diff --git a/CMakeExternals/MITKData.cmake b/CMakeExternals/MITKData.cmake index e764edaba2..52f4757489 100644 --- a/CMakeExternals/MITKData.cmake +++ b/CMakeExternals/MITKData.cmake @@ -1,36 +1,36 @@ #----------------------------------------------------------------------------- # MITK Data #----------------------------------------------------------------------------- # Sanity checks if(DEFINED MITK_DATA_DIR AND NOT EXISTS ${MITK_DATA_DIR}) message(FATAL_ERROR "MITK_DATA_DIR variable is defined but corresponds to non-existing directory") endif() set(proj MITK-Data) set(proj_DEPENDENCIES) set(MITK-Data_DEPENDS ${proj}) if(BUILD_TESTING) - set(revision_tag acedec01) + set(revision_tag 0b113ebe) # ^^^^^^^^ these are just to check correct length of hash part ExternalProject_Add(${proj} URL ${MITK_THIRDPARTY_DOWNLOAD_PREFIX_URL}/MITK-Data_${revision_tag}.tar.gz UPDATE_COMMAND "" CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND "" DEPENDS ${proj_DEPENDENCIES} ) set(MITK_DATA_DIR ${ep_source_dir}/${proj}) else() mitkMacroEmptyExternalProject(${proj} "${proj_DEPENDENCIES}") endif(BUILD_TESTING) diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp index 02a8ca2d37..261e98ffd5 100644 --- a/Modules/DiffusionImaging/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/Reconstruction/itkAnalyticalDiffusionQballReconstructionImageFilter.cpp @@ -1,818 +1,824 @@ /*=================================================================== 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 __itkAnalyticalDiffusionQballReconstructionImageFilter_cpp #define __itkAnalyticalDiffusionQballReconstructionImageFilter_cpp #include #include #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include #include #include "itkPointShell.h" using namespace boost::math; namespace itk { #define QBALL_ANAL_RECON_PI M_PI template< class T, class TG, class TO, int L, int NODF> AnalyticalDiffusionQballReconstructionImageFilter ::AnalyticalDiffusionQballReconstructionImageFilter() : m_GradientDirectionContainer(NULL), m_NumberOfGradientDirections(0), m_NumberOfBaselineImages(1), m_Threshold(NumericTraits< ReferencePixelType >::NonpositiveMin()), m_BValue(1.0), m_Lambda(0.0), m_DirectionsDuplicated(false), m_Delta1(0.001), m_Delta2(0.001), m_UseMrtrixBasis(false) { // At least 1 inputs is necessary for a vector image. // For images added one at a time we need at least six this->SetNumberOfRequiredInputs( 1 ); } template< class TReferenceImagePixelType, class TGradientImagePixelType, class TOdfPixelType, int NOrderL, int NrOdfDirections> typename itk::AnalyticalDiffusionQballReconstructionImageFilter< TReferenceImagePixelType,TGradientImagePixelType,TOdfPixelType, NOrderL,NrOdfDirections>::OdfPixelType itk::AnalyticalDiffusionQballReconstructionImageFilter ::Normalize( OdfPixelType odf, typename NumericTraits::AccumulateType b0 ) { switch( m_NormalizationMethod ) { case QBAR_STANDARD: { TOdfPixelType sum = 0; for(int i=0; i0) odf /= sum; return odf; break; } case QBAR_B_ZERO_B_VALUE: { for(int i=0; i vnl_vector itk::AnalyticalDiffusionQballReconstructionImageFilter ::PreNormalize( vnl_vector vec, typename NumericTraits::AccumulateType b0 ) { switch( m_NormalizationMethod ) { case QBAR_STANDARD: { + int n = vec.size(); + double b0f = (double)b0; + for(int i=0; i=1) vec[i] = 1-m_Delta2/2; else if (vec[i]>=1-m_Delta2) vec[i] = 1-m_Delta2/2-(1-vec[i])*(1-vec[i])/(2*m_Delta2); vec[i] = log(-log(vec[i])); } return vec; break; } } return vec; } template< class T, class TG, class TO, int L, int NODF> void AnalyticalDiffusionQballReconstructionImageFilter ::BeforeThreadedGenerateData() { // If we have more than 2 inputs, then each input, except the first is a // gradient image. The number of gradient images must match the number of // gradient directions. //const unsigned int numberOfInputs = this->GetNumberOfInputs(); // There need to be at least 6 gradient directions to be able to compute the // tensor basis if( m_NumberOfGradientDirections < (L*L + L + 2)/2 + L ) { itkExceptionMacro( << "Not enough gradient directions supplied (" << m_NumberOfGradientDirections << "). At least " << (L*L + L + 2)/2 + L << " needed for SH-order " << L); } // Input must be an itk::VectorImage. std::string gradientImageClassName( this->ProcessObject::GetInput(0)->GetNameOfClass()); if ( strcmp(gradientImageClassName.c_str(),"VectorImage") != 0 ) { itkExceptionMacro( << "There is only one Gradient image. I expect that to be a VectorImage. " << "But its of type: " << gradientImageClassName ); } this->ComputeReconstructionMatrix(); typename GradientImagesType::Pointer img = static_cast< GradientImagesType * >( this->ProcessObject::GetInput(0) ); m_BZeroImage = BZeroImageType::New(); m_BZeroImage->SetSpacing( img->GetSpacing() ); // Set the image spacing m_BZeroImage->SetOrigin( img->GetOrigin() ); // Set the image origin m_BZeroImage->SetDirection( img->GetDirection() ); // Set the image direction m_BZeroImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion()); m_BZeroImage->SetBufferedRegion( img->GetLargestPossibleRegion() ); m_BZeroImage->Allocate(); m_ODFSumImage = BZeroImageType::New(); m_ODFSumImage->SetSpacing( img->GetSpacing() ); // Set the image spacing m_ODFSumImage->SetOrigin( img->GetOrigin() ); // Set the image origin m_ODFSumImage->SetDirection( img->GetDirection() ); // Set the image direction m_ODFSumImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion()); m_ODFSumImage->SetBufferedRegion( img->GetLargestPossibleRegion() ); m_ODFSumImage->Allocate(); m_CoefficientImage = CoefficientImageType::New(); m_CoefficientImage->SetSpacing( img->GetSpacing() ); // Set the image spacing m_CoefficientImage->SetOrigin( img->GetOrigin() ); // Set the image origin m_CoefficientImage->SetDirection( img->GetDirection() ); // Set the image direction m_CoefficientImage->SetLargestPossibleRegion( img->GetLargestPossibleRegion()); m_CoefficientImage->SetBufferedRegion( img->GetLargestPossibleRegion() ); m_CoefficientImage->Allocate(); if(m_NormalizationMethod == QBAR_SOLID_ANGLE || m_NormalizationMethod == QBAR_NONNEG_SOLID_ANGLE) m_Lambda = 0.0; } template< class T, class TG, class TO, int L, int NODF> void AnalyticalDiffusionQballReconstructionImageFilter ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType ) { typename OutputImageType::Pointer outputImage = static_cast< OutputImageType * >(this->ProcessObject::GetPrimaryOutput()); ImageRegionIterator< OutputImageType > oit(outputImage, outputRegionForThread); oit.GoToBegin(); ImageRegionIterator< BZeroImageType > oit2(m_BZeroImage, outputRegionForThread); oit2.GoToBegin(); ImageRegionIterator< FloatImageType > oit3(m_ODFSumImage, outputRegionForThread); oit3.GoToBegin(); ImageRegionIterator< CoefficientImageType > oit4(m_CoefficientImage, outputRegionForThread); oit4.GoToBegin(); typedef ImageRegionConstIterator< GradientImagesType > GradientIteratorType; typedef typename GradientImagesType::PixelType GradientVectorType; typename GradientImagesType::Pointer gradientImagePointer = NULL; // Would have liked a dynamic_cast here, but seems SGI doesn't like it // The enum will ensure that an inappropriate cast is not done gradientImagePointer = static_cast< GradientImagesType * >( this->ProcessObject::GetInput(0) ); GradientIteratorType git(gradientImagePointer, outputRegionForThread ); git.GoToBegin(); // Compute the indicies of the baseline images and gradient images std::vector baselineind; // contains the indicies of // the baseline images std::vector gradientind; // contains the indicies of // the gradient images for(GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin(); gdcit != this->m_GradientDirectionContainer->End(); ++gdcit) { if(gdcit.Value().one_norm() <= 0.0) baselineind.push_back(gdcit.Index()); else gradientind.push_back(gdcit.Index()); } if( m_DirectionsDuplicated ) { int gradIndSize = gradientind.size(); for(int i=0; i::AccumulateType b0 = NumericTraits::Zero; // Average the baseline image pixels for(unsigned int i = 0; i < baselineind.size(); ++i) { b0 += b[baselineind[i]]; } b0 /= this->m_NumberOfBaselineImages; OdfPixelType odf(0.0); typename CoefficientImageType::PixelType coeffPixel(0.0); vnl_vector B(m_NumberOfGradientDirections); if( (b0 != 0) && (b0 >= m_Threshold) ) { for( unsigned int i = 0; i< m_NumberOfGradientDirections; i++ ) { B[i] = static_cast(b[gradientind[i]]); } B = PreNormalize(B, b0); if(m_NormalizationMethod == QBAR_SOLID_ANGLE) { vnl_vector coeffs(m_NumberCoefficients); coeffs = ( (*m_CoeffReconstructionMatrix) * B ); coeffs[0] += 1.0/(2.0*sqrt(QBALL_ANAL_RECON_PI)); odf = ( (*m_SphericalHarmonicBasisMatrix) * coeffs ).data_block(); coeffPixel = coeffs.data_block(); } else if(m_NormalizationMethod == QBAR_NONNEG_SOLID_ANGLE) { /** this would be the place to implement a non-negative * solver for quadratic programming problem: * min .5*|| Bc-s ||^2 subject to -CLPc <= 4*pi*ones * (refer to MICCAI 2009 Goh et al. "Estimating ODFs with PDF constraints") * .5*|| Bc-s ||^2 == .5*c'B'Bc - x'B's + .5*s's */ itkExceptionMacro( << "Nonnegative Solid Angle not yet implemented"); } else { vnl_vector coeffs(m_NumberCoefficients); coeffs = ( (*m_CoeffReconstructionMatrix) * B ); coeffs[0] += 1.0/(2.0*sqrt(QBALL_ANAL_RECON_PI)); coeffPixel = coeffs.data_block(); odf = ( (*m_ReconstructionMatrix) * B ).data_block(); } odf = Normalize(odf, b0); } oit.Set( odf ); oit2.Set( b0 ); float sum = 0; for (unsigned int k=0; k void AnalyticalDiffusionQballReconstructionImageFilter ::tofile2(vnl_matrix *pA, std::string fname) { vnl_matrix A = (*pA); std::ofstream myfile; std::locale C("C"); std::locale originalLocale = myfile.getloc(); myfile.imbue(C); myfile.open (fname.c_str()); myfile << "A1=["; for(unsigned int i=0; i void AnalyticalDiffusionQballReconstructionImageFilter ::Cart2Sph(double x, double y, double z, double *spherical) { double phi, theta, r; r = sqrt(x*x+y*y+z*z); if( r double AnalyticalDiffusionQballReconstructionImageFilter ::Yj(int m, int l, double theta, double phi, bool useMRtrixBasis) { if (!useMRtrixBasis) { if (m<0) return sqrt(2.0)*spherical_harmonic_r(l, -m, theta, phi); else if (m==0) return spherical_harmonic_r(l, m, theta, phi); else return pow(-1.0,m)*sqrt(2.0)*spherical_harmonic_i(l, m, theta, phi); } else { double plm = legendre_p(l,abs(m),-cos(theta)); double mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial(l-abs(m))/factorial(l+abs(m)))*plm; if (m>0) return mag*cos(m*phi); else if (m==0) return mag; else return mag*sin(-m*phi); } return 0; } template< class T, class TG, class TO, int L, int NODF> double AnalyticalDiffusionQballReconstructionImageFilter ::Legendre0(int l) { if( l%2 != 0 ) { return 0; } else { double prod1 = 1.0; for(int i=1;i void AnalyticalDiffusionQballReconstructionImageFilter ::ComputeReconstructionMatrix() { //for(int i=-6;i<7;i++) // std::cout << boost::math::legendre_p(6, i, 0.65657) << std::endl; if( m_NumberOfGradientDirections < (L*L + L + 2)/2 + L ) { itkExceptionMacro( << "Not enough gradient directions supplied (" << m_NumberOfGradientDirections << "). At least " << (L*L + L + 2)/2 + L << " needed for SH-order " << L); } { // check for duplicate diffusion gradients bool warning = false; for(GradientDirectionContainerType::ConstIterator gdcit1 = this->m_GradientDirectionContainer->Begin(); gdcit1 != this->m_GradientDirectionContainer->End(); ++gdcit1) { for(GradientDirectionContainerType::ConstIterator gdcit2 = this->m_GradientDirectionContainer->Begin(); gdcit2 != this->m_GradientDirectionContainer->End(); ++gdcit2) { if(gdcit1.Value() == gdcit2.Value() && gdcit1.Index() != gdcit2.Index()) { itkWarningMacro( << "Some of the Diffusion Gradients equal each other. Corresponding image data should be averaged before calling this filter." ); warning = true; break; } } if (warning) break; } // handle acquisition schemes where only half of the spherical // shell is sampled by the gradient directions. In this case, // each gradient direction is duplicated in negative direction. vnl_vector centerMass(3); centerMass.fill(0.0); int count = 0; for(GradientDirectionContainerType::ConstIterator gdcit1 = this->m_GradientDirectionContainer->Begin(); gdcit1 != this->m_GradientDirectionContainer->End(); ++gdcit1) { if(gdcit1.Value().one_norm() > 0.0) { centerMass += gdcit1.Value(); count ++; } } centerMass /= count; if(centerMass.two_norm() > 0.1) { m_DirectionsDuplicated = true; m_NumberOfGradientDirections *= 2; } } vnl_matrix *Q = new vnl_matrix(3, m_NumberOfGradientDirections); { int i = 0; for(GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin(); gdcit != this->m_GradientDirectionContainer->End(); ++gdcit) { if(gdcit.Value().one_norm() > 0.0) { double x = gdcit.Value().get(0); double y = gdcit.Value().get(1); double z = gdcit.Value().get(2); double cart[3]; Cart2Sph(x,y,z,cart); (*Q)(0,i) = cart[0]; (*Q)(1,i) = cart[1]; (*Q)(2,i++) = cart[2]; } } if(m_DirectionsDuplicated) { for(GradientDirectionContainerType::ConstIterator gdcit = this->m_GradientDirectionContainer->Begin(); gdcit != this->m_GradientDirectionContainer->End(); ++gdcit) { if(gdcit.Value().one_norm() > 0.0) { double x = gdcit.Value().get(0); double y = gdcit.Value().get(1); double z = gdcit.Value().get(2); double cart[3]; Cart2Sph(x,y,z,cart); (*Q)(0,i) = cart[0]; (*Q)(1,i) = cart[1]; (*Q)(2,i++) = cart[2]; } } } } int l = L; m_NumberCoefficients = (int)(l*l + l + 2.0)/2.0 + l; vnl_matrix* B = new vnl_matrix(m_NumberOfGradientDirections,m_NumberCoefficients); vnl_matrix* _L = new vnl_matrix(m_NumberCoefficients,m_NumberCoefficients); _L->fill(0.0); vnl_matrix* LL = new vnl_matrix(m_NumberCoefficients,m_NumberCoefficients); LL->fill(0.0); vnl_matrix* P = new vnl_matrix(m_NumberCoefficients,m_NumberCoefficients); P->fill(0.0); vnl_matrix* Inv = new vnl_matrix(m_NumberCoefficients,m_NumberCoefficients); P->fill(0.0); vnl_vector* lj = new vnl_vector(m_NumberCoefficients); m_LP = new vnl_vector(m_NumberCoefficients); for(unsigned int i=0; i temp((*_L)*(*_L)); LL->update(*_L); *LL *= *_L; //tofile2(LL,"LL"); for(int i=0; i(B->transpose()); //tofile2(&m_B_t,"m_B_t"); vnl_matrix B_t_B = (*m_B_t) * (*B); //tofile2(&B_t_B,"B_t_B"); vnl_matrix lambdaLL(m_NumberCoefficients,m_NumberCoefficients); lambdaLL.update((*LL)); lambdaLL *= m_Lambda; //tofile2(&lambdaLL,"lLL"); vnl_matrix tmp( B_t_B + lambdaLL); vnl_matrix_inverse *pseudoInverse = new vnl_matrix_inverse( tmp ); (*Inv) = pseudoInverse->pinverse(); //tofile2(Inv,"Inv"); vnl_matrix temp((*Inv) * (*m_B_t)); double fac1 = (1.0/(16.0*QBALL_ANAL_RECON_PI*QBALL_ANAL_RECON_PI)); switch(m_NormalizationMethod) { case QBAR_ADC_ONLY: case QBAR_RAW_SIGNAL: break; case QBAR_STANDARD: case QBAR_B_ZERO_B_VALUE: case QBAR_B_ZERO: case QBAR_NONE: temp = (*P) * temp; break; case QBAR_SOLID_ANGLE: temp = fac1 * (*P) * (*_L) * temp; break; case QBAR_NONNEG_SOLID_ANGLE: break; } //tofile2(&temp,"A"); m_CoeffReconstructionMatrix = new vnl_matrix(m_NumberCoefficients,m_NumberOfGradientDirections); for(int i=0; iodfs later int NOdfDirections = NODF; vnl_matrix_fixed* U = itk::PointShell >::DistributePointShell(); m_SphericalHarmonicBasisMatrix = new vnl_matrix(NOdfDirections,m_NumberCoefficients); vnl_matrix* sphericalHarmonicBasisMatrix2 = new vnl_matrix(NOdfDirections,m_NumberCoefficients); for(int i=0; i(NOdfDirections,m_NumberOfGradientDirections); *m_ReconstructionMatrix = (*m_SphericalHarmonicBasisMatrix) * (*m_CoeffReconstructionMatrix); } template< class T, class TG, class TO, int L, int NODF> void AnalyticalDiffusionQballReconstructionImageFilter ::SetGradientImage(const GradientDirectionContainerType *gradientDirection, const GradientImagesType *gradientImage ) { // Copy Gradient Direction Container this->m_GradientDirectionContainer = GradientDirectionContainerType::New(); for(GradientDirectionContainerType::ConstIterator it = gradientDirection->Begin(); it != gradientDirection->End(); it++) { this->m_GradientDirectionContainer->push_back(it.Value()); } unsigned int numImages = gradientDirection->Size(); this->m_NumberOfBaselineImages = 0; for(GradientDirectionContainerType::Iterator it = this->m_GradientDirectionContainer->Begin(); it != this->m_GradientDirectionContainer->End(); it++) { if(it.Value().one_norm() <= 0.0) { this->m_NumberOfBaselineImages++; } else // Normalize non-zero gradient directions { it.Value() = it.Value() / it.Value().two_norm(); } } this->m_NumberOfGradientDirections = numImages - this->m_NumberOfBaselineImages; // ensure that the gradient image we received has as many components as // the number of gradient directions if( gradientImage->GetVectorLength() != this->m_NumberOfBaselineImages + m_NumberOfGradientDirections ) { itkExceptionMacro( << m_NumberOfGradientDirections << " gradients + " << this->m_NumberOfBaselineImages << "baselines = " << m_NumberOfGradientDirections + this->m_NumberOfBaselineImages << " directions specified but image has " << gradientImage->GetVectorLength() << " components."); } this->ProcessObject::SetNthInput( 0, const_cast< GradientImagesType* >(gradientImage) ); } template< class T, class TG, class TO, int L, int NODF> void AnalyticalDiffusionQballReconstructionImageFilter ::PrintSelf(std::ostream& os, Indent indent) const { std::locale C("C"); std::locale originalLocale = os.getloc(); os.imbue(C); Superclass::PrintSelf(os,indent); os << indent << "OdfReconstructionMatrix: " << m_ReconstructionMatrix << std::endl; if ( m_GradientDirectionContainer ) os << indent << "GradientDirectionContainer: " << m_GradientDirectionContainer << std::endl; else os << indent << "GradientDirectionContainer: (Gradient directions not set)" << std::endl; os << indent << "NumberOfGradientDirections: " << m_NumberOfGradientDirections << std::endl; os << indent << "NumberOfBaselineImages: " << m_NumberOfBaselineImages << std::endl; os << indent << "Threshold for reference B0 image: " << m_Threshold << std::endl; os << indent << "BValue: " << m_BValue << std::endl; os.imbue( originalLocale ); } } #endif // __itkAnalyticalDiffusionQballReconstructionImageFilter_cpp diff --git a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkFiniteDiffOdfMaximaExtractionFilter.cpp b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkFiniteDiffOdfMaximaExtractionFilter.cpp index 4136c35c9b..5d6d751d14 100644 --- a/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkFiniteDiffOdfMaximaExtractionFilter.cpp +++ b/Modules/DiffusionImaging/DiffusionCore/Algorithms/itkFiniteDiffOdfMaximaExtractionFilter.cpp @@ -1,522 +1,520 @@ /*=================================================================== 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 __itkFiniteDiffOdfMaximaExtractionFilter_cpp #define __itkFiniteDiffOdfMaximaExtractionFilter_cpp #include "itkFiniteDiffOdfMaximaExtractionFilter.h" #include #include #include #include #include #include #include #include #include #include #include #include #include using namespace boost::math; namespace itk { static bool CompareVectors(const vnl_vector_fixed< double, 3 >& v1, const vnl_vector_fixed< double, 3 >& v2) { return (v1.magnitude()>v2.magnitude()); } template< class PixelType, int ShOrder, int NrOdfDirections > FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections> ::FiniteDiffOdfMaximaExtractionFilter() : m_NormalizationMethod(MAX_VEC_NORM) , m_MaxNumPeaks(2) , m_PeakThreshold(0.4) , m_AbsolutePeakThreshold(0) , m_ClusteringThreshold(0.9) , m_AngularThreshold(0.7) , m_NumCoeffs((ShOrder*ShOrder + ShOrder + 2)/2 + ShOrder) , m_Toolkit(FSL) { this->SetNumberOfRequiredInputs(1); } template< class PixelType, int ShOrder, int NrOdfDirections > void FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections> ::FindCandidatePeaks(OdfType& odf, double thr, std::vector< DirectionType >& container) { double gfa = odf.GetGeneralizedFractionalAnisotropy(); //Find the peaks using a finite difference method bool flag = true; vnl_vector_fixed< bool, NrOdfDirections > used; used.fill(false); //Find the peaks for (int i=0; ithr && val*gfa>m_AbsolutePeakThreshold) // limit to one hemisphere ??? { flag = true; std::vector< int > neighbours = odf.GetNeighbors(i); for (unsigned int j=0; j std::vector< vnl_vector_fixed< double, 3 > > FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections>::MeanShiftClustering(std::vector< vnl_vector_fixed< double, 3 > >& inDirs) { std::vector< DirectionType > outDirs; if (inDirs.empty()) return inDirs; DirectionType oldMean, currentMean, workingMean; std::vector< int > touched; // initialize touched.resize(inDirs.size(), 0); bool free = true; currentMean = inDirs[0]; // initialize first seed while (free) { oldMean.fill(0.0); // start mean-shift clustering float angle = 0.0; int counter = 0; while ((currentMean-oldMean).magnitude()>0.0001) { counter = 0; oldMean = currentMean; workingMean = oldMean; workingMean.normalize(); currentMean.fill(0.0); for (unsigned int i=0; i=m_ClusteringThreshold) { currentMean += inDirs[i]; touched[i] = 1; counter++; } else if (-angle>=m_ClusteringThreshold) { currentMean -= inDirs[i]; touched[i] = 1; counter++; } } } // found stable mean if (counter>0) { float mag = currentMean.magnitude(); if (mag>0) { currentMean /= mag; outDirs.push_back(currentMean); } } // find next unused seed free = false; for (unsigned int i=0; i void FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections> ::BeforeThreadedGenerateData() { typename CoefficientImageType::Pointer ShCoeffImage = static_cast< CoefficientImageType* >( this->ProcessObject::GetInput(0) ); itk::Vector spacing = ShCoeffImage->GetSpacing(); double minSpacing = spacing[0]; if (spacing[1]GetOrigin(); itk::Matrix 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 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* directions = odf.GetDirections(); vnl_matrix< double > sphCoords; std::vector< DirectionType > dirs; for (int i=0; iget_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; } template< class PixelType, int ShOrder, int NrOdfDirections > void FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections> ::AfterThreadedGenerateData() { MITK_INFO << "Generating vector field"; vtkSmartPointer m_VtkCellArray = vtkSmartPointer::New(); vtkSmartPointer m_VtkPoints = vtkSmartPointer::New(); typename CoefficientImageType::Pointer ShCoeffImage = static_cast< CoefficientImageType* >( this->ProcessObject::GetInput(0) ); ImageRegionConstIterator< CoefficientImageType > cit(ShCoeffImage, ShCoeffImage->GetLargestPossibleRegion() ); mitk::Vector3D spacing = ShCoeffImage->GetSpacing(); double minSpacing = spacing[0]; if (spacing[1]GetLargestPossibleRegion().GetSize()[0]*ShCoeffImage->GetLargestPossibleRegion().GetSize()[1]*ShCoeffImage->GetLargestPossibleRegion().GetSize()[2]; boost::progress_display disp(maxProgress); while( !cit.IsAtEnd() ) { ++disp; typename CoefficientImageType::IndexType index = cit.GetIndex(); if (m_MaskImage->GetPixel(index)==0) { ++cit; continue; } for (unsigned int i=0; iSize(); i++) { ItkDirectionImage::Pointer img = m_DirectionImageContainer->GetElement(i); itk::Vector< float, 3 > pixel = img->GetPixel(index); DirectionType dir; dir[0] = pixel[0]; dir[1] = pixel[1]; dir[2] = pixel[2]; vtkSmartPointer 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 ); 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); } ++cit; } vtkSmartPointer directionsPolyData = vtkSmartPointer::New(); directionsPolyData->SetPoints(m_VtkPoints); directionsPolyData->SetLines(m_VtkCellArray); m_OutputFiberBundle = mitk::FiberBundleX::New(directionsPolyData); for (unsigned int i=0; iSize(); i++) { ItkDirectionImage::Pointer img = m_DirectionImageContainer->GetElement(i); this->SetNthOutput(i, img); } } template< class PixelType, int ShOrder, int NrOdfDirections > 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; imax) 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; imax) 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; im_AngularThreshold && valm_DirectionImageContainer->Size() ) num = m_DirectionImageContainer->Size(); for (unsigned int i=0; i 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[0] = -dir[0]; -// dir[2] = -dir[2]; dir = m_MaskImage->GetDirection()*dir; itk::Vector< float, 3 > pixel; - pixel.SetElement(0, dir[0]); + 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"; } // convert cartesian to spherical coordinates template< class PixelType, int ShOrder, int NrOdfDirections > void FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections> ::Cart2Sph(const std::vector< DirectionType >& dir, vnl_matrix& sphCoords) { sphCoords.set_size(dir.size(), 2); for (unsigned int i=0; i vnl_matrix FiniteDiffOdfMaximaExtractionFilter< PixelType, ShOrder, NrOdfDirections> ::CalcShBasis(vnl_matrix& sphCoords) { int M = sphCoords.rows(); int j, m; double mag, plm; vnl_matrix shBasis; shBasis.set_size(M, m_NumCoeffs); for (int p=0; p(l,abs(m),cos(sphCoords(p,0))); mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial(l-abs(m))/factorial(l+abs(m)))*plm; if (m<0) shBasis(p,j) = sqrt(2.0)*mag*cos(fabs((double)m)*sphCoords(p,1)); else if (m==0) shBasis(p,j) = mag; else shBasis(p,j) = pow(-1.0, m)*sqrt(2.0)*mag*sin(m*sphCoords(p,1)); break; case MRTRIX: plm = legendre_p(l,abs(m),-cos(sphCoords(p,0))); mag = sqrt((double)(2*l+1)/(4.0*M_PI)*factorial(l-abs(m))/factorial(l+abs(m)))*plm; if (m>0) shBasis(p,j) = mag*cos(m*sphCoords(p,1)); else if (m==0) shBasis(p,j) = mag; else shBasis(p,j) = mag*sin(-m*sphCoords(p,1)); break; } j++; } } return shBasis; } } #endif // __itkFiniteDiffOdfMaximaExtractionFilter_cpp diff --git a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp index 40cabf5687..7f88865ef9 100644 --- a/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/Algorithms/itkStreamlineTrackingFilter.cpp @@ -1,890 +1,890 @@ /*=================================================================== 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 __itkStreamlineTrackingFilter_txx #define __itkStreamlineTrackingFilter_txx #include #include #include #include "itkStreamlineTrackingFilter.h" #include #include #include #define _USE_MATH_DEFINES #include namespace itk { template< class TTensorPixelType, class TPDPixelType> StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::StreamlineTrackingFilter() : m_FiberPolyData(NULL) , m_Points(NULL) , m_Cells(NULL) , m_FaImage(NULL) , m_NumberOfInputs(1) , m_FaThreshold(0.2) , m_MinCurvatureRadius(0) , m_StepSize(0) , m_MaxLength(10000) , m_MinTractLength(0.0) , m_SeedsPerVoxel(1) , m_F(1.0) , m_G(0.0) , m_Interpolate(true) , m_PointPistance(0.0) , m_ResampleFibers(false) , m_SeedImage(NULL) , m_MaskImage(NULL) { // At least 1 inputs is necessary for a vector image. // For images added one at a time we need at least six this->SetNumberOfRequiredInputs( 1 ); this->SetNumberOfIndexedInputs(3); } template< class TTensorPixelType, class TPDPixelType> double StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::RoundToNearest(double num) { return (num > 0.0) ? floor(num + 0.5) : ceil(num - 0.5); } template< class TTensorPixelType, class TPDPixelType> void StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::BeforeThreadedGenerateData() { m_FiberPolyData = FiberPolyDataType::New(); m_Points = vtkSmartPointer< vtkPoints >::New(); m_Cells = vtkSmartPointer< vtkCellArray >::New(); InputImageType* inputImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(0) ); m_ImageSize.resize(3); m_ImageSize[0] = inputImage->GetLargestPossibleRegion().GetSize()[0]; m_ImageSize[1] = inputImage->GetLargestPossibleRegion().GetSize()[1]; m_ImageSize[2] = inputImage->GetLargestPossibleRegion().GetSize()[2]; if (m_ImageSize[0]<3 || m_ImageSize[1]<3 || m_ImageSize[2]<3) m_Interpolate = false; m_ImageSpacing.resize(3); m_ImageSpacing[0] = inputImage->GetSpacing()[0]; m_ImageSpacing[1] = inputImage->GetSpacing()[1]; m_ImageSpacing[2] = inputImage->GetSpacing()[2]; double minSpacing; if(m_ImageSpacing[0]::New(); for (unsigned int i=0; iGetNumberOfThreads(); i++) { FiberPolyDataType poly = FiberPolyDataType::New(); m_PolyDataContainer->InsertElement(i, poly); } if (m_SeedImage.IsNull()) { // initialize mask image m_SeedImage = ItkUcharImgType::New(); m_SeedImage->SetSpacing( inputImage->GetSpacing() ); m_SeedImage->SetOrigin( inputImage->GetOrigin() ); m_SeedImage->SetDirection( inputImage->GetDirection() ); m_SeedImage->SetRegions( inputImage->GetLargestPossibleRegion() ); m_SeedImage->Allocate(); m_SeedImage->FillBuffer(1); } if (m_MaskImage.IsNull()) { // initialize mask image m_MaskImage = ItkUcharImgType::New(); m_MaskImage->SetSpacing( inputImage->GetSpacing() ); m_MaskImage->SetOrigin( inputImage->GetOrigin() ); m_MaskImage->SetDirection( inputImage->GetDirection() ); m_MaskImage->SetRegions( inputImage->GetLargestPossibleRegion() ); m_MaskImage->Allocate(); m_MaskImage->FillBuffer(1); } bool useUserFaImage = true; if (m_FaImage.IsNull()) { m_FaImage = ItkFloatImgType::New(); m_FaImage->SetSpacing( inputImage->GetSpacing() ); m_FaImage->SetOrigin( inputImage->GetOrigin() ); m_FaImage->SetDirection( inputImage->GetDirection() ); m_FaImage->SetRegions( inputImage->GetLargestPossibleRegion() ); m_FaImage->Allocate(); m_FaImage->FillBuffer(0.0); useUserFaImage = false; } m_NumberOfInputs = 0; for (unsigned int i=0; iGetNumberOfIndexedInputs(); i++) { if (this->ProcessObject::GetInput(i)==NULL) break; ItkPDImgType::Pointer pdImage = ItkPDImgType::New(); pdImage->SetSpacing( inputImage->GetSpacing() ); pdImage->SetOrigin( inputImage->GetOrigin() ); pdImage->SetDirection( inputImage->GetDirection() ); pdImage->SetRegions( inputImage->GetLargestPossibleRegion() ); pdImage->Allocate(); m_PdImage.push_back(pdImage); ItkDoubleImgType::Pointer emaxImage = ItkDoubleImgType::New(); emaxImage->SetSpacing( inputImage->GetSpacing() ); emaxImage->SetOrigin( inputImage->GetOrigin() ); emaxImage->SetDirection( inputImage->GetDirection() ); emaxImage->SetRegions( inputImage->GetLargestPossibleRegion() ); emaxImage->Allocate(); emaxImage->FillBuffer(1.0); m_EmaxImage.push_back(emaxImage); typename InputImageType::Pointer inputImage = static_cast< InputImageType * >( this->ProcessObject::GetInput(i) ); m_InputImage.push_back(inputImage); m_NumberOfInputs++; } MITK_INFO << "Processing " << m_NumberOfInputs << " tensor files"; typedef itk::DiffusionTensor3D TensorType; typename TensorType::EigenValuesArrayType eigenvalues; typename TensorType::EigenVectorsMatrixType eigenvectors; for (int x=0; xGetPixel(index); vnl_vector_fixed dir; tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors); dir[0] = eigenvectors(2, 0); dir[1] = eigenvectors(2, 1); dir[2] = eigenvectors(2, 2); dir.normalize(); m_PdImage.at(i)->SetPixel(index, dir); if (!useUserFaImage) m_FaImage->SetPixel(index, m_FaImage->GetPixel(index)+tensor.GetFractionalAnisotropy()); m_EmaxImage.at(i)->SetPixel(index, 2/eigenvalues[2]); } if (!useUserFaImage) m_FaImage->SetPixel(index, m_FaImage->GetPixel(index)/m_NumberOfInputs); } if (m_Interpolate) std::cout << "StreamlineTrackingFilter: using trilinear interpolation" << std::endl; else { if (m_MinCurvatureRadius<0.0) m_MinCurvatureRadius = 0.1*minSpacing; std::cout << "StreamlineTrackingFilter: using nearest neighbor interpolation" << std::endl; } if (m_MinCurvatureRadius<0.0) m_MinCurvatureRadius = 0.5*minSpacing; std::cout << "StreamlineTrackingFilter: Min. curvature radius: " << m_MinCurvatureRadius << std::endl; std::cout << "StreamlineTrackingFilter: FA threshold: " << m_FaThreshold << std::endl; std::cout << "StreamlineTrackingFilter: stepsize: " << m_StepSize << " mm" << std::endl; std::cout << "StreamlineTrackingFilter: f: " << m_F << std::endl; std::cout << "StreamlineTrackingFilter: g: " << m_G << std::endl; std::cout << "StreamlineTrackingFilter: starting streamline tracking using " << this->GetNumberOfThreads() << " threads." << std::endl; } template< class TTensorPixelType, class TPDPixelType> void StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::CalculateNewPosition(itk::ContinuousIndex& pos, vnl_vector_fixed& dir, typename InputImageType::IndexType& index) { vnl_matrix_fixed< double, 3, 3 > rot = m_InputImage.at(0)->GetDirection().GetTranspose(); dir = rot*dir; if (true) { dir *= m_StepSize; pos[0] += dir[0]/m_ImageSpacing[0]; pos[1] += dir[1]/m_ImageSpacing[1]; pos[2] += dir[2]/m_ImageSpacing[2]; index[0] = RoundToNearest(pos[0]); index[1] = RoundToNearest(pos[1]); index[2] = RoundToNearest(pos[2]); } else { dir[0] /= m_ImageSpacing[0]; dir[1] /= m_ImageSpacing[1]; dir[2] /= m_ImageSpacing[2]; int smallest = 0; double x = 100000; if (dir[0]>0) { if (fabs(fabs(RoundToNearest(pos[0])-pos[0])-0.5)>mitk::eps) x = fabs(pos[0]-RoundToNearest(pos[0])-0.5)/dir[0]; else x = fabs(pos[0]-std::ceil(pos[0])-0.5)/dir[0]; } else if (dir[0]<0) { if (fabs(fabs(RoundToNearest(pos[0])-pos[0])-0.5)>mitk::eps) x = -fabs(pos[0]-RoundToNearest(pos[0])+0.5)/dir[0]; else x = -fabs(pos[0]-std::floor(pos[0])+0.5)/dir[0]; } double s = x; double y = 100000; if (dir[1]>0) { if (fabs(fabs(RoundToNearest(pos[1])-pos[1])-0.5)>mitk::eps) y = fabs(pos[1]-RoundToNearest(pos[1])-0.5)/dir[1]; else y = fabs(pos[1]-std::ceil(pos[1])-0.5)/dir[1]; } else if (dir[1]<0) { if (fabs(fabs(RoundToNearest(pos[1])-pos[1])-0.5)>mitk::eps) y = -fabs(pos[1]-RoundToNearest(pos[1])+0.5)/dir[1]; else y = -fabs(pos[1]-std::floor(pos[1])+0.5)/dir[1]; } if (s>y) { s=y; smallest = 1; } double z = 100000; if (dir[2]>0) { if (fabs(fabs(RoundToNearest(pos[2])-pos[2])-0.5)>mitk::eps) z = fabs(pos[2]-RoundToNearest(pos[2])-0.5)/dir[2]; else z = fabs(pos[2]-std::ceil(pos[2])-0.5)/dir[2]; } else if (dir[2]<0) { if (fabs(fabs(RoundToNearest(pos[2])-pos[2])-0.5)>mitk::eps) z = -fabs(pos[2]-RoundToNearest(pos[2])+0.5)/dir[2]; else z = -fabs(pos[2]-std::floor(pos[2])+0.5)/dir[2]; } if (s>z) { s=z; smallest = 2; } // MITK_INFO << "---------------------------------------------"; // MITK_INFO << "s: " << s; // MITK_INFO << "dir: " << dir; // MITK_INFO << "old: " << pos[0] << ", " << pos[1] << ", " << pos[2]; pos[0] += dir[0]*s; pos[1] += dir[1]*s; pos[2] += dir[2]*s; switch (smallest) { case 0: if (dir[0]<0) index[0] = std::floor(pos[0]); else index[0] = std::ceil(pos[0]); index[1] = RoundToNearest(pos[1]); index[2] = RoundToNearest(pos[2]); break; case 1: if (dir[1]<0) index[1] = std::floor(pos[1]); else index[1] = std::ceil(pos[1]); index[0] = RoundToNearest(pos[0]); index[2] = RoundToNearest(pos[2]); break; case 2: if (dir[2]<0) index[2] = std::floor(pos[2]); else index[2] = std::ceil(pos[2]); index[1] = RoundToNearest(pos[1]); index[0] = RoundToNearest(pos[0]); } // double x = 100000; // if (dir[0]>0) // x = fabs(pos[0]-RoundToNearest(pos[0])-0.5)/dir[0]; // else if (dir[0]<0) // x = -fabs(pos[0]-RoundToNearest(pos[0])+0.5)/dir[0]; // double s = x; // double y = 100000; // if (dir[1]>0) // y = fabs(pos[1]-RoundToNearest(pos[1])-0.5)/dir[1]; // else if (dir[1]<0) // y = -fabs(pos[1]-RoundToNearest(pos[1])+0.5)/dir[1]; // if (s>y) // s=y; // double z = 100000; // if (dir[2]>0) // z = fabs(pos[2]-RoundToNearest(pos[2])-0.5)/dir[2]; // else if (dir[2]<0) // z = -fabs(pos[2]-RoundToNearest(pos[2])+0.5)/dir[2]; // if (s>z) // s=z; // s *= 1.001; // pos[0] += dir[0]*s; // pos[1] += dir[1]*s; // pos[2] += dir[2]*s; // index[0] = RoundToNearest(pos[0]); // index[1] = RoundToNearest(pos[1]); // index[2] = RoundToNearest(pos[2]); // MITK_INFO << "new: " << pos[0] << ", " << pos[1] << ", " << pos[2]; } } template< class TTensorPixelType, class TPDPixelType> bool StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::IsValidPosition(itk::ContinuousIndex& pos, typename InputImageType::IndexType &index, vnl_vector_fixed< double, 8 >& interpWeights, int imageIdx) { if (!m_InputImage.at(imageIdx)->GetLargestPossibleRegion().IsInside(index) || m_MaskImage->GetPixel(index)==0) return false; if (m_Interpolate) { double frac_x = pos[0] - index[0]; double frac_y = pos[1] - index[1]; double frac_z = pos[2] - index[2]; if (frac_x<0) { index[0] -= 1; frac_x += 1; } if (frac_y<0) { index[1] -= 1; frac_y += 1; } if (frac_z<0) { index[2] -= 1; frac_z += 1; } frac_x = 1-frac_x; frac_y = 1-frac_y; frac_z = 1-frac_z; // int coordinates inside image? if (index[0] < 0 || index[0] >= m_ImageSize[0]-1) return false; if (index[1] < 0 || index[1] >= m_ImageSize[1]-1) return false; if (index[2] < 0 || index[2] >= m_ImageSize[2]-1) return false; interpWeights[0] = ( frac_x)*( frac_y)*( frac_z); interpWeights[1] = (1-frac_x)*( frac_y)*( frac_z); interpWeights[2] = ( frac_x)*(1-frac_y)*( frac_z); interpWeights[3] = ( frac_x)*( frac_y)*(1-frac_z); interpWeights[4] = (1-frac_x)*(1-frac_y)*( frac_z); interpWeights[5] = ( frac_x)*(1-frac_y)*(1-frac_z); interpWeights[6] = (1-frac_x)*( frac_y)*(1-frac_z); interpWeights[7] = (1-frac_x)*(1-frac_y)*(1-frac_z); typename InputImageType::IndexType tmpIdx; double FA = m_FaImage->GetPixel(index) * interpWeights[0]; tmpIdx = index; tmpIdx[0]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[1]; tmpIdx = index; tmpIdx[1]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[2]; tmpIdx = index; tmpIdx[2]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[3]; tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[4]; tmpIdx = index; tmpIdx[1]++; tmpIdx[2]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[5]; tmpIdx = index; tmpIdx[2]++; tmpIdx[0]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[6]; tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++; FA += m_FaImage->GetPixel(tmpIdx) * interpWeights[7]; if (FAGetPixel(index) double StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::FollowStreamline(itk::ContinuousIndex pos, int dirSign, vtkPoints* points, std::vector< vtkIdType >& ids, int imageIdx) { double tractLength = 0; typedef itk::DiffusionTensor3D TensorType; typename TensorType::EigenValuesArrayType eigenvalues; typename TensorType::EigenVectorsMatrixType eigenvectors; vnl_vector_fixed< double, 8 > interpWeights; typename InputImageType::IndexType index, indexOld; indexOld[0] = -1; indexOld[1] = -1; indexOld[2] = -1; itk::Point worldPos; double distance = 0; double distanceInVoxel = 0; // starting index and direction index[0] = RoundToNearest(pos[0]); index[1] = RoundToNearest(pos[1]); index[2] = RoundToNearest(pos[2]); vnl_vector_fixed dir = m_PdImage.at(imageIdx)->GetPixel(index); dir *= dirSign; // reverse direction vnl_vector_fixed dirOld = dir; if (dir.magnitude()TransformContinuousIndexToPhysicalPoint( pos, worldPos ); - ids.push_back(points->InsertNextPoint(worldPos.GetDataPointer())); +// m_SeedImage->TransformContinuousIndexToPhysicalPoint( pos, worldPos ); +// ids.push_back(points->InsertNextPoint(worldPos.GetDataPointer())); return tractLength; } else if (distance>=m_PointPistance) { + tractLength += m_StepSize; + distanceInVoxel += m_StepSize; m_SeedImage->TransformContinuousIndexToPhysicalPoint( pos, worldPos ); ids.push_back(points->InsertNextPoint(worldPos.GetDataPointer())); distance = 0; } if (!m_Interpolate) // use nearest neighbour interpolation { if (indexOld!