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oImageDimensionsAndQuantification Class Reference

This class is designed to manage all dimensions and quantification related stuff. More...

#include <oImageDimensionsAndQuantification.hh>

Collaboration diagram for oImageDimensionsAndQuantification:
Collaboration graph

Public Member Functions

 oImageDimensionsAndQuantification ()
 The constructor of oImageDimensionsAndQuantification. More...
 
 ~oImageDimensionsAndQuantification ()
 The destructor of oImageDimensionsAndQuantification. More...
 
void SetDefault ()
 A function used to set number of threads and MPI instances to 1 and bypass the CheckParameters() function. More...
 
int CheckParameters ()
 A function used to check the parameters settings. More...
 
int Initialize ()
 A function used to initialize all that is needed. More...
 
void CheckNumberOfProjectionThreadsConsistencyWithDataFileSize (vDataFile **a2p_DataFile)
 
int DealWithBedPositions (vDataFile **a2p_DataFile)
 Deal with provided or default bed relative positions. More...
 
void ResetCurrentDynamicIndices ()
 Call the eponym function from the oDynamicDataManager class using the member object. More...
 
int InitDynamicData (string a_pathTo4DDataSplittingFile, int a_respMotionCorrectionFlag, int a_cardMotionCorrectionFlag, int a_doubleMotionCorrectionFlag, int a_invMotionCorrectionFlag, int a_nbRespGates, int a_nbCardGates)
 Call the eponym function from the oDynamicDataManager object in order to initialize its data. More...
 
int CheckDynamicParameters (int64_t a_nbEvents)
 Call the eponym function from the oDynamicDataManager object in order to check its parameters. More...
 
int DynamicSwitch (int64_t a_currentEventIndex, uint32_t a_currentTime, int a_bed, int a_th)
 Call the eponym function from the oDynamicDataManager class using the member object. More...
 
void SetRespMotionFlagOn ()
 Call the eponym function from the oDynamicDataManager class using the member object. More...
 
void SetCardMotionFlagOn ()
 Call the eponym function from the oDynamicDataManager class using the member object. More...
 
void SetPMotionFlagOn ()
 Call the eponym function from the oDynamicDataManager class using the member object. More...
 
int GetCurrentRespGate (int a_th)
 call the eponym function from the oDynamicDataManager object More...
 
int GetCurrentCardGate (int a_th)
 call the eponym function from the oDynamicDataManager object More...
 
int GetPMotionFirstIndexForLMS (int a_fr)
 
int GetNb1stMotImgsForLMS (int a_fr)
 call the eponym function from the oDynamicDataManager object More...
 
int GetNb2ndMotImgsForLMS ()
 call the eponym function from the oDynamicDataManager object More...
 
int GetCurrentRespImage (int a_th)
 call the eponym function from the oDynamicDataManager object More...
 
int GetCurrentCardImage (int a_th)
 call the eponym function from the oDynamicDataManager object More...
 
int GetCurrentTimeFrame (int a_th)
 call the eponym function from the oDynamicDataManager object More...
 
int GetCurrentPMotionIndex (int a_th)
 call the eponym function from the oDynamicDataManager object More...
 
int GetNbIPatMotionSubsets ()
 call the eponym function from the oDynamicDataManager object More...
 
void SetVerbose (int a_verbose)
 Set the member m_verboseLevel to the provided value. More...
 
int GetNbThreadsForProjection ()
 Get the number of threads used for projections. More...
 
int GetNbThreadsForImageComputation ()
 Get the number of threads used for image operations. More...
 
int GetNbThreadsMax ()
 Get the maximum between the number of threads used for projections and image operations. More...
 
int SetNbThreads (const string &a_nbThreads)
 Set the number of threads. More...
 
void SetMPIRankAndSize (int a_mpiRank, int a_mpiSize)
 Set the MPI rank of the MPI instance, and the MPI size (the number of instances) More...
 
int GetMPISize ()
 Get the MPI size (the number of MPI instances) More...
 
int GetMPIRank ()
 Get the MPI instance number (the rank) More...
 
int GetNbBeds ()
 Get the number of bed positions. More...
 
void SetNbBeds (int a_nbBeds)
 Set the number of bed positions and allocate the bed positions if not already done. More...
 
FLTNB GetBedPosition (int a_bedIndex)
 Get the bed position associated to a bed index. More...
 
bool GetProvidedBedPositionFlag ()
 Say if the bed relative position was provided from the datafile or not. More...
 
int GetNbTimeFrames ()
 Get the number of time frames. More...
 
int GetNbTimeBasisFunctions ()
 Get the number of time basis functions. More...
 
FLTNB GetTimeBasisCoefficient (int a_timeBasisFunction, int a_timeFrame)
 Get the time basis coefficients for the provided frame and basis function. More...
 
FLTNB GetFrameDurationInSec (int a_bed, int a_frame)
 Get the frame duration for the given bed, in seconds as a FLTNB. More...
 
FLTNB GetFrameTimeStartInSec (int a_bed, int a_frame)
 Get the frame time start for the given bed, in seconds as a FLTNB. More...
 
FLTNB GetFrameTimeStopInSec (int a_bed, int a_frame)
 Get the frame time stop for the given bed, in seconds as a FLTNB. More...
 
FLTNB GetFinalTimeStopInSec (int a_bed)
 Get the last frame time stop for the given bed, in seconds as a FLTNB. More...
 
uint32_t GetFrameDurationInMs (int a_bed, int a_frame)
 Get the frame duration for the given bed, in milliseconds as a uint32_t. More...
 
uint32_t GetFrameTimeStartInMs (int a_bed, int a_frame)
 Get the frame time start for the given bed, in milliseconds as a uint32_t. More...
 
uint32_t GetFrameTimeStopInMs (int a_bed, int a_frame)
 Get the frame time stop for the given bed, in milliseconds as a uint32_t. More...
 
uint32_t GetFinalTimeStopInMs (int a_bed)
 Get the last frame time stop for the given bed, in milliseconds as a uint32_t. More...
 
void SetFrames (const string &a_frameList)
 Set the frame list (a string that will be parsed by the InitializeFramingAndQuantification function) More...
 
void SetNbTimeBasisFunctions (int a_nbTimeBasisFunctions)
 Set the number of time basis functions. More...
 
void SetTimeBasisFunctionsFile (const string &a_timeBasisFunctionsFile)
 Set the file name containing the time basis functions coefficients. More...
 
int SetAcquisitionTime (int a_bed, FLTNB a_timeStartInSec, FLTNB a_durationInSec)
 Set the acquisition time if not already set by the SetTimeFrames() More...
 
bool GetTimeStaticFlag ()
 Get the time static flag that says if the reconstruction has only one frame or not. More...
 
int GetNbRespGates ()
 Get the number of respiratory gates. More...
 
int GetNbRespBasisFunctions ()
 Get the number of respiratory basis functions. More...
 
FLTNB GetRespBasisCoefficient (int a_respBasisFunction, int a_respGate)
 Get the respiratory basis coefficients for the provided respiratory gate and basis function. More...
 
void SetNbRespGates (int a_nbRespGates)
 Set the number of respiratory gates. More...
 
void SetNbRespBasisFunctions (int a_nbRespBasisFunctions)
 Set the number of respiratory basis functions. More...
 
void SetRespBasisFunctionsFile (const string &a_respBasisFunctionsFile)
 Set the file name containing the respiratory basis functions coefficients. More...
 
bool GetRespStaticFlag ()
 Get the respiratory static flag that says if the reconstruction has only one respiratory gate or not. More...
 
int GetNbCardGates ()
 Get the number of cardiac gates. More...
 
int GetNbCardBasisFunctions ()
 Get the number of cardiac basis functions. More...
 
