template<typename fitterT>
class mx::math::fit::fitGaussian2D< fitterT >

Class to manage fitting a 2D Gaussian to data via the levmarInterface.

Can fit either the symmetric Gaussian, or the rotated asymmetric Gaussian. Individual parameters can be fixed, except in the asymmetric case \(\sigma_x, \sigma_y, \theta\) must currently be fixed together.

In addition to the requirements on fitterT specified by levmarInterface this class also requires the following in fitterT

static const int nparams = 7; //where the number 7 is replaced by the number of parameters that fitterT expects to
fit.
 
void paramNormalizer( array2FitGaussian2D * arr,
                      realT *,
                      int); //A function which converts from input parameters to fitting parameters.  May do nothing.

Template Parameters

fitterT a type meeting the above requirements.

Test:: Scenario: Verify direction and accuracy of various image shifts [test doc]

Definition at line 301 of file fitGaussian.hpp.

#include <math/fit/fitGaussian.hpp>

Inheritance diagram for mx::math::fit::fitGaussian2D< fitterT >:

Public Member Functions
void	setFixed (bool G0, bool G, bool x0, bool y0, bool sigma_x, bool sigma_y, bool theta)
	Set whether each parameter is fixed.

void	setFixed (bool G0, bool G, bool x0, bool y0, bool sigma)
	Set whether each parameter is fixed.

void	setGuess (realT G0, realT G, realT x0, realT y0, realT sigma)
	Set the initial guess for a symmetric Gaussian.

void	setGuess (realT G0, realT G, realT x0, realT y0, realT sigma_x, realT sigma_y, realT theta)
	Set the initial guess for the general Gaussian.

void	setArray (realT *data, int nx, int ny)
	Set the data aray.

void	setArray (realT data, int nx, int ny, realT mask)
	Set the data aray, with a mask.

int	fit ()
	Do the fit.

realT	G0 ()
	Get the current value of G0, the constant.

realT	G ()
	Get the peak scaling.

realT	x0 ()
	Get the center x-coordinate.

realT	y0 ()
	Get the center y-coordinate.

realT	sigma ()
	Return the width parameter.

realT	fwhm ()
	Return the full-width at half maximum.

realT	sigma_x ()
	Return the width parameter on the long axis.

realT	sigma_y ()
	Return the width parameter on the short axis.

realT	theta ()
	Return the orientation of the long axis.

Public Member Functions inherited from mx::math::fit::levmarInterface< fitterT >
	levmarInterface ()
	Default constructor.

	levmarInterface (realT i_p, realT i_x, int i_m, int i_n, void *i_adata)
	Setup constructor.

	~levmarInterface ()
	Destructor.

void	nParams (int i_m)
	Set number of parameters, but don't allocate.

int	nParams ()
	Get the current number of parameters.

void	allocate_params ()
	Allocate parameters array based on previous call to nParams.

void	allocate_params (int i_m)
	Set number of parameters and allocate.

void	point_params (realT *i_p)
	Point the parameter pointer at an externally allocated array.

void	point_params (realT *i_p, int i_m)
	Point the parameter pointer at an externally allocated array.

void	set_params (realT *i_p)
	Copy parameters to the parameter array.

realT *	get_params ()
	Get current pointer array address.

void	set_itmax (int i_itmax)
	Set the maximum number of iterations.

int	get_itmax ()
	Get the maximum number of iterations.

void	allocate_work ()
	Allocate the work and covar matrices.

void	set_opts (int n, realT val)
	Set one of the minimization options to val.

void	set_opts_default (int n=-1)
	Set one or all of the minimization options to the default.

realT	get_opts (int n)
	Get the current value of an option.

int	fit ()
	Perform the fit.

realT	get_initial_norm ()
	Returns the L2-norm before minimization occurs.

realT	get_final_norm ()
	Returns the L2-norm at the end of the minimization.

int	get_iterations ()
	Get the number of iterations taken during the minimization.

int	get_reason_code ()
	Get a code specifying the reason minimization terminated.

std::string	get_reason_string ()
	Get the descriptive string describing the reason minimization terminated.

int	get_fevals ()
	Get the number of function evaluations during the minimization.

int	get_jevals ()
	Get the number of jacobian evaluations during the minimization.

int	get_nlinsys ()
	Get the number of linear system solutions during the minimization.

double	get_deltaT ()
	Get the elapsed time of the fit.

template<typename iosT , char comment = '#'>
iosT &	dumpParameters (iosT &ios)
	Output current parameters to a stream.

template<char comment = '#'>
std::ostream &	dumpParameters ()
	Dump the parameter vector to stdout.

template<typename iosT , char comment = '#'>
iosT &	dumpReport (iosT &ios, bool dumpParams=true)
	Output current parameters to a stream.

template<char comment = '#'>
std::ostream &	dumpReport (bool dumpParams=true)
	Dump a status report to stdout.