=index) // did we enter a new voxel? if yes, calculate new direction { double minAngle = 0; for (int img=0; img newDir = m_PdImage.at(img)->GetPixel(index); // get principal direction if (newDir.magnitude()GetPixel(index); double scale = m_EmaxImage.at(img)->GetPixel(index); newDir[0] = m_F*newDir[0] + (1-m_F)*( (1-m_G)*dirOld[0] + scale*m_G*(tensor[0]*dirOld[0] + tensor[1]*dirOld[1] + tensor[2]*dirOld[2])); newDir[1] = m_F*newDir[1] + (1-m_F)*( (1-m_G)*dirOld[1] + scale*m_G*(tensor[1]*dirOld[0] + tensor[3]*dirOld[1] + tensor[4]*dirOld[2])); newDir[2] = m_F*newDir[2] + (1-m_F)*( (1-m_G)*dirOld[2] + scale*m_G*(tensor[2]*dirOld[0] + tensor[4]*dirOld[1] + tensor[5]*dirOld[2])); newDir.normalize(); double angle = dot_product(dirOld, newDir); if (angle<0) { newDir *= -1; angle *= -1; } if (angle>minAngle) { minAngle = angle; dir = newDir; } } //double r = m_StepSize/(2*std::asin(std::acos(minAngle)/2)); vnl_vector_fixed v3 = dir+dirOld; v3 *= m_StepSize; double a = m_StepSize; double b = m_StepSize; double c = v3.magnitude(); double r = a*b*c/std::sqrt((a+b+c)*(a+b-c)*(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle) if (r1) { double minAngle = 0; for (int img=0; imgGetPixel(tmpIdx)); if (fabs(angle)>minAngle) { minAngle = angle; tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx); } } tensor = tmpTensor * interpWeights[0]; minAngle = 0; tmpIdx = index; tmpIdx[0]++; for (int img=0; imgGetPixel(tmpIdx)); if (fabs(angle)>minAngle) { minAngle = angle; tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx); } } tensor += tmpTensor * interpWeights[1]; minAngle = 0; tmpIdx = index; tmpIdx[1]++; for (int img=0; imgGetPixel(tmpIdx)); if (fabs(angle)>minAngle) { minAngle = angle; tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx); } } tensor += tmpTensor * interpWeights[2]; minAngle = 0; tmpIdx = index; tmpIdx[2]++; for (int img=0; imgGetPixel(tmpIdx)); if (fabs(angle)>minAngle) { minAngle = angle; tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx); } } tensor += tmpTensor * interpWeights[3]; minAngle = 0; tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; for (int img=0; imgGetPixel(tmpIdx)); if (fabs(angle)>minAngle) { minAngle = angle; tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx); } } tensor += tmpTensor * interpWeights[4]; minAngle = 0; tmpIdx = index; tmpIdx[1]++; tmpIdx[2]++; for (int img=0; imgGetPixel(tmpIdx)); if (fabs(angle)>minAngle) { minAngle = angle; tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx); } } tensor += tmpTensor * interpWeights[5]; minAngle = 0; tmpIdx = index; tmpIdx[2]++; tmpIdx[0]++; for (int img=0; imgGetPixel(tmpIdx)); if (fabs(angle)>minAngle) { minAngle = angle; tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx); } } tensor += tmpTensor * interpWeights[6]; minAngle = 0; tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++; for (int img=0; imgGetPixel(tmpIdx)); if (fabs(angle)>minAngle) { minAngle = angle; tmpTensor = m_InputImage.at(img)->GetPixel(tmpIdx); } } tensor += tmpTensor * interpWeights[7]; } else { tensor = m_InputImage.at(0)->GetPixel(index) * interpWeights[0]; typename InputImageType::IndexType tmpIdx = index; tmpIdx[0]++; tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[1]; tmpIdx = index; tmpIdx[1]++; tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[2]; tmpIdx = index; tmpIdx[2]++; tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[3]; tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[4]; tmpIdx = index; tmpIdx[1]++; tmpIdx[2]++; tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[5]; tmpIdx = index; tmpIdx[2]++; tmpIdx[0]++; tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[6]; tmpIdx = index; tmpIdx[0]++; tmpIdx[1]++; tmpIdx[2]++; tensor += m_InputImage.at(0)->GetPixel(tmpIdx) * interpWeights[7]; } tensor.ComputeEigenAnalysis(eigenvalues, eigenvectors); dir[0] = eigenvectors(2, 0); dir[1] = eigenvectors(2, 1); dir[2] = eigenvectors(2, 2); if (dir.magnitude() v3 = dir+dirOld; v3 *= m_StepSize; double a = m_StepSize; double b = m_StepSize; double c = v3.magnitude(); double r = a*b*c/std::sqrt((a+b+c)*(a+b-c)*(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle) if (r void StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::ThreadedGenerateData(const OutputImageRegionType& outputRegionForThread, ThreadIdType threadId) { FiberPolyDataType poly = m_PolyDataContainer->GetElement(threadId); vtkSmartPointer points = vtkSmartPointer::New(); vtkSmartPointer Cells = vtkSmartPointer::New(); typedef itk::DiffusionTensor3D TensorType; typedef ImageRegionConstIterator< InputImageType > InputIteratorType; typedef ImageRegionConstIterator< ItkUcharImgType > MaskIteratorType; typedef ImageRegionConstIterator< ItkFloatImgType > doubleIteratorType; typedef typename InputImageType::PixelType InputTensorType; MaskIteratorType sit(m_SeedImage, outputRegionForThread ); doubleIteratorType fit(m_FaImage, outputRegionForThread ); MaskIteratorType mit(m_MaskImage, outputRegionForThread ); for (int img=0; img worldPos; while( !sit.IsAtEnd() ) { if (sit.Value()==0 || fit.Value() line = vtkSmartPointer::New(); std::vector< vtkIdType > pointIDs; typename InputImageType::IndexType index = sit.GetIndex(); itk::ContinuousIndex start; unsigned int counter = 0; if (m_SeedsPerVoxel>1) { start[0] = index[0]+(double)(rand()%99-49)/100; start[1] = index[1]+(double)(rand()%99-49)/100; start[2] = index[2]+(double)(rand()%99-49)/100; } else { start[0] = index[0]; start[1] = index[1]; start[2] = index[2]; } // forward tracking double tractLength = FollowStreamline(start, 1, points, pointIDs, img); // add ids to line counter += pointIDs.size(); while (!pointIDs.empty()) { line->GetPointIds()->InsertNextId(pointIDs.back()); pointIDs.pop_back(); } // insert start point m_SeedImage->TransformContinuousIndexToPhysicalPoint( start, worldPos ); line->GetPointIds()->InsertNextId(points->InsertNextPoint(worldPos.GetDataPointer())); // backward tracking tractLength += FollowStreamline(start, -1, points, pointIDs, img); counter += pointIDs.size(); //MITK_INFO << "Tract length " << tractLength; if (tractLengthGetPointIds()->InsertNextId(pointIDs.at(i)); Cells->InsertNextCell(line); } ++sit; ++mit; ++fit; } } poly->SetPoints(points); poly->SetLines(Cells); std::cout << "Thread " << threadId << " finished tracking" << std::endl; } template< class TTensorPixelType, class TPDPixelType> vtkSmartPointer< vtkPolyData > StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::AddPolyData(FiberPolyDataType poly1, FiberPolyDataType poly2) { vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = poly1->GetLines(); vtkSmartPointer vNewPoints = poly1->GetPoints(); for( int i=0; iGetNumberOfLines(); i++ ) { vtkCell* cell = poly2->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } // initialize polydata vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); return vNewPolyData; } template< class TTensorPixelType, class TPDPixelType> void StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::AfterThreadedGenerateData() { MITK_INFO << "Generating polydata "; m_FiberPolyData = m_PolyDataContainer->GetElement(0); for (unsigned int i=1; iGetNumberOfThreads(); i++) { m_FiberPolyData = AddPolyData(m_FiberPolyData, m_PolyDataContainer->GetElement(i)); } MITK_INFO << "done"; } template< class TTensorPixelType, class TPDPixelType> void StreamlineTrackingFilter< TTensorPixelType, TPDPixelType> ::PrintSelf(std::ostream&, Indent) const { } } #endif // __itkDiffusionQballPrincipleDirectionsImageFilter_txx diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp index 5e7d62534d..cd192a0503 100755 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.cpp @@ -1,1945 +1,1945 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #define _USE_MATH_DEFINES #include "mitkFiberBundleX.h" #include #include #include #include "mitkImagePixelReadAccessor.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include const char* mitk::FiberBundleX::COLORCODING_ORIENTATION_BASED = "Color_Orient"; //const char* mitk::FiberBundleX::COLORCODING_FA_AS_OPACITY = "Color_Orient_FA_Opacity"; const char* mitk::FiberBundleX::COLORCODING_FA_BASED = "FA_Values"; const char* mitk::FiberBundleX::COLORCODING_CUSTOM = "custom"; const char* mitk::FiberBundleX::FIBER_ID_ARRAY = "Fiber_IDs"; using namespace std; mitk::FiberBundleX::FiberBundleX( vtkPolyData* fiberPolyData ) : m_CurrentColorCoding(NULL) , m_NumFibers(0) , m_FiberSampling(0) { m_FiberPolyData = vtkSmartPointer::New(); if (fiberPolyData != NULL) { m_FiberPolyData = fiberPolyData; //m_FiberPolyData->DeepCopy(fiberPolyData); this->DoColorCodingOrientationBased(); } this->UpdateFiberGeometry(); this->SetColorCoding(COLORCODING_ORIENTATION_BASED); this->GenerateFiberIds(); } mitk::FiberBundleX::~FiberBundleX() { } mitk::FiberBundleX::Pointer mitk::FiberBundleX::GetDeepCopy() { mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(m_FiberPolyData); newFib->SetColorCoding(m_CurrentColorCoding); return newFib; } vtkSmartPointer mitk::FiberBundleX::GeneratePolyDataByIds(std::vector fiberIds) { MITK_DEBUG << "\n=====FINAL RESULT: fib_id ======\n"; MITK_DEBUG << "Number of new Fibers: " << fiberIds.size(); // iterate through the vectorcontainer hosting all desired fiber Ids vtkSmartPointer newFiberPolyData = vtkSmartPointer::New(); vtkSmartPointer newLineSet = vtkSmartPointer::New(); vtkSmartPointer newPointSet = vtkSmartPointer::New(); // if FA array available, initialize fa double array // if color orient array is available init color array vtkSmartPointer faValueArray; vtkSmartPointer colorsT; //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; int componentSize = sizeof(rgba); if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_FA_BASED)){ MITK_DEBUG << "FA VALUES AVAILABLE, init array for new fiberbundle"; faValueArray = vtkSmartPointer::New(); } if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){ MITK_DEBUG << "colorValues available, init array for new fiberbundle"; colorsT = vtkUnsignedCharArray::New(); colorsT->SetNumberOfComponents(componentSize); colorsT->SetName(COLORCODING_ORIENTATION_BASED); } std::vector::iterator finIt = fiberIds.begin(); while ( finIt != fiberIds.end() ) { if (*finIt < 0 || *finIt>GetNumFibers()){ MITK_INFO << "FiberID can not be negative or >NumFibers!!! check id Extraction!" << *finIt; break; } vtkSmartPointer fiber = m_FiberIdDataSet->GetCell(*finIt);//->DeepCopy(fiber); vtkSmartPointer fibPoints = fiber->GetPoints(); vtkSmartPointer newFiber = vtkSmartPointer::New(); newFiber->GetPointIds()->SetNumberOfIds( fibPoints->GetNumberOfPoints() ); for(int i=0; iGetNumberOfPoints(); i++) { // MITK_DEBUG << "id: " << fiber->GetPointId(i); // MITK_DEBUG << fibPoints->GetPoint(i)[0] << " | " << fibPoints->GetPoint(i)[1] << " | " << fibPoints->GetPoint(i)[2]; newFiber->GetPointIds()->SetId(i, newPointSet->GetNumberOfPoints()); newPointSet->InsertNextPoint(fibPoints->GetPoint(i)[0], fibPoints->GetPoint(i)[1], fibPoints->GetPoint(i)[2]); if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_FA_BASED)){ // MITK_DEBUG << m_FiberIdDataSet->GetPointData()->GetArray(FA_VALUE_ARRAY)->GetTuple(fiber->GetPointId(i)); } if (m_FiberIdDataSet->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED)){ // MITK_DEBUG << "ColorValue: " << m_FiberIdDataSet->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetTuple(fiber->GetPointId(i))[0]; } } newLineSet->InsertNextCell(newFiber); ++finIt; } newFiberPolyData->SetPoints(newPointSet); newFiberPolyData->SetLines(newLineSet); MITK_DEBUG << "new fiberbundle polydata points: " << newFiberPolyData->GetNumberOfPoints(); MITK_DEBUG << "new fiberbundle polydata lines: " << newFiberPolyData->GetNumberOfLines(); MITK_DEBUG << "=====================\n"; // mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(newFiberPolyData); return newFiberPolyData; } // merge two fiber bundles mitk::FiberBundleX::Pointer mitk::FiberBundleX::AddBundle(mitk::FiberBundleX* fib) { if (fib==NULL) { MITK_WARN << "trying to call AddBundle with NULL argument"; return NULL; } MITK_INFO << "Adding fibers"; vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // add current fiber bundle for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } // add new fiber bundle for (int i=0; iGetFiberPolyData()->GetNumberOfCells(); i++) { vtkCell* cell = fib->GetFiberPolyData()->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p); vtkIdType id = vNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } // initialize polydata vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(vNewPolyData); return newFib; } // subtract two fiber bundles mitk::FiberBundleX::Pointer mitk::FiberBundleX::SubtractBundle(mitk::FiberBundleX* fib) { MITK_INFO << "Subtracting fibers"; vtkSmartPointer vNewPolyData = vtkSmartPointer::New(); vtkSmartPointer vNewLines = vtkSmartPointer::New(); vtkSmartPointer vNewPoints = vtkSmartPointer::New(); // iterate over current fibers boost::progress_display disp(m_NumFibers); for( int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (points==NULL || numPoints<=0) continue; int numFibers2 = fib->GetNumFibers(); bool contained = false; for( int i2=0; i2GetFiberPolyData()->GetCell(i2); int numPoints2 = cell2->GetNumberOfPoints(); vtkPoints* points2 = cell2->GetPoints(); if (points2==NULL)// || numPoints2<=0) continue; // check endpoints if (numPoints2==numPoints) { itk::Point point_start = GetItkPoint(points->GetPoint(0)); itk::Point point_end = GetItkPoint(points->GetPoint(numPoints-1)); itk::Point point2_start = GetItkPoint(points2->GetPoint(0)); itk::Point point2_end = GetItkPoint(points2->GetPoint(numPoints2-1)); if ((point_start.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps) || (point_start.SquaredEuclideanDistanceTo(point2_end)<=mitk::eps && point_end.SquaredEuclideanDistanceTo(point2_start)<=mitk::eps)) { // further checking ??? contained = true; break; } } } // add to result because fiber is not subtracted if (!contained) { vtkSmartPointer container = vtkSmartPointer::New(); for( int j=0; jInsertNextPoint(points->GetPoint(j)); container->GetPointIds()->InsertNextId(id); } vNewLines->InsertNextCell(container); } } if(vNewLines->GetNumberOfCells()==0) return NULL; // initialize polydata vNewPolyData->SetPoints(vNewPoints); vNewPolyData->SetLines(vNewLines); // initialize fiber bundle return mitk::FiberBundleX::New(vNewPolyData); } itk::Point mitk::FiberBundleX::GetItkPoint(double point[3]) { itk::Point itkPoint; itkPoint[0] = point[0]; itkPoint[1] = point[1]; itkPoint[2] = point[2]; return itkPoint; } /* * set polydata (additional flag to recompute fiber geometry, default = true) */ void mitk::FiberBundleX::SetFiberPolyData(vtkSmartPointer fiberPD, bool updateGeometry) { if (fiberPD == NULL) this->m_FiberPolyData = vtkSmartPointer::New(); else { m_FiberPolyData->DeepCopy(fiberPD); DoColorCodingOrientationBased(); } m_NumFibers = m_FiberPolyData->GetNumberOfLines(); if (updateGeometry) UpdateFiberGeometry(); SetColorCoding(COLORCODING_ORIENTATION_BASED); GenerateFiberIds(); } /* * return vtkPolyData */ vtkSmartPointer mitk::FiberBundleX::GetFiberPolyData() { return m_FiberPolyData; } void mitk::FiberBundleX::DoColorCodingOrientationBased() { //===== FOR WRITING A TEST ======================== // colorT size == tupelComponents * tupelElements // compare color results // to cover this code 100% also polydata needed, where colorarray already exists // + one fiber with exactly 1 point // + one fiber with 0 points //================================================= /* make sure that processing colorcoding is only called when necessary */ if ( m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) && m_FiberPolyData->GetNumberOfPoints() == m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)->GetNumberOfTuples() ) { // fiberstructure is already colorcoded MITK_DEBUG << " NO NEED TO REGENERATE COLORCODING! " ; this->ResetFiberOpacity(); this->SetColorCoding(COLORCODING_ORIENTATION_BASED); return; } /* Finally, execute color calculation */ vtkPoints* extrPoints = NULL; extrPoints = m_FiberPolyData->GetPoints(); int numOfPoints = 0; if (extrPoints!=NULL) numOfPoints = extrPoints->GetNumberOfPoints(); //colors and alpha value for each single point, RGBA = 4 components unsigned char rgba[4] = {0,0,0,0}; // int componentSize = sizeof(rgba); int componentSize = 4; vtkSmartPointer colorsT = vtkSmartPointer::New(); colorsT->Allocate(numOfPoints * componentSize); colorsT->SetNumberOfComponents(componentSize); colorsT->SetName(COLORCODING_ORIENTATION_BASED); /* checkpoint: does polydata contain any fibers */ int numOfFibers = m_FiberPolyData->GetNumberOfLines(); if (numOfFibers < 1) return; /* extract single fibers of fiberBundle */ vtkCellArray* fiberList = m_FiberPolyData->GetLines(); fiberList->InitTraversal(); for (int fi=0; fiGetNextCell(pointsPerFiber, idList); /* single fiber checkpoints: is number of points valid */ if (pointsPerFiber > 1) { /* operate on points of single fiber */ for (int i=0; i 0) { /* The color value of the current point is influenced by the previous point and next point. */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); vnl_vector_fixed< double, 3 > diff1; diff1 = currentPntvtk - nextPntvtk; vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; vnl_vector_fixed< double, 3 > diff; diff = (diff1 - diff2) / 2.0; diff.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff[2])); rgba[3] = (unsigned char) (255.0); } else if (i==0) { /* First point has no previous point, therefore only diff1 is taken */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > nextPntvtk(extrPoints->GetPoint(idList[i+1])[0], extrPoints->GetPoint(idList[i+1])[1], extrPoints->GetPoint(idList[i+1])[2]); vnl_vector_fixed< double, 3 > diff1; diff1 = currentPntvtk - nextPntvtk; diff1.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff1[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff1[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff1[2])); rgba[3] = (unsigned char) (255.0); } else if (i==pointsPerFiber-1) { /* Last point has no next point, therefore only diff2 is taken */ vnl_vector_fixed< double, 3 > currentPntvtk(extrPoints->GetPoint(idList[i])[0], extrPoints->GetPoint(idList[i])[1],extrPoints->GetPoint(idList[i])[2]); vnl_vector_fixed< double, 3 > prevPntvtk(extrPoints->GetPoint(idList[i-1])[0], extrPoints->GetPoint(idList[i-1])[1], extrPoints->GetPoint(idList[i-1])[2]); vnl_vector_fixed< double, 3 > diff2; diff2 = currentPntvtk - prevPntvtk; diff2.normalize(); rgba[0] = (unsigned char) (255.0 * std::fabs(diff2[0])); rgba[1] = (unsigned char) (255.0 * std::fabs(diff2[1])); rgba[2] = (unsigned char) (255.0 * std::fabs(diff2[2])); rgba[3] = (unsigned char) (255.0); } colorsT->InsertTupleValue(idList[i], rgba); } //end for loop } else if (pointsPerFiber == 1) { /* a single point does not define a fiber (use vertex mechanisms instead */ continue; } else { MITK_DEBUG << "Fiber with 0 points detected... please check your tractography algorithm!" ; continue; } }//end for loop m_FiberPolyData->GetPointData()->AddArray(colorsT); this->SetColorCoding(COLORCODING_ORIENTATION_BASED); //mini test, shall be ported to MITK TESTINGS! if (colorsT->GetSize() != numOfPoints*componentSize) MITK_DEBUG << "ALLOCATION ERROR IN INITIATING COLOR ARRAY"; } void mitk::FiberBundleX::DoColorCodingFaBased() { if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED) != 1 ) return; this->SetColorCoding(COLORCODING_FA_BASED); // this->GenerateFiberIds(); } void mitk::FiberBundleX::DoUseFaFiberOpacity() { if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED) != 1 ) return; if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_ORIENTATION_BASED) != 1 ) return; vtkDoubleArray* FAValArray = (vtkDoubleArray*) m_FiberPolyData->GetPointData()->GetArray(COLORCODING_FA_BASED); vtkUnsignedCharArray* ColorArray = dynamic_cast (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)); for(long i=0; iGetNumberOfTuples(); i++) { double faValue = FAValArray->GetValue(i); faValue = faValue * 255.0; ColorArray->SetComponent(i,3, (unsigned char) faValue ); } this->SetColorCoding(COLORCODING_ORIENTATION_BASED); // this->GenerateFiberIds(); } void mitk::FiberBundleX::ResetFiberOpacity() { vtkUnsignedCharArray* ColorArray = dynamic_cast (m_FiberPolyData->GetPointData()->GetArray(COLORCODING_ORIENTATION_BASED)); if (ColorArray==NULL) return; for(long i=0; iGetNumberOfTuples(); i++) ColorArray->SetComponent(i,3, 255.0 ); } void mitk::FiberBundleX::SetFAMap(mitk::Image::Pointer FAimage) { mitkPixelTypeMultiplex1( SetFAMap, FAimage->GetPixelType(), FAimage ); } template void mitk::FiberBundleX::SetFAMap(const mitk::PixelType, mitk::Image::Pointer FAimage) { MITK_DEBUG << "SetFAMap"; vtkSmartPointer faValues = vtkSmartPointer::New(); faValues->SetName(COLORCODING_FA_BASED); faValues->Allocate(m_FiberPolyData->GetNumberOfPoints()); faValues->SetNumberOfValues(m_FiberPolyData->GetNumberOfPoints()); mitk::ImagePixelReadAccessor readFAimage (FAimage, FAimage->GetVolumeData(0)); vtkPoints* pointSet = m_FiberPolyData->GetPoints(); for(long i=0; iGetNumberOfPoints(); ++i) { Point3D px; px[0] = pointSet->GetPoint(i)[0]; px[1] = pointSet->GetPoint(i)[1]; px[2] = pointSet->GetPoint(i)[2]; double faPixelValue = 1-readFAimage.GetPixelByWorldCoordinates(px); faValues->InsertValue(i, faPixelValue); } m_FiberPolyData->GetPointData()->AddArray(faValues); this->GenerateFiberIds(); if(m_FiberPolyData->GetPointData()->HasArray(COLORCODING_FA_BASED)) MITK_DEBUG << "FA VALUE ARRAY SET"; } void mitk::FiberBundleX::GenerateFiberIds() { if (m_FiberPolyData == NULL) return; vtkSmartPointer idFiberFilter = vtkSmartPointer::New(); idFiberFilter->SetInputData(m_FiberPolyData); idFiberFilter->CellIdsOn(); // idFiberFilter->PointIdsOn(); // point id's are not needed idFiberFilter->SetIdsArrayName(FIBER_ID_ARRAY); idFiberFilter->FieldDataOn(); idFiberFilter->Update(); m_FiberIdDataSet = idFiberFilter->GetOutput(); MITK_DEBUG << "Generating Fiber Ids...[done] | " << m_FiberIdDataSet->GetNumberOfCells(); } mitk::FiberBundleX::Pointer mitk::FiberBundleX::ExtractFiberSubset(ItkUcharImgType* mask, bool anyPoint, bool invert) { vtkSmartPointer polyData = m_FiberPolyData; if (anyPoint) { float minSpacing = 1; if(mask->GetSpacing()[0]GetSpacing()[1] && mask->GetSpacing()[0]GetSpacing()[2]) minSpacing = mask->GetSpacing()[0]; else if (mask->GetSpacing()[1] < mask->GetSpacing()[2]) minSpacing = mask->GetSpacing()[1]; else minSpacing = mask->GetSpacing()[2]; mitk::FiberBundleX::Pointer fibCopy = this->GetDeepCopy(); fibCopy->ResampleFibers(minSpacing/5); polyData = fibCopy->GetFiberPolyData(); } vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Extracting fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkCell* cellOriginal = m_FiberPolyData->GetCell(i); int numPointsOriginal = cellOriginal->GetNumberOfPoints(); vtkPoints* pointsOriginal = cellOriginal->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); if (numPoints>1 && numPointsOriginal) { if (anyPoint) { if (!invert) { for (int j=0; jGetPoint(j); itk::Point itkP; itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; itk::Index<3> idx; mask->TransformPhysicalPointToIndex(itkP, idx); if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) ) { for (int k=0; kGetPoint(k); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } break; } } } else { bool includeFiber = true; for (int j=0; jGetPoint(j); itk::Point itkP; itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; itk::Index<3> idx; mask->TransformPhysicalPointToIndex(itkP, idx); if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) ) { includeFiber = false; break; } } if (includeFiber) { for (int k=0; kGetPoint(k); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } } } } else { double* start = pointsOriginal->GetPoint(0); itk::Point itkStart; itkStart[0] = start[0]; itkStart[1] = start[1]; itkStart[2] = start[2]; itk::Index<3> idxStart; mask->TransformPhysicalPointToIndex(itkStart, idxStart); double* end = pointsOriginal->GetPoint(numPointsOriginal-1); itk::Point itkEnd; itkEnd[0] = end[0]; itkEnd[1] = end[1]; itkEnd[2] = end[2]; itk::Index<3> idxEnd; mask->TransformPhysicalPointToIndex(itkEnd, idxEnd); if ( mask->GetPixel(idxStart)>0 && mask->GetPixel(idxEnd)>0 && mask->GetLargestPossibleRegion().IsInside(idxStart) && mask->GetLargestPossibleRegion().IsInside(idxEnd) ) { for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } } } } vtkNewCells->InsertNextCell(container); } if (vtkNewCells->GetNumberOfCells()<=0) return NULL; vtkSmartPointer newPolyData = vtkSmartPointer::New(); newPolyData->SetPoints(vtkNewPoints); newPolyData->SetLines(vtkNewCells); return mitk::FiberBundleX::New(newPolyData); } mitk::FiberBundleX::Pointer mitk::FiberBundleX::RemoveFibersOutside(ItkUcharImgType* mask, bool invert) { float minSpacing = 1; if(mask->GetSpacing()[0]GetSpacing()[1] && mask->GetSpacing()[0]GetSpacing()[2]) minSpacing = mask->GetSpacing()[0]; else if (mask->GetSpacing()[1] < mask->GetSpacing()[2]) minSpacing = mask->GetSpacing()[1]; else minSpacing = mask->GetSpacing()[2]; mitk::FiberBundleX::Pointer fibCopy = this->GetDeepCopy(); fibCopy->ResampleFibers(minSpacing/10); vtkSmartPointer polyData =fibCopy->GetFiberPolyData(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Cutting fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); if (numPoints>1) { int newNumPoints = 0; for (int j=0; jGetPoint(j); itk::Point itkP; itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; itk::Index<3> idx; mask->TransformPhysicalPointToIndex(itkP, idx); if ( mask->GetPixel(idx)>0 && mask->GetLargestPossibleRegion().IsInside(idx) && !invert ) { vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); newNumPoints++; } else if ( (mask->GetPixel(idx)<=0 || !mask->GetLargestPossibleRegion().IsInside(idx)) && invert ) { vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); newNumPoints++; } else if (newNumPoints>0) { vtkNewCells->InsertNextCell(container); newNumPoints = 0; container = vtkSmartPointer::New(); } } if (newNumPoints>0) vtkNewCells->InsertNextCell(container); } } if (vtkNewCells->GetNumberOfCells()<=0) return NULL; vtkSmartPointer newPolyData = vtkSmartPointer::New(); newPolyData->SetPoints(vtkNewPoints); newPolyData->SetLines(vtkNewCells); mitk::FiberBundleX::Pointer newFib = mitk::FiberBundleX::New(newPolyData); newFib->ResampleFibers(minSpacing/2); return newFib; } mitk::FiberBundleX::Pointer mitk::FiberBundleX::ExtractFiberSubset(BaseData* roi) { if (roi==NULL || !