generates projection matrix for SPECT studies More...

#include "stir/recon_buildblock/ProjMatrixByBinSPECTUB.h"

Inheritance diagram for stir::ProjMatrixByBinSPECTUB:

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Public Member Functions
	ProjMatrixByBinSPECTUB ()
	Default constructor (calls set_defaults())

	ProjMatrixByBinSPECTUB (const ProjMatrixByBinSPECTUB &)=delete

	~ProjMatrixByBinSPECTUB () override
	Destructor (deallocates UB SPECT memory)

void	set_up (const shared_ptr< const ProjDataInfo > &proj_data_info_ptr, const shared_ptr< const DiscretisedDensity< 3, float >> &density_info_ptr) override
	Checks all necessary geometric info.

bool	get_keep_all_views_in_cache () const

void	set_keep_all_views_in_cache (bool value=true)
	Enable keeping the matrix in memory. More...

std::string	get_attenuation_type () const

void	set_attenuation_type (const std::string &value)
	Set type of attenuation modelling. More...

shared_ptr< const DiscretisedDensity< 3, float > >	get_attenuation_image_sptr () const

void	set_attenuation_image_sptr (const shared_ptr< const DiscretisedDensity< 3, float >> value)
	Sets attenuation image. More...

void	set_attenuation_image_sptr (const std::string &value)

void	set_resolution_model (const float collimator_sigma_0_in_mm, const float collimator_slope_in_mm, const bool full_3D=true)
	Set the parameters for the depth-dependent resolution model. More...

ProjMatrixByBinSPECTUB *	clone () const override

Public Member Functions inherited from stir::RegisteredParsingObject< ProjMatrixByBinSPECTUB, ProjMatrixByBin, ProjMatrixByBin >
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::ProjMatrixByBin
const DataSymmetriesForBins *	get_symmetries_ptr () const
	get a pointer to an object encoding all symmetries that are used by this ProjMatrixByBin

const shared_ptr< DataSymmetriesForBins >	get_symmetries_sptr () const
	get a shared_ptr to an object encoding all symmetries that are used by this ProjMatrixByBin

void	get_proj_matrix_elems_for_one_bin (ProjMatrixElemsForOneBin &, const Bin &) const
	The main method for getting a row of the matrix. More...

void	enable_cache (const bool v=true)

void	store_only_basic_bins_in_cache (const bool v=true)

bool	is_cache_enabled () const

bool	does_cache_store_only_basic_bins () const

void	clear_cache () const
	Remove all elements from the cache.

Public Member Functions inherited from stir::ParsingObject
	ParsingObject (const ParsingObject &)

ParsingObject &	operator= (const ParsingObject &)

void	ask_parameters ()

bool	parse (std::istream &f)

bool	parse (const char *const filename)

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 More...

void	start_timers (bool do_reset=false) const
	start all timers kept by this object More...

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 = "SPECT UB"
	Name which will be used when parsing a ProjMatrixByBin object.

Additional Inherited Members
Static Public Member Functions inherited from stir::RegisteredParsingObject< ProjMatrixByBinSPECTUB, ProjMatrixByBin, ProjMatrixByBin >
static ProjMatrixByBin *	read_from_stream (std::istream *)
	Construct a new object (of type Derived) by parsing the istream. More...

Static Public Member Functions inherited from stir::RegisteredObject< ProjMatrixByBin >
static ProjMatrixByBin *	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. More...

static ProjMatrixByBin *	ask_type_and_parameters ()
	ask the user for the type, and then calls read_registered_object(0, type) More...

static void	list_registered_names (std::ostream &stream)
	List all possible registered names to the stream. More...

Protected Types inherited from stir::RegisteredObject< ProjMatrixByBin >
typedef ProjMatrixByBin (	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.

Protected Member Functions inherited from stir::ProjMatrixByBin
	ProjMatrixByBin ()
	default ctor (calls set_defaults()) More...

Succeeded	get_cached_proj_matrix_elems_for_one_bin (ProjMatrixElemsForOneBin &) const
	The method that tries to get data from the cache. More...

void	cache_proj_matrix_elems_for_one_bin (const ProjMatrixElemsForOneBin &) const
	The method to store data in the cache.

Protected Member Functions inherited from stir::ParsingObject
virtual void	set_key_values ()
	This will be called before parsing or parameter_info is called. More...

