This class implements the general Markov Random Field kind of penalties. More...

#include <iPenaltyMarkovRandomField.hh>

Inheritance diagram for iPenaltyMarkovRandomField:

Collaboration diagram for iPenaltyMarkovRandomField:

Public Member Functions
	iPenaltyMarkovRandomField ()
	The constructor of iPenaltyMarkovRandomField. More...

	~iPenaltyMarkovRandomField ()
	The destructor of iPenaltyMarkovRandomField. More...

int	ReadConfigurationFile (const string &a_configurationFile)
	A function used to read options from a configuration file. More...

int	ReadOptionsList (const string &a_optionsList)
	A function used to read options from a list of options. More...

int	LocalPreProcessingStep (int a_tbf, int a_rbf, int a_cbf, INTNB a_voxel, int a_th)
	A public function computing a local pre-processing step for the penalty. More...

FLTNB	ComputePenaltyValue (int a_tbf, int a_rbf, int a_cbf, INTNB a_voxel, int a_th)
	Implementation of the pure virtual vPenalty::ComputePenaltyValue() More...

FLTNB	ComputeFirstDerivative (int a_tbf, int a_rbf, int a_cbf, INTNB a_voxel, int a_th)
	Implementation of the pure virtual vPenalty::ComputeFirstDerivative() More...

FLTNB	ComputeSecondDerivative (int a_tbf, int a_rbf, int a_cbf, INTNB a_voxel, int a_th)
	Implementation of the pure virtual vPenalty::ComputeSecondDerivative() More...

int	BuildSpecificNeighborhood (INTNB a_voxel, int a_th)
	Computes the specific neighborhood of a voxel, m2p_neighborhoodIndices, as well as mp_neighborhoodNbVoxels. More...

int	GetPotentialType ()

FLTNB *	GetProximityKernel ()

INTNB	GetNeighborhoodMaxNbVoxels ()

INTNB **	GetNeighborhoodIndices ()

Public Member Functions inherited from vPenalty
	vPenalty ()
	The constructor of vPenalty. More...

virtual	~vPenalty ()
	The destructor of vPenalty. More...

void	ShowHelp ()
	A function used to show help about the penalty. More...

int	CheckParameters ()
	A public function used to check the parameters settings. More...

int	Initialize ()
	A public function used to initialize the penalty. More...

virtual int	GlobalPreProcessingStep ()
	A public function computing a global pre-processing step for the penalty. More...

void	SetVerbose (int a_verbose)
	Set the verbose level. More...

void	SetImageDimensionsAndQuantification (oImageDimensionsAndQuantification *ap_ImageDimensionsAndQuantification)
	Set the pointer to the image dimensions in use. More...

void	SetImageSpace (oImageSpace *ap_ImageSpace)
	Set the pointer to the image space in use. More...

void	SetPenaltyStrength (FLTNB a_penaltyStrength)
	Set the penalty strength. More...

FLTNB	GetPenaltyStrength ()
	Get the penalty strength. More...

int	GetPenaltyDerivativesOrder ()
	Get the penalty deratives order. More...

void	SetPenaltyID (const string &a_penaltyID)
	Set the penalty ID. More...

const string &	GetPenaltyID ()

Private Member Functions
void	ShowHelpSpecific ()
	A function used to show help about the child penalty. More...

int	CheckSpecificParameters ()
	A private function used to check the parameters settings specific to the child penalty. More...

int	InitializeSpecific ()
	This function is used to initialize specific stuff to the child penalty. More...

int	BuildNeighborhoodKernel ()
	A function used to build the neighborhood kernel. More...

int	BuildProximityFactors ()
	A function used to build the kernel of the proximity factors. More...

int	ComputeSimilarityFactors (int a_tbf, int a_rbf, int a_cbf, INTNB a_voxel, int a_th)
	Computes the similarity factors of this specific voxel with respect to the similarity type used. More...

Additional Inherited Members
Protected Attributes inherited from vPenalty
string	m_penaltyID

oImageDimensionsAndQuantification *	mp_ImageDimensionsAndQuantification

oImageSpace *	mp_ImageSpace

int	m_verbose

int	m_penaltyDerivativesOrder

FLTNB	m_penaltyStrength

Detailed Description

This class implements the general Markov Random Field kind of penalties.

This class inherits from vPenalty and implements the general MRF penalties.

Definition at line 67 of file iPenaltyMarkovRandomField.hh.

