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 d98f6f20c5..76873960c7 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.cpp @@ -1,472 +1,648 @@ /*=================================================================== 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 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_FiberSeparationThreshold(30) , m_Spikes(0) , m_SpikeAmplitude(1) , m_KspaceLineOffset(0) , m_EddyStrength(0) , m_Tau(70) , m_CroppingFactor(1) + , m_DoAddNoise(false) + , m_DoAddGhosts(false) + , m_DoAddAliasing(false) + , m_DoAddSpikes(false) + , m_DoAddEddyCurrents(false) , m_DoAddGibbsRinging(false) , m_DoSimulateRelaxation(true) + , m_DoAddDistortions(false) , 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_NumBaseline(1) { + m_FiberGenerationParameters.m_RealTimeFibers = true; + m_FiberGenerationParameters.m_AdvancedOptions = false; + m_FiberGenerationParameters.m_Distribution = 0; + m_FiberGenerationParameters.m_Variance = 100; + m_FiberGenerationParameters.m_FiberDensity = 100; + m_FiberGenerationParameters.m_Sampling = 1; + m_FiberGenerationParameters.m_Tension = 0; + m_FiberGenerationParameters.m_Continuity = 0; + m_FiberGenerationParameters.m_Bias = 0; + m_FiberGenerationParameters.m_ConstantRadius = false; + m_FiberGenerationParameters.m_Rotation[0] = 0; + m_FiberGenerationParameters.m_Rotation[1] = 0; + m_FiberGenerationParameters.m_Rotation[2] = 0; + m_FiberGenerationParameters.m_Translation[0] = 0; + m_FiberGenerationParameters.m_Translation[1] = 0; + m_FiberGenerationParameters.m_Translation[2] = 0; + m_FiberGenerationParameters.m_Scale[0] = 1; + m_FiberGenerationParameters.m_Scale[1] = 1; + m_FiberGenerationParameters.m_Scale[2] = 1; + m_FiberGenerationParameters.m_IncludeFiducials = true; + 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() { 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 > 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() { 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) { 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() { return m_NumGradients; } template< class ScalarType > unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumBaselineVolumes() { return m_NumBaseline; } template< class ScalarType > unsigned int mitk::FiberfoxParameters< ScalarType >::GetNumVolumes() { return m_GradientDirections.size(); } template< class ScalarType > typename mitk::FiberfoxParameters< ScalarType >::GradientListType mitk::FiberfoxParameters< ScalarType >::GetGradientDirections() { return m_GradientDirections; } template< class ScalarType > typename mitk::FiberfoxParameters< ScalarType >::GradientType mitk::FiberfoxParameters< ScalarType >::GetGradientDirection(unsigned int i) { return m_GradientDirections.at(i); } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::SetNumWeightedGradients(int numGradients) { m_NumGradients = numGradients; GenerateGradientHalfShell(); } template< class ScalarType > void mitk::FiberfoxParameters< ScalarType >::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) { 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.realtime", m_FiberGenerationParameters.m_RealTimeFibers); + parameters.put("fiberfox.fibers.showadvanced", m_FiberGenerationParameters.m_AdvancedOptions); + parameters.put("fiberfox.fibers.distribution", m_FiberGenerationParameters.m_Distribution); + parameters.put("fiberfox.fibers.variance", m_FiberGenerationParameters.m_Variance); + parameters.put("fiberfox.fibers.density", m_FiberGenerationParameters.m_FiberDensity); + parameters.put("fiberfox.fibers.spline.sampling", m_FiberGenerationParameters.m_Sampling); + parameters.put("fiberfox.fibers.spline.tension", m_FiberGenerationParameters.m_Tension); + parameters.put("fiberfox.fibers.spline.continuity", m_FiberGenerationParameters.m_Continuity); + parameters.put("fiberfox.fibers.spline.bias", m_FiberGenerationParameters.m_Bias); + parameters.put("fiberfox.fibers.constantradius", m_FiberGenerationParameters.m_ConstantRadius); + parameters.put("fiberfox.fibers.rotation.x", m_FiberGenerationParameters.m_Rotation[0]); + parameters.put("fiberfox.fibers.rotation.y", m_FiberGenerationParameters.m_Rotation[1]); + parameters.put("fiberfox.fibers.rotation.z", m_FiberGenerationParameters.m_Rotation[2]); + parameters.put("fiberfox.fibers.translation.x", m_FiberGenerationParameters.m_Translation[0]); + parameters.put("fiberfox.fibers.translation.y", m_FiberGenerationParameters.m_Translation[1]); + parameters.put("fiberfox.fibers.translation.z", m_FiberGenerationParameters.m_Translation[2]); + parameters.put("fiberfox.fibers.scale.x", m_FiberGenerationParameters.m_Scale[0]); + parameters.put("fiberfox.fibers.scale.y", m_FiberGenerationParameters.m_Scale[1]); + parameters.put("fiberfox.fibers.scale.z", m_FiberGenerationParameters.m_Scale[2]); + parameters.put("fiberfox.fibers.includeFiducials", m_FiberGenerationParameters.m_IncludeFiducials); + + // image generation parameters + parameters.put("fiberfox.image.basic.size.x", m_ImageRegion.GetSize(0)); + parameters.put("fiberfox.image.basic.size.y", m_ImageRegion.GetSize(1)); + parameters.put("fiberfox.image.basic.size.z", m_ImageRegion.GetSize(2)); + parameters.put("fiberfox.image.basic.spacing.x", m_ImageSpacing[0]); + parameters.put("fiberfox.image.basic.spacing.y", m_ImageSpacing[1]); + parameters.put("fiberfox.image.basic.spacing.z", m_ImageSpacing[2]); + parameters.put("fiberfox.image.basic.origin.x", m_ImageOrigin[0]); + parameters.put("fiberfox.image.basic.origin.y", m_ImageOrigin[1]); + parameters.put("fiberfox.image.basic.origin.z", m_ImageOrigin[2]); + parameters.put("fiberfox.image.basic.direction.1", m_ImageDirection[0][0]); + parameters.put("fiberfox.image.basic.direction.2", m_ImageDirection[0][1]); + parameters.put("fiberfox.image.basic.direction.3", m_ImageDirection[0][2]); + parameters.put("fiberfox.image.basic.direction.4", m_ImageDirection[1][0]); + parameters.put("fiberfox.image.basic.direction.5", m_ImageDirection[1][1]); + parameters.put("fiberfox.image.basic.direction.6", m_ImageDirection[1][2]); + parameters.put("fiberfox.image.basic.direction.7", m_ImageDirection[2][0]); + parameters.put("fiberfox.image.basic.direction.8", m_ImageDirection[2][1]); + parameters.put("fiberfox.image.basic.direction.9", m_ImageDirection[2][2]); + + parameters.put("fiberfox.image.signalScale", m_SignalScale); + parameters.put("fiberfox.image.tEcho", m_tEcho); + parameters.put("fiberfox.image.tLine", m_tLine); + parameters.put("fiberfox.image.tInhom", m_tInhom); + parameters.put("fiberfox.image.bvalue", m_Bvalue); + parameters.put("fiberfox.image.simulatekspace", m_SimulateKspaceAcquisition); + + parameters.put("fiberfox.image.axonRadius", m_AxonRadius); + parameters.put("fiberfox.image.diffusiondirectionmode", m_DiffusionDirectionMode); + parameters.put("fiberfox.image.fiberseparationthreshold", m_FiberSeparationThreshold); + + parameters.put("fiberfox.image.artifacts.addnoise", m_DoAddNoise); + parameters.put("fiberfox.image.artifacts.addghosts", m_DoAddGhosts); + parameters.put("fiberfox.image.artifacts.addaliasing", m_DoAddAliasing); + parameters.put("fiberfox.image.artifacts.addspikes", m_DoAddSpikes); + parameters.put("fiberfox.image.artifacts.addeddycurrents", m_DoAddEddyCurrents); + parameters.put("fiberfox.image.artifacts.spikesnum", m_Spikes); + parameters.put("fiberfox.image.artifacts.spikesscale", m_SpikeAmplitude); + parameters.put("fiberfox.image.artifacts.kspaceLineOffset", m_KspaceLineOffset); + parameters.put("fiberfox.image.artifacts.eddyStrength", m_EddyStrength); + parameters.put("fiberfox.image.artifacts.eddyTau", m_Tau); + parameters.put("fiberfox.image.artifacts.aliasingfactor", m_CroppingFactor); + parameters.put("fiberfox.image.artifacts.addringing", m_DoAddGibbsRinging); + parameters.put("fiberfox.image.doSimulateRelaxation", m_DoSimulateRelaxation); + parameters.put("fiberfox.image.doDisablePartialVolume", m_DoDisablePartialVolume); + parameters.put("fiberfox.image.artifacts.doAddMotion", m_DoAddMotion); + parameters.put("fiberfox.image.artifacts.randomMotion", m_DoRandomizeMotion); + parameters.put("fiberfox.image.artifacts.doAddDistortions", m_DoAddDistortions); + parameters.put("fiberfox.image.artifacts.translation0", m_Translation[0]); + parameters.put("fiberfox.image.artifacts.translation1", m_Translation[1]); + parameters.put("fiberfox.image.artifacts.translation2", m_Translation[2]); + parameters.put("fiberfox.image.artifacts.rotation0", m_Rotation[0]); + parameters.put("fiberfox.image.artifacts.rotation1", m_Rotation[1]); + parameters.put("fiberfox.image.artifacts.rotation2", m_Rotation[2]); + + parameters.put("fiberfox.image.signalmodelstring", m_SignalModelString); + parameters.put("fiberfox.image.artifactmodelstring", m_ArtifactModelString); + parameters.put("fiberfox.image.outpath", m_OutputPath); + parameters.put("fiberfox.image.outputvolumefractions", m_OutputVolumeFractions); + parameters.put("fiberfox.image.showadvanced", m_AdvancedOptions); + parameters.put("fiberfox.image.basic.numgradients", m_NumGradients); + + 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()); + } + parameters.put("fiberfox.image.compartments."+boost::lexical_cast(i)+".ID", signalModel->m_CompartmentId); + } + + boost::property_tree::xml_writer_settings writerSettings(' ', 2); + boost::property_tree::xml_parser::write_xml(filename, parameters, std::locale(), writerSettings); +} + +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_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")) + m_FiberGenerationParameters.m_RealTimeFibers = v1.second.get("realtime", m_FiberGenerationParameters.m_RealTimeFibers); + m_FiberGenerationParameters.m_AdvancedOptions = v1.second.get("showadvanced", m_FiberGenerationParameters.m_AdvancedOptions); + m_FiberGenerationParameters.m_Distribution = v1.second.get("distribution", m_FiberGenerationParameters.m_Distribution); + m_FiberGenerationParameters.m_Variance = v1.second.get("variance", m_FiberGenerationParameters.m_Variance); + m_FiberGenerationParameters.m_FiberDensity = v1.second.get("density", m_FiberGenerationParameters.m_FiberDensity); + m_FiberGenerationParameters.m_Sampling = v1.second.get("spline.sampling", m_FiberGenerationParameters.m_Sampling); + m_FiberGenerationParameters.m_Tension = v1.second.get("spline.tension", m_FiberGenerationParameters.m_Tension); + m_FiberGenerationParameters.m_Continuity = v1.second.get("spline.continuity", m_FiberGenerationParameters.m_Continuity); + m_FiberGenerationParameters.m_Bias = v1.second.get("spline.bias", m_FiberGenerationParameters.m_Bias); + m_FiberGenerationParameters.m_ConstantRadius = v1.second.get("constantradius", m_FiberGenerationParameters.m_ConstantRadius); + m_FiberGenerationParameters.m_Rotation[0] = v1.second.get("rotation.x", m_FiberGenerationParameters.m_Rotation[0]); + m_FiberGenerationParameters.m_Rotation[1] = v1.second.get("rotation.y", m_FiberGenerationParameters.m_Rotation[1]); + m_FiberGenerationParameters.m_Rotation[2] = v1.second.get("rotation.z", m_FiberGenerationParameters.m_Rotation[2]); + m_FiberGenerationParameters.m_Translation[0] = v1.second.get("translation.x", m_FiberGenerationParameters.m_Translation[0]); + m_FiberGenerationParameters.m_Translation[1] = v1.second.get("translation.y", m_FiberGenerationParameters.m_Translation[1]); + m_FiberGenerationParameters.m_Translation[2] = v1.second.get("translation.z", m_FiberGenerationParameters.m_Translation[2]); + m_FiberGenerationParameters.m_Scale[0] = v1.second.get("scale.x", m_FiberGenerationParameters.m_Scale[0]); + m_FiberGenerationParameters.m_Scale[1] = v1.second.get("scale.y", m_FiberGenerationParameters.m_Scale[1]); + m_FiberGenerationParameters.m_Scale[2] = v1.second.get("scale.z", m_FiberGenerationParameters.m_Scale[2]); + m_FiberGenerationParameters.m_IncludeFiducials = v1.second.get("includeFiducials", m_FiberGenerationParameters.m_IncludeFiducials); + } + else if ( v1.first == "image" ) + { + m_ImageRegion.SetSize(0, v1.second.get("basic.size.x", m_ImageRegion.GetSize(0))); + m_ImageRegion.SetSize(1, v1.second.get("basic.size.y", m_ImageRegion.GetSize(1))); + m_ImageRegion.SetSize(2, v1.second.get("basic.size.z", m_ImageRegion.GetSize(2))); + m_ImageSpacing[0] = v1.second.get("basic.spacing.x", m_ImageSpacing[0]); + m_ImageSpacing[1] = v1.second.get("basic.spacing.y", m_ImageSpacing[1]); + m_ImageSpacing[2] = v1.second.get("basic.spacing.z", m_ImageSpacing[2]); + m_ImageOrigin[0] = v1.second.get("basic.origin.x", m_ImageOrigin[0]); + m_ImageOrigin[1] = v1.second.get("basic.origin.y", m_ImageOrigin[1]); + m_ImageOrigin[2] = v1.second.get("basic.origin.z", m_ImageOrigin[2]); + m_ImageDirection[0][0] = v1.second.get("basic.direction.1", m_ImageDirection[0][0]); + m_ImageDirection[0][1] = v1.second.get("basic.direction.2", m_ImageDirection[0][1]); + m_ImageDirection[0][2] = v1.second.get("basic.direction.3", m_ImageDirection[0][2]); + m_ImageDirection[1][0] = v1.second.get("basic.direction.4", m_ImageDirection[1][0]); + m_ImageDirection[1][1] = v1.second.get("basic.direction.5", m_ImageDirection[1][1]); + m_ImageDirection[1][2] = v1.second.get("basic.direction.6", m_ImageDirection[1][2]); + m_ImageDirection[2][0] = v1.second.get("basic.direction.7", m_ImageDirection[2][0]); + m_ImageDirection[2][1] = v1.second.get("basic.direction.8", m_ImageDirection[2][1]); + m_ImageDirection[2][2] = v1.second.get("basic.direction.9", m_ImageDirection[2][2]); + + m_SignalScale = v1.second.get("signalScale", m_SignalScale); + m_tEcho = v1.second.get("tEcho", m_tEcho); + m_tLine = v1.second.get("tLine", m_tLine); + m_tInhom = v1.second.get("tInhom", m_tInhom); + m_Bvalue = v1.second.get("bvalue", m_Bvalue); + m_SimulateKspaceAcquisition = v1.second.get("simulatekspace", m_SimulateKspaceAcquisition); + + m_AxonRadius = v1.second.get("axonRadius", m_AxonRadius); + int mode = v1.second.get("diffusiondirectionmode", 0); + switch (mode) { 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_DiffusionDirectionMode = 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("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); + m_DiffusionDirectionMode = 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("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_DiffusionDirectionMode = RANDOM_DIRECTIONS; break; + default: + m_DiffusionDirectionMode = FIBER_TANGENT_DIRECTIONS; } - } + m_FiberSeparationThreshold = v1.second.get("fiberseparationthreshold", m_FiberSeparationThreshold); + + m_DoAddNoise = v1.second.get("artifacts.addnoise", m_DoAddNoise); + m_DoAddGhosts = v1.second.get("artifacts.addghosts", m_DoAddGhosts); + m_DoAddAliasing = v1.second.get("artifacts.addaliasing", m_DoAddAliasing); + m_DoAddSpikes = v1.second.get("artifacts.addspikes", m_DoAddSpikes); + m_DoAddEddyCurrents = v1.second.get("artifacts.addeddycurrents", m_DoAddEddyCurrents); + m_Spikes = v1.second.get("artifacts.spikesnum", m_Spikes); + m_SpikeAmplitude = v1.second.get("artifacts.spikesscale", m_SpikeAmplitude); + m_KspaceLineOffset = v1.second.get("artifacts.kspaceLineOffset", m_KspaceLineOffset); + m_EddyStrength = v1.second.get("artifacts.eddyStrength", m_EddyStrength); + m_Tau = v1.second.get("artifacts.eddyTau", m_Tau); + m_CroppingFactor = v1.second.get("artifacts.aliasingfactor", m_CroppingFactor); + m_DoAddGibbsRinging = v1.second.get("artifacts.addringing", m_DoAddGibbsRinging); + m_DoSimulateRelaxation = v1.second.get("doSimulateRelaxation", m_DoSimulateRelaxation); + m_DoDisablePartialVolume = v1.second.get("doDisablePartialVolume", m_DoDisablePartialVolume); + m_DoAddMotion = v1.second.get("artifacts.doAddMotion", m_DoAddMotion); + m_DoRandomizeMotion = v1.second.get("artifacts.randomMotion", m_DoRandomizeMotion); + m_DoAddDistortions = v1.second.get("artifacts.doAddDistortions", m_DoAddDistortions); + m_Translation[0] = v1.second.get("artifacts.translation0", m_Translation[0]); + m_Translation[1] = v1.second.get("artifacts.translation1", m_Translation[1]); + m_Translation[2] = v1.second.get("artifacts.translation2", m_Translation[2]); + m_Rotation[0] = v1.second.get("artifacts.rotation0", m_Rotation[0]); + m_Rotation[1] = v1.second.get("artifacts.rotation1", m_Rotation[1]); + m_Rotation[2] = v1.second.get("artifacts.rotation2", m_Rotation[2]); + + m_SignalModelString = v1.second.get("signalmodelstring", m_SignalModelString); + m_ArtifactModelString = v1.second.get("artifactmodelstring", m_ArtifactModelString); + m_OutputPath = v1.second.get("outpath", m_OutputPath); + m_OutputVolumeFractions = v1.second.get("outputvolumefractions", m_OutputVolumeFractions); + m_AdvancedOptions = v1.second.get("showadvanced", m_AdvancedOptions); + m_NumGradients = v1.second.get("numgradients", m_NumGradients); + GenerateGradientHalfShell(); - // compartment 2 - switch (v1.second.get("compartment2.index")) - { - 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); - break; - } - case 1: + try { - 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); - 