diff --git a/Modules/ModelFit/src/Common/mitkMaskedDynamicImageStatisticsGenerator.cpp b/Modules/ModelFit/src/Common/mitkMaskedDynamicImageStatisticsGenerator.cpp index 60b95e0177..5fc4936c1c 100644 --- a/Modules/ModelFit/src/Common/mitkMaskedDynamicImageStatisticsGenerator.cpp +++ b/Modules/ModelFit/src/Common/mitkMaskedDynamicImageStatisticsGenerator.cpp @@ -1,197 +1,197 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "mitkMaskedDynamicImageStatisticsGenerator.h" #include "mitkImageTimeSelector.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "itkMaskedNaryStatisticsImageFilter.h" mitk::MaskedDynamicImageStatisticsGenerator::MaskedDynamicImageStatisticsGenerator() { m_Mask = NULL; m_DynamicImage = NULL; }; mitk::MaskedDynamicImageStatisticsGenerator::~MaskedDynamicImageStatisticsGenerator(){}; const mitk::MaskedDynamicImageStatisticsGenerator::ResultType& mitk::MaskedDynamicImageStatisticsGenerator::GetMaximum() { if(this->HasOutdatedResults()) { CheckValidInputs(); Generate(); } return m_Maximum; }; const mitk::MaskedDynamicImageStatisticsGenerator::ResultType& mitk::MaskedDynamicImageStatisticsGenerator::GetMinimum() { if(this->HasOutdatedResults()) { CheckValidInputs(); Generate(); } return m_Minimum; }; const mitk::MaskedDynamicImageStatisticsGenerator::ResultType& mitk::MaskedDynamicImageStatisticsGenerator::GetMean() { if(this->HasOutdatedResults()) { CheckValidInputs(); Generate(); } return m_Mean; }; const mitk::MaskedDynamicImageStatisticsGenerator::ResultType& mitk::MaskedDynamicImageStatisticsGenerator::GetSigma() { if(this->HasOutdatedResults()) { CheckValidInputs(); Generate(); } return m_Sigma; }; const mitk::MaskedDynamicImageStatisticsGenerator::ResultType& mitk::MaskedDynamicImageStatisticsGenerator::GetVariance() { if(this->HasOutdatedResults()) { CheckValidInputs(); Generate(); } return m_Variance; }; const mitk::MaskedDynamicImageStatisticsGenerator::ResultType& mitk::MaskedDynamicImageStatisticsGenerator::GetSum() { if(this->HasOutdatedResults()) { CheckValidInputs(); Generate(); } return m_Sum; }; template void mitk::MaskedDynamicImageStatisticsGenerator::DoCalculateStatistics(const itk::Image* /*image*/) { typedef itk::Image InputFrameImageType; typedef itk::MaskedNaryStatisticsImageFilter FilterType; typename FilterType::Pointer statFilter = FilterType::New(); //add the time frames to the fit filter unsigned int timeSteps = this->m_DynamicImage->GetTimeSteps(); std::vector frameCache; + mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); + imageTimeSelector->SetInput(this->m_DynamicImage); for (unsigned int i = 0; i < timeSteps; ++i) { typename InputFrameImageType::Pointer frameImage; - mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); - imageTimeSelector->SetInput(this->m_DynamicImage); imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); Image::Pointer frameMITKImage = imageTimeSelector->GetOutput(); frameCache.push_back(frameMITKImage); mitk::CastToItkImage(frameMITKImage, frameImage); statFilter->SetInput(i,frameImage); } if (this->m_InternalMask.IsNotNull()) { statFilter->SetMask(this->m_InternalMask); } statFilter->Update(); m_Maximum.SetSize(timeSteps); m_Minimum.SetSize(timeSteps); m_Mean.SetSize(timeSteps); m_Sigma.SetSize(timeSteps); m_Variance.SetSize(timeSteps); m_Sum.SetSize(timeSteps); for (unsigned int i = 0; i < timeSteps; ++i) { m_Maximum.SetElement(i,statFilter->GetMaximum()[i]); m_Minimum.SetElement(i,statFilter->GetMinimum()[i]); m_Mean.SetElement(i,statFilter->GetMean()[i]); m_Sigma.SetElement(i,statFilter->GetSigma()[i]); m_Variance.SetElement(i,statFilter->GetVariance()[i]); m_Sum.SetElement(i,statFilter->GetSum()[i]); } this->m_GenerationTimeStamp.Modified(); } void mitk::MaskedDynamicImageStatisticsGenerator::Generate() { if(this->m_Mask.IsNotNull()) { InternalMaskType::Pointer castedMask; CastToItkImage(m_Mask, castedMask); if (castedMask.IsNull()) { mitkThrow() << "Dynamic cast of mask went wrong. Internal Mask is NULL. Image statistics cannot be generated."; } this->m_InternalMask = castedMask; } else { this->m_InternalMask = NULL; } AccessFixedDimensionByItk(m_DynamicImage, mitk::MaskedDynamicImageStatisticsGenerator::DoCalculateStatistics, 4); } void mitk::MaskedDynamicImageStatisticsGenerator::CheckValidInputs() const { if (m_DynamicImage.IsNull()) { mitkThrow() << "Cannot generate statistics. Input dynamic image is not set."; } } bool mitk::MaskedDynamicImageStatisticsGenerator::HasOutdatedResults() const { bool result = this->GetMTime() > this->m_GenerationTimeStamp; if (m_DynamicImage.IsNotNull()) { if (m_DynamicImage->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } if (m_Mask.IsNotNull()) { if (m_Mask->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } return result; }; diff --git a/Modules/ModelFit/src/Common/mitkPixelBasedParameterFitImageGenerator.cpp b/Modules/ModelFit/src/Common/mitkPixelBasedParameterFitImageGenerator.cpp index a2046d8e69..e907d2934e 100644 --- a/Modules/ModelFit/src/Common/mitkPixelBasedParameterFitImageGenerator.cpp +++ b/Modules/ModelFit/src/Common/mitkPixelBasedParameterFitImageGenerator.cpp @@ -1,279 +1,279 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "itkCommand.h" #include "itkMultiOutputNaryFunctorImageFilter.h" #include "mitkPixelBasedParameterFitImageGenerator.h" #include "mitkImageTimeSelector.