rtk Namespace Reference

Namespaces
	Function
	Functor

Classes
class	AdditiveGaussianNoiseImageFilter
class	AddMatrixAndDiagonalImageFilter
class	ADMMTotalVariationConeBeamReconstructionFilter
class	ADMMTotalVariationConjugateGradientOperator
class	ADMMWaveletsConeBeamReconstructionFilter
class	ADMMWaveletsConjugateGradientOperator
class	AmsterdamShroudImageFilter
class	args_info_manager
class	AverageOutOfROIImageFilter
class	BackProjectionImageFilter
class	BackwardDifferenceDivergenceImageFilter
class	BioscanGeometryReader
class	BlockDiagonalMatrixVectorMultiplyImageFilter
class	BoellaardScatterCorrectionImageFilter
class	BoxShape
class	ConditionalMedianImageFilter
class	ConjugateGradientConeBeamReconstructionFilter
class	ConjugateGradientGetP_kPlusOneImageFilter
class	ConjugateGradientGetR_kPlusOneImageFilter
class	ConjugateGradientGetX_kPlusOneImageFilter
class	ConjugateGradientImageFilter
class	ConjugateGradientOperator
class	ConstantImageSource
class	ConvexShape
class	CyclicDeformationImageFilter
class	DaubechiesWaveletsConvolutionImageFilter
class	DaubechiesWaveletsDenoiseSequenceImageFilter
class	DbfField
class	DbfFile
class	DCMImagXImageIO
class	DCMImagXImageIOFactory
class	DeconstructImageFilter
class	DeconstructSoftThresholdReconstructImageFilter
class	DenoisingBPDQImageFilter
class	DePierroRegularizationImageFilter
class	DigisensGeometryReader
class	DigisensGeometryXMLFileReader
class	DisplacedDetectorForOffsetFieldOfViewImageFilter
class	DisplacedDetectorImageFilter
class	DivergenceOfGradientConjugateGradientOperator
class	DownsampleImageFilter
class	DPExtractShroudSignalImageFilter
class	DrawBoxImageFilter
class	DrawConeImageFilter
class	DrawConvexImageFilter
class	DrawCylinderImageFilter
class	DrawEllipsoidImageFilter
class	DrawGeometricPhantomImageFilter
class	DrawQuadricImageFilter
class	DrawSheppLoganFilter
class	DualEnergyNegativeLogLikelihood
class	EdfImageIO
class	EdfImageIOFactory
class	EdfRawToAttenuationImageFilter
class	ElektaSynergyGeometryReader
class	ElektaSynergyLookupTableImageFilter
class	ElektaSynergyRawLookupTableImageFilter
class	ElektaXVI5GeometryXMLFileReader
class	ExtractPhaseImageFilter
class	FDKBackProjectionImageFilter
class	FDKConeBeamReconstructionFilter
class	FDKWarpBackProjectionImageFilter
class	FDKWeightProjectionFilter
class	FFTProjectionsConvolutionImageFilter
class	FFTRampImageFilter
class	FieldOfViewImageFilter
class	ForbildPhantomFileReader
class	ForwardDifferenceGradientImageFilter
class	ForwardProjectionImageFilter
class	ForwardWarpImageFilter
class	FourDConjugateGradientConeBeamReconstructionFilter
class	FourDReconstructionConjugateGradientOperator
class	FourDROOSTERConeBeamReconstructionFilter
class	FourDSARTConeBeamReconstructionFilter
class	FourDToProjectionStackImageFilter
class	GeometricPhantom
class	GeometricPhantomFileReader
class	GetNewtonUpdateImageFilter
class	GlobalResourceProbe
class	HilbertImageFilter
class	HisImageIO
class	HisImageIOFactory
class	HncImageIO
class	HncImageIOFactory
class	HndImageIO
class	HndImageIOFactory
class	I0EstimationProjectionFilter
class	ImageToVectorImageFilter
class	ImagXGeometryReader
class	ImagXImageIO
class	ImagXImageIOFactory
class	ImagXXMLFileReader
class	ImportImageFilter
class	InterpolatorWithKnownWeightsImageFilter
class	IntersectionOfConvexShapes
class	IterationCommand
class	IterativeConeBeamReconstructionFilter
class	IterativeFDKConeBeamReconstructionFilter
class	JosephBackAttenuatedProjectionImageFilter
class	JosephBackProjectionImageFilter
class	JosephForwardAttenuatedProjectionImageFilter
class	JosephForwardProjectionImageFilter