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::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); - break; - } + if (v1.second.get("artifacts.noisetype")=="chisquare") + { + m_NoiseModel = new mitk::ChiSquareNoiseModel(); + m_NoiseModel->SetNoiseVariance(v1.second.get("artifacts.noisevariance")); + } } + catch(...){ } - // 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: - { - 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; - } - case 2: - { - mitk::DotModel* dotModel = new mitk::DotModel(); - dotModel->SetGradientList(m_GradientDirections); - dotModel->SetT2(v1.second.get("compartment3.dot.t2")); - m_NonFiberModelList.push_back(dotModel); - break; - } - } - // compartment 4 - switch (v1.second.get("compartment4.index")) + BOOST_FOREACH( boost::property_tree::ptree::value_type const& v2, v1.second.get_child("compartments") ) { - 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: - { - mitk::DotModel* dotModel = new mitk::DotModel(); - dotModel->SetGradientList(m_GradientDirections); - dotModel->SetT2(v1.second.get("compartment4.dot.t2")); - m_NonFiberModelList.push_back(dotModel); - break; - } + 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); + } + 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); + } + 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); + } + 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); + } + 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); + } + 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); + } + catch (...) { } } } } } 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 12d3adf709..2359106647 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/mitkFiberfoxParameters.h @@ -1,188 +1,219 @@ /*=================================================================== 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 using namespace std; namespace mitk { /** * \brief Datastructure to manage the Fiberfox signal generation parameters. * */ template< class ScalarType = double > class FiberfoxParameters { public: 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() { FiberfoxParameters< OutType > out; +// out.m_FiberGenerationParameters = m_FiberGenerationParameters; + 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_DiffusionDirectionMode = m_DiffusionDirectionMode; + // out.m_SignalGenerationMode = m_SignalGenerationMode; out.m_SimulateKspaceAcquisition = m_SimulateKspaceAcquisition; // TODO: copy constructor für singalmodelle und rauschen return out; } + /** Fiber generation */ + struct FiberGenerationParameters + { + bool m_RealTimeFibers; + bool m_AdvancedOptions; + int m_Distribution; + double m_Variance; + unsigned int m_FiberDensity; + double m_Sampling; + double m_Tension; + double m_Continuity; + double m_Bias; + bool m_ConstantRadius; + mitk::Vector3D m_Rotation; + mitk::Vector3D m_Translation; + mitk::Vector3D m_Scale; + bool m_IncludeFiducials; + } m_FiberGenerationParameters; + /** 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. double m_AxonRadius; ///< Determines compartment volume fractions (0 == automatic axon radius estimation) 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 */ 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_DoAddNoise; + bool m_DoAddGhosts; + bool m_DoAddAliasing; + bool m_DoAddSpikes; + bool m_DoAddEddyCurrents; bool m_DoAddGibbsRinging; ///< Add Gibbs ringing artifact bool m_DoSimulateRelaxation; ///< Add T2 relaxation effects + bool m_DoAddDistortions; ///< Add magnetic field distortions 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. + mitk::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. + bool m_OutputVolumeFractions; + bool m_AdvancedOptions; void PrintSelf(); ///< Print parameters to stdout. + void SaveParameters(string filename); ///< Save image generation parameters to .ffp file. void LoadParameters(string filename); ///< Load image generation parameters from .ffp file. void GenerateGradientHalfShell(); ///< Generates half shell of gradient directions (with m_NumGradients non-zero directions) std::vector< int > GetBaselineIndices(); unsigned int GetFirstBaselineIndex(); bool IsBaselineIndex(unsigned int idx); unsigned int GetNumWeightedVolumes(); unsigned int GetNumBaselineVolumes(); unsigned int GetNumVolumes(); GradientListType GetGradientDirections(); GradientType GetGradientDirection(unsigned int i); void SetNumWeightedGradients(int numGradients); ///< Automaticall calls GenerateGradientHalfShell() afterwards. void SetGradienDirections(GradientListType gradientList); void SetGradienDirections(mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientList); protected: - unsigned int m_NumBaseline; ///< Number of non-diffusion-weighted image volumes. 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. }; } #include "mitkFiberfoxParameters.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.h index 954a417a20..e060ec245a 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkAstroStickModel.h @@ -1,106 +1,109 @@ /*=================================================================== 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_AstroStickModel_H #define _MITK_AstroStickModel_H #include #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(); ~AstroStickModel(); 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; } 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 + ScalarType GetDiffusivity() { return m_Diffusivity; } + bool GetRandomizeSticks() { return m_RandomizeSticks; } + 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(); ~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; } + ScalarType GetDiffusivity() { return m_Diffusivity; } void SetBvalue(ScalarType bValue) { m_BValue = 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 }; } #include "mitkBallModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h index 7f6f48b973..e456b610ac 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDiffusionSignalModel.h @@ -1,83 +1,84 @@ /*=================================================================== 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; virtual void SetGradientList(GradientListType gradientList) = 0; void SetT2(double T2) { m_T2 = 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 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..f43662ae26 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkDotModel.h @@ -1,57 +1,57 @@ /*=================================================================== 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(); ~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.