SignalToNoiseEstimatorMedian< Container > Class Template Reference

Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based) More...

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

Inheritance diagram for SignalToNoiseEstimatorMedian< Container >:

Public Types
enum	IntensityThresholdCalculation { MANUAL = -1 , AUTOMAXBYSTDEV = 0 , AUTOMAXBYPERCENT = 1 }
	method to use for estimating the maximal intensity that is used for histogram calculation More...
typedef SignalToNoiseEstimator< Container >::PeakIterator	PeakIterator
typedef SignalToNoiseEstimator< Container >::PeakType	PeakType
typedef SignalToNoiseEstimator< Container >::GaussianEstimate	GaussianEstimate
Public Types inherited from SignalToNoiseEstimator< Container >
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
	SignalToNoiseEstimatorMedian ()
	default constructor
	SignalToNoiseEstimatorMedian (const SignalToNoiseEstimatorMedian &source)
	Copy Constructor.
Public Member Functions inherited from SignalToNoiseEstimator< Container >
	SignalToNoiseEstimator ()
	Constructor.
	SignalToNoiseEstimator (const SignalToNoiseEstimator &source)
	Copy constructor.
SignalToNoiseEstimator &	operator= (const SignalToNoiseEstimator &source)
	Assignment operator.
	~SignalToNoiseEstimator () override
	Destructor.
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.
virtual double	getSignalToNoise (const Size index) const
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.
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor.
virtual	~ProgressLogger ()
	Destructor.
	ProgressLogger (const ProgressLogger &other)
	Copy constructor.
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator.
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE!
LogType	getLogType () const
	Returns the type of progress log being used.
void	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging.
void	startProgress (SignedSize begin, SignedSize end, const std::string &label) const
	Initializes the progress display.
void	setProgress (SignedSize value) const
	Sets the current progress.
void	endProgress (UInt64 bytes_processed=0) const
void	nextProgress () const
	increment progress by 1 (according to range begin-end)

Assignment
double	max_intensity_
	maximal intensity considered during binning (values above get discarded)
double	auto_max_stdev_Factor_
	parameter for initial automatic estimation of "max_intensity_": a stdev multiplier
double	auto_max_percentile_
	parameter for initial automatic estimation of "max_intensity_" percentile or a stdev
int	auto_mode_
	determines which method shall be used for estimating "max_intensity_". valid are MANUAL=-1, AUTOMAXBYSTDEV=0 or AUTOMAXBYPERCENT=1
double	win_len_
	range of data points which belong to a window in Thomson
int	bin_count_
	number of bins in the histogram
int	min_required_elements_
	minimal number of elements a window needs to cover to be used
double	noise_for_empty_window_
bool	write_log_messages_
double	sparse_window_percent_
double	histogram_oob_percent_
SignalToNoiseEstimatorMedian &	operator= (const SignalToNoiseEstimatorMedian &source)
	~SignalToNoiseEstimatorMedian () override
	Destructor.
double	getSparseWindowPercent () const
	Returns how many percent of the windows were sparse.
double	getHistogramRightmostPercent () const
	Returns the percentage where the median was found in the rightmost bin.
void	computeSTN_ (const Container &c) override
void	updateMembers_ () override
	overridden function from DefaultParamHandler to keep members up to date, when a parameter is changed

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.
Protected Member Functions inherited from SignalToNoiseEstimator< Container >
GaussianEstimate	estimate_ (const PeakIterator &scan_first_, const PeakIterator &scan_last_) const
	calculate mean & stdev of intensities of a spectrum
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor.
Protected Attributes inherited from SignalToNoiseEstimator< Container >
std::vector< double >	stn_estimates_
	stores the noise estimate for each peak
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;.
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::SignalToNoiseEstimatorMedian< Container >

Estimates the signal/noise (S/N) ratio of each data point in a scan by using the median (histogram based)

