The PeakPickerMobilogram finds peaks a single mobilogram. More...

#include <OpenMS/ANALYSIS/OPENSWATH/PeakPickerMobilogram.h>

Inheritance diagram for PeakPickerMobilogram:

Collaboration diagram for PeakPickerMobilogram:

Classes
struct	PeakPositions
	Struct to hold peak positions. More...

Public Types
enum	FLOATINDICES { IDX_FWHM = 0 , IDX_ABUNDANCE = 1 , IDX_LEFTBORDER = 2 , IDX_RIGHTBORDER = 3 , IDX_OF_LEFTBORDER_IDX = 4 , IDX_OF_RIGHTBORDER_IDX = 5 , SIZE_OF_FLOATINDICES }
	indices into FloatDataArrays of resulting picked mobilogram More...

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

	~PeakPickerMobilogram () override
	Destructor. More...

void	pickMobilogram (const Mobilogram &mobilogram, Mobilogram &picked_mobilogram)
	Finds peaks in a single mobilogram and annotates left/right borders. More...

void	pickMobilogram (Mobilogram mobilogram, Mobilogram &picked_mobilogram, Mobilogram &smoothed_mobilogram)
	Finds peaks in a single mobilogram and annotates left/right borders. More...

void	filterTopPeak (Mobilogram &picked_mobilogram, std::vector< Mobilogram > &mobilograms, PeakPositions &peak_pos)
	Filters a vector of mobilograms for the highest peak based on the picked mobilogram. More...

void	filterTopPeak (Mobilogram &picked_mobilogram, Mobilogram &mobilogram, PeakPositions &peak_pos)
	Filters a single mobilogram for the highest peak based on the picked mobilogram. 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 Attributes
std::vector< double >	integrated_intensities_
	Temporary vector to hold the integrated intensities. More...

std::vector< Size >	left_width_
	Temporary vector to hold the peak left widths. More...

std::vector< Size >	right_width_
	Temporary vector to hold the peak right widths. More...

Protected Member Functions
void	pickMobilogram_ (const Mobilogram &mobilogram, Mobilogram &picked_mobilogram)

void	integratePeaks_ (const Mobilogram &mobilogram)
	Compute peak area (peak integration) More...

Size	findClosestPeak_ (const Mobilogram &mobilogram, double target_im, Size current_peak=0)
	Helper function to find the closest peak in a mobilogram to "target_im". More...

void	filterPeakIntensities_ (Mobilogram &mobilogram, size_t left_index, size_t right_index)
	Helper function to filter peak intensities in a mobilogram. More...

void	filterPeakIntensities_ (std::vector< Mobilogram > &mobilograms, size_t left_index, size_t right_index)
	Helper function to filter peak intensities for a vector of mobilograms. More...

PeakPositions	filterTopPeak_ (Mobilogram &picked_mobilogram, std::vector< Mobilogram > &mobilograms)
	Filter vector of mobilograms for the highest peak based on the picked mobilogram. More...

PeakPositions	filterTopPeak_ (Mobilogram &picked_mobilogram, Mobilogram &mobilograms)
	Filter single mobilogram for the highest peak based on the picked mobilogram. More...

void	removeOverlappingPeaks_ (const Mobilogram &mobilogram, Mobilogram &picked_mobilogram)
	Helper function to remove overlapping peaks in a single Chromatogram. More...

void	updateMembers_ () override
	Synchronize members with param class. More...

Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Static Protected Member Functions
static PeakPositions	findHighestPeak_ (const std::vector< double > intensities, const std::vector< Size > left_widths, const std::vector< Size > right_widths, const size_t im_size)
	Helper function to find the highest peak in a mobilogram. More...

static std::vector< double >	extractFloatValues_ (const OpenMS::DataArrays::FloatDataArray &floatDataArray)
	Helper function yo convert OpenMS FloatDataArray to a vector of doubles. More...

static std::vector< std::size_t >	extractIntValues_ (const OpenMS::DataArrays::FloatDataArray &floatDataArray)
	Helper function to convert OpenMS IntegerDataArray to a vector of std::size. More...

Protected Attributes
UInt	sgolay_frame_length_
	Frame length for the SGolay smoothing. More...

UInt	sgolay_polynomial_order_
	Polynomial order for the SGolay smoothing. More...

double	gauss_width_
	Width of the Gaussian smoothing. More...

bool	use_gauss_
	Whether to use Gaussian smoothing. More...

bool	remove_overlapping_
	Whether to resolve overlapping peaks. More...

double	peak_width_
	Forced peak with. More...

double	signal_to_noise_
	Signal to noise threshold. More...

double	sn_win_len_
	Signal to noise window length. More...

UInt	sn_bin_count_
	Signal to noise bin count. More...

bool	write_sn_log_messages_
	Whether to write out log messages of the SN estimator. More...

String	method_
	Peak picker method. More...

PeakPickerHiRes	pp_

SavitzkyGolayFilter	sgolay_

GaussFilter	gauss_

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
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...

Detailed Description

The PeakPickerMobilogram finds peaks a single mobilogram.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
sgolay_frame_length	int	9		The number of subsequent data points used for smoothing. This number has to be uneven. If it is not, 1 will be added.
sgolay_polynomial_order	int	3		Order of the polynomial that is fitted.
gauss_width	float	2.0e-03		Gaussian width in seconds, estimated peak size.
use_gauss	string	false	false, true	Use Gaussian filter for smoothing (alternative is Savitzky-Golay filter)
peak_width	float	-1.0		Force a certain minimal peak_width on the data (e.g. extend the peak at least by this amount on both sides) in seconds. -1 turns this feature off.
signal_to_noise	float	1.0	min: 0.0	Signal-to-noise threshold at which a peak will not be extended any more. Note that setting this too high (e.g. 1.0) can lead to peaks whose flanks are not fully captured.
sn_win_len	int	1		Signal to noise window length.
sn_bin_count	int	4		Signal to noise bin count.
write_sn_log_messages	string	false	true, false	Write out log messages of the signal-to-noise estimator in case of sparse windows or median in rightmost histogram bin
remove_overlapping_peaks	string	false	false, true	Try to remove overlapping peaks during peak picking
method	string	corrected	legacy, corrected, crawdad	Which method to choose for mobilogram peak-picking (OpenSWATH legacy on raw data, corrected picking on smoothed mobilogram).

Note:

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

It uses the PeakPickerHiRes internally to find interesting seed candidates. These candidates are then expanded and a right/left border of the peak is searched. Additionally, overlapping peaks can be removed.

Class Documentation

◆ OpenMS::PeakPickerMobilogram::PeakPositions

struct OpenMS::PeakPickerMobilogram::PeakPositions

Struct to hold peak positions.

Collaboration diagram for PeakPickerMobilogram::PeakPositions:

[legend]

Class Members
size_t	apex
size_t	left
size_t	right

Member Enumeration Documentation

◆ FLOATINDICES

enum FLOATINDICES

indices into FloatDataArrays of resulting picked mobilogram

Enumerator
IDX_FWHM
IDX_ABUNDANCE
IDX_LEFTBORDER
IDX_RIGHTBORDER
IDX_OF_LEFTBORDER_IDX
IDX_OF_RIGHTBORDER_IDX
SIZE_OF_FLOATINDICES

Constructor & Destructor Documentation

◆ PeakPickerMobilogram()

PeakPickerMobilogram ( )

Constructor.

◆ ~PeakPickerMobilogram()

~PeakPickerMobilogram ( )

inlineoverride

Destructor.

Member Function Documentation

◆ extractFloatValues_()

static std::vector<double> extractFloatValues_ ( const OpenMS::DataArrays::FloatDataArray & floatDataArray )

staticprotected

Helper function yo convert OpenMS FloatDataArray to a vector of doubles.

Parameters

[in] floatDataArray A const reference to a FloatDataArray object

Returns: A vector of doubles containing the values from the FloatDataArray

◆ extractIntValues_()

static std::vector<std::size_t> extractIntValues_ ( const OpenMS::DataArrays::FloatDataArray & floatDataArray )

staticprotected

Helper function to convert OpenMS IntegerDataArray to a vector of std::size.

Parameters

[in] floatDataArray A const reference to an FloatDataArray object

Returns: A vector of std::size containing the values from the IntegerDataArray

◆ filterPeakIntensities_() [1/2]

void filterPeakIntensities_	(	Mobilogram &	mobilogram,
		size_t	left_index,
		size_t	right_index
	)

protected

Helper function to filter peak intensities in a mobilogram.

This function takes a mobilogram and filters the peak intensities based on the left and right indices provided.

Note: This function modifies the input mobilogram in place.

Parameters

[in,out]	mobilogram	A Mobilogram object
[in]	left_index	The left index of the peak range to filter
[in]	right_index	The right index of the peak range to filter

◆ filterPeakIntensities_() [2/2]

void filterPeakIntensities_	(	std::vector< Mobilogram > &	mobilograms,
		size_t	left_index,
		size_t	right_index
	)

protected

Helper function to filter peak intensities for a vector of mobilograms.

This function takes a vector of mobilograms and filters the peak intensities based on the left and right indices provided.

Note: This function modifies the input mobilograms in place.

Parameters

[in,out]	mobilograms	A vector of Mobilogram objects
[in]	left_index	The left index of the peak range to filter
[in]	right_index	The right index of the peak range to filter

◆ filterTopPeak() [1/2]

void filterTopPeak	(	Mobilogram &	picked_mobilogram,
		Mobilogram &	mobilogram,
		PeakPositions &	peak_pos
	)

Filters a single mobilogram for the highest peak based on the picked mobilogram.

◆ filterTopPeak() [2/2]

void filterTopPeak	(	Mobilogram &	picked_mobilogram,
		std::vector< Mobilogram > &	mobilograms,
		PeakPositions &	peak_pos
	)

Filters a vector of mobilograms for the highest peak based on the picked mobilogram.

◆ filterTopPeak_() [1/2]

PeakPositions filterTopPeak_	(	Mobilogram &	picked_mobilogram,
		Mobilogram &	mobilograms
	)

protected

Filter single mobilogram for the highest peak based on the picked mobilogram.

◆ filterTopPeak_() [2/2]

PeakPositions filterTopPeak_	(	Mobilogram &	picked_mobilogram,
		std::vector< Mobilogram > &	mobilograms
	)

protected

Filter vector of mobilograms for the highest peak based on the picked mobilogram.

◆ findClosestPeak_()

Size findClosestPeak_	(	const Mobilogram &	mobilogram,
		double	target_im,
		Size	current_peak = `0`
	)

protected

Helper function to find the closest peak in a mobilogram to "target_im".

The search will start from the index current_peak, so the function is assuming the closest peak is to the right of current_peak.

It will return the index of the closest peak in the mobilogram.

◆ findHighestPeak_()

static PeakPositions findHighestPeak_	(	const std::vector< double >	intensities,
		const std::vector< Size >	left_widths,
		const std::vector< Size >	right_widths,
		const size_t	im_size
	)

staticprotected

Helper function to find the highest peak in a mobilogram.

This function takes the integrated intensities, left widths, right widths from the peak picker and finds the highest peak in the mobilogram. The left, apex, and right positions of the highest peak are returned.

If the peak picker found no peaks (i.e. intensities is empty), the returned PeakPositions object will have it's left, apex, and right set based on the input im_size. The peak picker could fail if the input mobilogram is sparse.

Note: The left, apex, and right positions are indices into the mobilogram.

Parameters

[in]	intensities	A vector of doubles containing the intensities of the peaks in the mobilogram
[in]	left_widths	A vector of Size values containing the left widths of the peaks in the mobilogram
[in]	right_widths	A vector of Size values containing the right widths of the peaks in the mobilogram
[in]	im_size	The size/length of the mobilogram

Returns: A PeakPositions object containing the left, apex, and right positions of the highest peak in the mobilogram

◆ integratePeaks_()

void integratePeaks_ ( const Mobilogram & mobilogram )

protected

Compute peak area (peak integration)

◆ pickMobilogram() [1/2]

void pickMobilogram	(	const Mobilogram &	mobilogram,
		Mobilogram &	picked_mobilogram
	)

Finds peaks in a single mobilogram and annotates left/right borders.

It uses a modified algorithm of the PeakPickerHiRes

This function will return a picked mobilogram

◆ pickMobilogram() [2/2]

void pickMobilogram	(	Mobilogram	mobilogram,
		Mobilogram &	picked_mobilogram,
		Mobilogram &	smoothed_mobilogram
	)

Finds peaks in a single mobilogram and annotates left/right borders.

It uses a modified algorithm of the PeakPickerHiRes

This function will return a picked mobilogram and a smoothed mobilogram

◆ pickMobilogram_()

void pickMobilogram_	(	const Mobilogram &	mobilogram,
		Mobilogram &	picked_mobilogram
	)

protected

◆ removeOverlappingPeaks_()

void removeOverlappingPeaks_	(	const Mobilogram &	mobilogram,
		Mobilogram &	picked_mobilogram
	)

protected

Helper function to remove overlapping peaks in a single Chromatogram.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ gauss_

GaussFilter gauss_

protected

◆ gauss_width_

double gauss_width_

protected

Width of the Gaussian smoothing.

◆ integrated_intensities_

std::vector<double> integrated_intensities_

Temporary vector to hold the integrated intensities.

◆ left_width_

std::vector<Size> left_width_

Temporary vector to hold the peak left widths.

◆ method_

String method_

protected

Peak picker method.

◆ peak_width_

double peak_width_

protected

Forced peak with.

◆ pp_

PeakPickerHiRes pp_

protected

◆ remove_overlapping_

bool remove_overlapping_

protected

Whether to resolve overlapping peaks.

◆ right_width_

std::vector<Size> right_width_

Temporary vector to hold the peak right widths.

◆ sgolay_

SavitzkyGolayFilter sgolay_

protected

◆ sgolay_frame_length_

UInt sgolay_frame_length_

protected

Frame length for the SGolay smoothing.

◆ sgolay_polynomial_order_

UInt sgolay_polynomial_order_

protected

Polynomial order for the SGolay smoothing.

◆ signal_to_noise_

double signal_to_noise_

protected

Signal to noise threshold.

◆ sn_bin_count_

UInt sn_bin_count_

protected

Signal to noise bin count.

◆ sn_win_len_

double sn_win_len_

protected

Signal to noise window length.

◆ use_gauss_

bool use_gauss_

protected

Whether to use Gaussian smoothing.

◆ write_sn_log_messages_

bool write_sn_log_messages_

protected

Whether to write out log messages of the SN estimator.

Classes

Public Types

Public Member Functions

Public Attributes

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::PeakPickerMobilogram::PeakPositions

Member Enumeration Documentation

◆ FLOATINDICES

Constructor & Destructor Documentation

◆ PeakPickerMobilogram()

◆ ~PeakPickerMobilogram()

Member Function Documentation

◆ extractFloatValues_()

◆ extractIntValues_()

◆ filterPeakIntensities_() [1/2]

◆ filterPeakIntensities_() [2/2]

◆ filterTopPeak() [1/2]

◆ filterTopPeak() [2/2]

◆ filterTopPeak_() [1/2]

◆ filterTopPeak_() [2/2]

◆ findClosestPeak_()

◆ findHighestPeak_()

◆ integratePeaks_()

◆ pickMobilogram() [1/2]

◆ pickMobilogram() [2/2]

◆ pickMobilogram_()

◆ removeOverlappingPeaks_()

◆ updateMembers_()

Member Data Documentation

◆ gauss_

◆ gauss_width_

◆ integrated_intensities_

◆ left_width_

◆ method_

◆ peak_width_

◆ pp_

◆ remove_overlapping_

◆ right_width_

◆ sgolay_

◆ sgolay_frame_length_

◆ sgolay_polynomial_order_

◆ signal_to_noise_

◆ sn_bin_count_

◆ sn_win_len_

◆ use_gauss_

◆ write_sn_log_messages_