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

#include <iDataFileSPECT.hh>

Inheritance diagram for iDataFileSPECT:

Collaboration diagram for iDataFileSPECT:

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

	~iDataFileSPECT ()
	iDataFileSPECT destructor. More...

int	ReadSpecificInfoInHeader (bool a_affectQuantificationFlag)
	Read through the header file and recover specific SPECT 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...

int	InitCorToDetectorDistance (FLTNB *ap_CORtoDetectorDistance)
	allocate memory for the ap_CORtoDetectorDistance 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	GetNbHeads ()

uint16_t	GetNbProjections ()

FLTNB *	GetAngles ()

FLTNB *	GetCORtoDetectorDistance ()

uint16_t	GetNbBins (int axis)

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

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

string	GetIsotope ()

void	SetNbBins (uint16_t a_binTrs, uint16_t a_binAxl)
	initialize the bin values More...

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

int	GetHeadRotDirection ()
	Simply return m_headRotDirection. More...

void	SetHeadRotDirection (int a_direction)
	initialize the rotation direction of the gamma camera(s) More...

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

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

bool	GetNormCorrectionFlag ()
	Simply return m_normCorrectionFlag. 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 SPECT from the provided datafile. More...

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

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

int	WriteHistoEvent (iEventHistoSPECT *ap_Event, int a_th)
	Write a SPECT histogram event. More...

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

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

Private Attributes
string	m_isotope

bool	m_eventKindFlag

bool	m_normCorrectionFlag

bool	m_ignoreNormCorrectionFlag

bool	m_scatCorrectionFlag

bool	m_ignoreScatCorrectionFlag

uint16_t	mp_nbOfBins [2]

FLTNB	m_acquisitionZoom

uint16_t	m_nbOfProjections

FLTNB *	mp_angles

uint16_t	m_nbHeads

FLTNB *	mp_CORtoDetectorDistance

int	m_headRotDirection

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 SPECT 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 47 of file iDataFileSPECT.hh.

Constructor & Destructor Documentation

iDataFileSPECT::iDataFileSPECT ( )

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

Definition at line 39 of file iDataFileSPECT.cc.

iDataFileSPECT::~iDataFileSPECT ( )

iDataFileSPECT destructor.

Definition at line 65 of file iDataFileSPECT.cc.

Member Function Documentation

int iDataFileSPECT::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 453 of file iDataFileSPECT.cc.

int iDataFileSPECT::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 506 of file iDataFileSPECT.cc.

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int iDataFileSPECT::CheckSpecificParameters ( )

privatevirtual

Check parameters specific to SPECT data.

Returns: 0 if success, and positive value otherwise.

Implements vDataFile.

Definition at line 423 of file iDataFileSPECT.cc.

int iDataFileSPECT::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 173 of file iDataFileSPECT.cc.

void iDataFileSPECT::DescribeSpecific ( )

virtual

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

Implements vDataFile.

Definition at line 396 of file iDataFileSPECT.cc.

iDataFileSPECT::GetAngles ( )

inline

Returns: pointers to angles of projections

Definition at line 167 of file iDataFileSPECT.hh.

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iDataFileSPECT::GetCORtoDetectorDistance ( )

inline

Returns: pointers to the COR to detector distances for each projection

Definition at line 173 of file iDataFileSPECT.hh.

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iDataFileSPECT::GetEventKindFlag ( )

inline

Simply return m_eventKindFlag.

Returns: m_eventKindFlag

Definition at line 238 of file iDataFileSPECT.hh.

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vEvent * iDataFileSPECT::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 306 of file iDataFileSPECT.cc.

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iDataFileSPECT::GetHeadRotDirection ( )

inline

Simply return m_headRotDirection.

Returns: m_headRotDirection

Definition at line 224 of file iDataFileSPECT.hh.

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iDataFileSPECT::GetIsotope ( )

inline

Returns: the isotope string value

Definition at line 202 of file iDataFileSPECT.hh.

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iDataFileSPECT::GetNbBins ( int axis )

inline

Parameters

axis	: axis corresponding to transaxial (0) or axial (1) bins

Returns: number of bins corresponding to the axis passed in parameter

Definition at line 180 of file iDataFileSPECT.hh.

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iDataFileSPECT::GetNbHeads ( )

inline

Returns: the number of heads

Definition at line 155 of file iDataFileSPECT.hh.

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iDataFileSPECT::GetNbProjections ( )

inline

Returns: total number of projections in the SPECT acquisition

Definition at line 161 of file iDataFileSPECT.hh.

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iDataFileSPECT::GetNormCorrectionFlag ( )

inline

Simply return m_normCorrectionFlag.

Returns: m_normCorrectionFlag

Definition at line 252 of file iDataFileSPECT.hh.

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iDataFileSPECT::GetScatCorrectionFlag ( )

inline

Simply return m_scatCorrectionFlag.

Returns: m_scatCorrectionFlag

Definition at line 245 of file iDataFileSPECT.hh.

