sirf Namespace Reference

Abstract base class for SIRF image data. More...

Classes
class	ANumRef
class	FloatRef
class	NumRef
class	ContainerBase
	Abstract data container. More...
class	DataContainer
	Abstract data container with numerical operations. More...
class	GeometricalInfo
class	VoxelisedGeometricalInfo
class	ImageData
class	JacobiCG
class	Wrapped_sptr
class	Operator
class	ImageDataWrap
class	Quaternion
	Class for quaternions. More...
class	AffineTransformation
	Class for affine transformations. More...
class	NiftiImageData
class	ImageWeightedMean
class	NiftiImageData3D
	Forward declarations. More...
class	NiftiBasedRegistration
	Base class for all NIfTI-based registrations. More...
class	NiftiImageData3DDisplacement
	Class for displacement SIRF image data. More...
class	NiftiImageData3DDeformation
	Class for deformation SIRF image data. More...
class	NiftiImageData3DTensor
	Class for tensor SIRF image data. More...
class	NiftyAladinSym
	NiftyReg's aladin class for rigid and affine registrations. More...
class	NiftyF3dSym
	NiftyReg's f3d class for non-rigid registrations. More...
class	NiftyRegistration
	Base class for all NiftyReg registrations. More...
class	NiftyResampler
	Resampling class based on nifty resample. More...
class	NonRigidTransformation
	Base class for non-rigid transformations. More...
class	Parser
class	ParserKeyBase
	Base for parser keys. More...
class	ParserKey0Arg
	Class for parser keys with 0 arguments. More...
class	ParserKey1Arg
	Class for parser keys with 1 argument. More...
class	ParserKey2Arg
	Class for parser keys with 2 arguments. More...
class	Transformation
	Forward declarations. More...
class	Registration
	Base class for all SIRF registration. More...
class	Resampler
class	BFOperator
	Backward projection of the forward projected image. More...
class	SPMRegistration
	Wrapper around SPM's registration class. More...
class	RemoveOversamplingProcessor
	Class for an xml-definition generator for oversampling removing chain. More...
class	SimpleReconstructionProcessor
	Class for an xml-definition generator for simple fully sampled reconstruction chain. More...
class	SimpleGRAPPAReconstructionProcessor
	Class for an xml-definition generator for simple undersampled GRAPPA reconstruction chain. More...
class	ExtractRealImagesProcessor
	Class for an xml-definition generator for real image extracting chain. More...
class	FourierEncoding
	Abstract class defining the interface to perform Fourier transforms. More...
class	CartesianFourierEncoding
	Class to perform a cartesian FFT. More...
class	aGadget
	Abstract base class for a gadget xml-definition generator. More...
class	Gadget
	Class for a gadget xml-definition generator. More...
class	IsmrmrdAcqMsgReader
	Class for GadgetIsmrmrdAcquisitionMessageReader gadget xml-definition generator. More...
class	IsmrmrdAcqMsgWriter
	Class for GadgetIsmrmrdAcquisitionMessageWriter gadget xml-definition generator. More...
class	IsmrmrdImgMsgReader
	Class for MRIImageReader gadget xml-definition generator. More...
class	ImageMessageWriter
	Base class for generators of xml-definitions of image writer gadgets. More...
class	IsmrmrdImgMsgWriter
	Class for MRIImageWriter gadget xml-definition generator. More...
class	DicomImageMessageWriter
	Class for DicomImageWriter gadget xml-definition generator. More...
class	NoiseAdjustGadget
	Class for the generator of xml definition of NoiseAdjustGadget. More...
class	PCACoilGadget
	Class for the generator of xml definition of PCACoilGadget. More...
class	CoilReductionGadget
	Class for the generator of xml definition of CoilReductionGadget. More...
class	AsymmetricEchoAdjustROGadget
	Class for the generator of xml definition of AsymmetricEchoAdjustROGadget. More...
class	RemoveROOversamplingGadget
	Class for the generator of xml definition of RemoveROOversamplingGadget. More...
class	AcquisitionAccumulateTriggerGadget
	Class for the generator of xml definition of AcquisitionAccumulateTriggerGadget. More...
