This class provides the two-dimensional optimization of the picked peak parameters. More...

#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/TwoDOptimization.h>

Inheritance diagram for TwoDOptimization:

Classes
struct	Data
	Helper struct (contains the size of an area and a raw data container) More...

class	TwoDOptFunctor

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

	TwoDOptimization (const TwoDOptimization &opt)
	Copy constructor. More...

	~TwoDOptimization () override
	Destructor. More...

TwoDOptimization &	operator= (const TwoDOptimization &opt)
	Assignment operator. More...

double	getMZTolerance () const
	Non-mutable access to the matching epsilon. More...

void	setMZTolerance (double tolerance_mz)
	Mutable access to the matching epsilon. More...

double	getMaxPeakDistance () const
	Non-mutable access to the maximal peak distance in a cluster. More...

void	setMaxPeakDistance (double max_peak_distance)
	Mutable access to the maximal peak distance in a cluster. More...

UInt	getMaxIterations () const
	Non-mutable access to the maximal number of iterations. More...

void	setMaxIterations (UInt max_iteration)
	Mutable access to the maximal number of iterations. More...

const OptimizationFunctions::PenaltyFactorsIntensity &	getPenalties () const
	Non-mutable access to the minimal number of adjacent scans. More...

void	setPenalties (OptimizationFunctions::PenaltyFactorsIntensity &penalties)
	Mutable access to the minimal number of adjacent scans. More...

template<typename InputSpectrumIterator >
void	optimize (InputSpectrumIterator first, InputSpectrumIterator last, PeakMap &ms_exp, bool real2D=true)
	Find two dimensional peak clusters and optimize their peak parameters. 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...

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...

Protected Member Functions
Auxiliary Functions for the search of matching regions
std::vector< double >::iterator	searchInScan_ (std::vector< double >::iterator scan_begin, std::vector< double >::iterator scan_end, double current_mz)

template<typename InputSpectrumIterator >
void	optimizeRegions_ (InputSpectrumIterator &first, InputSpectrumIterator &last, PeakMap &ms_exp)

template<typename InputSpectrumIterator >
void	optimizeRegionsScanwise_ (InputSpectrumIterator &first, InputSpectrumIterator &last, PeakMap &ms_exp)

template<typename InputSpectrumIterator >
void	getRegionEndpoints_ (PeakMap &exp, InputSpectrumIterator &first, InputSpectrumIterator &last, Size iso_map_idx, double noise_level, TwoDOptimization::Data &d)
	Get the indices of the first and last raw data point of this region. More...

void	findMatchingPeaks_ (std::multimap< double, IsotopeCluster >::iterator &it, PeakMap &ms_exp)
	Identify matching peak in a peak cluster. More...

void	updateMembers_ () override
	update members method from DefaultParamHandler to update the members More...

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

Protected Attributes
std::multimap< double, IsotopeCluster >	iso_map_
	stores the retention time of each isotopic cluster More...

std::multimap< double, IsotopeCluster >::const_iterator	curr_region_
	Pointer to the current region. More...

double	max_peak_distance_
	upper bound for distance between two peaks belonging to the same region More...

double	tolerance_mz_
	threshold for the difference in the peak position of two matching peaks More...

std::map< Int, std::vector< PeakIndex > >	matching_peaks_
	Indices of peaks in the adjacent scans matching peaks in the scan with no. ref_scan. More...

UInt	max_iteration_
	Convergence Parameter: Maximal number of iterations. More...

bool	real_2D_
	Optimization considering all scans of a cluster or optimization of each scan separately. More...

OptimizationFunctions::PenaltyFactorsIntensity	penalties_
	Penalty factors for some parameters in the optimization. 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

This class provides the two-dimensional optimization of the picked peak parameters.

Given the picked peaks, this class optimizes the peak parameters of each isotope pattern using a non-linear optimization. The peaks of adjacent scans are adjusted to achieve that a peak occurring in several scans has always the same m/z position. For the optimization the Levenberg-Marquardt algorithm provided from the Eigen is used. The optimized parameters are the m/z values, the left and right width, which shall be equal for a peak in all scans, and the peaks' heights.

