TraceFitter.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg$
// $Authors: Stephan Aiche, Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/FEATUREFINDER/FeatureFinderAlgorithmPickedHelperStructs.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/Peak1D.h>
#include <vector>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI TraceFitter :
    public DefaultParamHandler
  {
 
public:
    //TODO: This is copy and paste from LevMarqFitter1d.h. Make a generic wrapper for LM optimization
    class GenericFunctor
    {
public:
      int inputs() const;
      int values() const;
 
      GenericFunctor(int dimensions, int num_data_points);
 
      virtual ~GenericFunctor();
 
      virtual int operator()(const double* x, double* fvec) = 0;
 
      virtual int df(const double* x, double* J) = 0;
 
protected:
      const int m_inputs, m_values;
    };
 
    TraceFitter();
 
    TraceFitter(const TraceFitter& source);
 
    TraceFitter& operator=(const TraceFitter& source);
 
    ~TraceFitter() override;
 
    virtual void fit(FeatureFinderAlgorithmPickedHelperStructs::MassTraces& traces) = 0;
 
    virtual double getLowerRTBound() const = 0;
 
    virtual double getUpperRTBound() const = 0;
 
    virtual double getHeight() const = 0;
 
    virtual double getCenter() const = 0;
 
    virtual double getFWHM() const = 0;
 
    virtual double getValue(double rt) const = 0;
 
    double computeTheoretical(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace& trace, Size k) const;
 
    virtual bool checkMinimalRTSpan(const std::pair<double, double>& rt_bounds, const double min_rt_span) = 0;
 
    virtual bool checkMaximalRTSpan(const double max_rt_span) = 0;
 
    virtual double getArea() = 0;
 
    virtual std::string getGnuplotFormula(const FeatureFinderAlgorithmPickedHelperStructs::MassTrace& trace, const char function_name, const double baseline, const double rt_shift) = 0;
 
protected:
    struct ModelData
    {
      FeatureFinderAlgorithmPickedHelperStructs::MassTraces* traces_ptr; 
      bool weighted;                                                     
    };
 
    void updateMembers_() override;
 
    virtual void getOptimizedParameters_(const std::vector<double>& s) = 0;
 
    void optimize_(std::vector<double>& x_init, GenericFunctor& functor);
 
    SignedSize max_iterations_;
    bool weighted_;
 
  };
 
}