GenericFittingMiniApp.cpp File Reference

#include <string>
#include "itksys/SystemTools.hxx"
#include "mitkCommandLineParser.h"
#include <mitkIOUtil.h>
#include <mitkPixelBasedParameterFitImageGenerator.h>
#include <mitkROIBasedParameterFitImageGenerator.h>
#include <mitkLinearModelParameterizer.h>
#include <mitkGenericParamModelParameterizer.h>
#include <mitkModelFitInfo.h>
#include <mitkMaskedDynamicImageStatisticsGenerator.h>
#include <mitkLevenbergMarquardtModelFitFunctor.h>
#include <mitkNormalizedSumOfSquaredDifferencesFitCostFunction.h>
#include <mitkExtractTimeGrid.h>
#include <mitkModelFitCmdAppsHelper.h>
#include <mitkPreferenceListReaderOptionsFunctor.h>

Go to the source code of this file.

Functions
bool	verbose (false)
bool	roibased (false)
void	onFitEvent (::itk::Object *caller, const itk::EventObject &event, void *)
void	setupParser (mitkCommandLineParser &parser)
bool	configureApplicationSettings (std::map< std::string, us::Any > parsedArgs)
void	configureInitialParametersOfParameterizer (mitk::ModelParameterizerBase *parameterizer)
mitk::ModelFitFunctorBase::Pointer	createDefaultFitFunctor (const mitk::ModelParameterizerBase *parameterizer)
template<typename TParameterizer >
void	generateModelFit_PixelBased (mitk::modelFit::ModelFitInfo::Pointer &, mitk::ParameterFitImageGeneratorBase::Pointer &generator)
template<typename TParameterizer >
void	generateModelFit_ROIBased (mitk::modelFit::ModelFitInfo::Pointer &, mitk::ParameterFitImageGeneratorBase::Pointer &generator)
void	doFitting ()
int	main (int argc, char *argv[])

Variables
std::string	inFilename
std::string	outFileName
std::string	maskFileName
std::string	functionName
std::string	formular
mitk::Image::Pointer	image
mitk::Image::Pointer	mask

Function Documentation

configureApplicationSettings()

bool configureApplicationSettings

(

std::map< std::string, us::Any >

parsedArgs

)

Definition at line 103 of file GenericFittingMiniApp.cpp.

References us::any_cast(), formular, functionName, inFilename, maskFileName, outFileName, roibased(), and verbose().

Referenced by main().

configureInitialParametersOfParameterizer()

void configureInitialParametersOfParameterizer

(

mitk::ModelParameterizerBase *

parameterizer

)

Definition at line 142 of file GenericFittingMiniApp.cpp.

References formular, and mitk::GenericParamModelParameterizer::SetFunctionString().

Referenced by generateModelFit_PixelBased(), and generateModelFit_ROIBased().

createDefaultFitFunctor()

mitk::ModelFitFunctorBase::Pointer createDefaultFitFunctor

(

const mitk::ModelParameterizerBase *

parameterizer

)

Definition at line 154 of file GenericFittingMiniApp.cpp.

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

Referenced by generateModelFit_PixelBased(), and generateModelFit_ROIBased().

doFitting()

void doFitting

(

)

Definition at line 237 of file GenericFittingMiniApp.cpp.

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

Referenced by main().

generateModelFit_PixelBased()

template<typename TParameterizer >

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

Definition at line 177 of file GenericFittingMiniApp.cpp.

References configureInitialParametersOfParameterizer(), createDefaultFitFunctor(), and mitk::PixelBasedParameterFitImageGenerator::New().

generateModelFit_ROIBased()

template<typename TParameterizer >

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

Definition at line 203 of file GenericFittingMiniApp.cpp.

References configureInitialParametersOfParameterizer(), createDefaultFitFunctor(), mitk::ExtractTimeGrid(), mitk::MaskedDynamicImageStatisticsGenerator::New(), and mitk::ROIBasedParameterFitImageGenerator::New().

main()

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

[do processing]

Definition at line 287 of file GenericFittingMiniApp.cpp.

References configureApplicationSettings(), doFitting(), mitkCommandLineParser::helpText(), inFilename, maskFileName, MITK_ERROR, mitkThrow, mitkCommandLineParser::parseArguments(), roibased(), and setupParser().

onFitEvent()

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

Definition at line 47 of file GenericFittingMiniApp.cpp.

