SavitzkyGolayFilter.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Eva Lange $
// --------------------------------------------------------------------------

#ifndef OPENMS_FILTERING_SMOOTHING_SAVITZKYGOLAYFILTER_H
#define OPENMS_FILTERING_SMOOTHING_SAVITZKYGOLAYFILTER_H

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.h>

namespace OpenMS
{
  class OPENMS_DLLAPI SavitzkyGolayFilter :
    public ProgressLogger,
    public DefaultParamHandler
  {
public:
    SavitzkyGolayFilter();

    virtual ~SavitzkyGolayFilter();

    // low level template to filters spectra and chromatograms
    // raw data and meta data needs to be copied to the output container before calling this function
    template<class InputIt, class OutputIt>
    void filter(InputIt first, InputIt last, OutputIt d_first)
    {
      size_t n = std::distance(first, last);

      if (frame_size_ > n) { return; }

      int i;
      UInt j;
      int mid = (frame_size_ / 2);
      double help;

      // compute the transient on
      OutputIt out_it = d_first;

      for (i = 0; i <= mid; ++i)
      {
        InputIt it_forward = (first - i);
        help = 0;
        for (j = 0; j < frame_size_; ++j)
        {
          help += it_forward->getIntensity() * coeffs_[(i + 1) * frame_size_ - 1 - j];
          ++it_forward;
        }

        out_it->setPosition(first->getPosition());
        out_it->setIntensity(std::max(0.0, help));
        ++out_it;
        ++first;
      }

      // compute the steady state output
      InputIt it_help = (last - mid);

      while (first != it_help)
      {
        InputIt it_forward = (first - mid);
        help = 0;

        for (j = 0; j < frame_size_; ++j)
        {
          help += it_forward->getIntensity() * coeffs_[mid * frame_size_ + j];
          ++it_forward;
        }

        out_it->setPosition(first->getPosition());
        out_it->setIntensity(std::max(0.0, help));
        ++out_it;
        ++first;
      }

      // compute the transient off
      for (i = (mid - 1); i >= 0; --i)
      {
        InputIt it_forward = (first - (frame_size_ - i - 1));
        help = 0;

        for (j = 0; j < frame_size_; ++j)
        {
          help += it_forward->getIntensity() * coeffs_[i * frame_size_ + j];
          ++it_forward;
        }

        out_it->setPosition(first->getPosition());
        out_it->setIntensity(std::max(0.0, help));
        ++out_it;
        ++first;
      }

    }

    void filter(MSSpectrum & spectrum)
    {
      // copy the data AND META DATA to the output container
      MSSpectrum output = spectrum;
      // filter
      filter(spectrum.begin(), spectrum.end(), output.begin());
      // swap back
      std::swap(spectrum, output);
    }

    void filter(MSChromatogram & chromatogram)
    {
      // copy the data AND META DATA to the output container
      MSChromatogram output = chromatogram;
      // filter
      filter(chromatogram.begin(), chromatogram.end(), output.begin());
      // swap back
      std::swap(chromatogram, output);
    }

    void filterExperiment(PeakMap & map)
    {
      Size progress = 0;
      startProgress(0, map.size() + map.getChromatograms().size(), "smoothing data");
      for (Size i = 0; i < map.size(); ++i)
      {
        filter(map[i]);
        setProgress(++progress);
      }
      for (Size i = 0; i < map.getChromatograms().size(); ++i)
      {
        filter(map.getChromatogram(i));
        setProgress(++progress);
      }
      endProgress();
    }

protected:
    std::vector<double> coeffs_;

    UInt frame_size_;

    UInt order_;

    // Docu in base class
    virtual void updateMembers_();
  };

} // namespace OpenMS
#endif // OPENMS_FILTERING_SMOOTHING_SAVITZKYGOLAYFILTER_H