This class contains the implementation of the FBP3DRP algorithm. More...

#include "stir/analytic/FBP3DRP/FBP3DRPReconstruction.h"

Inheritance diagram for stir::FBP3DRPReconstruction:

[legend]

Public Member Functions
	FBP3DRPReconstruction ()
	Default constructor (calls set_defaults()).
	FBP3DRPReconstruction (const std::string &parameter_filename)
	Constructor, initialises everything from parameter file, or (when parameter_filename == "") by calling ask_parameters().
std::string	method_info () const override
	This method returns the type of the reconstruction algorithm during the reconstruction, here it is FBP3DRP.
Succeeded	set_up (shared_ptr< DiscretisedDensity< 3, float > > const &target_image_sptr) override
virtual void	do_process_viewgrams (RelatedViewgrams< float > &viewgrams, int rmin, int rmax, int orig_min_ring, int orig_max_ring)
void	ask_parameters ()
Public Member Functions inherited from stir::RegisteredParsingObject< FBP3DRPReconstruction, Reconstruction< DiscretisedDensity< 3, float > >, AnalyticReconstruction >
std::string	get_registered_name () const override
	Returns Derived::registered_name.
std::string	parameter_info () override
	Returns a string with all parameters and their values, in a form suitable for parsing again.
Public Member Functions inherited from stir::AnalyticReconstruction
virtual DiscretisedDensity< 3, float > *	construct_target_image_ptr () const
	construct an image from parameters set (e.g. during parsing)
Succeeded	reconstruct () override
	reconstruct and write to file
Succeeded	reconstruct (shared_ptr< TargetT > const &target_image_sptr) override
	executes the reconstruction storing result in `target_image_sptr`
void	set_input_data (const shared_ptr< ExamData > &) override
	set input data
const ProjData &	get_input_data () const override
	get input data
int	get_output_image_size_xy () const
void	set_output_image_size_xy (int)
int	get_output_image_size_z () const
void	set_output_image_size_z (int)
float	get_zoom_xy () const
void	set_zoom_xy (float)
float	get_zoom_z () const
void	set_zoom_z (float)
const CartesianCoordinate3D< float > &	get_offset () const
void	set_offset (const CartesianCoordinate3D< float > &)
Public Member Functions inherited from stir::Reconstruction< DiscretisedDensity< 3, float > >
	Reconstruction ()
	default constructor (calls set_defaults())
	~Reconstruction () override
	virtual destructor
virtual Succeeded	set_up (shared_ptr< DiscretisedDensity< 3, float > > const &target_data_sptr)
	operations prior to the reconstruction
void	set_output_filename_prefix (const std::string &)
	file name for output reconstructed images
void	set_output_file_format_ptr (const shared_ptr< OutputFileFormat< DiscretisedDensity< 3, float > > > &)
	defines the format of the output files
void	set_post_processor_sptr (const shared_ptr< DataProcessor< DiscretisedDensity< 3, float > > > &)
	post-filter
void	set_disable_output (bool _val)
	set_disable_output
shared_ptr< DiscretisedDensity< 3, float > >	get_target_image ()
	get_reconstructed_image
Public Member Functions inherited from stir::ParsingObject
	ParsingObject (const ParsingObject &)
ParsingObject &	operator= (const ParsingObject &)
bool	parse (std::istream &f)
bool	parse (const char *const filename)
void	ask_parameters ()
Public Member Functions inherited from stir::TimedObject
void	reset_timers ()
	reset all timers kept by this object
void	stop_timers () const
	stop all timers kept by this object
void	start_timers (bool do_reset=false) const
	start all timers kept by this object
double	get_CPU_timer_value () const
	get current value of the CPU timer (since first use or last reset)
double	get_wall_clock_timer_value () const
	get current value of the wall-clock timer (since first use or last reset)

Static Public Attributes
static const char *const	registered_name = "FBP3DRP"
	Name which will be used when parsing a ProjectorByBinPair object.

