libpappsomspp
Library for mass spectrometry
filtermorpho.cpp
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1/**
2 * \file pappsomspp/filers/filtermorpho.cpp
3 * \date 02/05/2019
4 * \author Olivier Langella
5 * \brief collection of morphological filters
6 */
7
8/*******************************************************************************
9 * Copyright (c) 2019 Olivier Langella <Olivier.Langella@u-psud.fr>.
10 *
11 * This file is part of the PAPPSOms++ library.
12 *
13 * PAPPSOms++ is free software: you can redistribute it and/or modify
14 * it under the terms of the GNU General Public License as published by
15 * the Free Software Foundation, either version 3 of the License, or
16 * (at your option) any later version.
17 *
18 * PAPPSOms++ is distributed in the hope that it will be useful,
19 * but WITHOUT ANY WARRANTY; without even the implied warranty of
20 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
21 * GNU General Public License for more details.
22 *
23 * You should have received a copy of the GNU General Public License
24 * along with PAPPSOms++. If not, see <http://www.gnu.org/licenses/>.
25 *
26 ******************************************************************************/
27
28#include "filtermorpho.h"
29#include "../../trace/trace.h"
30#include <QDebug>
31#include "../../exception/exceptionoutofrange.h"
32#include "../../exception/exceptionnotrecognized.h"
33
34using namespace pappso;
35
36FilterMorphoWindowBase::FilterMorphoWindowBase(std::size_t half_window_size)
37 : m_halfWindowSize(half_window_size)
38{
39}
41 const FilterMorphoWindowBase &other)
42 : m_halfWindowSize(other.m_halfWindowSize)
43{
44}
45std::size_t
47{
48 return m_halfWindowSize;
49}
50
53{
55
56 return *this;
57}
58
59
60Trace &
62{
63
64 qDebug() << " " << m_halfWindowSize << " data_points.size()"
65 << data_points.size();
66 if(m_halfWindowSize == 0)
67 return data_points;
68 if(data_points.size() <= m_halfWindowSize)
69 return data_points;
70 Trace old_trace(data_points);
71 auto it = old_trace.begin();
72 auto itend = old_trace.end() - m_halfWindowSize - 1;
73 auto it_target = data_points.begin();
74
75
76 std::size_t loop_begin = 0;
77 while((it != itend) && (loop_begin < m_halfWindowSize))
78 {
79 // maxYDataPoint(it_begin, it + m_halfWindowSize + 1);
80 // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
81 // << it->x << " " << m_halfWindowSize;
82 // it_target->x = it->x;
83 it_target->y =
84 getWindowValue(old_trace.begin(), it + m_halfWindowSize + 1);
85 it++;
86 it_target++;
87 loop_begin++;
88 }
89 // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
90 while(it != itend)
91 {
92 // it_target->x = it->x;
93 // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
94 // << it->x;
95 it_target->y =
97 it++;
98 it_target++;
99 }
100 // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
101 while(it != old_trace.end())
102 {
103 // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__ << " "
104 // << it->x;
105 // it_target->x = it->x;
106 it_target->y = getWindowValue(it - m_halfWindowSize, old_trace.end());
107 it++;
108 it_target++;
109 }
110 // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
111 // problem with move or swap : this lead to segmentation faults in some cases
112 // data_points = std::move(new_trace);
113 qDebug();
114 return data_points;
115}
116
117FilterMorphoSum::FilterMorphoSum(std::size_t half_window_size)
118 : FilterMorphoWindowBase(half_window_size)
119{
120}
