| OpenMS 2.5.0

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EGHFitter1D Class Reference

Exponential-Gaussian hybrid distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization. More...

`#include <OpenMS/SIMULATION/EGHFitter1D.h>`

Inheritance diagram for EGHFitter1D:

## Classes

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

## Public Member Functions

| EGHFitter1D ()
| Default constructor. More...
| EGHFitter1D (const EGHFitter1D &source)
| copy constructor More...
| ~EGHFitter1D () override
| destructor More...
virtual EGHFitter1D & | operator= (const EGHFitter1D &source)
| assignment operator More...
QualityType | fit1d (const RawDataArrayType &range, InterpolationModel *&model) override
| return interpolation model More...
Public Member Functions inherited from LevMarqFitter1D
| LevMarqFitter1D ()
| Default constructor. More...
| LevMarqFitter1D (const LevMarqFitter1D &source)
| copy constructor More...
| ~LevMarqFitter1D () override
| destructor More...
virtual LevMarqFitter1D & | operator= (const LevMarqFitter1D &source)
| assignment operator More...
Public Member Functions inherited from Fitter1D
| Fitter1D ()
| Default constructor. More...
| Fitter1D (const Fitter1D &source)
| copy constructor More...
| ~Fitter1D () override
| destructor More...
virtual Fitter1D & | operator= (const Fitter1D &source)
| assignment operator 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...

## Static Public Member Functions

static Fitter1D * | create ()
| create new EGHFitter1D object (function needed by Factory) More...
static const String | getProductName ()
| name of the model (needed by Factory) More...
Static Public Member Functions inherited from Fitter1D
static void | registerChildren ()
| register all derived classes here More...

## Protected Member Functions

virtual void | setInitialParameters_ (const RawDataArrayType &set)
| Compute start parameter. More...
void | updateMembers_ () override
| This method is used to update extra member variables at the end of the setParameters() method. More...
Protected Member Functions inherited from LevMarqFitter1D
void | optimize_ (Eigen::VectorXd &x_init, GenericFunctor &functor)
| Optimize start parameter. More...
void | updateMembers_ () override
| This method is used to update extra member variables at the end of the setParameters() method. More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

CoordinateType | height_
| Parameter of egh - peak height. More...
CoordinateType | tau_
| Parameter of egh - tau. More...
CoordinateType | sigma_square_
| Parameter of egh - sigma-square. More...
CoordinateType | retention_
| Parameter of egh - peak retention time. More...
Protected Attributes inherited from LevMarqFitter1D
bool | symmetric_
| Parameter indicates symmetric peaks. More...
Int | max_iteration_
| Maximum number of iterations. More...
Protected Attributes inherited from Fitter1D
CoordinateType | tolerance_stdev_box_
| standard derivation in bounding box More...
Math::BasicStatistics | statistics_
| basic statistics More...
CoordinateType | interpolation_step_
| interpolation step size 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...

## Additional Inherited Members

Public Types inherited from LevMarqFitter1D
typedef std::vector< double > | ContainerType
Public Types inherited from Fitter1D
typedef IsotopeCluster::IndexSet | IndexSet
| IndexSet. More...
typedef IsotopeCluster::ChargedIndexSet | ChargedIndexSet
| IndexSet with charge information. More...
typedef Feature::CoordinateType | CoordinateType
| Single coordinate. More...
typedef Feature::QualityType | QualityType
| Quality of a feature. More...
typedef Peak1D | PeakType
| Peak type data point type. More...
typedef std::vector< PeakType > | RawDataArrayType
| Peak type data container type using for the temporary storage of the input data. More...
typedef RawDataArrayType::iterator | PeakIterator
| Peak type data iterator. More...
Public Types inherited from FeatureFinderDefs
enum | Flag { UNUSED, USED }
| Flags that indicate if a peak is already used in a feature. More...
typedef IsotopeCluster::IndexPair | IndexPair
| Index to peak consisting of two UInts (scan index / peak index) More...
typedef IsotopeCluster::ChargedIndexSet | ChargedIndexSet
| Index to peak consisting of two UInts (scan index / peak index) with charge information. More...
typedef IsotopeCluster::IndexSet | IndexSet
| A set of peak indices. More...

## Detailed Description

Exponential-Gaussian hybrid distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (Eigen implementation) for parameter optimization.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
interpolation_step | float | 0.2 |  | Sampling rate for the interpolation of the model function.
tolerance_stdev_bounding_box | float | 3.0 |  | Bounding box has range [minimim of data, maximum of data] enlarged by tolerance_stdev_bounding_box times the standard deviation of the data.
max_iteration | int | 500 |  | Maximum number of iterations using by Levenberg-Marquardt algorithm.
statistics:mean | float | 1.0 |  | Centroid position of the model.
statistics:variance | float | 1.0 |  | Variance of the model.

Note:

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

## Class Documentation

## ◆ OpenMS::EGHFitter1D::Data

struct OpenMS::EGHFitter1D::Data

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

Class Members
typedef Peak1D | PeakType |
typedef vector< PeakType > | RawDataArrayType |

Class Members
Size | n |
RawDataArrayType | set |

## Constructor & Destructor Documentation

## ◆ EGHFitter1D() [1/2]

EGHFitter1D | ( |  | ) |

Default constructor.

## ◆ EGHFitter1D() [2/2]

EGHFitter1D | ( | const EGHFitter1D & | source | ) |

copy constructor

## ◆ ~EGHFitter1D()

~EGHFitter1D | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ create()

static Fitter1D* create | ( |  | ) |

inline static

create new EGHFitter1D object (function needed by Factory)

## ◆ fit1d()

QualityType fit1d | ( | const RawDataArrayType & | range,
|  | InterpolationModel *& | model
| ) |  |

override virtual

return interpolation model

Reimplemented from Fitter1D.

## ◆ getProductName()

static const String getProductName | ( |  | ) |

inline static

name of the model (needed by Factory)

## ◆ operator=()

virtual EGHFitter1D& operator= | ( | const EGHFitter1D & | source | ) |

virtual

assignment operator

## ◆ setInitialParameters_()

virtual void setInitialParameters_ | ( | const RawDataArrayType & | set | ) |

protected virtual

Compute start parameter.

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ height_

CoordinateType height_

protected

Parameter of egh - peak height.

## ◆ retention_

CoordinateType retention_

protected

Parameter of egh - peak retention time.

## ◆ sigma_square_

CoordinateType sigma_square_

protected

Parameter of egh - sigma-square.

## ◆ tau_

CoordinateType tau_

protected

Parameter of egh - tau.