tracedetectionmoulon.cpp

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/*******************************************************************************
 * Copyright (c) 2015 Olivier Langella <Olivier.Langella@moulon.inra.fr>.
 *
 * This file is part of the PAPPSOms++ library.
 *
 *     PAPPSOms++ is free software: you can redistribute it and/or modify
 *     it under the terms of the GNU General Public License as published by
 *     the Free Software Foundation, either version 3 of the License, or
 *     (at your option) any later version.
 *
 *     PAPPSOms++ is distributed in the hope that it will be useful,
 *     but WITHOUT ANY WARRANTY; without even the implied warranty of
 *     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *     GNU General Public License for more details.
 *
 *     You should have received a copy of the GNU General Public License
 *     along with PAPPSOms++.  If not, see <http://www.gnu.org/licenses/>.
 *
 * Contributors:
 *     Olivier Langella <Olivier.Langella@moulon.inra.fr> - initial API and
 *implementation
 ******************************************************************************/
#include "tracedetectionmoulon.h"
 
namespace pappso
{
TraceDetectionMoulon::TraceDetectionMoulon(unsigned int smoothing_half_window_length,
                                           pappso_double tic_start,
                                           pappso_double tic_stop)
  : m_xicFilterSmoothing(smoothing_half_window_length)
{
  m_ticStart = tic_start;
  m_ticStop  = tic_stop;
}
 
TraceDetectionMoulon::TraceDetectionMoulon(const TraceDetectionMoulon &other)
  : m_xicFilterSmoothing(other.m_xicFilterSmoothing)
{
  m_ticStart = other.m_ticStart;
  m_ticStop  = other.m_ticStop;
}
 
TraceDetectionMoulon::~TraceDetectionMoulon()
{
}
 
 
void
TraceDetectionMoulon::setFilterMorphoMean(const FilterMorphoMean &smooth)
{
  m_xicFilterSmoothing = smooth;
}
 
void
TraceDetectionMoulon::setTicStart(double tic_start)
{
  m_ticStart = tic_start;
}
void
TraceDetectionMoulon::setTicStop(double tic_stop)
{
  m_ticStop = tic_stop;
}
 
unsigned int
TraceDetectionMoulon::getSmoothingHalfEdgeWindows() const
{
  return m_xicFilterSmoothing.getHalfWindowSize();
}
 
pappso_double
TraceDetectionMoulon::getTicStart() const
{
  return m_ticStart;
}
 
pappso_double
TraceDetectionMoulon::getTicStop() const
{
  return m_ticStop;
}
 
void
TraceDetectionMoulon::detect(const Trace &xic,
                             TraceDetectionSinkInterface &sink,
                             bool remove_peak_base) const
{
 
  Trace xic_smoothed(xic);
 
  m_xicFilterSmoothing.filter(xic_smoothed);
 
  // detect peaks :
  bool banked(false);
  unsigned int nb_tic_start(0);
 
  std::vector<DataPoint>::const_iterator it_smoothed;
  std::vector<DataPoint>::const_iterator it, it_begin;
 
  // TracePeak *p_current_peak = nullptr;
 
  for(it_smoothed = xic_smoothed.begin(), it = xic.begin(); it_smoothed != xic_smoothed.end();
      ++it_smoothed, ++it)
    {
 
      if((nb_tic_start == 0) && (it_begin != xic.end()) && (banked == false))
        {
          // delete(p_current_peak);
          // p_current_peak = nullptr;
          it_begin = xic.end();
        }
 
      if(it_smoothed->y >= m_ticStart)
        {
          nb_tic_start++;
          if(it_begin == xic.end())
            {
              // p_current_peak = new TracePeak;
              // p_current_peak->setLeftBoundary(*it_smoothed);
              it_begin = it;
              banked   = false;
            }
          if((nb_tic_start == 2) && (banked == false))
            {
              banked = true;
            }
        }
      else
        {
          nb_tic_start = 0;
        }
      if(it_smoothed->y <= m_ticStop)
        {
          if(it_begin != xic.end())
            {
 
              if(banked)
                {
                  TracePeak peak(it_begin, it + 1, remove_peak_base);
                  sink.setTracePeak(peak);
                }
              banked = false;
            }
        }
    }
}
} // namespace pappso