Declaration of class stir::InputStreamFromROOTFileForCylindricalPET. More...

#include "stir/IO/InputStreamFromROOTFileForCylindricalPET.h"

Inheritance diagram for stir::InputStreamFromROOTFileForCylindricalPET:

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Public Member Functions
	InputStreamFromROOTFileForCylindricalPET ()
	Default constructor.

Succeeded	get_next_record (CListRecordROOT &record) override

Succeeded	set_up (const std::string &header_path) override
	Must be called before calling for the first event.

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

int	get_num_rings () const override
	Calculate the number of rings based on the crystal, module, submodule repeaters.

int	get_num_dets_per_ring () const override
	Calculate the number of detectors per ring based on the crystal, module, submodule repeaters.

int	get_num_axial_blocks_per_bucket_v () const override
	Get the number of axial modules.

int	get_num_transaxial_blocks_per_bucket_v () const override
	Get the number of transaxial modules.

int	get_num_axial_crystals_per_singles_unit () const override
	Calculate the number of axial crystals per singles unit based on the repeaters numbers and the readout deptth.

int	get_num_trans_crystals_per_singles_unit () const override
	Calculate the number of trans crystals per singles unit based on the repeaters numbers and the readout deptth.

void	set_submodule_repeater_x (int)

void	set_submodule_repeater_y (int)

void	set_submodule_repeater_z (int)

void	set_module_repeater_x (int)

void	set_module_repeater_y (int)

void	set_module_repeater_z (int)

void	set_rsector_repeater (int)

Public Member Functions inherited from stir::RegisteredParsingObject< InputStreamFromROOTFileForCylindricalPET, InputStreamFromROOTFile, InputStreamFromROOTFile >
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::InputStreamFromROOTFile
	InputStreamFromROOTFile ()
	Default constructor.

Succeeded	reset ()
	Go to the first event.

SavedPosition	save_get_position ()
	Save current position in a vector.

Succeeded	set_get_position (const SavedPosition &)
	Set current position.

std::vector< unsigned long int >	get_saved_get_positions () const
	Get the vector with the saved positions.

void	set_saved_get_positions (const std::vector< unsigned long int > &)
	Set a vector with saved positions.

unsigned long int	get_total_number_of_events () const
	Returns the total number of events.

std::string	get_ROOT_filename () const

int	get_num_axial_crystals_per_block_v () const
	Get the axial number of crystals per module.

int	get_num_transaxial_crystals_per_block_v () const
	Get the transaxial number of crystals per module.

float	get_low_energy_thres () const
	Lower energy threshold.

float	get_up_energy_thres () const
	Upper energy threshold.

void	set_singles_readout_depth (int)
	Set singles_readout_depth.

void	set_input_filename (const std::string &)

void	set_chain_name (const std::string &)

void	set_exclude_true_events (bool)

void	set_exclude_scattered_events (bool)

void	set_exclude_unscattered_events (bool)

void	set_exclude_random_events (bool)

void	set_low_energy_window (float)

void	set_upper_energy_window (float)

void	set_optional_ROOT_fields (bool)
	Set the read_optional_root_fields flag.

void	set_crystal_repeater_x (int)

void	set_crystal_repeater_y (int)

void	set_crystal_repeater_z (int)

int	get_num_virtual_axial_crystals_per_block () const

int	get_num_virtual_transaxial_crystals_per_block () const

void	set_num_virtual_axial_crystals_per_block (int)

void	set_num_virtual_transaxial_crystals_per_block (int)

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)

Static Public Attributes
static const char *const	registered_name = "GATE_Cylindrical_PET"
	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
	This will be called at the end of the parsing. More...

Protected Member Functions inherited from stir::InputStreamFromROOTFile
float	get_energy1_in_keV () const
	OpenGATE output ROOT energy information is given in MeV, these methods convert to keV.

float	get_energy2_in_keV () const

bool	check_brentry_randoms_scatter_energy_conditions (long long int brentry)
	Checks brentry satisfies the randoms, scatter and energy conditions.

void	GetEntryCheck (const int ret)
	Checks the return of branch->GetEntry(brentry) and errors if return <= 0.

