| OpenMS 2.5.0

Classes | Public Member Functions | Protected Member Functions | Protected Attributes | Static Protected Attributes | List of all members
EGHTraceFitter Class Reference

A RT Profile fitter using an Exponential Gaussian Hybrid background model. More...

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

Inheritance diagram for EGHTraceFitter:

## Classes

class | EGHTraceFunctor

## Public Member Functions

| EGHTraceFitter ()
| EGHTraceFitter (const EGHTraceFitter &other)
EGHTraceFitter & | operator= (const EGHTraceFitter &source)
| ~EGHTraceFitter () override
void | fit (FeatureFinderAlgorithmPickedHelperStructs::MassTraces &traces) override
double | getLowerRTBound () const override
double | getTau () const
double | getUpperRTBound () const override
double | getHeight () const override
double | getSigma () const
double | getCenter () const override
bool | checkMaximalRTSpan (const double max_rt_span) override
bool | checkMinimalRTSpan (const std::pair< double, double > &rt_bounds, const double min_rt_span) override
double | getValue (double rt) const override
double | getArea () override
double | getFWHM () const override
String | getGnuplotFormula (const FeatureFinderAlgorithmPickedHelperStructs::MassTrace &trace, const char function_name, const double baseline, const double rt_shift) override
Public Member Functions inherited from TraceFitter
| TraceFitter ()
| default constructor More...
| TraceFitter (const TraceFitter &source)
| copy constructor More...
virtual TraceFitter & | operator= (const TraceFitter &source)
| assignment operator More...
| ~TraceFitter () override
| destructor More...
double | computeTheoretical (const FeatureFinderAlgorithmPickedHelperStructs::MassTrace &trace, Size k)
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

std::pair< double, double > | getAlphaBoundaries_ (const double alpha) const
| Return an ordered pair of the positions where the EGH reaches a height of alpha * height of the EGH. More...
void | getOptimizedParameters_ (const Eigen::VectorXd &x_init) override
void | setInitialParameters_ (FeatureFinderAlgorithmPickedHelperStructs::MassTraces &traces)
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 TraceFitter
void | updateMembers_ () override
| This method is used to update extra member variables at the end of the setParameters() method. More...
void | optimize_ (Eigen::VectorXd &x_init, GenericFunctor &functor)
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

double | apex_rt_
double | height_
double | sigma_
double | tau_
std::pair< double, double > | sigma_5_bound_
double | region_rt_span_
Protected Attributes inherited from TraceFitter
SignedSize | max_iterations_
| Maximum number of iterations. More...
bool | weighted_
| Whether to weight mass traces by theoretical intensity during the optimization. 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...

## Static Protected Attributes

static const double | EPSILON_COEFS_ []
| Coefficients to calculate the proportionality factor for the peak area. More...
static const Size | NUM_PARAMS_

## Detailed Description

A RT Profile fitter using an Exponential Gaussian Hybrid background model.

Lan K, Jorgenson JW. A hybrid of exponential and gaussian functions as a simple model of asymmetric chromatographic peaks. Journal of Chromatography A. 915 (1-2)p. 1-13. Available at: http://linkinghub.elsevier.com/retrieve/pii/S0021967301005945

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
max_iteration | int | 500 |  | Maximum number of iterations used by the Levenberg-Marquardt algorithm.
weighted | string | false | true, false | Weight mass traces according to their theoretical intensities.

Note:

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

Experimental classes:
  Needs further testing on real data. Note that the tests are currently also focused on testing the EGH as replacement for the gaussian.

## Constructor & Destructor Documentation

## ◆ EGHTraceFitter() [1/2]

EGHTraceFitter | ( |  | ) |

## ◆ EGHTraceFitter() [2/2]

EGHTraceFitter | ( | const EGHTraceFitter & | other | ) |

## ◆ ~EGHTraceFitter()

~EGHTraceFitter | ( |  | ) |

override

## Member Function Documentation

## ◆ checkMaximalRTSpan()

bool checkMaximalRTSpan | ( | const double | max_rt_span | ) |

override virtual

Checks if the fitted model is not to big

Parameters

  max_rt_span | Maximum RT span in relation to extended area that the model is allowed to have

Implements TraceFitter.

