STIR  6.2.0
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stir::OSMAPOSLReconstruction< TargetT > Class Template Reference

Implementation of the Ordered Subsets version of Green's MAP One Step Late algorithm. More...

#include "stir/OSMAPOSL/OSMAPOSLReconstruction.h"

Inheritance diagram for stir::OSMAPOSLReconstruction< TargetT >:
Inheritance graph
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Public Member Functions

 OSMAPOSLReconstruction ()
 Default constructor (calling set_defaults())
 
 OSMAPOSLReconstruction (const std::string &parameter_filename)
 Constructor, initialises everything from parameter file, or (when parameter_filename == "") by calling ask_parameters().
 
OSMAPOSLReconstructionget_parameters ()
 accessor for the external parameters
 
const OSMAPOSLReconstructionget_parameters () const
 accessor for the external parameters
 
std::string method_info () const override
 gives method information
 
PoissonLogLikelihoodWithLinearModelForMean< TargetT > const & get_objective_function () const
 Return current objective function.
 
void ask_parameters () override
 prompts the user to enter parameter values manually
 
Succeeded set_up (shared_ptr< TargetT > const &target_image_ptr) override
 operations prior to the iterations
 
void update_estimate (TargetT &current_image_estimate) override
 the principal operations for updating the image iterates at each iteration
 
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.
void set_inter_update_filter_interval (const int)
 subiteration interval at which to apply inter-update filters
 
void set_inter_update_filter_ptr (const shared_ptr< DataProcessor< TargetT >> &)
 inter-update filter object
 
void set_maximum_relative_change (const double)
 restrict updates (larger relative updates will be thresholded)
 
void set_minimum_relative_change (const double)
 restrict updates (smaller relative updates will be thresholded)
 
void set_enforce_initial_positivity (const bool)
 
void set_write_update_image (const int)
 boolean value to determine if the update images have to be written to disk
 
void set_MAP_model (const std::string &)
 should be either additive or multiplicative
 
- Public Member Functions inherited from stir::RegisteredParsingObject< OSMAPOSLReconstruction< TargetT >, Reconstruction< TargetT >, IterativeReconstruction< TargetT > >
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::IterativeReconstruction< TargetT >
int get_subiteration_num () const
 accessor for the subiteration counter
 
int get_subset_num ()
 accessor for finding the current subset number More...
 
virtual TargetT * get_initial_data_ptr () const
 Gets a pointer to the initial data. More...
 
Succeeded reconstruct () override
 executes the reconstruction More...
 
Succeeded reconstruct (shared_ptr< TargetT > const &target_data_sptr) override
 executes the reconstruction with target_data_sptr as initial value More...
 
std::string make_filename_prefix_subiteration_num (const std::string &filename_prefix) const
 A utility function that creates a filename_prefix by appending the current subiteration number. More...
 
std::string make_filename_prefix_subiteration_num () const
 A utility function that creates the output filename_prefix for the current subiteration number. More...
 
Succeeded set_up (shared_ptr< TargetT > const &target_data_ptr) override
 operations prior to the reconstruction More...
 
GeneralisedObjectiveFunction< TargetT > const & get_objective_function () const
 
shared_ptr< GeneralisedObjectiveFunction< TargetT > > get_objective_function_sptr () const
 
const int get_max_num_full_iterations () const
 the maximum allowed number of full iterations
 
const int get_num_subsets () const
 the number of ordered subsets
 
const int get_num_subiterations () const
 the number of subiterations
 
const int get_start_subiteration_num () const
 value with which to initialize the subiteration counter
 
const int get_start_subset_num () const
 the starting subset number
 
const int get_save_interval () const
 subiteration interval at which data will be saved
 
const bool get_randomise_subset_order () const
 signals whether to randomise the subset order in each iteration
 
const DataProcessor< TargetT > & get_inter_iteration_filter () const
 inter-iteration filter
 
shared_ptr< DataProcessor< TargetT > > get_inter_iteration_filter_sptr ()
 
const int get_inter_iteration_filter_interval () const
 subiteration interval at which to apply inter-iteration filters
 
const int get_report_objective_function_values_interval () const
 subiteration interval at which to report the values of the objective function
 
void set_objective_function_sptr (const shared_ptr< GeneralisedObjectiveFunction< TargetT >> &)
 The objective function that will be optimised.
 
