File List

Here is a list of all documented files with brief descriptions:

[detail level 1234567]

▼ STIR
▼ examples
► C++
► General_Reconstruction
General_Reconstruction.h	Definition of class stir::General_Reconstruction
► using_installed_STIR
demo_create_image.cxx	A simple program that creates an image and fills it with a shape
► using_STIR_LOCAL
demo1.cxx	A simple program that backprojects some projection data
demo2.cxx	A small modification of demo1.cxx to ask the user for the back projector she wants to use
demo3.cxx	A modification of demo2.cxx that parses all parameters from a parameter file
demo4_obj_fun.cxx	An example of a method to compute the objective function value of an image and then perform basic iterative gradient ascent. All parameters are parsed from a parameter file
demo5_line_search.cxx	A class to compute a line search evaluation in the direction of the gradient of a given image and objective function. All parameters can be parsed from a parameter file. See demo5_line_search.par
▼ src
► analytic
► DDSR2D
DDSR2D.cxx	Main program for DDSR2D reconstruction
DDSR2DReconstruction.cxx	Implementation of class stir::DDSR2DReconstruction
► FBP2D
FBP2D.cxx	Main program for FBP2D reconstruction
FBP2DReconstruction.cxx	Implementation of class stir::FBP2DReconstruction
RampFilter.cxx	Implementation of class stir::RampFilter
► FBP3DRP
ColsherFilter.cxx	Colsher filter implementation
FBP3DRP.cxx	Main program for FBP3DRP reconstruction
FBP3DRPReconstruction.cxx	FBP3DRP reconstruction implementation
► GRD2D
GRD2D.cxx	Main program for GRD2D reconstruction
GRD2DReconstruction.cxx	Implementation of class stir::GRD2DReconstruction
► SRT2D
SRT2D.cxx	Main program for SRT2D reconstruction
SRT2DReconstruction.cxx	Implementation of class stir::SRT2DReconstruction
► SRT2DSPECT
SRT2DSPECT.cxx	Main program for SRT2DSPECT reconstruction
SRT2DSPECTReconstruction.cxx	Implementation of class stir::SRT2DSPECTReconstruction
► buildblock
ArcCorrection.cxx	Implementation of class stir::ArcCorrection
Array.cxx	Non-inline implementations for the Array class
ArrayFilter1DUsingConvolution.cxx	Implementations for class stir::ArrayFilter1DUsingConvolution
ArrayFilter1DUsingConvolutionSymmetricKernel.cxx	Implementations for class stir::ArrayFilter1DUsingConvolutionSymmetricKernel
ArrayFilter2DUsingConvolution.cxx	Implementations for class ArrayFilter2DUsingConvolution
ArrayFilter3DUsingConvolution.cxx	Implementations for class ArrayFilter3DUsingConvolution
ArrayFilterUsingRealDFTWithPadding.cxx	Implementation of class stir::ArrayFilterUsingRealDFTWithPadding
buildblock_registries.cxx	File that registers all stir::RegisterObject children in buildblock
ByteOrder.cxx	This file initialises ByteOrder::native_order
centre_of_gravity.cxx	Implementations of centre_of_gravity.h
ChainedDataProcessor.cxx	Implementations for class stir::ChainedDataProcessor
DataSymmetriesForViewSegmentNumbers.cxx	Implementations for class stir::DataSymmetriesForViewSegmentNumbers
DataWithProjDataInfo.cxx	Implementation of stir::DataWithProjDataInfo
date_time_functions.cxx	Functions for date-time conversions
DetectorCoordinateMap.cxx	Implementation of class stir::DetectorCoordinateMap
DiscretisedDensity.cxx	Implementations of non-inline functions of class stir::DiscretisedDensity
DynamicDiscretisedDensity.cxx	Implementation of class stir::DynamicDiscretisedDensity
DynamicProjData.cxx	Implementation of class stir::DynamicProjData
error.cxx	Defines the stir::error() function
ExamData.cxx	Implementation of stir::ExamData
ExamInfo.cxx	Implementation of stir::ExamInfo
extend_projdata.cxx	Implementation of functions to extension of direct sinograms in view direction
find_fwhm_in_image.cxx	Implementations of functions defined in find_fwhm_in_image.h
find_STIR_config.cxx	Implementation of functions to get configuration directory etc
GammaArrayFilter2D.cxx	Implementations for class stir::GammaArrayFilter2D
GammaImageFilter2D.cxx	Implementations for class stir::GammaImageFilter2D
GatedDiscretisedDensity.cxx	Implementation of class stir::GatedDiscretisedDensity
GatedProjData.cxx	Implementation of class stir::GatedProjData
GeneralisedPoissonNoiseGenerator.cxx	Implements stir::GeneralisedPoissonNoiseGenerator
GeometryBlocksOnCylindrical.cxx	Non-inline implementations of stir::GeometryBlocksOnCylindrical
HUToMuImageProcessor.cxx	Implementation of class stir::HUToMuImageProcessor
IndexRange.cxx	Implementations for the stir::IndexRange class
interfile_keyword_functions.cxx	Implementations for stir::standardise_interfile_keyword
interpolate_projdata.cxx	Perform B-Splines Interpolation of sinograms
inverse_SSRB.cxx	Implementation of stir::inverse_SSRB
KeyParser.cxx	Implementations for class stir::KeyParser
line.cxx	Implementations for class stir::Line
MaximalArrayFilter3D.cxx	Applies the dilation filter (i.e. voxel=max(neighbours))
MaximalImageFilter3D.cxx	Implementations for class stir::MaximalImageFilter3D
MedianArrayFilter3D.cxx	Implementations for class stir::MedianArrayFilter3D
MedianImageFilter3D.cxx	Implementations for class stir::MedianImageFilter3D
MinimalArrayFilter3D.cxx	Applies the erosion filter (i.e. voxel=min(neighbours))
MinimalImageFilter3D.cxx	Implementations for class MinimalImageFilter3D
ML_norm.cxx	Utilities for finding normalisation factors using an ML approach
MultipleDataSetHeader.cxx	Implementation of class stir::MultipleDataSetHeader
MultipleProjData.cxx	Implementation of class stir::MultipleProjData
multiply_crystal_factors.cxx	Implementation of stir::multiply_crystal_factors
NonseparableConvolutionUsingRealDFTImageFilter.cxx	Implementations for class stir::NonseparableConvolutionUsingRealDFTImageFilter
num_threads.cxx	Implementation of functions related to setting/getting the number of threads
NumericType.cxx	Implementations for the stir::NumericType class
overlap_interpolate.cxx	Implementation of stir::overlap_interpolate
ParseDiscretisedDensityParameters.cxx	Implementation of the stir::ParseDiscretisedDensityParameters class
ParsingObject.cxx	Non-linline implementations for class stir::ParsingObject
PatientPosition.cxx	Implementations of class stir::PatientPosition
ProjData.cxx	Implementations for non-inline functions of class stir::ProjData
ProjDataFromStream.cxx	Implementations for non-inline functions of class stir::ProjDataFromStream
ProjDataGEHDF5.cxx	Implementations for class stir::GE::RDF_HDF5::ProjDataGEHDF5
ProjDataInfo.cxx	Implementation of non-inline functions of class stir::ProjDataInfo
ProjDataInfoBlocksOnCylindricalNoArcCorr.cxx	Non-inline implementations of stir::ProjDataInfoBlocksOnCylindricalNoArcCorr
ProjDataInfoCylindrical.cxx	Non-inline implementations of stir::ProjDataInfoCylindrical
ProjDataInfoCylindricalArcCorr.cxx	Implementation of non-inline functions of class stir::ProjDataInfoCylindricalArcCorr
ProjDataInfoCylindricalNoArcCorr.cxx	Implementation of non-inline functions of class stir::ProjDataInfoCylindricalNoArcCorr
ProjDataInfoGeneric.cxx	Non-inline implementations of stir::ProjDataInfoGeneric
ProjDataInfoGenericNoArcCorr.cxx	Implementation of non-inline functions of class stir::ProjDataInfoGenericNoArcCorr
ProjDataInfoSubsetByView.cxx	Implementation of non-inline functions of class stir::ProjDataInfoSubsetByView
ProjDataInMemory.cxx	Implementations for non-inline functions of class stir::ProjDataInMemory
ProjDataInterfile.cxx	Implementation of class stir::ProjDataInterfile
Radionuclide.cxx	Implementations of inline functions of class stir::Radionuclide
RadionuclideDB.cxx	Implementation of class stir::RadionuclideDB
recon_array_functions.cxx	Implementations for functions declared in recon_array_functions.h
RelatedViewgrams.cxx	Implementations for class stir::RelatedViewgrams
scale_sinograms.cxx	Implementations of functions defined in scale_sinogram.h
Scanner.cxx	Implementations for class stir::Scanner
Segment.cxx	Implementations for non-inline functions of class stir::Segment
SegmentBySinogram.cxx	Implementations for non-inline functions of class stir::SegmentBySinogram
SegmentByView.cxx	Implementations for non-inline functions of class stir::SegmentByView
SeparableArrayFunctionObject.cxx	Implementations for stir::SeparableArrayFunctionObject
SeparableCartesianMetzImageFilter.cxx	Implementations for class stir::SeparableCartesianMetzImageFilter
SeparableConvolutionImageFilter.cxx	Implementation of class stir::SeparableConvolutionImageFilter
SeparableGaussianArrayFilter.cxx	Implementations for class stir::SeparableGaussianArrayFilter
SeparableGaussianImageFilter.cxx	Implementations for class stir::SeparableGaussianImageFilter
SeparableMetzArrayFilter.cxx	Implementations for class stir::SeparableMetzArrayFilter
Sinogram.cxx	Implementations for non-inline functions of class stir::Sinogram
SSRB.cxx	Implementation of stir::SSRB
ThresholdMinToSmallPositiveValueDataProcessor.cxx	Implementations for class stir::ThresholdMinToSmallPositiveValueDataProcessor
TimeFrameDefinitions.cxx	Implementation of class stir::TimeFrameDefinitions
TimeGateDefinitions.cxx	Implementation of class stir::TimeGateDefinitions
TruncateToCylindricalFOVImageProcessor.cxx	Implementations for class stir::TruncateToCylindricalFOVImageProcessor
utilities.cxx	Non-inline implementations for utility.h
Verbosity.cxx	Declaration of class stir::Verbosity
Viewgram.cxx	Implementations for non-inline functions of class stir::Viewgram
VoxelsOnCartesianGrid.cxx	Implementations of stir::VoxelsOnCartesianGrid
warning.cxx	Defines the stir::warning() function
WienerArrayFilter2D.cxx	Implementations for class stir::WienerArrayFilter2D
WienerImageFilter2D.cxx	Implementations for class stir::WienerImageFilter2D
zoom.cxx	Implementations of the stir::zoom functions
► data_buildblock
data_buildblock_registries.cxx	File that registers all stir::RegisterObject children in data_buildblock
randoms_from_singles.cxx	Implementation of stir::randoms_from_singles
SinglesRates.cxx	Implementation of stir::FrameSinglesRates and stir::SinglesRates
SinglesRatesForTimeFrames.cxx	Implementation of stir::SinglesRatesForTimeFrames
SinglesRatesForTimeSlices.cxx	Implementation of stir::SinglesRatesForTimeSlices
SinglesRatesFromECAT7.cxx	Implementation of stir::ecat::ecat7::SinglesRatesFromECAT7
SinglesRatesFromGEHDF5.cxx	Implementation of stir::GE::RDF_HDF5::SinglesRatesFromGEHDF5
SinglesRatesFromSglFile.cxx	Implementation of stir::ecat::ecat7::SinglesRatesFromECAT7
► display
display_array.cxx	Functions to display stir::Array objects (2d and 3d) and stir::RelatedViewgrams
gen.c	Utility functions used by the screen* files (internal use only)
gen.h	Declares some utility functions used by the screen* files
mathlinkhelp.c	Functions to write data to MathLink
screen.c	Very basic display routines for bitmaps (internal use only)
screen.h	Very basic display routines for bitmaps (internal use only)
screengen.c	Very basic display routines
► eval_buildblock
compute_ROI_values.cxx	Implementation of functions declared in stir/evaluation/compute_ROI_values.h
ROIValues.cxx	Implementation of class stir::ROI_values
► experimental
► buildblock
AbsTimeIntervalFromDynamicData.cxx	Declaration of class stir::AbsTimeIntervalFromDynamicData
AbsTimeIntervalFromECAT7ACF.cxx	Declaration of class stir::AbsTimeIntervalFromECAT7ACF
AbsTimeIntervalWithParsing.cxx	Declaration of class stir::AbsTimeIntervalWithParsing
DAVArrayFilter3D.cxx
DAVImageFilter3D.cxx
ModifiedInverseAveragingImageFilterAll.cxx	Implementations for class ModifiedInverseAveragingImageFilterAll
ModifiedInverseAverigingImageFilter.cxx	Implementations for class ModifiedInverseAverigingImageFilter
multiply_plane_scale_factorsImageProcessor.cxx	Implementations for class stir::multiply_plane_scale_factorsImageProcessor
NonseparableSpatiallyVaryingFilters.cxx	Implementations for class NonseparableSpatiallyVaryingFilters
NonseparableSpatiallyVaryingFilters3D.cxx	Implementations for class NonseparableSpatiallyVaryingFilters3D
Quaternion.cxx	Implementation of class Quaternion
► IO
ECAT7DynamicDiscretisedDensityOutputFileFormat.cxx	Implementation of class stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityOutputFileFormat
local_InputFileFormatRegistry.cxx	Instantiations for class stir::InputFileFormatRegistry
local_OutputFileFormat_default.cxx	Initialisation of the stir::OutputFileFormat::_default_sptr member
OutputFileFormat_default.cxx	Initialisation of the stir::OutputFileFormat::_default_sptr member
► iterative
► OSSPS
line_search.cxx	Disabled implementation of doing a simple line search (from the stir::OSSPSReconstruction class)
► listmode
CListModeDataLMF.cxx	Implementation of class stir::CListModeDataLMF
LmToProjDataWithMC.cxx	Implementation of class LmToProjDataWithMC
