This class implements a general linear dynamic model applied between the images of a dynamic acquisition
The model is applied on a voxel-by-voxel basis between the images of the frames and/or respiratory/cardiac gates. More...

#include <iLinearModel.hh>

Inheritance diagram for iLinearModel:

Collaboration diagram for iLinearModel:

Public Member Functions
	iLinearModel ()
	Constructor of iLinearModel. Simply set all data members to default values. More...

	~iLinearModel ()
	Destructor of iLinearModel. More...

int	CheckSpecificParameters ()
	This function is used to check whether all member variables have been correctly initialized or not. More...

int	CheckSpecificParametersForAllLinearModels ()
	This function is used to check parameters for all Linear Models. . More...

virtual int	ReadAndCheckConfigurationFileSpecific ()
	This function is used to read options from a configuration file. More...

int	ReadAndCheckOptionsList (string a_listOptions)
	This function is used to read parameters from a string. More...

int	ReadAndCheckConfigurationFileSpecificToAllLinearModels ()
	This function is used to read parameters that are generic for all Linear Models. . More...

int	InitializeSpecific ()
	This function is used to initialize the parametric images and basis functions for all Linear Models. More...

int	InitializeSpecificToAllLinearModels ()
	This function is used to initialize the parametric images and basis functions for all Linear Models. More...

void	ShowBasisFunctions ()
	This function is used to print the basis functions. More...

void	ShowHelp ()
	Print out specific help about the implementation of this model and its initialization. More...

int	EstimateModelParameters (oImageSpace *ap_Image, int a_ite, int a_sset)
	Estimate model parameters (parametric images and basis functions) More...

int	EstimateImageWithModel (oImageSpace *ap_Image, int a_ite, int a_sset)
	Re-estimate image using the linear parametric images and basis functions. More...

int	NestedEM (oImageSpace *ap_ImageS, int a_ite)
	Estimate parametric images and basis functions (if enabled) using the nested EM method. More...

int	EstimateParametersWithNNLS (oImageSpace *ap_ImageS, int a_ite)
	Estimate parametric images using the NNLS method. More...

int	Patlak_LS (oImageSpace *ap_ImageS, int a_ite)
	Estimate parametric images using linear regression. More...

Public Member Functions inherited from vDynamicModel
	vDynamicModel ()
	Constructor of vDynamicModel. Simply set all data members to default values. More...

virtual	~vDynamicModel ()
	Destructor of vDynamicModel. More...

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

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

virtual int	CheckParameters ()
	This function is used to check parameters after the latter have been all set using Set functions. More...

int	ReadAndCheckConfigurationFile (string a_fileOptions)
	This function is used to read options from a configuration file. It looks for the parameters implemented by the mother class, such as 'No image update', 'No parameters update', or 'Save parametric images'. More...

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

virtual int	EstimateModel (oImageSpace *ap_Image, int a_ite, int a_sset)
	This function checks if the EstimateModelParameters() function (specific to each model) must be called at this stage of the reconstruction depending on the m_xxxUpdateflags. More...

virtual int	EstimateImage (oImageSpace *ap_Image, int a_ite, int a_sset)

int	SaveParametricImages (int a_iteration, int a_subset=-1)
	This function is virtual it can be overloaded by children if required. More...

virtual int	ApplyOutputFOVMaskingOnParametricImages ()
	Mask the outside of the transaxial FOV based on the m_fovOutPercent. More...

bool	GetAICflag ()

bool	GetModelBasisFunctionsRequiredFlag ()

int	GetNbTimeBasisFunctions ()

FLTNB **	GetTimeBasisFunctions ()

virtual void	ComputeOutputParImage ()
	Compute output image using the m2p_parametricImages matrix Store the result in the m2p_outputParImages matrix. More...

int	NNLS (FLTNB *A, int m, int n, FLTNB B, FLTNB X, FLTNB rnorm, FLTNB wp, FLTNB zzp, int *indexp)
	Implementation of NNLS (non-negative least squares) algorithm Derived from Turku PET center libraries (authors: Vesa Oikonen and Kaisa Sederholm) This routine is based on the text and fortran code in C.L. Lawson and R.J. Hanson, Solving Least Squares Problems, Prentice-Hall, Englewood Cliffs, New Jersey, 1974. More...

