_Controls->m_TensionBox->value()); - filter->SetContinuity(m_Controls->m_ContinuityBox->value()); - filter->SetBias(m_Controls->m_BiasBox->value()); - filter->SetFiberSampling(m_Controls->m_FiberSamplingBox->value()); + filter->SetParameters(parameters.m_FiberGen); filter->Update(); vector< mitk::FiberBundleX::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_SelectedBundles.empty() && m_SelectedDWI.IsNull()) { 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_SelectedImage = 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(); } else if (!m_SelectedBundles.empty()) SimulateImageFromFibers(m_SelectedBundles.at(0)); else if (m_SelectedDWI.IsNotNull()) SimulateForExistingDwi(m_SelectedDWI); } void QmitkFiberfoxView::SimulateForExistingDwi(mitk::DataNode* imageNode) { if (!dynamic_cast*>(imageNode->GetData())) return; FiberfoxParameters parameters = UpdateImageParameters(); if (parameters.m_NoiseModel==NULL && - parameters.m_Spikes==0 && - parameters.m_FrequencyMap.IsNull() && - parameters.m_KspaceLineOffset<=0.000001 && - !parameters.m_DoAddGibbsRinging && - !(parameters.m_EddyStrength>0) && - parameters.m_CroppingFactor>0.999) + parameters.m_SignalGen.m_Spikes==0 && + parameters.m_SignalGen.m_FrequencyMap.IsNull() && + parameters.m_SignalGen.m_KspaceLineOffset<=0.000001 && + !parameters.m_SignalGen.m_DoAddGibbsRinging && + !(parameters.m_SignalGen.m_EddyStrength>0) && + parameters.m_SignalGen.m_CroppingFactor>0.999) { QMessageBox::information( NULL, "Simulation cancelled", "No valid artifact enabled! Motion artifacts and relaxation effects can NOT be added to an existing diffusion weighted image."); return; } mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(imageNode->GetData()); m_ArtifactsToDwiFilter = itk::AddArtifactsToDwiImageFilter< short >::New(); m_ArtifactsToDwiFilter->SetInput(diffImg->GetVectorImage()); - parameters.m_ParentNode = imageNode; + parameters.m_Misc.m_ParentNode = imageNode; m_ArtifactsToDwiFilter->SetParameters(parameters); m_Worker.m_FilterType = 1; m_Thread.start(QThread::LowestPriority); } void QmitkFiberfoxView::SimulateImageFromFibers(mitk::DataNode* fiberNode) { mitk::FiberBundleX::Pointer fiberBundle = dynamic_cast(fiberNode->GetData()); if (fiberBundle->GetNumFibers()<=0) return; FiberfoxParameters parameters = UpdateImageParameters(); m_TractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); - parameters.m_ParentNode = fiberNode; + parameters.m_Misc.m_ParentNode = fiberNode; if (m_SelectedDWI.IsNotNull()) { mitk::DiffusionImage::Pointer diffImg = dynamic_cast*>(m_SelectedDWI->GetData()); bool doSampling = false; for (unsigned int i=0; i* >(parameters.m_FiberModelList[i]) ) doSampling = true; for (unsigned int i=0; i* >(parameters.m_NonFiberModelList[i]) ) doSampling = true; // sample prototype signals if ( doSampling ) { const int shOrder = 2; typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, double > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); filter->SetGradientImage( diffImg->GetDirections(), diffImg->GetVectorImage() ); filter->SetBValue(diffImg->GetReferenceBValue()); filter->Update(); itk::Image< itk::DiffusionTensor3D< double >, 3 >::Pointer tensorImage = filter->GetOutput(); const int NumCoeffs = (shOrder*shOrder + shOrder + 2)/2 + shOrder; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter QballFilterType; QballFilterType::Pointer qballfilter = QballFilterType::New(); qballfilter->SetGradientImage( diffImg->GetDirections(), diffImg->GetVectorImage() ); qballfilter->SetBValue(diffImg->GetReferenceBValue()); qballfilter->SetLambda(0.006); qballfilter->SetNormalizationMethod(QballFilterType::QBAR_RAW_SIGNAL); qballfilter->Update(); QballFilterType::CoefficientImageType::Pointer itkFeatureImage = qballfilter->GetCoefficientImage(); itk::AdcImageFilter< short, double >::Pointer adcFilter = itk::AdcImageFilter< short, double >::New(); adcFilter->SetInput(diffImg->GetVectorImage()); adcFilter->SetGradientDirections(diffImg->GetDirections()); adcFilter->SetB_value(diffImg->GetReferenceBValue()); adcFilter->Update(); ItkDoubleImgType::Pointer