► listmode_utilities
change_lm_time_tags.cxx	Program to change time-tags of listmode data
get_singles_info.cxx	Utility program that lists the singles per bucket in a frame to a text file
lm_to_projdata_with_MC.cxx	Main for LmToProjDataWithMC
► motion
local_motion_registries.cxx	Registration of parsing objects related to motion
MatchTrackerAndScanner.cxx	Implementation of class stir::MatchTrackerAndScanner
NonRigidObjectTransformationUsingBSplines.cxx	Implementation of class stir::NonRigidObjectTransformationUsingBSplines
PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion.cxx	Declaration of class stir::PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion
Polaris_MT_File.cxx	Implementation of class stir::Polaris_MT_File
RigidObject3DMotion.cxx	Declaration of class stir::RigidObject3DMotion
RigidObject3DMotionFromPolaris.cxx	Implementation of class stir::RigidObject3DMotionFromPolaris
RigidObject3DTransformation.cxx	Implementation of class RigidObject3DTransformation
TimeFrameMotion.cxx	Stir::TimeFrameMotion
Transform3DObjectImageProcessor.cxx	Implementation of class stir::Transform3DObjectImageProcessor
transform_3d_object.cxx	Functions to re-interpolate an image or projection data to a new coordinate system
► motion_test
test_BSpline_transformations.cxx	Test program for non-rigid B-spline transformations with stir::NonRigidObjectTransformationUsingBSplines
► motion_utilities
find_motion_corrected_norm_factors.cxx	Utility to compute norm factors for motion corrected projection data
list_deformation_vectors.cxx	Utility to move an image according to average motion in the frame
list_polaris_info.cxx	Utility to list information from a Polaris file
match_tracker_and_scanner.cxx	A utility for finding the coordinate transformation between tracker and scanner coordinate systems
move_image.cxx	Utility to move an image according to average motion in the frame
move_projdata.cxx	Utility to move projection data according to average motion in the frame
non_rigid_transform.cxx	Non-rigid transformation with b-splines
remove_corrupted_sinograms.cxx	A utility that removes corrupted sinograms in the LMC method
report_movement.cxx	Utility to report RMSE w.r.t. reference position and within the frames
rigid_object_transform_image.cxx	A utility to re-interpolate an image to a new coordinate system
rigid_object_transform_projdata.cxx	A utility to perform a rigid object transformation on projection data
sync_polaris.cxx	Utility to synchronise Polaris data with a list mode file
► recon_buildblock
BinNormalisationFromML2D.cxx	Implementation for class stir::BinNormalisationFromML2D
BinNormalisationSinogramRescaling.cxx	Implementation for class BinNormalisationSinogramRescaling
BinNormalisationUsingProfile.cxx	Implementations for class BinNormalisationUsingProfile
DataSymmetriesForDensels_PET_CartesianGrid.cxx	Non-inline implementations for class stir::DataSymmetriesForDensels_PET_CartesianGrid
local_recon_buildblock_registries.cxx	File that registers all RegisterObject children in recon_buildblock
ParametricQuadraticPrior.cxx	Implementation of the stir::ParametricQuadraticPrior class
PoissonLogLikelihoodWithLinearModelForMeanAndDynamicProjData.cxx	Implementation of class stir::PoissonLogLikelihoodWithLinearModelForMeanAndDynamicProjData
PostsmoothingForwardProjectorByBin.cxx	Implementation of class PostsmoothingForwardProjectorByBin
ProjMatrixByBinSinglePhoton.cxx	Non-inline implementations for ProjMatrixByBinSinglePhoton
ProjMatrixByBinUsingSolidAngle.cxx	Non-inline implementations for stir::ProjMatrixByBinUsingSolidAngle
ProjMatrixByBinWithPositronRange.cxx	Non-inline implementations for stir::ProjMatrixByBinWithPositronRange
ProjMatrixByDensel.cxx	Implementation of the stir::ProjMatrixByDensel class
ProjMatrixByDenselOnCartesianGridUsingElement.cxx	Non-inline implementations for ProjMatrixByDenselOnCartesianGridUsingElement
ProjMatrixByDenselUsingRayTracing.cxx	Non-inline implementations for ProjMatrixByDenselUsingRayTracing
► recon_test
fwdtestDensel.cxx	Testing program for forward projection
test_ProjMatrixByBinUsingInterpolation.cxx	Test program for ProjMatrixByBinUsingInterpolation
► test
test_Fourier.cxx	Tests for function in the DFT group
test_LmToProjdataWithMC.cxx	Test program for LmToProjdataWithMC functions
test_proj_data_info_LOR.cxx	Test program to check consistency between projectors and LOR->detectors functions
test_Quaternion.cxx	Test program for class Quaternion
test_RigidObject3DTransformation.cxx	Test program for stir::RigidObject3DTransformation functions
► utilities
add_ecat7_header_to_sgl.cxx	Prepend contents of ECAT7 header to a new sgl file (from list mode acquisition)
add_side_shields.cxx	A preliminary utility to add side shields to an attenuation image
add_time_frame_info.cxx	Add the Time Frame Information to Dynamic Images
apply_plane_rescale_factors.cxx	This program rescales planes of an image according to a file with scale factors
Bland_Altman_plot.cxx	Writes the Bland-Altman values for two images in a text file
change_mhead_file_type.cxx	A small utility that changes the file type in an ECAT7 main header
CoG.cxx	This program computes the centre of gravity in each plane and writes its coordinates to file, together with a weight for each plane
compute_gradient.cxx
compute_plane_rescale_factors.cxx	This programme finds plane rescaling factors
create_normfactors.cxx	Create sample normalisation factors for the ML approach to normalisation
create_normfactors3D.cxx	Create sample normalisation factors for the ML approach to normalisation
fillwith1.cxx	A utility that just fills the projection data with 1
fillwithotherprojdata.cxx	A utility that just fills the projection data with input from somewhere else. Only useful when the first file is an a different file format (i.e. ECAT 7)
find_sinogram_rescaling_factors.cxx	Find sinogram rescaling factors
fit_cylinder.cxx
image_flip_x.cxx	A preliminary utility to flip the x-axis of an image
interpolate_blocks.cxx	A utility to set data corresponding to a certain detector block by interpolating from neighbouring data
interpolate_projdata.cxx	Interpolate projdata using BSplines
inverse_proj_data.cxx	Find the inverse of ProjData
inverse_SSRB.cxx	Create 4D projdata from 3D using stir::inverse_SSRB
line_profiles_through_projdata.cxx	Extracting profiles from projection data
list_TAC_ROI_values.cxx	Utility program for getting TAC for ROI values
make_grid_image.cxx	This program creates a simple grid image
normalizedbckproj.cxx	This programm was based on bck_project originnal code with the difference that here we normalize the final value of a single pixel with a sum of all values in the corresponding LOR
prepare_projdata.cxx	A utility preparing some projection data for further processing with iterative reconstructions. See stir::PrepareProjData
remove_sinograms.cxx	A utility to remove (or add) some sinograms at the end of each segment
set_blocks_to_value.cxx	A utility to set data corresponding to a certain detector block to a desired value
shift_projdata_along_axis.cxx	A utility to shift projection data along the axial direction
show_ecat7_header.cxx	Show contents of ECAT7 header
threshold_norm_data.cxx	Threshold normalisation data
zero_projdata_from_norm.cxx	Zero projection data when corresponding normalisation factors are too high
► include
► stir
► analytic
► DDSR2D
DDSR2DReconstruction.h	Declares the stir::DDSR2DReconstruction class
► FBP2D
FBP2DReconstruction.h	Declares the stir::FBP2DReconstruction class
RampFilter.h	Definition of class RampFilter, used for (2D) FBP
► FBP3DRP
ColsherFilter.h	Colsher filter class
FBP3DRPReconstruction.h	Declaration of class stir::FBP3DRPReconstruction
► GRD2D
GRD2DReconstruction.h	Declares the stir::GRD2DReconstruction class
► SRT2D
SRT2DReconstruction.h	Declares the stir::SRT2DReconstruction class
► SRT2DSPECT
SRT2DSPECTReconstruction.h	Declares the stir::SRT2DSPECTReconstruction class
► config
gcc.h	Configuration for gcc
visualc.h	Configuration for Visual C++
► data
randoms_from_singles.h	Declare stir:randoms_from_singles
SinglesRates.h	Declaration of class stir::SinglesRates
SinglesRates.inl	Implementation of class stir::SinglesRates
SinglesRatesForTimeFrames.h	Declaration of class stir::SinglesRatesForTimeFrames
SinglesRatesForTimeSlices.h	Declaration of class stir::SinglesRatesForTimeSlices
SinglesRatesFromECAT7.h	Declaration of class stir::ecat::ecat7::SinglesRatesFromECAT7
SinglesRatesFromGEHDF5.h	Declaration of class stir::GE::RDF_HDF5::SinglesRatesFromGEHDF5
SinglesRatesFromSglFile.h	Declaration of class stir::SinglesRatesFromSglFile
► detail
test_if_1d.h	Classes for use in implementation of stir::Array, stir::BasicCoordinate etc to test if it's a 1D array
► evaluation
compute_ROI_values.h	Declaration of various function that computes ROI values
ROIValues.h	Definition of class stir::ROIValues
► geometry
line_distances.h	A few functions to compute distances between lines etc
► IO
► test
test_IO.h	A simple program to test the stir::OutputFileFormat function
ecat6_types.h	ECAT 6 CTI matrix parameters
ecat6_utils.h	Declaration of ECAT 6 CTI functions to access data
ECAT6ImageInputFileFormat.h	Declaration of class stir::ecat::ecat6::ECAT6ImageInputFileFormat
ECAT6OutputFileFormat.h	Declaration of class stir::ecat::ecat7::ECAT6OutputFileFormat
ECAT7DynamicDiscretisedDensityInputFileFormat.h	Declaration of class stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityInputFileFormat
ECAT7DynamicDiscretisedDensityOutputFileFormat.h	Declaration of class stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityOutputFileFormat
ECAT7ImageInputFileFormat.h	Declaration of class stir::ecat::ecat7::ECAT7ImageInputFileFormat
ECAT7OutputFileFormat.h	Declaration of class stir::ecat::ecat7::ECAT7OutputFileFormat
ECAT7ParametricDensityOutputFileFormat.h	Declaration of class stir::ecat::ecat7::ECAT7ParametricDensityOutputFileFormat
ECAT8_32bitListmodeInputFileFormat.h	Declaration of class stir::ecat::ECAT8_32bitListmodeInputFileFormat
ECAT962ListmodeInputFileFormat.h	Declaration of class stir::ecat::ecat7::ECAT962ListmodeInputFileFormat
ECAT966ListmodeInputFileFormat.h	Declaration of class stir::ecat::ecat7::ECAT966ListmodeInputFileFormat
FileSignature.h	Declaration of class stir::FileSignature
GEHDF5ListmodeInputFileFormat.h	Declaration of class stir::GE::RDF_HDF5::IO::GEHDF5ListmodeInputFileFormat
GEHDF5Wrapper.h	Declaration of class stir::GE::RDF_HDF5::GEHDF5Wrapper
GEHDF5Wrapper.inl	Declaration of class stir::GE::RDF_HDF5::GEHDF5Wrapper
GIPL_ImageFormat.h	Applies the dilation filter (i.e. voxel=max(neighbours))
InputFileFormat.h	Declaration of class stir::InputFileFormat
InputFileFormatRegistry.h	Declaration of class stir::InputFileFormatRegistry, stir::RegisterInputFileFormat
InputFileFormatRegistry.txx
InputStreamFromROOTFile.h	Declaration of class stir::InputStreamFromROOTFile
InputStreamFromROOTFile.inl	Implementation of class stir::InputStreamFromROOTFile
InputStreamFromROOTFileForCylindricalPET.h	Declaration of class stir::InputStreamFromROOTFileForCylindricalPET
InputStreamFromROOTFileForCylindricalPET.inl	Implementation of class stir::InputStreamFromROOTFileForCylindricalPET
InputStreamFromROOTFileForECATPET.h	Declaration of class stir::InputStreamFromROOTFileForECATPET
InputStreamFromROOTFileForECATPET.inl
InputStreamWithRecords.h	Declaration of class stir::InputStreamWithRecords
InputStreamWithRecords.inl	Implementation of class stir::InputStreamWithRecords
InputStreamWithRecordsFromHDF5.h	Declaration of class stir::GE::RDF_HDF5::InputStreamWithRecordsFromHDF5
InputStreamWithRecordsFromHDF5.inl	Implementation of class stir::GE::RDF_HDF5::InputStreamWithRecordsFromHDF5
InputStreamWithRecordsFromUPENN.h	Declaration of class stir::InputStreamWithRecordsFromUPENN
InputStreamWithRecordsFromUPENN.inl
InputStreamWithRecordsFromUPENNbin.h	Declaration of class stir::InputStreamWithRecordsFromUPENNbin
InputStreamWithRecordsFromUPENNbin.inl	Implementation of class stir::InputStreamWithRecordsFromUPENNbin
InputStreamWithRecordsFromUPENNtxt.h	Declaration of class stir::InputStreamWithRecordsFromUPENNtxt
InputStreamWithRecordsFromUPENNtxt.inl	Implementation of class stir::InputStreamWithRecordsFromUPENNtxt
interfile.h	Declarations of functions which read/write Interfile data
InterfileDynamicDiscretisedDensityInputFileFormat.h	Declaration of class stir::InterfileDynamicDiscretisedDensityInputFileFormat
InterfileDynamicDiscretisedDensityOutputFileFormat.h	Declaration of class stir::InterfileDynamicDiscretisedDensityOutputFileFormat
InterfileHeader.h	This file declares the classes stir::InterfileHeader, stir::InterfileImageHeader, stir::InterfilePDFSHeader
