PeakPickerIM.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Author: Timo Sachsenberg, Mohammed Alhigaylan $
// $Maintainer: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/DATASTRUCTURES/Param.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
 
namespace OpenMS
{
  class OPENMS_DLLAPI PeakPickerIM : public DefaultParamHandler
  {
  public:
    PeakPickerIM();
 
    ~PeakPickerIM() override = default;
 
    void pickIMTraces(MSSpectrum& spectrum);
 
    using DefaultParamHandler::setParameters;
    using DefaultParamHandler::getParameters;
 
 
    void pickIMCluster(MSSpectrum& spec) const;
 
    void pickIMElutionProfiles(MSSpectrum& input) const;
 
  protected:
    void updateMembers_() override;
 
  private:
    double computeOptimalSamplingRate(const std::vector<MSSpectrum>& spectra);
 
    void sumFrame_(const MSSpectrum& input_spectrum, MSSpectrum& output_spectrum, double tolerance = 0.01, bool use_ppm = true);
 
    std::pair<double, double> ppmBounds(double mz, double ppm);
 
    std::vector<MSSpectrum> extractIonMobilityTraces(
      const MSSpectrum& picked_spectrum,
      const MSSpectrum& raw_spectrum);
 
    MSSpectrum computeCentroids_(const std::vector<MSSpectrum>& mobilogram_traces,
                              const std::vector<MSSpectrum>& picked_traces);
 
    double sum_tolerance_mz_{1.0};
    double gauss_ppm_tolerance_{5.0};
    double sum_tolerance_im_{0.0006};
    int sgolay_frame_length_{5};
    int sgolay_polynomial_order_{3};
    double ppm_tolerance_cluster_{50.0};
    double im_tolerance_cluster_{0.1};
 
    double ppm_tolerance_elution_{50.0};
  };
} // namespace OpenMS