Protected Member Functions
Succeeded	actual_reconstruct (shared_ptr< DiscretisedDensity< 3, float > > const &) override
	Implementation of the reconstruction.
void	do_best_fit (const Sinogram< float > &sino_measured, const Sinogram< float > &sino_calculated)
	Best fit of forward projected sinograms.
void	do_2D_reconstruction ()
	2D FBP implementation.
void	do_save_img (const char *file, const VoxelsOnCartesianGrid< float > &data) const
	Save image data.
void	do_read_image2D ()
	Read image estimated from 2D FBP.
void	do_3D_Reconstruction (VoxelsOnCartesianGrid< float > &image)
	3D reconstruction implementation.
void	do_arc_correction (RelatedViewgrams< float > &viewgrams) const
	Arc-correction viewgrams.
void	do_grow3D_viewgram (RelatedViewgrams< float > &viewgrams, int rmin, int rmax)
	Growing 8 viewgrams in both ring and bin directions.
void	do_forward_project_view (RelatedViewgrams< float > &viewgrams, int rmin, int rmax, int orig_min_ring, int orig_max_ring) const
	3D forward projection implentation by view.
void	do_colsher_filter_view (RelatedViewgrams< float > &viewgrams)
	Apply Colsher filter to 8 viewgrams.
void	do_3D_backprojection_view (RelatedViewgrams< float > const &viewgrams, int rmin, int rmax)
	3D backprojection implentation for 8 viewgrams.
void	do_log_file (const VoxelsOnCartesianGrid< float > &image)
	Saving CPU timing and values of reconstruction parameters into a log file.
virtual void	do_byview_initialise (const VoxelsOnCartesianGrid< float > &image) const
virtual void	do_byview_finalise (VoxelsOnCartesianGrid< float > &image)
bool	post_processing () override
	used to check acceptable parameter ranges, etc...
virtual void	check (DiscretisedDensity< 3, float > const &target_data) const
	do consistency checks
void	initialise (const std::string &parameter_filename)
	This function initialises all parameters, either via parsing, or by calling ask_parameters() (when parameter_filename is the empty string).
void	set_defaults () override
	Set defaults before parsing.
void	initialise_keymap () override
	Initialise all keywords.
bool	post_processing () override
	used to check acceptable parameters after parsing
virtual void	set_key_values ()
	This will be called before parsing or parameter_info is called.

Protected Attributes
int	display_level
	Switch to display intermediate images, 0,1,2.
int	save_intermediate_files
	Switch to save files after each segment, 0 or 1.
std::string	image_for_reprojection_filename
	Filename of image used in the reprojection step (default is empty).
int	num_segments_to_combine
	Number of segments to combine with SSRB before calling FBP.
int	PadS
	Transaxial extension for FFT.
int	PadZ
	Axial extension for FFT.
double	alpha_ramp
	Ramp filter: Alpha value.
double	fc_ramp
	Ramp filter: Cut off frequency.
double	alpha_colsher_axial
	Alpha parameter for Colsher filter in axial direction.
double	fc_colsher_axial
	Cut-off frequency for Colsher filter in axial direction.
double	alpha_colsher_planar
	Alpha parameter for Colsher filter in planar direction.
double	fc_colsher_planar
	Cut-off frequency for Colsher filter in planar direction.
int	colsher_stretch_factor_axial
	Define Colsher at larger size than used for filtering, axial direction.
int	colsher_stretch_factor_planar
	Define Colsher at larger size than used for filtering, planar direction.
int	fit_projections
	=1 => apply additional fitting procedure to forward projected data (DISABLED)
std::string	input_filename
	the input projection data file name
int	max_segment_num_to_process
	the maximum absolute ring difference number to use in the reconstruction
shared_ptr< ProjData >	proj_data_ptr
	points to the object for the total input projection data
ParseAndCreateFrom< TargetT, ProjData >	target_parameter_parser
std::string	output_filename_prefix
	file name for output reconstructed images
shared_ptr< OutputFileFormat< DiscretisedDensity< 3, float > > >	output_file_format_ptr
	defines the format of the output files
shared_ptr< DataProcessor< DiscretisedDensity< 3, float > > >	post_filter_sptr
	post-filter
bool	_already_set_up
shared_ptr< DiscretisedDensity< 3, float > >	target_data_sptr
	target_data_sptr
bool	_disable_output
	_disable_output
int	_verbosity
	Verbosity level.
KeyParser	parser

