The (abstract) base class for the projection data. More...

#include "stir/ProjData.h"

Inheritance diagram for stir::ProjData:

[legend]

Public Member Functions
	ProjData ()
	Empty constructor.

	ProjData (const shared_ptr< const ExamInfo > &exam_info_sptr, const shared_ptr< const ProjDataInfo > &proj_data_info_ptr)
	construct by specifying info. Data will be undefined.

virtual Viewgram< float >	get_viewgram (const int view, const int segment_num, const bool make_num_tangential_poss_odd=false, const int timing_pos=0) const =0
	Get viewgram.

Viewgram< float >	get_viewgram (const ViewgramIndices &) const
	Get viewgram.

virtual Succeeded	set_viewgram (const Viewgram< float > &)=0
	Set viewgram.

virtual Sinogram< float >	get_sinogram (const int ax_pos_num, const int segment_num, const bool make_num_tangential_poss_odd=false, const int timing_pos=0) const =0
	Get sinogram.

Sinogram< float >	get_sinogram (const SinogramIndices &) const
	Get sinogram.

virtual Succeeded	set_sinogram (const Sinogram< float > &)=0
	Set sinogram.

unique_ptr< ProjDataInMemory >	get_subset (const std::vector< int > &views) const
	construct projection data that stores a subset of the views

Viewgram< float >	get_empty_viewgram (const ViewgramIndices &) const
	Get empty viewgram.

Viewgram< float >	get_empty_viewgram (const int view, const int segment_num, const bool make_num_tangential_poss_odd=false, const int timing_pos=0) const
	Get empty viewgram.

Sinogram< float >	get_empty_sinogram (const SinogramIndices &) const
	Get empty_sinogram.

Sinogram< float >	get_empty_sinogram (const int ax_pos_num, const int segment_num, const bool make_num_tangential_poss_odd=false, const int timing_pos=0) const
	Get empty_sinogram.

SegmentByView< float >	get_empty_segment_by_view (const SegmentIndices &) const
	Get empty segment by view.

SegmentBySinogram< float >	get_empty_segment_by_sinogram (const SegmentIndices &) const
	Get empty segment by sino.

SegmentByView< float >	get_empty_segment_by_view (const int segment_num, const bool make_num_tangential_poss_odd=false, const int timing_pos=0) const
	Get empty segment view.

SegmentBySinogram< float >	get_empty_segment_by_sinogram (const int segment_num, const bool make_num_tangential_poss_odd=false, const int timing_pos=0) const
	Get empty segment sino.

virtual SegmentBySinogram< float >	get_segment_by_sinogram (const int segment_num, const int timing_pos=0) const
	Get segment by sinogram.

SegmentBySinogram< float >	get_segment_by_sinogram (const SegmentIndices &) const
	Get segment by sinogram.

virtual SegmentByView< float >	get_segment_by_view (const int segment_num, const int timing_pos=0) const
	Get segment by view.

SegmentByView< float >	get_segment_by_view (const SegmentIndices &) const
	Get segment by view.

virtual Succeeded	set_segment (const SegmentBySinogram< float > &)
	Set segment by sinogram.

virtual Succeeded	set_segment (const SegmentByView< float > &)
	Set segment by view.

virtual RelatedViewgrams< float >	get_related_viewgrams (const ViewgramIndices &, const shared_ptr< DataSymmetriesForViewSegmentNumbers > &, const bool make_num_tangential_poss_odd=false, const int timing_pos=0) const
	Get related viewgrams.

virtual Succeeded	set_related_viewgrams (const RelatedViewgrams< float > &viewgrams)
	Set related viewgrams.

