stir Namespace Reference

Namespace for the STIR library (and some/most of its applications) More...

Namespaces
	BSpline
	Namespace for functions and classes for B-Spline interpolation in the STIR library.
	detail
	Namespace for the implementation details of the STIR library.
	ecat
	Namespace for the ECAT IO part of the STIR library (and some/most of its applications)
	GE
	Namespace for the part of the STIR library that handles GE data (and some/most of its applications)

Classes
class	AbsTimeInterval
	Base class for specifying a time interval (in absolute time) More...
class	AbsTimeIntervalFromDynamicData
	class for specifying a time interval via a dynamic scan More...
class	AbsTimeIntervalFromECAT7ACF
	class for specifying a time interval via an ECAT7 .a file More...
class	AbsTimeIntervalWithParsing
	class for specifying a time interval via parsing of explicit times More...
class	AnalyticReconstruction
	base class for all analytic reconstruction algorithmsThis class provides extra functinoality (compared to Reconstruction) as it assumes that the TargetT is really a VoxelsOnCartesianGrid. More...
class	ArcCorrection
	A class to arc-correct projection data. More...
class	ArcCorrectionTests
	Test class for ArcCorrection. More...
class	Array
	This class defines multi-dimensional (numeric) arrays. More...
class	Array< 1, elemT >
	The 1-dimensional (partial) specialisation of Array. More...
class	ArrayFilter1DUsingConvolution
	This class implements convolution of a 1D array with an arbitrary (i.e. potentially non-symmetric) kernel. More...
class	ArrayFilter1DUsingConvolutionSymmetricKernel
	This class implements convolution of a 1D array with a symmetric kernel. More...
class	ArrayFilterTests
	Tests Array functionality. More...
class	ArrayFilterUsingRealDFTWithPadding
	This class implements convolution of an array of real numbers with an arbitrary (i.e. potentially non-symmetric) kernel using DFTs. More...
class	ArrayFunctionObject
	A class for operations on n-dimensional Arrays. More...
class	ArrayFunctionObject_1ArgumentImplementation
	A convenience class for children of ArrayFunctionObject. It implements the 2 argument operator() in terms of the in-place version. More...
class	ArrayFunctionObject_2ArgumentImplementation
	A convenience class for children of ArrayFunctionObject. It implements the in-place operator() in terms of the 2 argument version. More...
class	ArrayTests
	Tests Array functionality. More...
class	BackProjectorByBin
	Abstract base class for all back projectors. More...
class	BackProjectorByBinNiftyPET
	Class for NiftyPET's GPU back projector. More...
class	BackProjectorByBinParallelproj
	Class for Parallelproj's back projector. More...
class	BackProjectorByBinUsingInterpolation
	does backprojection by interpolating between the bins. More...
class	BackProjectorByBinUsingProjMatrixByBin
	This implements the BackProjectorByBin interface, given any ProjMatrixByBin object. More...
class	BackProjectorByBinUsingSquareProjMatrixByBin
	This implements the BackProjectorByBin interface, given any ProjMatrixByBin object. More...
class	BasicCoordinate
	class BasicCoordinate<int num_dimensions, typename coordT> defines num_dimensions -dimensional coordinates. More...
class	BeginEndAllFunction
	Helper class for NestedIterator when the 1st level iterator refers to a stir full iterator for the 2nd level iterator. More...
class	BeginEndFunction
	Helper class for NestedIterator when the 1st level iterator refers to an ordinary iterator for the 2nd level iterator. More...
class	Bin
	A class for storing coordinates and value of a single projection bin. More...
struct	BinAndCorr
	A small bundle of a Bin and its additive correction value. More...
class	BinNormalisation
	Abstract base class for implementing bin-wise normalisation of data. More...
class	BinNormalisationFromAttenuationImage
	A BinNormalisation class that gets attenuation correction factors from an attenuation image. More...
class	BinNormalisationFromML2D
	A BinNormalisation class that gets the normalisation factors from the files output by find_ML_normfactors. More...
class	BinNormalisationFromProjData
	A BinNormalisation class that gets the normalisation factors from a ProjData object. More...
class	BinNormalisationPETFromComponents
	A BinNormalisation class that uses component-based normalisation for PET. More...
class	BinNormalisationSinogramRescaling
	The BinNormalisationSinogramRescaling class gets normaliastion factors by dividing forward projection of the fitted cyl. to the precorrecred data. More...
class	BinNormalisationWithCalibration
class	BlocksTests
	Test class for Blocks. More...
class	BloodFrameData
	A class for storing plasma samples of a single study. More...
class	BoundaryConditions
	Preliminary class to specify boundary conditions for filters. More...
class	Box3D
	Three-dimensional cuboid box. More...
class	ByteOrder
	This class provides member functions to find out what byte-order your machine is and to swap numbers. More...
class	ByteOrderTests
	Test class for ByteOrder and the preprocessor defines from ByteOrderDefine.h. More...
class	CartesianCoordinate2D
	a templated class for 2-dimensional coordinates. More...
class	CartesianCoordinate3D
	a templated class for 3-dimensional coordinates. More...
class	ChainedBinNormalisation
	A BinNormalisation class that simply multiplies the factors given by 2 BinNormalisation objects. More...
class	ChainedDataProcessor
	A class in the DataProcessor hierarchy that calls 2 DataProcessors in sequence. More...
class	CListEvent
	Class for storing and using a coincidence event from a list mode file. More...
class	CListEventCylindricalScannerWithDiscreteDetectors
	Class for storing and using a coincidence event from a list mode file for a cylindrical scanner. More...
class	CListEventCylindricalScannerWithViewTangRingRingEncoding
	Helper class for listmode events when using 2d sinograms and ring-pairs is most efficient. More...
class	CListEventDataLMF
	Class for storing and using a coincidence event from a listmode file. More...
class	CListEventDataNeuroLF
	Class for record with coincidence data using NeuroLF bitfield definition. More...
class	CListEventDataSAFIR
	Class for record with coincidence data using SAFIR bitfield definition. More...
class	CListEventPENN
	Class for handling PENNPet Explorer events. More...
class	CListEventSAFIR
class	CListEventScannerWithDiscreteDetectors
	Class for storing and using a coincidence event from a list mode file for a cylindrical single layer scanner. More...
class	CListModeData
	The base class for reading PET (i.e. coincidence) list mode data.The only difference w.r.t. ListModeData is the used of CListRecord and a virtual function to check if delayeds are present. More...
class	CListModeDataLMF
	A class that reads the listmode data from an LMF file. More...
class	CListModeDataPENN
	Base class for listmode data for PENNPET Explorer scanner. More...
class	CListModeDataROOT
	class that reads ROOT files, generated by GATE, as listmode data. More...
class	CListModeDataSAFIR
	Class for reading SAFIR listmode data with variable geometry. More...
class	CListRecord
	Class for records in a PET list mode file. More...
class	CListRecordLMF
	A class for a general element of a listmode file. More...
class	CListRecordROOT
	A class for a general element of a listmode file for a Siemens scanner using the ROOT files. More...
class	CListRecordSAFIR
	Class for general SAFIR record, containing a union of data, time and raw record and providing access to certain elements. More...
class	CListTimeDataLMF
	A class for storing and using a timing 'event' from a listmode file. More...
class	CListTimeDataSAFIR
	Class for record with time data using SAFIR bitfield definition. More...
class	CListTimeROOT
	A class for storing and using a timing 'event' from a listmode file from the ECAT 8_32bit scanner. More...
class	ColsherFilter
	This class contains the Colsher filter used for 3D-PET reconstruction. More...
class	CombinedShape3D
	A class that allows combining several shapes using logical operations. More...
class	ConstBeginEndAllFunction
	Convenience class where the 2nd level iterator is a const_full_iterator. More...
class	ConstBeginEndFunction
	Convenience class where the 2nd level iterator is a const_iterator. More...
class	ConstPtrBeginEndAllFunction
	Convenience class where the 2nd level iterator is a const_full_iterator. More...
class	ConstPtrBeginEndFunction
	Convenience class where the 2nd level iterator is a const_iterator. More...
class	convert_array_Tests
	tests convert_array functionality More...
class	Coordinate2D
	a templated class for 2-dimensional coordinates. More...
class	Coordinate3D
	a templated class for 3-dimensional coordinates. More...
class	Coordinate4D
	a templated class for 4-dimensional coordinates. More...
class	coordinateTests
	Class with tests for BasicCoordinate, Coordinate3D et al. More...
struct	CopyFill
	Helper class for stir::copy_to and stir::fill_from. More...
struct	CopyFill< Array< num_dimensions, elemT > >
	Helper class for stir::copy_to and stir::fill_from. More...
struct	CopyFill< DynamicProjData >
	Copy all bins to a range specified by an iterator. More...
struct	CopyFill< MultipleProjData >
	Copy all bins to a range specified by an iterator. More...
struct	CopyFill< ProjData >
	Helper class for stir::copy_to and stir::fill_from. More...
class	CorrectProjDataApplication
	class to do precorrections More...
class	CPUTimer
	A class for measuring elapsed CPU time. More...
class	CreateTailMaskFromACFs
	The CreateTailMaskFromACFs class. More...
class	CudaRelativeDifferencePrior
	CUDA implementation of the Relative Difference prior. More...
class	DataProcessor
	Base class that defines an interface for classes that do data processing. More...
class	DataSymmetriesForBins
	A class for encoding/finding symmetries common to the geometry of the projection data and the discretised density. More...
class	DataSymmetriesForBins_PET_CartesianGrid
	Symmetries appropriate for a (cylindrical) PET scanner, and a discretised density on a Cartesian grid. More...
class	DataSymmetriesForBins_PET_CartesianGridTests
	Test class for DataSymmetriesForBins_PET_CartesianGrid. More...
class	DataSymmetriesForDensels
	A class for encoding/finding symmetries common to the geometry of the projection data and the discretised density. More...
class	DataSymmetriesForDensels_PET_CartesianGrid
	Symmetries appropriate for a (cylindrical) PET scanner, and a discretised density on a Cartesian grid. More...
class	DataSymmetriesForViewSegmentNumbers
	A class for encoding/finding symmetries. Works only on ViewSegmentNumbers (instead of Bin). More...
struct	DateTimeStrings
	A simple structure to hold 2 strings (date and time) More...
class	DateTimeTest
	Class with tests for date time functions. More...
class	DetectionPosition
	A class for storing coordinates of a detection. More...
class	DetectionPosition_Tests
	Class with tests for DetectionPosition. More...
class	DetectionPositionPair
	A class for storing 2 coordinates-sets of a detection, together with a timing-position index (for TOF), as suitable for PET. More...
class	DetectionPosMapTests
	Test class for Blocks. More...
class	DetectorCoordinateMap
class	DiscretisedDensity
	This abstract class is the basis for all image representations. More...
class	DiscretisedDensityOnCartesianGrid
	This abstract class is the basis for images on a Cartesian grid. More...
class	DiscretisedShape3D
	A class for shapes that have been discretised as a volume. More...
class	DistributedCachingInformation
	This class implements the logic needed to support caching in a distributed manner. More...
class	DistributedWorker
	This implements the Worker for the stir::distributable_computation() function. More...
class	DynamicDiscretisedDensity
	Class of multiple image frames, one for each time frame Each time frame is a DiscretisedDensity<3,float> More...
class	DynamicProjData
	Dynamic projection data. More...
class	Ellipsoid
	Three-dimensional ellipsoid. More...
class	EllipsoidalCylinder
	Three-dimensional ellipsoidal cylinder. More...
class	erfTests
	A simple class to test the erf and erfc functions. More...
class	ExamData
	base class for data objects such as ProjData etcProvides an ExamInfo member. More...
class	ExamInfo
	a class for storing information about 1 exam (or scan) More...
class	FactoryRegistry
	This class can be used to store 'factories' and their corresponding keys. It is essentially a map, but with some extra embelishments. More...
class	FBP2DReconstruction
	Reconstruction class for 2D Filtered Back Projection. More...
class	FBP3DRPReconstruction
	This class contains the implementation of the FBP3DRP algorithm. More...
class	FilenameTests
	Test class for filename functions defined in utility.h. More...
class	FilePath
	The FilePath class. More...
class	FileSignature
	A class to read/store the file signature. More...
class	Filter1D
	Preliminary class for 1D filtering using FFTs. More...
class	Filter2D
	2-dimensional filters (filtering done by FFTs) More...
class	FilterRootPrior
	A class in the GeneralisedPrior hierarchy. This implements 'generalised' priors a la the Median Root Prior (which was invented by Sakari Alenius). More...
class	find_fwhm_in_imageTests
	A simple class to test the find_fwhm_in_image function. More...
class	FindMCNormFactors
	Class to compute 'time-efficiency' factors for motino corrected projection data. More...
class	ForwardProjectorByBin
	Abstract base class for all forward projectors. More...
class	ForwardProjectorByBinNiftyPET
	Class for NiftyPET's GPU forward projector. More...
class	ForwardProjectorByBinParallelproj
	Class for Parallelproj's forward projector. More...
class	ForwardProjectorByBinUsingProjMatrixByBin
	This implements the ForwardProjectorByBin interface, given any ProjMatrixByBin objectIt stores a shared_ptr to a ProjMatrixByBin object, which will be used to get the relevant elements of the projection matrix. More...
class	ForwardProjectorByBinUsingRayTracing
	This class implements forward projection using Siddon's algorithm for ray tracing. That is, it computes length of intersection with the voxels. More...
class	FourierRebinning
	Class for Serial FORE Reconstruction. More...
class	FourierTests
	A simple class to test the erf and erfc functions. More...
class	FrameSinglesRates
	A single frame of singles information. More...
class	FullArrayIterator
	Class FullArrayIterator implements (forward) iterators that go through all elements of an Array. More...
class	GatedDiscretisedDensity
	Class of multiple image gates. More...
class	GatedSpatialTransformation
	Class for spatial transformations for gated images. More...
class	GeneralisedObjectiveFunction
	A base class for 'generalised' objective functions, i.e. objective functions for which at least a 'gradient' is defined. More...
class	GeneralisedPoissonNoiseGenerator
	Generates noise realisations according to Poisson statistics but allowing for scaling. More...
class	GeneralisedPoissonNoiseGeneratorTests
	Tests GeneralisedPoissonNoiseGenerator functionalityCurrently contains only simple tests to check mean and variance. More...
class	GeneralisedPrior
	A base class for 'generalised' priors, i.e. priors for which at least a 'gradient' is defined. More...
class	GeneralisedPriorTests
	Test class for QuadraticPrior, RelativeDifferencePrior, CudaRelativeDifferencePrior and LogcoshPrior. More...
class	GeometryBlocksOnCylindrical
	A helper class to build the crystal map based on scanner info. More...
class	GeometryBlocksOnCylindricalTests
	Test class for BlocksOnCylindrical geometry. More...
struct	HigherPrecision
	Helper class to get a type with higher precision. More...
class	HighResWallClockTimer
	High-resolution timer. More...
class	HUToMuImageProcessor
	A class in the DataProcessor hierarchy that convert from Hounsfield Units to mu-values. More...
class	ImagingModality
	Class for encoding the modality. More...
class	ImagingModalityTests
	Test class for ImagingModality. More...
class	IndexRange
	This class defines ranges which can be 'irregular'. More...
class	IndexRange2D
	a 'convenience' class for 2D index ranges. More...
class	IndexRange3D
	a 'convenience' class for 3D index ranges. Provides an easier constructor for regular ranges. More...
class	IndexRange4D
	A convenience class for 4D index ranges. More...
class	IndexRange< 1 >
	The (simple) 1 dimensional specialisation of IndexRange. More...
class	IndexRange_Tests
	Class with tests for IndexRange, IndexRange3D. More...
class	InputFileFormat
	Base-class for file-formats for reading. More...
class	InputFileFormatRegistry
	A class for registering (and finding) all input file formats. More...
class	InputStreamFromROOTFile
	A helper class to read data from a ROOT file Generated by GATE simulation toolkit. More...
class	InputStreamFromROOTFileForCylindricalPET
	Declaration of class stir::InputStreamFromROOTFileForCylindricalPET. More...
class	InputStreamFromROOTFileForECATPET
	Declaration of class stir::InputStreamFromROOTFileForECATPET. More...
class	InputStreamWithRecords
	A helper class to read data from a (presumably binary) stream. More...
class	InputStreamWithRecordsFromUPENN
	Base class for reading listmode files from the PENNPet Explorer scanner. More...
class	InputStreamWithRecordsFromUPENNbin
	Class for reading binary listmode files from the PENNPet Explorer scanner. More...
class	InputStreamWithRecordsFromUPENNtxt
	Class for reading listmode files in text format from the PENNPet Explorer scanner. More...
class	integrate_discrete_functionTests
	A simple class to test the integrate_discrete_function function. More...
struct	interfile_less
	A function object that compares Interfile keywords. More...
class	InterfileDynamicDiscretisedDensityInputFileFormat
	Class for reading images in Interfile file-format. More...
class	InterfileDynamicDiscretisedDensityOutputFileFormat
	Implementation of OutputFileFormat paradigm for the Interfile format. More...
class	InterfileHeader
	a class for Interfile keywords (and parsing) common to all types of data More...
class	InterfileImageHeader
	a class for Interfile keywords (and parsing) specific to images More...
class	InterfileImageInputFileFormat
	Class for reading images in Interfile file-format. More...
class	InterfileOutputFileFormat
	Implementation of OutputFileFormat paradigm for the Interfile format. More...
class	InterfileParametricDiscretisedDensityInputFileFormat
	Class for reading images in Interfile file-format. More...
class	InterfileParametricDiscretisedDensityOutputFileFormat
	Implementation of OutputFileFormat paradigm for the Interfile format. More...
class	InterfilePDFSHeader
	a class for Interfile keywords (and parsing) specific to projection data (i.e. ProjDataFromStream) More...
class	InterfilePDFSHeaderSPECT
	a class for Interfile keywords (and parsing) specific to SPECT projection data More...
class	InvertAxis
	a utility class to "invert" an axis More...
class	IOTests
	A simple class to test the OutputFileFormat function. More...
class	IOTests_DiscretisedDensity
	A simple class to test the OutputFileFormat function. More...
class	IOTests_DynamicDiscretisedDensity
	A simple class to test the OutputFileFormat function. More...
class	IOTests_ITKMulticomponent
	A simple class to test the reading of multicomponent ITK images. More...
class	IOTests_ParametricDiscretisedDensity
	A simple class to test the OutputFileFormat function. More...
class	IR_filterTests
	A simple class to test the IIR_filter and FIR_filter function. More...
class	IterativeReconstruction
	base class for iterative reconstruction objectsThis is the base class for all iterative reconstruction methods. It provides the basic iteration mechanisms. What each iteration does has to be implemented in a derived class. More...
class	ITKImageInputFileFormat
	Class for reading images using ITK. More...
class	ITKOutputFileFormat
	Implementation of OutputFileFormat paradigm using the ITK library for writing. More...
class	JacobianForIntBP
	The next class is used in BackProjectorByBinUsingInterpolation to take geometric things into account. It also includes some normalisation. (internal use only). More...
class	KeyArgument
	A class that enumerates the possible types that can be used to store parsed values. Used (only) by KeyParser. More...
class	KeyParser
	A class to parse Interfile headers. More...
class	KeyParserTests
	Test class for KeyParser. More...
class	KineticModel
	base class for all kinetic modelsAt present very basic. It just provides the parsing mechanism. More...
class	KOSMAPOSLReconstruction
	A reconstructor class appropriate for emission data. More...
class	Line
	A class used by the Interfile parser. More...
class	linear_regressionTests
	A simple class to test the linear_regression function. More...
class	ListEvent
	Class for storing and using gamma events from a list mode file. More...
class	ListGatingInput
	A class recording external input to the scanner (normally used for gating) More...
class	ListModeData
	The base class for reading list mode data. More...
class	ListModeData_dummy
	A class to trick the Objective function that we have list mode data, when we only have cache. More...
class	ListRecord
	A class for a general element of a list mode file. More...
class	ListTime
	A class for storing and using a timing record from a listmode file. More...
class	LmToProjData
	This class is used to bin listmode data to projection data, i.e. (3d) sinograms. More...
class	LmToProjDataAbstract
	This class is the abstract base class fir binning listmode data to projection data, i.e. (3d) sinograms. More...
class	LmToProjDataBootstrap
	Class for binning list mode data into projection data using the bootstrap procedure. More...
class	LmToProjDataWithMC
	Class for binning list mode files with motion correction. More...
class	LmToProjDataWithRandomRejection
	Class for binning list mode data into projection data using the bootstrap procedure. More...
class	LogcoshPrior
	A class in the GeneralisedPrior hierarchy. This implements a logcosh Gibbs prior. More...
class	LogCoshPriorTests
	tests for LogCoshPrior More...
class	LOR
	A base class for specifying an LOR with geometric coordinates. More...
class	LORAs2Points
	A class for LORs. More...
class	LORCylindricalCoordinates_z_and_radius
	An internal class for LORs. Do not use. More...
class	LORInAxialAndNoArcCorrSinogramCoordinates
	A class for LORs. More...
class	LORInAxialAndSinogramCoordinates
	A class for LORs. More...
class	LORInCylinderCoordinates
	A class for LORs. More...
class	map_element
	Class to store the Interfile keywords and their actions. More...
struct	MaskingParameters
	A struct to hold the parameters for image masking. More...
class	MatchTrackerAndScanner
	A class for finding the coordinate transformation between tracker and scanner coordinate systems. More...
class	MatrixTests
	Tests MatrixFunction.h functionality. More...
class	MaximalArrayFilter3D
	Implements erosion on 3D arrays. More...
class	MaximalImageFilter3D
	A class in the ImageProcessor hierarchy that implements maximal filtering. More...
class	MedianArrayFilter3D
	Implements median filtering on 3D arrays. More...
class	MedianImageFilter3D
	A class in the ImageProcessor hierarchy that implements median filtering. More...
class	MinimalArrayFilter3D
	Implements erosion on 3D arrays. More...
class	MinimalImageFilter3D
	A class in the ImageProcessor hierarchy that implements minimal filtering. More...
class	MinimalInterfileHeader
	a minimal class for Interfile keywords (and parsing) common to all types of data More...
class	ML_normTests
	Test class for ML_norm.h functions. More...
class	modellingTests
	A simple class to test modelling functions. More...
class	ModelMatrix
	A helper class to store the model matrix for a linear kinetic model. More...
class	MoveImage
	A class for moving an image according to average motion in the frame. More...
class	MoveProjData
	A class for moving projection data according to average motion in the frame. More...
class	MultiDynamicDiscretisedDensityInputFileFormat
	Class for reading images in Multi file-format. More...
class	MultiDynamicDiscretisedDensityOutputFileFormat
	Implementation of OutputFileFormat paradigm for the Multi format. More...
class	MultiParametricDiscretisedDensityInputFileFormat
	Class for reading images in Multi file-format. More...
class	MultiParametricDiscretisedDensityOutputFileFormat
	Implementation of OutputFileFormat paradigm for the Multi format. More...
class	MultipleProjDataTests
	Test class for MultipleProjData. More...
class	multiply_plane_scale_factorsImageProcessor
	Simply multiplies each plane in an image with a scale factor. More...
class	MyApp
	A class for moving an image according to average motion in the frame. More...
class	NestedIterator
	Class NestedIterator implements a (forward) iterator using a pair of 'nested' iterators. More...
class	NestedIteratorTests
	Tests NestedIterator functionality. More...
class	NiftyPETHelper
	Helper class for the wrapped NiftyPET projectors. More...
class	NonRigidObjectTransformationUsingBSplines
	Class to perform non-rigid object transformations in arbitrary dimensions. More...
class	NonseparableConvolutionUsingRealDFTImageFilter
	A class derived from DataProcessor for performing separable periodic convolutions with an array kernel. More...
struct	NormSquared
	A helper class that computes the square of the norm of numeric data. More...
class	NumericInfo
	class NumericInfo<NUMBER> defines properties for the type NUMBER. More...
class	NumericInfo< double >
	Basic properties of double. More...
class	NumericInfo< float >
	Basic properties of float. More...
class	NumericInfo< signed char >
	Basic properties of signed char. More...
class	NumericInfo< signed int >
	Basic properties of signed int. More...
class	NumericInfo< signed long >
	Basic properties of signed long. More...
class	NumericInfo< signed short >
	Basic properties of signed short. More...
class	NumericInfo< unsigned char >
	Basic properties of unsigned char. More...
class	NumericInfo< unsigned int >
	Basic properties of unsigned int. More...
class	NumericInfo< unsigned long >
	Basic properties of unsigned long. More...
class	NumericInfo< unsigned short >
	Basic properties of unsigned short. More...
class	NumericType
	provides names for some numeric types and methods for finding their properties. More...
class	NumericVectorWithOffset
	like VectorWithOffset, but with changes in various numeric operators More...
class	ObjectiveFunctionTests
	Test class for GeneralisedObjectiveFunction and GeneralisedPrior. More...
class	ObjectTransformation
	Base-class for performing (potentially non-rigid) object transformations. More...
class	OSMAPOSLReconstruction
	Implementation of the Ordered Subsets version of Green's MAP One Step Late algorithm. More...
class	OSSPSReconstruction
	Implementation of the relaxed Ordered Subsets Separable Paraboloidal Surrogate ( OSSPS) More...
class	OutputFileFormat
	Base class for classes that create output files. More...
class	OutputFileFormatTests
	A simple class to test the OutputFileFormat function. More...
class	overlap_interpolateTests
	Test class for stir::overlap_interpolate. More...
struct	Parametric2Single
	A helper class to find the type of a 'single' image for a corresponding parametric image. More...
class	ParametricDiscretisedDensity
	Class to store parametric images. More...
class	ParametricQuadraticPrior
	A class in the GeneralisedPrior hierarchy. This implements a quadratic Gibbs prior. More...
class	ParseAndCreateFrom
	template for adding keywords to a parser and creating an object More...
class	ParseAndCreateFrom< DiscretisedDensity< 3, elemT >, ExamDataT >
	parse keywords for creating a VoxelsOnCartesianGrid from ProjData etc More...
class	ParseAndCreateFrom< ParametricDiscretisedDensity< VoxelsOnCartesianGrid< elemT > >, ExamDataT >
	parse keywords for creating a parametric VoxelsOnCartesianGrid from DynamicProjData etc More...
class	ParseDiscretisedDensityParameters
	Class for adding parameters relevant to DiscretisedDensity to a parser. More...
class	ParsingObject
	A base class for objects that want to be able to parse parameter files. More...
class	PatientPosition
class	PatlakPlot
	Patlak kinetic model. More...
class	PENNListmodeInputFileFormat
	Base class for PENN listmode file format support. More...
class	PixelsOnCartesianGrid
	This class is used to represent pixelised densities on a rectangular grid (2D). More...
class	PlasmaData
	A class for storing plasma and blood samples of a single study. More...
class	PlasmaSample
class	PLSPrior
	A class in the GeneralisedPrior hierarchy. This implements the anatomical penalty function, Parallel Level Sets (PLS), also sometimes called Directional TV, proposed by Matthias J. Ehrhardt et. al in "PET Reconstruction With an Anatomical MRI Prior Using Parallel Level Sets", IEEE Trans. med. Imag., vol. 35, no. 9, Sept. 2016. https://doi.org/10.1109/TMI.2016.2549601 Note that PLS becomes smoothed TV when an uniform anatomical image is provided. More...
class	PLSPriorTests
	tests for PLSPrior More...
class	PointOnCylinder
	A class for a point on a cylinder. More...
class	PoissonLLReconstructionTests
	Base class for tests for iterative reconstruction that use PoissonLogLikelihoodWithLinearModelForMeanAndProjData. More...
class	PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData
	a base class for LogLikelihood of independent Poisson variables where the mean values are linear combinations of the kinetic parameters. More...
class	PoissonLogLikelihoodWithLinearModelForMean
	a base class for LogLikelihood of independent Poisson variables where the mean values are linear combinations of the parameters. More...
class	PoissonLogLikelihoodWithLinearModelForMeanAndDynamicProjData
	a base class for LogLikelihood of independent Poisson variables where the mean values are linear combinations of the frames. More...
class	PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion
	a base class for LogLikelihood of independent Poisson variables where the mean values are linear combinations of the gated images. More...
class	PoissonLogLikelihoodWithLinearModelForMeanAndListModeData
	An objective function class appropriate for PET list mode data. More...
class	PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin
	Class for PET list mode data from static images for a scanner with discrete detectors. More...
class	PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBinTests
	Test class for PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin. More...
class	PoissonLogLikelihoodWithLinearModelForMeanAndProjData
	An objective function class appropriate for PET emission data. More...
class	PoissonLogLikelihoodWithLinearModelForMeanAndProjDataTests
	Test class for PoissonLogLikelihoodWithLinearModelForMeanAndProjData. More...
class	Polaris_MT_File
	a class for parsing .mt files output by the Polaris software More...
class	PostsmoothingBackProjectorByBin
	A very preliminary class that first smooths the image, then back projects. More...
class	PostsmoothingForwardProjectorByBin
	A very preliminary class that first forward projects, and then smooths the viewgrams. More...
class	PrepareProjData
	A preliminary class to prepare files for iterative reconstruction. More...
class	PresmoothingForwardProjectorByBin
	A very preliminary class that first smooths the image, then forward projects. More...
class	PriorWithParabolicSurrogate
	this class implements priors with a parabolic surrogate curvature More...
class	ProjData
	The (abstract) base class for the projection data. More...
class	ProjDataFromStream
	A class which reads/writes projection data from/to a (binary) stream. More...
class	ProjDataInfo
	An (abstract base) class that contains information on the projection data. More...
class	ProjDataInfoBlocksOnCylindricalNoArcCorr
	Projection data info for data from a scanner with discrete dtectors organised by blocks. More...
class	ProjDataInfoCylindrical
	projection data info for data corresponding to a 'cylindrical' sampling. More...
class	ProjDataInfoCylindricalArcCorr
	Projection data info for arc-corrected data. More...
class	ProjDataInfoCylindricalArcCorrTests
	Test class for ProjDataInfoCylindricalArcCorr. More...
class	ProjDataInfoCylindricalNoArcCorr
	Projection data info for data which are not arc-corrected. More...
class	ProjDataInfoCylindricalNoArcCorrTests
	Test class for ProjDataInfoCylindricalNoArcCorr. More...
class	ProjDataInfoCylindricalTests
	Test class for ProjDataInfoCylindrical. More...
class	ProjDataInfoGeneric
	projection data info for data corresponding to 'Generic' sampling. More...
class	ProjDataInfoGenericNoArcCorr
	Projection data info for data for a scanner with discrete detectors. More...
class	ProjDataInfoSubsetByView
	Projection data info for data corresponding to a subset sampling by views. More...
class	ProjDataInfoTests
	Test class for ProjDataInfo. More...
class	ProjDataInMemory
	A class which reads/writes projection data from/to memory. More...
class	ProjDataInMemoryTests
	Test class for ProjDataInMemory. More...
class	ProjDataInterfile
	A class which reads/writes projection data from/to a (binary) stream, but creates the corresponding Interfile header. More...
class	ProjDataRebinning
	base class for all rebinning algorithms for 3D PET dataTODO describe what rebinning is and why you need it More...
class	ProjDataTests
	Test class for ProjData and ProjDataInMemory. More...
class	ProjectorByBinPair
	Abstract base class for all projector pairs. More...
class	ProjectorByBinPairUsingNiftyPET
	A projector pair based on NiftyPET projectors. More...
class	ProjectorByBinPairUsingParallelproj
	A projector pair based on Parallelproj projectors. More...
class	ProjectorByBinPairUsingProjMatrixByBin
	A projector pair based on a single matrix. More...
class	ProjectorByBinPairUsingSeparateProjectors
	A projector pair based on a single matrix. More...
class	ProjMatrixByBin
	This is the (abstract) base class for all projection matrices which are organised by 'bin'. More...
class	ProjMatrixByBinFromFile
	Reads/writes a projection matrix from/to file. More...
class	ProjMatrixByBinPinholeSPECTUB
	Generates projection matrix for pinhole SPECT studies. More...
class	ProjMatrixByBinSinglePhoton
	a 'projection matrix' to implement a model for a single photon acquisition in terms of the detector efficiencies. More...
class	ProjMatrixByBinSPECTUB
	generates projection matrix for SPECT studies More...
class	ProjMatrixByBinUsingInterpolation
	Computes projection matrix elements for VoxelsOnCartesianGrid images by using an interpolation model. More...
class	ProjMatrixByBinUsingInterpolationTests
	Test class for ProjMatrixByBinUsingInterpolation. More...
class	ProjMatrixByBinUsingRayTracing
	Computes projection matrix elements for VoxelsOnCartesianGrid images by using a Length of Intersection (LOI) model. More...
class	ProjMatrixByBinUsingSolidAngle
	Computes projection matrix elements for VoxelsOnCartesianGrid images by using a Solid Angle model. More...
class	ProjMatrixByBinWithPositronRange
	Computes projection matrix elements for VoxelsOnCartesianGrid images by using a Solid Angle model. More...
class	ProjMatrixByDensel
	This is the (abstract) base class for all projection matrices which are organised by 'Densel'. More...
class	ProjMatrixByDenselOnCartesianGridUsingElement
	Computes projection matrix elements for VoxelsOnCartesianGrid images by using a Length of Intersection (LOI) model. More...
class	ProjMatrixByDenselUsingRayTracing
	Computes projection matrix elements for VoxelsOnCartesianGrid images by using a Length of Intersection (LOI) model. More...
class	ProjMatrixElemsForOneBin
	This stores the non-zero projection matrix elements for every 'densel' that contributes to a given bin. More...
class	ProjMatrixElemsForOneBinValue
	Stores voxel coordinates and the value of the matrix element. More...
class	ProjMatrixElemsForOneDensel
	This stores the non-zero projection matrix elements for every 'voxel'. More...
class	ProjMatrixElemsForOneDenselValue
	Stores voxel coordinates and the value of the matrix element. More...
class	PtrBeginEndAllFunction
	Helper class for NestedIterator when the 1st level iterator refers to a pointer to a stir full iterator for the 2nd level iterator. More...
class	PtrBeginEndFunction
	Helper class for NestedIterator when the 1st level iterator refers to pointers to an ordinary iterator for the 2nd level iterator. More...
class	PullLinearInterpolator
	A function object to pull interpolated values from the input array into the grid points of the output array. More...
class	PullNearestNeighbourInterpolator
	A function object to pull interpolated values from the input array into the grid points of the output array. More...
class	PushNearestNeighbourInterpolator
	A function object to push values at the grid of the input array into the output array. More...
class	PushTransposeLinearInterpolator
	A function object to push values at the grid of the input array into the output array. More...
class	QuadraticPrior
	A class in the GeneralisedPrior hierarchy. This implements a quadratic Gibbs prior. More...
class	QuadraticPriorTests
	tests for QuadraticPrior More...
class	QuaternionTests
	Test class for Quaternion. More...
class	Radionuclide
	A class for storing radionuclide information. More...
class	RadionuclideTest
	Class with tests for stir::RadionuclideDB and stir::Radionuclide. More...
class	RampFilter
	The ramp filter used for (2D) FBP. More...
class	Reconstruction
	base class for all ReconstructionsAs there is not a lot of commonality between different reconstruction algorithms, this base class is rather basic. It essentially takes care of constructing a target image, calls the virtual reconstruct() function, and writes the result to file. More...
class	ReconstructionTests
	Base class for simple test on reconstruction. More...
class	RegisteredObject
	Helper class to provide registry mechanisms to a Base classSuppose you have a hierarchy of classes with (nearly) all public functionality provided by virtual functions of the Base (here called Root) class. The aim is then to be able to select at run-time which of the nodes will be used. More...
class	RegisteredObjectBase
	Base class for all classes that can parse .par files (and more?)The only reason that this class exists is such that KeyParser can store different types of objects, and get some basic info from it. More...
class	RegisteredParsingObject
	Parent class for all leaves in a RegisteredObject hierarchy that do parsing of parameter files. More...
struct	RegisterInputFileFormat
	A helper class to allow automatic registration to the default InputFileFormatRegistry. More...
class	RelatedBins
	This class contains all information about a set of bins related by symmetry. More...
class	RelatedDensels
	This class contains all information about a set of densels related by symmetry. More...
class	RelatedViewgrams
	A class for storing viewgrams which are related by symmetry. More...
class	RelativeDifferencePrior
	A class in the GeneralisedPrior hierarchy. This implements a Relative Difference prior. More...
class	RelativeDifferencePriorTests
	tests for RelativeDifferencePrior More...
class	ReportMovement
	A class for reporting the movement within the frame w.r.t. to the reference position. More...
struct	ResolutionIndex
	a structure that is used to hold the output of the function find_fwhm_in_image. More...
class	RigidObject3DMotion
	Base class for 3D rigid motion. More...
class	RigidObject3DMotionFromPolaris
	A class for handling motion information from the Polaris tracker. More...
class	RigidObject3DTransformation
	Class to perform rigid object transformations in 3 dimensions. More...
class	RigidObject3DTransformationTests
	Various tests on RigidObject3DTransformation. More...
class	ROITests
	Test class for compute_ROI_values and Shape3D hierarchy. More...
class	ROIValues
	A class to store and get results of an ROI calculation. More...
class	ROOTListmodeInputFileFormat
	The ROOTListmodeInputFileFormat class. More...
class	RunTests
	A base class for making test classesWith a derived class, an application could look like. More...
class	SAFIRCListmodeInputFileFormat
	Class for reading SAFIR coincidence listmode data. More...
class	Scanner
	A class for storing some info on the scanner. More...
class	ScannerTests
	Test class for Scanner. More...
class	ScatterEstimation
	Estimate the scatter probability using a model-based approach. More...
class	ScatterSimulation
	Simulate the scatter probability using a model-based approach. More...
class	ScatterSimulationTests
	Test class for ScatterSimulation. More...
class	Segment
	An (abstract base) class for storing 3d projection dataThis stores a subset of the data accessible via a ProjData object, where the SegmentIndices are fixed. More...
class	SegmentBySinogram
	A class for storing (3d) projection data with fixed SegmentIndices. More...
class	SegmentByView
	A class for storing (3d) projection data with fixed SegmentIndices. More...
class	SegmentIndices
	A very simple class to store segment numbers and any other indices that define a segment. More...
class	SeparableArrayFunctionObject
	This class implements an n -dimensional ArrayFunctionObject whose operation is separable. More...
class	SeparableArrayFunctionObject2
	This class implements an n -dimensional ArrayFunctionObject whose operation is separable. More...
class	SeparableCartesianMetzImageFilter
	A class in the DataProcessor hierarchy that implements Metz filtering (which includes Gaussian filtering). More...
class	SeparableConvolutionImageFilter
	A class derived from DataProcessor for performing separable non-periodic convolutions. More...
class	SeparableGaussianArrayFilter
	Separable Gaussian filtering in n - dimensions. More...
class	SeparableGaussianArrayFilterTests
	Tests SeparableGaussianArrayFilter functionalityCurrently only very basic tests on normalisation. More...
class	SeparableGaussianImageFilter
	A class in the DataProcessor hierarchy that implements Gaussian filtering. More...
class	SeparableMetzArrayFilter
	Separable Metz filtering in n - dimensions. More...
class	SeparableMetzArrayFilterTests
	Tests SeparableMetzArrayFilter functionalityCurrently only very basic tests on normalisation. More...
class	Shape3D
	The base class for all 3 dimensional shapes. More...
class	Shape3DWithOrientation
	Class for shapes with orientation. More...
class	SingleScatterSimulation
	PET single scatter simulation. More...
class	SinglesRates
	The base-class for using singles info. More...
class	SinglesRatesForTimeFrames
	A class for singles rates that are recorded in time frames. More...
class	SinglesRatesForTimeSlices
	A class for singles that are recorded at equal time intervals. More...
class	Sinogram
	A class for 2d projection data. More...
class	SinogramIndices
	A very simple class to store all dincies to get a (2D) Sinogram. More...
class	SpatialTransformation
	base class for any type of motion fieldsAt present very basic. It just provides the parsing mechanism. More...
class	SPECTListEvent
	Class for storing and using gamma events from a SPECT List mode file. More...
class	SPECTListModeData
	The base class for reading SPECT list mode data.This class (and SPECTListRecord) is specific to SPECT, i.e. to single gamma detection. However, the only difference with the PET part are the functions related to prompts and delayeds. SPECT is handled by calling all single photon events 'prompts'. More...
class	SPECTListRecord
	A class for a general element of a list mode file. More...
class	SqrtHessianRowSum
	Implementations of two square root Hessian row sum computation methods, as proposed by Tsai et al. (2020). More...
class	stir_mathTests
	Test class for the stir_math utility. More...
class	Succeeded
	a class containing an enumeration type that can be used by functions to signal successful operation or not More...
class	SumOfGeneralisedObjectiveFunctions
	A base class for sums of 'generalised' objective functions, i.e. objective functions for which at least a 'gradient' is defined. More...
class	SymmetryOperation
	Encodes symmetry operation on image coordinates and projection data coordinates. More...
class	TestBSplineTransformation
	Test class for Transformations. More...
class	TestDataProcessorProjectors
	Test class for GPU projectors. More...
class	TestFBP2D
	Test class for FBP2D. More...
class	TestFBP3DRP
	Test class for FBP3DRP. More...
class	TestGPUProjectors
	Test class for GPU projectors. More...
class	TestOSMAPOSL
	Test class for OSMAPOSL. More...
class	TestProjDataInfoSubsets
	Test class for subsets in ProjDataInfo. More...
class	ThresholdMinToSmallPositiveValueDataProcessor
	A class in the DataProcessor hierarchy for making sure all elements are strictly positive. More...
class	TimedBlock< TimerT=Timer >
	Helper class for measuring execution time of a block of code.It starts the timer in ctor, stops in dtor. Do not create unnamed instances of this class, as they are quite useless: you cannot predict destruction time. More...
class	TimedObject
	base class for all objects which need timers. At the moment, there's only a CPU timer. More...
class	TimeFrameDefinitions
	Class used for storing time frame durations. More...
class	TimeFrameMotion
	A class for encoding average motion in the frames. More...
class	TimeGateDefinitions
	Class used for storing time gate durations. More...
class	Timer
	A general base class for timers. Interface is like a stop watch. More...
class	TOF_Tests
	Test class for Time Of Flight. More...
class	Transform3DObjectImageProcessor
	A class in the ImageProcessor hierarchy that performs movement by reinterpolation. More...
class	TrivialBinNormalisation
	Trivial class which does not do any normalisation whatsoever. More...
class	TrivialDataSymmetriesForBins
	A class derived from DataSymmetriesForBins that says that there are no symmetries at all. More...
class	TrivialDataSymmetriesForViewSegmentNumbers
	A class for encoding/finding NO symmetries. Works only on ViewSegmentNumbers (instead of Bin). More...
class	TrivialSymmetryOperation
	A class implementing the trivial case where the symmetry operation does nothing at all. More...
class	TruncateToCylindricalFOVImageProcessor
	A class in the DataProcessor hierarchy that sets voxels to 0 outside a given radius. More...
struct	TypeForNumericType
	A helper class that specifies the C++ type for a particular NumericType. More...
class	Utah_phantom
	A class that represents a Utah phantom. More...
class	VectorWithOffset
	A templated class for vectors, but with indices starting not from 0. More...
class	VectorWithOffsetTests
	Test class for VectorWithOffset. More...
class	Verbosity
	This class enables the user to control the on-screen output. More...
class	Viewgram
	A class for 2d projection data. More...
class	ViewgramIndices
	A very simple class to store all dincies to get a (2D) Viewgram. More...
class	ViewSegmentNumbers
	alias for ViewgramIndices More...
class	VoxelsOnCartesianGrid
	This class is used to represent voxelised densities on a cuboid grid (3D). More...
class	VoxelsOnCartesianGridTests
	Test class for VoxelsOnCartesianGrid and image hierarchy. More...
class	warp_imageTests
	Class with tests for warp_image functions. More...
class	zoom_imageTests
	Test class for zoom_image (and centre_of_gravity) More...
class	ZoomOptions
	This class enables the user to choose between different zooming optionsThe 3 possible values determine a global scale factor used for the end result: (i) preserve sum (locally) (ii) preserve values (like interpolation) (iii) preserve projections: using a STIR forward projector on the zoomed image will give (approximately) the same projections. More...