122 : FilterMorphoWindowBase(other.m_halfWindowSize)
123{
124}
125
128{
130
131 return *this;
132}
133
134double
136 std::vector<DataPoint>::const_iterator begin,
137 std::vector<DataPoint>::const_iterator end) const
138{
139
140 qDebug();
141 return sumYTrace(begin, end, 0);
142}
143
144FilterMorphoMax::FilterMorphoMax(std::size_t half_window_size)
145 : FilterMorphoWindowBase(half_window_size)
146{
147}
149 : FilterMorphoWindowBase(other.m_halfWindowSize)
150{
151}
152
155{
157
158 return *this;
159}
160
161double
163 std::vector<DataPoint>::const_iterator begin,
164 std::vector<DataPoint>::const_iterator end) const
165{
166
167 // qDebug() << __FILE__ << " " << __FUNCTION__ << " " << __LINE__;
168 return maxYDataPoint(begin, end)->y;
169}
170
171std::size_t
173{
174 return m_halfWindowSize;
175}
176
177FilterMorphoMin::FilterMorphoMin(std::size_t half_window_size)
178 : FilterMorphoWindowBase(half_window_size)
179{
180}
182 : FilterMorphoWindowBase(other.m_halfWindowSize)
183{
184}
185
188{
190
191 return *this;
192}
193
194double
196 std::vector<DataPoint>::const_iterator begin,
197 std::vector<DataPoint>::const_iterator end) const
198{
199 return minYDataPoint(begin, end)->y;
200}
201
202std::size_t
204{
205 return m_halfWindowSize;
206}
207
208FilterMorphoMinMax::FilterMorphoMinMax(std::size_t half_window_size)
209 : m_filterMax(half_window_size), m_filterMin(half_window_size)
210{
211}
213 : m_filterMax(other.m_filterMax), m_filterMin(other.m_filterMin)
214{
215}
216
219{
220 m_filterMax = other.m_filterMax;
221 m_filterMin = other.m_filterMin;
222
223 return *this;
224}
225
226Trace &
228{
229 qDebug();
230 m_filterMax.filter(data_points);
231 m_filterMin.filter(data_points);
232 qDebug();
233 return data_points;
234}
235std::size_t
237{
238 return ((FilterMorphoMax)m_filterMax).getMaxHalfEdgeWindows();
239}
240
241
242FilterMorphoMaxMin::FilterMorphoMaxMin(std::size_t half_window_size)
243 : m_filterMin(half_window_size), m_filterMax(half_window_size)
244{
245}
247 : m_filterMin(other.m_filterMin), m_filterMax(other.m_filterMax)
248{
249}
250
253{
254 m_filterMin = other.m_filterMin;
255 m_filterMax = other.m_filterMax;
256
257 return *this;
258}
259
260Trace &
262{
263 qDebug();
264 m_filterMin.filter(data_points);
265 m_filterMax.filter(data_points);
266 qDebug();
267 return data_points;
268}
269std::size_t
271{
272 return ((FilterMorphoMax)m_filterMax).getMaxHalfEdgeWindows();
273}
274
276 : m_halfWindowSize(half_window_size)
277{
278}
279
281 : m_halfWindowSize(other.m_halfWindowSize)
282{
283}
284
286 const QString &strBuildParams)
287{
288 buildFilterFromString(strBuildParams);
289}
290
291void
293 const QString &strBuildParams)
294{
295 //"antiSpike|2"
296 if(strBuildParams.startsWith("antiSpike|"))
297 {
298 QStringList params = strBuildParams.split("|").back().split(";");
299
300 m_halfWindowSize = params.at(0).toUInt();
301 }
302 else
303 {
305 QString("building FilterMorphoAntiSpike from string %1 is not possible")
306 .arg(strBuildParams));
307 }
308}
309
310QString
312{
313 QString strCode = QString("antiSpike|%1").arg(m_halfWindowSize);
314
315 return strCode;
316}
317
318QString
320{
321 return "antiSpike";
322}
323
324
327{
329
330 return *this;
331}
332
333std::size_t
335{
336 return m_halfWindowSize;
337}
338Trace &
340{
341 // qDebug();
342 if(m_halfWindowSize == 0)
343 return data_points;
344 if(data_points.size() < m_halfWindowSize)
345 return data_points;
346 Trace old_trace(data_points);
