PeakPickerMobilogram.h

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// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Justin Sing $
// $Authors: Justin Sing $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/KERNEL/MSSpectrum.h>
#include <OpenMS/KERNEL/MSChromatogram.h>
#include <OpenMS/KERNEL/ChromatogramPeak.h>
#include <OpenMS/KERNEL/Mobilogram.h>
#include <OpenMS/KERNEL/MobilityPeak1D.h>
 
#include <OpenMS/PROCESSING/NOISEESTIMATION/SignalToNoiseEstimatorMedian.h>
#include <OpenMS/PROCESSING/SMOOTHING/SavitzkyGolayFilter.h>
#include <OpenMS/PROCESSING/SMOOTHING/GaussFilter.h>
 
#include <OpenMS/PROCESSING/CENTROIDING/PeakPickerHiRes.h>
#include <vector>
 
namespace OpenMS
{
    class OPENMS_DLLAPI PeakPickerMobilogram :
            public DefaultParamHandler
    {
    public:
        PeakPickerMobilogram();
 
        ~PeakPickerMobilogram() override {}
 
        enum FLOATINDICES { IDX_FWHM = 0, IDX_ABUNDANCE = 1, IDX_LEFTBORDER = 2, IDX_RIGHTBORDER = 3, IDX_OF_LEFTBORDER_IDX = 4, IDX_OF_RIGHTBORDER_IDX = 5, SIZE_OF_FLOATINDICES };
 
        struct PeakPositions {
            size_t left;    // Left position of the peak
            size_t apex;    // Apex (highest point) position of the peak
            size_t right;   // Right position of the peak
        };
 
        void pickMobilogram(const Mobilogram& mobilogram, Mobilogram& picked_mobilogram);
 
        void pickMobilogram(Mobilogram mobilogram, Mobilogram& picked_mobilogram, Mobilogram& smoothed_mobilogram);
 
        void filterTopPeak(Mobilogram& picked_mobilogram, std::vector<Mobilogram>& mobilograms, PeakPositions& peak_pos);
 
        void filterTopPeak(Mobilogram& picked_mobilogram, Mobilogram& mobilogram, PeakPositions& peak_pos);
 
        std::vector<double> integrated_intensities_;
 
        std::vector<Size> left_width_;
 
        std::vector<Size> right_width_;
 
      protected:
        void pickMobilogram_(const Mobilogram& mobilogram, Mobilogram& picked_mobilogram);
 
        void integratePeaks_(const Mobilogram& mobilogram);
 
        Size findClosestPeak_(const Mobilogram& mobilogram, double target_im, Size current_peak = 0);
 
        static PeakPositions findHighestPeak_(const std::vector<double> intensities,
                                       const std::vector<Size> left_widths,
                                       const std::vector<Size> right_widths,
                                       const size_t im_size);
 
        void filterPeakIntensities_(Mobilogram& mobilogram,
                               size_t left_index,
                               size_t right_index);
 
        void filterPeakIntensities_(std::vector<Mobilogram>& mobilograms,
                                size_t left_index,
                                size_t right_index);
 
        static std::vector<double> extractFloatValues_(const OpenMS::DataArrays::FloatDataArray& floatDataArray);
 
        static std::vector<std::size_t> extractIntValues_(const OpenMS::DataArrays::FloatDataArray& floatDataArray);
 
        PeakPositions filterTopPeak_(Mobilogram& picked_mobilogram, std::vector<Mobilogram>& mobilograms);
 
        PeakPositions filterTopPeak_(Mobilogram& picked_mobilogram, Mobilogram& mobilograms);
 
        void removeOverlappingPeaks_(const Mobilogram& mobilogram, Mobilogram& picked_mobilogram);
 
        void updateMembers_() override;
 
        // Members
        UInt sgolay_frame_length_;
        UInt sgolay_polynomial_order_;
        double gauss_width_;
        bool use_gauss_;
        bool remove_overlapping_;
 
        double peak_width_;
        double signal_to_noise_;
 
        double sn_win_len_;
        UInt sn_bin_count_;
        bool write_sn_log_messages_;
        String method_;
 
        PeakPickerHiRes pp_;
        SavitzkyGolayFilter sgolay_;
        GaussFilter gauss_;
    };
}