libpappsomspp
Library for mass spectrometry
pappso::TraceDetectionMoulon Class Reference

#include <tracedetectionmoulon.h>

Inheritance diagram for pappso::TraceDetectionMoulon:
pappso::TraceDetectionInterface

Public Member Functions

 TraceDetectionMoulon (unsigned int smoothing_half_window_length, pappso_double tic_start, pappso_double tic_stop)
 
 TraceDetectionMoulon (const TraceDetectionMoulon &other)
 
virtual ~TraceDetectionMoulon ()
 
void setFilterMorphoMean (const FilterMorphoMean &smooth)
 
void setTicStart (double tic_start)
 
void setTicStop (double tic_stop)
 
unsigned int getSmoothingHalfEdgeWindows () const
 
pappso_double getTicStart () const
 
pappso_double getTicStop () const
 
void detect (const Trace &xic, TraceDetectionSinkInterface &sink, bool remove_peak_base) const override
 detect peaks on a trace More...
 

Private Attributes

FilterMorphoMean m_xicFilterSmoothing
 
pappso_double m_ticStart
 
pappso_double m_ticStop
 

Detailed Description

Definition at line 34 of file tracedetectionmoulon.h.

Constructor & Destructor Documentation

◆ TraceDetectionMoulon() [1/2]

pappso::TraceDetectionMoulon::TraceDetectionMoulon ( unsigned int  smoothing_half_window_length,
pappso_double  tic_start,
pappso_double  tic_stop 
)

Definition at line 28 of file tracedetectionmoulon.cpp.

32  : m_xicFilterSmoothing(smoothing_half_window_length)
33 {
34  m_ticStart = tic_start;
35  m_ticStop = tic_stop;
36 }

References m_ticStart, and m_ticStop.

◆ TraceDetectionMoulon() [2/2]

pappso::TraceDetectionMoulon::TraceDetectionMoulon ( const TraceDetectionMoulon other)

Definition at line 38 of file tracedetectionmoulon.cpp.

39  : m_xicFilterSmoothing(other.m_xicFilterSmoothing)
40 {
41  m_ticStart = other.m_ticStart;
42  m_ticStop = other.m_ticStop;
43 }

References m_ticStart, and m_ticStop.

◆ ~TraceDetectionMoulon()

pappso::TraceDetectionMoulon::~TraceDetectionMoulon ( )
virtual

Definition at line 45 of file tracedetectionmoulon.cpp.

46 {
47 }

Member Function Documentation

◆ detect()

void pappso::TraceDetectionMoulon::detect ( const Trace trace,
TraceDetectionSinkInterface sink,
bool  remove_peak_base 
) const
overridevirtual

detect peaks on a trace

Parameters
tracethe trace to detect peaks on
sinkthe object to store peaks or stream it
remove_peak_baseif true, removes the area under the base of the peak

Implements pappso::TraceDetectionInterface.

Definition at line 86 of file tracedetectionmoulon.cpp.

89 {
90 
91  Trace xic_smoothed(xic);
92 
93  m_xicFilterSmoothing.filter(xic_smoothed);
94 
95  // detect peaks :
96  bool banked(false);
97  unsigned int nb_tic_start(0);
98 
99  std::vector<DataPoint>::const_iterator it_smoothed;
100  std::vector<DataPoint>::const_iterator it, it_begin;
101 
102  // TracePeak *p_current_peak = nullptr;
103 
104  for(it_smoothed = xic_smoothed.begin(), it = xic.begin();
105  it_smoothed != xic_smoothed.end();
106  ++it_smoothed, ++it)
107  {
108 
109  if((nb_tic_start == 0) && (it_begin != xic.end()) && (banked == false))
110  {
111  // delete(p_current_peak);
112  // p_current_peak = nullptr;
113  it_begin = xic.end();
114  }
115 
116  if(it_smoothed->y >= m_ticStart)
117  {
118  nb_tic_start++;
119  if(it_begin == xic.end())
120  {
121  // p_current_peak = new TracePeak;
122  // p_current_peak->setLeftBoundary(*it_smoothed);
123  it_begin = it;
124  banked = false;
125  }
126  if((nb_tic_start == 2) && (banked == false))
127  {
128  banked = true;
129  }
130  }
131  else
132  {
133  nb_tic_start = 0;
134  }
135  if(it_smoothed->y <= m_ticStop)
136  {
137  if(it_begin != xic.end())
138  {
139 
140  if(banked)
141  {
142  TracePeak peak(it_begin, it + 1, remove_peak_base);
143  sink.setTracePeak(peak);
144  }
145  banked = false;
146  }
147  }
148  }
149 }
virtual Trace & filter(Trace &data_points) const override

References pappso::FilterMorphoWindowBase::filter(), m_ticStart, m_ticStop, m_xicFilterSmoothing, and pappso::TraceDetectionSinkInterface::setTracePeak().

◆ getSmoothingHalfEdgeWindows()

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

◆ getTicStart()

pappso_double pappso::TraceDetectionMoulon::getTicStart ( ) const

Definition at line 74 of file tracedetectionmoulon.cpp.

75 {
76  return m_ticStart;
77 }

References m_ticStart.

◆ getTicStop()

pappso_double pappso::TraceDetectionMoulon::getTicStop ( ) const

Definition at line 80 of file tracedetectionmoulon.cpp.

81 {
82  return m_ticStop;
83 }

References m_ticStop.

◆ setFilterMorphoMean()

void pappso::TraceDetectionMoulon::setFilterMorphoMean ( const FilterMorphoMean smooth)

Definition at line 51 of file tracedetectionmoulon.cpp.

52 {
53  m_xicFilterSmoothing = smooth;
54 }

References m_xicFilterSmoothing.

◆ setTicStart()

void pappso::TraceDetectionMoulon::setTicStart ( double  tic_start)

Definition at line 57 of file tracedetectionmoulon.cpp.

58 {
59  m_ticStart = tic_start;
60 }

References m_ticStart.

◆ setTicStop()

void pappso::TraceDetectionMoulon::setTicStop ( double  tic_stop)

Definition at line 62 of file tracedetectionmoulon.cpp.

63 {
64  m_ticStop = tic_stop;
65 }

References m_ticStop.

Member Data Documentation

◆ m_ticStart

pappso_double pappso::TraceDetectionMoulon::m_ticStart
private

Definition at line 38 of file tracedetectionmoulon.h.

Referenced by TraceDetectionMoulon(), detect(), getTicStart(), and setTicStart().

◆ m_ticStop

pappso_double pappso::TraceDetectionMoulon::m_ticStop
private

Definition at line 39 of file tracedetectionmoulon.h.

Referenced by TraceDetectionMoulon(), detect(), getTicStop(), and setTicStop().

◆ m_xicFilterSmoothing

FilterMorphoMean pappso::TraceDetectionMoulon::m_xicFilterSmoothing
private

Definition at line 37 of file tracedetectionmoulon.h.

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


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