| OpenMS 2.5.0

Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
InterpolationModel Class Reference
Analysis » FeatureFinder

Abstract class for 1D-models that are approximated using linear interpolation. More...

`#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/InterpolationModel.h>`

Inheritance diagram for InterpolationModel:

## Public Types

typedef double | IntensityType
typedef DPosition< 1 > | PositionType
typedef double | CoordinateType
typedef Math::LinearInterpolation< double > | LinearInterpolation
Public Types inherited from BaseModel< 1 >
typedef double | IntensityType
typedef double | CoordinateType
typedef DPosition< D > | PositionType
typedef DPeak< D >::Type | PeakType
typedef std::vector< PeakType > | SamplesType

## Public Member Functions

| InterpolationModel ()
| Default constructor. More...
| InterpolationModel (const InterpolationModel &source)
| copy constructor More...
| ~InterpolationModel () override
| destructor More...
virtual InterpolationModel & | operator= (const InterpolationModel &source)
| assignment operator More...
IntensityType | getIntensity (const PositionType &pos) const override
| access model predicted intensity at position `pos` More...
IntensityType | getIntensity (CoordinateType coord) const
| access model predicted intensity at position `pos` More...
const LinearInterpolation & | getInterpolation () const
| Returns the interpolation class. More...
CoordinateType | getScalingFactor () const
| get the scaling for the model More...
virtual void | setOffset (CoordinateType offset)
| set the offset of the model More...
void | getSamples (SamplesType &cont) const override
| get reasonable set of samples from the model (i.e. for printing) More...
virtual CoordinateType | getCenter () const
| "center" of the model, particular definition (depends on the derived model) More...
virtual void | setSamples ()
| set sample/supporting points of interpolation wrt params. More...
void | setInterpolationStep (CoordinateType interpolation_step)
| Set the interpolation step for the linear interpolation of the model. More...
void | setScalingFactor (CoordinateType scaling)
Public Member Functions inherited from BaseModel< 1 >
| BaseModel ()
| Default constructor. More...
| BaseModel (const BaseModel &source)
| copy constructor More...
| ~BaseModel () override
| Destructor. More...
virtual BaseModel & | operator= (const BaseModel &source)
| assignment operator More...
void | registerChildren ()
void | registerChildren ()
virtual IntensityType | getIntensity (const PositionType &pos) const=0
| access model predicted intensity at position `pos` More...
virtual bool | isContained (const PositionType &pos) const
| check if position `pos` is part of the model regarding the models cut-off. More...
void | fillIntensity (PeakType &peak) const
| Convenience function to set the intensity of a peak to the predicted intensity at its current position, calling virtual void getIntensity(). More...
void | fillIntensities (PeakIterator begin, PeakIterator end) const
| Convenience function that applies fillIntensity() to an iterator range. More...
virtual IntensityType | getCutOff () const
| get cutoff value More...
virtual void | setCutOff (IntensityType cut_off)
| set cutoff value More...
virtual void | getSamples (std::ostream &os)
| fill stream with reasonable set of samples from the model (i.e. for printing) 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...

## Protected Member Functions

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 BaseModel< 1 >
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

LinearInterpolation | interpolation_
CoordinateType | interpolation_step_
CoordinateType | scaling_
Protected Attributes inherited from BaseModel< 1 >
IntensityType | cut_off_
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

Static Public Member Functions inherited from BaseModel< 1 >
static void | registerChildren ()
| register all derived classes here (implemented in file BaseModel_impl.h) More...

## Detailed Description

Abstract class for 1D-models that are approximated using linear interpolation.

Model wrapping LinearInterpolation for speed-up in calculation of predicted intensities Derived classes have to implement setSamples()

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
cutoff | float | 0.0 |  | Low intensity cutoff of the model. Peaks below this intensity are not considered part of the model.
interpolation_step | float | 0.1 |  | Sampling rate for the interpolation of the model function
intensity_scaling | float | 1.0 |  | Scaling factor used to adjust the model distribution to the intensities of the data

Note:

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

## Member Typedef Documentation

## ◆ CoordinateType

typedef double CoordinateType

## ◆ IntensityType

typedef double IntensityType

## ◆ LinearInterpolation

typedef Math::LinearInterpolation<double> LinearInterpolation

## ◆ PositionType

typedef DPosition<1> PositionType

## Constructor & Destructor Documentation

## ◆ InterpolationModel() [1/2]

InterpolationModel | ( |  | ) |

inline

Default constructor.

## ◆ InterpolationModel() [2/2]

InterpolationModel | ( | const InterpolationModel & | source | ) |

inline

copy constructor

## ◆ ~InterpolationModel()

~InterpolationModel | ( |  | ) |

inline override

destructor

## Member Function Documentation

## ◆ getCenter()

virtual CoordinateType getCenter | ( |  | ) | const

inline virtual

"center" of the model, particular definition (depends on the derived model)

Reimplemented in IsotopeModel, ExtendedIsotopeModel, EGHModel, BiGaussModel, GaussModel, and EmgModel.

## ◆ getIntensity() [1/2]

IntensityType getIntensity | ( | const PositionType & | pos | ) | const

inline override

access model predicted intensity at position `pos`

Referenced by MaxLikeliFitter1D::fitOffset_().

## ◆ getIntensity() [2/2]

IntensityType getIntensity | ( | CoordinateType | coord | ) | const

inline

access model predicted intensity at position `pos`

## ◆ getInterpolation()

const LinearInterpolation& getInterpolation | ( |  | ) | const

inline

Returns the interpolation class.

Referenced by MaxLikeliFitter1D::fitOffset_().

## ◆ getSamples()

void getSamples | ( | SamplesType & | cont | ) | const

inline override virtual

get reasonable set of samples from the model (i.e. for printing)

Implements BaseModel< 1 >.

## ◆ getScalingFactor()

CoordinateType getScalingFactor | ( |  | ) | const

inline

get the scaling for the model

A scaling factor of `scaling` means that the area under the model equals `scaling`. Default is 1.

## ◆ operator=()

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

inline virtual

assignment operator

References InterpolationModel::interpolation_, InterpolationModel::interpolation_step_, BaseModel< D >::operator=(), and InterpolationModel::scaling_.

## ◆ setInterpolationStep()

void setInterpolationStep | ( | CoordinateType | interpolation_step | ) |

inline

Set the interpolation step for the linear interpolation of the model.

For setting to take affect, call setSamples().

## ◆ setOffset()

virtual void setOffset | ( | CoordinateType | offset | ) |

inline virtual

set the offset of the model

The whole model will be shifted to the new offset without being recomputed all over. Setting takes affect immediately.

Reimplemented in IsotopeModel, ExtendedIsotopeModel, EGHModel, BiGaussModel, GaussModel, and EmgModel.

Referenced by MaxLikeliFitter1D::fitOffset_().

## ◆ setSamples()

virtual void setSamples | ( |  | ) |

inline virtual

set sample/supporting points of interpolation wrt params.

Reimplemented in ExtendedIsotopeModel, EGHModel, BiGaussModel, GaussModel, and EmgModel.

## ◆ setScalingFactor()

void setScalingFactor | ( | CoordinateType | scaling | ) |

inline

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

inline 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.

Reimplemented in IsotopeModel.

References BaseModel< D >::updateMembers_().

## Member Data Documentation

## ◆ interpolation_

LinearInterpolation interpolation_

protected

Referenced by InterpolationModel::operator=().

## ◆ interpolation_step_

CoordinateType interpolation_step_

protected

Referenced by InterpolationModel::operator=().

## ◆ scaling_

CoordinateType scaling_

protected

Referenced by InterpolationModel::operator=().