base class for all ReconstructionsAs there is not a lot of commonality between different reconstruction algorithms, this base class is rather basic. It essentially takes care of constructing a target image, calls the virtual reconstruct() function, and writes the result to file. More...

#include "stir/recon_buildblock/Reconstruction.h"

Inheritance diagram for stir::Reconstruction< TargetT >:

[legend]

Public Member Functions
	Reconstruction ()
	default constructor (calls set_defaults())

	~Reconstruction () override
	virtual destructor

virtual std::string	method_info () const =0
	gives method information

virtual Succeeded	reconstruct ()=0
	executes the reconstruction

virtual Succeeded	reconstruct (shared_ptr< TargetT > const &target_image_sptr)=0
	executes the reconstruction storing result in `target_image_sptr`

virtual Succeeded	set_up (shared_ptr< TargetT > const &target_data_sptr)
	operations prior to the reconstruction

Public Member Functions inherited from stir::RegisteredObjectBase
virtual std::string	get_registered_name () const =0
	Returns the name of the type of the object.

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 ()

virtual std::string	parameter_info ()

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)

Functions to set parameters
This can be used as alternative to the parsing mechanism. Warning Be careful with setting shared pointers. If you modify the objects in one place, all objects that use the shared pointer will be affected.
std::string	output_filename_prefix
	file name for output reconstructed images

shared_ptr< OutputFileFormat< TargetT > >	output_file_format_ptr
	defines the format of the output files

shared_ptr< DataProcessor< TargetT > >	post_filter_sptr
	post-filter

bool	_already_set_up

shared_ptr< TargetT >	target_data_sptr
	target_data_sptr

bool	_disable_output
	_disable_output

int	_verbosity
	Verbosity level.

void	set_output_filename_prefix (const std::string &)
	file name for output reconstructed images

void	set_output_file_format_ptr (const shared_ptr< OutputFileFormat< TargetT > > &)
	defines the format of the output files

void	set_post_processor_sptr (const shared_ptr< DataProcessor< TargetT > > &)
	post-filter

virtual void	set_input_data (const shared_ptr< ExamData > &)=0
	set input data

virtual const ExamData &	get_input_data () const =0
	get input data

void	set_disable_output (bool _val)
	set_disable_output

shared_ptr< TargetT >	get_target_image ()
	get_reconstructed_image

virtual void	check (TargetT 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

Additional Inherited Members
Static Public Member Functions inherited from stir::RegisteredObject< Reconstruction< TargetT > >
static Reconstruction< TargetT > *	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< TargetT > *	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< TargetT > >
typedef Reconstruction< TargetT > (	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.

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

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

KeyParser	parser

Detailed Description

template<typename TargetT>
class stir::Reconstruction< TargetT >

base class for all Reconstructions

As there is not a lot of commonality between different reconstruction algorithms, this base class is rather basic. It essentially takes care of constructing a target image, calls the virtual reconstruct() function, and writes the result to file.

For convenience, the class is derived from TimedObject. It is the responsibility of the derived class to run these timers though.

Parsing parameters

; post-processing after image reconstruction,see DataProcessor<TargetT>
; defaults to no processing ("None")
post-filter type :=

; output file(s) will be written with the following file name
output filename prefix :=
; output file(s) will use the following file format
; see OutputFileFormat<TargetT>
output file format :=

Member Function Documentation

◆ method_info()

template<typename TargetT>

virtual std::string stir::Reconstruction< TargetT >::method_info ( ) const

pure virtual

gives method information

Implemented in stir::FBP2DReconstruction, stir::FBP3DRPReconstruction, stir::OSMAPOSLReconstruction< TargetT >, stir::OSSPSReconstruction< TargetT >, stir::SRT2DReconstruction, and stir::SRT2DSPECTReconstruction.

Referenced by stir::IterativeReconstruction< TargetT >::end_of_iteration_processing().

◆ reconstruct() [1/2]

template<typename TargetT>

virtual Succeeded stir::Reconstruction< TargetT >::reconstruct ( )

pure virtual

executes the reconstruction

Returns: Succeeded::yes if everything was alright.

Implemented in stir::AnalyticReconstruction, and stir::IterativeReconstruction< TargetT >.

◆ reconstruct() [2/2]

template<typename TargetT>

virtual Succeeded stir::Reconstruction< TargetT >::reconstruct ( shared_ptr< TargetT > const & target_image_sptr )

pure virtual

executes the reconstruction storing result in target_image_sptr

Parameters

target_image_sptr The result of the reconstruction is stored in *target_image_sptr.

Returns: Succeeded::yes if everything was alright.

Developer\'s note

Because of C++ rules, overloading one of the reconstruct() functions in a derived class, will hide the other. So you have to overload both.

Warning: you need to call set_up() first.

Implemented in stir::AnalyticReconstruction, and stir::IterativeReconstruction< TargetT >.

References set_output_file_format_ptr(), set_output_filename_prefix(), set_post_processor_sptr(), set_up(), and target_data_sptr.

◆ set_up()

template<typename TargetT>

Succeeded stir::Reconstruction< TargetT >::set_up ( shared_ptr< TargetT > const & target_data_sptr )

virtual

operations prior to the reconstruction

Will do various consistency checks and return Succeeded::no if something is wrong.

Todo: Currently, set_up() is called by reconstruct(). This is in contrast with some other class hierarchies in STIR where set_up() has to be called before any actual processing. Maybe this should be made consistent.

Reimplemented in stir::IterativeReconstruction< TargetT >, stir::OSMAPOSLReconstruction< TargetT >, and stir::OSSPSReconstruction< TargetT >.

References stir::info(), post_filter_sptr, set_up(), target_data_sptr, and stir::warning().

