TOFCalibration.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakPickerCWT.h>

#include <OpenMS/MATH/MISC/MathFunctions.h>
#include <OpenMS/MATH/MISC/CubicSpline2d.h>

#include <vector>
#include <map>

//#define DEBUG_CALIBRATION
namespace OpenMS
{
  class OPENMS_DLLAPI TOFCalibration :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:

    TOFCalibration();

    ~TOFCalibration() override;


    /*
        @ brief Apply the external calibration using raw calibrant spectra.

        @exception Exception::UnableToCalibrate is thrown if not enough reference masses are observed.

    */
    void pickAndCalibrate(PeakMap & calib_spectra, PeakMap & exp, std::vector<double> & exp_masses);

    /*
        @ brief Apply the external calibration using picked calibrant spectra.

        @exception Exception::UnableToCalibrate is thrown if not enough reference masses are observed.

    */
    void calibrate(PeakMap & calib_spectra, PeakMap & exp, std::vector<double> & exp_masses);

    inline const std::vector<double> & getML1s() const {return ml1s_; }
    inline void setML1s(const std::vector<double> & ml1s)
    {
      ml1s_ = ml1s;
    }

    inline const std::vector<double> & getML2s() const {return ml2s_; }
    inline void setML2s(const std::vector<double> & ml2s)
    {
      ml2s_ = ml2s;
    }

    inline const std::vector<double> & getML3s() const {return ml3s_; }
    inline void setML3s(const std::vector<double> & ml3s)
    {
      ml3s_ = ml3s;
    }

private:
    PeakMap calib_peaks_ft_;


    std::vector<double> exp_masses_;

    std::map<double, std::vector<double> > errors_;

    std::vector<double> error_medians_;

    std::vector<double> calib_masses_;

    std::vector<double> ml1s_;
    std::vector<double> ml2s_;
    std::vector<double> ml3s_;

    std::vector<double> coeff_quad_fit_;

    double a_, b_, c_;


    void calculateCalibCoeffs_(PeakMap & calib_peaks_ft);


    void getMonoisotopicPeaks_(PeakMap & calib_peaks, std::vector<std::vector<unsigned int> > & monoiso_peaks);

    void applyTOFConversion_(PeakMap & calib_spectra);

    void matchMasses_(PeakMap & calib_peaks, 
                      std::vector<std::vector<unsigned int> > & monoiso_peaks, 
                      std::vector<unsigned int> & obs_masses, 
                      std::vector<double> & exp_masses, 
                      unsigned int idx);

    inline double mQ_(double ft, unsigned int spec)
    {
      return coeff_quad_fit_[3 * spec] + ft * coeff_quad_fit_[3 * spec + 1] + ft * ft * coeff_quad_fit_[3 * spec + 2];
    }

    inline double mQAv_(double ft)
    {
      return a_ + ft * b_ + ft * ft * c_;
    }

    void averageErrors_();

    void averageCoefficients_();
  };

} // namespace OpenMS