libpappsomspp
Library for mass spectrometry
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pappso::TraceDetectionZivy Class Reference

#include <tracedetectionzivy.h>

Inheritance diagram for pappso::TraceDetectionZivy:
pappso::TraceDetectionInterface

Public Member Functions

 TraceDetectionZivy (unsigned int smoothing_half_window_length, unsigned int minmax_half_window_length, unsigned int maxmin_half_window_length, pappso_double detection_threshold_on_minmax, pappso_double detection_threshold_on_maxmin)
 
virtual ~TraceDetectionZivy ()
 
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
 
pappso_double getDetectionThresholdOnMinmax () const
 
pappso_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
 
pappso_double m_detectionThresholdOnMinMax
 
pappso_double m_detectionThresholdOnMaxMin
 

Detailed Description

Definition at line 36 of file tracedetectionzivy.h.

Constructor & Destructor Documentation

◆ TraceDetectionZivy()

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

Definition at line 35 of file tracedetectionzivy.cpp.

41 : m_smooth(smoothing_half_window_length),
42 m_minMax(minmax_half_window_length),
43 m_maxMin(maxmin_half_window_length)
44{
45 m_detectionThresholdOnMaxMin = detection_threshold_on_maxmin;
46 m_detectionThresholdOnMinMax = detection_threshold_on_minmax;
47}
pappso_double m_detectionThresholdOnMaxMin
pappso_double m_detectionThresholdOnMinMax

References m_detectionThresholdOnMaxMin, and m_detectionThresholdOnMinMax.

◆ ~TraceDetectionZivy()

pappso::TraceDetectionZivy::~TraceDetectionZivy ( )
virtual

Definition at line 48 of file tracedetectionzivy.cpp.

49{
50}

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
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 109 of file tracedetectionzivy.cpp.

112{
113
114 // detect peak positions on close curve : a peak is an intensity value
115 // strictly greater than the two surrounding values. In case of
116 // equality (very rare, can happen with some old old spectrometers) we
117 // take the last equal point to be the peak
118 qDebug();
119 std::size_t size = xic.size();
120 if(size < 4)
121 {
122 qDebug() << QObject::tr(
123 "The original XIC is too small to detect peaks (%1)")
124 .arg(xic.size());
125 return;
126 }
128 return;
130 return;
131
132 Trace xic_minmax(xic); //"close" courbe du haut
134 {
135 qDebug() << "f";
136 m_smooth.filter(xic_minmax);
137 }
138
139 qDebug();
140 Trace xic_maxmin(xic_minmax); //"open" courbe du bas
141
142 qDebug();
143
144 try
145 {
146 qDebug() << "f1";
147 m_minMax.filter(xic_minmax);
148 qDebug() << "f2";
149 m_maxMin.filter(xic_maxmin);
150 }
151 catch(const ExceptionOutOfRange &e)
152 {
153 qDebug() << QObject::tr(
154 "The original XIC is too small to detect peaks (%1) :\n%2")
155 .arg(xic.size())
156 .arg(e.qwhat());
157 return;
158 }
159 qDebug() << "a";
160
161 std::vector<DataPoint>::const_iterator previous_rt = xic_minmax.begin();
162 std::vector<DataPoint>::const_iterator current_rt = (previous_rt + 1);
163 std::vector<DataPoint>::const_iterator last_rt = (xic_minmax.end() - 1);
164
165 std::vector<DataPoint>::const_iterator current_rt_on_maxmin =
166 (xic_maxmin.begin() + 1);
167
168 std::vector<DataPoint>::const_iterator xic_position = xic.begin();
169 qDebug() << "b";
170 while(current_rt != last_rt)
171 // for (unsigned int i = 1, count = 0; i < xic_minmax.size() - 1; )
172 {
173 // conditions to have a peak
174 if((previous_rt->y < current_rt->y) &&
175 (current_rt->y > m_detectionThresholdOnMinMax) &&
176 (current_rt_on_maxmin->y > m_detectionThresholdOnMaxMin))
177 {
178 // here we test the last condition to have a peak
179
180 // no peak case
181 if(current_rt->y < (current_rt + 1)->y)
182 {
183 //++i;
184 previous_rt = current_rt;
185 current_rt++;
186 current_rt_on_maxmin++;
187 }
188 // there is a peak here ! case
189 else if(current_rt->y > (current_rt + 1)->y)
190 {
191 // peak.setMaxXicElement(*current_rt);
192
193 // find left boundary
194 std::vector<DataPoint>::const_iterator it_left =
195 moveLowerYLeftDataPoint(xic_minmax, current_rt);
196 // walk back
197 it_left = moveLowerYRigthDataPoint(xic_minmax, it_left);
198 // peak.setLeftBoundary(*it_left);
199
200 // find right boundary
201 std::vector<DataPoint>::const_iterator it_right =
202 moveLowerYRigthDataPoint(xic_minmax, current_rt);
203 // walk back
204 it_right = moveLowerYLeftDataPoint(xic_minmax, it_right);
205 // peak.setRightBoundary(*it_right);
206
207 // integrate peak surface :
208 auto it =
209 findFirstEqualOrGreaterX(xic_position, xic.end(), it_left->x);
210 xic_position =
211 findFirstEqualOrGreaterX(it, xic.end(), it_right->x) + 1;
212 // peak.setArea(areaTrace(it, xic_position));
213
214 // find the maximum :
215 // peak.setMaxXicElement(*maxYDataPoint(it, xic_position));
216
217 // areaTrace()
218 TracePeak peak(it, xic_position, remove_peak_base);
219 sink.setTracePeak(peak);
220 // }
221 //++i;
222 previous_rt = current_rt;
223 current_rt++;
224 current_rt_on_maxmin++;
225 }
226 // equality case, skipping equal points
227 else
228 {
229 // while (v_minmax[i] == v_minmax[i + 1]) {
230 //++i;
231 current_rt++;
232 current_rt_on_maxmin++;
233
234 //++count;
235 }
236 }
237 // no chance to have a peak at all, continue looping
238 else
239 {
240 //++i;
241 previous_rt = current_rt;
242 current_rt++;
243 current_rt_on_maxmin++;
244 }
245 } // end loop for peaks
246 qDebug();
247}
Trace & filter(Trace &data_points) const override
std::size_t getMaxMinHalfEdgeWindows() const
std::size_t getMeanHalfEdgeWindows() const
std::size_t getMinMaxHalfEdgeWindows() const
Trace & filter(Trace &data_points) const override
virtual Trace & filter(Trace &data_points) const override
std::vector< DataPoint >::iterator findFirstEqualOrGreaterX(std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &value)
find the first element in which X is equal or greater than the value searched important : it implies ...
Definition trace.cpp:71
std::vector< DataPoint >::const_iterator moveLowerYLeftDataPoint(const Trace &trace, std::vector< DataPoint >::const_iterator begin)
Move left to the lower value.
Definition trace.cpp:223
std::vector< DataPoint >::const_iterator moveLowerYRigthDataPoint(const Trace &trace, std::vector< DataPoint >::const_iterator begin)
Move right to the lower value.
Definition trace.cpp:205

