This is the base class for reconstructions, containing a framework with iteration and data subset loops.
It contains all the managers and the images. More...

#include <vAlgorithm.hh>

Inheritance diagram for vAlgorithm:

Collaboration diagram for vAlgorithm:

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

virtual	~vAlgorithm ()
	vAlgorithm destructor. More...

int	Run ()
	Just call either the RunCPU or the RunGPU function as asked for. More...

int	RunCPU ()
	Perform the iterative loop of the algorithm. Function designed to be executed on the CPU only. More...

void	SetSaveSensitivityHistoFlag (bool a_saveSensitivityHistoFlag)
	Set the flag that specifies if the sensitivity image in histogram mode has to be saved for each subset/iteration. More...

void	SetSaveSubsetImageFlag (bool a_saveImageAfterSubsets)
	Set the flag that specifies if the image has to be saved for each subset. More...

void	SetSaveDynamicBasisCoefficientImages (bool a_saveDynamicBasisCoefficients)
	Set the flag that specifies if the dynamic basis functions coefficients images have to be saved. More...

void	SetOptimizerManager (oOptimizerManager *ap_OptimizerManager)
	Set the Optimizer Manager Object. More...

void	SetImageDimensionsAndQuantification (oImageDimensionsAndQuantification *ap_ImageDimensionsAndQuantification)
	Set the Image Dimensions and Quantification Object. More...

void	SetImageSpace (oImageSpace *ap_ImageSpace)
	Set the Image Space Object. More...

void	SetProjectorManager (oProjectorManager *ap_ProjectorManager)
	Set the Projector Manager Object. More...

void	SetImageConvolverManager (oImageConvolverManager *ap_ImageConvolverManager)
	Set the Image Convolver Manager Object. More...

void	SetImageProcessingManager (oImageProcessingManager *ap_ImageProcessingManager)
	Set the Image Processing Manager Object. More...

void	SetDynamicModelManager (oDynamicModelManager *ap_DynamicModelManager)
	Set the Dynamic Model Manager Object. More...

void	SetDeformationManager (oDeformationManager *ap_DeformationManager)
	Set the Deformation Manager Object. More...

void	SetDataFile (vDataFile **a2p_DataFile)
	Set the list of DataFile. More...

void	SetGPUflag (bool a_flagGPU)
	Set the GPU flag. More...

void	SetVerbose (int a_verboseLevel)
	Set Verbosity. More...

void	SetNbBeds (int a_nbBeds)
	Set number of beds (bed positions) More...

void	SetPathInitImage (string a_pathToInitialImage)
	Set path to an initial image. More...

void	SetPathToAttenuationImage (string a_pathToAttenuationImage)
	This function is used to set the path to the attenuation image. More...

void	SetPathToSensitivityImage (string a_pathToSensitivityImage)
	Set path to the sensitivity image. More...

void	SetPathToMultiModalImage (vector< string > a_pathToMultiModalImage)
	Set path to multimodal images. More...

void	SetPathToMaskImage (string a_pathToMaskImage)
	Set path to a mask image. More...

int	SetNbIterationsAndSubsets (const string &a_nbIterationsSubsets)
	Set the number of iterations and subsets. More...

int	SetOutputIterations (const string &a_outputIterations)
	Set the selected output iterations. More...

virtual int	InitSpecificOptions (string a_specificOptions)

virtual void	ShowHelpSpecific ()
	Show help for the child algorithm. More...

Protected Member Functions
virtual int	StepBeforeIterationLoop ()
	This function is called at the beginning of the RunCPU function. More...

virtual int	StepAfterIterationLoop ()
	This function is called at the end of the RunCPU function. More...

virtual int	StepBeforeSubsetLoop (int a_iteration)
	This function is called before starting the data subset loop. More...

virtual int	StepAfterSubsetLoop (int a_iteration)
	This function is called after finishing the data subset loop. More...

virtual int	StepPreProcessInsideSubsetLoop (int a_iteration, int a_subset)
	This function is called right after starting the data subset loop. More...

virtual int	StepPostProcessInsideSubsetLoop (int a_iteration, int a_subset)

virtual int	StepInnerLoopInsideSubsetLoop (int a_iteration, int a_subset, int a_bed)=0
	This function is called inside the subset loop. It contains the core operations of the algorithm and must be implemented by child classes. More...

virtual int	StepImageOutput (int a_iteration, int a_subset=-1)=0
	This function deals with everything about saving output images from the reconstruction. More...