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.h index 2c21e4f705..7cf83474ee 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkRawShModel.h @@ -1,79 +1,79 @@ /*=================================================================== 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_RawShModel_H #define _MITK_RawShModel_H #include 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(); ~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); 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; 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; }; } #include "mitkRawShModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h index 6af5a320f1..1523592cab 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkStickModel.h @@ -1,62 +1,63 @@ /*=================================================================== 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(); ~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 + ScalarType 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 }; } #include "mitkStickModel.cpp" #endif diff --git a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h index 4ebe00bc6e..06f16f8731 100644 --- a/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h +++ b/Modules/DiffusionImaging/FiberTracking/SignalModels/mitkTensorModel.h @@ -1,69 +1,72 @@ /*=================================================================== 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(); ~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; } + ScalarType GetDiffusivity1() { return m_KernelTensorMatrix[0][0]; } + ScalarType GetDiffusivity2() { return m_KernelTensorMatrix[1][1]; } + ScalarType GetDiffusivity3() { return m_KernelTensorMatrix[2][2]; } void SetFiberDirection(GradientType fiberDirection){ this->m_FiberDirection = fiberDirection; } void SetGradientList(GradientListType gradientList) { this->m_GradientList = gradientList; } 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 }; } #include "mitkTensorModel.cpp" #endif 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 9e934cfb9e..cbc63205ee 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxView.cpp @@ -1,2599 +1,2603 @@ /*=================================================================== 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); + + m_StickModel1.m_CompartmentId = 1; + m_StickModel2.m_CompartmentId = 2; + m_TensorModel1.m_CompartmentId = 1; + m_TensorModel2.m_CompartmentId = 2; + m_ZeppelinModel1.m_CompartmentId = 1; + m_ZeppelinModel2.m_CompartmentId = 2; + m_BallModel1.m_CompartmentId = 3; + m_BallModel2.m_CompartmentId = 4; + m_AstrosticksModel1.m_CompartmentId = 3; + m_AstrosticksModel2.m_CompartmentId = 4; + m_DotModel1.m_CompartmentId = 3; + m_DotModel2.m_CompartmentId = 4; + m_PrototypeModel1.m_CompartmentId = 1; + m_PrototypeModel3.m_CompartmentId = 3; + m_PrototypeModel4.m_CompartmentId = 4; } 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->InitializeFromVectorImage(); parameters.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); GetDataStorage()->Add(parameters.m_ResultNode, parameters.m_ParentNode); parameters.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); } } 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()); 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); m_ArtifactsToDwiFilter = NULL; break; } } mitk::BaseData::Pointer basedata = parameters.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()) { try{ QString outputFileName(parameters.m_OutputPath.c_str()); outputFileName += parameters.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; } 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_FiberGenerationParameters.m_AdvancedOptions = m_Controls->m_AdvancedOptionsBox->isChecked(); + parameters.m_AdvancedOptions = 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 += "/"; } if (m_MaskImageNode.IsNotNull()) { mitk::Image::Pointer mitkMaskImage = dynamic_cast(m_MaskImageNode->GetData()); mitk::CastToItkImage(mitkMaskImage, parameters.m_MaskImage); itk::ImageDuplicator::Pointer duplicator = itk::ImageDuplicator::New(); duplicator->SetInputImage(parameters.m_MaskImage); duplicator->Update(); parameters.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()); } 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(); } 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(); } // 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"; // N/2 ghosts + parameters.m_DoAddGhosts = 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)); } else parameters.m_KspaceLineOffset = 0; // Aliasing + parameters.m_DoAddAliasing = 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())); } // Spikes + parameters.m_DoAddSpikes = 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)); } // gibbs ringing parameters.