PeakIntegrator.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Douglas McCloskey, Pasquale Domenico Colaianni $
// $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/config.h> // OPENMS_DLLAPI
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/DATASTRUCTURES/ConvexHull2D.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/MATH/MISC/EmgGradientDescent.h>

namespace OpenMS
{
  class OPENMS_DLLAPI PeakIntegrator :
    public DefaultParamHandler
  {
public:
    PeakIntegrator();
    virtual ~PeakIntegrator();

    struct PeakArea
    {
      double area = 0.0;
      double height = 0.0;
      double apex_pos = 0.0;
      ConvexHull2D::PointArrayType hull_points;
    };

    struct PeakBackground
    {
      double area = 0.0;
      double height = 0.0;
    };

    struct PeakShapeMetrics
    {
      double width_at_5 = 0.0;
      double width_at_10 = 0.0;
      double width_at_50 = 0.0;
      double start_position_at_5 = 0.0;
      double start_position_at_10 = 0.0;
      double start_position_at_50 = 0.0;
      double end_position_at_5 = 0.0;
      double end_position_at_10 = 0.0;
      double end_position_at_50 = 0.0;
      double total_width = 0.0;
      double tailing_factor = 0.0;
      double asymmetry_factor = 0.0;
      double slope_of_baseline = 0.0;
      double baseline_delta_2_height = 0.0;
      Int points_across_baseline = 0;
      Int points_across_half_height = 0;
    };

    static constexpr const char* INTEGRATION_TYPE_INTENSITYSUM = "intensity_sum";
    static constexpr const char* INTEGRATION_TYPE_TRAPEZOID = "trapezoid";
    static constexpr const char* INTEGRATION_TYPE_SIMPSON = "simpson";
    static constexpr const char* BASELINE_TYPE_BASETOBASE = "base_to_base";
    static constexpr const char* BASELINE_TYPE_VERTICALDIVISION = "vertical_division";
    static constexpr const char* BASELINE_TYPE_VERTICALDIVISION_MIN = "vertical_division_min";
    static constexpr const char* BASELINE_TYPE_VERTICALDIVISION_MAX = "vertical_division_max";

    PeakArea integratePeak(
      const MSChromatogram& chromatogram, const double left, const double right
    ) const;

    PeakArea integratePeak(
      const MSChromatogram& chromatogram, MSChromatogram::ConstIterator& left, MSChromatogram::ConstIterator& right
    ) const;

    PeakArea integratePeak(
      const MSSpectrum& spectrum, const double left, const double right
    ) const;

    PeakArea integratePeak(
      const MSSpectrum& spectrum, MSSpectrum::ConstIterator& left, MSSpectrum::ConstIterator& right
    ) const;

    PeakBackground estimateBackground(
      const MSChromatogram& chromatogram, const double left, const double right,
      const double peak_apex_pos
    ) const;

    PeakBackground estimateBackground(
      const MSChromatogram& chromatogram, MSChromatogram::ConstIterator& left, MSChromatogram::ConstIterator& right,
      const double peak_apex_pos
    ) const;

    PeakBackground estimateBackground(
      const MSSpectrum& spectrum, const double left, const double right,
      const double peak_apex_pos
    ) const;

    PeakBackground estimateBackground(
      const MSSpectrum& spectrum, MSSpectrum::ConstIterator& left, MSSpectrum::ConstIterator& right,
      const double peak_apex_pos
    ) const;

    PeakShapeMetrics calculatePeakShapeMetrics(
      const MSChromatogram& chromatogram, const double left, const double right,
      const double peak_height, const double peak_apex_pos
    ) const;

    PeakShapeMetrics calculatePeakShapeMetrics(
      const MSChromatogram& chromatogram, MSChromatogram::ConstIterator& left, MSChromatogram::ConstIterator& right,
      const double peak_height, const double peak_apex_pos
    ) const;

    PeakShapeMetrics calculatePeakShapeMetrics(
      const MSSpectrum& spectrum, const double left, const double right,
      const double peak_height, const double peak_apex_pos
    ) const;

    PeakShapeMetrics calculatePeakShapeMetrics(
      const MSSpectrum& spectrum, MSSpectrum::ConstIterator& left, MSSpectrum::ConstIterator& right,
      const double peak_height, const double peak_apex_pos
    ) const;

    void getDefaultParameters(Param& params);

protected:
    void updateMembers_();

    template <typename PeakContainerT>
    PeakArea integratePeak_(
      const PeakContainerT& pc, double left, double right
    ) const;

    template <typename PeakContainerT>
    PeakBackground estimateBackground_(
      const PeakContainerT& pc, double left, double right,
      const double peak_apex_pos
    ) const;

    template <typename PeakContainerConstIteratorT>
    double simpson_(PeakContainerConstIteratorT it_begin, PeakContainerConstIteratorT it_end) const;

    template <typename PeakContainerT>
    PeakShapeMetrics calculatePeakShapeMetrics_(
      const PeakContainerT& pc, double left, double right,
      const double peak_height, const double peak_apex_pos
    ) const;

    template <typename PeakContainerConstIteratorT>
    double findPosAtPeakHeightPercent_(
      PeakContainerConstIteratorT it_begin,
      PeakContainerConstIteratorT it_end,
      const double peak_height,
      const double percent,
      const bool is_left_half
    ) const;

private:

    String integration_type_ = INTEGRATION_TYPE_INTENSITYSUM;
    String baseline_type_ = BASELINE_TYPE_BASETOBASE;

    bool fit_EMG_;
    EmgGradientDescent emg_;


    double simpson(MSChromatogram::ConstIterator it_begin, MSChromatogram::ConstIterator it_end) const;

    double simpson(MSSpectrum::ConstIterator it_begin, MSSpectrum::ConstIterator it_end) const;

    template <typename PeakContainerT>
    const PeakContainerT& EMGPreProcess_(
      const PeakContainerT& pc,
      PeakContainerT& emg_pc,
      double& left,
      double& right
    ) const;
  };
}