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
int	submodule_repeater_x

int	submodule_repeater_y

int	submodule_repeater_z

int	module_repeater_x

int	module_repeater_y

int	module_repeater_z

int	rsector_repeater

int	half_block
	In GATE, inside a block, the indeces start from the lower unit counting upwards. Therefore in order to align the crystals, between STIR and GATE we have to move half block more.

TBranches for Cylindrical PET
TBranch *	br_crystalID1 = nullptr

TBranch *	br_crystalID2 = nullptr

TBranch *	br_submoduleID1 = nullptr

TBranch *	br_submoduleID2 = nullptr

TBranch *	br_moduleID1 = nullptr

TBranch *	br_moduleID2 = nullptr

TBranch *	br_rsectorID1 = nullptr

TBranch *	br_rsectorID2 = nullptr

ROOT Variables, i.e. to hold data from each entry.
std::int32_t	crystalID1

std::int32_t	crystalID2

std::int32_t	submoduleID1

std::int32_t	submoduleID2

std::int32_t	moduleID1

std::int32_t	moduleID2

std::int32_t	rsectorID1

std::int32_t	rsectorID2

Protected Attributes inherited from stir::InputStreamFromROOTFile
std::string	filename
	Input data file name.

unsigned long int	starting_stream_position
	The starting position.

unsigned long int	nentries
	The total number of entries.

unsigned long int	current_position
	Current get position.

std::vector< unsigned long int >	saved_get_positions
	A vector with saved position indices.

std::string	chain_name
	The name of the ROOT chain to be read.

bool	read_optional_root_fields
	This variable can be used to setBranchAddress to ROOT fields that currently are not used by STIR. Because they might be related to medical image reconstruction or because STIR does not support a relevant use. Of course, just activating this flag does not mean that something meaningfull will happen. Please edit get_next_record() function accordingly.

bool	exclude_nonrandom
	Skip True events (eventID1 == eventID2). Default is false.

bool	exclude_scattered
	Skip scattered events (comptonphantom1 > 0 && comptonphantom2 > 0). Default is false.

bool	exclude_unscattered
	Skip unscattered events (comptonphantom1 == 0 && comptonphantom2 == 0)). Default is false.

bool	exclude_randoms
	Skip random events (eventID1 != eventID2). Default is false.

bool	check_energy_window_information
	Check energy window information (low_energy_window < energy < up_energy_window). Default is true.

float	low_energy_window
	Lower energy threshold. Default is 1000 (keV)

float	up_energy_window
	Upper energy threshold. Default is 0 (keV)

int	singles_readout_depth
	For the singles_readout_depth from GATE's online documentation: (here ) the readout depth depends upon how the electronic readout functions.