adcImage = adcFilter->GetOutput(); int b0Index; for (unsigned int i=0; iGetDirectionsWithoutMeasurementFrame()->Size(); i++) if ( diffImg->GetDirectionsWithoutMeasurementFrame()->GetElement(i).magnitude()<0.001 ) { b0Index = i; break; } double max = 0; { itk::ImageRegionIterator< itk::VectorImage< short, 3 > > it(diffImg->GetVectorImage(), diffImg->GetVectorImage()->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { - if (parameters.m_MaskImage.IsNotNull() && parameters.m_MaskImage->GetPixel(it.GetIndex())<=0) + if (parameters.m_SignalGen.m_MaskImage.IsNotNull() && parameters.m_SignalGen.m_MaskImage->GetPixel(it.GetIndex())<=0) { ++it; continue; } if (it.Get()[b0Index]>max) max = it.Get()[b0Index]; ++it; } } MITK_INFO << "Sampling signal kernels."; itk::ImageRegionIterator< itk::Image< itk::DiffusionTensor3D< double >, 3 > > it(tensorImage, tensorImage->GetLargestPossibleRegion()); while(!it.IsAtEnd()) { bool skipPixel = false; - if (parameters.m_MaskImage.IsNotNull() && parameters.m_MaskImage->GetPixel(it.GetIndex())<=0) + if (parameters.m_SignalGen.m_MaskImage.IsNotNull() && parameters.m_SignalGen.m_MaskImage->GetPixel(it.GetIndex())<=0) { ++it; continue; } for (unsigned int i=0; iGetDirections()->Size(); i++) { if (diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]!=diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i] || diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]<=0 || diffImg->GetVectorImage()->GetPixel(it.GetIndex())[i]>diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]) { skipPixel = true; break; } } if (skipPixel) { ++it; continue; } typedef itk::DiffusionTensor3D TensorType; TensorType::EigenValuesArrayType eigenvalues; TensorType::EigenVectorsMatrixType eigenvectors; TensorType tensor = it.Get(); double FA = tensor.GetFractionalAnisotropy(); double ADC = adcImage->GetPixel(it.GetIndex()); QballFilterType::CoefficientImageType::PixelType itkv = itkFeatureImage->GetPixel(it.GetIndex()); vnl_vector_fixed< double, NumCoeffs > coeffs; for (unsigned int c=0; c* model = dynamic_cast< RawShModel* >(parameters.m_FiberModelList[i]); if ( model && model->GetMaxNumKernels()>model->GetNumberOfKernels() && FA>model->GetFaRange().first && FAGetFaRange().second && ADC>model->GetAdcRange().first && ADCGetAdcRange().second) { if (model->SetShCoefficients( coeffs, (double)diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]/max )) { tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors); itk::Vector dir; dir[0] = eigenvectors(2, 0); dir[1] = eigenvectors(2, 1); dir[2] = eigenvectors(2, 2); model->m_PrototypeMaxDirection.push_back(dir); MITK_INFO << "WM KERNEL: " << it.GetIndex() << " (" << model->GetNumberOfKernels() << ")"; } } } for (unsigned int i=0; i* model = dynamic_cast< RawShModel* >(parameters.m_NonFiberModelList[i]); if ( model && model->GetMaxNumKernels()>model->GetNumberOfKernels() && FA>model->GetFaRange().first && FAGetFaRange().second && ADC>model->GetAdcRange().first && ADCGetAdcRange().second) { if (model->SetShCoefficients( coeffs, (double)diffImg->GetVectorImage()->GetPixel(it.GetIndex())[b0Index]/max )) MITK_INFO << "CSF/GM KERNEL: " << it.GetIndex() << " (" << model->GetNumberOfKernels() << ")"; } } ++it; } for (unsigned int i=0; i* model = dynamic_cast< RawShModel* >(parameters.m_FiberModelList[i]); if ( model && model->GetNumberOfKernels()<=0 ) { QMessageBox::information( NULL, "Simulation cancelled", "No suitable voxels found for fiber compartment "+QString::number(i)); return; } } for (unsigned int i=0; i* model = dynamic_cast< RawShModel* >(parameters.m_NonFiberModelList[i]); if ( model && model->GetNumberOfKernels()<=0 ) { QMessageBox::information( NULL, "Simulation cancelled", "No suitable voxels found for non-fiber compartment "+QString::number(i)); 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_Worker.m_FilterType = 0; 