(dynamic_cast(roi) || dynamic_cast(roi)) ) return NULL; std::vector tmp = ExtractFiberIdSubset(roi); if (tmp.size()<=0) return mitk::FiberBundleX::New(); vtkSmartPointer pTmp = GeneratePolyDataByIds(tmp); return mitk::FiberBundleX::New(pTmp); } std::vector mitk::FiberBundleX::ExtractFiberIdSubset(BaseData* roi) { std::vector result; if (roi==NULL) return result; mitk::PlanarFigureComposite::Pointer pfc = dynamic_cast(roi); if (!pfc.IsNull()) // handle composite { switch (pfc->getOperationType()) { case 0: // AND { result = this->ExtractFiberIdSubset(pfc->getChildAt(0)); std::vector::iterator it; for (int i=1; igetNumberOfChildren(); ++i) { std::vector inRoi = this->ExtractFiberIdSubset(pfc->getChildAt(i)); std::vector rest(std::min(result.size(),inRoi.size())); it = std::set_intersection(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() ); rest.resize( it - rest.begin() ); result = rest; } break; } case 1: // OR { result = ExtractFiberIdSubset(pfc->getChildAt(0)); std::vector::iterator it; for (int i=1; igetNumberOfChildren(); ++i) { it = result.end(); std::vector inRoi = ExtractFiberIdSubset(pfc->getChildAt(i)); result.insert(it, inRoi.begin(), inRoi.end()); } // remove duplicates sort(result.begin(), result.end()); it = unique(result.begin(), result.end()); result.resize( it - result.begin() ); break; } case 2: // NOT { for(long i=0; iGetNumFibers(); i++) result.push_back(i); std::vector::iterator it; for (long i=0; igetNumberOfChildren(); ++i) { std::vector inRoi = ExtractFiberIdSubset(pfc->getChildAt(i)); std::vector rest(result.size()-inRoi.size()); it = std::set_difference(result.begin(), result.end(), inRoi.begin(), inRoi.end(), rest.begin() ); rest.resize( it - rest.begin() ); result = rest; } break; } } } else if ( dynamic_cast(roi) ) // actual extraction { mitk::PlanarFigure::Pointer planarFigure = dynamic_cast(roi); Vector3D planeNormal = planarFigure->GetPlaneGeometry()->GetNormal(); planeNormal.Normalize(); Point3D planeOrigin = planarFigure->GetPlaneGeometry()->GetOrigin(); // define cutting plane by ROI geometry (PlanarFigure) vtkSmartPointer plane = vtkSmartPointer::New(); plane->SetOrigin(planeOrigin[0],planeOrigin[1],planeOrigin[2]); plane->SetNormal(planeNormal[0],planeNormal[1],planeNormal[2]); // get all fiber/plane intersection points vtkSmartPointer clipper = vtkSmartPointer::New(); clipper->SetInputData(m_FiberIdDataSet); clipper->SetClipFunction(plane); clipper->GenerateClipScalarsOn(); clipper->GenerateClippedOutputOn(); clipper->Update(); vtkSmartPointer clipperout = clipper->GetClippedOutput(); if (!clipperout->GetCellData()->HasArray(FIBER_ID_ARRAY)) return result; vtkSmartPointer distanceList = clipperout->GetPointData()->GetScalars(); vtkIdType numPoints = distanceList->GetNumberOfTuples(); std::vector pointsOnPlane; pointsOnPlane.reserve(numPoints); for (int i=0; iGetTuple(i)[0]; // check if point is on plane if (distance >= -0.01 && distance <= 0.01) pointsOnPlane.push_back(i); } if (pointsOnPlane.empty()) return result; // get all point IDs inside the ROI std::vector pointsInROI; pointsInROI.reserve(pointsOnPlane.size()); mitk::PlanarCircle::Pointer circleName = mitk::PlanarCircle::New(); mitk::PlanarPolygon::Pointer polyName = mitk::PlanarPolygon::New(); if ( planarFigure->GetNameOfClass() == circleName->GetNameOfClass() ) { //calculate circle radius mitk::Point3D V1w = planarFigure->GetWorldControlPoint(0); //centerPoint mitk::Point3D V2w = planarFigure->GetWorldControlPoint(1); //radiusPoint double radius = V1w.EuclideanDistanceTo(V2w); radius *= radius; for (unsigned int i=0; iGetPoint(pointsOnPlane[i], p); double dist = (p[0]-V1w[0])*(p[0]-V1w[0])+(p[1]-V1w[1])*(p[1]-V1w[1])+(p[2]-V1w[2])*(p[2]-V1w[2]); if( dist <= radius) pointsInROI.push_back(pointsOnPlane[i]); } } else if ( planarFigure->GetNameOfClass() == polyName->GetNameOfClass() ) { //create vtkPolygon using controlpoints from planarFigure polygon vtkSmartPointer polygonVtk = vtkSmartPointer::New(); for (unsigned int i=0; iGetNumberOfControlPoints(); ++i) { itk::Point p = planarFigure->GetWorldControlPoint(i); polygonVtk->GetPoints()->InsertNextPoint(p[0], p[1], p[2] ); } //prepare everything for using pointInPolygon function double n[3]; polygonVtk->ComputeNormal(polygonVtk->GetPoints()->GetNumberOfPoints(), static_cast(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), n); double bounds[6]; polygonVtk->GetPoints()->GetBounds(bounds); for (unsigned int i=0; iGetPoint(pointsOnPlane[i], p); int isInPolygon = polygonVtk->PointInPolygon(p, polygonVtk->GetPoints()->GetNumberOfPoints(), static_cast(polygonVtk->GetPoints()->GetData()->GetVoidPointer(0)), bounds, n); if( isInPolygon ) pointsInROI.push_back(pointsOnPlane[i]); } } if (pointsInROI.empty()) return result; // get the fiber IDs corresponding to all clipped points std::vector< long > pointToFiberMap; // pointToFiberMap[PointID] = FiberIndex pointToFiberMap.resize(clipperout->GetNumberOfPoints()); vtkCellArray* clipperlines = clipperout->GetLines(); clipperlines->InitTraversal(); for (int i=0, ic=0 ; iGetNumberOfCells(); i++, ic+=3) { // ic is the index counter for the cells hosting the desired information. each cell consits of 3 items. long fiberID = clipperout->GetCellData()->GetArray(FIBER_ID_ARRAY)->GetTuple(i)[0]; vtkIdType numPoints; vtkIdType* pointIDs; clipperlines->GetCell(ic, numPoints, pointIDs); for (long j=0; j=0) result.push_back( pointToFiberMap[pointsInROI[k]] ); else MITK_INFO << "ERROR in ExtractFiberIdSubset; impossible fiber id detected"; } // remove duplicates std::vector::iterator it; sort(result.begin(), result.end()); it = unique (result.begin(), result.end()); result.resize( it - result.begin() ); } return result; } void mitk::FiberBundleX::UpdateFiberGeometry() { vtkSmartPointer cleaner = vtkSmartPointer::New(); cleaner->SetInputData(m_FiberPolyData); cleaner->PointMergingOff(); cleaner->Update(); m_FiberPolyData = cleaner->GetOutput(); m_FiberLengths.clear(); m_MeanFiberLength = 0; m_MedianFiberLength = 0; m_LengthStDev = 0; m_NumFibers = m_FiberPolyData->GetNumberOfCells(); if (m_NumFibers<=0) // no fibers present; apply default geometry { m_MinFiberLength = 0; m_MaxFiberLength = 0; mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); - geometry->SetImageGeometry(true); + geometry->SetImageGeometry(false); float b[] = {0, 1, 0, 1, 0, 1}; geometry->SetFloatBounds(b); SetGeometry(geometry); return; } double b[6]; m_FiberPolyData->GetBounds(b); // calculate statistics for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); int p = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); float length = 0; for (int j=0; jGetPoint(j, p1); double p2[3]; points->GetPoint(j+1, p2); float dist = std::sqrt((p1[0]-p2[0])*(p1[0]-p2[0])+(p1[1]-p2[1])*(p1[1]-p2[1])+(p1[2]-p2[2])*(p1[2]-p2[2])); length += dist; } m_FiberLengths.push_back(length); m_MeanFiberLength += length; if (i==0) { m_MinFiberLength = length; m_MaxFiberLength = length; } else { if (lengthm_MaxFiberLength) m_MaxFiberLength = length; } } m_MeanFiberLength /= m_NumFibers; std::vector< float > sortedLengths = m_FiberLengths; std::sort(sortedLengths.begin(), sortedLengths.end()); for (int i=0; i1) m_LengthStDev /= (m_NumFibers-1); else m_LengthStDev = 0; m_LengthStDev = std::sqrt(m_LengthStDev); m_MedianFiberLength = sortedLengths.at(m_NumFibers/2); mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); geometry->SetFloatBounds(b); this->SetGeometry(geometry); m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } std::vector mitk::FiberBundleX::GetAvailableColorCodings() { std::vector availableColorCodings; int numColors = m_FiberPolyData->GetPointData()->GetNumberOfArrays(); for(int i=0; iGetPointData()->GetArrayName(i)); } //this controlstructure shall be implemented by the calling method if (availableColorCodings.empty()) MITK_DEBUG << "no colorcodings available in fiberbundleX"; return availableColorCodings; } char* mitk::FiberBundleX::GetCurrentColorCoding() { return m_CurrentColorCoding; } void mitk::FiberBundleX::SetColorCoding(const char* requestedColorCoding) { if (requestedColorCoding==NULL) return; if( strcmp (COLORCODING_ORIENTATION_BASED,requestedColorCoding) == 0 ) { this->m_CurrentColorCoding = (char*) COLORCODING_ORIENTATION_BASED; } else if( strcmp (COLORCODING_FA_BASED,requestedColorCoding) == 0 ) { this->m_CurrentColorCoding = (char*) COLORCODING_FA_BASED; } else if( strcmp (COLORCODING_CUSTOM,requestedColorCoding) == 0 ) { this->m_CurrentColorCoding = (char*) COLORCODING_CUSTOM; } else { MITK_DEBUG << "FIBERBUNDLE X: UNKNOWN COLORCODING in FIBERBUNDLEX Datastructure"; this->m_CurrentColorCoding = (char*) COLORCODING_CUSTOM; //will cause blank colorcoding of fibers } m_UpdateTime3D.Modified(); m_UpdateTime2D.Modified(); } itk::Matrix< double, 3, 3 > mitk::FiberBundleX::TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz) { rx = rx*M_PI/180; ry = ry*M_PI/180; rz = rz*M_PI/180; itk::Matrix< double, 3, 3 > rotX; rotX.SetIdentity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; itk::Matrix< double, 3, 3 > rotY; rotY.SetIdentity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; itk::Matrix< double, 3, 3 > rotZ; rotZ.SetIdentity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; itk::Matrix< double, 3, 3 > rot = rotZ*rotY*rotX; m = rot*m; return m; } itk::Point mitk::FiberBundleX::TransformPoint(vnl_vector_fixed< double, 3 > point, double rx, double ry, double rz, double tx, double ty, double tz) { rx = rx*M_PI/180; ry = ry*M_PI/180; rz = rz*M_PI/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; vnl_matrix_fixed< double, 3, 3 > rot = rotZ*rotY*rotX; mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); point[0] -= center[0]; point[1] -= center[1]; point[2] -= center[2]; point = rot*point; point[0] += center[0]+tx; point[1] += center[1]+ty; point[2] += center[2]+tz; itk::Point out; out[0] = point[0]; out[1] = point[1]; out[2] = point[2]; return out; } void mitk::FiberBundleX::TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz) { rx = rx*M_PI/180; ry = ry*M_PI/180; rz = rz*M_PI/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(rx); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(rx); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(ry); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(ry); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(rz); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(rz); rotZ[1][0] = -rotZ[0][1]; vnl_matrix_fixed< double, 3, 3 > rot = rotZ*rotY*rotX; mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vnl_vector_fixed< double, 3 > dir; dir[0] = p[0]-center[0]; dir[1] = p[1]-center[1]; dir[2] = p[2]-center[2]; dir = rot*dir; dir[0] += center[0]+tx; dir[1] += center[1]+ty; dir[2] += center[2]+tz; vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block()); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } void mitk::FiberBundleX::RotateAroundAxis(double x, double y, double z) { x = x*M_PI/180; y = y*M_PI/180; z = z*M_PI/180; vnl_matrix_fixed< double, 3, 3 > rotX; rotX.set_identity(); rotX[1][1] = cos(x); rotX[2][2] = rotX[1][1]; rotX[1][2] = -sin(x); rotX[2][1] = -rotX[1][2]; vnl_matrix_fixed< double, 3, 3 > rotY; rotY.set_identity(); rotY[0][0] = cos(y); rotY[2][2] = rotY[0][0]; rotY[0][2] = sin(y); rotY[2][0] = -rotY[0][2]; vnl_matrix_fixed< double, 3, 3 > rotZ; rotZ.set_identity(); rotZ[0][0] = cos(z); rotZ[1][1] = rotZ[0][0]; rotZ[0][1] = -sin(z); rotZ[1][0] = -rotZ[0][1]; mitk::BaseGeometry::Pointer geom = this->GetGeometry(); mitk::Point3D center = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vnl_vector_fixed< double, 3 > dir; dir[0] = p[0]-center[0]; dir[1] = p[1]-center[1]; dir[2] = p[2]-center[2]; dir = rotZ*rotY*rotX*dir; dir[0] += center[0]; dir[1] += center[1]; dir[2] += center[2]; vtkIdType id = vtkNewPoints->InsertNextPoint(dir.data_block()); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } void mitk::FiberBundleX::ScaleFibers(double x, double y, double z) { MITK_INFO << "Scaling fibers"; boost::progress_display disp(m_NumFibers); mitk::BaseGeometry* geom = this->GetGeometry(); mitk::Point3D c = geom->GetCenter(); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[0] -= c[0]; p[1] -= c[1]; p[2] -= c[2]; p[0] *= x; p[1] *= y; p[2] *= z; p[0] += c[0]; p[1] += c[1]; p[2] += c[2]; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } void mitk::FiberBundleX::TranslateFibers(double x, double y, double z) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[0] += x; p[1] += y; p[2] += z; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } void mitk::FiberBundleX::MirrorFibers(unsigned int axis) { if (axis>2) return; MITK_INFO << "Mirroring fibers"; boost::progress_display disp(m_NumFibers); vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); p[axis] = -p[axis]; vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } bool mitk::FiberBundleX::ApplyCurvatureThreshold(float minRadius, bool deleteFibers) { if (minRadius<0) return true; vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Applying curvature threshold"; boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); for (int i=0; iGetNumberOfCells(); i++) { ++disp ; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); // calculate curvatures vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j, p1); double p2[3]; points->GetPoint(j+1, p2); double p3[3]; points->GetPoint(j+2, p3); vnl_vector_fixed< float, 3 > v1, v2, v3; v1[0] = p2[0]-p1[0]; v1[1] = p2[1]-p1[1]; v1[2] = p2[2]-p1[2]; v2[0] = p3[0]-p2[0]; v2[1] = p3[1]-p2[1]; v2[2] = p3[2]-p2[2]; v3[0] = p1[0]-p3[0]; v3[1] = p1[1]-p3[1]; v3[2] = p1[2]-p3[2]; float a = v1.magnitude(); float b = v2.magnitude(); float c = v3.magnitude(); float r = a*b*c/std::sqrt((a+b+c)*(a+b-c)*(b+c-a)*(a-b+c)); // radius of triangle via Heron's formula (area of triangle) vtkIdType id = vtkNewPoints->InsertNextPoint(p1); container->GetPointIds()->InsertNextId(id); if (deleteFibers && rInsertNextCell(container); container = vtkSmartPointer::New(); } else if (j==numPoints-3) { id = vtkNewPoints->InsertNextPoint(p2); container->GetPointIds()->InsertNextId(id); id = vtkNewPoints->InsertNextPoint(p3); container->GetPointIds()->InsertNextId(id); vtkNewCells->InsertNextCell(container); } } } if (vtkNewCells->GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); return true; } bool mitk::FiberBundleX::RemoveShortFibers(float lengthInMM) { MITK_INFO << "Removing short fibers"; if (lengthInMM<=0 || lengthInMMm_MaxFiberLength) // can't remove all fibers { MITK_WARN << "Process aborted. No fibers would be left!"; return false; } vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); float min = m_MaxFiberLength; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (m_FiberLengths.at(i)>=lengthInMM) { vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); if (m_FiberLengths.at(i)GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); return true; } bool mitk::FiberBundleX::RemoveLongFibers(float lengthInMM) { if (lengthInMM<=0 || lengthInMM>m_MaxFiberLength) return true; if (lengthInMM vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Removing long fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); if (m_FiberLengths.at(i)<=lengthInMM) { vtkSmartPointer container = vtkSmartPointer::New(); for (int j=0; jGetPoint(j); vtkIdType id = vtkNewPoints->InsertNextPoint(p); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } } if (vtkNewCells->GetNumberOfCells()<=0) return false; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); return true; } void mitk::FiberBundleX::DoFiberSmoothing(float pointDistance, double tension, double continuity, double bias ) { if (pointDistance<=0) return; vtkSmartPointer vtkSmoothPoints = vtkSmartPointer::New(); //in smoothpoints the interpolated points representing a fiber are stored. //in vtkcells all polylines are stored, actually all id's of them are stored vtkSmartPointer vtkSmoothCells = vtkSmartPointer::New(); //cellcontainer for smoothed lines vtkIdType pointHelperCnt = 0; MITK_INFO << "Smoothing fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer newPoints = vtkSmartPointer::New(); for (int j=0; jInsertNextPoint(points->GetPoint(j)); float length = m_FiberLengths.at(i); int sampling = std::ceil(length/pointDistance); vtkSmartPointer xSpline = vtkSmartPointer::New(); vtkSmartPointer ySpline = vtkSmartPointer::New(); vtkSmartPointer zSpline = vtkSmartPointer::New(); xSpline->SetDefaultBias(bias); xSpline->SetDefaultTension(tension); xSpline->SetDefaultContinuity(continuity); ySpline->SetDefaultBias(bias); ySpline->SetDefaultTension(tension); ySpline->SetDefaultContinuity(continuity); zSpline->SetDefaultBias(bias); zSpline->SetDefaultTension(tension); zSpline->SetDefaultContinuity(continuity); vtkSmartPointer spline = vtkSmartPointer::New(); spline->SetXSpline(xSpline); spline->SetYSpline(ySpline); spline->SetZSpline(zSpline); spline->SetPoints(newPoints); vtkSmartPointer functionSource = vtkSmartPointer::New(); functionSource->SetParametricFunction(spline); functionSource->SetUResolution(sampling); functionSource->SetVResolution(sampling); functionSource->SetWResolution(sampling); functionSource->Update(); vtkPolyData* outputFunction = functionSource->GetOutput(); vtkPoints* tmpSmoothPnts = outputFunction->GetPoints(); //smoothPoints of current fiber vtkSmartPointer smoothLine = vtkSmartPointer::New(); smoothLine->GetPointIds()->SetNumberOfIds(tmpSmoothPnts->GetNumberOfPoints()); for (int j=0; jGetNumberOfPoints(); j++) { smoothLine->GetPointIds()->SetId(j, j+pointHelperCnt); vtkSmoothPoints->InsertNextPoint(tmpSmoothPnts->GetPoint(j)); } vtkSmoothCells->InsertNextCell(smoothLine); pointHelperCnt += tmpSmoothPnts->GetNumberOfPoints(); } m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkSmoothPoints); m_FiberPolyData->SetLines(vtkSmoothCells); UpdateColorCoding(); UpdateFiberGeometry(); m_FiberSampling = 10/pointDistance; } void mitk::FiberBundleX::DoFiberSmoothing(float pointDistance) { DoFiberSmoothing(pointDistance, 0, 0, 0 ); } unsigned long mitk::FiberBundleX::GetNumberOfPoints() { unsigned long points = 0; for (int i=0; iGetNumberOfCells(); i++) { vtkCell* cell = m_FiberPolyData->GetCell(i); points += cell->GetNumberOfPoints(); } return points; } void mitk::FiberBundleX::CompressFibers(float error) { vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); MITK_INFO << "Compressing fibers"; unsigned long numRemovedPoints = 0; boost::progress_display disp(m_FiberPolyData->GetNumberOfCells()); for (int i=0; iGetNumberOfCells(); i++) { ++disp; vtkCell* cell = m_FiberPolyData->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); // calculate curvatures std::vector< int > removedPoints; removedPoints.resize(numPoints, 0); removedPoints[0]=-1; removedPoints[numPoints-1]=-1; vtkSmartPointer container = vtkSmartPointer::New(); bool pointFound = true; while (pointFound) { pointFound = false; double minError = error; int removeIndex = -1; for (int j=0; jGetPoint(j, cand); vnl_vector_fixed< double, 3 > candV; candV[0]=cand[0]; candV[1]=cand[1]; candV[2]=cand[2]; int validP = -1; vnl_vector_fixed< double, 3 > pred; for (int k=j-1; k>=0; k--) if (removedPoints[k]<=0) { double ref[3]; points->GetPoint(k, ref); pred[0]=ref[0]; pred[1]=ref[1]; pred[2]=ref[2]; validP = k; break; } int validS = -1; vnl_vector_fixed< double, 3 > succ; for (int k=j+1; kGetPoint(k, ref); succ[0]=ref[0]; succ[1]=ref[1]; succ[2]=ref[2]; validS = k; break; } if (validP>=0 && validS>=0) { double a = (candV-pred).magnitude(); double b = (candV-succ).magnitude(); double c = (pred-succ).magnitude(); double s=0.5*(a+b+c); double hc=(2.0/c)*sqrt(fabs(s*(s-a)*(s-b)*(s-c))); if (hcGetPoint(j, cand); vtkIdType id = vtkNewPoints->InsertNextPoint(cand); container->GetPointIds()->InsertNextId(id); } } vtkNewCells->InsertNextCell(container); } if (vtkNewCells->GetNumberOfCells()>0) { MITK_INFO << "Removed points: " << numRemovedPoints; m_FiberPolyData = vtkSmartPointer::New(); m_FiberPolyData->SetPoints(vtkNewPoints); m_FiberPolyData->SetLines(vtkNewCells); UpdateColorCoding(); UpdateFiberGeometry(); } } // Resample fiber to get equidistant points void mitk::FiberBundleX::ResampleFibers(float pointDistance) { if (pointDistance<=0.00001) return; vtkSmartPointer newPoly = vtkSmartPointer::New(); vtkSmartPointer newCellArray = vtkSmartPointer::New(); vtkSmartPointer newPoints = vtkSmartPointer::New(); int numberOfLines = m_NumFibers; MITK_INFO << "Resampling fibers"; boost::progress_display disp(m_NumFibers); for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkSmartPointer container = vtkSmartPointer::New(); double* point = points->GetPoint(0); vtkIdType pointId = newPoints->InsertNextPoint(point); container->GetPointIds()->InsertNextId(pointId); float dtau = 0; int cur_p = 1; itk::Vector dR; float normdR = 0; for (;;) { while (dtau <= pointDistance && cur_p < numPoints) { itk::Vector v1; point = points->GetPoint(cur_p-1); v1[0] = point[0]; v1[1] = point[1]; v1[2] = point[2]; itk::Vector v2; point = points->GetPoint(cur_p); v2[0] = point[0]; v2[1] = point[1]; v2[2] = point[2]; dR = v2 - v1; normdR = std::sqrt(dR.GetSquaredNorm()); dtau += normdR; cur_p++; } if (dtau >= pointDistance) { itk::Vector v1; point = points->GetPoint(cur_p-1); v1[0] = point[0]; v1[1] = point[1]; v1[2] = point[2]; itk::Vector v2 = v1 - dR*( (dtau-pointDistance)/normdR ); pointId = newPoints->InsertNextPoint(v2.GetDataPointer()); container->GetPointIds()->InsertNextId(pointId); } else { point = points->GetPoint(numPoints-1); pointId = newPoints->InsertNextPoint(point); container->GetPointIds()->InsertNextId(pointId); break; } dtau = dtau-pointDistance; } newCellArray->InsertNextCell(container); } newPoly->SetPoints(newPoints); newPoly->SetLines(newCellArray); m_FiberPolyData = newPoly; UpdateFiberGeometry(); UpdateColorCoding(); m_FiberSampling = 10/pointDistance; } // reapply selected colorcoding in case polydata structure has changed void mitk::FiberBundleX::UpdateColorCoding() { char* cc = GetCurrentColorCoding(); if( strcmp (COLORCODING_ORIENTATION_BASED,cc) == 0 ) DoColorCodingOrientationBased(); else if( strcmp (COLORCODING_FA_BASED,cc) == 0 ) DoColorCodingFaBased(); } // reapply selected colorcoding in case polydata structure has changed bool mitk::FiberBundleX::Equals(mitk::FiberBundleX* fib, double eps) { if (fib==NULL) { MITK_INFO << "Reference bundle is NULL!"; return false; } if (m_NumFibers!=fib->GetNumFibers()) { MITK_INFO << "Unequal number of fibers!"; MITK_INFO << m_NumFibers << " vs. " << fib->GetNumFibers(); return false; } for (int i=0; iGetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); vtkCell* cell2 = fib->GetFiberPolyData()->GetCell(i); int numPoints2 = cell2->GetNumberOfPoints(); vtkPoints* points2 = cell2->GetPoints(); if (numPoints2!=numPoints) { MITK_INFO << "Unequal number of points in fiber " << i << "!"; MITK_INFO << numPoints2 << " vs. " << numPoints; return false; } for (int j=0; jGetPoint(j); double* p2 = points2->GetPoint(j); if (fabs(p1[0]-p2[0])>eps || fabs(p1[1]-p2[1])>eps || fabs(p1[2]-p2[2])>eps) { MITK_INFO << "Unequal points in fiber " << i << " at position " << j << "!"; MITK_INFO << "p1: " << p1[0] << ", " << p1[1] << ", " << p1[2]; MITK_INFO << "p2: " << p2[0] << ", " << p2[1] << ", " << p2[2]; return false; } } } return true; } /* ESSENTIAL IMPLEMENTATION OF SUPERCLASS METHODS */ void mitk::FiberBundleX::UpdateOutputInformation() { } void mitk::FiberBundleX::SetRequestedRegionToLargestPossibleRegion() { } bool mitk::FiberBundleX::RequestedRegionIsOutsideOfTheBufferedRegion() { return false; } bool mitk::FiberBundleX::VerifyRequestedRegion() { return true; } void mitk::FiberBundleX::SetRequestedRegion(const itk::DataObject* ) { } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h index 9684104e37..857e98adf5 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleX.h @@ -1,174 +1,172 @@ /*=================================================================== 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_FiberBundleX_H #define _MITK_FiberBundleX_H //includes for MITK datastructure #include #include #include //includes storing fiberdata #include #include #include #include #include //#include #include #include #include namespace mitk { /** * \brief Base Class for Fiber Bundles; */ class MitkFiberTracking_EXPORT FiberBundleX : public BaseData { public: typedef itk::Image ItkUcharImgType; // fiber colorcodings static const char* COLORCODING_ORIENTATION_BASED; static const char* COLORCODING_FA_BASED; static const char* COLORCODING_CUSTOM; static const char* FIBER_ID_ARRAY; virtual void UpdateOutputInformation(); virtual void SetRequestedRegionToLargestPossibleRegion(); virtual bool RequestedRegionIsOutsideOfTheBufferedRegion(); virtual bool VerifyRequestedRegion(); virtual void SetRequestedRegion(const itk::DataObject*); mitkClassMacro( FiberBundleX, BaseData ) itkFactorylessNewMacro(Self) itkCloneMacro(Self) mitkNewMacro1Param(Self, vtkSmartPointer) // custom constructor // colorcoding related methods void SetColorCoding(const char*); void SetFAMap(mitk::Image::Pointer); template void SetFAMap(const mitk::PixelType pixelType, mitk::Image::Pointer); void DoColorCodingOrientationBased(); void DoColorCodingFaBased(); void DoUseFaFiberOpacity(); void ResetFiberOpacity(); // fiber smoothing/resampling void CompressFibers(float error = 0.0); void ResampleFibers(float pointDistance = 1); void DoFiberSmoothing(float pointDistance); void DoFiberSmoothing(float pointDistance, double tension, double continuity, double bias ); bool RemoveShortFibers(float lengthInMM); bool RemoveLongFibers(float lengthInMM); bool ApplyCurvatureThreshold(float minRadius, bool deleteFibers); void MirrorFibers(unsigned int axis); void RotateAroundAxis(double x, double y, double z); void TranslateFibers(double x, double y, double z); void ScaleFibers(double x, double y, double z); void TransformFibers(double rx, double ry, double rz, double tx, double ty, double tz); itk::Point TransformPoint(vnl_vector_fixed< double, 3 > point, double rx, double ry, double rz, double tx, double ty, double tz); itk::Matrix< double, 3, 3 > TransformMatrix(itk::Matrix< double, 3, 3 > m, double rx, double ry, double rz); // add/subtract fibers FiberBundleX::Pointer AddBundle(FiberBundleX* fib); FiberBundleX::Pointer SubtractBundle(FiberBundleX* fib); // fiber subset extraction FiberBundleX::Pointer ExtractFiberSubset(BaseData* roi); std::vector ExtractFiberIdSubset(BaseData* roi); FiberBundleX::Pointer ExtractFiberSubset(ItkUcharImgType* mask, bool anyPoint, bool invert=false); FiberBundleX::Pointer RemoveFibersOutside(ItkUcharImgType* mask, bool invert=false); vtkSmartPointer GeneratePolyDataByIds( std::vector ); // TODO: make protected void GenerateFiberIds(); // TODO: make protected // get/set data void SetFiberPolyData(vtkSmartPointer, bool updateGeometry = true); vtkSmartPointer GetFiberPolyData(); std::vector< std::string > GetAvailableColorCodings(); char* GetCurrentColorCoding(); itkGetMacro( NumFibers, int) itkGetMacro( FiberSampling, int) itkGetMacro( MinFiberLength, float ) itkGetMacro( MaxFiberLength, float ) itkGetMacro( MeanFiberLength, float ) itkGetMacro( MedianFiberLength, float ) itkGetMacro( LengthStDev, float ) itkGetMacro( UpdateTime2D, itk::TimeStamp ) itkGetMacro( UpdateTime3D, itk::TimeStamp ) void RequestUpdate2D(){ m_UpdateTime2D.Modified(); } void RequestUpdate3D(){ m_UpdateTime3D.Modified(); } unsigned long GetNumberOfPoints(); // copy fiber bundle mitk::FiberBundleX::Pointer GetDeepCopy(); // compare fiber bundles bool Equals(FiberBundleX* fib, double eps=0.0001); - itkSetMacro( ReferenceImage, mitk::Image::Pointer ) - itkGetMacro( ReferenceImage, mitk::Image::Pointer ) + itkSetMacro( ReferenceGeometry, mitk::BaseGeometry::Pointer ) + itkGetMacro( ReferenceGeometry, mitk::BaseGeometry::Pointer ) protected: FiberBundleX( vtkPolyData* fiberPolyData = NULL ); virtual ~FiberBundleX(); itk::Point GetItkPoint(double point[3]); // calculate geometry from fiber extent void UpdateFiberGeometry(); // calculate colorcoding values according to m_CurrentColorCoding void UpdateColorCoding(); private: // actual fiber container vtkSmartPointer m_FiberPolyData; // contains fiber ids vtkSmartPointer m_FiberIdDataSet; char* m_CurrentColorCoding; int m_NumFibers; std::vector< float > m_FiberLengths; float m_MinFiberLength; float m_MaxFiberLength; float m_MeanFiberLength; float m_MedianFiberLength; float m_LengthStDev; int m_FiberSampling; itk::TimeStamp m_UpdateTime2D; itk::TimeStamp m_UpdateTime3D; - - mitk::Image::Pointer m_ReferenceImage; - + mitk::BaseGeometry::Pointer m_ReferenceGeometry; }; } // namespace mitk #endif /* _MITK_FiberBundleX_H */ diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp index 527341766a..22b31f140b 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.cpp @@ -1,302 +1,176 @@ /*=================================================================== 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 "mitkFiberBundleXReader.h" #include #include #include #include #include #include #include #include #include #include #include namespace mitk { void FiberBundleXReader ::GenerateData() { if ( ( ! m_OutputCache ) ) { Superclass::SetNumberOfRequiredOutputs(0); this->GenerateOutputInformation(); } if (!m_OutputCache) { itkWarningMacro("Output cache is empty!"); } Superclass::SetNumberOfRequiredOutputs(1); Superclass::SetNthOutput(0, m_OutputCache.GetPointer()); } void FiberBundleXReader::GenerateOutputInformation() { try { const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, NULL ); setlocale(LC_ALL, locale.c_str()); std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName); ext = itksys::SystemTools::LowerCase(ext); if (ext==".trk") { - MITK_INFO << "Importing fiber bundle from TrackVis ..."; m_OutputCache = OutputType::New(); - TrackVis trk; - trk.open(m_FileName); - trk.read(m_OutputCache); - MITK_INFO << "... done"; + TrackVisFiberReader reader; + reader.open(m_FileName); + reader.read(m_OutputCache); return; } vtkSmartPointer chooser=vtkSmartPointer::New(); chooser->SetFileName(m_FileName.c_str() ); if( chooser->IsFilePolyData()) { - MITK_INFO << "Reading vtk fiber bundle"; vtkSmartPointer reader = vtkSmartPointer::New(); reader->SetFileName( m_FileName.c_str() ); reader->Update(); if ( reader->GetOutput() != NULL ) { vtkSmartPointer fiberPolyData = reader->GetOutput(); m_OutputCache = OutputType::New(fiberPolyData); } } - else // try to read deprecated fiber bundle file format - { - MITK_INFO << "Reading xml fiber bundle"; - - vtkSmartPointer fiberPolyData = vtkSmartPointer::New(); - vtkSmartPointer cellArray = vtkSmartPointer::New(); - vtkSmartPointer points = vtkSmartPointer::New(); - TiXmlDocument doc( m_FileName ); - if(doc.LoadFile()) - { - TiXmlHandle hDoc(&doc); - TiXmlElement* pElem; - TiXmlHandle hRoot(0); - - pElem = hDoc.FirstChildElement().Element(); - - // save this for later - hRoot = TiXmlHandle(pElem); - - pElem = hRoot.FirstChildElement("geometry").Element(); - - // read geometry - mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); - - // read origin - mitk::Point3D origin; - double temp = 0; - pElem->Attribute("origin_x", &temp); - origin[0] = temp; - pElem->Attribute("origin_y", &temp); - origin[1] = temp; - pElem->Attribute("origin_z", &temp); - origin[2] = temp; - geometry->SetOrigin(origin); - - // read spacing - ScalarType spacing[3]; - pElem->Attribute("spacing_x", &temp); - spacing[0] = temp; - pElem->Attribute("spacing_y", &temp); - spacing[1] = temp; - pElem->Attribute("spacing_z", &temp); - spacing[2] = temp; - geometry->SetSpacing(spacing); - - // read transform - vtkMatrix4x4* m = vtkMatrix4x4::New(); - pElem->Attribute("xx", &temp); - m->SetElement(0,0,temp); - pElem->Attribute("xy", &temp); - m->SetElement(1,0,temp); - pElem->Attribute("xz", &temp); - m->SetElement(2,0,temp); - pElem->Attribute("yx", &temp); - m->SetElement(0,1,temp); - pElem->Attribute("yy", &temp); - m->SetElement(1,1,temp); - pElem->Attribute("yz", &temp); - m->SetElement(2,1,temp); - pElem->Attribute("zx", &temp); - m->SetElement(0,2,temp); - pElem->Attribute("zy", &temp); - m->SetElement(1,2,temp); - pElem->Attribute("zz", &temp); - m->SetElement(2,2,temp); - - m->SetElement(0,3,origin[0]); - m->SetElement(1,3,origin[1]); - m->SetElement(2,3,origin[2]); - m->SetElement(3,3,1); - geometry->SetIndexToWorldTransformByVtkMatrix(m); - - // read bounds - float bounds[] = {0, 0, 0, 0, 0, 0}; - pElem->Attribute("size_x", &temp); - bounds[1] = temp; - pElem->Attribute("size_y", &temp); - bounds[3] = temp; - pElem->Attribute("size_z", &temp); - bounds[5] = temp; - geometry->SetFloatBounds(bounds); - geometry->SetImageGeometry(true); - - pElem = hRoot.FirstChildElement("fiber_bundle").FirstChild().Element(); - for( ; pElem ; pElem=pElem->NextSiblingElement()) - { - TiXmlElement* pElem2 = pElem->FirstChildElement(); - - vtkSmartPointer container = vtkSmartPointer::New(); - - for( ; pElem2; pElem2=pElem2->NextSiblingElement()) - { - Point3D point; - pElem2->Attribute("pos_x", &temp); - point[0] = temp; - pElem2->Attribute("pos_y", &temp); - point[1] = temp; - pElem2->Attribute("pos_z", &temp); - point[2] = temp; - - geometry->IndexToWorld(point, point); - vtkIdType id = points->InsertNextPoint(point.GetDataPointer()); - container->GetPointIds()->InsertNextId(id); - - } - cellArray->InsertNextCell(container); - } - fiberPolyData->SetPoints(points); - fiberPolyData->SetLines(cellArray); - - vtkSmartPointer cleaner = vtkSmartPointer::New(); - cleaner->SetInputData(fiberPolyData); - cleaner->Update(); - fiberPolyData = cleaner->GetOutput(); - - m_OutputCache = OutputType::New(fiberPolyData); - } - else - { - MITK_INFO << "could not open xml file"; - throw "could not open xml file"; - } - } setlocale(LC_ALL, currLocale.c_str()); MITK_INFO << "Fiber bundle read"; } catch(...) { throw; } } void FiberBundleXReader::Update() { this->GenerateData(); } const char* FiberBundleXReader ::GetFileName() const { return m_FileName.c_str(); } void FiberBundleXReader ::SetFileName(const char* aFileName) { m_FileName = aFileName; } const char* FiberBundleXReader ::GetFilePrefix() const { return m_FilePrefix.c_str(); } void FiberBundleXReader ::SetFilePrefix(const char* aFilePrefix) { m_FilePrefix = aFilePrefix; } const char* FiberBundleXReader ::GetFilePattern() const { return m_FilePattern.c_str(); } void FiberBundleXReader ::SetFilePattern(const char* aFilePattern) { m_FilePattern = aFilePattern; } bool FiberBundleXReader ::CanReadFile(const std::string filename, const std::string /*filePrefix*/, const std::string /*filePattern*/) { // First check the extension if( filename == "" ) { return false; } std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename); ext = itksys::SystemTools::LowerCase(ext); if (ext == ".fib" || ext == ".trk") { return true; } return false; } BaseDataSource::DataObjectPointer FiberBundleXReader::MakeOutput(const DataObjectIdentifierType &name) { itkDebugMacro("MakeOutput(" << name << ")"); if( this->IsIndexedOutputName(name) ) { return this->MakeOutput( this->MakeIndexFromOutputName(name) ); } return static_cast(OutputType::New().GetPointer()); } BaseDataSource::DataObjectPointer FiberBundleXReader::MakeOutput(DataObjectPointerArraySizeType /*idx*/) { return OutputType::New().GetPointer(); } } //namespace MITK diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.h index dc864066d2..e05e54afe2 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXReader.h @@ -1,82 +1,77 @@ /*=================================================================== 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 __mitkFiberBundleXReader_h #define __mitkFiberBundleXReader_h #include #include #include #include #include namespace mitk { /** \brief */ class MitkFiberTracking_EXPORT FiberBundleXReader : public FileReader, public BaseDataSource { public: /** Types for the standardized TractContainer **/ /* direct linked includes of mitkFiberBundleX DataStructure */ typedef mitk::FiberBundleX OutputType; - mitkClassMacro( FiberBundleXReader, BaseDataSource ); + mitkClassMacro( FiberBundleXReader, BaseDataSource ) itkFactorylessNewMacro(Self) itkCloneMacro(Self) const char* GetFileName() const; void SetFileName(const char* aFileName); const char* GetFilePrefix() const; void SetFilePrefix(const char* aFilePrefix); const char* GetFilePattern() const; void SetFilePattern(const char* aFilePattern); static bool CanReadFile(const std::string filename, const std::string filePrefix, const std::string filePattern); -// itkGetMacro(GroupFiberBundleX, FiberGroupType::Pointer); -// itkGetMacro(TractContainer, ContainerType::Pointer); - virtual void Update(); BaseDataSource::DataObjectPointer MakeOutput(const DataObjectIdentifierType &name); - BaseDataSource::DataObjectPointer MakeOutput( DataObjectPointerArraySizeType idx); protected: /** Does the real work. */ virtual void GenerateData(); virtual void GenerateOutputInformation(); OutputType::Pointer m_OutputCache; std::string m_FileName; std::string m_FilePrefix; std::string m_FilePattern; - private: void operator=(const Self&); //purposely not implemented }; } //namespace MITK #endif // __mitkFiberBundleXReader_h diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp index 94a2815dae..757e6d1c1c 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkFiberBundleXWriter.cpp @@ -1,140 +1,140 @@ /*=================================================================== 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 "mitkFiberBundleXWriter.h" #include #include #include #include #include mitk::FiberBundleXWriter::FiberBundleXWriter() : m_FileName(""), m_FilePrefix(""), m_FilePattern(""), m_Success(false) { this->SetNumberOfRequiredInputs( 1 ); } mitk::FiberBundleXWriter::~FiberBundleXWriter() {} void mitk::FiberBundleXWriter::GenerateData() { try { const std::string& locale = "C"; const std::string& currLocale = setlocale( LC_ALL, NULL ); setlocale(LC_ALL, locale.c_str()); m_Success = false; InputType* input = this->GetInput(); if (input == NULL) { itkWarningMacro(<<"Sorry, input to FiberBundleXWriter is NULL!"); return; } else if ( m_FileName == "" ) { itkWarningMacro( << "Sorry, filename has not been set!" ); return ; } std::string ext = itksys::SystemTools::GetFilenameLastExtension(m_FileName); if (ext==".fib" || ext==".vtk") { MITK_INFO << "Writing fiber bundle as binary VTK"; vtkSmartPointer writer = vtkSmartPointer::New(); writer->SetInputData(input->GetFiberPolyData()); writer->SetFileName(m_FileName.c_str()); writer->SetFileTypeToBinary(); writer->Write(); } else if (ext==".afib") { itksys::SystemTools::ReplaceString(m_FileName,".afib",".fib"); MITK_INFO << "Writing fiber bundle as ascii VTK"; vtkSmartPointer writer = vtkSmartPointer::New(); writer->SetInputData(input->GetFiberPolyData()); writer->SetFileName(m_FileName.c_str()); writer->SetFileTypeToASCII(); writer->Write(); } else if (ext==".avtk") { itksys::SystemTools::ReplaceString(m_FileName,".avtk",".vtk"); MITK_INFO << "Writing fiber bundle as ascii VTK"; vtkSmartPointer writer = vtkSmartPointer::New(); writer->SetInputData(input->GetFiberPolyData()); writer->SetFileName(m_FileName.c_str()); writer->SetFileTypeToASCII(); writer->Write(); } else if (ext==".trk") { MITK_INFO << "Writing fiber bundle as TRK"; - TrackVis trk; + TrackVisFiberReader trk; trk.create(m_FileName, input); trk.writeHdr(); trk.append(input); } setlocale(LC_ALL, currLocale.c_str()); m_Success = true; MITK_INFO << "Fiber bundle written"; } catch(...) { throw; } } void mitk::FiberBundleXWriter::SetInputFiberBundleX( InputType* diffVolumes ) { this->ProcessObject::SetNthInput( 0, diffVolumes ); } mitk::FiberBundleX* mitk::FiberBundleXWriter::GetInput() { if ( this->GetNumberOfInputs() < 1 ) { return NULL; } else { return dynamic_cast ( this->ProcessObject::GetInput( 0 ) ); } } std::vector mitk::FiberBundleXWriter::GetPossibleFileExtensions() { std::vector possibleFileExtensions; possibleFileExtensions.push_back(".fib"); possibleFileExtensions.push_back(".afib"); possibleFileExtensions.push_back(".vtk"); possibleFileExtensions.push_back(".avtk"); possibleFileExtensions.push_back(".trk"); return possibleFileExtensions; } string mitk::FiberBundleXWriter::GetSupportedBaseData() const { return FiberBundleX::GetStaticNameOfClass(); } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.cpp b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.cpp index 6b49d112dc..e34d192642 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.cpp +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.cpp @@ -1,199 +1,237 @@ #include +#include -TrackVis::TrackVis() { filename = ""; fp = NULL; maxSteps = 20000; } +TrackVisFiberReader::TrackVisFiberReader() { m_Filename = ""; m_FilePointer = NULL; } -TrackVis::~TrackVis() { if (fp) fclose( fp ); } +TrackVisFiberReader::~TrackVisFiberReader() { if (m_FilePointer) fclose( m_FilePointer ); } // Create a TrackVis file and store standard metadata. The file is ready to append fibers. // --------------------------------------------------------------------------------------- -short TrackVis::create(string filename , mitk::FiberBundleX *fib) +short TrackVisFiberReader::create(string filename , mitk::FiberBundleX *fib) { // prepare the header for(int i=0; i<3 ;i++) { - if (fib->GetReferenceImage().IsNotNull()) + if (fib->GetReferenceGeometry().IsNotNull()) { - hdr.dim[i] = fib->GetReferenceImage()->GetDimension(i); - hdr.voxel_size[i] = fib->GetReferenceImage()->GetGeometry()->GetSpacing().GetElement(i); - m_Origin[i] = fib->GetReferenceImage()->GetGeometry()->GetOrigin().GetElement(i); + m_Header.dim[i] = fib->GetReferenceGeometry()->GetExtent(i); + m_Header.voxel_size[i] = fib->GetReferenceGeometry()->GetSpacing()[i]; + m_Header.origin[i] = fib->GetReferenceGeometry()->GetOrigin()[i]; } else { - hdr.dim[i] = 1; - hdr.voxel_size[i] = 1; - m_Origin[i] = 0; + m_Header.dim[i] = fib->GetGeometry()->GetExtent(i); + m_Header.voxel_size[i] = fib->GetGeometry()->GetSpacing()[i]; + m_Header.origin[i] = fib->GetGeometry()->GetOrigin()[i]; } - hdr.origin[i] = 0; } - hdr.n_scalars = 0; - hdr.n_properties = 0; - sprintf(hdr.voxel_order,"LPS"); - sprintf(hdr.pad2,"LPS"); - hdr.image_orientation_patient[0] = 1.0; - hdr.image_orientation_patient[1] = 0.0; - hdr.image_orientation_patient[2] = 0.0; - hdr.image_orientation_patient[3] = 0.0; - hdr.image_orientation_patient[4] = 1.0; - hdr.image_orientation_patient[5] = 0.0; - hdr.pad1[0] = 0; - hdr.pad1[1] = 0; - hdr.invert_x = 0; - hdr.invert_y = 0; - hdr.invert_z = 0; - hdr.swap_xy = 0; - hdr.swap_yz = 0; - hdr.swap_zx = 0; - hdr.n_count = 0; - hdr.version = 1; - hdr.hdr_size = 1000; + m_Header.n_scalars = 0; + m_Header.n_properties = 0; + sprintf(m_Header.voxel_order,"LPS"); + m_Header.image_orientation_patient[0] = 1.0; + m_Header.image_orientation_patient[1] = 0.0; + m_Header.image_orientation_patient[2] = 0.0; + m_Header.image_orientation_patient[3] = 0.0; + m_Header.image_orientation_patient[4] = 1.0; + m_Header.image_orientation_patient[5] = 0.0; + m_Header.pad1[0] = 0; + m_Header.pad1[1] = 0; + m_Header.pad2[0] = 0; + m_Header.pad2[1] = 0; + m_Header.invert_x = 0; + m_Header.invert_y = 0; + m_Header.invert_z = 0; + m_Header.swap_xy = 0; + m_Header.swap_yz = 0; + m_Header.swap_zx = 0; + m_Header.n_count = 0; + m_Header.version = 1; + m_Header.hdr_size = 1000; // write the header to the file - fp = fopen(filename.c_str(),"w+b"); - if (fp == NULL) + m_FilePointer = fopen(filename.c_str(),"w+b"); + if (m_FilePointer == NULL) { printf("[ERROR] Unable to create file '%s'\n",filename.c_str()); return 0; } - sprintf(hdr.id_string,"TRACK"); - if (fwrite((char*)&hdr, 1, 1000, fp) != 1000) + sprintf(m_Header.id_string,"TRACK"); + if (fwrite((char*)&m_Header, 1, 1000, m_FilePointer) != 1000) MITK_ERROR << "TrackVis::create : Error occurding during writing fiber."; - this->filename = filename; + this->m_Filename = filename; return 1; } // Open an existing TrackVis file and read metadata information. // The file pointer is positiond at the beginning of fibers data // ------------------------------------------------------------- -short TrackVis::open( string filename ) +short TrackVisFiberReader::open( string filename ) { - fp = fopen(filename.c_str(),"r+b"); - if (fp == NULL) + m_FilePointer = fopen(filename.c_str(),"r+b"); + if (m_FilePointer == NULL) { printf("[ERROR] Unable to open file '%s'\n",filename.c_str()); return 0; } - this->filename = filename; + this->m_Filename = filename; - return fread((char*)(&hdr), 1, 1000, fp); + return fread((char*)(&m_Header), 1, 1000, m_FilePointer); } // Append a fiber to the file // -------------------------- -short TrackVis::append(mitk::FiberBundleX *fib) +short TrackVisFiberReader::append(mitk::FiberBundleX *fib) { vtkPolyData* poly = fib->GetFiberPolyData(); for (int i=0; iGetNumFibers(); i++) { vtkCell* cell = poly->GetCell(i); int numPoints = cell->GetNumberOfPoints(); vtkPoints* points = cell->GetPoints(); unsigned int numSaved, pos = 0; //float* tmp = new float[3*maxSteps]; std::vector< float > tmp; tmp.reserve(3*numPoints); - if ( numPoints > maxSteps ) - { - printf( "[ERROR] Trying to write a fiber too long!\n" ); - return 0; - } - numSaved = numPoints; for(unsigned int i=0; iGetPoint(i); - tmp[pos++] = p[0] - m_Origin[0]; - tmp[pos++] = p[1] - m_Origin[1]; - tmp[pos++] = p[2] - m_Origin[2]; + tmp[pos++] = p[0]; + tmp[pos++] = p[1]; + tmp[pos++] = p[2]; } // write the coordinates to the file - if ( fwrite((char*)&numSaved, 1, 4, fp) != 4 ) + if ( fwrite((char*)&numSaved, 1, 4, m_FilePointer) != 4 ) { printf( "[ERROR] Problems saving the fiber!\n" ); return 1; } - if ( fwrite((char*)&(tmp.front()), 1, 4*pos, fp) != 4*pos ) + if ( fwrite((char*)&(tmp.front()), 1, 4*pos, m_FilePointer) != 4*pos ) { printf( "[ERROR] Problems saving the fiber!\n" ); return 1; } } return 0; } - - //// Read one fiber from the file //// ---------------------------- -short TrackVis::read( mitk::FiberBundleX* fib ) +short TrackVisFiberReader::read( mitk::FiberBundleX* fib ) { int numPoints; vtkSmartPointer vtkNewPoints = vtkSmartPointer::New(); vtkSmartPointer vtkNewCells = vtkSmartPointer::New(); - while (fread((char*)&numPoints, 1, 4, fp)==4) + while (fread((char*)&numPoints, 1, 4, m_FilePointer)==4) { - if ( numPoints >= maxSteps || numPoints <= 0 ) + if ( numPoints <= 0 ) { printf( "[ERROR] Trying to read a fiber with %d points!\n", numPoints ); return -1; } vtkSmartPointer container = vtkSmartPointer::New(); float tmp[3]; for(int i=0; iInsertNextPoint(tmp); container->GetPointIds()->InsertNextId(id); } vtkNewCells->InsertNextCell(container); } vtkSmartPointer fiberPolyData = vtkSmartPointer::New(); fiberPolyData->SetPoints(vtkNewPoints); fiberPolyData->SetLines(vtkNewCells); - fib->SetFiberPolyData(fiberPolyData); + + MITK_INFO << "Coordinate convention: " << m_Header.voxel_order; + + mitk::Geometry3D::Pointer geometry = mitk::Geometry3D::New(); + vtkSmartPointer< vtkMatrix4x4 > matrix = vtkSmartPointer< vtkMatrix4x4 >::New(); + matrix->Identity(); + + if (m_Header.voxel_order[0]=='R') + matrix->SetElement(0,0,-matrix->GetElement(0,0)); + if (m_Header.voxel_order[1]=='A') + matrix->SetElement(1,1,-matrix->GetElement(1,1)); + if (m_Header.voxel_order[2]=='I') + matrix->SetElement(2,2,-matrix->GetElement(2,2)); + + geometry->SetIndexToWorldTransformByVtkMatrix(matrix); + + vtkSmartPointer transformFilter = vtkSmartPointer::New(); + transformFilter->SetInputData(fiberPolyData); + transformFilter->SetTransform(geometry->GetVtkTransform()); + transformFilter->Update(); + fib->SetFiberPolyData(transformFilter->GetOutput()); + + mitk::Point3D origin; + origin[0]=m_Header.origin[0]; + origin[1]=m_Header.origin[1]; + origin[2]=m_Header.origin[2]; + geometry->SetOrigin(origin); + + mitk::Vector3D spacing; + spacing[0]=m_Header.voxel_size[0]; + spacing[1]=m_Header.voxel_size[1]; + spacing[2]=m_Header.voxel_size[2]; + geometry->SetSpacing(spacing); + + geometry->SetExtentInMM(0, m_Header.voxel_size[0]*m_Header.dim[0]); + geometry->SetExtentInMM(1, m_Header.voxel_size[1]*m_Header.dim[1]); + geometry->SetExtentInMM(2, m_Header.voxel_size[2]*m_Header.dim[2]); + + fib->SetReferenceGeometry(dynamic_cast(geometry.GetPointer())); return numPoints; } // Update the field in the header to the new FIBER TOTAL. // ------------------------------------------------------ -void TrackVis::updateTotal( int totFibers ) +void TrackVisFiberReader::updateTotal( int totFibers ) { - fseek(fp, 1000-12, SEEK_SET); - if (fwrite((char*)&totFibers, 1, 4, fp) != 4) + fseek(m_FilePointer, 1000-12, SEEK_SET); + if (fwrite((char*)&totFibers, 1, 4, m_FilePointer) != 4) MITK_ERROR << "[ERROR] Problems saving the fiber!"; } -void TrackVis::writeHdr() +void TrackVisFiberReader::writeHdr() { - fseek(fp, 0, SEEK_SET); - if (fwrite((char*)&hdr, 1, 1000, fp) != 1000) + fseek(m_FilePointer, 0, SEEK_SET); + if (fwrite((char*)&m_Header, 1, 1000, m_FilePointer) != 1000) MITK_ERROR << "[ERROR] Problems saving the fiber!"; } // Close the TrackVis file, but keep the metadata in the header. // ------------------------------------------------------------- -void TrackVis::close() +void TrackVisFiberReader::close() +{ + fclose(m_FilePointer); + m_FilePointer = NULL; +} + +bool TrackVisFiberReader::IsTransformValid() { - fclose(fp); - fp = NULL; + if (fabs(m_Header.image_orientation_patient[0])<=0.001 || fabs(m_Header.image_orientation_patient[3])<=0.001 || fabs(m_Header.image_orientation_patient[5])<=0.001) + return false; + return true; } diff --git a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.h b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.h index 56d0111c19..8d9ad1a8d9 100644 --- a/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.h +++ b/Modules/DiffusionImaging/FiberTracking/IODataStructures/FiberBundleX/mitkTrackvis.h @@ -1,83 +1,82 @@ /*=================================================================== 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 _TRACKVIS #define _TRACKVIS #include #include #include #include #include #include #include #include using namespace std; // Structure to hold metadata of a TrackVis file // --------------------------------------------- struct TrackVis_header { char id_string[6]; short int dim[3]; float voxel_size[3]; float origin[3]; short int n_scalars; char scalar_name[10][20]; short int n_properties; char property_name[10][20]; char reserved[508]; char voxel_order[4]; char pad2[4]; float image_orientation_patient[6]; char pad1[2]; unsigned char invert_x; unsigned char invert_y; unsigned char invert_z; unsigned char swap_xy; unsigned char swap_yz; unsigned char swap_zx; int n_count; int version; int hdr_size; }; // Class to handle TrackVis files. // ------------------------------- -class MitkFiberTracking_EXPORT TrackVis +class MitkFiberTracking_EXPORT TrackVisFiberReader { private: - string filename; - FILE* fp; - int maxSteps; // [TODO] should be related to the variable defined for fiber-tracking + string m_Filename; + FILE* m_FilePointer; public: - TrackVis_header hdr; - float m_Origin[3]; + TrackVis_header m_Header; - short create(string filename, mitk::FiberBundleX* fib); - short open( string filename ); - short read( mitk::FiberBundleX* fib ); - short append( mitk::FiberBundleX* fib ); + short create(string m_Filename, mitk::FiberBundleX* fib); + short open( string m_Filename ); + short read( mitk::FiberBundleX* fib ); + short append( mitk::FiberBundleX* fib ); void writeHdr(); void updateTotal( int totFibers ); void close(); + bool IsTransformValid(); - TrackVis(); - ~TrackVis(); + TrackVisFiberReader(); + ~TrackVisFiberReader(); }; #endif diff --git a/Modules/DiffusionImaging/MiniApps/CMakeLists.txt b/Modules/DiffusionImaging/MiniApps/CMakeLists.txt index 5f79886390..66e1fbdc43 100755 --- a/Modules/DiffusionImaging/MiniApps/CMakeLists.txt +++ b/Modules/DiffusionImaging/MiniApps/CMakeLists.txt @@ -1,64 +1,65 @@ option(BUILD_DiffusionMiniApps "Build commandline tools for diffusion" OFF) if(BUILD_DiffusionMiniApps OR MITK_BUILD_ALL_APPS) # needed include directories include_directories( ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR} ) project( MitkDiffusionMiniApps ) # fill in the standalone executables here set(DIFFUSIONMINIAPPS mitkDiffusionMiniApps ) # set additional files here set(DIFFUSIONCORE_ADDITIONAL_FILES MiniAppManager.cpp FileFormatConverter.cpp TensorReconstruction.cpp QballReconstruction.cpp DiffusionIndices.cpp CopyGeometry.cpp GibbsTracking.cpp StreamlineTracking.cpp FiberProcessing.cpp LocalDirectionalFiberPlausibility.cpp #TractogramAngularError.cpp FiberDirectionExtraction.cpp PeakExtraction.cpp PeaksAngularError.cpp MultishellMethods.cpp Fiberfox.cpp ExportShImage.cpp NetworkCreation.cpp NetworkStatistics.cpp DwiDenoising.cpp + TractometerMetrics.cpp ) # deprecated # FOREACH(tool ${DIFFUSIONMINIAPPS}) # ADD_EXECUTABLE( # ${tool} # ${tool}.cpp # ${DIFFUSIONCORE_ADDITIONAL_FILES} # ) # TARGET_LINK_LIBRARIES( # ${tool} # ${ALL_LIBRARIES} ) # ENDFOREACH(tool) mitk_create_executable(DiffusionMiniApps DEPENDS MitkDiffusionCore MitkFiberTracking MitkConnectomics PACKAGE_DEPENDS ITK|ITKDiffusionTensorImage ) if(EXECUTABLE_IS_ENABLED) MITK_INSTALL_TARGETS(EXECUTABLES ${EXECUTABLE_TARGET}) endif() endif() diff --git a/Modules/DiffusionImaging/MiniApps/CopyGeometry.cpp b/Modules/DiffusionImaging/MiniApps/CopyGeometry.cpp index 5f9c51eba6..5495b3093e 100755 --- a/Modules/DiffusionImaging/MiniApps/CopyGeometry.cpp +++ b/Modules/DiffusionImaging/MiniApps/CopyGeometry.cpp @@ -1,97 +1,93 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include "ctkCommandLineParser.h" using namespace mitk; #include "ctkCommandLineParser.h" int CopyGeometry(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Copy Geometry"); parser.setCategory("Preprocessing Tools"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("in", "i", ctkCommandLineParser::InputFile, "Input:", "input image", us::Any(), false); parser.addArgument("ref", "r", ctkCommandLineParser::InputFile, "Reference:", "reference image", us::Any(), false); parser.addArgument("out", "o", ctkCommandLineParser::OutputFile, "Output:", "output image", us::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string imageName = us::any_cast(parsedArgs["in"]); string refImage = us::any_cast(parsedArgs["ref"]); string outImage = us::any_cast(parsedArgs["out"]); try { - - MITK_INFO << "Loading image " << imageName; const std::string s1="", s2=""; std::vector infile = BaseDataIO::LoadBaseDataFromFile( refImage, s1, s2, false ); Image::Pointer source = dynamic_cast(infile.at(0).GetPointer()); infile = BaseDataIO::LoadBaseDataFromFile( imageName, s1, s2, false ); Image::Pointer target = dynamic_cast(infile.at(0).GetPointer()); mitk::BaseGeometry* s_geom = source->GetGeometry(); mitk::BaseGeometry* t_geom = target->GetGeometry(); t_geom->SetIndexToWorldTransform(s_geom->GetIndexToWorldTransform()); target->SetGeometry(t_geom); if ( dynamic_cast*>(target.GetPointer()) ) { - MITK_INFO << "Writing " << outImage; DiffusionImage::Pointer dwi = dynamic_cast*>(target.GetPointer()); NrrdDiffusionImageWriter::Pointer writer = NrrdDiffusionImageWriter::New(); writer->SetFileName(outImage); writer->SetInput(dwi); writer->Update(); } else mitk::IOUtil::SaveImage(target, outImage); } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } - MITK_INFO << "DONE"; return EXIT_SUCCESS; } RegisterDiffusionMiniApp(CopyGeometry); diff --git a/Modules/DiffusionImaging/MiniApps/DiffusionIndices.cpp b/Modules/DiffusionImaging/MiniApps/DiffusionIndices.cpp index 292e94f8f3..8e768840f7 100644 --- a/Modules/DiffusionImaging/MiniApps/DiffusionIndices.cpp +++ b/Modules/DiffusionImaging/MiniApps/DiffusionIndices.cpp @@ -1,152 +1,149 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include /** * Calculate indices derived from Qball or tensor images */ int DiffusionIndices(int argc, char* argv[]) { + MITK_INFO << "DiffusionIndices"; ctkCommandLineParser parser; parser.setTitle("Diffusion Indices"); parser.setCategory("Diffusion Related Measures"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input image (tensor, Q-ball or FSL/MRTrix SH-coefficient image)", us::Any(), false); parser.addArgument("index", "idx", ctkCommandLineParser::String, "Index:", "index (fa, gfa, ra, ad, rd, ca, l2, l3, md)", us::Any(), false); parser.addArgument("outFile", "o", ctkCommandLineParser::OutputFile, "Output:", "output file", us::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string inFileName = us::any_cast(parsedArgs["input"]); string index = us::any_cast(parsedArgs["index"]); string outFileName = us::any_cast(parsedArgs["outFile"]); string ext = itksys::SystemTools::GetFilenameLastExtension(outFileName); if (ext.empty()) outFileName += ".nrrd"; try { // load input image const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); if( boost::algorithm::ends_with(inFileName, ".qbi") && index=="gfa" ) { typedef itk::Vector OdfVectorType; typedef itk::Image ItkQballImageType; mitk::QBallImage::Pointer mitkQballImage = dynamic_cast(infile.at(0).GetPointer()); ItkQballImageType::Pointer itk_qbi = ItkQballImageType::New(); mitk::CastToItkImage(mitkQballImage, itk_qbi); typedef itk::DiffusionQballGeneralizedFaImageFilter GfaFilterType; GfaFilterType::Pointer gfaFilter = GfaFilterType::New(); gfaFilter->SetInput(itk_qbi); gfaFilter->SetComputationMethod(GfaFilterType::GFA_STANDARD); gfaFilter->Update(); - MITK_INFO << "Writing " << outFileName; - itk::ImageFileWriter< itk::Image >::Pointer fileWriter = itk::ImageFileWriter< itk::Image >::New(); fileWriter->SetInput(gfaFilter->GetOutput()); fileWriter->SetFileName(outFileName); fileWriter->Update(); } else if( boost::algorithm::ends_with(inFileName, ".dti") ) { typedef itk::Image< itk::DiffusionTensor3D, 3 > ItkTensorImage; mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast(infile.at(0).GetPointer()); ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); mitk::CastToItkImage(mitkTensorImage, itk_dti); typedef itk::TensorDerivedMeasurementsFilter MeasurementsType; MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itk_dti.GetPointer() ); if(index=="fa") measurementsCalculator->SetMeasure(MeasurementsType::FA); else if(index=="ra") measurementsCalculator->SetMeasure(MeasurementsType::RA); else if(index=="ad") measurementsCalculator->SetMeasure(MeasurementsType::AD); else if(index=="rd") measurementsCalculator->SetMeasure(MeasurementsType::RD); else if(index=="ca") measurementsCalculator->SetMeasure(MeasurementsType::CA); else if(index=="l2") measurementsCalculator->SetMeasure(MeasurementsType::L2); else if(index=="l3") measurementsCalculator->SetMeasure(MeasurementsType::L3); else if(index=="md") measurementsCalculator->SetMeasure(MeasurementsType::MD); else { MITK_WARN << "No valid diffusion index for input image (tensor image) defined"; return EXIT_FAILURE; } measurementsCalculator->Update(); - MITK_INFO << "Writing " << outFileName; - itk::ImageFileWriter< itk::Image >::Pointer fileWriter = itk::ImageFileWriter< itk::Image >::New(); fileWriter->SetInput(measurementsCalculator->GetOutput()); fileWriter->SetFileName(outFileName); fileWriter->Update(); } else MITK_INFO << "Diffusion index " << index << " not supported for supplied file type."; } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(DiffusionIndices); diff --git a/Modules/DiffusionImaging/MiniApps/DwiDenoising.cpp b/Modules/DiffusionImaging/MiniApps/DwiDenoising.cpp index 6e7ecdc5d0..28f0d0402d 100644 --- a/Modules/DiffusionImaging/MiniApps/DwiDenoising.cpp +++ b/Modules/DiffusionImaging/MiniApps/DwiDenoising.cpp @@ -1,168 +1,165 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include typedef mitk::DiffusionImage DiffusionImageType; typedef itk::Image ImageType; mitk::BaseData::Pointer LoadFile(std::string filename) { if( filename.empty() ) return NULL; const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( filename, s1, s2, false ); if( infile.empty() ) { MITK_INFO << "File " << filename << " could not be read!"; return NULL; } mitk::BaseData::Pointer baseData = infile.at(0); return baseData; } /** * Denoises DWI using the Nonlocal - Means algorithm */ int DwiDenoising(int argc, char* argv[]) { + MITK_INFO << "DwiDenoising"; ctkCommandLineParser parser; parser.setTitle("DWI Denoising"); parser.setCategory("Preprocessing Tools"); parser.setContributor("MBI"); parser.setDescription("Denoising for diffusion weighted images using a non-local means algorithm."); parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input image (DWI)", us::Any(), false); parser.addArgument("variance", "v", ctkCommandLineParser::Float, "Variance:", "noise variance", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask:", "brainmask for input image", us::Any(), true); parser.addArgument("search", "s", ctkCommandLineParser::Int, "Search radius:", "search radius", us::Any(), true); parser.addArgument("compare", "c", ctkCommandLineParser::Int, "Comparison radius:", "comparison radius", us::Any(), true); parser.addArgument("joint", "j", ctkCommandLineParser::Bool, "Joint information:", "use joint information"); parser.addArgument("rician", "r", ctkCommandLineParser::Bool, "Rician adaption:", "use rician adaption"); parser.changeParameterGroup("Output", "Output of this miniapp"); parser.addArgument("output", "o", ctkCommandLineParser::OutputFile, "Output:", "output image (DWI)", us::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string inFileName = us::any_cast(parsedArgs["input"]); double variance = static_cast(us::any_cast(parsedArgs["variance"])); string maskName; if (parsedArgs.count("mask")) maskName = us::any_cast(parsedArgs["mask"]); string outFileName = us::any_cast(parsedArgs["output"]); // boost::algorithm::erase_all(outFileName, ".dwi"); int search = 4; if (parsedArgs.count("search")) search = us::any_cast(parsedArgs["search"]); int compare = 1; if (parsedArgs.count("compare")) compare = us::any_cast(parsedArgs["compare"]); bool joint = false; if (parsedArgs.count("joint")) joint = true; bool rician = false; if (parsedArgs.count("rician")) rician = true; try { if( boost::algorithm::ends_with(inFileName, ".dwi")) { DiffusionImageType::Pointer dwi = dynamic_cast(LoadFile(inFileName).GetPointer()); itk::NonLocalMeansDenoisingFilter::Pointer filter = itk::NonLocalMeansDenoisingFilter::New(); filter->SetNumberOfThreads(12); filter->SetInputImage(dwi->GetVectorImage()); if (!maskName.empty()) { mitk::Image::Pointer mask = dynamic_cast(LoadFile(maskName).GetPointer()); ImageType::Pointer itkMask = ImageType::New(); mitk::CastToItkImage(mask, itkMask); filter->SetInputMask(itkMask); } filter->SetUseJointInformation(joint); filter->SetUseRicianAdaption(rician); filter->SetSearchRadius(search); filter->SetComparisonRadius(compare); filter->SetVariance(variance); filter->Update(); DiffusionImageType::Pointer output = DiffusionImageType::New(); output->SetVectorImage(filter->GetOutput()); output->SetReferenceBValue(dwi->GetReferenceBValue()); output->SetDirections(dwi->GetDirections()); output->InitializeFromVectorImage(); // std::stringstream name; // name << outFileName << "_NLM_" << search << "-" << compare << "-" << variance << ".dwi"; - MITK_INFO << "Writing: " << outFileName; - mitk::NrrdDiffusionImageWriter::Pointer writer = mitk::NrrdDiffusionImageWriter::New(); writer->SetInput(output); writer->SetFileName(outFileName/*.str()*/); writer->Update(); - - MITK_INFO << "Finish!"; } else { MITK_INFO << "Only supported for .dwi!"; } } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(DwiDenoising); diff --git a/Modules/DiffusionImaging/MiniApps/ExportShImage.cpp b/Modules/DiffusionImaging/MiniApps/ExportShImage.cpp index e81690ffb5..8bbd36c37b 100755 --- a/Modules/DiffusionImaging/MiniApps/ExportShImage.cpp +++ b/Modules/DiffusionImaging/MiniApps/ExportShImage.cpp @@ -1,140 +1,138 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include template int StartShConversion(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Export SH Image"); parser.setCategory("Preprocessing Tools"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "MITK SH image", us::Any(), false); parser.addArgument("output", "o", ctkCommandLineParser::InputFile, "Output", "MRtrix SH image", us::Any(), false); parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "SH order:", "spherical harmonics order"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string inFile = us::any_cast(parsedArgs["input"]); string outFile = us::any_cast(parsedArgs["output"]); try { typedef itk::Image< float, 4 > OutImageType; typedef itk::Image< itk::Vector< float, (shOrder*shOrder + shOrder + 2)/2 + shOrder >, 3 > InputImageType; typename InputImageType::Pointer itkInImage = InputImageType::New(); typedef itk::ImageFileReader< InputImageType > ReaderType; typename ReaderType::Pointer reader = ReaderType::New(); MITK_INFO << "reading " << inFile; reader->SetFileName(inFile.c_str()); reader->Update(); itkInImage = reader->GetOutput(); // extract directions from fiber bundle typename itk::ShCoefficientImageExporter::Pointer filter = itk::ShCoefficientImageExporter::New(); filter->SetInputImage(itkInImage); filter->GenerateData(); OutImageType::Pointer outImage = filter->GetOutputImage(); typedef itk::ImageFileWriter< OutImageType > WriterType; WriterType::Pointer writer = WriterType::New(); - MITK_INFO << "writing " << outFile; writer->SetFileName(outFile.c_str()); writer->SetInput(outImage); writer->Update(); - - MITK_INFO << "DONE"; } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } int ExportShImage(int argc, char* argv[]) { + MITK_INFO << "ExportShImage"; ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input image", "MITK SH image", us::Any(), false); parser.addArgument("output", "o", ctkCommandLineParser::OutputFile, "Output image", "MRtrix SH image", us::Any(), false); parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "Spherical harmonics order", "spherical harmonics order"); parser.setCategory("Preprocessing Tools"); parser.setTitle("Export SH Image"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; int shOrder = -1; if (parsedArgs.count("shOrder")) shOrder = us::any_cast(parsedArgs["shOrder"]); switch (shOrder) { case 4: return StartShConversion<4>(argc, argv); case 6: return StartShConversion<6>(argc, argv); case 8: return StartShConversion<8>(argc, argv); case 10: return StartShConversion<10>(argc, argv); case 12: return StartShConversion<12>(argc, argv); } return EXIT_FAILURE; } RegisterDiffusionMiniApp(ExportShImage); diff --git a/Modules/DiffusionImaging/MiniApps/FiberDirectionExtraction.cpp b/Modules/DiffusionImaging/MiniApps/FiberDirectionExtraction.cpp index e6cb2efd48..1488960489 100755 --- a/Modules/DiffusionImaging/MiniApps/FiberDirectionExtraction.cpp +++ b/Modules/DiffusionImaging/MiniApps/FiberDirectionExtraction.cpp @@ -1,185 +1,182 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include int FiberDirectionExtraction(int argc, char* argv[]) { + MITK_INFO << "FiberDirectionExtraction"; ctkCommandLineParser parser; parser.setTitle("Fiber Direction Extraction"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input tractogram (.fib, vtk ascii file format)", us::Any(), false); parser.addArgument("out", "o", ctkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask:", "mask image"); parser.addArgument("athresh", "a", ctkCommandLineParser::Float, "Angular threshold:", "angular threshold in degrees. closer fiber directions are regarded as one direction and clustered together.", 25, true); parser.addArgument("peakthresh", "t", ctkCommandLineParser::Float, "Peak size threshold:", "peak size threshold relative to largest peak in voxel", 0.2, true); parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "Verbose:", "output optional and intermediate calculation results"); parser.addArgument("numdirs", "d", ctkCommandLineParser::Int, "Max. num. directions:", "maximum number of fibers per voxel", 3, true); parser.addArgument("normalize", "n", ctkCommandLineParser::Bool, "Normalize:", "normalize vectors"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string fibFile = us::any_cast(parsedArgs["input"]); string maskImage(""); if (parsedArgs.count("mask")) maskImage = us::any_cast(parsedArgs["mask"]); float peakThreshold = 0.2; if (parsedArgs.count("peakthresh")) peakThreshold = us::any_cast(parsedArgs["peakthresh"]); float angularThreshold = 25; if (parsedArgs.count("athresh")) angularThreshold = us::any_cast(parsedArgs["athresh"]); string outRoot = us::any_cast(parsedArgs["out"]); bool verbose = false; if (parsedArgs.count("verbose")) verbose = us::any_cast(parsedArgs["verbose"]); int maxNumDirs = 3; if (parsedArgs.count("numdirs")) maxNumDirs = us::any_cast(parsedArgs["numdirs"]); bool normalize = false; if (parsedArgs.count("normalize")) normalize = us::any_cast(parsedArgs["normalize"]); try { 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(mitk::IOUtil::LoadDataNode(fibFile)->GetData()); // load/create mask image ItkUcharImgType::Pointer itkMaskImage = NULL; if (maskImage.compare("")!