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.

	~ProjData () override
	Destructor.

shared_ptr< const ProjDataInfo >	get_proj_data_info_sptr () const
	Get shared pointer to proj data info.

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. More...

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. More...

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. More...

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. More...

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. More...

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. More...

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

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. More...

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 More...

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

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

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

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 timgin 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.

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

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

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. More...

	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 More...

void	set_exam_info_sptr (shared_ptr< const ExamInfo > new_exam_info_sptr)

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. More...

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

Protected Attributes
shared_ptr< const ProjDataInfo >	proj_data_info_sptr

Protected Attributes inherited from stir::ExamData
shared_ptr< const ExamInfo >	exam_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::FileSignature::get_signature(), and stir::info().

Referenced by stir::CListModeDataSAFIR< CListRecordT >::CListModeDataSAFIR(), stir::ScatterSimulation::get_exam_info_sptr(), stir::ScatterEstimation::post_processing(), stir::TestDataProcessorProjectors::run_tests(), stir::TestProjDataInfoSubsets::run_tests(), stir::ScatterEstimation::set_up(), and stir::PoissonLogLikelihoodWithLinearModelForMeanAndProjDataTests::test_approximate_Hessian_concavity().

◆ 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.

Referenced by stir::NiftyPETHelper::convert_proj_data_stir_to_niftyPET(), stir::ArcCorrection::do_arc_correction(), and stir::TestProjDataInfoSubsets::TestProjDataInfoSubsets().

◆ 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.

Referenced by stir::get_scale_factors_per_sinogram(), stir::make_det_pair_data(), and stir::scale_sinograms().

◆ 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.

◆ 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 .

◆ 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 .

◆ 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

Get empty segment sino.

Deprecated:: Use get_empty_segment_by_sinogram(const SegmentIndices&) instead .

◆ get_segment_by_sinogram()

SegmentBySinogram< float > stir::ProjData::get_segment_by_sinogram	(	const int	segment_num,
		const int	timing_pos = `0`
	)		const

virtual

Get segment by sinogram.

Deprecated:: Use get_segment_by_sinogram(const SegmentIndices&) instead.

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

References stir::SegmentBySinogram< elemT >::set_viewgram().

Referenced by stir::ProjDataFromStream::get_segment_by_view(), norm(), and xapyb().

◆ get_segment_by_view()

SegmentByView< float > stir::ProjData::get_segment_by_view	(	const int	segment_num,
		const int	timing_pos = `0`
	)		const

virtual

Get segment by view.

Deprecated:: Use get_segment_by_view(const SegmentIndices&) instead.

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

References stir::SegmentByView< elemT >::set_viewgram().

Referenced by fill(), stir::GeneralisedPoissonNoiseGenerator::generate_random(), stir::ProjDataFromStream::get_segment_by_sinogram(), stir::ScatterEstimation::process_data(), and stir::transform_3d_object().

◆ fill() [1/2]

void stir::ProjData::fill ( const float value )

virtual

set all bins to the same value

will call error() if setting failed

Reimplemented in stir::ProjDataInMemory.

References stir::error(), and stir::Array< 3, elemT >::fill().

Referenced by stir::ProjDataInMemory::fill(), stir::ForwardProjectorByBin::forward_project(), stir::ScatterEstimation::upsample_and_fit_scatter_estimate(), and write_to_file().

◆ fill() [2/2]

void stir::ProjData::fill ( const ProjData & proj_data )

virtual

set all bins from another ProjData object

will call error() if setting failed or if the 'source' proj_data is not compatible. The current check requires at least the same segment numbers (but the source can have more), all other geometric parameters have to be the same.

Reimplemented in stir::ProjDataInMemory.

References stir::error(), get_max_segment_num(), get_min_segment_num(), get_proj_data_info_sptr(), and get_segment_by_view().

◆ standard_segment_sequence()

std::vector< int > stir::ProjData::standard_segment_sequence ( const ProjDataInfo & pdi )

static

Return a vector with segment numbers in a standard order.

This returns a vector filled as $ [0, 1, -1, 2, -2, ...] $ . In the (unlikely!) case that the segment range is not symmetric, the sequence just continues with valid segment numbers, e.g. $ [0, 1, -1, 2, 3 ] $ .

References stir::ProjDataInfo::get_max_segment_num(), stir::ProjDataInfo::get_min_segment_num(), and stir::ProjDataInfo::get_num_segments().

◆ fill_from()

template<typename iterT >

iterT stir::ProjData::fill_from ( iterT array_iter )

inline

set all bins from an array iterator

Returns: array_iter advanced over the number of bins (as std::copy)

Data are filled by SegmentBySinogram, with the TOF index running slowest (from - to +) and segment order given by standard_segment_sequence().

This order would be useful to fill data from a 4D array constructed as follows:

Array<4,float> array(IndexRange4D(p.get_num_tof_poss(), p.get_num_non_tof_sinograms(), p.get_num_views(),

p.get_num_tangential_poss()));

See also: copy_to() (consistency between these 2 is guaranteed)

Warning: there is no range-check on array_iter

◆ copy_to()

template<typename iterT >

iterT stir::ProjData::copy_to ( iterT array_iter ) const

inline

Copy all bins to a range specified by a (forward) iterator.

Returns: array_iter advanced over the number of bins (as std::copy)

Data are filled by SegmentBySinogram, with TOF index running slowest (from - to +) and segment order given by standard_segment_sequence().

See also: fill_from() (consistency between these 2 is guaranteed)

Warning: there is no range-check on array_iter

References stir::sum(), and stir::write_to_file().

◆ get_num_sinograms()

int stir::ProjData::get_num_sinograms ( ) const

inline

Get the total number of sinograms.

Note that this will count TOF sinograms as well.

See also: get_num_non_tof_sinograms()

◆ get_num_non_tof_sinograms()

int stir::ProjData::get_num_non_tof_sinograms ( ) const

inline

Get the number of non-tof sinograms.

Note that this is the sum of the number of axial poss over all segments.

See also: get_num_sinograms()

◆ axpby()

void stir::ProjData::axpby	(	const float	a,
		const ProjData &	x,
		const float	b,
		const ProjData &	y
	)

virtual

Deprecated:: a*x+b*y (use xapyb)

Reimplemented in stir::ProjDataInMemory.

References xapyb().

The documentation for this class was generated from the following files:

/home/sirfuser/devel/STIRdistrib/STIR/src/include/stir/ProjData.h
/home/sirfuser/devel/STIRdistrib/STIR/src/buildblock/ProjData.cxx
/home/sirfuser/devel/STIRdistrib/STIR/src/include/stir/ProjData.inl

Public Member Functions

Static Public Member Functions

Protected Attributes

Detailed Description

Member Function Documentation

◆ read_from_file()

◆ get_viewgram()

◆ get_sinogram()

◆ get_empty_viewgram()

◆ get_empty_sinogram()

◆ get_empty_segment_by_view()

◆ get_empty_segment_by_sinogram()

◆ get_segment_by_sinogram()

◆ get_segment_by_view()

◆ fill() [1/2]

◆ fill() [2/2]

◆ standard_segment_sequence()

◆ fill_from()

◆ copy_to()

◆ get_num_sinograms()

◆ get_num_non_tof_sinograms()

◆ axpby()