diff --git a/Modules/DiffusionImaging/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp b/Modules/DiffusionImaging/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp index 254fe1a463..eaa009d443 100644 --- a/Modules/DiffusionImaging/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp +++ b/Modules/DiffusionImaging/DiffusionCore/src/mitkDiffusionFunctionCollection.cpp @@ -1,704 +1,707 @@ /*=================================================================== 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 "mitkDiffusionFunctionCollection.h" #include "mitkNumericTypes.h" #include #include #include #include #include "itkVectorContainer.h" #include "vnl/vnl_vector.h" #include #include #include #include #include #include // Intersect a finite line (with end points p0 and p1) with all of the // cells of a vtkImageData std::vector< std::pair< itk::Index<3>, double > > mitk::imv::IntersectImage(const itk::Vector& spacing, itk::Index<3>& si, itk::Index<3>& ei, itk::ContinuousIndex& sf, itk::ContinuousIndex& ef) { std::vector< std::pair< itk::Index<3>, double > > out; if (si == ei) { double d[3]; for (int i=0; i<3; ++i) d[i] = static_cast(sf[i]-ef[i])*spacing[i]; double len = std::sqrt( d[0]*d[0] + d[1]*d[1] + d[2]*d[2] ); out.push_back( std::pair< itk::Index<3>, double >(si, len) ); return out; } double bounds[6]; double entrancePoint[3]; double exitPoint[3]; double startPoint[3]; double endPoint[3]; double t0, t1; for (unsigned int i=0; i<3; ++i) { startPoint[i] = static_cast(sf[i]); endPoint[i] = static_cast(ef[i]); if (si[i]>ei[i]) { auto t = si[i]; si[i] = ei[i]; ei[i] = t; } } for (auto x = si[0]; x<=ei[0]; ++x) for (auto y = si[1]; y<=ei[1]; ++y) for (auto z = si[2]; z<=ei[2]; ++z) { bounds[0] = static_cast(x) - 0.5; bounds[1] = static_cast(x) + 0.5; bounds[2] = static_cast(y) - 0.5; bounds[3] = static_cast(y) + 0.5; bounds[4] = static_cast(z) - 0.5; bounds[5] = static_cast(z) + 0.5; int entryPlane; int exitPlane; int hit = vtkBox::IntersectWithLine(bounds, startPoint, endPoint, t0, t1, entrancePoint, exitPoint, entryPlane, exitPlane); if (hit) { if (entryPlane>=0 && exitPlane>=0) { double d[3]; for (int i=0; i<3; ++i) d[i] = (exitPoint[i] - entrancePoint[i])*spacing[i]; double len = std::sqrt( d[0]*d[0] + d[1]*d[1] + d[2]*d[2] ); itk::Index<3> idx; idx[0] = x; idx[1] = y; idx[2] = z; out.push_back( std::pair< itk::Index<3>, double >(idx, len) ); } else if (entryPlane>=0) { double d[3]; for (int i=0; i<3; ++i) d[i] = (static_cast(ef[i]) - entrancePoint[i])*spacing[i]; double len = std::sqrt( d[0]*d[0] + d[1]*d[1] + d[2]*d[2] ); itk::Index<3> idx; idx[0] = x; idx[1] = y; idx[2] = z; out.push_back( std::pair< itk::Index<3>, double >(idx, len) ); } else if (exitPlane>=0) { double d[3]; for (int i=0; i<3; ++i) d[i] = (exitPoint[i]-static_cast(sf[i]))*spacing[i]; double len = std::sqrt( d[0]*d[0] + d[1]*d[1] + d[2]*d[2] ); itk::Index<3> idx; idx[0] = x; idx[1] = y; idx[2] = z; out.push_back( std::pair< itk::Index<3>, double >(idx, len) ); } } } return out; } //------------------------- SH-function ------------------------------------ double mitk::sh::factorial(int number) { if(number <= 1) return 1; double result = 1.0; for(int i=1; i<=number; i++) result *= i; return result; } void mitk::sh::Cart2Sph(double x, double y, double z, double *spherical) { double phi, th, rad; rad = sqrt(x*x+y*y+z*z); if( rad < mitk::eps ) { th = itk::Math::pi/2; phi = itk::Math::pi/2; } else { th = acos(z/rad); phi = atan2(y, x); } spherical[0] = phi; spherical[1] = th; spherical[2] = rad; } vnl_vector_fixed mitk::sh::Sph2Cart(const double& theta, const double& phi, const double& rad) { vnl_vector_fixed dir; dir[0] = rad * sin(theta) * cos(phi); dir[1] = rad * sin(theta) * sin(phi); dir[2] = rad * cos(theta); return dir; } double mitk::sh::legendre0(int l) { if( l%2 != 0 ) { return 0; } else { double prod1 = 1.0; for(int i=1;i(::boost::math::spherical_harmonic_r(static_cast(k), -m, theta, phi)); else if (m==0) return static_cast(::boost::math::spherical_harmonic_r(static_cast(k), m, theta, phi)); else return pow(-1.0,m)*sqrt(2.0)*static_cast(::boost::math::spherical_harmonic_i(static_cast(k), m, theta, phi)); } else { double plm = static_cast(::boost::math::legendre_p(k,abs(m),-cos(theta))); double mag = sqrt((2.0*k+1.0)/(4.0*itk::Math::pi)*::boost::math::factorial(k-abs(m))/::boost::math::factorial(k+abs(m)))*plm; if (m>0) return mag*static_cast(cos(m*phi)); else if (m==0) return mag; else return mag*static_cast(sin(-m*phi)); } return 0; } mitk::OdfImage::ItkOdfImageType::Pointer mitk::convert::GetItkOdfFromShImage(mitk::Image::Pointer mitkImage) { mitk::ShImage::Pointer mitkShImage = dynamic_cast(mitkImage.GetPointer()); if (mitkShImage.IsNull()) mitkThrow() << "Input image is not a SH image!"; mitk::OdfImage::ItkOdfImageType::Pointer output; switch (mitkShImage->ShOrder()) { case 2: { typedef itk::ShToOdfImageFilter< float, 2 > ShConverterType; typename ShConverterType::InputImageType::Pointer itkvol = ShConverterType::InputImageType::New(); mitk::CastToItkImage(mitkImage, itkvol); typename ShConverterType::Pointer converter = ShConverterType::New(); converter->SetInput(itkvol); converter->Update(); output = converter->GetOutput(); break; } case 4: { typedef itk::ShToOdfImageFilter< float, 4 > ShConverterType; typename ShConverterType::InputImageType::Pointer itkvol = ShConverterType::InputImageType::New(); mitk::CastToItkImage(mitkImage, itkvol); typename ShConverterType::Pointer converter = ShConverterType::New(); converter->SetInput(itkvol); converter->Update(); output = converter->GetOutput(); break; } case 6: { typedef itk::ShToOdfImageFilter< float, 6 > ShConverterType; typename ShConverterType::InputImageType::Pointer itkvol = ShConverterType::InputImageType::New(); mitk::CastToItkImage(mitkImage, itkvol); typename ShConverterType::Pointer converter = ShConverterType::New(); converter->SetInput(itkvol); converter->Update(); output = converter->GetOutput(); break; } case 8: { typedef itk::ShToOdfImageFilter< float, 8 > ShConverterType; typename ShConverterType::InputImageType::Pointer itkvol = ShConverterType::InputImageType::New(); mitk::CastToItkImage(mitkImage, itkvol); typename ShConverterType::Pointer converter = ShConverterType::New(); converter->SetInput(itkvol); converter->Update(); output = converter->GetOutput(); break; } case 10: { typedef itk::ShToOdfImageFilter< float, 10 > ShConverterType; typename ShConverterType::InputImageType::Pointer itkvol = ShConverterType::InputImageType::New(); mitk::CastToItkImage(mitkImage, itkvol); typename ShConverterType::Pointer converter = ShConverterType::New(); converter->SetInput(itkvol); converter->Update(); output = converter->GetOutput(); break; } case 12: { typedef itk::ShToOdfImageFilter< float, 12 > ShConverterType; typename ShConverterType::InputImageType::Pointer itkvol = ShConverterType::InputImageType::New(); mitk::CastToItkImage(mitkImage, itkvol); typename ShConverterType::Pointer converter = ShConverterType::New(); converter->SetInput(itkvol); converter->Update(); output = converter->GetOutput(); break; } default: mitkThrow() << "SH orders higher than 12 are not supported!"; } return output; } mitk::OdfImage::Pointer mitk::convert::GetOdfFromShImage(mitk::Image::Pointer mitkImage) { mitk::OdfImage::Pointer image = mitk::OdfImage::New(); auto img = GetItkOdfFromShImage(mitkImage); image->InitializeByItk( img.GetPointer() ); image->SetVolume( img->GetBufferPointer() ); return image; } mitk::OdfImage::ItkOdfImageType::Pointer mitk::convert::GetItkOdfFromTensorImage(mitk::Image::Pointer mitkImage) { typedef itk::TensorImageToOdfImageFilter< float, float > FilterType; FilterType::Pointer filter = FilterType::New(); filter->SetInput( GetItkTensorFromTensorImage(mitkImage) ); filter->Update(); return filter->GetOutput(); } mitk::TensorImage::ItkTensorImageType::Pointer mitk::convert::GetItkTensorFromTensorImage(mitk::Image::Pointer mitkImage) { typedef mitk::ImageToItk< mitk::TensorImage::ItkTensorImageType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(mitkImage); caster->Update(); return caster->GetOutput(); } mitk::PeakImage::ItkPeakImageType::Pointer mitk::convert::GetItkPeakFromPeakImage(mitk::Image::Pointer mitkImage) { typedef mitk::ImageToItk< mitk::PeakImage::ItkPeakImageType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(mitkImage); caster->SetCopyMemFlag(true); caster->Update(); return caster->GetOutput(); } mitk::OdfImage::Pointer mitk::convert::GetOdfFromTensorImage(mitk::Image::Pointer mitkImage) { mitk::OdfImage::Pointer image = mitk::OdfImage::New(); auto img = GetItkOdfFromTensorImage(mitkImage); image->InitializeByItk( img.GetPointer() ); image->SetVolume( img->GetBufferPointer() ); return image; } mitk::OdfImage::ItkOdfImageType::Pointer mitk::convert::GetItkOdfFromOdfImage(mitk::Image::Pointer mitkImage) { typedef mitk::ImageToItk< mitk::OdfImage::ItkOdfImageType > CasterType; CasterType::Pointer caster = CasterType::New(); caster->SetInput(mitkImage); caster->Update(); return caster->GetOutput(); } vnl_matrix mitk::sh::CalcShBasisForDirections(unsigned int sh_order, vnl_matrix U, bool mrtrix) { vnl_matrix sh_basis = vnl_matrix(U.cols(), (sh_order*sh_order + sh_order + 2)/2 + sh_order ); for(unsigned int i=0; i(sh_order); k+=2) { for(int m=-k; m<=k; m++) { int j = (k*k + k + 2)/2 + m - 1; double phi = U(0,i); double th = U(1,i); sh_basis(i,j) = mitk::sh::Yj(m,k,th,phi, mrtrix); } } } return sh_basis; } unsigned int mitk::sh::ShOrder(int num_coeffs) { int c=3, d=2-2*num_coeffs; int D = c*c-4*d; if (D>0) { int s = (-c+static_cast(sqrt(D)))/2; if (s<0) s = (-c-static_cast(sqrt(D)))/2; return static_cast(s); } else if (D==0) return static_cast(-c/2); return 0; } float mitk::sh::GetValue(const vnl_vector &coefficients, const int &sh_order, const double theta, const double phi, const bool mrtrix) { float val = 0; for(int k=0; k<=sh_order; k+=2) { for(int m=-k; m<=k; m++) { unsigned int j = static_cast((k*k + k + 2)/2 + m - 1); val += coefficients[j] * mitk::sh::Yj(m, k, theta, phi, mrtrix); } } return val; } float