Constructor & Destructor Documentation

◆ iPenaltyMarkovRandomField()

iPenaltyMarkovRandomField::iPenaltyMarkovRandomField ( )

The constructor of iPenaltyMarkovRandomField.

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 37 of file iPenaltyMarkovRandomField.cc.

◆ ~iPenaltyMarkovRandomField()

iPenaltyMarkovRandomField::~iPenaltyMarkovRandomField ( )

The destructor of iPenaltyMarkovRandomField.

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 built by this class.

Definition at line 73 of file iPenaltyMarkovRandomField.cc.

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Member Function Documentation

◆ BuildNeighborhoodKernel()

int iPenaltyMarkovRandomField::BuildNeighborhoodKernel ( )

private

A function used to build the neighborhood kernel.

This function build the table m2p_neighborhoodKernel, that prepare neighborhood indices operations. It is called only one time at initialization. The kernel will be used when computing the specific neighborhood of any voxel later on.

Returns: An integer reflecting the reading success; 0 if success, another value otherwise.

Definition at line 659 of file iPenaltyMarkovRandomField.cc.

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◆ BuildProximityFactors()

int iPenaltyMarkovRandomField::BuildProximityFactors ( )

private

A function used to build the kernel of the proximity factors.

This function build the table FLTNB* mp_proximityKernel

Returns: An integer reflecting the reading success; 0 if success, another value otherwise.

Definition at line 804 of file iPenaltyMarkovRandomField.cc.

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◆ BuildSpecificNeighborhood()

int iPenaltyMarkovRandomField::BuildSpecificNeighborhood	(	INTNB	a_voxel,
		int	a_th
	)

Computes the specific neighborhood of a voxel, m2p_neighborhoodIndices, as well as mp_neighborhoodNbVoxels.

Parameters

INTNB	a_voxel
int	a_th

This function computes the specific neighborhood of a voxel, from the neighborhood kernel and the provided index. From the neighborhood kernel that contains indices shifts, it computes the actual voxel indices of each neighbor and check if it is outside of boundaries. It records the index voxel if valid and -1 if not. This function use a thread index to be thread safe during computations.

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

Definition at line 895 of file iPenaltyMarkovRandomField.cc.

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◆ CheckSpecificParameters()

int iPenaltyMarkovRandomField::CheckSpecificParameters ( )

privatevirtual

A private function used to check the parameters settings specific to the child penalty.

This function is used to check that all parameters specific to the penalty are correctly set within allowed values. It is called by the CheckParameters() function of the mother class. It is the implementation of the pure virtual function inherited from the abstract mother class vPenalty.

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

Implements vPenalty.

Definition at line 430 of file iPenaltyMarkovRandomField.cc.

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◆ ComputeFirstDerivative()

FLTNB iPenaltyMarkovRandomField::ComputeFirstDerivative	(	int	a_tbf,
		int	a_rbf,
		int	a_cbf,
		INTNB	a_voxel,
		int	a_th
	)

virtual

Implementation of the pure virtual vPenalty::ComputeFirstDerivative()

Parameters

int	a_tbf
int	a_rbf
int	a_cbf
INTNB	a_voxel
int	a_th

This function computes the first derivative of the penalty. It is the implementation of the pure virtual vPenalty::ComputeFirstDerivative().

Returns: The derivative

Implements vPenalty.

Definition at line 1092 of file iPenaltyMarkovRandomField.cc.

◆ ComputePenaltyValue()

FLTNB iPenaltyMarkovRandomField::ComputePenaltyValue	(	int	a_tbf,
		int	a_rbf,
		int	a_cbf,
		INTNB	a_voxel,
		int	a_th
	)

virtual

Implementation of the pure virtual vPenalty::ComputePenaltyValue()

Parameters

int	a_tbf
int	a_rbf
int	a_cbf
INTNB	a_voxel
int	a_th

This function computes the value of the penalty function for the provided indices. It is the implementation of the pure virtual vPenalty::ComputePenaltyValue().

Returns: The penalty value

Implements vPenalty.

Definition at line 1006 of file iPenaltyMarkovRandomField.cc.

◆ ComputeSecondDerivative()

FLTNB iPenaltyMarkovRandomField::ComputeSecondDerivative	(	int	a_tbf,
		int	a_rbf,
		int	a_cbf,
		INTNB	a_voxel,
		int	a_th
	)

virtual

Implementation of the pure virtual vPenalty::ComputeSecondDerivative()

Parameters

int	a_tbf
int	a_rbf
int	a_cbf
INTNB	a_voxel
int	a_th

This function computes the second derivative of the penalty. It is the implementation of the pure virtual vPenalty::ComputeSecondDerivative().