Public Attributes
array2FitGaussian2D< realT >	arr

Public Attributes inherited from mx::math::fit::levmarInterface< fitterT >
realT *	x
	I: measurement vector. NULL implies a zero vector.

int	n
	I: measurement vector dimension.

realT	opts [LM_OPTS_SZ]
	Options passed to the minimization routines. See set_opts for details.

realT	info [LM_INFO_SZ]
	Information regarding the minimization.

double	deltaT
	Elapsed time of the fitting procedure.

realT *	work
	Working memory passed to the levmar routines.

int	work_sz
	The current size of the work array.

realT *	covar
	Covariance matrix corresponding to LS solution; mxm.

int	covar_sz
	The current size of the covar array.

bool	getCovar
	Controls whether the covar array is allocated.

void *	adata
	Pointer to possibly additional data, passed uninterpreted to func & jacf.

Additional Inherited Members
Protected Attributes inherited from mx::math::fit::levmarInterface< fitterT >
realT *	p
	Parameter array. On input is the initial estimates. On output has the estimated solution.

realT *	init_p
	Parameter array on input, saved for comparison.

int	m
	Parameter vector dimension (i.e. number of unknowns)

bool	own_p
	Flag indicating whether the p array is owned by this object (for de-allocation).

int	itmax
	Maximum number of iterations, default is 100.

Member Function Documentation

◆ fit()

template<typename fitterT >

int mx::math::fit::fitGaussian2D< fitterT >::fit ( )

inline

Do the fit.

Definition at line 441 of file fitGaussian.hpp.

References mx::math::fit::levmarInterface< fitterT >::fit(), and mx::math::six_fifths().

Referenced by SCENARIO().

◆ fwhm()

template<typename fitterT >

realT mx::math::fit::fitGaussian2D< fitterT >::fwhm ( )

inline

Return the full-width at half maximum.

This is a simple scaling of the sigma() result

Definition at line 495 of file fitGaussian.hpp.

References mx::math::func::sigma2fwhm(), and mx::math::six_fifths().

◆ G()

template<typename fitterT >

realT mx::math::fit::fitGaussian2D< fitterT >::G ( )

inline

Get the peak scaling.

Definition at line 465 of file fitGaussian.hpp.

◆ G0()

template<typename fitterT >

realT mx::math::fit::fitGaussian2D< fitterT >::G0 ( )

inline

Get the current value of G0, the constant.

Returns: the current value of G0.

Definition at line 459 of file fitGaussian.hpp.

◆ setArray() [1/2]

template<typename fitterT >

void mx::math::fit::fitGaussian2D< fitterT >::setArray	(	realT *	data,
		int	nx,
		int	ny
	)

inline

Set the data aray.

Parameters

[in]	data	The 2D array of data to fit.
[in]	nx	the x size of the data
[in]	ny	the y size of the data

Definition at line 402 of file fitGaussian.hpp.

Referenced by SCENARIO().

◆ setArray() [2/2]

template<typename fitterT >

void mx::math::fit::fitGaussian2D< fitterT >::setArray	(	realT *	data,
		int	nx,
		int	ny,
		realT *	mask
	)

inline

Set the data aray, with a mask.

Parameters

[in]	data	The 2D array of data to fit.
[in]	nx	the x size of the data
[in]	ny	the y size of the data
[in]	mask	Array of same size as data. Any 0 pixels in this array will be excluded from the fit.

Definition at line 415 of file fitGaussian.hpp.

References mx::math::six_fifths().

◆ setFixed() [1/2]

template<typename fitterT >

void mx::math::fit::fitGaussian2D< fitterT >::setFixed	(	bool	G0,
		bool	G,
		bool	x0,
		bool	y0,
		bool	sigma
	)

inline

Set whether each parameter is fixed.

Sets the parameter indices appropriately.

Parameters

[in]	G0	if true, then G0 will be not be part of the fit
[in]	G	if true, then G will be not be part of the fit
[in]	x0	if true, then x0 will be not be part of the fit
[in]	y0	if true, then y0 will be not be part of the fit
[in]	sigma	if true, then sigma will be not be part of the fit

Definition at line 353 of file fitGaussian.hpp.

