class that reads ROOT files, generated by GATE, as listmode data. More...

#include "stir/listmode/CListModeDataROOT.h"

Inheritance diagram for stir::CListModeDataROOT:

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Public Member Functions
	CListModeDataROOT (const std::string &hroot_filename_prefix)
	construct from the filename of the Interfile header

std::string	get_name () const override
	returns the header filename

void	set_defaults ()
	Set private members default values;.

shared_ptr< CListRecord >	get_empty_record_sptr () const override
	Get a pointer to an empty record.

Succeeded	get_next_record (CListRecord &record) const override
	Gets the next record in the listmode sequence.

Succeeded	reset () override
	Call this function if you want to re-start reading at the beginning.

SavedPosition	save_get_position () override
	Save the current reading position.

Succeeded	set_get_position (const SavedPosition &) override
	Set the position for reading to a previously saved point.

bool	has_delayeds () const override
	Return if the file stores delayed events as well (as opposed to prompts)

unsigned long int	get_total_number_of_events () const override
	Returns the total number of events in the listmode file.

Public Member Functions inherited from stir::ListModeData
	ListModeData ()
	Default constructor.

	ListModeData (shared_ptr< const ExamInfo > exam_info_sptr, shared_ptr< const ProjDataInfo > proj_data_info_sptr)

shared_ptr< ListRecord >	get_empty_record_sptr () const
	Get a pointer to an empty record.

virtual Succeeded	get_next_record (ListRecord &event) const
	Gets the next record in the listmode sequence.

const Scanner &	get_scanner () const
	Get reference to scanner.

Public Member Functions inherited from stir::ExamData
	ExamData ()
	ExamData.

	ExamData (const shared_ptr< const ExamInfo > &_this_exam)

virtual const ExamInfo &	get_exam_info () const

virtual shared_ptr< const ExamInfo >	get_exam_info_sptr () const
	Get shared pointer to exam info.

virtual void	set_exam_info (ExamInfo const &)
	change exam info

void	set_exam_info_sptr (shared_ptr< const ExamInfo > new_exam_info_sptr)

Public Member Functions inherited from stir::DataWithProjDataInfo
	DataWithProjDataInfo ()
	Default constructor sets internal member to 0.

	DataWithProjDataInfo (const shared_ptr< const ProjDataInfo > &proj_data_info_sptr_v)

virtual const ProjDataInfo &	get_proj_data_info () const

virtual shared_ptr< const ProjDataInfo >	get_proj_data_info_sptr () const
	Get shared pointer to ProjData info.

int	get_num_segments () const
	Get number of segments.

int	get_num_axial_poss (const int segment_num) const
	Get number of axial positions per segment.

int	get_num_views () const
	Get number of views.

int	get_num_tangential_poss () const
	Get number of tangential positions.

int	get_num_tof_poss () const
	Get number of TOF positions.

int	get_min_tof_pos_num () const
	Get the index of the first timing position.

int	get_max_tof_pos_num () const
	Get the index of the last timing position.

int	get_tof_mash_factor () const
	Get TOG mash factor.

int	get_min_segment_num () const
	Get minimum segment number.

int	get_max_segment_num () const
	Get maximum segment number.

int	get_min_axial_pos_num (const int segment_num) const
	Get mininum axial position per segmnet.

int	get_max_axial_pos_num (const int segment_num) const
	Get maximum axial position per segment.

int	get_min_view_num () const
	Get minimum view number.

int	get_max_view_num () const
	Get maximum view number.

int	get_min_tangential_pos_num () const
	Get minimum tangential position number.

int	get_max_tangential_pos_num () const
	Get maximum tangential position number.

Additional Inherited Members
Public Types inherited from stir::ListModeData
typedef ListModeData	hierarchy_base_type
	typedef used by read_from_file

typedef unsigned int	SavedPosition
	Use this typedef for save/set_get_position.

Protected Member Functions inherited from stir::CListModeData
shared_ptr< ListRecord >	get_empty_record_helper_sptr () const override

Succeeded	get_next (ListRecord &event) const override

Protected Member Functions inherited from stir::ListModeData
virtual void	set_proj_data_info_sptr (shared_ptr< const ProjDataInfo >)

Protected Attributes inherited from stir::ExamData
shared_ptr< const ExamInfo >	exam_info_sptr

Protected Attributes inherited from stir::DataWithProjDataInfo
shared_ptr< const ProjDataInfo >	proj_data_info_sptr

Detailed Description

class that reads ROOT files, generated by GATE, as listmode data.

Author: Nikos Efthimiou; Kris Thielemans

This class does not directly read the ROOT file but instead needs an Interfile-type header to specify the scanner (as this information is not stored in the ROOT file). We tend to name this header something.hroot but this is not mandatory.

Warning: There is currently no check if the scanner information is correct. This is dangerous for the geometry, but can also lead to crashes if the actual number of blocks/crystals etc is larger than what is specified in the scanner info.

