OptimizePick Class Reference

This class provides the non-linear optimization of the peak parameters. More...

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

List of all members.

Classes
struct	Data
Public Types
typedef std::vector< Peak1D >	RawDataVector
	Raw data vector type.
typedef RawDataVector::iterator	PeakIterator
	Raw data iterator type.
Public Member Functions
	OptimizePick ()
	Constructor.
	OptimizePick (const struct OptimizationFunctions::PenaltyFactors &penalties_, const int max_iteration_, const double eps_abs_, const double eps_rel_)
	Constructor to set the penalty factors, the number of optimization iterations as well as the threshold for the absolute and the relative error.
	~OptimizePick ()
	Destructor.
struct OptimizationFunctions::PenaltyFactors &	getPenalties () const
	Non-mutable access to the penalty factors.
struct OptimizationFunctions::PenaltyFactors &	getPenalties ()
	Mutable access to the penalty factors.
void	setPenalties (const struct OptimizationFunctions::PenaltyFactors &penalties)
	Mutable access to the penalty factors.
UInt	getNumberIterations () const
	Non-mutable access to the number of iterations.
unsigned int &	getNumberIterations ()
	Mutable access to the number of iterations.
void	setNumberIterations (const int max_iteration)
	Mutable access to the number of iterations.
DoubleReal	getMaxAbsError () const
	Non-mutable access to the maximum absolute error.
double &	getMaxAbsError ()
	Mutable access to the maximum absolute error.
void	setMaxAbsError (double eps_abs)
	Mutable access to the maximum absolute error.
DoubleReal	getMaxRelError () const
	Non-mutable access to the maximum relative error.
double &	getMaxRelError ()
	Mutable access to the maximum relative error.
void	setMaxRelError (double eps_rel)
	Mutable access to the maximum relative error.
void	optimize (std::vector< PeakShape > &peaks, Data &data)
	Start the optimization of the peak shapes peaks. The original peak shapes will be subsituted by the optimized peak shapes.
Protected Attributes
struct OptimizationFunctions::PenaltyFactors	penalties_
	Penalty factors.
unsigned int	max_iteration_
	Maximum number of iterations during optimization.
double	eps_abs_
	Maximum absolute and relative error used in the optimization.
double	eps_rel_

---

Detailed Description

This class provides the non-linear optimization of the peak parameters.

Given a vector of peak shapes, this class optimizes all peak shapes parameters using a non-linear optimization. For the non-linear optimization we use the Levenberg-Marquardt algorithm provided by the gsl.

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Member Typedef Documentation

typedef RawDataVector::iterator PeakIterator

Raw data iterator type.

typedef std::vector<Peak1D> RawDataVector

Raw data vector type.

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Constructor & Destructor Documentation

OptimizePick

(

)

[inline]

Constructor.

OptimizePick	(	const struct OptimizationFunctions::PenaltyFactors &	penalties_,
		const int	max_iteration_,
		const double	eps_abs_,
		const double	eps_rel_
	)

Constructor to set the penalty factors, the number of optimization iterations as well as the threshold for the absolute and the relative error.

~OptimizePick

(

)

Destructor.

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Member Function Documentation

DoubleReal getMaxAbsError

(

)

const [inline]

Non-mutable access to the maximum absolute error.

double& getMaxAbsError

(

)

[inline]

Mutable access to the maximum absolute error.

DoubleReal getMaxRelError

(

)

const [inline]

Non-mutable access to the maximum relative error.

double& getMaxRelError

(

)

[inline]

Mutable access to the maximum relative error.

unsigned int& getNumberIterations

(

)

[inline]

Mutable access to the number of iterations.

UInt getNumberIterations

(

)

const [inline]

Non-mutable access to the number of iterations.

struct OptimizationFunctions::PenaltyFactors& getPenalties

(

)

[inline, read]

Mutable access to the penalty factors.

struct OptimizationFunctions::PenaltyFactors& getPenalties

(

)

const [inline, read]

Non-mutable access to the penalty factors.

void optimize	(	std::vector< PeakShape > &	peaks,
		Data &	data
	)

Start the optimization of the peak shapes peaks. The original peak shapes will be subsituted by the optimized peak shapes.

Referenced by TwoDOptimization::optimizeRegionsScanwise_().

void setMaxAbsError

(

double

eps_abs

)

[inline]

Mutable access to the maximum absolute error.

void setMaxRelError

(

double

eps_rel

)

[inline]

Mutable access to the maximum relative error.

void setNumberIterations

(

const int

max_iteration

)

[inline]

Mutable access to the number of iterations.

void setPenalties

(

const struct OptimizationFunctions::PenaltyFactors &

penalties

)

[inline]

Mutable access to the penalty factors.

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Member Data Documentation

double eps_abs_ [protected]

Maximum absolute and relative error used in the optimization.

double eps_rel_ [protected]

unsigned int max_iteration_ [protected]

Maximum number of iterations during optimization.

struct OptimizationFunctions::PenaltyFactors penalties_ [protected]

Penalty factors.