SavitzkyGolayFilter.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Eva Lange $
// --------------------------------------------------------------------------
 
#pragma once
 
#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();
 
    ~SavitzkyGolayFilter() override;
 
    // 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
    void updateMembers_() override;
  };
 
} // namespace OpenMS