OptimizePick Class Reference

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

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

Collaboration diagram for OptimizePick:

Classes
struct	Data
class	OptPeakFunctor

Public Types
typedef std::vector< Peak1D >	RawDataVector
	Profile data vector type. More...
typedef RawDataVector::iterator	PeakIterator
	Profile data iterator type. More...

Public Member Functions
	OptimizePick ()
	Constructor. More...
	OptimizePick (const struct OptimizationFunctions::PenaltyFactors &penalties_, const int max_iteration_)
	Constructor to set the penalty factors, the number of optimization iterations as well as the threshold for the absolute and the relative error. More...
	~OptimizePick ()
	Destructor. More...
const struct OptimizationFunctions::PenaltyFactors &	getPenalties () const
	Non-mutable access to the penalty factors. More...
struct OptimizationFunctions::PenaltyFactors &	getPenalties ()
	Mutable access to the penalty factors. More...
void	setPenalties (const struct OptimizationFunctions::PenaltyFactors &penalties)
	Mutable access to the penalty factors. More...
UInt	getNumberIterations () const
	Non-mutable access to the number of iterations. More...
unsigned int &	getNumberIterations ()
	Mutable access to the number of iterations. More...
void	setNumberIterations (const int max_iteration)
	Mutable access to the number of iterations. More...
void	optimize (std::vector< PeakShape > &peaks, Data &data)
	Start the optimization of the peak shapes peaks. The original peak shapes will be substituted by the optimized peak shapes. More...

Protected Attributes
struct OptimizationFunctions::PenaltyFactors	penalties_
	Penalty factors. More...
unsigned int	max_iteration_
	Maximum number of iterations during optimization. More...

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 Eigen.

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Class Documentation

OpenMS::OptimizePick::Data

struct OpenMS::OptimizePick::Data

Collaboration diagram for OptimizePick::Data:

Class Members
vector< PeakShape >	peaks	This container contains the peak shapes to be optimized.
PenaltyFactors	penalties
vector< double >	positions	Positions and intensity values of the profile data.
vector< double >	signal

Member Typedef Documentation

PeakIterator

typedef RawDataVector::iterator PeakIterator

Profile data iterator type.

RawDataVector

typedef std::vector<Peak1D> RawDataVector

Profile data vector type.

Constructor & Destructor Documentation

OptimizePick() [1/2]

OptimizePick ( )

inline

Constructor.

OptimizePick() [2/2]

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

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

~OptimizePick()

~OptimizePick

(

)

Destructor.

Member Function Documentation

getNumberIterations() [1/2]

unsigned int& getNumberIterations ( )

inline

Mutable access to the number of iterations.

getNumberIterations() [2/2]

UInt getNumberIterations ( ) const

inline

Non-mutable access to the number of iterations.

getPenalties() [1/2]

struct OptimizationFunctions::PenaltyFactors& getPenalties ( )

inline

Mutable access to the penalty factors.

getPenalties() [2/2]

const struct OptimizationFunctions::PenaltyFactors& getPenalties ( ) const

inline

Non-mutable access to the penalty factors.

optimize()

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

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

Referenced by TwoDOptimization::optimizeRegionsScanwise_().

setNumberIterations()

void setNumberIterations ( const int  max_iteration )

inline

Mutable access to the number of iterations.

setPenalties()

void setPenalties ( const struct OptimizationFunctions::PenaltyFactors &  penalties )

inline

Mutable access to the penalty factors.

Member Data Documentation

max_iteration_

unsigned int max_iteration_

protected

Maximum number of iterations during optimization.

penalties_

struct OptimizationFunctions::PenaltyFactors penalties_

protected

Penalty factors.