FLTNB GetCardBasisCoefficient (int a_cardBasisFunction, int a_cardGate)
 Get the cardiac basis coefficients for the provided cardiac gate and basis function. More...
 
void SetNbCardGates (int a_nbCardGates)
 Set the number of cardiac gates. More...
 
void SetNbCardBasisFunctions (int a_nbCardBasisFunctions)
 Set the number of cardiac basis functions. More...
 
void SetCardBasisFunctionsFile (const string &a_cardBasisFunctionsFile)
 Set the file name containing the cardiac basis functions coefficients. More...
 
bool GetCardStaticFlag ()
 Get the cardiac static flag that says if the reconstruction has only one cardiac gate or not. More...
 
INTNB GetNbVoxX ()
 Get the number of voxels along the X axis. More...
 
INTNB GetNbVoxY ()
 Get the number of voxels along the Y axis. More...
 
INTNB GetNbVoxZ ()
 Get the number of voxels along the Z axis. More...
 
INTNB GetNbVoxXY ()
 Get the number of voxels in a slice. More...
 
INTNB GetNbVoxXYZ ()
 Get the total number of voxels. More...
 
INTNB GetNbVoxDiagonal ()
 Get an estimation of the number of voxels along the image diagonal. More...
 
void SetNbVoxX (INTNB a_nbVoxX)
 Set the number of voxels along the X axis. More...
 
void SetNbVoxY (INTNB a_nbVoxY)
 Set the number of voxels along the Y axis. More...
 
void SetNbVoxZ (INTNB a_nbVoxZ)
 Set the number of voxels along the Z axis. More...
 
FLTNB GetVoxSizeX ()
 Get the voxel's size along the X axis, in mm. More...
 
FLTNB GetVoxSizeY ()
 Get the voxel's size along the Y axis, in mm. More...
 
FLTNB GetVoxSizeZ ()
 Get the voxel's size along the Z axis, in mm. More...
 
FLTNB GetFOVSizeX ()
 Get the size of the field-of-view along the X axis, in mm. More...
 
FLTNB GetFOVSizeY ()
 Get the size of the field-of-view along the Y axis, in mm. More...
 
FLTNB GetFOVSizeZ ()
 Get the size of the field-of-view along the Z axis, in mm. More...
 
void SetVoxSizeX (FLTNB a_voxSizeX)
 Set the voxel's size along the X axis, in mm. More...
 
void SetVoxSizeY (FLTNB a_voxSizeY)
 Set the voxel's size along the Y axis, in mm. More...
 
void SetVoxSizeZ (FLTNB a_voxSizeZ)
 Set the voxel's size along the Z axis, in mm. More...
 
void SetFOVSizeX (FLTNB a_fovSizeX)
 Set the FOV's size along the X axis, in mm. More...
 
void SetFOVSizeY (FLTNB a_fovSizeY)
 Set the FOV's size along the Y axis, in mm. More...
 
void SetFOVSizeZ (FLTNB a_fovSizeZ)
 Set the FOV's size along the Z axis, in mm. More...
 
void SetFOVOutMasking (FLTNB a_fovOutPercent, INTNB a_nbSliceOutMask)
 Set the output FOV masking settings: transaxial unmasked FOV percent and number of extrem slices to removed. More...
 
FLTNB GetFOVOutPercent ()
 Get the percentage of transaxial unmasked FOV. More...
 
INTNB GetNbSliceOutMask ()
 Get the number of extrem slices that will be masked at each side. More...
 
int SetFlipOut (const string &a_flipOut)
 Set the output flip options, the parameter being a string potentially containing the letters x, y and z. More...
 
bool GetFlipOutX ()
 Get the boolean saying if the output image must be flipped along the X axis. More...
 
bool GetFlipOutY ()
 Get the boolean saying if the output image must be flipped along the Y axis. More...
 
bool GetFlipOutZ ()
 Get the boolean saying if the output image must be flipped along the Z axis. More...
 
FLTNB GetOffsetX ()
 Get the image offset along the X axis, in mm. More...
 
FLTNB GetOffsetY ()
 Get the image offset along the Y axis, in mm. More...
 
FLTNB GetOffsetZ ()
 Get the image offset along the Z axis, in mm. More...
 
void SetOffsetX (FLTNB a_offsetX)
 Set the image offset along the X axis, in mm. More...
 
void SetOffsetY (FLTNB a_offsetY)
 Set the image offset along the Y axis, in mm. More...
 
void SetOffsetZ (FLTNB a_offsetZ)
 Set the image offset along the Z axis, in mm. More...
 
FLTNB GetQuantificationFactor (int a_bed, int a_frame, int a_respGate, int a_cardGate)
 Get the quantification factor corresponding to the provided bed, frame, respiratory and cardiac gates. More...
 
int SetCalibrationFactor (int a_bed, FLTNB a_calibrationFactor)
 Set the calibration factor for the provided bed. More...
 
int SetPETIsotope (int a_bed, const string &a_isotope)
 Set the PET isotope for the provided bed. More...
 
int SetSPECTIsotope (int a_bed, const string &a_isotope)
 Set the SPECT isotope for the provided bed. More...
 
int SetDynamicSpecificQuantificationFactors (const string &a_quantificationFile)
 Apply specific quantification factors manually provided as an option. More...
 
void SetIgnoredCorrections (const string &a_ignoredCorrectionsList)
 Set the string specifying the corrections that will be ignored. More...
 
bool GetIgnoreAttnCorrectionFlag ()
 Get the boolean that says if the attenuation correction is ignored or not. More...
 
bool GetIgnoreNormCorrectionFlag ()
 Get the boolean that says if the normalization correction is ignored or not. More...
 
bool GetIgnoreScatCorrectionFlag ()
 Get the boolean that says if the scatter correction is ignored or not. More...
 
bool GetIgnoreRandCorrectionFlag ()
 Get the boolean that says if the random correction is ignored or not. More...
 
bool GetIgnoreDecaCorrectionFlag ()
 Get the boolean that says if the decay correction is ignored or not. More...
 
bool GetIgnoreBratCorrectionFlag ()
 Get the boolean that says if the branching ratio correction is ignored or not. More...
 
bool GetIgnoreFdurCorrectionFlag ()
 Get the boolean that says if the frame duration correction is ignored or not. More...
 
bool GetIgnoreCaliCorrectionFlag ()
 Get the boolean that says if the calibration correction is ignored or not. More...
 
int GetNbMultiModalImages ()
 Get the number of additional multimodal images. More...
 
void SetNbMultiModalImages (int a_nbMultiModalImages)
 Set the number of additional multimodal images. More...
 
bool IsInitialized ()
 Returns true if the object has been initialized. More...
 

Private Member Functions

int InitializeFramingAndQuantification ()
 A function used to initialize the framing and quantification tables. More...
 
int InitializeTimeBasisFunctions ()
 A function used to initialize the time basis functions. More...
 
int InitializeRespBasisFunctions ()
 A function used to initialize the respiratory basis functions. More...
 
int InitializeCardBasisFunctions ()
 A function used to initialize the cardiac basis functions. More...
 
int InitializeIgnoredCorrections ()
 A function used to initialize the ignored corrections. More...
 