class	LagCorrectionImageFilter
class	LaplacianImageFilter
class	LastDimensionL0GradientDenoisingImageFilter
class	LookupTableImageFilter
class	LUTbasedVariableI0RawToAttenuationImageFilter
class	MagnitudeThresholdImageFilter
class	MaskCollimationImageFilter
class	MatlabSparseMatrix
class	MechlemOneStepSpectralReconstructionFilter
class	MotionCompensatedFourDConjugateGradientConeBeamReconstructionFilter
class	MotionCompensatedFourDReconstructionConjugateGradientOperator
class	MotionCompensatedFourDROOSTERConeBeamReconstructionFilter
class	MultiplyByVectorImageFilter
class	NesterovUpdateImageFilter
class	NormalVariateNoiseFunctor
class	OraGeometryReader
class	OraImageIO
class	OraImageIOFactory
class	OraLookupTableImageFilter
class	OraXMLFileReader
class	OSEMConeBeamReconstructionFilter
class	OutputIterationCommand
class	ParkerShortScanImageFilter
class	PercentageProgressCommand
class	PhaseGatingImageFilter
class	PhaseReader
class	PhasesToInterpolationWeights
class	PolynomialGainCorrectionImageFilter
class	ProgressCommand
class	ProjectGeometricPhantomImageFilter
class	ProjectionGeometry
class	ProjectionsDecompositionNegativeLogLikelihood
class	ProjectionsReader
class	ProjectionsRegionConstIteratorRayBased
class	ProjectionsRegionConstIteratorRayBasedParallel
class	ProjectionsRegionConstIteratorRayBasedWithCylindricalPanel
class	ProjectionsRegionConstIteratorRayBasedWithFlatPanel
class	ProjectionStackToFourDImageFilter
class	QuadricShape
class	RayBoxIntersectionImageFilter
class	RayConvexIntersectionImageFilter
class	RayEllipsoidIntersectionImageFilter
class	RayQuadricIntersectionImageFilter
class	ReconstructImageFilter
class	ReconstructionConjugateGradientOperator
class	Reg1DExtractShroudSignalImageFilter
class	Reg23ProjectionGeometry
class	RegularizedConjugateGradientConeBeamReconstructionFilter
class	ReorderProjectionsImageFilter
class	ResourceProbesCollector
class	SARTConeBeamReconstructionFilter
class	ScatterGlareCorrectionImageFilter
class	Schlomka2008NegativeLogLikelihood
class	SelectOneProjectionPerCycleImageFilter
class	SeparableQuadraticSurrogateRegularizationImageFilter
class	SheppLoganPhantom
class	SheppLoganPhantomFilter
class	SignalToInterpolationWeights
class	SimplexSpectralProjectionsDecompositionImageFilter
class	SingularValueThresholdImageFilter
class	SoftThresholdImageFilter
class	SoftThresholdTVImageFilter
class	SpectralForwardModelImageFilter
class	SplatWithKnownWeightsImageFilter
class	SubSelectFromListImageFilter
class	SubSelectImageFilter
class	SumOfSquaresImageFilter
class	ThreeDCircularProjectionGeometry
class	ThreeDCircularProjectionGeometryXMLFileReader
class	ThreeDCircularProjectionGeometryXMLFileWriter
class	TotalNuclearVariationDenoisingBPDQImageFilter
class	TotalVariationDenoiseSequenceImageFilter
class	TotalVariationDenoisingBPDQImageFilter
class	TotalVariationImageFilter
class	UnwarpSequenceConjugateGradientOperator
class	UnwarpSequenceImageFilter
class	UpsampleImageFilter
class	VarianObiGeometryReader
class	VarianObiRawImageFilter
class	VarianObiXMLFileReader
class	VarianProBeamGeometryReader
class	VarianProBeamXMLFileReader
class	VectorImageToImageFilter
class	VerboseIterationCommand
class	WarpFourDToProjectionStackImageFilter
class	WarpProjectionStackToFourDImageFilter
class	WarpSequenceImageFilter
class	WatcherForResourceProbe
class	WaterPrecorrectionImageFilter
class	WeidingerForwardModelImageFilter
class	XimImageIO
class	XimImageIOFactory
class	XRadGeometryReader
class	XRadImageIO
class	XRadImageIOFactory
class	XRadRawToAttenuationImageFilter
class	ZengBackProjectionImageFilter
class	ZengForwardProjectionImageFilter

