Inherit from vDataFile. Class that manages the reading of a PET input file (header + data). More...

#include <iDataFilePET.hh>

Inheritance diagram for iDataFilePET:

Collaboration diagram for iDataFilePET:

Public Member Functions
	iDataFilePET ()
	iDataFilePET constructor. Initialize the member variables to their default values. More...

	~iDataFilePET ()
	iDataFilePET destructor. More...

int	ReadSpecificInfoInHeader (bool a_affectQuantificationFlag)
	Read through the header file and gather specific PET information. More...

int	WriteHeader ()
	Generate a header file according to the data output information. More...

int	ComputeSizeEvent ()
	Computation of the size of each event according to the mandatory/optional correction fields. More...

int	PrepareDataFile ()
	Store different kind of information inside arrays (data relative to specific correction as well as basic raw data for the case data is loaded in RAM) Use the flag provided by the user to determine how the data has to be sorted (preloaded or read on the fly) More...

int	WriteEvent (vEvent *ap_Event, int a_th)
	Write event according to the chosen type of data. More...

vEvent *	GetEventSpecific (char *ap_buffer, int a_th)
	Read an event from the position pointed by 'ap_buffer', parse the generic or modality-specific information, and store them in the (multithreaded) 'm2p_BufferEvent' object. More...

void	DescribeSpecific ()
	Implementation of the pure virtual eponym function that simply prints info about the datafile. More...

bool	GetTOFInfoFlag ()

bool	GetIgnoreTOFFlag ()

FLTNB	GetTOFResolution ()

int	GetNbTOFBins ()

FLTNB	GetTOFBinSize ()

FLTNB	GetTOFMeasurementRange ()

FLTNB	GetMaxAxialDiffmm ()

void	SetMaxNumberOfLinesPerEvent (uint16_t a_value)
	set the max number of line per event in the datafile More...

uint16_t	GetMaxNumberOfLinesPerEvent ()

void	SetIsotope (string a_value)
	initialize the isotope string value More...

string	GetIsotope ()

void	SetIgnoreTOFFlag (bool a_ignoreTOFFlag)
	Set a boolean that that if we ignore TOF information or not. More...

void	SetEventKindFlagOn ()
	set to true the flag indicating the presence of the kind of a list-mode event in the datafile TODO check if consistent with datafile type More...

void	SetAtnCorrectionFlagOn ()
	set to true the flag indicating the presence of attenuation correction factors in the datafile More...

void	SetNormCorrectionFlagOn ()
	set to true the flag indicating the presence of normalization correction factors in the datafile More...

void	SetScatterCorrectionFlagOn ()
	set to true the flag indicating the presence of scatter correction factors in the datafile More...

void	SetRandomCorrectionFlagOn ()
	set to true the flag indicating the presence of random correction factors in the datafile More...

bool	GetNormCorrectionFlag ()
	Simply return m_normCorrectionFlag. More...

bool	GetAtnCorrectionFlag ()
	Simply return m_atnCorrectionFlag. More...

bool	GetEventKindFlag ()
	Simply return m_eventKindFlag. More...

bool	GetScatCorrectionFlag ()
	Simply return m_scatCorrectionFlag. More...

bool	GetRandCorrectionFlag ()
	Simply return m_randCorrectionFlag. More...

int	PROJ_InitFile ()
	Initialize the fstream objets for output writing as well as some other variables specific to the Projection script (Event-based correction flags, Estimated size of data file) More...

int	PROJ_GetScannerSpecificParameters ()
	Get PET specific parameters for projections from the scanner object, through the scannerManager. More...