Private Attributes

oDynamicDataManager * mp_DynamicDataManager
 
int m_nbThreadsForProjection
 
int m_nbThreadsForImageComputation
 
int m_mpiRank
 
int m_mpiSize
 
int m_nbBeds
 
FLTNB * mp_bedPositions
 
bool m_providedBedPosition
 
string m_frameList
 
int m_nbTimeBasisFunctions
 
int m_nbTimeFrames
 
FLTNB ** m2p_timeBasisFunctions
 
uint32_t ** m2p_frameDurationsInMs
 
uint32_t ** m2p_frameTimeStartInMs
 
uint32_t ** m2p_frameTimeStopInMs
 
string m_timeBasisFunctionsFile
 
bool m_timeStaticFlag
 
FLTNB *** m3p_quantificationFactors
 
string m_ignoredCorrectionsList
 
bool m_ignoreAttnCorrectionFlag
 
bool m_ignoreNormCorrectionFlag
 
bool m_ignoreRandCorrectionFlag
 
bool m_ignoreScatCorrectionFlag
 
bool m_ignoreDecaCorrectionFlag
 
bool m_ignoreBratCorrectionFlag
 
bool m_ignoreFdurCorrectionFlag
 
bool m_ignoreCaliCorrectionFlag
 
int m_nbRespBasisFunctions
 
int m_nbRespGates
 
FLTNB ** m2p_respBasisFunctions
 
string m_respBasisFunctionsFile
 
bool m_respStaticFlag
 
int m_nbCardBasisFunctions
 
int m_nbCardGates
 
FLTNB ** m2p_cardBasisFunctions
 
string m_cardBasisFunctionsFile
 
bool m_cardStaticFlag
 
INTNB m_nbVoxX
 
INTNB m_nbVoxY
 
INTNB m_nbVoxZ
 
INTNB m_nbVoxXY
 
INTNB m_nbVoxXYZ
 
FLTNB m_voxSizeX
 
FLTNB m_voxSizeY
 
FLTNB m_voxSizeZ
 
FLTNB m_fovSizeX
 
FLTNB m_fovSizeY
 
FLTNB m_fovSizeZ
 
FLTNB m_offsetX
 
FLTNB m_offsetY
 
FLTNB m_offsetZ
 
FLTNB m_fovOutPercent
 
INTNB m_nbSliceOutMask
 
bool m_flipOutX
 
bool m_flipOutY
 
bool m_flipOutZ
 
bool m_checked
 
bool m_initialized
 
int m_verbose
 
int m_nbMultiModalImages
 

Detailed Description

This class is designed to manage all dimensions and quantification related stuff.

This class gather all dimensions information as well as quantification. It also manages the oDynamicDataManager which itself manages the dynamic data. Most classes in the project have a pointer to this class.

Definition at line 46 of file oImageDimensionsAndQuantification.hh.

Constructor & Destructor Documentation

oImageDimensionsAndQuantification::oImageDimensionsAndQuantification ( )

The constructor of oImageDimensionsAndQuantification.

This is the default and unique constructor. It does not take any parameter and its role is only to affect default values to each member of the class.

Definition at line 39 of file oImageDimensionsAndQuantification.cc.

oImageDimensionsAndQuantification::~oImageDimensionsAndQuantification ( )

The destructor of oImageDimensionsAndQuantification.

This is the default and unique destructor. It does not take any parameter and its role is only to free or delete all structures that were build by this class.

Definition at line 109 of file oImageDimensionsAndQuantification.cc.

Member Function Documentation

int oImageDimensionsAndQuantification::CheckDynamicParameters ( int64_t  a_nbEvents)

Call the eponym function from the oDynamicDataManager object in order to check its parameters.

Parameters
int64_ta_nbEvents
Returns
0 is success, positive value otherwise

Definition at line 1404 of file oImageDimensionsAndQuantification.cc.

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void oImageDimensionsAndQuantification::CheckNumberOfProjectionThreadsConsistencyWithDataFileSize ( vDataFile **  a2p_DataFile)
Parameters
vDataFile**a2p_DataFile

Reduce the number of projection threads to the lowest number of events in all datafiles, if the latter is below the former.

Definition at line 460 of file oImageDimensionsAndQuantification.cc.

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int oImageDimensionsAndQuantification::CheckParameters ( )

A function used to check the parameters settings.

This function does not take any parameter and is used to check that all mandatory members were correctly parameterized.

Returns
An integer reflecting the check status; 0 if no problem, another value otherwise.

Definition at line 299 of file oImageDimensionsAndQuantification.cc.

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int oImageDimensionsAndQuantification::DealWithBedPositions ( vDataFile **  a2p_DataFile)

Deal with provided or default bed relative positions.

Parameters
vDataFile**a2p_DataFile

If relative bed positions are provided from datafiles, then reposition them with respect to the CASToR referential. Otherwise, take the default bed displacement from the scanner and compute the bed relative positions. Finally, the bed positions used in the reconstruction are stored in the mp_bedPositions member.

Returns
An integer reflecting the initialization status; 0 if no problem, another value otherwise.

Definition at line 481 of file oImageDimensionsAndQuantification.cc.

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public inline int oImageDimensionsAndQuantification::DynamicSwitch ( int64_t  a_currentEventIndex,
uint32_t  a_currentTime,
int  a_bed,
int  a_th 
)
inline

Call the eponym function from the oDynamicDataManager class using the member object.

Parameters
a_currentEventIndex
a_currentTime
a_bed
a_th
Returns
An integer reflecting the dynamic evoluation (gate/frame change, involuntary motion)

Definition at line 202 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetBedPosition ( int  a_bedIndex)
inline

Get the bed position associated to a bed index.

Parameters
inta_bedIndex
Returns
The associated mp_bedPositions of the provided bed index. No check for overflow.

Definition at line 391 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetCardBasisCoefficient ( int  a_cardBasisFunction,
int  a_cardGate 
)
inline

Get the cardiac basis coefficients for the provided cardiac gate and basis function.

Parameters
inta_cardBasisFunction
inta_cardGate
Returns
m2p_cardBasisFunctions[a_cardBasisFunction][a_cardGate]

Definition at line 602 of file oImageDimensionsAndQuantification.hh.

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public inline bool oImageDimensionsAndQuantification::GetCardStaticFlag ( )
inline

Get the cardiac static flag that says if the reconstruction has only one cardiac gate or not.

Returns
m_cardStaticFlag

Definition at line 630 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetCurrentCardGate ( int  a_th)
inline

call the eponym function from the oDynamicDataManager object

Parameters
a_th
Returns
the current cardiac gate index

Definition at line 241 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetCurrentCardImage ( int  a_th)
inline

call the eponym function from the oDynamicDataManager object

Parameters
a_th
Returns
the index of the current cardiac image for reconstruction

Definition at line 280 of file oImageDimensionsAndQuantification.hh.

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int oImageDimensionsAndQuantification::GetCurrentPMotionIndex ( int  a_th)
inline

call the eponym function from the oDynamicDataManager object

Parameters
a_th
Returns
the index of the current involuntary motion gate

Definition at line 296 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetCurrentRespGate ( int  a_th)
inline

call the eponym function from the oDynamicDataManager object

Parameters
a_th
Returns
the current respiratory gate index

Definition at line 233 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetCurrentRespImage ( int  a_th)
inline

call the eponym function from the oDynamicDataManager object

Parameters
a_th
Returns
the index of the current respiratory image for reconstruction

Definition at line 272 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetCurrentTimeFrame ( int  a_th)
inline

call the eponym function from the oDynamicDataManager object

Parameters
a_th
Returns
the index of the current time frame

Definition at line 288 of file oImageDimensionsAndQuantification.hh.

