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

#include <iDataFileCT.hh>

Inheritance diagram for iDataFileCT:

Collaboration diagram for iDataFileCT:

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

	~iDataFileCT ()
	iDataFileCT destructor. More...

int	ReadSpecificInfoInHeader (bool a_affectQuantificationFlag)
	Read through the header file and recover specific CT 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=0)
	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...

int	InitAngles (FLTNB *ap_angles)
	allocate memory for the mp_angles variable using m_nbProjections and initialize the projection angles with the provided list of values More...

void	DescribeSpecific ()
	Implementation of the pure virtual eponym function that simply prints info about the datafile. 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 SPECT specific parameters for projections from the scanner object, through the scannerManager. More...

uint16_t	GetNbProjections ()

FLTNB *	GetAngles ()

void	SetEventKindFlagOn ()
	set to true the flag indicating the presence of the kind of a list-mode event in the datafile More...

void	SetNbProjections (uint16_t a_nbProjections)
	initialize the number of projections More...

int	GetDetectorRotDirection ()
	Simply return m_detectorRotDirection. More...

void	SetDetectorRotDirection (int a_direction)
	initialize the rotation direction of the CT detector More...

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

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

bool	GetBlankCorrectionFlag ()
	Simply return m_blankCorrectionFlag. 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 CT from the provided datafile. More...

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

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

int	WriteHistoEvent (iEventHistoCT *ap_Event, int a_th)
	Write a CT histogram event. More...

int	WriteListEvent (iEventListCT *ap_Event, int a_th)
	Write a CT list-mode event. More...

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

Private Attributes
bool	m_eventKindFlag

bool	m_blankCorrectionFlag

bool	m_ignoreBlankCorrectionFlag

bool	m_scatCorrectionFlag

bool	m_ignoreScatCorrectionFlag

uint16_t	m_nbOfProjections

FLTNB *	mp_angles

int	m_detectorRotDirection

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 CT 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 48 of file iDataFileCT.hh.

Constructor & Destructor Documentation

iDataFileCT::iDataFileCT ( )

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

Definition at line 39 of file iDataFileCT.cc.

iDataFileCT::~iDataFileCT ( )

iDataFileCT destructor.

Definition at line 59 of file iDataFileCT.cc.

Member Function Documentation

int iDataFileCT::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 403 of file iDataFileCT.cc.

int iDataFileCT::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 449 of file iDataFileCT.cc.

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int iDataFileCT::CheckSpecificParameters ( )

privatevirtual

Check parameters specific to CT data.

Returns: 0 if success, and positive value otherwise.

Implements vDataFile.

Definition at line 373 of file iDataFileCT.cc.

int iDataFileCT::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 141 of file iDataFileCT.cc.

void iDataFileCT::DescribeSpecific ( )

virtual

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

Implements vDataFile.

Definition at line 352 of file iDataFileCT.cc.

iDataFileCT::GetAngles ( )

inline

Returns: Angles for each projection of the acquisition

Definition at line 153 of file iDataFileCT.hh.

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iDataFileCT::GetBlankCorrectionFlag ( )

inline

Simply return m_blankCorrectionFlag.

Returns: m_blankCorrectionFlag

Definition at line 202 of file iDataFileCT.hh.

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iDataFileCT::GetDetectorRotDirection ( )

inline

Simply return m_detectorRotDirection.

Returns: m_detectorRotDirection

Definition at line 174 of file iDataFileCT.hh.

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iDataFileCT::GetEventKindFlag ( )

inline

Simply return m_eventKindFlag.

Returns: m_eventKindFlag

Definition at line 188 of file iDataFileCT.hh.

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vEvent * iDataFileCT::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 271 of file iDataFileCT.cc.

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iDataFileCT::GetNbProjections ( )

inline

Returns: total number of projections in the CT acquisition

Definition at line 147 of file iDataFileCT.hh.

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iDataFileCT::GetScatCorrectionFlag ( )

inline

Simply return m_scatCorrectionFlag.

Returns: m_scatCorrectionFlag

Definition at line 195 of file iDataFileCT.hh.

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int iDataFileCT::InitAngles ( FLTNB * ap_angles )

allocate memory for the mp_angles variable using m_nbProjections and initialize the projection angles with the provided list of values

Parameters

ap_angles

Returns: 0 if success, positive value otherwise

Definition at line 487 of file iDataFileCT.cc.

int iDataFileCT::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 192 of file iDataFileCT.cc.

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int iDataFileCT::PROJ_GetScannerSpecificParameters ( )

virtual

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

Returns: 0 if success, positive value otherwise

Implements vDataFile.

Definition at line 724 of file iDataFileCT.cc.

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int iDataFileCT::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 509 of file iDataFileCT.cc.

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int iDataFileCT::ReadSpecificInfoInHeader ( bool a_affectQuantificationFlag )

virtual

Read through the header file and recover specific CT 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 69 of file iDataFileCT.cc.

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iDataFileCT::SetDetectorRotDirection ( int a_direction )

inline

initialize the rotation direction of the CT detector

Parameters

a_direction

Definition at line 181 of file iDataFileCT.hh.

iDataFileCT::SetEventKindFlagOn ( )

inline

set to true the flag indicating the presence of the kind of a list-mode event in the datafile

This function is dedicated to datafile conversion scripts

Definition at line 160 of file iDataFileCT.hh.

iDataFileCT::SetNbProjections ( uint16_t a_nbProjections )

inline

initialize the number of projections

Parameters

a_nbProjections

Definition at line 167 of file iDataFileCT.hh.

int iDataFileCT::SetSpecificParametersFrom ( vDataFile * ap_DataFile )

privatevirtual

Initialize all parameters specific to CT from the provided datafile.

Returns: 0 if success, and positive value otherwise

Implements vDataFile.

Definition at line 123 of file iDataFileCT.cc.

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int iDataFileCT::WriteEvent	(	vEvent *	ap_Event,
		int	a_th = `0`
	)

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 561 of file iDataFileCT.cc.

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int iDataFileCT::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 671 of file iDataFileCT.cc.

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int iDataFileCT::WriteHistoEvent	(	iEventHistoCT *	ap_Event,
		int	a_th
	)

private

Write a CT 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 592 of file iDataFileCT.cc.

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int iDataFileCT::WriteListEvent	(	iEventListCT *	ap_Event,
		int	a_th
	)

private

Write a CT 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 630 of file iDataFileCT.cc.

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Member Data Documentation

bool iDataFileCT::m_blankCorrectionFlag

private

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

Definition at line 256 of file iDataFileCT.hh.

int iDataFileCT::m_detectorRotDirection

private

Head rotation direction (0=clockwise, 1=counterclockwise)

Definition at line 262 of file iDataFileCT.hh.

bool iDataFileCT::m_eventKindFlag

private

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

Definition at line 255 of file iDataFileCT.hh.

bool iDataFileCT::m_ignoreBlankCorrectionFlag

private

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

Definition at line 257 of file iDataFileCT.hh.

bool iDataFileCT::m_ignoreScatCorrectionFlag

private

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

Definition at line 259 of file iDataFileCT.hh.

uint16_t iDataFileCT::m_nbOfProjections

private

Total number of projections during the acquisition(for all the heads). No Default

Definition at line 260 of file iDataFileCT.hh.

bool iDataFileCT::m_scatCorrectionFlag

private

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

Definition at line 258 of file iDataFileCT.hh.

FLTNB* iDataFileCT::mp_angles

private

Angle [for each projection] in degrees. No Default

Definition at line 261 of file iDataFileCT.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