References mitk::ParameterFitImageGeneratorBase::GetProgress().

Referenced by doFitting().

roibased()

bool roibased

(

false

)

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

setupParser()

void setupParser

(

mitkCommandLineParser &

parser

)

[create parser]

[add arguments]

[add arguments]

Definition at line 59 of file GenericFittingMiniApp.cpp.

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

Referenced by main().

verbose()

bool verbose

(

false

)

Referenced by mitk::BaseDataCompare::AreEqual(), mitk::BaseGeometry::CheckIndexToWorldTransform(), configureApplicationSettings(), CreatePhantom_04_04_18_Parameters(), CreateSinglevessel_19_10_17_Parameters(), mitk::pa::Equal(), mitk::Equal(), mitk::EqualArray(), mitk::Label::Modified(), mitk::pa::MonteCarloThreadHandler::MonteCarloThreadHandler(), mitk::DataStorageCompare::Report(), mitk::TimeGeometry::UpdateWithoutBoundingBox(), mitk::pa::SpectralUnmixingSO2::Verbose(), and mitk::pa::SpectralUnmixingFilterBase::Verbose().

Variable Documentation

formular

std::string formular

Definition at line 42 of file GenericFittingMiniApp.cpp.

Referenced by configureApplicationSettings(), and configureInitialParametersOfParameterizer().

functionName

std::string functionName

Definition at line 41 of file GenericFittingMiniApp.cpp.

Referenced by configureApplicationSettings(), and doFitting().

image

mitk::Image::Pointer image

Examples:

Step3.cpp, and Step6.cpp.

Definition at line 43 of file GenericFittingMiniApp.cpp.