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public inline uint32_t oImageDimensionsAndQuantification::GetFinalTimeStopInMs ( int  a_bed)
inline

Get the last frame time stop for the given bed, in milliseconds as a uint32_t.

Parameters
inta_bed
Returns
m2p_frameTimeStopInMs[a_bed][m_nbTimeFrames-1]

Definition at line 490 of file oImageDimensionsAndQuantification.hh.

public inline FLTNB oImageDimensionsAndQuantification::GetFinalTimeStopInSec ( int  a_bed)
inline

Get the last frame time stop for the given bed, in seconds as a FLTNB.

Parameters
inta_bed
Returns
((FLTNB)(m2p_frameTimeStopInMs[a_bed][m_nbTimeFrames-1]))/1000.

Definition at line 455 of file oImageDimensionsAndQuantification.hh.

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public inline bool oImageDimensionsAndQuantification::GetFlipOutX ( )
inline

Get the boolean saying if the output image must be flipped along the X axis.

Returns
m_flipOutX

Definition at line 815 of file oImageDimensionsAndQuantification.hh.

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public inline bool oImageDimensionsAndQuantification::GetFlipOutY ( )
inline

Get the boolean saying if the output image must be flipped along the Y axis.

Returns
m_flipOutY

Definition at line 822 of file oImageDimensionsAndQuantification.hh.

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public inline bool oImageDimensionsAndQuantification::GetFlipOutZ ( )
inline

Get the boolean saying if the output image must be flipped along the Z axis.

Returns
m_flipOutZ

Definition at line 829 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetFOVOutPercent ( )
inline

Get the percentage of transaxial unmasked FOV.

Returns
m_fovOutPercent

Definition at line 794 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetFOVSizeX ( )
inline

Get the size of the field-of-view along the X axis, in mm.

Returns
m_fovSizeX

Definition at line 723 of file oImageDimensionsAndQuantification.hh.

public inline FLTNB oImageDimensionsAndQuantification::GetFOVSizeY ( )
inline

Get the size of the field-of-view along the Y axis, in mm.

Returns
m_fovSizeY

Definition at line 730 of file oImageDimensionsAndQuantification.hh.

public inline FLTNB oImageDimensionsAndQuantification::GetFOVSizeZ ( )
inline

Get the size of the field-of-view along the Z axis, in mm.

Returns
m_fovSizeZ

Definition at line 737 of file oImageDimensionsAndQuantification.hh.

public inline uint32_t oImageDimensionsAndQuantification::GetFrameDurationInMs ( int  a_bed,
int  a_frame 
)
inline

Get the frame duration for the given bed, in milliseconds as a uint32_t.

Parameters
inta_bed
inta_frame
Returns
m2p_frameDurationsInMs[a_bed][a_frame]

Definition at line 464 of file oImageDimensionsAndQuantification.hh.

public inline FLTNB oImageDimensionsAndQuantification::GetFrameDurationInSec ( int  a_bed,
int  a_frame 
)
inline

Get the frame duration for the given bed, in seconds as a FLTNB.

Parameters
inta_bed
inta_frame
Returns
((FLTNB)(m2p_frameDurationsInMs[a_bed][a_frame]))/1000.

Definition at line 429 of file oImageDimensionsAndQuantification.hh.

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public inline uint32_t oImageDimensionsAndQuantification::GetFrameTimeStartInMs ( int  a_bed,
int  a_frame 
)
inline

Get the frame time start for the given bed, in milliseconds as a uint32_t.

Parameters
inta_bed
inta_frame
Returns
m2p_frameTimeStartInMs[a_bed][a_frame]

Definition at line 473 of file oImageDimensionsAndQuantification.hh.

public inline FLTNB oImageDimensionsAndQuantification::GetFrameTimeStartInSec ( int  a_bed,
int  a_frame 
)
inline

Get the frame time start for the given bed, in seconds as a FLTNB.

Parameters
inta_bed
inta_frame
Returns
((FLTNB)(m2p_frameTimeStartInMs[a_bed][a_frame]))/1000.

Definition at line 438 of file oImageDimensionsAndQuantification.hh.

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public inline uint32_t oImageDimensionsAndQuantification::GetFrameTimeStopInMs ( int  a_bed,
int  a_frame 
)
inline

Get the frame time stop for the given bed, in milliseconds as a uint32_t.

Parameters
inta_bed
inta_frame
Returns
m2p_frameTimeStopInMs[a_bed][a_frame]

Definition at line 482 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetFrameTimeStopInSec ( int  a_bed,
int  a_frame 
)
inline

Get the frame time stop for the given bed, in seconds as a FLTNB.

Parameters
inta_bed
inta_frame
Returns
((FLTNB)(m2p_frameTimeStopInMs[a_bed][a_frame]))/1000.

Definition at line 447 of file oImageDimensionsAndQuantification.hh.

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public inline bool oImageDimensionsAndQuantification::GetIgnoreAttnCorrectionFlag ( )
inline

Get the boolean that says if the attenuation correction is ignored or not.

Returns
m_ignoreAttnCorrectionFlag

Definition at line 929 of file oImageDimensionsAndQuantification.hh.

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public inline bool oImageDimensionsAndQuantification::GetIgnoreBratCorrectionFlag ( )
inline

Get the boolean that says if the branching ratio correction is ignored or not.

Returns
m_ignoreBratCorrectionFlag

Definition at line 964 of file oImageDimensionsAndQuantification.hh.

public inline bool oImageDimensionsAndQuantification::GetIgnoreCaliCorrectionFlag ( )
inline

Get the boolean that says if the calibration correction is ignored or not.

Returns
m_ignoreCaliCorrectionFlag

Definition at line 978 of file oImageDimensionsAndQuantification.hh.

public inline bool oImageDimensionsAndQuantification::GetIgnoreDecaCorrectionFlag ( )
inline

Get the boolean that says if the decay correction is ignored or not.

Returns
m_ignoreDecaCorrectionFlag

Definition at line 957 of file oImageDimensionsAndQuantification.hh.

public inline bool oImageDimensionsAndQuantification::GetIgnoreFdurCorrectionFlag ( )
inline

Get the boolean that says if the frame duration correction is ignored or not.

Returns
m_ignoreFdurCorrectionFlag

Definition at line 971 of file oImageDimensionsAndQuantification.hh.

public inline bool oImageDimensionsAndQuantification::GetIgnoreNormCorrectionFlag ( )
inline

Get the boolean that says if the normalization correction is ignored or not.

Returns
m_ignoreNormCorrectionFlag

Definition at line 936 of file oImageDimensionsAndQuantification.hh.

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public inline bool oImageDimensionsAndQuantification::GetIgnoreRandCorrectionFlag ( )
inline

Get the boolean that says if the random correction is ignored or not.

Returns
m_ignoreRandCorrectionFlag

Definition at line 950 of file oImageDimensionsAndQuantification.hh.

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public inline bool oImageDimensionsAndQuantification::GetIgnoreScatCorrectionFlag ( )
inline

Get the boolean that says if the scatter correction is ignored or not.