Protected Attributes
int	m_OptimisationMethod

int	m_nbRgateBF

int	m_nbCgateBF

FLTNB **	m2p_respBasisFunctions

FLTNB **	m2p_cardBasisFunctions

FLTNB *	mp_corrBasisCoeffs

FLTNB *	mp_corrBasisFunctions

uint32_t	m_nbLinearModelCycles

int	m_basisFunctionsUpdStartIte

int	m_basisFunctionsUpdRatio

int	m_basisFunctionsUpdIdx

Protected Attributes inherited from vDynamicModel
oImageDimensionsAndQuantification *	mp_ID

int	m_verbose

int	m_nbTimeBF

int	m_nbWeightFactors

int	m_nbModelParam

int	m_nbRGModelParam

int	m_nbCGModelParam

string	m_AICfile

oArterialInputCurve *	mp_ArterialInputCurve

FLTNB **	m2p_parametricImages

FLTNB *	mp_blackListedvoxelsImage

FLTNB **	m2p_nestedModelTimeBasisFunctions

FLTNB **	m2p_outputParImages

FLTNB **	m2p_RGParametricImages

FLTNB **	m2p_CGParametricImages

string	m_fileOptions

string	m_listOptions

bool	m_checked

bool	m_initialized

bool	m_saveParImageFlag

bool	m_saveBlacklistedImageMaskFlag

bool	m_AICfileProvided

bool	m_ModelSpecificBasisFunctionsRequired

bool	m_noImageUpdateFlag

bool	m_noParametersUpdateFlag

int	m_startIteUpdateFlag

FLTNB *	mp_maskModel

INTNB	m_nbVoxelsMask

FLTNB *	mp_w

FLTNB ***	m3p_nnlsA

FLTNB **	m2p_nnlsB

FLTNB **	m2p_nnlsMat

FLTNB **	m2p_nnlsX

FLTNB **	m2p_nnlsWp

int **	m2p_nnlsIdx

uint16_t	m_nnlsN =0

Detailed Description

This class implements a general linear dynamic model applied between the images of a dynamic acquisition
The model is applied on a voxel-by-voxel basis between the images of the frames and/or respiratory/cardiac gates.

Definition at line 62 of file iLinearModel.hh.

Constructor & Destructor Documentation

◆ iLinearModel()

iLinearModel::iLinearModel ( )

Constructor of iLinearModel. Simply set all data members to default values.

Definition at line 41 of file iLinearModel.cc.

◆ ~iLinearModel()

iLinearModel::~iLinearModel ( )

Destructor of iLinearModel.

Definition at line 76 of file iLinearModel.cc.

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Member Function Documentation

◆ CheckSpecificParameters()

int iLinearModel::CheckSpecificParameters ( )

virtual

This function is used to check whether all member variables have been correctly initialized or not.

Returns: 0 if success, positive value otherwise.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearPatlakModel, and iLinearSpectralModel.

Definition at line 460 of file iLinearModel.cc.

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◆ CheckSpecificParametersForAllLinearModels()

int iLinearModel::CheckSpecificParametersForAllLinearModels ( )

This function is used to check parameters for all Linear Models.
.

Returns: 0 if success, other value otherwise.

Definition at line 487 of file iLinearModel.cc.

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◆ EstimateImageWithModel()

int iLinearModel::EstimateImageWithModel	(	oImageSpace *	ap_Image,
		int	a_ite,
		int	a_sset
	)

virtual

Re-estimate image using the linear parametric images and basis functions.

Parameters

ap_ImageS	: pointer to the ImageSpace
a_ite	: index of the actual iteration (not used)
a_sset	: index of the actual subset (not used)

Returns: 0 if success, other value otherwise.

Implements vDynamicModel.