mitk::sh::GetValue(const vnl_vector &coefficients, const int &sh_order, const vnl_vector_fixed &dir, const bool mrtrix) { double spherical[3]; mitk::sh::Cart2Sph(dir[0], dir[1], dir[2], spherical); float val = 0; for(int k=0; k<=sh_order; k+=2) { for(int m=-k; m<=k; m++) { int j = (k*k + k + 2)/2 + m - 1; val += coefficients[j] * mitk::sh::Yj(m, k, spherical[1], spherical[0], mrtrix); } } return val; } //------------------------- gradients-function ------------------------------------ mitk::gradients::GradientDirectionContainerType::Pointer mitk::gradients::ReadBvalsBvecs(std::string bvals_file, std::string bvecs_file, double& reference_bval) { mitk::gradients::GradientDirectionContainerType::Pointer directioncontainer = mitk::gradients::GradientDirectionContainerType::New(); std::vector bvec_entries; if (!itksys::SystemTools::FileExists(bvecs_file)) mitkThrow() << "bvecs file not existing: " << bvecs_file; else { std::string line; std::ifstream myfile (bvecs_file.c_str()); if (myfile.is_open()) { while (std::getline(myfile, line)) { std::vector strs; boost::split(strs,line,boost::is_any_of("\t \n")); for (auto token : strs) { if (!token.empty()) { try { bvec_entries.push_back(boost::lexical_cast(token)); } catch(...) { mitkThrow() << "Encountered invalid bvecs file entry >" << token << "<"; } } } } myfile.close(); } else { mitkThrow() << "bvecs file could not be opened: " << bvals_file; } } reference_bval = -1; std::vector bval_entries; if (!itksys::SystemTools::FileExists(bvals_file)) mitkThrow() << "bvals file not existing: " << bvals_file; else { std::string line; std::ifstream myfile (bvals_file.c_str()); if (myfile.is_open()) { while (std::getline(myfile, line)) { std::vector strs; boost::split(strs,line,boost::is_any_of("\t \n")); for (auto token : strs) { if (!token.empty()) { try { bval_entries.push_back(boost::lexical_cast(token)); if (bval_entries.back()>reference_bval) reference_bval = bval_entries.back(); } catch(...) { mitkThrow() << "Encountered invalid bvals file entry >" << token << "<"; } } } } myfile.close(); } else { mitkThrow() << "bvals file could not be opened: " << bvals_file; } } for(unsigned int i=0; i 0) + if (reference_bval>0) { - vec.normalize(); - vec[0] = sqrt(factor)*vec[0]; - vec[1] = sqrt(factor)*vec[1]; - vec[2] = sqrt(factor)*vec[2]; + double factor = b_val/reference_bval; + if(vec.magnitude() > 0) + { + vec.normalize(); + vec[0] = sqrt(factor)*vec[0]; + vec[1] = sqrt(factor)*vec[1]; + vec[2] = sqrt(factor)*vec[2]; + } } directioncontainer->InsertElement(i,vec); } return directioncontainer; } void mitk::gradients::WriteBvalsBvecs(std::string bvals_file, std::string bvecs_file, GradientDirectionContainerType::Pointer gradients, double reference_bval) { std::ofstream myfile; myfile.open (bvals_file.c_str()); for(unsigned int i=0; iSize(); i++) { double twonorm = gradients->ElementAt(i).two_norm(); myfile << std::round(reference_bval*twonorm*twonorm) << " "; } myfile.close(); std::ofstream myfile2; myfile2.open (bvecs_file.c_str()); for(int j=0; j<3; j++) { for(unsigned int i=0; iSize(); i++) { GradientDirectionType direction = gradients->ElementAt(i); direction.normalize(); myfile2 << direction.get(j) << " "; } myfile2 << std::endl; } } std::vector mitk::gradients::GetAllUniqueDirections(const BValueMap & refBValueMap, GradientDirectionContainerType *refGradientsContainer ) { IndiciesVector