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkModelFitFunctorPolicy.h" #include "mitkExtractTimeGrid.h" void mitk::PixelBasedParameterFitImageGenerator:: onFitProgressEvent(::itk::Object* caller, const ::itk::EventObject& /*eventObject*/) { this->InvokeEvent(::itk::ProgressEvent()); auto* process = dynamic_cast(caller); if (process) { this->m_Progress = process->GetProgress(); } }; template void mitk::PixelBasedParameterFitImageGenerator::DoPrepareMask(itk::Image* image) { m_InternalMask = dynamic_cast(image); if (m_InternalMask.IsNull()) { MITK_INFO << "Parameter Fit Generator. Need to cast mask for parameter fit."; using InputImageType = itk::Image; using CastFilterType = itk::CastImageFilter< InputImageType, InternalMaskType >; typename CastFilterType::Pointer spImageCaster = CastFilterType::New(); spImageCaster->SetInput(image); m_InternalMask = spImageCaster->GetOutput(); spImageCaster->Update(); } } template mitk::PixelBasedParameterFitImageGenerator::ParameterImageMapType StoreResultImages( mitk::ModelFitFunctorBase::ParameterNamesType ¶mNames, itk::ImageSource* source, mitk::ModelFitFunctorBase::ParameterNamesType::size_type startPos, mitk::ModelFitFunctorBase::ParameterNamesType::size_type& endPos ) { mitk::PixelBasedParameterFitImageGenerator::ParameterImageMapType result; for (mitk::ModelFitFunctorBase::ParameterNamesType::size_type j = 0; j < paramNames.size(); ++j) { if (source->GetNumberOfOutputs() < startPos+j) { mitkThrow() << "Error while generating fitted parameter images. Number of sources is too low and does not match expected parameter number. Output size: "<< source->GetNumberOfOutputs()<<"; number of param names: "<GetOutput(startPos+j); mitk::CastToMitkImage(outputImg, paramImage); result.insert(std::make_pair(paramNames[j],paramImage)); } endPos = startPos + paramNames.size(); return result; } template void mitk::PixelBasedParameterFitImageGenerator::DoParameterFit(itk::Image* /*image*/) { using InputFrameImageType = itk::Image; using ParameterImageType = itk::Image; using FitFilterType = itk::MultiOutputNaryFunctorImageFilter; typename FitFilterType::Pointer fitFilter = FitFilterType::New(); typename ::itk::MemberCommand::Pointer spProgressCommand = ::itk::MemberCommand::New(); spProgressCommand->SetCallbackFunction(this, &Self::onFitProgressEvent); fitFilter->AddObserver(::itk::ProgressEvent(), spProgressCommand); //add the time frames to the fit filter + mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); + imageTimeSelector->SetInput(this->m_DynamicImage); std::vector frameCache; for (unsigned int i = 0; i < this->m_DynamicImage->GetTimeSteps(); ++i) { typename InputFrameImageType::Pointer frameImage; - mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); - imageTimeSelector->SetInput(this->m_DynamicImage); imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); Image::Pointer frameMITKImage = imageTimeSelector->GetOutput(); frameCache.push_back(frameMITKImage); mitk::CastToItkImage(frameMITKImage, frameImage); fitFilter->SetInput(i,frameImage); } ModelBaseType::TimeGridType timeGrid = ExtractTimeGrid(m_DynamicImage); if (m_TimeGridByParameterizer) { if (timeGrid.GetSize() != m_ModelParameterizer->GetDefaultTimeGrid().GetSize()) { mitkThrow() << "Cannot do fitting. Filter is set to use default time grid of the parameterizer, but grid size does not match the number of input image frames. Grid size: " << m_ModelParameterizer->GetDefaultTimeGrid().GetSize() << "; frame count: " << timeGrid.GetSize(); } } else { this->m_ModelParameterizer->SetDefaultTimeGrid(timeGrid); } ModelFitFunctorPolicy functor; functor.SetModelFitFunctor(this->m_FitFunctor); functor.SetModelParameterizer(this->m_ModelParameterizer); fitFilter->SetFunctor(functor); if (this->m_InternalMask.IsNotNull()) { fitFilter->SetMask(this->m_InternalMask); } //generate the fits fitFilter->Update(); //convert the outputs into mitk images and fill the parameter image map ModelBaseType::Pointer refModel = this->m_ModelParameterizer->GenerateParameterizedModel(); ModelFitFunctorBase::ParameterNamesType paramNames = refModel->GetParameterNames(); ModelFitFunctorBase::ParameterNamesType derivedParamNames = refModel->GetDerivedParameterNames(); ModelFitFunctorBase::ParameterNamesType criterionNames = this->m_FitFunctor->GetCriterionNames(); ModelFitFunctorBase::ParameterNamesType evaluationParamNames = this->m_FitFunctor->GetEvaluationParameterNames(); ModelFitFunctorBase::ParameterNamesType debugParamNames = this->m_FitFunctor->GetDebugParameterNames(); if (fitFilter->GetNumberOfOutputs() != (paramNames.size() + derivedParamNames.size() + criterionNames.size() + evaluationParamNames.size() + debugParamNames.size())) { mitkThrow() << "Error while generating fitted parameter images. Fit filter output size does not match expected parameter number. Output size: "<< fitFilter->GetNumberOfOutputs(); } ModelFitFunctorBase::ParameterNamesType::size_type resultPos = 0; this->m_TempResultMap = StoreResultImages(paramNames,fitFilter,resultPos, resultPos); this->m_TempDerivedResultMap = StoreResultImages(derivedParamNames,fitFilter,resultPos, resultPos); this->m_TempCriterionResultMap = StoreResultImages(criterionNames,fitFilter,resultPos, resultPos); this->m_TempEvaluationResultMap = StoreResultImages(evaluationParamNames,fitFilter,resultPos, resultPos); //also add debug params (if generated) to the evaluation result map mitk::PixelBasedParameterFitImageGenerator::ParameterImageMapType debugMap = StoreResultImages(debugParamNames, fitFilter, resultPos, resultPos); this->m_TempEvaluationResultMap.insert(debugMap.begin(), debugMap.end()); } bool