Protected Attributes
int	m_nbIterations

int *	mp_nbSubsets

bool *	mp_outputIterations

int	m_verbose

bool	m_flagGPU

oImageDimensionsAndQuantification *	mp_ID

vDataFile **	m2p_DataFile

oProjectorManager *	mp_ProjectorManager

oOptimizerManager *	mp_OptimizerManager

oDeformationManager *	mp_DeformationManager

oDynamicModelManager *	mp_DynamicModelManager

oImageSpace *	mp_ImageSpace

oImageConvolverManager *	mp_ImageConvolverManager

oImageProcessingManager *	mp_ImageProcessingManager

int	m_nbBeds

string	m_pathToInitialImg

string	m_pathToAtnImg

string	m_pathToSensitivityImg

vector< string >	m_pathToMultiModalImg

string	m_pathToMaskImg

bool	m_saveSensitivityHistoFlag

bool	m_saveImageAfterSubsets

bool	m_saveDynamicBasisCoefficients

Detailed Description

This is the base class for reconstructions, containing a framework with iteration and data subset loops.
It contains all the managers and the images.

Definition at line 51 of file vAlgorithm.hh.

Constructor & Destructor Documentation

◆ vAlgorithm()

vAlgorithm::vAlgorithm ( )

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

Definition at line 39 of file vAlgorithm.cc.

◆ ~vAlgorithm()

vAlgorithm::~vAlgorithm ( )

virtual

vAlgorithm destructor.

Definition at line 73 of file vAlgorithm.cc.

Member Function Documentation

◆ InitSpecificOptions()

int vAlgorithm::InitSpecificOptions ( string a_specificOptions )

virtual

Parameters

a_specificOptions

Returns: 0

Reimplemented in iIterativeAlgorithm, and iRCPGSAlgorithm.

Definition at line 516 of file vAlgorithm.cc.

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◆ Run()

int vAlgorithm::Run ( )

Just call either the RunCPU or the RunGPU function as asked for.

Returns: 0 if success, positive value otherwise

Definition at line 233 of file vAlgorithm.cc.

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◆ RunCPU()

int vAlgorithm::RunCPU ( )

Perform the iterative loop of the algorithm. Function designed to be executed on the CPU only.

Loops over the iterations, data subsets, bed positions

StepBeforeIterationLoop()
/ Loop on iterations
| StepBeforeSubsetLoop(iteration)
| / Loop on data subsets
| | StepPreProcessInsideSubsetLoop(iteration,subset)
| | / Loop on bed positions
| | | StepInnerLoopInsideSubsetLoop(iteration,subset,bed)
| | StepPostProcessInsideSubsetLoop(iteration,subset)
| StepAfterSubsetLoop(iteration)
StepAfterIterationLoop()

Returns: 0 if success, positive value otherwise

Definition at line 252 of file vAlgorithm.cc.

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◆ SetDataFile()

public vAlgorithm::SetDataFile ( vDataFile ** a2p_DataFile )

inline

Set the list of DataFile.

Parameters

a2p_DataFile

Definition at line 190 of file vAlgorithm.hh.

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◆ SetDeformationManager()

public vAlgorithm::SetDeformationManager ( oDeformationManager * ap_DeformationManager )

inline

Set the Deformation Manager Object.

Parameters

ap_DeformationManager

Definition at line 183 of file vAlgorithm.hh.

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◆ SetDynamicModelManager()

public vAlgorithm::SetDynamicModelManager ( oDynamicModelManager * ap_DynamicModelManager )

inline

Set the Dynamic Model Manager Object.

Parameters

ap_DynamicModelManager

Definition at line 176 of file vAlgorithm.hh.