Functions
template<class TImageType >
itk::Matrix< double, TImageType::ImageDimension+1, TImageType::ImageDimension+1 >	GetIndexToPhysicalPointMatrix (const TImageType *image)
template<class TImageType >
itk::Matrix< double, TImageType::ImageDimension+1, TImageType::ImageDimension+1 >	GetPhysicalPointToIndexMatrix (const TImageType *image)
template<class TArgsInfo >
const std::vector< std::string >	GetProjectionsFileNamesFromGgo (const TArgsInfo &args_info)
RTK_EXPORT ThreeDCircularProjectionGeometry::Pointer	ReadGeometry (const std::string &filename)
static std::vector< double >	ReadSignalFile (std::string filename)
void RTK_EXPORT	RegisterIOFactories ()
template<class TArgsInfo , class TIterativeReconstructionFilter >
void	SetBackProjectionFromGgo (const TArgsInfo &args_info, TIterativeReconstructionFilter *recon)
template<class TConstantImageSourceType , class TArgsInfo >
void	SetConstantImageSourceFromGgo (typename TConstantImageSourceType::Pointer source, const TArgsInfo &args_info)
template<class TArgsInfo , class TIterativeReconstructionFilter >
void	SetForwardProjectionFromGgo (const TArgsInfo &args_info, TIterativeReconstructionFilter *recon)
template<class TProjectionsReaderType , class TArgsInfo >
void	SetProjectionsReaderFromGgo (typename TProjectionsReaderType::Pointer reader, const TArgsInfo &args_info)
template<typename OutputElementType , typename DetectorResponseImageType , typename ThresholdsType >
vnl_matrix< OutputElementType >	SpectralBinDetectorResponse (const DetectorResponseImageType *drm, const ThresholdsType &thresholds, const unsigned int numberOfEnergies)
template<typename ImageType >
void	WriteImage (typename ImageType::ConstPointer input, std::string name)
template<typename TGeometryPointer >
ITK_TEMPLATE_EXPORT void	WriteGeometry (TGeometryPointer &&geometry, const std::string &filename)

Function Documentation

GetIndexToPhysicalPointMatrix()

template<class TImageType >

itk::Matrix<double, TImageType::ImageDimension + 1, TImageType::ImageDimension + 1> rtk::GetIndexToPhysicalPointMatrix

(

const TImageType *

image

)

Get IndexToPhysicalPoint matrix from an image (no accessor provided by ITK).

The returned matrix is in homogeneous format.

Author

Simon Rit

Definition at line 40 of file rtkHomogeneousMatrix.h.

References Dimension, and point().

GetPhysicalPointToIndexMatrix()

template<class TImageType >

itk::Matrix<double, TImageType::ImageDimension + 1, TImageType::ImageDimension + 1> rtk::GetPhysicalPointToIndexMatrix

(

const TImageType *

image

)

Get PhysicalPointToIndex matrix from an image (no accessor provided by ITK).

The returned matrix is in homogeneous format.

Author

Simon Rit

Definition at line 77 of file rtkHomogeneousMatrix.h.

GetProjectionsFileNamesFromGgo()

template<class TArgsInfo >

const std::vector<std::string> rtk::GetProjectionsFileNamesFromGgo

(

const TArgsInfo &

args_info

)

Read a stack of 2D projections from gengetopt specifications.

This function sets a ProjectionsReader object from command line options stored in ggo struct. The projections are not buffered to allow streaming. The required options in the ggo struct are:

• verbose
• path: path containing projections
• regexp: regular expression to select projection files in path
• nsort: boolean to (des-)activate the numeric sort for expression matches
• submatch: index of the submatch that will be used to sort matches

Author

Simon Rit

Definition at line 117 of file rtkGgoFunctions.h.

References itk::ImageIOFactory::CreateImageIO(), itk::RegularExpressionSeriesFileNames::New(), itk::CommonEnums::ReadMode, and RegisterIOFactories().