Typedefs
typedef char	assert_unsigned_long_size[sizeof(unsigned long) - sizeof(unsigned char)]
typedef SegmentByView< elem_type >	segment_type
typedef VectorWithOffset< shared_ptr< segment_type > >	all_segments_type
typedef Array< 1, std::complex< float > >	ArrayC1
typedef Array< 1, float >	ArrayF1
typedef Array< 2, float >	ArrayF2
typedef Array< 2, std::complex< float > >	ArrayC2
typedef Array< 3, float >	ArrayF3
typedef Array< 3, std::complex< float > >	ArrayC3
typedef Coordinate3D< int >	Densel
	a typedef used for an element of a DiscretisedDensity More...
typedef std::vector< std::string >	ASCIIlist_type
typedef Array< 2, float >	GeoData
typedef Array< 2, float >	BlockData
typedef Array< 2, float >	DetectorEfficiencies
typedef FanProjData	BlockData3D
typedef VoxelsOnCartesianGrid< KineticParameters< 2, float > >	ParametricVoxelsOnCartesianGridBaseType
	Convenience typedef for base-type of Cartesian Voxelised Parametric Images with just two parameters.
typedef ParametricDiscretisedDensity< ParametricVoxelsOnCartesianGridBaseType >	ParametricVoxelsOnCartesianGrid
	Convenience typedef for Cartesian Voxelised Parametric Images with just two parameters.
using	ProjDataInfoBlocksOnCylindrical = ProjDataInfoGeneric
typedef Coordinate2D< int >	AxTangPosNumbers
	AxTangPosNumbers as a class that provides the 2 remaining coordinates for a Bin, aside from ViewSegmentNumbers. More...
typedef void	RPC_process_related_viewgrams_type(const shared_ptr< ForwardProjectorByBin > &forward_projector_sptr, const shared_ptr< BackProjectorByBin > &back_projector_sptr, RelatedViewgrams< float > *measured_viewgrams_ptr, int &count, int &count2, double *log_likelihood_ptr, const RelatedViewgrams< float > *additive_binwise_correction_ptr, const RelatedViewgrams< float > *mult_viewgrams_ptr)
	typedef for callback functions for distributable_computation() More...
typedef itk::Image< float, 3 >	ITKImageSingle
	Class for reading images in ITK file-format. More...
typedef itk::VectorImage< float, 3 >	ITKImageMulti
typedef DiscretisedDensity< 3, float >	STIRImageSingle
typedef VoxelsOnCartesianGrid< float >	STIRImageSingleConcrete
typedef DiscretisedDensity< 3, CartesianCoordinate3D< float > >	STIRImageMulti
typedef VoxelsOnCartesianGrid< CartesianCoordinate3D< float > >	STIRImageMultiConcrete
typedef itk::MetaDataObject< std::string >	MetaDataStringType
typedef DiscretisedDensity< 3, float >	target_type

Enumerations
enum	OUTPUT_CHANNEL { INFORMATION_CHANNEL, WARNING_CHANNEL, ERROR_CHANNEL }
enum	options {   _quit, _display_view, _display_sino, _absdiff,   _add_sino, _subtract_sino, _mult_sino, _div_sino,   _add_scalar, _mult_scalar, _div_scalar, _stats,   _pos_ind, _trunc_neg, _trim, _zero_ends,   _restart, _menu }

