PeakPickerCWT.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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// $Maintainer: Alexandra Zerck $
// $Authors: Eva Lange, Alexandra Zerck $
// --------------------------------------------------------------------------
//
#ifndef OPENMS_TRANSFORMATIONS_RAW2PEAK_PEAKPICKERCWT_H
#define OPENMS_TRANSFORMATIONS_RAW2PEAK_PEAKPICKERCWT_H

#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/PeakShape.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/OptimizePeakDeconvolution.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/ContinuousWaveletTransform.h>
#include <OpenMS/TRANSFORMATIONS/RAW2PEAK/ContinuousWaveletTransformNumIntegration.h>

//#define DEBUG_PEAK_PICKING
#undef DEBUG_PEAK_PICKING
//#define DEBUG_DECONV
namespace OpenMS
{
  class OPENMS_DLLAPI PeakPickerCWT :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:
    typedef MSSpectrum<>::iterator PeakIterator;
    typedef MSSpectrum<>::const_iterator ConstPeakIterator;

    PeakPickerCWT();

    virtual ~PeakPickerCWT();

    void pick(const MSSpectrum<> & input, MSSpectrum<> & output);

    void pickExperiment(const MSExperiment<> & input, MSExperiment<> & output);

    DoubleReal estimatePeakWidth(const MSExperiment<> & input);
protected:

    float peak_bound_;

    float peak_bound_ms2_level_;

    float signal_to_noise_;

    float fwhm_bound_;

    UInt radius_;

    float scale_;

    float peak_corr_bound_;

    float noise_level_;

    bool optimization_;

    bool deconvolution_;

    bool two_d_optimization_;


    void updateMembers_();

    void init_();


    struct OPENMS_DLLAPI PeakArea_
    {
      typedef MSSpectrum<>::iterator PeakIterator;

      PeakIterator left;
      PeakIterator max;
      PeakIterator right;
      PeakIterator left_behind_centroid;
      DPosition<1> centroid_position;
    };


    void getPeakArea_(const PeakArea_ & area, double & area_left, double & area_right);

    PeakShape fitPeakShape_(const PeakArea_ & area, bool enable_centroid_fit);

    double correlate_(const PeakShape & peak, const PeakArea_ & area, Int direction = 0) const;


    bool getMaxPosition_(PeakIterator first, PeakIterator last, const ContinuousWaveletTransform & wt, PeakArea_ & area, Int distance_from_scan_border, Int ms_level, DoubleReal peak_bound_cwt, DoubleReal peak_bound_ms2_level_cwt, Int direction = 1);


    bool getPeakEndPoints_(PeakIterator first, PeakIterator last, PeakArea_ & area, Int distance_from_scan_border, Int & peak_left_index, Int & peak_right_index, ContinuousWaveletTransformNumIntegration & wt);


    void getPeakCentroid_(PeakArea_ & area);

    double lorentz_(double height, double lambda, double pos, double x);

    void initializeWT_(ContinuousWaveletTransformNumIntegration & wt, DoubleReal & peak_bound_cwt, DoubleReal & peak_bound_ms2_level_cwt);


    bool deconvolutePeak_(PeakShape & shape, std::vector<PeakShape> & peak_shapes, DoubleReal peak_bound_cwt);

    Int getNumberOfPeaks_(ConstPeakIterator first, ConstPeakIterator last, std::vector<double> & peak_values,
                          Int direction, DoubleReal resolution, ContinuousWaveletTransformNumIntegration & wt, DoubleReal peak_bound_cwt);

    Int determineChargeState_(std::vector<double> & peak_values);

    void addPeak_(std::vector<PeakShape> & peaks_DC, PeakArea_ & area, double left_width, double right_width, OptimizePeakDeconvolution::Data & data);
  };  // end PeakPickerCWT

} // namespace OpenMS

#endif