#include <tracedetectionzivy.h>

Inheritance diagram for pappso::TraceDetectionZivy:

Public Member Functions
	TraceDetectionZivy (unsigned int smoothing_half_window_length, unsigned int minmax_half_window_length, unsigned int maxmin_half_window_length, double detection_threshold_on_minmax, double detection_threshold_on_maxmin)

	TraceDetectionZivy (const TraceDetectionZivy &other)

virtual	~TraceDetectionZivy ()

void	guessParametersFromMsRunReader (const MsRunReader &reader)

void	setFilterMorphoMean (const FilterMorphoMean &smooth)

void	setFilterMorphoMinMax (const FilterMorphoMinMax &m_minMax)

void	setFilterMorphoMaxMin (const FilterMorphoMaxMin &maxMin)

void	setDetectionThresholdOnMinmax (double detectionThresholdOnMinMax)

void	setDetectionThresholdOnMaxmin (double detectionThresholdOnMaxMin)

unsigned int	getSmoothingHalfEdgeWindows () const

unsigned int	getMaxMinHalfEdgeWindows () const

unsigned int	getMinMaxHalfEdgeWindows () const

double	getDetectionThresholdOnMinmax () const

double	getDetectionThresholdOnMaxmin () const

void	detect (const Trace &xic, TraceDetectionSinkInterface &sink, bool remove_peak_base) const override
	detect peaks on a trace

Private Attributes
FilterMorphoMean	m_smooth

FilterMorphoMinMax	m_minMax

FilterMorphoMaxMin	m_maxMin

double	m_detectionThresholdOnMinMax

double	m_detectionThresholdOnMaxMin

Detailed Description

Definition at line 37 of file tracedetectionzivy.h.

Constructor & Destructor Documentation

◆ TraceDetectionZivy() [1/2]

pappso::TraceDetectionZivy::TraceDetectionZivy	(	unsigned int	smoothing_half_window_length,
		unsigned int	minmax_half_window_length,
		unsigned int	maxmin_half_window_length,
		double	detection_threshold_on_minmax,
		double	detection_threshold_on_maxmin )

Definition at line 35 of file tracedetectionzivy.cpp.

  : m_smooth(smoothing_half_window_length),
    m_minMax(minmax_half_window_length),
    m_maxMin(maxmin_half_window_length)
{
  m_detectionThresholdOnMaxMin = detection_threshold_on_maxmin;
  m_detectionThresholdOnMinMax = detection_threshold_on_minmax;
}

References m_detectionThresholdOnMaxMin, m_detectionThresholdOnMinMax, m_maxMin, m_minMax, and m_smooth.

Referenced by TraceDetectionZivy().

◆ TraceDetectionZivy() [2/2]

pappso::TraceDetectionZivy::TraceDetectionZivy ( const TraceDetectionZivy & other )

Definition at line 48 of file tracedetectionzivy.cpp.

  : m_smooth(other.m_smooth), m_minMax(other.m_minMax), m_maxMin(other.m_maxMin)
{
  m_detectionThresholdOnMaxMin = other.m_detectionThresholdOnMaxMin;
  m_detectionThresholdOnMinMax = other.m_detectionThresholdOnMinMax;
}

References TraceDetectionZivy(), m_detectionThresholdOnMaxMin, m_detectionThresholdOnMinMax, m_maxMin, m_minMax, and m_smooth.

◆ ~TraceDetectionZivy()

pappso::TraceDetectionZivy::~TraceDetectionZivy ( )

virtual

Definition at line 54 of file tracedetectionzivy.cpp.

55{

56}

Member Function Documentation

◆ detect()

void pappso::TraceDetectionZivy::detect	(	const Trace &	trace,
		TraceDetectionSinkInterface &	sink,
		bool	remove_peak_base ) const

overridevirtual

detect peaks on a trace

Parameters

trace	the trace to detect peaks on
sink	the object to store peaks or stream it
remove_peak_base	if true, removes the area under the base of the peak

Implements pappso::TraceDetectionInterface.