◆ setFixed() [2/2]

template<typename fitterT >

void mx::math::fit::fitGaussian2D< fitterT >::setFixed	(	bool	G0,
		bool	G,
		bool	x0,
		bool	y0,
		bool	sigma_x,
		bool	sigma_y,
		bool	theta
	)

inline

Set whether each parameter is fixed.

Sets the parameter indices appropriately.

Parameters

[in]	G0	if true, then G0 will be not be part of the fit
[in]	G	if true, then G will be not be part of the fit
[in]	x0	if true, then x0 will be not be part of the fit
[in]	y0	if true, then y0 will be not be part of the fit
[in]	sigma_x	if true, then sigma_x will be not be part of the fit
[in]	sigma_y	if true, then sigma_y will be not be part of the fit
[in]	theta	if true, then theta will be not be part of the fit

Definition at line 337 of file fitGaussian.hpp.

◆ setGuess() [1/2]

template<typename fitterT >

void mx::math::fit::fitGaussian2D< fitterT >::setGuess	(	realT	G0,
		realT	G,
		realT	x0,
		realT	y0,
		realT	sigma
	)

inline

Set the initial guess for a symmetric Gaussian.

Also works for the general case, setting the same width in both directions.

Parameters

[in]	G0	the constant background level
[in]	G	the peak scaling
[in]	x0	the center x-coordinate
[in]	y0	the center y-coordinate
[in]	sigma	the width parameter

Definition at line 367 of file fitGaussian.hpp.

Referenced by SCENARIO().

◆ setGuess() [2/2]

template<typename fitterT >

void mx::math::fit::fitGaussian2D< fitterT >::setGuess	(	realT	G0,
		realT	G,
		realT	x0,
		realT	y0,
		realT	sigma_x,
		realT	sigma_y,
		realT	theta
	)

inline

Set the initial guess for the general Gaussian.

Parameters

[in]	G0	the constant background level
[in]	G	the peak scaling
[in]	x0	the center x-coordinate
[in]	y0	the center y-coordinate
[in]	sigma_x	the width parameter in the rotated x-direction (the long axis)
[in]	sigma_y	the width parameter in the rotated y-direction
[in]	theta	the angle of the long axis (always sigma_x)

Definition at line 382 of file fitGaussian.hpp.

◆ sigma()

template<typename fitterT >

realT mx::math::fit::fitGaussian2D< fitterT >::sigma ( )

inline

Return the width parameter.

As described for the symmetric Gaussian.

For the general Gaussian, this returns \( \sigma = \sqrt{ \sigma_x^2 + \sigma_y^2} \).

Definition at line 487 of file fitGaussian.hpp.

◆ sigma_x()

template<typename fitterT >

realT mx::math::fit::fitGaussian2D< fitterT >::sigma_x ( )

inline

Return the width parameter on the long axis.

Definition at line 501 of file fitGaussian.hpp.

◆ sigma_y()

template<typename fitterT >

realT mx::math::fit::fitGaussian2D< fitterT >::sigma_y ( )

inline

Return the width parameter on the short axis.

Definition at line 507 of file fitGaussian.hpp.

◆ theta()

template<typename fitterT >

realT mx::math::fit::fitGaussian2D< fitterT >::theta ( )

inline

Return the orientation of the long axis.

Definition at line 513 of file fitGaussian.hpp.

◆ x0()

template<typename fitterT >

realT mx::math::fit::fitGaussian2D< fitterT >::x0 ( )

inline

Get the center x-coordinate.

Definition at line 471 of file fitGaussian.hpp.

Referenced by SCENARIO().

◆ y0()

template<typename fitterT >

realT mx::math::fit::fitGaussian2D< fitterT >::y0 ( )

inline

Get the center y-coordinate.

Definition at line 477 of file fitGaussian.hpp.

Referenced by SCENARIO().

Member Data Documentation

◆ arr

template<typename fitterT >

array2FitGaussian2D<realT> mx::math::fit::fitGaussian2D< fitterT >::arr

Data array to pass to the levmar library. Contains the actual data plus the parameters if fixed.

Definition at line 308 of file fitGaussian.hpp.

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

math/fit/fitGaussian.hpp

Public Member Functions

Public Attributes

Additional Inherited Members

Member Function Documentation

◆ fit()

◆ fwhm()

◆ G()

◆ G0()

◆ setArray() [1/2]

◆ setArray() [2/2]

◆ setFixed() [1/2]

◆ setFixed() [2/2]

◆ setGuess() [1/2]

◆ setGuess() [2/2]

◆ sigma()

◆ sigma_x()

◆ sigma_y()

◆ theta()

◆ x0()

◆ y0()

Member Data Documentation

◆ arr