mitk::PixelBasedParameterFitImageGenerator::HasOutdatedResult() const { bool result = Superclass::HasOutdatedResult(); if (m_ModelParameterizer.IsNotNull()) { if (m_ModelParameterizer->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } if (m_FitFunctor.IsNotNull()) { if (m_FitFunctor->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } if (m_DynamicImage.IsNotNull()) { if (m_DynamicImage->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } if (m_Mask.IsNotNull()) { if (m_Mask->GetMTime() > this->m_GenerationTimeStamp) { result = true; } } return result; }; void mitk::PixelBasedParameterFitImageGenerator::CheckValidInputs() const { Superclass::CheckValidInputs(); if (m_DynamicImage.IsNull()) { mitkThrow() << "Cannot generate fitted parameter images. Input dynamic image is not set."; } }; void mitk::PixelBasedParameterFitImageGenerator::DoFitAndGetResults(ParameterImageMapType& parameterImages, ParameterImageMapType& derivedParameterImages, ParameterImageMapType& criterionImages, ParameterImageMapType& evaluationParameterImages) { this->m_Progress = 0; if(this->m_Mask.IsNotNull()) { AccessFixedDimensionByItk(m_Mask, mitk::PixelBasedParameterFitImageGenerator::DoPrepareMask, 3); } else { this->m_InternalMask = nullptr; } AccessFixedDimensionByItk(m_DynamicImage, mitk::PixelBasedParameterFitImageGenerator::DoParameterFit, 4); parameterImages = this->m_TempResultMap; derivedParameterImages = this->m_TempDerivedResultMap; criterionImages = this->m_TempCriterionResultMap; evaluationParameterImages = this->m_TempEvaluationResultMap; }; double mitk::PixelBasedParameterFitImageGenerator::GetProgress() const { return m_Progress; }; mitk::PixelBasedParameterFitImageGenerator::ParameterNamesType mitk::PixelBasedParameterFitImageGenerator::GetParameterNames() const { ParameterizerType::ModelBasePointer parameterizedModel = m_ModelParameterizer->GenerateParameterizedModel(); return parameterizedModel->GetParameterNames(); } mitk::PixelBasedParameterFitImageGenerator::ParameterNamesType mitk::PixelBasedParameterFitImageGenerator::GetDerivedParameterNames() const { ParameterizerType::ModelBasePointer parameterizedModel = m_ModelParameterizer->GenerateParameterizedModel(); return parameterizedModel->GetDerivedParameterNames(); } mitk::PixelBasedParameterFitImageGenerator::ParameterNamesType mitk::PixelBasedParameterFitImageGenerator::GetCriterionNames() const { return this->m_FitFunctor->GetCriterionNames(); } mitk::PixelBasedParameterFitImageGenerator::ParameterNamesType mitk::PixelBasedParameterFitImageGenerator::GetEvaluationParameterNames() const { auto evals = this->m_FitFunctor->GetEvaluationParameterNames(); auto debugs = this->m_FitFunctor->GetDebugParameterNames(); evals.insert(evals.end(), debugs.begin(), debugs.end()); return evals; } diff --git a/Modules/ModelFitUI/Qmitk/QmitkParameterFitBackgroundJob.cpp b/Modules/ModelFitUI/Qmitk/QmitkParameterFitBackgroundJob.cpp index 5f77a32368..2f25f4aeef 100644 --- a/Modules/ModelFitUI/Qmitk/QmitkParameterFitBackgroundJob.cpp +++ b/Modules/ModelFitUI/Qmitk/QmitkParameterFitBackgroundJob.cpp @@ -1,109 +1,121 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Software Development for Integrated Diagnostic and Therapy. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #include "QmitkParameterFitBackgroundJob.h" #include "mitkModelFitInfo.h" void ParameterFitBackgroundJob::OnFitEvent(::itk::Object* caller, const itk::EventObject & event) { itk::ProgressEvent progressEvent; itk::InitializeEvent initEvent; itk::StartEvent startEvent; itk::EndEvent endEvent; if (progressEvent.CheckEvent(&event)) { mitk::ParameterFitImageGeneratorBase* castedReporter = dynamic_cast(caller); emit JobProgress(castedReporter->GetProgress()); } else if (initEvent.CheckEvent(&event)) { emit JobStatusChanged(QString("Initializing parameter fit generator")); } else if (startEvent.CheckEvent(&event)) { emit JobStatusChanged(QString("Started fitting process.")); } else if (endEvent.CheckEvent(&event)) { emit JobStatusChanged(QString("Finished fitting process.")); } } ParameterFitBackgroundJob:: -ParameterFitBackgroundJob(mitk::ParameterFitImageGeneratorBase* generator, const mitk::modelFit::ModelFitInfo* fitInfo, mitk::DataNode* parentNode) +ParameterFitBackgroundJob(mitk::ParameterFitImageGeneratorBase* generator, const mitk::modelFit::ModelFitInfo* fitInfo, mitk::DataNode* parentNode) : ParameterFitBackgroundJob(generator, fitInfo, parentNode, {}) +{ +}; + +ParameterFitBackgroundJob:: +ParameterFitBackgroundJob(mitk::ParameterFitImageGeneratorBase* generator, const mitk::modelFit::ModelFitInfo* fitInfo, mitk::DataNode* parentNode, mitk::modelFit::ModelFitResultNodeVectorType additionalRelevantNodes) { if (!generator) { mitkThrow() << "Cannot create parameter fit background job. Passed fit generator is NULL."; } if (!fitInfo) { mitkThrow() << "Cannot create parameter fit background job. Passed model traits interface is NULL."; } m_Generator = generator; m_ModelFitInfo = fitInfo; m_ParentNode = parentNode; + m_AdditionalRelevantNodes = additionalRelevantNodes; m_spCommand = ::itk::MemberCommand::New(); m_spCommand->SetCallbackFunction(this, &ParameterFitBackgroundJob::OnFitEvent); m_ObserverID = m_Generator->AddObserver(::itk::AnyEvent(), m_spCommand); }; mitk::DataNode* ParameterFitBackgroundJob:: GetParentNode() const { return m_ParentNode; }; +mitk::modelFit::ModelFitResultNodeVectorType ParameterFitBackgroundJob::GetAdditionalRelevantNodes() const +{ + return m_AdditionalRelevantNodes; +}; + + ParameterFitBackgroundJob:: ~ParameterFitBackgroundJob() { m_Generator->RemoveObserver(m_ObserverID); }; void ParameterFitBackgroundJob:: run() { try { emit JobStatusChanged(QString("Started fit session.Generate UID: ")+QString::fromStdString(m_ModelFitInfo->uid)); m_Generator->Generate(); emit JobStatusChanged(QString("Generate result nodes.")); m_Results = mitk::modelFit::CreateResultNodeMap(m_Generator->GetParameterImages(), m_Generator->GetDerivedParameterImages(), m_Generator->GetCriterionImages(), m_Generator->GetEvaluationParameterImages(), m_ModelFitInfo); emit ResultsAreAvailable(m_Results, this); } catch (::std::exception& e) { emit Error(QString("Error while fitting data. Details: ")+QString::fromLatin1(e.what())); } catch (...) { emit Error(QString("Unkown error when fitting the data.")); } emit Finished(); }; diff --git a/Modules/ModelFitUI/Qmitk/QmitkParameterFitBackgroundJob.h b/Modules/ModelFitUI/Qmitk/QmitkParameterFitBackgroundJob.h index 0cb5b505d3..17dda9b0fe 100644 --- a/Modules/ModelFitUI/Qmitk/QmitkParameterFitBackgroundJob.h +++ b/Modules/ModelFitUI/Qmitk/QmitkParameterFitBackgroundJob.h @@ -1,78 +1,84 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Software Development for Integrated Diagnostic and Therapy. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef __QMITK_PARAMETER_FIT_BACKGROUND_JOB_H #define __QMITK_PARAMETER_FIT_BACKGROUND_JOB_H //QT #include #include //MITK #include #include #include #include // ITK #include #include "MitkModelFitUIExports.h" class MITKMODELFITUI_EXPORT ParameterFitBackgroundJob : public QObject, public QRunnable { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: ParameterFitBackgroundJob(mitk::ParameterFitImageGeneratorBase* generator, const mitk::modelFit::ModelFitInfo* fitInfo, mitk::DataNode* parentNode = NULL); - ~ParameterFitBackgroundJob(); + /** */ + ParameterFitBackgroundJob(mitk::ParameterFitImageGeneratorBase* generator, const mitk::modelFit::ModelFitInfo* fitInfo, mitk::DataNode* parentNode, mitk::modelFit::ModelFitResultNodeVectorType additionalRelevantNodes); + + ~ParameterFitBackgroundJob(); void run(); /**Returns the node (if defined), that is the parent object for the results of the job. May be null.*/ mitk::DataNode* GetParentNode() const; + mitk::modelFit::ModelFitResultNodeVectorType GetAdditionalRelevantNodes() const; + signals: void Finished(); void Error(QString err); void ResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType resultMap, const ParameterFitBackgroundJob* pJob); void JobProgress(double progress); void JobStatusChanged(QString info); protected: //Inputs mitk::ParameterFitImageGeneratorBase::Pointer m_Generator; mitk::modelFit::ModelFitInfo::ConstPointer m_ModelFitInfo; mitk::DataNode::Pointer m_ParentNode; + mitk::modelFit::ModelFitResultNodeVectorType m_AdditionalRelevantNodes; // Results mitk::modelFit::ModelFitResultNodeVectorType m_Results; ::itk::MemberCommand::Pointer m_spCommand; unsigned long m_ObserverID; void OnFitEvent(::itk::Object *, const itk::EventObject &event); }; #endif diff --git a/Modules/Pharmacokinetics/include/mitkConcentrationCurveGenerator.h b/Modules/Pharmacokinetics/include/mitkConcentrationCurveGenerator.h index 2f44a4b1a3..a10283ffe5 100644 --- a/Modules/Pharmacokinetics/include/mitkConcentrationCurveGenerator.h +++ b/Modules/Pharmacokinetics/include/mitkConcentrationCurveGenerator.h @@ -1,146 +1,146 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef CONCENTRATIONCURVEGENERATOR_H #define CONCENTRATIONCURVEGENERATOR_H #include #include #include "mitkConvertToConcentrationAbsoluteFunctor.h" #include "mitkConvertToConcentrationRelativeFunctor.h" #include "MitkPharmacokineticsExports.h" namespace mitk { /** \class ConcentrationCurveGenerator * \brief Converts a given 4D mitk::Image with MR signal values into a 4D mitk::Image with corresponding contrast agent concentration values * * From a given 4D image, the Generator takes the 3D image of the first time point as baseline image. It then loops over all time steps, casts * the current 3D image to itk and passes it to the ConvertToconcentrationFunctor. The returned 3D image has now values of concentration type and is stored at its timepoint * in the return image. */ class MITKPHARMACOKINETICS_EXPORT ConcentrationCurveGenerator : public itk::Object { public: mitkClassMacroItkParent(ConcentrationCurveGenerator, itk::Object); itkNewMacro(Self); //typedef itk::Image ImageType; typedef itk::Image ConvertedImageType; /** Getter and Setter for 4D mitk::Image*/ - itkSetObjectMacro(DynamicImage,Image); + itkSetConstObjectMacro(DynamicImage,Image); itkGetConstObjectMacro(DynamicImage,Image); /** Parameters Relevant for conversion Calculation; Have to be Set externally (Sequence Dependend)*/ itkSetMacro(RelaxationTime, double); itkGetConstReferenceMacro(RelaxationTime, double); itkSetMacro(Relaxivity, double); itkGetConstReferenceMacro(Relaxivity, double); itkSetMacro(RecoveryTime, double); itkGetConstReferenceMacro(RecoveryTime, double); itkSetMacro(FlipAngle, double); itkGetConstReferenceMacro(FlipAngle, double); itkSetMacro(Factor, double); itkGetConstReferenceMacro(Factor, double); /** Getter and Setter for T10 Map image*/ - itkSetObjectMacro(T10Image,Image); + itkSetConstObjectMacro(T10Image,Image); itkGetConstObjectMacro(T10Image,Image); itkSetMacro(T2Factor, double); itkGetConstReferenceMacro(T2Factor, double); itkSetMacro(T2EchoTime, double); itkGetConstReferenceMacro(T2EchoTime, double); /** @brief