diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.cpp b/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.cpp index 35ac6847cf..64cef01de2 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.cpp +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.cpp @@ -1,1000 +1,880 @@ /*============================================================================ 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 "mitkWorkbenchUtil.h" #include "PerfusionDataSimulationView.h" #include "itkUnaryFunctorImageFilter.h" #include #include "mitkImageCast.h" #include "mitkImageTimeSelector.h" #include "mitkITKImageImport.h" #include "mitkGaussianNoiseFunctor.h" #include "mitkTwoCompartmentExchangeModel.h" #include "mitkTwoCompartmentExchangeModelParameterizer.h" #include "mitkTwoCompartmentExchangeModelFactory.h" -#include "mitkNumericTwoCompartmentExchangeModel.h" -#include "mitkNumericTwoCompartmentExchangeModelParameterizer.h" -#include "mitkNumericTwoCompartmentExchangeModelFactory.h" #include "mitkExtendedToftsModel.h" #include "mitkExtendedToftsModelFactory.h" #include "mitkExtendedToftsModelParameterizer.h" #include "mitkTwoTissueCompartmentModel.h" #include "mitkTwoTissueCompartmentModelParameterizer.h" #include "mitkTwoTissueCompartmentModelFactory.h" #include "mitkOneTissueCompartmentModel.h" #include "mitkOneTissueCompartmentModelParameterizer.h" #include "mitkOneTissueCompartmentModelFactory.h" #include "mitkModelSignalImageGenerator.h" #include #include #include #include #include "mitkSimpleFunctorBase.h" #include "mitkArbitraryTimeGeometry.h" #include #include const std::string PerfusionDataSimulationView::VIEW_ID = "org.mitk.views.pharmacokinetics.simulation"; 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; } inline double FindeMaxConcentration(std::vector Concentration) { double maximum = Concentration[0]; for (std::vector::size_type i =0; isetFocus(); } void PerfusionDataSimulationView::CreateQtPartControl(QWidget* parent) { m_Controls.setupUi(parent); m_Controls.GenerateBtn->setEnabled(false); m_Controls.groupBox_TM->hide(); m_Controls.groupBox_2CXM->hide(); m_Controls.groupBox_2TCM->hide(); m_Controls.groupBox_1TCM->hide(); m_Controls.groupBox_CNR->hide(); this->InitModelComboBox(); /** #2 @todo Reduce code ? */ m_Controls.comboBox_F->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_F->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_PS->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_PS->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_fp->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_fp->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_fi->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_fi->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_Ktrans->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_Ktrans->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_vp->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_vp->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_ve->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_ve->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_K1->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_K1->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_K2->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_K2->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_K3->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_K3->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_K4->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_K4->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_VB->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_VB->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_k1->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_k1->SetPredicate(m_IsNotABinaryImagePredicate); m_Controls.comboBox_k2->SetDataStorage(this->GetDataStorage()); m_Controls.comboBox_k2->SetPredicate(m_IsNotABinaryImagePredicate); connect(m_Controls.AifFileBtn, SIGNAL(clicked()), this, SLOT(LoadAIFFile())); connect(m_Controls.ModelSelection, SIGNAL(currentIndexChanged(int)), this, SLOT(OnModellSet(int))); connect(m_Controls.GenerateBtn, SIGNAL(clicked()), this, SLOT(OnGenerateDataButtonClicked())); connect(m_Controls.comboBox_F, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_PS, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_fp, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_fi, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_VB, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_K1, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_K2, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_K3, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_K4, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_k1, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_k2, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_Ktrans, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_vp, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.comboBox_ve, SIGNAL(currentIndexChanged(int)), this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.CNRSpinBox, SIGNAL(valueChanged(double)),this, SLOT(OnSimulationConfigurationChanged())); connect(m_Controls.NoiseCheckBox, SIGNAL(stateChanged(int)),this, SLOT(OnSimulationConfigurationChanged())); // UpdateDataSelection(); } void PerfusionDataSimulationView::UpdateDataSelection() { } //void PerfusionDataSimulationView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, // const QList& selectedNodes) //{ // UpdateDataSelection(); // m_Controls.GenerateBtn->setEnabled(CheckModelSettings()); //} void PerfusionDataSimulationView::OnSimulationConfigurationChanged() { // UpdateDataSelection(); m_Controls.groupBox_CNR->setVisible(m_Controls.NoiseCheckBox->isChecked()); this->m_CNR = m_Controls.CNRSpinBox->value(); m_Controls.GenerateBtn->setEnabled( CheckModelSettings() ); } void PerfusionDataSimulationView::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; } } bool isToftsFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; - bool is2CXMFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr || dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; + bool is2CXMFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; bool is2TCMFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; bool is1TCMFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; m_Controls.groupBox_TM->setVisible(isToftsFactory); m_Controls.groupBox_2CXM->setVisible(is2CXMFactory ); m_Controls.groupBox_2TCM->setVisible(is2TCMFactory ); m_Controls.groupBox_1TCM->setVisible(is1TCMFactory ); m_Controls.GenerateBtn->setEnabled( CheckModelSettings() ); // UpdateDataSelection(); } bool PerfusionDataSimulationView::CheckModelSettings() { bool ok = true; if(m_selectedModelFactory.IsNull()) { return false; } if(this->m_AterialInputFunction.GetSize() == 0 || this->m_TimeGrid.GetSize() == 0) { return false; } bool isToftsFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; - bool is2CXMFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr || dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; + bool is2CXMFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; bool is2TCMFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; bool is1TCMFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; if(isToftsFactory) { ok = ok && m_Controls.comboBox_Ktrans->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_vp->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_ve->GetSelectedNode().IsNotNull(); } else if(is2CXMFactory) { ok = ok && m_Controls.comboBox_F->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_PS->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_fp->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_fi->GetSelectedNode().IsNotNull(); } else if(is2TCMFactory) { ok = ok && m_Controls.comboBox_K1->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_K2->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_K3->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_K4->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_VB->GetSelectedNode().IsNotNull(); } else if(is1TCMFactory) { ok = ok && m_Controls.comboBox_k1->GetSelectedNode().IsNotNull(); ok = ok && m_Controls.comboBox_k2->GetSelectedNode().IsNotNull(); } else { return false; } if(m_Controls.NoiseCheckBox->isChecked()) { if(m_CNR !