Medical Imaging Interaction Toolkit  2018.4.99-389bf124
Medical Imaging Interaction Toolkit
Functions | Variables
MRPerfusionMiniApp.cpp File Reference
#include <string>
#include "itksys/SystemTools.hxx"
#include "mitkCommandLineParser.h"
#include <mitkIOUtil.h>
#include <mitkPreferenceListReaderOptionsFunctor.h>
#include <mitkImageTimeSelector.h>
#include <mitkImageCast.h>
#include <mitkPixelBasedParameterFitImageGenerator.h>
#include <mitkROIBasedParameterFitImageGenerator.h>
#include <mitkModelFitInfo.h>
#include <mitkModelFitCmdAppsHelper.h>
#include <mitkMaskedDynamicImageStatisticsGenerator.h>
#include <mitkLevenbergMarquardtModelFitFunctor.h>
#include <mitkNormalizedSumOfSquaredDifferencesFitCostFunction.h>
#include <mitkExtractTimeGrid.h>
#include <mitkAterialInputFunctionGenerator.h>
#include <mitkModelFitResultHelper.h>
#include <mitkDescriptivePharmacokineticBrixModelParameterizer.h>
#include <mitkDescriptivePharmacokineticBrixModelValueBasedParameterizer.h>
#include <mitkDescriptivePharmacokineticBrixModelFactory.h>
#include <mitkExtendedToftsModelParameterizer.h>
#include <mitkExtendedToftsModelFactory.h>
#include <mitkTwoCompartmentExchangeModelParameterizer.h>
#include <mitkTwoCompartmentExchangeModelFactory.h>
#include <mitkThreeStepLinearModelParameterizer.h>
#include <mitkThreeStepLinearModelFactory.h>
#include <mitkModelFactoryBase.h>

Go to the source code of this file.

Functions

bool useConstraints (false)
 
bool verbose (false)
 
bool roibased (false)
 
bool preview (false)
 
float aifHematocritLevel (0)
 
float brixInjectionTime (0)
 
void onFitEvent (::itk::Object *caller, const itk::EventObject &event, void *)
 
void setupParser (mitkCommandLineParser &parser)
 
bool configureApplicationSettings (std::map< std::string, us::Any > parsedArgs)
 
mitk::ModelFitFunctorBase::Pointer createDefaultFitFunctor (const mitk::ModelParameterizerBase *parameterizer, const mitk::ModelFactoryBase *modelFactory)
 
mitk::Image::Pointer getMask3D ()
 
void getAIF (mitk::AIFBasedModelBase::AterialInputFunctionType &aif, mitk::AIFBasedModelBase::AterialInputFunctionType &aifTimeGrid)
 
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<typename TParameterizer , typename TFactory >
void generateAIFbasedModelFit_PixelBased (mitk::modelFit::ModelFitInfo::Pointer &modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer &generator)
 
template<typename TParameterizer , typename TFactory >
void generateAIFbasedModelFit_ROIBased (mitk::modelFit::ModelFitInfo::Pointer &modelFitInfo, mitk::ParameterFitImageGeneratorBase::Pointer &generator)
 
void storeResultImage (const std::string &name, mitk::Image *image, mitk::modelFit::Parameter::Type nodeType, const mitk::modelFit::ModelFitInfo *modelFitInfo)
 
void createFitGenerator (mitk::modelFit::ModelFitInfo::Pointer &fitSession, mitk::ParameterFitImageGeneratorBase::Pointer &generator)
 
void doFitting ()
 
void doPreview ()
 
int main (int argc, char *argv[])
 

Variables

std::string inFilename
 
std::string outFileName
 
std::string maskFileName
 
std::string aifMaskFileName
 
std::string aifImageFileName
 
mitk::Image::Pointer image
 
mitk::Image::Pointer mask
 
mitk::Image::Pointer aifImage
 
mitk::Image::Pointer aifMask
 
std::string modelName
 
const std::string MODEL_NAME_3SL
 
const std::string MODEL_NAME_descriptive
 
const std::string MODEL_NAME_tofts
 
const std::string MODEL_NAME_2CX
 

Function Documentation

◆ aifHematocritLevel()

float aifHematocritLevel ( 0  )

Referenced by configureApplicationSettings(), and getAIF().

◆ brixInjectionTime()

float brixInjectionTime ( 0  )

Referenced by configureApplicationSettings(), generateDescriptiveBrixModel_PixelBased(), and generateDescriptiveBrixModel_ROIBased().

◆ configureApplicationSettings()

bool configureApplicationSettings ( std::map< std::string, us::Any >  parsedArgs)

Definition at line 146 of file MRPerfusionMiniApp.cpp.

