SignalToNoiseEstimator.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
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// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
//
 
#pragma once
 
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
 
#include <vector>
#include <cmath>
 
namespace OpenMS
{
  class MSExperiment;
 
  template <typename Container = MSSpectrum>
  class SignalToNoiseEstimator :
    public DefaultParamHandler, public ProgressLogger
  {
public:
 
    typedef typename Container::const_iterator PeakIterator;
    typedef typename PeakIterator::value_type PeakType;
 
 
 
    inline SignalToNoiseEstimator() :
      DefaultParamHandler("SignalToNoiseEstimator"),
      ProgressLogger()
    {
    }
 
    inline SignalToNoiseEstimator(const SignalToNoiseEstimator & source) :
      DefaultParamHandler(source),
      ProgressLogger(source),
      stn_estimates_(source.stn_estimates_)
    {}
 
    inline SignalToNoiseEstimator & operator=(const SignalToNoiseEstimator & source)
    {
      if (&source == this) return *this;
 
      DefaultParamHandler::operator=(source);
      ProgressLogger::operator=(source);
      stn_estimates_ = source.stn_estimates_;
      return *this;
    }
 
    ~SignalToNoiseEstimator() override
    {}
 
    virtual void init(const Container& c)
    {
      computeSTN_(c);
    }
 
    virtual double getSignalToNoise(const Size index) const
    {
      OPENMS_POSTCONDITION(index < stn_estimates_.size(),"SignalToNoiseEstimator estimates beyond container size was requested.");
      return stn_estimates_[index];
    }
 
protected:
 
    virtual void computeSTN_(const Container& c) = 0;
 
 
 
    struct GaussianEstimate
    {
      double mean;   
      double variance; 
    };
 
 
    inline GaussianEstimate estimate_(const PeakIterator & scan_first_, const PeakIterator & scan_last_) const
    {
      int size = 0;
      // add up
      double v = 0;
      double m = 0;
      PeakIterator run = scan_first_;
      while (run != scan_last_)
      {
        m += (*run).getIntensity();
        ++size;
        ++run;
      }
      //average
      m = m / size;
 
      //determine variance
      run = scan_first_;
      while (run != scan_last_)
      {
        double tmp(m - (*run).getIntensity());
        v += tmp * tmp;
        ++run;
      }
      v = v / ((double)size); // divide by n
 
      GaussianEstimate value = {m, v};
      return value;
    }
 
    //MEMBERS:
 
    std::vector<double> stn_estimates_;
  };
 
  OPENMS_DLLAPI float estimateNoiseFromRandomScans(const MSExperiment& exp, const UInt ms_level, const UInt n_scans = 10, const double percentile = 80);
 
} // namespace OpenMS