InterfileHeaderSiemens.h	This file declares the classes stir::InterfileHeaderSiemens, stir::InterfileRawDataHeaderSiemens, stir::InterfilePDFSHeaderSiemens, stir::InterfileListmodeHeaderSiemens, stir:InterfileNormHeaderSiemens
InterfileImageInputFileFormat.h	Declaration of class stir::InterfileImageInputFileFormat
InterfileOutputFileFormat.h	Declaration of class stir::InterfileOutputFileFormat
InterfileParametricDiscretisedDensityInputFileFormat.h	Declaration of class stir::InterfileParametricDiscretisedDensityInputFileFormat
InterfileParametricDiscretisedDensityOutputFileFormat.h	Declaration of class stir::InterfileParametricDiscretisedDensityOutputFileFormat
InterfilePDFSHeaderSPECT.h	This file declares the class stir::InterfilePDFSHeaderSPECT
ITKImageInputFileFormat.h	Declaration of class stir::ITKInputFileFormat
ITKOutputFileFormat.h	Declaration of class stir::ITKOutputFileFormat
MultiDynamicDiscretisedDensityInputFileFormat.h	Declaration of class stir::MultiDynamicDiscretisedDensityInputFileFormat
MultiDynamicDiscretisedDensityOutputFileFormat.h	Declaration of class stir::MultiDynamicDiscretisedDensityOutputFileFormat
MultiParametricDiscretisedDensityInputFileFormat.h	Declaration of class stir::MultiParametricDiscretisedDensityInputFileFormat
MultiParametricDiscretisedDensityOutputFileFormat.h	Declaration of class stir::MultiParametricDiscretisedDensityOutputFileFormat
OutputFileFormat.h	Declaration of class stir::OutputFileFormat
OutputFileFormat.txx
PENNListmodeInputFileFormat.h
read_data.h	Declarations of stir::read_data() functions for reading Arrays from file
read_data.inl	Implementation of stir::read_data() functions for reading stir::Array's from file
read_data_1d.h	Declaration of stir::read_data_1d() functions for reading 1D stir::Array objects from file
read_data_1d.inl	Implementation of stir::read_data_1d() functions
read_from_file.h	Declaration of stir::read_from_file functions (providing easy access to class stir::InputFileFormatRegistry)
ROOTListmodeInputFileFormat.h
SAFIRCListmodeInputFileFormat.h	Declaration of class stir::SAFIRCListmodeInputFileFormat
stir_ecat6.h	Declaration of routines which convert ECAT6 things into our building blocks and vice versa
stir_ecat7.h	Declaration of routines which convert CTI things into our building blocks and vice versa
stir_ecat_common.h	Declaration of routines which convert ECAT things into our building blocks and vice versa
write_data.h	Declarations of stir::write_data() functions for writing Arrays to file
write_data.inl	Implementation of stir::write_data() functions for writing stir::Array's to file
write_data_1d.h	Declaration of stir::write_data_1d() functions for writing 1D stir::Array objects to file
write_data_1d.inl	Implementation of stir::write_data_1d() functions
write_to_file.h	Declaration of stir::write_to_file function (providing easy access to the default stir::OutputFileFormat)
► KOSMAPOSL
KOSMAPOSLReconstruction.h	Declaration of class stir::KOSMAPOSLReconstruction
► listmode
► NiftyPET_listmode
LmToProjDataNiftyPET.h	Wrapper to NiftyPET's listmode to projection data converter
CListEventCylindricalScannerWithDiscreteDetectors.h	Declarations of class stir::CListEventCylindricalScannerWithDiscreteDetectors
CListEventCylindricalScannerWithViewTangRingRingEncoding.h	Definition of class stir::CListEventCylindricalScannerWithViewTangRingRingEncoding
CListEventCylindricalScannerWithViewTangRingRingEncoding.inl	Implementation for stir::CListEventCylindricalScannerWithViewTangRingRingEncoding
CListEventScannerWithDiscreteDetectors.h	Declarations of class stir::CListEventScannerWithDiscreteDetectors
CListEventScannerWithDiscreteDetectors.inl	Implementations of class stir::CListEventScannerWithDiscreteDetectors
CListModeData.h	Declaration of class stir::CListModeData
CListModeDataECAT.h	Declaration of class stir::CListModeDataECAT
CListModeDataECAT8_32bit.h	Declaration of class stir::ecat::CListModeDataECAT8_32bit
CListModeDataGEHDF5.h	Declaration of class stir::GE::RDF_HDF5::CListModeDataGEHDF5
CListModeDataPENN.h	Declaration of class stir::CListModeDataPENN
CListModeDataROOT.h	Declaration of class stir::CListModeDataROOT
CListModeDataSAFIR.h	Declaration of class stir::CListModeDataSAFIR
CListRecord.h	Declarations of classes stir::CListRecord, and stir::CListEvent which are used for list mode data
CListRecordECAT8_32bit.h	Classes for listmode events for the ECAT 8 format
CListRecordECAT962.h	Classes for listmode events for the ECAT 962 (aka Exact HR+)
CListRecordECAT966.h	Classes for listmode events for the ECAT 966 (aka Exact 3d)
CListRecordGEHDF5.h	Classes for listmode records of GE RDF9 data
CListRecordPENN.h	Classes for listmode events for the PENNPET Explorer scanner
CListRecordROOT.h	Classes for listmode events for GATE simulated ROOT data
CListRecordROOT.inl	Implementation of class stir::InputStreamFromROOTFile
CListRecordSAFIR.h	Declaration of class stir::CListEventSAFIR and stir::CListRecordSAFIR with supporting classes
CListRecordSAFIR.inl	Inline implementation of class stir::CListEventSAFIR and stir::CListRecordSAFIR with supporting classes
ListEvent.h	Declarations of classe stir::ListEvent which is used for list mode data
ListGatingInput.h	Declarations of class stir::ListGatingInput, which is used for list mode data
ListModeData.h	Declaration of class stir::ListModeData
ListModeData_dummy.h	Declaration of class stir::ListModeData_dummy
ListRecord.h	Declarations of classes stir::ListRecord which is used for list mode data
ListRecordWithGatingInput.h	Declarations of classes stir::ListRecordWithGatingInput which is used for list mode data
ListTime.h	Declarations of class stir::ListTime which is used for list mode data
LmToProjData.h	Declaration of the stir::LmToProjData class which is used to bin listmode data to (3d) sinograms
LmToProjDataAbstract.h	Abstract base class for listmode to projection data conversion
LmToProjDataBootstrap.h	Class for binning list mode files with the bootstrap method
LmToProjDataWithRandomRejection.h	Class for binning list mode files with the bootstrap method
SPECTListEvent.h	Declarations of classe stir::SPECTListEvent which is used for list mode data
SPECTListModeData.h	Declaration of class stir::GSPECTListModeData
SPECTListRecord.h	Declarations of classes stir::SPECTListRecord which is used for list mode data
SPECTListRecordWithGatingInput.h	Declarations of classes stir::SPECTListRecordWithGatingInput which is used for list mode data
► modelling
KineticModel.h	Definition of class stir::KineticModel
KineticParameters.h	Declaration of class stir::KineticParameters
ModelMatrix.h	Declaration of class stir::ModelMatrix<num_param>
ModelMatrix.inl
ParametricDiscretisedDensity.h	Declaration of class stir::ParametricDiscretisedDensity
ParseAndCreateParametricDiscretisedDensityFrom.h	Definition of the stir::ParseAndCreateFrom class for stir::ParametricDiscretisedDensity
ParseAndCreateParametricDiscretisedDensityFrom.inl	Implementation of the stir::ParseAndCreateFrom class for stir:ParametricDiscretisedDensity
PatlakPlot.h	Implementation of functions of class stir::PatlakPlot
PlasmaData.h	Declaration of class stir::PlasmaData
PlasmaData.inl	Implementations of inline functions of class stir::PlasmaData
PlasmaSample.h	Declaration of class stir::PlasmaData
PlasmaSample.inl	Implementations of inline functions of class stir::PlasmaData
► numerics
BSplines.h	Implementation of the basic components and declarations for B-Splines Interpolation
BSplines1DRegularGrid.h	Implementation of the B-Splines Interpolation
BSplines1DRegularGrid.inl	Implementation of the B-Splines Interpolation
BSplines_coef.inl	Implementation of the (cubic) B-Splines Interpolation
BSplines_weights.inl	Implementation of the B-Splines Interpolation
BSplinesDetail.inl	Implementation of the B-Splines Interpolation
BSplinesRegularGrid.h	Implementation of the n-dimensional B-Splines Interpolation
BSplinesRegularGrid.inl	Implementation of the B-Splines Interpolation
determinant.h	Declaration of stir::determinant() function for matrices
divide.h	Implementation of stir::divide
divide.inl	Implementation of stir::divide
erf.h
erf.inl
FastErf.h	Implementation of an erf interpolation
FastErf.inl	Implementation of an erf interpolation
fftshift.h	Functions to rearrange Fourier data so that DC (zero frequency) is centered
fourier.h	Functions for computing FFTs
ieeefp.h	Definition of work-around macros STIR_isnan and STIR_finite for a few non-portable IEEE floating point functions
integrate_discrete_function.h	Declaration of stir::integrate_discrete_function function
integrate_discrete_function.inl
IR_filters.h	Implementation of the IIR and FIR filters
IR_filters.inl	Implements the IR_filters
MatrixFunction.h	Declaration of functions for matrices
MatrixFunction.inl	Implementation of functions for matrices
max_eigenvector.h	Declaration of functions for computing eigenvectors
norm.h	Declaration of the stir::norm(), stir::norm_squared() functions and stir::NormSquared unary function
norm.inl	Implementation of the stir::norm(), stir::norm_squared() functions and stir::NormSquared unary function
overlap_interpolate.h	Declaration of stir::overlap_interpolate
overlap_interpolate.inl	Implementation of inline versions of stir::overlap_interpolate
sampling_functions.h	Sampling functions (currently only stir::sample_function_on_regular_grid)
sampling_functions.inl
stir_NumericalRecipes.h	Functions to convert from data in Numerical Recipes format to STIR arrays
► OSMAPOSL
OSMAPOSLReconstruction.h	Declaration of class stir::OSMAPOSLReconstruction
► OSSPS
OSSPSReconstruction.h	Declaration of class stir::OSSPSReconstruction
► recon_buildblock
► CUDA
CudaGibbsPenalty.h	Declaration of the stir::CudaGibbsPenalty class
CudaRelativeDifferencePrior.h	Implementation of the stir::CudaRelativeDifferencePrior class
► NiftyPET_projector
BackProjectorByBinNiftyPET.h	Back projection class using NiftyPET's GPU implementation
ForwardProjectorByBinNiftyPET.h	Forward projection class using NiftyPET's GPU implementation
NiftyPETHelper.h	Helper class for NiftyPET's GPU implementation
ProjectorByBinPairUsingNiftyPET.h	Declares class stir::ProjectorByBinPairUsingNiftyPET
► Parallelproj_projector
BackProjectorByBinParallelproj.h	Back projection class using Parallelproj's implementation
ForwardProjectorByBinParallelproj.h	Forward projection class using Parallelproj's GPU implementation
ParallelprojHelper.h	Defines stir::detail::ParallelprojHelper
ProjectorByBinPairUsingParallelproj.h	Declares class stir::ProjectorByBinPairUsingParallelproj
► test
ObjectiveFunctionTests.h	Test skeleton for stir::GeneralisedObjectiveFunction and stir::GeneralisedPrior
PoissonLLReconstructionTests.h	Test class for iterative reconstructions using stir::PoissonLogLikelihoodWithLinearModelForMeanAndProjData
ReconstructionTests.h	Test class for reconstructions
AnalyticReconstruction.h	Declares the stir::AnalyticReconstruction class
BackProjectorByBin.h	Declares class stir::BackProjectorByBin
BackProjectorByBinUsingInterpolation.h	Declares class stir::BackProjectorByBinUsingInterpolation
BackProjectorByBinUsingProjMatrixByBin.h	Declaration of class stir::BackprojectorByBinUsingProjMatrixByBin
BackProjectorByBinUsingSquareProjMatrixByBin.h
BinNormalisation.h	Declaration of class stir::BinNormalisation
BinNormalisationFromAttenuationImage.h	Declaration of class stir::BinNormalisationFromAttenuationImage
BinNormalisationFromECAT7.h	Declaration of class stir::ecat::ecat7::BinNormalisationFromECAT7
BinNormalisationFromECAT8.h	Declaration of class stir::ecat::BinNormalisationFromECAT8
BinNormalisationFromGEHDF5.h	Declaration of class stir::GE_RDF_HDF5::BinNormalisationFromGEHDF5
BinNormalisationFromProjData.h	Declaration of class stir::BinNormalisationFromProjData
BinNormalisationPETFromComponents.h	Declaration of class stir::BinNormalisationPETFromComponents
BinNormalisationSPECT.h	Declaration of class BinNormalisationSPECT
BinNormalisationWithCalibration.h	Declaration of class stir::BinNormalisationWithCalibration
ChainedBinNormalisation.h	Declaration of class stir::ChainedBinNormalisation
DataSymmetriesForBins.h	Declaration of class stir::DataSymmetriesForBins
DataSymmetriesForBins.inl	Inline implementations for class stir::DataSymmetriesForBins
DataSymmetriesForBins_PET_CartesianGrid.h	Declaration of class stir::DataSymmetriesForBins_PET_CartesianGrid
DataSymmetriesForBins_PET_CartesianGrid.inl	Inline implementations for class stir::DataSymmetriesForBins_PET_CartesianGrid
DataSymmetriesForDensels.h	Declaration of class stir::DataSymmetriesForDensels