Returns
m_ignoreScatCorrectionFlag

Definition at line 943 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetMPIRank ( )
inline

Get the MPI instance number (the rank)

Returns
m_mpiRank

Definition at line 369 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetMPISize ( )
inline

Get the MPI size (the number of MPI instances)

Returns
m_mpiSize

Definition at line 362 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNb1stMotImgsForLMS ( int  a_fr)
inline

call the eponym function from the oDynamicDataManager object

Parameters
a_fr= frame index
Returns
the number of respiratory images for sensitivity

Definition at line 257 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNb2ndMotImgsForLMS ( )
inline

call the eponym function from the oDynamicDataManager object

Returns
the number of cardiac images for sensitivity

Definition at line 264 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNbBeds ( )
inline

Get the number of bed positions.

Returns
m_nbBeds

Definition at line 376 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNbCardBasisFunctions ( )
inline

Get the number of cardiac basis functions.

Returns
m_nbCardBasisFunctions

Definition at line 593 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNbCardGates ( )
inline

Get the number of cardiac gates.

Returns
m_nbCardGates

Definition at line 586 of file oImageDimensionsAndQuantification.hh.

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int oImageDimensionsAndQuantification::GetNbIPatMotionSubsets ( )
inline

call the eponym function from the oDynamicDataManager object

Returns
the total number of involuntary patient motion triggers

Definition at line 304 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNbMultiModalImages ( )
inline

Get the number of additional multimodal images.

Returns
m_nbMultiModalImages

Definition at line 985 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNbRespBasisFunctions ( )
inline

Get the number of respiratory basis functions.

Returns
m_nbRespBasisFunctions

Definition at line 542 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNbRespGates ( )
inline

Get the number of respiratory gates.

Returns
m_nbRespGates

Definition at line 535 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetNbSliceOutMask ( )
inline

Get the number of extrem slices that will be masked at each side.

Returns
m_nbSliceOutMask

Definition at line 801 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNbThreadsForImageComputation ( )
inline

Get the number of threads used for image operations.

Returns
m_nbThreadsForImageComputation

Definition at line 330 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNbThreadsForProjection ( )
inline

Get the number of threads used for projections.

Returns
m_nbThreadsForProjection

Definition at line 323 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNbThreadsMax ( )
inline

Get the maximum between the number of threads used for projections and image operations.

Returns
max(m_nbThreadsForProjection,m_nbThreadsForImageComputation)

Definition at line 337 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNbTimeBasisFunctions ( )
inline

Get the number of time basis functions.

Returns
m_nbTimeBasisFunctions

Definition at line 411 of file oImageDimensionsAndQuantification.hh.

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public inline int oImageDimensionsAndQuantification::GetNbTimeFrames ( )
inline

Get the number of time frames.

Returns
m_nbTimeFrames

Definition at line 404 of file oImageDimensionsAndQuantification.hh.

public inline INTNB oImageDimensionsAndQuantification::GetNbVoxDiagonal ( )
inline

Get an estimation of the number of voxels along the image diagonal.

Returns
An estimation of the number of voxels along the image diagonal

Definition at line 672 of file oImageDimensionsAndQuantification.hh.

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public inline INTNB oImageDimensionsAndQuantification::GetNbVoxX ( )
inline

Get the number of voxels along the X axis.

Returns
m_nbVoxX

Definition at line 637 of file oImageDimensionsAndQuantification.hh.

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public inline INTNB oImageDimensionsAndQuantification::GetNbVoxXY ( )
inline

Get the number of voxels in a slice.

Returns
m_nbVoxXY

Definition at line 658 of file oImageDimensionsAndQuantification.hh.

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public inline INTNB oImageDimensionsAndQuantification::GetNbVoxXYZ ( )
inline

Get the total number of voxels.

Returns
m_nbVoxXYZ

Definition at line 665 of file oImageDimensionsAndQuantification.hh.

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public inline INTNB oImageDimensionsAndQuantification::GetNbVoxY ( )
inline

Get the number of voxels along the Y axis.

Returns
m_nbVoxY

Definition at line 644 of file oImageDimensionsAndQuantification.hh.

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public inline INTNB oImageDimensionsAndQuantification::GetNbVoxZ ( )
inline

Get the number of voxels along the Z axis.

Returns
m_nbVoxZ

Definition at line 651 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetOffsetX ( )
inline

Get the image offset along the X axis, in mm.

Returns
m_offsetX

Definition at line 836 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetOffsetY ( )
inline

Get the image offset along the Y axis, in mm.

Returns
m_offsetY

Definition at line 843 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetOffsetZ ( )
inline

Get the image offset along the Z axis, in mm.

Returns
m_offsetZ

Definition at line 850 of file oImageDimensionsAndQuantification.hh.

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int oImageDimensionsAndQuantification::GetPMotionFirstIndexForLMS ( int  a_fr)
inline

Definition at line 249 of file oImageDimensionsAndQuantification.hh.

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public inline bool oImageDimensionsAndQuantification::GetProvidedBedPositionFlag ( )
inline

Say if the bed relative position was provided from the datafile or not.

Returns
m_providedBedPosition

Definition at line 398 of file oImageDimensionsAndQuantification.hh.

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FLTNB oImageDimensionsAndQuantification::GetQuantificationFactor ( int  a_bed,
int  a_frame,
int  a_respGate,
int  a_cardGate 
)

Get the quantification factor corresponding to the provided bed, frame, respiratory and cardiac gates.

Parameters
inta_bed
inta_frame
inta_respGate
inta_cardGate

Definition at line 1161 of file oImageDimensionsAndQuantification.cc.

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public inline FLTNB oImageDimensionsAndQuantification::GetRespBasisCoefficient ( int  a_respBasisFunction,
int  a_respGate 
)
inline

Get the respiratory basis coefficients for the provided respiratory gate and basis function.

Parameters
inta_respBasisFunction
inta_respGate
Returns
m2p_respBasisFunctions[a_respBasisFunction][a_respGate]

Definition at line 551 of file oImageDimensionsAndQuantification.hh.

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public inline bool oImageDimensionsAndQuantification::GetRespStaticFlag ( )
inline

Get the respiratory static flag that says if the reconstruction has only one respiratory gate or not.

Returns
m_respStaticFlag

Definition at line 579 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetTimeBasisCoefficient ( int  a_timeBasisFunction,
int  a_timeFrame 
)
inline

Get the time basis coefficients for the provided frame and basis function.

Parameters
inta_timeBasisFunction
inta_timeFrame
Returns
m2p_timeBasisFunctions[a_timeBasisFunction][a_timeFrame]

Definition at line 420 of file oImageDimensionsAndQuantification.hh.

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public inline bool oImageDimensionsAndQuantification::GetTimeStaticFlag ( )
inline

Get the time static flag that says if the reconstruction has only one frame or not.

Returns
m_timeStaticFlag

Definition at line 528 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetVoxSizeX ( )
inline

Get the voxel's size along the X axis, in mm.

Returns
m_voxSizeX

Definition at line 702 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetVoxSizeY ( )
inline

Get the voxel's size along the Y axis, in mm.

Returns
m_voxSizeY

Definition at line 709 of file oImageDimensionsAndQuantification.hh.

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public inline FLTNB oImageDimensionsAndQuantification::GetVoxSizeZ ( )
inline

Get the voxel's size along the Z axis, in mm.