Calls Convert and returns the 4D mitk::image in Concentration units*/ itkSetMacro(isTurboFlashSequence,bool); itkGetConstReferenceMacro(isTurboFlashSequence,bool); itkSetMacro(AbsoluteSignalEnhancement,bool); itkGetConstReferenceMacro(AbsoluteSignalEnhancement,bool); itkSetMacro(RelativeSignalEnhancement,bool); itkGetConstReferenceMacro(RelativeSignalEnhancement,bool); itkSetMacro(UsingT1Map,bool); itkGetConstReferenceMacro(UsingT1Map,bool); itkSetMacro(isT2weightedImage,bool); itkGetConstReferenceMacro(isT2weightedImage,bool); Image::Pointer GetConvertedImage(); protected: ConcentrationCurveGenerator(); ~ConcentrationCurveGenerator(); template - mitk::Image::Pointer convertToConcentration(mitk::Image::Pointer inputImage,mitk::Image::Pointer baselineImage); + mitk::Image::Pointer convertToConcentration(const mitk::Image* inputImage, const mitk::Image* baselineImage); /** Calls ConvertToconcentrationFunctor for passed 3D itk::image*/ -mitk::Image::Pointer ConvertSignalToConcentrationCurve(mitk::Image::Pointer inputImage, mitk::Image::Pointer baselineImage); + mitk::Image::Pointer ConvertSignalToConcentrationCurve(const mitk::Image* inputImage, const mitk::Image* baselineImage); /** @brief Takes the 3D image of the first timepoint to set as baseline image*/ void PrepareBaselineImage(); /** @brief loops over all timepoints, casts the current timepoint 3D mitk::image to itk and passes it to ConvertSignalToConcentrationCurve */ virtual void Convert(); private: - Image::Pointer m_DynamicImage; - Image::Pointer m_BaselineImage; - Image::Pointer m_T10Image; + Image::ConstPointer m_DynamicImage; + Image::ConstPointer m_BaselineImage; + Image::ConstPointer m_T10Image; Image::Pointer m_ConvertedImage; bool m_isT2weightedImage; bool m_isTurboFlashSequence; bool m_AbsoluteSignalEnhancement; bool m_RelativeSignalEnhancement; bool m_UsingT1Map; double m_Factor; //=Repetition Time TR double m_RecoveryTime; //= pre-CA T1 time double m_RelaxationTime; //= contrast agent relaxivity double m_Relaxivity; double m_FlipAngle; double m_T2Factor; double m_T2EchoTime; }; } #endif // CONCENTRATIONCURVEGENERATOR_H diff --git a/Modules/Pharmacokinetics/src/Common/mitkConcentrationCurveGenerator.cpp b/Modules/Pharmacokinetics/src/Common/mitkConcentrationCurveGenerator.cpp index cc3676fbd7..8ded94876d 100644 --- a/Modules/Pharmacokinetics/src/Common/mitkConcentrationCurveGenerator.cpp +++ b/Modules/Pharmacokinetics/src/Common/mitkConcentrationCurveGenerator.cpp @@ -1,265 +1,252 @@ #include "mitkConcentrationCurveGenerator.h" #include "mitkConvertToConcentrationTurboFlashFunctor.h" #include "mitkConvertT2ConcentrationFunctor.h" #include "mitkConvertToConcentrationViaT1Functor.h" #include "mitkImageTimeSelector.h" #include "mitkImageCast.h" #include "mitkITKImageImport.h" #include "mitkModelBase.h" #include "mitkExtractTimeGrid.h" #include "mitkArbitraryTimeGeometry.h" #include "itkImageIOBase.h" #include "itkBinaryFunctorImageFilter.h" #include "itkTernaryFunctorImageFilter.h" mitk::ConcentrationCurveGenerator::ConcentrationCurveGenerator() : m_isT2weightedImage(false), m_isTurboFlashSequence(false), m_AbsoluteSignalEnhancement(false), m_RelativeSignalEnhancement(0.0), m_UsingT1Map(false), m_Factor(0.0), m_RecoveryTime(0.0), m_RelaxationTime(0.0), m_Relaxivity(0.0), m_FlipAngle(0.0), m_T2Factor(0.0), m_T2EchoTime(0.0) { } mitk::ConcentrationCurveGenerator::~ConcentrationCurveGenerator() { } mitk::Image::Pointer mitk::ConcentrationCurveGenerator::GetConvertedImage() { if(this->m_DynamicImage.IsNull()) { itkExceptionMacro( << "Dynamic Image not set!"); } else { Convert(); } return m_ConvertedImage; } void mitk::ConcentrationCurveGenerator::Convert() { mitk::Image::Pointer tempImage = mitk::Image::New(); mitk::PixelType pixeltype = mitk::MakeScalarPixelType(); tempImage->Initialize(pixeltype,*this->m_DynamicImage->GetTimeGeometry()); mitk::TimeGeometry::Pointer timeGeometry = (this->m_DynamicImage->GetTimeGeometry())->Clone(); tempImage->SetTimeGeometry(timeGeometry); PrepareBaselineImage(); mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(this->m_DynamicImage); - - for(unsigned int i = 0; i< this->m_DynamicImage->GetTimeSteps(); ++i) { imageTimeSelector->SetTimeNr(i); imageTimeSelector->UpdateLargestPossibleRegion(); mitk::Image::Pointer mitkInputImage = imageTimeSelector->GetOutput(); mitk::Image::Pointer outputImage = mitk::Image::New(); outputImage = ConvertSignalToConcentrationCurve(mitkInputImage,this->m_BaselineImage); mitk::ImageReadAccessor accessor(outputImage); tempImage->SetVolume(accessor.GetData(), i); } this->m_ConvertedImage = tempImage; } void mitk::ConcentrationCurveGenerator::PrepareBaselineImage() { mitk::ImageTimeSelector::Pointer imageTimeSelector = mitk::ImageTimeSelector::New(); imageTimeSelector->SetInput(this->m_DynamicImage); imageTimeSelector->SetTimeNr(0); imageTimeSelector->UpdateLargestPossibleRegion(); this->m_BaselineImage = imageTimeSelector->GetOutput(); } -mitk::Image::Pointer mitk::ConcentrationCurveGenerator::ConvertSignalToConcentrationCurve(mitk::Image::Pointer inputImage,mitk::Image::Pointer baselineImage) +mitk::Image::Pointer mitk::ConcentrationCurveGenerator::ConvertSignalToConcentrationCurve(const mitk::Image* inputImage, const mitk::Image* baselineImage) { - - - mitk::PixelType m_PixelType = inputImage->GetPixelType(); mitk::Image::Pointer