void set_max_num_full_iterations (const int)
 the maximum allowed number of full iterations
 
void set_num_subsets (const int)
 the number of ordered subsets
 
void set_num_subiterations (const int)
 the number of subiterations
 
void set_start_subiteration_num (const int)
 value with which to initialize the subiteration counter
 
void set_start_subset_num (const int)
 the starting subset number
 
void set_save_interval (const int)
 subiteration interval at which data will be saved
 
void set_randomise_subset_order (const bool)
 signals whether to randomise the subset order in each iteration
 
void set_inter_iteration_filter_ptr (const shared_ptr< DataProcessor< TargetT >> &)
 inter-iteration filter
 
void set_inter_iteration_filter_interval (const int)
 subiteration interval at which to apply inter-iteration filters
 
void set_report_objective_function_values_interval (const int)
 subiteration interval at which to report the values of the objective function
 
void set_input_data (const shared_ptr< ExamData > &arg) override
 set_input_data More...
 
const ExamDataget_input_data () const override
 get input data More...
 
- Public Member Functions inherited from stir::Reconstruction< TargetT >
 Reconstruction ()
 default constructor (calls set_defaults())
 
 ~Reconstruction () override
 virtual destructor
 
void set_disable_output (bool _val)
 set_disable_output More...
 
shared_ptr< TargetT > get_target_image ()
 get_reconstructed_image More...
 
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
 
- Public Member Functions inherited from stir::ParsingObject
 ParsingObject (const ParsingObject &)
 
ParsingObjectoperator= (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 = "OSMAPOSL"
 Name which will be used when parsing a OSMAPOSLReconstruction object.
 

Protected Member Functions

void set_defaults () override
 Set defaults before parsing.
 
void initialise_keymap () override
 Initialise all keywords.
 
bool post_processing () override
 used to check acceptable parameter ranges, etc...
 
virtual void compute_sub_gradient_without_penalty_plus_sensitivity (TargetT &gradient, const TargetT &current_estimate, const int subset_num)
 
virtual const TargetT & get_subset_sensitivity (const int subset_num)
 
virtual void apply_multiplicative_update (TargetT &current_image_estimate, const TargetT &multiplicative_update_image)
 
- Protected Member Functions inherited from stir::IterativeReconstruction< TargetT >
virtual void end_of_iteration_processing (TargetT &current_estimate)
 operations for the end of the iteration More...
 
void set_defaults () override
 Set defaults before parsing.
 
void initialise_keymap () override
 Initialise all keywords.
 
bool post_processing () override
 used to check acceptable parameter ranges, etc...
 
- Protected Member Functions inherited from stir::Reconstruction< TargetT >
virtual void check (TargetT const &target_data) const
 do consistency checks More...
 
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). More...
 
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 More...
 
- Protected Member Functions inherited from stir::ParsingObject
virtual void set_key_values ()
 This will be called before parsing or parameter_info is called. More...
 