Referenced by SetProjectionsReaderFromGgo().

ReadGeometry()

RTK_EXPORT ThreeDCircularProjectionGeometry::Pointer rtk::ReadGeometry

(

const std::string &

filename

)

Convenience function for reading a geometry XML file.

The function reads the geometry from the specified XML file, and returns the geometry that it has read.

ReadSignalFile()

static std::vector<double> rtk::ReadSignalFile ( std::string  filename )

inlinestatic

A few functions that are used either in the applications or for debugging purposes.

Author

Cyril Mory

Definition at line 42 of file rtkGeneralPurposeFunctions.h.

RegisterIOFactories()

void RTK_EXPORT rtk::RegisterIOFactories

(

)

Register all rtk IO factories.

Referenced by GetProjectionsFileNamesFromGgo().

SetBackProjectionFromGgo()

template<class TArgsInfo , class TIterativeReconstructionFilter >

void rtk::SetBackProjectionFromGgo	(	const TArgsInfo &	args_info,
		TIterativeReconstructionFilter *	recon
	)

Set the correct RTK backprojection type from gengetopt Given a gengetopt bp_arg option from the rtkprojectors_section.ggo, will set the corresponding enum value from rtk::IterativeConeBeamReconstructionFilter.

Author

Simon Rit

Definition at line 282 of file rtkGgoFunctions.h.

SetConstantImageSourceFromGgo()

template<class TConstantImageSourceType , class TArgsInfo >

void rtk::SetConstantImageSourceFromGgo	(	typename TConstantImageSourceType::Pointer	source,
		const TArgsInfo &	args_info
	)

Create 3D image from gengetopt specifications.

This function sets a ConstantImageSource object from command line options stored in ggo struct. The image is not buffered to allow streaming. The image is filled with zeros. The required options in the ggo struct are:

• dimension: image size in pixels
• spacing: image spacing in coordinate units
• origin: image origin in coordinate units

Author

Simon Rit

Definition at line 50 of file rtkGgoFunctions.h.

References Dimension, and TRY_AND_EXIT_ON_ITK_EXCEPTION.

SetForwardProjectionFromGgo()

template<class TArgsInfo , class TIterativeReconstructionFilter >

void rtk::SetForwardProjectionFromGgo	(	const TArgsInfo &	args_info,
		TIterativeReconstructionFilter *	recon
	)

Set the correct RTK forward projection type from gengetopt Given a gengetopt fp_arg option from the rtkprojectors_section.ggo, will set the corresponding enum value from rtk::IterativeConeBeamReconstructionFilter.

Author

Simon Rit

Definition at line 319 of file rtkGgoFunctions.h.

SetProjectionsReaderFromGgo()

template<class TProjectionsReaderType , class TArgsInfo >

void rtk::SetProjectionsReaderFromGgo	(	typename TProjectionsReaderType::Pointer	reader,
		const TArgsInfo &	args_info
	)

Definition at line 178 of file rtkGgoFunctions.h.

References Dimension, GetProjectionsFileNamesFromGgo(), and TRY_AND_EXIT_ON_ITK_EXCEPTION.

SpectralBinDetectorResponse()

template<typename OutputElementType , typename DetectorResponseImageType , typename ThresholdsType >

vnl_matrix<OutputElementType> rtk::SpectralBinDetectorResponse	(	const DetectorResponseImageType *	drm,
		const ThresholdsType &	thresholds,
		const unsigned int	numberOfEnergies
	)

WriteGeometry()

template<typename TGeometryPointer >

ITK_TEMPLATE_EXPORT void rtk::WriteGeometry	(	TGeometryPointer &&	geometry,
		const std::string &	filename
	)

Convenience function for writing an geometry.

The geometry parameter may be a either SmartPointer or a raw pointer and const or non-const.

Definition at line 93 of file rtkThreeDCircularProjectionGeometryXMLFileWriter.h.

References rtk::ThreeDCircularProjectionGeometryXMLFileWriter::New().

WriteImage()

template<typename ImageType >

void rtk::WriteImage	(	typename ImageType::ConstPointer	input,
		std::string	name
	)

Definition at line 71 of file rtkGeneralPurposeFunctions.h.