References aifHematocritLevel(), aifImageFileName, aifMaskFileName, us::any_cast(), brixInjectionTime(), inFilename, maskFileName, MODEL_NAME_tofts, modelName, outFileName, preview(), roibased(), useConstraints(), and verbose().

Referenced by main().

◆ createDefaultFitFunctor()

mitk::ModelFitFunctorBase::Pointer createDefaultFitFunctor ( const mitk::ModelParameterizerBase *  parameterizer,
const mitk::ModelFactoryBase *  modelFactory 
)

Definition at line 214 of file MRPerfusionMiniApp.cpp.

References mitk::ModelFactoryBase::CreateDefaultConstraints(), mitk::ModelParameterizerBase::GenerateParameterizedModel(), mitk::NormalizedSumOfSquaredDifferencesFitCostFunction::New(), mitk::LevenbergMarquardtModelFitFunctor::New(), and useConstraints().

Referenced by Generate3StepLinearModelFit_PixelBased(), Generate3StepLinearModelFit_ROIBased(), generateAIFbasedModelFit_PixelBased(), generateAIFbasedModelFit_ROIBased(), generateDescriptiveBrixModel_PixelBased(), and generateDescriptiveBrixModel_ROIBased().

◆ createFitGenerator()

void createFitGenerator ( mitk::modelFit::ModelFitInfo::Pointer &  fitSession,
mitk::ParameterFitImageGeneratorBase::Pointer &  generator 
)

Definition at line 669 of file MRPerfusionMiniApp.cpp.

References Generate3StepLinearModelFit_PixelBased(), Generate3StepLinearModelFit_ROIBased(), generateDescriptiveBrixModel_PixelBased(), generateDescriptiveBrixModel_ROIBased(), MODEL_NAME_2CX, MODEL_NAME_3SL, MODEL_NAME_descriptive, MODEL_NAME_tofts, modelName, and roibased().

Referenced by doFitting(), and doPreview().

◆ doFitting()

void doFitting ( )

Definition at line 730 of file MRPerfusionMiniApp.cpp.

References createFitGenerator(), mitkThrow, onFitEvent(), outFileName, and mitk::storeModelFitGeneratorResults().

Referenced by main().

◆ doPreview()

void doPreview ( )

Definition at line 755 of file MRPerfusionMiniApp.cpp.

References createFitGenerator(), mitkThrow, outFileName, and mitk::previewModelFitGeneratorResults().

Referenced by main().

◆ Generate3StepLinearModelFit_PixelBased()

void Generate3StepLinearModelFit_PixelBased ( mitk::modelFit::ModelFitInfo::Pointer &  modelFitInfo,
mitk::ParameterFitImageGeneratorBase::Pointer &  generator 
)

Definition at line 425 of file MRPerfusionMiniApp.cpp.

References createDefaultFitFunctor(), mitk::modelFit::CreateFitInfoFromModelParameterizer(), mitk::EnsureModelFitUID(), mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), getMask3D(), mitk::ThreeStepLinearModelFactory::New(), mitk::ThreeStepLinearModelParameterizer::New(), and mitk::PixelBasedParameterFitImageGenerator::New().

Referenced by createFitGenerator().

◆ Generate3StepLinearModelFit_ROIBased()

void Generate3StepLinearModelFit_ROIBased ( mitk::modelFit::ModelFitInfo::Pointer &  modelFitInfo,
mitk::ParameterFitImageGeneratorBase::Pointer &  generator 
)

Definition at line 460 of file MRPerfusionMiniApp.cpp.

References createDefaultFitFunctor(), mitk::modelFit::CreateFitInfoFromModelParameterizer(), mitk::EnsureModelFitUID(), mitk::ExtractTimeGrid(), mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), getMask3D(), mitk::ThreeStepLinearModelFactory::New(), mitk::ThreeStepLinearModelParameterizer::New(), mitk::MaskedDynamicImageStatisticsGenerator::New(), and mitk::ROIBasedParameterFitImageGenerator::New().

Referenced by createFitGenerator().

◆ generateAIFbasedModelFit_PixelBased()

template<typename TParameterizer , typename TFactory >
void generateAIFbasedModelFit_PixelBased ( mitk::modelFit::ModelFitInfo::Pointer &  modelFitInfo,
mitk::ParameterFitImageGeneratorBase::Pointer &  generator 
)

Definition at line 515 of file MRPerfusionMiniApp.cpp.

References createDefaultFitFunctor(), mitk::modelFit::CreateFitInfoFromModelParameterizer(), mitk::EnsureModelFitUID(), mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), getAIF(), getMask3D(), and mitk::PixelBasedParameterFitImageGenerator::New().

