TraceFitter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Timo Sachsenberg$
// $Authors: Stephan Aiche, Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmPickedHelperStructs.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/Peak1D.h>
 
// forward decl
namespace Eigen
{
    template<typename _Scalar, int _Rows, int _Cols, int _Options, int _MaxRows, int _MaxCols>
    class Matrix;
    using MatrixXd = Matrix<double, -1, -1, 0, -1, -1>;
    using VectorXd = Matrix<double, -1, 1, 0, -1, 1>;
}
 
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 Eigen::VectorXd& x, Eigen::VectorXd& fvec) = 0;
      // compute Jacobian matrix for the different parameters
      virtual int df(const Eigen::VectorXd& x, Eigen::MatrixXd& 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 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 Eigen::VectorXd& s) = 0;
    void optimize_(Eigen::VectorXd& x_init, GenericFunctor& functor);
 
    SignedSize max_iterations_;
    bool weighted_;
 
  };
 
}