This class represents the abstract base class of a signal to noise estimator. More...

#include <OpenMS/PROCESSING/NOISEESTIMATION/SignalToNoiseEstimator.h>

Inheritance diagram for SignalToNoiseEstimator< Container >:

Collaboration diagram for SignalToNoiseEstimator< Container >:

Classes
struct	GaussianEstimate
	protected struct to store parameters my, sigma for a Gaussian distribution More...

Type definitions
typedef Container::const_iterator	PeakIterator

typedef PeakIterator::value_type	PeakType

std::vector< double >	stn_estimates_
	stores the noise estimate for each peak More...

	SignalToNoiseEstimator ()
	Constructor. More...

	SignalToNoiseEstimator (const SignalToNoiseEstimator &source)
	Copy constructor. More...

SignalToNoiseEstimator &	operator= (const SignalToNoiseEstimator &source)
	Assignment operator. More...

	~SignalToNoiseEstimator () override
	Destructor. More...

virtual void	init (const Container &c)
	Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately. More...

virtual double	getSignalToNoise (const Size index) const

virtual void	computeSTN_ (const Container &c)=0
	computes the S/N values when init() is called More...

GaussianEstimate	estimate_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_) const
	calculate mean & stdev of intensities of a spectrum More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD , GUI , NONE }
	Possible log types. 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...

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...

Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...

virtual	~ProgressLogger ()
	Destructor. More...

	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...

ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...

void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...

LogType	getLogType () const
	Returns the type of progress log being used. More...

void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. More...

void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...

void	setProgress (SignedSize value) const
	Sets the current progress. More...

void	endProgress (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) 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 inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

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

Protected Attributes inherited from ProgressLogger
LogType	type_

time_t	last_invoke_

ProgressLoggerImpl *	current_logger_

Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

template<typename Container = MSSpectrum>
class OpenMS::SignalToNoiseEstimator< Container >

This class represents the abstract base class of a signal to noise estimator.

A signal to noise estimator should provide the signal to noise ratio of all raw data points in a given interval [first_,last_).

Class Documentation

◆ OpenMS::SignalToNoiseEstimator::GaussianEstimate

struct OpenMS::SignalToNoiseEstimator::GaussianEstimate

template<typename Container = MSSpectrum>
struct OpenMS::SignalToNoiseEstimator< Container >::GaussianEstimate

protected struct to store parameters my, sigma for a Gaussian distribution

Accessors are : mean and variance

Collaboration diagram for SignalToNoiseEstimator< Container >::GaussianEstimate:

[legend]

Class Members
double	mean	mean of estimated Gaussian
double	variance	variance of estimated Gaussian

Member Typedef Documentation

◆ PeakIterator

typedef Container::const_iterator PeakIterator

◆ PeakType

typedef PeakIterator::value_type PeakType

Constructor & Destructor Documentation

◆ SignalToNoiseEstimator() [1/2]

SignalToNoiseEstimator ( )

inline

Constructor.

◆ SignalToNoiseEstimator() [2/2]

SignalToNoiseEstimator ( const SignalToNoiseEstimator< Container > & source )

inline

Copy constructor.

◆ ~SignalToNoiseEstimator()

~SignalToNoiseEstimator ( )

inlineoverride

Destructor.

Member Function Documentation

◆ computeSTN_()

virtual void computeSTN_ ( const Container & c )

protectedpure virtual

computes the S/N values when init() is called

Exceptions

Throws Exception::InvalidValue

Referenced by SignalToNoiseEstimator< Container >::init().

◆ estimate_()

GaussianEstimate estimate_	(	const PeakIterator &	scan_first_,
		const PeakIterator &	scan_last_
	)		const

inlineprotected

calculate mean & stdev of intensities of a spectrum

Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), and SignalToNoiseEstimatorMedian< Container >::computeSTN_().

◆ getSignalToNoise()

virtual double getSignalToNoise ( const Size index ) const

inlinevirtual

Return to signal/noise estimate for date point index

Note: you will get a warning to stderr if more than 20% of the noise estimates used sparse windows

References OPENMS_POSTCONDITION, and SignalToNoiseEstimator< Container >::stn_estimates_.

Referenced by SignalToNoiseOpenMS< ContainerT >::getValueAtRT(), and PeakPickerIterative::pickRecenterPeaks_().

◆ init()

virtual void init ( const Container & c )

inlinevirtual

Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately.

References OpenMS::Constants::c, and SignalToNoiseEstimator< Container >::computeSTN_().

Referenced by PeakPickerIterative::pick(), and SignalToNoiseOpenMS< ContainerT >::SignalToNoiseOpenMS().

◆ operator=()

SignalToNoiseEstimator& operator= ( const SignalToNoiseEstimator< Container > & source )

inline

Assignment operator.

References DefaultParamHandler::operator=(), ProgressLogger::operator=(), and SignalToNoiseEstimator< Container >::stn_estimates_.

Referenced by SignalToNoiseEstimatorMeanIterative< Container >::operator=(), and SignalToNoiseEstimatorMedian< Container >::operator=().

Member Data Documentation

◆ stn_estimates_

std::vector<double> stn_estimates_

protected

stores the noise estimate for each peak

Referenced by SignalToNoiseEstimator< Container >::getSignalToNoise(), and SignalToNoiseEstimator< Container >::operator=().

Classes

Type definitions

Additional Inherited Members

Detailed Description

template<typename Container = MSSpectrum> class OpenMS::SignalToNoiseEstimator< Container >

Class Documentation

◆ OpenMS::SignalToNoiseEstimator::GaussianEstimate

template<typename Container = MSSpectrum> struct OpenMS::SignalToNoiseEstimator< Container >::GaussianEstimate

Member Typedef Documentation

◆ PeakIterator

◆ PeakType

Constructor & Destructor Documentation

◆ SignalToNoiseEstimator() [1/2]

◆ SignalToNoiseEstimator() [2/2]

◆ ~SignalToNoiseEstimator()

Member Function Documentation

◆ computeSTN_()

◆ estimate_()

◆ getSignalToNoise()

◆ init()

◆ operator=()

Member Data Documentation

◆ stn_estimates_

template<typename Container = MSSpectrum>
class OpenMS::SignalToNoiseEstimator< Container >

template<typename Container = MSSpectrum>
struct OpenMS::SignalToNoiseEstimator< Container >::GaussianEstimate