=0) { MITK_INFO << "Using mask image"; itkMaskImage = ItkUcharImgType::New(); mitk::Image::Pointer mitkMaskImage = dynamic_cast(mitk::IOUtil::LoadDataNode(maskImage)->GetData()); mitk::CastToItkImage(mitkMaskImage, itkMaskImage); } // extract directions from fiber bundle itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); fOdfFilter->SetFiberBundle(inputTractogram); fOdfFilter->SetMaskImage(itkMaskImage); fOdfFilter->SetAngularThreshold(cos(angularThreshold*M_PI/180)); fOdfFilter->SetNormalizeVectors(normalize); fOdfFilter->SetUseWorkingCopy(false); fOdfFilter->SetSizeThreshold(peakThreshold); fOdfFilter->SetMaxNumDirections(maxNumDirs); fOdfFilter->Update(); ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); // write direction images for (unsigned int i=0; iSize(); i++) { itk::TractsToVectorImageFilter::ItkDirectionImageType::Pointer itkImg = directionImageContainer->GetElement(i); typedef itk::ImageFileWriter< itk::TractsToVectorImageFilter::ItkDirectionImageType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_DIRECTION_"); outfilename.append(boost::lexical_cast(i)); outfilename.append(".nrrd"); - MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(itkImg); writer->Update(); } if (verbose) { // write vector field mitk::FiberBundleX::Pointer directions = fOdfFilter->GetOutputFiberBundle(); mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(directions.GetPointer()) ) { string outfilename = outRoot; outfilename.append("_VECTOR_FIELD.fib"); (*it)->SetFileName( outfilename.c_str() ); (*it)->DoWrite( directions.GetPointer() ); } } // write num direction image { ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage(); typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_NUM_DIRECTIONS.nrrd"); - MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(numDirImage); writer->Update(); } } - - MITK_INFO << "DONE"; } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(FiberDirectionExtraction); diff --git a/Modules/DiffusionImaging/MiniApps/FiberExtraction.cpp b/Modules/DiffusionImaging/MiniApps/FiberExtraction.cpp index 6b536d7874..cab8803780 100755 --- a/Modules/DiffusionImaging/MiniApps/FiberExtraction.cpp +++ b/Modules/DiffusionImaging/MiniApps/FiberExtraction.cpp @@ -1,159 +1,158 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include int FiberExtraction(int argc, char* argv[]) { + MITK_INFO << "FiberExtraction"; ctkCommandLineParser parser; parser.setTitle("Fiber Extraction"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setContributor("MBI"); parser.setDescription(""); parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::String, "Input:", "input tractogram (.fib, vtk ascii file format)", us::Any(), false); parser.addArgument("out", "o", ctkCommandLineParser::String, "Output:", "output tractogram", us::Any(), false); parser.addArgument("planfirgure1", "pf1", ctkCommandLineParser::String, "Figure 1:", "first ROI", us::Any(), false); parser.addArgument("planfirgure2", "pf2", ctkCommandLineParser::String, "Figure 2:", "second ROI", us::Any()); parser.addArgument("operation", "op", ctkCommandLineParser::String, "Operation:", "logical operation (AND, OR, NOT)", us::Any()); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string inFib = us::any_cast(parsedArgs["input"]); string outFib = us::any_cast(parsedArgs["out"]); string pf1_path = us::any_cast(parsedArgs["planfirgure1"]); string operation(""); string pf2_path(""); if (parsedArgs.count("operation")) { operation = us::any_cast(parsedArgs["operation"]); if (parsedArgs.count("planfirgure2") && (operation=="AND" || operation=="OR")) pf2_path = us::any_cast(parsedArgs["planfirgure2"]); } try { typedef itk::Image ItkUcharImgType; // load fiber bundle mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast(mitk::IOUtil::LoadDataNode(inFib)->GetData()); mitk::FiberBundleX::Pointer result; mitk::BaseData::Pointer input1 = mitk::IOUtil::LoadDataNode(pf1_path)->GetData(); mitk::PlanarFigure::Pointer pf1 = dynamic_cast(input1.GetPointer()); if (pf1.IsNotNull()) { mitk::BaseData::Pointer input2; mitk::PlanarFigure::Pointer pf2; if (!pf2_path.empty()) { input2 = mitk::IOUtil::LoadDataNode(pf2_path)->GetData(); pf2 = dynamic_cast(input2.GetPointer()); } mitk::PlanarFigureComposite::Pointer pfc = mitk::PlanarFigureComposite::New(); if (operation.empty()) { result = inputTractogram->ExtractFiberSubset(input1); } else if (operation=="NOT") { pfc->setOperationType(mitk::PFCOMPOSITION_NOT_OPERATION); pfc->addPlanarFigure(input1); result = inputTractogram->ExtractFiberSubset(pfc); } else if (operation=="AND" && pf2.IsNotNull()) { pfc->setOperationType(mitk::PFCOMPOSITION_AND_OPERATION); pfc->addPlanarFigure(input1); pfc->addPlanarFigure(input2); result = inputTractogram->ExtractFiberSubset(pfc); } else if (operation=="OR" && pf2.IsNotNull()) { pfc->setOperationType(mitk::PFCOMPOSITION_OR_OPERATION); pfc->addPlanarFigure(input1); pfc->addPlanarFigure(input2); result = inputTractogram->ExtractFiberSubset(pfc); } else { MITK_INFO << "Could not process input:"; MITK_INFO << pf1_path; MITK_INFO << pf2_path; MITK_INFO << operation; } } else { ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New(); mitk::Image::Pointer mitkMaskImage = dynamic_cast(mitk::IOUtil::LoadDataNode(pf1_path)->GetData()); mitk::CastToItkImage(mitkMaskImage, itkMaskImage); if (operation=="NOT") result = inputTractogram->ExtractFiberSubset(itkMaskImage, true, true); else result = inputTractogram->ExtractFiberSubset(itkMaskImage, true, false); } if (result.IsNotNull()) mitk::IOUtil::SaveBaseData(result, outFib); else MITK_INFO << "No valid fiber bundle extracted."; - - MITK_INFO << "DONE"; } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(FiberExtraction); diff --git a/Modules/DiffusionImaging/MiniApps/FiberProcessing.cpp b/Modules/DiffusionImaging/MiniApps/FiberProcessing.cpp index 4cc65437d9..52d81f0705 100644 --- a/Modules/DiffusionImaging/MiniApps/FiberProcessing.cpp +++ b/Modules/DiffusionImaging/MiniApps/FiberProcessing.cpp @@ -1,240 +1,240 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include mitk::FiberBundleX::Pointer LoadFib(std::string filename) { const std::string s1="", s2=""; std::vector fibInfile = mitk::BaseDataIO::LoadBaseDataFromFile( filename, s1, s2, false ); if( fibInfile.empty() ) MITK_INFO << "File " << filename << " could not be read!"; mitk::BaseData::Pointer baseData = fibInfile.at(0); return dynamic_cast(baseData.GetPointer()); } int FiberProcessing(int argc, char* argv[]) { + MITK_INFO << "FiberProcessing"; ctkCommandLineParser parser; parser.setTitle("Fiber Processing"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input fiber bundle (.fib)", us::Any(), false); parser.addArgument("outFile", "o", ctkCommandLineParser::OutputFile, "Output:", "output fiber bundle (.fib)", us::Any(), false); parser.addArgument("resample", "r", ctkCommandLineParser::Float, "Resample:", "Resample fiber with the given point distance (in mm)"); parser.addArgument("smooth", "s", ctkCommandLineParser::Float, "Smooth:", "Smooth fiber with the given point distance (in mm)"); parser.addArgument("minLength", "l", ctkCommandLineParser::Float, "Minimum length:", "Minimum fiber length (in mm)"); parser.addArgument("maxLength", "m", ctkCommandLineParser::Float, "Maximum length:", "Maximum fiber length (in mm)"); parser.addArgument("minCurv", "a", ctkCommandLineParser::Float, "Minimum curvature radius:", "Minimum curvature radius (in mm)"); parser.addArgument("mirror", "p", ctkCommandLineParser::Int, "Invert coordinates:", "Invert fiber coordinates XYZ (e.g. 010 to invert y-coordinate of each fiber point)"); parser.addArgument("copyAndJoin", "c", ctkCommandLineParser::Bool, "Copy & Join:", "Create a copy of the input fiber bundle (applied after resample/smooth/minLength/maxLength/minCurv/mirror) and join copy with original (applied after rotate/scale/translate)"); //parser.addArgument("join", "j", ctkCommandLineParser::Bool, "Join the original and copied fiber bundle (applied after rotate/scale/translate)"); parser.addArgument("rotate-x", "rx", ctkCommandLineParser::Float, "Rotate x-axis:", "Rotate around x-axis (if copy is given the copy is rotated, in deg)"); parser.addArgument("rotate-y", "ry", ctkCommandLineParser::Float, "Rotate y-axis:", "Rotate around y-axis (if copy is given the copy is rotated, in deg)"); parser.addArgument("rotate-z", "rz", ctkCommandLineParser::Float, "Rotate z-axis:", "Rotate around z-axis (if copy is given the copy is rotated, in deg)"); parser.addArgument("scale-x", "sx", ctkCommandLineParser::Float, "Scale x-axis:", "Scale in direction of x-axis (if copy is given the copy is scaled)"); parser.addArgument("scale-y", "sy", ctkCommandLineParser::Float, "Scale y-axis:", "Scale in direction of y-axis (if copy is given the copy is scaled)"); parser.addArgument("scale-z", "sz", ctkCommandLineParser::Float, "Scale z-axis", "Scale in direction of z-axis (if copy is given the copy is scaled)"); parser.addArgument("translate-x", "tx", ctkCommandLineParser::Float, "Translate x-axis:", "Translate in direction of x-axis (if copy is given the copy is translated, in mm)"); parser.addArgument("translate-y", "ty", ctkCommandLineParser::Float, "Translate y-axis:", "Translate in direction of y-axis (if copy is given the copy is translated, in mm)"); parser.addArgument("translate-z", "tz", ctkCommandLineParser::Float, "Translate z-axis:", "Translate in direction of z-axis (if copy is given the copy is translated, in mm)"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; float pointDist = -1; if (parsedArgs.count("resample")) pointDist = us::any_cast(parsedArgs["resample"]); float smoothDist = -1; if (parsedArgs.count("smooth")) smoothDist = us::any_cast(parsedArgs["smooth"]); float minFiberLength = -1; if (parsedArgs.count("minLength")) minFiberLength = us::any_cast(parsedArgs["minLength"]); float maxFiberLength = -1; if (parsedArgs.count("maxLength")) maxFiberLength = us::any_cast(parsedArgs["maxLength"]); float curvThres = -1; if (parsedArgs.count("minCurv")) curvThres = us::any_cast(parsedArgs["minCurv"]); int axis = 0; if (parsedArgs.count("mirror")) axis = us::any_cast(parsedArgs["mirror"]); bool copyAndJoin = false; if(parsedArgs.count("copyAndJoin")) copyAndJoin = us::any_cast(parsedArgs["copyAndJoin"]); float rotateX = 0; if (parsedArgs.count("rotate-x")) rotateX = us::any_cast(parsedArgs["rotate-x"]); float rotateY = 0; if (parsedArgs.count("rotate-y")) rotateY = us::any_cast(parsedArgs["rotate-y"]); float rotateZ = 0; if (parsedArgs.count("rotate-z")) rotateZ = us::any_cast(parsedArgs["rotate-z"]); float scaleX = 0; if (parsedArgs.count("scale-x")) scaleX = us::any_cast(parsedArgs["scale-x"]); float scaleY = 0; if (parsedArgs.count("scale-y")) scaleY = us::any_cast(parsedArgs["scale-y"]); float scaleZ = 0; if (parsedArgs.count("scale-z")) scaleZ = us::any_cast(parsedArgs["scale-z"]); float translateX = 0; if (parsedArgs.count("translate-x")) translateX = us::any_cast(parsedArgs["translate-x"]); float translateY = 0; if (parsedArgs.count("translate-y")) translateY = us::any_cast(parsedArgs["translate-y"]); float translateZ = 0; if (parsedArgs.count("translate-z")) translateZ = us::any_cast(parsedArgs["translate-z"]); string inFileName = us::any_cast(parsedArgs["input"]); string outFileName = us::any_cast(parsedArgs["outFile"]); try { mitk::FiberBundleX::Pointer fib = LoadFib(inFileName); if (minFiberLength>0) fib->RemoveShortFibers(minFiberLength); if (maxFiberLength>0) fib->RemoveLongFibers(maxFiberLength); if (curvThres>0) fib->ApplyCurvatureThreshold(curvThres, false); if (pointDist>0) fib->ResampleFibers(pointDist); if (smoothDist>0) fib->DoFiberSmoothing(smoothDist); if (axis/100==1) fib->MirrorFibers(0); if ((axis%100)/10==1) fib->MirrorFibers(1); if (axis%10==1) fib->MirrorFibers(2); if (copyAndJoin == true) { MITK_INFO << "Create copy"; mitk::FiberBundleX::Pointer fibCopy = fib->GetDeepCopy(); if (rotateX > 0 || rotateY > 0 || rotateZ > 0){ MITK_INFO << "Rotate " << rotateX << " " << rotateY << " " << rotateZ; fibCopy->RotateAroundAxis(rotateX, rotateY, rotateZ); } if (translateX > 0 || translateY > 0 || translateZ > 0) fibCopy->TranslateFibers(translateX, translateY, translateZ); if (scaleX > 0 || scaleY > 0 || scaleZ > 0) fibCopy->ScaleFibers(scaleX, scaleY, scaleZ); MITK_INFO << "Join copy with original"; fib = fib->AddBundle(fibCopy.GetPointer()); } else { if (rotateX > 0 || rotateY > 0 || rotateZ > 0){ MITK_INFO << "Rotate " << rotateX << " " << rotateY << " " << rotateZ; fib->RotateAroundAxis(rotateX, rotateY, rotateZ); } if (translateX > 0 || translateY > 0 || translateZ > 0){ fib->TranslateFibers(translateX, translateY, translateZ); } if (scaleX > 0 || scaleY > 0 || scaleZ > 0) fib->ScaleFibers(scaleX, scaleY, scaleZ); } mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(fib.GetPointer()) ) { - MITK_INFO << "writing " << outFileName; (*it)->SetFileName( outFileName.c_str() ); (*it)->DoWrite( fib.GetPointer() ); } } } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(FiberProcessing); diff --git a/Modules/DiffusionImaging/MiniApps/Fiberfox.cpp b/Modules/DiffusionImaging/MiniApps/Fiberfox.cpp index 8dfba05cc5..b433de1774 100755 --- a/Modules/DiffusionImaging/MiniApps/Fiberfox.cpp +++ b/Modules/DiffusionImaging/MiniApps/Fiberfox.cpp @@ -1,84 +1,85 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include "boost/property_tree/ptree.hpp" #include "boost/property_tree/xml_parser.hpp" #include "boost/foreach.hpp" /** TODO: Proritype signal komplett speichern oder bild mit speichern. */ /** TODO: Tarball aus images und parametern? */ /** TODO: Artefakte auf bild in miniapp */ namespace mitk { int Fiberfox(int argc, char* argv[]) { + MITK_INFO << "Fiberfox"; ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("out", "o", ctkCommandLineParser::OutputFile, "Output root:", "output root", us::Any(), false); parser.addArgument("parameters", "p", ctkCommandLineParser::InputFile, "Parameter file:", "fiberfox parameter file", us::Any(), false); parser.addArgument("fiberbundle", "f", ctkCommandLineParser::String, "Fiberbundle:", "", us::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string outName = us::any_cast(parsedArgs["out"]); string paramName = us::any_cast(parsedArgs["parameters"]); string fibFile = ""; if (parsedArgs.count("fiberbundle")) fibFile = us::any_cast(parsedArgs["fiberbundle"]); { FiberfoxParameters parameters; parameters.LoadParameters(paramName); mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast(mitk::IOUtil::LoadDataNode(fibFile)->GetData()); itk::TractsToDWIImageFilter< short >::Pointer tractsToDwiFilter = itk::TractsToDWIImageFilter< short >::New(); tractsToDwiFilter->SetParameters(parameters); tractsToDwiFilter->SetFiberBundle(inputTractogram); tractsToDwiFilter->Update(); DiffusionImage::Pointer image = DiffusionImage::New(); image->SetVectorImage( tractsToDwiFilter->GetOutput() ); image->SetReferenceBValue( parameters.m_SignalGen.m_Bvalue ); image->SetDirections( parameters.m_SignalGen.GetGradientDirections() ); image->InitializeFromVectorImage(); NrrdDiffusionImageWriter::Pointer writer = NrrdDiffusionImageWriter::New(); writer->SetFileName(outName); writer->SetInput(image); writer->Update(); } return EXIT_SUCCESS; } } RegisterDiffusionMiniApp(Fiberfox); diff --git a/Modules/DiffusionImaging/MiniApps/FileFormatConverter.cpp b/Modules/DiffusionImaging/MiniApps/FileFormatConverter.cpp index 675b71e0f2..896b1456de 100755 --- a/Modules/DiffusionImaging/MiniApps/FileFormatConverter.cpp +++ b/Modules/DiffusionImaging/MiniApps/FileFormatConverter.cpp @@ -1,100 +1,96 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include "ctkCommandLineParser.cpp" using namespace mitk; int FileFormatConverter(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setTitle("Format Converter"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("in", "i", ctkCommandLineParser::InputFile, "Input:", "input file", us::Any(), false); parser.addArgument("out", "o", ctkCommandLineParser::OutputFile, "Output:", "output file", us::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string inName = us::any_cast(parsedArgs["in"]); string outName = us::any_cast(parsedArgs["out"]); try { - MITK_INFO << "Loading " << inName; const std::string s1="", s2=""; std::vector infile = BaseDataIO::LoadBaseDataFromFile( inName, s1, s2, false ); mitk::BaseData::Pointer baseData = infile.at(0); if ( dynamic_cast*>(baseData.GetPointer()) ) { - MITK_INFO << "Writing " << outName; DiffusionImage::Pointer dwi = dynamic_cast*>(baseData.GetPointer()); NrrdDiffusionImageWriter::Pointer writer = NrrdDiffusionImageWriter::New(); writer->SetFileName(outName); writer->SetInput(dwi); writer->Update(); } else if ( dynamic_cast(baseData.GetPointer()) ) { Image::Pointer image = dynamic_cast(baseData.GetPointer()); mitk::IOUtil::SaveImage(image, outName); } else if ( dynamic_cast(baseData.GetPointer()) ) { - MITK_INFO << "Writing " << outName; FiberBundleXWriter::Pointer fibWriter = FiberBundleXWriter::New(); fibWriter->SetFileName(outName.c_str()); fibWriter->DoWrite( dynamic_cast(baseData.GetPointer()) ); } else MITK_INFO << "File type currently not supported!"; } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } - MITK_INFO << "DONE"; return EXIT_SUCCESS; } RegisterDiffusionMiniApp(FileFormatConverter); diff --git a/Modules/DiffusionImaging/MiniApps/GibbsTracking.cpp b/Modules/DiffusionImaging/MiniApps/GibbsTracking.cpp index 1c1de05216..7bd0f14b97 100755 --- a/Modules/DiffusionImaging/MiniApps/GibbsTracking.cpp +++ b/Modules/DiffusionImaging/MiniApps/GibbsTracking.cpp @@ -1,251 +1,252 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include template typename itk::ShCoefficientImageImporter< float, shOrder >::QballImageType::Pointer TemplatedConvertShCoeffs(mitk::Image* mitkImg, int toolkit, bool noFlip = false) { typedef itk::ShCoefficientImageImporter< float, shOrder > FilterType; typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(mitkImg); caster->Update(); itk::Image< float, 4 >::Pointer itkImage = caster->GetOutput(); typename FilterType::Pointer filter = FilterType::New(); if (noFlip) { filter->SetInputImage(itkImage); } else { MITK_INFO << "Flipping image"; itk::FixedArray flipAxes; flipAxes[0] = true; flipAxes[1] = true; flipAxes[2] = false; flipAxes[3] = false; itk::FlipImageFilter< itk::Image< float, 4 > >::Pointer flipper = itk::FlipImageFilter< itk::Image< float, 4 > >::New(); flipper->SetInput(itkImage); flipper->SetFlipAxes(flipAxes); flipper->Update(); itk::Image< float, 4 >::Pointer flipped = flipper->GetOutput(); itk::Matrix< double,4,4 > m = itkImage->GetDirection(); m[0][0] *= -1; m[1][1] *= -1; flipped->SetDirection(m); itk::Point< float, 4 > o = itkImage->GetOrigin(); o[0] -= (flipped->GetLargestPossibleRegion().GetSize(0)-1); o[1] -= (flipped->GetLargestPossibleRegion().GetSize(1)-1); flipped->SetOrigin(o); filter->SetInputImage(flipped); } switch (toolkit) { case 0: filter->SetToolkit(FilterType::FSL); break; case 1: filter->SetToolkit(FilterType::MRTRIX); break; default: filter->SetToolkit(FilterType::FSL); } filter->GenerateData(); return filter->GetQballImage(); } int GibbsTracking(int argc, char* argv[]) { + MITK_INFO << "GibbsTracking"; ctkCommandLineParser parser; parser.setTitle("Gibbs Tracking"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input image (tensor, Q-ball or FSL/MRTrix SH-coefficient image)", us::Any(), false); parser.addArgument("parameters", "p", ctkCommandLineParser::InputFile, "Parameters:", "parameter file (.gtp)", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask:", "binary mask image"); parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "SH coefficient:", "sh coefficient convention (FSL, MRtrix)", string("FSL"), true); parser.addArgument("outFile", "o", ctkCommandLineParser::OutputFile, "Output:", "output fiber bundle (.fib)", us::Any(), false); parser.addArgument("noFlip", "f", ctkCommandLineParser::Bool, "No flip:", "do not flip input image to match MITK coordinate convention"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; string inFileName = us::any_cast(parsedArgs["input"]); string paramFileName = us::any_cast(parsedArgs["parameters"]); string outFileName = us::any_cast(parsedArgs["outFile"]); bool noFlip = false; if (parsedArgs.count("noFlip")) noFlip = us::any_cast(parsedArgs["noFlip"]); try { // instantiate gibbs tracker typedef itk::Vector OdfVectorType; typedef itk::Image ItkQballImageType; typedef itk::GibbsTrackingFilter GibbsTrackingFilterType; GibbsTrackingFilterType::Pointer gibbsTracker = GibbsTrackingFilterType::New(); // load input image const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); mitk::Image::Pointer mitkImage = dynamic_cast(infile.at(0).GetPointer()); // try to cast to qball image if( boost::algorithm::ends_with(inFileName, ".qbi") ) { MITK_INFO << "Loading qball image ..."; mitk::QBallImage::Pointer mitkQballImage = dynamic_cast(infile.at(0).GetPointer()); ItkQballImageType::Pointer itk_qbi = ItkQballImageType::New(); mitk::CastToItkImage(mitkQballImage, itk_qbi); gibbsTracker->SetQBallImage(itk_qbi.GetPointer()); } else if( boost::algorithm::ends_with(inFileName, ".dti") ) { MITK_INFO << "Loading tensor image ..."; typedef itk::Image< itk::DiffusionTensor3D, 3 > ItkTensorImage; mitk::TensorImage::Pointer mitkTensorImage = dynamic_cast(infile.at(0).GetPointer()); ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); mitk::CastToItkImage(mitkTensorImage, itk_dti); gibbsTracker->SetTensorImage(itk_dti); } else if ( boost::algorithm::ends_with(inFileName, ".nii") ) { MITK_INFO << "Loading sh-coefficient image ..."; int nrCoeffs = mitkImage->GetLargestPossibleRegion().GetSize()[3]; int c=3, d=2-2*nrCoeffs; double D = c*c-4*d; int shOrder; if (D>0) { shOrder = (-c+sqrt(D))/2.0; if (shOrder<0) shOrder = (-c-sqrt(D))/2.0; } else if (D==0) shOrder = -c/2.0; MITK_INFO << "using SH-order " << shOrder; int toolkitConvention = 0; if (parsedArgs.count("shConvention")) { string convention = us::any_cast(parsedArgs["shConvention"]).c_str(); if ( boost::algorithm::equals(convention, "MRtrix") ) { toolkitConvention = 1; MITK_INFO << "Using MRtrix style sh-coefficient convention"; } else MITK_INFO << "Using FSL style sh-coefficient convention"; } else MITK_INFO << "Using FSL style sh-coefficient convention"; switch (shOrder) { case 4: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<4>(mitkImage, toolkitConvention, noFlip)); break; case 6: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<6>(mitkImage, toolkitConvention, noFlip)); break; case 8: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<8>(mitkImage, toolkitConvention, noFlip)); break; case 10: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<10>(mitkImage, toolkitConvention, noFlip)); break; case 12: gibbsTracker->SetQBallImage(TemplatedConvertShCoeffs<12>(mitkImage, toolkitConvention, noFlip)); break; default: MITK_INFO << "SH-order " << shOrder << " not supported"; } } else return EXIT_FAILURE; // global tracking if (parsedArgs.count("mask")) { typedef itk::Image MaskImgType; mitk::Image::Pointer mitkMaskImage = mitk::IOUtil::LoadImage(us::any_cast(parsedArgs["mask"])); MaskImgType::Pointer itk_mask = MaskImgType::New(); mitk::CastToItkImage(mitkMaskImage, itk_mask); gibbsTracker->SetMaskImage(itk_mask); } gibbsTracker->SetDuplicateImage(false); gibbsTracker->SetLoadParameterFile( paramFileName ); // gibbsTracker->SetLutPath( "" ); gibbsTracker->Update(); mitk::FiberBundleX::Pointer mitkFiberBundle = mitk::FiberBundleX::New(gibbsTracker->GetFiberBundle()); - mitkFiberBundle->SetReferenceImage(mitkImage); + mitkFiberBundle->SetReferenceGeometry(mitkImage->GetGeometry()); mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(mitkFiberBundle.GetPointer()) ) { (*it)->SetFileName( outFileName.c_str() ); (*it)->DoWrite( mitkFiberBundle.GetPointer() ); } } } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(GibbsTracking); diff --git a/Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp b/Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp index 30006c4102..2ec21daa9d 100755 --- a/Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp +++ b/Modules/DiffusionImaging/MiniApps/LocalDirectionalFiberPlausibility.cpp @@ -1,304 +1,309 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include int LocalDirectionalFiberPlausibility(int argc, char* argv[]) { + MITK_INFO << "LocalDirectionalFiberPlausibility"; ctkCommandLineParser parser; parser.setTitle("Local Directional Fiber Plausibility"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input tractogram (.fib, vtk ascii file format)", us::Any(), false); parser.addArgument("reference", "r", ctkCommandLineParser::StringList, "Reference images:", "reference direction images", us::Any(), false); parser.addArgument("out", "o", ctkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::StringList, "Masks:", "mask images"); parser.addArgument("athresh", "a", ctkCommandLineParser::Float, "Angular threshold:", "angular threshold in degrees. closer fiber directions are regarded as one direction and clustered together.", 25, true); parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "Verbose:", "output optional and intermediate calculation results"); parser.addArgument("ignore", "n", ctkCommandLineParser::Bool, "Ignore:", "don't increase error for missing or too many directions"); + parser.addArgument("fileID", "id", ctkCommandLineParser::String, "ID:", "optional ID field"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; ctkCommandLineParser::StringContainerType referenceImages = us::any_cast(parsedArgs["reference"]); ctkCommandLineParser::StringContainerType maskImages; if (parsedArgs.count("mask")) maskImages = us::any_cast(parsedArgs["mask"]); string fibFile = us::any_cast(parsedArgs["input"]); float angularThreshold = 25; if (parsedArgs.count("athresh")) angularThreshold = us::any_cast(parsedArgs["athresh"]); string outRoot = us::any_cast(parsedArgs["out"]); bool verbose = false; if (parsedArgs.count("verbose")) verbose = us::any_cast(parsedArgs["verbose"]); bool ignore = false; if (parsedArgs.count("ignore")) ignore = us::any_cast(parsedArgs["ignore"]); + string fileID = ""; + if (parsedArgs.count("fileID")) + fileID = us::any_cast(parsedArgs["fileID"]); + + try { typedef itk::Image ItkUcharImgType; typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; typedef itk::EvaluateDirectionImagesFilter< float > EvaluationFilterType; // load fiber bundle mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast(mitk::IOUtil::LoadDataNode(fibFile)->GetData()); // load reference directions ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New(); for (unsigned int i=0; i(mitk::IOUtil::LoadDataNode(referenceImages.at(i))->GetData()); typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(img); caster->Update(); ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput(); referenceImageContainer->InsertElement(referenceImageContainer->Size(),itkImg); } catch(...){ MITK_INFO << "could not load: " << referenceImages.at(i); } } ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New(); ItkDirectionImage3DType::Pointer dirImg = referenceImageContainer->GetElement(0); itkMaskImage->SetSpacing( dirImg->GetSpacing() ); itkMaskImage->SetOrigin( dirImg->GetOrigin() ); itkMaskImage->SetDirection( dirImg->GetDirection() ); itkMaskImage->SetLargestPossibleRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->SetBufferedRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->SetRequestedRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->Allocate(); itkMaskImage->FillBuffer(1); // extract directions from fiber bundle itk::TractsToVectorImageFilter::Pointer fOdfFilter = itk::TractsToVectorImageFilter::New(); fOdfFilter->SetFiberBundle(inputTractogram); fOdfFilter->SetMaskImage(itkMaskImage); fOdfFilter->SetAngularThreshold(cos(angularThreshold*M_PI/180)); fOdfFilter->SetNormalizeVectors(true); fOdfFilter->SetUseWorkingCopy(false); fOdfFilter->Update(); ItkDirectionImageContainerType::Pointer directionImageContainer = fOdfFilter->GetDirectionImageContainer(); if (verbose) { // write vector field mitk::FiberBundleX::Pointer directions = fOdfFilter->GetOutputFiberBundle(); mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(directions.GetPointer()) ) { string outfilename = outRoot; outfilename.append("_VECTOR_FIELD.fib"); (*it)->SetFileName( outfilename.c_str() ); (*it)->DoWrite( directions.GetPointer() ); } } // write direction images for (unsigned int i=0; iSize(); i++) { itk::TractsToVectorImageFilter::ItkDirectionImageType::Pointer itkImg = directionImageContainer->GetElement(i); typedef itk::ImageFileWriter< itk::TractsToVectorImageFilter::ItkDirectionImageType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_DIRECTION_"); outfilename.append(boost::lexical_cast(i)); outfilename.append(".nrrd"); - MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(itkImg); writer->Update(); } // write num direction image { ItkUcharImgType::Pointer numDirImage = fOdfFilter->GetNumDirectionsImage(); typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_NUM_DIRECTIONS.nrrd"); - MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(numDirImage); writer->Update(); } } string logFile = outRoot; logFile.append("_ANGULAR_ERROR.csv"); ofstream file; file.open (logFile.c_str()); if (maskImages.size()>0) { for (unsigned int i=0; i(mitk::IOUtil::LoadDataNode(maskImages.at(i))->GetData()); mitk::CastToItkImage(mitkMaskImage, itkMaskImage); // evaluate directions EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New(); evaluationFilter->SetImageSet(directionImageContainer); evaluationFilter->SetReferenceImageSet(referenceImageContainer); evaluationFilter->SetMaskImage(itkMaskImage); evaluationFilter->SetIgnoreMissingDirections(ignore); evaluationFilter->Update(); if (verbose) { EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0); typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_ERROR_IMAGE.nrrd"); - MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(angularErrorImage); writer->Update(); } - string sens = itksys::SystemTools::GetFilenameWithoutExtension(itksys::SystemTools::GetFilenameName(fibFile)); + string maskFileName = itksys::SystemTools::GetFilenameWithoutExtension(maskImages.at(i)); + unsigned found = maskFileName.find_last_of("_"); + + string sens = itksys::SystemTools::GetFilenameWithoutLastExtension(fibFile); + if (!fileID.empty()) + sens = fileID; sens.append(","); - sens.append(itksys::SystemTools::GetFilenameWithoutExtension(itksys::SystemTools::GetFilenameName(maskImages.at(i)))); + sens.append(maskFileName.substr(found+1)); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMeanAngularError())); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMedianAngularError())); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMaxAngularError())); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMinAngularError())); sens.append(","); sens.append(boost::lexical_cast(std::sqrt(evaluationFilter->GetVarAngularError()))); sens.append(";\n"); file << sens; } } else { // evaluate directions EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New(); evaluationFilter->SetImageSet(directionImageContainer); evaluationFilter->SetReferenceImageSet(referenceImageContainer); evaluationFilter->SetMaskImage(itkMaskImage); evaluationFilter->SetIgnoreMissingDirections(ignore); evaluationFilter->Update(); if (verbose) { EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0); typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_ERROR_IMAGE.nrrd"); - MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(angularErrorImage); writer->Update(); } - string sens = itksys::SystemTools::GetFilenameWithoutExtension(itksys::SystemTools::GetFilenameName(fibFile)); - sens.append(","); - - sens.append("FULL"); + string sens = itksys::SystemTools::GetFilenameWithoutLastExtension(fibFile); + if (!fileID.empty()) + sens = fileID; sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMeanAngularError())); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMedianAngularError())); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMaxAngularError())); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMinAngularError())); sens.append(","); sens.append(boost::lexical_cast(std::sqrt(evaluationFilter->GetVarAngularError()))); sens.append(";\n"); file << sens; } file.close(); - - MITK_INFO << "DONE"; } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(LocalDirectionalFiberPlausibility); diff --git a/Modules/DiffusionImaging/MiniApps/MultishellMethods.cpp b/Modules/DiffusionImaging/MiniApps/MultishellMethods.cpp index 0368b6b6a0..3a81eabccf 100644 --- a/Modules/DiffusionImaging/MiniApps/MultishellMethods.cpp +++ b/Modules/DiffusionImaging/MiniApps/MultishellMethods.cpp @@ -1,230 +1,229 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include int MultishellMethods(int argc, char* argv[]) { + MITK_INFO << "MultishellMethods"; ctkCommandLineParser parser; parser.setTitle("Multishell Methods"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("in", "i", ctkCommandLineParser::InputFile, "Input:", "input file", us::Any(), false); parser.addArgument("out", "o", ctkCommandLineParser::OutputFile, "Output:", "output file", us::Any(), false); parser.addArgument("adc", "D", ctkCommandLineParser::Bool, "ADC:", "ADC Average", us::Any(), false); parser.addArgument("akc", "K", ctkCommandLineParser::Bool, "Kurtosis fit:", "Kurtosis Fit", us::Any(), false); parser.addArgument("biexp", "B", ctkCommandLineParser::Bool, "BiExp fit:", "BiExp fit", us::Any(), false); parser.addArgument("targetbvalue", "b", ctkCommandLineParser::String, "b Value:", "target bValue (mean, min, max)", us::Any(), false); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string inName = us::any_cast(parsedArgs["in"]); string outName = us::any_cast(parsedArgs["out"]); bool applyADC = us::any_cast(parsedArgs["adc"]); bool applyAKC = us::any_cast(parsedArgs["akc"]); bool applyBiExp = us::any_cast(parsedArgs["biexp"]); string targetType = us::any_cast(parsedArgs["targetbvalue"]); try { MITK_INFO << "Loading " << inName; const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( inName, s1, s2, false ); mitk::BaseData::Pointer baseData = infile.at(0); if ( dynamic_cast*>(baseData.GetPointer()) ) { - MITK_INFO << "Writing " << outName; mitk::DiffusionImage::Pointer dwi = dynamic_cast*>(baseData.GetPointer()); typedef itk::RadialMultishellToSingleshellImageFilter FilterType; typedef itk::DwiGradientLengthCorrectionFilter CorrectionFilterType; CorrectionFilterType::Pointer roundfilter = CorrectionFilterType::New(); roundfilter->SetRoundingValue( 1000 ); roundfilter->SetReferenceBValue(dwi->GetReferenceBValue()); roundfilter->SetReferenceGradientDirectionContainer(dwi->GetDirections()); roundfilter->Update(); dwi->SetReferenceBValue( roundfilter->GetNewBValue() ); dwi->SetDirections( roundfilter->GetOutputGradientDirectionContainer()); // filter input parameter const mitk::DiffusionImage::BValueMap &originalShellMap = dwi->GetBValueMap(); const mitk::DiffusionImage::ImageType *vectorImage = dwi->GetVectorImage(); const mitk::DiffusionImage::GradientDirectionContainerType::Pointer gradientContainer = dwi->GetDirections(); const unsigned int &bValue = dwi->GetReferenceBValue(); // filter call vnl_vector bValueList(originalShellMap.size()-1); double targetBValue = bValueList.mean(); mitk::DiffusionImage::BValueMap::const_iterator it = originalShellMap.begin(); ++it; int i = 0 ; for(; it != originalShellMap.end(); ++it) bValueList.put(i++,it->first); if( targetType == "mean" ) targetBValue = bValueList.mean(); else if( targetType == "min" ) targetBValue = bValueList.min_value(); else if( targetType == "max" ) targetBValue = bValueList.max_value(); if(applyADC) { FilterType::Pointer filter = FilterType::New(); filter->SetInput(vectorImage); filter->SetOriginalGradientDirections(gradientContainer); filter->SetOriginalBValueMap(originalShellMap); filter->SetOriginalBValue(bValue); itk::ADCAverageFunctor::Pointer functor = itk::ADCAverageFunctor::New(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); filter->SetFunctor(functor); filter->Update(); // create new DWI image mitk::DiffusionImage::Pointer outImage = mitk::DiffusionImage::New(); outImage->SetVectorImage( filter->GetOutput() ); outImage->SetReferenceBValue( targetBValue ); outImage->SetDirections( filter->GetTargetGradientDirections() ); outImage->InitializeFromVectorImage(); mitk::NrrdDiffusionImageWriter::Pointer writer = mitk::NrrdDiffusionImageWriter::New(); writer->SetFileName((string(outName) + "_ADC.dwi")); writer->SetInput(outImage); writer->Update(); } if(applyAKC) { FilterType::Pointer filter = FilterType::New(); filter->SetInput(vectorImage); filter->SetOriginalGradientDirections(gradientContainer); filter->SetOriginalBValueMap(originalShellMap); filter->SetOriginalBValue(bValue); itk::KurtosisFitFunctor::Pointer functor = itk::KurtosisFitFunctor::New(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); filter->SetFunctor(functor); filter->Update(); // create new DWI image mitk::DiffusionImage::Pointer outImage = mitk::DiffusionImage::New(); outImage->SetVectorImage( filter->GetOutput() ); outImage->SetReferenceBValue( targetBValue ); outImage->SetDirections( filter->GetTargetGradientDirections() ); outImage->InitializeFromVectorImage(); mitk::NrrdDiffusionImageWriter::Pointer writer = mitk::NrrdDiffusionImageWriter::New(); writer->SetFileName((string(outName) + "_AKC.dwi")); writer->SetInput(outImage); writer->Update(); } if(applyBiExp) { FilterType::Pointer filter = FilterType::New(); filter->SetInput(vectorImage); filter->SetOriginalGradientDirections(gradientContainer); filter->SetOriginalBValueMap(originalShellMap); filter->SetOriginalBValue(bValue); itk::BiExpFitFunctor::Pointer functor = itk::BiExpFitFunctor::New(); functor->setListOfBValues(bValueList); functor->setTargetBValue(targetBValue); filter->SetFunctor(functor); filter->Update(); // create new DWI image mitk::DiffusionImage::Pointer outImage = mitk::DiffusionImage::New(); outImage->SetVectorImage( filter->GetOutput() ); outImage->SetReferenceBValue( targetBValue ); outImage->SetDirections( filter->GetTargetGradientDirections() ); outImage->InitializeFromVectorImage(); mitk::NrrdDiffusionImageWriter::Pointer writer = mitk::NrrdDiffusionImageWriter::New(); writer->SetFileName((string(outName) + "_BiExp.dwi")); writer->SetInput(outImage); writer->Update(); } } } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } - MITK_INFO << "DONE"; return EXIT_SUCCESS; } RegisterDiffusionMiniApp(MultishellMethods); diff --git a/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp b/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp index 99e1acb9af..6104af810f 100755 --- a/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp +++ b/Modules/DiffusionImaging/MiniApps/PeakExtraction.cpp @@ -1,382 +1,380 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include mitk::Image::Pointer LoadData(std::string filename) { if( filename.empty() ) return NULL; const std::string s1="", s2=""; std::vector infile = mitk::BaseDataIO::LoadBaseDataFromFile( filename, s1, s2, false ); if( infile.empty() ) { MITK_INFO << "File " << filename << " could not be read!"; return NULL; } mitk::BaseData::Pointer baseData = infile.at(0); return dynamic_cast(baseData.GetPointer()); } template int StartPeakExtraction(int argc, char* argv[]) { + MITK_INFO << "StartPeakExtraction"; ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("image", "i", ctkCommandLineParser::InputFile, "Input image", "sh coefficient image", us::Any(), false); parser.addArgument("outroot", "o", ctkCommandLineParser::OutputDirectory, "Output directory", "output root", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask", "mask image"); parser.addArgument("normalization", "n", ctkCommandLineParser::Int, "Normalization", "0=no norm, 1=max norm, 2=single vec norm", 1, true); parser.addArgument("numpeaks", "p", ctkCommandLineParser::Int, "Max. number of peaks", "maximum number of extracted peaks", 2, true); parser.addArgument("peakthres", "r", ctkCommandLineParser::Float, "Peak threshold", "peak threshold relative to largest peak", 0.4, true); parser.addArgument("abspeakthres", "a", ctkCommandLineParser::Float, "Absolute peak threshold", "absolute peak threshold weighted with local GFA value", 0.06, true); parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "Use specified SH-basis", "use specified SH-basis (MITK, FSL, MRtrix)", string("MITK"), true); parser.addArgument("noFlip", "f", ctkCommandLineParser::Bool, "No flip", "do not flip input image to match MITK coordinate convention"); parser.setCategory("Preprocessing Tools"); parser.setTitle("Peak Extraction"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string imageName = us::any_cast(parsedArgs["image"]); string outRoot = us::any_cast(parsedArgs["outroot"]); // optional arguments string maskImageName(""); if (parsedArgs.count("mask")) maskImageName = us::any_cast(parsedArgs["mask"]); int normalization = 1; if (parsedArgs.count("normalization")) normalization = us::any_cast(parsedArgs["normalization"]); int numPeaks = 2; if (parsedArgs.count("numpeaks")) numPeaks = us::any_cast(parsedArgs["numpeaks"]); float peakThres = 0.4; if (parsedArgs.count("peakthres")) peakThres = us::any_cast(parsedArgs["peakthres"]); float absPeakThres = 0.06; if (parsedArgs.count("abspeakthres")) absPeakThres = us::any_cast(parsedArgs["abspeakthres"]); bool noFlip = false; if (parsedArgs.count("noFlip")) noFlip = us::any_cast(parsedArgs["noFlip"]); MITK_INFO << "image: " << imageName; MITK_INFO << "outroot: " << outRoot; if (!maskImageName.empty()) MITK_INFO << "mask: " << maskImageName; else MITK_INFO << "no mask image selected"; MITK_INFO << "numpeaks: " << numPeaks; MITK_INFO << "peakthres: " << peakThres; MITK_INFO << "abspeakthres: " << absPeakThres; MITK_INFO << "shOrder: " << shOrder; try { mitk::Image::Pointer image = LoadData(imageName); mitk::Image::Pointer mask = LoadData(maskImageName); typedef itk::Image ItkUcharImgType; typedef itk::FiniteDiffOdfMaximaExtractionFilter< float, shOrder, 20242 > MaximaExtractionFilterType; typename MaximaExtractionFilterType::Pointer filter = MaximaExtractionFilterType::New(); int toolkitConvention = 0; if (parsedArgs.count("shConvention")) { string convention = us::any_cast(parsedArgs["shConvention"]).c_str(); if ( boost::algorithm::equals(convention, "FSL") ) { toolkitConvention = 1; MITK_INFO << "Using FSL SH-basis"; } else if ( boost::algorithm::equals(convention, "MRtrix") ) { toolkitConvention = 2; MITK_INFO << "Using MRtrix SH-basis"; } else MITK_INFO << "Using MITK SH-basis"; } else MITK_INFO << "Using MITK SH-basis"; ItkUcharImgType::Pointer itkMaskImage = NULL; if (mask.IsNotNull()) { try{ itkMaskImage = ItkUcharImgType::New(); mitk::CastToItkImage(mask, itkMaskImage); filter->SetMaskImage(itkMaskImage); } catch(...) { } } if (toolkitConvention>0) { MITK_INFO << "Converting coefficient image to MITK format"; typedef itk::ShCoefficientImageImporter< float, shOrder > ConverterType; typedef mitk::ImageToItk< itk::Image< float, 4 > > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(image); caster->Update(); itk::Image< float, 4 >::Pointer itkImage = caster->GetOutput(); typename ConverterType::Pointer converter = ConverterType::New(); if (noFlip) { converter->SetInputImage(itkImage); } else { MITK_INFO << "Flipping image"; itk::FixedArray flipAxes; flipAxes[0] = true; flipAxes[1] = true; flipAxes[2] = false; flipAxes[3] = false; itk::FlipImageFilter< itk::Image< float, 4 > >::Pointer flipper = itk::FlipImageFilter< itk::Image< float, 4 > >::New(); flipper->SetInput(itkImage); flipper->SetFlipAxes(flipAxes); flipper->Update(); itk::Image< float, 4 >::Pointer flipped = flipper->GetOutput(); itk::Matrix< double,4,4 > m = itkImage->GetDirection(); m[0][0] *= -1; m[1][1] *= -1; flipped->SetDirection(m); itk::Point< float, 4 > o = itkImage->GetOrigin(); o[0] -= (flipped->GetLargestPossibleRegion().GetSize(0)-1); o[1] -= (flipped->GetLargestPossibleRegion().GetSize(1)-1); flipped->SetOrigin(o); converter->SetInputImage(flipped); } MITK_INFO << "Starting conversion"; switch (toolkitConvention) { case 1: converter->SetToolkit(ConverterType::FSL); filter->SetToolkit(MaximaExtractionFilterType::FSL); break; case 2: converter->SetToolkit(ConverterType::MRTRIX); filter->SetToolkit(MaximaExtractionFilterType::MRTRIX); break; default: converter->SetToolkit(ConverterType::FSL); filter->SetToolkit(MaximaExtractionFilterType::FSL); break; } converter->GenerateData(); filter->SetInput(converter->GetCoefficientImage()); } else { try{ typedef mitk::ImageToItk< typename MaximaExtractionFilterType::CoefficientImageType > CasterType; typename CasterType::Pointer caster = CasterType::New(); caster->SetInput(image); caster->Update(); filter->SetInput(caster->GetOutput()); } catch(...) { MITK_INFO << "wrong image type"; return EXIT_FAILURE; } } filter->SetMaxNumPeaks(numPeaks); filter->SetPeakThreshold(peakThres); filter->SetAbsolutePeakThreshold(absPeakThres); filter->SetAngularThreshold(1); switch (normalization) { case 0: filter->SetNormalizationMethod(MaximaExtractionFilterType::NO_NORM); break; case 1: filter->SetNormalizationMethod(MaximaExtractionFilterType::MAX_VEC_NORM); break; case 2: filter->SetNormalizationMethod(MaximaExtractionFilterType::SINGLE_VEC_NORM); break; } MITK_INFO << "Starting extraction"; filter->Update(); // write direction images { typedef typename MaximaExtractionFilterType::ItkDirectionImageContainer ItkDirectionImageContainer; typename ItkDirectionImageContainer::Pointer container = filter->GetDirectionImageContainer(); for (unsigned int i=0; iSize(); i++) { typename MaximaExtractionFilterType::ItkDirectionImage::Pointer itkImg = container->GetElement(i); if (itkMaskImage.IsNotNull()) { itkImg->SetDirection(itkMaskImage->GetDirection()); itkImg->SetOrigin(itkMaskImage->GetOrigin()); } string outfilename = outRoot; outfilename.append("_DIRECTION_"); outfilename.append(boost::lexical_cast(i)); outfilename.append(".nrrd"); - MITK_INFO << "writing " << outfilename; typedef itk::ImageFileWriter< typename MaximaExtractionFilterType::ItkDirectionImage > WriterType; typename WriterType::Pointer writer = WriterType::New(); writer->SetFileName(outfilename); writer->SetInput(itkImg); writer->Update(); } } // write num directions image { ItkUcharImgType::Pointer numDirImage = filter->GetNumDirectionsImage(); if (itkMaskImage.IsNotNull()) { numDirImage->SetDirection(itkMaskImage->GetDirection()); numDirImage->SetOrigin(itkMaskImage->GetOrigin()); } string outfilename = outRoot.c_str(); outfilename.append("_NUM_DIRECTIONS.nrrd"); - MITK_INFO << "writing " << outfilename; typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; WriterType::Pointer writer = WriterType::New(); writer->SetFileName(outfilename); writer->SetInput(numDirImage); writer->Update(); } // write vector field { mitk::FiberBundleX::Pointer directions = filter->GetOutputFiberBundle(); string outfilename = outRoot.c_str(); outfilename.append("_VECTOR_FIELD.fib"); mitk::FiberBundleXWriter::Pointer fibWriter = mitk::FiberBundleXWriter::New(); fibWriter->SetFileName(outfilename.c_str()); fibWriter->DoWrite(directions.GetPointer()); } } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } - MITK_INFO << "DONE"; return EXIT_SUCCESS; } int PeakExtraction(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("image", "i", ctkCommandLineParser::InputFile, "Input image", "sh coefficient image", us::Any(), false); parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "Spherical harmonics order", "spherical harmonics order"); parser.addArgument("outroot", "o", ctkCommandLineParser::OutputDirectory, "Output directory", "output root", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask", "mask image"); parser.addArgument("normalization", "n", ctkCommandLineParser::Int, "Normalization", "0=no norm, 1=max norm, 2=single vec norm", 1, true); parser.addArgument("numpeaks", "p", ctkCommandLineParser::Int, "Max. number of peaks", "maximum number of extracted peaks", 2, true); parser.addArgument("peakthres", "r", ctkCommandLineParser::Float, "Peak threshold", "peak threshold relative to largest peak", 0.4, true); parser.addArgument("abspeakthres", "a", ctkCommandLineParser::Float, "Absolute peak threshold", "absolute peak threshold weighted with local GFA value", 0.06, true); parser.addArgument("shConvention", "s", ctkCommandLineParser::String, "Use specified SH-basis", "use specified SH-basis (MITK, FSL, MRtrix)", string("MITK"), true); parser.addArgument("noFlip", "f", ctkCommandLineParser::Bool, "No flip", "do not flip input image to match MITK coordinate convention"); parser.setCategory("Preprocessing Tools"); parser.setTitle("Peak Extraction"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; int shOrder = -1; if (parsedArgs.count("shOrder")) shOrder = us::any_cast(parsedArgs["shOrder"]); switch (shOrder) { case 4: return StartPeakExtraction<4>(argc, argv); case 6: return StartPeakExtraction<6>(argc, argv); case 8: return StartPeakExtraction<8>(argc, argv); case 10: return StartPeakExtraction<10>(argc, argv); case 12: return StartPeakExtraction<12>(argc, argv); } return EXIT_FAILURE; } RegisterDiffusionMiniApp(PeakExtraction); diff --git a/Modules/DiffusionImaging/MiniApps/PeaksAngularError.cpp b/Modules/DiffusionImaging/MiniApps/PeaksAngularError.cpp index b3747772f2..9b5d4bbe10 100755 --- a/Modules/DiffusionImaging/MiniApps/PeaksAngularError.cpp +++ b/Modules/DiffusionImaging/MiniApps/PeaksAngularError.cpp @@ -1,210 +1,208 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include int PeaksAngularError(int argc, char* argv[]) { + MITK_INFO << "PeaksAngularError"; ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("test", "t", ctkCommandLineParser::StringList, "Test images", "test direction images", us::Any(), false); parser.addArgument("reference", "r", ctkCommandLineParser::StringList, "Reference images", "reference direction images", us::Any(), false); parser.addArgument("out", "o", ctkCommandLineParser::OutputDirectory, "Output directory", "output root", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::InputFile, "Mask", "mask image"); parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "Verbose", "output optional and intermediate calculation results"); parser.addArgument("ignore", "i", ctkCommandLineParser::Bool, "Ignore", "don't increase error for missing or too many directions"); parser.setCategory("Preprocessing Tools"); parser.setTitle("Peaks Angular Error"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; ctkCommandLineParser::StringContainerType testImages = us::any_cast(parsedArgs["test"]); ctkCommandLineParser::StringContainerType referenceImages = us::any_cast(parsedArgs["reference"]); string maskImage(""); if (parsedArgs.count("mask")) maskImage = us::any_cast(parsedArgs["mask"]); string outRoot = us::any_cast(parsedArgs["out"]); bool verbose = false; if (parsedArgs.count("verbose")) verbose = us::any_cast(parsedArgs["verbose"]); bool ignore = false; if (parsedArgs.count("ignore")) ignore = us::any_cast(parsedArgs["ignore"]); try { typedef itk::Image ItkUcharImgType; typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< unsigned int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; typedef itk::EvaluateDirectionImagesFilter< float > EvaluationFilterType; ItkDirectionImageContainerType::Pointer directionImageContainer = ItkDirectionImageContainerType::New(); for (unsigned int i=0; i(mitk::IOUtil::LoadDataNode(testImages.at(i))->GetData()); typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(img); caster->Update(); ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput(); directionImageContainer->InsertElement(directionImageContainer->Size(),itkImg); } catch(...){ MITK_INFO << "could not load: " << referenceImages.at(i); } } // load reference directions ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New(); for (unsigned int i=0; i(mitk::IOUtil::LoadDataNode(referenceImages.at(i))->GetData()); typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(img); caster->Update(); ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput(); referenceImageContainer->InsertElement(referenceImageContainer->Size(),itkImg); } catch(...){ MITK_INFO << "could not load: " << referenceImages.at(i); } } // load/create mask image ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New(); if (maskImage.compare("")==0) { ItkDirectionImage3DType::Pointer dirImg = referenceImageContainer->GetElement(0); itkMaskImage->SetSpacing( dirImg->GetSpacing() ); itkMaskImage->SetOrigin( dirImg->GetOrigin() ); itkMaskImage->SetDirection( dirImg->GetDirection() ); itkMaskImage->SetLargestPossibleRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->SetBufferedRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->SetRequestedRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->Allocate(); itkMaskImage->FillBuffer(1); } else { mitk::Image::Pointer mitkMaskImage = dynamic_cast(mitk::IOUtil::LoadDataNode(maskImage)->GetData()); mitk::CastToItkImage(mitkMaskImage, itkMaskImage); } // evaluate directions EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New(); evaluationFilter->SetImageSet(directionImageContainer); evaluationFilter->SetReferenceImageSet(referenceImageContainer); evaluationFilter->SetMaskImage(itkMaskImage); evaluationFilter->SetIgnoreMissingDirections(ignore); evaluationFilter->Update(); if (verbose) { EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0); typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_ERROR_IMAGE.nrrd"); - MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(angularErrorImage); writer->Update(); } string logFile = outRoot; logFile.append("_ANGULAR_ERROR.csv"); ofstream file; file.open (logFile.c_str()); string sens = "Mean:"; sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMeanAngularError())); sens.append(";\n"); sens.append("Median:"); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMedianAngularError())); sens.append(";\n"); sens.append("Maximum:"); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMaxAngularError())); sens.append(";\n"); sens.append("Minimum:"); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMinAngularError())); sens.append(";\n"); sens.append("STDEV:"); sens.append(","); sens.append(boost::lexical_cast(std::sqrt(evaluationFilter->GetVarAngularError()))); sens.append(";\n"); file << sens; file.close(); - - MITK_INFO << "DONE"; } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(PeaksAngularError); diff --git a/Modules/DiffusionImaging/MiniApps/QballReconstruction.cpp b/Modules/DiffusionImaging/MiniApps/QballReconstruction.cpp index d0531a20ba..68392158d1 100644 --- a/Modules/DiffusionImaging/MiniApps/QballReconstruction.cpp +++ b/Modules/DiffusionImaging/MiniApps/QballReconstruction.cpp @@ -1,244 +1,243 @@ /*=================================================================== 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 "MiniAppManager.h" #include "mitkBaseDataIOFactory.h" #include #include "mitkDiffusionImage.h" #include "itkAnalyticalDiffusionQballReconstructionImageFilter.h" #include #include "ctkCommandLineParser.h" #include #include using namespace mitk; /** * Perform Q-ball reconstruction using a spherical harmonics basis */ int QballReconstruction(int argc, char* argv[]) { + MITK_INFO << "QballReconstruction"; ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input file", "input raw dwi (.dwi or .fsl/.fslgz)", us::Any(), false); parser.addArgument("outFile", "o", ctkCommandLineParser::OutputFile, "Output file", "output file", us::Any(), false); parser.addArgument("shOrder", "sh", ctkCommandLineParser::Int, "Spherical harmonics order", "spherical harmonics order", 4, true); parser.addArgument("b0Threshold", "t", ctkCommandLineParser::Int, "b0 threshold", "baseline image intensity threshold", 0, true); parser.addArgument("lambda", "r", ctkCommandLineParser::Float, "Lambda", "ragularization factor lambda", 0.006, true); parser.addArgument("csa", "csa", ctkCommandLineParser::Bool, "Constant solid angle consideration", "use constant solid angle consideration"); parser.addArgument("outputCoeffs", "shc", ctkCommandLineParser::Bool, "Output coefficients", "output file containing the SH coefficients"); parser.addArgument("mrtrix", "mb", ctkCommandLineParser::Bool, "MRtrix", "use MRtrix compatible spherical harmonics definition"); parser.setCategory("Preprocessing Tools"); parser.setTitle("Qball Reconstruction"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; std::string inFileName = us::any_cast(parsedArgs["input"]); std::string outfilename = us::any_cast(parsedArgs["outFile"]); outfilename = itksys::SystemTools::GetFilenamePath(outfilename)+"/"+itksys::SystemTools::GetFilenameWithoutExtension(outfilename); int threshold = 0; if (parsedArgs.count("b0Threshold")) threshold = us::any_cast(parsedArgs["b0Threshold"]); int shOrder = 4; if (parsedArgs.count("shOrder")) shOrder = us::any_cast(parsedArgs["shOrder"]); float lambda = 0.006; if (parsedArgs.count("lambda")) lambda = us::any_cast(parsedArgs["lambda"]); int normalization = 0; if (parsedArgs.count("csa") && us::any_cast(parsedArgs["csa"])) normalization = 6; bool outCoeffs = false; if (parsedArgs.count("outputCoeffs")) outCoeffs = us::any_cast(parsedArgs["outputCoeffs"]); bool mrTrix = false; if (parsedArgs.count("mrtrix")) mrTrix = us::any_cast(parsedArgs["mrtrix"]); try { - MITK_INFO << "Loading image ..."; const std::string s1="", s2=""; std::vector infile = BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); DiffusionImage::Pointer dwi = dynamic_cast*>(infile.at(0).GetPointer()); dwi->AverageRedundantGradients(0.001); mitk::QBallImage::Pointer image = mitk::QBallImage::New(); mitk::Image::Pointer coeffsImage = mitk::Image::New(); MITK_INFO << "SH order: " << shOrder; MITK_INFO << "lambda: " << lambda; MITK_INFO << "B0 threshold: " << threshold; switch ( shOrder ) { case 4: { typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold( threshold ); filter->SetLambda(lambda); filter->SetUseMrtrixBasis(mrTrix); if (normalization==0) filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); else filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() ); coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() ); break; } case 6: { typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold( threshold ); filter->SetLambda(lambda); filter->SetUseMrtrixBasis(mrTrix); if (normalization==0) filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); else filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() ); coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() ); break; } case 8: { typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold( threshold ); filter->SetLambda(lambda); filter->SetUseMrtrixBasis(mrTrix); if (normalization==0) filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); else filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() ); coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() ); break; } case 10: { typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold( threshold ); filter->SetLambda(lambda); filter->SetUseMrtrixBasis(mrTrix); if (normalization==0) filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); else filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() ); coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() ); break; } case 12: { typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold( threshold ); filter->SetLambda(lambda); if (normalization==0) filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); else filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() ); coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() ); break; } default: { MITK_INFO << "Supplied SH order not supported. Using default order of 4."; typedef itk::AnalyticalDiffusionQballReconstructionImageFilter FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold( threshold ); filter->SetLambda(lambda); filter->SetUseMrtrixBasis(mrTrix); if (normalization==0) filter->SetNormalizationMethod(FilterType::QBAR_STANDARD); else filter->SetNormalizationMethod(FilterType::QBAR_SOLID_ANGLE); filter->Update(); image->InitializeByItk( filter->GetOutput() ); image->SetVolume( filter->GetOutput()->GetBufferPointer() ); coeffsImage->InitializeByItk( filter->GetCoefficientImage().GetPointer() ); coeffsImage->SetVolume( filter->GetCoefficientImage()->GetBufferPointer() ); } } std::string coeffout = outfilename; coeffout += "_shcoeffs.nrrd"; outfilename += ".qbi"; - MITK_INFO << "writing image " << outfilename; mitk::IOUtil::SaveBaseData(image, outfilename); if (outCoeffs) mitk::IOUtil::SaveImage(coeffsImage, coeffout); } catch ( itk::ExceptionObject &err) { MITK_INFO << "Exception: " << err; } catch ( std::exception err) { MITK_INFO << "Exception: " << err.what(); } catch ( ... ) { MITK_INFO << "Exception!"; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(QballReconstruction); diff --git a/Modules/DiffusionImaging/MiniApps/StreamlineTracking.cpp b/Modules/DiffusionImaging/MiniApps/StreamlineTracking.cpp index 6d78c197e7..4e71015370 100755 --- a/Modules/DiffusionImaging/MiniApps/StreamlineTracking.cpp +++ b/Modules/DiffusionImaging/MiniApps/StreamlineTracking.cpp @@ -1,187 +1,187 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include int StreamlineTracking(int argc, char* argv[]) { + MITK_INFO << "StreamlineTracking"; ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::StringList, "Input image", "input tensor image (.dti)", us::Any(), false); parser.addArgument("seed", "si", ctkCommandLineParser::InputFile, "Seed image", "binary seed image", us::Any(), true); parser.addArgument("mask", "mi", ctkCommandLineParser::InputFile, "Mask", "binary mask image", us::Any(), true); parser.addArgument("faImage", "fai", ctkCommandLineParser::InputFile, "FA image", "FA image", us::Any(), true); parser.addArgument("minFA", "fa", ctkCommandLineParser::Float, "Min. FA threshold", "minimum fractional anisotropy threshold", 0.15, true); parser.addArgument("minCurv", "c", ctkCommandLineParser::Float, "Min. curvature radius", "minimum curvature radius in mm (default = 0.5*minimum-spacing)"); parser.addArgument("stepSize", "s", ctkCommandLineParser::Float, "Step size", "step size in mm (default = 0.1*minimum-spacing)"); parser.addArgument("tendf", "f", ctkCommandLineParser::Float, "Weight f", "Weighting factor between first eigenvector (f=1 equals FACT tracking) and input vector dependent direction (f=0).", 1.0, true); parser.addArgument("tendg", "g", ctkCommandLineParser::Float, "Weight g", "Weighting factor between input vector (g=0) and tensor deflection (g=1 equals TEND tracking)", 0.0, true); parser.addArgument("numSeeds", "n", ctkCommandLineParser::Int, "Seeds per voxel", "Number of seeds per voxel.", 1, true); parser.addArgument("minLength", "l", ctkCommandLineParser::Float, "Min. fiber length", "minimum fiber length in mm", 20, true); parser.addArgument("interpolate", "ip", ctkCommandLineParser::Bool, "Interpolate", "Use linear interpolation", false, true); parser.addArgument("outFile", "o", ctkCommandLineParser::String, "Output file", "output fiber bundle (.fib)", us::Any(), false); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setTitle("Streamline Tracking"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; ctkCommandLineParser::StringContainerType inputImages = us::any_cast(parsedArgs["input"]); string dtiFileName; string outFileName = us::any_cast(parsedArgs["outFile"]); float minFA = 0.15; float minCurv = -1; float stepSize = -1; float tendf = 1; float tendg = 0; float minLength = 20; int numSeeds = 1; bool interpolate = false; if (parsedArgs.count("minCurv")) minCurv = us::any_cast(parsedArgs["minCurv"]); if (parsedArgs.count("minFA")) minFA = us::any_cast(parsedArgs["minFA"]); if (parsedArgs.count("stepSize")) stepSize = us::any_cast(parsedArgs["stepSize"]); if (parsedArgs.count("tendf")) tendf = us::any_cast(parsedArgs["tendf"]); if (parsedArgs.count("tendg")) tendg = us::any_cast(parsedArgs["tendg"]); if (parsedArgs.count("minLength")) minLength = us::any_cast(parsedArgs["minLength"]); if (parsedArgs.count("numSeeds")) numSeeds = us::any_cast(parsedArgs["numSeeds"]); if (parsedArgs.count("interpolate")) interpolate = us::any_cast(parsedArgs["interpolate"]); try { typedef itk::StreamlineTrackingFilter< float > FilterType; FilterType::Pointer filter = FilterType::New(); mitk::Image::Pointer mitkImage = NULL; MITK_INFO << "Loading tensor images ..."; typedef itk::Image< itk::DiffusionTensor3D, 3 > ItkTensorImage; dtiFileName = inputImages.at(0); for (unsigned int i=0; i(mitk::IOUtil::LoadDataNode(inputImages.at(i))->GetData()); mitk::TensorImage::Pointer img = dynamic_cast(mitk::IOUtil::LoadDataNode(inputImages.at(i))->GetData()); ItkTensorImage::Pointer itk_dti = ItkTensorImage::New(); mitk::CastToItkImage(img, itk_dti); filter->SetInput(i, itk_dti); } catch(...){ MITK_INFO << "could not load: " << inputImages.at(i); } } MITK_INFO << "Loading seed image ..."; typedef itk::Image< unsigned char, 3 > ItkUCharImageType; mitk::Image::Pointer mitkSeedImage = NULL; if (parsedArgs.count("seed")) mitkSeedImage = mitk::IOUtil::LoadImage(us::any_cast(parsedArgs["seed"])); MITK_INFO << "Loading mask image ..."; mitk::Image::Pointer mitkMaskImage = NULL; if (parsedArgs.count("mask")) mitkMaskImage = mitk::IOUtil::LoadImage(us::any_cast(parsedArgs["mask"])); // instantiate tracker filter->SetSeedsPerVoxel(numSeeds); filter->SetFaThreshold(minFA); filter->SetMinCurvatureRadius(minCurv); filter->SetStepSize(stepSize); filter->SetF(tendf); filter->SetG(tendg); filter->SetInterpolate(interpolate); filter->SetMinTractLength(minLength); if (mitkSeedImage.IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(mitkSeedImage, mask); filter->SetSeedImage(mask); } if (mitkMaskImage.IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(mitkMaskImage, mask); filter->SetMaskImage(mask); } filter->Update(); vtkSmartPointer fiberBundle = filter->GetFiberPolyData(); if ( fiberBundle->GetNumberOfLines()==0 ) { MITK_INFO << "No fibers reconstructed. Check parametrization."; return EXIT_FAILURE; } mitk::FiberBundleX::Pointer fib = mitk::FiberBundleX::New(fiberBundle); - fib->SetReferenceImage(mitkImage); + fib->SetReferenceGeometry(mitkImage->GetGeometry()); mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) { if ( (*it)->CanWriteBaseDataType(fib.GetPointer()) ) { (*it)->SetFileName( outFileName.c_str() ); (*it)->DoWrite( fib.GetPointer() ); } } } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } - MITK_INFO << "DONE"; return EXIT_SUCCESS; } RegisterDiffusionMiniApp(StreamlineTracking); diff --git a/Modules/DiffusionImaging/MiniApps/TensorDerivedMapsExtraction.cpp b/Modules/DiffusionImaging/MiniApps/TensorDerivedMapsExtraction.cpp index 29a5323c70..6f4b744a57 100644 --- a/Modules/DiffusionImaging/MiniApps/TensorDerivedMapsExtraction.cpp +++ b/Modules/DiffusionImaging/MiniApps/TensorDerivedMapsExtraction.cpp @@ -1,195 +1,196 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include "mitkImage.h" #include #include "mitkITKImageImport.h" #include #include #include #include #include "itkTensorDerivedMeasurementsFilter.h" #include "itkDiffusionTensor3DReconstructionImageFilter.h" #include "ctkCommandLineParser.h" #include #include #include typedef short DiffusionPixelType; typedef double TTensorPixelType; static void ExtractMapsAndSave(mitk::TensorImage::Pointer tensorImage, std::string filename, std::string postfix = "") { mitk::Image* image = dynamic_cast (tensorImage.GetPointer()); typedef itk::DiffusionTensor3D< TTensorPixelType > TensorPixelType; typedef itk::Image< TensorPixelType, 3 > TensorImageType; TensorImageType::Pointer itkvol = TensorImageType::New(); mitk::CastToItkImage(image, itkvol); typedef itk::TensorDerivedMeasurementsFilter MeasurementsType; MeasurementsType::Pointer measurementsCalculator = MeasurementsType::New(); measurementsCalculator->SetInput(itkvol.GetPointer() ); mitk::Image::Pointer map = mitk::Image::New(); // FA measurementsCalculator->SetMeasure(MeasurementsType::FA); measurementsCalculator->Update(); map->InitializeByItk( measurementsCalculator->GetOutput() ); map->SetVolume( measurementsCalculator->GetOutput()->GetBufferPointer() ); mitk::IOUtil::SaveImage(map, filename + "_dti_FA" + postfix + ".nrrd"); // MD measurementsCalculator->SetMeasure(MeasurementsType::MD); measurementsCalculator->Update(); map->InitializeByItk( measurementsCalculator->GetOutput() ); map->SetVolume( measurementsCalculator->GetOutput()->GetBufferPointer() ); mitk::IOUtil::SaveImage(map, filename + "_dti_MD" + postfix + ".nrrd"); // AD measurementsCalculator->SetMeasure(MeasurementsType::AD); measurementsCalculator->Update(); map->InitializeByItk( measurementsCalculator->GetOutput() ); map->SetVolume( measurementsCalculator->GetOutput()->GetBufferPointer() ); mitk::IOUtil::SaveImage(map, filename + "_dti_AD" + postfix + ".nrrd"); // CA measurementsCalculator->SetMeasure(MeasurementsType::CA); measurementsCalculator->Update(); map->InitializeByItk( measurementsCalculator->GetOutput() ); map->SetVolume( measurementsCalculator->GetOutput()->GetBufferPointer() ); mitk::IOUtil::SaveImage(map, filename + "_dti_CA" + postfix + ".nrrd"); // RA measurementsCalculator->SetMeasure(MeasurementsType::RA); measurementsCalculator->Update(); map->InitializeByItk( measurementsCalculator->GetOutput() ); map->SetVolume( measurementsCalculator->GetOutput()->GetBufferPointer() ); mitk::IOUtil::SaveImage(map, filename + "_dti_RA" + postfix + ".nrrd"); // RD measurementsCalculator->SetMeasure(MeasurementsType::RD); measurementsCalculator->Update(); map->InitializeByItk( measurementsCalculator->GetOutput() ); map->SetVolume( measurementsCalculator->GetOutput()->GetBufferPointer() ); mitk::IOUtil::SaveImage(map, filename + "_dti_RD" + postfix + ".nrrd"); } int TensorDerivedMapsExtraction(int argc, char* argv[]) { + MITK_INFO << "TensorDerivedMapsExtraction"; ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("help", "h", ctkCommandLineParser::String, "Help", "Show this help text"); parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input file", "input dwi file", us::Any(),false); parser.addArgument("out", "o", ctkCommandLineParser::String, "Output folder", "output folder and base name, e.g. /tmp/outPatient1 ", us::Any(),false); parser.setCategory("Diffusion Related Measures"); parser.setTitle("Tensor Derived Maps Extraction"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0 || parsedArgs.count("help") || parsedArgs.count("h")) { std::cout << "\n\nMiniApp Description: \nPerforms tensor reconstruction on DWI file," << endl; std::cout << "and computes tensor derived measures." << endl; std::cout << "\n\n For out parameter /tmp/outPatient1 it will produce :"<< endl; std::cout << " /tmp/outPatient1_dti.dti , /tmp/outPatient1_dti_FA.nrrd, ..."