Returns: The derivative

Implements vPenalty.

Definition at line 1187 of file iPenaltyMarkovRandomField.cc.

◆ ComputeSimilarityFactors()

int iPenaltyMarkovRandomField::ComputeSimilarityFactors	(	int	a_tbf,
		int	a_rbf,
		int	a_cbf,
		INTNB	a_voxel,
		int	a_th
	)

private

Computes the similarity factors of this specific voxel with respect to the similarity type used.

Parameters

int	a_tbf
int	a_rbf
int	a_cbf
INTNB	a_voxel
int	a_th

Store the results in m2p_similarityFactors

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

Definition at line 938 of file iPenaltyMarkovRandomField.cc.

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◆ GetNeighborhoodIndices()

public inline INTNB ** iPenaltyMarkovRandomField::GetNeighborhoodIndices ( )

inline

Returns: m2p_neighborhoodIndices

Definition at line 202 of file iPenaltyMarkovRandomField.hh.

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◆ GetNeighborhoodMaxNbVoxels()

public inline INTNB iPenaltyMarkovRandomField::GetNeighborhoodMaxNbVoxels ( )

inline

Returns: m_neighborhoodMaxNbVoxels

Definition at line 197 of file iPenaltyMarkovRandomField.hh.

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◆ GetPotentialType()

public inline int iPenaltyMarkovRandomField::GetPotentialType ( )

inline

Returns: m_potentialType

Definition at line 187 of file iPenaltyMarkovRandomField.hh.

◆ GetProximityKernel()

public inline FLTNB * iPenaltyMarkovRandomField::GetProximityKernel ( )

inline

Returns: mp_proximityKernel

Definition at line 192 of file iPenaltyMarkovRandomField.hh.

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◆ InitializeSpecific()

int iPenaltyMarkovRandomField::InitializeSpecific ( )

privatevirtual

This function is used to initialize specific stuff to the child penalty.

It is called by the public Initialize() function from the mother.

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

Implements vPenalty.

Definition at line 532 of file iPenaltyMarkovRandomField.cc.

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◆ LocalPreProcessingStep()

int iPenaltyMarkovRandomField::LocalPreProcessingStep	(	int	a_tbf,
		int	a_rbf,
		int	a_cbf,
		INTNB	a_voxel,
		int	a_th
	)

virtual

A public function computing a local pre-processing step for the penalty.

Parameters

int	a_tbf
int	a_rbf
int	a_cbf
INTNB	a_voxel
int	a_th

This function overloads the mother class function that does nothing. The idea here is to build the specific neighborhood of the given voxel and to compute all related weights.

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

Reimplemented from vPenalty.

Definition at line 983 of file iPenaltyMarkovRandomField.cc.

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◆ ReadConfigurationFile()

int iPenaltyMarkovRandomField::ReadConfigurationFile ( const string & a_configurationFile )

virtual

A function used to read options from a configuration file.

Parameters

const string& a_configurationFile

This function implements the reading of all options associated to the child penalty, from a configuration file. It is the implementation of the pure virtual function inherited from the abstract class vPenalty. It checks the reading status but not the options values that will be checked by the CheckSpecificParameters() function.

Returns: An integer reflecting the reading success; 0 if success, another value otherwise.

Implements vPenalty.

Definition at line 193 of file iPenaltyMarkovRandomField.cc.

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◆ ReadOptionsList()

int iPenaltyMarkovRandomField::ReadOptionsList ( const string & a_optionsList )

virtual

A function used to read options from a list of options.

Parameters

const string& a_optionsList

This function implements the reading of all options associated to the child penalty, from a list of options. It is the implementation of the pure virtual function inherited from the abstract class vPenalty. It checks the reading status but not the options values that will be checked by the CheckSpecificParameters() function.

Returns: An integer reflecting the reading success; 0 if success, another value otherwise.

Implements vPenalty.

Definition at line 418 of file iPenaltyMarkovRandomField.cc.

◆ ShowHelpSpecific()

void iPenaltyMarkovRandomField::ShowHelpSpecific ( )

privatevirtual

A function used to show help about the child penalty.