RelatedViewgrams< float >	get_empty_related_viewgrams (const ViewgramIndices &viewgram_indices, const shared_ptr< DataSymmetriesForViewSegmentNumbers > &symmetries_ptr, const bool make_num_tangential_poss_odd=false, const int timing_pos=0) const
	Get empty related viewgrams, where the symmetries_ptr specifies the symmetries to use.

virtual void	fill (const float value)
	set all bins to the same value

virtual void	fill (const ProjData &)
	set all bins from another ProjData object

template<typename iterT>
iterT	fill_from (iterT array_iter)
	set all bins from an array iterator

template<typename iterT>
iterT	copy_to (iterT array_iter) const
	Copy all bins to a range specified by a (forward) iterator.

int	get_num_sinograms () const
	Get the total number of sinograms.

int	get_num_non_tof_sinograms () const
	Get the number of non-tof sinograms.

std::size_t	size_all () const
	Get the total size of the data.

std::vector< int >	get_original_view_nums () const
	forward ProjDataInfo::get_original_view_nums()

Succeeded	write_to_file (const std::string &filename) const
	writes data to a file in Interfile format

arithmetic operations
return sum of all elements
virtual float	sum () const

virtual float	find_max () const
	return maximum value of all elements

virtual float	find_min () const
	return minimum value of all elements

virtual double	norm () const
	return L2-norm (sqrt of sum of squares)

virtual double	norm_squared () const
	return L2-norm squared (sum of squares)

virtual self_type &	operator+= (const self_type &v)
	adding elements of `v` to the current data

virtual self_type &	operator-= (const self_type &v)
	subtracting elements of `v` from the current data

virtual self_type &	operator*= (const self_type &v)
	multiplying elements of the current data with elements of `v`

virtual self_type &	operator/= (const self_type &v)
	dividing all elements of the current data by elements of `v`

virtual self_type &	operator+= (const float v)
	adding an `float` to the elements of the current data

virtual self_type &	operator-= (const float v)
	subtracting an `float` from the elements of the current data

virtual self_type &	operator*= (const float v)
	multiplying the elements of the current data with an `float`

virtual self_type &	operator/= (const float v)
	dividing the elements of the current data by an `float`

virtual STIR_DEPRECATED void	axpby (const float a, const ProjData &x, const float b, const ProjData &y)

virtual void	xapyb (const ProjData &x, const float a, const ProjData &y, const float b)
	set values of the array to xa+yb, where a and b are scalar, and x and y are ProjData

virtual void	xapyb (const ProjData &x, const ProjData &a, const ProjData &y, const ProjData &b)
	set values of the array to xa+yb, where a, b, x and y are ProjData

virtual void	sapyb (const float a, const ProjData &y, const float b)
	set values of the array to selfa+yb where a and b are scalar, y is ProjData

virtual void	sapyb (const ProjData &a, const ProjData &y, const ProjData &b)
	set values of the array to selfa+yb where a, b and y are ProjData

Public Member Functions inherited from stir::ExamData
	ExamData ()
	ExamData.

	ExamData (const shared_ptr< const ExamInfo > &_this_exam)

virtual const ExamInfo &	get_exam_info () const

virtual shared_ptr< const ExamInfo >	get_exam_info_sptr () const
	Get shared pointer to exam info.

virtual void	set_exam_info (ExamInfo const &)
	change exam info

void	set_exam_info_sptr (shared_ptr< const ExamInfo > new_exam_info_sptr)

Public Member Functions inherited from stir::DataWithProjDataInfo
	DataWithProjDataInfo ()
	Default constructor sets internal member to 0.

	DataWithProjDataInfo (const shared_ptr< const ProjDataInfo > &proj_data_info_sptr_v)

virtual const ProjDataInfo &	get_proj_data_info () const

virtual shared_ptr< const ProjDataInfo >	get_proj_data_info_sptr () const
	Get shared pointer to ProjData info.

int	get_num_segments () const
	Get number of segments.

int	get_num_axial_poss (const int segment_num) const
	Get number of axial positions per segment.

int	get_num_views () const
	Get number of views.

int	get_num_tangential_poss () const
	Get number of tangential positions.

int	get_num_tof_poss () const
	Get number of TOF positions.

int	get_min_tof_pos_num () const
	Get the index of the first timing position.

int	get_max_tof_pos_num () const
	Get the index of the last timing position.

int	get_tof_mash_factor () const
	Get TOG mash factor.

int	get_min_segment_num () const
	Get minimum segment number.

int	get_max_segment_num () const
	Get maximum segment number.

int	get_min_axial_pos_num (const int segment_num) const
	Get mininum axial position per segmnet.

int	get_max_axial_pos_num (const int segment_num) const
	Get maximum axial position per segment.

int	get_min_view_num () const
	Get minimum view number.

int	get_max_view_num () const
	Get maximum view number.

int	get_min_tangential_pos_num () const
	Get minimum tangential position number.

int	get_max_tangential_pos_num () const
	Get maximum tangential position number.