Public Member Functions inherited from vDataFile
	vDataFile ()
	vDataFile constructor. More...

virtual	~vDataFile ()
	vDataFile destructor. More...

int	ReadInfoInHeader (bool a_affectQuantificationFlag=true)
	Read and check general information from the header datafile Call the ReadSpecificInformationInHeader() function implemented in child classes. More...

int	SetParametersFrom (vDataFile *ap_DataFile)
	Initialize all parameters from the provided datafile. More...

int	CheckParameters ()
	Check the initialization of member variables Call the CheckSpecificParameters() function implemented in child classes. More...

int	InitializeMappedFile ()
	Check the datafile existency, map it to memory and get the raw char* pointer. . More...

int	OpenFileForWriting (string a_suffix="")
	Open a binary file stream for writing, with eventually the suffix appended to the file name. More...

int	CloseFile ()
	Close as many binary file stream for writing. More...

vEvent *	GetEvent (int64_t a_eventIndex, int a_th=0)

void	GetEventIndexStartAndStop (int64_t ap_indexStart, int64_t ap_indexStop, int a_subsetNum=0, int a_NbSubsets=1)
	Compute the index start and stop of the events loop with respect to the current subset and MPI size and rank. More...

int	CheckConsistencyWithAnotherBedDataFile (vDataFile *ap_DataFile)
	Check consistency between 'this' and the provided datafile as two bed positions. More...

void	Describe ()
	A function used to describe the generic parts of the datafile. More...

int	PROJ_WriteData ()
	Write/Merge chunk of data in a general data file. More...

int	PROJ_DeleteTmpDataFile ()
	Delete temporary datafile used for multithreaded output writing if needed. More...

vEvent *	PROJ_GenerateEvent (int idx_elt1, int idx_elt2, int a_th)
	Generate a standard event and set up its ID Used by the projection, list-mode sensitivity generation, and datafile converter scripts. More...

int	GetBedIndex ()

int	GetDataMode ()

string	GetDataModeToString ()

int	GetDataType ()

string	GetDataTypeToString ()

int	GetDataSpec ()

string	GetDataSpecToString ()

int64_t	GetSize ()

int64_t	GetEventSize ()

string	GetHeaderDataFileName ()

string	GetDataFileName ()

int64_t	GetStartTime ()

int64_t	GetDuration ()

FLTNB	GetCalibrationFactor ()

FLTNB *	GetPOIResolution ()

bool *	GetPOIDirectionFlag ()

bool	GetPOIInfoFlag ()

bool	GetIgnorePOIFlag ()

virtual int	GetMaxRingDiff ()
	Return an error by default. This function is surcharged by the PET (and CT) scanner daughter class. More...

void	SetDataMode (int a_dataMode)
	set the data mode More...

void	SetDataType (int a_dataType)
	set the data type More...

void	SetBedIndex (int a_bedIndex)
	set the bed index corresponding to this data file More...

bool	GetBedPositionFlag ()

FLTNB	GetRelativeBedPosition ()

void	SetVerbose (int a_verboseLevel)
	set verbosity More...

int	GetVerbose ()
	Get the verbose level. More...

void	SetImageDimensionsAndQuantification (oImageDimensionsAndQuantification *ap_ImageDimensionsAndQuantification)
	set the pointer to the oImageDimensionsAndQuantification object More...

void	SetPOIResolution (FLTNB ap_value[3])
	initialize the POI resolution (for list-mode) More...

void	SetIgnorePOIFlag (bool a_ignorePOIFlag)
	Set a boolean that that if we ignore POI information or not. More...

void	SetHeaderDataFileName (const string &a_headerFileName)
	set the data header file name More...

void	SetBinaryDataFileName (const string &a_dataFileName)
	set the data binary file name More...

void	SetCalibrationFactor (FLTNB a_value)
	initialize the global calibration factor with a FLTNB value More...

void	SetNbEvents (int64_t a_value)
	initialize the number of events with a int64_t value More...

void	SetStartTime (FLTNB a_value)

void	SetDuration (FLTNB a_value)

string	GetScannerName ()

virtual int	Shuffle (int64_t)
	!!!\ This function has been modified to be used specifically with a More...

