SavitzkyGolayFilter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Alexandra Zerck $
// $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/MSExperiment.h>

#include <gsl/gsl_vector.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_linalg.h>
#include <gsl/gsl_permutation.h>
#include <gsl/gsl_pow_int.h>

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

    virtual ~SavitzkyGolayFilter();

    template <typename PeakType>
    void filter(MSSpectrum<PeakType> & spectrum)
    {
      UInt n = (UInt)spectrum.size();

      typename MSSpectrum<PeakType>::iterator first = spectrum.begin();
      typename MSSpectrum<PeakType>::iterator last = spectrum.end();

      //copy the data AND META DATA to the output container
      MSSpectrum<PeakType> output = spectrum;

      if (frame_size_ > n)
      {
        return;
      }

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

      typename MSSpectrum<PeakType>::iterator it_forward;
      typename MSSpectrum<PeakType>::iterator it_help;
      typename MSSpectrum<PeakType>::iterator out_it = output.begin();

      // compute the transient on
      for (i = 0; i <= mid; ++i)
      {
        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
      it_help = (last - mid);
      while (first != it_help)
      {
        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)
      {
        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;
      }

      spectrum = output;
    }

    template <typename PeakType>
    void filterExperiment(MSExperiment<PeakType> & map)
    {
      startProgress(0, map.size(), "smoothing data");
      for (Size i = 0; i < map.size(); ++i)
      {
        filter(map[i]);
        setProgress(i);
      }
      endProgress();
    }

protected:
    std::vector<DoubleReal> coeffs_;
    UInt frame_size_;
    UInt order_;
    // Docu in base class
    virtual void updateMembers_();

  };

} // namespace OpenMS
#endif // OPENMS_FILTERING_SMOOTHING_SAVITZKYGOLAYFILTER_H