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::FiberBundleX::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("QmitkFiberProcessingView") << "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::FiberBundleX::Pointer fib = dynamic_cast((*it)->GetData()); mitk::FiberBundleX::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 = mitk::PlanarEllipse::New(); pe->DeepCopy(dynamic_cast(fiducialNode->GetData())); 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("QmitkFiberProcessingView") << "Select at least two fiber bundles!"; return; } std::vector::const_iterator it = m_SelectedBundles.begin(); mitk::FiberBundleX::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_FiberBundleLabel->setText("mandatory"); 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); if (m_SelectedFiducial.IsNotNull()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_FlipButton->setEnabled(true); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_SelectedImage.IsNotNull() || !m_SelectedBundles.empty()) { m_Controls->m_TransformBundlesButton->setEnabled(true); m_Controls->m_CircleButton->setEnabled(true); m_Controls->m_FiberGenMessage->setVisible(false); m_Controls->m_AlignOnGrid->setEnabled(true); } if (m_MaskImageNode.IsNotNull() || m_SelectedImage.IsNotNull()) { m_Controls->m_GeometryMessage->setVisible(true); m_Controls->m_GeometryFrame->setEnabled(false); } if (m_SelectedDWI.IsNotNull()) { 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); } if (!m_SelectedBundles.empty()) { m_Controls->m_CopyBundlesButton->setEnabled(true); m_Controls->m_GenerateFibersButton->setEnabled(true); m_Controls->m_FiberBundleLabel->setText(m_SelectedBundles.at(0)->GetName().c_str()); if (m_SelectedBundles.size()>1) m_Controls->m_JoinBundlesButton->setEnabled(true); } } 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_SelectedImage = NULL; m_SelectedDWI = NULL; m_MaskImageNode = NULL; m_Controls->m_TissueMaskLabel->setText("optional"); // iterate all selected objects, adjust warning visibility for( int i=0; i*>(node->GetData()) ) { m_SelectedDWI = node; m_SelectedImage = node; m_SelectedImages.push_back(node); } else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { m_SelectedImages.push_back(node); m_SelectedImage = node; bool isbinary = false; node->GetPropertyValue("binary", isbinary); if (isbinary) { m_MaskImageNode = node; m_Controls->m_TissueMaskLabel->setText(m_MaskImageNode->GetName().c_str()); } } 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::FiberBundleX::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() { MITK_DEBUG << "EnableCrosshairNavigation"; // enable the crosshair navigation if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "enabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(true); // linkedRenderWindow->EnableSlicingPlanes(true); } if (m_Controls->m_RealTimeFibers->isChecked()) GenerateFibers(); } void QmitkFiberfoxView::DisableCrosshairNavigation() { MITK_DEBUG << "DisableCrosshairNavigation"; // disable the crosshair navigation during the drawing if (mitk::ILinkedRenderWindowPart* linkedRenderWindow = dynamic_cast(this->GetRenderWindowPart())) { MITK_DEBUG << "disabling linked navigation"; linkedRenderWindow->EnableLinkedNavigation(false); // linkedRenderWindow->EnableSlicingPlanes(false); } } 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/QmitkFiberfoxView.h b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h index fc4f611076..dbe58f859b 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.h @@ -1,228 +1,209 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include #include #include #include "ui_QmitkFiberfoxViewControls.