This is the main class for iterative reconstructions, that manages the iteration loops.
This class manages an iterative reconstruction of any kind, using a vDataFile, and through the use of an oProjector, an oOptimizer, a oConvolver, a oImageSpace. More...

#include <oIterativeAlgorithm.hh>

Collaboration diagram for oIterativeAlgorithm:

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

virtual	~oIterativeAlgorithm ()
	oIterativeAlgorithm destructor. More...

int	Iterate ()
	Just call either the IterateCPU or the IterateGPU function as asked for. More...

int	IterateCPU ()
	Perform the iterative loop of the algorithm, call the different object for optimization, projection, update, etc. 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	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)
	Set the selected output iterations. More...

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

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

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

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

virtual int	StepPreProcessInsideSubsetLoop (int a_iteration, int a_subset)
	This function is called right after starting the subset loop. Apply any kind of processing on the forward image before projections. More...

virtual int	StepPostProcessInsideSubsetLoop (int a_iteration, int a_subset)

virtual int	StepInnerLoopInsideSubsetLoop (int a_iteration, int a_subset, int a_bed)
	This function is called inside the subset loop and manages the main loop over the events The loop over the events is multithreaded, and involves a thread lock in the case of image-based deformation. More...

void	ThreadBarrierIncrement ()
	Increment (thread safe) the m_nbThreadsWaiting variable. More...

bool	ThreadBarrierFlag ()
	Check if the m_releaseThreads boolean is enabled or not. More...

bool	ThreadBarrierCheck ()
	Check if all the threads are currently in waiting condition. More...

void	ThreadBarrierSetOff ()
	Disable the thread locking variable (thread safe), and reset the number of waiting threads to 0. More...

void	ThreadBarrierSetOn ()
	Enable the thread locking variable (thread safe), and reset the number of waiting threads to 0. 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_generalizedImplementation

Detailed Description

This is the main class for iterative reconstructions, that manages the iteration loops.
This class manages an iterative reconstruction of any kind, using a vDataFile, and through the use of an oProjector, an oOptimizer, a oConvolver, a oImageSpace.

Definition at line 53 of file oIterativeAlgorithm.hh.

Constructor & Destructor Documentation

oIterativeAlgorithm::oIterativeAlgorithm ( )

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

Definition at line 46 of file oIterativeAlgorithm.cc.

oIterativeAlgorithm::~oIterativeAlgorithm ( )

virtual

oIterativeAlgorithm destructor.

Definition at line 81 of file oIterativeAlgorithm.cc.

Member Function Documentation

int oIterativeAlgorithm::InitSpecificOptions ( string a_specificOptions )

virtual

Set the selected output iterations.

Parameters

a_specificOptions

Not Implemented yet

Returns: 0

Definition at line 1036 of file oIterativeAlgorithm.cc.

int oIterativeAlgorithm::Iterate ( )

Just call either the IterateCPU or the IterateGPU function as asked for.

Returns: 0 if success, positive value otherwise

Definition at line 262 of file oIterativeAlgorithm.cc.

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int oIterativeAlgorithm::IterateCPU ( )

Perform the iterative loop of the algorithm, call the different object for optimization, projection, update, etc. Function designed to be executed on the CPU only.

Loops over the iterations, subsets, bed position
Call functions related to each steps of iterative reconstruction:

StepBeforeIterationLoop()
/ Loop on iterations
| StepBeforeSubsetLoop(iteration)
| / Loop on 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 301 of file oIterativeAlgorithm.cc.

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public oIterativeAlgorithm::SetDataFile ( vDataFile ** a2p_DataFile )

inline

Set the list of DataFile.

Parameters

a2p_DataFile

Definition at line 178 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetDeformationManager ( oDeformationManager * ap_DeformationManager )

inline

Set the Deformation Manager Object.

Parameters

ap_DeformationManager

Definition at line 172 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetDynamicModelManager ( oDynamicModelManager * ap_DynamicModelManager )

inline

Set the Dynamic Model Manager Object.

Parameters

ap_DynamicModelManager

Definition at line 166 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetGPUflag ( bool a_flagGPU )

inline

Set the GPU flag.

Parameters

a_flagGPU

Definition at line 184 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetImageConvolverManager ( oImageConvolverManager * ap_ImageConvolverManager )

inline

Set the Image Convolver Manager Object.

Parameters

ap_ImageConvolverManager

Definition at line 154 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetImageDimensionsAndQuantification ( oImageDimensionsAndQuantification * ap_ImageDimensionsAndQuantification )

inline

Set the Image Dimensions and Quantification Object.

Parameters

ap_ImageDimensionsAndQuantification

Definition at line 136 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetImageProcessingManager ( oImageProcessingManager * ap_ImageProcessingManager )

inline

Set the Image Processing Manager Object.

Parameters

ap_ImageProcessingManager

Definition at line 160 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetImageSpace ( oImageSpace * ap_ImageSpace )

inline

Set the Image Space Object.

