A BinNormalisation class that gets attenuation correction factors from an attenuation image. More...

#include "stir/recon_buildblock/BinNormalisationFromAttenuationImage.h"

Inheritance diagram for stir::BinNormalisationFromAttenuationImage:

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Public Member Functions
	BinNormalisationFromAttenuationImage ()
	Default constructor.

	BinNormalisationFromAttenuationImage (const std::string &filename, shared_ptr< ForwardProjectorByBin > const &=shared_ptr< ForwardProjectorByBin >())
	Constructor that reads the image from a file.

	BinNormalisationFromAttenuationImage (const shared_ptr< const DiscretisedDensity< 3, float > > &attenuation_image_ptr, shared_ptr< ForwardProjectorByBin > const &=shared_ptr< ForwardProjectorByBin >())
	Constructor that takes the image as an argument.

Succeeded	set_up (const shared_ptr< const ExamInfo > &exam_info_sptr, const shared_ptr< const ProjDataInfo > &) override
	Checks if we can handle certain projection data.

void	apply (RelatedViewgrams< float > &viewgrams) const override
	Normalise some data.

void	undo (RelatedViewgrams< float > &viewgrams) const override
	Undo the normalisation of some data.

float	get_bin_efficiency (const Bin &bin) const override
	Return the 'efficiency' factor for a single bin.

void	apply (ProjData &, shared_ptr< DataSymmetriesForViewSegmentNumbers >=shared_ptr< DataSymmetriesForViewSegmentNumbers >()) const
	normalise some data

void	undo (ProjData &, shared_ptr< DataSymmetriesForViewSegmentNumbers >=shared_ptr< DataSymmetriesForViewSegmentNumbers >()) const
	undo the normalisation of some data

Public Member Functions inherited from stir::RegisteredParsingObject< BinNormalisationFromAttenuationImage, BinNormalisation >
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::BinNormalisation
virtual float	get_calibration_factor () const

virtual bool	is_trivial () const
	check if we would be multiplying with 1 (i.e. do nothing)

virtual bool	is_TOF_only_norm () const
	returns if the object can only handle TOF data

void	apply (ProjData &, shared_ptr< DataSymmetriesForViewSegmentNumbers >=shared_ptr< DataSymmetriesForViewSegmentNumbers >()) const
	normalise some data

void	undo (ProjData &, shared_ptr< DataSymmetriesForViewSegmentNumbers >=shared_ptr< DataSymmetriesForViewSegmentNumbers >()) const
	undo the normalisation of some data

void	set_exam_info_sptr (const shared_ptr< const ExamInfo > _exam_info_sptr)

shared_ptr< const ExamInfo >	get_exam_info_sptr () const

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 ()

Static Public Attributes
static const char *const	registered_name = "From Attenuation Image"
	Name which will be used when parsing a BinNormalisation object.

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

Static Public Member Functions inherited from stir::RegisteredObject< BinNormalisation >
static BinNormalisation *	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 BinNormalisation *	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< BinNormalisation >
typedef BinNormalisation (	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::BinNormalisation
virtual void	check (const ProjDataInfo &proj_data_info) const
	check if the argument is the same as what was used for set_up()

virtual void	check (const ExamInfo &exam_info) const

virtual void	set_key_values ()
	This will be called before parsing or parameter_info is called.

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

Protected Attributes inherited from stir::BinNormalisation
bool	_already_set_up

shared_ptr< const ProjDataInfo >	proj_data_info_sptr

KeyParser	parser

Detailed Description

A BinNormalisation class that gets attenuation correction factors from an attenuation image.

This forwards projects the attenuation image, multiplies with -1, and exponentiates to obtain the attenuation correction factors.

Default forward projector is ForwardProjectorByBinUsingRayTracing.

Warning: Attenuation image data are supposed to be in units cm^-1. (Reference: water has mu .096 cm^-1.)

Todo: Add mechanism for caching the attenuation correction factors, such that they will be calculated only once. However, caching should by default be disabled, as most applications need them only once anyway.

Parsing details

Bin Normalisation From Attenuation Image:=
attenuation_image_filename := <ASCII>
forward projector type := <ASCII>
End Bin Normalisation From Attenuation Image :=

Constructor & Destructor Documentation

◆ BinNormalisationFromAttenuationImage() [1/3]

stir::BinNormalisationFromAttenuationImage::BinNormalisationFromAttenuationImage ( )

Default constructor.

Warning: You should not call any member functions for any object just constructed with this constructor. Initialise the object properly first by parsing.

References BinNormalisationFromAttenuationImage().

Referenced by BinNormalisationFromAttenuationImage(), and BinNormalisationFromAttenuationImage().

