Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgFitter1D.h>

Inheritance diagram for EmgFitter1D:

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Collaboration diagram for EmgFitter1D:

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Classes
struct	Data
	Helper struct (contains the size of an area and a raw data container) More...

class	EgmFitterFunctor

Public Member Functions
	EmgFitter1D ()
	Default constructor. More...

	EmgFitter1D (const EmgFitter1D &source)
	copy constructor More...

	~EmgFitter1D () override
	destructor More...

virtual EmgFitter1D &	operator= (const EmgFitter1D &source)
	assignment operator More...

QualityType	fit1d (const RawDataArrayType &range, std::unique_ptr< InterpolationModel > &model) override
	return interpolation model More...

Public Member Functions inherited from LevMarqFitter1D
	LevMarqFitter1D ()
	Default constructor. More...

	LevMarqFitter1D (const LevMarqFitter1D &source)
	copy constructor More...

	~LevMarqFitter1D () override
	destructor More...

virtual LevMarqFitter1D &	operator= (const LevMarqFitter1D &source)
	assignment operator More...

Public Member Functions inherited from Fitter1D
	Fitter1D ()
	Default constructor. More...

	Fitter1D (const Fitter1D &source)
	copy constructor More...

	~Fitter1D () override
	destructor More...

virtual Fitter1D &	operator= (const Fitter1D &source)
	assignment operator More...

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...

Static Public Member Functions
static Fitter1D *	create ()
	create new EmgFitter1D object (function needed by Factory) More...

static const String	getProductName ()
	name of the model (needed by Factory) More...

Static Public Member Functions inherited from Fitter1D
static void	registerChildren ()
	register all derived classes here More...

Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions
virtual void	setInitialParameters_ (const RawDataArrayType &set)
	Compute start parameter. More...

void	setInitialParametersMOM_ (const RawDataArrayType &set)

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 LevMarqFitter1D
void	optimize_ (Eigen::VectorXd &x_init, GenericFunctor &functor) const
	Optimize start parameter. More...

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 DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
CoordinateType	height_
	Parameter of emg - peak height. More...

CoordinateType	width_
	Parameter of emg - peak width. More...

CoordinateType	symmetry_
	Parameter of emg - peak symmetry. More...

CoordinateType	retention_
	Parameter of emg - peak retention time. More...

Protected Attributes inherited from LevMarqFitter1D
bool	symmetric_
	Parameter indicates symmetric peaks. More...

Int	max_iteration_
	Maximum number of iterations. More...

Protected Attributes inherited from Fitter1D
CoordinateType	tolerance_stdev_box_
	standard derivation in bounding box More...

Math::BasicStatistics	statistics_
	basic statistics More...

CoordinateType	interpolation_step_
	interpolation step size 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...

Additional Inherited Members
Public Types inherited from LevMarqFitter1D
typedef std::vector< double >	ContainerType

Public Types inherited from Fitter1D
typedef IsotopeCluster::IndexSet	IndexSet
	IndexSet. More...

typedef IsotopeCluster::ChargedIndexSet	ChargedIndexSet
	IndexSet with charge information. More...

typedef Feature::CoordinateType	CoordinateType
	Single coordinate. More...

typedef Feature::QualityType	QualityType
	Quality of a feature. More...

typedef Peak1D	PeakType
	Peak type data point type. More...

typedef std::vector< PeakType >	RawDataArrayType
	Peak type data container type using for the temporary storage of the input data. More...

typedef RawDataArrayType::iterator	PeakIterator
	Peak type data iterator. More...

Public Types inherited from FeatureFinderDefs
enum	Flag { UNUSED , USED }
	Flags that indicate if a peak is already used in a feature. More...

typedef IsotopeCluster::IndexPair	IndexPair
	Index to peak consisting of two UInts (scan index / peak index) More...

typedef IsotopeCluster::ChargedIndexSet	ChargedIndexSet
	Index to peak consisting of two UInts (scan index / peak index) with charge information. More...

typedef IsotopeCluster::IndexSet	IndexSet
	A set of peak indices. More...

Detailed Description

Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
interpolation_step	float	0.2		Sampling rate for the interpolation of the model function.
tolerance_stdev_bounding_box	float	3.0		Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data.
max_iteration	int	500		Maximum number of iterations using by Levenberg-Marquardt algorithm.
init_mom	string	false	true, false	Initialize parameters using method of moments estimators.
statistics:mean	float	1.0		Centroid position of the model.
statistics:variance	float	1.0		Variance of the model.

Note:

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

Class Documentation

◆ OpenMS::EmgFitter1D::Data

struct OpenMS::EmgFitter1D::Data

Helper struct (contains the size of an area and a raw data container)

Collaboration diagram for EmgFitter1D::Data:

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Class Members
typedef Peak1D	PeakType
typedef vector< PeakType >	RawDataArrayType

Class Members
Size	n
RawDataArrayType	set

Constructor & Destructor Documentation

◆ EmgFitter1D() [1/2]

EmgFitter1D ( )

Default constructor.

◆ EmgFitter1D() [2/2]

EmgFitter1D ( const EmgFitter1D & source )

copy constructor

◆ ~EmgFitter1D()

~EmgFitter1D ( )

override

destructor

Member Function Documentation

◆ create()

static Fitter1D* create ( )

inlinestatic

create new EmgFitter1D object (function needed by Factory)

◆ fit1d()

QualityType fit1d	(	const RawDataArrayType &	range,
		std::unique_ptr< InterpolationModel > &	model
	)

overridevirtual

return interpolation model

Reimplemented from Fitter1D.

Referenced by EmgScoring::fitRT_().

◆ getProductName()

static const String getProductName ( )

inlinestatic

name of the model (needed by Factory)

◆ operator=()

virtual EmgFitter1D& operator= ( const EmgFitter1D & source )

virtual

assignment operator

◆ setInitialParameters_()

virtual void setInitialParameters_ ( const RawDataArrayType & set )

protectedvirtual

Compute start parameter.

◆ setInitialParametersMOM_()

void setInitialParametersMOM_ ( const RawDataArrayType & set )

protected

Compute start parameters using method of moments (usually reduces nr. of iterations needed at some additional one-time costs

◆ 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_

CoordinateType height_

protected

Parameter of emg - peak height.

◆ retention_

CoordinateType retention_

protected

Parameter of emg - peak retention time.

◆ symmetry_

CoordinateType symmetry_

protected

Parameter of emg - peak symmetry.

◆ width_

CoordinateType width_

protected

Parameter of emg - peak width.

Classes

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::EmgFitter1D::Data

Constructor & Destructor Documentation

◆ EmgFitter1D() [1/2]

◆ EmgFitter1D() [2/2]

◆ ~EmgFitter1D()

Member Function Documentation

◆ create()

◆ fit1d()

◆ getProductName()

◆ operator=()

◆ setInitialParameters_()

◆ setInitialParametersMOM_()

◆ updateMembers_()

Member Data Documentation

◆ height_

◆ retention_

◆ symmetry_

◆ width_