◆ generateAIFbasedModelFit_ROIBased()

template<typename TParameterizer , typename TFactory >
void generateAIFbasedModelFit_ROIBased ( mitk::modelFit::ModelFitInfo::Pointer &  modelFitInfo,
mitk::ParameterFitImageGeneratorBase::Pointer &  generator 
)

Definition at line 569 of file MRPerfusionMiniApp.cpp.

References createDefaultFitFunctor(), mitk::modelFit::CreateFitInfoFromModelParameterizer(), mitk::EnsureModelFitUID(), mitk::ExtractTimeGrid(), mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), getAIF(), getMask3D(), mitk::MaskedDynamicImageStatisticsGenerator::New(), and mitk::ROIBasedParameterFitImageGenerator::New().

◆ generateDescriptiveBrixModel_PixelBased()

void generateDescriptiveBrixModel_PixelBased ( mitk::modelFit::ModelFitInfo::Pointer &  modelFitInfo,
mitk::ParameterFitImageGeneratorBase::Pointer &  generator 
)

Definition at line 316 of file MRPerfusionMiniApp.cpp.

References brixInjectionTime(), mitk::CastToItkImage(), createDefaultFitFunctor(), mitk::modelFit::CreateFitInfoFromModelParameterizer(), mitk::EnsureModelFitUID(), mitk::ModelFitConstants::FIT_TYPE_VALUE_PIXELBASED(), getMask3D(), mitk::ImageTimeSelector::New(), mitk::DescriptivePharmacokineticBrixModelFactory::New(), mitk::DescriptivePharmacokineticBrixModelParameterizer::New(), and mitk::PixelBasedParameterFitImageGenerator::New().

Referenced by createFitGenerator().

◆ generateDescriptiveBrixModel_ROIBased()

void generateDescriptiveBrixModel_ROIBased ( mitk::modelFit::ModelFitInfo::Pointer &  modelFitInfo,
mitk::ParameterFitImageGeneratorBase::Pointer &  generator 
)

Definition at line 365 of file MRPerfusionMiniApp.cpp.

References brixInjectionTime(), createDefaultFitFunctor(), mitk::modelFit::CreateFitInfoFromModelParameterizer(), mitk::EnsureModelFitUID(), mitk::ExtractTimeGrid(), mitk::ModelFitConstants::FIT_TYPE_VALUE_ROIBASED(), getMask3D(), mitk::DescriptivePharmacokineticBrixModelFactory::New(), mitk::DescriptivePharmacokineticBrixModelValueBasedParameterizer::New(), mitk::MaskedDynamicImageStatisticsGenerator::New(), and mitk::ROIBasedParameterFitImageGenerator::New().

Referenced by createFitGenerator().

◆ getAIF()

void getAIF ( mitk::AIFBasedModelBase::AterialInputFunctionType &  aif,
mitk::AIFBasedModelBase::AterialInputFunctionType &  aifTimeGrid 
)

Definition at line 267 of file MRPerfusionMiniApp.cpp.

References aifHematocritLevel(), aifImage, aifMask, image, MITK_INFO, mitkThrow, mitk::ImageTimeSelector::New(), and mitk::AterialInputFunctionGenerator::New().

Referenced by generateAIFbasedModelFit_PixelBased(), and generateAIFbasedModelFit_ROIBased().

◆ getMask3D()

mitk::Image::Pointer getMask3D ( )

Helper that ensures that the mask (if it exists) is always 3D image. If the mask is originally an 4D image, the first time step will be used.

Definition at line 243 of file MRPerfusionMiniApp.cpp.

References mask, MITK_INFO, and mitk::ImageTimeSelector::New().

Referenced by Generate3StepLinearModelFit_PixelBased(), Generate3StepLinearModelFit_ROIBased(), generateAIFbasedModelFit_PixelBased(), generateAIFbasedModelFit_ROIBased(), generateDescriptiveBrixModel_PixelBased(), and generateDescriptiveBrixModel_ROIBased().

◆ main()

int main ( int  argc,
char *  argv[] 
)

[do processing]

Definition at line 772 of file MRPerfusionMiniApp.cpp.

References aifImageFileName, aifMaskFileName, configureApplicationSettings(), doFitting(), doPreview(), mitkCommandLineParser::helpText(), inFilename, maskFileName, MITK_ERROR, mitkThrow, MODEL_NAME_3SL, MODEL_NAME_descriptive, modelName, mitkCommandLineParser::parseArguments(), preview(), roibased(), and setupParser().

