This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data). More...

#include <OpenMS/PROCESSING/CENTROIDING/PeakPickerIterative.h>

Inheritance diagram for PeakPickerIterative:

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Collaboration diagram for PeakPickerIterative:

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Public Member Functions
	PeakPickerIterative ()
	Constructor. More...

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

	~PeakPickerIterative () override
	Destructor. More...

void	pick (const MSSpectrum &input, MSSpectrum &output)

void	pickExperiment (const PeakMap &input, PeakMap &output)

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...

Private Member Functions
void	pickRecenterPeaks_ (const MSSpectrum &input, std::vector< PeakCandidate > &PeakCandidates, SignalToNoiseEstimatorMedian< MSSpectrum > &snt) const

Private Attributes
double	signal_to_noise_

double	peak_width_

double	spacing_difference_

int	sn_bin_count_

int	nr_iterations_

double	sn_win_len_

bool	check_width_internally_

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

This class implements a peak-picking algorithm for high-resolution MS data (specifically designed for TOF-MS data).

This peak-picking algorithm detects ion signals in profile data and reconstructs the corresponding peak shape by identifying the left and right borders of the peak. It reports the area under the peak as intensity and the weighted m/z values as the m/z value as well as left/right border. Furthermore, it next tries to improve the peak positioning iteratively using the m/z center computed in the last iteration. This allows for refinement in the peak boundaries and more accurate determination of peak center and borders.

Its approach is similar to the PeakPickerHiRes but additionally uses an iterative approach to find and re-center peaks.

First, it uses the PeakPickerHiRes to find seeds or candidate peaks.
Next it uses n iterations to re-center those peaks and compute left/right borders for each peak.
Finally it removes peaks that are within the borders of other peaks.

So far, this peak picker was mainly tested on high resolution TOF-MS data.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
signal_to_noise_	float	1.0		Signal to noise value, each peak is required to be above this value (turn off by setting it to 0.0)
peak_width	float	0.0		Expected peak width half width in Dalton - peaks will be extended until this half width is reached (even if the intensitity is increasing). In conjunction with check_width_internally it will also be used to remove peaks whose spacing is larger than this value.
spacing_difference	float	1.5		Difference between peaks in multiples of the minimal difference to continue. The higher this value is set, the further apart peaks are allowed to be to still extend a peak. E.g. if the value is set to 1.5 and in a current peak the minimal spacing between peaks is 10 mDa, then only peaks at most 15 mDa apart will be added to the peak.
sn_bin_count_	int	30		Bin count for the Signal to Noise estimation.
nr_iterations_	int	5	min: 1	Nr of iterations to perform (how many times the peaks are re-centered).
sn_win_len_	float	20.0		Window length for the Signal to Noise estimation.
check_width_internally	string	false	true, false	Delete peaks where the spacing is larger than the peak width (should be set to true to avoid artefacts)
ms1_only	string	false	true, false	Only do MS1
clear_meta_data	string	false	true, false	Delete meta data about peak width

Note:

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

Note: The peaks must be sorted according to ascending m/z!

Constructor & Destructor Documentation

◆ PeakPickerIterative()

PeakPickerIterative ( )

inline

Constructor.

◆ ~PeakPickerIterative()

~PeakPickerIterative ( )

inlineoverride

Destructor.

Member Function Documentation

◆ pick()

void pick	(	const MSSpectrum &	input,
		MSSpectrum &	output
	)

inline

References SpectrumSettings::CENTROID, OpenMS::copySpectrumMeta(), DefaultParamHandler::getDefaults(), MSSpectrum::getFloatDataArrays(), DefaultParamHandler::getParameters(), SignalToNoiseEstimator< Container >::init(), OpenMS::Constants::k, OPENMS_LOG_DEBUG, PeakPickerHiRes::pick(), Peak1D::setIntensity(), Peak1D::setMZ(), DefaultParamHandler::setParameters(), SpectrumSettings::setType(), Param::setValue(), OpenMS::sort_peaks_by_intensity(), and MSSpectrum::sortByPosition().

◆ pickExperiment()

void pickExperiment	(	const PeakMap &	input,
		PeakMap &	output
	)

inline

References MSExperiment::clear(), MSExperiment::resize(), and MSExperiment::size().

◆ pickRecenterPeaks_()

void pickRecenterPeaks_	(	const MSSpectrum &	input,
		std::vector< PeakCandidate > &	PeakCandidates,
		SignalToNoiseEstimatorMedian< MSSpectrum > &	snt
	)		const

inlineprivate

References SignalToNoiseEstimator< Container >::getSignalToNoise(), and OpenMS::Constants::k.

◆ updateMembers_()

void updateMembers_ ( )

inlineoverridevirtual

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

◆ check_width_internally_

bool check_width_internally_

private

◆ nr_iterations_

int nr_iterations_

private

◆ peak_width_

double peak_width_

private

◆ signal_to_noise_

double signal_to_noise_

private

◆ sn_bin_count_

int sn_bin_count_

private

◆ sn_win_len_

double sn_win_len_

private

◆ spacing_difference_

double spacing_difference_

private

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PeakPickerIterative()

◆ ~PeakPickerIterative()

Member Function Documentation

◆ pick()

◆ pickExperiment()

◆ pickRecenterPeaks_()

◆ updateMembers_()

Member Data Documentation

◆ check_width_internally_

◆ nr_iterations_

◆ peak_width_

◆ signal_to_noise_

◆ sn_bin_count_

◆ sn_win_len_

◆ spacing_difference_