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int iDataFileSPECT::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 550 of file iDataFileSPECT.cc.

int iDataFileSPECT::InitCorToDetectorDistance ( FLTNB * ap_CORtoDetectorDistance )

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

Parameters

ap_CORtoDetectorDistance

Returns: 0 if success, positive value otherwise

Definition at line 572 of file iDataFileSPECT.cc.

int iDataFileSPECT::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 228 of file iDataFileSPECT.cc.

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int iDataFileSPECT::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 842 of file iDataFileSPECT.cc.

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int iDataFileSPECT::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 594 of file iDataFileSPECT.cc.

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int iDataFileSPECT::ReadSpecificInfoInHeader ( bool a_affectQuantificationFlag )

virtual

Read through the header file and recover specific SPECT 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 iDataFileSPECT.cc.

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iDataFileSPECT::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 187 of file iDataFileSPECT.hh.

iDataFileSPECT::SetHeadRotDirection ( int a_direction )

inline

initialize the rotation direction of the gamma camera(s)

Parameters

a_direction

Definition at line 231 of file iDataFileSPECT.hh.

iDataFileSPECT::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 196 of file iDataFileSPECT.hh.

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iDataFileSPECT::SetNbBins	(	uint16_t	a_binTrs,
		uint16_t	a_binAxl
	)

inline

initialize the bin values

Parameters

a_binTrs
a_binAxl

Definition at line 210 of file iDataFileSPECT.hh.

iDataFileSPECT::SetNbProjections ( uint16_t a_nbProjections )

inline

initialize the number of projections

Parameters

a_nbProjections

Definition at line 217 of file iDataFileSPECT.hh.

int iDataFileSPECT::SetSpecificParametersFrom ( vDataFile * ap_DataFile )

privatevirtual

Initialize all parameters specific to SPECT from the provided datafile.

Returns: 0 if success, and positive value otherwise

Implements vDataFile.

Definition at line 150 of file iDataFileSPECT.cc.

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int iDataFileSPECT::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 650 of file iDataFileSPECT.cc.

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int iDataFileSPECT::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 778 of file iDataFileSPECT.cc.

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int iDataFileSPECT::WriteHistoEvent	(	iEventHistoSPECT *	ap_Event,
		int	a_th
	)

private

Write a SPECT 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 681 of file iDataFileSPECT.cc.

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int iDataFileSPECT::WriteListEvent	(	iEventListSPECT *	ap_Event,
		int	a_th
	)

private

Write a SPECT 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 719 of file iDataFileSPECT.cc.

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Member Data Documentation

FLTNB iDataFileSPECT::m_acquisitionZoom

private

Zoom used during the acquisition to limit the area of detection for monolithic detectors

Definition at line 312 of file iDataFileSPECT.hh.

bool iDataFileSPECT::m_eventKindFlag

private

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

Definition at line 306 of file iDataFileSPECT.hh.

int iDataFileSPECT::m_headRotDirection

private

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

Definition at line 322 of file iDataFileSPECT.hh.

bool iDataFileSPECT::m_ignoreNormCorrectionFlag

private

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

Definition at line 308 of file iDataFileSPECT.hh.

bool iDataFileSPECT::m_ignoreScatCorrectionFlag

private

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

Definition at line 310 of file iDataFileSPECT.hh.

string iDataFileSPECT::m_isotope

private

Isotope. Default value =unknown

Definition at line 305 of file iDataFileSPECT.hh.

uint16_t iDataFileSPECT::m_nbHeads

private

Number of heads in the SPECT systems. Default =1

Definition at line 316 of file iDataFileSPECT.hh.

uint16_t iDataFileSPECT::m_nbOfProjections

private

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

Definition at line 313 of file iDataFileSPECT.hh.

bool iDataFileSPECT::m_normCorrectionFlag

private

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

Definition at line 307 of file iDataFileSPECT.hh.

bool iDataFileSPECT::m_scatCorrectionFlag

private

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

Definition at line 309 of file iDataFileSPECT.hh.

FLTNB* iDataFileSPECT::mp_angles

private

Angle [for each projection] in degrees. If SPECT system contains several heads, first head angles should be entered first, followed by 2nd head angles, etc.. No Default

Definition at line 314 of file iDataFileSPECT.hh.

FLTNB* iDataFileSPECT::mp_CORtoDetectorDistance

private

Distance camera surface to COR (mm) [for each projection].
if not provided, the distance given for each heads in the camera description file is taken and considered constant for each projections related to each head
if provided then: if positive value (either a constant value, or a value specific to each projection) then it overwrites the one given in the camera file
if negative, the distance given for each heads in the camera description file is taken and considered constant for each projections related to each head
Default value = Recovered from the camera description file

Definition at line 317 of file iDataFileSPECT.hh.

uint16_t iDataFileSPECT::mp_nbOfBins[2]

private

Transaxial/Axial number of bins. Default value =1,1

Definition at line 311 of file iDataFileSPECT.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