## ◆ checkMinimalRTSpan()

bool checkMinimalRTSpan | ( | const std::pair< double, double > & | rt_bounds,
|  | const double | min_rt_span
| ) |  |

override virtual

Checks if the fitted model fills out at least 'min_rt_span' of the RT span

Parameters

  rt_bounds | RT boundaries of the fitted model
  min_rt_span | Minimum RT span in relation to extended area that has to remain after model fitting

Implements TraceFitter.

## ◆ fit()

void fit | ( | FeatureFinderAlgorithmPickedHelperStructs::MassTraces & | traces | ) |

override virtual

Main method of the TraceFitter which triggers the actual fitting.

Implements TraceFitter.

## ◆ getAlphaBoundaries_()

std::pair<double, double> getAlphaBoundaries_ | ( | const double | alpha | ) | const

protected

Return an ordered pair of the positions where the EGH reaches a height of alpha * height of the EGH.

Parameters

  alpha | The alpha at which the boundaries should be computed

## ◆ getArea()

double getArea | ( |  | ) |

override virtual

Returns the peak area of the fitted model

Implements TraceFitter.

## ◆ getCenter()

double getCenter | ( |  | ) | const

override virtual

Returns the center position of the fitted model

Implements TraceFitter.

## ◆ getFWHM()

double getFWHM | ( |  | ) | const

override virtual

Returns the mass trace width at half max (FWHM)

Implements TraceFitter.

## ◆ getGnuplotFormula()

String getGnuplotFormula | ( | const FeatureFinderAlgorithmPickedHelperStructs::MassTrace & | trace,
|  | const char | function_name,
|  | const double | baseline,
|  | const double | rt_shift
| ) |  |

override virtual

Returns a textual representation of the fitted model function, that can be plotted using Gnuplot

Parameters

  trace | The mass trace that should be plotted
  function_name | The name of the function (e.g. f(x) -> function_name = f)
  baseline | The intensity of the baseline
  rt_shift | A shift value, that allows to plot all RT profiles side by side, even if they would overlap in reality. This should be 0 for the first mass trace and increase by a fixed value for each mass trace.

Implements TraceFitter.

## ◆ getHeight()

double getHeight | ( |  | ) | const

override virtual

Returns the height of the fitted model

Implements TraceFitter.

## ◆ getLowerRTBound()

double getLowerRTBound | ( |  | ) | const

override virtual

Returns the lower bound of the fitted RT model

Implements TraceFitter.

## ◆ getOptimizedParameters_()

void getOptimizedParameters_ | ( | const Eigen::VectorXd & |  | ) |

override protected virtual

Updates all member variables to the fitted values stored in the solver.

Parameters

  s | The solver containing the fitted parameter values.

Implements TraceFitter.

## ◆ getSigma()

double getSigma | ( |  | ) | const

## ◆ getTau()

double getTau | ( |  | ) | const

## ◆ getUpperRTBound()

double getUpperRTBound | ( |  | ) | const

override virtual

Returns the upper bound of the fitted RT model

Implements TraceFitter.

## ◆ getValue()

double getValue | ( | double | rt | ) | const

override virtual

Evaluate the fitted model at a time point

Implements TraceFitter.

## ◆ operator=()

EGHTraceFitter& operator= | ( | const EGHTraceFitter & | source | ) |

## ◆ setInitialParameters_()

void setInitialParameters_ | ( | FeatureFinderAlgorithmPickedHelperStructs::MassTraces & | traces | ) |

protected

## ◆ 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

## ◆ apex_rt_

double apex_rt_

protected

## ◆ EPSILON_COEFS_

const double EPSILON_COEFS_[]

static protected

Coefficients to calculate the proportionality factor for the peak area.

## ◆ height_

double height_

protected

## ◆ NUM_PARAMS_

const Size NUM_PARAMS_

static protected

## ◆ region_rt_span_

double region_rt_span_

protected

## ◆ sigma_

double sigma_

protected

## ◆ sigma_5_bound_

std::pair<double, double> sigma_5_bound_

protected

## ◆ tau_

double tau_

protected