Method calibrate

src/openms/source/FILTERING/CALIBRATION/InternalCalibration.cpp:278–551

  }

  bool InternalCalibration::calibrate(PeakMap& exp, 
                                      const IntList& target_mslvl,
                                      MZTrafoModel::MODELTYPE model_type,
                                      double rt_chunk,
                                      bool use_RANSAC,
                                      double post_ppm_median,
                                      double post_ppm_MAD,
                                      const String& file_models,
                                      const String& file_models_plot,
                                      const String& file_residuals,
                                      const String& file_residuals_plot,
                                      const String& rscript_executable_)
  {
    QString rscript_executable = rscript_executable_.toQString();

    // ensure sorting; required for finding RT ranges and lock masses
    if (!exp.isSorted(true))
    {
      exp.sortSpectra(true);
    }

    startProgress(0, exp.size(), "Applying calibration to data");

    std::vector<MZTrafoModel> tms; // each spectrum gets its own model (params are cheap to store)
    std::map<Size, Size> invalid_models; // indices from tms[] -> exp[]; where model creation failed (e..g, not enough calibration points)
    bool hasValidModels(false); // was at least one model valid?
    bool global_model = (rt_chunk < 0);
    if (global_model)
    { // build one global modal
      OPENMS_LOG_INFO << "Building a global model..." << std::endl;
      tms.emplace_back();
      tms[0].train(cal_data_, model_type, use_RANSAC);
      if (MZTrafoModel::isValidModel(tms[0]))
      {
        applyTransformation(exp, target_mslvl, tms[0]);
        hasValidModels = true;
      }
    }
    else
    { // one model per spectrum (not all might be needed, if certain MS levels are excluded from calibration)
      tms.reserve(exp.size());
      // go through spectra and calibrate
      Size i(0), i_mslvl(0);
      for (PeakMap::Iterator it = exp.begin(); it != exp.end(); ++it, ++i)
      {
        setProgress(i);

        // skip this MS level?
        if (!(ListUtils::contains(target_mslvl, it->getMSLevel()) ||     // scan m/z needs correction
              ListUtils::contains(target_mslvl, it->getMSLevel() - 1)))  // precursor m/z needs correction
        {
          continue;
        }

        //
        // build model
        //
        tms.emplace_back();