DataSymmetriesForDensels.inl	Inline implementations for class stir::DataSymmetriesForDensels
distributable.h	Declaration of the main functions that perform parallel processing
distributable.txx
distributable_main.h	Declaration of the stir::distributable_main function
distributableMPICacheEnabled.h	Declaration of the main function that performs parallel processing
distributed_functions.h	Declaration of functions in the distributed namespace
distributed_test_functions.h	Declaration of test functions for the distributed namespace
DistributedCachingInformation.h
DistributedWorker.h	Declares the stir::DistributedWorker class
FilterRootPrior.h	Declaration of class stir::FilterRootPriot
find_basic_vs_nums_in_subsets.h	Implementation for stir::detail::find_basic_vs_nums_in_subset
ForwardProjectorByBin.h	Base class for forward projectors which work on 'large' collections of bins: given the whole image, fill in a stir::RelatedViewgrams<float> object
ForwardProjectorByBinUsingProjMatrixByBin.h	Definition of stir::ForwardProjectorByBinUsingProjMatrixByBin
ForwardProjectorByBinUsingRayTracing.h	Declaration of class stir::ForwardProjectorByBinUsingRayTracing
FourierRebinning.h	Class for FORE Reconstruction
GeneralisedObjectiveFunction.h	Declaration of class stir::GeneralisedObjectiveFunction
GeneralisedPrior.h	Declaration of class stir::GeneralisedPrior
GeneralisedPrior.inl	Inline implementations for class stir::GeneralisedPrior
GibbsPenalty.h	Declaration of the stir::GibbsPenalty class
GibbsPenalty.inl	Implementation of the stir::GibbsPenalty class
GibbsQuadraticPenalty.h	Declaration of class stir::GibbsQuadraticPenalty, stir::CudaGibbsQuadraticPenalty and the potential function stir::QuadraticPotential
GibbsRelativeDifferencePenalty.h	Declaration of class stir::CudaRelativeDifferencePenalty, stir::CudaGibbsRelativeDifferencePenalty and the potential function stir::RelativeDifferencePotential
IterativeReconstruction.h	Declares the stir::IterativeReconstruction class
LogcoshPrior.h	Declaration of class stir::LogcoshPrior
ML_estimate_component_based_normalisation.h	Declaration of stir::ML_estimate_component_based_normalisation
PinholeSPECTUB_Tools.h
PinholeSPECTUB_Weight3d.h
PLSPrior.h	Declaration of class stir::PLSPrior
PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData.h	Declaration of class stir::PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData
PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData.txx
PoissonLogLikelihoodWithLinearModelForMean.h	Declaration of class stir::PoissonLogLikelihoodWithLinearModelForMean
PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion.h	Declaration of class stir::PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion
PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion.txx
PoissonLogLikelihoodWithLinearModelForMeanAndListModeData.h	Declaration of class stir::PoissonLogLikelihoodWithLinearModelForMeanAndListModeData
PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin.h	Declaration of class stir::PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin
PoissonLogLikelihoodWithLinearModelForMeanAndProjData.h	Declaration of class stir::PoissonLogLikelihoodWithLinearModelForMeanAndProjData
PostsmoothingBackProjectorByBin.h	Declaration of class stir::PostsmoothingBackProjectorByBin
PresmoothingForwardProjectorByBin.h	Declaration of class stir::PresmoothingForwardProjectorByBin
PriorWithParabolicSurrogate.h	Declaration of class stir::PriorWithParabolicSurrogate
ProjDataRebinning.h	Declares the stir::ProjDataRebinning class
ProjectorByBinPair.h	Declares class stir::ProjectorByBinPair
ProjectorByBinPairUsingProjMatrixByBin.h	Declares class stir::ProjectorByBinPairUsingProjMatrixByBin
ProjectorByBinPairUsingSeparateProjectors.h	Declares class stir::ProjectorByBinPairUsingSeparateProjectors
ProjMatrixByBin.h	Declaration of stir::ProjMatrixByBin and its helpers classes
ProjMatrixByBin.inl	Implementations of inline functions for class stir::ProjMatrixByBin
ProjMatrixByBinFromFile.h	Stir::ProjMatrixByBinFromFile's definition
ProjMatrixByBinPinholeSPECTUB.h	Stir::ProjMatrixByBinPinholeSPECTUB's definition
ProjMatrixByBinSPECTUB.h	Stir::ProjMatrixByBinSPECTUB's definition
ProjMatrixByBinUsingInterpolation.h	Stir::ProjMatrixByBinUsingInterpolation's definition
ProjMatrixByBinUsingRayTracing.h	Stir::ProjMatrixByBinUsingRayTracing's definition
ProjMatrixElemsForOneBin.h	Declaration of class stir::ProjMatrixElemsForOneBin
ProjMatrixElemsForOneBin.inl	Inline implementations for class stir::ProjMatrixelemesForOneBin
ProjMatrixElemsForOneBinValue.h	Declaration of class stir::ProjMatrixElemsForOneBinValue
ProjMatrixElemsForOneBinValue.inl	Inline implementations for class stir::ProjMatrixElemsForOneBinValue
ProjMatrixElemsForOneDensel.h	Declaration of class stir::ProjMatrixElemsForOneDensel
ProjMatrixElemsForOneDensel.inl	Inline implementations for class stir::ProjMatrixElemsForOneDensel
ProjMatrixElemsForOneDenselValue.h	Declaration of class stir::ProjMatrixElemsForOneDenselValue
ProjMatrixElemsForOneDenselValue.inl	Inline implementations for class stir::ProjMatrixElemsForOneDenselValue
QuadraticPrior.h	Declaration of class stir::QuadraticPrior
RayTraceVoxelsOnCartesianGrid.h	Declaration of stir::RayTraceVoxelsOnCartesianGrid
Reconstruction.h	Declares the stir::Reconstruction class
RelatedBins.h	Declaration of class stir::RelatedBins
RelatedBins.inl	Implementations of inline functions of class stir::RelatedBins
RelatedDensels.h	Declaration of class stir::RelatedDensels
RelatedDensels.inl	Implementations of inline functions of class stir::RelatedDensels
RelativeDifferencePrior.h	Declaration of class stir::RelativeDifferencePrior
SPECTUB_Tools.h
SPECTUB_Weight3d.h
SqrtHessianRowSum.h	Declaration of class stir::SqrtHessianRowSum
SumOfGeneralisedObjectiveFunctions.h	Declaration of class stir::SumOfGeneralisedObjectiveFunctions
SumOfGeneralisedObjectiveFunctions.inl	Implementation of class stir::SumOfGeneralisedObjectiveFunctions
SymmetryOperation.h	Declaration of 2 classes: stir::SymmetryOperation and stir::TrivialSymmetryOperation
SymmetryOperations_PET_CartesianGrid.h	Declaration of all symmetry classes for PET (cylindrical) scanners and cartesian images
SymmetryOperations_PET_CartesianGrid.inl	Implementation of all symmetry classes for PET scanners and cartesian images
TrivialBinNormalisation.h	Declaration of class stir::TrivialBinNormalisation
TrivialDataSymmetriesForBins.h	Declaration of class stir::TrivialDataSymmetriesForBins
► scatter
CreateTailMaskFromACFs.h	Compute a mask for the "tails" in the sinogram
ScatterEstimation.h	Definition of class stir::ScatterEstimation
ScatterEstimation.inl
ScatterSimulation.h	Definition of class stir::ScatterSimulation
ScatterSimulation.inl	Inline functions of stir::ScatterSimulation (cross sections)
SingleScatterSimulation.h	Definition of class stir::SingleScatterSimulation
► Shape
Box3D.h	Declaration of class stir::Box3D
CombinedShape3D.h	Declaration of class stir::CombinedShape3D
CombinedShape3D.inl	Inline implementations of class stir::CombinedShape3D
DiscretisedShape3D.h	Declaration of class stir::DiscretisedShape3D
DiscretisedShape3D.inl	Inline-implementations of class stir::DiscretisedShape3D
Ellipsoid.h	Declaration of class stir::Ellipsoid
EllipsoidalCylinder.h	Declaration of class stir::EllipsoidalCylinder
EllipsoidalCylinder.inl	Inline-implementations of class stir::EllipsoidalCylinder
GenerateImage.h	Declaration of class stir::GenerateImage
Shape3D.h	Declaration of class stir::Shape3D
Shape3D.inl	Inline-implementations of class stir::Shape3D
Shape3DWithOrientation.h	Declaration of class stir::Shape3DWithOrientation
► spatial_transformation
GatedSpatialTransformation.h	Declaration of class stir::GatedSpatialTransformation
InvertAxis.h	This invert the selected image axis
SpatialTransformation.h	Definition of class stir::SpatialTransformation
warp_image.h	This warps an image
ArcCorrection.h	Declaration of class stir::ArcCorrection
Array.h	Defines the stir::Array class for multi-dimensional (numeric) arrays
Array.inl	Inline implementations for the stir::Array class
Array_complex_numbers.h	Defines additional numerical operations for arrays of complex numbers
array_index_functions.h	Variety of useful functions for indexing stir::Array objects
array_index_functions.inl	Implementation of functions in stir/array_index_functions.h
ArrayFilter1DUsingConvolution.h	Declaration of class stir::ArrayFilter1DUsingConvolution
ArrayFilter1DUsingConvolutionSymmetricKernel.h	Declaration of class stir::ArrayFilter1DUsingConvolutionSymmetricKernel
ArrayFilter2DUsingConvolution.h	Declaration of class ArrayFilter2DUsingConvolution
ArrayFilter3DUsingConvolution.h	Declaration of class ArrayFilter3DUsingConvolution
ArrayFilterUsingRealDFTWithPadding.h	Declaration of class stir::ArrayFilterUsingRealDFTWithPadding
ArrayFunction.h	This include file provides some additional functionality for stir::Array objects
ArrayFunction.inl	Implementations for ArrayFunction.h
ArrayFunctionObject.h	Declaration of class stir::ArrayFunctionObject
ArrayFunctionObject_1ArgumentImplementation.h	Declaration of class stir::ArrayFunctionObject_1ArgumentImplementation
ArrayFunctionObject_2ArgumentImplementation.h	Declaration of class stir::ArrayFunctionObject_2ArgumentImplementation
ArrayFwd.h	Forward declaration of stir::Array class for multi-dimensional (numeric) arrays
assign.h	Defines the stir::assign function to assign values to different data types
assign_to_subregion.h	Declares the stir::assign_to_subregion function
assign_to_subregion.inl	Implementation of the stir::assign_to_subregion function
BasicCoordinate.h	This file declares class stir::BasicCoordinate and some functions acting on stir::BasicCoordinate objects
BasicCoordinate.inl	(inline) implementations for stir::BasicCoordinate
Bin.h	Declaration of class stir::Bin
Bin.inl	Implementations of inline functions of class stir::Bin
BoundaryConditions.h	Declaration of class stir::BoundaryConditions
ByteOrder.h	This file declares the stir::ByteOrder class
ByteOrder.inl	This file declares the stir::ByteOrder class
ByteOrderDefine.h	Definition of STIRIsNativeByteOrderBigEndian and STIRIsNativeByteOrderLittleEndian preprocessor symbols
CartesianCoordinate2D.h	Defines the stir::CartesianCoordinate2D<coordT> class
CartesianCoordinate2D.inl	Inline implementations for the stir::CartesianCoordinate2D<coordT> class
CartesianCoordinate3D.h	Defines the stir::CartesianCoordinate3D<coordT> class
CartesianCoordinate3D.inl	Inline implementations for the stir::CartesianCoordinate3D<coordT> class
centre_of_gravity.h	This file contains functions to compute the centre of gravity of arrays and images
ChainedDataProcessor.h	Declaration of class stir::ChainedDataProcessor
common.h	Basic configuration include file
convert_array.h	This file declares the stir::convert_array functions. This is a function to convert stir::Array objects to a different numeric type
convert_array.inl	Implementation of stir::convert_array
convert_range.h	This file declares the stir::convert_range and stir::find_scale_factor functions
convert_range.inl	Implementation of stir::convert_range
Coordinate2D.h	Defines the stir::Coordinate2D<coordT> class
Coordinate2D.inl	Inline implementations for the stir::Coordinate2D class
Coordinate3D.h	Defines the stir::Coordinate3D<coordT> class
Coordinate3D.inl	Inline implementations for the stir::Coordinate3D class
Coordinate4D.h	Defines the stir::Coordinate4D<coordT> class
Coordinate4D.inl	Inline implementations for the stir::Coordinate4D class
copy_fill.h	Declaration of stir::copy_to and stir::fill_from templates
CPUTimer.h	Declares the stir::CPUTimer class
CPUTimer.inl	Inline implementations for stir::CPUTimer
cross_product.h	Defines the cross-product of 2 CartesianCoordinate3D numbers
cuda_utilities.h	Some utilities for STIR and CUDA
DataProcessor.h	Declaration of class stir::DataProcessor
DataProcessor.inl	Inline implementations for class stir::DataProcessor
DataSymmetriesForViewSegmentNumbers.h	Declaration of class stir::DataSymmetriesForViewSegmentNumbers
DataWithProjDataInfo.h	Declaration of stir::DataWithProjDataInfo
DataWithProjDataInfo.inl	Inline implementations of stir::DataWithProjDataInfo
date_time_functions.h	Functions for date-time conversions
decay_correction_factor.h	Simple functions to compute the decay correction factor
Densel.h	Declaration of typedef stir::Densel
deprecated.h	This file declares a deprecation macro
DetectionPosition.h	Declaration of class stir::DetectionPosition
DetectionPosition.inl	Implementation of inline methods of class stir::DetectionPosition
DetectionPositionPair.h	Declaration of class stir::DetectionPositionPair
DetectionPositionPair.inl	Implementation of inline methods of class stir::DetectionPositionPair
DetectorCoordinateMap.h	Declaration of class stir::DetectorCoordinateMap
DiscretisedDensity.h	Defines the stir::DiscretisedDensity class
DiscretisedDensity.inl	Inline implementation for stir::DiscretisedDensity
DiscretisedDensityOnCartesianGrid.h	Defines the stir::DiscretisedDensityOnCartesianGrid class
DiscretisedDensityOnCartesianGrid.inl	Inline implementations for stir::DiscretisedDensityOnCartesianGrid
display.h	Functions to display 2D and 3D stir::Array and stir::RelatedViewgrams objects
display.inl	Functions to display 2D and 3D stir::Array objects
doxygen_doc_for_boost.h	Documentation for some boost functions
doxygengroups.h
doxygenmain.h
DynamicDiscretisedDensity.h	Declaration of class stir::DynamicDiscretisedDensity
DynamicDiscretisedDensity.inl	Inline implementations of class stir::DynamicDiscretisedDensity
DynamicProjData.h	Declaration of class stir::DynamicProjData
error.h	Declaration of stir::error()
ExamData.h	Declaration of stir::ExamData
ExamInfo.h	This file declares the class stir::ExamInfo
ExamInfo.inl	This file declares the class stir::ExamInfo
extend_projdata.h
extract_line.h	Declaration of stir::extract_line
extract_line.inl	Implementation of stir::extract_line
FactoryRegistry.h	Declaration of class stir::FactoryRegistry
FactoryRegistry.inl	Inline implementations for stir::FactoryRegistry
FilePath.h	Declaration of class stir::FilePath This is a class implementing basic filesytem functionality. Parts of this class were copied from Functions for filename manipulations
FilePath.inl	Implementations of inline functions for class stir::FilePath
find_fwhm_in_image.h	A collection of functions to measure resolution
find_fwhm_in_image.inl	A collection of functions to measure resolution
find_STIR_config.h	Declaration of functions to get configuration directory etc
format.h	Include for formatting function. Use standard library version if available (C++20 and newer). Otherwise use fmt::format, which is included into STIR as a git submodule
FullArrayIterator.h	This file declares the stir::FullArrayIterator class
FullArrayIterator.inl	Inline implementations for stir::FullArrayIterator
GammaArrayFilter2D.h	Declaration of class stir::GammaArrayFilter2D
GammaImageFilter2D.h	Declaration of class stir::GammaImageFilter2D
GatedDiscretisedDensity.h	Implementation of class stir::GatedDiscretisedDensity
GatedProjData.h	Declaration of class stir::GatedProjData
GeneralisedPoissonNoiseGenerator.h	Declares stir::GeneralisedPoissonNoiseGenerator
GeometryBlocksOnCylindrical.h	Declaration of class stir::GeometryBlocksOnCylindrical
getopt.h
HigherPrecision.h	Class stir::HigherPrecision
HighResWallClockTimer.h	High-resolution wall-clock timer stir::HighResWallClockTimer
HUToMuImageProcessor.h	Declaration of class stir::HUToMuImageProcessor
ImagingModality.h	Declaration of class stir::ImagingModality
index_at_maximum.h	Declaration of stir:index_at_maximum() and stir::indices_at_maximum()
IndexRange.h	This file defines the stir::IndexRange class
IndexRange.inl	Inline definitions for the IndexRange class
IndexRange2D.h	This file declares the class stir::IndexRange2D
IndexRange2D.inl	Inline implementations for stir::IndexRange2D
IndexRange3D.h	This file declares the class stir::IndexRange3D
IndexRange3D.inl	Inline implementations for stir::IndexRange3D
IndexRange4D.h	This file declares the class stir::IndexRange4D
IndexRange4D.inl	Inline implementations for stir::IndexRange4D
info.h	Declaration of stir::info()
interfile_keyword_functions.h	Functions useful for manipulating Interfile keywords
interpolate.h	Declares functions for interpolation
interpolate_projdata.h
inverse_SSRB.h
is_null_ptr.h	Definition of stir::is_null_ptr functions
KeyParser.h	Declaration of class stir::KeyParser
line.h	Declaration of class stir::Line
linear_regression.h	Declaration of stir::linear_regression()
linear_regression.inl	Implementation of inline functions for stir::linear_regression()
LORCoordinates.h	Defines various classes for specifying a line in 3 dimensions
LORCoordinates.inl	Implementations for LORCoordinates.h
make_array.h	Declaration of functions for constructing arrays stir::make_1d_array etc
make_array.inl	Implementation of functions for constructing arrays stir::make_1d_array etc
MaximalArrayFilter3D.h	Applies the dilation filter (i.e. voxel=max(neighbours))
MaximalImageFilter3D.h	Implementations for class stir::MaximalImageFilter3D
MedianArrayFilter3D.h	Declaration of class stir::MedianArrayFilter3D
MedianImageFilter3D.h	Declaration of class stir::MedianImageFilter3D.h
min_positive_element.h	Declares the stir::min_positive_element() function
MinimalArrayFilter3D.h	Applies the erosion filter (i.e. voxel=min(neighbours))
MinimalImageFilter3D.h	Implementations for class MinimalImageFilter3D
ML_norm.h	Preliminary things for ML normalisation factor estimation
modulo.h	Defines stir::modulo() and related functions
more_algorithms.h	Declaration of some functions missing from std::algorithm
more_algorithms.inl	Implementation of some functions missing from std::algorithm
MultipleDataSetHeader.h	Declaration of class stir::MultipleDataSetHeader
MultipleDataSetHeader.inl	Inline implementations of class stir::MultipleDataSetHeader
MultipleProjData.h	Declaration of class stir::MultipleProjData
multiply_crystal_factors.h	Declaration of stir::multiply_crystal_factors
NestedIterator.h	This file declares the stir::NestedIterator class and supporting function objects
NestedIterator.inl	Inline implementations for stir::NestedIterator
NestedIteratorHelpers.h	This file defines supporting function objects for stir::NestedIterator
NonseparableConvolutionUsingRealDFTImageFilter.h	Declaration of class NonseparableConvolutionUsingRealDFTImageFilter
num_threads.h	Implementation of functions related to setting/getting the number of threads
NumericInfo.h	This file declares the class stir::NumericInfo
NumericType.h	This file declares the stir::NumericType class
NumericType.inl	Implementation of inline methods of class stir::NumericType
NumericVectorWithOffset.h	Defines the stir::NumericVectorWithOffset class
NumericVectorWithOffset.inl	Inline implementations for stir::NumericVectorWithOffset
ParseAndCreateFrom.h	Definition of the stir::ParseAndCreateFrom class
ParseAndCreateFrom.inl	Implementation of the stir::ParseAndCreateFrom class for stir:DiscretisedDensity
ParseDiscretisedDensityParameters.h	Definition of the stir::ParseDiscretisedDensityParameters class
ParsingObject.h	Declaration of class stir::ParsingObject
PatientPosition.h	Declaration of class stir::PatientPosition
PixelsOnCartesianGrid.h	Defines the stir::PixelsOnCartesianGrid class
PixelsOnCartesianGrid.inl	Inline implementations for the stir::PixelsOnCartesianGrid class
PostFiltering.h	Declaration the helper class PostFiltering
PostFiltering.inl
ProjData.h	Declaration of class stir::ProjData
ProjData.inl	Implementations for inline functions of class stir::ProjData
ProjDataFromStream.h	Declaration of class stir::ProjDataFromStream
ProjDataFromStream.inl	Inline implementations for class stir::ProjDataFromStream
ProjDataGEHDF5.h	Declaration of class stir::GE::RDF_HDF5::ProjDataFromGEHDF5
ProjDataInfo.h	Declaration of class stir::ProjDataInfo
ProjDataInfo.inl	Implementations of inline functions for class stir::ProjDataInfo
ProjDataInfoBlocksOnCylindrical.h	Declaration of class stir::ProjDataInfoBlocksOnCylindrical
ProjDataInfoBlocksOnCylindricalNoArcCorr.h	Declaration of class stir::ProjDataInfoBlocksOnCylindricalNoArcCorr
ProjDataInfoCylindrical.h	Declaration of class stir::ProjDataInfoCylindrical
ProjDataInfoCylindrical.inl	Implementation of inline functions of class stir::ProjDataInfoCylindrical
ProjDataInfoCylindricalArcCorr.h	Declaration of class stir::ProjDataInfoCylindricalArcCorr
ProjDataInfoCylindricalArcCorr.inl	Implementation of inline functions of class stir::ProjDataInfoCylindricalArcCorr
ProjDataInfoCylindricalNoArcCorr.h	Declaration of class stir::ProjDataInfoCylindricalNoArcCorr
ProjDataInfoCylindricalNoArcCorr.inl	Implementation of inline functions of class ProjDataInfoCylindricalNoArcCorr
ProjDataInfoGeneric.h
ProjDataInfoGenericNoArcCorr.h	Declaration of class stir::ProjDataInfoGenericNoArcCorr
ProjDataInfoGenericNoArcCorr.inl	Implementation of inline functions of class stir::ProjDataInfoGenericNoArcCorr
ProjDataInfoSubsetByView.h	Declaration of class stir::ProjDataInfoSubsetByView
ProjDataInMemory.h	Declaration of class stir::ProjDataInMemory
ProjDataInterfile.h	Declaration of class stir::ProjDataInterfile
Radionuclide.h	Declaration of class stir::Radionuclide
RadionuclideDB.h	Declaration of class stir::RadionuclideDB
recon_array_functions.h	Variety of useful functions
RegisteredObject.h	Declaration of class stiir::RegisteredObject
RegisteredObject.inl	Inline implementations for class stir::RegisteredObject
RegisteredObjectBase.h	Declaration of class stir::RegisteredObjectBase
RegisteredParsingObject.h	Declaration of class stir::RegisteredParsingObject
RegisteredParsingObject.inl	Inline implementations for class stir::RegisteredParsingObject
RelatedViewgrams.h	Declaration of class stir::RelatedViewgrams
RelatedViewgrams.inl	Inline implementations for class stir::RelatedViewgrams
round.h	Declaration of the stir::round functions
round.inl	Implementation of the stir::round functions
RunTests.h	Defines the stir::RunTests class
scale_sinograms.h	Declaration of stir::scale_sinograms and stir::get_scale_factors_per_sinogram
Scanner.h	Declaration of class stir::Scanner
Scanner.inl	Implementation of inline functions of class Scanner
Segment.h	Declaration of class stir::Segment
Segment.inl	Implementation of inline functions of class stir::Segment
SegmentBySinogram.h	Declaration of class stir::SegmentBySinogram
SegmentBySinogram.inl	Implementations of inline functions of class stir::SegmentBySinogram
SegmentByView.h	Declaration of class stir::SegmentByView
SegmentByView.inl	Implementations of inline functions of class stir::SegmentByView
SegmentIndices.h	Definition of class stir::SegmentIndices
SegmentIndices.inl	Inline implementations for class stir::SegmentIndices
SeparableArrayFunctionObject.h	Declaration of class stir::SeparableArrayFunctionObject
SeparableCartesianMetzImageFilter.h	Declaration of class stir::SeparableCartesianMetzImageFilter
SeparableConvolutionImageFilter.h	Declaration of class stir::SeparableConvolutionImageFilter
SeparableGaussianArrayFilter.h	Declaration of class stir::SeparableGaussianArrayFilter
SeparableGaussianImageFilter.h	Declaration of class stir::SeparableGaussianImageFilter
SeparableMetzArrayFilter.h	Declaration of class stir::SeparableMetzArrayFilter
shared_ptr.h	Import of std::shared_ptr, std::dynamic_pointer_cast and std::static_pointer_cast into the stir namespace
Sinogram.h	Declaration of class stir::Sinogram
Sinogram.inl	Implementations of inline functions of class stir::Sinogram
SinogramIndices.h	Definition of class stir::SinogramIndices
SinogramIndices.inl	Inline implementations for class stir::SinogramIndices
SSRB.h	Declaration of stir::SSRB functions
stir_math.h
StirException.h
stream.h	Input/output of basic vector-like types to/from streams
stream.inl	Input/output of basic vector-like types to/from streams
Succeeded.h	Declaration of class stir::Succeeded
TextWriter.h
thresholding.h	Declaration of functions that threshold sequences (specified by iterators)
ThresholdMinToSmallPositiveValueDataProcessor.h	Declaration of class stir::ThresholdMinToSmallPositiveValueDataProcessor
TimedBlock.h	Class stir::TimedBlock
TimedObject.h	Declares the stir::TimedObject class
TimedObject.inl	Inline implementations for stir::TimedObject
TimeFrameDefinitions.h	Declaration of class stir::TimeFrameDefinitions
TimeGateDefinitions.h	Declaration of class stir::TimeGateDefinitions
Timer.h	This declares the stir::Timer class
Timer.inl	Inline implementations for stir::Timer
TOF_conversions.h	Implementations of inline functions for TOF time to mm
TrivialDataSymmetriesForViewSegmentNumbers.h	Declaration of class stir::TrivialDataSymmetriesForViewSegmentNumbers
TrivialDataSymmetriesForViewSegmentNumbers.inl	Implementation of inline-methods of class stir::TrivialDataSymmetriesForViewSegmentNumbers
TruncateToCylindricalFOVImageProcessor.h	Declaration of class stir::TruncateToCylindricalFOVImageProcessor
type_traits.h	Defines various type traits, checking for iterators etc
unique_ptr.h	Import of std::unique_ptr into the stir namespace, together with work-arounds for other compilers
utilities.h	This file declares various utility functions