We currently support only ROOT output using the 'Cylindrical PET' and 'ECAT' systems from GATE.

The Scanner geometry is set in multiple places. In hroot there is the option to use the Scanner name to pull a Scanner from the library. Another option is to use Scanner::User_defined_scanner and set the members: num_rings, num_detectors_per_ring, max_num_non_arccorrected_bins, inner_ring_diameter, average_depth_of_interaction, ring_spacing and bin_size, manually.

In any case this scanner must checkout the geometry created by the repeaters section (which will initialise the InputStreamFromROOTFile. And of course, match the Scanner used by other parts of STIR (e.g. ProjDataInfo e.t.c).

Finally, in the case that Scanner::Unknown_scanner the algorithm will try to create the scanner from the members. Subject to concistency checks, of course.

Example headers

If the scanner is known to stir::Scanner, you can use this

ROOT header :=
Originating system := Siemens mMR

; specify GATE output format (could be GATE_ECAT_PET as well)
GATE scanner type := GATE_Cylindrical_PET
GATE_Cylindrical_PET Parameters :=
  ; name of the actual ROOT file
  name of data file := mysim.root

  ; See elsewhere for other parameters
End GATE_Cylindrical_PET Parameters :=

end ROOT header :=

Below is an example using a user-defined scanner.

ROOT header :=
Originating system := User_defined_scanner
Number of rings                          := 4
Number of detectors per ring             := 504
Inner ring diameter (cm)                 := 65.6
Average depth of interaction (cm)        := 0.7
Distance between rings (cm)              := 0.40625
Default bin size (cm)                    := 0.208626
Maximum number of non-arc-corrected bins := 344
; optional keywords to create "virtual" crystals to accomodate for gaps between blocks
; if you do not specify these, the STIR defaults (determined by the "originating system")
; will be used (which are zero for a User_defined_scanner)
Number of virtual axial crystals per block := 0
Number of virtual transaxial crystals per block:= 0

GATE scanner type := GATE_Cylindrical_PET
GATE_Cylindrical_PET Parameters :=
  ; name of the actual ROOT file
  name of data file := mysim.root

  ; See elsewhere for other parameters
End GATE_Cylindrical_PET Parameters :=

end ROOT header :=

Member Function Documentation

◆ get_name()

std::string stir::CListModeDataROOT::get_name ( ) const

overridevirtual

returns the header filename

Implements stir::ListModeData.

◆ get_empty_record_sptr()

shared_ptr< CListRecord > stir::CListModeDataROOT::get_empty_record_sptr ( ) const

overridevirtual

Get a pointer to an empty record.

This is mainly/only useful to get a record of the correct type, that can then be passed to get_next_record().

Implements stir::CListModeData.

References stir::DataWithProjDataInfo::get_proj_data_info_sptr().

◆ get_next_record()

Succeeded stir::CListModeDataROOT::get_next_record ( CListRecord & event ) const

overridevirtual

Gets the next record in the listmode sequence.

Implements stir::CListModeData.

◆ reset()

Succeeded stir::CListModeDataROOT::reset ( )

overridevirtual

Call this function if you want to re-start reading at the beginning.

Implements stir::ListModeData.

◆ save_get_position()

CListModeData::SavedPosition stir::CListModeDataROOT::save_get_position ( )

overridevirtual

Save the current reading position.

Note that the return value is not related to the number of events already read. In particular, you cannot do any arithmetic on it to skip a few events. This is different from e.g. std::streampos.

Warning: There is a maximum number of times this function can be called. This is determined by the SavedPosition type. Once you save more positions, the first positions will be overwritten. There is currently no way of finding out after how many times this will happen (but it's a large number...).; These saved positions are only valid for the lifetime of the ListModeData object.; A derived class might disable this facility. It will/should then always return Succeeded::no when calling set_get_position().

Implements stir::ListModeData.

◆ set_get_position()

Succeeded stir::CListModeDataROOT::set_get_position ( const SavedPosition & )

overridevirtual

Set the position for reading to a previously saved point.

Implements stir::ListModeData.

◆ has_delayeds()

bool stir::CListModeDataROOT::has_delayeds ( ) const

inlineoverridevirtual

Return if the file stores delayed events as well (as opposed to prompts)

Implements stir::CListModeData.

◆ get_total_number_of_events()

unsigned long stir::CListModeDataROOT::get_total_number_of_events ( ) const

inlineoverridevirtual

Returns the total number of events in the listmode file.

Warning: This function currently works only a limited number of input types (including ROOT). By default it will throw an error.

Reimplemented from stir::ListModeData.

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

/home/kris/devel/STIRdistrib/STIR/src/include/stir/listmode/CListModeDataROOT.h
/home/kris/devel/STIRdistrib/STIR/src/listmode_buildblock/CListModeDataROOT.cxx

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ get_name()

◆ get_empty_record_sptr()

◆ get_next_record()

◆ reset()

◆ save_get_position()

◆ set_get_position()

◆ has_delayeds()

◆ get_total_number_of_events()