diff --git a/Modules/Pharmacokinetics/include/mitkOneTissueCompartmentModel.h b/Modules/Pharmacokinetics/include/mitkOneTissueCompartmentModel.h index 6da9c3a278..be2ab24e38 100644 --- a/Modules/Pharmacokinetics/include/mitkOneTissueCompartmentModel.h +++ b/Modules/Pharmacokinetics/include/mitkOneTissueCompartmentModel.h @@ -1,94 +1,92 @@ /*============================================================================ 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 mitkOneTissueCompartmentModel_h #define mitkOneTissueCompartmentModel_h #include "mitkAIFBasedModelBase.h" #include "MitkPharmacokineticsExports.h" namespace mitk { - /** @class OneTissueCompartmentModel - * @brief Implementation of the Model function of the Tofts pharmacokinetic model, using an Aterial Input Function - * The Model calculates the Concentration-Time-Curve as a convolution of the plasma curve Cp (the AIF) and a tissue specific - * residue function (in this case an exponential: R(t) = ktrans * exp(-ktrans/ve * (t)) ). - * C(t) = vp * Cp(t) + conv(Cp(t),R(t)) - * The parameters ktrans, ve and ve are subject to the fitting routine*/ - class MITKPHARMACOKINETICS_EXPORT OneTissueCompartmentModel : public AIFBasedModelBase { public: typedef OneTissueCompartmentModel Self; typedef AIFBasedModelBase Superclass; typedef itk::SmartPointer< Self > Pointer; typedef itk::SmartPointer< const Self > ConstPointer; /** Method for creation through the object factory. */ itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Run-time type information (and related methods). */ itkTypeMacro(OneTissueCompartmentModel, ModelBase); - static const std::string MODEL_DISPLAY_NAME; - - static const std::string NAME_PARAMETER_k1; + static const std::string NAME_PARAMETER_K1; static const std::string NAME_PARAMETER_k2; - static const std::string UNIT_PARAMETER_k1; + static const std::string UNIT_PARAMETER_K1; static const std::string UNIT_PARAMETER_k2; - static const unsigned int POSITION_PARAMETER_k1; + static const unsigned int POSITION_PARAMETER_K1; static const unsigned int POSITION_PARAMETER_k2; static const unsigned int NUMBER_OF_PARAMETERS; + static const unsigned int NUMBER_OF_DERIVED_PARAMETERS; + + static const std::string MODEL_DISPLAY_NAME; + + static const std::string MODEL_TYPE; + std::string GetModelDisplayName() const override; std::string GetModelType() const override; ParameterNamesType GetParameterNames() const override; ParametersSizeType GetNumberOfParameters() const override; ParamterUnitMapType GetParameterUnits() const override; + ParametersSizeType GetNumberOfDerivedParameters() const override; protected: OneTissueCompartmentModel(); ~OneTissueCompartmentModel() override; /** * Actual implementation of the clone method. This method should be reimplemeted * in subclasses to clone the extra required parameters. */ itk::LightObject::Pointer InternalClone() const override; ModelResultType ComputeModelfunction(const ParametersType& parameters) const override; void PrintSelf(std::ostream& os, ::itk::Indent indent) const override; private: //No copy constructor allowed OneTissueCompartmentModel(const Self& source); void operator=(const Self&); //purposely not implemented }; } #endif diff --git a/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModel.cpp b/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModel.cpp index a4d455583e..eac58bc877 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModel.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModel.cpp @@ -1,138 +1,149 @@ /*============================================================================ 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 "mitkOneTissueCompartmentModel.h" #include "mitkConvolutionHelper.h" #include #include const std::string mitk::OneTissueCompartmentModel::MODEL_DISPLAY_NAME = "One Tissue Compartment Model"; -const std::string mitk::OneTissueCompartmentModel::NAME_PARAMETER_k1 = "K1"; -const std::string mitk::OneTissueCompartmentModel::NAME_PARAMETER_k2 = "k2"; +const std::string mitk::OneTissueCompartmentModel::NAME_PARAMETER_K1 = "K_1"; +const std::string mitk::OneTissueCompartmentModel::NAME_PARAMETER_k2 = "k_2"; -const std::string mitk::OneTissueCompartmentModel::UNIT_PARAMETER_k1 = "1/min"; +const std::string mitk::OneTissueCompartmentModel::UNIT_PARAMETER_K1 = "1/min"; const std::string mitk::OneTissueCompartmentModel::UNIT_PARAMETER_k2 = "1/min"; -const unsigned int mitk::OneTissueCompartmentModel::POSITION_PARAMETER_k1 = 0; +const unsigned int mitk::OneTissueCompartmentModel::POSITION_PARAMETER_K1 = 0; const unsigned int mitk::OneTissueCompartmentModel::POSITION_PARAMETER_k2 = 1; const unsigned int mitk::OneTissueCompartmentModel::NUMBER_OF_PARAMETERS = 2; +const unsigned int mitk::OneTissueCompartmentModel::NUMBER_OF_DERIVED_PARAMETERS = 0; + +const std::string mitk::OneTissueCompartmentModel::MODEL_TYPE = "Dynamic.PET"; + std::string mitk::OneTissueCompartmentModel::GetModelDisplayName() const { return MODEL_DISPLAY_NAME; }; std::string mitk::OneTissueCompartmentModel::GetModelType() const { - return "Dynamic.PET"; + return MODEL_TYPE; }; mitk::OneTissueCompartmentModel::OneTissueCompartmentModel() { } mitk::OneTissueCompartmentModel::~OneTissueCompartmentModel() { } mitk::OneTissueCompartmentModel::ParameterNamesType mitk::OneTissueCompartmentModel::GetParameterNames() const { ParameterNamesType result; - result.push_back(NAME_PARAMETER_k1); + result.push_back(NAME_PARAMETER_K1); result.push_back(NAME_PARAMETER_k2); return result; } mitk::OneTissueCompartmentModel::ParametersSizeType mitk::OneTissueCompartmentModel::GetNumberOfParameters() const { return NUMBER_OF_PARAMETERS; } mitk::OneTissueCompartmentModel::ParamterUnitMapType mitk::OneTissueCompartmentModel::GetParameterUnits() const { ParamterUnitMapType result; - result.insert(std::make_pair(NAME_PARAMETER_k1, UNIT_PARAMETER_k1)); + result.insert(std::make_pair(NAME_PARAMETER_K1, UNIT_PARAMETER_K1)); result.insert(std::make_pair(NAME_PARAMETER_k2, UNIT_PARAMETER_k2)); return result; }; + +mitk::OneTissueCompartmentModel::ParametersSizeType +mitk::OneTissueCompartmentModel::GetNumberOfDerivedParameters() const +{ + return NUMBER_OF_DERIVED_PARAMETERS; +}; + mitk::OneTissueCompartmentModel::ModelResultType mitk::OneTissueCompartmentModel::ComputeModelfunction( const ParametersType& parameters) const { if (this->m_TimeGrid.GetSize() == 0) { itkExceptionMacro("No Time Grid Set! Cannot Calculate Signal"); } AterialInputFunctionType aterialInputFunction; aterialInputFunction = GetAterialInputFunction(this->m_TimeGrid); unsigned int timeSteps = this->m_TimeGrid.GetSize(); //Model Parameters - double K1 = (double) parameters[POSITION_PARAMETER_k1] / 60.0; + double K1 = (double) parameters[POSITION_PARAMETER_K1] / 60.0; double k2 = (double) parameters[POSITION_PARAMETER_k2] / 60.0; mitk::ModelBase::ModelResultType convolution = mitk::convoluteAIFWithExponential(this->m_TimeGrid, aterialInputFunction, k2); //Signal that will be returned by ComputeModelFunction mitk::ModelBase::ModelResultType signal(timeSteps); signal.fill(0.0); mitk::ModelBase::ModelResultType::iterator signalPos = signal.begin(); for (mitk::ModelBase::ModelResultType::const_iterator res = convolution.begin(); res != convolution.end(); ++res, ++signalPos) { *signalPos = K1 * (*res); } return signal; } itk::LightObject::Pointer mitk::OneTissueCompartmentModel::InternalClone() const { OneTissueCompartmentModel::Pointer newClone = OneTissueCompartmentModel::New(); newClone->SetTimeGrid(this->m_TimeGrid); return newClone.GetPointer(); }; void mitk::OneTissueCompartmentModel::PrintSelf(std::ostream& os, ::itk::Indent indent) const { Superclass::PrintSelf(os, indent); }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelFactory.cpp b/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelFactory.cpp index b9c28d3295..5a2b2c9d1e 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelFactory.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelFactory.cpp @@ -1,46 +1,46 @@ /*============================================================================ 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 "mitkOneTissueCompartmentModelFactory.h" #include #include #include mitk::ConstraintCheckerBase::Pointer mitk::OneTissueCompartmentModelFactory::CreateDefaultConstraints() const { SimpleBarrierConstraintChecker::Pointer constraints = SimpleBarrierConstraintChecker::New(); - constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_k1, 0.0); + constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_K1, 0.0); constraints->SetLowerBarrier(ModelType::POSITION_PARAMETER_k2, 0.0); - constraints->SetUpperBarrier (ModelType::POSITION_PARAMETER_k1, 1.0); + constraints->SetUpperBarrier (ModelType::POSITION_PARAMETER_K1, 1.0); constraints->SetUpperBarrier(ModelType::POSITION_PARAMETER_k2, 1.0); return constraints.GetPointer(); }; mitk::ModelParameterizerBase::ParametersType mitk::OneTissueCompartmentModelFactory::GetDefaultInitialParameterization() const { return OneTissueCompartmentModelParameterizer::New()->GetDefaultInitialParameterization(); }; mitk::OneTissueCompartmentModelFactory::OneTissueCompartmentModelFactory() { }; mitk::OneTissueCompartmentModelFactory::~OneTissueCompartmentModelFactory() { }; diff --git a/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelParameterizer.cpp b/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelParameterizer.cpp index 017db227a0..1dc058f326 100644 --- a/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelParameterizer.cpp +++ b/Modules/Pharmacokinetics/src/Models/mitkOneTissueCompartmentModelParameterizer.cpp @@ -1,32 +1,32 @@ /*============================================================================ 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 "mitkOneTissueCompartmentModelParameterizer.h" mitk::OneTissueCompartmentModelParameterizer::ParametersType mitk::OneTissueCompartmentModelParameterizer::GetDefaultInitialParameterization() const { ParametersType initialParameters; initialParameters.SetSize(2); - initialParameters[mitk::OneTissueCompartmentModel::POSITION_PARAMETER_k1] = 0.5; + initialParameters[mitk::OneTissueCompartmentModel::POSITION_PARAMETER_K1] = 0.5; initialParameters[mitk::OneTissueCompartmentModel::POSITION_PARAMETER_k2] = 0.5; return initialParameters; }; mitk::OneTissueCompartmentModelParameterizer::OneTissueCompartmentModelParameterizer() { }; mitk::OneTissueCompartmentModelParameterizer::~OneTissueCompartmentModelParameterizer() { }; 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 9a250cb94a..3bdf80080f 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 +1,1000 @@ /*============================================================================ 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 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 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 */ 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)); + 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 independend 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) + if(pos->first == mitk::OneTissueCompartmentModel::NAME_PARAMETER_K1) { - generator->SetParameterInputImage(mitk::OneTissueCompartmentModel::POSITION_PARAMETER_k1, pos->second); + 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(); }