int main(int argc, char* argv[]) { mitkCommandLineParser parser; parser.setTitle("Multishell Methods"); parser.setCategory("Fiber Tracking and Processing Methods"); parser.setDescription(""); parser.setContributor("MBI"); parser.setArgumentPrefix("--", "-"); parser.addArgument("in", "i", mitkCommandLineParser::InputFile, "Input:", "input file", us::Any(), false); parser.addArgument("out", "o", mitkCommandLineParser::OutputFile, "Output:", "output file", us::Any(), false); parser.addArgument("adc", "D", mitkCommandLineParser::Bool, "ADC:", "ADC Average", us::Any(), false); parser.addArgument("akc", "K", mitkCommandLineParser::Bool, "Kurtosis fit:", "Kurtosis Fit", us::Any(), false); parser.addArgument("biexp", "B", mitkCommandLineParser::Bool, "BiExp fit:", "BiExp fit", us::Any(), false); parser.addArgument("targetbvalue", "b", mitkCommandLineParser::String, "b Value:", "target bValue (mean, min, max)", us::Any(), false); map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string inName = us::any_cast<string>(parsedArgs["in"]); string outName = us::any_cast<string>(parsedArgs["out"]); bool applyADC = us::any_cast<bool>(parsedArgs["adc"]); bool applyAKC = us::any_cast<bool>(parsedArgs["akc"]); bool applyBiExp = us::any_cast<bool>(parsedArgs["biexp"]); string targetType = us::any_cast<string>(parsedArgs["targetbvalue"]); try { std::cout << "Loading " << inName; mitk::Image::Pointer dwi = mitk::IOUtil::LoadImage(inName); if ( mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage( dwi ) ) { typedef itk::RadialMultishellToSingleshellImageFilter<short, short> FilterType; typedef itk::DwiGradientLengthCorrectionFilter CorrectionFilterType; CorrectionFilterType::Pointer roundfilter = CorrectionFilterType::New(); roundfilter->SetRoundingValue( 1000 ); roundfilter->SetReferenceBValue(mitk::DiffusionPropertyHelper::GetReferenceBValue( dwi )); roundfilter->SetReferenceGradientDirectionContainer(mitk::DiffusionPropertyHelper::GetGradientContainer(dwi)); roundfilter->Update(); dwi->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( roundfilter->GetNewBValue() ) ); dwi->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( roundfilter->GetOutputGradientDirectionContainer() ) ); // filter input parameter const mitk::DiffusionPropertyHelper::BValueMapType &originalShellMap = mitk::DiffusionPropertyHelper::GetBValueMap(dwi); mitk::DiffusionPropertyHelper::ImageType::Pointer vectorImage = mitk::DiffusionPropertyHelper::ImageType::New(); mitk::CastToItkImage(dwi, vectorImage); const mitk::DiffusionPropertyHelper::GradientDirectionsContainerType::Pointer gradientContainer = mitk::DiffusionPropertyHelper::GetGradientContainer(dwi); const unsigned int &bValue = mitk::DiffusionPropertyHelper::GetReferenceBValue( dwi ); // filter call vnl_vector<double> bValueList(originalShellMap.size()-1); double targetBValue = bValueList.mean(); mitk::DiffusionPropertyHelper::BValueMapType::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::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() ); outImage->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( targetBValue ) ); outImage->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( filter->GetTargetGradientDirections() ) ); mitk::DiffusionPropertyHelper propertyHelper( outImage ); propertyHelper.InitializeImage(); mitk::IOUtil::Save(outImage, (outName + "_ADC.dwi").c_str()); } 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::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() ); outImage->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( targetBValue ) ); outImage->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( filter->GetTargetGradientDirections() ) ); mitk::DiffusionPropertyHelper propertyHelper( outImage ); propertyHelper.InitializeImage(); mitk::IOUtil::Save(outImage, (string(outName) + "_AKC.dwi").c_str()); } 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::Image::Pointer outImage = mitk::GrabItkImageMemory( filter->GetOutput() ); outImage->SetProperty( mitk::DiffusionPropertyHelper::REFERENCEBVALUEPROPERTYNAME.c_str(), mitk::FloatProperty::New( targetBValue ) ); outImage->SetProperty( mitk::DiffusionPropertyHelper::GRADIENTCONTAINERPROPERTYNAME.c_str(), mitk::GradientDirectionsProperty::New( filter->GetTargetGradientDirections() ) ); mitk::DiffusionPropertyHelper propertyHelper( outImage ); propertyHelper.InitializeImage(); mitk::IOUtil::Save(outImage, (string(outName) + "_BiExp.dwi").c_str()); } } } catch (itk::ExceptionObject e) { std::cout << e; return EXIT_FAILURE; } catch (std::exception e) { std::cout << e.what(); return EXIT_FAILURE; } catch (...) { std::cout << "ERROR!?!"; return EXIT_FAILURE; } return EXIT_SUCCESS; }