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◆ SetGPUflag()

public vAlgorithm::SetGPUflag ( bool a_flagGPU )

inline

Set the GPU flag.

Parameters

a_flagGPU

Definition at line 197 of file vAlgorithm.hh.

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◆ SetImageConvolverManager()

public vAlgorithm::SetImageConvolverManager ( oImageConvolverManager * ap_ImageConvolverManager )

inline

Set the Image Convolver Manager Object.

Parameters

ap_ImageConvolverManager

Definition at line 162 of file vAlgorithm.hh.

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◆ SetImageDimensionsAndQuantification()

public vAlgorithm::SetImageDimensionsAndQuantification ( oImageDimensionsAndQuantification * ap_ImageDimensionsAndQuantification )

inline

Set the Image Dimensions and Quantification Object.

Parameters

ap_ImageDimensionsAndQuantification

Definition at line 141 of file vAlgorithm.hh.

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◆ SetImageProcessingManager()

public vAlgorithm::SetImageProcessingManager ( oImageProcessingManager * ap_ImageProcessingManager )

inline

Set the Image Processing Manager Object.

Parameters

ap_ImageProcessingManager

Definition at line 169 of file vAlgorithm.hh.

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◆ SetImageSpace()

public vAlgorithm::SetImageSpace ( oImageSpace * ap_ImageSpace )

inline

Set the Image Space Object.

Parameters

ap_ImageSpace

Definition at line 148 of file vAlgorithm.hh.

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◆ SetNbBeds()

public vAlgorithm::SetNbBeds ( int a_nbBeds )

inline

Set number of beds (bed positions)

Parameters

a_nbBeds

Definition at line 211 of file vAlgorithm.hh.

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◆ SetNbIterationsAndSubsets()

int vAlgorithm::SetNbIterationsAndSubsets ( const string & a_nbIterationsSubsets )

Set the number of iterations and subsets.

Parameters

a_nbIterationsSubsets

The provided string is a list of iteration:subset pairs separated by commas.

Returns: 0 if success, positive value otherwise

Definition at line 85 of file vAlgorithm.cc.

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◆ SetOptimizerManager()

public vAlgorithm::SetOptimizerManager ( oOptimizerManager * ap_OptimizerManager )

inline

Set the Optimizer Manager Object.

Parameters

ap_OptimizerManager

Definition at line 134 of file vAlgorithm.hh.

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◆ SetOutputIterations()

int vAlgorithm::SetOutputIterations ( const string & a_outputIterations )

Set the selected output iterations.

Parameters

a_outputIterations

The provided string is a list of couple a:b separated by commas.
It means that we save one iteration over a until b is reached.
"b" must be incrementing for each successive couples. If the list is empty, we save all iterations by default.
If the list is equal to "-1", then we save only the last iteration.

Returns: 0 if success, positive value otherwise

Definition at line 144 of file vAlgorithm.cc.

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◆ SetPathInitImage()

public vAlgorithm::SetPathInitImage ( string a_pathToInitialImage )

inline

Set path to an initial image.

Parameters

a_pathToInitialImage

Definition at line 218 of file vAlgorithm.hh.

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◆ SetPathToAttenuationImage()

public vAlgorithm::SetPathToAttenuationImage ( string a_pathToAttenuationImage )

inline

This function is used to set the path to the attenuation image.

Parameters

string a_pathToAttenuationImage

Definition at line 225 of file vAlgorithm.hh.

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◆ SetPathToMaskImage()

public vAlgorithm::SetPathToMaskImage ( string a_pathToMaskImage )

inline

Set path to a mask image.

Parameters

a_pathToMaskImage

Definition at line 246 of file vAlgorithm.hh.

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◆ SetPathToMultiModalImage()

public vAlgorithm::SetPathToMultiModalImage ( vector< string > a_pathToMultiModalImage )

inline

Set path to multimodal images.

Parameters

a_pathToMultiModalImage

Definition at line 239 of file vAlgorithm.hh.

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◆ SetPathToSensitivityImage()

public vAlgorithm::SetPathToSensitivityImage ( string a_pathToSensitivityImage )

inline

Set path to the sensitivity image.