Referenced by mitk::PixelManipulationTool::Activated(), mitk::DataCollectionSingleImageIterator< TDataType, ImageDimension >::AddImage(), BPFunction(), mitk::GIFVolumetricDensityStatistics::CalculateFeatures(), mitk::GIFVolumetricStatistics::CalculateFeatures(), mitk::PixelManipulationTool::CalculateImage(), mitk::AdaptiveRegionGrowingTool::CanHandle(), mitk::FastMarchingTool3D::CanHandle(), mitk::PaintbrushTool::CheckIfCurrentSliceHasChanged(), CheckIntersectionWithPointCloud(), CheckIntersectionWithRotatedGeometry(), CheckIntersectionWithRotatedGeometry90(), mitk::NodePredicateDimension::CheckNode(), CheckPlanesInsideBoundingBox(), CheckPlanesInsideBoundingBoxOnlyOnOneSlice(), CheckPlanesOutsideOfBoundingBox(), QmitkImageStatisticsTreeModel::Clear(), mitk::CLUtil::ClosingBinary(), mitk::ImageStatisticsHolder::ComputeImageStatistics(), QmitkStatisticsCalculator::ComputeLesionVolume(), mitk::ConvertLabelSetImageToImage(), mitk::GrabCutOpenCVImageFilter::ConvertMaskToModelPointsList(), ConvertToConcentrationTest(), DescriptionParameterBackgroundJob::CreateResultNodes(), mitk::ModelSignalImageGenerator::DoPrepareMask(), mitk::PixelBasedDescriptionParameterImageGenerator::DoPrepareMask(), mitk::PixelBasedParameterFitImageGenerator::DoPrepareMask(), EnsureDataImageInCollection(), mitk::DCUtilities::EnsureDoubleImageInDC(), EnsureLabelImageInCollection(), mitk::DCUtilities::EnsureUCharImageInDC(), ExecuteWaveletTransformation(), mitk::CollectionWriter::ExportCollectionToFolder(), mitk::ContourModelUtils::FillContourInSlice(), mitk::CollectionReader::FolderToCollection(), mitk::ImageToUnstructuredGridFilter::GenerateData(), mitk::FeatureBasedEdgeDetectionFilter::GenerateData(), mitk::ItkImageFileReader::GenerateData(), mitk::ManualSegmentationToSurfaceFilter::GenerateData(), mitk::BandpassFilter::GenerateData(), mitk::TrackedUltrasound::GenerateData(), mitk::PadImageFilter::GenerateData(), mitk::ImageToPointCloudFilter::GenerateData(), mitk::USCombinedModality::GenerateData(), mitk::RGBToRGBACastImageFilter::GenerateData(), mitk::ImageToSurfaceFilter::GenerateData(), mitk::USIGTLDevice::GenerateData(), mitk::LabeledImageToSurfaceFilter::GenerateData(), mitk::ImageWriter::GenerateData(), mitk::USVideoDevice::GenerateData(), mitk::USDevice::GenerateData(), mitk::LabelSetImageVtkMapper2D::GenerateDataForRenderer(), mitk::ImageVtkMapper2D::GenerateDataForRenderer(), mitk::ImageGenerator::GenerateGradientImage(), GenerateGradientWithDimXImage(), mitk::generateMappedResultNode(), GenerateMaskImage(), generateModelFitTestStorage(), mitk::LabeledImageToSurfaceFilter::GenerateOutputInformation(), mitk::GenerateTestFrame(), mitk::GenerateTestImage(), mitk::GenerateTestMask(), mitk::GenerateTestMaskMITK(), mitk::SegTool2D::GetAffectedImageSliceAs2DImage(), mitk::LabeledImageToSurfaceFilter::GetAvailableLabels(), mitk::ApplyDiffImageOperation::GetDiffImage(), mitk::Tool::GetIconPath(), mitk::CompressedImageContainer::GetImage(), mitk::SemanticRelationsTestHelper::GetInvalidCaseID(), mitk::SemanticRelationsTestHelper::GetInvalidDate(), mitk::SemanticRelationsTestHelper::GetInvalidID(), mitk::SemanticRelationsTestHelper::GetInvalidModality(), mitk::DataCollection::GetItkImage(), mitk::OverwriteDirectedPlaneImageFilter::GetLastDifferenceImage(), mitk::OverwriteSliceImageFilter::GetLastDifferenceImage(), mitk::USDiPhASImageSource::GetNextRawImage(), mitk::ImageToOpenCVImageFilter::GetOpenCVMat(), mitk::SemanticRelationsTestHelper::GetPatientOneCTImage(), mitk::SemanticRelationsTestHelper::GetPatientOneMRImage(), mitk::SemanticRelationsTestHelper::GetPatientOneOtherCTImage(), mitk::SemanticRelationsTestHelper::GetPatientThreeCTImage(), mitk::SemanticRelationsTestHelper::GetPatientThreeMRImage(), mitk::SemanticRelationsTestHelper::GetPatientTwoPETImage(), mitk::USDiPhASImageSource::GetPixelValues(), QmitkSemanticRelationsUIHelper::GetPixmapFromImageNode(), GetPixmapFromImageNode(), mitk::PlanarFigureMaskGenerator::GetReferenceImage(), mitk::DiffSliceOperation::GetSlice(), mitk::ImageStatisticsCalculator::GetStatistics(), mitk::LabeledImageToSurfaceFilter::GetVolumeForLabel(), mitk::ItkImageIO::GetWriterConfidenceLevel(), mitk::USDevice::GrabImage(), QmitkStdMultiWidget::HandleCrosshairPositionEventDelayed(), mitk::USDiPhASImageSource::ImageDataCallback(), berry::AbstractUICTKPlugin::ImageDescriptorFromPlugin(), mitk::ImageStatisticsCalculator::ImageStatisticsCalculator(), ImageVtkDataReferenceCheck(), QmitkImageStatisticsCalculationJob::Initialize(), QmitkImageStatisticsCalculationRunnable::Initialize(), mitk::Image::Initialize(), QmitkDataNodeOpenInAction::InitializeAction(), mitk::SourceImageRelationRule::