// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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
{
  /**
   @brief This class implements an external calibration for TOF data using external calibrant spectra.

   The procedure is very similar to the one described in Gobom et al. (Anal Chem. 2002, 74 (15) pp 3915-23).
   The input experiment data need to be flight times. They are converted into m/z-values using the
       calibrant spectra. The calibrant spectra and their expected masses are used to determine the
       quadratic dependence of TOF and m/z values.

       @note The input spectra need to contain flight times.

       @note The peaks must be sorted according to ascending m/z!

     @ingroup SignalProcessing
*/
  class OPENMS_DLLAPI TOFCalibration :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:

    /// Default constructor
    TOFCalibration();

    /// Destructor
    ~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);

    /// Non-mutable access to the first calibration constant
    inline const std::vector<double> & getML1s() const {return ml1s_; }
    ///mutable access to the first calibration constant
    inline void setML1s(const std::vector<double> & ml1s)
    {
      ml1s_ = ml1s;
    }

    /// Non-mutable access to the second calibration constant
    inline const std::vector<double> & getML2s() const {return ml2s_; }
    /// mutable access to the second calibration constant
    inline void setML2s(const std::vector<double> & ml2s)
    {
      ml2s_ = ml2s;
    }

    /// Non-mutable access to the third calibration constant
    inline const std::vector<double> & getML3s() const {return ml3s_; }
    /// mutable access to the third calibration constant
    inline void setML3s(const std::vector<double> & ml3s)
    {
      ml3s_ = ml3s;
    }

private:
    ///the calibrant spectra still using flight times instead of m/z-values
    PeakMap calib_peaks_ft_;


    /// the expected calibrant masses
    std::vector<double> exp_masses_;

    /// error in ppm after quadratic fit
    std::map<double, std::vector<double> > errors_;

    /// median errors
    std::vector<double> error_medians_;

    ///
    std::vector<double> calib_masses_;

    ///calibration constants from the instrument needed for the conversion of the calibrant spectra
    std::vector<double> ml1s_;
    std::vector<double> ml2s_;
    std::vector<double> ml3s_;

    /// all coefficients of the quadratic fit
    std::vector<double> coeff_quad_fit_;

    /// mean coefficients
    double a_, b_, c_;


    /// Calculates the coefficients of the quadratic fit used for external calibration.
    void calculateCalibCoeffs_(PeakMap & calib_peaks_ft);


    /// determines the monoisotopic peaks
    void getMonoisotopicPeaks_(PeakMap & calib_peaks, std::vector<std::vector<unsigned int> > & monoiso_peaks);

    /**
             @brief Applies the conversion from TOF to m/z-values to all peaks

             Either a 2-point or a 3-point time of flight conversion can be used, as well as
             different constants for each calibrant spectra or one set for all of them.

             The 2-point equation is mass = ml1/10^12 * (TOF * 1000 - ml2).
             The 3-point equation is time = ml2 + sqrt(10^12/ml1 * mass) +  ml3*mass.

        */
    void applyTOFConversion_(PeakMap & calib_spectra);

    /// determine the monoisotopic masses that have matching expected masses
    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);

    /// Calculate the mass value for a given flight time using the coefficients of the quadratic fit in a specific spectrum.
    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];
    }

    /// Calculate the mass value for a given flight time using the averaged coefficients of the quadratic fit.
    inline double mQAv_(double ft) const
    {
      return a_ + ft * b_ + ft * ft * c_;
    }

    /// Calculate the average errors of the reference masses over all scans
    void averageErrors_();

    /// Average the coefficients of the quadratic fit
    void averageCoefficients_();
  };

} // namespace OpenMS