Returns
m_voxSizeZ

Definition at line 716 of file oImageDimensionsAndQuantification.hh.

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int oImageDimensionsAndQuantification::InitDynamicData ( string  a_pathTo4DDataSplittingFile,
int  a_respMotionCorrectionFlag,
int  a_cardMotionCorrectionFlag,
int  a_doubleMotionCorrectionFlag,
int  a_invMotionCorrectionFlag,
int  a_nbRespGates,
int  a_nbCardGates 
)

Call the eponym function from the oDynamicDataManager object in order to initialize its data.

Parameters
a_pathTo4DDataSplittingFile
a_respMotionCorrectionFlag
a_cardMotionCorrectionFlag
a_doubleMotionCorrectionFlag
a_invMotionCorrectionFlag
a_nbRespGates
a_nbCardGates#
Returns
0 is success, positive value otherwise

Definition at line 1380 of file oImageDimensionsAndQuantification.cc.

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int oImageDimensionsAndQuantification::Initialize ( )

A function used to initialize all that is needed.

This function does not take any parameter and is used to initialize everything that should be initialized. It initializes image dimensions, dynamic basis functions and quantification factors.

Returns
An integer reflecting the initialization status; 0 if no problem, another value otherwise.

Definition at line 355 of file oImageDimensionsAndQuantification.cc.

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int oImageDimensionsAndQuantification::InitializeCardBasisFunctions ( )
private

A function used to initialize the cardiac basis functions.

This function is called by the Initialize() function. If provided, it parses the file containing the cardiac basis functions coefficients.

Returns
An integer reflecting the initialization status; 0 if no problem, another value otherwise.

Definition at line 828 of file oImageDimensionsAndQuantification.cc.

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int oImageDimensionsAndQuantification::InitializeFramingAndQuantification ( )
private

A function used to initialize the framing and quantification tables.

This function is called by the Initialize() function.

Returns
An integer reflecting the initialization status; 0 if no problem, another value otherwise.

Definition at line 556 of file oImageDimensionsAndQuantification.cc.

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int oImageDimensionsAndQuantification::InitializeIgnoredCorrections ( )
private

A function used to initialize the ignored corrections.

This function is called by the Initialize() function. It parses the ignored correction string (correction keywords separated by commas) and set the associated boolean members

Returns
An integer reflecting the initialization status; 0 if no problem, another value otherwise.

Definition at line 877 of file oImageDimensionsAndQuantification.cc.

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int oImageDimensionsAndQuantification::InitializeRespBasisFunctions ( )
private

A function used to initialize the respiratory basis functions.

This function is called by the Initialize() function. If provided, it parses the file containing the respiratory basis functions coefficients.

Returns
An integer reflecting the initialization status; 0 if no problem, another value otherwise.

Definition at line 778 of file oImageDimensionsAndQuantification.cc.

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int oImageDimensionsAndQuantification::InitializeTimeBasisFunctions ( )
private

A function used to initialize the time basis functions.

This function is called by the Initialize() function. If provided, it parses the file containing the time basis functions coefficients.

Returns
An integer reflecting the initialization status; 0 if no problem, another value otherwise.

Definition at line 729 of file oImageDimensionsAndQuantification.cc.

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public inline bool oImageDimensionsAndQuantification::IsInitialized ( )
inline

Returns true if the object has been initialized.

Definition at line 999 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::ResetCurrentDynamicIndices ( )
inline

Call the eponym function from the oDynamicDataManager class using the member object.

Definition at line 168 of file oImageDimensionsAndQuantification.hh.

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int oImageDimensionsAndQuantification::SetAcquisitionTime ( int  a_bed,
FLTNB  a_timeStartInSec,
FLTNB  a_durationInSec 
)

Set the acquisition time if not already set by the SetTimeFrames()

Parameters
inta_bed
FLTNBa_timeStartInSec
FLTNBa_durationInSec

This function is called from the vDataFile once the acquisition start and duration are read in the header

Returns
0 if no problem, another value otherwise

Definition at line 934 of file oImageDimensionsAndQuantification.cc.

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int oImageDimensionsAndQuantification::SetCalibrationFactor ( int  a_bed,
FLTNB  a_calibrationFactor 
)

Set the calibration factor for the provided bed.

Parameters
inta_bed
FLTNBa_calibrationFactor

Apply it to all frames and gates

Returns
0 if no problem, another value otherwise

Definition at line 1011 of file oImageDimensionsAndQuantification.cc.

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public inline void oImageDimensionsAndQuantification::SetCardBasisFunctionsFile ( const string &  a_cardBasisFunctionsFile)
inline

Set the file name containing the cardiac basis functions coefficients.

Parameters
conststring& a_cardBasisFunctionsFile

Definition at line 623 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetCardMotionFlagOn ( )
inline

Call the eponym function from the oDynamicDataManager class using the member object.

Definition at line 219 of file oImageDimensionsAndQuantification.hh.

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void oImageDimensionsAndQuantification::SetDefault ( )

A function used to set number of threads and MPI instances to 1 and bypass the CheckParameters() function.

The m_checked flag is set to true

Definition at line 281 of file oImageDimensionsAndQuantification.cc.

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int oImageDimensionsAndQuantification::SetDynamicSpecificQuantificationFactors ( const string &  a_quantificationFile)

Apply specific quantification factors manually provided as an option.

Parameters
conststring& a_quantificationFile

It does not set the quantification factors, it applies them (it is an update, not an affectation)

Returns
0 if no problem, another value otherwise

Definition at line 1052 of file oImageDimensionsAndQuantification.cc.

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int oImageDimensionsAndQuantification::SetFlipOut ( const string &  a_flipOut)

Set the output flip options, the parameter being a string potentially containing the letters x, y and z.

Parameters
conststring& a_flipOut
Returns
0 if no problem, another value if the string is not correctly set

Definition at line 154 of file oImageDimensionsAndQuantification.cc.

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public inline void oImageDimensionsAndQuantification::SetFOVOutMasking ( FLTNB  a_fovOutPercent,
INTNB  a_nbSliceOutMask 
)
inline

Set the output FOV masking settings: transaxial unmasked FOV percent and number of extrem slices to removed.

Parameters
FLTNBa_fovOutPercent
INTNBa_nbSliceOutMask

Definition at line 787 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetFOVSizeX ( FLTNB  a_fovSizeX)
inline

Set the FOV's size along the X axis, in mm.

Parameters
FLTNBa_fovSizeX

Definition at line 765 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetFOVSizeY ( FLTNB  a_fovSizeY)
inline

Set the FOV's size along the Y axis, in mm.

Parameters
FLTNBa_fovSizeY

Definition at line 772 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetFOVSizeZ ( FLTNB  a_fovSizeZ)
inline

Set the FOV's size along the Z axis, in mm.

Parameters
FLTNBa_fovSizeZ

Definition at line 779 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetFrames ( const string &  a_frameList)
inline

Set the frame list (a string that will be parsed by the InitializeFramingAndQuantification function)

Parameters
conststring& a_frameList

Definition at line 497 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetIgnoredCorrections ( const string &  a_ignoredCorrectionsList)
inline

Set the string specifying the corrections that will be ignored.