Private Member Functions
int	SetSpecificParametersFrom (vDataFile *ap_DataFile)
	Initialize all parameters specific to PET from the provided datafile. More...

int	CheckSpecificParameters ()
	Check parameters specific to PET data. More...

int	WriteListEvent (iEventListPET *ap_Event, int a_th=0)
	Write a PET list-mode event. More...

int	WriteHistoEvent (iEventHistoPET *ap_Event, int a_th)
	Write a PET histogram event. More...

int	CheckFileSizeConsistency ()
	This function is implemented in child classes Check if file size is consistent. More...

int	CheckSpecificConsistencyWithAnotherDataFile (vDataFile *ap_DataFile)
	Check consistency between 'this' and the provided datafile, for specific characteristics. More...

Private Attributes
uint16_t	m_maxNumberOfLinesPerEvent

FLTNB	m_maxAxialDiffmm

string	m_isotope

bool	m_eventKindFlag

bool	m_atnCorrectionFlag

bool	m_ignoreAttnCorrectionFlag

bool	m_normCorrectionFlag

bool	m_ignoreNormCorrectionFlag

bool	m_scatCorrectionFlag

bool	m_ignoreScatCorrectionFlag

bool	m_randCorrectionFlag

bool	m_ignoreRandCorrectionFlag

bool	m_TOFInfoFlag

bool	m_ignoreTOFFlag

FLTNB	m_resolutionTOF

int	m_nbBinsTOF

FLTNB	m_binSizeTOF

FLTNB	m_TOFMeasurementRange

Additional Inherited Members
Protected Attributes inherited from vDataFile
oImageDimensionsAndQuantification *	mp_ID

int	m_verbose

string	m_headerFileName

string	m_dataFileName

int64_t	m_nbEvents

int	m_dataMode

int	m_dataType

int	m_dataSpec

FLTNB	m_startTimeInSec

FLTNB	m_durationInSec

FLTNB	m_calibrationFactor

int	m_bedIndex

FLTNB	m_relativeBedPosition

bool	m_bedPositionFlag

string	m_scannerName

bool	m_POIInfoFlag

bool	m_ignorePOIFlag

bool	mp_POIDirectionFlag [3]

FLTNB	mp_POIResolution [3]

int64_t	m_sizeEvent

fstream **	m2p_dataFile

vEvent **	m2p_BufferEvent

int64_t	m_mpi1stEvent

int64_t	m_mpiLastEvent

int64_t	m_mpiNbEvents

oMemoryMapped *	mp_MappedFile

char *	mp_mappedMemory

Detailed Description

Inherit from vDataFile. Class that manages the reading of a PET input file (header + data).

It contains several arrays corresponding to the different kind of informations the data file could contain.
As many booleans as arrays say if the data are here or not. The data file can be either completely loaded, or read event by event during reconstruction.
MPI is coming here to cut the data file into peaces (also either can be loaded or read on-the-fly).

Definition at line 44 of file iDataFilePET.hh.

Constructor & Destructor Documentation

iDataFilePET::iDataFilePET ( )

iDataFilePET constructor. Initialize the member variables to their default values.

Definition at line 39 of file iDataFilePET.cc.

iDataFilePET::~iDataFilePET ( )

iDataFilePET destructor.

Definition at line 69 of file iDataFilePET.cc.

Member Function Documentation

int iDataFilePET::CheckFileSizeConsistency ( )

privatevirtual

This function is implemented in child classes
Check if file size is consistent.

Returns: 0 if success, and positive value otherwise.

Implements vDataFile.

Definition at line 663 of file iDataFilePET.cc.

int iDataFilePET::CheckSpecificConsistencyWithAnotherDataFile ( vDataFile * ap_DataFile )

privatevirtual

Check consistency between 'this' and the provided datafile, for specific characteristics.

Parameters

vDataFile* ap_DataFile

Implementation of the pure virtual function from vDataFile. It checks correction flags, etc.

Returns: 0 if the provided datafile is consistent with 'this', another value otherwise

Implements vDataFile.

Definition at line 724 of file iDataFilePET.cc.

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int iDataFilePET::CheckSpecificParameters ( )

privatevirtual

Check parameters specific to PET data.

Returns: 0 if success, and positive value otherwise.

