A RT Profile fitter using an Exponential Gaussian Hybrid background model. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/EGHTraceFitter.h>

Inheritance diagram for EGHTraceFitter:

Classes
class	EGHTraceFunctor

Public Member Functions
	EGHTraceFitter ()

	EGHTraceFitter (const EGHTraceFitter &other)

EGHTraceFitter &	operator= (const EGHTraceFitter &source)

virtual	~EGHTraceFitter ()

void	fit (FeatureFinderAlgorithmPickedHelperStructs::MassTraces &traces)

double	getLowerRTBound () const

double	getTau () const

double	getUpperRTBound () const

double	getHeight () const

double	getSigma () const

double	getCenter () const

bool	checkMaximalRTSpan (const double max_rt_span)

bool	checkMinimalRTSpan (const std::pair< double, double > &rt_bounds, const double min_rt_span)

double	getValue (double rt) const

double	getArea ()

double	getFWHM () const

String	getGnuplotFormula (const FeatureFinderAlgorithmPickedHelperStructs::MassTrace &trace, const char function_name, const double baseline, const double rt_shift)

Public Member Functions inherited from TraceFitter
	TraceFitter ()
	default constructor More...

	TraceFitter (const TraceFitter &source)
	copy constructor More...

virtual TraceFitter &	operator= (const TraceFitter &source)
	assignment operator More...

virtual	~TraceFitter ()
	destructor More...

double	computeTheoretical (const FeatureFinderAlgorithmPickedHelperStructs::MassTrace &trace, Size k)

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Protected Member Functions
std::pair< double, double >	getAlphaBoundaries_ (const double alpha) const
	Return an ordered pair of the positions where the EGH reaches a height of alpha * height of the EGH. More...

void	getOptimizedParameters_ (const Eigen::VectorXd &x_init)

void	setInitialParameters_ (FeatureFinderAlgorithmPickedHelperStructs::MassTraces &traces)

virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

Protected Member Functions inherited from TraceFitter
void	optimize_ (Eigen::VectorXd &x_init, GenericFunctor &functor)

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
double	apex_rt_

double	height_

double	sigma_

double	tau_

std::pair< double, double >	sigma_5_bound_

double	region_rt_span_

Protected Attributes inherited from TraceFitter
SignedSize	max_iterations_
	Maximum number of iterations. More...

bool	weighted_
	Whether to weight mass traces by theoretical intensity during the optimization. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Static Protected Attributes
static const double	EPSILON_COEFS_ []
	Coefficients to calculate the proportionality factor for the peak area. More...

static const Size	NUM_PARAMS_

Detailed Description

A RT Profile fitter using an Exponential Gaussian Hybrid background model.

Lan K, Jorgenson JW. A hybrid of exponential and gaussian functions as a simple model of asymmetric chromatographic peaks. Journal of Chromatography A. 915 (1-2)p. 1-13. Available at: http://linkinghub.elsevier.com/retrieve/pii/S0021967301005945

Parameters of this class are:

Name	Type	Default	Restrictions	Description
max_iteration	int	500		Maximum number of iterations used by the Levenberg-Marquardt algorithm.
weighted	string	false	true, false	Weight mass traces according to their theoretical intensities.

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Experimental classes:: Needs further testing on real data. Note that the tests are currently also focused on testing the EGH as replacement for the gaussian.

Constructor & Destructor Documentation

◆ EGHTraceFitter() [1/2]

EGHTraceFitter ( )

◆ EGHTraceFitter() [2/2]

EGHTraceFitter ( const EGHTraceFitter & other )

◆ ~EGHTraceFitter()

virtual ~EGHTraceFitter ( )

virtual

Member Function Documentation

◆ checkMaximalRTSpan()

bool checkMaximalRTSpan ( const double max_rt_span )

virtual

Checks if the fitted model is not to big

Parameters

max_rt_span Maximum RT span in relation to extended area that the model is allowed to have

Implements TraceFitter.

◆ checkMinimalRTSpan()

bool checkMinimalRTSpan	(	const std::pair< double, double > &	rt_bounds,
		const double	min_rt_span
	)

virtual

Checks if the fitted model fills out at least 'min_rt_span' of the RT span

Parameters

rt_bounds	RT boundaries of the fitted model
min_rt_span	Minimum RT span in relation to extended area that has to remain after model fitting

Implements TraceFitter.

