Abstract data container. More...

Classes
class	AcquisitionAccumulateTriggerGadget

class	AcquisitionFinishGadget

class	AcquisitionsInfo

class	AcquisitionsProcessor
	A particular type of Gadget chain that has AcquisitionData on input and output. More...

class	AcquisitionsVector
	A vector implementation of the abstract MR acquisition data container class. More...

class	AffineTransformation
	Class for affine transformations. More...

class	aGadget
	Abstract base class for a gadget xml-definition generator. More...

class	ANumRef

class	AsymmetricEchoAdjustROGadget

class	AutoScaleGadget

class	BucketToBufferGadget

class	CartesianFourierEncoding
	Class to perform a cartesian FFT. More...

class	CartesianTrajectoryPrep
	Class to get cartesian encoding phase encoding locations. More...

class	CoilImagesVector
	A coil images container based on the GadgetronImagesVector class. More...

class	CoilReductionGadget

class	CoilSensitivitiesVector
	A coil sensitivities container based on the GadgetronImagesVector class. More...

class	ComplexToFloatGadget

class	DataContainer

class	DicomFinishGadget

class	DicomImageMessageWriter
	Class for DicomImageWriter gadget xml-definition generator. More...

class	ExtractGadget

class	ExtractRealImagesProcessor
	Class for an xml-definition generator for real image extracting chain. More...

class	FatWaterGadget

class	FloatRef

class	FloatToFixPointGadget

class	FloatToShortGadget

class	FloatToUShortGadget

class	FourierEncoding
	Abstract class defining the interface to perform Fourier transforms. More...

class	Gadget
	Class for a gadget xml-definition generator. More...

class	GadgetChain
	Gadget chain class. More...

class	GadgetHandle
	Shared pointer wrap-up for the abstract gadget class aGadget. More...

struct	GadgetMessageConfigurationFile

struct	GadgetMessageIdentifier

struct	GadgetMessageScript

class	GadgetronClientAcquisitionMessageCollector
	Class for accumulating acquisitions sent by Gadgetron server. More...

class	GadgetronClientBlobMessageReader

class	GadgetronClientConnector
	Class for communicating with Gadgetron server. More...

class	GadgetronClientException

class	GadgetronClientImageMessageCollector
	Class for accumulating ISMRMRD images sent by Gadgetron server. More...

class	GadgetronClientMessageReader
	Abstract base class for receiving messages from Gadgetron server. More...

class	GadgetronImagesVector
	A vector implementation of the abstract Gadgetron image data container class. More...

class	GenericReconCartesianFFTGadget

class	GenericReconCartesianGrappaGadget

class	GenericReconCartesianReferencePrepGadget

class	GenericReconFieldOfViewAdjustmentGadget

class	GenericReconImageArrayScalingGadget

class	GeometricalInfo

class	GoldenAngle2DTrajprep
	Implementation to set anglular increment for 2D radial trajectory based on doi:10.1109/TMI.2006.885337. More...

class	GPUCGSenseGadget

class	GPURadialPrepGadget

class	GPURadialSensePrepGadget

class	GPUSenseGadget

class	Gridder
	Class to perform a NUFFT for 2D data. More...

class	GRPETrajectoryPrep
	Class to set the golden-angle radial phase encoding (GRPE) trajectory. More...

class	GTConnector
	Shared pointer wrap-up for GadgetronClientConnector. More...

class	ImageArraySplitGadget

class	ImageData

class	ImageDataWrap

class	ImageFinishGadget

class	ImageMessageWriter

class	ImagesProcessor
	A particular type of Gadget chain that has ImageData on input and output. More...

class	ImagesReconstructor
	A particular type of Gadget chain that has AcquisitionData on input and ImageData on output. More...

class	ImageWeightedMean

class	ImageWrap
	Wrapper for ISMRMRD::Image. More...

class	IsmrmrdAcqMsgReader
	Class for GadgetIsmrmrdAcquisitionMessageReader gadget xml-definition generator. More...

class	IsmrmrdAcqMsgWriter
	Class for GadgetIsmrmrdAcquisitionMessageWriter gadget xml-definition generator. More...

class	ISMRMRDImageData
	Abstract Gadgetron image data container class. More...

class	IsmrmrdImgMsgReader
	Class for MRIImageReader gadget xml-definition generator. More...

class	IsmrmrdImgMsgWriter
	Class for MRIImageWriter gadget xml-definition generator. More...

class	JacobiCG

class	KSpaceSubset
	Class to keep track of order in k-space. More...