outputImage; if(inputImage->GetPixelType().GetComponentType() != baselineImage->GetPixelType().GetComponentType()) { mitkThrow() << "Input Image and Baseline Image have different Pixel Types. Data not supported"; } if(m_PixelType.GetComponentType() == itk::ImageIOBase::USHORT) { outputImage = convertToConcentration(inputImage, baselineImage); } else if(m_PixelType.GetComponentType() == itk::ImageIOBase::UINT) { outputImage = convertToConcentration(inputImage, baselineImage); } else if(m_PixelType.GetComponentType() == itk::ImageIOBase::INT) { outputImage = convertToConcentration(inputImage, baselineImage); } else if(m_PixelType.GetComponentType() == itk::ImageIOBase::SHORT) { outputImage = convertToConcentration(inputImage, baselineImage); } - /*else if(m_PixelType.GetComponentType() == itk::ImageIOBase::ULONG) - { - outputImage = convertToConcentration(inputImage, baselineImage); - } - else if(m_PixelType.GetComponentType() == itk::ImageIOBase::LONG) - { - outputImage = convertToConcentration(inputImage, baselineImage); - }*/ else if(m_PixelType.GetComponentType() == itk::ImageIOBase::DOUBLE) { outputImage = convertToConcentration(inputImage, baselineImage); } else if(m_PixelType.GetComponentType() == itk::ImageIOBase::FLOAT) { outputImage = convertToConcentration(inputImage, baselineImage); } else { mitkThrow() << "PixelType is "< -mitk::Image::Pointer mitk::ConcentrationCurveGenerator::convertToConcentration(mitk::Image::Pointer inputImage,mitk::Image::Pointer baselineImage) +mitk::Image::Pointer mitk::ConcentrationCurveGenerator::convertToConcentration(const mitk::Image* inputImage, const mitk::Image* baselineImage) { typedef itk::Image InputImageType; typename InputImageType::Pointer itkInputImage = InputImageType::New(); typename InputImageType::Pointer itkBaselineImage = InputImageType::New(); mitk::CastToItkImage(inputImage, itkInputImage ); mitk::CastToItkImage(baselineImage, itkBaselineImage ); mitk::Image::Pointer outputImage; if(this->m_isT2weightedImage) { typedef mitk::ConvertT2ConcentrationFunctor ConversionFunctorT2Type; typedef itk::BinaryFunctorImageFilter FilterT2Type; ConversionFunctorT2Type ConversionT2Functor; ConversionT2Functor.initialize(this->m_T2Factor, this->m_T2EchoTime); typename FilterT2Type::Pointer ConversionT2Filter = FilterT2Type::New(); ConversionT2Filter->SetFunctor(ConversionT2Functor); ConversionT2Filter->SetInput1(itkInputImage); ConversionT2Filter->SetInput2(itkBaselineImage); ConversionT2Filter->Update(); outputImage = mitk::ImportItkImage(ConversionT2Filter->GetOutput())->Clone(); } else { if(this->m_isTurboFlashSequence) { typedef mitk::ConvertToConcentrationTurboFlashFunctor ConversionFunctorTurboFlashType; typedef itk::BinaryFunctorImageFilter FilterTurboFlashType; ConversionFunctorTurboFlashType ConversionTurboFlashFunctor; ConversionTurboFlashFunctor.initialize(this->m_RelaxationTime, this->m_Relaxivity, this->m_RecoveryTime); typename FilterTurboFlashType::Pointer ConversionTurboFlashFilter = FilterTurboFlashType::New(); ConversionTurboFlashFilter->SetFunctor(ConversionTurboFlashFunctor); ConversionTurboFlashFilter->SetInput1(itkInputImage); ConversionTurboFlashFilter->SetInput2(itkBaselineImage); ConversionTurboFlashFilter->Update(); outputImage = mitk::ImportItkImage(ConversionTurboFlashFilter->GetOutput())->Clone(); } else if(this->m_UsingT1Map) { typename InputImageType::Pointer itkT10Image = InputImageType::New(); mitk::CastToItkImage(m_T10Image, itkT10Image); typedef mitk::ConvertToConcentrationViaT1CalcFunctor ConvertToConcentrationViaT1CalcFunctorType; typedef itk::TernaryFunctorImageFilter FilterT1MapType; ConvertToConcentrationViaT1CalcFunctorType ConversionT1MapFunctor; ConversionT1MapFunctor.initialize(this->m_Relaxivity, this->m_RecoveryTime, this->m_FlipAngle); typename FilterT1MapType::Pointer ConversionT1MapFilter = FilterT1MapType::New(); ConversionT1MapFilter->SetFunctor(ConversionT1MapFunctor); ConversionT1MapFilter->SetInput1(itkInputImage); ConversionT1MapFilter->SetInput2(itkBaselineImage); ConversionT1MapFilter->SetInput3(itkT10Image); ConversionT1MapFilter->Update(); outputImage = mitk::ImportItkImage(ConversionT1MapFilter->GetOutput())->Clone(); } else if(this->m_AbsoluteSignalEnhancement) { typedef mitk::ConvertToConcentrationAbsoluteFunctor ConversionFunctorAbsoluteType; typedef itk::BinaryFunctorImageFilter FilterAbsoluteType; ConversionFunctorAbsoluteType ConversionAbsoluteFunctor; ConversionAbsoluteFunctor.initialize(this->m_Factor); typename FilterAbsoluteType::Pointer ConversionAbsoluteFilter = FilterAbsoluteType::New(); ConversionAbsoluteFilter->SetFunctor(ConversionAbsoluteFunctor); ConversionAbsoluteFilter->SetInput1(itkInputImage); ConversionAbsoluteFilter->SetInput2(itkBaselineImage); ConversionAbsoluteFilter->Update(); outputImage = mitk::ImportItkImage(ConversionAbsoluteFilter->GetOutput())->Clone(); } else if(this->m_RelativeSignalEnhancement) { typedef mitk::ConvertToConcentrationRelativeFunctor ConversionFunctorRelativeType; typedef itk::BinaryFunctorImageFilter FilterRelativeType; ConversionFunctorRelativeType ConversionRelativeFunctor; ConversionRelativeFunctor.initialize(this->m_Factor); typename FilterRelativeType::Pointer ConversionRelativeFilter = FilterRelativeType::New(); ConversionRelativeFilter->SetFunctor(ConversionRelativeFunctor); ConversionRelativeFilter->SetInput1(itkInputImage); ConversionRelativeFilter->SetInput2(itkBaselineImage); ConversionRelativeFilter->Update(); outputImage = mitk::ImportItkImage(ConversionRelativeFilter->GetOutput())->Clone(); } } return