TOFCalibration.h

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// $Maintainer: Alexandra Zerck $
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#ifndef OPENMS_FILTERING_CALIBRATION_TOFCALIBRATION_H
#define OPENMS_FILTERING_CALIBRATION_TOFCALIBRATION_H


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

#include <iostream>
#include <vector>
#include <map>
#include <gsl/gsl_multifit.h>
#include <gsl/gsl_spline.h>

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

    TOFCalibration();

    ~TOFCalibration();


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

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

    */
    template <typename PeakType>
    void pickAndCalibrate(MSExperiment<Peak1D> & calib_spectra, MSExperiment<PeakType> & 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.

    */
    template <typename PeakType>
    void calibrate(MSExperiment<Peak1D> & calib_spectra, MSExperiment<PeakType> & 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:
    MSExperiment<> 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_;


    gsl_interp_accel * acc_;

    gsl_spline * spline_;

    void calculateCalibCoeffs_(MSExperiment<> & calib_peaks_ft);


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

    void applyTOFConversion_(MSExperiment<> & calib_spectra);

    void matchMasses_(MSExperiment<> & 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_();
  };

  template <typename PeakType>
  void TOFCalibration::pickAndCalibrate(MSExperiment<Peak1D> & calib_spectra, MSExperiment<PeakType> & exp, std::vector<double> & exp_masses)
  {
    MSExperiment<Peak1D> p_calib_spectra;

    // pick peaks
    PeakPickerCWT pp;
    pp.setParameters(param_.copy("PeakPicker:", true));
    pp.pickExperiment(calib_spectra, p_calib_spectra);

    //calibrate
    calibrate(p_calib_spectra, exp, exp_masses);
  }

  template <typename PeakType>
  void TOFCalibration::calibrate(MSExperiment<Peak1D> & calib_spectra, MSExperiment<PeakType> & exp, std::vector<double> & exp_masses)
  {
    exp_masses_ = exp_masses;
    calculateCalibCoeffs_(calib_spectra);
    double m;
    for (unsigned int spec = 0; spec <  exp.size(); ++spec)
    {
      for (unsigned int peak = 0; peak <  exp[spec].size(); ++peak)
      {
        m = mQAv_(exp[spec][peak].getMZ());
        exp[spec][peak].setPos(m - gsl_spline_eval(spline_, m, acc_));
      }
    }
  }

} // namespace OpenMS

#endif // OPENMS_FILTERING_CALIBRATION_TOFCALIBRATION_H