int MultishellMethods(int argc, char* argv[]) { ctkCommandLineParser parser; parser.setArgumentPrefix("--", "-"); parser.addArgument("in", "i", ctkCommandLineParser::String, "input file", us::Any(), false); parser.addArgument("out", "o", ctkCommandLineParser::String, "output file", us::Any(), false); parser.addArgument("adc", "D", ctkCommandLineParser::Bool, "ADC Average", us::Any(), false); parser.addArgument("akc", "K", ctkCommandLineParser::Bool, "Kurtosis Fit", us::Any(), false); parser.addArgument("biexp", "B", ctkCommandLineParser::Bool, "BiExp fit", us::Any(), false); parser.addArgument("targetbvalue", "b", ctkCommandLineParser::String, "target bValue (mean, min, max)", us::Any(), false); map<string, us::Any> parsedArgs = parser.parseArguments(argc, argv); if (parsedArgs.size()==0) return EXIT_FAILURE; // mandatory arguments string inName = us::any_cast<string>(parsedArgs["in"]); string outName = us::any_cast<string>(parsedArgs["out"]); bool applyADC = us::any_cast<bool>(parsedArgs["adc"]); bool applyAKC = us::any_cast<bool>(parsedArgs["akc"]); bool applyBiExp = us::any_cast<bool>(parsedArgs["biexp"]); string targetType = us::any_cast<string>(parsedArgs["targetbvalue"]); try { MITK_INFO << "Loading " << inName; const std::string s1="", s2=""; std::vector<mitk::BaseData::Pointer> infile = mitk::BaseDataIO::LoadBaseDataFromFile( inName, s1, s2, false ); mitk::BaseData::Pointer baseData = infile.at(0); if ( dynamic_cast<mitk::DiffusionImage<short>*>(baseData.GetPointer()) ) { MITK_INFO << "Writing " << outName; mitk::DiffusionImage<short>::Pointer dwi = dynamic_cast<mitk::DiffusionImage<short>*>(baseData.GetPointer()); typedef itk::RadialMultishellToSingleshellImageFilter<short, short> 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<short>::BValueMap &originalShellMap = dwi->GetBValueMap(); const mitk::DiffusionImage<short>::ImageType *vectorImage = dwi->GetVectorImage(); const mitk::DiffusionImage<short>::GradientDirectionContainerType::Pointer gradientContainer = dwi->GetDirections(); const unsigned int &bValue = dwi->GetReferenceBValue(); // filter call vnl_vector<double> bValueList(originalShellMap.size()-1); double targetBValue = bValueList.mean(); mitk::DiffusionImage<short>::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<short>::Pointer outImage = mitk::DiffusionImage<short>::New(); outImage->SetVectorImage( filter->GetOutput() ); outImage->SetReferenceBValue( targetBValue ); outImage->SetDirections( filter->GetTargetGradientDirections() ); outImage->InitializeFromVectorImage(); mitk::NrrdDiffusionImageWriter<short>::Pointer writer = mitk::NrrdDiffusionImageWriter<short>::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<short>::Pointer outImage = mitk::DiffusionImage<short>::New(); outImage->SetVectorImage( filter->GetOutput() ); outImage->SetReferenceBValue( targetBValue ); outImage->SetDirections( filter->GetTargetGradientDirections() ); outImage->InitializeFromVectorImage(); mitk::NrrdDiffusionImageWriter<short>::Pointer writer = mitk::NrrdDiffusionImageWriter<short>::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<short>::Pointer outImage = mitk::DiffusionImage<short>::New(); outImage->SetVectorImage( filter->GetOutput() ); outImage->SetReferenceBValue( targetBValue ); outImage->SetDirections( filter->GetTargetGradientDirections() ); outImage->InitializeFromVectorImage(); mitk::NrrdDiffusionImageWriter<short>::Pointer writer = mitk::NrrdDiffusionImageWriter<short>::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; }
