Fitter for RT profiles using a Gaussian background model. More...

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

Inheritance diagram for GaussTraceFitter:

Classes
class	GaussTraceFunctor

Public Member Functions
	GaussTraceFitter ()

	GaussTraceFitter (const GaussTraceFitter &other)

GaussTraceFitter &	operator= (const GaussTraceFitter &source)

	~GaussTraceFitter () override

void	fit (FeatureFinderAlgorithmPickedHelperStructs::MassTraces &traces) override

double	getLowerRTBound () const override

double	getUpperRTBound () const override

double	getHeight () const override

double	getCenter () const override

double	getFWHM () const override

double	getSigma () const
	Returns the sigma of the fitted gaussian model. More...

bool	checkMaximalRTSpan (const double max_rt_span) override

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

double	getValue (double rt) const override

double	getArea () override

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

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...

	~TraceFitter () override
	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
void	getOptimizedParameters_ (const Eigen::VectorXd &x_init) override

void	setInitialParameters_ (FeatureFinderAlgorithmPickedHelperStructs::MassTraces &traces)

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

Protected Member Functions inherited from TraceFitter
void	updateMembers_ () override
	This method is used to update extra member variables at the end of the setParameters() method. More...

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	sigma_

double	x0_

double	height_

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 Size	NUM_PARAMS_

Detailed Description

Fitter for RT profiles using a Gaussian background model.

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.

Todo:: More docu

Constructor & Destructor Documentation

◆ GaussTraceFitter() [1/2]

GaussTraceFitter ( )

◆ GaussTraceFitter() [2/2]

GaussTraceFitter ( const GaussTraceFitter & other )

◆ ~GaussTraceFitter()

~GaussTraceFitter ( )

override

Member Function Documentation

◆ checkMaximalRTSpan()

bool checkMaximalRTSpan ( const double max_rt_span )

overridevirtual

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
	)

overridevirtual

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 )

overridevirtual

Main method of the TraceFitter which triggers the actual fitting.

Implements TraceFitter.

◆ getArea()

double getArea ( )

overridevirtual

Returns the peak area of the fitted model

Implements TraceFitter.

◆ getCenter()

double getCenter ( ) const

overridevirtual

Returns the center position of the fitted model

Implements TraceFitter.

◆ getFWHM()

double getFWHM ( ) const

overridevirtual

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
	)

overridevirtual

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

overridevirtual

Returns the height of the fitted model

Implements TraceFitter.

◆ getLowerRTBound()

double getLowerRTBound ( ) const

overridevirtual

Returns the lower bound of the fitted RT model

Implements TraceFitter.

◆ getOptimizedParameters_()

void getOptimizedParameters_ ( const Eigen::VectorXd & )

overrideprotectedvirtual

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

Returns the sigma of the fitted gaussian model.

◆ getUpperRTBound()

double getUpperRTBound ( ) const

overridevirtual

Returns the upper bound of the fitted RT model

Implements TraceFitter.

◆ getValue()

double getValue ( double rt ) const

overridevirtual

Evaluate the fitted model at a time point

Implements TraceFitter.

◆ operator=()

GaussTraceFitter& operator= ( const GaussTraceFitter & source )

◆ setInitialParameters_()

void setInitialParameters_ ( FeatureFinderAlgorithmPickedHelperStructs::MassTraces & traces )

protected

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

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 DefaultParamHandler.

Member Data Documentation

◆ height_

double height_

protected

◆ NUM_PARAMS_

const Size NUM_PARAMS_

staticprotected

◆ region_rt_span_

double region_rt_span_

protected

◆ sigma_

double sigma_

protected

◆ x0_

double x0_

protected

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ GaussTraceFitter() [1/2]

◆ GaussTraceFitter() [2/2]

◆ ~GaussTraceFitter()

Member Function Documentation

◆ checkMaximalRTSpan()

◆ checkMinimalRTSpan()

◆ fit()

◆ getArea()

◆ getCenter()

◆ getFWHM()

◆ getGnuplotFormula()

◆ getHeight()

◆ getLowerRTBound()

◆ getOptimizedParameters_()

◆ getSigma()

◆ getUpperRTBound()

◆ getValue()

◆ operator=()

◆ setInitialParameters_()

◆ updateMembers_()

Member Data Documentation

◆ height_

◆ NUM_PARAMS_

◆ region_rt_span_

◆ sigma_

◆ x0_