void FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections> ::BeforeThreadedGenerateData() { typename CoefficientImageType::Pointer ShCoeffImage = static_cast< CoefficientImageType* >( this->ProcessObject::GetInput(0) ); itk::Vector<double,3> spacing = ShCoeffImage->GetSpacing(); double minSpacing = spacing[0]; if (spacing[1]<minSpacing) minSpacing = spacing[1]; if (spacing[2]<minSpacing) minSpacing = spacing[2]; mitk::Point3D origin = ShCoeffImage->GetOrigin(); itk::Matrix<double, 3, 3> direction = ShCoeffImage->GetDirection(); ImageRegion<3> imageRegion = ShCoeffImage->GetLargestPossibleRegion(); if (m_MaskImage.IsNotNull()) { origin = m_MaskImage->GetOrigin(); direction = m_MaskImage->GetDirection(); imageRegion = m_MaskImage->GetLargestPossibleRegion(); } m_DirectionImageContainer = ItkDirectionImageContainer::New(); for (unsigned int i=0; i<m_MaxNumPeaks; i++) { itk::Vector< float, 3 > nullVec; nullVec.Fill(0.0); ItkDirectionImage::Pointer img = ItkDirectionImage::New(); img->SetSpacing( spacing ); img->SetOrigin( origin ); img->SetDirection( direction ); img->SetRegions( imageRegion ); img->Allocate(); img->FillBuffer(nullVec); m_DirectionImageContainer->InsertElement(m_DirectionImageContainer->Size(), img); } if (m_MaskImage.IsNull()) { 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); } 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); this->SetNumberOfIndexedOutputs(m_MaxNumPeaks); // calculate SH basis OdfType odf; vnl_matrix_fixed<double, 3, NrOdfDirections>* directions = odf.GetDirections(); vnl_matrix< double > sphCoords; std::vector< DirectionType > dirs; for (int i=0; i<NrOdfDirections; i++) dirs.push_back(directions->get_column(i)); Cart2Sph(dirs, sphCoords); // convert candidate peaks to spherical angles m_ShBasis = CalcShBasis(sphCoords); // evaluate spherical harmonics at each peak MITK_INFO << "Starting finite differences maximum extraction"; MITK_INFO << "ODF sampling points: " << NrOdfDirections; MITK_INFO << "SH order: " << ShOrder; MITK_INFO << "Maximum peaks: " << m_MaxNumPeaks; MITK_INFO << "Relative threshold: " << m_PeakThreshold; MITK_INFO << "Absolute threshold: " << m_AbsolutePeakThreshold; MITK_INFO << "Clustering threshold: " << m_ClusteringThreshold; MITK_INFO << "Angular threshold: " << m_AngularThreshold; }
void FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections> ::ThreadedGenerateData( const OutputImageRegionType& outputRegionForThread, ThreadIdType threadID ) { typename CoefficientImageType::Pointer ShCoeffImage = static_cast< CoefficientImageType* >( this->ProcessObject::GetInput(0) ); ImageRegionConstIterator< CoefficientImageType > cit(ShCoeffImage, outputRegionForThread ); OdfType odf; while( !cit.IsAtEnd() ) { typename CoefficientImageType::IndexType index = cit.GetIndex(); if (m_MaskImage->GetPixel(index)==0) { ++cit; continue; } CoefficientPixelType c = cit.Get(); // calculate ODF double max = 0; odf.Fill(0.0); for (int i=0; i<NrOdfDirections; i++) { for (int j=0; j<m_NumCoeffs; j++) odf[i] += c[j]*m_ShBasis(i,j); if (odf[i]>max) max = odf[i]; } if (max<0.0001) { ++cit; continue; } std::vector< DirectionType > candidates, peaks, temp; peaks.clear(); max *= m_PeakThreshold; // relative threshold FindCandidatePeaks(odf, max, candidates); // find all local maxima candidates = MeanShiftClustering(candidates); // cluster maxima vnl_matrix< double > shBasis, sphCoords; Cart2Sph(candidates, sphCoords); // convert candidate peaks to spherical angles shBasis = CalcShBasis(sphCoords); // evaluate spherical harmonics at each peak max = 0.0; for (unsigned int i=0; i<candidates.size(); i++) // scale peaks according to ODF value { double val = 0; for (int j=0; j<m_NumCoeffs; j++) val += c[j]*shBasis(i,j); if (val>max) max = val; peaks.push_back(candidates[i]*val); } std::sort( peaks.begin(), peaks.end(), CompareVectors ); // sort peaks // kick out directions to close to a larger direction (too far away to cluster but too close to keep) unsigned int m = peaks.size(); if ( m>m_DirectionImageContainer->Size() ) m = m_DirectionImageContainer->Size(); for (unsigned int i=0; i<m; i++) { DirectionType v1 = peaks.at(i); double val = v1.magnitude(); if (val<max*m_PeakThreshold || val<m_AbsolutePeakThreshold) break; bool flag = true; for (unsigned int j=0; j<peaks.size(); j++) if (i!