PeakPickerCWT.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 2002-2017.
//
// 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: Timo Sachsenberg $
// $Authors: Eva Lange, Alexandra Zerck $
// --------------------------------------------------------------------------
//
#ifndef OPENMS_TRANSFORMATIONS_RAW2PEAK_PEAKPICKERCWT_H
#define OPENMS_TRANSFORMATIONS_RAW2PEAK_PEAKPICKERCWT_H

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/KERNEL/MSExperiment.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 PeakShape;

  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) const;

    void pickExperiment(const PeakMap & input, PeakMap & output);

    double estimatePeakWidth(const PeakMap & 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_();

    struct OPENMS_DLLAPI PeakArea_
    {
      typedef MSSpectrum::iterator PeakIterator;
      PeakIterator left;  //< iterator to the leftmost valid point
      PeakIterator max;   //< iterator to the maximum position
      PeakIterator right; //< iterator to the rightmost valid point (inclusive)
      DPosition<1> centroid_position; //< The estimated centroid position in m/z
    };

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

    PeakShape fitPeakShape_(const PeakArea_ & area) const;

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


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


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


    void getPeakCentroid_(PeakArea_ & area) const;

    inline double lorentz_(const double height, const double lambda, const double pos, const double x) const
    {
      const double x2 = lambda * (x - pos);
      return height / (1 + x2*x2);
    }

    void initializeWT_(ContinuousWaveletTransformNumIntegration& wt, const double peak_bound_in, double& peak_bound_ms_cwt) const;


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

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

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

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

} // namespace OpenMS

#endif