MaxLikeliFitter1D.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: $
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#pragma once
 
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/Fitter1D.h>
#include <OpenMS/MATH/STATISTICS/StatisticFunctions.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/InterpolationModel.h>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI MaxLikeliFitter1D :
    public Fitter1D
  {
 
public:
 
    MaxLikeliFitter1D() :
      Fitter1D()
    {
    }
 
    MaxLikeliFitter1D(const MaxLikeliFitter1D & source) :
      Fitter1D(source)
    {
    }
 
    ~MaxLikeliFitter1D() override
    {
    }
 
    virtual MaxLikeliFitter1D & operator=(const MaxLikeliFitter1D & source)
    {
      if (&source == this) return *this;
 
      Fitter1D::operator=(source);
 
      return *this;
    }
 
protected:
 
    QualityType fitOffset_(InterpolationModel * model, const RawDataArrayType & set, const CoordinateType stdev1, const CoordinateType stdev2, const CoordinateType offset_step)
    {
      const CoordinateType offset_min = model->getInterpolation().supportMin() - stdev1;
      const CoordinateType offset_max = model->getInterpolation().supportMin() + stdev2;
 
      CoordinateType offset;
      QualityType correlation;
 
      //test model with default offset
      std::vector<float> real_data;
      real_data.reserve(set.size());
      std::vector<float> model_data;
      model_data.reserve(set.size());
 
      for (Size i = 0; i < set.size(); ++i)
      {
        real_data.push_back(set[i].getIntensity());
        model_data.push_back(model->getIntensity(DPosition<1>(set[i].getPosition())));
      }
 
      CoordinateType max_offset = model->getInterpolation().getOffset();
      QualityType max_correlation = Math::pearsonCorrelationCoefficient(real_data.begin(), real_data.end(), model_data.begin(), model_data.end());
 
      //test different offsets
      for (offset = offset_min; offset <= offset_max; offset += offset_step)
      {
        // set offset
        model->setOffset(offset);
 
        // get samples
        model_data.clear();
        for (Size i = 0; i < set.size(); ++i)
        {
          model_data.push_back(model->getIntensity(DPosition<1>(set[i].getPosition())));
        }
 
        correlation = Math::pearsonCorrelationCoefficient(real_data.begin(), real_data.end(), model_data.begin(), model_data.end());
 
        if (correlation > max_correlation)
        {
          max_correlation = correlation;
          max_offset = offset;
        }
      }
 
      model->setOffset(max_offset);
 
      return max_correlation;
    }
 
    void updateMembers_() override
    {
      Fitter1D::updateMembers_();
    }
 
  };
}