TraceFitter.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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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_;

  };

}