Definition at line 113 of file tracedetectionzivy.cpp.

{
 
  // detect peak positions on close curve : a peak is an intensity value
  // strictly greater than the two surrounding values. In case of
  // equality (very rare, can happen with some old old spectrometers) we
  // take the last equal point to be the peak
  qDebug();
  std::size_t size = xic.size();
  if(size < 4)
    {
      qDebug() << QObject::tr("The original XIC is too small to detect peaks (%1)").arg(xic.size());
      return;
    }
  if(size <= m_maxMin.getMaxMinHalfEdgeWindows())
    return;
  if(size <= m_minMax.getMinMaxHalfEdgeWindows())
    return;
 
  Trace xic_minmax(xic); //"close" courbe du haut
  if(m_smooth.getHalfWindowSize() != 0)
    {
      qDebug() << "f";
      m_smooth.filter(xic_minmax);
    }
 
  qDebug();
  Trace xic_maxmin(xic_minmax); //"open" courbe du bas
 
  qDebug();
 
  try
    {
      qDebug() << "f1";
      m_minMax.filter(xic_minmax);
      qDebug() << "f2";
      m_maxMin.filter(xic_maxmin);
    }
  catch(const ExceptionOutOfRange &e)
    {
      qDebug() << QObject::tr("The original XIC is too small to detect peaks (%1) :\n%2")
                    .arg(xic.size())
                    .arg(e.qwhat());
      return;
    }
  qDebug() << "a";
 
  std::vector<DataPoint>::const_iterator previous_rt = xic_minmax.begin();
  std::vector<DataPoint>::const_iterator current_rt  = (previous_rt + 1);
  std::vector<DataPoint>::const_iterator last_rt     = (xic_minmax.end() - 1);
 
  std::vector<DataPoint>::const_iterator current_rt_on_maxmin = (xic_maxmin.begin() + 1);
 
  std::vector<DataPoint>::const_iterator xic_position = xic.begin();
  qDebug() << "b";
  while(current_rt != last_rt)
    // for (unsigned int i = 1, count = 0; i < xic_minmax.size() - 1; )
    {
      // conditions to have a peak
      if((previous_rt->y < current_rt->y) && (current_rt->y > m_detectionThresholdOnMinMax) &&
         (current_rt_on_maxmin->y > m_detectionThresholdOnMaxMin))
        {
          // here we test the last condition to have a peak
 
          // no peak case
          if(current_rt->y < (current_rt + 1)->y)
            {
              //++i;
              previous_rt = current_rt;
              current_rt++;
              current_rt_on_maxmin++;
            }
          // there is a peak here ! case
          else if(current_rt->y > (current_rt + 1)->y)
            {
              // peak.setMaxXicElement(*current_rt);
 
              // find left boundary
              std::vector<DataPoint>::const_iterator it_left =
                moveLowerYLeftDataPoint(xic_minmax, current_rt);
              // walk back
              it_left = moveLowerYRigthDataPoint(xic_minmax, it_left);
              // peak.setLeftBoundary(*it_left);
 
              // find right boundary
              std::vector<DataPoint>::const_iterator it_right =
                moveLowerYRigthDataPoint(xic_minmax, current_rt);
              // walk back
              it_right = moveLowerYLeftDataPoint(xic_minmax, it_right);
              // peak.setRightBoundary(*it_right);
 
              // integrate peak surface :
              auto it      = findFirstEqualOrGreaterX(xic_position, xic.end(), it_left->x);
              xic_position = findFirstEqualOrGreaterX(it, xic.end(), it_right->x) + 1;
              // peak.setArea(areaTrace(it, xic_position));
 
              // find the maximum :
              // peak.setMaxXicElement(*maxYDataPoint(it, xic_position));
 