This function must describe what the module does and how to use it. It describes in details the different parameters of the penalty, and how to set them through the use of a configuration file or a list of options. It is the implementation of the pure virtual function inherited from the abstract class vPenalty. It is called by the public ShowHelp() function.

Implements vPenalty.

Definition at line 119 of file iPenaltyMarkovRandomField.cc.

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Member Data Documentation

◆ m2p_neighborhoodIndices

INTNB** iPenaltyMarkovRandomField::m2p_neighborhoodIndices

private

Neighborhood indices of a specific voxel. First index is on the threads, second one contains the list of the voxels in the neighborhood (as many as m_neighborhoodMaxNbVoxels). It follows strictly the same order than m2p_neighborhoodKernel, with the convention -1: out of image boundaries

Definition at line 290 of file iPenaltyMarkovRandomField.hh.

◆ m2p_neighborhoodKernel

INTNB** iPenaltyMarkovRandomField::m2p_neighborhoodKernel

private

Neighborhood of a virtual voxel of coordinates 0, 0, 0 without boundary. First index on neighboring voxels, second one on indexes

Definition at line 288 of file iPenaltyMarkovRandomField.hh.

◆ m2p_similarityFactors

FLTNB** iPenaltyMarkovRandomField::m2p_similarityFactors

private

Similarity factors of the neighborhood. First index on threads, second on neighboring voxels, as for m2p_neighborhoodIndices

Definition at line 280 of file iPenaltyMarkovRandomField.hh.

◆ m_neighborhoodBoxExcludeCorners

int iPenaltyMarkovRandomField::m_neighborhoodBoxExcludeCorners

private

In case of a box neighborhood, remove the corners as in some papers, or not (keep them by default)

Definition at line 286 of file iPenaltyMarkovRandomField.hh.

◆ m_neighborhoodBoxOrder

int iPenaltyMarkovRandomField::m_neighborhoodBoxOrder

private

In case of a box neighborhood, order of the box

Definition at line 285 of file iPenaltyMarkovRandomField.hh.

◆ m_neighborhoodMaxNbVoxels

INTNB iPenaltyMarkovRandomField::m_neighborhoodMaxNbVoxels

private

Maximum number of voxels in the neighborhood

Definition at line 287 of file iPenaltyMarkovRandomField.hh.

◆ m_neighborhoodShape

int iPenaltyMarkovRandomField::m_neighborhoodShape

private

Type of neighborhood (sphere, box)

Definition at line 283 of file iPenaltyMarkovRandomField.hh.

◆ m_neighborhoodSphereRadius

FLTNB iPenaltyMarkovRandomField::m_neighborhoodSphereRadius

private

In case of a spherical neighborhood, radius of the sphere

Definition at line 284 of file iPenaltyMarkovRandomField.hh.

◆ m_potentialGemanMcClureDelta

FLTNB iPenaltyMarkovRandomField::m_potentialGemanMcClureDelta

private

Parameter of the Geman and McClure's potential function

Definition at line 269 of file iPenaltyMarkovRandomField.hh.

◆ m_potentialGreenLogCoshDelta

FLTNB iPenaltyMarkovRandomField::m_potentialGreenLogCoshDelta

private

Parameter of the Green's log-cosh potential function

Definition at line 270 of file iPenaltyMarkovRandomField.hh.

◆ m_potentialHebertLeahyMu

FLTNB iPenaltyMarkovRandomField::m_potentialHebertLeahyMu

private

Parameter of the Hebert and Leahy's potential function

Definition at line 271 of file iPenaltyMarkovRandomField.hh.

◆ m_potentialHuberDelta

FLTNB iPenaltyMarkovRandomField::m_potentialHuberDelta

private

Parameter of the piecewise Huber potential function

Definition at line 272 of file iPenaltyMarkovRandomField.hh.

◆ m_potentialRelativeDifferenceGamma

FLTNB iPenaltyMarkovRandomField::m_potentialRelativeDifferenceGamma

private

Parameter of the relative difference potential function

Definition at line 268 of file iPenaltyMarkovRandomField.hh.

◆ m_potentialType

int iPenaltyMarkovRandomField::m_potentialType

private

Type of the potential function used (e.g. quadratic)

Definition at line 267 of file iPenaltyMarkovRandomField.hh.

◆ m_proximityCharacteristicDistance

FLTNB iPenaltyMarkovRandomField::m_proximityCharacteristicDistance

private

When the proximity factors are the exponential distance squared, this is the characteristic distance

Definition at line 275 of file iPenaltyMarkovRandomField.hh.