utilities.inl	Inline implementations for utility.h
VectorWithOffset.h	Defines the stir::VectorWithOffset class
VectorWithOffset.inl	Inline implementations of stir::VectorWithOffset
Verbosity.h	Declaration of class stir::Verbosity
Viewgram.h	Declaration of class stir::Viewgram
Viewgram.inl	Inline implementations of class stir::Viewgram
ViewgramIndices.h	Definition of class stir::ViewgramIndices
ViewgramIndices.inl	Inline implementations for class stir::ViewgramIndices
ViewSegmentNumbers.h	Definition of class stir::ViewSegmentNumbers, alias to stir::ViewgramIndices
ViewSegmentNumbers.inl	Inline implementations for class stir::ViewSegmentNumbers
VoxelsOnCartesianGrid.h	Defines the stir::VoxelsOnCartesianGrid class
VoxelsOnCartesianGrid.inl	Inline implementations for the stir::VoxelsOnCartesianGrid class
warning.h	Declaration of stir::warning()
WienerArrayFilter2D.h	Declaration of class stir::WienerArrayFilter2D
WienerImageFilter2D.h	Declaration of class stir::WienerImageFilter2D.h
zoom.h	This file declares various zooming functions
ZoomOptions.h	Declaration of class stir::ZoomOptions
► stir_experimental
► listmode
CListModeDataLMF.h	Declaration of class stir::CListModeDataLMF
CListRecordLMF.h	Preliminary code to handle listmode events
LmToProjDataWithMC.h	Declaration of class stir::LmToProjDataWithMC
► modelling
BloodFrame.h	Declaration of class stir::PlasmaData
BloodFrame.inl
BloodFrameData.h	Declaration of class stir::BloodFrameData
BloodFrameData.inl
OneParamModel.h
OneParamModel.inl
► motion
bin_interpolate.h	Functions to interpolate sinograms
MatchTrackerAndScanner.h	Definition of class stir::MatchTrackerAndScanner
NonRigidObjectTransformationUsingBSplines.h	Declaration of class stir::NonRigidObjectTransformationUsingBSplines
ObjectTransformation.h	Declaration of class stir::ObjectTransformation
PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion.h	Declaration of class stir::PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion
Polaris_MT_File.h	Declaration of class stir::Polaris_MT_File
RigidObject3DMotion.h	Declaration of class stir::RigidObject3DMotion
RigidObject3DMotionFromPolaris.h	Declaration of class stir::RigidObject3DMotionFromPolaris
RigidObject3DTransformation.h	Declaration of class stir::RigidObject3DTransformation
TimeFrameMotion.h	Stir::TimeFrameMotion
Transform3DObjectImageProcessor.h	Declaration of class stir::Transform3DObjectImageProcessor
transform_3d_object.h	Declaration of functions to re-interpolate an image or projection data to a new coordinate system
transform_3d_object.inl	Functions to re-interpolate an image
► numerics
linear_extrapolation.h	Stir::linear_extrapolation
more_interpolators.h	Functions to interpolate data
more_interpolators.inl	Functions to interpolate data
► phantoms
CylindersWithLineSource.h
Utah.h	Inline implementations for stir::Utah_phantom
► recon_buildblock
BinNormalisationFromML2D.h	Declaration of class stir::BinNormalisationFromML2D
BinNormalisationSinogramRescaling.h	Declaration of class stir::BinNormalisationSinogramRescaling
BinNormalisationUsingProfile.h	Declaration of class BinNormalisationUsingProfile
DataSymmetriesForDensels_PET_CartesianGrid.h	Declaration of class stir::DataSymmetriesForDensels_PET_CartesianGrid
DataSymmetriesForDensels_PET_CartesianGrid.inl	Inline implementations for class DataSymmetriesForDensels_PET_CartesianGrid
ParametricQuadraticPrior.h	Declaration of class stir::ParametricQuadraticPrior
PoissonLogLikelihoodWithLinearModelForMeanAndDynamicProjData.h	Declaration of class stir::PoissonLogLikelihoodWithLinearModelForMeanAndDynamicProjData
PostsmoothingForwardProjectorByBin.h	Declaration of class PostsmoothingForwardProjectorByBin
ProjMatrixByBinSinglePhoton.h	ProjMatrixByBinSinglePhoton's definition
ProjMatrixByBinUsingSolidAngle.h	ProjMatrixByBinUsingSolidAngle's definition
ProjMatrixByBinWithPositronRange.h	ProjMatrixByBinWithPositronRange's definition
ProjMatrixByDensel.h	Declaration of ProjMatrixByDensel and its helpers classes
ProjMatrixByDensel.inl	Implementations of inline functions for class ProjMatrixByDensel
ProjMatrixByDenselOnCartesianGridUsingElement.h	ProjMatrixByDenselOnCartesianGridUsingElement's definition
ProjMatrixByDenselUsingRayTracing.h	ProjMatrixByDenselUsingRayTracing's definition
AbsTimeInterval.h	Declaration of class stir::AbsTimeInterval
AbsTimeIntervalFromDynamicData.h	Declaration of class stir::AbsTimeIntervalFromDynamicData
AbsTimeIntervalFromECAT7ACF.h	Declaration of class stir::AbsTimeIntervalFromECAT7ACF
AbsTimeIntervalWithParsing.h	Declaration of class stir::AbsTimeIntervalWithParsing
DAVArrayFilter3D.h
DAVImageFilter3D.h	Implementation of stir::DAVImageFilter3D
doxygengroups.h
fft.h	Declaration of FFT routines
Filter.h	Filter classes (filter defined in Fourier space)
fwd_and_bck_manipulation_for_SAF.h
local_helping_functions.h
ModifiedInverseAveragingImageFilterAll.h	This is a messy, first, attempt to design spatially varying filter Given the kernel which in this case is a lospass filter with a DC gain 1 the filter is design such that the output kernel varies depending on the k0 and k1 ( for more details on these factors look at Fessler)
ModifiedInverseAverigingArrayFilter.h	This is a messy first attempt to design spatially varying filter Given the kernel which in this case is a lospass filter with a DC gain 1 the filter is design such that the output kernel varies depending on the k0 and k1 ( for more details on these factors look at Fessler)
ModifiedInverseAverigingImageFilter.h	This is a messy, first, attempt to design spatially varying filter Given the kernel which in this case is a lospass filter with a DC gain 1 the filter is design such that the output kernel varies depending on the k0 and k1 ( for more details on these factors look at Fessler)
multiply_plane_scale_factorsImageProcessor.h	Declaration of class multiply_plane_scale_factorsImageProcessor
NonseparableSpatiallyVaryingFilters.h	This is a messy, first, attempt to design spatially varying filter Given the kernel which in this case is a lospass filter with a DC gain 1 the filter is design such that the output kernel varies depending on the k0 and k1 ( for more details on these factors look at Fessler)
NonseparableSpatiallyVaryingFilters3D.h	This is a messy, first, attempt to design spatially varying filter Given the kernel which in this case is a lospass filter with a DC gain 1 the filter is design such that the output kernel varies depending on the k0 and k1 ( for more details on these factors look at Fessler)
Quaternion.h	Declaration of class stir::Quaternion
Quaternion.inl	Implementation of class stir::Quaternion
SeparableGaussianArrayFilter.h
SeparableGaussianImageFilter.h	Declaration of class SeparableGaussianImageFilter
SeparableLowPassArrayFilter.h
SeparableLowPassArrayFilter2.h
SeparableLowPassImageFilter.h	Declaration of class SeparableLowPassImageFilter
► IO
ecat6_utils.cxx	Implementation of ECAT 6 CTI functions to access data
ECAT6OutputFileFormat.cxx	Implementation of class stir::ECAT6OutputFileFormat
ECAT7DynamicDiscretisedDensityInputFileFormat.cxx	Implementation of class stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityInputFileFormat
ECAT7DynamicDiscretisedDensityOutputFileFormat.cxx	Implementation of class stir::ecat::ecat7::ECAT7DynamicDiscretisedDensityOutputFileFormat
ECAT7OutputFileFormat.cxx	Implementation of class stir::ecat::ecat7::ECAT7OutputFileFormat
ECAT7ParametricDensityOutputFileFormat.cxx	Implementation of class stir::ecat::ecat7::ECAT7ParametricDensityOutputFileFormat
GEHDF5ListmodeInputFileFormat.cxx	Implementations of class stir::GE::RDF_HDF5::IO::GEHDF5ListmodeInputFileFormat
GEHDF5Wrapper.cxx	Declaration of class stir::GE::RDF_HDF5::GEHDF5Wrapper
GIPL_ImageFormat.cxx	Class for reading GIPL data
InputFileFormatRegistry.cxx	Instantiations for class stir::InputFileFormatRegistry
InputStreamFromROOTFile.cxx	Implementation of class stir::InputStreamFromROOTFile
InputStreamWithRecordsFromUPENN.cxx	Implementation of class stir::InputStreamWithRecordsFromUPENN
InputStreamWithRecordsFromUPENNbin.cxx	Implementation of class stir::InputStreamWithRecordsFromUPENNbin
InputStreamWithRecordsFromUPENNtxt.cxx	Implementation of class stir::InputStreamWithRecordsFromUPENNtxt
interfile.cxx	Implementation of functions which read/write Interfile data
InterfileDynamicDiscretisedDensityOutputFileFormat.cxx	Implementation of class stir::InterfileDynamicDiscretisedDensityOutputFileFormat
InterfileHeader.cxx	Implementations for the stir::InterfileHeader class
InterfileHeaderSiemens.cxx	Implementations for the stir::InterfileHeaderSiemens classes
InterfileOutputFileFormat.cxx	Implementation of class stir::InterfileOutputFileFormat
InterfileParametricDiscretisedDensityOutputFileFormat.cxx	Implementation of class stir::InterfileParametricDiscretisedDensityOutputFileFormat
InterfilePDFSHeaderSPECT.cxx	This file implements the classes stir::InterfilePDFSHeaderSPECT
IO_registries.cxx	File that registers all stir::RegisterObject children in IO
ITKImageInputFileFormat.cxx	Declaration of class stir::ITKImageInputFileFormat
ITKOutputFileFormat.cxx	Implementation of class stir::ITKOutputFileFormat
MultiDynamicDiscretisedDensityInputFileFormat.cxx	Implementation of class stir::MultiDynamicDiscretisedDensityInputFileFormat
MultiDynamicDiscretisedDensityOutputFileFormat.cxx	Implementation of class stir::MultiDynamicDiscretisedDensityOutputFileFormat
MultiParametricDiscretisedDensityOutputFileFormat.cxx	Implementation of class stir::MultiParametricDiscretisedDensityOutputFileFormat
OutputFileFormat.cxx	Instantiations of the stir::OutputFileFormat class
OutputFileFormat_default.cxx	Initialisation of the stir::OutputFileFormat::_default_sptr member
stir_ecat6.cxx	Implementation of routines which convert CTI things into our building blocks and vice versa
stir_ecat7.cxx	Implementation of routines which convert ECAT7 things into our building blocks and vice versa
stir_ecat_common.cxx	Implementation of routines which convert ECAT6, ECAT7 and ECAT8 things into our building blocks and vice versa
► iterative
► KOSMAPOSL
KOSMAPOSL.cxx	Main() for KOSMAPOSLReconstruction
KOSMAPOSLReconstruction.cxx	Implementation of the stir::KOSMAPOSLReconstruction class
► OSMAPOSL
OSMAPOSL.cxx	Main() for OSMAPOSLReconstruction
OSMAPOSLReconstruction.cxx	Implementation of the stir::OSMAPOSLReconstruction class
► OSSPS
OSSPS.cxx	Main() for stir::OSSPSReconstruction
OSSPSReconstruction.cxx	Implementation of the stir::OSSPSReconstruction class
► POSMAPOSL
POSMAPOSL.cxx	Main() for stir::OSMAPOSLReconstruction on parametric images
► POSSPS
POSSPS.cxx	Main() for stir::OSSPS for parametric images
► listmode_buildblock
► NiftyPET_listmode
LmToProjDataNiftyPET.cxx	Implementation of class stir::LmToProjDataNiftyPET
CListEvent.cxx	Implementations of class stir::CListEvent
CListModeDataECAT.cxx	Implementation of class stir::CListModeDataECAT
CListModeDataECAT8_32bit.cxx	Implementation of class stir::CListModeDataECAT8_32bit
CListModeDataGEHDF5.cxx	Implementation of class stir::GE::RDF_HDF5::CListModeDataGEHDF5
CListModeDataPENN.cxx	Implementation of class stir::CListModeDataPENN
CListModeDataROOT.cxx	Implementation of class stir::CListModeDataROOT
CListModeDataSAFIR.cxx	Implementation of class stir::CListModeDataSAFIR
CListRecordECAT8_32bit.cxx	Implementation of classes stir::ecat::CListEventECAT8_32bit and stir::ecat::CListRecordECAT8_32bit for listmode events for the ECAT8 32bit listmode file format
CListRecordECAT962.cxx	Implementation of classes CListEventECAT962 and CListRecordECAT962 for listmode events for the ECAT 962 (aka Exact HR+)
CListRecordECAT966.cxx	Implementation of classes CListEventECAT966 and CListRecordECAT966 for listmode events for the ECAT 966 (aka Exact 3d)
CListRecordPENN.cxx	Implementation of classes CListEventPENN
CListRecordROOT.cxx	Implementation of classes stir::ecat::CListEventROOT and stir::ecat::CListRecordROOT for listmode events for the ROOT as listmode file format
ListEvent.cxx	Implementations of class stir::ListEvent
ListModeData.cxx	Implementation of class stir::ListModeData
LmToProjData.cxx	Implementation of class stir::LmToProjData
LmToProjDataAbstract.cxx	Implementation of class stir::LmToProjDataAbstract
LmToProjDataBootstrap.cxx	Class stir::LmToProjDataBootstrap for rebinning listmode files with the bootstrap method
LmToProjDataWithRandomRejection.cxx	Class stir::LmToProjDataWithRandomRejection for rebinning listmode files rejection some events randomly
► listmode_utilities
add_ecat7_header_to_sgl.cxx	Prepend contents of ECAT7 header to a new sgl file (from list mode acquisition)
