LinearResampler.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 2002-2017.
//
// 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 $
// --------------------------------------------------------------------------

#ifndef OPENMS_FILTERING_TRANSFORMERS_LINEARRESAMPLER_H
#define OPENMS_FILTERING_TRANSFORMERS_LINEARRESAMPLER_H

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

#include <limits>
#include <cmath>

namespace OpenMS
{
  class OPENMS_DLLAPI LinearResampler :
    public DefaultParamHandler,
    public ProgressLogger
  {

public:

    LinearResampler() :
      DefaultParamHandler("LinearResampler")
    {
      defaults_.setValue("spacing", 0.05, "Spacing of the resampled output peaks.");
      defaultsToParam_();
    }

    ~LinearResampler()
    {
    }

    void raster(MSSpectrum& spectrum)
    {
      //return if nothing to do
      if (spectrum.empty()) return;

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

      double end_pos = (last - 1)->getMZ();
      double start_pos = first->getMZ();
      int number_raw_points = static_cast<int>(spectrum.size());
      int number_resampled_points = static_cast<int>(ceil((end_pos - start_pos) / spacing_ + 1));

      std::vector<Peak1D> resampled_peak_container;
      resampled_peak_container.resize(number_resampled_points);

      // generate the resampled peaks at positions origin+i*spacing_
      std::vector<Peak1D>::iterator it = resampled_peak_container.begin();
      for (int i = 0; i < number_resampled_points; ++i)
      {
        it->setMZ(start_pos + i * spacing_);
        ++it;
      }

      // spread the intensity h of the data point at position x to the left and right
      // adjacent resampled peaks
      double distance_left = 0.;
      double distance_right = 0.;
      int left_index = 0;
      int right_index = 0;

      it = resampled_peak_container.begin();
      for (int i = 0; i < number_raw_points; ++i)
      {
        int help = static_cast<int>(floor(((first + i)->getMZ() - start_pos) / spacing_));
        left_index = (help < 0) ? 0 : help;
        help = distance(first, last) - 1;
        right_index = (left_index >= help) ? help : left_index + 1;

        // compute the distance between x and the left adjacent resampled peak
        distance_left = fabs((first + i)->getMZ() - (it + left_index)->getMZ()) / spacing_;
        //std::cout << "Distance left " << distance_left << std::endl;
        // compute the distance between x and the right adjacent resampled peak
        distance_right = fabs((first + i)->getMZ() - (it + right_index)->getMZ());
        //std::cout << "Distance right " << distance_right << std::endl;


        // add the distance_right*h to the left resampled peak and distance_left*h to the right resampled peak
        double intensity = static_cast<double>((it + left_index)->getIntensity());
        intensity += static_cast<double>((first + i)->getIntensity()) * distance_right / spacing_;
        (it + left_index)->setIntensity(intensity);
        intensity = static_cast<double>((it + right_index)->getIntensity());
        intensity += static_cast<double>((first + i)->getIntensity()) * distance_left;
        (it + right_index)->setIntensity(intensity);
      }

      spectrum.swap(resampled_peak_container);
    }

    void rasterExperiment(PeakMap& exp)
    {
      startProgress(0, exp.size(), "resampling of data");
      for (Size i = 0; i < exp.size(); ++i)
      {
        raster(exp[i]);
        setProgress(i);
      }
      endProgress();
    }

protected:

    double spacing_;

    virtual void updateMembers_()
    {
      spacing_ =  param_.getValue("spacing");
    }

  };


} // namespace OpenMS

#endif // OPENMS_FILTERING_TRANSFORMERS_LINEARRESAMPLER_H