class	BucketToBufferGadget
	Class for the generator of xml definition of BucketToBufferGadget. More...
class	GenericReconCartesianReferencePrepGadget
	Class for the generator of xml definition of GenericReconCartesianReferencePrepGadget. More...
class	GenericReconEigenChannelGadget
	Class for the generator of xml definition of GenericReconEigenChannelGadget. More...
class	GenericReconPartialFourierHandlingFilterGadget
	Class for the generator of xml definition of GenericReconPartialFourierHandlingFilterGadget. More...
class	GenericReconKSpaceFilteringGadget
	Class for the generator of xml definition of GenericReconKSpaceFilteringGadget. More...
class	SimpleReconGadget
	Class for the generator of xml definition of SimpleReconGadget. More...
class	FFTGadget
	Class for the generator of xml definition of FFTGadget. More...
class	CombineGadget
	Class for the generator of xml definition of CombineGadget. More...
class	GenericReconCartesianFFTGadget
	Class for the generator of xml definition of GenericReconCartesianFFTGadget. More...
class	GenericReconCartesianGrappaGadget
	Class for the generator of xml definition of GenericReconCartesianGrappaGadget. More...
class	GenericReconFieldOfViewAdjustmentGadget
	Class for the generator of xml definition of GenericReconFieldOfViewAdjustmentGadget. More...
class	GenericReconImageArrayScalingGadget
	Class for the generator of xml definition of GenericReconImageArrayScalingGadget. More...
class	FatWaterGadget
	Class for the generator of xml definition of FatWaterGadget. More...
class	ImageArraySplitGadget
	Class for the generator of xml definition of ImageArraySplitGadget. More...
class	PhysioInterpolationGadget
	Class for the generator of xml definition of PhysioInterpolationGadget. More...
class	GPURadialPrepGadget
	Class for the generator of xml definition of GPURadialPrepGadget. More...
class	GPURadialSensePrepGadget
	Class for the generator of xml definition of GPURadialSensePrepGadget. More...
class	GPUSenseGadget
	Class for the generator of xml definition of GPUSenseGadget. More...
class	GPUCGSenseGadget
	Class for the generator of xml definition of GPUCGSenseGadget. More...
class	ExtractGadget
	Class for the generator of xml definition of ExtractGadget. More...
class	AutoScaleGadget
	Class for the generator of xml definition of AutoScaleGadget. More...
class	ComplexToFloatGadget
	Class for the generator of xml definition of ComplexToFloatGadget. More...
class	FloatToFixPointGadget
	Class for the generator of xml definition of FloatToFixPointGadget. More...
class	FloatToUShortGadget
	Class for the generator of xml definition of FloatToUShortGadget. More...
class	FloatToShortGadget
	Class for the generator of xml definition of FloatToShortGadget. More...
class	ImageFinishGadget
	Class for the generator of xml definition of ImageFinishGadget. More...
class	DicomFinishGadget
	Class for the generator of xml definition of DicomFinishGadget. More...
class	AcquisitionFinishGadget
	Class for the generator of xml definition of AcquisitionFinishGadget. More...
class	SimpleReconGadgetSet
	Class for xml-definition generator for a simple fully sumpled reconstruction gadget set. More...
struct	GadgetMessageIdentifier
struct	GadgetMessageConfigurationFile
struct	GadgetMessageScript
class	GadgetronClientException
class	GadgetronClientMessageReader
	Abstract base class for receiving messages from Gadgetron server. More...
class	GadgetronClientAcquisitionMessageCollector
	Class for accumulating acquisitions sent by Gadgetron server. More...
class	GadgetronClientImageMessageCollector
	Class for accumulating ISMRMRD images sent by Gadgetron server. More...
class	GadgetronClientBlobMessageReader
class	GadgetronClientConnector
	Class for communicating with Gadgetron server. More...
class	AcquisitionsInfo
class	IgnoreMask
	Class enabling ignoring acquisitions with certain ISMRMRD acquisition flags. More...
class	KSpaceSubset