References pappso::FilterMorphoWindowBase::filter(), pappso::FilterMorphoMinMax::filter(), pappso::FilterMorphoMaxMin::filter(), pappso::findFirstEqualOrGreaterX(), pappso::FilterMorphoMaxMin::getMaxMinHalfEdgeWindows(), pappso::FilterMorphoMean::getMeanHalfEdgeWindows(), pappso::FilterMorphoMinMax::getMinMaxHalfEdgeWindows(), 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 102 of file tracedetectionzivy.cpp.

103{
105};

References m_detectionThresholdOnMaxMin.

◆ getDetectionThresholdOnMinmax()

pappso_double pappso::TraceDetectionZivy::getDetectionThresholdOnMinmax ( ) const

Definition at line 97 of file tracedetectionzivy.cpp.

98{
100};

References m_detectionThresholdOnMinMax.

◆ getMaxMinHalfEdgeWindows()

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

◆ getMinMaxHalfEdgeWindows()

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

◆ getSmoothingHalfEdgeWindows()

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

◆ setDetectionThresholdOnMaxmin()

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

Definition at line 75 of file tracedetectionzivy.cpp.

77{
78 m_detectionThresholdOnMaxMin = detectionThresholdOnMaxMin;
79}

References m_detectionThresholdOnMaxMin.

◆ setDetectionThresholdOnMinmax()

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

Definition at line 69 of file tracedetectionzivy.cpp.

71{
72 m_detectionThresholdOnMinMax = detectionThresholdOnMinMax;
73}

References m_detectionThresholdOnMinMax.

◆ setFilterMorphoMaxMin()

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

Definition at line 63 of file tracedetectionzivy.cpp.

64{
65 m_maxMin = maxMin;
66}

References m_maxMin.

◆ setFilterMorphoMean()

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

Definition at line 53 of file tracedetectionzivy.cpp.

54{
55 m_smooth = smooth;
56}

References m_smooth.

◆ setFilterMorphoMinMax()

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

Definition at line 58 of file tracedetectionzivy.cpp.

59{
60 m_minMax = minMax;
61}

References m_minMax.

Member Data Documentation

◆ m_detectionThresholdOnMaxMin

pappso_double pappso::TraceDetectionZivy::m_detectionThresholdOnMaxMin
private

◆ m_detectionThresholdOnMinMax

pappso_double pappso::TraceDetectionZivy::m_detectionThresholdOnMinMax
private

◆ m_maxMin

FilterMorphoMaxMin pappso::TraceDetectionZivy::m_maxMin
private

Definition at line 69 of file tracedetectionzivy.h.

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

◆ m_minMax

FilterMorphoMinMax pappso::TraceDetectionZivy::m_minMax
private

Definition at line 68 of file tracedetectionzivy.h.

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

◆ m_smooth

FilterMorphoMean pappso::TraceDetectionZivy::m_smooth
private

Definition at line 67 of file tracedetectionzivy.h.

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


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