LinearResampler.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 2002-2020.
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// $Maintainer: Timo Sachsenberg $
// $Authors: Eva Lange $
// --------------------------------------------------------------------------
 
#pragma once
 
#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() override
    {
    }
 
    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_;
 
    void updateMembers_() override
    {
      spacing_ =  param_.getValue("spacing");
    }
 
  };
 
 
} // namespace OpenMS