conv_NiftyPET_stir.cxx	Convert between NiftyPET and STIR imagees and projdata
list_lm_countrates.cxx	Utility to generate a count rate curve for some listmode data The count rate curve is just a list of the total number of prompts and delayeds in subsequent time intervals. The current output is a file with 4 columns:
list_lm_events.cxx	Program to show info about listmode data
list_lm_info.cxx	A utility that lists info on the listmode data on stdout
lm_fansums.cxx	Program to compute detector fansums directly from listmode data
lm_to_projdata.cxx	Program to bin listmode data to 3d sinograms
lm_to_projdata_bootstrap.cxx	Program to bin listmode data to projection data using bootstrapping (uses stir::LmToProjDataBootstrap)
lm_to_projdata_NiftyPET.cxx	Program to bin listmode data to 3d sinograms using STIR's NiftyPET wrapper
lm_to_projdata_with_random_rejection.cxx	Program to bin listmode data to projection data using random rejection of counts (uses stir::LmToProjDataWithRandomRejection)
print_sgl_values.cxx	Utility program that prints out values from an sgl file
rebin_sgl_file.cxx	Utility program scans the singles file looking for anomalous values
scan_sgl_file.cxx	Utility program scans the singles file looking for anomalous values
► modelling_buildblock
modelling_registries.cxx	File that registers all stir::RegisterObject children in modelling
ParametricDiscretisedDensity.cxx	Declaration of class stir::ParametricDiscretisedDensity
► modelling_utilities
apply_patlak_to_images.cxx	Apply the Patlak linear fit using Dynamic Images
extract_single_images_from_parametric_image.cxx	Split parametric image into individual images
get_dynamic_images_from_parametric_images.cxx	Multiplies Parametric Images with the Model Matrix creating Dynamic Images
make_parametric_image_from_components.cxx	Create parametric image from individual components
mult_image_parameters.cxx	It multiplies the two parametric images and produces one-parameter image
mult_model_with_dyn_images.cxx	Multiplies Dynamic Images with the Model Matrix creating image in the Parametric Space
write_patlak_matrix.cxx	Write the Model Matrix for the Patlak plot (e.g., for debugging)
► numerics_buildblock
determinant.cxx	Implementation of stir::determinant() function for matrices
fourier.cxx	Functions for computing discrete fourier transforms
► recon_buildblock
► NiftyPET_projector
BackProjectorByBinNiftyPET.cxx	Non-inline implementations for stir::BackProjectorByBinNiftyPET
ForwardProjectorByBinNiftyPET.cxx	Non-inline implementations for stir::ForwardProjectorByBinNiftyPET
NiftyPETHelper.cxx	Non-inline implementations for stir::NiftyPETHelper
ProjectorByBinPairUsingNiftyPET.cxx	Non-inline implementations for stir::ProjectorByBinPairUsingNiftyPET
► Parallelproj_projector
BackProjectorByBinParallelproj.cxx	Non-inline implementations for stir::BackProjectorByBinParallelproj
ForwardProjectorByBinParallelproj.cxx	Non-inline implementations for stir::ForwardProjectorByBinParallelproj
ParallelprojHelper.cxx	Non-inline implementations for stir::ParallelprojHelper
ProjectorByBinPairUsingParallelproj.cxx	Non-inline implementations for stir::ProjectorByBinPairUsingParallelproj
AnalyticReconstruction.cxx	Implementation of the stir::AnalyticReconstruction class
BackProjectorByBin.cxx	Non-inline implementations for stir::BackProjectorByBin
BackProjectorByBinUsingInterpolation.cxx	Non-inline implementations for BackProjectorByBinUsingInterpolation
BackProjectorByBinUsingInterpolation_3DCho.cxx	This file defines two private static functions from stir::BackProjectorByBinUsingInterpolation
BackProjectorByBinUsingInterpolation_linear.cxx	This file defines two private static functions from stir::BackProjectorByBinUsingInterpolation, for the case of piecewise linear interpolation
BackProjectorByBinUsingInterpolation_piecewise_linear.cxx	This file defines two private static functions from stir::BackProjectorByBinUsingInterpolation, for the case of piecewise linear interpolation
BackProjectorByBinUsingProjMatrixByBin.cxx	Non-inline implementations for stir::BackProjectorByBinUsingProjMatrixByBin
BackProjectorByBinUsingSquareProjMatrixByBin.cxx	Non-inline implementations for stir::BackProjectorByBinUsingSquareProjMatrixByBin
BinNormalisation.cxx	Implementation for class stir::BinNormalisation
BinNormalisationFromAttenuationImage.cxx	Implementation for class stir::BinNormalisationFromAttenuationImage
BinNormalisationFromECAT7.cxx	Implementation for class stir::ecat::ecat7::BinNormalisationFromECAT7
BinNormalisationFromECAT8.cxx	Implementation for class stir::ecat::BinNormalisationFromECAT8
BinNormalisationFromGEHDF5.cxx	Implementation for class stir::GE:RDF_HDF5::BinNormalisationFromGEHDF5
BinNormalisationFromProjData.cxx	Implementation for class stir::BinNormalisationFromProjData
BinNormalisationPETFromComponents.cxx	Implementation for class stir::BinNormalisationPETFromComponents
BinNormalisationSPECT.cxx	Implementation for class stir::BinNormalisationSPECT
BinNormalisationWithCalibration.cxx	Implementation for class stir::BinNormalisationWithCalibration
ChainedBinNormalisation.cxx	Implementation for class stir::ChainedBinNormalisation
DataSymmetriesForBins.cxx	Implementations for class stir::DataSymmetriesForBins
DataSymmetriesForBins_PET_CartesianGrid.cxx	Non-inline implementations for class stir::DataSymmetriesForBins_PET_CartesianGrid
DataSymmetriesForDensels.cxx	Implementations for class stir::DataSymmetriesForDensels
distributable.cxx	Implementation of stir::distributable_computation() and related functions
distributableMPICacheEnabled.cxx	Implementation of stir::distributable_computation_cache_enabled()
distributed_functions.cxx	Implementation of functions in distributed namespace
distributed_test_functions.cxx	Implementation of test functions in distributed namespace
DistributedCachingInformation.cxx	Implementation of class stir::DistributedCachingInformation
DistributedWorker.cxx	Implementation of stir::DistributedWorker()
FilterRootPrior.cxx	Implementation of the stir::FilterRootPrior class
find_basic_vs_nums_in_subset.cxx	Implementation for stir::detail::find_basic_vs_nums_in_subset
ForwardProjectorByBin.cxx	Non-inline implementations for stir::ForwardProjectorByBin
ForwardProjectorByBinUsingProjMatrixByBin.cxx	Implementations for stir::ForwardProjectorByBinUsingProjMatrixByBin
ForwardProjectorByBinUsingRayTracing.cxx	Implementations of non-static methods of stir::ForwardProjectorByBinUsingRayTracing
ForwardProjectorByBinUsingRayTracing_Siddon.cxx	Implementation of Siddon's algorithm
FourierRebinning.cxx	FORE kernel
GeneralisedObjectiveFunction.cxx	Declaration of class stir::GeneralisedObjectiveFunction
GeneralisedPrior.cxx	Implementation of the stir::GeneralisedPrior
IterativeReconstruction.cxx	Implementation of the stir::IterativeReconstruction class
LogcoshPrior.cxx	Implementation of the stir::LogcoshPrior class
ML_estimate_component_based_normalisation.cxx	Implementation of ML_estimate_component_based_normalisation
PLSPrior.cxx	Implementation of the stir::PLSPrior class
PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData.cxx	Instantiations for class stir::PoissonLogLikelihoodWithLinearKineticModelAndDynamicProjectionData
PoissonLogLikelihoodWithLinearModelForMean.cxx	Implementation of class stir::PoissonLogLikelihoodWithLinearModelForMean
PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion.cxx	Instantiations for class stir::PoissonLogLikelihoodWithLinearModelForMeanAndGatedProjDataWithMotion
PoissonLogLikelihoodWithLinearModelForMeanAndListModeData.cxx	Declaration of class stir::PoissonLogLikelihoodWithLinearModelForMeanAndListModeData
PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin.cxx	Implementation of class stir::PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin
PoissonLogLikelihoodWithLinearModelForMeanAndProjData.cxx	Declaration of class stir::PoissonLogLikelihoodWithLinearModelForMeanAndProjData
PostsmoothingBackProjectorByBin.cxx	Implementation of class stir::PostsmoothingBackProjectorByBin
PresmoothingForwardProjectorByBin.cxx	Implementation of class stir::PresmoothingForwardProjectorByBin
ProjDataRebinning.cxx	Implementation of the ProjDataRebinning class
ProjectorByBinPair.cxx	Non-inline implementations for stir::ProjectorByBinPair
ProjectorByBinPairUsingProjMatrixByBin.cxx	Non-inline implementations for stir::ProjectorByBinPairUsingProjMatrixByBin
ProjectorByBinPairUsingSeparateProjectors.cxx	Non-inline implementations for stir::ProjectorByBinPairUsingSeparateProjectors
ProjMatrixByBin.cxx	Implementation of the stir::ProjMatrixByBin class
ProjMatrixByBinFromFile.cxx	Implementation of class stir::ProjMatrixByBinFromFile
ProjMatrixByBinPinholeSPECTUB.cxx	Implementation of class stir::ProjMatrixByBinPinholeSPECTUB
ProjMatrixByBinSPECTUB.cxx	Implementation of class stir::ProjMatrixByBinSPECTUB
ProjMatrixByBinUsingInterpolation.cxx	Non-inline implementations for stir::ProjMatrixByBinUsingInterpolation
ProjMatrixByBinUsingRayTracing.cxx	Non-inline implementations for stir::ProjMatrixByBinUsingRayTracing
ProjMatrixElemsForOneBin.cxx	Non-inline implementations for stir::ProjMatrixElemsForOneBin
ProjMatrixElemsForOneDensel.cxx	Non-inline implementations for stir::ProjMatrixElemsForOneDensel
QuadraticPrior.cxx	Implementation of the stir::QuadraticPrior class
RayTraceVoxelsOnCartesianGrid.cxx	Implementation of RayTraceVoxelsOnCartesianGrid
recon_buildblock_registries.cxx	File that registers all stir::RegisterObject children in recon_buildblock
Reconstruction.cxx	Implementation of the stir::Reconstruction class
RelativeDifferencePrior.cxx	Implementation of the stir::RelativeDifferencePrior class
SqrtHessianRowSum.cxx	Declaration of class stir::SqrtHessianRowSum
SymmetryOperation.cxx	Implementations of non-inline functions for class SymmetryOperation
SymmetryOperations_PET_CartesianGrid.cxx	Non-inline implementations for all symmetry operations for PET scanners and Cartesian grid images
TrivialBinNormalisation.cxx	Implementations for class stir::TrivialBinNormalisation
TrivialDataSymmetriesForBins.cxx	Non-inline implementations for class stir::TrivialDataSymmetriesForBins
► recon_test
bcktest.cxx	Test program for back projection
fwdtest.cxx	Testing program for forward projection
recontest.cxx	Demo for Realtime reconstruction initialization
test_blocks_on_cylindrical_projectors.cxx	Test program for back projection and forward projection using stir::ProjDataInfoBlockOnCylindrical
test_data_processor_projectors.cxx	Test program for forward and backwards projectors with pre- and post- data processors (smoothing in this case)
test_DataSymmetriesForBins_PET_CartesianGrid.cxx	Test program for stir::DataSymmetriesForBins_PET_CartesianGrid
test_FBP2D.cxx	Test program for FBP2D
test_FBP3DRP.cxx	Test program for FBP3DRP
test_geometry_blocks_on_cylindrical.cxx	Test program to ensure the axial coordinates of blocks on cylindrical are monotonic with axial indices
test_OSMAPOSL.cxx	Test program for OSMAPOSL
test_PoissonLogLikelihoodWithLinearModelForMeanAndListModeWithProjMatrixByBin.cxx	Test program for stir::PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin
test_PoissonLogLikelihoodWithLinearModelForMeanAndProjData.cxx	Test program for stir::PoissonLogLikelihoodWithLinearModelForMeanAndProjData
test_priors.cxx	Test program for stir::QuadraticPrior, stir::RelativeDifferencePrior, and stir::LogcoshPrior
► scatter_buildblock
cached_single_scatter_integrals.cxx	Implementations of functions defined in stir::ScatterEstimationByBin
sample_scatter_points.cxx	Implementation of stir::ScatterEstimationByBin::sample_scatter_points
scatter_detection_modelling.cxx	Implementations of detection modelling in stir::ScatterEstimationByBin
scatter_estimate_for_one_scatter_point.cxx	Implementation of stir::SingleScatterSimulation::simulate_for_one_scatter_point
scatter_registries.cxx	File that registers all stir::RegisterObject children in scatter estimation
ScatterEstimation.cxx	Implementation of most functions in stir::ScatterEstimation
ScatterSimulation.cxx	Definition of class stir::ScatterSimulation
single_scatter_estimate.cxx	Implementation of stir::SingleScatterSimulation::actual_scatter_estimate
single_scatter_integrals.cxx	Implementations of integrating functions in stir::ScatterEstimationByBin
upsample_and_fit_scatter_estimate.cxx	Implementation of stir::ScatterEstimationByBin::upsample_and_fit_scatter_estimate
► scatter_utilities
create_tail_mask_from_ACFs.cxx	Compute a mask for the "tails" in the sinogram
estimate_scatter.cxx	Estimates a coarse scatter sinogram
simulate_scatter.cxx	Simulates a coarse scatter sinogram