◆ m_proximityType

int iPenaltyMarkovRandomField::m_proximityType

private

Type of weighting based on proximity (e.g. the inverse of the euclidian distance between voxels)

Definition at line 274 of file iPenaltyMarkovRandomField.hh.

◆ m_similarityBowsherNbVoxels

INTNB iPenaltyMarkovRandomField::m_similarityBowsherNbVoxels

private

The number of voxels kept from the Bowsher's threashold

Definition at line 281 of file iPenaltyMarkovRandomField.hh.

◆ m_similarityBowsherThreshold

FLTNB iPenaltyMarkovRandomField::m_similarityBowsherThreshold

private

Percentage of the neighborhood voxels for defining the most similar Bowsher neighbor voxels

Definition at line 279 of file iPenaltyMarkovRandomField.hh.

◆ m_similarityType

int iPenaltyMarkovRandomField::m_similarityType

private

Type of weighting based on similarity (e.g. joint entropy)

Definition at line 278 of file iPenaltyMarkovRandomField.hh.

◆ mp_neighborhoodNbVoxels

INTNB* iPenaltyMarkovRandomField::mp_neighborhoodNbVoxels

private

Number of voxels in a specific neighborhood. The index is on threads

Definition at line 289 of file iPenaltyMarkovRandomField.hh.

◆ mp_proximityKernel

FLTNB* iPenaltyMarkovRandomField::mp_proximityKernel

private

Precomputation of the proximity factors. Index is on neighboring voxels, as for m2p_neighborhoodKernel

Definition at line 276 of file iPenaltyMarkovRandomField.hh.

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

Private Attributes
int	m_potentialType

FLTNB	m_potentialRelativeDifferenceGamma

FLTNB	m_potentialGemanMcClureDelta

FLTNB	m_potentialGreenLogCoshDelta

FLTNB	m_potentialHebertLeahyMu

FLTNB	m_potentialHuberDelta

int	m_proximityType

FLTNB	m_proximityCharacteristicDistance

FLTNB *	mp_proximityKernel

int	m_similarityType

FLTNB	m_similarityBowsherThreshold

FLTNB **	m2p_similarityFactors

INTNB	m_similarityBowsherNbVoxels

int	m_neighborhoodShape

FLTNB	m_neighborhoodSphereRadius

int	m_neighborhoodBoxOrder

int	m_neighborhoodBoxExcludeCorners

INTNB	m_neighborhoodMaxNbVoxels

INTNB **	m2p_neighborhoodKernel

INTNB *	mp_neighborhoodNbVoxels

INTNB **	m2p_neighborhoodIndices

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ iPenaltyMarkovRandomField()

◆ ~iPenaltyMarkovRandomField()

Member Function Documentation

◆ BuildNeighborhoodKernel()

◆ BuildProximityFactors()

◆ BuildSpecificNeighborhood()

◆ CheckSpecificParameters()

◆ ComputeFirstDerivative()

◆ ComputePenaltyValue()

◆ ComputeSecondDerivative()

◆ ComputeSimilarityFactors()

◆ GetNeighborhoodIndices()

◆ GetNeighborhoodMaxNbVoxels()

◆ GetPotentialType()

◆ GetProximityKernel()

◆ InitializeSpecific()

◆ LocalPreProcessingStep()

◆ ReadConfigurationFile()

◆ ReadOptionsList()

◆ ShowHelpSpecific()

Member Data Documentation

◆ m2p_neighborhoodIndices

◆ m2p_neighborhoodKernel

◆ m2p_similarityFactors

◆ m_neighborhoodBoxExcludeCorners

◆ m_neighborhoodBoxOrder

◆ m_neighborhoodMaxNbVoxels

◆ m_neighborhoodShape

◆ m_neighborhoodSphereRadius

◆ m_potentialGemanMcClureDelta

◆ m_potentialGreenLogCoshDelta

◆ m_potentialHebertLeahyMu

◆ m_potentialHuberDelta

◆ m_potentialRelativeDifferenceGamma

◆ m_potentialType

◆ m_proximityCharacteristicDistance

◆ m_proximityType

◆ m_similarityBowsherNbVoxels

◆ m_similarityBowsherThreshold

◆ m_similarityType

◆ mp_neighborhoodNbVoxels

◆ mp_proximityKernel