=0 && m_MaxConcentration !=0) { this->m_Sigma = m_MaxConcentration/m_CNR; } if(m_Sigma==0) { return false; } } return ok; } void PerfusionDataSimulationView::InitModelComboBox() const { this->m_Controls.ModelSelection->clear(); this->m_Controls.ModelSelection->addItem(tr("No model selected")); for (ModelFactoryStackType::const_iterator pos = m_FactoryStack.begin(); pos != m_FactoryStack.end(); ++pos) { this->m_Controls.ModelSelection->addItem(QString::fromStdString((*pos)->GetClassID())); } this->m_Controls.ModelSelection->setCurrentIndex(0); }; void PerfusionDataSimulationView::LoadAIFFile() { QFileDialog dialog; dialog.setNameFilter(tr("Images (*.csv")); QString fileName = dialog.getOpenFileName(); m_Controls.AifFilePath->setText( fileName ); std::string aifFilePath = fileName.toStdString(); //Read Input typedef boost::tokenizer< boost::escaped_list_separator > Tokenizer; ///////////////////////////////////////////////////////////////////////////////////////////////// //AIF Data std::vector inputFunction; std::vector inputGrid; std::ifstream in1(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()); // if (vec1.size() < 3) continue; inputGrid.push_back(convertToDouble(vec1[0])); inputFunction.push_back(convertToDouble(vec1[1])); } this->m_MaxConcentration = FindeMaxConcentration(inputFunction); itk::Array aif; itk::Array grid; aif.SetSize(inputFunction.size()); grid.SetSize(inputGrid.size()); aif.fill(0.0); grid.fill(0.0); itk::Array::iterator aifPos = aif.begin(); for(std::vector::const_iterator pos = inputFunction.begin(); pos != inputFunction.end(); ++pos, ++aifPos) { *aifPos = *pos; } itk::Array::iterator gridPos = grid.begin(); for(std::vector::const_iterator pos = inputGrid.begin(); pos != inputGrid.end(); ++pos, ++gridPos) { *gridPos = *pos; } this->m_AterialInputFunction = aif; this->m_TimeGrid = grid; m_Controls.GenerateBtn->setEnabled( CheckModelSettings() ); // UpdateDataSelection(); } -/** @todo #2 Same function for Numeric and analytic version of FillParameterMap2CXM +/** @todo #2 Same function for analytic version of FillParameterMap2CXM */ void PerfusionDataSimulationView::FillParameterMap2CXM() { ParameterMapType stack; mitk::DataNode::Pointer m_selectedNode = m_Controls.comboBox_F->GetSelectedNode(); mitk::Image::Pointer m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_F,m_selectedImage)); m_selectedNode = m_Controls.comboBox_PS->GetSelectedNode(); m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_PS,m_selectedImage)); m_selectedNode = m_Controls.comboBox_fp->GetSelectedNode(); m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_vp,m_selectedImage)); m_selectedNode = m_Controls.comboBox_fi->GetSelectedNode(); m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_ve,m_selectedImage)); this->m_ParameterImageMap = stack; } -void PerfusionDataSimulationView::FillParameterMapNumeric2CXM() -{ - ParameterMapType stack; - - mitk::DataNode::Pointer m_selectedNode = m_Controls.comboBox_F->GetSelectedNode(); - mitk::Image::Pointer m_selectedImage = dynamic_cast(m_selectedNode->GetData()); - stack.insert(std::make_pair(mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_F,m_selectedImage)); - - m_selectedNode = m_Controls.comboBox_PS->GetSelectedNode(); - m_selectedImage = dynamic_cast(m_selectedNode->GetData()); - stack.insert(std::make_pair(mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_PS,m_selectedImage)); - - m_selectedNode = m_Controls.comboBox_fp->GetSelectedNode(); - m_selectedImage = dynamic_cast(m_selectedNode->GetData()); - stack.insert(std::make_pair(mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_vp,m_selectedImage)); - - m_selectedNode = m_Controls.comboBox_fi->GetSelectedNode(); - m_selectedImage = dynamic_cast(m_selectedNode->GetData()); - stack.insert(std::make_pair(mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_ve,m_selectedImage)); - - this->m_ParameterImageMap = stack; - -} void PerfusionDataSimulationView::FillParameterMapETM() { ParameterMapType stack; mitk::DataNode::Pointer