Additional Inherited Members
Public Types inherited from stir::AnalyticReconstruction
typedef DiscretisedDensity< 3, float >	TargetT
Static Public Member Functions inherited from stir::RegisteredParsingObject< FBP3DRPReconstruction, Reconstruction< DiscretisedDensity< 3, float > >, AnalyticReconstruction >
static Reconstruction< DiscretisedDensity< 3, float > > *	read_from_stream (std::istream *)
	Construct a new object (of type Derived) by parsing the istream.
Static Public Member Functions inherited from stir::RegisteredObject< Reconstruction< DiscretisedDensity< 3, float > > >
static Reconstruction< DiscretisedDensity< 3, float > > *	read_registered_object (std::istream *in, const std::string &registered_name)
	Construct a new object (of a type derived from Root, its actual type determined by the registered_name parameter) by parsing the istream.
static Reconstruction< DiscretisedDensity< 3, float > > *	ask_type_and_parameters ()
	ask the user for the type, and then calls read_registered_object(0, type)
static void	list_registered_names (std::ostream &stream)
	List all possible registered names to the stream.
Protected Types inherited from stir::RegisteredObject< Reconstruction< DiscretisedDensity< 3, float > > >
typedef Reconstruction< DiscretisedDensity< 3, float > > ()	RootFactory(std::istream *)
	The type of a root factory is a function, taking an istream* as argument, and returning a Root*.
typedef FactoryRegistry< std::string, RootFactory, interfile_less >	RegistryType
	The type of the registry.
Static Protected Member Functions inherited from stir::RegisteredObject< Reconstruction< DiscretisedDensity< 3, float > > >
static RegistryType &	registry ()
	Static function returning the registry.

Detailed Description

This class contains the implementation of the FBP3DRP algorithm.

This class implements the 3DRP algorithm (Kinahan and Rogers) as a specific case of a 3D FBP reconstruction algorithm.

Some care is taken to achieve a fairly general implementation. For instance, the number of sinograms in the oblique segments is arbitrary (i.e. does not have to be related to what you would get from a cylindrical PET scanner). Also, scale factors are inserted such that the reconstructed image has (almost) the same scale independent of the number of segments that is used.

Nevertheless, this is an analytic algorithm, and it implements a discrete version of a continuous inversion formula. This will work best (but of course slowest) when the number of segments is large.

This implementation is specific for data using sampling corresponding to cylindrical PET scanners. This dependency essentially only occurs in the backprojection where a Jacobian is necessary in this case, and where the number of ring differences in each segment is taken into account. It would be not too difficult to make a version that works on e.g. spherical sampling.

About zooming (rescaling + offset):

1) The 2D FBP process works at full resolution, i.e on the original number of bins, and with a pixel size equal to the bin size. 2) For the process of oblique sinograms:

Forward projection works at full resolution i.e forward projection works from images without zooming and complete missing projection data on normal sinograms
Colsher filter is then applied on complete data
3D backprojection then puts this data into an image with appropriate voxel sizes, i.e. it is up to the backprojector to perform the zooming.
So, no zooming is needed on the final image.

Constructor & Destructor Documentation

◆ FBP3DRPReconstruction() [1/2]

stir::FBP3DRPReconstruction::FBP3DRPReconstruction ( )

Default constructor (calls set_defaults()).

References FBP3DRPReconstruction().

Referenced by FBP3DRPReconstruction(), and FBP3DRPReconstruction().

◆ FBP3DRPReconstruction() [2/2]

stir::FBP3DRPReconstruction::FBP3DRPReconstruction ( const std::string & parameter_filename )

explicit

Constructor, initialises everything from parameter file, or (when parameter_filename == "") by calling ask_parameters().

References FBP3DRPReconstruction(), and stir::Reconstruction< DiscretisedDensity< 3, float > >::initialise().

Member Function Documentation

◆ method_info()

std::string stir::FBP3DRPReconstruction::method_info ( ) const

overridevirtual

This method returns the type of the reconstruction algorithm during the reconstruction, here it is FBP3DRP.

Implements stir::Reconstruction< DiscretisedDensity< 3, float > >.

References method_info().

Referenced by method_info().

◆ actual_reconstruct()

Succeeded stir::FBP3DRPReconstruction::actual_reconstruct ( shared_ptr< DiscretisedDensity< 3, float > > const & target_image_ptr )

overrideprotectedvirtual

Implementation of the reconstruction.