Static Public Member Functions
static shared_ptr< ProjData >	read_from_file (const std::string &filename, const std::ios::openmode open_mode=std::ios::in)
	A static member to get the projection data from a file.

static std::vector< int >	standard_segment_sequence (const ProjDataInfo &pdi)
	Return a vector with segment numbers in a standard order.

Additional Inherited Members
Protected Attributes inherited from stir::ExamData
shared_ptr< const ExamInfo >	exam_info_sptr

Protected Attributes inherited from stir::DataWithProjDataInfo
shared_ptr< const ProjDataInfo >	proj_data_info_sptr

Detailed Description

The (abstract) base class for the projection data.

Projection data are supposed to be indexed by 4 coordinates (corresponding to the most general case of projection data in all directions of a 3D volume):

segment_num : indexes polar angle theta, or ring difference (segment_num==0 are the projections orthogonal to the scanner axis)
view_num : indexes azimuthal angle phi
axial_pos_num : indexes different positions along the scanner axis (corresponding to 'z', or different rings)
tangential_pos_num : indexes different positions in a direction tangential to the scanner cylinder. (sometimes called 'bin' or 'element')
timing_pos_num : indexes different positions in the LOR, based on the photon detection time difference.

The number of axial positions is allowed to depend on segment_num.

Different 'subsets' of the 4D data are possible by fixing one or more of the 4 coordinates. Currently we support the following cases

SegmentBySinogram (fixed segment_num)
SegmentByView (fixed segment_num)
Viewgram (fixed segment_num and view_num)
Sinogram (fixed segment_num and axial_pos_num)
RelatedViewgrams (different Viewgrams related by symmetry)

This abstract class provides the general interface for accessing the projection data. This works with get_ and set_ pairs. (Generally, the 4D dataset might be too big to be kept in memory.) In addition, there are get_empty_ functions that just create the corresponding object of appropriate sizes etc. but filled with 0.

One important member of this class is get_proj_data_info_sptr() which allows access to a ProjDataInfo object, which describes the dimensions of the data, the scanner type, the geometry ...

Warning: The arguments 'make_num_tangential_poss_odd' are temporary and will be deleted in the next release.

Member Function Documentation

◆ read_from_file()

shared_ptr< ProjData > stir::ProjData::read_from_file	(	const std::string &	filename,
		const std::ios::openmode	openmode = std::ios::in )

static

A static member to get the projection data from a file.

This function will attempt to determine the type of projection data in the file, construct an object of the appropriate type, and return a pointer to the object.

The return value is a shared_ptr, to make sure that the caller will delete the object.

If more than 1 projection data set is in the file, only the first is read.

When the file is not readable for some reason, the program is aborted by calling error().

Currently supported:

Interfile (using read_interfile_PDFS())
ECAT 7 3D sinograms and attenuation files >li> GE RDF9 (in HDF5)

Developer's note: ideally the return value would be an stir::unique_ptr.

References stir::GE::RDF_HDF5::GEHDF5Wrapper::check_GE_signature(), stir::error(), stir::FileSignature::get_signature(), stir::info(), stir::ecat::ecat7::is_ECAT7_attenuation_file(), stir::ecat::ecat7::is_ECAT7_emission_file(), stir::ecat::ecat7::is_ECAT7_file(), stir::is_interfile_signature(), read_from_file(), and stir::read_interfile_PDFS().

Referenced by stir::CListModeDataSAFIR< CListRecordT >::CListModeDataSAFIR(), stir::ReconstructionTests< TargetT >::construct_input_data(), stir::AnalyticReconstruction::post_processing(), stir::FindMCNormFactors::post_processing(), stir::LmToProjData::post_processing(), stir::MoveProjData::post_processing(), stir::PoissonLogLikelihoodWithLinearModelForMeanAndProjData< TargetT >::post_processing(), stir::ProjDataRebinning::post_processing(), stir::ScatterEstimation::post_processing(), read_from_file(), stir::ProjDataInMemory::read_from_file(), stir::DataSymmetriesForBins_PET_CartesianGridTests::run_tests(), stir::ProjMatrixByBinUsingInterpolationTests::run_tests(), stir::stir_mathTests::run_tests(), stir::TestDataProcessorProjectors::run_tests(), stir::TestProjDataInfoSubsets::run_tests(), stir::TestProjDataInfoSubsetsSPECTUB::run_tests(), stir::PoissonLogLikelihoodWithLinearModelForMeanAndProjData< DiscretisedDensity< 3, float > >::set_num_subsets(), and stir::ScatterEstimation::set_up().