Implements vDataFile.

Definition at line 590 of file iDataFilePET.cc.

int iDataFilePET::ComputeSizeEvent ( )

virtual

Computation of the size of each event according to the mandatory/optional correction fields.

Returns: 0 is success, positive value otherwise

Implements vDataFile.

Definition at line 139 of file iDataFilePET.cc.

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void iDataFilePET::DescribeSpecific ( )

virtual

Implementation of the pure virtual eponym function that simply prints info about the datafile.

Implements vDataFile.

Definition at line 557 of file iDataFilePET.cc.

iDataFilePET::GetAtnCorrectionFlag ( )

inline

Simply return m_atnCorrectionFlag.

Returns: m_atnCorrectionFlag

Definition at line 239 of file iDataFilePET.hh.

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iDataFilePET::GetEventKindFlag ( )

inline

Simply return m_eventKindFlag.

Returns: m_eventKindFlag

Definition at line 246 of file iDataFilePET.hh.

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vEvent * iDataFilePET::GetEventSpecific	(	char *	ap_buffer,
		int	a_th
	)

virtual

Read an event from the position pointed by 'ap_buffer', parse the generic or modality-specific information, and store them in the (multithreaded) 'm2p_BufferEvent' object.

Parameters

ap_buffer	: address pointing to the event to recover
a_th	: index of the thread from which the function was called

Returns: the thread-specific 'm2p_BufferEvent' object containing the modality-specific information for the event

Implements vDataFile.

Definition at line 355 of file iDataFilePET.cc.

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iDataFilePET::GetIgnoreTOFFlag ( )

inline

Returns: m_ignoreTOFFlag

Definition at line 125 of file iDataFilePET.hh.

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iDataFilePET::GetIsotope ( )

inline

Returns: the isotope string value

Definition at line 182 of file iDataFilePET.hh.

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iDataFilePET::GetMaxAxialDiffmm ( )

inline

Returns: max ring difference in the acquisition

Definition at line 155 of file iDataFilePET.hh.

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iDataFilePET::GetMaxNumberOfLinesPerEvent ( )

inline

Returns: the max number of line per event in the datafile

Definition at line 167 of file iDataFilePET.hh.

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iDataFilePET::GetNbTOFBins ( )

inline

Returns: number of TOF bins in the acquisition

Definition at line 137 of file iDataFilePET.hh.

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iDataFilePET::GetNormCorrectionFlag ( )

inline

Simply return m_normCorrectionFlag.

Returns: m_normCorrectionFlag

Definition at line 232 of file iDataFilePET.hh.

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iDataFilePET::GetRandCorrectionFlag ( )

inline

Simply return m_randCorrectionFlag.

Returns: m_randCorrectionFlag

Definition at line 260 of file iDataFilePET.hh.

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iDataFilePET::GetScatCorrectionFlag ( )

inline

Simply return m_scatCorrectionFlag.

Returns: m_scatCorrectionFlag

Definition at line 253 of file iDataFilePET.hh.

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iDataFilePET::GetTOFBinSize ( )

inline

Returns: size of TOF bins in the acquisition

Definition at line 143 of file iDataFilePET.hh.

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iDataFilePET::GetTOFInfoFlag ( )

inline

Returns: m_TOFInfoFlag

Definition at line 119 of file iDataFilePET.hh.

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iDataFilePET::GetTOFMeasurementRange ( )

inline

Returns: Maximum range of values for TOF delta measurements

Definition at line 149 of file iDataFilePET.hh.

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iDataFilePET::GetTOFResolution ( )

inline

Returns: TOF resolution for the acquisition

Definition at line 131 of file iDataFilePET.hh.

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int iDataFilePET::PrepareDataFile ( )

virtual

Store different kind of information inside arrays (data relative to specific correction as well as basic raw data for the case data is loaded in RAM)
Use the flag provided by the user to determine how the data has to be sorted (preloaded or read on the fly)

Returns: 0 is success, positive value otherwise

Implements vDataFile.