	Class to keep track of order in k-space. More...
class	MRAcquisitionData
	Abstract MR acquisition data container class. More...
class	AcquisitionsVector
	A vector implementation of the abstract MR acquisition data container class. More...
class	ISMRMRDImageData
	Abstract Gadgetron image data container class. More...
class	GadgetronImagesVector
	A vector implementation of the abstract Gadgetron image data container class. More...
class	CoilImagesVector
	A coil images container based on the GadgetronImagesVector class. More...
class	CoilSensitivitiesVector
	A coil sensitivities container based on the GadgetronImagesVector class. More...
class	ImageWrap
	Wrapper for ISMRMRD::Image. More...
class	GTConnector
	Shared pointer wrap-up for GadgetronClientConnector. More...
class	GadgetHandle
	Shared pointer wrap-up for the abstract gadget class aGadget. More...
class	GadgetChain
	Gadget chain class. More...
class	AcquisitionsProcessor
	A particular type of Gadget chain that has AcquisitionData on input and output. More...
class	ImagesReconstructor
	A particular type of Gadget chain that has AcquisitionData on input and ImageData on output. More...
class	ImagesProcessor
	A particular type of Gadget chain that has ImageData on input and output. More...
class	MRAcquisitionModel
	A class for MR acquisition modelling. More...
class	Gridder
	Class to perform a NUFFT for 2D data. More...
class	RPEFourierEncoding
	Implementation to perform a non-cartesian FFT for RPE MR data. More...
class	NonCartesian2DEncoding
class	TrajectoryPreparation
	Abstract class defining the interface to set trajectories. More...
class	CartesianTrajectoryPrep
	Class to get cartesian encoding phase encoding locations. More...
class	GRPETrajectoryPrep
	Class to set the golden-angle radial phase encoding (GRPE) trajectory. More...
class	NonCartesian2DTrajPrep
	Interface to set the 2D radial trajectory. More...
class	Radial2DTrajprep
	Implementation to set anglular increment for 2D radial trajectory based on (Pi=3.141...)/#Angles. More...
class	GoldenAngle2DTrajprep
	Implementation to set anglular increment for 2D radial trajectory based on doi:10.1109/TMI.2006.885337. More...
class	xGadgetronUtilities
class	Mutex
class	SIRFUtilities
class	ProjDataFile
	STIR ProjDataInterfile wrapper with additional file managing features. More...
class	STIRAcquisitionData
	STIR ProjData wrapper with added functionality. More...
class	STIRAcquisitionDataInFile
	In-file implementation of STIRAcquisitionData. More...
class	STIRAcquisitionDataInMemory
	In-memory implementation of STIRAcquisitionData. More...
class	STIRListmodeData
class	STIRImageData
	STIR DiscretisedDensity<3, float> wrapper with added functionality. More...
class	ListmodeToSinograms
	Listmode-to-sinograms converter. More...
class	PETAcquisitionSensitivityModel
	Class for PET scanner detector efficiencies model. More...
class	PETAcquisitionModel
	Class for a PET acquisition model. More...
class	PETSingleScatterSimulator
	Class for simulating the scatter contribution to PET data. More...
class	PETScatterEstimator
	Class for estimating the scatter contribution in PET projection data. More...
class	PETAcquisitionModelUsingMatrix
	Ray tracing matrix implementation of the PET acquisition model. More...
class	PETAcquisitionModelUsingRayTracingMatrix
class	PETAttenuationModel
	Attenuation model. More...
class	xSTIR_Box3D
	Accessor classes. More...
class	xSTIR_GeneralisedPrior3DF
class	xSTIR_QuadraticPrior3DF
class	xSTIR_LogcoshPrior3DF
class	xSTIR_RelativeDifferencePrior3DF
class	xSTIR_PLSPrior3DF
class	xSTIR_GeneralisedObjectiveFunction3DF
class	xSTIR_PoissonLogLikelihoodWithLinearModelForMeanAndProjData3DF
class	xSTIR_PoissonLLhLinModMeanListDataProjMatBin3DF
class	xSTIR_IterativeReconstruction3DF
class	xSTIR_OSMAPOSLReconstruction3DF
class	xSTIR_KOSMAPOSLReconstruction3DF
class	xSTIR_OSSPSReconstruction3DF
class	xSTIR_FBP2DReconstruction
class	xSTIR_SeparableGaussianImageFilter