◆ get_viewgram()

virtual Viewgram< float > stir::ProjData::get_viewgram	(	const int	view,
		const int	segment_num,
		const bool	make_num_tangential_poss_odd = false,
		const int	timing_pos = 0 ) const

pure virtual

Get viewgram.

Deprecated: Use get_viewgram(const ViewgramIndices&) instead.

Implemented in stir::ProjDataFromStream, and stir::ProjDataInMemory.

References get_viewgram().

Referenced by get_related_viewgrams(), get_segment_by_sinogram(), get_segment_by_view(), get_subset(), get_viewgram(), and get_viewgram().

◆ set_viewgram()

virtual Succeeded stir::ProjData::set_viewgram ( const Viewgram< float > & )

pure virtual

Set viewgram.

Implemented in stir::ProjDataFromStream, and stir::ProjDataInMemory.

Referenced by set_related_viewgrams(), set_segment(), and set_segment().

◆ get_sinogram()

virtual Sinogram< float > stir::ProjData::get_sinogram	(	const int	ax_pos_num,
		const int	segment_num,
		const bool	make_num_tangential_poss_odd = false,
		const int	timing_pos = 0 ) const

pure virtual

Get sinogram.

Deprecated: Use get_sinogram(const SinogramIndices&) instead .

Implemented in stir::ProjDataFromStream, and stir::ProjDataInMemory.

References get_sinogram().

Referenced by stir::get_scale_factors_per_sinogram(), get_sinogram(), get_sinogram(), stir::inverse_SSRB(), stir::ecat::ecat6::ProjData_to_ECAT6(), stir::scale_sinograms(), and stir::SSRB().

◆ set_sinogram()

virtual Succeeded stir::ProjData::set_sinogram ( const Sinogram< float > & )

pure virtual

Set sinogram.

Implemented in stir::ProjDataFromStream, and stir::ProjDataInMemory.

References fill(), get_empty_related_viewgrams(), get_empty_segment_by_sinogram(), get_empty_segment_by_view(), get_empty_sinogram(), get_empty_viewgram(), get_related_viewgrams(), get_segment_by_sinogram(), get_segment_by_view(), get_subset(), ProjData(), set_related_viewgrams(), set_segment(), and standard_segment_sequence().

Referenced by stir::inverse_SSRB(), stir::scale_sinograms(), and stir::SSRB().

◆ get_empty_viewgram()

Viewgram< float > stir::ProjData::get_empty_viewgram	(	const int	view,
		const int	segment_num,
		const bool	make_num_tangential_poss_odd = false,
		const int	timing_pos = 0 ) const

Get empty viewgram.

Deprecated: Use get_viewgram(const ViewgramIndices&) instead.

References get_empty_viewgram().

◆ get_empty_sinogram()

Sinogram< float > stir::ProjData::get_empty_sinogram	(	const int	ax_pos_num,
		const int	segment_num,
		const bool	make_num_tangential_poss_odd = false,
		const int	timing_pos = 0 ) const

Get empty_sinogram.

Deprecated: Use get_sinogram(const SinogramIndices&) instead .

References get_empty_sinogram().

◆ get_empty_segment_by_view()

SegmentByView< float > stir::ProjData::get_empty_segment_by_view	(	const int	segment_num,
		const bool	make_num_tangential_poss_odd = false,
		const int	timing_pos = 0 ) const

Get empty segment view.

Deprecated: Use get_empty_segment_by_sinogram(const SegmentIndices&) instead .

References get_empty_segment_by_view().

◆ get_empty_segment_by_sinogram()

SegmentBySinogram< float > stir::ProjData::get_empty_segment_by_sinogram	(	const int	segment_num,
		const bool	make_num_tangential_poss_odd = false,
		const int	timing_pos = 0 ) const