Definition at line 212 of file iDataFilePET.cc.

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int iDataFilePET::PROJ_GetScannerSpecificParameters ( )

virtual

Get PET specific parameters for projections from the scanner object, through the scannerManager.

Returns: 0 if success, positive value otherwise

Implements vDataFile.

Definition at line 1177 of file iDataFilePET.cc.

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int iDataFilePET::PROJ_InitFile ( )

virtual

Initialize the fstream objets for output writing as well as some other variables specific to the Projection script (Event-based correction flags, Estimated size of data file)

Returns: 0 if success, and positive value otherwise.

Implements vDataFile.

Definition at line 816 of file iDataFilePET.cc.

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int iDataFilePET::ReadSpecificInfoInHeader ( bool a_affectQuantificationFlag )

virtual

Read through the header file and gather specific PET information.

Parameters

bool	a_affectQuantificationFlag

If the parameter flag is on, then affect the quantification factors from the oImageDimensionsAndQuantification after reading relevant information

Returns: 0 is success, positive value otherwise

Implements vDataFile.

Definition at line 76 of file iDataFilePET.cc.

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void iDataFilePET::SetAtnCorrectionFlagOn ( )

inline

set to true the flag indicating the presence of attenuation correction factors in the datafile

This function is dedicated to datafile conversion scripts

Definition at line 204 of file iDataFilePET.hh.

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iDataFilePET::SetEventKindFlagOn ( )

inline

set to true the flag indicating the presence of the kind of a list-mode event in the datafile TODO check if consistent with datafile type

This function is dedicated to datafile conversion scripts

Definition at line 197 of file iDataFilePET.hh.

iDataFilePET::SetIgnoreTOFFlag ( bool a_ignoreTOFFlag )

inline

Set a boolean that that if we ignore TOF information or not.

Parameters

a_flag

Definition at line 189 of file iDataFilePET.hh.

iDataFilePET::SetIsotope ( string a_value )

inline

initialize the isotope string value

Parameters

a_value

The name should corresponds to one corresponding tag in the isotope configuration file in config/. This function is dedicated to datafile conversion scripts

Definition at line 176 of file iDataFilePET.hh.

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iDataFilePET::SetMaxNumberOfLinesPerEvent ( uint16_t a_value )

inline

set the max number of line per event in the datafile

Definition at line 161 of file iDataFilePET.hh.

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iDataFilePET::SetNormCorrectionFlagOn ( )

inline

set to true the flag indicating the presence of normalization correction factors in the datafile

This function is dedicated to datafile conversion scripts

Definition at line 211 of file iDataFilePET.hh.

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iDataFilePET::SetRandomCorrectionFlagOn ( )

inline

set to true the flag indicating the presence of random correction factors in the datafile

This function is dedicated to datafile conversion scripts

Definition at line 225 of file iDataFilePET.hh.

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iDataFilePET::SetScatterCorrectionFlagOn ( )

inline

set to true the flag indicating the presence of scatter correction factors in the datafile

This function is dedicated to datafile conversion scripts

Definition at line 218 of file iDataFilePET.hh.

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int iDataFilePET::SetSpecificParametersFrom ( vDataFile * ap_DataFile )

privatevirtual

Initialize all parameters specific to PET from the provided datafile.

Returns: 0 if success, and positive value otherwise

Implements vDataFile.

Definition at line 114 of file iDataFilePET.cc.

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int iDataFilePET::WriteEvent	(	vEvent *	ap_Event,
		int	a_th
	)

virtual

Write event according to the chosen type of data.

Parameters

ap_Event	: event containing the data to write
a_th	: index of the thread from which the function was called

Returns: 0 if success, and positive value otherwise.

Implements vDataFile.

Definition at line 890 of file iDataFilePET.cc.

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int iDataFilePET::WriteHeader ( )

virtual

Generate a header file according to the data output information.

Returns: 0 if success, and positive value otherwise.

Implements vDataFile.

Definition at line 1087 of file iDataFilePET.cc.

