libopenms-dev 1.11.1-3 / usr / include / OpenMS / TRANSFORMATIONS / FEATUREFINDER / EmgFitter1D.h

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// $Maintainer: Clemens Groepl $
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#ifndef OPENMS_TRANSFORMATIONS_FEATUREFINDER_EMGFITTER1D_H
#define OPENMS_TRANSFORMATIONS_FEATUREFINDER_EMGFITTER1D_H

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/LevMarqFitter1D.h>

namespace OpenMS
{
  /**
    @brief Exponentially modified gaussian distribution fitter (1-dim.) using Levenberg-Marquardt algorithm (GSL implementation) for parameter optimization.

    @htmlinclude OpenMS_EmgFitter1D.parameters
  */
  class OPENMS_DLLAPI EmgFitter1D :
    public LevMarqFitter1D
  {
public:

    /// Default constructor
    EmgFitter1D();

    /// copy constructor
    EmgFitter1D(const EmgFitter1D & source);

    /// destructor
    virtual ~EmgFitter1D();

    /// assignment operator
    virtual EmgFitter1D & operator=(const EmgFitter1D & source);

    /// create new EmgFitter1D object (function needed by Factory)
    static Fitter1D * create()
    {
      return new EmgFitter1D();
    }

    /// name of the model (needed by Factory)
    static const String getProductName()
    {
      return "EmgFitter1D";
    }

    /// return interpolation model
    QualityType fit1d(const RawDataArrayType & range, InterpolationModel * & model);

protected:

    /// Helper struct (contains the size of an area and a raw data container)
    struct Data
    {
      typedef Peak1D PeakType;
      typedef std::vector<PeakType> RawDataArrayType;

      Size n;
      RawDataArrayType set;
    };

    /// Compute start parameter
    virtual void setInitialParameters_(const RawDataArrayType & set);

    /// Evaluation of the target function for nonlinear optimization
    static Int residual_(const gsl_vector * x, void * params, gsl_vector * f);

    /// Compute the Jacobian matrix, where each row of the matrix corresponds to a point in the data
    static Int jacobian_(const gsl_vector * x, void * params, gsl_matrix * J);

    /// Driver function for the evaluation of function and jacobian
    static Int evaluate_(const gsl_vector * x, void * params, gsl_vector * f, gsl_matrix * J);

    /** Diplay the intermediate state of the solution. The solver state contains
        the vector s->x which is the current position, and the vector s->f with
        corresponding function values */
    void printState_(Int iter, gsl_multifit_fdfsolver * s);

    /// Parameter of emg - peak height
    CoordinateType height_;
    /// Parameter of emg - peak width
    CoordinateType width_;
    /// Parameter of emg - peak symmetry
    CoordinateType symmetry_;
    /// Parameter of emg - peak retention time
    CoordinateType retention_;

    void updateMembers_();
  };

}

#endif // OPENMS_TRANSFORMATIONS_FEATUREFINDER_EMGFITTER1D_H