Functions
template<class T >
T	find_unweighted_centre_of_gravity_1d (const VectorWithOffset< T > &row)
	Compute centre of gravity of a vector but without dividing by its sum. More...
template<class T >
T	find_unweighted_centre_of_gravity (const Array< 1, T > &)
	Compute centre of gravity of a 1D Array but without dividing by its sum. More...
template<int num_dimensions, class T >
BasicCoordinate< num_dimensions, T >	find_unweighted_centre_of_gravity (const Array< num_dimensions, T > &)
	Compute centre of gravity of an Array but without dividing by its sum. More...
template<int num_dimensions, class T >
BasicCoordinate< num_dimensions, T >	find_centre_of_gravity (const Array< num_dimensions, T > &)
	Compute centre of gravity of an Array. More...
template<class T >
void	find_centre_of_gravity_in_mm_per_plane (VectorWithOffset< CartesianCoordinate3D< float >> &allCoG, VectorWithOffset< T > &weights, const VoxelsOnCartesianGrid< T > &image)
	Computes centre of gravity for each plane. More...
template<class T >
CartesianCoordinate3D< float >	find_centre_of_gravity_in_mm (const VoxelsOnCartesianGrid< T > &image)
	Computes centre of gravity of an image. More...
template void	find_centre_of_gravity_in_mm_per_plane (VectorWithOffset< CartesianCoordinate3D< float >> &allCoG, VectorWithOffset< float > &weights, const VoxelsOnCartesianGrid< float > &image)
template CartesianCoordinate3D< float >	find_centre_of_gravity_in_mm (const VoxelsOnCartesianGrid< float > &image)
int	time_zone_offset_in_secs ()
	returns the current time_zone in seconds (without DST)The result is independent of DST.
int	current_time_zone_and_DST_offset_in_secs ()
	returns the current time_zone in seconds (taking DST into account) More...
std::string	DICOM_date_time_to_DT (const std::string &date, const std::string &time, const std::string &TZ="")
	concatenate date, time and optional time_zone info.Minimal checks on format are performed, calling error() if input is incorrect.
double	DICOM_datetime_to_secs_since_Unix_epoch (const std::string &str, bool silent=false)
	convert DICOM DT string to seconds since the Unix epoch (i.e. 1 Jan 1970 00:00:00 UTC) More...
std::string	secs_since_Unix_epoch_to_DICOM_datetime (double secs, int time_zone_offset_in_secs=current_time_zone_and_DST_offset_in_secs())
	convert epoch to DICOM DT string in specified time zone (+3600 is CET)
DateTimeStrings	DICOM_datetime_to_Interfile (const std::string &str)
	Convert from DICOM DT to Interfile.
std::string	Interfile_datetime_to_DICOM (const DateTimeStrings &)
	Convert from Interfile to DICOM DT.
double	Interfile_datetime_to_secs_since_Unix_epoch (const DateTimeStrings &, bool silent=false)
	convert Interfile DateTime strings to seconds since the Unix epoch (i.e. 1 Jan 1970 00:00:00 UTC)Interfile uses a format year 1900:01:01, time 02:01:00.00. More...
DateTimeStrings	secs_since_Unix_epoch_to_Interfile_datetime (double secs, int time_zone_offset_in_secs=current_time_zone_and_DST_offset_in_secs())
	convert epoch to Interfile date-times string in specified time zone (+3600 is CET)
void	error (const char *const s,...)
	Print error with format string a la printf and throw exception. More...
template<class elemT >
std::list< ResolutionIndex< 3, float > >	find_fwhm_in_image (DiscretisedDensity< 3, elemT > &input_image, const unsigned int num_maxima, const float level, const int dimension, const bool nema)
	Finds FWHM, FWTM etc (in mm) for a number of point sources or a line source. More...
template<class elemT >
BasicCoordinate< 3, int >	maximum_location_per_slice (const Array< 3, elemT > &input_array, const int slice, const int dimension)
	finds the maximum of the Input_Array in the given slice at the given dimension (z=1, y=2, x=3), and returns its location as a vector in BasicCoordinate Field (only 3D implementation).
template<class elemT >
Array< 1, elemT >	interpolate_line (const Array< 3, elemT > &input_array, const BasicCoordinate< 3, int > &max_location, const BasicCoordinate< 3, bool > &do_direction, const int dimension)
	extract a line from the given array after determining its locatin with a parabolic fit More...
template<class RandomAccessIterType >
float	parabolic_3points_fit (const RandomAccessIterType &begin_iter, const RandomAccessIterType &end_iter)
template<class RandomAccessIterType >
float	parabolic_3points_fit_x0 (const RandomAccessIterType &begin_iter, const RandomAccessIterType &end_iter)
template std::list< ResolutionIndex< 3, float > >	find_fwhm_in_image (DiscretisedDensity< 3, float > &input_image, const unsigned int num_maxima, const float level, const int dimension, const bool nema)
std::string	find_STIR_config_file (const std::string &filename)
	find full path of a config file More...
std::string	get_STIR_config_dir ()
	find string with the (full) path of the directory where looks for STIR configuration files More...
std::string	get_STIR_doc_dir ()
	find string with the (full) path of the directory where the STIR documentation was installed More...
std::string	get_STIR_examples_dir ()
	find string with the (full) path of the directory where the STIR examples are installed More...
string	standardise_interfile_keyword (const std::string &keyword)
	Put a (Interfile) keyword into a standard form. More...
Succeeded	inverse_SSRB (ProjData &proj_data_4D, const ProjData &proj_data_3D)
	Perform Inverse Single Slice Rebinning and write output to ProjData4D format. More...
template<>
Succeeded	get_param_from_string (string &param, const string &s)
template<>
Succeeded	get_vparam_from_string (vector< string > &param, const string &s)
void	make_det_pair_data (DetPairData &det_pair_data, const ProjDataInfo &proj_data_info, const int segment_num, const int ax_pos_num)
	Makes a DetPairData of appropriate dimensions and fills it with 0.
void	make_det_pair_data (DetPairData &det_pair_data, const ProjData &proj_data, const int segment_num, const int ax_pos_num)
void	apply_block_norm (DetPairData &det_pair_data, const BlockData &block_data, const bool apply)
void	apply_geo_norm (DetPairData &det_pair_data, const GeoData &geo_data, const bool apply)
void	apply_efficiencies (DetPairData &det_pair_data, const Array< 1, float > &efficiencies, const bool apply)
void	make_fan_sum_data (Array< 1, float > &data_fan_sums, const DetPairData &det_pair_data)
void	make_geo_data (GeoData &geo_data, const DetPairData &det_pair_data)
void	make_block_data (BlockData &block_data, const DetPairData &det_pair_data)
void	iterate_efficiencies (Array< 1, float > &efficiencies, const Array< 1, float > &data_fan_sums, const DetPairData &model)
void	iterate_geo_norm (GeoData &norm_geo_data, const GeoData &measured_geo_data, const DetPairData &model)
void	iterate_block_norm (BlockData &norm_block_data, const BlockData &measured_block_data, const DetPairData &model)
double	KL (const DetPairData &d1, const DetPairData &d2, const double threshold)
std::ostream &	operator<< (std::ostream &s, const GeoData3D &geo_data)
std::istream &	operator>> (std::istream &s, GeoData3D &geo_data)
std::ostream &	operator<< (std::ostream &s, const FanProjData &fan_data)
std::istream &	operator>> (std::istream &s, FanProjData &fan_data)
void	get_fan_info (int &num_rings, int &num_detectors_per_ring, int &max_ring_diff, int &fan_size, const ProjDataInfo &proj_data_info)
void	set_det_pair_data (ProjData &proj_data, const DetPairData &det_pair_data, const int segment_num, const int ax_pos_num)
void	make_fan_data_remove_gaps (FanProjData &fan_data, const ProjData &proj_data)
void	set_fan_data_add_gaps (ProjData &proj_data, const FanProjData &fan_data, const float gap_value)
void	apply_block_norm (FanProjData &fan_data, const BlockData3D &block_data, const bool apply)
void	apply_geo_norm (FanProjData &fan_data, const GeoData3D &geo_data, const bool apply)
void	apply_efficiencies (FanProjData &fan_data, const DetectorEfficiencies &efficiencies, const bool apply)
void	make_fan_sum_data (Array< 2, float > &data_fan_sums, const FanProjData &fan_data)
void	make_fan_sum_data (Array< 2, float > &data_fan_sums, const ProjData &proj_data)
void	make_fan_sum_data (Array< 2, float > &data_fan_sums, const DetectorEfficiencies &efficiencies, const int max_ring_diff, const int half_fan_size)
void	make_geo_data (GeoData3D &geo_data, const FanProjData &fan_data)
void	make_block_data (BlockData3D &block_data, const FanProjData &fan_data)
void	iterate_efficiencies (DetectorEfficiencies &efficiencies, const Array< 2, float > &data_fan_sums, const FanProjData &model)
void	iterate_efficiencies (DetectorEfficiencies &efficiencies, const Array< 2, float > &data_fan_sums, const int max_ring_diff, const int half_fan_size)
void	iterate_geo_norm (GeoData3D &norm_geo_data, const GeoData3D &measured_geo_data, const FanProjData &model)
void	iterate_block_norm (BlockData3D &norm_block_data, const BlockData3D &measured_block_data, const FanProjData &model)
double	KL (const FanProjData &d1, const FanProjData &d2, const double threshold)
template<class TProjDataInfo >
void	multiply_crystal_factors_help (ProjData &proj_data, const TProjDataInfo &proj_data_info, const Array< 2, float > &efficiencies, float global_factor)
void	multiply_crystal_factors (ProjData &proj_data, const Array< 2, float > &efficiencies, const float global_factor)
	Construct proj-data as a multiple of crystal efficiencies (or singles) More...
template void	multiply_crystal_factors_help (ProjData &, const ProjDataInfoCylindricalNoArcCorr &, const Array< 2, float > &, const float)
template void	multiply_crystal_factors_help (ProjData &, const ProjDataInfoBlocksOnCylindricalNoArcCorr &, const Array< 2, float > &, const float)
int	get_max_num_threads ()
	Get current maximum number of threads. More...
void	set_num_threads (const int num_threads=0)
	Set current number of threads. More...
int	get_default_num_threads ()
	Get default number of threads. More...
void	set_default_num_threads ()
	set current number of threads to the default More...
template<typename T >
void	overlap_interpolate (VectorWithOffset< T > &out_data, const VectorWithOffset< T > &in_data, const float zoom, const float offset, const bool assign_rest_with_zeroes=true)
	'overlap' interpolation (i.e. count preserving) for vectors. More...
template void	overlap_interpolate (VectorWithOffset< float > &out_data, const VectorWithOffset< float > &in_data, const float zoom, const float offset, const bool assign_rest_with_zeroes)
template void	overlap_interpolate (VectorWithOffset< double > &out_data, const VectorWithOffset< double > &in_data, const float zoom, const float offset, const bool assign_rest_with_zeroes)
template void	overlap_interpolate (VectorWithOffset< Array< 1, float >> &out_data, const VectorWithOffset< Array< 1, float >> &in_data, const float zoom, const float offset, const bool assign_rest_with_zeroes)
template void	overlap_interpolate (VectorWithOffset< Array< 2, float >> &out_data, const VectorWithOffset< Array< 2, float >> &in_data, const float zoom, const float offset, const bool assign_rest_with_zeroes)
void	truncate_rim (Viewgram< float > &viewgram, const int rim_truncation_sino)
	sets the first and last rim_truncation_sino bins at the 'edges' to zero
void	truncate_rim (SegmentByView< float > &seg, const int rim_truncation_sino)
	sets the first and last rim_truncation_sino bins at the 'edges' to zero
void	truncate_rim (SegmentBySinogram< float > &seg, const int rim_truncation_sino)
void	truncate_rim (DiscretisedDensity< 3, float > &image_input, const int rim_truncation_image, const bool strictly_less_than_radius=true)
	sets to zero voxels within rim_truncation_image of the FOV rim
void	divide_and_truncate (Viewgram< float > &numerator, const Viewgram< float > &denominator, const int rim_truncation_sino, int &count, int &count2, double *f=NULL)
	divide viewgrams and set 'edge bins' to zero, put answer in numerator
void	divide_and_truncate (RelatedViewgrams< float > &numerator, const RelatedViewgrams< float > &denominator, const int rim_truncation_sino, int &count, int &count2, double *f=NULL)
	divide related viewgrams and set 'edge bins' to zero, put answer in numerator
void	divide_array (SegmentByView< float > &numerator, const SegmentByView< float > &denominator)
	simple division of two sinograms, x/0 = 0
void	divide_array (DiscretisedDensity< 3, float > &numerator, const DiscretisedDensity< 3, float > &denominator)
	simple division of two images, x/0 = 0
void	accumulate_loglikelihood (Viewgram< float > &projection_data, const Viewgram< float > &estimated_projections, const int rim_truncation_sino, double *accum)
	compute the log term of the loglikelihood function for given part of the projection space
void	multiply_and_add (DiscretisedDensity< 3, float > &image_res, const DiscretisedDensity< 3, float > &image_scaled, float scalar)
float	neg_trunc (float x)
	truncates negative values to zero
void	truncate_end_planes (DiscretisedDensity< 3, float > &input_image, int input_num_planes=1)
	sets the end planes of the image to zero
Succeeded	scale_sinograms (ProjData &output_proj_data, const ProjData &input_proj_data, const Array< 2, float > scale_factors_per_sinogram)
	apply a scale factor for every sinogram More...
Array< 2, float >	get_scale_factors_per_sinogram (const ProjData &numerator_proj_data, const ProjData &denominator_proj_data, const ProjData &weights_proj_data)
	find scale factors between two different sinograms More...
template<typename elemT >
void	build_gauss (VectorWithOffset< elemT > &kernel, int res, float s2, float sampling_interval)
template<typename elemT >
void	build_metz (VectorWithOffset< elemT > &kernel, float N, float fwhm, float MmPerVox, int max_kernel_size)
ProjDataInfo *	SSRB (const ProjDataInfo &in_proj_data_info, const int num_segments_to_combine, const int num_views_to_combine=1, const int num_tangential_poss_to_trim=0, const int max_in_segment_num_to_process=-1, const int num_tof_bins_to_combine=1)
	construct new ProjDataInfo that is appropriate for rebinned data More...
void	SSRB (const std::string &output_filename, const ProjData &in_projdata, const int num_segments_to_combine, const int num_views_to_combine=1, const int num_tangential_poss_to_trim=0, const bool do_normalisation=true, const int max_in_segment_num_to_process=-1, const int num_tof_bins_to_combine=1)
	Perform Single Slice Rebinning and write output to file. More...
void	SSRB (ProjData &out_projdata, const ProjData &in_projdata, const bool do_normalisation=true)
	Perform Single Slice Rebinning and write output to ProjData. More...
void	writeText (const char *text, OUTPUT_CHANNEL channel)
template<class FSTREAM >
void	ask_filename_and_open (FSTREAM &s, const string &prompt, const string &default_extension, ios::openmode mode, bool abort_if_failed)
template void	ask_filename_and_open (ifstream &s, const string &prompt, const string &default_extension, ios::openmode mode, bool abort_if_failed)
template void	ask_filename_and_open (ofstream &s, const string &prompt, const string &default_extension, ios::openmode mode, bool abort_if_failed)
template void	ask_filename_and_open (fstream &s, const string &prompt, const string &default_extension, ios::openmode mode, bool abort_if_failed)
void *	read_stream_in_memory (istream &input, streamsize &file_size)
void	warning (const char *const s,...)
	Print warning with format string a la printf. More...
void	randoms_from_singles (ProjData &proj_data, const SinglesRates &singles, float coincidence_time_window=-1.F, float radionuclide_halflife=-1.F)
	Estimate randoms from singles (RFS) More...
template<class elemT , class SCALE , class CHARP >
void	display_bitmap (const Array< 3, elemT > &plane_stack, const VectorWithOffset< SCALE > &scale_factors, const VectorWithOffset< CHARP > &text, double maxi, const char *const title, int scale)
template<class elemT , class SCALE , class CHARP >
void	display_mathlink (const Array< 3, elemT > &plane_stack, const VectorWithOffset< SCALE > &scale_factors, const VectorWithOffset< CHARP > &text, double maxi, const char *const title, int scale)
template<class elemT , class SCALE , class CHARP >
void	display_pgm (const Array< 3, elemT > &plane_stack, const VectorWithOffset< SCALE > &scale_factors, const VectorWithOffset< CHARP > &text, double maxi, const char *const title, int scale)
template<class elemT , class SCALE , class CHARP >
void	display (const Array< 3, elemT > &plane_stack, const VectorWithOffset< SCALE > &scale_factors, const VectorWithOffset< CHARP > &text, double maxi, const char *const title, int scale)
template<class elemT >
void	display (const RelatedViewgrams< elemT > &v1, double maxi=0, const char *const title=0, int zoom=0)
	Convenience function to display all viewgrams in a RelatedViewgrams object.
void	display (const DetPairData &det_pair_data, const char *const title)
void	display (const FanProjData &fan_data, const char *const title)
template void	display (const Array< 3, short > &plane_stack, const VectorWithOffset< short > &scale_factors, const VectorWithOffset< char *> &text, double maxi, const char *const title, int scale)
template void	display (const Array< 3, short > &plane_stack, const VectorWithOffset< float > &scale_factors, const VectorWithOffset< char *> &text, double maxi, const char *const title, int scale)
template void	display (const Array< 3, float > &plane_stack, const VectorWithOffset< float > &scale_factors, const VectorWithOffset< char *> &text, double maxi, const char *const title, int scale)
template void	display (const Array< 3, short > &plane_stack, const VectorWithOffset< short > &scale_factors, const VectorWithOffset< const char *> &text, double maxi, const char *const title, int scale)
template void	display (const Array< 3, short > &plane_stack, const VectorWithOffset< float > &scale_factors, const VectorWithOffset< const char *> &text, double maxi, const char *const title, int scale)
template void	display (const Array< 3, float > &plane_stack, const VectorWithOffset< float > &scale_factors, const VectorWithOffset< const char *> &text, double maxi, const char *const title, int scale)
template void	display (const RelatedViewgrams< float > &vs, double maxi, const char *const title, int zoom)
void	find_inverse_and_bck_densels (DiscretisedDensity< 3, float > &image, VectorWithOffset< SegmentByView< float > *> &all_segments, VectorWithOffset< SegmentByView< float > *> &attenuation_segmnets, const int min_z, const int max_z, const int min_y, const int max_y, const int min_x, const int max_x, ProjMatrixByDensel &proj_matrix, bool do_attenuation, const float threshold, bool normalize_result)
void	do_segments_densels_fwd (const VoxelsOnCartesianGrid< float > &image, ProjData &proj_data, VectorWithOffset< SegmentByView< float > *> &all_segments, const int min_z, const int max_z, const int min_y, const int max_y, const int min_x, const int max_x, ProjMatrixByDensel &proj_matrix)
void	fwd_densels_all (VectorWithOffset< SegmentByView< float > *> &all_segments, shared_ptr< ProjMatrixByDensel > proj_matrix_ptr, shared_ptr< ProjData > proj_data_ptr, const int min_z, const int max_z, const int min_y, const int max_y, const int min_x, const int max_x, const DiscretisedDensity< 3, float > &in_density)
void	divide_complex_arrays (Array< 1, float > &out_array, const Array< 1, float > &array_nom, const Array< 1, float > &array_denom)
void	mulitply_complex_arrays (Array< 1, float > &out_array, const Array< 1, float > &array_nom, const Array< 1, float > &array_denom)
void	mulitply_complex_arrays (Array< 1, float > &array_nom, const Array< 1, float > &array_denom)
void	divide_complex_arrays (Array< 1, float > &array_nom, const Array< 1, float > &array_denom)
void	create_kernel_3d (Array< 3, float > &kernel_3d, const VectorWithOffset< float > &kernel_1d)
void	create_kernel_2d (Array< 2, float > &kernel_2d, const VectorWithOffset< float > &kernel_1d)
void	padd_filter_coefficients_3D_and_make_them_symmetric (VectorWithOffset< VectorWithOffset< VectorWithOffset< float >>> &padded_filter_coefficients_3D, VectorWithOffset< VectorWithOffset< VectorWithOffset< float >>> &filter_coefficients)
void	convert_array_3D_into_1D_array (Array< 1, float > &out_array, const Array< 3, float > &in_array)
void	convert_array_1D_into_3D_array (Array< 3, float > &out_array, const Array< 1, float > &in_array)
void	convert_array_2D_into_1D_array (Array< 1, float > &out_array, Array< 2, float > &in_array)
void	convert_array_1D_into_2D_array (Array< 2, float > &out_array, Array< 1, float > &in_array)
void	precompute_filter_coefficients_for_second_apporach (VoxelsOnCartesianGrid< float > &precomputed_coefficients, const VoxelsOnCartesianGrid< float > &input_image, VoxelsOnCartesianGrid< float > &sensitivity_image, VoxelsOnCartesianGrid< float > &normalised_bck)
void	construct_scaled_filter_coefficients_3D (VectorWithOffset< VectorWithOffset< VectorWithOffset< float >>> &new_filter_coefficients_3D_array, VectorWithOffset< float > kernel_1d, const float kapa0_over_kapa1)
void	construct_scaled_filter_coefficients_2D (Array< 2, float > &new_filter_coefficients_2D_array, VectorWithOffset< float > kernel_1d, const float kapa0_over_kapa1)
void	construct_scaled_filter_coefficients_3D (Array< 3, float > &new_filter_coefficients_3D_array, VectorWithOffset< float > kernel_1d, const float kapa0_over_kapa1)
void	construct_scaled_filter_coefficients_2D (Array< 2, float > &new_filter_coefficients_2D_array, Array< 2, float > &kernel_2d, const float kapa0_over_kapa1, int number_of_coefficients_before_padding)
void	construct_scaled_filter_coefficients_3D (Array< 3, float > &new_filter_coefficients_2D_array, Array< 3, float > &kernel_3d, const float kapa0_over_kapa1)
RigidObject3DTransformation	compose (const RigidObject3DTransformation &apply_last, const RigidObject3DTransformation &apply_first)
	Composition of 2 transformations. More...
std::ostream &	operator<< (std::ostream &out, const RigidObject3DTransformation &rigid_object_transformation)
	Output to (text) stream. More...
std::istream &	operator>> (std::istream &, RigidObject3DTransformation &rigid_object_transformation)
	Input from (text) stream. More...
Succeeded	transform_3d_object (DiscretisedDensity< 3, float > &out_density, const DiscretisedDensity< 3, float > &in_density, const RigidObject3DTransformation &transformation_in_to_out)
	transform image data More...
Succeeded	transpose_of_transform_3d_object (DiscretisedDensity< 3, float > &out_density, const DiscretisedDensity< 3, float > &in_density, const RigidObject3DTransformation &transformation_in_to_out)
	transform image data using transposed matrix More...
Array< 3, BasicCoordinate< 3, float > >	find_grid_coords_of_transformed_centres (const DiscretisedDensity< 3, float > &source_density, const DiscretisedDensity< 3, float > &target_density, const ObjectTransformation< 3, float > &transformation_source_to_target)
Array< 3, std::pair< BasicCoordinate< 3, float >, float > >	find_grid_coords_of_transformed_centres_and_jacobian (const DiscretisedDensity< 3, float > &source_density, const DiscretisedDensity< 3, float > &target_density, const ObjectTransformation< 3, float > &transformation_source_to_target)
Succeeded	transform_3d_object (ProjData &out_proj_data, const ProjData &in_proj_data, const RigidObject3DTransformation &object_transformation)
	transform projection data More...
Succeeded	transform_3d_object (ProjData &out_proj_data, const ProjData &in_proj_data, const RigidObject3DTransformation &rigid_object_transformation, const int min_in_segment_num_to_process, const int max_in_segment_num_to_process)
	transform projection data More...
int	sign (const float x)
float	trapezoid_integral (const float s, const float m2, const float m3)
template<typename T >
T	cube (const T x)
float	convolution_2_trapezoids (const float x, const float m21, const float m31, const float m22, const float m32)
float	VOI (const float s_voxel, const float half_bin_size, const float halfcosminsin, const float halfcosplussin)
float	SA_rotated_voxel (const float s_voxel, const float half_voxel_size, const float m2, const float m3)
float	SAapprox (const float s_voxel, const float half_voxel_size, const float m2, const float m3, const float halfcosminsin, const float halfcosplussin)
float	SA (const float s_voxel, const float half_voxel_size, const float m2, const float m3, const float halfcosminsin, const float halfcosplussin)
template<typename T >
bool	coordinates_less (const BasicCoordinate< 3, T > &el1, const BasicCoordinate< 3, T > &el2)
template<typename elemT >
void	discrete_fourier_transform (VectorWithOffset< elemT > &data, int isign)
float	rand1 ()
void	do_block (vector< Bin > &list_of_bins_in_block, const int axial_block_num, const int tangential_block_num, const ProjDataInfoCylindricalNoArcCorr &proj_data_info, const int axial_num_crystals_in_block, const int tangential_num_crystals_in_block)
bool	bin_coordinates_by_view_less (const Bin &b1, const Bin &b2)
void	sort_and_make_unique (vector< Bin > &list_of_bins)
void	find_inverse (ProjData *proj_data_ptr_out, const ProjData *proj_data_ptr_in)
void	do_segments (DiscretisedDensity< 3, float > &image, ProjData &proj_data_org, const int start_segment_num, const int end_segment_num, const int start_view, const int end_view, BackProjectorByBin &back_projector, bool fill_with_1)
void	find_inverse (ProjData &proj_data_out, const ProjData &proj_data_in, const int min_segment_num, const int max_segment_num)
template<int num_dimensions, typename elemT >
const Array< num_dimensions - 1, elemT > &	get (const Array< num_dimensions, elemT > &a, const BasicCoordinate< 1, int > &c)
template<class elemT >
Array< 1, elemT > &	in_place_log (Array< 1, elemT > &v)
	Replace elements by their logarithm, 1D version. More...
template<int num_dimensions, class elemT >
Array< num_dimensions, elemT > &	in_place_log (Array< num_dimensions, elemT > &v)
	apply log to each element of the multi-dimensional array More...
template<class elemT >
Array< 1, elemT > &	in_place_exp (Array< 1, elemT > &v)
	Replace elements by their exponentiation, 1D version. More...
template<int num_dimensions, class elemT >
Array< num_dimensions, elemT > &	in_place_exp (Array< num_dimensions, elemT > &v)
	apply exp to each element of the multi-dimensional array More...
template<class elemT >
Array< 1, elemT > &	in_place_abs (Array< 1, elemT > &v)
	Replace elements by their absolute value, 1D version. More...
template<int num_dimensions, class elemT >
Array< num_dimensions, elemT > &	in_place_abs (Array< num_dimensions, elemT > &v)
	store absolute value of each element of the multi-dimensional array More...
template<class T , class FUNCTION >
T &	in_place_apply_function (T &v, FUNCTION f)
	apply any function(object) to each element of the multi-dimensional array More...
template<int num_dim, typename elemT , typename FunctionObjectPtr >
void	in_place_apply_array_function_on_1st_index (Array< num_dim, elemT > &array, FunctionObjectPtr f)
	Apply a function object on all possible 1d arrays extracted by keeping all indices fixed, except the first one. More...
template<int num_dim, typename elemT , typename FunctionObjectPtr >
void	apply_array_function_on_1st_index (Array< num_dim, elemT > &out_array, const Array< num_dim, elemT > &in_array, FunctionObjectPtr f)
	apply any function(object) to each element of the multi-dimensional array, storing results in a different array More...
template<int num_dim, typename elemT , typename FunctionObjectPtrIter >
void	in_place_apply_array_functions_on_each_index (Array< num_dim, elemT > &array, FunctionObjectPtrIter start, FunctionObjectPtrIter stop)
	Apply a sequence of 1d array-function objects on every dimension of the input array. More...
template<typename elemT , typename FunctionObjectPtrIter >
void	in_place_apply_array_functions_on_each_index (Array< 1, elemT > &array, FunctionObjectPtrIter start, FunctionObjectPtrIter stop)
	1d specialisation of the above.
template<int num_dim, typename elemT , typename FunctionObjectPtrIter >
void	apply_array_functions_on_each_index (Array< num_dim, elemT > &out_array, const Array< num_dim, elemT > &in_array, FunctionObjectPtrIter start, FunctionObjectPtrIter stop)
	Apply a sequence of 1d array-function objects on every dimension of the input array, store in output array. More...
template<int num_dim, typename elemT >
void	apply_array_functions_on_each_index (Array< num_dim, elemT > &out_array, const Array< num_dim, elemT > &in_array, ActualFunctionObjectPtrIter start, ActualFunctionObjectPtrIter stop)
	Apply a sequence of 1d array-function objects of a specific type on every dimension of the input array, store in output array. More...
template<typename elemT >
void	apply_array_functions_on_each_index (Array< 1, elemT > &out_array, const Array< 1, elemT > &in_array, ActualFunctionObjectPtrIter start, ActualFunctionObjectPtrIter stop)
	1d specialisation of above
template<typename elemT , typename FunctionObjectPtrIter >
void	apply_array_functions_on_each_index (Array< 1, elemT > &out_array, const Array< 1, elemT > &in_array, FunctionObjectPtrIter start, FunctionObjectPtrIter stop)
	1d specialisation for general function objects
template<int num_dim, typename elemT >
void	transform_array_to_periodic_indices (Array< num_dim, elemT > &out_array, const Array< num_dim, elemT > &in_array)
template<int num_dim, typename elemT >
void	transform_array_from_periodic_indices (Array< num_dim, elemT > &out_array, const Array< num_dim, elemT > &in_array)
template<int num_dimensions, typename elemT >
void	transform_array_to_periodic_indices (Array< num_dimensions, elemT > &out_array, const Array< num_dimensions, elemT > &in_array)
template<int num_dimensions, typename elemT >
void	transform_array_from_periodic_indices (Array< num_dimensions, elemT > &out_array, const Array< num_dimensions, elemT > &in_array)
template<class elemT >
void	assign_to_subregion (Array< 3, elemT > &input_array, const BasicCoordinate< 3, int > &mask_location, const BasicCoordinate< 3, int > &half_size, const elemT &value)
	assign a value to a sub-region of an array More...
template<int num_dimensions, typename coordT >
coordT	inner_product (const BasicCoordinate< num_dimensions, coordT > &p1, const BasicCoordinate< num_dimensions, coordT > &p2)
	compute sum_i p1[i] * p2[i] More...
template<int num_dimensions, typename coordT >
double	norm_squared (const BasicCoordinate< num_dimensions, coordT > &p1)
	compute (inner_product(p1,p1)) More...
template<int num_dimensions, typename coordT >
double	norm (const BasicCoordinate< num_dimensions, coordT > &p1)
	compute sqrt(inner_product(p1,p1)) More...
template<int num_dimensions, typename coordT >
double	angle (const BasicCoordinate< num_dimensions, coordT > &p1, const BasicCoordinate< num_dimensions, coordT > &p2)
	compute angle between 2 directions More...
template<int num_dimensions, typename coordT >
double	cos_angle (const BasicCoordinate< num_dimensions, coordT > &p1, const BasicCoordinate< num_dimensions, coordT > &p2)
	compute cos of the angle between 2 directions More...
template<int num_dimensions, typename coordT >
BasicCoordinate< num_dimensions+1, coordT >	join (const coordT &a, const BasicCoordinate< num_dimensions, coordT > &c)
	make a longer BasicCoordinate, by prepending c with the single coordT More...
template<int num_dimensions, class coordT >
BasicCoordinate< num_dimensions+1, coordT >	join (const BasicCoordinate< num_dimensions, coordT > &c, const coordT &a)
	make a longer BasicCoordinate, by appending the coordT to c More...
template<int num_dimensions, class coordT >
BasicCoordinate< num_dimensions - 1, coordT >	cut_last_dimension (const BasicCoordinate< num_dimensions, coordT > &c)
	make a shorter BasicCoordinate, by cutting the last element from c More...
template<int num_dimensions, typename coordT >
BasicCoordinate< num_dimensions - 1, coordT >	cut_first_dimension (const BasicCoordinate< num_dimensions, coordT > &c)
	make a shorter BasicCoordinate, by cutting the first element from c More...
template<int num_dimensions>
BasicCoordinate< num_dimensions, float >	convert_int_to_float (const BasicCoordinate< num_dimensions, int > &cint)
	converts a BasicCoordinate<int> to BasicCoordinate<float> More...
template<class NUMBER >
NUMBER	square (const NUMBER &x)
	returns the square of a number, templated. More...
template<int num_dimensions, class T1 , class T2 , class scaleT >
void	find_scale_factor (scaleT &scale_factor, const Array< num_dimensions, T1 > &data_in, const NumericInfo< T2 > info_for_out_type)
	A function that finds a scale factor to use when converting data to a new type. More...
template<int num_dimensions, class T1 , class T2 , class scaleT >
Array< num_dimensions, T2 >	convert_array (scaleT &scale_factor, const Array< num_dimensions, T1 > &data_in, const NumericInfo< T2 > info2)
	A function that returns a new Array (of the same dimension) with elements of type T2. More...
template<int num_dimensions, class T1 , class T2 , class scaleT >
void	convert_array (Array< num_dimensions, T2 > &data_out, scaleT &scale_factor, const Array< num_dimensions, T1 > &data_in)
	Converts the data_in Array to data_out (with elements of different types) such that data_in == data_out * scale_factor. More...
template<class InputIteratorT , class T2 , class scaleT >
void	find_scale_factor (scaleT &scale_factor, const InputIteratorT &begin, const InputIteratorT &end, const NumericInfo< T2 > info_for_out_type)
	A function that finds a scale factor to use when converting data to a new type. More...
template<class OutputIteratorT , class InputIteratorT , class scaleT >
void	convert_range (const OutputIteratorT &out_begin, scaleT &scale_factor, const InputIteratorT &in_begin, const InputIteratorT &in_end)
	Converts the data in the input range to the output range (with elements of different types) such that data_in == data_out * scale_factor. More...
template<class IteratorT , class scaleT >
void	convert_range (const IteratorT &out_begin, scaleT &scale_factor, const IteratorT &in_begin, const IteratorT &in_end)
template<typename T , typename iterT >
iterT	copy_to (const T &stir_object, iterT iter)
	Copy all bins to a range specified by a iterator. More...
template<typename T , typename iterT >
void	fill_from (T &stir_object, iterT iter, iterT iter_end)
	set all elements of stir_object from an iterator More...
template<class coordT >
CartesianCoordinate3D< coordT >	cross_product (const CartesianCoordinate3D< coordT > &a, const CartesianCoordinate3D< coordT > &b)
	the cross-product for 3-dimensional coordinates. More...
template<int num_dimensions, typename elemT >
void	array_to_device (elemT *dev_data, const Array< num_dimensions, elemT > &stir_array)
template<int num_dimensions, typename elemT >
void	array_to_host (Array< num_dimensions, elemT > &stir_array, const elemT *dev_data)
double	decay_correction_factor (const double isotope_halflife, const double start_time, const double end_time)
	Compute decay-correction factor for a time frame. More...