This method implements the reconstruction by giving as input the emission sinogram data corrected for attenuation, scatter, dead time, and returns the output reconstructed image

Implements stir::AnalyticReconstruction.

References actual_reconstruct(), alpha_colsher_axial, alpha_colsher_planar, stir::Reconstruction< DiscretisedDensity< 3, float > >::check(), colsher_stretch_factor_axial, colsher_stretch_factor_planar, display_level, do_2D_reconstruction(), do_3D_Reconstruction(), do_best_fit(), do_log_file(), do_read_image2D(), stir::error(), fc_colsher_axial, fc_colsher_planar, stir::Array< num_dimensions, elemT >::find_max(), fit_projections, stir::DataWithProjDataInfo::get_proj_data_info_sptr(), image_for_reprojection_filename, stir::AnalyticReconstruction::max_segment_num_to_process, stir::Reconstruction< DiscretisedDensity< 3, float > >::output_filename_prefix, stir::RegisteredParsingObject< FBP3DRPReconstruction, Reconstruction< DiscretisedDensity< 3, float > >, AnalyticReconstruction >::parameter_info(), stir::AnalyticReconstruction::proj_data_ptr, and stir::warning().

Referenced by actual_reconstruct().

◆ do_best_fit()

void stir::FBP3DRPReconstruction::do_best_fit	(	const Sinogram< float > &	sino_measured,
		const Sinogram< float > &	sino_calculated )

protected

Best fit of forward projected sinograms.

References stir::determinant(), do_best_fit(), stir::Array< num_dimensions, elemT >::find_max(), stir::DataWithProjDataInfo::get_max_tangential_pos_num(), stir::DataWithProjDataInfo::get_max_view_num(), stir::DataWithProjDataInfo::get_min_tangential_pos_num(), stir::DataWithProjDataInfo::get_min_view_num(), stir::DataWithProjDataInfo::get_num_tangential_poss(), stir::DataWithProjDataInfo::get_num_views(), stir::Array< num_dimensions, elemT >::sum(), and stir::warning().

Referenced by actual_reconstruct(), and do_best_fit().

◆ do_2D_reconstruction()

void stir::FBP3DRPReconstruction::do_2D_reconstruction ( )

protected

2D FBP implementation.

References stir::Reconstruction< DiscretisedDensity< 3, float > >::_disable_output, alpha_ramp, display_level, do_2D_reconstruction(), do_save_img(), fc_ramp, stir::max_filename_length, num_segments_to_combine, stir::Reconstruction< DiscretisedDensity< 3, float > >::output_filename_prefix, PadS, stir::RegisteredParsingObject< Derived, Base, Parent >::parameter_info(), stir::AnalyticReconstruction::proj_data_ptr, stir::AnalyticReconstruction::reconstruct(), and save_intermediate_files.

Referenced by actual_reconstruct(), and do_2D_reconstruction().

◆ do_save_img()

void stir::FBP3DRPReconstruction::do_save_img	(	const char *	file,
		const VoxelsOnCartesianGrid< float > &	data ) const

protected

Save image data.

References do_save_img(), stir::Array< num_dimensions, elemT >::find_max(), stir::Array< num_dimensions, elemT >::find_min(), stir::Reconstruction< DiscretisedDensity< 3, float > >::output_file_format_ptr, and stir::Array< num_dimensions, elemT >::sum().

Referenced by do_2D_reconstruction(), do_3D_Reconstruction(), and do_save_img().

◆ do_read_image2D()

void stir::FBP3DRPReconstruction::do_read_image2D ( )

protected

Read image estimated from 2D FBP.

References do_read_image2D(), image_for_reprojection_filename, and stir::read_from_file().

Referenced by actual_reconstruct(), and do_read_image2D().

◆ do_3D_Reconstruction()

void stir::FBP3DRPReconstruction::do_3D_Reconstruction ( VoxelsOnCartesianGrid< float > & image )

protected

3D reconstruction implementation.