Protected Attributes

bool enforce_initial_positivity
 operations prior to the iterations More...
 
bool do_rim_truncation
 determines wether voxels outside a circular FOV will be set to 0 or not More...
 
int inter_update_filter_interval
 subiteration interval at which to apply inter-update filters
 
shared_ptr< DataProcessor< TargetT > > inter_update_filter_ptr
 inter-update filter object
 
double maximum_relative_change
 restrict updates (larger relative updates will be thresholded)
 
double minimum_relative_change
 restrict updates (smaller relative updates will be thresholded)
 
int write_update_image
 boolean value to determine if the update images have to be written to disk
 
std::string MAP_model
 should be either additive or multiplicative
 
- Protected Attributes inherited from stir::IterativeReconstruction< TargetT >
shared_ptr< GeneralisedObjectiveFunction< TargetT > > objective_function_sptr
 
int subiteration_num
 the subiteration counter
 
bool terminate_iterations
 used to abort the loop over iterations
 
int max_num_full_iterations
 the maximum allowed number of full iterations
 
int num_subsets
 the number of ordered subsets
 
int num_subiterations
 the number of subiterations
 
int start_subiteration_num
 value with which to initialize the subiteration counter
 
std::string initial_data_filename
 name of the file containing the data for intializing the reconstruction
 
int start_subset_num
 the starting subset number
 
int save_interval
 subiteration interval at which data will be saved
 
bool randomise_subset_order
 signals whether to randomise the subset order in each iteration
 
shared_ptr< DataProcessor< TargetT > > inter_iteration_filter_ptr
 inter-iteration filter
 
int inter_iteration_filter_interval
 subiteration interval at which to apply inter-iteration filters
 
int report_objective_function_values_interval
 subiteration interval at which to report the values of the objective function More...
 
- Protected Attributes inherited from stir::Reconstruction< TargetT >
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 More...
 
int _verbosity
 Verbosity level.
 
- Protected Attributes inherited from stir::ParsingObject
KeyParser parser
 

Friends

void do_sensitivity (const char *const par_filename)
 

Additional Inherited Members

- Static Public Member Functions inherited from stir::RegisteredParsingObject< OSMAPOSLReconstruction< TargetT >, Reconstruction< TargetT >, IterativeReconstruction< TargetT > >
static Reconstruction< TargetT > * 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< 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. More...
 
static Reconstruction< TargetT > * 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< 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_lessRegistryType
 The type of the registry.
 
- Static Protected Member Functions inherited from stir::RegisteredObject< Reconstruction< TargetT > >
static RegistryTyperegistry ()
 Static function returning the registry. More...
 

Detailed Description

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

Implementation of the Ordered Subsets version of Green's MAP One Step Late algorithm.

See Jacobson et al, PMB for a description of the implementation.

When no prior info is specified, this reduces to 'standard' OSEM.

Two different forms of the prior are implemented. (For background, see Mustavic&Thielemans, proc. IEEE MIC 2001).

When MAP_model == "additive" this implements the standard form of OSL (with a small modification for allowing subsets):

lambda_new = lambda / ((p_v + beta*prior_gradient)/ num_subsets) *
sum_subset backproj(measured/forwproj(lambda))

with $p_v = sum_b p_{bv}$. actually, we restrict 1 + beta*prior_gradient/p_v between .1 and 10

On the other hand, when MAP_model == "multiplicative" it implements

lambda_new = lambda / (p_v*(1 + beta*prior_gradient)/ num_subsets) *
sum_subset backproj(measured/forwproj(lambda))

with $p_v = sum_b p_{bv}$. actually, we restrict 1 + beta*prior_gradient between .1 and 10.

Note that all this assumes 'balanced subsets', i.e.

\[\sum_{b \in \rm{subset}} p_{bv} = { \sum_b p_{bv} \over \rm{numsubsets} } \]

Warning
This class should be the last in a Reconstruction hierarchy.

Member Data Documentation

◆ enforce_initial_positivity

template<typename TargetT>
bool stir::OSMAPOSLReconstruction< TargetT >::enforce_initial_positivity
protected

operations prior to the iterations

determines whether non-positive values in the initial image will be set to small positive ones

◆ do_rim_truncation

template<typename TargetT>
bool stir::OSMAPOSLReconstruction< TargetT >::do_rim_truncation
protected

determines wether voxels outside a circular FOV will be set to 0 or not

Currently this circular FOV is slightly smaller than the actual image size (1 pixel at each end or so).

Deprecated:

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