upsample_and_fit_single_scatter.cxx	Upsample a coarse scatter estimate and fit it to emission data using a weight/mask projection data
► Shape_buildblock
Box3D.cxx	Non-inline implementations for class stir::Box3D
DiscretisedShape3D.cxx	Non-inline implementations for class stir::DiscretisedShape3D
Ellipsoid.cxx	Non-inline implementations for class stir::Ellipsoid
EllipsoidalCylinder.cxx	Non-inline implementations for class stir::EllipsoidalCylinder
GenerateImage.cxx	Declaration of class stir::GenerateImage
Shape3D.cxx	Non-inline implementations for class stir::Shape3D
Shape3DWithOrientation.cxx	Non-inline implementations for class stir::Shape3DWithOrientation
Shape_buildblock_registries.cxx	File that registers all stir::RegisteredObject children in Shape_buildblock
► SimSET
conv_SimSET_projdata_to_STIR.cxx	This program converts SimSET 3D sinograms to STIR format
conv_to_SimSET_att_image.cxx	Convert a transmission image into SimSET attenuation file input
write_phg_image_info.c	Write object-spec for PHG parameter file for SimSET
► spatial_transformation_buildblock
GatedSpatialTransformation.cxx	Implementations of inline functions of class stir::GatedSpatialTransformation
InvertAxis.cxx	Implementation of function stir::invert_axis
spatial_transformation_registries.cxx	File that registers all stir::RegisterObject children in spatial_transformation
SpatialTransformation.cxx	Implementations of inline functions of class stir::SpatialTransformation
warp_image.cxx	Implementation of function stir::warp_image
► test
► IO
test_IO_DiscretisedDensity.cxx	A simple program to test the stir::OutputFileFormat function
test_IO_DynamicDiscretisedDensity.cxx	A simple program to test the stir::OutputFileFormat function
test_IO_ITKMulticomponent.cxx	A simple program to test the reading of multicomponent images with ITK
test_IO_ParametricDiscretisedDensity.cxx	A simple program to test the stir::OutputFileFormat function
► modelling
test_modelling.cxx	Tests parts of the modelling implementation
test_ParametricDiscretisedDensity.cxx	Testing stir::ParametricDiscretisedDensity class
► NiftyPET_projector
test_ProjectorNiftyPET_adjoint.cxx	Test that the NiftyPET forward and back projectors are adjoint to one another
► numerics
BSplines_timing.cxx	Allows executing timing tests for the stir::BSpline::BSplinesRegularGrid class
test_BSplines.cxx	Tests the BSplines
test_BSplinesRegularGrid.cxx	Tests the stir::BSplinesRegularGrid class for the stir::Array 2D case
test_BSplinesRegularGrid1D.cxx	Tests the stir::BSplinesRegularGrid class for the stir::Array 1D case
test_erf.cxx	Tests the error function stir::erf and its complementary
test_Fourier.cxx	Tests for function in the DFT group
test_integrate_discrete_function.cxx	Test stir::integrate_discrete_function
test_IR_filters.cxx	Tests the implementation of the IR_filters
test_matrices.cxx	Tests for functions in MatrixFunction.h etc
test_overlap_interpolate.cxx	Test program for stir::overlap_interpolate
test_ArcCorrection.cxx	Test program for stir::ArcCorrection
test_Array.cxx	Tests for the stir::Array class
test_ArrayFilter.cxx	Tests for the stir::ArrayFilter classes
test_ByteOrder.cxx	Test program for stir::ByteOrder and ByteOrderDefine.h
test_convert_array.cxx	Tests for the stir::convert_array functions
test_coordinates.cxx	A simple program to test the Coordinate classes
test_DateTime.cxx	A simple program to test the date-time conversions
test_DetectionPosition.cxx	A simple program to test the stir::DetectionPosition class
test_DetectorCoordinateMap.cxx	Test program for detection position map using stir::ProjDataInfoBlockOnCylindrical
test_display.cxx	Very simple test program for stir::display()
test_DynamicDiscretisedDensity.cxx	Tests the stir::DynamicDiscretisedDensity class
test_filename_functions.cxx	Test program for filename functions defined in utility.h
test_find_fwhm_in_image.cxx	A simple program to test stir::find_fwhm_in_image
test_GeneralisedPoissonNoiseGenerator.cxx	Tests for the stir::GeneralisedPoissonNoiseGenerator class
test_ImagingModality.cxx	Test program for stir::ImagingModality
test_IndexRange.cxx	A simple program to test the stir::IndexRange class
test_interpolate.cxx	Interactive test program for overlap_interpolate
test_interpolate_projdata.cxx	Tests for stir::ProjData interpolation as used by the scatter estimation
test_KeyParser.cxx	Test program for stir::KeyParser
test_linear_regression.cxx	A simple programme to test the stir::linear_regression function
test_ML_norm.cxx	Test program for ML_norm.h functionality
test_multiple_proj_data.cxx	Test program for stir::MultipleProjData
test_NestedIterator.cxx	Tests for the stir::NestedIterator class
test_OutputFileFormat.cxx	A simple program to test the stir::OutputFileFormat function
test_proj_data.cxx	Test program for stir::ProjData and stir::ProjDataInMemory
test_proj_data_in_memory.cxx	Test program for stir::ProjDataInMemory
test_proj_data_info.cxx	Test program for stir::ProjDataInfo hierarchy
test_proj_data_info_subsets_pet.cxx	Test program for subsetting stir::ProjDataInfo via stir::ProjDataInfoSubsetByView
test_proj_data_info_subsets_spect.cxx	Test program for subsetting stir::ProjDataInfo via stir::ProjDataInfoSubsetByView for SPECT data
test_proj_data_maths.cxx	Test maths of stir::ProjData
test_radionuclide.cxx	A simple program to test stir::RadionuclideDB and stir::Radionuclide
test_ROIs.cxx	Test program for ROI functionality (and a bit of stir::Shape3D hierarchy)
test_Scanner.cxx	Test program for stir::Scanner hierarchy
test_ScatterSimulation.cxx	Test program for stir::ScatterSimulation
test_SeparableGaussianArrayFilter.cxx	Tests for the stir::SeparableGaussianArrayFilter class
test_SeparableMetzArrayFilter.cxx	Tests for the stir::SeparableMetzArrayFilter class
test_stir_math.cxx	Test program for the stir_math utility
test_VectorWithOffset.cxx	Test program for stir::VectorWithOffset
test_VoxelsOnCartesianGrid.cxx	Test program for stir::VoxelsOnCartesianGrid and image hierarchy
test_warp_image.cxx	A simple program to test the warp image functions
test_zoom_image.cxx	Test program for stir::zoom_image (and stir::centre_of_gravity)
► utilities
► ecat
conv_to_ecat6.cxx	Conversion from interfile (or any format that we can read) to ECAT 6 cti (image and sinogram data)
conv_to_ecat7.cxx	Conversion from interfile (or any format that we can read) to ECAT 7 cti (image and sinogram data)
convecat6_if.cxx	Conversion from ECAT 6 cti to interfile (image and sinogram data)
copy_ecat7_header.cxx	Copy contents of an ECAT7 header from 1 file to another
ecat_swap_corners.cxx	A (slightly dangerous) utility to perform so-called corner-swapping for ECAT6 projection data
ifheaders_for_ecat7.cxx	Utility to make Interfile headers for ECAT7 data
is_ecat7_file.cxx	A simple utility that allows to check if a file is in the ECAT7 format
print_ecat_singles_values.cxx	Utility program that prints out values from an sgl file
► GE
print_GE_singles_values.cxx	Utility program that prints out singles values from an RDF file
► UPENN
conv_UPENN_projdata_to_STIR.cxx	Convert PennPET Explorer-type of sinogram to STIR-type The PennPET projdata skip over the gaps, the –gaps options adds them back to STIR's projdata. Without the –gaps flag the output will match the input (as closely as possibly). –inv: should be used for the attenuation correction –up_treshold should be used with normalisation (typically 13)
abs_image.cxx	It produces the absolute value image of an image
apply_normfactors.cxx	Apply normalisation factors using an ML approach
apply_normfactors3D.cxx	Apply normalisation factors estimated using the ML code to projection data
attenuation_coefficients_to_projections.cxx	Takes the logarithm of attenuation coefficients to 'convert' them to line integrals
back_project.cxx	Back project an image
calculate_attenuation_coefficients.cxx	Calculates attenuation coefficients (as an alternative to correct_projdata)
compare_image.cxx	Compare images to see if they are identical, allowing for small differences
compare_projdata.cxx	Compare 2 files with sinogram data
compute_sqrt_Hessian_row_sum.cxx	Computes the Square Root of the Hessian Row Sum of the objective function
construct_randoms_from_GEsingles.cxx	Construct randoms as a product of singles estimates
construct_randoms_from_singles.cxx	Construct randoms as a product of singles estimates
conv_GATE_raw_ECAT_projdata_to_interfile.cxx	This program converts GATE ECAT output (.ima) into STIR interfile format
conv_gipl_to_interfile.cxx	This program converts Images from GIPL (Guy's Imaging Processing Lab) format to Interfile Format
conv_interfile_to_gipl.cxx	This program converts Images from Interfile Format to GIPL (Guy's Imaging Processing Lab) format
convert_to_binary_image.cxx	This program outputs a binary image (voxel values 0 or 1) where all values strictly below a threshold are set to 0, and others to 1
correct_projdata.cxx	A utility applying/undoing some corrections on projection data
create_multi_header.cxx	Create a "Multi" header for a set of data
create_projdata_template.cxx	A utility that creates a template projection data
ctac_to_mu_values.cxx	Produces an image of mu-values from a CT/CTAC
display_projdata.cxx	This program displays projection data by segment
do_linear_regression.cxx	A simple programme to perform weighted least squares
estimate_triple_energy_window_scatter_sinogram.cxx	Calculate Triple energy window scatter
extract_segments.cxx	This program extracts projection data by segment into 3d image files
extract_single_images_from_dynamic_image.cxx	Split dynamic image into individual images
find_fwhm_in_image.cxx	List of FWHM and location of maximum in the image
find_maxima_in_image.cxx	List coordinates of maxima in the image to stdout
find_ML_normfactors.cxx	Find normalisation factors using an ML approach
find_ML_normfactors3D.cxx	Find normalisation factors using an ML approach
find_ML_singles_from_delayed.cxx	Find singles (and hence randoms) from delayed events using an ML approach
find_normfactors_from_cylinder_data.cxx	Find normalisation factors given projection data of a cylinder (direct method)
find_recovery_coefficients_in_image_quality_phantom_nema_nu4.cxx	Utility program for calculating recovery coeficient values in the image quality phantom described in NEMA NU 4
find_sum_projection_of_viewgram_and_sinogram.cxx	This program reads a projection data file and squeezes a given sinogrm or viewgram of it (from a 2D matrix to a 1D vector)
forward_project.cxx	Forward project an image
generate_image.cxx	A utility to generate images consisting of uniform objects added/subtracted together
get_time_frame_info.cxx	Prints start time and duration of a frame to stdout
invert_axis.cxx	This program inverts x y or z axis
list_detector_and_bin_info.cxx	A utility that lists bin and detector info for a given (cylindrical) scanner on stdout
list_image_info.cxx	This program lists basic image info. It works for dynamic images
list_image_values.cxx	Utility to extract image values along profiles (or another box-shape)
list_projdata_info.cxx	A utility that lists size info on the projection data on stdout
list_ROI_values.cxx	Utility program for getting ROI values
manip_image.cxx	This program performs operations on image data
manip_projdata.cxx	Process sinogram data
poisson_noise.cxx	Generates a noise realisation according to Poisson statistics for some projection data
postfilter.cxx	This program performs filtering on image data
rebin_projdata.cxx	A utility to rebin projection data
separate_true_from_random_scatter_for_necr.cxx	This program gets a projection data file of a mouse/rat scatter phantom measured according to NEMA NU 4. It seperates number of true events from number of random+scatter events
shift_image.cxx	This program shifts the origin of an image
shift_image_origin.cxx	This program shifts the origin of an image
SPECT_dicom_to_interfile.cxx	Convert SPECT DICOM projection data to Interfile
SSRB.cxx	Main program for stir::SSRB
stir_config.cxx	Prints configuration directory and STIR version
stir_list_registries.cxx	Prints all registered names for many registries
stir_math.cxx	Add or multiply data, with some other basic math manipulations
stir_timings.cxx	Perform timings
stir_write_pgm.cxx	This program writes a PGM bitmap for an image (preliminary)
warp_and_accumulate_gated_images.cxx	This program corrects the motion from an image
warp_image.cxx	This program warps an image
write_proj_matrix_by_bin.cxx	Program that writes a projection matrix by bin to file
zeropad_planes.cxx	This program zero pads the start & end planes of an image
zoom_image.cxx	This program serves as a stand-alone zoom/trim utility for image files Run without arguments to get a usage message