Static Protected Member Functions inherited from stir::RegisteredObject< ProjMatrixByBin >
static RegistryType &	registry ()
	Static function returning the registry. More...

Protected Attributes inherited from stir::ProjMatrixByBin
shared_ptr< DataSymmetriesForBins >	symmetries_sptr

bool	cache_disabled

bool	cache_stores_only_basic_bins

bool	tof_enabled
	If activated TOF reconstruction will be performed.

shared_ptr< const VoxelsOnCartesianGrid< float > >	image_info_sptr
	We need a local copy of the discretised density in order to find the cartesian coordinates of each voxel.

shared_ptr< const ProjDataInfo >	proj_data_info_sptr
	We need a local copy of the proj_data_info to get the integration boundaries and RayTracing.

Protected Attributes inherited from stir::ParsingObject
KeyParser	parser

Detailed Description

generates projection matrix for SPECT studies

This functionality is described in Berta Marti Fuster, Carles Falcon, Charalampos Tsoumpas, Lefteris Livieratos, Pablo Aguiar, Albert Cot, Domenec Ros and Kris Thielemans, Integration of advanced 3D SPECT modeling into the open-source STIR framework, Med. Phys. 40, 092502 (2013); http://dx.doi.org/10.1118/1.4816676

Warning: this class currently only works with VoxelsOnCartesianGrid.

Sample parameter file

  Projection Matrix By Bin SPECT UB Parameters:=
    ; width of PSF
    maximum number of sigmas:= 2.0

    ;PSF type of correction { 2D // 3D // Geometrical }
    psf type:= 2D
    ; next 2 parameters define the PSF. They are ignored if psf_type is "Geometrical"
    ; the PSF is modelled as a Gaussian with sigma dependent on the distance from the collimator
    ; sigma_at_depth = collimator_slope * depth_in_cm + collimator sigma 0(cm)
    collimator slope := 0.0163
    collimator sigma 0(cm) := 0.1466

    ;Attenuation correction { Simple // Full // No }
    attenuation type := Simple
    ;Values in attenuation map in cm-1
    attenuation map := attMapRec.hv

    ;Mask properties { Cylinder // Attenuation Map // Explicit Mask // No}
    mask type := Explicit Mask
    mask file := mask.hv

    ; if next variable is set to 0, only a single view is kept in memory
   keep all views in cache:=1

End Projection Matrix By Bin SPECT UB Parameters:=

Member Function Documentation

◆ set_keep_all_views_in_cache()

void stir::ProjMatrixByBinSPECTUB::set_keep_all_views_in_cache ( bool value = true )

Enable keeping the matrix in memory.

This speeds-up the calculations, but can use a lot of memory.

You have to call set_up() after this (unless the value didn't change).

◆ set_attenuation_type()

void stir::ProjMatrixByBinSPECTUB::set_attenuation_type ( const std::string & value )

Set type of attenuation modelling.

Has to be "no", "simple" or "full"

You have to call set_up() after this (unless the value didn't change).

References stir::error().

◆ set_attenuation_image_sptr()

void stir::ProjMatrixByBinSPECTUB::set_attenuation_image_sptr ( const shared_ptr< const DiscretisedDensity< 3, float >> value )

Sets attenuation image.

The image has to have same characteristics as the emission image currently.

Will call set_attenuation_type() to set to "simple" if it was set to "no".

You have to call set_up() after this.

References stir::info(), and stir::read_from_file().

◆ set_resolution_model()

void stir::ProjMatrixByBinSPECTUB::set_resolution_model	(	const float	collimator_sigma_0_in_mm,
		const float	collimator_slope_in_mm,
		const bool	full_3D = `true`
	)

Set the parameters for the depth-dependent resolution model.

The detector and collimator blurring is modelled as a Gaussian with sigma dependent on the distance from the collimator.

 sigma_at_depth = collimator_slope * depth_in_mm + collimator sigma 0

Set slope and sigma_0 to zero for "geometrical" modelling.

Warning: Values are in mm

You have to call set_up() after this.

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

/home/sirfuser/devel/STIRdistrib/STIR/src/include/stir/recon_buildblock/ProjMatrixByBinSPECTUB.h
/home/sirfuser/devel/STIRdistrib/STIR/src/recon_buildblock/ProjMatrixByBinSPECTUB.cxx

Public Member Functions