diff --git a/Modules/Pharmacokinetics/autoload/Models/mitkPharmacokineticModelsActivator.cpp b/Modules/Pharmacokinetics/autoload/Models/mitkPharmacokineticModelsActivator.cpp index 26ea2d0521..d67c683c15 100644 --- a/Modules/Pharmacokinetics/autoload/Models/mitkPharmacokineticModelsActivator.cpp +++ b/Modules/Pharmacokinetics/autoload/Models/mitkPharmacokineticModelsActivator.cpp @@ -1,80 +1,82 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include //MR perfusion models #include "mitkDescriptivePharmacokineticBrixModelFactory.h" #include "mitkExtendedToftsModelFactory.h" #include "mitkStandardToftsModelFactory.h" #include "mitkTwoCompartmentExchangeModelFactory.h" #include "mitkNumericTwoCompartmentExchangeModelFactory.h" //PET perfusion models #include "mitkOneTissueCompartmentModelFactory.h" #include "mitkExtendedOneTissueCompartmentModelFactory.h" #include "mitkTwoTissueCompartmentModelFactory.h" #include "mitkTwoTissueCompartmentFDGModelFactory.h" #include "mitkNumericTwoTissueCompartmentModelFactory.h" //general models +#include "mitkTwoStepLinearModelFactory.h" #include "mitkThreeStepLinearModelFactory.h" namespace mitk { /* * This is the module activator for the IO aspects of the "pharmacokinetics" module. */ class PharmacokineticModelsActivator : public us::ModuleActivator { public: template void RegisterProvider(us::ModuleContext* context) { auto provider = new TProvider(); provider->RegisterService(context); m_RegisteredProviders.push_back(std::unique_ptr(provider)); } void Load(us::ModuleContext* context) override { m_RegisteredProviders.clear(); RegisterProvider >(context); RegisterProvider >(context); + RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); RegisterProvider >(context); } void Unload(us::ModuleContext* ) override { } private: std::vector > m_RegisteredProviders; }; } US_EXPORT_MODULE_ACTIVATOR(mitk::PharmacokineticModelsActivator) diff --git a/Modules/Pharmacokinetics/cmdapps/MRPerfusionMiniApp.cpp b/Modules/Pharmacokinetics/cmdapps/MRPerfusionMiniApp.cpp index 6ebefbef87..03af6417c2 100644 --- a/Modules/Pharmacokinetics/cmdapps/MRPerfusionMiniApp.cpp +++ b/Modules/Pharmacokinetics/cmdapps/MRPerfusionMiniApp.cpp @@ -1,874 +1,890 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // std includes #include // itk includes #include "itksys/SystemTools.hxx" // CTK includes #include "mitkCommandLineParser.h" // MITK includes #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include +#include +#include #include std::string inFilename; std::string outFileName; std::string maskFileName; std::string aifMaskFileName; std::string aifImageFileName; mitk::Image::Pointer image; mitk::Image::Pointer mask; mitk::Image::Pointer aifImage; mitk::Image::Pointer aifMask; bool useConstraints(false); bool verbose(false); bool roibased(false); bool preview(false); std::string modelName; float aifHematocritLevel(0); float brixInjectionTime(0); +const std::string MODEL_NAME_2SL = "2SL"; const std::string MODEL_NAME_3SL = "3SL"; const std::string MODEL_NAME_descriptive = "descriptive"; const std::string MODEL_NAME_tofts = "tofts"; const std::string MODEL_NAME_2CX = "2CX"; void onFitEvent(::itk::Object* caller, const itk::EventObject & event, void* /*data*/) { itk::ProgressEvent progressEvent; if (progressEvent.CheckEvent(&event)) { mitk::ParameterFitImageGeneratorBase* castedReporter = dynamic_cast(caller); std::cout <GetProgress()*100 << "% "; } } void setupParser(mitkCommandLineParser& parser) { // set general information about your MiniApp parser.setCategory("Dynamic Data Analysis Tools"); parser.setTitle("MR Perfusion"); parser.setDescription("MiniApp that allows to fit MRI perfusion models and generates the according parameter maps. IMPORTANT!!!: The app assumes that the input images (signal and AIF) are concentration images. If your images do not hold this assumption, convert the image date before using this app (e.g. by using the signal-to-concentration-converter mini app."); parser.setContributor("DKFZ MIC"); //! [create parser] //! [add arguments] // how should arguments be prefixed parser.setArgumentPrefix("--", "-"); // add each argument, unless specified otherwise each argument is optional // see mitkCommandLineParser::addArgument for more information parser.beginGroup("Model parameters"); parser.addArgument( "model", "l", mitkCommandLineParser::String, "Model function", "Model that should be used to fit the concentration signal. Options are: \""+MODEL_NAME_descriptive+"\" (descriptive pharmacokinetic Brix model),\""+MODEL_NAME_3SL+"\" (three step linear model), \""+MODEL_NAME_tofts+"\" (extended tofts model) or \""+MODEL_NAME_2CX+"\" (two compartment exchange model).", us::Any(std::string(MODEL_NAME_tofts))); parser.addArgument( "injectiontime", "j", mitkCommandLineParser::Float, "Injection time [min]", "Injection time of the bolus. This information is needed for the descriptive pharmacokinetic Brix model.", us::Any()); parser.endGroup(); parser.beginGroup("Required I/O parameters"); parser.addArgument( "input", "i", mitkCommandLineParser::File, "Input file", "input 3D+t image file", us::Any(), false, false, false, mitkCommandLineParser::Input); parser.addArgument("output", "o", mitkCommandLineParser::File, "Output file template", "where to save the output parameter images. The specified path will be used as template to determine the format (via extension) and the name \"root\". For each parameter a suffix will be added to the name.", us::Any(), false, false, false, mitkCommandLineParser::Output); parser.endGroup(); parser.beginGroup("AIF parameters"); parser.addArgument( "aifmask", "n", mitkCommandLineParser::File, "AIF mask file", "Mask that defines the spatial image region that should be used as AIF for models that need one. Must have the same geometry as the AIF input image!", us::Any(), true, false, false, mitkCommandLineParser::Input); parser.addArgument( "aifimage", "a", mitkCommandLineParser::File, "AIF image file", "3D+t image that defines the image that containes the AIF signal. If this flag is not set and the model needs a AIF, the CLI will assume that the AIF is encoded in the normal image. Must have the same geometry as the AIF mask!", us::Any(), true, false, false, mitkCommandLineParser::Input); parser.addArgument( "hematocrit", "h", mitkCommandLineParser::Float, "Hematocrit Level", "Value needed for correct AIF computation. Only needed if model needs an AIF. Default value is 0.45.", us::Any(0.45)); parser.endGroup(); parser.beginGroup("Optional parameters"); parser.addArgument( "mask", "m", mitkCommandLineParser::File, "Mask file", "Mask that defines the spatial image region that should be fitted. Must have the same geometry as the input image!", us::Any(), true, false, false, mitkCommandLineParser::Input); parser.addArgument( "verbose", "v", mitkCommandLineParser::Bool, "Verbose Output", "Whether to produce verbose output"); parser.addArgument( "roibased", "r", mitkCommandLineParser::Bool, "Roi based fitting", "Will compute a mean intesity signal over the ROI before fitting it. If this mode is used a mask must be specified."); parser.addArgument( "constraints", "c", mitkCommandLineParser::Bool, "Constraints", "Indicates if constraints should be used for the fitting (if flag is set the default contraints will be used.).", us::Any(false)); parser.addArgument( "preview", "p", mitkCommandLineParser::Bool, "Preview outputs", "The application previews the outputs (filename, type) it would produce with the current settings."); parser.addArgument("help", "h", mitkCommandLineParser::Bool, "Help:", "Show this help text"); parser.endGroup(); //! [add arguments] } bool configureApplicationSettings(std::map parsedArgs) { if (parsedArgs.size() == 0) return false; // parse, cast and set required arguments modelName = MODEL_NAME_tofts; if (parsedArgs.count("model")) { modelName = us::any_cast(parsedArgs["model"]); } inFilename = us::any_cast(parsedArgs["input"]); outFileName = us::any_cast(parsedArgs["output"]); if (parsedArgs.count("mask")) { maskFileName = us::any_cast(parsedArgs["mask"]); } if (parsedArgs.count("aifimage")) { aifImageFileName = us::any_cast(parsedArgs["aifimage"]); } if (parsedArgs.count("aifmask")) { aifMaskFileName = us::any_cast(parsedArgs["aifmask"]); } verbose = false; if (parsedArgs.count("verbose")) { verbose = us::any_cast(parsedArgs["verbose"]); } preview = false; if (parsedArgs.count("preview")) { preview = us::any_cast(parsedArgs["preview"]); } roibased = false; if (parsedArgs.count("roibased")) { roibased = us::any_cast(parsedArgs["roibased"]); } useConstraints = false; if (parsedArgs.count("constraints")) { useConstraints = us::any_cast(parsedArgs["constraints"]); } aifHematocritLevel = 0.45; if (parsedArgs.count("hematocrit")) { aifHematocritLevel = us::any_cast(parsedArgs["hematocrit"]); } brixInjectionTime = 0.0; if (parsedArgs.count("injectiontime")) { brixInjectionTime = us::any_cast(parsedArgs["injectiontime"]); } return true; } mitk::ModelFitFunctorBase::Pointer createDefaultFitFunctor( const mitk::ModelParameterizerBase* parameterizer, const mitk::ModelFactoryBase* modelFactory) { mitk::LevenbergMarquardtModelFitFunctor::Pointer fitFunctor = mitk::LevenbergMarquardtModelFitFunctor::New(); mitk::NormalizedSumOfSquaredDifferencesFitCostFunction::Pointer chi2 = mitk::NormalizedSumOfSquaredDifferencesFitCostFunction::New(); fitFunctor->RegisterEvaluationParameter("Chi^2", chi2); if (useConstraints) { fitFunctor->SetConstraintChecker(modelFactory->CreateDefaultConstraints().GetPointer()); } mitk::ModelBase::Pointer refModel = parameterizer->GenerateParameterizedModel(); ::itk::LevenbergMarquardtOptimizer::ScalesType scales; scales.SetSize(refModel->GetNumberOfParameters()); scales.Fill(1.0); fitFunctor->SetScales(scales); fitFunctor->SetDebugParameterMaps(true); return fitFunctor.GetPointer(); } /**Helper that ensures that the mask (if it exists) is always 3D image. If the mask is originally an 4D image, the first time step will be used.*/ mitk::Image::Pointer getMask3D() { mitk::Image::Pointer result; if (mask.IsNotNull()) { result = mask; //mask settings if (mask->GetTimeSteps() > 1) { MITK_INFO << "Selected mask has multiple timesteps. Only use first timestep to mask model fit."; mitk::ImageTimeSelector::Pointer maskedImageTimeSelector = mitk::ImageTimeSelector::New(); maskedImageTimeSelector->SetInput(mask); maskedImageTimeSelector->SetTimeNr(0); maskedImageTimeSelector->UpdateLargestPossibleRegion(); result = maskedImageTimeSelector->GetOutput(); } } return result; } void getAIF(mitk::AIFBasedModelBase::AterialInputFunctionType& aif, mitk::AIFBasedModelBase::AterialInputFunctionType& aifTimeGrid) { if (aifMask.IsNotNull()) { aif.clear(); aifTimeGrid.clear(); mitk::AterialInputFunctionGenerator::Pointer aifGenerator = mitk::AterialInputFunctionGenerator::New(); //Hematocrit level aifGenerator->SetHCL(aifHematocritLevel); std::cout << "AIF hematocrit level: " << aifHematocritLevel << std::endl; mitk::Image::Pointer selectedAIFMask = aifMask; //mask settings if (aifMask->GetTimeSteps() > 1) { MITK_INFO << "Selected AIF mask has multiple timesteps. Only use first timestep to mask model fit."; mitk::ImageTimeSelector::Pointer maskedImageTimeSelector = mitk::ImageTimeSelector::New(); maskedImageTimeSelector->SetInput(aifMask); maskedImageTimeSelector->SetTimeNr(0); maskedImageTimeSelector->UpdateLargestPossibleRegion(); aifMask = maskedImageTimeSelector->GetOutput(); } aifGenerator->SetMask(aifMask); mitk::Image::Pointer selectedAIFImage = image; //image settings if (aifImage.IsNotNull()) { selectedAIFImage = aifImage; } aifGenerator->SetDynamicImage(selectedAIFImage); aif = aifGenerator->GetAterialInputFunction(); aifTimeGrid = aifGenerator->GetAterialInputFunctionTimeGrid(); } else { mitkThrow() << "Cannot generate AIF. AIF mask was not specified or correctly loaded."; } } void