OptimizePeakDeconvolution.h

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#ifndef OPENMS_TRANSFORMATIONS_RAW2PEAK_OPTIMIZEPEAKDECONVOLUTION_H
#define OPENMS_TRANSFORMATIONS_RAW2PEAK_OPTIMIZEPEAKDECONVOLUTION_H

#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakShape.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/OptimizePick.h>
#include <gsl/gsl_vector.h>
#include <gsl/gsl_multifit_nlin.h>
#include <gsl/gsl_blas.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

//#define DEBUG_DECONV
#include <iostream>
#ifdef DEBUG_DECONV
#include <iostream>
#include <fstream>
#endif
#include <vector>

namespace OpenMS
{

  namespace OptimizationFunctions
  {

    struct OPENMS_DLLAPI PenaltyFactorsIntensity :
      public PenaltyFactors
    {
      PenaltyFactorsIntensity() :
        PenaltyFactors(), height(0){}
      PenaltyFactorsIntensity(const PenaltyFactorsIntensity & p) :
        PenaltyFactors(p), height(p.height) {}
      inline PenaltyFactorsIntensity & operator=(const PenaltyFactorsIntensity & p)
      {
        height = p.height;
        pos = p.pos;
        lWidth = p.lWidth;
        rWidth = p.rWidth;

        return *this;
      }

      ~PenaltyFactorsIntensity(){}

      DoubleReal height;


    };



  } //namespace OptimizationFunctions

  class OPENMS_DLLAPI OptimizePeakDeconvolution :
    public DefaultParamHandler
  {
public:
    typedef std::vector<Peak1D> RawDataVector;
    typedef RawDataVector::iterator PeakIterator;

    struct Data
    {
      std::vector<PeakShape> peaks;
      std::vector<DoubleReal> positions;
      std::vector<DoubleReal> signal;
      OptimizationFunctions::PenaltyFactorsIntensity penalties;
      Int charge;
    };




    OptimizePeakDeconvolution();

    OptimizePeakDeconvolution(const OptimizePeakDeconvolution & opt) :
      DefaultParamHandler(opt),
      penalties_(opt.penalties_),
      charge_(opt.charge_){}

    virtual ~OptimizePeakDeconvolution(){}

    inline OptimizePeakDeconvolution & operator=(const OptimizePeakDeconvolution & opt)
    {
      DefaultParamHandler::operator=(opt);
      penalties_ = opt.penalties_;
      charge_ = opt.charge_;

      return *this;
    }




    inline const OptimizationFunctions::PenaltyFactorsIntensity & getPenalties() const { return penalties_; }
    inline void setPenalties(const OptimizationFunctions::PenaltyFactorsIntensity & penalties)
    {
      penalties_ = penalties;
      param_.setValue("penalties:left_width", penalties_.lWidth);
      param_.setValue("penalties:right_width", penalties_.rWidth);
      param_.setValue("penalties:height", penalties_.height);
      param_.setValue("penalties:position", penalties_.pos);
    }

    inline Int getCharge() const { return charge_; }
    inline void setCharge(const Int charge) { charge_ = charge; }


    bool optimize(std::vector<PeakShape> & peaks, Data & data);

protected:
    // Penalty factors for some parameter in the optimization
    OptimizationFunctions::PenaltyFactorsIntensity penalties_;

    Int charge_;

    static const DoubleReal dist_;

    Size getNumberOfPeaks_(Int charge, std::vector<PeakShape> & temp_shapes, Data & data);

    // After each iteration the fwhm of all peaks is checked whether it isn't too large
    bool checkFWHM_(std::vector<PeakShape> & peaks, gsl_multifit_fdfsolver * & fit);

    void updateMembers_();
  }; // class

} // namespace OpenMS


#endif