              // areaTrace()
              TracePeak peak(it, xic_position, remove_peak_base);
              sink.setTracePeak(peak);
              // }
              //++i;
              previous_rt = current_rt;
              current_rt++;
              current_rt_on_maxmin++;
            }
          // equality case, skipping equal points
          else
            {
              // while (v_minmax[i] == v_minmax[i + 1]) {
              //++i;
              current_rt++;
              current_rt_on_maxmin++;
 
              //++count;
            }
        }
      // no chance to have a peak at all, continue looping
      else
        {
          //++i;
          previous_rt = current_rt;
          current_rt++;
          current_rt_on_maxmin++;
        }
    } // end loop for peaks
  qDebug();
}

References pappso::findFirstEqualOrGreaterX(), m_detectionThresholdOnMaxMin, m_detectionThresholdOnMinMax, m_maxMin, m_minMax, m_smooth, pappso::moveLowerYLeftDataPoint(), pappso::moveLowerYRigthDataPoint(), pappso::PappsoException::qwhat(), and pappso::TraceDetectionSinkInterface::setTracePeak().

◆ getDetectionThresholdOnMaxmin()

pappso_double pappso::TraceDetectionZivy::getDetectionThresholdOnMaxmin ( ) const

Definition at line 106 of file tracedetectionzivy.cpp.

{
  return m_detectionThresholdOnMaxMin;
};

References m_detectionThresholdOnMaxMin.

Referenced by pappso::masschroq::QuantificationMethod::getJsonObject(), and pappso::masschroq::QuantificationMethod::getProjectParameters().

◆ getDetectionThresholdOnMinmax()

pappso_double pappso::TraceDetectionZivy::getDetectionThresholdOnMinmax ( ) const

Definition at line 101 of file tracedetectionzivy.cpp.

{
  return m_detectionThresholdOnMinMax;
};

References m_detectionThresholdOnMinMax.

Referenced by pappso::masschroq::QuantificationMethod::getJsonObject(), and pappso::masschroq::QuantificationMethod::getProjectParameters().

◆ getMaxMinHalfEdgeWindows()

unsigned int pappso::TraceDetectionZivy::getMaxMinHalfEdgeWindows ( ) const

Definition at line 90 of file tracedetectionzivy.cpp.

{
  return m_maxMin.getMaxMinHalfEdgeWindows();
};

References m_maxMin.

Referenced by pappso::masschroq::QuantificationMethod::getJsonObject(), and pappso::masschroq::QuantificationMethod::getProjectParameters().

◆ getMinMaxHalfEdgeWindows()

unsigned int pappso::TraceDetectionZivy::getMinMaxHalfEdgeWindows ( ) const

Definition at line 96 of file tracedetectionzivy.cpp.

{
  return m_minMax.getMinMaxHalfEdgeWindows();
};

References m_minMax.

Referenced by pappso::masschroq::QuantificationMethod::getJsonObject(), and pappso::masschroq::QuantificationMethod::getProjectParameters().

◆ getSmoothingHalfEdgeWindows()

unsigned int pappso::TraceDetectionZivy::getSmoothingHalfEdgeWindows ( ) const

Definition at line 85 of file tracedetectionzivy.cpp.

{
  return m_smooth.getHalfWindowSize();
};

References m_smooth.

Referenced by pappso::masschroq::QuantificationMethod::getJsonObject(), and pappso::masschroq::QuantificationMethod::getProjectParameters().

◆ guessParametersFromMsRunReader()

void pappso::TraceDetectionZivy::guessParametersFromMsRunReader ( const MsRunReader & reader )

Definition at line 248 of file tracedetectionzivy.cpp.

{
  // reader.
}

◆ setDetectionThresholdOnMaxmin()

void pappso::TraceDetectionZivy::setDetectionThresholdOnMaxmin ( double detectionThresholdOnMaxMin )

Definition at line 80 of file tracedetectionzivy.cpp.

{
  m_detectionThresholdOnMaxMin = detectionThresholdOnMaxMin;
}

References m_detectionThresholdOnMaxMin.