=j) { DirectionType v2 = peaks.at(j); double val2 = v2.magnitude(); double angle = fabs(dot_product(v1,v2)/(val*val2)); if (angle>m_AngularThreshold && val<val2) { flag = false; break; } } if (flag) temp.push_back(v1); } peaks = temp; // fill output image unsigned int num = peaks.size(); if ( num>m_DirectionImageContainer->Size() ) num = m_DirectionImageContainer->Size(); for (unsigned int i=0; i<num; i++) { vnl_vector<double> dir = peaks.at(i); ItkDirectionImage::Pointer img = m_DirectionImageContainer->GetElement(i); switch (m_NormalizationMethod) { case NO_NORM: break; case SINGLE_VEC_NORM: dir.normalize(); break; case MAX_VEC_NORM: dir /= max; break; } dir = m_MaskImage->GetDirection()*dir; itk::Vector< float, 3 > pixel; pixel.SetElement(0, -dir[0]); pixel.SetElement(1, dir[1]); pixel.SetElement(2, dir[2]); img->SetPixel(index, pixel); } m_NumDirectionsImage->SetPixel(index, num); ++cit; } MITK_INFO << "Thread " << threadID << " finished extraction"; }
void FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections> ::BeforeThreadedGenerateData() { typename CoefficientImageType::Pointer ShCoeffImage = static_cast< CoefficientImageType* >( this->ProcessObject::GetInput(0) ); itk::Vector<double,3> spacing = ShCoeffImage->GetSpacing(); double minSpacing = spacing[0]; if (spacing[1]<minSpacing) minSpacing = spacing[1]; if (spacing[2]<minSpacing) minSpacing = spacing[2]; mitk::Point3D origin = ShCoeffImage->GetOrigin(); itk::Matrix<double, 3, 3> direction = ShCoeffImage->GetDirection(); ImageRegion<3> imageRegion = ShCoeffImage->GetLargestPossibleRegion(); if (m_MaskImage.IsNotNull()) { origin = m_MaskImage->GetOrigin(); direction = m_MaskImage->GetDirection(); imageRegion = m_MaskImage->GetLargestPossibleRegion(); } itk::Vector<double, 3> spacing3 = ShCoeffImage->GetSpacing(); itk::Point<float, 3> origin3 = ShCoeffImage->GetOrigin(); itk::Matrix<double, 3, 3> direction3 = ShCoeffImage->GetDirection(); itk::ImageRegion<3> imageRegion3 = ShCoeffImage->GetLargestPossibleRegion(); itk::Vector<double, 4> spacing4; itk::Point<float, 4> origin4; itk::Matrix<double, 4, 4> direction4; itk::ImageRegion<4> imageRegion4; spacing4[0] = spacing3[0]; spacing4[1] = spacing3[1]; spacing4[2] = spacing3[2]; spacing4[3] = 1; origin4[0] = origin3[0]; origin4[1] = origin3[1]; origin4[2] = origin3[2]; origin4[3] = 0; for (int r=0; r<3; r++) for (int c=0; c<3; c++) direction4[r][c] = direction3[r][c]; direction4[3][3] = 1; imageRegion4.SetSize(0, imageRegion3.GetSize()[0]); imageRegion4.SetSize(1, imageRegion3.GetSize()[1]); imageRegion4.SetSize(2, imageRegion3.GetSize()[2]); imageRegion4.SetSize(3, m_MaxNumPeaks*3); m_PeakImage = PeakImageType::New(); m_PeakImage->SetSpacing( spacing4 ); m_PeakImage->SetOrigin( origin4 ); m_PeakImage->SetDirection( direction4 ); m_PeakImage->SetRegions( imageRegion4 ); m_PeakImage->Allocate(); m_PeakImage->FillBuffer(0.0); if (m_MaskImage.IsNull()) { 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); } 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); // calculate SH basis OdfType odf; vnl_matrix< double > sphCoords; std::vector< DirectionType > dirs; for (int i=0; i<NrOdfDirections; i++) { DirectionType odf_dir; odf_dir[0] = odf.GetDirection(i)[0]; odf_dir[1] = odf.GetDirection(i)[1]; odf_dir[2] = odf.GetDirection(i)[2]; dirs.push_back(odf_dir); } Cart2Sph(dirs, sphCoords); // convert candidate peaks to spherical angles m_ShBasis = CalcShBasis(sphCoords); // evaluate spherical harmonics at each peak MITK_INFO << "Starting finite differences maximum extraction"; MITK_INFO << "ODF sampling points: " << NrOdfDirections; MITK_INFO << "SH order: " << ShOrder; MITK_INFO << "Maximum peaks: " << m_MaxNumPeaks; MITK_INFO << "Relative threshold: " << m_PeakThreshold; MITK_INFO << "Absolute threshold: " << m_AbsolutePeakThreshold; MITK_INFO << "Clustering threshold: " << m_ClusteringThreshold; MITK_INFO << "Angular threshold: " << m_AngularThreshold; }