Referenced by reconstruct(), stir::IterativeReconstruction< TargetT >::set_up(), and set_up().

◆ set_input_data()

template<typename TargetT>

virtual void stir::Reconstruction< TargetT >::set_input_data ( const shared_ptr< ExamData > & )

pure virtual

set input data

Implemented in stir::AnalyticReconstruction, and stir::IterativeReconstruction< TargetT >.

◆ get_input_data()

template<typename TargetT>

virtual const ExamData & stir::Reconstruction< TargetT >::get_input_data ( ) const

pure virtual

get input data

Will throw an exception if it wasn't set first

Implemented in stir::AnalyticReconstruction, and stir::IterativeReconstruction< TargetT >.

References get_target_image(), and set_disable_output().

◆ set_disable_output()

template<typename TargetT>

void stir::Reconstruction< TargetT >::set_disable_output ( bool _val )

set_disable_output

Parameters

_val

Author: Nikos Efthimiou

This function is called if the user deside to mute any output images. The best way to do this is to use the "disable output" key in the par file.

Warning: The "output filename prefix" has to be set.

References set_disable_output().

Referenced by get_input_data(), and set_disable_output().

◆ get_target_image()

template<typename TargetT>

shared_ptr< TargetT > stir::Reconstruction< TargetT >::get_target_image ( )

get_reconstructed_image

Author: Nikos Efthimiou

Returns

References get_target_image(), and target_data_sptr.

Referenced by get_input_data(), and get_target_image().

◆ check()

template<typename TargetT>

void stir::Reconstruction< TargetT >::check ( TargetT const & target_data ) const

protectedvirtual

do consistency checks

calls error() if anything is wrong, in particular when set_up() hasn't been called yet.

If overriding this function in a derived class, you need to call this one.

References check(), stir::error(), and target_data_sptr.

Referenced by check(), stir::IterativeReconstruction< TargetT >::reconstruct(), stir::OSMAPOSLReconstruction< TargetT >::update_estimate(), and stir::OSSPSReconstruction< TargetT >::update_estimate().

◆ initialise()

template<typename TargetT>

void stir::Reconstruction< TargetT >::initialise ( const std::string & parameter_filename )

protected

This function initialises all parameters, either via parsing, or by calling ask_parameters() (when parameter_filename is the empty string).

It should be called in the constructor of the last class in the hierarchy. At that time, all Interfile keys will have been initialised, and ask_parameters() will be the appropriate virtual function, such that questions are asked for all parameters.

Todo: It currently calls error() when something goes wrong. It should return Succeeded (or throw an exception).

References stir::error(), initialise(), and set_defaults().

Referenced by initialise(), stir::KOSMAPOSLReconstruction< TargetT >::KOSMAPOSLReconstruction(), stir::OSMAPOSLReconstruction< TargetT >::OSMAPOSLReconstruction(), and stir::OSSPSReconstruction< TargetT >::OSSPSReconstruction().

◆ set_defaults()

template<typename TargetT>

void stir::Reconstruction< TargetT >::set_defaults ( )

overrideprotectedvirtual

Set defaults before parsing.

Reimplemented from stir::ParsingObject.

References _disable_output, _verbosity, stir::OutputFileFormat< DataT >::default_sptr(), output_file_format_ptr, output_filename_prefix, post_filter_sptr, and set_defaults().

Referenced by initialise(), Reconstruction(), stir::AnalyticReconstruction::set_defaults(), stir::IterativeReconstruction< TargetT >::set_defaults(), and set_defaults().

◆ initialise_keymap()

template<typename TargetT>

void stir::Reconstruction< TargetT >::initialise_keymap ( )

overrideprotectedvirtual

Initialise all keywords.

Reimplemented from stir::ParsingObject.

References _disable_output, _verbosity, initialise_keymap(), output_file_format_ptr, output_filename_prefix, and post_filter_sptr.

Referenced by stir::AnalyticReconstruction::initialise_keymap(), stir::IterativeReconstruction< TargetT >::initialise_keymap(), and initialise_keymap().

◆ post_processing()

template<typename TargetT>

bool stir::Reconstruction< TargetT >::post_processing ( )

overrideprotectedvirtual

used to check acceptable parameters after parsing

The function should be used to set members that have are not set directly by the parsing. For example, parsing might set input_filename, and post_processing() might then read in the data and set the corresponding Reconstruction parameter.

Consistency checks mostly belong in set_up(). The reason for this is that for instance a GUI might not use the parsing mechanism and set parameters by calling various set_ functions (such as set_post_processor_sptr() ).

Reimplemented from stir::ParsingObject.

References _disable_output, stir::RegisteredObjectBase::get_registered_name(), post_processing(), and stir::warning().

Referenced by stir::AnalyticReconstruction::post_processing(), stir::IterativeReconstruction< TargetT >::post_processing(), and post_processing().

Member Data Documentation

◆ _disable_output

template<typename TargetT>

bool stir::Reconstruction< TargetT >::_disable_output

protected

_disable_output

Author: Nikos Efthimiou

This member mutes the creatation and write into an output image. You want to use it if you call for reconstruction from within some other code and want to use directly the output image.

Referenced by stir::IterativeReconstruction< TargetT >::end_of_iteration_processing(), initialise_keymap(), post_processing(), set_defaults(), and stir::OSMAPOSLReconstruction< TargetT >::update_estimate().

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

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

Public Member Functions

Functions to set parameters

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ method_info()

◆ reconstruct() [1/2]

◆ reconstruct() [2/2]

◆ set_up()

◆ set_input_data()

◆ get_input_data()

◆ set_disable_output()

◆ get_target_image()

◆ check()

◆ initialise()

◆ set_defaults()

◆ initialise_keymap()

◆ post_processing()

Member Data Documentation

◆ _disable_output