| OpenMS 2.5.0

Classes | Public Types | Public Member Functions | Protected Attributes | List of all members
OptimizePick Class Reference

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

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

## 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.

## Class Documentation

## ◆ OpenMS::OptimizePick::Data

struct OpenMS::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]

UInt getNumberIterations | ( |  | ) | const

inline

Non-mutable access to the number of iterations.

## ◆ getNumberIterations() [2/2]

unsigned int& getNumberIterations | ( |  | ) |

inline

Mutable access to the number of iterations.

## ◆ getPenalties() [1/2]

const struct OptimizationFunctions::PenaltyFactors& getPenalties | ( |  | ) | const

inline

Non-mutable access to the penalty factors.

## ◆ getPenalties() [2/2]

struct OptimizationFunctions::PenaltyFactors& getPenalties | ( |  | ) |

inline

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.