void QmitkSimpleRegistrationView::OnRegResultIsAvailable(mitk::MAPRegistrationWrapper::Pointer spResultRegistration, const QmitkRegistrationJob* job) { mitk::Image::Pointer movingImage = dynamic_cast<mitk::Image*>(m_MovingImageNode->GetData()); mitk::Image::Pointer image; if (m_RegistrationType==0 && !m_Controls->m_ResampleBox->isChecked()) { image = mitk::ImageMappingHelper::refineGeometry(movingImage, spResultRegistration, true); mitk::DiffusionPropertyHelper::CopyProperties(movingImage, image, true); auto reg = spResultRegistration->GetRegistration(); typedef mitk::DiffusionImageCorrectionFilter CorrectionFilterType; CorrectionFilterType::Pointer corrector = CorrectionFilterType::New(); corrector->SetImage( image ); corrector->CorrectDirections( mitk::MITKRegistrationHelper::getAffineMatrix(reg, false)->GetMatrix().GetVnlMatrix() ); } else { if (!mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(movingImage)) { image = mitk::ImageMappingHelper::map(movingImage, spResultRegistration, false, 0, job->m_spTargetData->GetGeometry(), false, 0, mitk::ImageMappingInterpolator::BSpline_3); } else { typedef itk::ComposeImageFilter < ITKDiffusionVolumeType > ComposeFilterType; ComposeFilterType::Pointer composer = ComposeFilterType::New(); ItkDwiType::Pointer itkVectorImagePointer = mitk::DiffusionPropertyHelper::GetItkVectorImage(movingImage); for (unsigned int i=0; i<itkVectorImagePointer->GetVectorLength(); ++i) { itk::ExtractDwiChannelFilter< short >::Pointer filter = itk::ExtractDwiChannelFilter< short >::New(); filter->SetInput( itkVectorImagePointer); filter->SetChannelIndex(i); filter->Update(); mitk::Image::Pointer gradientVolume = mitk::Image::New(); gradientVolume->InitializeByItk( filter->GetOutput() ); gradientVolume->SetImportChannel( filter->GetOutput()->GetBufferPointer() ); mitk::Image::Pointer registered_mitk_image = mitk::ImageMappingHelper::map(gradientVolume, spResultRegistration, false, 0, job->m_spTargetData->GetGeometry(), false, 0, mitk::ImageMappingInterpolator::BSpline_3); ITKDiffusionVolumeType::Pointer registered_itk_image = ITKDiffusionVolumeType::New(); mitk::CastToItkImage(registered_mitk_image, registered_itk_image); composer->SetInput(i, registered_itk_image); } composer->Update(); image = mitk::GrabItkImageMemory( composer->GetOutput() ); mitk::DiffusionPropertyHelper::CopyProperties(movingImage, image, true); auto reg = spResultRegistration->GetRegistration(); typedef mitk::DiffusionImageCorrectionFilter CorrectionFilterType; CorrectionFilterType::Pointer corrector = CorrectionFilterType::New(); corrector->SetImage( image ); corrector->CorrectDirections( mitk::MITKRegistrationHelper::getAffineMatrix(reg, false)->GetMatrix().GetVnlMatrix() ); } } if (mitk::DiffusionPropertyHelper::IsDiffusionWeightedImage(image)) mitk::DiffusionPropertyHelper::InitializeImage( image ); mitk::DataNode::Pointer resultNode = mitk::DataNode::New(); resultNode->SetData(image); if (m_MovingImageNode.IsNotNull()) { m_MovingImageNode->SetVisibility(false); QString name = m_MovingImageNode->GetName().c_str(); if (m_RegistrationType==0) resultNode->SetName((name+"_registered (rigid)").toStdString().c_str()); else resultNode->SetName((name+"_registered (affine)").toStdString().c_str()); } else { if (m_RegistrationType==0) resultNode->SetName("Registered (rigid)"); else resultNode->SetName("Registered (affine)"); } // resultNode->SetOpacity(0.6); // resultNode->SetColor(0.0, 0.0, 1.0); GetDataStorage()->Add(resultNode); mitk::RenderingManager::GetInstance()->InitializeViews( resultNode->GetData()->GetTimeGeometry(), mitk::RenderingManager::REQUEST_UPDATE_ALL, true); if (m_Controls->m_RegOutputBox->isChecked()) { mitk::DataNode::Pointer registration_node = mitk::DataNode::New(); registration_node->SetData(spResultRegistration); if (m_RegistrationType==0) registration_node->SetName("Registration Object (rigid)"); else registration_node->SetName("Registration Object (affine)"); GetDataStorage()->Add(registration_node, resultNode); } this->GetRenderWindowPart()->RequestUpdate(); m_Controls->m_RegistrationStartButton->setEnabled(true); m_Controls->m_RegistrationStartButton->setText("Start Registration"); m_MovingImageNode = nullptr; TractoChanged(); }