Parameters

ap_ImageSpace

Definition at line 142 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetNbBeds ( int a_nbBeds )

inline

Set number of beds (bed positions)

Parameters

a_nbBeds

Definition at line 196 of file oIterativeAlgorithm.hh.

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int oIterativeAlgorithm::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 226 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetOptimizerManager ( oOptimizerManager * ap_OptimizerManager )

inline

Set the Optimizer Manager Object.

Parameters

ap_OptimizerManager

Definition at line 130 of file oIterativeAlgorithm.hh.

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int oIterativeAlgorithm::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 169 of file oIterativeAlgorithm.cc.

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public oIterativeAlgorithm::SetPathInitImage ( string a_pathToInitialImage )

inline

Set path to an initial image.

Parameters

a_pathToInitialImage

Definition at line 202 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetPathToAttenuationImage ( string a_pathToAttenuationImage )

inline

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

Parameters

string a_pathToAttenuationImage

Definition at line 208 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetPathToMaskImage ( string a_pathToMaskImage )

inline

Set path to a mask image.

Parameters

a_pathToMaskImage

Definition at line 226 of file oIterativeAlgorithm.hh.

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

inline

Set path to multimodal images.

Parameters

a_pathToMultiModalImage

Definition at line 220 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetPathToSensitivityImage ( string a_pathToSensitivityImage )

inline

Set path to the sensitivity image.

Parameters

a_pathToSensitivityImage

Definition at line 214 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetProjectorManager ( oProjectorManager * ap_ProjectorManager )

inline

Set the Projector Manager Object.

Parameters

ap_ProjectorManager

Definition at line 148 of file oIterativeAlgorithm.hh.

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public void oIterativeAlgorithm::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 118 of file oIterativeAlgorithm.hh.

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public void oIterativeAlgorithm::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 124 of file oIterativeAlgorithm.hh.

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public oIterativeAlgorithm::SetVerbose ( int a_verboseLevel )

inline

Set Verbosity.

Parameters

a_verboseLevel

Definition at line 190 of file oIterativeAlgorithm.hh.

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int oIterativeAlgorithm::StepAfterIterationLoop ( )

protectedvirtual

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

Free Memory for the imageSpace and some managers

Returns: 0 if success, positive value otherwise.

Definition at line 1006 of file oIterativeAlgorithm.cc.

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int oIterativeAlgorithm::StepAfterSubsetLoop ( int a_iteration )

protectedvirtual

This function is called after finishing the subset loop.

Parameters

a_iteration : iteration index

Clean the main images from never visited voxels
Apply post-convolution/post-processing if needed
Write output images on disk as requested by the user

Definition at line 935 of file oIterativeAlgorithm.cc.

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int oIterativeAlgorithm::StepBeforeIterationLoop ( )

protectedvirtual

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

Initialization and memory allocation for the imageSpace and some managers

Returns: 0 if success, positive value otherwise.

Definition at line 430 of file oIterativeAlgorithm.cc.

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int oIterativeAlgorithm::StepBeforeSubsetLoop ( int a_iteration )

protectedvirtual

This function is called before starting the subset loop.

Parameters

a_iteration : iteration index

Returns: 0 if success, positive value otherwise.

Definition at line 495 of file oIterativeAlgorithm.cc.

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

protectedvirtual

This function is called inside the subset loop and manages the main loop over the events
The loop over the events is multithreaded, and involves a thread lock in the case of image-based deformation.

Parameters

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

Step 1: Get the current event for that thread index
Step 2: Call the dynamic switch function that updates the current frame and gate numbers, and also detects involuntary patient motion
Perform image-based deformation if needed (thread lock is required)
Step 3: Compute the projection line
Step 4: Optimize in the data space (forward-proj, update, backward-proj)

Definition at line 579 of file oIterativeAlgorithm.cc.

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

protectedvirtual

Definition at line 802 of file oIterativeAlgorithm.cc.

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

protectedvirtual

This function is called right after starting the subset loop. Apply any kind of processing on the forward image before projections.

This function is called right after starting the subset loop.
Apply any kind of image processing on the backward image and main image after backprojections.

Parameters

a_iteration	: iteration index
a_subset	: subset index

Copy current main image into forward image matrix
Reinitialize backward image and 4D gating indices
Apply image processing/convolution on the forward image matrix (image to be projeted)

Parameters

a_iteration	: iteration index
a_subset	: subset index

Synchronize parallel results
Apply image deformation/processing/convolution on the backward image
Update the image using the optimizer functions
Apply dynamic model/image processing/convolution on the main image

Returns: 0 if success, positive value otherwise.

Definition at line 519 of file oIterativeAlgorithm.cc.

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bool oIterativeAlgorithm::ThreadBarrierCheck ( )

protected

Check if all the threads are currently in waiting condition.

Returns: true if all the threads are waiting, false otherwise

Definition at line 1099 of file oIterativeAlgorithm.cc.