outputImage; } 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 e197e697c0..649a5d8e92 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 @@ -1,1400 +1,1402 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #include "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 #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); 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.groupBoxTurboFlash->hide(); m_Controls.radioButtonNoConversion->setChecked(true); m_Controls.factorSpinBox->setEnabled(false); m_Controls.groupBox_viaT1Map->hide(); 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.factorSpinBox, SIGNAL(valueChanged(double)), 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()) != NULL; bool isToftsFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL || dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; bool is2CXMFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL || dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; bool isNum2CXMFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; m_Controls.groupAIF->setVisible(isToftsFactory || is2CXMFactory); m_Controls.groupDescBrix->setVisible(isDescBrixFactory); m_Controls.groupNum2CXM->setVisible(isNum2CXMFactory); m_Controls.groupConcentration->setVisible(isToftsFactory || is2CXMFactory); 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()); } void MRPerfusionView::OnModellSet(int index) { m_selectedModelFactory = NULL; 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 = NULL; mitk::modelFit::ModelFitInfo::Pointer fitSession = NULL; bool isDescBrixFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; bool is3LinearFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; bool isExtToftsFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; bool isStanToftsFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; bool is2CXMFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; bool isNum2CXMFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; if (isDescBrixFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { GenerateDescriptiveBrixModel_PixelBased(fitSession, generator); } else { GenerateDescriptiveBrixModel_ROIBased(fitSession, generator); } } else if (is3LinearFactory) { if (this->m_Controls.radioPixelBased->isChecked()) { Generate3StepLinearModelFit_PixelBased(fitSession, generator); } else { Generate3StepLinearModelFit_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 = NULL; m_selectedMask = NULL; 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 = NULL; this->m_selectedImage = NULL; 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(); 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()) != NULL; bool is3LinearFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; bool isToftsFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL|| dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; bool is2CXMFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; bool isNum2CXMFactory = dynamic_cast (m_selectedModelFactory.GetPointer()) != NULL; 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) { 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); } else if (this->m_Controls.radioButton_absoluteEnhancement->isChecked() || this->m_Controls.radioButton_relativeEnchancement->isChecked()) { ok = ok && (m_Controls.factorSpinBox->value() > 0); } 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()); } else if (this->m_Controls.radioButtonNoConversion->isChecked()) { ok = ok; } 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); } else if (this->m_Controls.radioButton_absoluteEnhancement->isChecked() || this->m_Controls.radioButton_relativeEnchancement->isChecked()) { ok = ok && (m_Controls.factorSpinBox->value() > 0); } 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()); } else if (this->m_Controls.radioButtonNoConversion->isChecked()) { ok = ok; } 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; } 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& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { mitk::PixelBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::PixelBasedParameterFitImageGenerator::New(); mitk::ThreeStepLinearModelParameterizer::Pointer modelParameterizer = mitk::ThreeStepLinearModelParameterizer::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& modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer& generator) { if (m_selectedMask.IsNull()) { return; } mitk::ROIBasedParameterFitImageGenerator::Pointer fitGenerator = mitk::ROIBasedParameterFitImageGenerator::New(); mitk::ThreeStepLinearModelParameterizer::Pointer modelParameterizer = mitk::ThreeStepLinearModelParameterizer::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(); - mitk::Image::Pointer concentrationImage; - mitk::DataNode::Pointer concentrationNode; - GetConcentrationImage(concentrationImage, concentrationNode, false); + 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(concentrationImage); + fitGenerator->SetDynamicImage(this->m_inputImage); fitGenerator->SetFitFunctor(fitFunctor); generator = fitGenerator.GetPointer(); //Create model info modelFitInfo = mitk::modelFit::CreateFitInfoFromModelParameterizer(modelParameterizer, - concentrationNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), this->GetFitName(), + 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(); - mitk::Image::Pointer concentrationImage; - mitk::DataNode::Pointer concentrationNode; - GetConcentrationImage(concentrationImage, concentrationNode, false); + 