References stir::Reconstruction< DiscretisedDensity< 3, float > >::_disable_output, do_3D_Reconstruction(), do_save_img(), stir::Array< num_dimensions, elemT >::find_max(), stir::Array< num_dimensions, elemT >::find_min(), stir::AnalyticReconstruction::max_segment_num_to_process, stir::Reconstruction< DiscretisedDensity< 3, float > >::output_filename_prefix, stir::AnalyticReconstruction::proj_data_ptr, save_intermediate_files, stir::SegmentIndices::segment_num(), stir::Array< num_dimensions, elemT >::sum(), and stir::ViewgramIndices::view_num().

Referenced by actual_reconstruct(), and do_3D_Reconstruction().

◆ do_arc_correction()

void stir::FBP3DRPReconstruction::do_arc_correction ( RelatedViewgrams< float > & viewgrams ) const

protected

Arc-correction viewgrams.

References do_arc_correction().

Referenced by do_arc_correction().

◆ do_grow3D_viewgram()

void stir::FBP3DRPReconstruction::do_grow3D_viewgram	(	RelatedViewgrams< float > &	viewgrams,
		int	rmin,
		int	rmax )

protected

Growing 8 viewgrams in both ring and bin directions.

References do_grow3D_viewgram(), stir::DataWithProjDataInfo::get_max_tangential_pos_num(), stir::DataWithProjDataInfo::get_min_tangential_pos_num(), and stir::RelatedViewgrams< elemT >::grow().

Referenced by do_grow3D_viewgram().

◆ do_forward_project_view()

void stir::FBP3DRPReconstruction::do_forward_project_view	(	RelatedViewgrams< float > &	viewgrams,
		int	rmin,
		int	rmax,
		int	orig_min_ring,
		int	orig_max_ring ) const

protected

3D forward projection implentation by view.

References display_level, do_forward_project_view(), stir::error(), stir::RelatedViewgrams< elemT >::find_max(), and fit_projections.

Referenced by do_forward_project_view().

◆ do_colsher_filter_view()

void stir::FBP3DRPReconstruction::do_colsher_filter_view ( RelatedViewgrams< float > & viewgrams )

protected

Apply Colsher filter to 8 viewgrams.

References _PI, alpha_colsher_axial, alpha_colsher_planar, stir::RelatedViewgrams< elemT >::begin(), display_level, do_colsher_filter_view(), stir::RelatedViewgrams< elemT >::end(), stir::error(), fc_colsher_axial, fc_colsher_planar, stir::RelatedViewgrams< elemT >::find_max(), stir::RelatedViewgrams< elemT >::get_basic_segment_num(), stir::DataWithProjDataInfo::get_num_tangential_poss(), stir::RelatedViewgrams< elemT >::get_num_viewgrams(), stir::DataWithProjDataInfo::get_proj_data_info_sptr(), stir::AnalyticReconstruction::max_segment_num_to_process, PadS, and PadZ.

Referenced by do_colsher_filter_view().

◆ do_3D_backprojection_view()

void stir::FBP3DRPReconstruction::do_3D_backprojection_view	(	RelatedViewgrams< float > const &	viewgrams,
		int	rmin,
		int	rmax )

protected

3D backprojection implentation for 8 viewgrams.

References do_3D_backprojection_view().

Referenced by do_3D_backprojection_view().

◆ do_log_file()

void stir::FBP3DRPReconstruction::do_log_file ( const VoxelsOnCartesianGrid< float > & image )

protected

Saving CPU timing and values of reconstruction parameters into a log file.

References do_log_file(), stir::TimedObject::get_CPU_timer_value(), stir::max_filename_length, stir::Reconstruction< DiscretisedDensity< 3, float > >::output_filename_prefix, stir::RegisteredParsingObject< FBP3DRPReconstruction, Reconstruction< DiscretisedDensity< 3, float > >, AnalyticReconstruction >::parameter_info(), and stir::warning().

Referenced by actual_reconstruct(), and do_log_file().

Member Data Documentation

◆ display_level

int stir::FBP3DRPReconstruction::display_level

protected

Switch to display intermediate images, 0,1,2.

Referenced by actual_reconstruct(), do_2D_reconstruction(), do_colsher_filter_view(), and do_forward_project_view().

◆ save_intermediate_files

int stir::FBP3DRPReconstruction::save_intermediate_files

protected

Switch to save files after each segment, 0 or 1.

Referenced by do_2D_reconstruction(), and do_3D_Reconstruction().