class	ListmodeToSinograms
	Listmode-to-sinograms converter. More...

class	MRAcquisitionData
	Abstract MR acquisition data container class. More...

class	MRAcquisitionModel
	A class for MR acquisition modelling. More...

class	Mutex

class	NiftiBasedRegistration
	Base class for all NIfTI-based registrations. More...

class	NiftiImageData

class	NiftiImageData3D
	Forward declarations. More...

class	NiftiImageData3DDeformation
	Class for deformation SIRF image data. More...

class	NiftiImageData3DDisplacement
	Class for displacement 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	NoiseAdjustGadget

class	NonCartesian2DEncoding

class	NonCartesian2DTrajPrep
	Interface to set the 2D radial trajectory. More...

class	NonRigidTransformation
	Base class for non-rigid transformations. More...

class	NumRef

class	Operator

class	Parser

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	ParserKeyBase
	Base for parser keys. More...

class	PCACoilGadget

class	PETAcquisitionData
	STIR ProjData wrapper with added functionality. More...

class	PETAcquisitionDataInFile
	In-file implementation of PETAcquisitionData. More...

class	PETAcquisitionDataInMemory
	In-memory implementation of PETAcquisitionData. More...

class	PETAcquisitionModel
	Class for a PET acquisition model. More...

class	PETAcquisitionModelUsingMatrix
	Ray tracing matrix implementation of the PET acquisition model. More...

class	PETAcquisitionModelUsingRayTracingMatrix

class	PETAcquisitionSensitivityModel
	Class for PET scanner detector efficiencies model. More...

class	PETAttenuationModel
	Attenuation model. More...

class	PETScatterEstimator
	Class for estimating the scatter contribution in PET projection data. More...

class	PETSingleScatterSimulator
	Class for simulating the scatter contribution to PET data. More...

class	PhysioInterpolationGadget

class	ProjDataFile
	STIR ProjDataInterfile wrapper with additional file managing features. More...

class	Quaternion
	Class for quaternions. More...

class	Radial2DTrajprep
	Implementation to set anglular increment for 2D radial trajectory based on (Pi=3.141...)/#Angles. More...

class	Registration
	Base class for all SIRF registration. More...

class	RemoveOversamplingProcessor
	Class for an xml-definition generator for oversampling removing chain. More...

class	RemoveROOversamplingGadget

class	Resampler

class	RPEFourierEncoding
	Implementation to perform a non-cartesian FFT for RPE MR data. More...

class	SimpleGRAPPAReconstructionProcessor
	Class for an xml-definition generator for simple undersampled GRAPPA reconstruction chain. More...

class	SimpleReconGadget

class	SimpleReconGadgetSet
	Class for xml-definition generator for a simple fully sumpled reconstruction gadget set. More...

class	SimpleReconstructionProcessor
	Class for an xml-definition generator for simple fully sampled reconstruction chain. More...

class	SIRFUtilities

class	SPMRegistration
	Wrapper around SPM's registration class. More...

class	STIRImageData
	STIR DiscretisedDensity<3, float> wrapper with added functionality. More...

class	TrajectoryPreparation
	Abstract class defining the interface to set trajectories. More...

class	Transformation
	Forward declarations. More...

class	VoxelisedGeometricalInfo

class	xGadgetronUtilities

class	xSTIR_FBP2DReconstruction

class	xSTIR_GeneralisedObjectiveFunction3DF

class	xSTIR_GeneralisedPrior3DF
	Accessor classes. More...

class	xSTIR_IterativeReconstruction3DF

class	xSTIR_OSMAPOSLReconstruction3DF

class	xSTIR_OSSPSReconstruction3DF

class	xSTIR_PLSPrior3DF

class	xSTIR_PoissonLogLikelihoodWithLinearModelForMeanAndProjData3DF

class	xSTIR_QuadraticPrior3DF

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 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::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

Functions
bool	iequals (const std::string &a, const std::string &b)
	Case insensitive string comparison, replaces boost::iequals.

void	fix_path_separator (std::string &path)

template<typename Type >
NumberType::Type	TypeID (Type t)

std::string	getenv (const char *name, bool throws=false)

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_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_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_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_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)

Detailed Description

Abstract data container.

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

Abstract base class for SIRF image data.

A class for a set of generally heterogeneous items of data.

Has vector features: norm, dot product, linear combination, which rely on the same features of the items.

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...

Classes

Typedefs

Functions

Detailed Description

Typedef Documentation

◆ ImageDataProcessor