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"; } // add distortions + parameters.m_DoAddDistortions = m_Controls->m_AddDistortions->isChecked(); if (m_Controls->m_AddDistortions->isChecked() && m_Controls->m_FrequencyMapBox->GetSelectedNode().IsNotNull()) { mitk::DataNode::Pointer fMapNode = m_Controls->m_FrequencyMapBox->GetSelectedNode(); mitk::Image* img = dynamic_cast(fMapNode->GetData()); 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)) { parameters.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_EddyStrength = 0; + parameters.m_DoAddEddyCurrents = 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)); } // 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(); 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])); } // 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(); // adjust echo time if needed if ( parameters.m_tEcho < parameters.m_ImageRegion.GetSize(1)*parameters.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"); } // Noise + parameters.m_DoAddNoise = 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")); break; } case 1: { parameters.m_NoiseModel = new mitk::ChiSquareNoiseModel(); parameters.m_ArtifactModelString += "_CHISQUARED-"; parameters.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_NoiseModel->SetNoiseVariance(noiseVariance); parameters.m_ArtifactModelString += QString::number(noiseVariance).toStdString(); parameters.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); y += y%2; if ( y>parameters.m_ImageRegion.GetSize(1) ) parameters.m_tLine *= (double)parameters.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()) { + 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_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(1.0/(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::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: { 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()) ); 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()) ); 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()) ); break; } case 4: { 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") ); break; } } parameters.m_FiberSeparationThreshold = m_Controls->m_SeparationAngleBox->value(); switch (m_Controls->m_DiffusionDirectionBox->currentIndex()) { case 0: parameters.m_DiffusionDirectionMode = FiberfoxParameters::FIBER_TANGENT_DIRECTIONS; break; case 1: parameters.m_DiffusionDirectionMode = FiberfoxParameters::MAIN_FIBER_DIRECTIONS; break; case 2: parameters.m_DiffusionDirectionMode = FiberfoxParameters::RANDOM_DIRECTIONS; parameters.m_DoAddMotion = false; parameters.m_DoAddGibbsRinging = false; parameters.m_KspaceLineOffset = 0.0; parameters.m_FrequencyMap = NULL; parameters.m_CroppingFactor = 1.0; parameters.m_EddyStrength = 0; break; default: parameters.m_DiffusionDirectionMode = FiberfoxParameters::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_FiberGenerationParameters.m_RealTimeFibers = m_Controls->m_RealTimeFibers->isChecked(); + parameters.m_FiberGenerationParameters.m_AdvancedOptions = m_Controls->m_AdvancedOptionsBox->isChecked(); + parameters.m_FiberGenerationParameters.m_Distribution = m_Controls->m_DistributionBox->currentIndex(); + parameters.m_FiberGenerationParameters.m_Variance = m_Controls->m_VarianceBox->value(); + parameters.m_FiberGenerationParameters.m_FiberDensity = m_Controls->m_FiberDensityBox->value(); + parameters.m_FiberGenerationParameters.m_IncludeFiducials = m_Controls->m_IncludeFiducials->isChecked(); + parameters.m_FiberGenerationParameters.m_ConstantRadius = m_Controls->m_ConstantRadiusBox->isChecked(); + parameters.m_FiberGenerationParameters.m_Sampling = m_Controls->m_FiberSamplingBox->value(); + parameters.m_FiberGenerationParameters.m_Tension = m_Controls->m_TensionBox->value(); + parameters.m_FiberGenerationParameters.m_Continuity = m_Controls->m_ContinuityBox->value(); + parameters.m_FiberGenerationParameters.m_Bias = m_Controls->m_BiasBox->value(); + parameters.m_FiberGenerationParameters.m_Rotation[0] = m_Controls->m_XrotBox->value(); + parameters.m_FiberGenerationParameters.m_Rotation[1] = m_Controls->m_YrotBox->value(); + parameters.m_FiberGenerationParameters.m_Rotation[2] = m_Controls->m_ZrotBox->value(); + parameters.m_FiberGenerationParameters.m_Translation[0] = m_Controls->m_XtransBox->value(); + parameters.m_FiberGenerationParameters.m_Translation[1] = m_Controls->m_YtransBox->value(); + parameters.m_FiberGenerationParameters.m_Translation[2] = m_Controls->m_ZtransBox->value(); + parameters.m_FiberGenerationParameters.m_Scale[0] = m_Controls->m_XscaleBox->value(); + parameters.m_FiberGenerationParameters.m_Scale[1] = m_Controls->m_YscaleBox->value(); + parameters.m_FiberGenerationParameters.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<> ffParamaters; + ffParamaters.LoadParameters(filename.toStdString()); + + m_Controls->m_RealTimeFibers->setChecked(ffParamaters.m_FiberGenerationParameters.m_RealTimeFibers); + m_Controls->m_AdvancedOptionsBox->setChecked(ffParamaters.m_FiberGenerationParameters.m_AdvancedOptions); + m_Controls->m_DistributionBox->setCurrentIndex(ffParamaters.m_FiberGenerationParameters.m_Distribution); + m_Controls->m_VarianceBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Variance); + m_Controls->m_FiberDensityBox->setValue(ffParamaters.m_FiberGenerationParameters.m_FiberDensity); + m_Controls->m_IncludeFiducials->setChecked(ffParamaters.m_FiberGenerationParameters.m_IncludeFiducials); + m_Controls->m_ConstantRadiusBox->setChecked(ffParamaters.m_FiberGenerationParameters.m_ConstantRadius); + m_Controls->m_FiberSamplingBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Sampling); + m_Controls->m_TensionBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Tension