generateDescriptiveBrixModel_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::PixelBasedParameterFitImageGenerator::New(); mitk::DescriptivePharmacokineticBrixModelParameterizer::Pointer modelParameterizer = mitk::DescriptivePharmacokineticBrixModelParameterizer::New(); mitk::Image::Pointer mask3D = getMask3D(); //Model configuration (static parameters) can be done now modelParameterizer->SetTau(brixInjectionTime); std::cout << "Injection time [min]: " << brixInjectionTime << std::endl; mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(image); imageTimeSelector->SetTimeNr(0); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::DescriptivePharmacokineticBrixModelParameterizer::BaseImageType::Pointer baseImage; mitk::CastToItkImage(imageTimeSelector->GetOutput(), baseImage); modelParameterizer->SetBaseImage(baseImage); //Specify fitting strategy and criterion parameters mitk::ModelFactoryBase::Pointer factory = mitk::DescriptivePharmacokineticBrixModelFactory::New().GetPointer(); mitk::ModelFitFunctorBase::Pointer fitFunctor = createDefaultFitFunctor(modelParameterizer, factory); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); std::string roiUID = ""; if (mask3D.IsNotNull()) { fitGenerator->SetMask(mask3D); roiUID = mitk::EnsureModelFitUID(mask); } fitGenerator->SetDynamicImage(image); fitGenerator->SetFitFunctor(fitFunctor); generator = fitGenerator.GetPointer(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, image, mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), roiUID); } void generateDescriptiveBrixModel_ROIBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::Image::Pointer mask3D = getMask3D(); if (mask3D.IsNull()) { return; } mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::ROIBasedParameterFitImageGenerator::New(); mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::Pointer modelParameterizer = mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::New(); //Compute ROI signal mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator = mitk::MaskedDynamicImageStatisticsGenerator::New(); signalGenerator->SetMask(mask3D); signalGenerator->SetDynamicImage(image); signalGenerator->Generate(); mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean(); //Model configuration (static parameters) can be done now modelParameterizer->SetTau(brixInjectionTime); std::cout << "Injection time [min]: " << brixInjectionTime << std::endl; modelParameterizer->SetBaseValue(roiSignal[0]); //Specify fitting strategy and criterion parameters mitk::ModelFactoryBase::Pointer factory = mitk::DescriptivePharmacokineticBrixModelFactory::New().GetPointer(); mitk::ModelFitFunctorBase::Pointer fitFunctor = createDefaultFitFunctor(modelParameterizer, factory); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); fitGenerator->SetMask(mask3D); fitGenerator->SetFitFunctor(fitFunctor); fitGenerator->SetSignal(roiSignal); fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(image)); generator = fitGenerator.GetPointer(); std::string roiUID = mitk::EnsureModelFitUID(mask); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, image, mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos = roiSignal.begin(); pos != roiSignal.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("ROI", infoSignal); } - -void Generate3StepLinearModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& +template +void GenerateLinearModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::PixelBasedParameterFitImageGenerator::New(); - mitk::ThreeStepLinearModelParameterizer::Pointer modelParameterizer = - mitk::ThreeStepLinearModelParameterizer::New(); + typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); mitk::Image::Pointer mask3D = getMask3D(); //Specify fitting strategy and criterion parameters - mitk::ModelFactoryBase::Pointer factory = mitk::ThreeStepLinearModelFactory::New().GetPointer(); + mitk::ModelFactoryBase::Pointer factory = TFactory::New().GetPointer(); mitk::ModelFitFunctorBase::Pointer fitFunctor = createDefaultFitFunctor(modelParameterizer, factory); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); std::string roiUID = ""; if (mask3D.IsNotNull()) { fitGenerator->SetMask(mask3D); roiUID = mitk::EnsureModelFitUID(mask); } fitGenerator->SetDynamicImage(image); fitGenerator->SetFitFunctor(fitFunctor); generator = fitGenerator.GetPointer(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, image, mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), roiUID); } -void Generate3StepLinearModelFit_ROIBased(mitk::modelFit::ModelFitInfo::Pointer& +template +void GenerateLinearModelFit_ROIBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::Image::Pointer mask3D = getMask3D(); if (mask3D.IsNull()) { return; } mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::ROIBasedParameterFitImageGenerator::New(); - mitk::ThreeStepLinearModelParameterizer::Pointer modelParameterizer = - mitk::ThreeStepLinearModelParameterizer::New(); + typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); //Compute ROI signal mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator = mitk::MaskedDynamicImageStatisticsGenerator::New(); signalGenerator->SetMask(mask3D); signalGenerator->SetDynamicImage(image); signalGenerator->Generate(); mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean(); //Specify fitting strategy and criterion parameters - mitk::ModelFactoryBase::Pointer factory = mitk::ThreeStepLinearModelFactory::New().GetPointer(); + mitk::ModelFactoryBase::Pointer factory = TFactory::New().GetPointer(); mitk::ModelFitFunctorBase::Pointer fitFunctor = createDefaultFitFunctor(modelParameterizer, factory); + //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); fitGenerator->SetMask(mask3D); fitGenerator->SetFitFunctor(fitFunctor); fitGenerator->SetSignal(roiSignal); fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(image)); generator = fitGenerator.GetPointer(); std::string roiUID = mitk::EnsureModelFitUID(mask); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, image, mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos = roiSignal.begin(); pos != roiSignal.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("ROI", infoSignal); } template void generateAIFbasedModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::PixelBasedParameterFitImageGenerator::New(); typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); mitk::AIFBasedModelBase::AterialInputFunctionType aif; mitk::AIFBasedModelBase::AterialInputFunctionType aifTimeGrid; getAIF(aif, aifTimeGrid); modelParameterizer->SetAIF(aif); modelParameterizer->SetAIFTimeGrid(aifTimeGrid); mitk::Image::Pointer mask3D = getMask3D(); //Specify fitting strategy and criterion parameters mitk::ModelFactoryBase::Pointer factory = TFactory::New().GetPointer(); mitk::ModelFitFunctorBase::Pointer fitFunctor = createDefaultFitFunctor(modelParameterizer, factory); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); std::string roiUID = ""; if (mask3D.IsNotNull()) { fitGenerator->SetMask(mask3D); roiUID = mitk::EnsureModelFitUID(mask); } fitGenerator->SetDynamicImage(image); fitGenerator->SetFitFunctor(fitFunctor); generator = fitGenerator.GetPointer(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, image, mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::AIFBasedModelBase::AterialInputFunctionType::const_iterator pos = aif.begin(); pos != aif.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("AIF", infoSignal); } template void generateAIFbasedModelFit_ROIBased( mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::Image::Pointer mask3D = getMask3D(); if (mask3D.IsNull()) { return; } mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::ROIBasedParameterFitImageGenerator::New(); typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); mitk::AIFBasedModelBase::AterialInputFunctionType aif; mitk::AIFBasedModelBase::AterialInputFunctionType aifTimeGrid; getAIF(aif, aifTimeGrid); modelParameterizer->SetAIF(aif); modelParameterizer->SetAIFTimeGrid(aifTimeGrid); //Compute ROI signal mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator = mitk::MaskedDynamicImageStatisticsGenerator::New(); signalGenerator->SetMask(mask3D); signalGenerator->SetDynamicImage(image); signalGenerator->Generate(); mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean(); //Specify fitting strategy and criterion parameters mitk::ModelFactoryBase::Pointer factory = TFactory::New().GetPointer(); mitk::ModelFitFunctorBase::Pointer fitFunctor = createDefaultFitFunctor(modelParameterizer, factory); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); fitGenerator->SetMask(mask3D); fitGenerator->SetFitFunctor(fitFunctor); fitGenerator->SetSignal(roiSignal); fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(image)); generator = fitGenerator.GetPointer(); std::string roiUID = mitk::EnsureModelFitUID(mask); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, image, mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos = roiSignal.begin(); pos != roiSignal.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("ROI", infoSignal); infoSignal.clear(); for (mitk::AIFBasedModelBase::AterialInputFunctionType::const_iterator pos = aif.begin(); pos != aif.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("AIF", infoSignal); } void storeResultImage(const std::string& name, mitk::Image* image, mitk::modelFit::Parameter::Type nodeType, const mitk::modelFit::ModelFitInfo* modelFitInfo) { mitk::modelFit::SetModelFitDataProperties(image, name, nodeType, modelFitInfo); std::string ext = ::itksys::SystemTools::GetFilenameLastExtension(outFileName); std::string dir = itksys::SystemTools::GetFilenamePath(outFileName); dir = itksys::SystemTools::ConvertToOutputPath(dir); std::string rootName = itksys::SystemTools::GetFilenameWithoutLastExtension(outFileName); std::string fileName = rootName + "_" + name + ext; std::vector pathElements; pathElements.push_back(dir); pathElements.push_back(fileName); std::string fullOutPath = itksys::SystemTools::ConvertToOutputPath(dir + "/" + fileName); mitk::IOUtil::Save(image, fullOutPath); std::cout << "Store result (parameter: "<(fitSession, generator); + } + else + { + GenerateLinearModelFit_ROIBased(fitSession, generator); + } + } + else if (is2SLFactory) + { + std::cout << "Model: two step linear model" << std::endl; + if (!roibased) + { + GenerateLinearModelFit_PixelBased(fitSession, generator); } else { - Generate3StepLinearModelFit_ROIBased(fitSession, generator); + GenerateLinearModelFit_ROIBased(fitSession, generator); } } else if (isToftsFactory) { std::cout << "Model: extended tofts model" << std::endl; if (!roibased) { generateAIFbasedModelFit_PixelBased(fitSession, generator); } else { generateAIFbasedModelFit_ROIBased(fitSession, generator); } } else if (is2CXMFactory) { std::cout << "Model: two compartment exchange model" << std::endl; if (!roibased) { generateAIFbasedModelFit_PixelBased(fitSession, generator); } else { generateAIFbasedModelFit_ROIBased(fitSession, generator); } } else { std::cerr << "ERROR. Model flag is unknown. Given flag: " << modelName << std::endl; } } void doFitting() { mitk::ParameterFitImageGeneratorBase::Pointer generator = nullptr; mitk::modelFit::ModelFitInfo::Pointer fitSession = nullptr; ::itk::CStyleCommand::Pointer command = ::itk::CStyleCommand::New(); command->SetCallback(onFitEvent); createFitGenerator(fitSession, generator); if (generator.IsNotNull() ) { std::cout << "Started fitting process..." << std::endl; generator->AddObserver(::itk::AnyEvent(), command); generator->Generate(); std::cout << std::endl << "Finished fitting process" << std::endl; mitk::storeModelFitGeneratorResults(outFileName, generator, fitSession); } else { mitkThrow() << "Fitting error! Could not initialize fitting job."; } } void doPreview() { mitk::ParameterFitImageGeneratorBase::Pointer generator = nullptr; mitk::modelFit::ModelFitInfo::Pointer fitSession = nullptr; createFitGenerator(fitSession, generator); if (generator.IsNotNull()) { mitk::previewModelFitGeneratorResults(outFileName, generator); } else { mitkThrow() << "Fitting error! Could not initialize fitting job."; } } int main(int argc, char* argv[]) { mitkCommandLineParser parser; setupParser(parser); const std::map& parsedArgs = parser.parseArguments(argc, argv); mitk::PreferenceListReaderOptionsFunctor readerFilterFunctor = mitk::PreferenceListReaderOptionsFunctor({ "MITK DICOM Reader v2 (classic config)" }, { "MITK DICOM Reader" }); if (!configureApplicationSettings(parsedArgs)) { return EXIT_FAILURE; }; // Show a help message if (parsedArgs.count("help") || parsedArgs.count("h")) { std::cout << parser.helpText(); return EXIT_SUCCESS; } //! [do processing] try { image = mitk::IOUtil::Load(inFilename, &readerFilterFunctor); std::cout << "Input: " << inFilename << std::endl; if (!maskFileName.empty()) { mask = mitk::IOUtil::Load(maskFileName, &readerFilterFunctor); std::cout << "Mask: " << maskFileName << std::endl; } else { std::cout << "Mask: none" << std::endl; } if (modelName != MODEL_NAME_descriptive && modelName != MODEL_NAME_3SL) { if (!aifMaskFileName.empty()) { aifMask = mitk::IOUtil::Load(aifMaskFileName, &readerFilterFunctor); std::cout << "AIF mask: " << aifMaskFileName << std::endl; } else { mitkThrow() << "Error. Cannot fit. Choosen model needs an AIF. Please specify AIF mask (--aifmask)."; } if (!aifImageFileName.empty()) { aifImage = mitk::IOUtil::Load(aifImageFileName, &readerFilterFunctor); std::cout << "AIF image: " << aifImageFileName << std::endl; } else { std::cout << "AIF image: none (using signal image)" << std::endl; } } if (roibased && mask.IsNull()) { mitkThrow() << "Error. Cannot fit. Please specify mask if you select roi based fitting."; } std::cout << "Style: "; if (roibased) { std::cout << "ROI based"; } else { std::cout << "pixel based"; } std::cout << std::endl; if (preview) { doPreview(); } else { doFitting(); } std::cout << "Processing finished." << std::endl; return EXIT_SUCCESS; } catch (const itk::ExceptionObject& e) { MITK_ERROR << e.what(); return EXIT_FAILURE; } catch (const std::exception& e) { MITK_ERROR << e.what(); return EXIT_FAILURE; } catch (...) { MITK_ERROR << "Unexpected error encountered."; return EXIT_FAILURE; } } diff --git a/Modules/Pharmacokinetics/files.cmake b/Modules/Pharmacokinetics/files.cmake index bc0e5e5661..03780a2490 100644 --- a/Modules/Pharmacokinetics/files.cmake +++ b/Modules/Pharmacokinetics/files.cmake @@ -1,64 +1,67 @@ file(GLOB_RECURSE H_FILES RELATIVE "${CMAKE_CURRENT_SOURCE_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include/*") set(CPP_FILES Common/mitkAterialInputFunctionGenerator.cpp Common/mitkAIFParametrizerHelper.cpp Common/mitkConcentrationCurveGenerator.cpp Common/mitkDescriptionParameterImageGeneratorBase.cpp Common/mitkPixelBasedDescriptionParameterImageGenerator.cpp DescriptionParameters/mitkCurveDescriptionParameterBase.cpp DescriptionParameters/mitkAreaUnderTheCurveDescriptionParameter.cpp DescriptionParameters/mitkAreaUnderFirstMomentDescriptionParameter.cpp DescriptionParameters/mitkMeanResidenceTimeDescriptionParameter.cpp DescriptionParameters/mitkTimeToPeakCurveDescriptionParameter.cpp DescriptionParameters/mitkMaximumCurveDescriptionParameter.cpp Functors/mitkCurveParameterFunctor.cpp Models/mitkAIFBasedModelBase.cpp Models/mitkDescriptivePharmacokineticBrixModel.cpp Models/mitkDescriptivePharmacokineticBrixModelFactory.cpp Models/mitkDescriptivePharmacokineticBrixModelValueBasedParameterizer.cpp Models/mitkDescriptivePharmacokineticBrixModelParameterizer.cpp Models/mitkThreeStepLinearModel.cpp Models/mitkThreeStepLinearModelFactory.cpp Models/mitkThreeStepLinearModelParameterizer.cpp Models/mitkTwoCompartmentExchangeModel.cpp Models/mitkTwoCompartmentExchangeModelFactory.cpp Models/mitkTwoCompartmentExchangeModelParameterizer.cpp Models/mitkNumericTwoCompartmentExchangeModel.cpp Models/mitkNumericTwoCompartmentExchangeModelFactory.cpp Models/mitkNumericTwoCompartmentExchangeModelParameterizer.cpp Models/mitkExtendedToftsModel.cpp Models/mitkExtendedToftsModelFactory.cpp Models/mitkExtendedToftsModelParameterizer.cpp Models/mitkStandardToftsModel.cpp Models/mitkStandardToftsModelFactory.cpp Models/mitkStandardToftsModelParameterizer.cpp Models/mitkOneTissueCompartmentModel.cpp Models/mitkOneTissueCompartmentModelFactory.cpp Models/mitkOneTissueCompartmentModelParameterizer.cpp Models/mitkExtendedOneTissueCompartmentModel.cpp Models/mitkExtendedOneTissueCompartmentModelFactory.cpp Models/mitkExtendedOneTissueCompartmentModelParameterizer.cpp + Models/mitkTwoStepLinearModel.cpp + Models/mitkTwoStepLinearModelFactory.cpp + Models/mitkTwoStepLinearModelParameterizer.cpp Models/mitkTwoTissueCompartmentModel.cpp Models/mitkTwoTissueCompartmentModelFactory.cpp Models/mitkTwoTissueCompartmentModelParameterizer.cpp Models/mitkTwoTissueCompartmentFDGModel.cpp Models/mitkTwoTissueCompartmentFDGModelFactory.cpp Models/mitkTwoTissueCompartmentFDGModelParameterizer.cpp Models/mitkNumericTwoTissueCompartmentModel.cpp Models/mitkNumericTwoTissueCompartmentModelFactory.cpp Models/mitkNumericTwoTissueCompartmentModelParameterizer.cpp SimulationFramework/mitkImageGenerationHelper.cpp ) set(HXX_FILES mitkDICOMSegmentationConstants.h ) set(MOC_H_FILES ) diff --git a/Modules/Pharmacokinetics/include/mitkTwoStepLinearModel.h b/Modules/Pharmacokinetics/include/mitkTwoStepLinearModel.h new file mode 100644 index 0000000000..62f0d544b8 --- /dev/null +++ b/Modules/Pharmacokinetics/include/mitkTwoStepLinearModel.h @@ -0,0 +1,105 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#ifndef MITKTWOSTEPLINEARMODEL_H +#define MITKTWOSTEPLINEARMODEL_H + +#include "mitkModelBase.h" + +#include "MitkPharmacokineticsExports.h" + +namespace mitk +{ + + class MITKPHARMACOKINETICS_EXPORT TwoStepLinearModel : public mitk::ModelBase + { + + public: + typedef TwoStepLinearModel Self; + typedef mitk::ModelBase Superclass; + typedef itk::SmartPointer< Self > Pointer; + typedef itk::SmartPointer< const Self > ConstPointer; + + typedef Superclass::ParameterNameType ParameterNameType; + typedef Superclass::ParametersSizeType ParametersSizeType; + + /** Method for creation through the object factory. */ + itkFactorylessNewMacro(Self); + itkCloneMacro(Self); + + /** Run-time type information (and related methods). */ + itkTypeMacro(TwoStepLinearModel, ModelBase) + + static const std::string MODELL_NAME; + static const std::string NAME_PARAMETER_y1; + static const std::string NAME_PARAMETER_t; + static const std::string NAME_PARAMETER_a1; + static const std::string NAME_PARAMETER_a2; + + static const unsigned int POSITION_PARAMETER_y1; + static const unsigned int POSITION_PARAMETER_t; + static const unsigned int POSITION_PARAMETER_a1; + static const unsigned int POSITION_PARAMETER_a2; + + static const unsigned int NUMBER_OF_PARAMETERS; + + virtual std::string GetModelDisplayName() const override; + + virtual std::string GetModelType() const override; + + virtual FunctionStringType GetFunctionString() const override; + + virtual std::string GetXName() const override; + + virtual ParameterNamesType GetParameterNames() const override; + + virtual ParametersSizeType GetNumberOfParameters() const override; + + virtual ParameterNamesType GetStaticParameterNames() const override; + + virtual ParametersSizeType GetNumberOfStaticParameters() const override; + + virtual ParameterNamesType GetDerivedParameterNames() const override; + + virtual ParametersSizeType GetNumberOfDerivedParameters() const override; + + + protected: + TwoStepLinearModel() {}; + virtual ~TwoStepLinearModel(){}; + + + /** + * Actual implementation of the clone method. This method should be reimplemeted + * in subclasses to clone the extra required parameters. + */ + virtual itk::LightObject::Pointer InternalClone() const; + + virtual ModelResultType ComputeModelfunction(const ParametersType& parameters) const; + virtual DerivedParameterMapType ComputeDerivedParameters(const mitk::ModelBase::ParametersType& + parameters) const; + + virtual void SetStaticParameter(const ParameterNameType& name, + const StaticParameterValuesType& values); + virtual StaticParameterValuesType GetStaticParameterValue(const ParameterNameType& name) const; + + private: + + //No copy constructor allowed + TwoStepLinearModel(const Self& source); + void operator=(const Self&); //purposely not implemented + + }; +} + + +#endif // MITKTWOSTEPLINEARMODEL_H diff --git a/Modules/Pharmacokinetics/include/mitkTwoStepLinearModelFactory.h b/Modules/Pharmacokinetics/include/mitkTwoStepLinearModelFactory.h new file mode 100644 index 0000000000..6068d67ab2 --- /dev/null +++ b/Modules/Pharmacokinetics/include/mitkTwoStepLinearModelFactory.h @@ -0,0 +1,55 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#ifndef MITKTWOSTEPLINEARMODELFACTORY_H +#define MITKTWOSTEPLINEARMODELFACTORY_H + +#include + +#include "mitkConcreteModelFactoryBase.h" +#include "mitkTwoStepLinearModel.h" +#include "mitkTwoStepLinearModelParameterizer.h" + +#include "MitkPharmacokineticsExports.h" + +namespace mitk +{ + + class MITKPHARMACOKINETICS_EXPORT TwoStepLinearModelFactory : public ConcreteModelFactoryBase + { + public: + mitkClassMacroItkParent(TwoStepLinearModelFactory, ConcreteModelFactoryBase); + itkFactorylessNewMacro(Self); + + /** This function returns the default parameterization (e.g. initial parametrization for fitting) + defined by the model developer for for the given model.*/ + virtual ParametersType GetDefaultInitialParameterization() const; + + protected: + virtual ModelParameterizerBase::Pointer DoCreateParameterizer(const modelFit::ModelFitInfo* fit) + const; + + TwoStepLinearModelFactory(); + + virtual ~TwoStepLinearModelFactory(); + + private: + + //No copy constructor allowed + TwoStepLinearModelFactory(const Self& source); + void operator=(const Self&); //purposely not implemented + + }; + +} + +#endif // MITKTWOSTEPLINEARMODELFACTORY_H diff --git a/Modules/Pharmacokinetics/include/mitkTwoStepLinearModelParameterizer.h b/Modules/Pharmacokinetics/include/mitkTwoStepLinearModelParameterizer.h new file mode 100644 index 0000000000..6edb67b745 --- /dev/null +++ b/Modules/Pharmacokinetics/include/mitkTwoStepLinearModelParameterizer.h @@ -0,0 +1,63 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#ifndef MITKTWOSTEPLINEARMODELPARAMETERIZER_H +#define MITKTWOSTEPLINEARMODELPARAMETERIZER_H + +#include "mitkConcreteModelParameterizerBase.h" +#include "mitkTwoStepLinearModel.h" + +namespace mitk +{ + +class MITKPHARMACOKINETICS_EXPORT TwoStepLinearModelParameterizer : public + mitk::ConcreteModelParameterizerBase +{ +public: + typedef TwoStepLinearModelParameterizer Self; + typedef mitk::ConcreteModelParameterizerBase Superclass; + typedef itk::SmartPointer< Self > Pointer; + typedef itk::SmartPointer< const Self > ConstPointer; + + itkTypeMacro(TwoStepLinearModelParameterizer, ConcreteModelParameterizerBase); + itkFactorylessNewMacro(Self); + + typedef typename Superclass::ModelBaseType ModelBaseType; + typedef typename Superclass::ModelBasePointer ModelBasePointer; + + typedef typename Superclass::ModelType ModelType; + typedef typename Superclass::ModelPointer ModelPointer; + + typedef typename Superclass::StaticParameterValueType StaticParameterValueType; + typedef typename Superclass::StaticParameterValuesType StaticParameterValuesType; + typedef typename Superclass::StaticParameterMapType StaticParameterMapType; + + typedef typename Superclass::IndexType IndexType; + + /** This function returns the default parameterization (e.g. initial parametrization for fitting) + defined by the model developer for for the given model.