Definition at line 1913 of file iLinearModel.cc.

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◆ EstimateModelParameters()

int iLinearModel::EstimateModelParameters	(	oImageSpace *	ap_Image,
		int	a_ite,
		int	a_sset
	)

virtual

Estimate model parameters (parametric images and basis functions)

Parameters

ap_ImageS	: pointer to the ImageSpace
a_ite	: index of the actual iteration (not used)
a_sset	: index of the actual subset (not used)

Returns: 0 if success, other value otherwise.

Implements vDynamicModel.

Definition at line 1022 of file iLinearModel.cc.

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◆ EstimateParametersWithNNLS()

int iLinearModel::EstimateParametersWithNNLS	(	oImageSpace *	ap_ImageS,
		int	a_ite
	)

Estimate parametric images using the NNLS method.

Parameters

ap_ImageS	: pointer to the ImageSpace
a_ite	: index of the actual iteration (not used)

Returns: 0 if success, other value otherwise.

Definition at line 1601 of file iLinearModel.cc.

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◆ InitializeSpecific()

int iLinearModel::InitializeSpecific ( )

virtual

This function is used to initialize the parametric images and basis functions for all Linear Models.

Returns: 0 if success, other value otherwise.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearPatlakModel, and iLinearSpectralModel.

Definition at line 983 of file iLinearModel.cc.

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◆ InitializeSpecificToAllLinearModels()

int iLinearModel::InitializeSpecificToAllLinearModels ( )

This function is used to initialize the parametric images and basis functions for all Linear Models.

Returns: 0 if success, other value otherwise.

Definition at line 552 of file iLinearModel.cc.

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◆ NestedEM()

int iLinearModel::NestedEM	(	oImageSpace *	ap_ImageS,
		int	a_ite
	)

Estimate parametric images and basis functions (if enabled) using the nested EM method.

Parameters

ap_ImageS	: pointer to the ImageSpace
a_ite	: index of the actual iteration (not used)

Returns: 0 if success, other value otherwise.

Definition at line 1104 of file iLinearModel.cc.

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◆ Patlak_LS()

int iLinearModel::Patlak_LS	(	oImageSpace *	ap_ImageS,
		int	a_ite
	)

Estimate parametric images using linear regression.

Parameters

ap_ImageS	: pointer to the ImageSpace
a_ite	: index of the actual iteration (not used)

Returns: 0 if success, other value otherwise.

Definition at line 1840 of file iLinearModel.cc.

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◆ ReadAndCheckConfigurationFileSpecific()

int iLinearModel::ReadAndCheckConfigurationFileSpecific ( )

virtual

This function is used to read options from a configuration file.

Returns: 0 if success, other value otherwise.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearPatlakModel, and iLinearSpectralModel.

Definition at line 252 of file iLinearModel.cc.

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◆ ReadAndCheckConfigurationFileSpecificToAllLinearModels()

int iLinearModel::ReadAndCheckConfigurationFileSpecificToAllLinearModels ( )

This function is used to read parameters that are generic for all Linear Models.
.

Returns: 0 if success, other value otherwise.

Definition at line 276 of file iLinearModel.cc.

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◆ ReadAndCheckOptionsList()

int iLinearModel::ReadAndCheckOptionsList ( string a_listOptions )

virtual

This function is used to read parameters from a string.

Parameters

const string& a_optionsList : a list of parameters separated by commas

Returns: 0 if success, other value otherwise.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearPatlakModel, and iLinearSpectralModel.

Definition at line 431 of file iLinearModel.cc.

◆ ShowBasisFunctions()

void iLinearModel::ShowBasisFunctions ( )

This function is used to print the basis functions.

Definition at line 951 of file iLinearModel.cc.

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◆ ShowHelp()

void iLinearModel::ShowHelp ( )

virtual

Print out specific help about the implementation of this model and its initialization.

Implements vDynamicModel.

Reimplemented in iLinearModelTemplate, iLinearPatlakModel, and iLinearSpectralModel.

Definition at line 139 of file iLinearModel.cc.