For each datapoint in the given scan, we collect a range of data points around it (param: win_len). The noise for a datapoint is estimated to be the median of the intensities of the current window. If the number of elements in the current window is not sufficient (param: MinReqElements), the noise level is set to a default value (param: noise_for_empty_window). The whole computation is histogram based, so the user will need to supply a number of bins (param: bin_count), which determines the level of error and runtime. The maximal intensity for a datapoint to be included in the histogram can be either determined automatically (params: AutoMaxIntensity, auto_mode) by two different methods or can be set directly by the user (param: max_intensity). Within the histogram bin that contains the median, the noise value is linearly interpolated between that bin's edges (assuming a uniform distribution of points within the bin), rather than using the bin's center. This keeps the estimate close to continuous as the underlying data changes, instead of only ever taking one of bin_count discrete values. If the (estimated) max_intensity value is too low and the median is found to be in the last (&highest) bin, a warning will be given. In this case you should increase max_intensity (and optionally the bin_count).

Changing any of the parameters will invalidate the S/N values (which will invoke a recomputation on the next request).

Note

If more than 20 percent of windows have less than min_required_elements of elements, a warning is issued to OPENMS_LOG_WARN and noise estimates in those windows are set to the constant noise_for_empty_window.

If more than 1 percent of median estimations had to rely on the last(=rightmost) bin (which gives an unreliable result), a warning is issued to OPENMS_LOG_WARN. In this case you should increase max_intensity (and optionally the bin_count).

You can disable logging this error by setting write_log_messages and read out the values

@htmlinclude OpenMS_SignalToNoiseEstimatorMedian.parameters

Member Typedef Documentation

GaussianEstimate

template<typename Container = MSSpectrum>

typedef SignalToNoiseEstimator<Container>::GaussianEstimate GaussianEstimate

PeakIterator

template<typename Container = MSSpectrum>

typedef SignalToNoiseEstimator<Container>::PeakIterator PeakIterator

PeakType

template<typename Container = MSSpectrum>

typedef SignalToNoiseEstimator<Container>::PeakType PeakType

Member Enumeration Documentation

IntensityThresholdCalculation

template<typename Container = MSSpectrum>

enum IntensityThresholdCalculation

method to use for estimating the maximal intensity that is used for histogram calculation

Enumerator
MANUAL
AUTOMAXBYSTDEV
AUTOMAXBYPERCENT

Constructor & Destructor Documentation

SignalToNoiseEstimatorMedian() [1/2]

template<typename Container = MSSpectrum>

SignalToNoiseEstimatorMedian ( )

inline

default constructor

References DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), Param::setMaxFloat(), Param::setMaxInt(), Param::setMinFloat(), Param::setMinInt(), DefaultParamHandler::setName(), Param::setValidStrings(), and Param::setValue().

SignalToNoiseEstimatorMedian() [2/2]

template<typename Container = MSSpectrum>

SignalToNoiseEstimatorMedian ( const SignalToNoiseEstimatorMedian< Container > &  source )

inline

Copy Constructor.

References SignalToNoiseEstimatorMedian< Container >::updateMembers_().

~SignalToNoiseEstimatorMedian()

template<typename Container = MSSpectrum>

~SignalToNoiseEstimatorMedian ( )

inlineoverride

Destructor.

Member Function Documentation

computeSTN_()

template<typename Container = MSSpectrum>

void computeSTN_ ( const Container &  c )

inlineoverrideprotectedvirtual

Calculate signal-to-noise values for all data points given, by using a sliding window approach

Parameters

[in]

c

Raw data, usually an MSSpectrum

Exceptions

Throws

Exception::InvalidValue

start progress estimation

Implements SignalToNoiseEstimator< Container >.

References SignalToNoiseEstimatorMedian< Container >::auto_max_percentile_, SignalToNoiseEstimatorMedian< Container >::auto_max_stdev_Factor_, SignalToNoiseEstimatorMedian< Container >::auto_mode_, SignalToNoiseEstimatorMedian< Container >::AUTOMAXBYPERCENT, SignalToNoiseEstimatorMedian< Container >::AUTOMAXBYSTDEV, SignalToNoiseEstimatorMedian< Container >::bin_count_, ProgressLogger::endProgress(), SignalToNoiseEstimator< Container >::estimate_(), SignalToNoiseEstimatorMedian< Container >::histogram_oob_percent_, SignalToNoiseEstimatorMedian< Container >::max_intensity_, SignalToNoiseEstimator< Container >::GaussianEstimate::mean, SignalToNoiseEstimatorMedian< Container >::min_required_elements_, SignalToNoiseEstimatorMedian< Container >::noise_for_empty_window_, OPENMS_LOG_WARN, ProgressLogger::setProgress(), SignalToNoiseEstimatorMedian< Container >::sparse_window_percent_, ProgressLogger::startProgress(), SignalToNoiseEstimator< Container >::stn_estimates_, OpenMS::StringUtils::toStr(), SignalToNoiseEstimator< Container >::GaussianEstimate::variance, SignalToNoiseEstimatorMedian< Container >::win_len_, and SignalToNoiseEstimatorMedian< Container >::write_log_messages_.