double	decay_correction_factor (const double isotope_halflife, const double rel_time)
	Computes the decay-correction factor for activity at a given time point. More...
template<class elemT , class scaleT , class CHARP >
void	display (const Array< 3, elemT > &plane_stack, const VectorWithOffset< scaleT > &scale_factors, const VectorWithOffset< CHARP > &text, double maxi, const char *const title, int zoom)
template<class elemT , class scaleT , class CHARP >
void	display (const Array< 3, elemT > &plane_stack, const VectorWithOffset< scaleT > &scale_factors, const VectorWithOffset< CHARP > &text, double maxi, const char *const title)
template<class elemT , class scaleT , class CHARP >
void	display (const Array< 3, elemT > &plane_stack, const VectorWithOffset< scaleT > &scale_factors, const VectorWithOffset< CHARP > &text, double maxi)
template<class elemT , class scaleT , class CHARP >
void	display (const Array< 3, elemT > &plane_stack, const VectorWithOffset< scaleT > &scale_factors, const VectorWithOffset< CHARP > &text)
template<class elemT >
void	display (const Array< 3, elemT > &plane_stack, double maxi, const char *const title, int zoom)
template<class elemT >
void	display (const Array< 3, elemT > &plane_stack, double maxi, const char *const title)
template<class elemT >
void	display (const Array< 3, elemT > &plane_stack, double maxi)
template<class elemT >
void	display (const Array< 3, elemT > &plane_stack)
template<class elemT >
void	display (const Array< 2, elemT > &plane, const char *const text, double maxi, int zoom)
template<class elemT >
void	display (const Array< 2, elemT > &plane, const char *const text, double maxi)
template<class elemT >
void	display (const Array< 2, elemT > &plane, const char *const text)
template<class elemT >
void	display (const Array< 2, elemT > &plane)
template<typename iterT >
void	fill_from (DynamicProjData &stir_object, iterT iter, iterT)
	set all elements of a MultipleProjData from an iterator More...
template<class STRING >
void	error (const STRING &string)
	Use this function for writing error messages and throwing an exception. More...
template<class elemT >
Array< 1, elemT >	extract_line (const Array< 3, elemT > &, const BasicCoordinate< 3, int > &index, const int dimension)
	extracts a line from an array in the direction of the specified dimension. More...
template<class RandomAccessIterType >
float	find_level_width (const RandomAccessIterType &begin_iterator, const RandomAccessIterType &max_iterator, const RandomAccessIterType &end_iterator, const float level_height)
	find width at a level More...
template<class RandomAccessIterType >
float	find_level_width (const RandomAccessIterType &begin_iterator, const RandomAccessIterType &end_iterator, const float level_height)
	find width at a level More...
template<class coordT >
coordT	coordinate_between_2_lines (CartesianCoordinate3D< coordT > &result, const LORAs2Points< coordT > &line0, const LORAs2Points< coordT > &line1)
	find a point half-way between 2 lines and their distance More...
template<class coordT >
coordT	distance_between_line_and_point (const LORAs2Points< coordT > &line, const CartesianCoordinate3D< coordT > &r1)
	find the distance between a point and a line
template<class coordT >
void	project_point_on_a_line (const CartesianCoordinate3D< coordT > &p1, const CartesianCoordinate3D< coordT > &p2, CartesianCoordinate3D< coordT > &r1)
	Project a point on a line. More...
template<class elemT >
int	index_at_maximum (const VectorWithOffset< elemT > &v)
	Finds the index where the maximum occurs in a (1-dimensional) vector. More...
template<class elemT >
BasicCoordinate< 3, int >	indices_at_maximum (const Array< 3, elemT > &input_array)
	Finds the first (3-dimensional) index where the maximum occurs in a (3-dimensional) array. More...
template<class STRING >
void	info (const STRING &string, const int verbosity_level=1)
	Use this function for writing informational messages. More...
bool	is_interfile_signature (const char *const signature)
	Checks if the signature corresponds to the start of an interfile header. More...
VoxelsOnCartesianGrid< float > *	read_interfile_image (std::istream &input, const std::string &directory_for_data="")
	This reads the first 3d image in an Interfile header file, given as a stream. More...
VoxelsOnCartesianGrid< float > *	read_interfile_image (const std::string &filename)
	This reads the first 3d image in an Interfile header file, given as a filename. More...
DynamicDiscretisedDensity *	read_interfile_dynamic_image (std::istream &input, const std::string &directory_for_data)
	Read dynamic image.
DynamicDiscretisedDensity *	read_interfile_dynamic_image (const std::string &filename)
	Read dynamic image.
ParametricDiscretisedDensity< VoxelsOnCartesianGrid< KineticParameters< 2, float > > > *	read_interfile_parametric_image (std::istream &input, const std::string &directory_for_data)
	Read parametric image.
ParametricDiscretisedDensity< VoxelsOnCartesianGrid< KineticParameters< 2, float > > > *	read_interfile_parametric_image (const std::string &filename)
	Read parametric image.
Succeeded	write_basic_interfile_image_header (const std::string &header_file_name, const std::string &image_file_name, const ExamInfo &exam_info, const IndexRange< 3 > &index_range, const CartesianCoordinate3D< float > &voxel_size, const CartesianCoordinate3D< float > &origin, const NumericType output_type, const ByteOrder byte_order, const VectorWithOffset< float > &scaling_factors, const VectorWithOffset< unsigned long > &file_offsets, const std::vector< std::string > &data_type_descriptions=std::vector< std::string >())
	This outputs an Interfile header for an image. More...
const VectorWithOffset< unsigned long >	compute_file_offsets (int number_of_time_frames, const NumericType output_type, const Coordinate3D< int > &dim, unsigned long initial_offset=0)
	a utility function that computes the file offsets of subsequent images
template<class elemT >
Succeeded	write_basic_interfile (const std::string &filename, const Array< 3, elemT > &image, const CartesianCoordinate3D< float > &voxel_size, const CartesianCoordinate3D< float > &origin, const NumericType output_type=NumericType::FLOAT, const float scale=0, const ByteOrder byte_order=ByteOrder::native)
	This outputs an Interfile header and data for a Array<3,elemT> object. More...
template<class elemT >
Succeeded	write_basic_interfile (const std::string &filename, const ExamInfo &exam_info, const Array< 3, elemT > &image, const CartesianCoordinate3D< float > &voxel_size, const CartesianCoordinate3D< float > &origin, const NumericType output_type=NumericType::FLOAT, const float scale=0, const ByteOrder byte_order=ByteOrder::native)
	This outputs an Interfile header and data for a Array<3,elemT> object. More...
template<class elemT >
Succeeded	write_basic_interfile (const std::string &filename, const Array< 3, elemT > &image, const NumericType output_type=NumericType::FLOAT, const float scale=0, const ByteOrder byte_order=ByteOrder::native)
	This outputs an Interfile header and data for a Array<3,elemT> object, assuming unit voxel sizes. More...
Succeeded	write_basic_interfile (const std::string &filename, const VoxelsOnCartesianGrid< float > &image, const NumericType output_type=NumericType::FLOAT, const float scale=0, const ByteOrder byte_order=ByteOrder::native)
	This outputs an Interfile header and data for a VoxelsOnCartesianGrid<float> object. More...
Succeeded	write_basic_interfile (const std::string &filename, const DiscretisedDensity< 3, float > &image, const NumericType output_type=NumericType::FLOAT, const float scale=0, const ByteOrder byte_order=ByteOrder::native)
	This outputs an Interfile header and data for a DiscretisedDensity<3,float> object. More...
Succeeded	write_basic_interfile (const std::string &filename, const ParametricDiscretisedDensity< VoxelsOnCartesianGrid< KineticParameters< 2, float >>> &image, const NumericType output_type=NumericType::FLOAT, const float scale=0, const ByteOrder byte_order=ByteOrder::native)
Succeeded	write_basic_interfile (const std::string &filename, const DynamicDiscretisedDensity &image, const NumericType output_type=NumericType::FLOAT, const float scale=0, const ByteOrder byte_order=ByteOrder::native)
ProjDataFromStream *	read_interfile_PDFS (std::istream &input, const std::string &directory_for_data="", const std::ios::openmode openmode=std::ios::in)
	This reads the first 3D sinogram from an Interfile header, given as a stream. More...
ProjDataFromStream *	read_interfile_PDFS (const std::string &filename, const std::ios::openmode open_mode)
	This reads the first 3D sinogram from an Interfile header, given as a filename. More...
Succeeded	write_basic_interfile_PDFS_header (const std::string &header_filename, const std::string &data_filename, const ProjDataFromStream &pdfs)
	This writes an Interfile header appropriate for the ProjDataFromStream object. More...
Succeeded	write_basic_interfile_PDFS_header (const std::string &data_filename, const ProjDataFromStream &pdfs)
	This function writes an Interfile header for the pdfs object. More...
template<int num_dimensions, class IStreamT , class elemT >
Succeeded	read_data (IStreamT &s, Array< num_dimensions, elemT > &data, const ByteOrder byte_order=ByteOrder::native)
	Read the data of an Array from file. More...
template<int num_dimensions, class IStreamT , class elemT , class InputType , class ScaleT >
Succeeded	read_data (IStreamT &s, Array< num_dimensions, elemT > &data, NumericInfo< InputType > input_type, ScaleT &scale_factor, const ByteOrder byte_order=ByteOrder::native)
	Read the data of an Array from file as a different type. More...
template<int num_dimensions, class IStreamT , class elemT , class ScaleT >
Succeeded	read_data (IStreamT &s, Array< num_dimensions, elemT > &data, NumericType type, ScaleT &scale, const ByteOrder byte_order=ByteOrder::native)
	Read the data of an Array from file as a different type. More...
template<class DataT , class FileT >
unique_ptr< DataT >	read_from_file (const FileSignature &signature, FileT file)
	Function that reads data from file using the default InputFileFormatRegistry, using the provided FileSignature to find the matching file format. More...
template<class DataT , class FileT >
unique_ptr< DataT >	read_from_file (FileT file)
	Function that reads data from file using the default InputFileFormatRegistry. More...
template<int num_dimensions, class OStreamT , class elemT >
Succeeded	write_data (OStreamT &s, const Array< num_dimensions, elemT > &data, const ByteOrder byte_order=ByteOrder::native, const bool can_corrupt_data=false)
	Write the data of an Array to file. More...
template<int num_dimensions, class OStreamT , class elemT , class OutputType , class ScaleT >
Succeeded	write_data (OStreamT &s, const Array< num_dimensions, elemT > &data, NumericInfo< OutputType > output_type, ScaleT &scale_factor, const ByteOrder byte_order=ByteOrder::native, const bool can_corrupt_data=false)
	Write the data of an Array to file as a different type. More...
template<int num_dimensions, class OStreamT , class elemT , class OutputType , class ScaleT >
Succeeded	write_data_with_fixed_scale_factor (OStreamT &s, const Array< num_dimensions, elemT > &data, NumericInfo< OutputType > output_type, const ScaleT scale_factor, const ByteOrder byte_order=ByteOrder::native, const bool can_corrupt_data=false)
	Write the data of an Array to file as a different type but using a given scale factor. More...
template<int num_dimensions, class OStreamT , class elemT , class ScaleT >
Succeeded	write_data (OStreamT &s, const Array< num_dimensions, elemT > &data, NumericType type, ScaleT &scale, const ByteOrder byte_order=ByteOrder::native, const bool can_corrupt_data=false)
	Write the data of an Array to file as a different type. More...
template<class DataT >
std::string	write_to_file (const std::string &filename, const DataT &data)
	Function that writes data to file using the default OutputFileFormat. More...
template<class Value , class DataType , class CoordinatesType >
void	linear_regression (Value &constant, Value &scale, Value &chi_square, Value &variance_of_constant, Value &variance_of_scale, Value &covariance_of_constant_with_scale, const VectorWithOffset< DataType > &measured_data, const VectorWithOffset< CoordinatesType > &coordinates, const VectorWithOffset< float > &weights, const bool use_estimated_variance=true)
	Implements standard linear regression on VectorWithOffset data. More...
template<class Value , class DataIter , class CoordinatesIter , class WeightsIter >
void	linear_regression (Value &constant, Value &scale, Value &chi_square, Value &variance_of_constant, Value &variance_of_scale, Value &covariance_of_constant_with_scale, DataIter measured_data_begin, DataIter measured_data_end, CoordinatesIter coords_begin, WeightsIter weights_begin, const bool use_estimated_variance=true)
	Implements standard linear regression. More...
template<class ValueIter , class DataIter , class CoordinatesIter , class WeightsIter >
void	linear_regression (ValueIter regression_values_begin, DataIter data_begin, DataIter data_end, CoordinatesIter coords_begin, WeightsIter weights_begin, const bool use_estimated_variance=true)
template<class coordT1 , class coordT2 >
Succeeded	find_LOR_intersections_with_cylinder (LORInCylinderCoordinates< coordT1 > &, const LORAs2Points< coordT2 > &, const double radius)
	Given an LOR, find its intersection with a (infintely long) cylinder. More...
template<class coordT1 , class coordT2 >
Succeeded	find_LOR_intersections_with_cylinder (LORAs2Points< coordT1 > &intersection_coords, const LORAs2Points< coordT2 > &coords, const double radius)
	Given an LOR, find its intersection with a (infintely long) cylinder. More...
template<class coordT1 , class coordT2 >
Succeeded	find_LOR_intersections_with_cylinder (LORInAxialAndNoArcCorrSinogramCoordinates< coordT1 > &lor, const LORAs2Points< coordT2 > &cart_coords, const double radius)
	Given an LOR, find its intersection with a (infintely long) cylinder. More...
template<class coordT1 , class coordT2 >
Succeeded	find_LOR_intersections_with_cylinder (LORInAxialAndSinogramCoordinates< coordT1 > &lor, const LORAs2Points< coordT2 > &cart_coords, const double radius)
	Given an LOR, find its intersection with a (infintely long) cylinder. More...
template<class T >
VectorWithOffset< T >	make_vector (const T &a0)
template<class T >
VectorWithOffset< T >	make_vector (const T &a0, const T &a1)
template<class T >
VectorWithOffset< T >	make_vector (const T &a0, const T &a1, const T &a2)
template<class T >
VectorWithOffset< T >	make_vector (const T &a0, const T &a1, const T &a2, const T &a3)
template<class T >
VectorWithOffset< T >	make_vector (const T &a0, const T &a1, const T &a2, const T &a3, const T &a4)
template<class T >
VectorWithOffset< T >	make_vector (const T &a0, const T &a1, const T &a2, const T &a3, const T &a4, const T &a5)
template<class T >
VectorWithOffset< T >	make_vector (const T &a0, const T &a1, const T &a2, const T &a3, const T &a4, const T &a5, const T &a6)
template<class T >
VectorWithOffset< T >	make_vector (const T &a0, const T &a1, const T &a2, const T &a3, const T &a4, const T &a5, const T &a6, const T &a7)
template<class T >
VectorWithOffset< T >	make_vector (const T &a0, const T &a1, const T &a2, const T &a3, const T &a4, const T &a5, const T &a6, const T &a7, const T &a8)
template<class T >
VectorWithOffset< T >	make_vector (const T &a0, const T &a1, const T &a2, const T &a3, const T &a4, const T &a5, const T &a6, const T &a7, const T &a8, const T &a9)
template<class T >
Array< 1, T >	make_1d_array (const T &a0)
template<class T >
Array< 1, T >	make_1d_array (const T &a0, const T &a1)
template<class T >
Array< 1, T >	make_1d_array (const T &a0, const T &a1, const T &a2)
template<class T >
Array< 1, T >	make_1d_array (const T &a0, const T &a1, const T &a2, const T &a3)
template<class T >
Array< 1, T >	make_1d_array (const T &a0, const T &a1, const T &a2, const T &a3, const T &a4)
template<class T >
Array< 1, T >	make_1d_array (const T &a0, const T &a1, const T &a2, const T &a3, const T &a4, const T &a5)
template<class T >
Array< 1, T >	make_1d_array (const T &a0, const T &a1, const T &a2, const T &a3, const T &a4, const T &a5, const T &a6)
template<class T >
Array< 1, T >	make_1d_array (const T &a0, const T &a1, const T &a2, const T &a3, const T &a4, const T &a5, const T &a6, const T &a7)
template<class T >
Array< 1, T >	make_1d_array (const T &a0, const T &a1, const T &a2, const T &a3, const T &a4, const T &a5, const T &a6, const T &a7, const T &a8)
template<class T >
Array< 1, T >	make_1d_array (const T &a0, const T &a1, const T &a2, const T &a3, const T &a4, const T &a5, const T &a6, const T &a7, const T &a8, const T &a9)
template<int num_dimensions, class T >
Array< num_dimensions+1, T >	make_array (const Array< num_dimensions, T > &a0)
template<int num_dimensions, class T >
Array< num_dimensions+1, T >	make_array (const Array< num_dimensions, T > &a0, const Array< num_dimensions, T > &a1)
template<int num_dimensions, class T >
Array< num_dimensions+1, T >	make_array (const Array< num_dimensions, T > &a0, const Array< num_dimensions, T > &a1, const Array< num_dimensions, T > &a2)
template<int num_dimensions, class T >
Array< num_dimensions+1, T >	make_array (const Array< num_dimensions, T > &a0, const Array< num_dimensions, T > &a1, const Array< num_dimensions, T > &a2, const Array< num_dimensions, T > &a3)
template<int num_dimensions, class T >
Array< num_dimensions+1, T >	make_array (const Array< num_dimensions, T > &a0, const Array< num_dimensions, T > &a1, const Array< num_dimensions, T > &a2, const Array< num_dimensions, T > &a3, const Array< num_dimensions, T > &a4)
template<int num_dimensions, class T >
Array< num_dimensions+1, T >	make_array (const Array< num_dimensions, T > &a0, const Array< num_dimensions, T > &a1, const Array< num_dimensions, T > &a2, const Array< num_dimensions, T > &a3, const Array< num_dimensions, T > &a4, Array< num_dimensions, T > &a5)
template<int num_dimensions, class T >
Array< num_dimensions+1, T >	make_array (const Array< num_dimensions, T > &a0, const Array< num_dimensions, T > &a1, const Array< num_dimensions, T > &a2, const Array< num_dimensions, T > &a3, const Array< num_dimensions, T > &a4, Array< num_dimensions, T > &a5, const Array< num_dimensions, T > &a6)
template<int num_dimensions, class T >
Array< num_dimensions+1, T >	make_array (const Array< num_dimensions, T > &a0, const Array< num_dimensions, T > &a1, const Array< num_dimensions, T > &a2, const Array< num_dimensions, T > &a3, const Array< num_dimensions, T > &a4, Array< num_dimensions, T > &a5, const Array< num_dimensions, T > &a6, const Array< num_dimensions, T > &a7)
template<int num_dimensions, class T >
Array< num_dimensions+1, T >	make_array (const Array< num_dimensions, T > &a0, const Array< num_dimensions, T > &a1, const Array< num_dimensions, T > &a2, const Array< num_dimensions, T > &a3, const Array< num_dimensions, T > &a4, Array< num_dimensions, T > &a5, const Array< num_dimensions, T > &a6, const Array< num_dimensions, T > &a7, const Array< num_dimensions, T > &a8)
template<int num_dimensions, class T >
Array< num_dimensions+1, T >	make_array (const Array< num_dimensions - 1, T > &a0, const Array< num_dimensions - 1, T > &a1, const Array< num_dimensions - 1, T > &a2, const Array< num_dimensions - 1, T > &a3, const Array< num_dimensions - 1, T > &a4, Array< num_dimensions - 1, T > &a5, const Array< num_dimensions - 1, T > &a6, const Array< num_dimensions - 1, T > &a7, const Array< num_dimensions - 1, T > &a8, const Array< num_dimensions - 1, T > &a9)
template<int num_dimensions, class T >
Array< num_dimensions+1, T >	make_array (const Array< num_dimensions, T > &a0, const Array< num_dimensions, T > &a1, const Array< num_dimensions, T > &a2, const Array< num_dimensions, T > &a3, const Array< num_dimensions, T > &a4, Array< num_dimensions, T > &a5, const Array< num_dimensions, T > &a6, const Array< num_dimensions, T > &a7, const Array< num_dimensions, T > &a8, const Array< num_dimensions, T > &a9)
template<typename ForwardIter_t >
ForwardIter_t	min_positive_element (ForwardIter_t start, ForwardIter_t end)
	Finds where the smallest strictly positive element occurs. More...
double	KL (const double a, const double b, const double threshold_a=0)
template<int num_dimensions, typename elemT >
double	KL (const Array< num_dimensions, elemT > &a, const Array< num_dimensions, elemT > &b, const double threshold_a=0)
template<int num_dimensions, class T , class T2 >
void	assign (KineticParameters< num_dimensions, T > &v, const T2 &y)
template<class iterT >
iterT	abs_max_element (iterT start, iterT end)
	Like std::max_element, but comparing after taking absolute value. More...
template<class IterT , class elemT >
elemT	sum (IterT start, IterT end, elemT init)
	Compute the sum of a sequence using operator+=(), using an initial value. More...
template<class IterT >
std::iterator_traits< IterT >::value_type	sum (IterT start, IterT end)
	Compute the sum of a sequence using operator+=(). More...
template<class IterT >
std::iterator_traits< IterT >::value_type	average (IterT start, IterT end)
	Compute the average of a sequence using sum(start,end). More...
template<typename iterT >
void	fill_from (MultipleProjData &stir_object, iterT iter, iterT)
	set all elements of a MultipleProjData from an iterator More...
template<class elemT >
elemT	determinant (const Array< 2, elemT > &m)
	Compute the determinant of a matrix. More...
template<class NumeratorIterT , class DenominatorIterT , class small_numT >
void	divide (const NumeratorIterT &numerator_begin, const NumeratorIterT &numerator_end, const DenominatorIterT &denominator_begin, const small_numT small_num)
	division of two ranges, 0/0 = 0 More...
template<typename T >
void	fourier (T &c, const int sign=1)
	Compute multi-dimensional discrete fourier transform. More...
template<typename T >
void	inverse_fourier (T &c, const int sign=1)
	Compute the inverse of the multi-dimensional discrete fourier transform. More...
template<typename T >
void	fourier_1d (T &c, const int sign)
	Compute one-dimensional discrete fourier transform of an array. More...
template<typename T >
void	inverse_fourier_1d (T &c, const int sign=1)
	Compute the inverse of the one-dimensional discrete fourier transform. More...
template<typename T >
Array< 1, std::complex< T > >	fourier_1d_for_real_data (const Array< 1, T > &c, const int sign=1)
	Compute one-dimensional discrete fourier transform of a real array (of even size). More...
template<typename T >
Array< 1, T >	inverse_fourier_1d_for_real_data (const Array< 1, std::complex< T >> &c, const int sign=1)
	Compute the inverse of the one-dimensional discrete fourier transform of a real array (of even size). More...
template<typename T >
Array< 1, T >	inverse_fourier_1d_for_real_data_corrupting_input (Array< 1, std::complex< T >> &c, const int sign)
	As inverse_fourier_1d_for_real_data(), but avoiding the copy of the input array. More...
template<int num_dimensions, typename T >
Array< num_dimensions, std::complex< T > >	fourier_for_real_data (const Array< num_dimensions, T > &c, const int sign=1)
	Compute discrete fourier transform of a real array (with the last dimensions of even size). More...
template<int num_dimensions, typename T >
Array< num_dimensions, T >	inverse_fourier_for_real_data (const Array< num_dimensions, std::complex< T >> &c, const int sign=1)
	Compute the inverse of the discrete fourier transform of a real array (with the last dimension of even size). More...
template<int num_dimensions, typename T >
Array< num_dimensions, T >	inverse_fourier_for_real_data_corrupting_input (Array< num_dimensions, std::complex< T >> &c, const int sign=1)
	As inverse_fourier_for_real_data(), but avoiding the copy of the input array. More...
template<int num_dimensions, typename T >
Array< num_dimensions, std::complex< T > >	pos_frequencies_to_all (const Array< num_dimensions, std::complex< T >> &c)
	Adds negative frequencies to the last dimension of a complex array by complex conjugation. More...
template<typename elemT >
elemT	integrate_discrete_function (const std::vector< elemT > &coordinates, const std::vector< elemT > &values, const int interpolation_order=1)
	numerical integration of a 1D functionThis is a simple integral implementation using rectangular (=0) or trapezoidal (=1) approximation. It currently integrates over the complete range specified. More...
template<class RandIter1 , class RandIter2 , class RandIter3 , class RandIter4 >
void	IIR_filter (RandIter1 output_begin_iterator, RandIter1 output_end_iterator, const RandIter2 input_begin_iterator, const RandIter2 input_end_iterator, const RandIter3 input_factor_begin_iterator, const RandIter3 input_factor_end_iterator, const RandIter4 pole_begin_iterator, const RandIter4 pole_end_iterator, const bool if_initial_exists)
template<class RandIter1 , class RandIter2 , class RandIter3 >
void	FIR_filter (RandIter1 output_begin_iterator, RandIter1 output_end_iterator, const RandIter2 input_begin_iterator, const RandIter2 input_end_iterator, const RandIter3 input_factor_begin_iterator, const RandIter3 input_factor_end_iterator, const bool if_initial_exists)
template<class elemT >
std::complex< elemT >	inner_product (const Array< 1, std::complex< elemT >> &v1, const Array< 1, std::complex< elemT >> &v2)
template<int num_dimensions, class elemT >
BasicCoordinate< num_dimensions, elemT >	matrix_multiply (const Array< 2, elemT > &m, const BasicCoordinate< num_dimensions, elemT > &vec)
template<class elemT >
Succeeded	absolute_max_eigenvector_using_power_method (elemT &max_eigenvalue, Array< 1, elemT > &max_eigenvector, const Array< 2, elemT > &m, const Array< 1, elemT > &start, const double tolerance=.01, const unsigned long max_num_iterations=10000UL)
	Compute the eigenvalue with the largest absolute value and corresponding eigenvector of a matrix by using the power method. More...
template<class elemT >
Succeeded	absolute_max_eigenvector_using_shifted_power_method (elemT &max_eigenvalue, Array< 1, elemT > &max_eigenvector, const Array< 2, elemT > &m, const Array< 1, elemT > &start, const elemT shift, const double tolerance=.03, const unsigned long max_num_iterations=10000UL)
	Compute the eigenvalue with the largest absolute value and corresponding eigenvector of a matrix by using the shifted power method. More...
template<class elemT >
Succeeded	max_eigenvector_using_power_method (elemT &max_eigenvalue, Array< 1, elemT > &max_eigenvector, const Array< 2, elemT > &m, const Array< 1, elemT > &start, const double tolerance=.03, const unsigned long max_num_iterations=10000UL)
	Compute the eigenvalue with the largest value and corresponding eigenvector of a matrix by using the power method. More...
template<typename out_iter_t , typename out_coord_iter_t , typename in_iter_t , typename in_coord_iter_t >
void	overlap_interpolate (const out_iter_t out_begin, const out_iter_t out_end, const out_coord_iter_t out_coord_begin, const out_coord_iter_t out_coord_end, const in_iter_t in_begin, in_iter_t in_end, const in_coord_iter_t in_coord_begin, const in_coord_iter_t in_coord_end, const bool only_add_to_output=false, const bool assign_rest_with_zeroes=true)
	'overlap' interpolation for iterators, with arbitrary 'bin' sizes. More...
template<class FunctionType , class elemT , class positionT >
void	sample_function_on_regular_grid (Array< 3, elemT > &out, FunctionType func, const BasicCoordinate< 3, positionT > &offset, const BasicCoordinate< 3, positionT > &step)
	Generic function to get the values of a 3D function on a regular grid. More...
template<typename elemT , typename FunctionType , typename Lambda >
void	sample_function_using_index_converter (Array< 3, elemT > &out, FunctionType func, Lambda &&index_converter)
	Generic function to get the values of a 3D function on a grid. More...
double	norm (const ProjDataInMemory &p)
double	norm_squared (const ProjDataInMemory &p)
void	setup_distributable_computation (const shared_ptr< ProjectorByBinPair > &proj_pair_sptr, const shared_ptr< const ExamInfo > &exam_info_sptr, const shared_ptr< const ProjDataInfo > proj_data_info_sptr, const shared_ptr< const DiscretisedDensity< 3, float >> &target_sptr, const bool zero_seg0_end_planes, const bool distributed_cache_enabled)
	set-up parameters before calling distributable_computation() More...
void	end_distributable_computation ()
	clean-up after a sequence of computations More...
void	distributable_computation (const shared_ptr< ForwardProjectorByBin > &forward_projector_sptr, const shared_ptr< BackProjectorByBin > &back_projector_sptr, const shared_ptr< DataSymmetriesForViewSegmentNumbers > &symmetries_sptr, DiscretisedDensity< 3, float > *output_image_ptr, const DiscretisedDensity< 3, float > *input_image_ptr, const shared_ptr< ProjData > &proj_data_ptr, const bool read_from_proj_data, int subset_num, int num_subsets, int min_segment_num, int max_segment_num, bool zero_seg0_end_planes, double *double_out_ptr, const shared_ptr< ProjData > &additive_binwise_correction, const shared_ptr< BinNormalisation > normalise_sptr, const double start_time_of_frame, const double end_time_of_frame, RPC_process_related_viewgrams_type *RPC_process_related_viewgrams, DistributedCachingInformation *caching_info_ptr, int min_timing_pos_num, int max_timing_pos_num)
	This function essentially implements a loop over segments and all views in the current subset.Output is in output_image_ptr and in float_out_ptr (but only if they are not NULL). What the output is, is really determined by the call-back function RPC_process_related_viewgrams. More...
template<typename CallBackT >
void	LM_distributable_computation (const shared_ptr< ProjMatrixByBin > PM_sptr, const shared_ptr< ProjDataInfo > &proj_data_info_sptr, DiscretisedDensity< 3, float > *output_image_ptr, const DiscretisedDensity< 3, float > *input_image_ptr, const std::vector< BinAndCorr > &record_cache, const int subset_num, const int num_subsets, const bool has_add, const bool accumulate, double *double_out_ptr, CallBackT &&call_back)
	This function essentially implements a loop over a cached listmode file. More...
void	ML_estimate_component_based_normalisation (const std::string &out_filename_prefix, const ProjData &measured_data, const ProjData &model_data, int num_eff_iterations, int num_iterations, bool do_geo, bool do_block, bool do_symmetry_per_block, bool do_KL, bool do_display)
	Find normalisation factors using a maximum likelihood approach.
bool	operator== (const ProjMatrixElemsForOneBinValue &el1, const ProjMatrixElemsForOneBinValue &el2)
bool	operator< (const ProjMatrixElemsForOneBinValue &el1, const ProjMatrixElemsForOneBinValue &el2)
bool	operator== (const ProjMatrixElemsForOneDenselValue &el1, const ProjMatrixElemsForOneDenselValue &el2)
bool	operator< (const ProjMatrixElemsForOneDenselValue &el1, const ProjMatrixElemsForOneDenselValue &el2)
void	RayTraceVoxelsOnCartesianGrid (ProjMatrixElemsForOneBin &lor, const CartesianCoordinate3D< float > &start_point, const CartesianCoordinate3D< float > &end_point, const CartesianCoordinate3D< float > &voxel_size, const float normalisation_constant=1.F)
	RayTraceVoxelsOnCartesianGrid finds the Length of Intersections (LOIs) of an LOR with a grid of voxels and appends them to the ProjMatrixElemsForOneBin object. More...
template<typename integerT >
void	round_to (integerT &result, const double x)
void	round_to (unsigned &result, const double x)
void	round_to (unsigned long &result, const double x)
VoxelsOnCartesianGrid< float >	warp_image (const shared_ptr< DiscretisedDensity< 3, float >> &density_sptr, const shared_ptr< DiscretisedDensity< 3, float >> &motion_x_sptr, const shared_ptr< DiscretisedDensity< 3, float >> &motion_y_sptr, const shared_ptr< DiscretisedDensity< 3, float >> &motion_z_sptr, const BSpline::BSplineType spline_type, const bool extend_borders)
template<typename elemT >
std::ostream &	operator<< (std::ostream &str, const VectorWithOffset< elemT > &v)
	Outputs a VectorWithOffset to a stream. More...
template<int num_dimensions, typename coordT >
std::ostream &	operator<< (std::ostream &str, const BasicCoordinate< num_dimensions, coordT > &v)
	Outputs a BasicCoordinate to a stream. More...
template<typename elemT >
std::ostream &	operator<< (std::ostream &str, const std::vector< elemT > &v)
	Outputs a vector to a stream. More...
std::ostream &	operator<< (std::ostream &out, const Bin &bin)
	Outputs a Bin to a stream.Output is of the form. More...
template<class T >
std::ostream &	operator<< (std::ostream &out, const DetectionPosition< T > &det_pos)
	Outputs a DetectionPosition to a stream.Output is of the form. More...
template<class T >
std::ostream &	operator<< (std::ostream &out, const DetectionPositionPair< T > &det_pos)
	Outputs a DetectionPosition to a stream.Output is of the form. More...
template<typename elemT >
std::istream &	operator>> (std::istream &str, std::vector< elemT > &v)
	Inputs a vector from a stream. More...
template<typename elemT >
std::istream &	operator>> (std::istream &str, VectorWithOffset< elemT > &v)
	Inputs a VectorWithOffset from a stream. More...
template<int num_dimensions, typename coordT >
std::istream &	operator>> (std::istream &str, BasicCoordinate< num_dimensions, coordT > &v)
	Inputs a coordinate from a stream. More...
double	mm_to_tof_delta_time (const float dist)
float	tof_delta_time_to_mm (const double delta_time)
char *	strupr (char *const str)
	make C-string uppercase
template<class STRING >
void	warning (const STRING &string, const int verbosity_level=1)
	Use this function for writing warning messages. More...
void	four1 (Array< 1, float > &data, int nn, int isign)
	1-dimensional FFT More...
void	fourn (Array< 1, float > &data, Array< 1, int > &nn, int ndim, int isign)
	n-dimensional FFT More...
void	convlvC (Array< 1, float > &data, const Array< 1, float > &filter, int n)
	Convolve data with a filter which is given in frequency space. More...
void	rlft3 (Array< 3, float > &data, Array< 2, float > &speq, int nn1, int nn2, int nn3, int isign)
	3D FFT of real numbers
void	realft (Array< 1, float > &data, int n, int isign)
	Calculates the Fourier Transform of a set of 2n real-valued data points. More...
void	fwd_project (ProjData &proj_data, VoxelsOnCartesianGrid< float > *vox_image_ptr, const int start_segment_num, const int end_segment_num, const int start_axial_pos_num, const int end_axial_pos_num, const int start_view, const int end_view, const int start_tang_pos_num, const int end_tang_pos_num)
Coordinate4D< int >	sign (const Coordinate4D< float > &c)
Coordinate4D< float >	abs (const Coordinate4D< float > &c)
void	add_to_bin (VectorWithOffset< shared_ptr< SegmentByView< float >>> &segments, const Bin &bin, const float value)
template<class ObjectTransformationT , class PushInterpolatorT >