Parameters

a_pathToSensitivityImage

Definition at line 232 of file vAlgorithm.hh.

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◆ SetProjectorManager()

public vAlgorithm::SetProjectorManager ( oProjectorManager * ap_ProjectorManager )

inline

Set the Projector Manager Object.

Parameters

ap_ProjectorManager

Definition at line 155 of file vAlgorithm.hh.

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◆ SetSaveDynamicBasisCoefficientImages()

public void vAlgorithm::SetSaveDynamicBasisCoefficientImages ( bool a_saveDynamicBasisCoefficients )

inline

Set the flag that specifies if the dynamic basis functions coefficients images have to be saved.

Parameters

bool	a_saveDynamicBasisCoefficients

Definition at line 127 of file vAlgorithm.hh.

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◆ SetSaveSensitivityHistoFlag()

public void vAlgorithm::SetSaveSensitivityHistoFlag ( bool a_saveSensitivityHistoFlag )

inline

Set the flag that specifies if the sensitivity image in histogram mode has to be saved for each subset/iteration.

Parameters

bool	a_saveSensitivityHistoFlag

Definition at line 113 of file vAlgorithm.hh.

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◆ SetSaveSubsetImageFlag()

public void vAlgorithm::SetSaveSubsetImageFlag ( bool a_saveImageAfterSubsets )

inline

Set the flag that specifies if the image has to be saved for each subset.

Parameters

bool	a_saveImageAfterSubsets

Definition at line 120 of file vAlgorithm.hh.

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◆ SetVerbose()

public vAlgorithm::SetVerbose ( int a_verboseLevel )

inline

Set Verbosity.

Parameters

a_verboseLevel

Definition at line 204 of file vAlgorithm.hh.

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◆ ShowHelpSpecific()

public virtual vAlgorithm::ShowHelpSpecific ( )

inlinevirtual

Show help for the child algorithm.

Reimplemented in iRCPGSAlgorithm.

Definition at line 279 of file vAlgorithm.hh.

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◆ StepAfterIterationLoop()

int vAlgorithm::StepAfterIterationLoop ( )

protectedvirtual

This function is called at the end of the RunCPU function.

Returns: 0 if success, positive value otherwise.

Reimplemented in iIterativeAlgorithm, and iRCPGSAlgorithm.

Definition at line 483 of file vAlgorithm.cc.

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◆ StepAfterSubsetLoop()

int vAlgorithm::StepAfterSubsetLoop ( int a_iteration )

protectedvirtual

This function is called after finishing the data subset loop.

Parameters

a_iteration : iteration index

Returns: 0 if success, positive value otherwise.

Reimplemented in iIterativeAlgorithm, and iRCPGSAlgorithm.

Definition at line 472 of file vAlgorithm.cc.

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◆ StepBeforeIterationLoop()

int vAlgorithm::StepBeforeIterationLoop ( )

protectedvirtual

This function is called at the beginning of the RunCPU function.

Returns: 0 if success, positive value otherwise.

Reimplemented in iIterativeAlgorithm, and iRCPGSAlgorithm.

Definition at line 388 of file vAlgorithm.cc.

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◆ StepBeforeSubsetLoop()

int vAlgorithm::StepBeforeSubsetLoop ( int a_iteration )

protectedvirtual

This function is called before starting the data subset loop.

Parameters

a_iteration : iteration index

Returns: 0 if success, positive value otherwise.

Reimplemented in iIterativeAlgorithm, and iRCPGSAlgorithm.

Definition at line 439 of file vAlgorithm.cc.

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◆ StepImageOutput()

int vAlgorithm::StepImageOutput	(	int	a_iteration,
		int	a_subset = `-1`
	)

protectedpure virtual

This function deals with everything about saving output images from the reconstruction.

Implemented in iIterativeAlgorithm, and iRCPGSAlgorithm.

Definition at line 505 of file vAlgorithm.cc.