*/ + virtual ParametersType GetDefaultInitialParameterization() const; + +protected: + TwoStepLinearModelParameterizer(){}; + + virtual ~TwoStepLinearModelParameterizer(){}; + +private: + + //No copy constructor allowed + TwoStepLinearModelParameterizer(const Self& source); + void operator=(const Self&); //purposely not implemented +};} + + +#endif // MITKTWOSTEPLINEARMODELPARAMETERIZER_H diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModel.cpp new file mode 100644 index 0000000000..6846ce111c --- /dev/null +++ b/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModel.cpp @@ -0,0 +1,184 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#include "mitkTwoStepLinearModel.h" + +const std::string mitk::TwoStepLinearModel::MODELL_NAME = "Two Step Linear Model"; + +const std::string mitk::TwoStepLinearModel::NAME_PARAMETER_y1 = "BaseValue"; +const std::string mitk::TwoStepLinearModel::NAME_PARAMETER_a1 = "Slope_1"; +const std::string mitk::TwoStepLinearModel::NAME_PARAMETER_t = "Change_Point"; +const std::string mitk::TwoStepLinearModel::NAME_PARAMETER_a2 = "Slope_2"; + +const unsigned int mitk::TwoStepLinearModel::POSITION_PARAMETER_y1 = 0; +const unsigned int mitk::TwoStepLinearModel::POSITION_PARAMETER_t = 1; +const unsigned int mitk::TwoStepLinearModel::POSITION_PARAMETER_a1 = 2; +const unsigned int mitk::TwoStepLinearModel::POSITION_PARAMETER_a2 = 3; + +const unsigned int mitk::TwoStepLinearModel::NUMBER_OF_PARAMETERS = 4; + +std::string mitk::TwoStepLinearModel::GetModelDisplayName() const +{ + return MODELL_NAME; +}; + +std::string mitk::TwoStepLinearModel::GetModelType() const +{ + return "Generic"; +}; + +mitk::TwoStepLinearModel::FunctionStringType mitk::TwoStepLinearModel::GetFunctionString() const +{ + return "Slope_1*t+Y_intercept_1 if tSetTimeGrid(this->m_TimeGrid); + + return newClone.GetPointer(); +}; diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelFactory.cpp b/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelFactory.cpp new file mode 100644 index 0000000000..837ce05078 --- /dev/null +++ b/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelFactory.cpp @@ -0,0 +1,35 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + + +#include "mitkTwoStepLinearModelFactory.h" +#include "mitkConcreteModelParameterizerBase.h" + +mitk::TwoStepLinearModelFactory::TwoStepLinearModelFactory() +{ +}; + +mitk::TwoStepLinearModelFactory::~TwoStepLinearModelFactory() +{ +}; + +mitk::ModelParameterizerBase::ParametersType +mitk::TwoStepLinearModelFactory::GetDefaultInitialParameterization() const +{ + return TwoStepLinearModelParameterizer::New()->GetDefaultInitialParameterization(); +}; + +mitk::ModelParameterizerBase::Pointer mitk::TwoStepLinearModelFactory::DoCreateParameterizer( + const modelFit::ModelFitInfo* /*fit*/) const +{ + return ConcreteModelParameterizerBase::New().GetPointer(); +}; diff --git a/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelParameterizer.cpp b/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelParameterizer.cpp new file mode 100644 index 0000000000..29f6b5287c --- /dev/null +++ b/Modules/Pharmacokinetics/src/Models/mitkTwoStepLinearModelParameterizer.cpp @@ -0,0 +1,28 @@ +/*============================================================================ + +The Medical Imaging Interaction Toolkit (MITK) + +Copyright (c) German Cancer Research Center (DKFZ) +All rights reserved. + +Use of this source code is governed by a 3-clause BSD license that can be +found in the LICENSE file. + +============================================================================*/ + +#include "mitkTwoStepLinearModelParameterizer.h" + +mitk::TwoStepLinearModelParameterizer::ParametersType +mitk::TwoStepLinearModelParameterizer::GetDefaultInitialParameterization() const +{ + ParametersType initialParameters; + initialParameters.SetSize(4); + initialParameters[mitk:: TwoStepLinearModel::POSITION_PARAMETER_y1] = 0.0; + initialParameters[mitk:: TwoStepLinearModel::POSITION_PARAMETER_t] = 50; + initialParameters[mitk:: TwoStepLinearModel::POSITION_PARAMETER_a1] = 1.0; + initialParameters[mitk:: TwoStepLinearModel::POSITION_PARAMETER_a2] = -1.0; + + return initialParameters; +}; + + diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.cpp b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.cpp index 6634588751..66f443e717 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.cpp +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.cpp @@ -1,1429 +1,1460 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "MRPerfusionView.h" #include "boost/tokenizer.hpp" #include "boost/math/constants/constants.hpp" #include #include "mitkWorkbenchUtil.h" #include "mitkAterialInputFunctionGenerator.h" #include "mitkConcentrationCurveGenerator.h" #include #include #include #include "mitkThreeStepLinearModelFactory.h" #include "mitkThreeStepLinearModelParameterizer.h" +#include "mitkTwoStepLinearModelFactory.h" +#include "mitkTwoStepLinearModelParameterizer.h" #include #include #include #include #include "mitkTwoCompartmentExchangeModelFactory.h" #include "mitkTwoCompartmentExchangeModelParameterizer.h" #include "mitkNumericTwoCompartmentExchangeModelFactory.h" #include "mitkNumericTwoCompartmentExchangeModelParameterizer.h" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // Includes for image casting between ITK and MITK #include #include "mitkImageCast.h" #include "mitkITKImageImport.h" #include #include const std::string MRPerfusionView::VIEW_ID = "org.mitk.gui.qt.pharmacokinetics.mri"; inline double convertToDouble(const std::string& data) { std::istringstream stepStream(data); stepStream.imbue(std::locale("C")); double value = 0.0; if (!(stepStream >> value) || !(stepStream.eof())) { mitkThrow() << "Cannot convert string to double. String: " << data; } return value; } void MRPerfusionView::SetFocus() { m_Controls.btnModelling->setFocus(); } void MRPerfusionView::CreateQtPartControl(QWidget* parent) { m_Controls.setupUi(parent); m_Controls.btnModelling->setEnabled(false); m_Controls.errorMessageLabel->hide(); this->InitModelComboBox(); connect(m_Controls.btnModelling, SIGNAL(clicked()), this, SLOT(OnModellingButtonClicked())); connect(m_Controls.comboModel, SIGNAL(currentIndexChanged(int)), this, SLOT(OnModellSet(int))); connect(m_Controls.radioPixelBased, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); //AIF setting m_Controls.groupAIF->hide(); m_Controls.btnAIFFile->setEnabled(false); m_Controls.btnAIFFile->setEnabled(false); m_Controls.radioAIFImage->setChecked(true); m_Controls.comboAIFMask->SetDataStorage(this->GetDataStorage()); m_Controls.comboAIFMask->SetPredicate(m_IsMaskPredicate); m_Controls.comboAIFMask->setVisible(true); m_Controls.comboAIFMask->setEnabled(true); m_Controls.comboAIFImage->SetDataStorage(this->GetDataStorage()); m_Controls.comboAIFImage->SetPredicate(m_IsNoMaskImagePredicate); m_Controls.comboAIFImage->setEnabled(false); m_Controls.checkDedicatedAIFImage->setEnabled(true); m_Controls.HCLSpinBox->setValue(mitk::AterialInputFunctionGenerator::DEFAULT_HEMATOCRIT_LEVEL); m_Controls.spinBox_baselineEndTimeStep->setMinimum(0); m_Controls.spinBox_baselineStartTimeStep->setMinimum(0); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.comboAIFMask, SLOT(setVisible(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.labelAIFMask, SLOT(setVisible(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.checkDedicatedAIFImage, SLOT(setVisible(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.comboAIFMask, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.checkDedicatedAIFImage, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.checkDedicatedAIFImage, SLOT(setVisible(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), m_Controls.comboAIFImage, SLOT(setVisible(bool))); connect(m_Controls.checkDedicatedAIFImage, SIGNAL(toggled(bool)), m_Controls.comboAIFImage, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFImage, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioAIFFile, SIGNAL(toggled(bool)), m_Controls.btnAIFFile, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFFile, SIGNAL(toggled(bool)), m_Controls.aifFilePath, SLOT(setEnabled(bool))); connect(m_Controls.radioAIFFile, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.btnAIFFile, SIGNAL(clicked()), this, SLOT(LoadAIFfromFile())); //Brix setting m_Controls.groupDescBrix->hide(); connect(m_Controls.injectiontime, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); //Num2CX setting m_Controls.groupNum2CXM->hide(); connect(m_Controls.odeStepSize, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); //Model fit configuration m_Controls.groupBox_FitConfiguration->hide(); m_Controls.checkBox_Constraints->setEnabled(false); m_Controls.constraintManager->setEnabled(false); m_Controls.initialValuesManager->setEnabled(false); m_Controls.initialValuesManager->setDataStorage(this->GetDataStorage()); connect(m_Controls.radioButton_StartParameters, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.initialValuesManager, SIGNAL(initialValuesChanged(void)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioButton_StartParameters, SIGNAL(toggled(bool)), m_Controls.initialValuesManager, SLOT(setEnabled(bool))); connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), m_Controls.constraintManager, SLOT(setEnabled(bool))); connect(m_Controls.checkBox_Constraints, SIGNAL(toggled(bool)), m_Controls.constraintManager, SLOT(setVisible(bool))); //Concentration m_Controls.groupConcentration->hide(); + m_Controls.groupBoxEnhancement->hide(); m_Controls.groupBoxTurboFlash->hide(); m_Controls.radioButtonNoConversion->setChecked(true); - m_Controls.factorSpinBox->setEnabled(false); - m_Controls.spinBox_baselineStartTimeStep->setEnabled(false); - m_Controls.spinBox_baselineEndTimeStep->setEnabled(false); m_Controls.groupBox_viaT1Map->hide(); + m_Controls.spinBox_baselineStartTimeStep->setValue(0); m_Controls.spinBox_baselineEndTimeStep->setValue(0); connect(m_Controls.radioButtonTurboFlash, SIGNAL(toggled(bool)), m_Controls.groupBoxTurboFlash, SLOT(setVisible(bool))); connect(m_Controls.radioButtonTurboFlash, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.relaxationtime, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); connect(m_Controls.recoverytime, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); connect(m_Controls.relaxivity, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioButton_absoluteEnhancement, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioButton_relativeEnchancement, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); - connect(m_Controls.radioButton_absoluteEnhancement, SIGNAL(toggled(bool)), m_Controls.factorSpinBox, SLOT(setEnabled(bool))); - connect(m_Controls.radioButton_relativeEnchancement, SIGNAL(toggled(bool)), m_Controls.factorSpinBox, SLOT(setEnabled(bool))); + connect(m_Controls.radioButton_absoluteEnhancement, SIGNAL(toggled(bool)), m_Controls.groupBoxEnhancement, SLOT(setVisible(bool))); + connect(m_Controls.radioButton_relativeEnchancement, SIGNAL(toggled(bool)), m_Controls.groupBoxEnhancement, SLOT(setVisible(bool))); connect(m_Controls.factorSpinBox, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); connect(m_Controls.spinBox_baselineStartTimeStep, SIGNAL(valueChanged(int)), this, SLOT(UpdateGUIControls())); connect(m_Controls.spinBox_baselineEndTimeStep, SIGNAL(valueChanged(int)), this, SLOT(UpdateGUIControls())); connect(m_Controls.radioButtonUsingT1, SIGNAL(toggled(bool)), m_Controls.groupBox_viaT1Map, SLOT(setVisible(bool))); connect(m_Controls.radioButtonUsingT1, SIGNAL(toggled(bool)), this, SLOT(UpdateGUIControls())); connect(m_Controls.FlipangleSpinBox, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); connect(m_Controls.RelaxivitySpinBox, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); connect(m_Controls.TRSpinBox, SIGNAL(valueChanged(double)), this, SLOT(UpdateGUIControls())); m_Controls.ComboT1Map->SetDataStorage(this->GetDataStorage()); m_Controls.ComboT1Map->SetPredicate(m_IsNoMaskImagePredicate); m_Controls.ComboT1Map->setEnabled(false); connect(m_Controls.radioButtonUsingT1, SIGNAL(toggled(bool)), m_Controls.ComboT1Map, SLOT(setEnabled(bool))); UpdateGUIControls(); } bool