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include /*! \brief View for fiber based diffusion software phantoms (Fiberfox). See "Fiberfox: Facilitating the creation of realistic white matter software phantoms" (DOI: 10.1002/mrm.25045) for details. \sa QmitkFunctionality \ingroup Functionalities */ // Forward Qt class declarations using namespace std; class QmitkFiberfoxView; class QmitkFiberfoxWorker : public QObject { Q_OBJECT public: QmitkFiberfoxWorker(QmitkFiberfoxView* view); int m_FilterType; public slots: void run(); private: QmitkFiberfoxView* m_View; }; class QmitkFiberfoxView : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const string VIEW_ID; QmitkFiberfoxView(); virtual ~QmitkFiberfoxView(); virtual void CreateQtPartControl(QWidget *parent); void SetFocus(); typedef itk::Image ItkDoubleImgType; typedef itk::Image ItkUcharImgType; typedef itk::Vector GradientType; typedef vector GradientListType; template vector > MakeGradientList(); protected slots: void SetOutputPath(); ///< path where image is automatically saved to after the simulation is finished void LoadParameters(); ///< load fiberfox parameters void SaveParameters(); ///< save fiberfox parameters void BeforeThread(); void AfterThread(); void KillThread(); ///< abort simulation void UpdateSimulationStatus(); ///< print simulation progress and satus messages void OnDrawROI(); ///< adds new ROI, handles interactors etc. void OnAddBundle(); ///< adds new fiber bundle to datastorage void OnFlipButton(); ///< negate one coordinate of the fiber waypoints in the selcted planar figure. needed in case of unresolvable twists void GenerateFibers(); ///< generate fibers from the selected ROIs void GenerateImage(); ///< start image simulation void JoinBundles(); ///< merges selcted fiber bundles into one void CopyBundles(); ///< add copy of the selected bundle to the datamanager void ApplyTransform(); ///< rotate and shift selected bundles void AlignOnGrid(); ///< shift selected fiducials to nearest voxel center void Comp1ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 1 void Comp2ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 2 void Comp3ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 3 void Comp4ModelFrameVisibility(int index); ///< only show parameters of selected signal model for compartment 4 void ShowAdvancedOptions(int state); /** update fibers if any parameter changes */ void OnFiberDensityChanged(int value); void OnFiberSamplingChanged(double value); void OnTensionChanged(double value); void OnContinuityChanged(double value); void OnBiasChanged(double value); void OnVarianceChanged(double value); void OnDistributionChanged(int value); void OnConstantRadius(int value); /** update GUI elements */ void OnAddNoise(int value); void OnAddGhosts(int value); void OnAddDistortions(int value); void OnAddEddy(int value); void OnAddSpikes(int value); void OnAddAliasing(int value); void OnAddMotion(int value); protected: /// \brief called by QmitkFunctionality when DataManager's selection has changed virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList&); GradientListType GenerateHalfShell(int NPoints); ///< generate vectors distributed over the halfsphere Ui::QmitkFiberfoxViewControls* m_Controls; void SimulateForExistingDwi(mitk::DataNode* imageNode); ///< add artifacts to existing diffusion weighted image void SimulateImageFromFibers(mitk::DataNode* fiberNode); ///< simulate new diffusion weighted image template< class ScalarType > FiberfoxParameters< ScalarType > UpdateImageParameters(); ///< update fiberfox paramater object (template parameter defines noise model type) void UpdateGui(); ///< enable/disbale buttons etc. according to current datamanager selection void PlanarFigureSelected( itk::Object* object, const itk::EventObject& ); void EnableCrosshairNavigation(); ///< enable crosshair navigation if planar figure interaction ends void DisableCrosshairNavigation(); ///< disable crosshair navigation if planar figure interaction starts void NodeAdded( const mitk::DataNode* node ); ///< add observers void NodeRemoved(const mitk::DataNode* node); ///< remove observers /** structure to keep track of planar figures and observers */ struct QmitkPlanarFigureData { QmitkPlanarFigureData() : m_Figure(0) , m_EndPlacementObserverTag(0) , m_SelectObserverTag(0) , m_StartInteractionObserverTag(0) , m_EndInteractionObserverTag(0) , m_Flipped(0) { } mitk::PlanarFigure* m_Figure; unsigned