SignalToNoiseEstimator.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 2002-2018.
//
// 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: Chris Bielow $
// $Authors: $
// --------------------------------------------------------------------------
//

#pragma once

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

#include <vector>
#include <cmath>
#include <map>

namespace OpenMS
{
  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(),
      first_(),
      last_(),
      is_result_valid_(false)
    {
    }

    inline SignalToNoiseEstimator(const SignalToNoiseEstimator & source) :
      DefaultParamHandler(source),
      ProgressLogger(source),
      stn_estimates_(source.stn_estimates_),
      first_(source.first_),
      last_(source.last_),
      is_result_valid_(source.is_result_valid_)
    {}

    inline SignalToNoiseEstimator & operator=(const SignalToNoiseEstimator & source)
    {
      if (&source == this) return *this;

      DefaultParamHandler::operator=(source);
      ProgressLogger::operator=(source);
      stn_estimates_ = source.stn_estimates_;
      first_ = source.first_;
      last_  = source.last_;
      return *this;
    }

    ~SignalToNoiseEstimator() override
    {}


    virtual void init(const PeakIterator & it_begin, const PeakIterator & it_end)
    {
      first_ = it_begin;
      last_ = it_end;
      computeSTN_(first_, last_);
      is_result_valid_ = true;
    }

    virtual void init(const Container & c)
    {
      init(c.begin(), c.end());
    }

    virtual double getSignalToNoise(const PeakIterator & data_point)
    {
      if (!is_result_valid_)
      {
        // recompute ...
        init(first_, last_);
      }

      return stn_estimates_[*data_point];
    }

    virtual double getSignalToNoise(const PeakType & data_point)
    {
      if (!is_result_valid_)
      {
        // recompute ...
        init(first_, last_);
      }

      return stn_estimates_[data_point];
    }

protected:

    virtual void computeSTN_(const PeakIterator & scan_first_, const PeakIterator & scan_last_) = 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::map<PeakType, double, typename PeakType::PositionLess> stn_estimates_;

    PeakIterator first_;
    PeakIterator last_;
    mutable bool is_result_valid_;
  };

} // namespace OpenMS