<< endl; std::cout << "\n\n Parameters:"<< endl; std::cout << parser.helpText(); return EXIT_SUCCESS; } std::string inputFile = us::any_cast(parsedArgs["input"]); std::string baseFileName = us::any_cast(parsedArgs["out"]); std::string dtiFileName = "_dti.dti"; MITK_INFO << "BaseFileName: " << baseFileName; mitk::Image::Pointer inputImage = mitk::IOUtil::LoadImage(inputFile); mitk::DiffusionImage* diffusionImage = static_cast*>(inputImage.GetPointer()); if (diffusionImage == NULL) // does NULL pointer check make sense after static cast ? { MITK_ERROR << "Invalid Input Image. Must be DWI. Aborting."; return -1; } mitk::DiffusionImage* vols = dynamic_cast *> (inputImage.GetPointer()); typedef itk::DiffusionTensor3DReconstructionImageFilter< DiffusionPixelType, DiffusionPixelType, TTensorPixelType > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer tensorReconstructionFilter = TensorReconstructionImageFilterType::New(); typedef mitk::DiffusionImage DiffusionImageType; typedef DiffusionImageType::GradientDirectionContainerType GradientDirectionContainerType; GradientDirectionContainerType::Pointer gradientContainerCopy = GradientDirectionContainerType::New(); for(GradientDirectionContainerType::ConstIterator it = vols->GetDirections()->Begin(); it != vols->GetDirections()->End(); it++) { gradientContainerCopy->push_back(it.Value()); } tensorReconstructionFilter->SetGradientImage( gradientContainerCopy, vols->GetVectorImage() ); tensorReconstructionFilter->SetBValue(vols->GetReferenceBValue()); tensorReconstructionFilter->SetThreshold(50); tensorReconstructionFilter->Update(); typedef itk::Image, 3> TensorImageType; TensorImageType::Pointer tensorImage = tensorReconstructionFilter->GetOutput(); tensorImage->SetDirection( vols->GetVectorImage()->GetDirection() ); mitk::TensorImage::Pointer tensorImageMitk = mitk::TensorImage::New(); tensorImageMitk->InitializeByItk(tensorImage.GetPointer()); tensorImageMitk->SetVolume( tensorImage->GetBufferPointer() ); itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); io->SetFileType( itk::ImageIOBase::Binary ); io->UseCompressionOn(); itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< double >, 3 > >::Pointer writer = itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< double >, 3 > >::New(); writer->SetInput(tensorReconstructionFilter->GetOutput()); writer->SetFileName(baseFileName + dtiFileName); writer->SetImageIO(io); writer->UseCompressionOn(); writer->Update(); ExtractMapsAndSave(tensorImageMitk,baseFileName); return EXIT_SUCCESS; } RegisterDiffusionMiniApp(TensorDerivedMapsExtraction); diff --git a/Modules/DiffusionImaging/MiniApps/TensorReconstruction.cpp b/Modules/DiffusionImaging/MiniApps/TensorReconstruction.cpp index 446bcb6dfa..e73a4a4d01 100644 --- a/Modules/DiffusionImaging/MiniApps/TensorReconstruction.cpp +++ b/Modules/DiffusionImaging/MiniApps/TensorReconstruction.cpp @@ -1,102 +1,100 @@ /*=================================================================== 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 "MiniAppManager.h" #include "mitkBaseDataIOFactory.h" #include "mitkDiffusionImage.h" #include "mitkBaseData.h" #include #include #include #include #include "ctkCommandLineParser.h" #include using namespace mitk; /** * Convert files from one ending to the other */ int TensorReconstruction(int argc, char* argv[]) { + MITK_INFO << "TensorReconstruction"; ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input file", "input raw dwi (.dwi or .fsl/.fslgz)", us::Any(), false); parser.addArgument("outFile", "o", ctkCommandLineParser::OutputFile, "Output file", "output file", us::Any(), false); parser.addArgument("b0Threshold", "t", ctkCommandLineParser::Int, "b0 threshold", "baseline image intensity threshold", 0, true); parser.setCategory("Preprocessing Tools"); parser.setTitle("Tensor Reconstruction"); parser.setDescription(""); parser.setContributor("MBI"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; std::string inFileName = us::any_cast(parsedArgs["input"]); std::string outfilename = us::any_cast(parsedArgs["outFile"]); outfilename = itksys::SystemTools::GetFilenamePath(outfilename)+"/"+itksys::SystemTools::GetFilenameWithoutExtension(outfilename); outfilename += ".dti"; int threshold = 0; if (parsedArgs.count("b0Threshold")) threshold = us::any_cast(parsedArgs["b0Threshold"]); try { - MITK_INFO << "Loading image ..."; const std::string s1="", s2=""; std::vector infile = BaseDataIO::LoadBaseDataFromFile( inFileName, s1, s2, false ); DiffusionImage::Pointer dwi = dynamic_cast*>(infile.at(0).GetPointer()); - MITK_INFO << "B0 threshold: " << threshold; typedef itk::DiffusionTensor3DReconstructionImageFilter< short, short, float > TensorReconstructionImageFilterType; TensorReconstructionImageFilterType::Pointer filter = TensorReconstructionImageFilterType::New(); filter->SetGradientImage( dwi->GetDirections(), dwi->GetVectorImage() ); filter->SetBValue(dwi->GetReferenceBValue()); filter->SetThreshold(threshold); filter->Update(); // Save tensor image - MITK_INFO << "writing image " << outfilename; itk::NrrdImageIO::Pointer io = itk::NrrdImageIO::New(); io->SetFileType( itk::ImageIOBase::Binary ); io->UseCompressionOn(); itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< float >, 3 > >::Pointer writer = itk::ImageFileWriter< itk::Image< itk::DiffusionTensor3D< float >, 3 > >::New(); writer->SetInput(filter->GetOutput()); writer->SetFileName(outfilename); writer->SetImageIO(io); writer->UseCompressionOn(); writer->Update(); } catch ( itk::ExceptionObject &err) { MITK_INFO << "Exception: " << err; } catch ( std::exception err) { MITK_INFO << "Exception: " << err.what(); } catch ( ... ) { MITK_INFO << "Exception!"; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(TensorReconstruction); diff --git a/Modules/DiffusionImaging/MiniApps/TractogramAngularError.cpp b/Modules/DiffusionImaging/MiniApps/TractogramAngularError.cpp index 2b745330de..aa2a25ef82 100755 --- a/Modules/DiffusionImaging/MiniApps/TractogramAngularError.cpp +++ b/Modules/DiffusionImaging/MiniApps/TractogramAngularError.cpp @@ -1,205 +1,202 @@ /*=================================================================== 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 "MiniAppManager.h" #include #include #include #include #include #include #include #include "ctkCommandLineParser.h" #include #include #include #include #include #include #include #define _USE_MATH_DEFINES #include int TractogramAngularError(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("input", "i", ctkCommandLineParser::String, "input tractogram (.fib, vtk ascii file format)", us::Any(), false); parser.addArgument("reference", "r", ctkCommandLineParser::StringList, "reference direction images", us::Any(), false); parser.addArgument("out", "o", ctkCommandLineParser::String, "output root", us::Any(), false); parser.addArgument("mask", "m", ctkCommandLineParser::String, "mask image"); parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "output optional and intermediate calculation results"); parser.addArgument("ignore", "n", ctkCommandLineParser::Bool, "don't increase error for missing or too many directions"); parser.addArgument("trilinear", "t", ctkCommandLineParser::Bool, "use trilinear instead of nearest neighbor interpolation"); map parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; ctkCommandLineParser::StringContainerType referenceImages = us::any_cast(parsedArgs["reference"]); string fibFile = us::any_cast(parsedArgs["input"]); string maskImage(""); if (parsedArgs.count("mask")) maskImage = us::any_cast(parsedArgs["mask"]); string outRoot = us::any_cast(parsedArgs["out"]); bool verbose = false; if (parsedArgs.count("verbose")) verbose = us::any_cast(parsedArgs["verbose"]); bool ignore = false; if (parsedArgs.count("ignore")) ignore = us::any_cast(parsedArgs["ignore"]); bool interpolate = false; if (parsedArgs.count("interpolate")) interpolate = us::any_cast(parsedArgs["interpolate"]); try { RegisterDiffusionCoreObjectFactory(); RegisterFiberTrackingObjectFactory(); typedef itk::Image ItkUcharImgType; typedef itk::Image< itk::Vector< float, 3>, 3 > ItkDirectionImage3DType; typedef itk::VectorContainer< int, ItkDirectionImage3DType::Pointer > ItkDirectionImageContainerType; typedef itk::EvaluateTractogramDirectionsFilter< float > EvaluationFilterType; // load fiber bundle mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast(mitk::IOUtil::LoadDataNode(fibFile)->GetData()); if (!inputTractogram) return EXIT_FAILURE; // load reference directions ItkDirectionImageContainerType::Pointer referenceImageContainer = ItkDirectionImageContainerType::New(); for (int i=0; i(mitk::IOUtil::LoadDataNode(referenceImages.at(i))->GetData()); typedef mitk::ImageToItk< ItkDirectionImage3DType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(img); caster->Update(); ItkDirectionImage3DType::Pointer itkImg = caster->GetOutput(); referenceImageContainer->InsertElement(referenceImageContainer->Size(),itkImg); } catch(...){ MITK_INFO << "could not load: " << referenceImages.at(i); } } // load/create mask image ItkUcharImgType::Pointer itkMaskImage = ItkUcharImgType::New(); if (maskImage.compare("")==0) { ItkDirectionImage3DType::Pointer dirImg = referenceImageContainer->GetElement(0); itkMaskImage->SetSpacing( dirImg->GetSpacing() ); itkMaskImage->SetOrigin( dirImg->GetOrigin() ); itkMaskImage->SetDirection( dirImg->GetDirection() ); itkMaskImage->SetLargestPossibleRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->SetBufferedRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->SetRequestedRegion( dirImg->GetLargestPossibleRegion() ); itkMaskImage->Allocate(); itkMaskImage->FillBuffer(1); } else { mitk::Image::Pointer mitkMaskImage = dynamic_cast(mitk::IOUtil::LoadDataNode(maskImage)->GetData()); mitk::CastToItkImage(mitkMaskImage, itkMaskImage); } // evaluate directions EvaluationFilterType::Pointer evaluationFilter = EvaluationFilterType::New(); evaluationFilter->SetTractogram(inputTractogram); evaluationFilter->SetReferenceImageSet(referenceImageContainer); evaluationFilter->SetMaskImage(itkMaskImage); evaluationFilter->SetIgnoreMissingDirections(ignore); evaluationFilter->SetUseInterpolation(interpolate); evaluationFilter->Update(); if (verbose) { EvaluationFilterType::OutputImageType::Pointer angularErrorImage = evaluationFilter->GetOutput(0); typedef itk::ImageFileWriter< EvaluationFilterType::OutputImageType > WriterType; WriterType::Pointer writer = WriterType::New(); string outfilename = outRoot; outfilename.append("_ERROR_IMAGE.nrrd"); - MITK_INFO << "writing " << outfilename; writer->SetFileName(outfilename.c_str()); writer->SetInput(angularErrorImage); writer->Update(); } string logFile = outRoot; logFile.append("_ANGULAR_ERROR.csv"); ofstream file; file.open (logFile.c_str()); string sens = "Mean:"; sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMeanAngularError())); sens.append(";\n"); sens.append("Median:"); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMedianAngularError())); sens.append(";\n"); sens.append("Maximum:"); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMaxAngularError())); sens.append(";\n"); sens.append("Minimum:"); sens.append(","); sens.append(boost::lexical_cast(evaluationFilter->GetMinAngularError())); sens.append(";\n"); sens.append("STDEV:"); sens.append(","); sens.append(boost::lexical_cast(std::sqrt(evaluationFilter->GetVarAngularError()))); sens.append(";\n"); file << sens; file.close(); - - MITK_INFO << "DONE"; } catch (itk::ExceptionObject e) { MITK_INFO << e; return EXIT_FAILURE; } catch (std::exception e) { MITK_INFO << e.what(); return EXIT_FAILURE; } catch (...) { MITK_INFO << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; } RegisterDiffusionMiniApp(TractogramAngularError); diff --git a/Modules/DiffusionImaging/MiniApps/TractometerMetrics.cpp b/Modules/DiffusionImaging/MiniApps/TractometerMetrics.cpp new file mode 100755 index 0000000000..e3f4bac9c0 --- /dev/null +++ b/Modules/DiffusionImaging/MiniApps/TractometerMetrics.cpp @@ -0,0 +1,405 @@ +/*=================================================================== + +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 "MiniAppManager.h" +#include +#include +#include +#include +#include +#include +#include "ctkCommandLineParser.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#define _USE_MATH_DEFINES +#include + +int TractometerMetrics(int argc, char* argv[]) +{ + MITK_INFO << "TractometerMetrics"; + ctkCommandLineParser parser; + + parser.setTitle("Tractometer Metrics"); + parser.setCategory("Fiber Tracking and Processing Methods"); + parser.setDescription(""); + parser.setContributor("MBI"); + + parser.setArgumentPrefix("--", "-"); + parser.addArgument("input", "i", ctkCommandLineParser::InputFile, "Input:", "input tractogram (.fib, vtk ascii file format)", us::Any(), false); + parser.addArgument("out", "o", ctkCommandLineParser::OutputDirectory, "Output:", "output root", us::Any(), false); + parser.addArgument("labels", "l", ctkCommandLineParser::StringList, "Label pairs:", "label pairs", false); + parser.addArgument("labelimage", "li", ctkCommandLineParser::String, "Label image:", "label image", false); + parser.addArgument("verbose", "v", ctkCommandLineParser::Bool, "Verbose:", "output valid, invalid and no connections as fiber bundles"); + + parser.addArgument("fileID", "id", ctkCommandLineParser::String, "ID:", "optional ID field"); + + map parsedArgs = parser.parseArguments(argc, argv); + if (parsedArgs.size()==0) + return EXIT_FAILURE; + + ctkCommandLineParser::StringContainerType labelpairs = us::any_cast(parsedArgs["labels"]); + + string fibFile = us::any_cast(parsedArgs["input"]); + string labelImageFile = us::any_cast(parsedArgs["labelimage"]); + + string outRoot = us::any_cast(parsedArgs["out"]); + + string fileID = ""; + if (parsedArgs.count("fileID")) + fileID = us::any_cast(parsedArgs["fileID"]); + + bool verbose = false; + if (parsedArgs.count("verbose")) + verbose = us::any_cast(parsedArgs["verbose"]); + + try + { + typedef itk::Image ItkShortImgType; + typedef itk::Image ItkUcharImgType; + + // load fiber bundle + mitk::FiberBundleX::Pointer inputTractogram = dynamic_cast(mitk::IOUtil::LoadDataNode(fibFile)->GetData()); + + mitk::Image::Pointer img = dynamic_cast(mitk::IOUtil::LoadDataNode(labelImageFile)->GetData()); + typedef mitk::ImageToItk< ItkShortImgType > CasterType; + CasterType::Pointer caster = CasterType::New(); + caster->SetInput(img); + caster->Update(); + ItkShortImgType::Pointer labelImage = caster->GetOutput(); + + string path = itksys::SystemTools::GetFilenamePath(labelImageFile); + + std::vector< bool > detected; + std::vector< std::pair< int, int > > labelsvector; + std::vector< ItkUcharImgType::Pointer > bundleMasks; + short max = 0; + for (unsigned int i=0; i l; + l.first = boost::lexical_cast(labelpairs.at(i)); + l.second = boost::lexical_cast(labelpairs.at(i+1)); + MITK_INFO << labelpairs.at(i); + MITK_INFO << labelpairs.at(i+1); + if (l.first>max) + max=l.first; + if (l.second>max) + max=l.second; + + labelsvector.push_back(l); + detected.push_back(false); + + mitk::Image::Pointer img = dynamic_cast(mitk::IOUtil::LoadDataNode(path+"/Bundle"+boost::lexical_cast(labelsvector.size())+"_MASK.nrrd")->GetData()); + typedef mitk::ImageToItk< ItkUcharImgType > CasterType; + CasterType::Pointer caster = CasterType::New(); + caster->SetInput(img); + caster->Update(); + ItkUcharImgType::Pointer bundle = caster->GetOutput(); + bundleMasks.push_back(bundle); + } + vnl_matrix< unsigned char > matrix; matrix.set_size(max, max); matrix.fill(0); + + vtkSmartPointer polyData = inputTractogram->GetFiberPolyData(); + + int validConnections = 0; + int noConnection = 0; + int validBundles = 0; + int invalidBundles = 0; + int invalidConnections = 0; + + ItkUcharImgType::Pointer coverage = ItkUcharImgType::New(); + coverage->SetSpacing(labelImage->GetSpacing()); + coverage->SetOrigin(labelImage->GetOrigin()); + coverage->SetDirection(labelImage->GetDirection()); + coverage->SetLargestPossibleRegion(labelImage->GetLargestPossibleRegion()); + coverage->SetBufferedRegion( labelImage->GetLargestPossibleRegion() ); + coverage->SetRequestedRegion( labelImage->GetLargestPossibleRegion() ); + coverage->Allocate(); + coverage->FillBuffer(0); + + vtkSmartPointer noConnPoints = vtkSmartPointer::New(); + vtkSmartPointer noConnCells = vtkSmartPointer::New(); + + vtkSmartPointer invalidPoints = vtkSmartPointer::New(); + vtkSmartPointer invalidCells = vtkSmartPointer::New(); + + vtkSmartPointer validPoints = vtkSmartPointer::New(); + vtkSmartPointer validCells = vtkSmartPointer::New(); + + boost::progress_display disp(inputTractogram->GetNumFibers()); + for (int i=0; iGetNumFibers(); i++) + { + ++disp; + + vtkCell* cell = polyData->GetCell(i); + int numPoints = cell->GetNumberOfPoints(); + vtkPoints* points = cell->GetPoints(); + + + if (numPoints>1) + { + double* start = points->GetPoint(0); + itk::Point itkStart; + itkStart[0] = start[0]; itkStart[1] = start[1]; itkStart[2] = start[2]; + itk::Index<3> idxStart; + labelImage->TransformPhysicalPointToIndex(itkStart, idxStart); + + double* end = points->GetPoint(numPoints-1); + itk::Point itkEnd; + itkEnd[0] = end[0]; itkEnd[1] = end[1]; itkEnd[2] = end[2]; + itk::Index<3> idxEnd; + labelImage->TransformPhysicalPointToIndex(itkEnd, idxEnd); + + + if ( labelImage->GetPixel(idxStart)==0 || labelImage->GetPixel(idxEnd)==0 ) + { + noConnection++; + + if (verbose) + { + vtkSmartPointer container = vtkSmartPointer::New(); + for (int j=0; jGetPoint(j); + vtkIdType id = noConnPoints->InsertNextPoint(p); + container->GetPointIds()->InsertNextId(id); + } + noConnCells->InsertNextCell(container); + } + } + else + { + bool invalid = true; + for (unsigned int i=0; i l = labelsvector.at(i); + if ( (labelImage->GetPixel(idxStart)==l.first && labelImage->GetPixel(idxEnd)==l.second) || + (labelImage->GetPixel(idxStart)==l.second && labelImage->GetPixel(idxEnd)==l.first) ) + { + for (int j=0; jGetPoint(j); + + itk::Point itkP; + itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; + itk::Index<3> idx; + bundle->TransformPhysicalPointToIndex(itkP, idx); + + if ( !bundle->GetPixel(idx)>0 && bundle->GetLargestPossibleRegion().IsInside(idx) ) + { + outside=true; + } + } + + if (!outside) + { + validConnections++; + if (detected.at(i)==false) + validBundles++; + detected.at(i) = true; + invalid = false; + + + vtkSmartPointer container = vtkSmartPointer::New(); + for (int j=0; jGetPoint(j); + vtkIdType id = validPoints->InsertNextPoint(p); + container->GetPointIds()->InsertNextId(id); + + itk::Point itkP; + itkP[0] = p[0]; itkP[1] = p[1]; itkP[2] = p[2]; + itk::Index<3> idx; + coverage->TransformPhysicalPointToIndex(itkP, idx); + if ( coverage->GetLargestPossibleRegion().IsInside(idx) ) + coverage->SetPixel(idx, 1); + } + validCells->InsertNextCell(container); + } + break; + } + } + if (invalid==true) + { + invalidConnections++; + int x = labelImage->GetPixel(idxStart)-1; + int y = labelImage->GetPixel(idxEnd)-1; + if (x>=0 && y>0 && x container = vtkSmartPointer::New(); + for (int j=0; jGetPoint(j); + vtkIdType id = invalidPoints->InsertNextPoint(p); + container->GetPointIds()->InsertNextId(id); + } + invalidCells->InsertNextCell(container); + } + } + } + } + } + + if (verbose) + { + mitk::CoreObjectFactory::FileWriterList fileWriters = mitk::CoreObjectFactory::GetInstance()->GetFileWriters(); + vtkSmartPointer noConnPolyData = vtkSmartPointer::New(); + noConnPolyData->SetPoints(noConnPoints); + noConnPolyData->SetLines(noConnCells); + mitk::FiberBundleX::Pointer noConnFib = mitk::FiberBundleX::New(noConnPolyData); + for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) + { + if ( (*it)->CanWriteBaseDataType(noConnFib.GetPointer()) ) { + (*it)->SetFileName( (outRoot+"_NC.fib").c_str() ); + (*it)->DoWrite( noConnFib.GetPointer() ); + } + } + + vtkSmartPointer invalidPolyData = vtkSmartPointer::New(); + invalidPolyData->SetPoints(invalidPoints); + invalidPolyData->SetLines(invalidCells); + mitk::FiberBundleX::Pointer invalidFib = mitk::FiberBundleX::New(invalidPolyData); + for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) + { + if ( (*it)->CanWriteBaseDataType(invalidFib.GetPointer()) ) { + (*it)->SetFileName( (outRoot+"_IC.fib").c_str() ); + (*it)->DoWrite( invalidFib.GetPointer() ); + } + } + + vtkSmartPointer validPolyData = vtkSmartPointer::New(); + validPolyData->SetPoints(validPoints); + validPolyData->SetLines(validCells); + mitk::FiberBundleX::Pointer validFib = mitk::FiberBundleX::New(validPolyData); + for (mitk::CoreObjectFactory::FileWriterList::iterator it = fileWriters.begin() ; it != fileWriters.end() ; ++it) + { + if ( (*it)->CanWriteBaseDataType(validFib.GetPointer()) ) { + (*it)->SetFileName( (outRoot+"_VC.fib").c_str() ); + (*it)->DoWrite( validFib.GetPointer() ); + } + } + + { + typedef itk::ImageFileWriter< ItkUcharImgType > WriterType; + WriterType::Pointer writer = WriterType::New(); + writer->SetFileName(outRoot+"_ABC.nrrd"); + writer->SetInput(coverage); + writer->Update(); + } + } + + // calculate coverage + int wmVoxels = 0; + int coveredVoxels = 0; + itk::ImageRegionIterator it (coverage, coverage->GetLargestPossibleRegion()); + while(!it.IsAtEnd()) + { + bool wm = false; + for (unsigned int i=0; iGetPixel(it.GetIndex())>0) + { + wm = true; + wmVoxels++; + break; + } + } + if (wm && it.Get()>0) + coveredVoxels++; + ++it; + } + + int numFibers = inputTractogram->GetNumFibers(); + double nc = (double)noConnection/numFibers; + double vc = (double)validConnections/numFibers; + double ic = (double)invalidConnections/numFibers; + if (numFibers==0) + { + nc = 0.0; + vc = 0.0; + ic = 0.0; + } + int vb = validBundles; + int ib = invalidBundles; + double abc = (double)coveredVoxels/wmVoxels; + + MITK_INFO << "NC: " << nc; + MITK_INFO << "VC: " << vc; + MITK_INFO << "IC: " << ic; + MITK_INFO << "VB: " << vb; + MITK_INFO << "IB: " << ib; + MITK_INFO << "ABC: " << abc; + + string logFile = outRoot; + logFile.append("_TRACTOMETER.csv"); + ofstream file; + file.open (logFile.c_str()); + { + string sens = itksys::SystemTools::GetFilenameWithoutLastExtension(fibFile); + if (!fileID.empty()) + sens = fileID; + sens.append(","); + + sens.append(boost::lexical_cast(nc)); + sens.append(","); + + sens.append(boost::lexical_cast(validBundles)); + sens.append(","); + + sens.append(boost::lexical_cast(invalidBundles)); + sens.append(","); + + sens.append(boost::lexical_cast(abc)); + sens.append(";\n"); + file << sens; + } + file.close(); + } + catch (itk::ExceptionObject e) + { + MITK_INFO << e; + return EXIT_FAILURE; + } + catch (std::exception e) + { + MITK_INFO << e.what(); + return EXIT_FAILURE; + } + catch (...) + { + MITK_INFO << "ERROR!?!"; + return EXIT_FAILURE; + } + return EXIT_SUCCESS; +} +RegisterDiffusionMiniApp(TractometerMetrics); diff --git a/Modules/DiffusionImaging/MiniApps/files.cmake b/Modules/DiffusionImaging/MiniApps/files.cmake index 98428da34c..08d6ac21d1 100644 --- a/Modules/DiffusionImaging/MiniApps/files.cmake +++ b/Modules/DiffusionImaging/MiniApps/files.cmake @@ -1,31 +1,32 @@ set(CPP_FILES mitkDiffusionMiniApps.cpp MiniAppManager.cpp BatchedFolderRegistration.cpp DicomFolderDump.cpp FileFormatConverter.cpp TensorReconstruction.cpp TensorDerivedMapsExtraction.cpp QballReconstruction.cpp DiffusionIndices.cpp ExtractImageStatistics.cpp CopyGeometry.cpp GibbsTracking.cpp StreamlineTracking.cpp FiberProcessing.cpp LocalDirectionalFiberPlausibility.cpp #TractogramAngularError.cpp FiberDirectionExtraction.cpp ImageResampler.cpp PeakExtraction.cpp PeaksAngularError.cpp MultishellMethods.cpp Fiberfox.cpp ExportShImage.cpp NetworkCreation.cpp NetworkStatistics.cpp DwiDenoising.cpp FiberExtraction.cpp FiberJoin.cpp + TractometerMetrics.cpp ) diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingView.cpp index fb81c52ed1..c16cc2172b 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkGibbsTrackingView.cpp @@ -1,761 +1,761 @@ /*=================================================================== 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 "QmitkGibbsTrackingView.h" #include // Qt #include #include #include // MITK #include #include #include #include #include // ITK #include #include #include // MISC #include QmitkTrackingWorker::QmitkTrackingWorker(QmitkGibbsTrackingView* view) : m_View(view) { } void QmitkTrackingWorker::run() { m_View->m_GlobalTracker = QmitkGibbsTrackingView::GibbsTrackingFilterType::New(); m_View->m_GlobalTracker->SetQBallImage(m_View->m_ItkQBallImage); m_View->m_GlobalTracker->SetTensorImage(m_View->m_ItkTensorImage); m_View->m_GlobalTracker->SetMaskImage(m_View->m_MaskImage); m_View->m_GlobalTracker->SetStartTemperature((float)m_View->m_Controls->m_StartTempSlider->value()/100); m_View->m_GlobalTracker->SetEndTemperature((float)m_View->m_Controls->m_EndTempSlider->value()/10000); m_View->m_GlobalTracker->SetIterations(m_View->m_Iterations); m_View->m_GlobalTracker->SetParticleWeight((float)m_View->m_Controls->m_ParticleWeightSlider->value()/10000); m_View->m_GlobalTracker->SetParticleWidth((float)(m_View->m_Controls->m_ParticleWidthSlider->value())/10); m_View->m_GlobalTracker->SetParticleLength((float)(m_View->m_Controls->m_ParticleLengthSlider->value())/10); m_View->m_GlobalTracker->SetInexBalance((float)m_View->m_Controls->m_InExBalanceSlider->value()/10); m_View->m_GlobalTracker->SetMinFiberLength(m_View->m_Controls->m_FiberLengthSlider->value()); m_View->m_GlobalTracker->SetCurvatureThreshold(cos((float)m_View->m_Controls->m_CurvatureThresholdSlider->value()*M_PI/180)); m_View->m_GlobalTracker->SetRandomSeed(m_View->m_Controls->m_RandomSeedSlider->value()); try{ m_View->m_GlobalTracker->Update(); } catch( mitk::Exception e ) { MITK_ERROR << "Internal error occured: " << e.what() << "\nAborting"; } m_View->m_TrackingThread.quit(); } const std::string QmitkGibbsTrackingView::VIEW_ID = "org.mitk.views.gibbstracking"; QmitkGibbsTrackingView::QmitkGibbsTrackingView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget(NULL) , m_FiberBundle(NULL) , m_MaskImage(NULL) , m_TensorImage(NULL) , m_QBallImage(NULL) , m_ItkQBallImage(NULL) , m_ItkTensorImage(NULL) , m_ImageNode(NULL) , m_MaskImageNode(NULL) , m_FiberBundleNode(NULL) , m_ThreadIsRunning(false) , m_ElapsedTime(0) , m_Iterations(10000000) , m_LastStep(0) , m_GlobalTracker(NULL) , m_TrackingWorker(this) { m_TrackingWorker.moveToThread(&m_TrackingThread); connect(&m_TrackingThread, SIGNAL(started()), this, SLOT(BeforeThread())); connect(&m_TrackingThread, SIGNAL(started()), &m_TrackingWorker, SLOT(run())); connect(&m_TrackingThread, SIGNAL(finished()), this, SLOT(AfterThread())); connect(&m_TrackingThread, SIGNAL(terminated()), this, SLOT(AfterThread())); m_TrackingTimer = new QTimer(this); } QmitkGibbsTrackingView::~QmitkGibbsTrackingView() { delete m_TrackingTimer; } // update tracking status and generate fiber bundle void QmitkGibbsTrackingView::TimerUpdate() { int currentStep = m_GlobalTracker->GetCurrentStep(); mitk::ProgressBar::GetInstance()->Progress(currentStep-m_LastStep); UpdateTrackingStatus(); GenerateFiberBundle(); m_LastStep = currentStep; } // tell global tractography filter to stop after current step void QmitkGibbsTrackingView::StopGibbsTracking() { if (m_GlobalTracker.IsNull()) return; //mitk::ProgressBar::GetInstance()->Progress(m_GlobalTracker->GetSteps()-m_LastStep+1); m_GlobalTracker->SetAbortTracking(true); m_Controls->m_TrackingStop->setEnabled(false); m_Controls->m_TrackingStop->setText("Stopping Tractography ..."); } // update gui elements and generate fiber bundle after tracking is finished void QmitkGibbsTrackingView::AfterThread() { m_ThreadIsRunning = false; m_TrackingTimer->stop(); mitk::ProgressBar::GetInstance()->Progress(m_GlobalTracker->GetSteps()-m_LastStep+1); UpdateGUI(); if( !m_GlobalTracker->GetIsInValidState() ) { QMessageBox::critical( NULL, "Gibbs Tracking", "An internal error occured. Tracking aborted.\n Please check the log for details." ); m_FiberBundleNode = NULL; return; } UpdateTrackingStatus(); if(m_Controls->m_ParticleWeightSlider->value()==0) { m_Controls->m_ParticleWeightLabel->setText(QString::number(m_GlobalTracker->GetParticleWeight())); m_Controls->m_ParticleWeightSlider->setValue(m_GlobalTracker->GetParticleWeight()*10000); } if(m_Controls->m_ParticleWidthSlider->value()==0) { m_Controls->m_ParticleWidthLabel->setText(QString::number(m_GlobalTracker->GetParticleWidth())); m_Controls->m_ParticleWidthSlider->setValue(m_GlobalTracker->GetParticleWidth()*10); } if(m_Controls->m_ParticleLengthSlider->value()==0) { m_Controls->m_ParticleLengthLabel->setText(QString::number(m_GlobalTracker->GetParticleLength())); m_Controls->m_ParticleLengthSlider->setValue(m_GlobalTracker->GetParticleLength()*10); } GenerateFiberBundle(); m_FiberBundleNode = 0; m_GlobalTracker = 0; // images not needed anymore ( relevant only for computation ) // we need to release them to remove the memory access block created through CastToItk<> calls this->m_ItkQBallImage = 0; this->m_ItkTensorImage = 0; } // start tracking timer and update gui elements before tracking is started void QmitkGibbsTrackingView::BeforeThread() { m_ThreadIsRunning = true; m_TrackingTime = QTime::currentTime(); m_ElapsedTime = 0; m_TrackingTimer->start(1000); m_LastStep = 0; UpdateGUI(); } // setup gui elements and signal/slot connections void QmitkGibbsTrackingView::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::QmitkGibbsTrackingViewControls; m_Controls->setupUi( parent ); AdvancedSettings(); connect( m_TrackingTimer, SIGNAL(timeout()), this, SLOT(TimerUpdate()) ); connect( m_Controls->m_TrackingStop, SIGNAL(clicked()), this, SLOT(StopGibbsTracking()) ); connect( m_Controls->m_TrackingStart, SIGNAL(clicked()), this, SLOT(StartGibbsTracking()) ); connect( m_Controls->m_AdvancedSettingsCheckbox, SIGNAL(clicked()), this, SLOT(AdvancedSettings()) ); connect( m_Controls->m_SaveTrackingParameters, SIGNAL(clicked()), this, SLOT(SaveTrackingParameters()) ); connect( m_Controls->m_LoadTrackingParameters, SIGNAL(clicked()), this, SLOT(LoadTrackingParameters()) ); connect( m_Controls->m_IterationsSlider, SIGNAL(valueChanged(int)), this, SLOT(SetIterations(int)) ); connect( m_Controls->m_ParticleWidthSlider, SIGNAL(valueChanged(int)), this, SLOT(SetParticleWidth(int)) ); connect( m_Controls->m_ParticleLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(SetParticleLength(int)) ); connect( m_Controls->m_InExBalanceSlider, SIGNAL(valueChanged(int)), this, SLOT(SetInExBalance(int)) ); connect( m_Controls->m_FiberLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(SetFiberLength(int)) ); connect( m_Controls->m_ParticleWeightSlider, SIGNAL(valueChanged(int)), this, SLOT(SetParticleWeight(int)) ); connect( m_Controls->m_StartTempSlider, SIGNAL(valueChanged(int)), this, SLOT(SetStartTemp(int)) ); connect( m_Controls->m_EndTempSlider, SIGNAL(valueChanged(int)), this, SLOT(SetEndTemp(int)) ); connect( m_Controls->m_CurvatureThresholdSlider, SIGNAL(valueChanged(int)), this, SLOT(SetCurvatureThreshold(int)) ); connect( m_Controls->m_RandomSeedSlider, SIGNAL(valueChanged(int)), this, SLOT(SetRandomSeed(int)) ); connect( m_Controls->m_OutputFileButton, SIGNAL(clicked()), this, SLOT(SetOutputFile()) ); } } void QmitkGibbsTrackingView::SetInExBalance(int value) { m_Controls->m_InExBalanceLabel->setText(QString::number((float)value/10)); } void QmitkGibbsTrackingView::SetFiberLength(int value) { m_Controls->m_FiberLengthLabel->setText(QString::number(value)+"mm"); } void QmitkGibbsTrackingView::SetRandomSeed(int value) { if (value>=0) m_Controls->m_RandomSeedLabel->setText(QString::number(value)); else m_Controls->m_RandomSeedLabel->setText("auto"); } void QmitkGibbsTrackingView::SetParticleWeight(int value) { if (value>0) m_Controls->m_ParticleWeightLabel->setText(QString::number((float)value/10000)); else m_Controls->m_ParticleWeightLabel->setText("auto"); } void QmitkGibbsTrackingView::SetStartTemp(int value) { m_Controls->m_StartTempLabel->setText(QString::number((float)value/100)); } void QmitkGibbsTrackingView::SetEndTemp(int value) { m_Controls->m_EndTempLabel->setText(QString::number((float)value/10000)); } void QmitkGibbsTrackingView::SetParticleWidth(int value) { if (value>0) m_Controls->m_ParticleWidthLabel->setText(QString::number((float)value/10)+" mm"); else m_Controls->m_ParticleWidthLabel->setText("auto"); } void QmitkGibbsTrackingView::SetParticleLength(int value) { if (value>0) m_Controls->m_ParticleLengthLabel->setText(QString::number((float)value/10)+" mm"); else m_Controls->m_ParticleLengthLabel->setText("auto"); } void QmitkGibbsTrackingView::SetCurvatureThreshold(int value) { m_Controls->m_CurvatureThresholdLabel->setText(QString::number(value)+"°"); } void QmitkGibbsTrackingView::SetIterations(int value) { switch(value) { case 0: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^4"); m_Iterations = 10000; break; case 1: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^4"); m_Iterations = 50000; break; case 2: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^5"); m_Iterations = 100000; break; case 3: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^5"); m_Iterations = 500000; break; case 4: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^6"); m_Iterations = 1000000; break; case 5: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^6"); m_Iterations = 5000000; break; case 6: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^7"); m_Iterations = 10000000; break; case 7: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^7"); m_Iterations = 50000000; break; case 8: m_Controls->m_IterationsLabel->setText("Iterations: 1x10^8"); m_Iterations = 100000000; break; case 9: m_Controls->m_IterationsLabel->setText("Iterations: 5x10^8"); m_Iterations = 500000000; break; } } void QmitkGibbsTrackingView::StdMultiWidgetAvailable(QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkGibbsTrackingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } // called if datamanager selection changes void QmitkGibbsTrackingView::OnSelectionChanged( std::vector nodes ) { if (m_ThreadIsRunning) return; m_ImageNode = NULL; m_MaskImageNode = NULL; // iterate all selected objects for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) m_ImageNode = node; else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) m_ImageNode = node; else if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { mitk::Image::Pointer img = dynamic_cast(node->GetData()); if (img->GetPixelType().GetPixelType()==itk::ImageIOBase::SCALAR) m_MaskImageNode = node; } } UpdateGUI(); } // update gui elements displaying trackings status void QmitkGibbsTrackingView::UpdateTrackingStatus() { if (m_GlobalTracker.IsNull()) return; m_ElapsedTime += m_TrackingTime.elapsed()/1000; m_TrackingTime.restart(); unsigned long hours = m_ElapsedTime/3600; unsigned long minutes = (m_ElapsedTime%3600)/60; unsigned long seconds = m_ElapsedTime%60; m_Controls->m_ProposalAcceptance->setText(QString::number(m_GlobalTracker->GetProposalAcceptance()*100)+"%"); m_Controls->m_TrackingTimeLabel->setText( QString::number(hours)+QString("h ")+QString::number(minutes)+QString("m ")+QString::number(seconds)+QString("s") ); m_Controls->m_NumConnectionsLabel->setText( QString::number(m_GlobalTracker->GetNumConnections()) ); m_Controls->m_NumParticlesLabel->setText( QString::number(m_GlobalTracker->GetNumParticles()) ); m_Controls->m_CurrentStepLabel->setText( QString::number(100*(float)(m_GlobalTracker->GetCurrentStep()-1)/m_GlobalTracker->GetSteps())+"%" ); m_Controls->m_AcceptedFibersLabel->setText( QString::number(m_GlobalTracker->GetNumAcceptedFibers()) ); } // update gui elements (enable/disable elements and set tooltips) void QmitkGibbsTrackingView::UpdateGUI() { if (m_ImageNode.IsNotNull()) { m_Controls->m_QballImageLabel->setText(m_ImageNode->GetName().c_str()); m_Controls->m_DataFrame->setTitle("Input Data"); } else { m_Controls->m_QballImageLabel->setText("mandatory"); m_Controls->m_DataFrame->setTitle("Please Select Input Data"); } if (m_MaskImageNode.IsNotNull()) m_Controls->m_MaskImageLabel->setText(m_MaskImageNode->GetName().c_str()); else m_Controls->m_MaskImageLabel->setText("optional"); if (!m_ThreadIsRunning && m_ImageNode.IsNotNull()) { m_Controls->m_TrackingStop->setEnabled(false); m_Controls->m_TrackingStart->setEnabled(true); m_Controls->m_LoadTrackingParameters->setEnabled(true); m_Controls->m_IterationsSlider->setEnabled(true); m_Controls->m_AdvancedFrame->setEnabled(true); m_Controls->m_TrackingStop->setText("Stop Tractography"); m_Controls->m_TrackingStart->setToolTip("Start tractography. No further change of parameters possible."); m_Controls->m_TrackingStop->setToolTip(""); } else if (!m_ThreadIsRunning) { m_Controls->m_TrackingStop->setEnabled(false); m_Controls->m_TrackingStart->setEnabled(false); m_Controls->m_LoadTrackingParameters->setEnabled(true); m_Controls->m_IterationsSlider->setEnabled(true); m_Controls->m_AdvancedFrame->setEnabled(true); m_Controls->m_TrackingStop->setText("Stop Tractography"); m_Controls->m_TrackingStart->setToolTip("No Q-Ball image selected."); m_Controls->m_TrackingStop->setToolTip(""); } else { m_Controls->m_TrackingStop->setEnabled(true); m_Controls->m_TrackingStart->setEnabled(false); m_Controls->m_LoadTrackingParameters->setEnabled(false); m_Controls->m_IterationsSlider->setEnabled(false); m_Controls->m_AdvancedFrame->setEnabled(false); m_Controls->m_AdvancedFrame->setVisible(false); m_Controls->m_AdvancedSettingsCheckbox->setChecked(false); m_Controls->m_TrackingStart->setToolTip("Tracking in progress."); m_Controls->m_TrackingStop->setToolTip("Stop tracking and display results."); } } // show/hide advanced settings frame void QmitkGibbsTrackingView::AdvancedSettings() { m_Controls->m_AdvancedFrame->setVisible(m_Controls->m_AdvancedSettingsCheckbox->isChecked()); } // set mask image data node void QmitkGibbsTrackingView::SetMask() { std::vector nodes = GetDataManagerSelection(); if (nodes.empty()) { m_MaskImageNode = NULL; m_Controls->m_MaskImageLabel->setText("-"); return; } for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if (node.IsNotNull() && dynamic_cast(node->GetData())) { m_MaskImageNode = node; m_Controls->m_MaskImageLabel->setText(node->GetName().c_str()); return; } } } // check for mask and qbi and start tracking thread void QmitkGibbsTrackingView::StartGibbsTracking() { if(m_ThreadIsRunning) { MITK_WARN("QmitkGibbsTrackingView")<<"Thread already running!"; return; } m_GlobalTracker = NULL; if (m_ImageNode.IsNull()) { QMessageBox::information( NULL, "Warning", "Please load and select a qball image before starting image processing."); return; } if (dynamic_cast(m_ImageNode->GetData())) m_QBallImage = dynamic_cast(m_ImageNode->GetData()); else if (dynamic_cast(m_ImageNode->GetData())) m_TensorImage = dynamic_cast(m_ImageNode->GetData()); if (m_QBallImage.IsNull() && m_TensorImage.IsNull()) return; // cast qbi to itk m_ItkTensorImage = NULL; m_ItkQBallImage = NULL; m_MaskImage = NULL; if (m_QBallImage.IsNotNull()) { m_ItkQBallImage = ItkQBallImgType::New(); mitk::CastToItkImage(m_QBallImage, m_ItkQBallImage); } else { m_ItkTensorImage = ItkTensorImage::New(); mitk::CastToItkImage(m_TensorImage, m_ItkTensorImage); } // mask image found? // catch exceptions thrown by the itkAccess macros try{ if(m_MaskImageNode.IsNotNull()) { if (dynamic_cast(m_MaskImageNode->GetData())) mitk::CastToItkImage(dynamic_cast(m_MaskImageNode->GetData()), m_MaskImage); } } catch(...){}; unsigned int steps = m_Iterations/10000; if (steps<10) steps = 10; m_LastStep = 1; mitk::ProgressBar::GetInstance()->AddStepsToDo(steps); // start worker thread m_TrackingThread.start(QThread::LowestPriority); } // generate mitkFiberBundle from tracking filter output void QmitkGibbsTrackingView::GenerateFiberBundle() { if (m_GlobalTracker.IsNull() || (!