double	least_significant_clock_bit

int	crystal_repeater_x

int	crystal_repeater_y

int	crystal_repeater_z

TChain *	stream_ptr

std::int32_t	eventID1

std::int32_t	eventID2

std::int32_t	runID

std::int32_t	sourceID1

std::int32_t	sourceID2

double	time1

double	time2

float	energy1

float	energy2

float	rotation_angle

float	sinogramS

float	sinogramTheta

float	axialPos

int32_t	comptonphantom1

int32_t	comptonphantom2

float	globalPosX1

float	globalPosX2

float	globalPosY1

float	globalPosY2

float	globalPosZ1

float	globalPosZ2

float	sourcePosX1

float	sourcePosX2

float	sourcePosY1

float	sourcePosY2

float	sourcePosZ1

float	sourcePosZ2

TBranch *	br_time1 = nullptr

TBranch *	br_time2 = nullptr

TBranch *	br_eventID1 = nullptr

TBranch *	br_eventID2 = nullptr

TBranch *	br_energy1 = nullptr

TBranch *	br_energy2 = nullptr

TBranch *	br_comptonPhantom1 = nullptr

TBranch *	br_comptonPhantom2 = nullptr

TBranch *	br_axialPos = nullptr

TBranch *	br_globalPosX1 = nullptr

TBranch *	br_globalPosX2 = nullptr

TBranch *	br_globalPosY1 = nullptr

TBranch *	br_globalPosY2 = nullptr

TBranch *	br_globalPosZ1 = nullptr

TBranch *	br_globalPosZ2 = nullptr

TBranch *	br_rotation_angle = nullptr

TBranch *	br_runID = nullptr

TBranch *	br_sinogramS = nullptr

TBranch *	br_sinogramTheta = nullptr

TBranch *	br_sourceID1 = nullptr

TBranch *	br_sourceID2 = nullptr

TBranch *	br_sourcePosX1 = nullptr

TBranch *	br_sourcePosX2 = nullptr

TBranch *	br_sourcePosY1 = nullptr

TBranch *	br_sourcePosY2 = nullptr

TBranch *	br_sourcePosZ1 = nullptr

TBranch *	br_sourcePosZ2 = nullptr

int	num_virtual_axial_crystals_per_block

int	num_virtual_transaxial_crystals_per_block

Protected Attributes inherited from stir::ParsingObject
KeyParser	parser

Additional Inherited Members
Public Types inherited from stir::InputStreamFromROOTFile
typedef std::vector< long long int >::size_type	SavedPosition

Static Public Member Functions inherited from stir::RegisteredParsingObject< InputStreamFromROOTFileForCylindricalPET, InputStreamFromROOTFile, InputStreamFromROOTFile >
static InputStreamFromROOTFile *	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< InputStreamFromROOTFile >
static InputStreamFromROOTFile *	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 InputStreamFromROOTFile *	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< InputStreamFromROOTFile >
typedef InputStreamFromROOTFile (	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< InputStreamFromROOTFile >
static RegistryType &	registry ()
	Static function returning the registry. More...

Detailed Description

Declaration of class stir::InputStreamFromROOTFileForCylindricalPET.

From (here ) a cylindrical PET scanner has five levels rsector module submodule crystal layer

The geometry is defined through the repeaters. In the example header file found below. The values in the repeaters must match the values in the simulation macro file.

Warning: In case that in the simulation a level is skipped then the repeater has to be set to 1.

  GATE scanner type := GATE_Cylindrical_PET
      GATE_Cylindrical_PET Parameters :=
      name of data file := ${INPUT_ROOT_FILE}
      name of input TChain := Coincidences

      number of Rsectors := 504
      number of modules_X := 1
      number of modules_Y := 1
      number of modules_Z := 1
      number of submodules_X := 1
      number of submodules_Y := 1
      number of submodules_Z := 1
      number of crystals_X := 1
      number of crystals_Y := 1
      number of crystals_Z := 4

      Singles readout depth := 1
      exclude scattered events := ${EXCLUDE_SCATTERED}
      exclude random events := ${EXCLUDE_RANDOM}
      low energy window (keV) := 0
      upper energy window (keV):= 10000

  End GATE_Cylindrical_PET Parameters :=

Author: Nikos Efthimiou

Member Function Documentation

◆ get_next_record()

Succeeded stir::InputStreamFromROOTFileForCylindricalPET::get_next_record ( CListRecordROOT & record )

overridevirtual

Returns the next record in the ROOT file. The code is adapted from Sadek A. Nehmeh and CR Schmidtlein, downloaded from here

Implements stir::InputStreamFromROOTFile.

References stir::InputStreamFromROOTFile::check_brentry_randoms_scatter_energy_conditions(), stir::InputStreamFromROOTFile::current_position, stir::InputStreamFromROOTFile::get_num_axial_crystals_per_block_v(), stir::InputStreamFromROOTFile::get_num_transaxial_crystals_per_block_v(), stir::InputStreamFromROOTFile::GetEntryCheck(), half_block, stir::CListRecordROOT::init_from_data(), and stir::InputStreamFromROOTFile::nentries.

◆ post_processing()

bool stir::InputStreamFromROOTFileForCylindricalPET::post_processing ( )

overrideprotectedvirtual

This will be called at the end of the parsing.

Returns: false if everything OK, true if not

Reimplemented from stir::InputStreamFromROOTFile.

References stir::InputStreamFromROOTFile::post_processing().

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

/home/sirfuser/devel/STIRdistrib/STIR/src/include/stir/IO/InputStreamFromROOTFileForCylindricalPET.h
/home/sirfuser/devel/STIRdistrib/STIR/src/include/stir/IO/InputStreamFromROOTFileForCylindricalPET.inl
/home/sirfuser/devel/STIRdistrib/STIR/src/IO/InputStreamFromROOTFileForCylindricalPET.cxx

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ get_next_record()

◆ post_processing()