MRPerfusionView::IsTurboFlashSequenceFlag() const { return this->m_Controls.radioButtonTurboFlash->isChecked(); }; void MRPerfusionView::UpdateGUIControls() { m_Controls.lineFitName->setPlaceholderText(QString::fromStdString(this->GetDefaultFitName())); m_Controls.lineFitName->setEnabled(!m_FittingInProgress); m_Controls.checkBox_Constraints->setEnabled(m_modelConstraints.IsNotNull()); bool isDescBrixFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; bool isToftsFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr || dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; bool is2CXMFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr || dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; bool isNum2CXMFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; + bool isSLFactory = dynamic_cast + (m_selectedModelFactory.GetPointer()) != nullptr || + dynamic_cast + (m_selectedModelFactory.GetPointer()) != nullptr; + m_Controls.groupAIF->setVisible(isToftsFactory || is2CXMFactory); m_Controls.groupDescBrix->setVisible(isDescBrixFactory); m_Controls.groupNum2CXM->setVisible(isNum2CXMFactory); - m_Controls.groupConcentration->setVisible(isToftsFactory || is2CXMFactory); + m_Controls.groupConcentration->setVisible(isToftsFactory || is2CXMFactory || isSLFactory); m_Controls.groupBox_FitConfiguration->setVisible(m_selectedModelFactory); m_Controls.groupBox->setEnabled(!m_FittingInProgress); m_Controls.comboModel->setEnabled(!m_FittingInProgress); m_Controls.groupAIF->setEnabled(!m_FittingInProgress); m_Controls.groupDescBrix->setEnabled(!m_FittingInProgress); m_Controls.groupNum2CXM->setEnabled(!m_FittingInProgress); m_Controls.groupConcentration->setEnabled(!m_FittingInProgress); m_Controls.groupBox_FitConfiguration->setEnabled(!m_FittingInProgress); m_Controls.radioROIbased->setEnabled(m_selectedMask.IsNotNull()); m_Controls.btnModelling->setEnabled(m_selectedImage.IsNotNull() && m_selectedModelFactory.IsNotNull() && !m_FittingInProgress && CheckModelSettings()); m_Controls.spinBox_baselineStartTimeStep->setEnabled(m_Controls.radioButtonTurboFlash->isChecked() || m_Controls.radioButton_absoluteEnhancement->isChecked() || m_Controls.radioButton_relativeEnchancement->isChecked() || m_Controls.radioButtonUsingT1->isChecked()); m_Controls.spinBox_baselineEndTimeStep->setEnabled(m_Controls.radioButton_absoluteEnhancement->isChecked() || m_Controls.radioButton_relativeEnchancement->isChecked() || m_Controls.radioButtonUsingT1->isChecked() || m_Controls.radioButtonTurboFlash->isChecked()); } void MRPerfusionView::OnModellSet(int index) { m_selectedModelFactory = nullptr; if (index > 0) { if (static_cast(index) <= m_FactoryStack.size() ) { m_selectedModelFactory = m_FactoryStack[index - 1]; } else { MITK_WARN << "Invalid model index. Index outside of the factory stack. Factory stack size: "<< m_FactoryStack.size() << "; invalid index: "<< index; } } if (m_selectedModelFactory) { this->m_modelConstraints = dynamic_cast (m_selectedModelFactory->CreateDefaultConstraints().GetPointer()); m_Controls.initialValuesManager->setInitialValues(m_selectedModelFactory->GetParameterNames(), m_selectedModelFactory->GetDefaultInitialParameterization()); if (this->m_modelConstraints.IsNull()) { this->m_modelConstraints = mitk::SimpleBarrierConstraintChecker::New(); } m_Controls.constraintManager->setChecker(this->m_modelConstraints, this->m_selectedModelFactory->GetParameterNames()); } UpdateGUIControls(); } std::string MRPerfusionView::GetFitName() const { std::string fitName = m_Controls.lineFitName->text().toStdString(); if (fitName.empty()) { fitName = m_Controls.lineFitName->placeholderText().toStdString(); } return fitName; } std::string MRPerfusionView::GetDefaultFitName() const { std::string defaultName = "undefined model"; if (this->m_selectedModelFactory.IsNotNull()) { defaultName = this->m_selectedModelFactory->GetClassID(); } if (this->m_Controls.radioPixelBased->isChecked()) { defaultName += "_pixel"; } else { defaultName += "_roi"; } return defaultName; } void MRPerfusionView::OnModellingButtonClicked() { //check if all static parameters set if (m_selectedModelFactory.IsNotNull() && CheckModelSettings()) { m_HasGeneratedNewInput = false; m_HasGeneratedNewInputAIF = false; mitk::ParameterFitImageGeneratorBase::Pointer generator = nullptr; mitk::modelFit::ModelFitInfo::Pointer fitSession = nullptr; bool isDescBrixFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; bool is3LinearFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; + bool is2LinearFactory = dynamic_cast + (m_selectedModelFactory.GetPointer()) != nullptr; bool isExtToftsFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; bool isStanToftsFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; bool is2CXMFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; bool isNum2CXMFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; if (isDescBrixFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateDescriptiveBrixModel_PixelBased(fitSession, generator); } else { GenerateDescriptiveBrixModel_ROIBased(fitSession, generator); } } + else if (is2LinearFactory) + { + if (this->m_Controls.radioPixelBased->isChecked()) + { + GenerateLinearModelFit_PixelBased(fitSession, generator); + } + else + { + GenerateLinearModelFit_ROIBased(fitSession, generator); + } + } else if (is3LinearFactory) { - if (this->m_Controls.radioPixelBased->isChecked()) - { - Generate3StepLinearModelFit_PixelBased(fitSession, generator); - } - else - { - Generate3StepLinearModelFit_ROIBased(fitSession, generator); - } + if (this->m_Controls.radioPixelBased->isChecked()) + { + GenerateLinearModelFit_PixelBased(fitSession, generator); + } + else + { + GenerateLinearModelFit_ROIBased(fitSession, generator); + } } else if (isStanToftsFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateAIFbasedModelFit_PixelBased(fitSession, generator); } else { GenerateAIFbasedModelFit_ROIBased(fitSession, generator); } } else if (isExtToftsFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateAIFbasedModelFit_PixelBased(fitSession, generator); } else { GenerateAIFbasedModelFit_ROIBased(fitSession, generator); } } else if (is2CXMFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateAIFbasedModelFit_PixelBased(fitSession, generator); } else { GenerateAIFbasedModelFit_ROIBased(fitSession, generator); } } else if (isNum2CXMFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateAIFbasedModelFit_PixelBased(fitSession, generator); } else { GenerateAIFbasedModelFit_ROIBased(fitSession, generator); } } //add other models with else if if (generator.IsNotNull() && fitSession.IsNotNull()) { m_FittingInProgress = true; UpdateGUIControls(); DoFit(fitSession, generator); } else { QMessageBox box; box.setText("Fitting error!"); box.setInformativeText("Could not establish fitting job. Error when setting ab generator, model parameterizer or session info."); box.setStandardButtons(QMessageBox::Ok); box.setDefaultButton(QMessageBox::Ok); box.setIcon(QMessageBox::Warning); box.exec(); } } else { QMessageBox box; box.setText("Static parameters for model are not set!"); box.setInformativeText("Some static parameters, that are needed for calculation are not set and equal to zero. Modeling not possible"); box.setStandardButtons(QMessageBox::Ok); box.setDefaultButton(QMessageBox::Ok); box.setIcon(QMessageBox::Warning); box.exec(); } } void MRPerfusionView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList& selectedNodes) { m_selectedMaskNode = nullptr; m_selectedMask = nullptr; m_Controls.errorMessageLabel->setText(""); m_Controls.masklabel->setText("No (valid) mask selected."); m_Controls.timeserieslabel->setText("No (valid) series selected."); QList nodes = selectedNodes; if (nodes.size() > 0 && this->m_IsNoMaskImagePredicate->CheckNode(nodes.front())) { this->m_selectedNode = nodes.front(); auto selectedImage = dynamic_cast(this->m_selectedNode->GetData()); m_Controls.timeserieslabel->setText((this->m_selectedNode->GetName()).c_str()); if (selectedImage != this->m_selectedImage) { if (selectedImage) { this->m_Controls.initialValuesManager->setReferenceImageGeometry(selectedImage->GetGeometry()); } else { this->m_Controls.initialValuesManager->setReferenceImageGeometry(nullptr); } } this->m_selectedImage = selectedImage; nodes.pop_front(); } else { this->m_selectedNode = nullptr; this->m_selectedImage = nullptr; this->m_Controls.initialValuesManager->setReferenceImageGeometry(nullptr); } if (nodes.size() > 0 && this->m_IsMaskPredicate->CheckNode(nodes.front())) { this->m_selectedMaskNode = nodes.front(); this->m_selectedMask = dynamic_cast(this->m_selectedMaskNode->GetData()); if (this->m_selectedMask->GetTimeSteps() > 1) { MITK_INFO << "Selected mask has multiple timesteps. Only use first timestep to mask model fit. Mask name: " << m_selectedMaskNode->GetName(); mitk::ImageTimeSelector::Pointer maskedImageTimeSelector = mitk::ImageTimeSelector::New(); maskedImageTimeSelector->SetInput(this->m_selectedMask); maskedImageTimeSelector->SetTimeNr(0); maskedImageTimeSelector->UpdateLargestPossibleRegion(); this->m_selectedMask = maskedImageTimeSelector->GetOutput(); } m_Controls.masklabel->setText((this->m_selectedMaskNode->GetName()).c_str()); } if (m_selectedMask.IsNull()) { this->m_Controls.radioPixelBased->setChecked(true); } m_Controls.errorMessageLabel->show(); if (this->m_selectedImage.IsNotNull()) { m_Controls.spinBox_baselineStartTimeStep->setMaximum((this->m_selectedImage->GetDimension(3))-1); m_Controls.spinBox_baselineEndTimeStep->setMaximum((this->m_selectedImage->GetDimension(3)) - 1); } UpdateGUIControls(); } bool MRPerfusionView::CheckModelSettings() const { bool ok = true; //check wether any model is set at all. Otherwise exit with false if (m_selectedModelFactory.IsNotNull()) { bool isDescBrixFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; bool is3LinearFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; + bool is2LinearFactory = dynamic_cast + (m_selectedModelFactory.GetPointer()) != nullptr; bool isToftsFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr|| dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; bool is2CXMFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; bool isNum2CXMFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != nullptr; if (isDescBrixFactory) { //if all static parameters for this model are set, exit with true, Otherwise exit with false ok = m_Controls.injectiontime->value() > 0; } - else if (is3LinearFactory) + else if (is3LinearFactory || is2LinearFactory) { if (this->m_Controls.radioButtonTurboFlash->isChecked() ) { ok = ok && (m_Controls.recoverytime->value() > 0); ok = ok && (m_Controls.relaxationtime->value() > 0); ok = ok && (m_Controls.relaxivity->value() > 0); ok = ok && (m_Controls.AifRecoverytime->value() > 0); ok = ok && CheckBaselineSelectionSettings(); } else if (this->m_Controls.radioButton_absoluteEnhancement->isChecked() || this->m_Controls.radioButton_relativeEnchancement->isChecked() ) { ok = ok && (m_Controls.factorSpinBox->value() > 0); ok = ok && CheckBaselineSelectionSettings(); } else if (this->m_Controls.radioButtonUsingT1->isChecked() ) { ok = ok && (m_Controls.FlipangleSpinBox->value() > 0); ok = ok && (m_Controls.TRSpinBox->value() > 0); ok = ok && (m_Controls.RelaxivitySpinBox->value() > 0); ok = ok && (m_Controls.ComboT1Map->GetSelectedNode().IsNotNull()); ok = ok && CheckBaselineSelectionSettings(); } + else if (this->m_Controls.radioButtonNoConversion->isChecked()) + { + ok = true; + } else { ok = false; } } else if (isToftsFactory || is2CXMFactory || isNum2CXMFactory) { if (this->m_Controls.radioAIFImage->isChecked()) { ok = ok && m_Controls.comboAIFMask->GetSelectedNode().IsNotNull(); if (this->m_Controls.checkDedicatedAIFImage->isChecked()) { ok = ok && m_Controls.comboAIFImage->GetSelectedNode().IsNotNull(); } } else if (this->m_Controls.radioAIFFile->isChecked()) { ok = ok && (this->AIFinputGrid.size() != 0) && (this->AIFinputFunction.size() != 0); } else { ok = false; } if (this->m_Controls.radioButtonTurboFlash->isChecked() ) { ok = ok && (m_Controls.recoverytime->value() > 0); ok = ok && (m_Controls.relaxationtime->value() > 0); ok = ok && (m_Controls.relaxivity->value() > 0); ok = ok && (m_Controls.AifRecoverytime->value() > 0); ok = ok && CheckBaselineSelectionSettings(); } else if (this->m_Controls.radioButton_absoluteEnhancement->isChecked() || this->m_Controls.radioButton_relativeEnchancement->isChecked() ) { ok = ok && (m_Controls.factorSpinBox->value() > 0); ok = ok && CheckBaselineSelectionSettings(); } else if (this->m_Controls.radioButtonUsingT1->isChecked() ) { ok = ok && (m_Controls.FlipangleSpinBox->value() > 0); ok = ok && (m_Controls.TRSpinBox->value() > 0); ok = ok && (m_Controls.RelaxivitySpinBox->value() > 0); ok = ok && (m_Controls.ComboT1Map->GetSelectedNode().IsNotNull()); ok = ok && CheckBaselineSelectionSettings(); } + else if (this->m_Controls.radioButtonNoConversion->isChecked()) + { + ok = ok && true; + } else { ok = false; } if (isNum2CXMFactory) { ok = ok && (this->m_Controls.odeStepSize->value() > 0); } } //add other models as else if and check wether all needed static parameters are set else { ok = false; } if (this->m_Controls.radioButton_StartParameters->isChecked() && !this->m_Controls.initialValuesManager->hasValidInitialValues()) { std::string warning = "Warning. Invalid start parameters. At least one parameter as an invalid image setting as source."; MITK_ERROR << warning; m_Controls.infoBox->append(QString("") + QString::fromStdString(warning) + QString("")); ok = false; }; } else { ok = false; } return ok; } bool MRPerfusionView::CheckBaselineSelectionSettings() const { return m_Controls.spinBox_baselineStartTimeStep->value() <= m_Controls.spinBox_baselineEndTimeStep->value(); } void MRPerfusionView::ConfigureInitialParametersOfParameterizer(mitk::ModelParameterizerBase* parameterizer) const { if (m_Controls.radioButton_StartParameters->isChecked()) { //use user defined initial parameters mitk::InitialParameterizationDelegateBase::Pointer paramDelegate = m_Controls.initialValuesManager->getInitialParametrizationDelegate(); parameterizer->SetInitialParameterizationDelegate(paramDelegate); } } void MRPerfusionView::GenerateDescriptiveBrixModel_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::PixelBasedParameterFitImageGenerator::New(); mitk::DescriptivePharmacokineticBrixModelParameterizer::Pointer modelParameterizer = mitk::DescriptivePharmacokineticBrixModelParameterizer::New(); //Model configuration (static parameters) can be done now modelParameterizer->SetTau(m_Controls.injectiontime->value()); mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(this->m_selectedImage); imageTimeSelector->SetTimeNr(0); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::DescriptivePharmacokineticBrixModelParameterizer::BaseImageType::Pointer baseImage; mitk::CastToItkImage(imageTimeSelector->GetOutput(), baseImage); modelParameterizer->SetBaseImage(baseImage); this->ConfigureInitialParametersOfParameterizer(modelParameterizer); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); std::string roiUID = ""; if (m_selectedMask.IsNotNull()) { fitGenerator->SetMask(m_selectedMask); roiUID = mitk::EnsureModelFitUID(this->m_selectedMaskNode); } fitGenerator->SetDynamicImage(m_selectedImage); fitGenerator->SetFitFunctor(fitFunctor); generator = fitGenerator.GetPointer(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), this->GetFitName(), roiUID); } void MRPerfusionView::GenerateDescriptiveBrixModel_ROIBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { if (m_selectedMask.IsNull()) { return; } mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::ROIBasedParameterFitImageGenerator::New(); mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::Pointer modelParameterizer = mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::New(); //Compute ROI signal mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator = mitk::MaskedDynamicImageStatisticsGenerator::New(); signalGenerator->SetMask(m_selectedMask); signalGenerator->SetDynamicImage(m_selectedImage); signalGenerator->Generate(); mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean(); //Model configuration (static parameters) can be done now modelParameterizer->SetTau(m_Controls.injectiontime->value()); modelParameterizer->SetBaseValue(roiSignal[0]); this->ConfigureInitialParametersOfParameterizer(modelParameterizer); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); fitGenerator->SetMask(m_selectedMask); fitGenerator->SetFitFunctor(fitFunctor); fitGenerator->SetSignal(roiSignal); fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(m_selectedImage)); generator = fitGenerator.GetPointer(); std::string roiUID = mitk::EnsureModelFitUID(this->m_selectedMaskNode); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), this->GetFitName(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos = roiSignal.begin(); pos != roiSignal.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("ROI", infoSignal); } -void MRPerfusionView::Generate3StepLinearModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& +template +void MRPerfusionView::GenerateLinearModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::PixelBasedParameterFitImageGenerator::New(); - mitk::ThreeStepLinearModelParameterizer::Pointer modelParameterizer = - mitk::ThreeStepLinearModelParameterizer::New(); + typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); this->ConfigureInitialParametersOfParameterizer(modelParameterizer); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); std::string roiUID = ""; if (m_selectedMask.IsNotNull()) { fitGenerator->SetMask(m_selectedMask); roiUID = mitk::EnsureModelFitUID(this->m_selectedMaskNode); } fitGenerator->SetDynamicImage(m_selectedImage); fitGenerator->SetFitFunctor(fitFunctor); generator = fitGenerator.GetPointer(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), this->GetFitName(), roiUID); } -void MRPerfusionView::Generate3StepLinearModelFit_ROIBased(mitk::modelFit::ModelFitInfo::Pointer& +template +void MRPerfusionView::GenerateLinearModelFit_ROIBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { if (m_selectedMask.IsNull()) { return; } mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::ROIBasedParameterFitImageGenerator::New(); - mitk::ThreeStepLinearModelParameterizer::Pointer modelParameterizer = - mitk::ThreeStepLinearModelParameterizer::New(); + typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); //Compute ROI signal mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator = mitk::MaskedDynamicImageStatisticsGenerator::New(); signalGenerator->SetMask(m_selectedMask); signalGenerator->SetDynamicImage(m_selectedImage); signalGenerator->Generate(); mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean(); //Model configuration (static parameters) can be done now this->ConfigureInitialParametersOfParameterizer(modelParameterizer); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); fitGenerator->SetMask(m_selectedMask); fitGenerator->SetFitFunctor(fitFunctor); fitGenerator->SetSignal(roiSignal); fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(m_selectedImage)); generator = fitGenerator.GetPointer(); std::string roiUID = mitk::EnsureModelFitUID(this->m_selectedMaskNode); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, m_selectedNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), this->GetFitName(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos = roiSignal.begin(); pos != roiSignal.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("ROI", infoSignal); } template void MRPerfusionView::GenerateAIFbasedModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::PixelBasedParameterFitImageGenerator::New(); typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); PrepareConcentrationImage(); mitk::AIFBasedModelBase::AterialInputFunctionType aif; mitk::AIFBasedModelBase::AterialInputFunctionType aifTimeGrid; GetAIF(aif, aifTimeGrid); modelParameterizer->SetAIF(aif); modelParameterizer->SetAIFTimeGrid(aifTimeGrid); this->ConfigureInitialParametersOfParameterizer(modelParameterizer); mitk::NumericTwoCompartmentExchangeModelParameterizer* numTCXParametrizer = dynamic_cast (modelParameterizer.GetPointer()); if (numTCXParametrizer) { numTCXParametrizer->SetODEINTStepSize(this->m_Controls.odeStepSize->value()); } //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); std::string roiUID = ""; if (m_selectedMask.IsNotNull()) { fitGenerator->SetMask(m_selectedMask); roiUID = mitk::EnsureModelFitUID(this->m_selectedMaskNode); } fitGenerator->SetDynamicImage(this->m_inputImage); fitGenerator->SetFitFunctor(fitFunctor); generator = fitGenerator.GetPointer(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, this->m_inputImage, mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), this->GetFitName(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::AIFBasedModelBase::AterialInputFunctionType::const_iterator pos = aif.begin(); pos != aif.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("AIF", infoSignal); } template void MRPerfusionView::GenerateAIFbasedModelFit_ROIBased( mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { if (m_selectedMask.IsNull()) { return; } mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::ROIBasedParameterFitImageGenerator::New(); typename TParameterizer::Pointer modelParameterizer = TParameterizer::New(); PrepareConcentrationImage(); mitk::AIFBasedModelBase::AterialInputFunctionType aif; mitk::AIFBasedModelBase::AterialInputFunctionType aifTimeGrid; GetAIF(aif, aifTimeGrid); modelParameterizer->SetAIF(aif); modelParameterizer->SetAIFTimeGrid(aifTimeGrid); this->ConfigureInitialParametersOfParameterizer(modelParameterizer); mitk::NumericTwoCompartmentExchangeModelParameterizer* numTCXParametrizer = dynamic_cast (modelParameterizer.GetPointer()); if (numTCXParametrizer) { numTCXParametrizer->SetODEINTStepSize(this->m_Controls.odeStepSize->value()); } //Compute ROI signal mitk::MaskedDynamicImageStatisticsGenerator::Pointer signalGenerator = mitk::MaskedDynamicImageStatisticsGenerator::New(); signalGenerator->SetMask(m_selectedMask); signalGenerator->SetDynamicImage(this->m_inputImage); signalGenerator->Generate(); mitk::MaskedDynamicImageStatisticsGenerator::ResultType roiSignal = signalGenerator->GetMean(); //Specify fitting strategy and criterion parameters mitk::ModelFitFunctorBase::Pointer fitFunctor = CreateDefaultFitFunctor(modelParameterizer); //Parametrize fit generator fitGenerator->SetModelParameterizer(modelParameterizer); fitGenerator->SetMask(m_selectedMask); fitGenerator->SetFitFunctor(fitFunctor); fitGenerator->SetSignal(roiSignal); fitGenerator->SetTimeGrid(mitk::ExtractTimeGrid(this->m_inputImage)); generator = fitGenerator.GetPointer(); std::string roiUID = mitk::EnsureModelFitUID(this->m_selectedMaskNode); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, this->m_inputImage, mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), this->GetFitName(), roiUID); mitk::ScalarListLookupTable::ValueType infoSignal; for (mitk::MaskedDynamicImageStatisticsGenerator::ResultType::const_iterator pos = roiSignal.begin(); pos != roiSignal.