m_selectedNode = m_Controls.comboBox_Ktrans->GetSelectedNode(); mitk::Image::Pointer m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::ExtendedToftsModel::NAME_PARAMETER_Ktrans,m_selectedImage)); m_selectedNode = m_Controls.comboBox_vp->GetSelectedNode(); m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::ExtendedToftsModel::NAME_PARAMETER_vp,m_selectedImage)); m_selectedNode = m_Controls.comboBox_ve->GetSelectedNode(); m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::ExtendedToftsModel::NAME_PARAMETER_ve,m_selectedImage)); this->m_ParameterImageMap = stack; } void PerfusionDataSimulationView::FillParameterMap2TCM() { ParameterMapType stack; mitk::DataNode::Pointer m_selectedNode = m_Controls.comboBox_K1->GetSelectedNode(); mitk::Image::Pointer m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoTissueCompartmentModel::NAME_PARAMETER_K1,m_selectedImage)); m_selectedNode = m_Controls.comboBox_K2->GetSelectedNode(); m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k2,m_selectedImage)); m_selectedNode = m_Controls.comboBox_K3->GetSelectedNode(); m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k3,m_selectedImage)); m_selectedNode = m_Controls.comboBox_K4->GetSelectedNode(); m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k4,m_selectedImage)); m_selectedNode = m_Controls.comboBox_VB->GetSelectedNode(); m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::TwoTissueCompartmentModel::NAME_PARAMETER_vb,m_selectedImage)); this->m_ParameterImageMap = stack; } void PerfusionDataSimulationView::FillParameterMap1TCM() { ParameterMapType stack; mitk::DataNode::Pointer m_selectedNode = m_Controls.comboBox_k1->GetSelectedNode(); mitk::Image::Pointer m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::OneTissueCompartmentModel::NAME_PARAMETER_K1,m_selectedImage)); m_selectedNode = m_Controls.comboBox_k2->GetSelectedNode(); m_selectedImage = dynamic_cast(m_selectedNode->GetData()); stack.insert(std::make_pair(mitk::OneTissueCompartmentModel::NAME_PARAMETER_k2,m_selectedImage)); this->m_ParameterImageMap = stack; } void PerfusionDataSimulationView::OnGenerateDataButtonClicked() { mitk::Image::Pointer m_DynamicImage = mitk::Image::New(); bool isToftsFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; bool isPhysBrixFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; - bool isNumPhysBrixFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; bool is2TCMFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; bool is1TCMFactory = dynamic_cast(m_selectedModelFactory.GetPointer()) != nullptr; if(isToftsFactory) { this->FillParameterMapETM(); m_DynamicImage = this->GenerateETModelData(); } if (isPhysBrixFactory) { this->FillParameterMap2CXM(); m_DynamicImage = this->Generate2CXModelData(); } - if (isNumPhysBrixFactory) - { - this->FillParameterMapNumeric2CXM(); - m_DynamicImage = this->GenerateNumeric2CXModelData(); - } if (is2TCMFactory) { this->FillParameterMap2TCM(); m_DynamicImage = this->Generate2TCModelData(); } if (is1TCMFactory) { this->FillParameterMap1TCM(); m_DynamicImage = this->Generate1TCModelData(); } mitk::DataNode::Pointer resultNode = mitk::DataNode::New(); std::string nameOfResultImage = "SimulationData_"; nameOfResultImage.append(m_selectedModelFactory->GetModelDisplayName()); resultNode->SetProperty("name", mitk::StringProperty::New(nameOfResultImage) ); resultNode->SetData(m_DynamicImage); // set data of new node this->GetDataStorage()->Add(resultNode); } mitk::Image::Pointer PerfusionDataSimulationView::Generate2CXModelData() { mitk::ModelSignalImageGenerator::Pointer generator = mitk::ModelSignalImageGenerator::New(); mitk::TwoCompartmentExchangeModelParameterizer::Pointer modelParameterizer = mitk::TwoCompartmentExchangeModelParameterizer::New(); /** @todo #2 necessary? Generator need to have a map with Parameters in order of Model in order to pass vector parameters correctly to Model. * I wanted to make it independent from the order the images are passed on */ for(ParameterMapType::const_iterator pos = this->m_ParameterImageMap.begin(); pos != this->m_ParameterImageMap.end(); ++pos) { if(pos->first == mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_F) { generator->SetParameterInputImage(mitk::TwoCompartmentExchangeModel::POSITION_PARAMETER_F, pos->second); } if(pos->first == mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_PS) { generator->SetParameterInputImage(mitk::TwoCompartmentExchangeModel::POSITION_PARAMETER_PS, pos->second); } if(pos->first == mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_ve) { generator->SetParameterInputImage(mitk::TwoCompartmentExchangeModel::POSITION_PARAMETER_ve, pos->second); } if(pos->first == mitk::TwoCompartmentExchangeModel::NAME_PARAMETER_vp) { generator->SetParameterInputImage(mitk::TwoCompartmentExchangeModel::POSITION_PARAMETER_vp, pos->second); } } modelParameterizer->SetAIF(this->m_AterialInputFunction); modelParameterizer->SetAIFTimeGrid(this->m_TimeGrid); modelParameterizer->SetDefaultTimeGrid(this->m_TimeGrid); generator->SetParameterizer(modelParameterizer); mitk::Image::Pointer generatedImage = generator->GetGeneratedImage(); mitk::Image::Pointer resultImage = mitk::Image::New(); if(m_Controls.NoiseCheckBox->isChecked()) { typedef itk::Image ImageType; mitk::Image::Pointer tempImage = mitk::Image::New(); tempImage->Initialize(generatedImage); mitk::ArbitraryTimeGeometry* timeGeometry = dynamic_cast (generatedImage->GetTimeGeometry()); tempImage->SetTimeGeometry(timeGeometry); ImageType::Pointer itkImage = ImageType::New(); mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(generatedImage); for(unsigned int i = 0; i< generatedImage->GetTimeSteps(); ++i) { imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::Image::Pointer mitkInputImage = imageTimeSelector->GetOutput(); mitk::CastToItkImage(mitkInputImage, itkImage ); typedef mitk::GaussianNoiseFunctor NoiseFunctorType; typedef itk::UnaryFunctorImageFilter NoiseFilterType; NoiseFilterType::Pointer noiseFilter = NoiseFilterType::New(); NoiseFunctorType noiseFunctor; noiseFunctor.SetMean(0.0); noiseFunctor.SetSigma(this->m_Sigma); noiseFilter->SetFunctor(noiseFunctor); noiseFilter->SetInput(itkImage); mitk::Image::Pointer outputImage = mitk::ImportItkImage(noiseFilter->GetOutput())->Clone(); mitk::ImageReadAccessor accessor(outputImage); tempImage->SetVolume(accessor.GetData(), i); } resultImage = tempImage->Clone(); } else { resultImage = generatedImage; } return resultImage; } -/** @todo #2 Synergie? Function implementation for every Model to complicated? - */ -mitk::Image::Pointer PerfusionDataSimulationView::GenerateNumeric2CXModelData() -{ -mitk::ModelSignalImageGenerator::Pointer generator = mitk::ModelSignalImageGenerator::New(); -mitk::NumericTwoCompartmentExchangeModelParameterizer::Pointer modelParameterizer = mitk::NumericTwoCompartmentExchangeModelParameterizer::New(); - -for(ParameterMapType::const_iterator pos = this->m_ParameterImageMap.begin(); pos != this->m_ParameterImageMap.end(); ++pos) -{ - if(pos->first == mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_F) - { - generator->SetParameterInputImage(mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_F, pos->second); - } - if(pos->first == mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_PS) - { - generator->SetParameterInputImage(mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_PS, pos->second); - } - if(pos->first == mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_ve) - { - generator->SetParameterInputImage(mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_ve, pos->second); - } - if(pos->first == mitk::NumericTwoCompartmentExchangeModel::NAME_PARAMETER_vp) - { - generator->SetParameterInputImage(mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_vp, pos->second); - } -} - -modelParameterizer->SetAIF(this->m_AterialInputFunction); -modelParameterizer->SetAIFTimeGrid(this->m_TimeGrid); -modelParameterizer->SetDefaultTimeGrid(this->m_TimeGrid); -modelParameterizer->SetODEINTStepSize(0.05); - -generator->SetParameterizer(modelParameterizer); - -mitk::Image::Pointer generatedImage = generator->GetGeneratedImage(); - - -mitk::Image::Pointer resultImage = mitk::Image::New(); -if(m_Controls.NoiseCheckBox->isChecked()) -{ - typedef itk::Image ImageType; - - mitk::Image::Pointer tempImage = mitk::Image::New(); - tempImage->Initialize(generatedImage); - - mitk::ArbitraryTimeGeometry* timeGeometry = dynamic_cast (generatedImage->GetTimeGeometry()); - - tempImage->SetTimeGeometry(timeGeometry); - - ImageType::Pointer itkImage = ImageType::New(); - mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); - imageTimeSelector->SetInput(generatedImage); - - for(unsigned int i = 0; i< generatedImage->GetTimeSteps(); ++i) - { - imageTimeSelector->SetTimeNr(i); - imageTimeSelector->UpdateLargestPossibleRegion(); - - mitk::Image::Pointer mitkInputImage = imageTimeSelector->GetOutput(); - - mitk::CastToItkImage(mitkInputImage, itkImage ); - - typedef mitk::GaussianNoiseFunctor NoiseFunctorType; - typedef itk::UnaryFunctorImageFilter NoiseFilterType; - NoiseFilterType::Pointer noiseFilter = NoiseFilterType::New(); - NoiseFunctorType noiseFunctor; - noiseFunctor.SetMean(0.0); - noiseFunctor.SetSigma(this->m_Sigma); - noiseFilter->SetFunctor(noiseFunctor); - - noiseFilter->SetInput(itkImage); - - mitk::Image::Pointer outputImage = mitk::ImportItkImage(noiseFilter->GetOutput())->Clone(); - - mitk::ImageReadAccessor accessor(outputImage); - tempImage->SetVolume(accessor.GetData(), i); - } - - resultImage = tempImage->Clone(); -} -else -{ - resultImage = generatedImage; -} -return resultImage; -} mitk::Image::Pointer PerfusionDataSimulationView::GenerateETModelData() { mitk::ModelSignalImageGenerator::Pointer generator = mitk::ModelSignalImageGenerator::New(); mitk::ExtendedToftsModelParameterizer::Pointer modelParameterizer = mitk::ExtendedToftsModelParameterizer::New(); for(ParameterMapType::const_iterator pos = this->m_ParameterImageMap.begin(); pos != this->m_ParameterImageMap.end(); ++pos) { if(pos->first == mitk::ExtendedToftsModel::NAME_PARAMETER_Ktrans) { generator->SetParameterInputImage(mitk::ExtendedToftsModel::POSITION_PARAMETER_Ktrans, pos->second); } if(pos->first == mitk::ExtendedToftsModel::NAME_PARAMETER_vp) { generator->SetParameterInputImage(mitk::ExtendedToftsModel::POSITION_PARAMETER_vp, pos->second); } if(pos->first == mitk::ExtendedToftsModel::NAME_PARAMETER_ve) { generator->SetParameterInputImage(mitk::ExtendedToftsModel::POSITION_PARAMETER_ve, pos->second); } } modelParameterizer->SetAIF(this->m_AterialInputFunction); modelParameterizer->SetAIFTimeGrid(this->m_TimeGrid); modelParameterizer->SetDefaultTimeGrid(this->m_TimeGrid); generator->SetParameterizer(modelParameterizer); mitk::Image::Pointer generatedImage = generator->GetGeneratedImage(); mitk::Image::Pointer resultImage = mitk::Image::New(); if(m_Controls.NoiseCheckBox->isChecked()) { typedef itk::Image ImageType; mitk::Image::Pointer tempImage = mitk::Image::New(); tempImage->Initialize(generatedImage); mitk::ArbitraryTimeGeometry* timeGeometry = dynamic_cast (generatedImage->GetTimeGeometry()); tempImage->SetTimeGeometry(timeGeometry); ImageType::Pointer itkImage = ImageType::New(); mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(generatedImage); for(unsigned int i = 0; i< generatedImage->GetTimeSteps(); ++i) { imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::Image::Pointer mitkInputImage = imageTimeSelector->GetOutput(); mitk::CastToItkImage(mitkInputImage, itkImage ); typedef mitk::GaussianNoiseFunctor NoiseFunctorType; typedef itk::UnaryFunctorImageFilter NoiseFilterType; NoiseFilterType::Pointer noiseFilter = NoiseFilterType::New(); NoiseFunctorType noiseFunctor; noiseFunctor.SetMean(0.0); noiseFunctor.SetSigma(this->m_Sigma); noiseFilter->SetFunctor(noiseFunctor); noiseFilter->SetInput(itkImage); mitk::Image::Pointer outputImage = mitk::ImportItkImage(noiseFilter->GetOutput())->Clone(); mitk::ImageReadAccessor accessor(outputImage); tempImage->SetVolume(accessor.GetData(), i); } resultImage = tempImage->Clone(); } else { resultImage = generatedImage; } return resultImage; } mitk::Image::Pointer PerfusionDataSimulationView::Generate2TCModelData() { mitk::ModelSignalImageGenerator::Pointer generator = mitk::ModelSignalImageGenerator::New(); mitk::TwoTissueCompartmentModelParameterizer::Pointer modelParameterizer = mitk::TwoTissueCompartmentModelParameterizer::New(); for(ParameterMapType::const_iterator pos = this->m_ParameterImageMap.begin(); pos != this->m_ParameterImageMap.end(); ++pos) { if(pos->first == mitk::TwoTissueCompartmentModel::NAME_PARAMETER_K1) { generator->SetParameterInputImage(mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_K1, pos->second); } if(pos->first == mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k2) { generator->SetParameterInputImage(mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_k2, pos->second); } if(pos->first == mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k3) { generator->SetParameterInputImage(mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_k3, pos->second); } if(pos->first == mitk::TwoTissueCompartmentModel::NAME_PARAMETER_k4) { generator->SetParameterInputImage(mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_k4, pos->second); } if(pos->first == mitk::TwoTissueCompartmentModel::NAME_PARAMETER_vb) { generator->SetParameterInputImage(mitk::TwoTissueCompartmentModel::POSITION_PARAMETER_vb, pos->second); } } modelParameterizer->SetAIF(this->m_AterialInputFunction); modelParameterizer->SetAIFTimeGrid(this->m_TimeGrid); modelParameterizer->SetDefaultTimeGrid(this->m_TimeGrid); generator->SetParameterizer(modelParameterizer); mitk::Image::Pointer generatedImage = generator->GetGeneratedImage(); mitk::Image::Pointer resultImage = mitk::Image::New(); if(m_Controls.NoiseCheckBox->isChecked()) { typedef itk::Image ImageType; mitk::Image::Pointer tempImage = mitk::Image::New(); tempImage->Initialize(generatedImage); mitk::ArbitraryTimeGeometry* timeGeometry = dynamic_cast (generatedImage->GetTimeGeometry()); tempImage->SetTimeGeometry(timeGeometry); ImageType::Pointer itkImage = ImageType::New(); mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(generatedImage); for(unsigned int i = 0; i< generatedImage->GetTimeSteps(); ++i) { imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::Image::Pointer mitkInputImage = imageTimeSelector->GetOutput(); mitk::CastToItkImage(mitkInputImage, itkImage ); typedef mitk::GaussianNoiseFunctor NoiseFunctorType; typedef itk::UnaryFunctorImageFilter NoiseFilterType; NoiseFilterType::Pointer noiseFilter = NoiseFilterType::New(); NoiseFunctorType noiseFunctor; noiseFunctor.SetMean(0.0); noiseFunctor.SetSigma(this->m_Sigma); noiseFilter->SetFunctor(noiseFunctor); noiseFilter->SetInput(itkImage); mitk::Image::Pointer outputImage = mitk::ImportItkImage(noiseFilter->GetOutput())->Clone(); mitk::ImageReadAccessor accessor(outputImage); tempImage->SetVolume(accessor.GetData(), i); } resultImage = tempImage->Clone(); } else { resultImage = generatedImage; } return resultImage; } mitk::Image::Pointer PerfusionDataSimulationView::Generate1TCModelData() { mitk::ModelSignalImageGenerator::Pointer generator = mitk::ModelSignalImageGenerator::New(); mitk::OneTissueCompartmentModelParameterizer::Pointer modelParameterizer = mitk::OneTissueCompartmentModelParameterizer::New(); for(ParameterMapType::const_iterator pos = this->m_ParameterImageMap.begin(); pos != this->m_ParameterImageMap.end(); ++pos) { if(pos->first == mitk::OneTissueCompartmentModel::NAME_PARAMETER_K1) { generator->SetParameterInputImage(mitk::OneTissueCompartmentModel::POSITION_PARAMETER_K1, pos->second); } if(pos->first == mitk::OneTissueCompartmentModel::NAME_PARAMETER_k2) { generator->SetParameterInputImage(mitk::OneTissueCompartmentModel::POSITION_PARAMETER_k2, pos->second); } } modelParameterizer->SetAIF(this->m_AterialInputFunction); modelParameterizer->SetAIFTimeGrid(this->m_TimeGrid); modelParameterizer->SetDefaultTimeGrid(this->m_TimeGrid); generator->SetParameterizer(modelParameterizer); mitk::Image::Pointer generatedImage = generator->GetGeneratedImage(); mitk::Image::Pointer resultImage = mitk::Image::New(); if(m_Controls.NoiseCheckBox->isChecked()) { typedef itk::Image ImageType; mitk::Image::Pointer tempImage = mitk::Image::New(); tempImage->Initialize(generatedImage); mitk::ArbitraryTimeGeometry* timeGeometry = dynamic_cast (generatedImage->GetTimeGeometry()); tempImage->SetTimeGeometry(timeGeometry); ImageType::Pointer itkImage = ImageType::New(); mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(generatedImage); for(unsigned int i = 0; i< generatedImage->GetTimeSteps(); ++i) { imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::Image::Pointer mitkInputImage = imageTimeSelector->GetOutput(); mitk::CastToItkImage(mitkInputImage, itkImage ); typedef mitk::GaussianNoiseFunctor NoiseFunctorType; typedef itk::UnaryFunctorImageFilter NoiseFilterType; NoiseFilterType::Pointer noiseFilter = NoiseFilterType::New(); NoiseFunctorType noiseFunctor; noiseFunctor.SetMean(0.0); noiseFunctor.SetSigma(this->m_Sigma); noiseFilter->SetFunctor(noiseFunctor); noiseFilter->SetInput(itkImage); mitk::Image::Pointer outputImage = mitk::ImportItkImage(noiseFilter->GetOutput())->Clone(); mitk::ImageReadAccessor accessor(outputImage); tempImage->SetVolume(accessor.GetData(), i); } resultImage = tempImage->Clone(); } else { resultImage = generatedImage; } return resultImage; } PerfusionDataSimulationView::PerfusionDataSimulationView() { m_Sigma = 0; m_CNR=0; m_MaxConcentration=0; m_selectedModelFactory = nullptr; mitk::ModelFactoryBase::Pointer 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); factory = mitk::TwoTissueCompartmentModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); factory = mitk::OneTissueCompartmentModelFactory::New().GetPointer(); m_FactoryStack.push_back(factory); m_IsNotABinaryImagePredicate = mitk::NodePredicateAnd::New( mitk::TNodePredicateDataType::New(), mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true))), mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer(); } diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.h b/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.h index 7956d413f1..27cf365e0a 100644 --- a/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.h +++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.simulation/src/internal/PerfusionDataSimulationView.h @@ -1,114 +1,112 @@ /*============================================================================ 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 PerfusionDataSimulationView_h #define PerfusionDataSimulationView_h #include #include #include "ui_PerfusionDataSimulationViewControls.h" #include "mitkModelBase.h" #include #include "itkArray.h" #include "mitkImage.h" #include /*! * @brief Test Plugin for SUV calculations of PET images */ class PerfusionDataSimulationView : public QmitkAbstractView { Q_OBJECT public: /*! @brief The view's unique ID - required by MITK */ static const std::string VIEW_ID; PerfusionDataSimulationView(); protected slots: /*! * @brief Is triggered of the update button is clicked and the selected node should get the (new) iso level set. */ void OnGenerateDataButtonClicked(); void LoadAIFFile(); void OnModellSet(int); void OnSimulationConfigurationChanged(); void UpdateDataSelection(); protected: typedef std::map ParameterMapType; // 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; void InitModelComboBox() const; mitk::Image::Pointer Generate2CXModelData(); - mitk::Image::Pointer GenerateNumeric2CXModelData(); mitk::Image::Pointer GenerateETModelData(); void FillParameterMap2CXM(); - void FillParameterMapNumeric2CXM(); void FillParameterMapETM(); ///////////////////// dynamic PET Models/////////////// mitk::Image::Pointer Generate2TCModelData(); mitk::Image::Pointer Generate1TCModelData(); void FillParameterMap2TCM(); void FillParameterMap1TCM(); bool CheckModelSettings(); // Variables /*! @brief The view's UI controls */ Ui::PerfusionDataSimulationViewControls m_Controls; mitk::DataNode::Pointer m_selectedNode; ParameterMapType m_ParameterImageMap; itk::Array m_AterialInputFunction; itk::Array m_TimeGrid; mitk::ModelFactoryBase::Pointer m_selectedModelFactory; private: typedef std::vector ModelFactoryStackType; ModelFactoryStackType m_FactoryStack; mitk::NodePredicateBase::Pointer m_IsNotABinaryImagePredicate; double m_CNR, m_MaxConcentration, m_Sigma; }; #endif