Typedefs
typedef std::map< std::string, int >	Dimensions
typedef GeometricalInfo< 3, 3 >	GeometricalInfo3D
typedef VoxelisedGeometricalInfo< 3 >	VoxelisedGeometricalInfo3D
typedef VoxelisedGeometricalInfo< 3 >::TransformMatrix	TransformMatrix3D
using	SIRF_DEPRECATED_USING = NiftyResampler< float >
typedef ISMRMRDImageData	GadgetronImageData
typedef Gadgetron::hoNDArray< std::complex< float > >	CFGThoNDArr
typedef Gridder< 2 >	Gridder2D
typedef TrajectoryPreparation< 2 >	TrajectoryPreparation2D
typedef TrajectoryPreparation< 3 >	TrajectoryPreparation3D
typedef STIRAcquisitionData	PETAcquisitionData
typedef STIRAcquisitionDataInFile	PETAcquisitionDataInFile
typedef STIRAcquisitionDataInMemory	PETAcquisitionDataInMemory
typedef Image3DF::full_iterator	Image3DFIterator
typedef Image3DF::const_full_iterator	Image3DFIterator_const
typedef stir::DiscretisedDensity< 3, float >	Image3DF
typedef stir::shared_ptr< Image3DF >	sptrImage3DF
typedef stir::shared_ptr< stir::ProjData >	sptrProjData
typedef stir::CartesianCoordinate3D< float >	Coord3DF
typedef stir::CartesianCoordinate3D< int >	Coord3DI
typedef stir::VoxelsOnCartesianGrid< float >	Voxels3DF
typedef stir::shared_ptr< Voxels3DF >	sptrVoxels3DF
typedef stir::shared_ptr< stir::Shape3D >	sptrShape3D
typedef stir::Reconstruction< Image3DF >	Reconstruction3DF
typedef stir::IterativeReconstruction< Image3DF >	IterativeReconstruction3DF
typedef stir::GeneralisedObjectiveFunction< Image3DF >	ObjectiveFunction3DF
typedef stir::PoissonLogLikelihoodWithLinearModelForMean< Image3DF >	PoissonLogLhLinModMean3DF
typedef stir::ProjectorByBinPairUsingProjMatrixByBin	ProjectorPairUsingMatrix
typedef stir::ProjMatrixByBinUsingRayTracing	RayTracingMatrix
typedef stir::ProjMatrixByBinSPECTUB	SPECTUBMatrix
typedef stir::GeneralisedPrior< Image3DF >	Prior3DF
typedef stir::QuadraticPrior< float >	QuadPrior3DF
typedef stir::LogcoshPrior< float >	LogPrior3DF
typedef stir::RelativeDifferencePrior< float >	RDPrior3DF
typedef stir::PLSPrior< float >	PLSPrior3DF
typedef stir::DataProcessor< Image3DF >	DataProcessor3DF
typedef stir::TruncateToCylindricalFOVImageProcessor< float >	CylindricFilter3DF
typedef DataProcessor3DF	ImageDataProcessor
	A typedef to use SIRF terminology for DataProcessors. More...
typedef PETAcquisitionModel	AcqMod3DF
typedef PETAcquisitionModelUsingMatrix	AcqModUsingMatrix3DF
typedef std::shared_ptr< AcqMod3DF >	sptrAcqMod3DF
typedef xSTIR_PoissonLogLikelihoodWithLinearModelForMeanAndProjData3DF	PoissonLogLhLinModMeanProjData3DF
typedef xSTIR_PoissonLLhLinModMeanListDataProjMatBin3DF	PoissonLLhLinModMeanListDataProjMatBin3DF