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("ROI", infoSignal); infoSignal.clear(); for (mitk::AIFBasedModelBase::AterialInputFunctionType::const_iterator pos = aif.begin(); pos != aif.end(); ++pos) { infoSignal.push_back(*pos); } modelFitInfo->inputData.SetTableValue("AIF", infoSignal); } void MRPerfusionView::DoFit(const mitk::modelFit::ModelFitInfo* fitSession, mitk::ParameterFitImageGeneratorBase* generator) { std::stringstream message; message << "" << "Fitting Data Set . . ." << ""; m_Controls.errorMessageLabel->setText(message.str().c_str()); m_Controls.errorMessageLabel->show(); ///////////////////////// //create job and put it into the thread pool mitk::modelFit::ModelFitResultNodeVectorType additionalNodes; if (m_HasGeneratedNewInput) { additionalNodes.push_back(m_inputNode); } if (m_HasGeneratedNewInputAIF) { additionalNodes.push_back(m_inputAIFNode); } ParameterFitBackgroundJob* pJob = new ParameterFitBackgroundJob(generator, fitSession, this->m_selectedNode, additionalNodes); pJob->setAutoDelete(true); connect(pJob, SIGNAL(Error(QString)), this, SLOT(OnJobError(QString))); connect(pJob, SIGNAL(Finished()), this, SLOT(OnJobFinished())); connect(pJob, SIGNAL(ResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType, const ParameterFitBackgroundJob*)), this, SLOT(OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType, const ParameterFitBackgroundJob*)), Qt::BlockingQueuedConnection); connect(pJob, SIGNAL(JobProgress(double)), this, SLOT(OnJobProgress(double))); connect(pJob, SIGNAL(JobStatusChanged(QString)), this, SLOT(OnJobStatusChanged(QString))); QThreadPool* threadPool = QThreadPool::globalInstance(); threadPool->start(pJob); } MRPerfusionView::MRPerfusionView() : m_FittingInProgress(false), m_HasGeneratedNewInput(false), m_HasGeneratedNewInputAIF(false) { m_selectedImage = nullptr; m_selectedMask = nullptr; mitk::ModelFactoryBase::Pointer factory = mitk::DescriptivePharmacokineticBrixModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); + factory = mitk::TwoStepLinearModelFactory::New().GetPointer(); + m_FactoryStack.push_back(factory); factory = mitk::ThreeStepLinearModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::StandardToftsModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::ExtendedToftsModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::TwoCompartmentExchangeModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::NumericTwoCompartmentExchangeModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage"); mitk::NodePredicateDataType::Pointer isImage = mitk::NodePredicateDataType::New("Image"); mitk::NodePredicateProperty::Pointer isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true)); mitk::NodePredicateAnd::Pointer isLegacyMask = mitk::NodePredicateAnd::New(isImage, isBinary); mitk::NodePredicateOr::Pointer isMask = mitk::NodePredicateOr::New(isLegacyMask, isLabelSet); mitk::NodePredicateAnd::Pointer isNoMask = mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isMask)); this->m_IsMaskPredicate = mitk::NodePredicateAnd::New(isMask, mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer(); this->m_IsNoMaskImagePredicate = mitk::NodePredicateAnd::New(isNoMask, mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer(); } void MRPerfusionView::OnJobFinished() { this->m_Controls.infoBox->append(QString("Fitting finished.")); this->m_FittingInProgress = false; this->UpdateGUIControls(); }; void MRPerfusionView::OnJobError(QString err) { MITK_ERROR << err.toStdString().c_str(); m_Controls.infoBox->append(QString("") + err + QString("")); }; void MRPerfusionView::OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType results, const ParameterFitBackgroundJob* pJob) { //Store the resulting parameter fit image via convenience helper function in data storage //(handles the correct generation of the nodes and their properties) mitk::modelFit::StoreResultsInDataStorage(this->GetDataStorage(), results, pJob->GetParentNode()); //this stores the concentration image and AIF concentration image, if generated for this fit in the storage. //if not generated for this fit, relevant nodes are empty. mitk::modelFit::StoreResultsInDataStorage(this->GetDataStorage(), pJob->GetAdditionalRelevantNodes(), pJob->GetParentNode()); }; void MRPerfusionView::OnJobProgress(double progress) { QString report = QString("Progress. ") + QString::number(progress); this->m_Controls.infoBox->append(report); }; void MRPerfusionView::OnJobStatusChanged(QString info) { this->m_Controls.infoBox->append(info); } void MRPerfusionView::InitModelComboBox() const { this->m_Controls.comboModel->clear(); this->m_Controls.comboModel->addItem(tr("No model selected")); for (ModelFactoryStackType::const_iterator pos = m_FactoryStack.begin(); pos != m_FactoryStack.end(); ++pos) { this->m_Controls.comboModel->addItem(QString::fromStdString((*pos)->GetClassID())); } this->m_Controls.comboModel->setCurrentIndex(0); }; mitk::DataNode::Pointer MRPerfusionView::GenerateConcentrationNode(mitk::Image* image, const std::string& nodeName) const { if (!image) { mitkThrow() << "Cannot generate concentration node. Passed image is null. parameter name: "; } mitk::DataNode::Pointer result = mitk::DataNode::New(); result->SetData(image); result->SetName(nodeName); result->SetVisibility(true); mitk::EnsureModelFitUID(result); return result; }; mitk::Image::Pointer MRPerfusionView::ConvertConcentrationImage(bool AIFMode) { //Compute Concentration image mitk::ConcentrationCurveGenerator::Pointer concentrationGen = mitk::ConcentrationCurveGenerator::New(); if (m_Controls.checkDedicatedAIFImage->isChecked() && AIFMode) { concentrationGen->SetDynamicImage(this->m_selectedAIFImage); } else { concentrationGen->SetDynamicImage(this->m_selectedImage); } concentrationGen->SetisTurboFlashSequence(IsTurboFlashSequenceFlag()); concentrationGen->SetAbsoluteSignalEnhancement(m_Controls.radioButton_absoluteEnhancement->isChecked()); concentrationGen->SetRelativeSignalEnhancement(m_Controls.radioButton_relativeEnchancement->isChecked()); concentrationGen->SetUsingT1Map(m_Controls.radioButtonUsingT1->isChecked()); if (IsTurboFlashSequenceFlag()) { if (AIFMode) { concentrationGen->SetRecoveryTime(m_Controls.AifRecoverytime->value()); } else { concentrationGen->SetRecoveryTime(m_Controls.recoverytime->value()); } concentrationGen->SetRelaxationTime(m_Controls.relaxationtime->value()); concentrationGen->SetRelaxivity(m_Controls.relaxivity->value()); concentrationGen->SetBaselineStartTimeStep(m_Controls.spinBox_baselineStartTimeStep->value()); concentrationGen->SetBaselineEndTimeStep(m_Controls.spinBox_baselineEndTimeStep->value()); } else if (this->m_Controls.radioButtonUsingT1->isChecked()) { concentrationGen->SetRecoveryTime(m_Controls.TRSpinBox->value()); concentrationGen->SetRelaxivity(m_Controls.RelaxivitySpinBox->value()); concentrationGen->SetT10Image(dynamic_cast(m_Controls.ComboT1Map->GetSelectedNode()->GetData())); concentrationGen->SetBaselineStartTimeStep(m_Controls.spinBox_baselineStartTimeStep->value()); concentrationGen->SetBaselineEndTimeStep(m_Controls.spinBox_baselineEndTimeStep->value()); //Convert Flipangle from degree to radiant double alpha = m_Controls.FlipangleSpinBox->value()/360*2* boost::math::constants::pi(); concentrationGen->SetFlipAngle(alpha); } else { concentrationGen->SetFactor(m_Controls.factorSpinBox->value()); concentrationGen->SetBaselineStartTimeStep(m_Controls.spinBox_baselineStartTimeStep->value()); concentrationGen->SetBaselineEndTimeStep(m_Controls.spinBox_baselineEndTimeStep->value()); } mitk::Image::Pointer concentrationImage = concentrationGen->GetConvertedImage(); return concentrationImage; } void MRPerfusionView::GetAIF(mitk::AIFBasedModelBase::AterialInputFunctionType& aif, mitk::AIFBasedModelBase::AterialInputFunctionType& aifTimeGrid) { if (this->m_Controls.radioAIFFile->isChecked()) { aif.clear(); aifTimeGrid.clear(); aif.SetSize(AIFinputFunction.size()); aifTimeGrid.SetSize(AIFinputGrid.size()); aif.fill(0.0); aifTimeGrid.fill(0.0); itk::Array::iterator aifPos = aif.begin(); for (std::vector::const_iterator pos = AIFinputFunction.begin(); pos != AIFinputFunction.end(); ++pos, ++aifPos) { *aifPos = *pos; } itk::Array::iterator gridPos = aifTimeGrid.begin(); for (std::vector::const_iterator pos = AIFinputGrid.begin(); pos != AIFinputGrid.end(); ++pos, ++gridPos) { *gridPos = *pos; } } else if (this->m_Controls.radioAIFImage->isChecked()) { aif.clear(); aifTimeGrid.clear(); mitk::AterialInputFunctionGenerator::Pointer aifGenerator = mitk::AterialInputFunctionGenerator::New(); //Hematocrit level aifGenerator->SetHCL(this->m_Controls.HCLSpinBox->value()); //mask settings this->m_selectedAIFMaskNode = m_Controls.comboAIFMask->GetSelectedNode(); this->m_selectedAIFMask = dynamic_cast(this->m_selectedAIFMaskNode->GetData()); if (this->m_selectedAIFMask->GetTimeSteps() > 1) { MITK_INFO << "Selected AIF mask has multiple timesteps. Only use first timestep to mask model fit. AIF Mask name: " << m_selectedAIFMaskNode->GetName() ; mitk::ImageTimeSelector::Pointer maskedImageTimeSelector = mitk::ImageTimeSelector::New(); maskedImageTimeSelector->SetInput(this->m_selectedAIFMask); maskedImageTimeSelector->SetTimeNr(0); maskedImageTimeSelector->UpdateLargestPossibleRegion(); this->m_selectedAIFMask = maskedImageTimeSelector->GetOutput(); } if (this->m_selectedAIFMask.IsNotNull()) { aifGenerator->SetMask(this->m_selectedAIFMask); } //image settings if (this->m_Controls.checkDedicatedAIFImage->isChecked()) { this->m_selectedAIFImageNode = m_Controls.comboAIFImage->GetSelectedNode(); this->m_selectedAIFImage = dynamic_cast(this->m_selectedAIFImageNode->GetData()); } else { this->m_selectedAIFImageNode = m_selectedNode; this->m_selectedAIFImage = m_selectedImage; } this->PrepareAIFConcentrationImage(); aifGenerator->SetDynamicImage(this->m_inputAIFImage); aif = aifGenerator->GetAterialInputFunction(); aifTimeGrid = aifGenerator->GetAterialInputFunctionTimeGrid(); } else { mitkThrow() << "Cannot generate AIF. View is in a invalide state. No AIF mode selected."; } } void MRPerfusionView::LoadAIFfromFile() { QFileDialog dialog; dialog.setNameFilter(tr("Images (*.csv")); QString fileName = dialog.getOpenFileName(); m_Controls.aifFilePath->setText(fileName); std::string m_aifFilePath = fileName.toStdString(); //Read Input typedef boost::tokenizer< boost::escaped_list_separator > Tokenizer; ///////////////////////////////////////////////////////////////////////////////////////////////// //AIF Data std::ifstream in1(m_aifFilePath.c_str()); if (!in1.is_open()) { m_Controls.errorMessageLabel->setText("Could not open AIF File!"); } std::vector< std::string > vec1; std::string line1; while (getline(in1, line1)) { Tokenizer tok(line1); vec1.assign(tok.begin(), tok.end()); this->AIFinputGrid.push_back(convertToDouble(vec1[0])); this->AIFinputFunction.push_back(convertToDouble(vec1[1])); } } void MRPerfusionView::PrepareConcentrationImage() { mitk::Image::Pointer concentrationImage = this->m_selectedImage; mitk::DataNode::Pointer concentrationNode = this->m_selectedNode; m_HasGeneratedNewInput = false; if (!this->m_Controls.radioButtonNoConversion->isChecked()) { concentrationImage = this->ConvertConcentrationImage(false); concentrationNode = GenerateConcentrationNode(concentrationImage, "Concentration"); m_HasGeneratedNewInput = true; } m_inputImage = concentrationImage; m_inputNode = concentrationNode; mitk::EnsureModelFitUID(concentrationNode); } void MRPerfusionView::PrepareAIFConcentrationImage() { mitk::Image::Pointer concentrationImage = this->m_selectedImage; mitk::DataNode::Pointer concentrationNode = this->m_selectedNode; m_HasGeneratedNewInputAIF = false; if (this->m_Controls.checkDedicatedAIFImage->isChecked()) { concentrationImage = this->m_selectedAIFImage; concentrationNode = this->m_selectedAIFImageNode; } if (!this->m_Controls.radioButtonNoConversion->isChecked()) { if (!IsTurboFlashSequenceFlag() && !this->m_Controls.checkDedicatedAIFImage->isChecked()) { if (m_inputImage.IsNull()) { mitkThrow() << "Cannot get AIF concentration image. Invalid view state. Input image is not defined yet, but should be."; } //we can directly use the concentration input image/node (generated by GetConcentrationImage) also for the AIF concentrationImage = this->m_inputImage; concentrationNode = this->m_inputNode; } else { concentrationImage = this->ConvertConcentrationImage(true); concentrationNode = GenerateConcentrationNode(concentrationImage, "AIF Concentration"); m_HasGeneratedNewInputAIF = true; } } m_inputAIFImage = concentrationImage; m_inputAIFNode = concentrationNode; mitk::EnsureModelFitUID(concentrationNode); } mitk::ModelFitFunctorBase::Pointer MRPerfusionView::CreateDefaultFitFunctor( const mitk::ModelParameterizerBase* parameterizer) const { mitk::LevenbergMarquardtModelFitFunctor::Pointer fitFunctor = mitk::LevenbergMarquardtModelFitFunctor::New(); mitk::NormalizedSumOfSquaredDifferencesFitCostFunction::Pointer chi2 = mitk::NormalizedSumOfSquaredDifferencesFitCostFunction::New(); fitFunctor->RegisterEvaluationParameter("Chi^2", chi2); if (m_Controls.checkBox_Constraints->isChecked()) { fitFunctor->SetConstraintChecker(m_modelConstraints); } mitk::ModelBase::Pointer refModel = parameterizer->GenerateParameterizedModel(); ::itk::LevenbergMarquardtOptimizer::ScalesType scales; scales.SetSize(refModel->GetNumberOfParameters()); scales.Fill(1.0); fitFunctor->SetScales(scales); fitFunctor->SetDebugParameterMaps(m_Controls.checkDebug->isChecked()); return fitFunctor.GetPointer(); } diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.h b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.h index a5410d2e49..51ca7e5bce 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.h +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionView.h @@ -1,213 +1,214 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef MRPerfusionView_h #define MRPerfusionView_h #include #include "QmitkAbstractView.h" #include "itkCommand.h" #include "ui_MRPerfusionViewControls.h" #include "mitkModelBase.h" #include "QmitkParameterFitBackgroundJob.h" #include "mitkModelFitResultHelper.h" #include "mitkModelFactoryBase.h" #include "mitkLevenbergMarquardtModelFitFunctor.h" #include "mitkSimpleBarrierConstraintChecker.h" #include "mitkAIFBasedModelBase.h" /*! * @brief Test Plugin for SUV calculations of PET images */ class MRPerfusionView : public QmitkAbstractView { Q_OBJECT public: /*! @brief The view's unique ID - required by MITK */ static const std::string VIEW_ID; MRPerfusionView(); protected slots: void OnModellingButtonClicked(); void OnJobFinished(); void OnJobError(QString err); void OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType results, const ParameterFitBackgroundJob* pJob); void OnJobProgress(double progress); void OnJobStatusChanged(QString info); void OnModellSet(int); void LoadAIFfromFile(); /**Sets visibility and enabled state of the GUI depending on the settings and workflow state.*/ void UpdateGUIControls(); protected: typedef QList SelectedDataNodeVectorType; // Overridden base class functions /*! * @brief Sets up the UI controls and connects the slots and signals. Gets * called by the framework to create the GUI at the right time. * @param[in,out] parent The parent QWidget, as this class itself is not a QWidget * subclass. */ void CreateQtPartControl(QWidget* parent) override; /*! * @brief Sets the focus to the plot curve button. Gets called by the framework to set the * focus on the right widget. */ void SetFocus() override; /*! @brief Generates a configured fit generator and the corresponding modelinfo for a descriptive brix model with pixel based strategy. * @remark add GenerateFunction for each model in the Combo box*/ void GenerateDescriptiveBrixModel_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator); void GenerateDescriptiveBrixModel_ROIBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator); - void Generate3StepLinearModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, + template + void GenerateLinearModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator); - void Generate3StepLinearModelFit_ROIBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, + template + void GenerateLinearModelFit_ROIBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator); template void GenerateAIFbasedModelFit_ROIBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator); - template void GenerateAIFbasedModelFit_PixelBased(mitk::modelFit::ModelFitInfo::Pointer& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator); /** Helper function that configures the initial parameter strategy of a parameterizer according to the settings of the GUI.*/ void ConfigureInitialParametersOfParameterizer(mitk::ModelParameterizerBase* parameterizer) const; /*! Starts the fitting job with the passed generator and session info*/ void DoFit(const mitk::modelFit::ModelFitInfo* fitSession, mitk::ParameterFitImageGeneratorBase* generator); /**Checks if the settings in the GUI are valid for the chosen model.*/ bool CheckModelSettings() const; bool CheckBaselineSelectionSettings() const; void InitModelComboBox() const; /*! Helper method that generates a node for the passed concentration image.*/ mitk::DataNode::Pointer GenerateConcentrationNode(mitk::Image* image, const std::string& nodeName) const; /*! \brief called by QmitkFunctionality when DataManager's selection has changed */ void OnSelectionChanged(berry::IWorkbenchPart::Pointer source, const QList& selectedNodes) override; // Variables /*! @brief The view's UI controls */ Ui::MRPerfusionViewControls m_Controls; /* Nodes selected by user/ui for the fit */ mitk::DataNode::Pointer m_selectedNode; mitk::DataNode::Pointer m_selectedMaskNode; mitk::DataNode::Pointer m_selectedAIFMaskNode; mitk::DataNode::Pointer m_selectedAIFImageNode; /* Images selected by user/ui for the fit */ mitk::Image::Pointer m_selectedImage; mitk::Image::Pointer m_selectedMask; mitk::Image::Pointer m_selectedAIFMask; mitk::Image::Pointer m_selectedAIFImage; mitk::ModelFactoryBase::Pointer m_selectedModelFactory; mitk::SimpleBarrierConstraintChecker::Pointer m_modelConstraints; private: bool IsTurboFlashSequenceFlag() const; bool m_FittingInProgress; typedef std::vector ModelFactoryStackType; ModelFactoryStackType m_FactoryStack; /**Converts the selected image to a concentration image based on the given gui settings. AIFMode controls if the concentration image for the fit input or the AIF will be converted.*/ mitk::Image::Pointer ConvertConcentrationImage(bool AIFMode); /**Helper function that (depending on the gui settings) prepares m_inputNode and m_inputImage. Either by directly pass back the selected image/node or the newly generated concentration image/node. After calling this method m_inputImage are always what should be used as input image for the fitting.*/ void PrepareConcentrationImage(); /**Helper function that (depending on the gui settings) prepares m_inputAIFNode and m_inputAIFImage. Either by directly pass back the selected image/node or the newly generated concentration image/node. After calling this method m_inputAIFImage are always what should be used as AIF image for the fitting.*/ void PrepareAIFConcentrationImage(); /**Helper function that (depending on the gui settings) generates and passes back the AIF and its time grid that should be used for fitting. @remark the parameters aif and aifTimeGrid will be initialized accordingly if the method returns.*/ void GetAIF(mitk::AIFBasedModelBase::AterialInputFunctionType& aif, mitk::AIFBasedModelBase::AterialInputFunctionType& aifTimeGrid); /**Helper function that generates a default fitting functor * default is a levenberg marquart based optimizer with all scales set to 1.0. * Constraint setter will be set based on the gui setting and a evaluation parameter * "sum of squared differences" will always be set.*/ mitk::ModelFitFunctorBase::Pointer CreateDefaultFitFunctor(const mitk::ModelParameterizerBase* parameterizer) const; /**Returns the default fit name, derived from the current GUI settings.*/ std::string GetDefaultFitName() const; /**Returns the current set name of the fit (either default name or use defined name).*/ std::string GetFitName() const; std::vector AIFinputGrid; std::vector AIFinputFunction; mitk::NodePredicateBase::Pointer m_IsNoMaskImagePredicate; mitk::NodePredicateBase::Pointer m_IsMaskPredicate; /* Node used for the fit (my be the selected image or converted ones (depending on the ui settings */ mitk::DataNode::Pointer m_inputNode; mitk::DataNode::Pointer m_inputAIFNode; bool m_HasGeneratedNewInput; bool m_HasGeneratedNewInputAIF; /* Image used for the fit (my be the selected image or converted ones (depending on the ui settings */ mitk::Image::Pointer m_inputImage; mitk::Image::Pointer m_inputAIFImage; }; #endif diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionViewControls.ui b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionViewControls.ui index 63dfa422d3..d50deb67e5 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionViewControls.ui +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.mri/src/internal/MRPerfusionViewControls.ui @@ -1,726 +1,715 @@ MRPerfusionViewControls 0 0 - 556 + 489 1124 0 0 QmitkTemplate Selected Time Series: No series selected. Selected Mask: No mask selected. Fitting strategy 5 5 5 5 5 Pixel based true ROI based Message - Select pharmacokinetic modell... AIF Mask: Select AIF from Image: 20 0 0 AIF Mask: false Dedicated AIF Image: false 0 0 0 Select AIF from File: false Browse 5 Hematocrit Level [ ]: 1.000000000000000 0.010000000000000 Descriptive Brix-Model Parameters: QFormLayout::AllNonFixedFieldsGrow Injection Time [min]: Numeric Two Compartment Exchange Model Parameters: ODE Int Step Size [s]: 3 0.001000000000000 0.050000000000000 0 0 Model Fit Configuration 0 0 0 0 - 526 - 132 + 484 + 68 Start parameter Enter Fit Starting Parameters 0 0 0 0 - 158 - 232 + 484 + 244 Constraints Enter Constraints for Fit Parameters 0 0 0 200 0 - -108 - 516 - 452 + -17 + 433 + 473 Conversion: Signal to Concentration - - - 9 - - - - - No Signal Conversion - - - true - - - + - + 10 - + - Using T1 Map + No Signal Conversion + + + true - - - 10 - - - - - Parameters: - - - - - - Flip Angle [ ° ] : - - - - - - - Repetition Time TR [ms] : - - - - - - - T1 Map [ms] : - - - - - - - - - - 10000.000000000000000 - - - - - - - Relaxivity [mM⁻¹ s⁻¹] : - - - - - - - - - - - - - - - - - - - - 6 - - - - - - + - Conversion Factor k: + Absolute Signal Enhancement - - - - - - Start Time Frame - - - - - - - - - - End Time Frame - - - - - - - - - + Relative Signal Enhancement - - - - Absolute Signal Enhancement - - - - - - - - + + - Baseline Range Selection: - - - Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter + Using T1 Map - - - - - - 2 - TurboFLASH Sequence - - - 5 + + + Qt::Vertical - - 20 + + + 20 + 40 + - - - - true - - - Turbo FLASH Parameters: - - - - - - Recovery Time [s]: - - - - - + + + + + + + + + + Enhancement Parameters: + + + + + + Conversion Factor k: + + + + + + + + + + Baseline Range Selection: + + + Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter + + + + + + + - + - AIF Recovery Time [s]: + Start Time Frame - - - - - - - - + + - Relaxation Time [s]: + End Time Frame - - - - - - Relaxivity [ ]: - - + - - - + + + + + + + + T1 Map Parameters: + + + + + + Flip Angle [ ° ] : + + + + + + + Repetition Time TR [ms] : + + + + + + + Relaxivity [mM⁻¹ s⁻¹] : + + + + + + + + + + + + + T1 Map [ms] : + + + + + + + 10000.000000000000000 + + + + + + + + + + + + + true + + + Turbo FLASH Parameters: + + + + + + Recovery Time [s]: + + + + + + + + + + AIF Recovery Time [s]: + + + + + + + + + + + + + Relaxation Time [s]: + + + + + + + + + + Relaxivity [ ]: + + + + + 5 Fitting name: <html><head/><body><p>Name/prefix that should be used for the fitting results.</p><p>May be explicitly defined by the user.</p></body></html> default fit name Start Modelling Generate debug parameter images 0 0 true Qt::Vertical 20 40 QmitkSimpleBarrierManagerWidget QWidget
QmitkSimpleBarrierManagerWidget.h
 QmitkInitialValuesManagerWidget QWidget
QmitkInitialValuesManagerWidget.h
 QmitkDataStorageComboBox QWidget
QmitkDataStorageComboBox.h