int m_EndPlacementObserverTag; unsigned int m_SelectObserverTag; unsigned int m_StartInteractionObserverTag; unsigned int m_EndInteractionObserverTag; unsigned int m_Flipped; }; std::map m_DataNodeToPlanarFigureData; ///< map each planar figure uniquely to a QmitkPlanarFigureData mitk::DataNode::Pointer m_SelectedFiducial; ///< selected planar ellipse mitk::DataNode::Pointer m_SelectedImage; mitk::DataNode::Pointer m_SelectedDWI; vector< mitk::DataNode::Pointer > m_SelectedBundles; vector< mitk::DataNode::Pointer > m_SelectedBundles2; vector< mitk::DataNode::Pointer > m_SelectedFiducials; vector< mitk::DataNode::Pointer > m_SelectedImages; mitk::DataNode::Pointer m_MaskImageNode; - /** intra and inter axonal compartments */ - mitk::StickModel m_StickModel1; - mitk::StickModel m_StickModel2; - mitk::TensorModel m_ZeppelinModel1; - mitk::TensorModel m_ZeppelinModel2; - mitk::TensorModel m_TensorModel1; - mitk::TensorModel m_TensorModel2; - mitk::RawShModel m_PrototypeModel1; - - /** extra axonal compartment models */ - mitk::BallModel m_BallModel1; - mitk::BallModel m_BallModel2; - mitk::AstroStickModel m_AstrosticksModel1; - mitk::AstroStickModel m_AstrosticksModel2; - mitk::DotModel m_DotModel1; - mitk::DotModel m_DotModel2; - mitk::RawShModel m_PrototypeModel3; - mitk::RawShModel m_PrototypeModel4; - QString m_ParameterFile; ///< parameter file name // GUI thread QmitkFiberfoxWorker m_Worker; ///< runs filter QThread m_Thread; ///< worker thread bool m_ThreadIsRunning; QTimer* m_SimulationTimer; QTime m_SimulationTime; QString m_SimulationStatusText; /** Image filters that do all the simulations. */ itk::TractsToDWIImageFilter< short >::Pointer m_TractsToDwiFilter; itk::AddArtifactsToDwiImageFilter< short >::Pointer m_ArtifactsToDwiFilter; friend class QmitkFiberfoxWorker; }; 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 c4274ce619..cf15c8a6b3 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui @@ -1,3037 +1,3083 @@ QmitkFiberfoxViewControls 0 0 - 435 - 2305 + 443 + 2332 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. -360.000000000000000 360.000000000000000 0.100000000000000 Axis: false Rotation angle (in degree) around y-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation: false Translation (in mm) in direction of the z-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 Translation (in mm) in direction of the y-axis. -1000.000000000000000 1000.000000000000000 0.100000000000000 X false Rotation: false Z false Rotation angle (in degree) around z-axis. -360.000000000000000 360.000000000000000 0.100000000000000 Translation (in mm) in direction of the x-axis. -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 - - + + - Data + Extra-axonal Compartments - - - - - - - - - - - - - - Tissue Mask: - - - false - - - - - - - <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> - - - true - - - - - - - - - - - - - - - - Fiber Bundle: - - - false - - - - - - - <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> - - - true - - - - - - - - - - - - - - - - Save path: - - - false - - - - - + + + QFrame::NoFrame QFrame::Raised - + 0 0 0 0 - - 0 - - + - - + Volume Fraction: - - - ... + + + - - - - - - - Noise and other Artifacts - - - - - - Qt::Horizontal + + + + Select signal model for extra-axonal compartment. + + + Ball Model + + + + + Astrosticks Model + + + + + Dot Model + + + + + PrototypeSignal + + - - - - Add Noise - - - false + + + + + + + + + + + + + + + + Qt::Horizontal - - + + + + + + + + + + + - Add ringing artifacts occuring at strong edges in the image. + Select signal model for extra-axonal compartment. + + + -- + + + + + Ball Model + + + + + Astrosticks Model + + + + + Dot Model + + + + + Prototype Signal + + + + + + + + + + + + + + Qt::Vertical + + + + 20 + 40 + + + + + + + + Image Settings + + + + - Add Gibbs Ringing - - - false + Advanced Options - - - - true - + + QFrame::NoFrame QFrame::Raised - - - 