◆ fit()

void fit ( FeatureFinderAlgorithmPickedHelperStructs::MassTraces & traces )

virtual

Main method of the TraceFitter which triggers the actual fitting.

Implements TraceFitter.

◆ getAlphaBoundaries_()

std::pair<double, double> getAlphaBoundaries_ ( const double alpha ) const

protected

Return an ordered pair of the positions where the EGH reaches a height of alpha * height of the EGH.

Parameters

alpha The alpha at which the boundaries should be computed

◆ getArea()

double getArea ( )

virtual

Returns the peak area of the fitted model

Implements TraceFitter.

◆ getCenter()

double getCenter ( ) const

virtual

Returns the center position of the fitted model

Implements TraceFitter.

◆ getFWHM()

double getFWHM ( ) const

virtual

Returns the mass trace width at half max (FWHM)

Implements TraceFitter.

◆ getGnuplotFormula()

String getGnuplotFormula	(	const FeatureFinderAlgorithmPickedHelperStructs::MassTrace &	trace,
		const char	function_name,
		const double	baseline,
		const double	rt_shift
	)

virtual

Returns a textual representation of the fitted model function, that can be plotted using Gnuplot

Parameters

trace	The mass trace that should be plotted
function_name	The name of the function (e.g. f(x) -> function_name = f)
baseline	The intensity of the baseline
rt_shift	A shift value, that allows to plot all RT profiles side by side, even if they would overlap in reality. This should be 0 for the first mass trace and increase by a fixed value for each mass trace.

Implements TraceFitter.

◆ getHeight()

double getHeight ( ) const

virtual

Returns the height of the fitted model

Implements TraceFitter.

◆ getLowerRTBound()

double getLowerRTBound ( ) const

virtual

Returns the lower bound of the fitted RT model

Implements TraceFitter.

◆ getOptimizedParameters_()

void getOptimizedParameters_ ( const Eigen::VectorXd & )

protectedvirtual

Updates all member variables to the fitted values stored in the solver.

Parameters

s	The solver containing the fitted parameter values.

Implements TraceFitter.

◆ getSigma()

double getSigma ( ) const

◆ getTau()

double getTau ( ) const

◆ getUpperRTBound()

double getUpperRTBound ( ) const

virtual

Returns the upper bound of the fitted RT model

Implements TraceFitter.

◆ getValue()

double getValue ( double rt ) const

virtual

Evaluate the fitted model at a time point

Implements TraceFitter.

◆ operator=()

EGHTraceFitter& operator= ( const EGHTraceFitter & source )

◆ setInitialParameters_()

void setInitialParameters_ ( FeatureFinderAlgorithmPickedHelperStructs::MassTraces & traces )

protected

◆ updateMembers_()

virtual void updateMembers_ ( )

protectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from TraceFitter.

Member Data Documentation

◆ apex_rt_

double apex_rt_

protected

◆ EPSILON_COEFS_

const double EPSILON_COEFS_[]

staticprotected

Coefficients to calculate the proportionality factor for the peak area.

◆ height_

double height_

protected

◆ NUM_PARAMS_

const Size NUM_PARAMS_

staticprotected

◆ region_rt_span_

double region_rt_span_

protected

◆ sigma_

double sigma_

protected

◆ sigma_5_bound_

std::pair<double, double> sigma_5_bound_

protected

◆ tau_

double tau_

protected

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ EGHTraceFitter() [1/2]

◆ EGHTraceFitter() [2/2]

◆ ~EGHTraceFitter()

Member Function Documentation

◆ checkMaximalRTSpan()

◆ checkMinimalRTSpan()

◆ fit()

◆ getAlphaBoundaries_()

◆ getArea()

◆ getCenter()

◆ getFWHM()

◆ getGnuplotFormula()

◆ getHeight()

◆ getLowerRTBound()

◆ getOptimizedParameters_()

◆ getSigma()

◆ getTau()

◆ getUpperRTBound()

◆ getValue()

◆ operator=()

◆ setInitialParameters_()

◆ updateMembers_()

Member Data Documentation

◆ apex_rt_

◆ EPSILON_COEFS_

◆ height_

◆ NUM_PARAMS_

◆ region_rt_span_

◆ sigma_

◆ sigma_5_bound_

◆ tau_