); + m_Controls->m_ContinuityBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Continuity); + m_Controls->m_BiasBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Bias); + m_Controls->m_XrotBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Rotation[0]); + m_Controls->m_YrotBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Rotation[1]); + m_Controls->m_ZrotBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Rotation[2]); + m_Controls->m_XtransBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Translation[0]); + m_Controls->m_YtransBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Translation[1]); + m_Controls->m_ZtransBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Translation[2]); + m_Controls->m_XscaleBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Scale[0]); + m_Controls->m_YscaleBox->setValue(ffParamaters.m_FiberGenerationParameters.m_Scale[1]); + m_Controls->m_ZscaleBox->setValue(ffParamaters.m_FiberGenerationParameters.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(ffParamaters.m_ImageRegion.GetSize(0)); + m_Controls->m_SizeY->setValue(ffParamaters.m_ImageRegion.GetSize(1)); + m_Controls->m_SizeZ->setValue(ffParamaters.m_ImageRegion.GetSize(2)); + m_Controls->m_SpacingX->setValue(ffParamaters.m_ImageSpacing[0]); + m_Controls->m_SpacingY->setValue(ffParamaters.m_ImageSpacing[1]); + m_Controls->m_SpacingZ->setValue(ffParamaters.m_ImageSpacing[2]); + m_Controls->m_NumGradientsBox->setValue(ffParamaters.GetNumWeightedVolumes()); + m_Controls->m_BvalueBox->setValue(ffParamaters.m_Bvalue); + m_Controls->m_AdvancedOptionsBox_2->setChecked(ffParamaters.m_AdvancedOptions); + m_Controls->m_SignalScaleBox->setValue(ffParamaters.m_SignalScale); + m_Controls->m_TEbox->setValue(ffParamaters.m_tEcho); + m_Controls->m_LineReadoutTimeBox->setValue(ffParamaters.m_tLine); + m_Controls->m_T2starBox->setValue(ffParamaters.m_tInhom); + m_Controls->m_FiberRadius->setValue(ffParamaters.m_AxonRadius); + m_Controls->m_RelaxationBox->setChecked(ffParamaters.m_DoSimulateRelaxation); + m_Controls->m_EnforcePureFiberVoxelsBox->setChecked(ffParamaters.m_DoDisablePartialVolume); + m_Controls->m_VolumeFractionsBox->setChecked(ffParamaters.m_OutputVolumeFractions); + + if (ffParamaters.m_NoiseModel!=NULL) + { + m_Controls->m_AddNoise->setChecked(ffParamaters.m_DoAddNoise); + if (dynamic_cast*>(ffParamaters.m_NoiseModel)) + m_Controls->m_NoiseDistributionBox->setCurrentIndex(0); + else if (dynamic_cast*>(ffParamaters.m_NoiseModel)) + m_Controls->m_NoiseDistributionBox->setCurrentIndex(1); + m_Controls->m_NoiseLevel->setValue(ffParamaters.m_NoiseModel->GetNoiseVariance()); + } + else + m_Controls->m_AddNoise->setChecked(false); + + m_Controls->m_AddGhosts->setChecked(ffParamaters.m_DoAddGhosts); + m_Controls->m_kOffsetBox->setValue(ffParamaters.m_KspaceLineOffset); + m_Controls->m_AddAliasing->setChecked(ffParamaters.m_DoAddAliasing); + m_Controls->m_WrapBox->setValue(100*(1-ffParamaters.m_CroppingFactor)); + m_Controls->m_AddDistortions->setChecked(ffParamaters.m_DoAddDistortions); + m_Controls->m_AddSpikes->setChecked(ffParamaters.m_DoAddSpikes); + m_Controls->m_SpikeNumBox->setValue(ffParamaters.m_Spikes); + m_Controls->m_SpikeScaleBox->setValue(ffParamaters.m_SpikeAmplitude); + m_Controls->m_AddEddy->setChecked(ffParamaters.m_DoAddEddyCurrents); + m_Controls->m_EddyGradientStrength->setValue(ffParamaters.m_EddyStrength); + m_Controls->m_AddGibbsRinging->setChecked(ffParamaters.m_DoAddGibbsRinging); + m_Controls->m_AddMotion->setChecked(ffParamaters.m_DoAddMotion); + m_Controls->m_RandomMotion->setChecked(ffParamaters.m_DoRandomizeMotion); + m_Controls->m_MaxTranslationBoxX->setValue(ffParamaters.m_Translation[0]); + m_Controls->m_MaxTranslationBoxY->setValue(ffParamaters.m_Translation[1]); + m_Controls->m_MaxTranslationBoxZ->setValue(ffParamaters.m_Translation[2]); + m_Controls->m_MaxRotationBoxX->setValue(ffParamaters.m_Rotation[0]); + m_Controls->m_MaxRotationBoxY->setValue(ffParamaters.m_Rotation[1]); + m_Controls->m_MaxRotationBoxZ->setValue(ffParamaters.m_Rotation[2]); + m_Controls->m_DiffusionDirectionBox->setCurrentIndex(ffParamaters.m_DiffusionDirectionMode); + m_Controls->m_SeparationAngleBox->setValue(ffParamaters.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; } - if( v1.first == "image" ) + case 2: { - 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::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; + } + case 4: + { + 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; 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); } 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->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) { 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; 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; 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) { ++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) { ++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/QmitkFiberfoxViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui index 28d2196f47..cf15c8a6b3 100755 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkFiberfoxViewControls.ui @@ -1,3110 +1,3083 @@ QmitkFiberfoxViewControls 0 0 443 - 2305 + 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 - - + + - Intra-axonal Compartment + Extra-axonal Compartments - - - - - - + + + + + QFrame::NoFrame + + + QFrame::Raised + + + + 0 + + + 0 + + + 0 + + + 0 + + + + + Volume Fraction: + + + + + + + + + + + + - - + + - Select signal model for intra-axonal compartment. + Select signal model for extra-axonal compartment. - Stick Model + Ball Model - Zeppelin Model + Astrosticks Model - Tensor Model + Dot Model PrototypeSignal - - + + - - + + + + + + + + + + + + + Qt::Horizontal + + + + + + + + + + + + + + + + Select signal model for extra-axonal compartment. + + + + -- + + + + + Ball Model + + + + + Astrosticks Model + + + + + Dot Model + + + + + Prototype Signal + + + + + + - - - - true - - - Stop current simulation. - - - Abort Simulation + + + + Qt::Vertical - - - :/QmitkDiffusionImaging/general_icons/abort.ico:/QmitkDiffusionImaging/general_icons/abort.ico + + + 20 + 40 + - + Image Settings Advanced Options QFrame::NoFrame QFrame::Raised 0 0 0 0 6 Gradient Directions: Number of gradient directions distributed over the half sphere. 