Succeeded	transform_3d_object_push_interpolation (DiscretisedDensity< 3, float > &out_density, const DiscretisedDensity< 3, float > &in_density, const ObjectTransformationT &transformation_in_to_out, const PushInterpolatorT &interpolator, const bool do_jacobian)
	transform image data More...
template<class ObjectTransformationT , class PullInterpolatorT >
Succeeded	transform_3d_object_pull_interpolation (DiscretisedDensity< 3, float > &out_density, const DiscretisedDensity< 3, float > &in_density, const ObjectTransformationT &transformation_out_to_in, const PullInterpolatorT &interpolator, const bool do_jacobian)
	transform image data More...
template<class T2 >
void	assign (std::pair< BasicCoordinate< 3, float >, float > &x, T2 y)
template<typename in_elemT >
void	linear_extrapolation (std::vector< in_elemT > &input_vector)
template<class elemT , class positionT >
elemT	pull_nearest_neighbour_interpolate (const Array< 3, elemT > &in, const BasicCoordinate< 3, positionT > &point_in_input_coords)
	Pull value from the input array using nearest neigbour interpolation. More...
template<int num_dimensions, class elemT , class positionT , class valueT >
void	push_nearest_neighbour_interpolate (Array< num_dimensions, elemT > &out, const BasicCoordinate< num_dimensions, positionT > &point_in_output_coords, valueT value)
	Push value into the output array using nearest neigbour interpolation. More...
template<class elemT , class positionT >
elemT	pull_linear_interpolate (const Array< 3, elemT > &in, const BasicCoordinate< 3, positionT > &point_in_input_coords)
	Returns an interpolated value according to point_in_input_coords.
template<class elemT , class positionT , class valueT >
void	push_transpose_linear_interpolate (Array< 3, elemT > &out, const BasicCoordinate< 3, positionT > &point_in_output_coords, valueT value)
	Push value into the output array using the transpose of linear interpolation.
template<typename coordT >
Quaternion< coordT >	conjugate (const Quaternion< coordT > &)
template<typename coordT >
Quaternion< coordT >	inverse (const Quaternion< coordT > &)
template<typename coordT >
coordT	norm_squared (const Quaternion< coordT > &q)
template<typename coordT >
coordT	norm (const Quaternion< coordT > &q)
template<class NUMBER >
Succeeded	write_basic_interfile (const string &filename, const ExamInfo &exam_info, const Array< 3, NUMBER > &image, const CartesianCoordinate3D< float > &voxel_size, const CartesianCoordinate3D< float > &origin, const NumericType output_type, const float scale, const ByteOrder byte_order)
template<class NUMBER >
Succeeded	write_basic_interfile (const string &filename, const Array< 3, NUMBER > &image, const CartesianCoordinate3D< float > &voxel_size, const CartesianCoordinate3D< float > &origin, const NumericType output_type, const float scale, const ByteOrder byte_order)
Succeeded	write_basic_interfile (const string &filename, const ParametricVoxelsOnCartesianGrid &image, const NumericType output_type, const float scale, const ByteOrder byte_order)
ProjDataFromStream *	read_interfile_PDFS_Siemens (istream &input, const string &directory_for_data, const ios::openmode open_mode)
ProjDataFromStream *	read_interfile_PDFS (istream &input, const string &directory_for_data, const ios::openmode open_mode)
ProjDataFromStream *	read_interfile_PDFS (const string &filename, const ios::openmode open_mode)
template Succeeded	write_basic_interfile (const string &filename, const Array< 3, signed short > &, const CartesianCoordinate3D< float > &voxel_size, const CartesianCoordinate3D< float > &origin, const NumericType output_type, const float scale, const ByteOrder byte_order)
template Succeeded	write_basic_interfile (const string &filename, const Array< 3, unsigned short > &, const CartesianCoordinate3D< float > &voxel_size, const CartesianCoordinate3D< float > &origin, const NumericType output_type, const float scale, const ByteOrder byte_order)
template Succeeded	write_basic_interfile (const string &filename, const Array< 3, float > &, const CartesianCoordinate3D< float > &voxel_size, const CartesianCoordinate3D< float > &origin, const NumericType output_type, const float scale, const ByteOrder byte_order)
template Succeeded	write_basic_interfile (const string &filename, const Array< 3, signed short > &image, const NumericType output_type, const float scale, const ByteOrder byte_order)
template Succeeded	write_basic_interfile (const string &filename, const Array< 3, unsigned short > &image, const NumericType output_type, const float scale, const ByteOrder byte_order)
template Succeeded	write_basic_interfile (const string &filename, const Array< 3, float > &image, const NumericType output_type, const float scale, const ByteOrder byte_order)
void	find_segment_sequence (vector< int > &segment_sequence, VectorWithOffset< int > &sorted_num_rings_per_segment, VectorWithOffset< int > &sorted_min_ring_diff, VectorWithOffset< int > &sorted_max_ring_diff, vector< int > &num_rings_per_segment, const vector< int > &min_ring_difference, const vector< int > &max_ring_difference)
template<>
STIRImageMultiConcrete::full_value_type	ITK_pixel_to_STIR_pixel (typename ITKImageMulti::PixelType itk_pixel, const STIRImageMultiConcrete &stir_image, bool is_displacement_field)
template<typename ITKImageType >
ITKImageType::Pointer	orient_ITK_image (const typename ITKImageType::Pointer itk_image_orig, const shared_ptr< ExamInfo > exam_info_sptr)
template<>
STIRImageSingle *	read_file_itk (const std::string &filename)
template<>
STIRImageMulti *	read_file_itk (const std::string &filename)
template float	determinant (const Array< 2, float > &)
template double	determinant (const Array< 2, double > &)
template std::complex< float >	determinant (const Array< 2, std::complex< float >> &)
template std::complex< double >	determinant (const Array< 2, std::complex< double >> &)
template void	fourier (Array< 3, std::complex< float >> &c, const int sign)
template void	fourier (Array< 2, std::complex< float >> &c, const int sign)
template void	fourier (Array< 1, std::complex< float >> &c, const int sign)
template void	fourier (VectorWithOffset< std::complex< float >> &c, const int sign)
	INSTANTIATE (1, float)
	INSTANTIATE (2, float)
	INSTANTIATE (3, float)
void	check_values (const shared_ptr< const ProjDataInfoCylindricalArcCorr > proj_data_info_sptr, const float delta, const double cphi, const double sphi, const int s, const int ring0, const int X1, const int Y1, const int Z1, const double ds, const double dz, const float num_planes_per_axial_pos, const float axial_pos_to_z_offset)
template<class dataType >
dataType *	create_heap_array (const unsigned numel, const dataType val=dataType(0))
void	get_stir_indices_and_dims (int stir_dim[3], Coordinate3D< int > &min_indices, Coordinate3D< int > &max_indices, const DiscretisedDensity< 3, float > &stir)
unsigned	convert_NiftyPET_im_3d_to_1d_idx (const unsigned x, const unsigned y, const unsigned z)
std::vector< int >	get_buckets (unsigned int *bck, const unsigned B, const unsigned nitag)
	Get bucket singles (from mmrhist.py)
void	check_im_sizes (const int stir_dim[3], const int np_dim[3])
void	check_voxel_spacing (const DiscretisedDensity< 3, float > &stir)
void	get_vals_for_proj_data_conversion (std::vector< int > &sizes, std::vector< int > &segment_sequence, int &num_sinograms, int &min_view, int &max_view, int &min_tang_pos, int &max_tang_pos, const ProjDataInfo &proj_data_info, const std::vector< float > &np_vec)
void	get_stir_segment_and_axial_pos_from_NiftyPET_sino (int &segment, int &axial_pos, const unsigned np_sino, const std::vector< int > &sizes, const std::vector< int > &segment_sequence)
void	get_NiftyPET_sino_from_stir_segment_and_axial_pos (unsigned &np_sino, const int segment, const int axial_pos, const std::vector< int > &sizes, const std::vector< int > &segment_sequence)
template<bool do_gradient, bool do_value>
void	LM_gradient_and_value (DiscretisedDensity< 3, float > &output_image, const ProjMatrixElemsForOneBin &row, const float add_term, const Bin &measured_bin, const DiscretisedDensity< 3, float > &input_image, double *value_ptr)
void	LM_Hessian (DiscretisedDensity< 3, float > &output_image, const ProjMatrixElemsForOneBin &row, const float add_term, const Bin &measured_bin, const DiscretisedDensity< 3, float > &input_image, const DiscretisedDensity< 3, float > &rhs)
void	LM_gradient_distributable_computation (const shared_ptr< ProjMatrixByBin > PM_sptr, const shared_ptr< ProjDataInfo > &proj_data_info_sptr, DiscretisedDensity< 3, float > *output_image_ptr, const DiscretisedDensity< 3, float > *input_image_ptr, const std::vector< BinAndCorr > &record_ptr, const int subset_num, const int num_subsets, const bool has_add, const bool accumulate, double *value_ptr)
void	LM_Hessian_distributable_computation (const shared_ptr< ProjMatrixByBin > PM_sptr, const shared_ptr< ProjDataInfo > &proj_data_info_sptr, DiscretisedDensity< 3, float > *output_image_ptr, const DiscretisedDensity< 3, float > *input_image_ptr, const DiscretisedDensity< 3, float > *rhs_ptr, const std::vector< BinAndCorr > &record_ptr, const int subset_num, const int num_subsets, const bool has_add, const bool accumulate)
void	distributable_compute_gradient (const shared_ptr< ForwardProjectorByBin > &forward_projector_sptr, const shared_ptr< BackProjectorByBin > &back_projector_sptr, const shared_ptr< DataSymmetriesForViewSegmentNumbers > &symmetries_sptr, DiscretisedDensity< 3, float > &output_image, const DiscretisedDensity< 3, float > &input_image, const shared_ptr< ProjData > &proj_dat, int subset_num, int num_subsets, int min_segment, int max_segment, bool zero_seg0_end_planes, double *log_likelihood_ptr, shared_ptr< ProjData > const &additive_binwise_correction, shared_ptr< BinNormalisation > const &normalisation_sptr, DistributedCachingInformation *caching_info_ptr, int min_timing_pos_num, int max_timing_pos_num, const bool add_sensitivity)
void	distributable_accumulate_loglikelihood (const shared_ptr< ForwardProjectorByBin > &forward_projector_sptr, const shared_ptr< BackProjectorByBin > &back_projector_sptr, const shared_ptr< DataSymmetriesForViewSegmentNumbers > &symmetries_sptr, const DiscretisedDensity< 3, float > &input_image, const shared_ptr< ProjData > &proj_dat, int subset_num, int num_subsets, int min_segment, int max_segment, bool zero_seg0_end_planes, double *log_likelihood_ptr, shared_ptr< ProjData > const &additive_binwise_correction, shared_ptr< BinNormalisation > const &normalisation_sptr, const double start_time_of_frame, const double end_time_of_frame, DistributedCachingInformation *caching_info_ptr, int min_timing_pos_num, int max_timing_pos_num)
void	distributable_sensitivity_computation (const shared_ptr< BackProjectorByBin > &back_projector_sptr, const shared_ptr< DataSymmetriesForViewSegmentNumbers > &symmetries_sptr, DiscretisedDensity< 3, float > &sensitivity, const DiscretisedDensity< 3, float > &input_image, const shared_ptr< ProjData > &proj_dat, int subset_num, int num_subsets, int min_segment, int max_segment, bool zero_seg0_end_planes, double *log_likelihood_ptr, shared_ptr< ProjData > const &additive_binwise_correction, shared_ptr< BinNormalisation > const &normalisation_sptr, const double start_time_of_frame, const double end_time_of_frame, DistributedCachingInformation *caching_info_ptr, int min_timing_pos_num, int max_timing_pos_num)
template<bool add_sensitivity>
void	RPC_process_related_viewgrams_gradient (const shared_ptr< ForwardProjectorByBin > &forward_projector_sptr, const shared_ptr< BackProjectorByBin > &back_projector_sptr, RelatedViewgrams< float > *measured_viewgrams_ptr, int &count, int &count2, double *log_likelihood_ptr, const RelatedViewgrams< float > *additive_binwise_correction_ptr, const RelatedViewgrams< float > *mult_viewgrams_ptr)
void	RPC_process_related_viewgrams_accumulate_loglikelihood (const shared_ptr< ForwardProjectorByBin > &forward_projector_sptr, const shared_ptr< BackProjectorByBin > &back_projector_sptr, RelatedViewgrams< float > *measured_viewgrams_ptr, int &count, int &count2, double *log_likelihood_ptr, const RelatedViewgrams< float > *additive_binwise_correction_ptr, const RelatedViewgrams< float > *mult_viewgrams_ptr)
void	RPC_process_related_viewgrams_sensitivity_computation (const shared_ptr< ForwardProjectorByBin > &forward_projector_sptr, const shared_ptr< BackProjectorByBin > &back_projector_sptr, RelatedViewgrams< float > *measured_viewgrams_ptr, int &count, int &count2, double *log_likelihood_ptr, const RelatedViewgrams< float > *additive_binwise_correction_ptr, const RelatedViewgrams< float > *mult_viewgrams_ptr)
void	do_segments (DiscretisedDensity< 3, float > &image, ProjData &proj_data_org, const int start_timing_num, const int end_timing_num, const int start_segment_num, const int end_segment_num, const int start_axial_pos_num, const int end_axial_pos_num, const int start_tang_pos_num, const int end_tang_pos_num, const int start_view, const int end_view, BackProjectorByBin *back_projector_ptr, bool fill_with_1)
template<typename T >
shared_ptr< T[]>	vec_to_shared (std::vector< T > &v)
void	set_Gaussian_filter_fwhm (SeparableCartesianMetzImageFilter< float > &filter, const float fwhm_z, const float fwhm_y, const float fwhm_x)
void	michelogram (const ProjDataInfoCylindrical &proj_data_info)
std::vector< int >	_calc_regularly_sampled_views_for_subset (int subset_n, int num_subsets, int num_views)
void	update_comparison (SegmentByView< float > &input1, const SegmentByView< float > &input2, float &max_pos_error, float &max_neg_error, float &amplitude)
void	do_math (enum options operation, SegmentByView< float > &sino1, SegmentByView< float > &sino2, float &accum_max, float &accum_min, float &accum_sum, bool accumulators_initialized)
void	do_math (enum options operation, SegmentByView< float > &sino1, SegmentBySinogram< float > &seg_sinogram, float &accum_max, float &accum_min, float &accum_sum, bool accumulators_initialized, float scalar=0.0)
void	make_buffer_header (const char *data_filename, const char *header_filename, ProjData &input_sino, int limit_segments, NumericType::Type output_type=NumericType::FLOAT)
void	show_math_menu ()
float	pos_indicate (float x)
shared_ptr< ProjData >	ask_proj_data (const char *const input_query)
template<typename STIRImageType >
STIRImageType *	ask_image (const char *const input_query)
template<typename STIRImageType >
shared_ptr< OutputFileFormat< STIRImageType > >	set_up_output_format (const std::string &filename)
Array< 3, float >	extend_segment (const SegmentBySinogram< float > &segment, const int view_extension=5, const int axial_extension=5, const int tangential_extension=5)
	Extension of direct projection data. More...
Succeeded	interpolate_projdata (ProjData &proj_data_out, const ProjData &proj_data_in, const BSpline::BSplineType spline_type, const bool remove_interleaving=false)
	Perform B-Splines Interpolation. More...
Succeeded	interpolate_projdata (ProjData &proj_data_out, const ProjData &proj_data_in, const BasicCoordinate< 3, BSpline::BSplineType > &these_types, const bool remove_interleaving)
Functions for user input
bool	ask (const std::string &prompt, bool default_value)
	A function to ask a yes/no question from the user. More...
string	ask_string (const std::string &prompt, const std::string &default_value="")
	A function to ask a string from the user.
string	ask_filename_with_extension (const std::string &prompt, const std::string &default_extension)
	Asks for a filename (appending an extension if none is provided). More...
char *	ask_filename_with_extension (char *file_in_directory_name, const std::string &prompt, const std::string &default_extension)
	Asks for a filename (appending an extension if none is provided) and stores the string where file_in_directory_name points to. More...
template<class NUMBER >
NUMBER	ask_num (const std::string &prompt, NUMBER minimum_value, NUMBER maximum_value, NUMBER default_value)
	A function to ask a number from the user. More...
template<class FSTREAM >
void	ask_filename_and_open (FSTREAM &s, const std::string &prompt, const std::string &default_extension, std::ios::openmode mode, bool abort_if_failed)
	Asks for a filename (with default extension) and opens the stream s with mode giving the specifics. More...
template<class FSTREAM >
void	ask_filename_and_open (FSTREAM &s, const std::string &prompt, const std::string &default_extension, std::ios::openmode mode)
	as above, but with default abort_if_failed = true
Functions for stream/file manipulations
FILE *&	open_read_binary (FILE *&fptr, const std::string &name)
	opens a FILE for reading binary data. Calls error() when it does not succeed. More...
FILE *&	open_write_binary (FILE *&fptr, const std::string &name)
	opens a FILE for writing binary data. Calls error() when it does not succeed. More...
void	close_file (FILE *&fptr)
	closes a FILE without error checking. More...
streamsize	find_remaining_size (std::istream &input)
	Find number of remaining characters in the stream. More...
void *	read_stream_in_memory (std::istream &input, std::streamsize &file_size)
	reads data into memory, returning a pointer to the memory More...
template<class IFSTREAM >
IFSTREAM &	open_read_binary (IFSTREAM &s, const std::string &name)
	opens a stream for reading binary data. Calls error() when it does not succeed. More...
template<class OFSTREAM >
OFSTREAM &	open_write_binary (OFSTREAM &s, const std::string &name)
	opens a stream for writing binary data. Calls error() when it does not succeed. More...
template<class FSTREAM >
void	close_file (FSTREAM &s)
	closes a stream without error checking. More...
Functions for filename manipulations
These functions work on different platforms, i.e. Unix, VAX, Windows. Also on older MacOS versions. Warning Functions that work on char* might be removed at some point.
const char *	find_filename (const char *const filename_with_directory)
	return a pointer to the start of the filename (i.e. after directory specifications) More...
string::size_type	find_pos_of_filename (const std::string &filename_with_directory)
	return the position of the start of the filename (i.e. after directory specifications) More...
string	get_filename (const std::string &filename_with_directory)
	return a std::string containing only the filename (i.e. after directory specifications) More...
char *	get_directory_name (char *directory_name, const char *const filename_with_directory)
	Copies the directory part from 'filename_with_directory' into 'directory_name' and returns the 'directory_name' pointer. More...
string	get_directory_name (const std::string &filename_with_directory)
	Returns a string with the directory part from 'filename_with_directory'. More...
string::size_type	find_pos_of_extension (const std::string &file_in_directory_name)
	find the position of the '.' of the extension More...
string &	add_extension (std::string &file_in_directory_name, const std::string &extension)
	Append extension if none present.
string &	replace_extension (std::string &file_in_directory_name, const std::string &extension)
	Replace extension (or append if none present)
bool	is_absolute_pathname (const char *const filename_with_directory)
	Checks if the filename points to an absolute location, or is a relative (e.g. to current directory) pathname.
bool	is_absolute_pathname (const std::string &filename_with_directory)
	Checks if the filename points to an absolute location, or is a relative (e.g. to current directory) pathname.
char *	prepend_directory_name (char *filename_with_directory, const char *const directory_name)
	Prepend directory_name to the filename, but only if !is_absolute_pathname(filename_with_directory) More...
Functions for interpolating data to new pixel/bin sizes
void	zoom_viewgrams (RelatedViewgrams< float > &viewgrams, const float zoom, const int min_tang_pos_num, const int max_tang_pos_num, const float x_offset_in_mm=0, const float y_offset_in_mm=0)
	zoom a RelatedViewgrams object, replacing it with the new data More...
void	zoom_viewgram (Viewgram< float > &viewgram, const float zoom, const int min_tang_pos_num, const int max_tang_pos_num, const float x_offset_in_mm=0, const float y_offset_in_mm=0)
	zoom viewgram, replacing it with the new data More...
void	zoom_viewgram (Viewgram< float > &out_viewgram, const Viewgram< float > &in_viewgram, const float x_offset_in_mm=0, const float y_offset_in_mm=0)
	zoom in_viewgram, replacing out_viewgram with the new data More...
void	zoom_image_in_place (VoxelsOnCartesianGrid< float > &image, const float zoom, const float x_offset_in_mm, const float y_offset_in_mm, const int new_size, const ZoomOptions=ZoomOptions::preserve_sum)
	zoom image, replacing the first argument with the new data More...
VoxelsOnCartesianGrid< float >	zoom_image (const VoxelsOnCartesianGrid< float > &image, const float zoom, const float x_offset_in_mm, const float y_offset_in_mm, const int new_size, const ZoomOptions=ZoomOptions::preserve_sum)
	zoom image, replacing the first argument with the new data More...
void	zoom_image_in_place (VoxelsOnCartesianGrid< float > &image, const CartesianCoordinate3D< float > &zooms, const CartesianCoordinate3D< float > &offsets_in_mm, const BasicCoordinate< 3, int > &new_sizes, const ZoomOptions=ZoomOptions::preserve_sum)
	zoom image, replacing the first argument with the new data. Full 3D shifts and zooms. More...
VoxelsOnCartesianGrid< float >	zoom_image (const VoxelsOnCartesianGrid< float > &image, const CartesianCoordinate3D< float > &zooms, const CartesianCoordinate3D< float > &offsets_in_mm, const BasicCoordinate< 3, int > &new_sizes, const ZoomOptions=ZoomOptions::preserve_sum)
	zoom image, returning the new image More...
void	zoom_image (VoxelsOnCartesianGrid< float > &image_out, const VoxelsOnCartesianGrid< float > &image_in, const ZoomOptions=ZoomOptions::preserve_sum)
	zoom image_in according to dimensions, origin and voxel_size of image_out. More...
void	zoom_image (PixelsOnCartesianGrid< float > &image2D_out, const PixelsOnCartesianGrid< float > &image2D_in, const ZoomOptions=ZoomOptions::preserve_sum)
	zoom image2D_in according to dimensions, origin and pixel_size of image2D_out. More...
Functions to compute ROI values
Shapes can be first discretised using Shape3D::construct_volume or a Shape3D parsed. This can make fuzzy boundaries (when the num_samples argument is not (1,1,1), or when DiscretisedShape3D needs zooming). Mean and stddev are computed using weighted versions, taking this smoothness into account, while ROI_min and max are ignore those weights.
void	compute_ROI_values_per_plane (VectorWithOffset< ROIValues > &values, const DiscretisedDensity< 3, float > &density, const Shape3D &shape, const CartesianCoordinate3D< int > &num_samples)
void	compute_ROI_values_per_plane (VectorWithOffset< ROIValues > &values, const DiscretisedDensity< 3, float > &density, const DiscretisedDensity< 3, float > &discretised_shape)
ROIValues	compute_total_ROI_values (const VectorWithOffset< ROIValues > &values)
ROIValues	compute_total_ROI_values (const DiscretisedDensity< 3, float > &image, const Shape3D &shape, const CartesianCoordinate3D< int > &num_samples)
ROIValues	compute_total_ROI_values (const DiscretisedDensity< 3, float > &image, const DiscretisedDensity< 3, float > &discretised_shape)
void	compute_plane_range_ROI_values_per_plane (VectorWithOffset< ROIValues > &values, const DiscretisedDensity< 3, float > &density, const CartesianCoordinate2D< int > &plane_range, const Shape3D &shape, const CartesianCoordinate3D< int > &num_samples)
float	compute_CR_hot (ROIValues &val1, ROIValues &val2)
float	compute_CR_cold (ROIValues &val1, ROIValues &val2)
float	compute_uniformity (ROIValues &val)
VectorWithOffset< float >	compute_CR_hot_per_plane (VectorWithOffset< ROIValues > &val1, VectorWithOffset< ROIValues > &val2)
VectorWithOffset< float >	compute_CR_cold_per_plane (VectorWithOffset< ROIValues > &val1, VectorWithOffset< ROIValues > &val2)
VectorWithOffset< float >	compute_uniformity_per_plane (VectorWithOffset< ROIValues > &val)
numerical operations for arrays of complex numbers
template<int num_dimensions, typename elemT >
Array< num_dimensions, std::complex< elemT > > &	operator*= (Array< num_dimensions, std::complex< elemT >> &lhs, const elemT &rhs)
template<int num_dimensions, typename elemT >
Array< num_dimensions, std::complex< elemT > > &	operator/= (Array< num_dimensions, std::complex< elemT >> &lhs, const elemT &rhs)
template<int num_dimensions, typename elemT >
Array< num_dimensions, std::complex< elemT > > &	operator+= (Array< num_dimensions, std::complex< elemT >> &lhs, const elemT &rhs)
template<int num_dimensions, typename elemT >
Array< num_dimensions, std::complex< elemT > > &	operator-= (Array< num_dimensions, std::complex< elemT >> &lhs, const elemT &rhs)
void	assign (std::complex< double > &x, const int y)
void	assign (std::complex< float > &x, const int y)
template<int num_dimensions, int num_dimensions2, typename elemT >
const Array< num_dimensions - num_dimensions2, elemT > &	get (const Array< num_dimensions, elemT > &a, const BasicCoordinate< num_dimensions2, int > &c)
	an alternative for array indexing using BasicCoordinate objects More...
template<int num_dimensions, typename elemT >
const elemT &	get (const Array< num_dimensions, elemT > &a, const BasicCoordinate< num_dimensions, int > &c)
	an alternative for array indexing using BasicCoordinate objects More...
template<int num_dimensions, typename T >
BasicCoordinate< num_dimensions, int >	get_min_indices (const Array< num_dimensions, T > &a)
	Get the first multi-dimensional index of the array. More...
template<int num_dimensions, typename T , int num_dimensions2>
bool	next (BasicCoordinate< num_dimensions, int > &indices, const Array< num_dimensions2, T > &a)
	Given an index into an array, increment it to the next one. More...
templated functions for assigning values
When writing templated code, it is sometimes not possible to use operator=() for assignment, e.g. when the classes do not support that operator. The assign template tries to alleviate this problem by providing several overloads when the first argument is a (STIR) container. Usage assign(x,y); // logically equivalent to x=y; Design consideration We could have overloaded operator=() instead, but that would probably lead to surprising conversions.
template<class T , class T2 >
void	assign (T &x, const T2 &y)
template<class T , class T2 >
void	assign (std::vector< T > &v, const T2 &y)
template<int num_dimensions, class T , class T2 >
void	assign (BasicCoordinate< num_dimensions, T > &v, const T2 &y)
template<class T , class T2 >
void	assign (VectorWithOffset< T > &v, const T2 &y)
template<int num_dimensions, class T , class T2 >
void	assign (Array< num_dimensions, T > &v, const T2 &y)
void	assign (double &x, const int y)
void	assign (float &x, const int y)
Utility functions to make BasicCoordinate objects.
Warning Because of template rules of C++, all arguments of the make_coordinate function have to have exactly the same type. For instance, const BasicCoordinate<3,float> a = make_coordinate(1.F,2.F,0.F);
template<class T >
BasicCoordinate< 1, T >	make_coordinate (const T &a1)
template<class T >
BasicCoordinate< 2, T >	make_coordinate (const T &a1, const T &a2)
template<class T >
BasicCoordinate< 3, T >	make_coordinate (const T &a1, const T &a2, const T &a3)
template<class T >
BasicCoordinate< 4, T >	make_coordinate (const T &a1, const T &a2, const T &a3, const T &a4)
template<class T >
BasicCoordinate< 5, T >	make_coordinate (const T &a1, const T &a2, const T &a3, const T &a4, const T &a5)
template<class T >
BasicCoordinate< 6, T >	make_coordinate (const T &a1, const T &a2, const T &a3, const T &a4, const T &a5, const T &a6)
testing of (smart) pointers
A utility function that checks if an ordinary or smart pointer is null with identical syntax for all types.
template<typename T >
bool	is_null_ptr (T const *const ptr)
template<typename T >
bool	is_null_ptr (shared_ptr< T > const &sptr)
template<typename T >
bool	is_null_ptr (unique_ptr< T > const &aptr)
bool	is_null_ptr (const std::nullptr_t)
Functions for modulo computations
double	modulo (const double a, const double b)
	Like std::fmod() but with guaranteed nonnegative result. More...
float	modulo (const float a, const float b)
	modulo for floats More...
int	modulo (const int a, const int b)
	Like the normal modulus operator (%) but with guaranteed nonnegative result. More...
template<int num_dimensions, typename T >
BasicCoordinate< num_dimensions, T >	modulo (const BasicCoordinate< num_dimensions, T > &a, const BasicCoordinate< num_dimensions, T > &b)
	Performs the modulus operation on each element of the coordinates. More...
template<typename FloatOrDouble >
FloatOrDouble	from_min_pi_plus_pi_to_0_2pi (const FloatOrDouble phi)
	A function to convert an angle from one range to another. More...
template<typename FloatOrDouble >
FloatOrDouble	to_0_2pi (const FloatOrDouble phi)
	Convert angle to standard range. More...
A collection of error functions.
The erf() is a high precision implementation of the error function. The erfc() is the complementary of the erf(), which should be equal to 1-erf(), but with higher precision when erf is close to 1. Todo: replace with boost::erf
double	erf (double)
double	erfc (double)
functions specific for 1D Arrays
template<class elemT >
elemT	inner_product (const Array< 1, elemT > &v1, const Array< 1, elemT > &v2)
	Inner product of 2 1D arrays. More...
template<class elemT >
double	angle (const Array< 1, elemT > &v1, const Array< 1, elemT > &v2)
	angle between 2 1D arrays
functions for matrices
template<class elemT >
Array< 1, elemT >	matrix_multiply (const Array< 2, elemT > &m, const Array< 1, elemT > &vec)
	matrix with vector multiplication More...
template<int dimension, class elemT >
BasicCoordinate< dimension, elemT >	matrix_multiply (const Array< 2, elemT > &m, const BasicCoordinate< dimension, elemT > &vec)
	matrix multiplication with vector (given as BasicCoordinate) More...
template<class elemT >
Array< 2, elemT >	matrix_multiply (const Array< 2, elemT > &m1, const Array< 2, elemT > &m2)
	matrix multiplication More...
template<class elemT >
Array< 2, elemT >	matrix_transpose (const Array< 2, elemT > &m)
	matrix transposition
template<class elemT >
Array< 2, elemT >	diagonal_matrix (const unsigned dimension, const elemT value)
	construct a diagonal matrix with all elements on the diagonal equal More...
template<int dimension, class elemT >
Array< 2, elemT >	diagonal_matrix (const BasicCoordinate< dimension, elemT > &values)
	construct a diagonal matrix More...
Functions to compute the norm
template<typename elemT >
double	norm_squared (const elemT t)
	Returns the square of the norm of a number. More...
template<typename elemT >
double	norm (const elemT t)
	Returns the norm of a number. More...
double	norm (const double t)
double	norm (const float t)
template<class Iter >
double	norm_squared (Iter begin, Iter end)
	Returns the square of the l2-norm of a sequence. More...
template<class Iter >
double	norm (Iter begin, Iter end)
	Returns the l2-norm of a sequence. More...
template<class elemT >
double	norm (const Array< 1, elemT > &v1)
	l2 norm of a 1D array More...
template<class elemT >
double	norm_squared (const Array< 1, elemT > &v1)
	square of the l2 norm of a 1D array More...
functions to convert from data in Numerical Recipes format to STIR arrays.
void	stir_to_nr (const VectorWithOffset< std::complex< float >> &c, VectorWithOffset< float > &nr_data)
void	stir_to_nr (const Array< 2, std::complex< float >> &c2d, VectorWithOffset< float > &nr_data)
void	stir_to_nr (const VectorWithOffset< Array< 1, std::complex< float >>> &c2d, VectorWithOffset< float > &nr_data)
void	nr_to_stir (const VectorWithOffset< float > &nr_data, VectorWithOffset< std::complex< float >> &c)
void	nr_to_stir (const VectorWithOffset< float > &nr_data, Array< 2, std::complex< float >> &c2d)
void	nr_to_stir (const VectorWithOffset< float > &nr_data, VectorWithOffset< Array< 1, std::complex< float >>> &c2d)
int	distributable_main (int argc, char **argv)
void	distributable_computation_cache_enabled (const shared_ptr< ForwardProjectorByBin > &forward_projector_ptr, const shared_ptr< BackProjectorByBin > &back_projector_ptr, const shared_ptr< DataSymmetriesForViewSegmentNumbers > &symmetries_ptr, DiscretisedDensity< 3, float > *output_image_ptr, const DiscretisedDensity< 3, float > *input_image_ptr, const shared_ptr< ProjData > &proj_data_sptr, const bool read_from_proj_data, int subset_num, int num_subsets, int min_segment_num, int max_segment_num, bool zero_seg0_end_planes, double *double_out_ptr, const shared_ptr< ProjData > &additive_binwise_correction, const shared_ptr< BinNormalisation > normalise_sptr, const double start_time_of_frame, const double end_time_of_frame, RPC_process_related_viewgrams_type *RPC_process_related_viewgrams, DistributedCachingInformation *caching_info_ptr, int min_timing_pos_num, int max_timing_pos_num)
	This function essentially implements a loop over segments and all views in the current subset in the parallel case. More...
void	test_image_estimate (shared_ptr< stir::DiscretisedDensity< 3, float >> input_image_ptr)
Functions for rounding floating point numbers
int	round (const float x)
	Implements rounding of floating point numbers. More...
int	round (const double x)
	Implements rounding of double numbers. More...
template<int num_dimensions, class elemT >
BasicCoordinate< num_dimensions, int >	round (const BasicCoordinate< num_dimensions, elemT > &x)
	Implements rounding of a BasicCoordinate object. More...
template<typename integerT >
void	round_to (integerT &result, const float x)
	Implements rounding of floating point numbers to other integer types. More...
template<int num_dimensions, class integerT , class elemT >
void	round_to (BasicCoordinate< num_dimensions, integerT > &result, const BasicCoordinate< num_dimensions, elemT > &x)
	Implements rounding of a BasicCoordinate object to other integer types. More...
Functions for thresholding numbers and sequences
template<typename forw_iterT , typename elemT >
void	threshold_upper_lower (forw_iterT begin, forw_iterT end, const elemT new_min, const elemT new_max)
	Threshold a sequence from above and below. More...
template<typename forw_iterT , typename elemT >
void	threshold_upper (forw_iterT begin, forw_iterT end, const elemT new_max)
	Threshold a sequence from above. More...
template<typename forw_iterT , typename elemT >
void	threshold_lower (forw_iterT begin, forw_iterT end, const elemT new_min)
	Threshold a sequence from below. More...
template<typename ForwardIter_t , typename elemT >
void	threshold_min_to_small_positive_value (ForwardIter_t begin, ForwardIter_t end, const elemT &small_number)
	sets non-positive values in the sequence to small positive ones More...

