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

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

Inheritance diagram for SignalToNoiseEstimator< Container >:

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

Public Types
Type definitions
typedef Container::const_iterator	PeakIterator

typedef PeakIterator::value_type	PeakType

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

Public Member Functions
	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 PeakIterator &it_begin, const PeakIterator &it_end)
	Set the start and endpoint of the raw data interval, for which signal to noise ratios will be estimated immediately. 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 PeakIterator &data_point)

virtual double	getSignalToNoise (const PeakType &data_point)

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...

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

	~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	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 () const
	Ends the progress display. More...

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Protected Member Functions
virtual void	computeSTN_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_)=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...

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
std::map< PeakType, double, typename PeakType::PositionLess >	stn_estimates_
	stores the noise estimate for each peak More...

PeakIterator	first_
	points to the first raw data point in the interval More...

PeakIterator	last_
	points to the right position next to the last raw data point in the interval More...

bool	is_result_valid_
	flag: set to true if SignalToNoise estimates are calculated and none of the params were changed. otherwise false. 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_

Additional Inherited Members
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...

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_).

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 PeakIterator &	scan_first_,
		const PeakIterator &	scan_last_
	)

protectedpure virtual

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

Exceptions

Throws Exception::InvalidValue

Implemented in SignalToNoiseEstimatorMedian< Container >, SignalToNoiseEstimatorMedian< OpenMS::MSChromatogram >, SignalToNoiseEstimatorMedian< ContainerT >, and SignalToNoiseEstimatorMeanIterative< Container >.

Referenced by SignalToNoiseEstimator< ContainerT >::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< ContainerT >::computeSTN_().

◆ getSignalToNoise() [1/2]

virtual double getSignalToNoise ( const PeakIterator & data_point )

inlinevirtual

Return to signal/noise estimate for data point data_point

Note: the first query to this function will take longer, as all SignalToNoise values are calculated; you will get a warning to stderr if more than 20% of the noise estimates used sparse windows

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

◆ getSignalToNoise() [2/2]

virtual double getSignalToNoise ( const PeakType & data_point )

inlinevirtual

◆ init() [1/2]

virtual void init	(	const PeakIterator &	it_begin,
		const PeakIterator &	it_end
	)

inlinevirtual

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

Referenced by SignalToNoiseEstimator< ContainerT >::getSignalToNoise(), SignalToNoiseEstimator< ContainerT >::init(), and SignalToNoiseOpenMS< ContainerT >::SignalToNoiseOpenMS().

◆ init() [2/2]

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.

◆ operator=()

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

inline

Assignment operator.

Member Data Documentation

◆ first_

PeakIterator first_

protected

points to the first raw data point in the interval

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

◆ is_result_valid_

bool is_result_valid_

mutableprotected

flag: set to true if SignalToNoise estimates are calculated and none of the params were changed. otherwise false.

Referenced by SignalToNoiseEstimator< ContainerT >::getSignalToNoise(), SignalToNoiseEstimator< ContainerT >::init(), SignalToNoiseEstimatorMeanIterative< Container >::updateMembers_(), and SignalToNoiseEstimatorMedian< ContainerT >::updateMembers_().

◆ last_

PeakIterator last_

protected

points to the right position next to the last raw data point in the interval

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

◆ stn_estimates_

std::map<PeakType, double, typename PeakType::PositionLess> stn_estimates_

protected

stores the noise estimate for each peak

Referenced by SignalToNoiseEstimatorMeanIterative< Container >::computeSTN_(), SignalToNoiseEstimatorMedian< ContainerT >::computeSTN_(), SignalToNoiseEstimator< ContainerT >::getSignalToNoise(), and SignalToNoiseEstimator< ContainerT >::operator=().

Classes

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

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

Member Typedef Documentation

◆ PeakIterator

◆ PeakType

Constructor & Destructor Documentation

◆ SignalToNoiseEstimator() [1/2]

◆ SignalToNoiseEstimator() [2/2]

◆ ~SignalToNoiseEstimator()

Member Function Documentation

◆ computeSTN_()

◆ estimate_()

◆ getSignalToNoise() [1/2]

◆ getSignalToNoise() [2/2]

◆ init() [1/2]

◆ init() [2/2]

◆ operator=()

Member Data Documentation

◆ first_

◆ is_result_valid_

◆ last_

◆ stn_estimates_

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