Member Data Documentation

◆ m2p_cardBasisFunctions

FLTNB** iLinearModel::m2p_cardBasisFunctions

protected

Vector containing the cardiac gating model temporal basis functions
2 pointers:
1: index of the temporal function
2: coefficient of the functions for each cardiac gate

Definition at line 205 of file iLinearModel.hh.

◆ m2p_respBasisFunctions

FLTNB** iLinearModel::m2p_respBasisFunctions

protected

Vector containing the respiratory gating model temporal basis functions
2 pointers:
1: index of the temporal function
2: coefficient of the functions for each respiratory gate

Definition at line 201 of file iLinearModel.hh.

◆ m_basisFunctionsUpdIdx

int iLinearModel::m_basisFunctionsUpdIdx

protected

Index to compute the ratio for the parametric images/basis functions updates cycle

Definition at line 217 of file iLinearModel.hh.

◆ m_basisFunctionsUpdRatio

int iLinearModel::m_basisFunctionsUpdRatio

protected

Ratio for the parametric images/basis functions updates cycle.
Cycles consist in 'm_basisFunctionsUpdRate' iterations of the parametric images, following by 'm_basisFunctionsUpdRate' iterations of the basis functions

Definition at line 215 of file iLinearModel.hh.

◆ m_basisFunctionsUpdStartIte

int iLinearModel::m_basisFunctionsUpdStartIte

protected

Starting iteration for the update of basis functions.
If negative, no update of the basis functions is performed (only parametric images are updated)

Definition at line 213 of file iLinearModel.hh.

◆ m_nbCgateBF

int iLinearModel::m_nbCgateBF

protected

Number of time basis functions applied to cardiac gates in the model

Definition at line 197 of file iLinearModel.hh.

◆ m_nbLinearModelCycles

uint32_t iLinearModel::m_nbLinearModelCycles

protected

Number of iteration of the model (one cycle consists in several updates of either the parametric images or the basis function)

Definition at line 212 of file iLinearModel.hh.

◆ m_nbRgateBF

int iLinearModel::m_nbRgateBF

protected

Number of time basis functions applied to respiratory gates in the model

Definition at line 196 of file iLinearModel.hh.

◆ m_OptimisationMethod

int iLinearModel::m_OptimisationMethod

protected

Number indicating the method to estimate parameters, from the available options.

Definition at line 195 of file iLinearModel.hh.

◆ mp_corrBasisCoeffs

FLTNB* iLinearModel::mp_corrBasisCoeffs

protected

Image matrix containing correction factors for the parametric images updates

Definition at line 210 of file iLinearModel.hh.

◆ mp_corrBasisFunctions

FLTNB* iLinearModel::mp_corrBasisFunctions

protected

Vector containing correction factors for the temporal basis functions updates

Definition at line 211 of file iLinearModel.hh.

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

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ iLinearModel()

◆ ~iLinearModel()

Member Function Documentation

◆ CheckSpecificParameters()

◆ CheckSpecificParametersForAllLinearModels()

◆ EstimateImageWithModel()

◆ EstimateModelParameters()

◆ EstimateParametersWithNNLS()

◆ InitializeSpecific()

◆ InitializeSpecificToAllLinearModels()

◆ NestedEM()

◆ Patlak_LS()

◆ ReadAndCheckConfigurationFileSpecific()

◆ ReadAndCheckConfigurationFileSpecificToAllLinearModels()

◆ ReadAndCheckOptionsList()

◆ ShowBasisFunctions()

◆ ShowHelp()

Member Data Documentation

◆ m2p_cardBasisFunctions

◆ m2p_respBasisFunctions

◆ m_basisFunctionsUpdIdx

◆ m_basisFunctionsUpdRatio

◆ m_basisFunctionsUpdStartIte

◆ m_nbCgateBF

◆ m_nbLinearModelCycles

◆ m_nbRgateBF

◆ m_OptimisationMethod

◆ mp_corrBasisCoeffs

◆ mp_corrBasisFunctions