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◆ StepInnerLoopInsideSubsetLoop()

vAlgorithm::StepInnerLoopInsideSubsetLoop	(	int	a_iteration,
		int	a_subset,
		int	a_bed
	)

protectedpure virtual

This function is called inside the subset loop.
It contains the core operations of the algorithm and must be implemented by child classes.

Parameters

a_iteration	: iteration index
a_subset	: subset index
a_bed	: bed position

Returns: 0 if success, positive value otherwise.

Implemented in iIterativeAlgorithm, and iRCPGSAlgorithm.

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◆ StepPostProcessInsideSubsetLoop()

int vAlgorithm::StepPostProcessInsideSubsetLoop	(	int	a_iteration,
		int	a_subset
	)

protectedvirtual

Reimplemented in iIterativeAlgorithm, and iRCPGSAlgorithm.

Definition at line 461 of file vAlgorithm.cc.

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◆ StepPreProcessInsideSubsetLoop()

int vAlgorithm::StepPreProcessInsideSubsetLoop	(	int	a_iteration,
		int	a_subset
	)

protectedvirtual

This function is called right after starting the data subset loop.

This function is called right after starting the subset loop.
.

Parameters

a_iteration	: iteration index
a_subset	: subset index

Returns: 0 if success, positive value otherwise.

Reimplemented in iIterativeAlgorithm, and iRCPGSAlgorithm.

Definition at line 450 of file vAlgorithm.cc.

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Member Data Documentation

◆ m2p_DataFile

vDataFile** vAlgorithm::m2p_DataFile

protected

Pointer to the array of vDataFile object

Definition at line 353 of file vAlgorithm.hh.

◆ m_flagGPU

bool vAlgorithm::m_flagGPU

protected

Do we use GPU or not (default=false)

Definition at line 351 of file vAlgorithm.hh.

◆ m_nbBeds

int vAlgorithm::m_nbBeds

protected

number of bed FOVs (1 datafile by bed) (default=-1)

Definition at line 361 of file vAlgorithm.hh.

◆ m_nbIterations

int vAlgorithm::m_nbIterations

protected

Number of iterations (default=1)

Definition at line 347 of file vAlgorithm.hh.

◆ m_pathToAtnImg

string vAlgorithm::m_pathToAtnImg

protected

String of the path to the attenuation images

Definition at line 363 of file vAlgorithm.hh.

◆ m_pathToInitialImg

string vAlgorithm::m_pathToInitialImg

protected

String containing the path to an initialization image

Definition at line 362 of file vAlgorithm.hh.

◆ m_pathToMaskImg

string vAlgorithm::m_pathToMaskImg

protected

String containing the path to a mask image

Definition at line 366 of file vAlgorithm.hh.

◆ m_pathToMultiModalImg

vector<string> vAlgorithm::m_pathToMultiModalImg

protected

String vector containing paths to multimodal images

Definition at line 365 of file vAlgorithm.hh.

◆ m_pathToSensitivityImg

string vAlgorithm::m_pathToSensitivityImg

protected

String containing the path to a sensitivity image

Definition at line 364 of file vAlgorithm.hh.

◆ m_saveDynamicBasisCoefficients

bool vAlgorithm::m_saveDynamicBasisCoefficients

protected

Flag specifying that the dynamic basis coefficient images will be saved

Definition at line 369 of file vAlgorithm.hh.

◆ m_saveImageAfterSubsets

bool vAlgorithm::m_saveImageAfterSubsets

protected

Flag specifying that the image has to be saved after each subset

Definition at line 368 of file vAlgorithm.hh.

◆ m_saveSensitivityHistoFlag

bool vAlgorithm::m_saveSensitivityHistoFlag

protected

Flag specifying that the sensitivity image has to be saved for each subset/iteration in histogram mode

Definition at line 367 of file vAlgorithm.hh.

◆ m_verbose

int vAlgorithm::m_verbose

protected

Verbosity (default=-1)

Definition at line 350 of file vAlgorithm.hh.

◆ mp_DeformationManager

oDeformationManager* vAlgorithm::mp_DeformationManager

protected

Pointer to the Deformation Manager object

Definition at line 356 of file vAlgorithm.hh.