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bool oIterativeAlgorithm::ThreadBarrierFlag ( )

protected

Check if the m_releaseThreads boolean is enabled or not.

Returns: true if the threads can be released, false otherwise

Definition at line 1079 of file oIterativeAlgorithm.cc.

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void oIterativeAlgorithm::ThreadBarrierIncrement ( )

protected

Increment (thread safe) the m_nbThreadsWaiting variable.

Definition at line 1058 of file oIterativeAlgorithm.cc.

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void oIterativeAlgorithm::ThreadBarrierSetOff ( )

protected

Disable the thread locking variable (thread safe), and reset the number of waiting threads to 0.

Definition at line 1117 of file oIterativeAlgorithm.cc.

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void oIterativeAlgorithm::ThreadBarrierSetOn ( )

protected

Enable the thread locking variable (thread safe), and reset the number of waiting threads to 0.

Definition at line 1137 of file oIterativeAlgorithm.cc.

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Member Data Documentation

vDataFile** oIterativeAlgorithm::m2p_DataFile

protected

Pointer to the array of vDataFile object

Definition at line 386 of file oIterativeAlgorithm.hh.

bool oIterativeAlgorithm::m_flagGPU

protected

Do we use GPU or not (default=false)

Definition at line 384 of file oIterativeAlgorithm.hh.

bool oIterativeAlgorithm::m_generalizedImplementation

protected

No purpose yet. For upcoming features

Definition at line 402 of file oIterativeAlgorithm.hh.

int oIterativeAlgorithm::m_nbBeds

protected

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

Definition at line 394 of file oIterativeAlgorithm.hh.

int oIterativeAlgorithm::m_nbIterations

protected

Number of iterations (default=1)

Definition at line 380 of file oIterativeAlgorithm.hh.

string oIterativeAlgorithm::m_pathToAtnImg

protected

String of the path to the attenuation images

Definition at line 396 of file oIterativeAlgorithm.hh.

string oIterativeAlgorithm::m_pathToInitialImg

protected

String containing the path to an initialization image

Definition at line 395 of file oIterativeAlgorithm.hh.

string oIterativeAlgorithm::m_pathToMaskImg

protected

String containing the path to a mask image

Definition at line 399 of file oIterativeAlgorithm.hh.

vector<string> oIterativeAlgorithm::m_pathToMultiModalImg

protected

String vector containing paths to multimodal images

Definition at line 398 of file oIterativeAlgorithm.hh.

string oIterativeAlgorithm::m_pathToSensitivityImg

protected

String containing the path to a sensitivity image

Definition at line 397 of file oIterativeAlgorithm.hh.

bool oIterativeAlgorithm::m_saveImageAfterSubsets

protected

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

Definition at line 401 of file oIterativeAlgorithm.hh.

bool oIterativeAlgorithm::m_saveSensitivityHistoFlag

protected

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

Definition at line 400 of file oIterativeAlgorithm.hh.

int oIterativeAlgorithm::m_verbose

protected

Verbosity (default=-1)

Definition at line 383 of file oIterativeAlgorithm.hh.

oDeformationManager* oIterativeAlgorithm::mp_DeformationManager

protected

Pointer to the Deformation Manager object

Definition at line 389 of file oIterativeAlgorithm.hh.

oDynamicModelManager* oIterativeAlgorithm::mp_DynamicModelManager

protected

Pointer to the Dynamic Model Manager object

Definition at line 390 of file oIterativeAlgorithm.hh.

oImageDimensionsAndQuantification* oIterativeAlgorithm::mp_ID

protected

Pointer to the oImageDimensionsAndQuantification object

Definition at line 385 of file oIterativeAlgorithm.hh.

oImageConvolverManager* oIterativeAlgorithm::mp_ImageConvolverManager

protected

Pointer to the Image Convolver Manager object

Definition at line 392 of file oIterativeAlgorithm.hh.

oImageProcessingManager* oIterativeAlgorithm::mp_ImageProcessingManager

protected

Pointer to the Image Processing Manager object

Definition at line 393 of file oIterativeAlgorithm.hh.

oImageSpace* oIterativeAlgorithm::mp_ImageSpace

protected

Pointer to the Image Space object

Definition at line 391 of file oIterativeAlgorithm.hh.

int* oIterativeAlgorithm::mp_nbSubsets

protected

Number of subsets (default=1)

Definition at line 381 of file oIterativeAlgorithm.hh.

oOptimizerManager* oIterativeAlgorithm::mp_OptimizerManager

protected

Pointer to the Optimizer Manager object

Definition at line 388 of file oIterativeAlgorithm.hh.

bool* oIterativeAlgorithm::mp_outputIterations

protected

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

Definition at line 382 of file oIterativeAlgorithm.hh.

oProjectorManager* oIterativeAlgorithm::mp_ProjectorManager

protected

Pointer to the Projector Manager object

Definition at line 387 of file oIterativeAlgorithm.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

Member Function Documentation

Member Data Documentation