IsDestinationCandidate(), vtkMitkGPUVolumeRayCastMapper::IsRenderSupported(), mitk::CLUtil::itkCountVoxel(), Step6::Load(), mitk::DicomSeriesReader::LoadDicom(), mitk::LogoAnnotation::LoadLogoImageFromPath(), main(), mitkDICOMLocaleTestWithReferenceImage(), mitkDICOMTestingSanityTest(), mitkImageAccessorTest(), mitkImageSliceSelectorTest(), mitkImageTest(), mitkImageVtkMapper2DResliceInterpolationPropertyTest(), mitkImageVtkMapper2DSwivelTest(), mitkLabeledImageToSurfaceFilterTest(), mitkLevelWindowTest(), mitkPlaneGeometryDataMapper2DTest(), mitkRegistrationBaseTest(), mitkTimeGeometryTest(), mitkVolumeCalculatorTest(), mitkVtkPropRendererTest(), mitk::PaintbrushTool::MouseMoved(), mitk::CropOpenCVImageFilter::OnFilterImage(), mitk::SetRegionTool::OnMouseReleased(), mitk::ContourTool::OnMouseReleased(), mitk::CorrectorTool2D::OnMouseReleased(), QmitkAdaptiveRegionGrowingToolGUI::OnPointAdded(), mitk::BinaryThresholdTool::OnRoiDataChanged(), mitk::BinaryThresholdULTool::OnRoiDataChanged(), mitk::PixelBasedParameterFitImageGenerator::PixelBasedParameterFitImageGenerator(), mitk::PlanarFigureMaskGenerator::PlanarFigureMaskGenerator(), mitk::CalculateVolumetryTool::ProcessOneWorkingData(), mitk::AutoCropTool::ProcessOneWorkingData(), mitk::CreateSurfaceTool::ProcessOneWorkingData(), mitk::CalculateGrayValueStatisticsTool::ProcessOneWorkingData(), mitk::CESTDICOMReaderService::Read(), mitk::RawImageFileReaderService::Read(), mitk::ItkImageIO::Read(), mitk::LabelSetImageIO::Read(), mitk::DICOMSegmentationIO::Read(), mitk::ReadVoxel(), mitk::ShowSegmentationAsSmoothedSurface::ReadyToRun(), mitk::SegmentationSink::ReadyToRun(), mitk::CalculateSegmentationVolume::ReadyToRun(), mitk::LabelSetImageToSurfaceThreadedFilter::ReadyToRun(), mitk::ShowSegmentationAsSurface::ReadyToRun(), mitk::LevelWindowManager::RecalculateLevelWindowForSelectedComponent(), mitk::SurfaceInterpolationController::RemoveAllInterpolationSessions(), mitk::TransformationOperation::ResampleImage(), mitk::ROIBasedParameterFitImageGenerator::ROIBasedParameterFitImageGenerator(), ReinitAction::Run(), mitk::CollectionWriter::SaveCollection(), mitk::LabelSetImageSerializer::Serialize(), mitk::ImageSerializer::Serialize(), mitk::LevelWindow::SetAuto(), QmitkSliceWidget::SetData(), QmitkTransferFunctionGeneratorWidget::SetDataNode(), mitk::CoreObjectFactory::SetDefaultProperties(), mitk::VolumeMapperVtkSmart3D::SetDefaultProperties(), mitk::GPUVolumeMapper3D::SetDefaultProperties(), mitk::ImageVtkMapper2D::SetDefaultProperties(), mitk::DoseImageVtkMapper2D::SetDefaultProperties(), mitk::MaskUtilities< TPixel, VImageDimension >::SetImage(), mitk::DiffSliceOperation::SetImage(), mitk::OclImageFilter::SetInput(), mitk::ClippedSurfaceBoundsCalculator::SetInput(), mitk::ImageStatisticsCalculator::SetInputImage(), mitk::OpenCVToMitkImageFilter::SetOpenCVMat(), mitk::MaskAndCutRoiImageFilter::SetRegionOfInterest(), mitk::USDevice::SetSpacing(), mitk::BinaryThresholdTool::SetupPreviewNode(), mitk::BinaryThresholdULTool::SetupPreviewNode(), mitk::CollectionReader::StartElement(), mitk::SurfaceToImageFilter::Stencil3DImage(), TestDataStorage(), TestRandomPixelAccess(), mitk::ShowSegmentationAsSmoothedSurface::ThreadedUpdateFunction(), mitk::CalculateSegmentationVolume::ThreadedUpdateFunction(), mitk::LabelSetImageToSurfaceThreadedFilter::ThreadedUpdateFunction(), mitk::ShowSegmentationAsSurface::ThreadedUpdateFunction(), mitk::ShowSegmentationAsSmoothedSurface::ThreadedUpdateSuccessful(), mitk::LabelSetImageToSurfaceThreadedFilter::ThreadedUpdateSuccessful(), mitk::ShowSegmentationAsSurface::ThreadedUpdateSuccessful(), mitk::DataCollectionSingleImageIterator< TDataType, ImageDimension >::ToBegin(), mitk::DataCollectionImageIterator< TDataType, ImageDimension >::ToBegin(), mitk::ToFDebugHelper::ToFDebugHelper::ShowCVDistanceImage(), mitk::CLUtil::Transform(), mitk::RawImageFileReader::TypedGenerateData(), mitk::LabelSetImageVtkMapper2D::Update(), mitk::ToFCameraMITKPlayerController::UpdateCamera(), QmitkDataNodeColorMapAction::UseWholePixelRange(), mitk::USImageVideoSource::USImageCropping::USImageCropping(), mitk::pa::Volume::Volume(), mitk::ItkImageIO::Write(), mitk::SegTool2D::WriteBackSegmentationResult(), mitk::SegTool2D::WriteSliceToVolume(), mitk::IgnorePixelMaskGenerator::~IgnorePixelMaskGenerator(), mitk::ImageToItk< TOutputImage >::~ImageToItk(), mitk::ModelSignalImageGenerator::~ModelSignalImageGenerator(), mitk::PixelBasedDescriptionParameterImageGenerator::~PixelBasedDescriptionParameterImageGenerator(), mitk::RTDoseReaderService::~RTDoseReaderService(), and mitk::TimeFramesRegistrationHelper::~TimeFramesRegistrationHelper().