◆ mp_DynamicModelManager

oDynamicModelManager* vAlgorithm::mp_DynamicModelManager

protected

Pointer to the Dynamic Model Manager object

Definition at line 357 of file vAlgorithm.hh.

◆ mp_ID

oImageDimensionsAndQuantification* vAlgorithm::mp_ID

protected

Pointer to the oImageDimensionsAndQuantification object

Definition at line 352 of file vAlgorithm.hh.

◆ mp_ImageConvolverManager

oImageConvolverManager* vAlgorithm::mp_ImageConvolverManager

protected

Pointer to the Image Convolver Manager object

Definition at line 359 of file vAlgorithm.hh.

◆ mp_ImageProcessingManager

oImageProcessingManager* vAlgorithm::mp_ImageProcessingManager

protected

Pointer to the Image Processing Manager object

Definition at line 360 of file vAlgorithm.hh.

◆ mp_ImageSpace

oImageSpace* vAlgorithm::mp_ImageSpace

protected

Pointer to the Image Space object

Definition at line 358 of file vAlgorithm.hh.

◆ mp_nbSubsets

int* vAlgorithm::mp_nbSubsets

protected

Number of subsets (default=1)

Definition at line 348 of file vAlgorithm.hh.

◆ mp_OptimizerManager

oOptimizerManager* vAlgorithm::mp_OptimizerManager

protected

Pointer to the Optimizer Manager object

Definition at line 355 of file vAlgorithm.hh.

◆ mp_outputIterations

bool* vAlgorithm::mp_outputIterations

protected

A boolean for each iteration saying if we save it or not

Definition at line 349 of file vAlgorithm.hh.

◆ mp_ProjectorManager

oProjectorManager* vAlgorithm::mp_ProjectorManager

protected

Pointer to the Projector Manager object

Definition at line 354 of file vAlgorithm.hh.

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

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ vAlgorithm()

◆ ~vAlgorithm()

Member Function Documentation

◆ InitSpecificOptions()

◆ Run()

◆ RunCPU()

◆ SetDataFile()

◆ SetDeformationManager()

◆ SetDynamicModelManager()

◆ SetGPUflag()

◆ SetImageConvolverManager()

◆ SetImageDimensionsAndQuantification()

◆ SetImageProcessingManager()

◆ SetImageSpace()

◆ SetNbBeds()

◆ SetNbIterationsAndSubsets()

◆ SetOptimizerManager()

◆ SetOutputIterations()

◆ SetPathInitImage()

◆ SetPathToAttenuationImage()

◆ SetPathToMaskImage()

◆ SetPathToMultiModalImage()

◆ SetPathToSensitivityImage()

◆ SetProjectorManager()

◆ SetSaveDynamicBasisCoefficientImages()

◆ SetSaveSensitivityHistoFlag()

◆ SetSaveSubsetImageFlag()

◆ SetVerbose()

◆ ShowHelpSpecific()

◆ StepAfterIterationLoop()

◆ StepAfterSubsetLoop()

◆ StepBeforeIterationLoop()

◆ StepBeforeSubsetLoop()

◆ StepImageOutput()

◆ StepInnerLoopInsideSubsetLoop()

◆ StepPostProcessInsideSubsetLoop()

◆ StepPreProcessInsideSubsetLoop()

Member Data Documentation

◆ m2p_DataFile

◆ m_flagGPU

◆ m_nbBeds

◆ m_nbIterations

◆ m_pathToAtnImg

◆ m_pathToInitialImg

◆ m_pathToMaskImg

◆ m_pathToMultiModalImg

◆ m_pathToSensitivityImg

◆ m_saveDynamicBasisCoefficients

◆ m_saveImageAfterSubsets

◆ m_saveSensitivityHistoFlag

◆ m_verbose

◆ mp_DeformationManager

◆ mp_DynamicModelManager

◆ mp_ID

◆ mp_ImageConvolverManager

◆ mp_ImageProcessingManager

◆ mp_ImageSpace

◆ mp_nbSubsets

◆ mp_OptimizerManager

◆ mp_outputIterations

◆ mp_ProjectorManager