コード例 #1
0
  void MapAlignmentTransformer::transformRetentionTimes(
    MSExperiment<>& msexp, const TransformationDescription& trafo,
    bool store_original_rt)
  {
    msexp.clearRanges();

    // Transform spectra
    for (MSExperiment<>::iterator mse_iter = msexp.begin();
         mse_iter != msexp.end(); ++mse_iter)
    {
      double rt = mse_iter->getRT();
      if (store_original_rt) storeOriginalRT_(*mse_iter, rt);
      mse_iter->setRT(trafo.apply(rt));
    }

    // Also transform chromatograms
    for (Size i = 0; i < msexp.getNrChromatograms(); ++i)
    {
      MSChromatogram<ChromatogramPeak>& chromatogram = msexp.getChromatogram(i);
      vector<double> original_rts;
      if (store_original_rt) original_rts.reserve(chromatogram.size());
      for (Size j = 0; j < chromatogram.size(); j++)
      {
        double rt = chromatogram[j].getRT();
        if (store_original_rt) original_rts.push_back(rt);
        chromatogram[j].setRT(trafo.apply(rt));
      }
      if (store_original_rt && !chromatogram.metaValueExists("original_rt"))
      {
        chromatogram.setMetaValue("original_rt", original_rts);
      }
    }

    msexp.updateRanges();
  }
コード例 #2
0
  ExitCodes main_(int, const char **)
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------
    in = getStringOption_("in");
    out = getStringOption_("out");
    String process_option = getStringOption_("processOption");

    Param filter_param = getParam_().copy("algorithm:", true);
    writeDebug_("Parameters passed to filter", filter_param, 3);

    SavitzkyGolayFilter sgolay;
    sgolay.setLogType(log_type_);
    sgolay.setParameters(filter_param);

    if (process_option == "lowmemory")
    {
      return doLowMemAlgorithm(sgolay);
    }

    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------
    MzMLFile mz_data_file;
    mz_data_file.setLogType(log_type_);
    MSExperiment<Peak1D> exp;
    mz_data_file.load(in, exp);

    if (exp.empty() && exp.getChromatograms().size() == 0)
    {
      LOG_WARN << "The given file does not contain any conventional peak data, but might"
                  " contain chromatograms. This tool currently cannot handle them, sorry.";
      return INCOMPATIBLE_INPUT_DATA;
    }
    //check for peak type (profile data required)
    if (!exp.empty() && PeakTypeEstimator().estimateType(exp[0].begin(), exp[0].end()) == SpectrumSettings::PEAKS)
    {
      writeLog_("Warning: OpenMS peak type estimation indicates that this is not profile data!");
    }

    //check if spectra are sorted
    for (Size i = 0; i < exp.size(); ++i)
    {
      if (!exp[i].isSorted())
      {
        writeLog_("Error: Not all spectra are sorted according to peak m/z positions. Use FileFilter to sort the input!");
        return INCOMPATIBLE_INPUT_DATA;
      }
    }

    //check if chromatograms are sorted
    for (Size i = 0; i < exp.getChromatograms().size(); ++i)
    {
      if (!exp.getChromatogram(i).isSorted())
      {
        writeLog_("Error: Not all chromatograms are sorted according to peak m/z positions. Use FileFilter to sort the input!");
        return INCOMPATIBLE_INPUT_DATA;
      }
    }

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------
    sgolay.filterExperiment(exp);

    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------

    //annotate output with data processing info
    addDataProcessing_(exp, getProcessingInfo_(DataProcessing::SMOOTHING));

    mz_data_file.store(out, exp);

    return EXECUTION_OK;
  }