Functions
bool	iequals (const std::string &a, const std::string &b)
	Case insensitive string comparison, replaces boost::iequals.
template<typename Type >
NumberType::Type	TypeID (Type t)
std::string	getenv (const char *name, bool throws=false)
char	path_separator ()
	return the path-separator used by the OS More...
void *	cReg_NiftiImageDataParameter (const DataHandle *handle, const char *name)
void *	cReg_setRegistrationParameter (void *hp, const char *name, const void *hv)
void *	cReg_setNiftyRegistrationParameter (void *hp, const char *name, const void *hv)
void *	cReg_setNiftyF3dSymParameter (void *hp, const char *name, const void *hv)
void *	cReg_setNiftyResamplerParameter (void *hp, const char *name, const void *hv)
void *	cReg_NiftyResamplerParameter (const DataHandle *handle, const char *name)
void *	cReg_ImageWeightedMeanParameter (const DataHandle *handle, const char *name)
void *	cReg_AffineTransformationParameter (const DataHandle *handle, const char *name)
template<class A >
std::string	get_typename (A)
	Get template type as human-readable name.
void *	cGT_acquisitionParameter (void *ptr_acq, const char *name)
void *	cGT_acquisitionsParameter (void *ptr_acq, const char *name)
void *	cGT_imageParameter (void *ptr_im, const char *name)
void *	cGT_AcquisitionModelParameter (void *ptr_am, const char *name)
void *	cGT_setCSParameter (void *ptr, const char *par, const void *val)
void	match_img_header_to_acquisition (CFImage &img, const ISMRMRD::Acquisition &acq)
void	preprocess_acquisition_data (MRAcquisitionData &ad)
void	set_unit_dcf (MRAcquisitionData &ad)
void	set_acq_default_orientation (std::string path_in, std::string path_out)
void	write_cfimage_to_raw (const std::string &fname_prefix, const CFImage &img)
void	write_cfimage_to_raw (const std::string &fname_prefix, const ImageWrap &iw)
void	write_imagevector_to_raw (const std::string &fname_prefix, const sirf::GadgetronImagesVector &iv)
sirf::MRAcquisitionModel	get_prepared_MRAcquisitionModel (const MRAcquisitionData &ad)
void *	cSTIR_setImageDataParameter (void *hp, const char *name, const void *hv)
void *	cSTIR_AcquisitionDataParameter (void *hp, const char *name)
void *	cSTIR_ImageDataParameter (void *hp, const char *name)
void *	cSTIR_setListmodeToSinogramsParameter (void *hp, const char *name, const void *hv)
void *	cSTIR_setShapeParameter (void *hp, const char *name, const void *hv)
void *	cSTIR_shapeParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setBox3DParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_Box3DParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setEllipsoidParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_ellipsoidParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setEllipsoidalCylinderParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_ellipsoidalCylinderParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setRayTracingMatrixParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_rayTracingMatrixParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setSPECTUBMatrixParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_SPECTUBMatrixParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setPinholeSPECTUBMatrixParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_PinholeSPECTUBMatrixParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setAcquisitionModelParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_AcquisitionModelParameter (DataHandle *hm, const char *name)
void *	cSTIR_setAcqModUsingMatrixParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_acqModUsingMatrixParameter (DataHandle *hp, const char *name)
void *	cSTIR_setTruncateToCylindricalFOVImageProcessorParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_truncateToCylindricalFOVImageProcessorParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setSeparableGaussianImageFilterParameter (void *hp, const char *name, const void *hv)
void *	cSTIR_setGeneralisedPriorParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_generalisedPriorParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setQuadraticPriorParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_QuadraticPriorParameter (DataHandle *hp, const char *name)
void *	cSTIR_setLogcoshPriorParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_LogcoshPriorParameter (DataHandle *hp, const char *name)
void *	cSTIR_setRelativeDifferencePriorParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_RelativeDifferencePriorParameter (DataHandle *hp, const char *name)
void *	cSTIR_setPLSPriorParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_PLSPriorParameter (DataHandle *hp, const char *name)
void *	cSTIR_generalisedObjectiveFunctionParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setScatterSimulatorParameter (const DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_setScatterEstimatorParameter (const DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_ScatterEstimatorParameter (DataHandle *hp, const char *name)
void *	cSTIR_setGeneralisedObjectiveFunctionParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_setPoissonLogLikelihoodWithLinearModelForMeanParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_setPoissonLogLikelihoodWithLinearModelForMeanAndProjDataParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_setPoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBinParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBinParameter (DataHandle *handle, const char *name)
void *	cSTIR_PoissonLogLikelihoodWithLinearModelForMeanAndProjDataParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setReconstructionParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_setIterativeReconstructionParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_iterativeReconstructionParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setOSMAPOSLParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_OSMAPOSLParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setOSSPSParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_OSSPSParameter (const DataHandle *handle, const char *name)
void *	cSTIR_setFBP2DParameter (DataHandle *hp, const char *name, const DataHandle *hv)
void *	cSTIR_FBP2DParameter (DataHandle *hp, const char *name)
template<typename T >
std::string	append_path (std::string path, T a)
template<typename T , typename... Ts>
std::string	append_path (std::string path, T a, Ts... args)
std::string	examples_data_path (const char *data_type)

Detailed Description

Abstract base class for SIRF image data.

Serialized ISMRMRD acquisition header (cf. ismrmrd.h).

Typedef Documentation

ImageDataProcessor

typedef DataProcessor3DF sirf::ImageDataProcessor

A typedef to use SIRF terminology for DataProcessors.

\todo We should have a sirf::ImageDataProcessor which takes a sirf::ImageData, but that's too much work for now...

PETAcquisitionData

typedef STIRAcquisitionData sirf::PETAcquisitionData

Backward compatibility - to be removed in SIRF 4

Function Documentation

append_path()

template<typename T >

std::string sirf::append_path	(	std::string	path,
		T	a
	)

concatenate path strings

Example:

std::string filename = "somefile.txt";
std:string full_path = append_path("/usr/local", "share", filename);

warning

The code does not check if there are already trailing path-separators, nor if the resulting path exists.

examples_data_path()

std::string sirf::examples_data_path

(

const char *

data_type

)

Returns where the examples are installed

Example:

std::string p = examples_data_path("PET");

path_separator()

char sirf::path_separator

(

)

return the path-separator used by the OS

Usually this will return a forward-slash, but it could be a backslash on Windows.