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int iDataFilePET::WriteHistoEvent	(	iEventHistoPET *	ap_Event,
		int	a_th
	)

private

Write a PET histogram event.

Parameters

ap_Event	: event containing the data to write
a_th	: index of the thread from which the function was called

Returns: 0 if success, and positive value otherwise.

Definition at line 920 of file iDataFilePET.cc.

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int iDataFilePET::WriteListEvent	(	iEventListPET *	ap_Event,
		int	a_th = `0`
	)

private

Write a PET list-mode event.

Parameters

ap_Event	: event containing the data to write
a_th	: index of the thread from which the function was called

Returns: 0 if success, and positive value otherwise.

Definition at line 988 of file iDataFilePET.cc.

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Member Data Documentation

bool iDataFilePET::m_atnCorrectionFlag

private

Flag that says if attenuation correction terms are included in the data. Default = false

Definition at line 333 of file iDataFilePET.hh.

FLTNB iDataFilePET::m_binSizeTOF

private

Size of TOF bins for histogram mode. Default = -1.0

Definition at line 345 of file iDataFilePET.hh.

bool iDataFilePET::m_eventKindFlag

private

Flag for informations about the event nature (true, scatter, random) in the data. Default = false

Definition at line 332 of file iDataFilePET.hh.

bool iDataFilePET::m_ignoreAttnCorrectionFlag

private

Flag to say if we ignore the attenuation correction even if present. Default = false

Definition at line 334 of file iDataFilePET.hh.

bool iDataFilePET::m_ignoreNormCorrectionFlag

private

Flag to say if we ignore the normalization correction even if present. Default = false

Definition at line 336 of file iDataFilePET.hh.

bool iDataFilePET::m_ignoreRandCorrectionFlag

private

Flag to say if we ignore the random correction even if present. Default = false

Definition at line 340 of file iDataFilePET.hh.

bool iDataFilePET::m_ignoreScatCorrectionFlag

private

Flag to say if we ignore the scatter correction even if present. Default = false

Definition at line 338 of file iDataFilePET.hh.

bool iDataFilePET::m_ignoreTOFFlag

private

Flag to say if we ignore the TOF data even if present, or not. Default = false

Definition at line 342 of file iDataFilePET.hh.

string iDataFilePET::m_isotope

private

Isotope. Default = unknown

Definition at line 331 of file iDataFilePET.hh.

FLTNB iDataFilePET::m_maxAxialDiffmm

private

Max axial difference in mm between 2 crystals in a LOR. Default value calculated from the scanner files

Definition at line 330 of file iDataFilePET.hh.

uint16_t iDataFilePET::m_maxNumberOfLinesPerEvent

private

Number of lines in each event in the datafile. Default = 1

Definition at line 329 of file iDataFilePET.hh.

int iDataFilePET::m_nbBinsTOF

private

Number of TOF bins for histogram mode. Default = 1

Definition at line 344 of file iDataFilePET.hh.

bool iDataFilePET::m_normCorrectionFlag

private

Flag that says if normalization correction terms are included in the data. Default = false

Definition at line 335 of file iDataFilePET.hh.

bool iDataFilePET::m_randCorrectionFlag

private

Flag that says if random correction terms are included in the data. Default = false

Definition at line 339 of file iDataFilePET.hh.

FLTNB iDataFilePET::m_resolutionTOF

private

TOF resolution in ps. Default = -1.0

Definition at line 343 of file iDataFilePET.hh.

bool iDataFilePET::m_scatCorrectionFlag

private

Flag that says if scatter correction terms are included in the data. Default = false

Definition at line 337 of file iDataFilePET.hh.

bool iDataFilePET::m_TOFInfoFlag

private

Flag that says if TOF information is included in the data. Default = false

Definition at line 341 of file iDataFilePET.hh.

FLTNB iDataFilePET::m_TOFMeasurementRange

private

Maximum range of values for TOF delta time measurements (delta t max - delta t min) in ps

Definition at line 346 of file iDataFilePET.hh.

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation