Compute the area, background and shape metrics of a peak. More...

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

Inheritance diagram for PeakIntegrator:

Collaboration diagram for PeakIntegrator:

Classes
struct	PeakArea

struct	PeakBackground

struct	PeakShapeMetrics

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

	~PeakIntegrator () override
	Destructor. More...

PeakArea	integratePeak (const MSChromatogram &chromatogram, const double left, const double right) const
	Compute the area of a peak contained in a MSChromatogram. More...

PeakArea	integratePeak (const MSChromatogram &chromatogram, MSChromatogram::ConstIterator &left, MSChromatogram::ConstIterator &right) const
	Compute the area of a peak contained in a MSChromatogram. More...

PeakArea	integratePeak (const MSSpectrum &spectrum, const double left, const double right) const
	Compute the area of a peak contained in a MSSpectrum. More...

PeakArea	integratePeak (const MSSpectrum &spectrum, MSSpectrum::ConstIterator &left, MSSpectrum::ConstIterator &right) const
	Compute the area of a peak contained in a MSSpectrum. More...

PeakBackground	estimateBackground (const MSChromatogram &chromatogram, const double left, const double right, const double peak_apex_pos) const
	Estimate the background of a peak contained in a MSChromatogram. More...

PeakBackground	estimateBackground (const MSChromatogram &chromatogram, MSChromatogram::ConstIterator &left, MSChromatogram::ConstIterator &right, const double peak_apex_pos) const
	Estimate the background of a peak contained in a MSChromatogram. More...

PeakBackground	estimateBackground (const MSSpectrum &spectrum, const double left, const double right, const double peak_apex_pos) const
	Estimate the background of a peak contained in a MSSpectrum. More...

PeakBackground	estimateBackground (const MSSpectrum &spectrum, MSSpectrum::ConstIterator &left, MSSpectrum::ConstIterator &right, const double peak_apex_pos) const
	Estimate the background of a peak contained in a MSSpectrum. More...

PeakShapeMetrics	calculatePeakShapeMetrics (const MSChromatogram &chromatogram, const double left, const double right, const double peak_height, const double peak_apex_pos) const
	Calculate peak's shape metrics. More...

PeakShapeMetrics	calculatePeakShapeMetrics (const MSChromatogram &chromatogram, MSChromatogram::ConstIterator &left, MSChromatogram::ConstIterator &right, const double peak_height, const double peak_apex_pos) const
	Calculate peak's shape metrics. More...

PeakShapeMetrics	calculatePeakShapeMetrics (const MSSpectrum &spectrum, const double left, const double right, const double peak_height, const double peak_apex_pos) const
	Calculate peak's shape metrics. More...

PeakShapeMetrics	calculatePeakShapeMetrics (const MSSpectrum &spectrum, MSSpectrum::ConstIterator &left, MSSpectrum::ConstIterator &right, const double peak_height, const double peak_apex_pos) const
	Calculate peak's shape metrics. More...

void	getDefaultParameters (Param &params)

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...

Static Public Attributes
Constant expressions for parameters
Constants expressions used throughout the code and tests to set the integration and baseline types.
static constexpr const char *	INTEGRATION_TYPE_INTENSITYSUM = "intensity_sum"

static constexpr const char *	INTEGRATION_TYPE_TRAPEZOID = "trapezoid"
	Integration type: trapezoid. More...

static constexpr const char *	INTEGRATION_TYPE_SIMPSON = "simpson"
	Integration type: simpson. More...

static constexpr const char *	BASELINE_TYPE_BASETOBASE = "base_to_base"
	Baseline type: base to base. More...

static constexpr const char *	BASELINE_TYPE_VERTICALDIVISION = "vertical_division"
	Baseline type: vertical division (min of end points; only for backwards compatibility) More...

static constexpr const char *	BASELINE_TYPE_VERTICALDIVISION_MIN = "vertical_division_min"
	Baseline type: vertical division (min of end points) More...

static constexpr const char *	BASELINE_TYPE_VERTICALDIVISION_MAX = "vertical_division_max"
	Baseline type: vertical division (max of end points) More...

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

template<typename PeakContainerT >
PeakArea	integratePeak_ (const PeakContainerT &pc, double left, double right) const

template<typename PeakContainerT >
PeakBackground	estimateBackground_ (const PeakContainerT &pc, double left, double right, const double peak_apex_pos) const

template<typename PeakContainerConstIteratorT >
double	simpson_ (PeakContainerConstIteratorT it_begin, PeakContainerConstIteratorT it_end) const
	Simpson's rule algorithm. More...

template<typename PeakContainerT >
PeakShapeMetrics	calculatePeakShapeMetrics_ (const PeakContainerT &pc, double left, double right, const double peak_height, const double peak_apex_pos) const

template<typename PeakContainerConstIteratorT >
double	findPosAtPeakHeightPercent_ (PeakContainerConstIteratorT it_left, PeakContainerConstIteratorT it_right, PeakContainerConstIteratorT it_end, const double peak_height, const double percent, const bool is_left_half) const
	Find the position (RT/MZ) at a given percentage of peak's height. More...

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

Private Member Functions
template<typename PeakContainerT >
const PeakContainerT &	EMGPreProcess_ (const PeakContainerT &pc, PeakContainerT &emg_pc, double &left, double &right) const
	Fit the peak to the EMG model. More...

Private Attributes
bool	fit_EMG_
	Enable/disable EMG peak model fitting. More...

EmgGradientDescent	emg_

Parameters
The user is supposed to select a value for these parameters. By default, the integration_type_ is "intensity_sum" and the baseline_type_ is "base_to_base".
String	integration_type_ = INTEGRATION_TYPE_INTENSITYSUM

String	baseline_type_ = BASELINE_TYPE_BASETOBASE

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...

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...

Detailed Description

Compute the area, background and shape metrics of a peak.

The area computation is performed in integratePeak() and it supports integration by simple sum of the intensity, integration by Simpson's rule implementations for an odd number of unequally spaced points or integration by the trapezoid rule.

The background computation is performed in estimateBackground() and it supports three different approaches to baseline correction, namely computing a rectangular shape under the peak based on the minimum value of the peak borders (vertical_division_min), a rectangular shape based on the maximum value of the beak borders (vertical_division_max) or a trapezoidal shape based on a straight line between the peak borders (base_to_base).

Peak shape metrics are computed in calculatePeakShapeMetrics() and multiple metrics are supported.

The containers supported by the methods are MSChromatogram and MSSpectrum.

Warning: integratePeak() using Simpson's rule can result in negative areas despite strictly positive intensities in the input dataset. An example is given in the class test (see area = -665788.77).

Class Documentation

◆ OpenMS::PeakIntegrator::PeakArea

struct OpenMS::PeakIntegrator::PeakArea

Collaboration diagram for PeakIntegrator::PeakArea:

[legend]

Class Members
double	apex_pos	The position of the point with highest intensity
double	area	The peak's computed area
double	height	The peak's highest intensity
PointArrayType	hull_points	The peak's hull points

◆ OpenMS::PeakIntegrator::PeakBackground

struct OpenMS::PeakIntegrator::PeakBackground

Collaboration diagram for PeakIntegrator::PeakBackground:

[legend]

Class Members
double	area	The background area estimation
double	height	The background height

◆ OpenMS::PeakIntegrator::PeakShapeMetrics

struct OpenMS::PeakIntegrator::PeakShapeMetrics

Collaboration diagram for PeakIntegrator::PeakShapeMetrics:

[legend]

Class Members
double	asymmetry_factor	The asymmetry factor is a measure of peak tailing. It is defined as the distance from the center line of the peak to the back slope divided by the distance from the center line of the peak to the front slope, with all measurements made at 10% of the maximum peak height. asymmetry_factor = As = b/a where a is min width to peak maximum at 10% max peak height b is max width to peak maximum at 10% max peak height
double	baseline_delta_2_height	The change in baseline divided by the height is a way of comparing the influence of the change of baseline on the peak height.
double	end_position_at_10	The end position at which the intensity is 10% the peak's height.
double	end_position_at_5	The end position at which the intensity is 5% the peak's height.
double	end_position_at_50	The end position at which the intensity is 50% the peak's height.
Int	points_across_baseline	The number of points across the baseline.
Int	points_across_half_height	The number of points across half the peak's height.
double	slope_of_baseline	The slope of the baseline is a measure of slope change. It is approximated as the difference in baselines between the peak start and peak end.
double	start_position_at_10	The start position at which the intensity is 10% the peak's height.
double	start_position_at_5	The start position at which the intensity is 5% the peak's height.
double	start_position_at_50	The start position at which the intensity is 50% the peak's height.
double	tailing_factor	The tailing factor is a measure of peak tailing. It is defined as the distance from the front slope of the peak to the back slope divided by twice the distance from the center line of the peak to the front slope, with all measurements made at 5% of the maximum peak height. tailing_factor = Tf = W0.05/2a where W0.05 is peak width at 5% max peak height a = min width to peak maximum at 5% max peak height b = max width to peak maximum at 5% max peak height 0.9 < Tf < 1.2 front Tf < 0.9 tailing Tf > 1.2
double	total_width	The peak's total width.
double	width_at_10	The width of the peak at 10% the peak's height.
double	width_at_5	The width of the peak at 5% the peak's height.
double	width_at_50	The width of the peak at 50% the peak's height.

Constructor & Destructor Documentation

◆ PeakIntegrator()

PeakIntegrator ( )

Constructor.

◆ ~PeakIntegrator()

~PeakIntegrator ( )

override

Destructor.

Member Function Documentation

◆ calculatePeakShapeMetrics() [1/4]

PeakShapeMetrics calculatePeakShapeMetrics	(	const MSChromatogram &	chromatogram,
		const double	left,
		const double	right,
		const double	peak_height,
		const double	peak_apex_pos
	)		const

Calculate peak's shape metrics.

The calculated characteristics are the start and end times at 0.05, 0.10 and 0.5 the peak's height. Also the widths at those positions are calculated. Other values: the peak's total width, its tailing factor, asymmetry factor, baseline delta to height and the slope of the baseline. The number of points across the baseline and also at half height are saved.

Note: Make sure the chromatogram is sorted with respect to retention time.

Parameters

[in]	chromatogram	The chromatogram which contains the peak
[in]	left	The left retention time boundary
[in]	right	The right retention time boundary
[in]	peak_height	The peak's highest intensity
[in]	peak_apex_pos	The position of the point with highest intensity

Returns: A struct containing the calculated peak shape metrics

◆ calculatePeakShapeMetrics() [2/4]

PeakShapeMetrics calculatePeakShapeMetrics	(	const MSChromatogram &	chromatogram,
		MSChromatogram::ConstIterator &	left,
		MSChromatogram::ConstIterator &	right,
		const double	peak_height,
		const double	peak_apex_pos
	)		const

Calculate peak's shape metrics.

The calculated characteristics are the start and end times at 0.05, 0.10 and 0.5 the peak's height. Also the widths at those positions are calculated. Other values: the peak's total width, its tailing factor, asymmetry factor, baseline delta to height and the slope of the baseline. The number of points across the baseline and also at half height are saved.

Note: Make sure the chromatogram is sorted with respect to retention time.

Parameters

[in]	chromatogram	The chromatogram which contains the peak
[in]	left	The iterator to the first point
[in]	right	The iterator to the last point
[in]	peak_height	The peak's highest intensity
[in]	peak_apex_pos	The position of the point with highest intensity

Returns: A struct containing the calculated peak shape metrics

◆ calculatePeakShapeMetrics() [3/4]

PeakShapeMetrics calculatePeakShapeMetrics	(	const MSSpectrum &	spectrum,
		const double	left,
		const double	right,
		const double	peak_height,
		const double	peak_apex_pos
	)		const

Calculate peak's shape metrics.

The calculated characteristics are the start and end positions at 0.05, 0.10 and 0.5 the peak's height. Also the widths at those positions are calculated. Other values: the peak's total width, its tailing factor, asymmetry factor, baseline delta to height and the slope of the baseline. The number of points across the baseline and also at half height are saved.

Note: Make sure the spectrum is sorted with respect to mass-to-charge ratio.

Parameters

[in]	spectrum	The spectrum which contains the peak
[in]	left	The left mass-to-charge ratio boundary
[in]	right	The right mass-to-charge ratio boundary
[in]	peak_height	The peak's highest intensity
[in]	peak_apex_pos	The position of the point with highest intensity

Returns: A struct containing the calculated peak shape metrics

◆ calculatePeakShapeMetrics() [4/4]

PeakShapeMetrics calculatePeakShapeMetrics	(	const MSSpectrum &	spectrum,
		MSSpectrum::ConstIterator &	left,
		MSSpectrum::ConstIterator &	right,
		const double	peak_height,
		const double	peak_apex_pos
	)		const

Calculate peak's shape metrics.

The calculated characteristics are the start and end positions at 0.05, 0.10 and 0.5 the peak's height. Also the widths at those positions are calculated. Other values: the peak's total width, its tailing factor, asymmetry factor, baseline delta to height and the slope of the baseline. The number of points across the baseline and also at half height are saved.

Note: Make sure the spectrum is sorted with respect to mass-to-charge ratio.

Parameters

[in]	spectrum	The spectrum which contains the peak
[in]	left	The iterator to the first point
[in]	right	The iterator to the last point
[in]	peak_height	The peak's highest intensity
[in]	peak_apex_pos	The position of the point with highest intensity

Returns: A struct containing the calculated peak shape metrics

◆ calculatePeakShapeMetrics_()

PeakShapeMetrics calculatePeakShapeMetrics_	(	const PeakContainerT &	pc,
		double	left,
		double	right,
		const double	peak_height,
		const double	peak_apex_pos
	)		const

inlineprotected

◆ EMGPreProcess_()

const PeakContainerT& EMGPreProcess_	(	const PeakContainerT &	pc,
		PeakContainerT &	emg_pc,
		double &	left,
		double &	right
	)		const

inlineprivate

Fit the peak to the EMG model.

The fitting process happens only if fit_EMG_ is true. left and right are updated accordingly.

Template Parameters

PeakContainerT Either a MSChromatogram or a MSSpectrum

Parameters

[in]	pc	Input peak
[out]	emg_pc	Will possibly contain the processed peak
[in]	left	RT or MZ value of the first point of interest
[in]	right	RT or MZ value of the first point of interest

Returns: A const reference to emg_pc if the fitting is executed, pc otherwise.

References EmgGradientDescent::fitEMGPeakModel().

◆ estimateBackground() [1/4]

PeakBackground estimateBackground	(	const MSChromatogram &	chromatogram,
		const double	left,
		const double	right,
		const double	peak_apex_pos
	)		const

Estimate the background of a peak contained in a MSChromatogram.

The user can choose to compute one of two background types: "vertical_sum" and "base_to_base". For the former case, the area is computed as a rectangle with delta RT being the base and the minimum intensity on boundaries as the height. For the latter case, the area is computed as a rectangle trapezoid. Similar to the "vertical_sum" solution, this technique also takes into account the area between the intensities on boundaries.

For both cases, the parameter integration_type_ decides which formula to use to compute the area. The user should make sure to use the same integration_type between calls of estimateBackground() and integratePeak().

Note: Make sure the chromatogram is sorted with respect to retention time.

Exceptions

Exception::InvalidParameter for class parameter baseline_type.

Parameters

[in]	chromatogram	The chromatogram which contains the peak
[in]	left	The left retention time boundary
[in]	right	The right retention time boundary
[in]	peak_apex_pos	The position of the point with highest intensity

Returns: A struct containing the informations about the peak's background area and height

◆ estimateBackground() [2/4]

PeakBackground estimateBackground	(	const MSChromatogram &	chromatogram,
		MSChromatogram::ConstIterator &	left,
		MSChromatogram::ConstIterator &	right,
		const double	peak_apex_pos
	)		const

Estimate the background of a peak contained in a MSChromatogram.

The user can choose to compute one of two background types: "vertical_sum" and "base_to_base". For the former case, the area is computed as a rectangle with delta RT being the base and the minimum intensity on boundaries as the height. For the latter case, the area is computed as a rectangle trapezoid. Similar to the "vertical_sum" solution, this technique also takes into account the area between the intensities on boundaries.

For both cases, the parameter integration_type_ decides which formula to use to compute the area. The user should make sure to use the same integration_type between calls of estimateBackground() and integratePeak().

Note: Make sure the chromatogram is sorted with respect to retention time.

Exceptions

Exception::InvalidParameter for class parameter baseline_type.

Parameters

[in]	chromatogram	The chromatogram which contains the peak
[in]	left	The iterator to the first point
[in]	right	The iterator to the last point
[in]	peak_apex_pos	The position of the point with highest intensity

Returns: A struct containing the informations about the peak's background area and height

◆ estimateBackground() [3/4]

PeakBackground estimateBackground	(	const MSSpectrum &	spectrum,
		const double	left,
		const double	right,
		const double	peak_apex_pos
	)		const

Estimate the background of a peak contained in a MSSpectrum.

The user can choose to compute one of two background types: "vertical_sum" and "base_to_base". For the former case, the area is computed as a rectangle with delta MZ being the base and the minimum intensity on boundaries as the height. For the latter case, the area is computed as a rectangle trapezoid. Similar to the "vertical_sum" solution, this technique also takes into account the area between the intensities on boundaries.

For both cases, the parameter integration_type_ decides which formula to use to compute the area. The user should make sure to use the same integration_type between calls of estimateBackground() and integratePeak().

Note: Make sure the spectrum is sorted with respect to mass-to-charge ratio.

Exceptions

Exception::InvalidParameter for class parameter baseline_type.

Parameters

[in]	spectrum	The spectrum which contains the peak
[in]	left	The left mass-to-charge ratio boundary
[in]	right	The right mass-to-charge ratio boundary
[in]	peak_apex_pos	The position of the point with highest intensity

Returns: A struct containing the informations about the peak's background area and height

◆ estimateBackground() [4/4]

PeakBackground estimateBackground	(	const MSSpectrum &	spectrum,
		MSSpectrum::ConstIterator &	left,
		MSSpectrum::ConstIterator &	right,
		const double	peak_apex_pos
	)		const

Estimate the background of a peak contained in a MSSpectrum.

The user can choose to compute one of two background types: "vertical_sum" and "base_to_base". For the former case, the area is computed as a rectangle with delta MZ being the base and the minimum intensity on boundaries as the height. For the latter case, the area is computed as a rectangle trapezoid. Similar to the "vertical_sum" solution, this technique also takes into account the area between the intensities on boundaries.

For both cases, the parameter integration_type_ decides which formula to use to compute the area. The user should make sure to use the same integration_type between calls of estimateBackground() and integratePeak().

Note: Make sure the spectrum is sorted with respect to mass-to-charge ratio.

Exceptions

Exception::InvalidParameter for class parameter baseline_type.

Parameters

[in]	spectrum	The spectrum which contains the peak
[in]	left	The iterator to the first point
[in]	right	The iterator to the last point
[in]	peak_apex_pos	The position of the point with highest intensity

Returns: A struct containing the informations about the peak's background area and height

◆ estimateBackground_()

PeakBackground estimateBackground_	(	const PeakContainerT &	pc,
		double	left,
		double	right,
		const double	peak_apex_pos
	)		const

inlineprotected

References PeakIntegrator::PeakBackground::area, and PeakIntegrator::PeakBackground::height.

◆ findPosAtPeakHeightPercent_()

double findPosAtPeakHeightPercent_	(	PeakContainerConstIteratorT	it_left,
		PeakContainerConstIteratorT	it_right,
		PeakContainerConstIteratorT	it_end,
		const double	peak_height,
		const double	percent,
		const bool	is_left_half
	)		const

inlineprotected

Find the position (RT/MZ) at a given percentage of peak's height.

Note

The method expects that the iterators span half of the peak's width. Examples:

Left half case: the range would be [leftMostPt, peakApexPos)
Right half case: the range would be [peakApexPos + 1, rightMostPt + 1)

The method assumes a convex peak. If 5%, 10%, or 50% peak heights are not found on either side of the peak, the closest left (for left peak height percentages) and closest right (for right peak height percentages) will be used.

Parameters

[in]	it_left	The iterator to the first point (must not be past the end)
[in]	it_right	The iterator to the last point (might be past the end)
[in]	it_end	The end-iterator of the container
[in]	peak_height	The peak's height
[in]	percent	At which percentage of the peak height we want to find the position (common values: 0.05, 0.1, 0.5)
[in]	is_left_half	According to which half of the peak, the algorithm proceeds to the correct direction

Returns: The position found

◆ getDefaultParameters()

void getDefaultParameters ( Param & params )

◆ integratePeak() [1/4]

PeakArea integratePeak	(	const MSChromatogram &	chromatogram,
		const double	left,
		const double	right
	)		const

Compute the area of a peak contained in a MSChromatogram.

The value of integration_type_ decides which integration technique to use:

"trapezoid" for the trapezoidal rule
"simpson" for the Simpson's rule (for unequally spaced points, Shklov, 1960)
"intensity_sum" for the simple sum of the intensities

Note: Make sure the chromatogram is sorted with respect to retention time.

Exceptions

Exception::InvalidParameter for class parameter integration_type.

Parameters

[in]	chromatogram	The chromatogram which contains the peak
[in]	left	The left retention time boundary
[in]	right	The right retention time boundary

Returns: A struct containing the informations about the peak's area, height and position

◆ integratePeak() [2/4]

PeakArea integratePeak	(	const MSChromatogram &	chromatogram,
		MSChromatogram::ConstIterator &	left,
		MSChromatogram::ConstIterator &	right
	)		const

Compute the area of a peak contained in a MSChromatogram.

The value of integration_type_ decides which integration technique to use:

"trapezoid" for the trapezoidal rule
"simpson" for the Simpson's rule (for unequally spaced points, Shklov, 1960)
"intensity_sum" for the simple sum of the intensities

Note: Make sure the chromatogram is sorted with respect to retention time.

Exceptions

Exception::InvalidParameter for class parameter integration_type.

Parameters

[in]	chromatogram	The chromatogram which contains the peak
[in]	left	The iterator to the first point
[in]	right	The iterator to the last point

Returns: A struct containing the informations about the peak's area, height and position

◆ integratePeak() [3/4]

PeakArea integratePeak	(	const MSSpectrum &	spectrum,
		const double	left,
		const double	right
	)		const

Compute the area of a peak contained in a MSSpectrum.

The value of integration_type_ decides which integration technique to use:

"trapezoid" for the trapezoidal rule
"simpson" for the Simpson's rule (for unequally spaced points, Shklov, 1960)
"intensity_sum" for the simple sum of the intensities

Note: Make sure the spectrum is sorted with respect to mass-to-charge ratio.

Exceptions

Exception::InvalidParameter for class parameter integration_type.

Parameters

[in]	spectrum	The spectrum which contains the peak
[in]	left	The left mass-to-charge ratio boundary
[in]	right	The right mass-to-charge ratio boundary

Returns: A struct containing the informations about the peak's area, height and position

◆ integratePeak() [4/4]

PeakArea integratePeak	(	const MSSpectrum &	spectrum,
		MSSpectrum::ConstIterator &	left,
		MSSpectrum::ConstIterator &	right
	)		const

Compute the area of a peak contained in a MSSpectrum.

The value of integration_type_ decides which integration technique to use:

"trapezoid" for the trapezoidal rule
"simpson" for the Simpson's rule (for unequally spaced points, Shklov, 1960)
"intensity_sum" for the simple sum of the intensities

Note: Make sure the spectrum is sorted with respect to mass-to-charge ratio.

Exceptions

Exception::InvalidParameter for class parameter integration_type.

Parameters

[in]	spectrum	The spectrum which contains the peak
[in]	left	The iterator to the first point
[in]	right	The iterator to the last point

Returns: A struct containing the informations about the peak's area, height and position

◆ integratePeak_()

PeakArea integratePeak_	(	const PeakContainerT &	pc,
		double	left,
		double	right
	)		const

inlineprotected

References PeakIntegrator::PeakArea::apex_pos, PeakIntegrator::PeakArea::area, PeakIntegrator::PeakArea::height, PeakIntegrator::PeakArea::hull_points, OPENMS_LOG_WARN, and OPENMS_PRECONDITION.

◆ simpson_()

double simpson_	(	PeakContainerConstIteratorT	it_begin,
		PeakContainerConstIteratorT	it_end
	)		const

inlineprotected

Simpson's rule algorithm.

This implementation expects an odd number of points. The formula used supports unequally spaced points.

Note: Make sure the container (chromatogram or spectrum) is sorted with respect to position (RT or m/z).

Warning: An odd number of points is expected!

Parameters

[in]	it_begin	The iterator to the first point
[in]	it_end	The iterator to the past-the-last point

Returns: The computed area

References OpenMS::Constants::h, and OpenMS::Constants::k.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

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

◆ baseline_type_

String baseline_type_ = BASELINE_TYPE_BASETOBASE

private

The baseline type to use in estimateBackground(). Possible values are: "vertical_division_max", "vertical_division_min", "base_to_base".

◆ BASELINE_TYPE_BASETOBASE

constexpr const char* BASELINE_TYPE_BASETOBASE = "base_to_base"

staticconstexpr

Baseline type: base to base.

◆ BASELINE_TYPE_VERTICALDIVISION

constexpr const char* BASELINE_TYPE_VERTICALDIVISION = "vertical_division"

staticconstexpr

Baseline type: vertical division (min of end points; only for backwards compatibility)

◆ BASELINE_TYPE_VERTICALDIVISION_MAX

constexpr const char* BASELINE_TYPE_VERTICALDIVISION_MAX = "vertical_division_max"

staticconstexpr

Baseline type: vertical division (max of end points)

◆ BASELINE_TYPE_VERTICALDIVISION_MIN

constexpr const char* BASELINE_TYPE_VERTICALDIVISION_MIN = "vertical_division_min"

staticconstexpr

Baseline type: vertical division (min of end points)

◆ emg_

EmgGradientDescent emg_

private

◆ fit_EMG_

bool fit_EMG_

private

Enable/disable EMG peak model fitting.

◆ integration_type_

String integration_type_ = INTEGRATION_TYPE_INTENSITYSUM

private

The integration technique to use in integratePeak() and estimateBackground(). Possible values are: "trapezoid", "simpson", "intensity_sum".

◆ INTEGRATION_TYPE_INTENSITYSUM

constexpr const char* INTEGRATION_TYPE_INTENSITYSUM = "intensity_sum"

staticconstexpr

Integration type: intensity sum

◆ INTEGRATION_TYPE_SIMPSON

constexpr const char* INTEGRATION_TYPE_SIMPSON = "simpson"

staticconstexpr

Integration type: simpson.

◆ INTEGRATION_TYPE_TRAPEZOID

constexpr const char* INTEGRATION_TYPE_TRAPEZOID = "trapezoid"

staticconstexpr

Integration type: trapezoid.

Classes

Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::PeakIntegrator::PeakArea

◆ OpenMS::PeakIntegrator::PeakBackground

◆ OpenMS::PeakIntegrator::PeakShapeMetrics

Constructor & Destructor Documentation

◆ PeakIntegrator()

◆ ~PeakIntegrator()

Member Function Documentation

◆ calculatePeakShapeMetrics() [1/4]

◆ calculatePeakShapeMetrics() [2/4]

◆ calculatePeakShapeMetrics() [3/4]

◆ calculatePeakShapeMetrics() [4/4]

◆ calculatePeakShapeMetrics_()

◆ EMGPreProcess_()

◆ estimateBackground() [1/4]

◆ estimateBackground() [2/4]

◆ estimateBackground() [3/4]

◆ estimateBackground() [4/4]

◆ estimateBackground_()

◆ findPosAtPeakHeightPercent_()

◆ getDefaultParameters()

◆ integratePeak() [1/4]

◆ integratePeak() [2/4]

◆ integratePeak() [3/4]

◆ integratePeak() [4/4]

◆ integratePeak_()

◆ simpson_()

◆ updateMembers_()

Member Data Documentation

◆ baseline_type_

◆ BASELINE_TYPE_BASETOBASE

◆ BASELINE_TYPE_VERTICALDIVISION

◆ BASELINE_TYPE_VERTICALDIVISION_MAX

◆ BASELINE_TYPE_VERTICALDIVISION_MIN

◆ emg_

◆ fit_EMG_

◆ integration_type_

◆ INTEGRATION_TYPE_INTENSITYSUM

◆ INTEGRATION_TYPE_SIMPSON

◆ INTEGRATION_TYPE_TRAPEZOID