inFilename

std::string inFilename

Definition at line 36 of file GenericFittingMiniApp.cpp.

Referenced by configureApplicationSettings(), and main().

mask

mitk::Image::Pointer mask

Definition at line 44 of file GenericFittingMiniApp.cpp.

Referenced by mitk::GIFVolumetricDensityStatistics::CalculateFeatures(), mitk::GIFVolumetricStatistics::CalculateFeatures(), QmitkImageStatisticsTreeModel::Clear(), QmitkStatisticsCalculator::ComputeLesionVolume(), mitk::GrabCutOpenCVImageFilter::ConvertMaskToModelPointsList(), mitk::LabelSetImage::CreateLabelMask(), CreateNewMask(), mitk::ImageLiveWireContourModelFilter::DumpMaskImage(), mitk::TimeFramesRegistrationHelper::Generate(), mitk::MaskImageFilter::GenerateData(), mitk::MaskImageFilter::GenerateInputRequestedRegion(), mitk::GrabCutOpenCVImageFilter::GetMaskFromPointSets(), mitk::AbstractGlobalImageFeature::GetOptionPrefix(), mitk::GrabCutOpenCVImageFilter::GetResultContourWithPixel(), mitk::IgnorePixelMaskGenerator::InternalCalculateMask(), vtkMitkGPUVolumeRayCastMapper::IsRenderSupported(), mitk::CLUtil::itkCountVoxel(), itkMaskedNaryStatisticsImageFilterTest(), itkMaskedStatisticsImageFilterTest(), itkMultiOutputNaryFunctorImageFilterTest(), main(), QmitkMaskStampWidget::OnStamp(), ProcessFeatureImages(), mitk::MRNormLinearStatisticBasedFilter::SetMask(), mitk::MaskImageFilter::SetMask(), mitk::ImageStatisticsCalculator::SetMask(), mitk::MaskUtilities< TPixel, VImageDimension >::SetMask(), mitk::HotspotMaskGenerator::SetMask(), itk::LocalIntensityFilter< TInputImage >::SetMask(), mitk::MRNormTwoRegionsBasedFilter::SetMask1(), mitk::MRNormTwoRegionsBasedFilter::SetMask2(), itk::SmoothedClassProbabilites< TImage >::SetMaskImage(), mitk::MaskedAlgorithmHelper::SetMasks(), mitk::ImageStatisticsCalculator::SetSecondaryMask(), mitk::CLUtil::Transform(), and mitk::MaskedAlgorithmHelper::~MaskedAlgorithmHelper().

maskFileName

std::string maskFileName

Definition at line 38 of file GenericFittingMiniApp.cpp.

Referenced by configureApplicationSettings(), and main().

outFileName

std::string outFileName

Definition at line 37 of file GenericFittingMiniApp.cpp.

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