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 2002-2023.
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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) const
    {
      return a_ + ft * b_ + ft * ft * c_;
    }
 
    void averageErrors_();
 
    void averageCoefficients_();
  };
 
} // namespace OpenMS