directioncontainer; auto mapIterator = refBValueMap.begin(); if(refBValueMap.find(0) != refBValueMap.end() && refBValueMap.size() > 1) mapIterator++; //skip bzero Values for( ; mapIterator != refBValueMap.end(); mapIterator++){ IndiciesVector currentShell = mapIterator->second; while(currentShell.size()>0) { unsigned int wntIndex = currentShell.back(); currentShell.pop_back(); auto containerIt = directioncontainer.begin(); bool directionExist = false; while(containerIt != directioncontainer.end()) { if (fabs(dot_product(refGradientsContainer->ElementAt(*containerIt), refGradientsContainer->ElementAt(wntIndex))) > 0.9998) { directionExist = true; break; } containerIt++; } if(!directionExist) { directioncontainer.push_back(wntIndex); } } } return directioncontainer; } bool mitk::gradients::CheckForDifferingShellDirections(const BValueMap & refBValueMap, GradientDirectionContainerType::ConstPointer refGradientsContainer) { auto mapIterator = refBValueMap.begin(); if(refBValueMap.find(0) != refBValueMap.end() && refBValueMap.size() > 1) mapIterator++; //skip bzero Values for( ; mapIterator != refBValueMap.end(); mapIterator++){ auto mapIterator_2 = refBValueMap.begin(); if(refBValueMap.find(0) != refBValueMap.end() && refBValueMap.size() > 1) mapIterator_2++; //skip bzero Values for( ; mapIterator_2 != refBValueMap.end(); mapIterator_2++){ if(mapIterator_2 == mapIterator) continue; IndiciesVector currentShell = mapIterator->second; IndiciesVector testShell = mapIterator_2->second; for (unsigned int i = 0; i< currentShell.size(); i++) if (fabs(dot_product(refGradientsContainer->ElementAt(currentShell[i]), refGradientsContainer->ElementAt(testShell[i]))) <= 0.9998) { return true; } } } return false; } vnl_matrix mitk::gradients::ComputeSphericalFromCartesian(const IndiciesVector & refShell, const GradientDirectionContainerType * refGradientsContainer) { vnl_matrix Q(3, refShell.size()); Q.fill(0.0); for(unsigned int i = 0; i < refShell.size(); i++) { GradientDirectionType dir = refGradientsContainer->ElementAt(refShell[i]); double x = dir.normalize().get(0); double y = dir.normalize().get(1); double z = dir.normalize().get(2); double cart[3]; mitk::sh::Cart2Sph(x,y,z,cart); Q(0,i) = cart[0]; Q(1,i) = cart[1]; Q(2,i) = cart[2]; } return Q; } vnl_matrix mitk::gradients::ComputeSphericalHarmonicsBasis(const vnl_matrix & QBallReference, const unsigned int & LOrder) { vnl_matrix SHBasisOutput(QBallReference.cols(), (LOrder+1)*(LOrder+2)*0.5); SHBasisOutput.fill(0.0); for(unsigned int i=0; i 1){ mapIterator++; //skip bzero Values vnl_vector_fixed vec; vec.fill(0.0); directioncontainer->push_back(vec); } for( ; mapIterator != bValueMap.end(); mapIterator++){ IndiciesVector currentShell = mapIterator->second; while(currentShell.size()>0) { unsigned int wntIndex = currentShell.back(); currentShell.pop_back(); mitk::gradients::GradientDirectionContainerType::Iterator containerIt = directioncontainer->Begin(); bool directionExist = false; while(containerIt != directioncontainer->End()) { if (fabs(dot_product(containerIt.Value(), origninalGradentcontainer->ElementAt(wntIndex))) > 0.9998) { directionExist = true; break; } containerIt++; } if(!directionExist) { GradientDirectionType dir(origninalGradentcontainer->ElementAt(wntIndex)); directioncontainer->push_back(dir.normalize()); } } } return directioncontainer; }