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OptimizePick Class Reference

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

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

Classes

struct  Data
 

Public Types

typedef std::vector< Peak1DRawDataVector
 Raw data vector type. More...
 
typedef RawDataVector::iterator PeakIterator
 Raw data iterator type. More...
 

Public Member Functions

 OptimizePick ()
 Constructor. More...
 
 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. More...
 
 ~OptimizePick ()
 Destructor. More...
 
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...
 
DoubleReal getMaxAbsError () const
 Non-mutable access to the maximum absolute error. More...
 
doublegetMaxAbsError ()
 Mutable access to the maximum absolute error. More...
 
void setMaxAbsError (double eps_abs)
 Mutable access to the maximum absolute error. More...
 
DoubleReal getMaxRelError () const
 Non-mutable access to the maximum relative error. More...
 
doublegetMaxRelError ()
 Mutable access to the maximum relative error. More...
 
void setMaxRelError (double eps_rel)
 Mutable access to the maximum relative error. More...
 
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. More...
 

Protected Attributes

struct
OptimizationFunctions::PenaltyFactors 
penalties_
 Penalty factors. More...
 
unsigned int max_iteration_
 Maximum number of iterations during optimization. More...
 
double eps_abs_
 Maximum absolute and relative error used in the optimization. More...
 
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.

Member Typedef Documentation

typedef RawDataVector::iterator PeakIterator

Raw data iterator type.

typedef std::vector<Peak1D> RawDataVector

Raw data vector type.

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.

Destructor.

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.

UInt getNumberIterations ( ) const
inline

Non-mutable access to the number of iterations.

unsigned int& getNumberIterations ( )
inline

Mutable access to the number of iterations.

struct OptimizationFunctions::PenaltyFactors& getPenalties ( ) const
inline

Non-mutable access to the penalty factors.

struct OptimizationFunctions::PenaltyFactors& getPenalties ( )
inline

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.

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.


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:35 using doxygen 1.8.5