Todo:: Works only with defined types due to pointers to the data in the optimization namespace! Change that or remove templates (Alexandra)

Parameters of this class are:

Name	Type	Default	Description
iterations	int	10	maximal number of iterations for the fitting step
penalties:position	float	0.0	If the position changes more than 0.2Da during the fitting it can be penalized
penalties:height	float	1.0	penalty term for the fitting of the intensity:If it gets negative during the fitting it can be penalized.
penalties:left_width	float	0.0	penalty term for the fitting of the left width:If the left width gets too broad or negative during the fitting it can be penalized.
penalties:right_width	float	0.0	penalty term for the fitting of the right width:If the right width gets too broad or negative during the fitting it can be penalized.
2d:tolerance_mz	float	2.2	mz tolerance for cluster construction
2d:max_peak_distance	float	1.2	maximal peak distance in mz in a cluster

Note:

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

Class Documentation

◆ OpenMS::TwoDOptimization::Data

struct OpenMS::TwoDOptimization::Data

Helper struct (contains the size of an area and a raw data container)

Class Members
multimap< double, IsotopeCluster >::iterator	iso_map_iter
map< Int, vector< PeakIndex > >	matching_peaks
PenaltyFactorsIntensity	penalties
PeakMap	picked_peaks
vector< double >	positions
ConstIterator	raw_data_first
vector< double >	signal
vector< pair< SignedSize, SignedSize > >	signal2D
Size	total_nr_peaks

Constructor & Destructor Documentation

◆ TwoDOptimization() [1/2]

TwoDOptimization ( )

Constructor.

◆ TwoDOptimization() [2/2]

TwoDOptimization ( const TwoDOptimization & opt )

Copy constructor.

◆ ~TwoDOptimization()

~TwoDOptimization ( )

inlineoverride

Destructor.

Member Function Documentation

◆ findMatchingPeaks_()

void findMatchingPeaks_	(	std::multimap< double, IsotopeCluster >::iterator &	it,
		PeakMap &	ms_exp
	)

protected

Identify matching peak in a peak cluster.

Referenced by TwoDOptimization::optimizeRegions_().

◆ getMaxIterations()

UInt getMaxIterations ( ) const

inline

Non-mutable access to the maximal number of iterations.

◆ getMaxPeakDistance()

double getMaxPeakDistance ( ) const

inline

Non-mutable access to the maximal peak distance in a cluster.

◆ getMZTolerance()

double getMZTolerance ( ) const

inline

Non-mutable access to the matching epsilon.

◆ getPenalties()

const OptimizationFunctions::PenaltyFactorsIntensity& getPenalties ( ) const

inline

Non-mutable access to the minimal number of adjacent scans.

◆ getRegionEndpoints_()

void getRegionEndpoints_	(	PeakMap &	exp,
		InputSpectrumIterator &	first,
		InputSpectrumIterator &	last,
		Size	iso_map_idx,
		double	noise_level,
		TwoDOptimization::Data &	d
	)

protected

Get the indices of the first and last raw data point of this region.

References TwoDOptimization::iso_map_, MSExperiment::RTBegin(), MSSpectrum::setRT(), TwoDOptimization::Data::signal2D, and MSExperiment::size().

Referenced by TwoDOptimization::optimizeRegions_(), and TwoDOptimization::optimizeRegionsScanwise_().

◆ operator=()

TwoDOptimization& operator= ( const TwoDOptimization & opt )

Assignment operator.

◆ optimize()

void optimize	(	InputSpectrumIterator	first,
		InputSpectrumIterator	last,
		PeakMap &	ms_exp,
		bool	real2D = `true`
	)

Find two dimensional peak clusters and optimize their peak parameters.

Note

For the peak spectra, the following meta data arrays (see MSSpectrum) have to be present and have to be named just as listed here:

intensity (index:1)
leftWidth (index:3)
rightWidth (index:4)
peakShape (index:5)

Parameters

first	begin of the raw data spectra iterator range
last	end of the raw data spectra iterator range
ms_exp	peak map corresponding to the raw data in the range from `first` to `last`
real2D	flag if the optimization should be two dimensional or on each scan separately

Exceptions

Exception::IllegalArgument is thrown if required meta information from peak picking is missing (area, shape, left width, right width) or if the input data is invalid in some other way

References MSExperiment::begin(), IsotopeCluster::ChargedIndexSet::charge, TwoDOptimization::curr_region_, MSExperiment::empty(), MSExperiment::end(), seqan::find(), Param::getValue(), TwoDOptimization::iso_map_, TwoDOptimization::max_peak_distance_, TwoDOptimization::optimizeRegions_(), TwoDOptimization::optimizeRegionsScanwise_(), DefaultParamHandler::param_, IsotopeCluster::peaks, TwoDOptimization::real_2D_, IsotopeCluster::scans, TwoDOptimization::searchInScan_(), MSSpectrum::setRT(), and MSExperiment::size().