Variables
const int	LINE_ERROR = -1
const int	LINE_OK = 0
const float	SMALL_NUM = 0.000001F
const float	ZERO_TOL = 0.000001F
const double	TPI = 6.28318530717958647692
const double	MAX_INTERVAL_DIFFERENCE = 0.05
template	DAVArrayFilter3D< float >
template	DAVImageFilter3D< float >
template	ModifiedInverseAveragingImageFilterAll< float >
template	ModifiedInverseAverigingArrayFilter< 3, float >
template	ModifiedInverseAverigingImageFilter< float >
template	NonseparableSpatiallyVaryingFilters< float >
template	NonseparableSpatiallyVaryingFilters3D< float >
template	SeparableLowPassArrayFilter< 3, float >
template	SeparableLowPassImageFilter< float >
const int	FORWARDFFT = 1
const int	INVERSEFFT = -1
constexpr double	speed_of_light_in_mm_per_ps = 0.299792458
	Define the speed of light in mm / ps.
constexpr double	speed_of_light_in_mm_per_ps_div2 = speed_of_light_in_mm_per_ps * 0.5
	This ratio is used often.
const int	max_filename_length = 1000
	some large value to say how long filenames can be in the (deprecated) function ask_filename_with_extension(char *,const std::string&, const std::string&)
constexpr float	max_quotient = 10000.F
const int	rim_truncation_sino = 0
const float	cache_init_value = -1234567.89E10F
Task-ids currently understood by stir::DistributedWorker
const int	task_stop_processing = 0
const int	task_setup_distributable_computation = 200
const int	task_do_distributable_gradient_computation = 42
const int	task_do_distributable_loglikelihood_computation = 43
const int	task_do_distributable_sensitivity_computation = 44
Tag-names currently used by stir::distributable_computation and related functions
const int	AVAILABLE_NOTIFICATION_TAG = 2
const int	END_ITERATION_TAG = 3
const int	END_RECONSTRUCTION_TAG = 4
const int	END_NOTIFICATION_TAG = 5
const int	BINWISE_CORRECTION_TAG = 6
const int	BINWISE_MULT_TAG = 66
const int	REUSE_VIEWGRAM_TAG = 10
const int	NEW_VIEWGRAM_TAG = 11
const int	USE_DOUBLE_ARG_TAG = 70
const int	USE_OUTPUT_IMAGE_ARG_TAG = 71