(m_Controls->m_VisualizationCheckbox->isChecked() || m_Controls->m_VisualizeOnceButton->isChecked()) && m_ThreadIsRunning)) return; if (m_Controls->m_VisualizeOnceButton->isChecked()) m_Controls->m_VisualizeOnceButton->setChecked(false); vtkSmartPointer fiberBundle = m_GlobalTracker->GetFiberBundle(); if ( m_GlobalTracker->GetNumAcceptedFibers()==0 ) return; m_FiberBundle = mitk::FiberBundleX::New(fiberBundle); - m_FiberBundle->SetReferenceImage(dynamic_cast(m_ImageNode->GetData())); + m_FiberBundle->SetReferenceGeometry(dynamic_cast(m_ImageNode->GetData())->GetGeometry()); if (m_FiberBundleNode.IsNotNull()){ GetDefaultDataStorage()->Remove(m_FiberBundleNode); m_FiberBundleNode = 0; } m_FiberBundleNode = mitk::DataNode::New(); m_FiberBundleNode->SetData(m_FiberBundle); QString name("FiberBundle_"); name += m_ImageNode->GetName().c_str(); name += "_Gibbs"; m_FiberBundleNode->SetName(name.toStdString()); m_FiberBundleNode->SetVisibility(true); if (!m_OutputFileName.isEmpty()) { QString filename = m_OutputFileName; mitk::FiberBundleXWriter::Pointer writer = mitk::FiberBundleXWriter::New(); writer->SetFileName(filename.toStdString()); writer->SetInputFiberBundleX(m_FiberBundle.GetPointer()); try { writer->Update(); QMessageBox::information(NULL, "Fiber bundle saved to", filename); } catch (itk::ExceptionObject &ex) { QMessageBox::information(NULL, "Fiber bundle could not be saved", QString("%1\n%2\n%3\n%4\n%5\n%6").arg(ex.GetNameOfClass()).arg(ex.GetFile()).arg(ex.GetLine()).arg(ex.GetLocation()).arg(ex.what()).arg(ex.GetDescription())); if(m_ImageNode.IsNull()) GetDataStorage()->Add(m_FiberBundleNode); else GetDataStorage()->Add(m_FiberBundleNode, m_ImageNode); } } else { if(m_ImageNode.IsNull()) GetDataStorage()->Add(m_FiberBundleNode); else GetDataStorage()->Add(m_FiberBundleNode, m_ImageNode); } } void QmitkGibbsTrackingView::SetOutputFile() { // SELECT FOLDER DIALOG m_OutputFileName = QFileDialog::getSaveFileName(0, tr("Set file name"), QDir::currentPath()+"/FiberBundle.fib", tr("Fiber Bundle (*.fib)") ); if (m_OutputFileName.isEmpty()) m_Controls->m_OutputFileLabel->setText("N/A"); else m_Controls->m_OutputFileLabel->setText(m_OutputFileName); } // save current tracking paramters as xml file (.gtp) void QmitkGibbsTrackingView::SaveTrackingParameters() { TiXmlDocument documentXML; TiXmlDeclaration* declXML = new TiXmlDeclaration( "1.0", "", "" ); documentXML.LinkEndChild( declXML ); TiXmlElement* mainXML = new TiXmlElement("global_tracking_parameter_file"); mainXML->SetAttribute("file_version", "0.1"); documentXML.LinkEndChild(mainXML); TiXmlElement* paramXML = new TiXmlElement("parameter_set"); paramXML->SetAttribute("iterations", QString::number(m_Iterations).toStdString()); paramXML->SetAttribute("particle_length", QString::number((float)m_Controls->m_ParticleLengthSlider->value()/10).toStdString()); paramXML->SetAttribute("particle_width", QString::number((float)m_Controls->m_ParticleWidthSlider->value()/10).toStdString()); paramXML->SetAttribute("particle_weight", QString::number((float)m_Controls->m_ParticleWeightSlider->value()/10000).toStdString()); paramXML->SetAttribute("temp_start", QString::number((float)m_Controls->m_StartTempSlider->value()/100).toStdString()); paramXML->SetAttribute("temp_end", QString::number((float)m_Controls->m_EndTempSlider->value()/10000).toStdString()); paramXML->SetAttribute("inexbalance", QString::number((float)m_Controls->m_InExBalanceSlider->value()/10).toStdString()); paramXML->SetAttribute("fiber_length", QString::number(m_Controls->m_FiberLengthSlider->value()).toStdString()); paramXML->SetAttribute("curvature_threshold", QString::number(m_Controls->m_CurvatureThresholdSlider->value()).toStdString()); mainXML->LinkEndChild(paramXML); QString filename = QFileDialog::getSaveFileName( 0, tr("Save Parameters"), QDir::currentPath()+"/param.gtp", tr("Global Tracking Parameters (*.gtp)") ); if(filename.isEmpty() || filename.isNull()) return; if(!filename.endsWith(".gtp")) filename += ".gtp"; documentXML.SaveFile( filename.toStdString() ); } void QmitkGibbsTrackingView::UpdateIteraionsGUI(unsigned long iterations) { switch(iterations) { case 10000: m_Controls->m_IterationsSlider->setValue(0); m_Controls->m_IterationsLabel->setText("Iterations: 10^4"); break; case 50000: m_Controls->m_IterationsSlider->setValue(1); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^4"); break; case 100000: m_Controls->m_IterationsSlider->setValue(2); m_Controls->m_IterationsLabel->setText("Iterations: 10^5"); break; case 500000: m_Controls->m_IterationsSlider->setValue(3); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^5"); break; case 1000000: m_Controls->m_IterationsSlider->setValue(4); m_Controls->m_IterationsLabel->setText("Iterations: 10^6"); break; case 5000000: m_Controls->m_IterationsSlider->setValue(5); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^6"); break; case 10000000: m_Controls->m_IterationsSlider->setValue(6); m_Controls->m_IterationsLabel->setText("Iterations: 10^7"); break; case 50000000: m_Controls->m_IterationsSlider->setValue(7); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^7"); break; case 100000000: m_Controls->m_IterationsSlider->setValue(8); m_Controls->m_IterationsLabel->setText("Iterations: 10^8"); break; case 500000000: m_Controls->m_IterationsSlider->setValue(9); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^8"); break; case 1000000000: m_Controls->m_IterationsSlider->setValue(10); m_Controls->m_IterationsLabel->setText("Iterations: 10^9"); break; case 5000000000: m_Controls->m_IterationsSlider->setValue(11); m_Controls->m_IterationsLabel->setText("Iterations: 5x10^9"); break; } } // load current tracking paramters from xml file (.gtp) void QmitkGibbsTrackingView::LoadTrackingParameters() { QString filename = QFileDialog::getOpenFileName(0, tr("Load Parameters"), QDir::currentPath(), tr("Global Tracking Parameters (*.gtp)") ); if(filename.isEmpty() || filename.isNull()) return; TiXmlDocument doc( filename.toStdString() ); doc.LoadFile(); TiXmlHandle hDoc(&doc); TiXmlElement* pElem; TiXmlHandle hRoot(0); pElem = hDoc.FirstChildElement().Element(); hRoot = TiXmlHandle(pElem); pElem = hRoot.FirstChildElement("parameter_set").Element(); QString iterations(pElem->Attribute("iterations")); m_Iterations = iterations.toULong(); UpdateIteraionsGUI(m_Iterations); QString particleLength(pElem->Attribute("particle_length")); float pLength = particleLength.toFloat(); QString particleWidth(pElem->Attribute("particle_width")); float pWidth = particleWidth.toFloat(); if (pLength==0) m_Controls->m_ParticleLengthLabel->setText("auto"); else m_Controls->m_ParticleLengthLabel->setText(particleLength+" mm"); if (pWidth==0) m_Controls->m_ParticleWidthLabel->setText("auto"); else m_Controls->m_ParticleWidthLabel->setText(particleWidth+" mm"); m_Controls->m_ParticleWidthSlider->setValue(pWidth*10); m_Controls->m_ParticleLengthSlider->setValue(pLength*10); QString partWeight(pElem->Attribute("particle_weight")); m_Controls->m_ParticleWeightSlider->setValue(partWeight.toFloat()*10000); m_Controls->m_ParticleWeightLabel->setText(partWeight); QString startTemp(pElem->Attribute("temp_start")); m_Controls->m_StartTempSlider->setValue(startTemp.toFloat()*100); m_Controls->m_StartTempLabel->setText(startTemp); QString endTemp(pElem->Attribute("temp_end")); m_Controls->m_EndTempSlider->setValue(endTemp.toFloat()*10000); m_Controls->m_EndTempLabel->setText(endTemp); QString inExBalance(pElem->Attribute("inexbalance")); m_Controls->m_InExBalanceSlider->setValue(inExBalance.toFloat()*10); m_Controls->m_InExBalanceLabel->setText(inExBalance); QString fiberLength(pElem->Attribute("fiber_length")); m_Controls->m_FiberLengthSlider->setValue(fiberLength.toInt()); m_Controls->m_FiberLengthLabel->setText(fiberLength+"mm"); QString curvThres(pElem->Attribute("curvature_threshold")); m_Controls->m_CurvatureThresholdSlider->setValue(curvThres.toInt()); m_Controls->m_CurvatureThresholdLabel->setText(curvThres+"°"); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionViewControls.ui index 22858ce939..16461ab945 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkOdfMaximaExtractionViewControls.ui @@ -1,479 +1,500 @@ QmitkOdfMaximaExtractionViewControls 0 0 - 392 + 395 761 Form false Extract ODF peaks using a semicontinuous method (Aganj et al. 2010). EXPERIMENTAL! Start Analytical Extraction (only SH order 4) Please Select Input Data Select a tensor image or a SH coefficient image (generate using Q-Ball reconstruction view). ShCoeff/DTI: Mask Image: <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> true Parameters QFrame::NoFrame QFrame::Raised - + + 0 + + + 0 + + + 0 + + 0 6 Vector normalization: <html><head/><body><p>The vector fields are always coorected for image spacing and using the lagest eigenvalue in case of the tensor peak extraction. This is done for visualizytion purposes. The output direction images are not affected.</p></body></html> 1 No Normalization MAX Normalize Single Vec Normalization false QFrame::NoFrame QFrame::Raised - + + 0 + + + 0 + + + 0 + + 0 6 SH Order: Absolute threshold: false Absolute peak threshold (only used for the finite differences method). The value is additionally scaled by 1/GFA. 3 0.000000000000000 1.000000000000000 0.001000000000000 0.010000000000000 Max. Peaks: false Peak threshold relative to the largest peak per voxel. 0.000000000000000 1.000000000000000 0.050000000000000 0.400000000000000 false Maximum number of peaks to extract. 1 1000 3 Relative threshold: false 1 2 4 6 8 10 12 Clustering angle: Cluster close directions. Define "close" here. 90 - 25 + 30 Angular threshold: Discard smaller peaks in the defined angle around the maximum peaks. 0 90 0 Qt::Vertical 20 259 Import From Other Tools false Generate Q-Ball image and MITK compatible SH coefficient from other toolkits. Import SH - Coefficients Define SH coefficient convention (depends on toolkit) + + 1 + FSL MRtrix false Generate vector field and direction images from the FSL qboot peak extraction output. Import Peak Image false Extract ODF peaks using finite differences on the densely sampled ODF surface. Start Finite Differences Extraction false Extract principal eigenvectors of input tensors. Start Tensor Principal Direction Extraction Output QFormLayout::AllNonFixedFieldsGrow Only for visualization purposes! The vectors are automatically corrected for image spacing and for the largest eigenvalue in case of the tensor peak extraction. Vector Field true Output unsigned char image containing the number of directions per voxel. #Directions per Voxel false Output one image per extracted direction containing the direction vecors as pixel values. Direction Images false diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStochasticFiberTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStochasticFiberTrackingView.cpp index c50dda8e7b..d2dd9a171d 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStochasticFiberTrackingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStochasticFiberTrackingView.cpp @@ -1,290 +1,290 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include #include // Qmitk #include "QmitkStochasticFiberTrackingView.h" #include "QmitkStdMultiWidget.h" // Qt #include // MITK #include #include // VTK #include #include #include #include #include #include const std::string QmitkStochasticFiberTrackingView::VIEW_ID = "org.mitk.views.stochasticfibertracking"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace berry; QmitkStochasticFiberTrackingView::QmitkStochasticFiberTrackingView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_SeedRoi( NULL ) , m_DiffusionImage( NULL ) { } // Destructor QmitkStochasticFiberTrackingView::~QmitkStochasticFiberTrackingView() { } void QmitkStochasticFiberTrackingView::CreateQtPartControl( QWidget *parent ) { if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkStochasticFiberTrackingViewControls; m_Controls->setupUi( parent ); connect( m_Controls->commandLinkButton, SIGNAL(clicked()), this, SLOT(DoFiberTracking()) ); connect( m_Controls->m_SeedsPerVoxelSlider, SIGNAL(valueChanged(int)), this, SLOT(OnSeedsPerVoxelChanged(int)) ); connect( m_Controls->m_MaxCacheSizeSlider, SIGNAL(valueChanged(int)), this, SLOT(OnMaxCacheSizeChanged(int)) ); connect( m_Controls->m_MaxTractLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(OnMaxTractLengthChanged(int)) ); } } void QmitkStochasticFiberTrackingView::OnSeedsPerVoxelChanged(int value) { m_Controls->m_SeedsPerVoxelLabel->setText(QString("Seeds per Voxel: ")+QString::number(value)); } void QmitkStochasticFiberTrackingView::OnMaxTractLengthChanged(int value) { m_Controls->m_MaxTractLengthLabel->setText(QString("Max. Tract Length: ")+QString::number(value)); } void QmitkStochasticFiberTrackingView::OnMaxCacheSizeChanged(int value) { m_Controls->m_MaxCacheSizeLabel->setText(QString("Max. Cache Size: ")+QString::number(value)+"GB"); } void QmitkStochasticFiberTrackingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkStochasticFiberTrackingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkStochasticFiberTrackingView::OnSelectionChanged( std::vector nodes ) { m_DiffusionImageNode = NULL; m_DiffusionImage = NULL; m_SeedRoi = NULL; m_Controls->m_DiffusionImageLabel->setText("mandatory"); m_Controls->m_RoiImageLabel->setText("mandatory"); for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { if( dynamic_cast*>(node->GetData()) ) { m_DiffusionImageNode = node; m_DiffusionImage = dynamic_cast*>(node->GetData()); m_Controls->m_DiffusionImageLabel->setText(node->GetName().c_str()); } else { bool isBinary = false; node->GetPropertyValue("binary", isBinary); if (isBinary) { m_SeedRoi = dynamic_cast(node->GetData()); m_Controls->m_RoiImageLabel->setText(node->GetName().c_str()); } } } } if(m_DiffusionImage.IsNotNull() && m_SeedRoi.IsNotNull()) { m_Controls->m_InputData->setTitle("Input Data"); m_Controls->commandLinkButton->setEnabled(true); } else { m_Controls->m_InputData->setTitle("Please Select Input Data"); m_Controls->commandLinkButton->setEnabled(false); } } void QmitkStochasticFiberTrackingView::DoFiberTracking() { typedef itk::VectorImage< short int, 3 > DWIVectorImageType; typedef itk::Image< float, 3 > FloatImageType; typedef itk::Image< unsigned int, 3 > CImageType; typedef itk::StochasticTractographyFilter< DWIVectorImageType, FloatImageType, CImageType > TrackingFilterType; typedef itk::DTITubeSpatialObject<3> DTITubeType; typedef itk::DTITubeSpatialObjectPoint<3> DTITubePointType; typedef itk::SceneSpatialObject<3> SceneSpatialObjectType; /* get Gradients/Direction of dwi */ itk::VectorContainer< unsigned int, vnl_vector_fixed >::Pointer Pdir = m_DiffusionImage->GetDirections(); /* bValueContainer, Container includes b-values according to corresponding gradient-direction*/ TrackingFilterType::bValueContainerType::Pointer vecCont = TrackingFilterType::bValueContainerType::New(); /* for each gradient set b-Value; for 0-gradient set b-value eq. 0 */ for ( int i=0; i<(int)Pdir->size(); ++i) { vnl_vector_fixed valsGrad = Pdir->at(i); if (valsGrad.get(0) == 0 && valsGrad.get(1) == 0 && valsGrad.get(2) == 0) { //set 0-Gradient to bValue 0 vecCont->InsertElement(i,0); }else{ vecCont->InsertElement(i,m_DiffusionImage->GetReferenceBValue()); } } /* define measurement frame (identity-matrix 3x3) */ TrackingFilterType::MeasurementFrameType measurement_frame = m_DiffusionImage->GetMeasurementFrame(); /* generate white matterImage (dummy?)*/ FloatImageType::Pointer wmImage = FloatImageType::New(); wmImage->SetSpacing( m_DiffusionImage->GetVectorImage()->GetSpacing() ); wmImage->SetOrigin( m_DiffusionImage->GetVectorImage()->GetOrigin() ); wmImage->SetDirection( m_DiffusionImage->GetVectorImage()->GetDirection() ); wmImage->SetLargestPossibleRegion( m_DiffusionImage->GetVectorImage()->GetLargestPossibleRegion() ); wmImage->SetBufferedRegion( wmImage->GetLargestPossibleRegion() ); wmImage->SetRequestedRegion( wmImage->GetLargestPossibleRegion() ); wmImage->Allocate(); itk::ImageRegionIterator ot(wmImage, wmImage->GetLargestPossibleRegion() ); while (!ot.IsAtEnd()) { ot.Set(1); ++ot; } /* init TractographyFilter */ TrackingFilterType::Pointer trackingFilter = TrackingFilterType::New(); trackingFilter->SetPrimaryInput(m_DiffusionImage->GetVectorImage().GetPointer()); trackingFilter->SetbValues(vecCont); trackingFilter->SetGradients(Pdir); trackingFilter->SetMeasurementFrame(measurement_frame); trackingFilter->SetWhiteMatterProbabilityImage(wmImage); trackingFilter->SetTotalTracts(m_Controls->m_SeedsPerVoxelSlider->value()); trackingFilter->SetMaxLikelihoodCacheSize(m_Controls->m_MaxCacheSizeSlider->value()*1000); trackingFilter->SetMaxTractLength(m_Controls->m_MaxTractLengthSlider->value()); //itk::Image< char, 3 > mitk::ImageToItk< itk::Image< unsigned char, 3 > >::Pointer binaryImageToItk1 = mitk::ImageToItk< itk::Image< unsigned char, 3 > >::New(); binaryImageToItk1->SetInput( m_SeedRoi ); binaryImageToItk1->Update(); vtkSmartPointer vPoints = vtkSmartPointer::New(); vtkSmartPointer vCellArray = vtkSmartPointer::New(); itk::ImageRegionConstIterator< BinaryImageType > it(binaryImageToItk1->GetOutput(), binaryImageToItk1->GetOutput()->GetRequestedRegion()); it.GoToBegin(); mitk::BaseGeometry* geom = m_DiffusionImage->GetGeometry(); while(!it.IsAtEnd()) { itk::ImageConstIterator::PixelType tmpPxValue = it.Get(); if(tmpPxValue != 0){ mitk::Point3D point; itk::ImageRegionConstIterator< BinaryImageType >::IndexType seedIdx = it.GetIndex(); trackingFilter->SetSeedIndex(seedIdx); trackingFilter->Update(); /* get results from Filter */ /* write each single tract into member container */ TrackingFilterType::TractContainerType::Pointer container_tmp = trackingFilter->GetOutputTractContainer(); TrackingFilterType::TractContainerType::Iterator elIt = container_tmp->Begin(); TrackingFilterType::TractContainerType::Iterator end = container_tmp->End(); bool addTract = true; while( elIt != end ){ TrackingFilterType::TractContainerType::Element tract = elIt.Value(); TrackingFilterType::TractContainerType::Element::ObjectType::VertexListType::ConstPointer vertexlist = tract->GetVertexList(); vtkSmartPointer vPolyLine = vtkSmartPointer::New(); for( int j=0; j<(int)vertexlist->Size(); j++) { TrackingFilterType::TractContainerType::Element::ObjectType::VertexListType::Element vertex = vertexlist->GetElement(j); mitk::Point3D index; index[0] = (float)vertex[0]; index[1] = (float)vertex[1]; index[2] = (float)vertex[2]; if (geom->IsIndexInside(index)) { geom->IndexToWorld(index, point); vtkIdType id = vPoints->InsertNextPoint(point.GetDataPointer()); vPolyLine->GetPointIds()->InsertNextId(id); } else { addTract = false; break; } } if (addTract) vCellArray->InsertNextCell(vPolyLine); ++elIt; } } ++it; } vtkSmartPointer fiberPolyData = vtkSmartPointer::New(); fiberPolyData->SetPoints(vPoints); fiberPolyData->SetLines(vCellArray); mitk::FiberBundleX::Pointer fib = mitk::FiberBundleX::New(fiberPolyData); - fib->SetReferenceImage(dynamic_cast(m_DiffusionImageNode->GetData())); + fib->SetReferenceGeometry(dynamic_cast(m_DiffusionImageNode->GetData())->GetGeometry()); mitk::DataNode::Pointer fbNode = mitk::DataNode::New(); fbNode->SetData(fib); QString name("FiberBundle_"); name += m_DiffusionImageNode->GetName().c_str(); name += "_Probabilistic"; fbNode->SetName(name.toStdString()); fbNode->SetVisibility(true); GetDataStorage()->Add(fbNode, m_DiffusionImageNode); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.cpp b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.cpp index fb6386a883..5e3eeeeab5 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.cpp +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingView.cpp @@ -1,286 +1,286 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include #include // Qmitk #include "QmitkStreamlineTrackingView.h" #include "QmitkStdMultiWidget.h" // Qt #include // MITK #include #include #include #include #include #include #include #include // VTK #include #include #include #include #include #include const std::string QmitkStreamlineTrackingView::VIEW_ID = "org.mitk.views.streamlinetracking"; const std::string id_DataManager = "org.mitk.views.datamanager"; using namespace berry; QmitkStreamlineTrackingView::QmitkStreamlineTrackingView() : QmitkFunctionality() , m_Controls( 0 ) , m_MultiWidget( NULL ) , m_MaskImage( NULL ) , m_SeedRoi( NULL ) { } // Destructor QmitkStreamlineTrackingView::~QmitkStreamlineTrackingView() { } void QmitkStreamlineTrackingView::CreateQtPartControl( QWidget *parent ) { if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkStreamlineTrackingViewControls; m_Controls->setupUi( parent ); m_Controls->m_FaImageBox->SetDataStorage(this->GetDataStorage()); mitk::TNodePredicateDataType::Pointer isImagePredicate = mitk::TNodePredicateDataType::New(); mitk::NodePredicateProperty::Pointer isBinaryPredicate = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateNot::Pointer isNotBinaryPredicate = mitk::NodePredicateNot::New( isBinaryPredicate ); mitk::NodePredicateAnd::Pointer isNotABinaryImagePredicate = mitk::NodePredicateAnd::New( isImagePredicate, isNotBinaryPredicate ); mitk::NodePredicateDimension::Pointer dimensionPredicate = mitk::NodePredicateDimension::New(3); m_Controls->m_FaImageBox->SetPredicate( mitk::NodePredicateAnd::New(isNotABinaryImagePredicate, dimensionPredicate) ); connect( m_Controls->commandLinkButton, SIGNAL(clicked()), this, SLOT(DoFiberTracking()) ); connect( m_Controls->m_SeedsPerVoxelSlider, SIGNAL(valueChanged(int)), this, SLOT(OnSeedsPerVoxelChanged(int)) ); connect( m_Controls->m_MinTractLengthSlider, SIGNAL(valueChanged(int)), this, SLOT(OnMinTractLengthChanged(int)) ); connect( m_Controls->m_FaThresholdSlider, SIGNAL(valueChanged(int)), this, SLOT(OnFaThresholdChanged(int)) ); connect( m_Controls->m_AngularThresholdSlider, SIGNAL(valueChanged(int)), this, SLOT(OnAngularThresholdChanged(int)) ); connect( m_Controls->m_StepsizeSlider, SIGNAL(valueChanged(int)), this, SLOT(OnStepsizeChanged(int)) ); connect( m_Controls->m_fSlider, SIGNAL(valueChanged(int)), this, SLOT(OnfChanged(int)) ); connect( m_Controls->m_gSlider, SIGNAL(valueChanged(int)), this, SLOT(OngChanged(int)) ); } } void QmitkStreamlineTrackingView::OnfChanged(int value) { m_Controls->m_fLabel->setText(QString("f: ")+QString::number((float)value/100)); } void QmitkStreamlineTrackingView::OngChanged(int value) { m_Controls->m_gLabel->setText(QString("g: ")+QString::number((float)value/100)); } void QmitkStreamlineTrackingView::OnAngularThresholdChanged(int value) { if (value<0) m_Controls->m_AngularThresholdLabel->setText(QString("Min. Curvature Radius: auto")); else m_Controls->m_AngularThresholdLabel->setText(QString("Min. Curvature Radius: ")+QString::number((float)value/10)+QString("mm")); } void QmitkStreamlineTrackingView::OnSeedsPerVoxelChanged(int value) { m_Controls->m_SeedsPerVoxelLabel->setText(QString("Seeds per Voxel: ")+QString::number(value)); } void QmitkStreamlineTrackingView::OnMinTractLengthChanged(int value) { m_Controls->m_MinTractLengthLabel->setText(QString("Min. Tract Length: ")+QString::number(value)+QString("mm")); } void QmitkStreamlineTrackingView::OnFaThresholdChanged(int value) { m_Controls->m_FaThresholdLabel->setText(QString("FA Threshold: ")+QString::number((float)value/100)); } void QmitkStreamlineTrackingView::OnStepsizeChanged(int value) { if (value==0) m_Controls->m_StepsizeLabel->setText(QString("Stepsize: auto")); else m_Controls->m_StepsizeLabel->setText(QString("Stepsize: ")+QString::number((float)value/10)+QString("mm")); } void QmitkStreamlineTrackingView::StdMultiWidgetAvailable (QmitkStdMultiWidget &stdMultiWidget) { m_MultiWidget = &stdMultiWidget; } void QmitkStreamlineTrackingView::StdMultiWidgetNotAvailable() { m_MultiWidget = NULL; } void QmitkStreamlineTrackingView::OnSelectionChanged( std::vector nodes ) { m_TensorImageNodes.clear(); m_TensorImages.clear(); m_SeedRoi = NULL; m_MaskImage = NULL; m_Controls->m_TensorImageLabel->setText("mandatory"); m_Controls->m_RoiImageLabel->setText("optional"); m_Controls->m_MaskImageLabel->setText("optional"); for( std::vector::iterator it = nodes.begin(); it != nodes.end(); ++it ) { mitk::DataNode::Pointer node = *it; if( node.IsNotNull() && dynamic_cast(node->GetData()) ) { if( dynamic_cast(node->GetData()) ) { m_TensorImageNodes.push_back(node); m_TensorImages.push_back(dynamic_cast(node->GetData())); } else { bool isBinary = false; node->GetPropertyValue("binary", isBinary); if (isBinary && m_SeedRoi.IsNull()) { m_SeedRoi = dynamic_cast(node->GetData()); m_Controls->m_RoiImageLabel->setText(node->GetName().c_str()); } else if (isBinary) { m_MaskImage = dynamic_cast(node->GetData()); m_Controls->m_MaskImageLabel->setText(node->GetName().c_str()); } } } } if(!m_TensorImageNodes.empty()) { if (m_TensorImageNodes.size()>1) m_Controls->m_TensorImageLabel->setText(m_TensorImageNodes.size()+" tensor images selected"); else m_Controls->m_TensorImageLabel->setText(m_TensorImageNodes.at(0)->GetName().c_str()); m_Controls->m_InputData->setTitle("Input Data"); m_Controls->commandLinkButton->setEnabled(true); } else { m_Controls->m_InputData->setTitle("Please Select Input Data"); m_Controls->commandLinkButton->setEnabled(false); } } void QmitkStreamlineTrackingView::DoFiberTracking() { if (m_TensorImages.empty()) return; typedef itk::Image< itk::DiffusionTensor3D, 3> TensorImageType; typedef mitk::ImageToItk CastType; typedef mitk::ImageToItk CastType2; typedef itk::StreamlineTrackingFilter< float > FilterType; FilterType::Pointer filter = FilterType::New(); for (int i=0; i<(int)m_TensorImages.size(); i++) { CastType::Pointer caster = CastType::New(); caster->SetInput(m_TensorImages.at(i)); caster->Update(); filter->SetInput(i, caster->GetOutput()); } if (m_Controls->m_UseFaImage->isChecked()) { mitk::ImageToItk::Pointer floatCast = mitk::ImageToItk::New(); floatCast->SetInput(dynamic_cast(m_Controls->m_FaImageBox->GetSelectedNode()->GetData())); floatCast->Update(); filter->SetFaImage(floatCast->GetOutput()); } //filter->SetNumberOfThreads(1); filter->SetSeedsPerVoxel(m_Controls->m_SeedsPerVoxelSlider->value()); filter->SetFaThreshold((float)m_Controls->m_FaThresholdSlider->value()/100); filter->SetMinCurvatureRadius((float)m_Controls->m_AngularThresholdSlider->value()/10); filter->SetStepSize((float)m_Controls->m_StepsizeSlider->value()/10); filter->SetF((float)m_Controls->m_fSlider->value()/100); filter->SetG((float)m_Controls->m_gSlider->value()/100); filter->SetInterpolate(m_Controls->m_InterpolationBox->isChecked()); filter->SetMinTractLength(m_Controls->m_MinTractLengthSlider->value()); if (m_SeedRoi.IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(m_SeedRoi, mask); filter->SetSeedImage(mask); } if (m_MaskImage.IsNotNull()) { ItkUCharImageType::Pointer mask = ItkUCharImageType::New(); mitk::CastToItkImage(m_MaskImage, mask); filter->SetMaskImage(mask); } filter->Update(); vtkSmartPointer fiberBundle = filter->GetFiberPolyData(); if ( fiberBundle->GetNumberOfLines()==0 ) { QMessageBox warnBox; warnBox.setWindowTitle("Warning"); warnBox.setText("No fiberbundle was generated!"); warnBox.setDetailedText("No fibers were generated using the parameters: \n\n" + m_Controls->m_FaThresholdLabel->text() + "\n" + m_Controls->m_AngularThresholdLabel->text() + "\n" + m_Controls->m_fLabel->text() + "\n" + m_Controls->m_gLabel->text() + "\n" + m_Controls->m_StepsizeLabel->text() + "\n" + m_Controls->m_MinTractLengthLabel->text() + "\n" + m_Controls->m_SeedsPerVoxelLabel->text() + "\n\nPlease check your parametersettings."); warnBox.setIcon(QMessageBox::Warning); warnBox.exec(); return; } mitk::FiberBundleX::Pointer fib = mitk::FiberBundleX::New(fiberBundle); - fib->SetReferenceImage(dynamic_cast(m_TensorImageNodes.at(0)->GetData())); + fib->SetReferenceGeometry(dynamic_cast(m_TensorImageNodes.at(0)->GetData())->GetGeometry()); if (m_Controls->m_ResampleFibersBox->isChecked()) fib->CompressFibers(m_Controls->m_FiberErrorBox->value()); mitk::DataNode::Pointer node = mitk::DataNode::New(); node->SetData(fib); QString name("FiberBundle_"); name += m_TensorImageNodes.at(0)->GetName().c_str(); name += "_Streamline"; node->SetName(name.toStdString()); node->SetVisibility(true); GetDataStorage()->Add(node, m_TensorImageNodes.at(0)); } diff --git a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingViewControls.ui b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingViewControls.ui index b314c425aa..2526c4aa11 100644 --- a/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.diffusionimaging/src/internal/QmitkStreamlineTrackingViewControls.ui @@ -1,431 +1,431 @@ QmitkStreamlineTrackingViewControls 0 0 382 538 0 0 QmitkTemplate 3 3 0 Qt::Vertical QSizePolicy::Expanding 20 220 false Start Tractography Parameters Weighting factor between input vector (g=0) and tensor deflection (g=1 equals TEND tracking) 0 100 0 Qt::Horizontal Stepsize in mm (auto = 0.1*minimal spacing) 0 100 0 Qt::Horizontal - Minimally allowed curcature radius (in mm, interpolated auto = 0.5 minimal spacing, noninterpolated auto = 0.1 minimal spacing) + Minimally allowed curcature radius (in mm, interpolated auto = 0.5 minimal spacing, noninterpolated auto = 0.5 * minimal spacing) -1 50 -1 Qt::Horizontal - Min. Tract Length: 40mm + Min. Tract Length: 20mm FA Threshold: 0.2 g: 0 Qt::Horizontal QSizePolicy::Fixed 200 0 Seeds per Voxel: 1 Number of tracts started in each voxel of the seed ROI. 1 100 Qt::Horizontal Step Size: auto Weighting factor between first eigenvector (f=1 equals FACT tracking) and input vector dependent direction (f=0). 0 100 100 Qt::Horizontal Fractional Anisotropy Threshold 0 100 20 Qt::Horizontal Minimum tract length in mm. 0 500 - 40 + 20 Qt::Horizontal Default is nearest neighbor interpolation. Enable Trilinear Interpolation - false + true f: 1 Min. Curvature Radius: auto Resample fibers using the specified error constraint. Compress Fibers - true + false Maximum error in mm. 3 10.000000000000000 0.010000000000000 0.100000000000000 Please Select Input Data <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> true - <html><head/><body><p><span style=" color:#969696;">optional</span></p></body></html> true Only track insida mask area. Mask Image: Binary seed ROI. If not specified, the whole image area is seeded. Seed ROI: <html><head/><body><p><span style=" color:#ff0000;">mandatory</span></p></body></html> true Input DTI Tensor Image: Check to use selected FA image instead of internally calculated one. Recommended for multi-tensor tractography. FA image false QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h