◆ optimizeRegions_()

void optimizeRegions_	(	InputSpectrumIterator &	first,
		InputSpectrumIterator &	last,
		PeakMap &	ms_exp
	)

protected

Performs 2D optimization of all regions

References TwoDOptimization::findMatchingPeaks_(), TwoDOptimization::getRegionEndpoints_(), TwoDOptimization::iso_map_, TwoDOptimization::Data::iso_map_iter, OpenMS::Constants::k, PeakShape::LORENTZ_PEAK, TwoDOptimization::Data::matching_peaks, TwoDOptimization::matching_peaks_, TwoDOptimization::Data::penalties, TwoDOptimization::penalties_, TwoDOptimization::Data::picked_peaks, TwoDOptimization::Data::raw_data_first, TwoDOptimization::Data::signal2D, and TwoDOptimization::Data::total_nr_peaks.

Referenced by TwoDOptimization::optimize().

◆ optimizeRegionsScanwise_()

void optimizeRegionsScanwise_	(	InputSpectrumIterator &	first,
		InputSpectrumIterator &	last,
		PeakMap &	ms_exp
	)

protected

◆ searchInScan_()

std::vector<double>::iterator searchInScan_	(	std::vector< double >::iterator	scan_begin,
		std::vector< double >::iterator	scan_end,
		double	current_mz
	)

protected

Referenced by TwoDOptimization::optimize().

◆ setMaxIterations()

void setMaxIterations ( UInt max_iteration )

inline

Mutable access to the maximal number of iterations.

◆ setMaxPeakDistance()

void setMaxPeakDistance ( double max_peak_distance )

inline

Mutable access to the maximal peak distance in a cluster.

◆ setMZTolerance()

void setMZTolerance ( double tolerance_mz )

inline

Mutable access to the matching epsilon.

◆ setPenalties()

void setPenalties ( OptimizationFunctions::PenaltyFactorsIntensity & penalties )

inline

Mutable access to the minimal number of adjacent scans.

References PenaltyFactorsIntensity::height, PenaltyFactors::lWidth, PenaltyFactors::pos, and PenaltyFactors::rWidth.

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

update members method from DefaultParamHandler to update the members

Reimplemented from DefaultParamHandler.

Member Data Documentation

◆ curr_region_

std::multimap<double, IsotopeCluster>::const_iterator curr_region_

protected

Pointer to the current region.

Referenced by TwoDOptimization::optimize().

◆ iso_map_

std::multimap<double, IsotopeCluster> iso_map_

protected

stores the retention time of each isotopic cluster

Referenced by TwoDOptimization::getRegionEndpoints_(), TwoDOptimization::optimize(), TwoDOptimization::optimizeRegions_(), and TwoDOptimization::optimizeRegionsScanwise_().

◆ matching_peaks_

std::map<Int, std::vector<PeakIndex> > matching_peaks_

protected

Indices of peaks in the adjacent scans matching peaks in the scan with no. ref_scan.

Referenced by TwoDOptimization::optimizeRegions_().

◆ max_iteration_

UInt max_iteration_

protected

Convergence Parameter: Maximal number of iterations.

◆ max_peak_distance_

double max_peak_distance_

protected

upper bound for distance between two peaks belonging to the same region

Referenced by TwoDOptimization::optimize().

◆ penalties_

OptimizationFunctions::PenaltyFactorsIntensity penalties_

protected

Penalty factors for some parameters in the optimization.

Referenced by TwoDOptimization::optimizeRegions_().

◆ real_2D_

bool real_2D_

protected

Optimization considering all scans of a cluster or optimization of each scan separately.

Referenced by TwoDOptimization::optimize().

◆ tolerance_mz_

double tolerance_mz_

protected

threshold for the difference in the peak position of two matching peaks

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Class Documentation

◆ OpenMS::TwoDOptimization::Data

Constructor & Destructor Documentation

◆ TwoDOptimization() [1/2]

◆ TwoDOptimization() [2/2]

◆ ~TwoDOptimization()

Member Function Documentation

◆ findMatchingPeaks_()

◆ getMaxIterations()

◆ getMaxPeakDistance()

◆ getMZTolerance()

◆ getPenalties()

◆ getRegionEndpoints_()

◆ operator=()

◆ optimize()

◆ optimizeRegions_()

◆ optimizeRegionsScanwise_()

◆ searchInScan_()

◆ setMaxIterations()

◆ setMaxPeakDistance()

◆ setMZTolerance()

◆ setPenalties()

◆ updateMembers_()

Member Data Documentation

◆ curr_region_

◆ iso_map_

◆ matching_peaks_

◆ max_iteration_

◆ max_peak_distance_

◆ penalties_

◆ real_2D_

◆ tolerance_mz_