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(concentrationImage); + 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(concentrationImage)); + 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, - concentrationNode->GetData(), mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), this->GetFitName(), + 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); + 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) +MRPerfusionView::MRPerfusionView() : m_FittingInProgress(false), m_HasGeneratedNewInput(false), m_HasGeneratedNewInputAIF(false) { m_selectedImage = NULL; m_selectedMask = NULL; mitk::ModelFactoryBase::Pointer factory = mitk::DescriptivePharmacokineticBrixModelFactory::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()); m_Controls.errorMessageLabel->setText(""); m_Controls.errorMessageLabel->hide(); }; 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::AddConcentrationImage(mitk::Image* image, +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); - this->GetDataStorage()->Add(result, m_selectedNode); - 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()); } 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())); //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()); } 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; } - mitk::Image::Pointer concentrationImage; - mitk::DataNode::Pointer concentrationNode; - this->GetConcentrationImage(concentrationImage, concentrationNode, true); + this->PrepareAIFConcentrationImage(); - aifGenerator->SetDynamicImage(concentrationImage); + 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()); - // if (vec1.size() < 3) continue; - 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::GetConcentrationImage(mitk::Image::Pointer& concentrationImage, - mitk::DataNode::Pointer& concentrationNode, bool AIFMode) +void MRPerfusionView::PrepareAIFConcentrationImage() { - if (this->m_Controls.radioButtonNoConversion->isChecked()) + mitk::Image::Pointer concentrationImage = this->m_selectedImage; + mitk::DataNode::Pointer concentrationNode = this->m_selectedNode; + m_HasGeneratedNewInputAIF = false; + + if (this->m_Controls.checkDedicatedAIFImage->isChecked()) { - if (this->m_Controls.checkDedicatedAIFImage->isChecked() && AIFMode) - { - concentrationImage = this->m_selectedAIFImage; - concentrationNode = this->m_selectedAIFImageNode; - } - else - { - concentrationImage = this->m_selectedImage; - concentrationNode = this->m_selectedNode; - } + concentrationImage = this->m_selectedAIFImage; + concentrationNode = this->m_selectedAIFImageNode; } - else + + if (!this->m_Controls.radioButtonNoConversion->isChecked()) { - if (AIFMode && !IsTurboFlashSequenceFlag() && !this->m_Controls.checkDedicatedAIFImage->isChecked()) + if (!IsTurboFlashSequenceFlag() && !this->m_Controls.checkDedicatedAIFImage->isChecked()) { - //we can directly use the input image/node for the AIF if (m_inputImage.IsNull()) { mitkThrow() << - "Cannot get AIF concentration image. Invalid view state. Input image is not defined yet, but should be."; + "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(AIFMode); - - if (AIFMode) - { - concentrationNode = AddConcentrationImage(concentrationImage, "AIF Concentration"); - } - else - { - concentrationNode = AddConcentrationImage(concentrationImage, "Concentration"); - } + concentrationImage = this->ConvertConcentrationImage(true); + concentrationNode = GenerateConcentrationNode(concentrationImage, "AIF Concentration"); + m_HasGeneratedNewInputAIF = true; } } - if (AIFMode) - { - m_inputAIFImage = concentrationImage; - m_inputAIFNode = concentrationNode; - } - else - { - m_inputImage = concentrationImage; - m_inputNode = concentrationNode; - } + 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 ad27f0cb52..7a67e7400b 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 @@ -1,205 +1,212 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #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); /*! * @brief Sets the focus to the plot curve button. Gets called by the framework to set the * focus on the right widget. */ void SetFocus(); /*! @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, mitk::ParameterFitImageGeneratorBase::Pointer& generator); void Generate3StepLinearModelFit_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; void InitModelComboBox() const; - /*! Helper method that adds an concentration image as child node to the current m_selectedNode and returns this new child node.*/ - mitk::DataNode::Pointer AddConcentrationImage(mitk::Image* image, const std::string& nodeName) 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 + /*! \brief called by QmitkFunctionality when DataManager's selection has changed */ virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer source, const QList& selectedNodes); // 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; - /* 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; - - /* 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; - 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) directly pass back the selected image/node - or the newly generated concentration image/node. The result is always what should be used as input for - the fitting. If AIFMode is true the function will generate the data for the AIF.*/ - void GetConcentrationImage(mitk::Image::Pointer& concentrationImage, - mitk::DataNode::Pointer& concentrationNode, 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