getHistogramRightmostPercent()

template<typename Container = MSSpectrum>

double getHistogramRightmostPercent ( ) const

inline

Returns the percentage where the median was found in the rightmost bin.

References SignalToNoiseEstimatorMedian< Container >::histogram_oob_percent_.

getSparseWindowPercent()

template<typename Container = MSSpectrum>

double getSparseWindowPercent ( ) const

inline

Returns how many percent of the windows were sparse.

References SignalToNoiseEstimatorMedian< Container >::sparse_window_percent_.

operator=()

template<typename Container = MSSpectrum>

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

inline

References SignalToNoiseEstimator< Container >::operator=(), and SignalToNoiseEstimatorMedian< Container >::updateMembers_().

updateMembers_()

template<typename Container = MSSpectrum>

void updateMembers_ ( )

inlineoverrideprotectedvirtual

overridden function from DefaultParamHandler to keep members up to date, when a parameter is changed

Reimplemented from DefaultParamHandler.

References SignalToNoiseEstimatorMedian< Container >::auto_max_percentile_, SignalToNoiseEstimatorMedian< Container >::auto_max_stdev_Factor_, SignalToNoiseEstimatorMedian< Container >::auto_mode_, SignalToNoiseEstimatorMedian< Container >::bin_count_, Param::getValue(), SignalToNoiseEstimatorMedian< Container >::max_intensity_, SignalToNoiseEstimatorMedian< Container >::min_required_elements_, SignalToNoiseEstimatorMedian< Container >::noise_for_empty_window_, DefaultParamHandler::param_, SignalToNoiseEstimator< Container >::stn_estimates_, ParamValue::toBool(), SignalToNoiseEstimatorMedian< Container >::win_len_, and SignalToNoiseEstimatorMedian< Container >::write_log_messages_.

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

Member Data Documentation

auto_max_percentile_

template<typename Container = MSSpectrum>

double auto_max_percentile_

protected

parameter for initial automatic estimation of "max_intensity_" percentile or a stdev

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

auto_max_stdev_Factor_

template<typename Container = MSSpectrum>

double auto_max_stdev_Factor_

protected

parameter for initial automatic estimation of "max_intensity_": a stdev multiplier

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

auto_mode_

template<typename Container = MSSpectrum>

int auto_mode_

protected

determines which method shall be used for estimating "max_intensity_". valid are MANUAL=-1, AUTOMAXBYSTDEV=0 or AUTOMAXBYPERCENT=1

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

bin_count_

template<typename Container = MSSpectrum>

int bin_count_

protected

number of bins in the histogram

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

histogram_oob_percent_

template<typename Container = MSSpectrum>

double histogram_oob_percent_

protected

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

max_intensity_

template<typename Container = MSSpectrum>

double max_intensity_

protected

maximal intensity considered during binning (values above get discarded)

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

min_required_elements_

template<typename Container = MSSpectrum>

int min_required_elements_

protected

minimal number of elements a window needs to cover to be used

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

noise_for_empty_window_

template<typename Container = MSSpectrum>

double noise_for_empty_window_

protected

used as noise value for windows which cover less than "min_required_elements_" use a very high value if you want to get a low S/N result

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

sparse_window_percent_

template<typename Container = MSSpectrum>

double sparse_window_percent_

protected

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

win_len_

template<typename Container = MSSpectrum>

double win_len_

protected

range of data points which belong to a window in Thomson

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

write_log_messages_

template<typename Container = MSSpectrum>

bool write_log_messages_

protected

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