◆ setDetectionThresholdOnMinmax()

void pappso::TraceDetectionZivy::setDetectionThresholdOnMinmax ( double detectionThresholdOnMinMax )

Definition at line 75 of file tracedetectionzivy.cpp.

{
  m_detectionThresholdOnMinMax = detectionThresholdOnMinMax;
}

References m_detectionThresholdOnMinMax.

◆ setFilterMorphoMaxMin()

void pappso::TraceDetectionZivy::setFilterMorphoMaxMin ( const FilterMorphoMaxMin & maxMin )

Definition at line 69 of file tracedetectionzivy.cpp.

{
  m_maxMin = maxMin;
}

References m_maxMin.

◆ setFilterMorphoMean()

void pappso::TraceDetectionZivy::setFilterMorphoMean ( const FilterMorphoMean & smooth )

Definition at line 59 of file tracedetectionzivy.cpp.

{
  m_smooth = smooth;
}

References m_smooth.

◆ setFilterMorphoMinMax()

void pappso::TraceDetectionZivy::setFilterMorphoMinMax ( const FilterMorphoMinMax & m_minMax )

Definition at line 64 of file tracedetectionzivy.cpp.

{
  m_minMax = minMax;
}

References m_minMax.

Member Data Documentation

◆ m_detectionThresholdOnMaxMin

double pappso::TraceDetectionZivy::m_detectionThresholdOnMaxMin

private

Definition at line 74 of file tracedetectionzivy.h.

Referenced by TraceDetectionZivy(), TraceDetectionZivy(), detect(), getDetectionThresholdOnMaxmin(), and setDetectionThresholdOnMaxmin().

◆ m_detectionThresholdOnMinMax

double pappso::TraceDetectionZivy::m_detectionThresholdOnMinMax

private

Definition at line 73 of file tracedetectionzivy.h.

Referenced by TraceDetectionZivy(), TraceDetectionZivy(), detect(), getDetectionThresholdOnMinmax(), and setDetectionThresholdOnMinmax().

◆ m_maxMin

FilterMorphoMaxMin pappso::TraceDetectionZivy::m_maxMin

private

Definition at line 72 of file tracedetectionzivy.h.

Referenced by TraceDetectionZivy(), TraceDetectionZivy(), detect(), getMaxMinHalfEdgeWindows(), and setFilterMorphoMaxMin().

◆ m_minMax

FilterMorphoMinMax pappso::TraceDetectionZivy::m_minMax

private

Definition at line 71 of file tracedetectionzivy.h.

Referenced by TraceDetectionZivy(), TraceDetectionZivy(), detect(), getMinMaxHalfEdgeWindows(), and setFilterMorphoMinMax().

◆ m_smooth

FilterMorphoMean pappso::TraceDetectionZivy::m_smooth

private

Definition at line 70 of file tracedetectionzivy.h.

Referenced by TraceDetectionZivy(), TraceDetectionZivy(), detect(), getSmoothingHalfEdgeWindows(), and setFilterMorphoMean().

The documentation for this class was generated from the following files:

pappsomspp/core/processing/detection/tracedetectionzivy.h
pappsomspp/core/processing/detection/tracedetectionzivy.cpp

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TraceDetectionZivy() [1/2]

◆ TraceDetectionZivy() [2/2]

◆ ~TraceDetectionZivy()

Member Function Documentation

◆ detect()

◆ getDetectionThresholdOnMaxmin()

◆ getDetectionThresholdOnMinmax()

◆ getMaxMinHalfEdgeWindows()

◆ getMinMaxHalfEdgeWindows()

◆ getSmoothingHalfEdgeWindows()

◆ guessParametersFromMsRunReader()

◆ setDetectionThresholdOnMaxmin()

◆ setDetectionThresholdOnMinmax()

◆ setFilterMorphoMaxMin()

◆ setFilterMorphoMean()

◆ setFilterMorphoMinMax()

Member Data Documentation

◆ m_detectionThresholdOnMaxMin

◆ m_detectionThresholdOnMinMax

◆ m_maxMin

◆ m_minMax

◆ m_smooth