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

#include <OpenMS/FEATUREFINDER/EGHTraceFitter.h>

Inheritance diagram for EGHTraceFitter:

Collaboration diagram for EGHTraceFitter:

Classes
class	EGHTraceFunctor

Public Member Functions
	EGHTraceFitter ()

	EGHTraceFitter (const EGHTraceFitter &other)

EGHTraceFitter &	operator= (const EGHTraceFitter &source)

	~EGHTraceFitter () override

void	fit (FeatureFinderAlgorithmPickedHelperStructs::MassTraces &traces) override
	Run the LM fit on `traces`.

double	getLowerRTBound () const override
	Lower RT bound of the fitted RT model.

double	getTau () const

double	getUpperRTBound () const override
	Upper RT bound of the fitted RT model.

double	getHeight () const override
	Height of the fitted RT model at its centre.

double	getSigma () const

double	getCenter () const override
	Centre of the fitted RT model.

bool	checkMaximalRTSpan (const double max_rt_span) override
	Whether the fitted RT model stays within `max_rt_span` of the extended search area.

bool	checkMinimalRTSpan (const std::pair< double, double > &rt_bounds, const double min_rt_span) override
	Whether the fitted RT model covers at least `min_rt_span` of the extended search area.

double	getValue (double rt) const override
	Evaluate the fitted model at retention time `rt`.

double	getArea () override
	Area under the fitted RT model.

double	getFWHM () const override
	Full width at half maximum of the fitted RT model.

std::string	getGnuplotFormula (const FeatureFinderAlgorithmPickedHelperStructs::MassTrace &trace, const char function_name, const double baseline, const double rt_shift) override
	Gnuplot expression of the fitted model for `trace`.

Public Member Functions inherited from TraceFitter
	TraceFitter ()
	Default constructor; registers the `"max_iteration"` and `"weighted"` defaults on DefaultParamHandler.

	TraceFitter (const TraceFitter &source)
	Copy constructor.

TraceFitter &	operator= (const TraceFitter &source)
	Assignment operator.

	~TraceFitter () override
	Destructor.

double	computeTheoretical (const FeatureFinderAlgorithmPickedHelperStructs::MassTrace &trace, Size k) const
	Evaluate the fitted model at the RT of the `k-th` peak of `trace`, scaled by the trace's theoretical intensity.

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

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor.

virtual	~DefaultParamHandler ()
	Destructor.

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

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

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

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

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

const std::string &	getName () const
	Non-mutable access to the name.

void	setName (const std::string &name)
	Mutable access to the name.

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

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.

void	getOptimizedParameters_ (const std::vector< double > &x_init) override
	Subclass hook: copy the optimised parameter vector back into the subclass's model fields.

void	setInitialParameters_ (FeatureFinderAlgorithmPickedHelperStructs::MassTraces &traces)

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

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.

void	optimize_ (std::vector< double > &x_init, GenericFunctor &functor)
	Run Levenberg-Marquardt on `functor` starting from `x_init`.

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

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 LM iterations; refreshed from `"max_iteration"` in updateMembers_.

bool	weighted_
	Whether mass traces are weighted by theoretical intensity during fitting; refreshed from `"weighted"` in updateMembers_.

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

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

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

std::string	error_name_
	Name that is displayed in error messages during the parameter checking.

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

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

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

static const Size	NUM_PARAMS_

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const std::string &key_prefix="")
	Writes all parameters to meta values.

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()

~EGHTraceFitter ( )

override

Member Function Documentation

◆ checkMaximalRTSpan()

bool checkMaximalRTSpan ( const double max_rt_span )

overridevirtual

Whether the fitted RT model stays within max_rt_span of the extended search area.

Parameters

[in] max_rt_span Maximum allowed RT span of the fitted model relative to the extended search area, as a fraction.

Returns: true when the model does not exceed max_rt_span of the search area.

Implements TraceFitter.

◆ checkMinimalRTSpan()

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

overridevirtual

Whether the fitted RT model covers at least min_rt_span of the extended search area.

Parameters

[in]	rt_bounds	RT boundaries of the extended search area (lower, upper).
[in]	min_rt_span	Minimum RT span the fitted model must cover relative to `rt_bounds`, as a fraction.

Returns: true when the model spans at least min_rt_span of the search area.

Implements TraceFitter.

◆ fit()

void fit ( FeatureFinderAlgorithmPickedHelperStructs::MassTraces & traces )

overridevirtual

Run the LM fit on traces.

Subclasses fill the model parameters and (typically) call optimize_ on a problem-specific functor.

Parameters

[in,out] traces Mass traces to fit; subclasses may set additional bookkeeping on traces.

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

[in] alpha The alpha at which the boundaries should be computed

◆ getArea()

double getArea ( )

overridevirtual

Area under the fitted RT model.

Returns: Integrated intensity of the fitted model.

Implements TraceFitter.

◆ getCenter()

double getCenter ( ) const

overridevirtual

Centre of the fitted RT model.

Returns: Centre retention time of the fitted model.

Implements TraceFitter.

◆ getFWHM()

double getFWHM ( ) const

overridevirtual

Full width at half maximum of the fitted RT model.

Returns: FWHM in retention-time units.

Implements TraceFitter.

◆ getGnuplotFormula()

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

overridevirtual

Gnuplot expression of the fitted model for trace.

Parameters

[in]	trace	Mass trace whose theoretical intensity scales the expression.
[in]	function_name	Name of the function in the resulting expression (e.g. `'f'` for `"f(x)"`).
[in]	baseline	Intensity of the plotted baseline.
[in]	rt_shift	RT offset added to the expression so several traces can be plotted side by side (typically `0` for the first trace and incremented for subsequent traces).

Returns: Gnuplot expression as a String.

Implements TraceFitter.

◆ getHeight()

double getHeight ( ) const

overridevirtual

Height of the fitted RT model at its centre.

Returns: Model intensity at the centre RT.

Implements TraceFitter.

◆ getLowerRTBound()

double getLowerRTBound ( ) const

overridevirtual

Lower RT bound of the fitted RT model.

Returns: Lower RT bound (retention-time units).

Implements TraceFitter.

◆ getOptimizedParameters_()

void getOptimizedParameters_ ( const std::vector< double > & s )

overrideprotectedvirtual

Subclass hook: copy the optimised parameter vector back into the subclass's model fields.

Called by optimize_ after the LM solver has converged.

Parameters

[in] s Optimised parameter vector (size matches the functor's inputs).

Implements TraceFitter.

◆ getSigma()

double getSigma ( ) const

◆ getTau()

double getTau ( ) const

◆ getUpperRTBound()

double getUpperRTBound ( ) const

overridevirtual

Upper RT bound of the fitted RT model.

Returns: Upper RT bound (retention-time units).

Implements TraceFitter.

◆ getValue()

double getValue ( double rt ) const

overridevirtual

Evaluate the fitted model at retention time rt.

Parameters

[in] rt Retention time at which to evaluate the model.

Returns: Model intensity at rt.

Implements TraceFitter.

◆ operator=()

EGHTraceFitter & operator= ( const EGHTraceFitter & 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

◆ 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

Additional Inherited Members

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_