Parameters
conststring& a_ignoredCorrectionsList

Definition at line 922 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetMPIRankAndSize ( int  a_mpiRank,
int  a_mpiSize 
)
inline

Set the MPI rank of the MPI instance, and the MPI size (the number of instances)

Parameters
inta_mpiRank
inta_mpiSize

Definition at line 355 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetNbBeds ( int  a_nbBeds)
inline

Set the number of bed positions and allocate the bed positions if not already done.

Parameters
inta_nbBeds

Definition at line 383 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetNbCardBasisFunctions ( int  a_nbCardBasisFunctions)
inline

Set the number of cardiac basis functions.

Parameters
inta_nbCardBasisFunctions

Definition at line 616 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetNbCardGates ( int  a_nbCardGates)
inline

Set the number of cardiac gates.

Parameters
inta_nbCardGates

Definition at line 609 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetNbMultiModalImages ( int  a_nbMultiModalImages)
inline

Set the number of additional multimodal images.

Parameters
inta_nbMultiModalImages

Definition at line 992 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetNbRespBasisFunctions ( int  a_nbRespBasisFunctions)
inline

Set the number of respiratory basis functions.

Parameters
inta_nbRespBasisFunctions

Definition at line 565 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetNbRespGates ( int  a_nbRespGates)
inline

Set the number of respiratory gates.

Parameters
inta_nbRespGates

Definition at line 558 of file oImageDimensionsAndQuantification.hh.

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int oImageDimensionsAndQuantification::SetNbThreads ( const string &  a_nbThreads)

Set the number of threads.

Parameters
conststring& a_nbThreads

The string parameter can be a set of two parameters separated by a comma, the first for the number of threads for projections and the second for the number of threads for image operations. If no comma, then the number of threads is the same for all operations.

Returns
0 if correctly set, another value otherwise

Definition at line 223 of file oImageDimensionsAndQuantification.cc.

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public inline void oImageDimensionsAndQuantification::SetNbTimeBasisFunctions ( int  a_nbTimeBasisFunctions)
inline

Set the number of time basis functions.

Parameters
inta_nbTimeBasisFunctions

Definition at line 504 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetNbVoxX ( INTNB  a_nbVoxX)
inline

Set the number of voxels along the X axis.

Parameters
INTNBa_nbVoxX

Definition at line 681 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetNbVoxY ( INTNB  a_nbVoxY)
inline

Set the number of voxels along the Y axis.

Parameters
INTNBa_nbVoxY

Definition at line 688 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetNbVoxZ ( INTNB  a_nbVoxZ)
inline

Set the number of voxels along the Z axis.

Parameters
INTNBa_nbVoxZ

Definition at line 695 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetOffsetX ( FLTNB  a_offsetX)
inline

Set the image offset along the X axis, in mm.

Parameters
FLTNBa_offsetX

Definition at line 857 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetOffsetY ( FLTNB  a_offsetY)
inline

Set the image offset along the Y axis, in mm.

Parameters
FLTNBa_offsetY

Definition at line 864 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetOffsetZ ( FLTNB  a_offsetZ)
inline

Set the image offset along the Z axis, in mm.

Parameters
FLTNBa_offsetZ

Definition at line 871 of file oImageDimensionsAndQuantification.hh.

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int oImageDimensionsAndQuantification::SetPETIsotope ( int  a_bed,
const string &  a_isotope 
)

Set the PET isotope for the provided bed.

Parameters
inta_bed
conststring& a_isotope

Apply decay and branching ratio corrections if the PET isotope is found in the database of the config/ directory

Returns
0 if no problem, another value otherwise

Definition at line 1198 of file oImageDimensionsAndQuantification.cc.

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public inline void oImageDimensionsAndQuantification::SetPMotionFlagOn ( )
inline

Call the eponym function from the oDynamicDataManager class using the member object.

Definition at line 225 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetRespBasisFunctionsFile ( const string &  a_respBasisFunctionsFile)
inline

Set the file name containing the respiratory basis functions coefficients.

Parameters
conststring& a_respBasisFunctionsFile

Definition at line 572 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetRespMotionFlagOn ( )
inline

Call the eponym function from the oDynamicDataManager class using the member object.

Definition at line 213 of file oImageDimensionsAndQuantification.hh.

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int oImageDimensionsAndQuantification::SetSPECTIsotope ( int  a_bed,
const string &  a_isotope 
)

Set the SPECT isotope for the provided bed.

Parameters
inta_bed
conststring& a_isotope

Apply decay and branching ratio corrections if the SPECT isotope is found in the database of the config/ directory

Returns
0 if no problem, another value otherwise

Definition at line 1178 of file oImageDimensionsAndQuantification.cc.

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public inline void oImageDimensionsAndQuantification::SetTimeBasisFunctionsFile ( const string &  a_timeBasisFunctionsFile)
inline

Set the file name containing the time basis functions coefficients.

Parameters
conststring& a_timeBasisFunctionsFile

Definition at line 511 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetVerbose ( int  a_verbose)
inline

Set the member m_verboseLevel to the provided value.

Parameters
inta_verboseLevel

Definition at line 316 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetVoxSizeX ( FLTNB  a_voxSizeX)
inline

Set the voxel's size along the X axis, in mm.

Parameters
FLTNBa_voxSizeX

Definition at line 744 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetVoxSizeY ( FLTNB  a_voxSizeY)
inline

Set the voxel's size along the Y axis, in mm.

Parameters
FLTNBa_voxSizeY

Definition at line 751 of file oImageDimensionsAndQuantification.hh.

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public inline void oImageDimensionsAndQuantification::SetVoxSizeZ ( FLTNB  a_voxSizeZ)
inline

Set the voxel's size along the Z axis, in mm.

Parameters
FLTNBa_voxSizeZ

Definition at line 758 of file oImageDimensionsAndQuantification.hh.

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Member Data Documentation

FLTNB** oImageDimensionsAndQuantification::m2p_cardBasisFunctions
private

The table of cardiac basis functions coefficients

Definition at line 1046 of file oImageDimensionsAndQuantification.hh.

uint32_t** oImageDimensionsAndQuantification::m2p_frameDurationsInMs
private

The table of frame durations, per bed position

Definition at line 1021 of file oImageDimensionsAndQuantification.hh.

uint32_t** oImageDimensionsAndQuantification::m2p_frameTimeStartInMs
private

The table of frame time start, per bed position

Definition at line 1022 of file oImageDimensionsAndQuantification.hh.

uint32_t** oImageDimensionsAndQuantification::m2p_frameTimeStopInMs
private

The table of frame time stop, per bed position

Definition at line 1023 of file oImageDimensionsAndQuantification.hh.

FLTNB** oImageDimensionsAndQuantification::m2p_respBasisFunctions
private

The table of respiratory basis functions coefficients

Definition at line 1040 of file oImageDimensionsAndQuantification.hh.

FLTNB** oImageDimensionsAndQuantification::m2p_timeBasisFunctions
private

The table of time basis functions coefficients

Definition at line 1020 of file oImageDimensionsAndQuantification.hh.

FLTNB*** oImageDimensionsAndQuantification::m3p_quantificationFactors
private

The table of quantification factors, per bed, per frame, per gate

Definition at line 1027 of file oImageDimensionsAndQuantification.hh.

string oImageDimensionsAndQuantification::m_cardBasisFunctionsFile
private

The file containing the cardiac basis coefficients

Definition at line 1047 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_cardStaticFlag
private

A boolean saying if only one cardiac gate is being reconstructed

Definition at line 1048 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_checked
private

A boolean that says if the function CheckParameters() has been called

Definition at line 1072 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_flipOutX
private

A boolean saying if the images must be flipped along the X axis before being saved (default: false)

Definition at line 1068 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_flipOutY
private

A boolean saying if the images must be flipped along the Y axis before being saved (default: false)

Definition at line 1069 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_flipOutZ
private

A boolean saying if the images must be flipped along the Z axis before being saved (default: false)

Definition at line 1070 of file oImageDimensionsAndQuantification.hh.