◆ image_for_reprojection_filename

std::string stir::FBP3DRPReconstruction::image_for_reprojection_filename

protected

Filename of image used in the reprojection step (default is empty).

If the filename is empty, FBP is used (with filter parameters as specified further).

Warning: This image must have the correct scale. That is, if you use the forward projector on it, you get sinograms of the same scale as the input sinograms. There is NO check on this.

Referenced by actual_reconstruct(), and do_read_image2D().

◆ num_segments_to_combine

int stir::FBP3DRPReconstruction::num_segments_to_combine

protected

Number of segments to combine with SSRB before calling FBP.

default -1 will use SSRB only when the data are not yet axially compressed

Referenced by do_2D_reconstruction().

◆ PadS

int stir::FBP3DRPReconstruction::PadS

protected

Transaxial extension for FFT.

Referenced by do_2D_reconstruction(), and do_colsher_filter_view().

◆ PadZ

int stir::FBP3DRPReconstruction::PadZ

protected

Axial extension for FFT.

Referenced by do_colsher_filter_view().

◆ alpha_ramp

double stir::FBP3DRPReconstruction::alpha_ramp

protected

Ramp filter: Alpha value.

Referenced by do_2D_reconstruction().

◆ fc_ramp

double stir::FBP3DRPReconstruction::fc_ramp

protected

Ramp filter: Cut off frequency.

Referenced by do_2D_reconstruction().

◆ alpha_colsher_axial

double stir::FBP3DRPReconstruction::alpha_colsher_axial

protected

Alpha parameter for Colsher filter in axial direction.

Referenced by actual_reconstruct(), and do_colsher_filter_view().

◆ fc_colsher_axial

double stir::FBP3DRPReconstruction::fc_colsher_axial

protected

Cut-off frequency for Colsher filter in axial direction.

Referenced by actual_reconstruct(), and do_colsher_filter_view().

◆ alpha_colsher_planar

double stir::FBP3DRPReconstruction::alpha_colsher_planar

protected

Alpha parameter for Colsher filter in planar direction.

Referenced by actual_reconstruct(), and do_colsher_filter_view().

◆ fc_colsher_planar

double stir::FBP3DRPReconstruction::fc_colsher_planar

protected

Cut-off frequency for Colsher filter in planar direction.

Referenced by actual_reconstruct(), and do_colsher_filter_view().

◆ colsher_stretch_factor_axial

int stir::FBP3DRPReconstruction::colsher_stretch_factor_axial

protected

Define Colsher at larger size than used for filtering, axial direction.

Referenced by actual_reconstruct().

◆ colsher_stretch_factor_planar

int stir::FBP3DRPReconstruction::colsher_stretch_factor_planar

protected

Define Colsher at larger size than used for filtering, planar direction.

Referenced by actual_reconstruct().

◆ fit_projections

int stir::FBP3DRPReconstruction::fit_projections

protected

=1 => apply additional fitting procedure to forward projected data (DISABLED)

Referenced by actual_reconstruct(), and do_forward_project_view().

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

/home/kris/devel/STIRdistrib/STIR/src/include/stir/analytic/FBP3DRP/FBP3DRPReconstruction.h
/home/kris/devel/STIRdistrib/STIR/src/analytic/FBP3DRP/FBP3DRPReconstruction.cxx

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ FBP3DRPReconstruction() [1/2]

◆ FBP3DRPReconstruction() [2/2]

Member Function Documentation

◆ method_info()

◆ actual_reconstruct()

◆ do_best_fit()

◆ do_2D_reconstruction()

◆ do_save_img()

◆ do_read_image2D()

◆ do_3D_Reconstruction()

◆ do_arc_correction()

◆ do_grow3D_viewgram()

◆ do_forward_project_view()

◆ do_colsher_filter_view()

◆ do_3D_backprojection_view()

◆ do_log_file()

Member Data Documentation

◆ display_level

◆ save_intermediate_files

◆ image_for_reprojection_filename

◆ num_segments_to_combine

◆ PadS

◆ PadZ

◆ alpha_ramp

◆ fc_ramp

◆ alpha_colsher_axial

◆ fc_colsher_axial

◆ alpha_colsher_planar

◆ fc_colsher_planar

◆ colsher_stretch_factor_axial

◆ colsher_stretch_factor_planar

◆ fit_projections