6 - + 0 0 0 0 + + 6 + - - - + + + Gradient Directions: + + + + + + + Number of gradient directions distributed over the half sphere. + + + 0 + + + 10000 + + + 1 + + + 30 + + + + + + + - Shrink FOV (%): + <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 - - + + - Shrink FOV by this percentage. - - - 1 + b-value in s/mm² - 0.000000000000000 + 0 - 90.000000000000000 + 10000 - 0.100000000000000 + 100 - 25.000000000000000 + 1000 - - - - Qt::Horizontal + + + + 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 - - - - Num. Spikes: - - - + + 6 + - + - The number of randomly occurring signal spikes. + TE in milliseconds - + 1 - - - - - - Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice. + + 10000 - 0.100000000000000 + 1 - 0.100000000000000 + 100 - - - Scale: + + + + + + + + + - - - - - - - - - !!!EXPERIMENTAL!!! - - - Add Eddy Current Effects - - - false - - - - - - - Add Spikes - - - false - - - - - - - QFrame::NoFrame - - - QFrame::Raised - - - - 0 - - - 0 - - - 0 - - - 0 - - - - Variance: + <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> + + + false - - + + - Variance of selected noise distribution. - - - 4 - - - 0.000000000000000 + T2* relaxation time (in milliseconds). - 999999999.000000000000000 + 100.000000000000000 - 0.001000000000000 + 0.100000000000000 - 50.000000000000000 + 1.000000000000000 - - + + + + Output one image per compartment containing the corresponding volume fractions per voxel. + - Distribution: + Output Volume Fractions + + + false - - - - Noise distribution - + + - Rician + Fiber tangent - Chi-squared + Main fiber directions + + + + + Random - - - - - - - Add N/2 Ghosts - - - false - - - - - - - true - - - QFrame::NoFrame - - - QFrame::Raised - - - - 6 - - - 0 - - - 0 - - - 0 - - - 0 - - - + + - + <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 + + + + + + + Fiber Radius: + + + + + + + + + - Frequency Map: + Line Readout Time: false - - + + - Select image specifying the frequency inhomogeneities (in Hz). + + + + + + + + + + <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 + + + + + + + Diffusion Direction: + + + + + + + Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). + + + 1 + + + 10000 + + + 1 + + + 50 + + + + + + + TE in milliseconds + + + 1 + + + 10000 + + + 1 + + + 100 + + + + + + + Signal Scale: + + + + + + + Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. + + + 0 + + + 1000 + + + 0 + + + + + + + Separation Angle: + + + + + + + Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. + + + Disable Partial Volume Effects + + + false + + + + + + + 1 + + + 90.000000000000000 + + + 45.000000000000000 - - - - Qt::Horizontal - - - - - - - Qt::Horizontal - - - - - - - Qt::Horizontal - - - - - - - true - + + QFrame::NoFrame QFrame::Raised - - - QFormLayout::AllNonFixedFieldsGrow - - - 6 - + 0 - 6 + 0 0 0 - - - - Toggle between random movement and linear movement. + + + + 3 + + + 0.100000000000000 + + + 50.000000000000000 + + + 0.100000000000000 + + + 2.000000000000000 + + + + - Randomize motion + Image Spacing: - - true + + + + + + 3 + + + 0.100000000000000 + + + 50.000000000000000 + + + 0.100000000000000 + + + 2.000000000000000 - - - - Rotation + + + + 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 + + + 11 + + + + + + + Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. + + + 1 + + + 1000 + + + 1 + + + 11 + + + + + + + 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 + + + + + + + + + + + + + + + + + + + + + + + true + + + Stop current simulation. + + + Abort Simulation + + + + :/QmitkDiffusionImaging/general_icons/abort.ico:/QmitkDiffusionImaging/general_icons/abort.ico + + + + + + + Data + + + + + + + + + + + + + + + Tissue Mask: + + + false + + + + + + + <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> + + + true + + + + + + + + + + + + + + + + Fiber Bundle: + + + false + + + + + + + <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> + + + true + + + + + + + + + + + + + + + + Save path: + + + false + + + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + 0 + + + 0 + + + 0 + + + + + - - - - 0 - - - 9 - - - 0 - - - 0 - - - - - - - - - - - - - - Degree: - - - false - - - - - - - - - - - - - - - - x - - - false - - - - - - - - - - - - - - - - Axis: - - - false - - - - - - - Maximum rotation around x-axis. - - - 1 - - - 360.000000000000000 - - - 1.000000000000000 - - - 0.000000000000000 - - - - - - - Maximum rotation around z-axis. - - - 1 - - - 360.000000000000000 - - - 1.000000000000000 - - - 15.000000000000000 - - - - - - - - - - - - - - - - y - - - false - - - - - - - - - - - - - - - - z - - - false - - - - - - - Maximum rotation around y-axis. - - - 1 - - - 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 - - - 1.000000000000000 - - - 0.000000000000000 - - - - - - - Maximum translation along y-axis. - - - 1 - - - 1000.000000000000000 - - - 1.000000000000000 - - - 0.000000000000000 - - - - - - - Maximum translation along z-axis. - - - 1 - - - 1000.000000000000000 - - - 1.000000000000000 - - - 0.000000000000000 - - - - - - - - Add Motion Artifacts - - - false + + + + + + + + 8 + + + + true + + + + + + + Noise and other Artifacts + + + + + + Qt::Horizontal - - + + - Add Distortions + Add Noise false - - + + + + Add ringing artifacts occuring at strong edges in the image. + - Add Aliasing + Add Gibbs Ringing false - - + + true QFrame::NoFrame QFrame::Raised - + 6 0 0 0 0 - + - K-Space Line Offset: + Shrink FOV (%): false - + - A larger offset increases the inensity of the ghost image. + Shrink FOV by this percentage. - 3 + 1 + + + 0.000000000000000 - 1.000000000000000 + 90.000000000000000 - 0.010000000000000 + 0.100000000000000 - 0.250000000000000 + 25.000000000000000 - - - - true + + + + Qt::Horizontal + + + + QFrame::NoFrame QFrame::Raised - - - QFormLayout::AllNonFixedFieldsGrow - - - 6 - + 0 0 0 0 - - - - - - - - - - - + + - Magnitude: - - - false + Num. Spikes: - - + + - Maximum magnitude of eddy current induced magnetic field inhomogeneities (in mT). + The number of randomly occurring signal spikes. - - 5 + + 1 - - 1000.000000000000000 + + + + + + Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice. - 0.001000000000000 + 0.100000000000000 - 0.005000000000000 + 0.100000000000000 - - - - color: rgb(255, 0, 0); - + + - Experimental! + Scale: - - - - Qt::Horizontal + + + + !!!EXPERIMENTAL!!! + + + Add Eddy Current Effects + + + false - - - - Qt::Horizontal + + + + Add Spikes + + + false - - - - - - - Image Settings - - - - + + QFrame::NoFrame QFrame::Raised - + 0 0 0 0 - - 6 - - - - - TE in milliseconds - - - 1 - - - 10000 - - - 1 - - - 100 - - - - - - - - - - - - - + - <html><head/><body><p>Echo Time <span style=" font-style:italic;">TE</span>: </p></body></html> - - - false - - - - - - - Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). - - - 1 - - - 10000 - - - 1 - - - 50 + Variance: - - + + - Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. - - - Disable Partial Volume Effects - - - false + Variance of selected noise distribution. - - - - - - T2* relaxation time (in milliseconds). + + 4 + + + 0.000000000000000 - 100.000000000000000 + 999999999.000000000000000 - 0.100000000000000 + 0.001000000000000 - 1.000000000000000 + 50.000000000000000 - - - - Output one image per compartment containing the corresponding volume fractions per voxel. - + + - Output Volume Fractions - - - false + Distribution: - - + + - - - - - - - - - - <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 + Noise distribution + + + Rician + + + + + Chi-squared + + - - + + + + + + + Add N/2 Ghosts + + + false + + + + + + + true + + + QFrame::NoFrame + + + QFrame::Raised + + + + 6 + + + 0 + + + 0 + + + 0 + + + 0 + + + - Line Readout Time: + Frequency Map: false - - + + - Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. - - - 0 - - - 1000 - - - 0 - - - - - - - Fiber Radius: + Select image specifying the frequency inhomogeneities (in Hz). + + + + + + + Qt::Horizontal + + + + + + + Qt::Horizontal + + + + + + + Qt::Horizontal + + + + + + + true + + + QFrame::NoFrame + + + QFrame::Raised + + + + QFormLayout::AllNonFixedFieldsGrow + + + 6 + + + 0 + + + 6 + + + 0 + + + 0 + - - - Signal Scale: - - - - - + - <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> + Toggle between random movement and linear movement. - Simulate Signal Relaxation + Randomize motion true - - - - TE in milliseconds - - - 1 - - - 10000 - - - 1 - - - 100 + + + + Rotation + + + + 0 + + + 9 + + + 0 + + + 0 + + + + + + + + + + + + + + Degree: + + + false + + + + + + + + + + + + + + + + x + + + false + + + + + + + + + + + + + + + + Axis: + + + false + + + + + + + Maximum rotation around x-axis. + + + 1 + + + 360.000000000000000 + + + 1.000000000000000 + + + 0.000000000000000 + + + + + + + Maximum rotation around z-axis. + + + 1 + + + 360.000000000000000 + + + 1.000000000000000 + + + 15.000000000000000 + + + + + + + + + + + + + + + + y + + + false + + + + + + + + + + + + + + + + z + + + false + + + + + + + Maximum rotation around y-axis. + + + 1 + + + 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 + + + 1.000000000000000 + + + 0.000000000000000 + + + + + + + Maximum translation along y-axis. + + + 1 + + + 1000.000000000000000 + + + 1.000000000000000 + + + 0.000000000000000 + + + + + + + Maximum translation along z-axis. + + + 1 + + + 1000.000000000000000 + + + 1.000000000000000 + + + 0.000000000000000 + + + + - - - - color: rgb(255, 0, 0); - + + - Using geometry of selected image! + Add Motion Artifacts + + + false - - - - color: rgb(255, 0, 0); + + + + Add Distortions + + + false + + + + - Using gradients of selected DWI! + Add Aliasing + + + false - - + + + + true + QFrame::NoFrame QFrame::Raised - + + + 6 + 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 - - - 11 - - - - - + - Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. + - - 1 + + - - 1000 + + - - 1 + + K-Space Line Offset: - - 11 + + false - - + + - Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. + A larger offset increases the inensity of the ghost image. - - 1 + + 3 - 1000 + 1.000000000000000 - 1 + 0.010000000000000 - 3 + 0.250000000000000 - - + + + + true + QFrame::NoFrame QFrame::Raised - + + + QFormLayout::AllNonFixedFieldsGrow + + + 6 + 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> + Magnitude: false - + - b-value in s/mm² + Maximum magnitude of eddy current induced magnetic field inhomogeneities (in mT). - - 0 + + 5 - 10000 + 1000.000000000000000 - 100 + 0.001000000000000 - 1000 + 0.005000000000000 + + + + + + + color: rgb(255, 0, 0); + + + Experimental! - - - - Advanced Options + + + + Qt::Horizontal + + + + + + + Qt::Horizontal 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 PrototypeSignal - - - - true - - - Stop current simulation. - - - Abort Simulation - - - - :/QmitkDiffusionImaging/general_icons/abort.ico:/QmitkDiffusionImaging/general_icons/abort.ico - - - - - - - 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 - - - - - PrototypeSignal - - - - - - - - - - - - - - - - - - - - Qt::Horizontal - - - - - - - - - - - - - - - - Select signal model for extra-axonal compartment. - - - - -- - - - - - Ball Model - - - - - Astrosticks Model - - - - - Dot Model - - - - - Prototype Signal - - - - - - - - - - - - - - Qt::Vertical - - - - 20 - 40 - - - - - - - - Inter-axonal Compartment - - - - - - Select signal model for intra-axonal compartment. - - - - -- - - - - - Stick Model - - - - - Zeppelin Model - - - - - Tensor Model - - - - - - - - - - - - - - - - - - - - - - - - 8 - - - - true - - - 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 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_GenerateImageButton m_SizeX m_SizeY m_SizeZ m_SpacingX m_SpacingY m_SpacingZ m_NumGradientsBox m_BvalueBox m_AdvancedOptionsBox_2 m_SignalScaleBox m_TEbox m_LineReadoutTimeBox m_T2starBox m_FiberRadius m_RelaxationBox m_EnforcePureFiberVoxelsBox m_VolumeFractionsBox m_Compartment1Box m_Compartment2Box m_Compartment3Box m_Compartment4Box m_AddNoise 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