0 10000 1 30 <html><head/><body><p>b-Value<span style=" font-style:italic;"> [s/mm</span><span style=" font-style:italic; vertical-align:super;">2</span><span style=" font-style:italic;">]</span>:</p></body></html> false b-value in s/mm² 0 10000 100 1000 color: rgb(255, 0, 0); Using geometry of selected image! color: rgb(255, 0, 0); Using gradients of selected DWI! QFrame::NoFrame QFrame::Raised 0 0 0 0 6 - - + + 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 + T2* relaxation time (in milliseconds). - 10000 + 100.000000000000000 - 1 + 0.100000000000000 - 50 + 1.000000000000000 - - + + - Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. + Output one image per compartment containing the corresponding volume fractions per voxel. - Disable Partial Volume Effects + Output Volume Fractions false - - - - T2* relaxation time (in milliseconds). - - - 100.000000000000000 - - - 0.100000000000000 - - - 1.000000000000000 - + + + + + Fiber tangent + + + + + Main fiber directions + + + + + Random + + - + - Output one image per compartment containing the corresponding volume fractions per voxel. + <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> - Output Volume Fractions + Simulate Signal Relaxation - false + true - - + + + + Fiber Radius: + + + + + - <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> + Line Readout Time: false - - + + - Line Readout Time: + <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: + + + + + - Fiber radius used to calculate volume fractions (in µm). Set to 0 for automatic radius estimation. + Relaxation time due to magnetic field inhomogeneities (T2', in milliseconds). - 0 + 1 - 1000 + 10000 + + + 1 - 0 + 50 - - - - Fiber Radius: + + + + 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: + + + + + - <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> + Disable partial volume. Treat voxel content as fiber-only if at least one fiber is present. - Simulate Signal Relaxation + Disable Partial Volume Effects - true + false - - - - TE in milliseconds - - + + + 1 - 10000 - - - 1 + 90.000000000000000 - 100 + 45.000000000000000 QFrame::NoFrame QFrame::Raised 0 0 0 0 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Spacing: 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 3 0.100000000000000 50.000000000000000 0.100000000000000 2.000000000000000 Image Dimensions: Fiber sampling factor which determines the accuracy of the calculated fiber and non-fiber volume fractions. 1 1000 1 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 - - - - - 8 - - - + + + 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 - ... - - - - 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 + + + + + 8 + - - - 20 - 40 - + + true - + - + Noise and other Artifacts Qt::Horizontal Add Noise false Add ringing artifacts occuring at strong edges in the image. Add Gibbs Ringing false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Shrink FOV (%): false Shrink FOV by this percentage. 1 0.000000000000000 90.000000000000000 0.100000000000000 25.000000000000000 Qt::Horizontal QFrame::NoFrame QFrame::Raised 0 0 0 0 Num. Spikes: The number of randomly occurring signal spikes. 1 Spike amplitude relative to the largest signal amplitude of the corresponding k-space slice. 0.100000000000000 0.100000000000000 Scale: !!!EXPERIMENTAL!!! Add Eddy Current Effects false Add Spikes false QFrame::NoFrame QFrame::Raised 0 0 0 0 Variance: Variance of selected noise distribution. 4 0.000000000000000 999999999.000000000000000 0.001000000000000 50.000000000000000 Distribution: Noise distribution Rician Chi-squared Add N/2 Ghosts false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 Frequency Map: false 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 Toggle between random movement and linear movement. Randomize motion true Rotation 0 9 0 0 Degree: false x false Axis: false Maximum rotation around x-axis. 1 360.000000000000000 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 Add Distortions false Add Aliasing false true QFrame::NoFrame QFrame::Raised 6 0 0 0 0 K-Space Line Offset: false A larger offset increases the inensity of the ghost image. 3 1.000000000000000 0.010000000000000 0.250000000000000 true QFrame::NoFrame QFrame::Raised QFormLayout::AllNonFixedFieldsGrow 6 0 0 0 0 Magnitude: false Maximum magnitude of eddy current induced magnetic field inhomogeneities (in mT). 5 1000.000000000000000 0.001000000000000 0.005000000000000 color: rgb(255, 0, 0); Experimental! 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 - - - QFrame::NoFrame - - - QFrame::Raised + + + Intra-axonal Compartment - - - 0 - - - 0 - - - 0 - - - 0 - - - 0 - - - + + + + + + + + + + + Select signal model for intra-axonal compartment. + - Fiber tangent + Stick Model - Main fiber directions + Zeppelin Model - Random + Tensor Model + + + + + PrototypeSignal - - - - - - Diffusion Direction: - - - - Separation Angle: - - + - - - - 1 - - - 90.000000000000000 - - - 45.000000000000000 - - + + 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