◆ BinNormalisationFromAttenuationImage() [2/3]

stir::BinNormalisationFromAttenuationImage::BinNormalisationFromAttenuationImage	(	const std::string &	filename,
		shared_ptr< ForwardProjectorByBin > const &	forward_projector_ptr = shared_ptr<ForwardProjectorByBin>() )

Constructor that reads the image from a file.

Default forward projector is ForwardProjectorByBinUsingRayTracing.

References BinNormalisationFromAttenuationImage().

◆ BinNormalisationFromAttenuationImage() [3/3]

stir::BinNormalisationFromAttenuationImage::BinNormalisationFromAttenuationImage	(	const shared_ptr< const DiscretisedDensity< 3, float > > &	attenuation_image_ptr,
		shared_ptr< ForwardProjectorByBin > const &	forward_projector_ptr = shared_ptr<ForwardProjectorByBin>() )

Constructor that takes the image as an argument.

Default forward projector is ForwardProjectorByBinUsingRayTracing. The image pointed to by attenuation_image_ptr is NOT modified.

Member Function Documentation

◆ set_up()

Succeeded stir::BinNormalisationFromAttenuationImage::set_up	(	const shared_ptr< const ExamInfo > &	exam_info_sptr,
		const shared_ptr< const ProjDataInfo > &	proj_data_info_ptr )

overridevirtual

Checks if we can handle certain projection data.

This test is essentially checking if the forward projector can handle the data by calling ForwardProjectorByBin::set_up().

Reimplemented from stir::BinNormalisation.

References stir::error(), and stir::BinNormalisation::set_up().

◆ apply() [1/2]

void stir::BinNormalisationFromAttenuationImage::apply ( RelatedViewgrams< float > & viewgrams ) const

overridevirtual

Normalise some data.

This means multiply with the data in the projdata object passed in the constructor.

Reimplemented from stir::BinNormalisation.

References stir::RelatedViewgrams< elemT >::begin(), stir::BinNormalisation::check(), stir::RelatedViewgrams< elemT >::end(), stir::RelatedViewgrams< elemT >::get_empty_copy(), stir::DataWithProjDataInfo::get_proj_data_info_sptr(), and stir::in_place_exp().

◆ undo() [1/2]

void stir::BinNormalisationFromAttenuationImage::undo ( RelatedViewgrams< float > & viewgrams ) const

overridevirtual

Undo the normalisation of some data.

This means divide with the data in the projdata object passed in the constructor.

Reimplemented from stir::BinNormalisation.

References stir::RelatedViewgrams< elemT >::begin(), stir::BinNormalisation::check(), stir::RelatedViewgrams< elemT >::end(), stir::RelatedViewgrams< elemT >::get_empty_copy(), stir::DataWithProjDataInfo::get_proj_data_info_sptr(), and stir::in_place_exp().

◆ get_bin_efficiency()

float stir::BinNormalisationFromAttenuationImage::get_bin_efficiency ( const Bin & bin ) const

overridevirtual

Return the 'efficiency' factor for a single bin.

With the notation of the class documentation, this returns the factor $\mathrm{norm}_b$ .

Warning: Some derived classes might implement this very inefficiently.

Implements stir::BinNormalisation.

References stir::error().

◆ apply() [2/2]

void stir::BinNormalisation::apply	(	ProjData &	proj_data,
		shared_ptr< DataSymmetriesForViewSegmentNumbers >	symmetries_sptr = shared_ptr<DataSymmetriesForViewSegmentNumbers>() ) const

normalise some data

This would be used for instance to precorrect unnormalised data. With the notation of the class documentation, this would divide by the factors $\mathrm{norm}_b$ .

This just loops over all RelatedViewgrams.

The default value for the symmetries means that TrivialDataSymmetriesForBins will be used.

◆ undo() [2/2]

void stir::BinNormalisation::undo	(	ProjData &	proj_data,
		shared_ptr< DataSymmetriesForViewSegmentNumbers >	symmetries_sptr = shared_ptr<DataSymmetriesForViewSegmentNumbers>() ) const

undo the normalisation of some data

This would be used for instance to bring geometrically forward projected data to the mean of the measured data. With the notation of the class documentation, this would multiply by the factors $\mathrm{norm}_b$ .

This just loops over all RelatedViewgrams.

The default value for the symmetries means that TrivialDataSymmetriesForBins will be used.

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

/home/kris/devel/STIRdistrib/STIR/src/include/stir/recon_buildblock/BinNormalisationFromAttenuationImage.h
/home/kris/devel/STIRdistrib/STIR/src/recon_buildblock/BinNormalisationFromAttenuationImage.cxx

Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BinNormalisationFromAttenuationImage() [1/3]

◆ BinNormalisationFromAttenuationImage() [2/3]

◆ BinNormalisationFromAttenuationImage() [3/3]

Member Function Documentation

◆ set_up()

◆ apply() [1/2]

◆ undo() [1/2]

◆ get_bin_efficiency()

◆ apply() [2/2]

◆ undo() [2/2]