EmgScoring.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 2002-2020.
//
// 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: Hannes Roest $
// $Authors: Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <vector>
#include <boost/math/special_functions/fpclassify.hpp> // for isnan
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgFitter1D.h>
#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/EmgModel.h>
#include <OpenMS/FILTERING/SMOOTHING/GaussFilter.h>
 
#include <OpenMS/KERNEL/MRMFeature.h>
#include <OpenMS/KERNEL/MRMTransitionGroup.h>
 
#include <OpenMS/KERNEL/StandardTypes.h>
 
 
namespace OpenMS
{
 
  class EmgScoring
  {
 
  public :
 
    EmgScoring() { }
 
    ~EmgScoring() { }
 
    void setFitterParam(Param param)
    {
      fitter_emg1D_.setParameters(param);
    }
 
    Param getDefaults()
    {
      return fitter_emg1D_.getDefaults();
    }
 
    template<typename SpectrumType, class TransitionT>
    double calcElutionFitScore(MRMFeature & mrmfeature, MRMTransitionGroup<SpectrumType, TransitionT> & transition_group)
    {
      std::vector<double> fit_scores;
      double avg_score = 0;
      bool smooth_data = false;
      for (Size k = 0; k < transition_group.size(); k++)
      {
        // get the id, then find the corresponding transition and features within this peakgroup
        String native_id = transition_group.getChromatograms()[k].getNativeID();
        Feature f = mrmfeature.getFeature(native_id);
        OPENMS_PRECONDITION(f.getConvexHulls().size() == 1, "Convex hulls need to have exactly one hull point structure");
 
        // TODO what if score is -1 ?? e.g. if it is undefined
        double fscore = elutionModelFit(f.getConvexHulls()[0].getHullPoints(), smooth_data);
        fit_scores.push_back(fscore);
        avg_score += fscore;
      }
 
      avg_score /= transition_group.size();
      return avg_score;
    }
 
    // Fxn from FeatureFinderAlgorithmMRM
    // TODO: check whether we can leave out some of the steps here, e.g. gaussian smoothing
    double elutionModelFit(ConvexHull2D::PointArrayType current_section, bool smooth_data)
    {
      // We need at least 2 datapoints in order to create a fit
      if (current_section.size() < 2)
      {
        return -1;
      }
 
      // local PeakType is a small hack since here we *need* data of type
      // Peak1D, otherwise our fitter will not accept it.
      typedef Peak1D LocalPeakType;
 
      // -- cut line 301 of FeatureFinderAlgorithmMRM
      std::vector<LocalPeakType> data_to_fit;
      prepareFit_(current_section, data_to_fit, smooth_data);
      InterpolationModel * model_rt = nullptr;
      double quality = fitRT_(data_to_fit, model_rt);
      // cut line 354 of FeatureFinderAlgorithmMRM
      delete model_rt;
 
      return quality;
 
    }
 
  protected:
    template<class LocalPeakType>
    double fitRT_(std::vector<LocalPeakType> & rt_input_data, InterpolationModel * & model)
    {
      double quality;
      //Param param;
 
      /*EmgFitter
       param.setValue( "tolerance_stdev_bounding_box", tolerance_stdev_box_);
       param.setValue( "statistics:mean", rt_stat_.mean() );
       param.setValue( "statistics:variance", rt_stat_.variance() );
       param.setValue( "interpolation_step", interpolation_step_rt_ );
       param.setValue( "max_iteration", max_iteration_);
       param.setValue( "deltaAbsError", deltaAbsError_);
       param.setValue( "deltaRelError", deltaRelError_);
       */
 
      // Set parameter for fitter
      //fitter_emg1D.setParameters(param);
      // Construct model for rt
      quality = fitter_emg1D_.fit1d(rt_input_data, model);
 
      // Check quality
      if (boost::math::isnan(quality)) quality = -1.0;
      return quality;
    }
 
    // Fxn from FeatureFinderAlgorithmMRM
    // TODO: check whether we can leave out some of the steps here, e.g. gaussian smoothing
    template<class LocalPeakType>
    void prepareFit_(const ConvexHull2D::PointArrayType & current_section, std::vector<LocalPeakType> & data_to_fit, bool smooth_data)
    {
      // typedef Peak1D LocalPeakType;
      PeakSpectrum filter_spec;
      // first smooth the data to prevent outliers from destroying the fit
      for (ConvexHull2D::PointArrayType::const_iterator it = current_section.begin(); it != current_section.end(); it++)
      {
        LocalPeakType p;
        p.setMZ(it->getX());
        p.setIntensity(it->getY());
        filter_spec.push_back(p);
      }
 
      // add two peaks at the beginning and at the end for better fit
      // therefore calculate average distance first
      std::vector<double> distances;
      for (Size j = 1; j < filter_spec.size(); ++j)
      {
        distances.push_back(filter_spec[j].getMZ() - filter_spec[j - 1].getMZ());
      }
      double dist_average = std::accumulate(distances.begin(), distances.end(), 0.0) / (double) distances.size();
 
      // append peaks
      Peak1D new_peak;
      new_peak.setIntensity(0);
      new_peak.setMZ(filter_spec.back().getMZ() + dist_average);
      filter_spec.push_back(new_peak);
      new_peak.setMZ(filter_spec.back().getMZ() + dist_average);
      filter_spec.push_back(new_peak);
      new_peak.setMZ(filter_spec.back().getMZ() + dist_average);
      filter_spec.push_back(new_peak);
 
      // prepend peaks
      new_peak.setMZ(filter_spec.front().getMZ() - dist_average);
      filter_spec.insert(filter_spec.begin(), new_peak);
      new_peak.setMZ(filter_spec.front().getMZ() - dist_average);
      filter_spec.insert(filter_spec.begin(), new_peak);
      new_peak.setMZ(filter_spec.front().getMZ() - dist_average);
      filter_spec.insert(filter_spec.begin(), new_peak);
 
      // To get an estimate of the peak quality, we probably should not smooth
      // and/or transform the data.
      if (smooth_data)
      {
        GaussFilter filter;
        Param filter_param(filter.getParameters());
        filter.setParameters(filter_param);
        filter_param.setValue("gaussian_width", 4 * dist_average);
        filter.setParameters(filter_param);
        filter.filter(filter_spec);
      }
 
      // transform the data for fitting and fit RT profile
      for (Size j = 0; j != filter_spec.size(); ++j)
      {
        LocalPeakType p;
        p.setPosition(filter_spec[j].getMZ());
        p.setIntensity(filter_spec[j].getIntensity());
        data_to_fit.push_back(p);
      }
    }
 
    EmgFitter1D fitter_emg1D_;
  };
}