Detailed Description

Namespace for the STIR library (and some/most of its applications)

Test class for exporting and importing ProjData as arrays.

Addition for SAFIR listmode input file format.

Declaration of class stir::DistributedCachingInformation.

A class in that reads the radionuclide information from a Json file.

implementation of stir::sample_function_on_regular_grid and stir::sample_function_using_index_converter

This namespace encompasses the whole library. All classes, functions and symbols are in this namespace. This has the effect that conflicts with any other library is impossible (except if that library uses the same namespace...).

Author

Kris Thielemans

Charalampos Tsoumpas

Markus Jehl

Values for half life branching ratio are taken from: http://www.lnhb.fr/donnees-nucleaires/donnees-nucleaires-tableau/

The class also supports using "aliases" for radionuclide names. This is useful as different manufacturers use different conventions.

STIR comes with a default database and lookup table. The database uses DICOM conventions for the names. The lookup table provides alternatives for GE and Siemens (in STIR 5.0).

Format of the radionuclide database

This file is in JSON format. An example is distributed with STIR, a brief extract follows

{
    "nuclides": [

        {
            "name":  "^18^Fluorine",
            "decays": [
                {  "modality": "PET",
                   "keV": 511,
                   "branching_ratio": 0.9686,
                   "half_life": 6584.04
                }
            ]
        },
        {
            "name": "^99m^Technetium",
            "decays": [
                {  "modality": "nucmed",
                   "keV": 140.511,
                   "branching_ratio": 0.885,
                   "half_life": 21624.12
                }
            ]

        },
      # more entries like the above
   ]
}

Format of the radionuclide name look-up database

This file is in JSON format. An example is distributed with STIR, a brief extract follows

[
     [ "^18^Fluorine", "18F", "F-18" ],
     [ "^11^Carbon", "11C", "C-11" ]
]

The first name is the one that will be used to find an entry in the radionuclide database.

Note that both files need to have the same number of radionuclides..

Author

Tobias Beisel

Kris Thielemans

Addition for ROOT support - Nikos Efthimiou

Author

Nikos Efthimiou

Kris Thielemans

Typedef Documentation

AxTangPosNumbers

typedef Coordinate2D<int> stir::AxTangPosNumbers

AxTangPosNumbers as a class that provides the 2 remaining coordinates for a Bin, aside from ViewSegmentNumbers.

TODO? something more sofisticated than a typedef

Function Documentation

standardise_interfile_keyword()

std::string stir::standardise_interfile_keyword

(

const std::string &

keyword

)

Put a (Interfile) keyword into a standard form.

This follows Interfile 3.3 conventions:

• The characters space, tab, underscore, ! are all treated as white space.
• Starting and trailing white space is trimmed.
• Repeated white space is replaced with a single space
• All letters are made lowercase.

Referenced by stir::SAFIRCListmodeInputFileFormat< EventDataType >::can_read(), DICOM_date_time_to_DT(), DICOM_datetime_to_secs_since_Unix_epoch(), stir::ImagingModality::get_name(), stir::Scanner::get_scanner_from_name(), Interfile_datetime_to_DICOM(), is_interfile_signature(), stir::ProjMatrixByBinFromFile::ProjMatrixByBinFromFile(), and stir::KeyParser::standardise_keyword().

ask()

bool stir::ask	(	const std::string &	prompt,
		bool	default_value
	)

A function to ask a yes/no question from the user.

Parameters

prompt	a text string which is supposed to be a question
default_value	When set to true , the default is Yes.

The question is currently presented as

prompt [Y/N D:default_value]:

Simply pressing 'enter' will select the default value. Otherwise, the first charachter of the response will be checked against y/Y/n/N to determine the return value. If it is none of these, the question will be asked again.

Referenced by stir::ProjDataInfo::ask_parameters(), stir::OSSPSReconstruction< TargetT >::ask_parameters(), stir::OSMAPOSLReconstruction< TargetT >::ask_parameters(), stir::IterativeReconstruction< TargetT >::ask_parameters(), stir::VoxelsOnCartesianGrid< elemT >::grow_z_range(), stir::Scanner::list_names(), and stir::ProjDataFromStream::set_segment().

open_read_binary() [1/2]

FILE *& stir::open_read_binary	(	FILE *&	fptr,
		const std::string &	name
	)

opens a FILE for reading binary data. Calls error() when it does not succeed.

Warning

probably does not work if you are not in the C-locale

References error().

Referenced by stir::FileSignature::FileSignature(), stir::InputStreamWithRecords< RecordT, OptionsT >::InputStreamWithRecords(), stir::InputFileFormat< ListModeData >::read_from_file(), stir::ProjDataFromStream::set_segment(), and stir::ecat::BinNormalisationFromECAT8::set_up().

open_write_binary() [1/2]

FILE *& stir::open_write_binary	(	FILE *&	fptr,
		const std::string &	name
	)

opens a FILE for writing binary data. Calls error() when it does not succeed.

Warning

probably does not work if you are not in the C-locale

References error().

Referenced by stir::ProjMatrixByBin::get_cached_proj_matrix_elems_for_one_bin().

close_file() [1/2]

void stir::close_file

(

FILE *&

fptr

)

closes a FILE without error checking.

This function is only provided in case you need to write code that works with both std::fstream and stdio FILE.

find_filename()

const char * stir::find_filename

(

const char *const

filename_with_directory

)

return a pointer to the start of the filename (i.e. after directory specifications)

The returned pointer is between filename_with_directory and (filename_with_directory+strlen(filename_with_directory)+1). This highest value is used when it looks like a directory name.

Deprecated:

use find_pos_of_filename()

Warning

This function works only with string manipulations. There is no check if the 'filename' part actually corresponds to a directory on disk.

Referenced by add_extension(), find_pos_of_extension(), get_directory_name(), stir::FilenameTests::run_tests(), stir::ecat::ecat7::write_basic_interfile_header_for_ECAT7(), and write_basic_interfile_PDFS_header().

find_pos_of_filename()

std::string::size_type stir::find_pos_of_filename

(

const std::string &

filename_with_directory

)

return the position of the start of the filename (i.e. after directory specifications)

The returned number is between 0 and filename_with_directory.size()+1. This highest value is used when it's a directory name.

Warning

This function works only with string manipulations. There is no check if the 'filename' part actually corresponds to a directory on disk.

Referenced by find_pos_of_extension(), get_directory_name(), get_filename(), and stir::FilenameTests::run_tests().

get_filename()

std::string stir::get_filename

(

const std::string &

filename_with_directory

)

return a std::string containing only the filename (i.e. after directory specifications)

Warning

This function works only with string manipulations. There is no check if the 'filename' part actually corresponds to a directory on disk.

References find_pos_of_filename().

Referenced by stir::FilePath::get_filename_no_extension(), and stir::RigidObject3DMotionFromPolaris::synchronise().

get_directory_name() [1/2]

char * stir::get_directory_name	(	char *	directory_name,
		const char *const	filename_with_directory
	)

Copies the directory part from 'filename_with_directory' into 'directory_name' and returns the 'directory_name' pointer.

Warning

This function works only with string manipulations. There is no check if the 'filename' part actually corresponds to a directory on disk.

assumes that directory_name points to enough allocated space

Deprecated:

Use get_directory_name(const std::string&)

References find_filename().

Referenced by stir::ecat::CListModeDataECAT8_32bit::get_empty_record_sptr(), read_interfile_dynamic_image(), read_interfile_image(), read_interfile_parametric_image(), stir::FilenameTests::run_tests(), and stir::ecat::BinNormalisationFromECAT8::set_up().

get_directory_name() [2/2]

std::string stir::get_directory_name

(

const std::string &

filename_with_directory

)

Returns a string with the directory part from 'filename_with_directory'.

If there was no directory information present, the return value is the string "." (i.e. the current directory). (It was the empty string prior to STIR 3.0).

Warning

This function works only with string manipulations. There is no check if the 'filename' part actually corresponds to a directory on disk.

References find_pos_of_filename().

find_pos_of_extension()

std::string::size_type stir::find_pos_of_extension

(

const std::string &

file_in_directory_name

)

find the position of the '.' of the extension

If no '.' is found in the filename part (i.e. ignoring the directory name), the function returns std::string::npos

References add_extension(), find_filename(), and find_pos_of_filename().

Referenced by stir::FilePath::add_extension(), add_extension(), stir::FilePath::get_extension(), stir::FilePath::get_filename_no_extension(), stir::ecat::ecat7::ECAT966ListmodeInputFileFormat::read_from_file(), stir::FilePath::replace_extension(), replace_extension(), and write_basic_interfile_PDFS_header().

prepend_directory_name()

char * stir::prepend_directory_name	(	char *	filename_with_directory,
		const char *const	directory_name
	)

Prepend directory_name to the filename, but only if !is_absolute_pathname(filename_with_directory)

If necessary, a directory separator is inserted. If 'directory_name' == 0, nothing happens.

Returns

a pointer to the start of the new filename

Warning

this function assumes that filename_with_directory points to sufficient allocated space to contain the new string.

References is_absolute_pathname().

Referenced by stir::ecat::CListModeDataECAT8_32bit::get_empty_record_sptr(), stir::FilenameTests::run_tests(), and stir::ecat::BinNormalisationFromECAT8::set_up().

ask_filename_with_extension() [1/2]

std::string stir::ask_filename_with_extension	(	const std::string &	prompt,
		const std::string &	default_extension
	)

Asks for a filename (appending an extension if none is provided).

Example:

std::string filename =
ask_filename_with_extension("Input file name ?", ".img");

Warning

starting or ending spaces are NOT stripped.

References add_extension().

Referenced by stir::OSSPSReconstruction< TargetT >::ask_parameters(), stir::IterativeReconstruction< TargetT >::ask_parameters(), stir::AnalyticReconstruction::initialise_keymap(), and stir::ProjDataFromStream::set_segment().

ask_filename_with_extension() [2/2]

char * stir::ask_filename_with_extension	(	char *	file_in_directory_name,
		const std::string &	prompt,
		const std::string &	default_extension
	)

Asks for a filename (appending an extension if none is provided) and stores the string where file_in_directory_name points to.

Deprecated:

Use ask_filename_with_extension(const std::string&, const std::string&);

Example:

char filename[max_filename_length];
ask_filename_with_extension(filename, "Input file name ?", ".img");

Warning

file_in_directory_name has to be preallocated (with size max_filename_length)

starting or ending spaces are NOT stripped.

find_remaining_size()

std::streamsize stir::find_remaining_size

(

std::istream &

input

)

Find number of remaining characters in the stream.

At the end of this function, the 'input' stream will be positioned at the original_position.

Warning

Works only properly for binary streams.

Referenced by ask_filename_and_open(), stir::VoxelsOnCartesianGrid< elemT >::grow_z_range(), and stir::ProjDataFromStream::set_segment().

zoom_viewgrams()

void stir::zoom_viewgrams	(	RelatedViewgrams< float > &	viewgrams,
		const float	zoom,
		const int	min_tang_pos_num,
		const int	max_tang_pos_num,
		const float	x_offset_in_mm = 0,
		const float	y_offset_in_mm = 0
	)

zoom a RelatedViewgrams object, replacing it with the new data

See also

zoom.h for parameter info

References stir::RelatedViewgrams< elemT >::begin(), stir::RelatedViewgrams< elemT >::end(), error(), stir::RelatedViewgrams< elemT >::get_basic_timing_pos_num(), stir::RelatedViewgrams< elemT >::get_basic_view_segment_num(), stir::RelatedViewgrams< elemT >::get_proj_data_info_sptr(), stir::RelatedViewgrams< elemT >::get_symmetries_ptr(), and zoom_viewgram().

Referenced by stir::BackProjectorByBinUsingInterpolation::use_piecewise_linear_interpolation().

zoom_viewgram() [1/2]

void stir::zoom_viewgram	(	Viewgram< float > &	viewgram,
		const float	zoom,
		const int	min_tang_pos_num,
		const int	max_tang_pos_num,
		const float	x_offset_in_mm = 0,
		const float	y_offset_in_mm = 0
	)

zoom viewgram, replacing it with the new data

See also

zoom.h for parameter info

References error(), stir::Viewgram< elemT >::get_max_tangential_pos_num(), stir::Viewgram< elemT >::get_min_tangential_pos_num(), stir::Viewgram< elemT >::get_proj_data_info_sptr(), stir::Viewgram< elemT >::get_segment_num(), stir::Viewgram< elemT >::get_timing_pos_num(), stir::Viewgram< elemT >::get_view_num(), and zoom_viewgram().

zoom_viewgram() [2/2]

void stir::zoom_viewgram	(	Viewgram< float > &	out_viewgram,
		const Viewgram< float > &	in_viewgram,
		const float	x_offset_in_mm = 0,
		const float	y_offset_in_mm = 0
	)

zoom in_viewgram, replacing out_viewgram with the new data

This version of zoom_viewgram gets the info on the new sizes, sampling etc. from out_viewgram.

See also

zoom.h for parameter info

References stir::Viewgram< elemT >::get_max_axial_pos_num(), stir::Viewgram< elemT >::get_min_axial_pos_num(), stir::Viewgram< elemT >::get_proj_data_info_sptr(), stir::Viewgram< elemT >::get_segment_num(), stir::Viewgram< elemT >::get_timing_pos_num(), and stir::Viewgram< elemT >::get_view_num().

Referenced by zoom_viewgram(), and zoom_viewgrams().

zoom_image_in_place() [1/2]

void stir::zoom_image_in_place	(	VoxelsOnCartesianGrid< float > &	image,
		const float	zoom,
		const float	x_offset_in_mm,
		const float	y_offset_in_mm,
		const int	new_size,
		const ZoomOptions	= ZoomOptions::preserve_sum
	)

zoom image, replacing the first argument with the new data

See also

zoom.h for parameter info

References zoom_image().

zoom_image() [1/4]

VoxelsOnCartesianGrid< float > stir::zoom_image	(	const VoxelsOnCartesianGrid< float > &	image,
		const float	zoom,
		const float	x_offset_in_mm,
		const float	y_offset_in_mm,
		const int	new_size,
		const ZoomOptions	= ZoomOptions::preserve_sum
	)

zoom image, replacing the first argument with the new data

See also

zoom.h for parameter info

References stir::VoxelsOnCartesianGrid< elemT >::get_x_size().

Referenced by stir::DiscretisedShape3D::construct_volume(), stir::ScatterSimulation::downsample_density_image_for_scatter_points(), and stir::ScatterSimulation::downsample_images_to_scanner_size().

zoom_image_in_place() [2/2]

void stir::zoom_image_in_place	(	VoxelsOnCartesianGrid< float > &	image,
		const CartesianCoordinate3D< float > &	zooms,
		const CartesianCoordinate3D< float > &	offsets_in_mm,
		const BasicCoordinate< 3, int > &	new_sizes,
		const ZoomOptions	= ZoomOptions::preserve_sum
	)

zoom image, replacing the first argument with the new data. Full 3D shifts and zooms.

See also

zoom.h for parameter info.

Zooming is done such that the physical coordinates of a point (as returned by DiscretisedDensity<3,float>::get_physical_coordinates_for_indices) remain the same.

The index range of the new image is according to the standard STIR conventions (z starts from 0, but x and y from -(new_size/2)). The origin is then chosen such that the geometric centres of the images satisfy

offsets_in_mm == new_middle - old_middle

The geometric centre is determined by the average of the physical coordinates of the min and max indices.

Warning

: For even-sized images, this convention can lead to somewhat non-intuitive results (half-pixel shifts etc).

References zoom_image().

zoom_image() [2/4]

VoxelsOnCartesianGrid< float > stir::zoom_image	(	const VoxelsOnCartesianGrid< float > &	image,
		const CartesianCoordinate3D< float > &	zooms,
		const CartesianCoordinate3D< float > &	offsets_in_mm,
		const BasicCoordinate< 3, int > &	new_sizes,
		const ZoomOptions	= ZoomOptions::preserve_sum
	)

zoom image, returning the new image

See also

zoom.h for parameter info

zoom_image_in_place

zoom_image() [3/4]

void stir::zoom_image	(	VoxelsOnCartesianGrid< float > &	image_out,
		const VoxelsOnCartesianGrid< float > &	image_in,
		const ZoomOptions	= ZoomOptions::preserve_sum
	)

zoom image_in according to dimensions, origin and voxel_size of image_out.

See also

zoom.h for parameter info

Zooming is done such that the physical coordinates of a point (as returned by DiscretisedDensity<3,float>::get_physical_coordinates_for_indices) remain the same.