FLTNB oImageDimensionsAndQuantification::m_fovOutPercent
private

The percentage of the transaxial field-of-view not masked before saving reconstructed images (default: 0. = none)

Definition at line 1065 of file oImageDimensionsAndQuantification.hh.

FLTNB oImageDimensionsAndQuantification::m_fovSizeX
private

The size of the field-of-view along the X axis, in mm

Definition at line 1058 of file oImageDimensionsAndQuantification.hh.

FLTNB oImageDimensionsAndQuantification::m_fovSizeY
private

The size of the field-of-view along the Y axis, in mm

Definition at line 1059 of file oImageDimensionsAndQuantification.hh.

FLTNB oImageDimensionsAndQuantification::m_fovSizeZ
private

The size of the field-of-view along the Z axis, in mm

Definition at line 1060 of file oImageDimensionsAndQuantification.hh.

string oImageDimensionsAndQuantification::m_frameList
private

A string containing the list of reconstructed frames

Definition at line 1017 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_ignoreAttnCorrectionFlag
private

A boolean saying if the attenuation correction is ignored

Definition at line 1029 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_ignoreBratCorrectionFlag
private

A boolean saying if the branching ratio correction is ignored

Definition at line 1034 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_ignoreCaliCorrectionFlag
private

A boolean saying if the calibration correction is ignored

Definition at line 1036 of file oImageDimensionsAndQuantification.hh.

string oImageDimensionsAndQuantification::m_ignoredCorrectionsList
private

The string containing the list of corrections to be ignored

Definition at line 1028 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_ignoreDecaCorrectionFlag
private

A boolean saying if the decay correction is ignored

Definition at line 1033 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_ignoreFdurCorrectionFlag
private

A boolean saying if the frame duration correction is ignored

Definition at line 1035 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_ignoreNormCorrectionFlag
private

A boolean saying if the normalization correction is ignored

Definition at line 1030 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_ignoreRandCorrectionFlag
private

A boolean saying if the random correction is ignored

Definition at line 1031 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_ignoreScatCorrectionFlag
private

A boolean saying if the scatter correction is ignored

Definition at line 1032 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_initialized
private

A boolean that says if the function Initialize() has been called

Definition at line 1074 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_mpiRank
private

The rank of the MPI instance

Definition at line 1010 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_mpiSize
private

The size of the MPI process (i.e. the number of instances)

Definition at line 1011 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_nbBeds
private

The number of bed positions simultaneously reconstructed

Definition at line 1013 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_nbCardBasisFunctions
private

The number of cardiac basis functions

Definition at line 1044 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_nbCardGates
private

The number of cardiac gates

Definition at line 1045 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_nbMultiModalImages
private

The number of additional multimodal images

Definition at line 1077 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_nbRespBasisFunctions
private

The number of respiratory basis functions

Definition at line 1038 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_nbRespGates
private

The number of respiratory gates

Definition at line 1039 of file oImageDimensionsAndQuantification.hh.

INTNB oImageDimensionsAndQuantification::m_nbSliceOutMask
private

The number of extrem slices to be masked from both sides of the axial FOV before saving reconstruction images (default: 0)

Definition at line 1066 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_nbThreadsForImageComputation
private

The number of threads for image operations

Definition at line 1008 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_nbThreadsForProjection
private

The number of threads for projections

Definition at line 1007 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_nbTimeBasisFunctions
private

The number of time basis functions

Definition at line 1018 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_nbTimeFrames
private

The number of time frames

Definition at line 1019 of file oImageDimensionsAndQuantification.hh.

INTNB oImageDimensionsAndQuantification::m_nbVoxX
private

The number of voxels along the X axis

Definition at line 1050 of file oImageDimensionsAndQuantification.hh.

INTNB oImageDimensionsAndQuantification::m_nbVoxXY
private

The number of voxels in a slice

Definition at line 1053 of file oImageDimensionsAndQuantification.hh.

INTNB oImageDimensionsAndQuantification::m_nbVoxXYZ
private

The total number of voxels

Definition at line 1054 of file oImageDimensionsAndQuantification.hh.

INTNB oImageDimensionsAndQuantification::m_nbVoxY
private

The number of voxels along the Y axis

Definition at line 1051 of file oImageDimensionsAndQuantification.hh.

INTNB oImageDimensionsAndQuantification::m_nbVoxZ
private

The number of voxels along the Z axis

Definition at line 1052 of file oImageDimensionsAndQuantification.hh.

FLTNB oImageDimensionsAndQuantification::m_offsetX
private

The image offset along the X axis, in mm (default: 0.)

Definition at line 1061 of file oImageDimensionsAndQuantification.hh.

FLTNB oImageDimensionsAndQuantification::m_offsetY
private

The image offset along the Y axis, in mm (default: 0.)

Definition at line 1062 of file oImageDimensionsAndQuantification.hh.

FLTNB oImageDimensionsAndQuantification::m_offsetZ
private

The image offset along the Z axis, in mm (default: 0.)

Definition at line 1063 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_providedBedPosition
private

A flag saying if the bed position has been provided from the datafile

Definition at line 1015 of file oImageDimensionsAndQuantification.hh.

string oImageDimensionsAndQuantification::m_respBasisFunctionsFile
private

The file containing the respiratory basis coefficients

Definition at line 1041 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_respStaticFlag
private

A boolean saying if only one respiratory gate is being reconstructed

Definition at line 1042 of file oImageDimensionsAndQuantification.hh.

string oImageDimensionsAndQuantification::m_timeBasisFunctionsFile
private

The file containing the time basis coefficients

Definition at line 1024 of file oImageDimensionsAndQuantification.hh.

bool oImageDimensionsAndQuantification::m_timeStaticFlag
private

A boolean saying if only one frame is being reconstructed

Definition at line 1025 of file oImageDimensionsAndQuantification.hh.

int oImageDimensionsAndQuantification::m_verbose
private

The verbose level

Definition at line 1076 of file oImageDimensionsAndQuantification.hh.

FLTNB oImageDimensionsAndQuantification::m_voxSizeX
private

The voxel's size along the X axis, in mm

Definition at line 1055 of file oImageDimensionsAndQuantification.hh.

FLTNB oImageDimensionsAndQuantification::m_voxSizeY
private

The voxel's size along the Y axis, in mm

Definition at line 1056 of file oImageDimensionsAndQuantification.hh.

FLTNB oImageDimensionsAndQuantification::m_voxSizeZ
private

The voxel's size along the Z axis, in mm

Definition at line 1057 of file oImageDimensionsAndQuantification.hh.

FLTNB* oImageDimensionsAndQuantification::mp_bedPositions
private

The bed positions used during the reconstruction

Definition at line 1014 of file oImageDimensionsAndQuantification.hh.

oDynamicDataManager* oImageDimensionsAndQuantification::mp_DynamicDataManager
private

oDynamicDataManager object related to dynamic raw data management

Definition at line 1005 of file oImageDimensionsAndQuantification.hh.

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