◆ onFitEvent()

void onFitEvent ( ::itk::Object *  caller,
const itk::EventObject &  event,
void *   
)

Definition at line 77 of file MRPerfusionMiniApp.cpp.

References mitk::ParameterFitImageGeneratorBase::GetProgress().

Referenced by doFitting().

◆ preview()

bool preview ( false  )

Referenced by configureApplicationSettings(), and main().

◆ roibased()

bool roibased ( false  )

Referenced by configureApplicationSettings(), createFitGenerator(), and main().

◆ setupParser()

void setupParser ( mitkCommandLineParser &  parser)

[create parser]

[add arguments]

[add arguments]

Definition at line 89 of file MRPerfusionMiniApp.cpp.

References mitkCommandLineParser::addArgument(), mitkCommandLineParser::beginGroup(), mitkCommandLineParser::Bool, mitkCommandLineParser::endGroup(), mitkCommandLineParser::File, mitkCommandLineParser::Float, mitkCommandLineParser::Input, MODEL_NAME_2CX, MODEL_NAME_3SL, MODEL_NAME_descriptive, MODEL_NAME_tofts, mitkCommandLineParser::Output, mitkCommandLineParser::setArgumentPrefix(), mitkCommandLineParser::setCategory(), mitkCommandLineParser::setContributor(), mitkCommandLineParser::setDescription(), mitkCommandLineParser::setTitle(), and mitkCommandLineParser::String.

Referenced by main().

◆ storeResultImage()

void storeResultImage ( const std::string &  name,
mitk::Image *  image,
mitk::modelFit::Parameter::Type  nodeType,
const mitk::modelFit::ModelFitInfo *  modelFitInfo 
)

Definition at line 644 of file MRPerfusionMiniApp.cpp.

References outFileName, mitk::IOUtil::Save(), and mitk::modelFit::SetModelFitDataProperties().

◆ useConstraints()

bool useConstraints ( false  )

Referenced by configureApplicationSettings(), and createDefaultFitFunctor().

◆ verbose()

bool verbose ( false  )

Referenced by configureApplicationSettings().

Variable Documentation

◆ aifImage

mitk::Image::Pointer aifImage

Definition at line 59 of file MRPerfusionMiniApp.cpp.

Referenced by getAIF().

◆ aifImageFileName

std::string aifImageFileName

Definition at line 55 of file MRPerfusionMiniApp.cpp.

Referenced by configureApplicationSettings(), and main().

◆ aifMask

mitk::Image::Pointer aifMask

Definition at line 60 of file MRPerfusionMiniApp.cpp.

Referenced by getAIF().

◆ aifMaskFileName

std::string aifMaskFileName

Definition at line 54 of file MRPerfusionMiniApp.cpp.

Referenced by configureApplicationSettings(), and main().

◆ image

mitk::Image::Pointer image

Definition at line 57 of file MRPerfusionMiniApp.cpp.

Referenced by getAIF().

◆ inFilename

std::string inFilename

Definition at line 51 of file MRPerfusionMiniApp.cpp.

Referenced by configureApplicationSettings(), and main().

◆ mask

mitk::Image::Pointer mask

Definition at line 58 of file MRPerfusionMiniApp.cpp.

Referenced by getMask3D().

◆ maskFileName

std::string maskFileName

Definition at line 53 of file MRPerfusionMiniApp.cpp.

Referenced by configureApplicationSettings(), and main().

◆ MODEL_NAME_2CX

const std::string MODEL_NAME_2CX

Definition at line 75 of file MRPerfusionMiniApp.cpp.

Referenced by createFitGenerator(), and setupParser().

◆ MODEL_NAME_3SL

const std::string MODEL_NAME_3SL

Definition at line 72 of file MRPerfusionMiniApp.cpp.

Referenced by createFitGenerator(), main(), and setupParser().

◆ MODEL_NAME_descriptive

const std::string MODEL_NAME_descriptive

Definition at line 73 of file MRPerfusionMiniApp.cpp.

Referenced by createFitGenerator(), main(), and setupParser().

◆ MODEL_NAME_tofts

const std::string MODEL_NAME_tofts

Definition at line 74 of file MRPerfusionMiniApp.cpp.

Referenced by configureApplicationSettings(), createFitGenerator(), and setupParser().

◆ modelName

std::string modelName

Definition at line 67 of file MRPerfusionMiniApp.cpp.

Referenced by configureApplicationSettings(), createFitGenerator(), main(), and mitk::DICOMPMIO::Write().

◆ outFileName

std::string outFileName

Definition at line 52 of file MRPerfusionMiniApp.cpp.

Referenced by configureApplicationSettings(), doFitting(), doPreview(), and storeResultImage().