The code also provides for three possible rescaling options: (i) preserving the image values: should be used when zooming an attenuation image (ii) preserving the image projectors: should be used when zooming an activity image (iii) preserving the image sum: default

References stir::ExamData::set_exam_info().

zoom_image() [4/4]

void stir::zoom_image	(	PixelsOnCartesianGrid< float > &	image2D_out,
		const PixelsOnCartesianGrid< float > &	image2D_in,
		const ZoomOptions	= ZoomOptions::preserve_sum
	)

zoom image2D_in according to dimensions, origin and pixel_size of image2D_out.

See also

zoom.h for parameter info

References stir::DiscretisedDensity< num_dimensions, elemT >::get_origin(), stir::PixelsOnCartesianGrid< elemT >::get_pixel_size(), overlap_interpolate(), and stir::ExamData::set_exam_info().

Referenced by zoom_image_in_place().

get() [1/2]

template<int num_dimensions, int num_dimensions2, typename elemT >

const Array< num_dimensions - num_dimensions2, elemT > & stir::get ( const Array< num_dimensions, elemT > &  a, const BasicCoordinate< num_dimensions2, int > &  c  )

inline

an alternative for array indexing using BasicCoordinate objects

Case where the index has lower dimension than the array

References cut_first_dimension().

Referenced by info(), and warning().

get() [2/2]

template<int num_dimensions, typename elemT >

const elemT & stir::get ( const Array< num_dimensions, elemT > &  a, const BasicCoordinate< num_dimensions, int > &  c  )

inline

an alternative for array indexing using BasicCoordinate objects

Case where the index has the same dimension as the array

get_min_indices()

template<int num_dimensions, typename T >

BasicCoordinate< num_dimensions, int > stir::get_min_indices ( const Array< num_dimensions, T > &  a )

inline

Get the first multi-dimensional index of the array.

Todo:

If the array

• a is empty, we return an object where all indices are 0. It would be better to throw an exception.

next()

template<int num_dimensions, typename T , int num_dimensions2>

bool stir::next ( BasicCoordinate< num_dimensions, int > &  indices, const Array< num_dimensions2, T > &  a  )

inline

Given an index into an array, increment it to the next one.

Returns

true if the next index was still within the array, false otherwise

This can be used to iterate through an array using code such as

Array<num_dimensions2, T> array = ...;
BasicCoordinate<num_dimensions, int> indices =
   get_min_indices(array);
do
{ something with indices }
while (next(indices, array));

Warning

The above loop will fail for empty arrays

display() [1/2]

template<class elemT >

void stir::display ( const Array< 3, elemT > &  plane_stack, double  maxi, const char *const  title, int  zoom  )

inline

See also

Display functions(const Array<3,elemT>&, const VectorWithOffset<scaleT>& , const VectorWithOffset<CHARP>& , double, const char * const , int zoom) for more info. This function sets the 'text' parameter to a sequence of numbers.

display() [2/2]

template<class elemT >

void stir::display ( const Array< 2, elemT > &  plane, const char *const  text, double  maxi, int  zoom  )

inline

See also

Display functions(const Array<3,elemT>&, const VectorWithOffset<scaleT>& , const VectorWithOffset<CHARP>& , double, const char * const , int zoom) for more info.

index_at_maximum()

template<class elemT >

int stir::index_at_maximum

(

const VectorWithOffset< elemT > &

v

)

Finds the index where the maximum occurs in a (1-dimensional) vector.

If the maximum occurs more than once, the smallest index is returned.

If the vector is empty, the function returns 0.

Todo:

make iterator version, or something that works on std::vector

indices_at_maximum()

template<class elemT >

BasicCoordinate<3, int> stir::indices_at_maximum

(

const Array< 3, elemT > &

input_array

)

Finds the first (3-dimensional) index where the maximum occurs in a (3-dimensional) array.

Todo:

generalise to arbitrary dimensions

implementation currently cycles through the data twice

References stir::Array< num_dimensions, elemT >::find_max(), stir::VectorWithOffset< T >::get_max_index(), and stir::VectorWithOffset< T >::get_min_index().

Referenced by maximum_location_per_slice(), and stir::MatchTrackerAndScanner::run().

modulo() [1/4]

double stir::modulo ( const double  a, const double  b  )

inline

Like std::fmod() but with guaranteed nonnegative result.

std::fmod(a,b) return a number of the same sign as a. This is often inconvenient as the result of this is that the range of std::fmod(a,b) is from -fabs(b) to +fabs(b).

In contrast, modulo(a,b) always returns a nonnegative result. To be precise:

modulo(a,b) returns the value a-i*b, for the integer i such that, if b is nonzero, the result is greater or equal to 0 and less than the magnitude of b.

Error handling (i.e. b=0) is as for std::fmod().

Warning

When assigning the result to a float, the implied rounding might give you float which is (a tiny bit) larger than fabs(b).

Referenced by stir::ProjDataInfoCylindricalNoArcCorr::find_scanner_coordinates_given_cartesian_coordinates(), and stir::ProjDataInfoCylindricalNoArcCorr::get_bin().

modulo() [2/4]

float stir::modulo ( const float  a, const float  b  )

inline

modulo for floats

See also

modulo(double,double) The reason for this function is that rounding from double to float might make the result of the calculation with doubles larger than b.

Warning

Because of C++ promotion of floats to doubles, it is very easy to call the modulo(double,double) version inadvertently. So, you should probably not rely too much on the result being less than b.

References modulo().

modulo() [3/4]

int stir::modulo ( const int  a, const int  b  )

inline

Like the normal modulus operator (%) but with guaranteed nonnegative result.

Result will be larger than or equal to 0, and (strictly) smaller than abs(b).

modulo() [4/4]

template<int num_dimensions, typename T >

BasicCoordinate<num_dimensions, T> stir::modulo ( const BasicCoordinate< num_dimensions, T > &  a, const BasicCoordinate< num_dimensions, T > &  b  )

inline

Performs the modulus operation on each element of the coordinates.

Returns

A BasicCoordinate such that for all d

result[d] = modulo(a[d], b[d] 

Referenced by modulo(), and to_0_2pi().

from_min_pi_plus_pi_to_0_2pi()

template<typename FloatOrDouble >

FloatOrDouble stir::from_min_pi_plus_pi_to_0_2pi ( const FloatOrDouble  phi )

inline

A function to convert an angle from one range to another.

This is mainly useful for converting results from e.g. std::atan2 to a range .

References _PI.

Referenced by stir::LORAs2Points< float >::change_representation_for_block(), find_LOR_intersections_with_cylinder(), and stir::DetectorCoordinateMap::set_detector_map().

to_0_2pi()

template<typename FloatOrDouble >

FloatOrDouble stir::to_0_2pi ( const FloatOrDouble  phi )

inline

Convert angle to standard range.

Identical to modulo(phi, static_cast<FloatOrDouble>(2*_PI))

References _PI, and modulo().

Referenced by stir::ProjDataInfoCylindricalNoArcCorr::find_scanner_coordinates_given_cartesian_coordinates(), stir::ProjDataInfoCylindricalArcCorr::get_bin(), stir::ProjDataInfoCylindricalNoArcCorr::get_bin(), and stir::LORInAxialAndNoArcCorrSinogramCoordinates< coordT >::LORInAxialAndNoArcCorrSinogramCoordinates().

fill_from()

template<typename iterT >

void stir::fill_from	(	MultipleProjData &	stir_object,
		iterT	iter,
		iterT
	)

set all elements of a MultipleProjData from an iterator

Implementation that resorts to MultipleProjData::fill_from

Warning

there is no size/range-check on iter

matrix_multiply() [1/3]

template<class elemT >

Array< 1, elemT > stir::matrix_multiply ( const Array< 2, elemT > &  m, const Array< 1, elemT > &  vec  )

inline

matrix with vector multiplication

Index ranges have to be compatible (checked with assert).

Referenced by absolute_max_eigenvector_using_power_method(), stir::RigidObject3DTransformation::transform_point(), and stir::Shape3DWithOrientation::transform_to_shape_coords().

matrix_multiply() [2/3]

template<int dimension, class elemT >

BasicCoordinate<dimension, elemT> stir::matrix_multiply ( const Array< 2, elemT > &  m, const BasicCoordinate< dimension, elemT > &  vec  )

inline

matrix multiplication with vector (given as BasicCoordinate)

matrix size has to be compatible with dimension. Matrix index range has to start from 1. All of this is only checked with assert().

matrix_multiply() [3/3]

template<class elemT >

Array< 2, elemT > stir::matrix_multiply ( const Array< 2, elemT > &  m1, const Array< 2, elemT > &  m2  )

inline

matrix multiplication

Index ranges have to be compatible (checked with assert).

diagonal_matrix() [1/2]

template<class elemT >

Array< 2, elemT > stir::diagonal_matrix ( const unsigned  dimension, const elemT  value  )

inline

construct a diagonal matrix with all elements on the diagonal equal

Parameters

[in]	dimension	specifies the size of the matrix
[in]	value	gives the value on the diagonal. Note that its type determines the type of the return value.

Example

// a 3x3 identity matrix
Array<2,float> iden = diagonal_matrix(3, 1.F);

Index-range of the matrix will be 0 till dimensions-1.

Referenced by absolute_max_eigenvector_using_shifted_power_method(), stir::Shape3DWithOrientation::get_direction_vectors(), and stir::Shape3DWithOrientation::set_defaults().

diagonal_matrix() [2/2]

template<int dimension, class elemT >

Array< 2, elemT > stir::diagonal_matrix ( const BasicCoordinate< dimension, elemT > &  values )

inline

construct a diagonal matrix

Parameters

[in]

values

gives the values on the diagonal. Note that its type determines the type of the return value.

Example

// a 3x3 diagonal matrix with values 1,2,3 on the diagonal
Array<2,float> diag = diagonal_matrix(Coordinate3D<float>(1,2,3));

Index-range of the matrix will be 0 till dimensions-1. (Note that this is different from values).

norm_squared() [1/3]

template<typename elemT >

double stir::norm_squared ( const elemT  t )

inline

Returns the square of the norm of a number.

See also

norm(elemT)

norm() [1/3]

template<typename elemT >

double stir::norm ( const elemT  t )

inline

Returns the norm of a number.

This is the same as the absolute value, but works also for std::complex<T>.

norm_squared() [2/3]

template<class Iter >

double stir::norm_squared ( Iter  begin, Iter  end  )

inline

Returns the square of the l2-norm of a sequence.

The l2-norm is defined as the sqrt of the sum of squares of the norms of each element in the sequence.

References norm_squared().

norm() [2/3]

template<class Iter >

double stir::norm ( Iter  begin, Iter  end  )

inline

Returns the l2-norm of a sequence.

The l2-norm is defined as the sqrt of the sum of squares of the norms of each element in the sequence.

See also

norm(const Array<1,elemT>&) for a convenience function for Array objects.

References norm_squared().

norm() [3/3]

template<class elemT >

double stir::norm ( const Array< 1, elemT > &  v1 )

inline

l2 norm of a 1D array

This returns the sqrt of the sum of the square of the absolute values of the elements of v1.

References stir::VectorWithOffset< T >::begin(), stir::VectorWithOffset< T >::end(), and norm().

norm_squared() [3/3]

template<class elemT >

double stir::norm_squared ( const Array< 1, elemT > &  v1 )

inline

square of the l2 norm of a 1D array

This returns the sum of the square of the absolute values of the elements of v1.

References stir::VectorWithOffset< T >::begin(), stir::VectorWithOffset< T >::end(), and norm_squared().

round() [1/3]

int stir::round ( const float  x )

inline

Implements rounding of floating point numbers.

round() has the property that

round(x) == -round(-x)

The usual (int)(x+.5) has machine dependent behaviour for negative numbers.

.5 is rounded to 1 (and hence -.5 to -1).

Warning

There is no check on overflow (i.e. if x is too large to fit in an int).

Referenced by stir::Scanner::check_consistency(), stir::DiscretisedShape3D::construct_volume(), stir::DataSymmetriesForBins_PET_CartesianGrid::DataSymmetriesForBins_PET_CartesianGrid(), stir::DataSymmetriesForDensels_PET_CartesianGrid::DataSymmetriesForDensels_PET_CartesianGrid(), stir::ScatterSimulation::downsample_density_image_for_scatter_points(), stir::ScatterSimulation::downsample_scanner(), stir::DetectorCoordinateMap::find_detection_position_given_cartesian_coordinate(), stir::ProjDataInfoCylindricalNoArcCorr::find_scanner_coordinates_given_cartesian_coordinates(), stir::ProjDataInfoCylindricalArcCorr::get_bin(), stir::ProjDataInfoCylindricalNoArcCorr::get_bin(), stir::DiscretisedDensity< 3, float >::get_indices_closest_to_LPS_coordinates(), stir::DiscretisedDensity< 3, float >::get_indices_closest_to_relative_coordinates(), stir::DiscretisedShape3D::get_voxel_weight(), stir::ProjDataInfoCylindrical::ProjDataInfoCylindrical(), pull_linear_interpolate(), pull_nearest_neighbour_interpolate(), push_nearest_neighbour_interpolate(), push_transpose_linear_interpolate(), stir::SinglesRatesForTimeSlices::rebin(), stir::coordinateTests::run_tests(), secs_since_Unix_epoch_to_DICOM_datetime(), stir::GeneralisedPoissonNoiseGenerator::seed(), stir::DetectorCoordinateMap::set_detector_map(), stir::ForwardProjectorByBinUsingRayTracing::set_up(), stir::BackProjectorByBinUsingInterpolation::set_up(), SSRB(), time_zone_offset_in_secs(), stir::BackProjectorByBinUsingInterpolation::use_piecewise_linear_interpolation(), and stir::HUToMuImageProcessor< TargetT >::virtual_set_up().

round() [2/3]

int stir::round ( const double  x )

inline

Implements rounding of double numbers.

See also

round(const float)

round() [3/3]

template<int num_dimensions, class elemT >

BasicCoordinate< num_dimensions, int > stir::round ( const BasicCoordinate< num_dimensions, elemT > &  x )

inline

Implements rounding of a BasicCoordinate object.

See also

round(const float)

round_to() [1/2]

template<typename integerT >

void stir::round_to ( integerT &  result, const float  x  )

inline

Implements rounding of floating point numbers to other integer types.

This function is templated in the output type for convenience of implementation.

Warning

if an unsigned type is used for integerT, the result for negative x will be system dependent

See also

round(const float)

Todo:

add code to check that integerT is really an integer type at compilation time

Referenced by stir::DynamicDiscretisedDensity::write_to_ecat7().

round_to() [2/2]

template<int num_dimensions, class integerT , class elemT >

void stir::round_to ( BasicCoordinate< num_dimensions, integerT > &  result, const BasicCoordinate< num_dimensions, elemT > &  x  )

inline

Implements rounding of a BasicCoordinate object to other integer types.

See also

round_to(integerT, float)

operator<<() [1/3]

template<typename elemT >

std::ostream & stir::operator<< ( std::ostream &  str, const VectorWithOffset< elemT > &  v  )

inline

Outputs a VectorWithOffset to a stream.

Output is of the form

{1, 2, 3}

with an endl at the end.

This can be used for higher dimensional arrays as well, where each 1D subobject will be on its own line.

operator<<() [2/3]

template<int num_dimensions, typename coordT >

std::ostream & stir::operator<< ( std::ostream &  str, const BasicCoordinate< num_dimensions, coordT > &  v  )

inline

Outputs a BasicCoordinate to a stream.

Output is of the form

{1, 2, 3}

with no endl at the end.

operator<<() [3/3]

template<typename elemT >

std::ostream & stir::operator<< ( std::ostream &  str, const std::vector< elemT > &  v  )

inline

Outputs a vector to a stream.

Output is of the form

{1, 2, 3}

with an endl at the end.

For each element of the vector std::ostream::operator<<() will be called.

operator>>() [1/3]

template<typename elemT >

std::istream & stir::operator>> ( std::istream &  str, std::vector< elemT > &  v  )

inline

Inputs a vector from a stream.

Input is of the form

{1, 2, 3}

Input is stopped when either the beginning '{', an intermediate ',' or the trailing '}' is not found. The size of the vector will be the number of correctly read elemT elements.

For each element of the vector std::istream::operator>>(element) will be called.

elemT needs to have a default constructor.

operator>>() [2/3]

template<typename elemT >

std::istream & stir::operator>> ( std::istream &  str, VectorWithOffset< elemT > &  v  )

inline

Inputs a VectorWithOffset from a stream.

Input is of the form

{1, 2, 3}

As Array<>'s are constructed from nested VectorWithOffset objects, you can input say a 2d array as

{{1,2}, {2,4,5}, {5}}

Input is stopped when either the beginning '{', an intermediate ',' or the trailing '}' is not found. The size of the vector will be the number of correctly read elemT elements.

v.get_min_index() will be 0 at the end of the call.

For each element of the vector std::istream::operator>>(element) will be called.

elemT needs to have a default constructor.

operator>>() [3/3]

template<int num_dimensions, typename coordT >

std::istream & stir::operator>> ( std::istream &  str, BasicCoordinate< num_dimensions, coordT > &  v  )

inline

Inputs a coordinate from a stream.

Input is of the form

{1, 2, 3}

Input is stopped when either the beginning '{', an intermediate ',' or the trailing '}' is not found. If the number of correctly read elements is not num_dimensions, the last few will have undefined values.

For each element of the vector std::istream::operator>>(element) will be called.

elemT needs to have a default constructor.

Referenced by operator<<().

threshold_upper_lower()

template<typename forw_iterT , typename elemT >

void stir::threshold_upper_lower ( forw_iterT  begin, forw_iterT  end, const elemT  new_min, const elemT  new_max  )

inline

Threshold a sequence from above and below.

Type requirements:

• forw_iterT is a forward iterator
• elemT must be assignable to *forw_iterT
• bool operator>(*forw_iterT, elemT) must exist

Referenced by stir::stir_mathTests::run_tests(), and stir::OSSPSReconstruction< TargetT >::update_estimate().

threshold_upper()

template<typename forw_iterT , typename elemT >

void stir::threshold_upper ( forw_iterT  begin, forw_iterT  end, const elemT  new_max  )

inline

Threshold a sequence from above.

See also

threshold_upper_lower for type requirements

Referenced by stir::VectorWithOffset< shared_ptr< stir::BinNormalisation > >::apply_upper_threshold(), and stir::ScatterEstimation::upsample_and_fit_scatter_estimate().

threshold_lower()

template<typename forw_iterT , typename elemT >

void stir::threshold_lower ( forw_iterT  begin, forw_iterT  end, const elemT  new_min  )

inline

Threshold a sequence from below.

See also

threshold_upper_lower for type requirements

Referenced by stir::VectorWithOffset< shared_ptr< stir::BinNormalisation > >::apply_lower_threshold(), stir::MatchTrackerAndScanner::run(), threshold_min_to_small_positive_value(), and stir::ScatterEstimation::upsample_and_fit_scatter_estimate().

threshold_min_to_small_positive_value()

template<typename ForwardIter_t , typename elemT >

void stir::threshold_min_to_small_positive_value	(	ForwardIter_t	begin,
		ForwardIter_t	end,
		const elemT &	small_number
	)

sets non-positive values in the sequence to small positive ones

Thresholds the sequence from below to *min_positive_element()*small_number. However, if all values are less than or equal to 0, they are set to small_number.

Parameters

begin	start of the sequence. Usually object.begin().
end	end of the sequence in iterator sense (so actually one beyond the last element). Usually object.end().
small_number	see above

The iterator type has to satisfy the requirements of a forward iterator, and its value_type has to be comparable using < and <=.

References min_positive_element(), and threshold_lower().

Referenced by stir::OSSPSReconstruction< TargetT >::update_estimate().

ask_num()

template<class NUMBER >

NUMBER stir::ask_num ( const std::string &  str, NUMBER  minimum_value, NUMBER  maximum_value, NUMBER  default_value  )

inline

A function to ask a number from the user.

The question is currently presented as

str_text : [minimum_value, maximum_value, D: default_value]:

Simply pressing 'enter' will select the default value. Otherwise, range checking is performed, and the question asked again if necessary.

Referenced by stir::ProjDataInfo::ask_parameters(), stir::ScatterSimulation::ask_parameters(), stir::OSSPSReconstruction< TargetT >::ask_parameters(), stir::OSMAPOSLReconstruction< TargetT >::ask_parameters(), stir::IterativeReconstruction< TargetT >::ask_parameters(), stir::VoxelsOnCartesianGrid< elemT >::grow_z_range(), stir::AnalyticReconstruction::initialise_keymap(), stir::Scanner::list_names(), and stir::ProjDataFromStream::set_segment().

ask_filename_and_open()

template<class FSTREAM >

void stir::ask_filename_and_open	(	FSTREAM &	s,
		const std::string &	prompt,
		const std::string &	default_extension,
		std::ios::openmode	mode,
		bool	abort_if_failed
	)

Asks for a filename (with default extension) and opens the stream s with mode giving the specifics.

Example: open a binary input file, aborting if it is not found

ifstream in;
ask_filename_and_open(s, "Input file ?", ".hv", std::ios::in | std::ios::binary);

Note: this function is templated to allow s to be of different types ifstream, ofstream, fstream

read_stream_in_memory()

void* stir::read_stream_in_memory	(	std::istream &	input,
		std::streamsize &	file_size
	)

reads data into memory, returning a pointer to the memory

If the file_size parameter is zero, the stream is read till EOF and 'file_size' is set to the number of bytes in the file. Otherwise 'file_size' bytes are read.

The data is read from the current position in the stream. At the end of this function, the 'input' stream will be positioned at original_position + file_size.

Referenced by ask_filename_and_open().

open_read_binary() [2/2]

template<class IFSTREAM >

IFSTREAM & stir::open_read_binary ( IFSTREAM &  s, const std::string &  name  )

inline

opens a stream for reading binary data. Calls error() when it does not succeed.

Warning

probably does not work if you are not in the C-locale

References error().

Referenced by ask_filename_and_open().

open_write_binary() [2/2]

template<class OFSTREAM >

OFSTREAM & stir::open_write_binary ( OFSTREAM &  s, const std::string &  name  )

inline

opens a stream for writing binary data. Calls error() when it does not succeed.

Templated such that it works on std::ofstream and std::fstream.

Warning

probably does not work if you are not in the C-locale

References error().

Referenced by ask_filename_and_open().

close_file() [2/2]

template<class FSTREAM >

void stir::close_file ( FSTREAM &  s )

inline

closes a stream without error checking.

Templated such that it works on std::ofstream, std::ifstream and std::fstream.

This function is only provided in case you need to write code that works with both std::fstream and stdio FILE.

Referenced by ask_filename_and_open().

four1()

void stir::four1	(	Array< 1, float > &	data,
		int	nn,
		int	isign
	)

1-dimensional FFT

Replaces data by its discrete Fourier transform, if isign is input as 1; or replaces data by nn times its inverse discrete Fourier transform, if isign is input as -1. data is a complex array of length nn, input as a real array data[1..2*nn]. nn MUST be an integer power of 2 ( this is not checked for !).

fourn()

void stir::fourn	(	Array< 1, float > &	data,
		Array< 1, int > &	nn,
		int	ndim,
		int	isign
	)

n-dimensional FFT

Replaces data by its ndim-dimensional discrete Fourier transform, if isign is input as 1. nn[1..ndim] is an integer array containing the lengths of each dimension (number of complex values), which MUST all be powers of 2. data is a real array of length twice the product of thes lengths, in which the data are stored as in a multidimensional complex array: real and imaginary parts of each element are in consecutive locations , and the rightmost index of the array increases most rapidly as one proceeds along data. For a two-dimensional array, this is equivalent to storing the array by rows . If isign is in input as -1 , data is replaced by its inverse transform time the product of the lengths of all dimensions.

convlvC()

void stir::convlvC	(	Array< 1, float > &	data,
		const Array< 1, float > &	filter,
		int	n
	)

Convolve data with a filter which is given in frequency space.

Parameters

data	has to have a min_index == 1
filter	has to in the format produced by realft.
n	has to be equal to th elength of data

Warning

Currently, only the real elements of the filter will be used. (Historical reason?) So, the result will be incorrect of the filter has complex components (i.e. its spatial kernel is not symmetric).

realft()

void stir::realft	(	Array< 1, float > &	data,
		int	n,
		int	isign
	)

Calculates the Fourier Transform of a set of 2n real-valued data points.

Replaces this data ( which is stored in array data[1..2n]) by the positive frequency half of its complex Fourier Transform. The real-valued first and last components of the complex transform are returned as element data[1] and data[2] respectively. n must be a power of 2. The routine also calculates the inverse transform of a complex data array if it is the transform of real data. (Result in this case must be multiplied by 1/n.)