347 auto it = old_trace.begin();
348 auto it_target = data_points.begin();
349 auto itw = old_trace.begin();
350
351 auto itend = old_trace.end() - m_halfWindowSize - 1;
352 // new_trace.reserve(data_points.size());
353
354 // qDebug();
355 while((it != old_trace.end()) &&
356 (std::distance(old_trace.begin(), it) < (int)m_halfWindowSize))
357 {
358 // no anti spike at the begining of the signal
359 it++;
360 it_target++;
361 }
362 // qDebug();
363 while((it != itend) && (it != old_trace.end()))
364 {
365 // qDebug();
366 auto itwend = it + m_halfWindowSize + 1;
367 itw = findDifferentYvalue(it - m_halfWindowSize, it + 1, 0);
368 if(itw == it)
369 {
370 // qDebug();
371 itw = findDifferentYvalue(it + 1, itwend, 0);
372 if(itw == itwend)
373 {
374 it_target->y = 0;
375 }
376 // qDebug();
377 }
378
379 // qDebug();
380 it++;
381 it_target++;
382 }
383
384 return data_points;
385}
386
387
388FilterMorphoMedian::FilterMorphoMedian(std::size_t half_window_size)
389 : FilterMorphoWindowBase(half_window_size)
390{
391}
393 : FilterMorphoWindowBase(other.m_halfWindowSize)
394{
395}
396
399{
401
402 return *this;
403}
404
405double
407 std::vector<DataPoint>::const_iterator begin,
408 std::vector<DataPoint>::const_iterator end) const
409{
410 return medianYTrace(begin, end);
411}
412
413
414FilterMorphoMean::FilterMorphoMean(std::size_t half_window_size)
415 : FilterMorphoWindowBase(half_window_size)
416{
417}
419 : FilterMorphoWindowBase(other.m_halfWindowSize)
420{
421}
422
425{
427
428 return *this;
429}
430
431std::size_t
433{
434 return m_halfWindowSize;
435}
436
437double
439 std::vector<DataPoint>::const_iterator begin,
440 std::vector<DataPoint>::const_iterator end) const
441{
442 return meanYTrace(begin, end);
443}
444
445
447 std::size_t median_half_window_size, std::size_t minmax_half_window_size)
448 : m_filterMorphoMedian(median_half_window_size),
449 m_filterMorphoMinMax(minmax_half_window_size)
450{
451}
452
454 const FilterMorphoBackground &other)
455 : m_filterMorphoMedian(other.m_filterMorphoMedian),
456 m_filterMorphoMinMax(other.m_filterMorphoMinMax)
457{
458}
459
462{
465
466 return *this;
467}
468
469Trace &
471{
472 m_filterMorphoMedian.filter(data_points);
473 m_filterMorphoMinMax.filter(data_points);
474
475 // finally filter negative values
476 for(DataPoint &point : data_points)
477 {
478 if(point.y < 0)
479 {
480 point.y = 0;
481 }
482 }
483 return data_points;
484}
485const FilterMorphoMedian &
487{
489}
490const FilterMorphoMinMax &
492{
494}
excetion to use when an item type is not recognized
anti spike filter set to zero alone values inside the window
Definition: filtermorpho.h:158
FilterMorphoAntiSpike & operator=(const FilterMorphoAntiSpike &other)
std::size_t getHalfWindowSize() const
void buildFilterFromString(const QString &strBuildParams) override
build this filter using a string
QString toString() const override
QString name() const override
FilterMorphoAntiSpike(std::size_t half_window_size)
Trace & filter(Trace &data_points) const override
compute background of a trace compute background noise on a trace
Definition: filtermorpho.h:229
Trace & filter(Trace &data_points) const override
FilterMorphoBackground(std::size_t median_half_window_size, std::size_t minmax_half_window_size)
FilterMorphoMedian m_filterMorphoMedian
Definition: filtermorpho.h:231
const FilterMorphoMedian & getFilterMorphoMedian() const
FilterMorphoBackground & operator=(const FilterMorphoBackground &other)
const FilterMorphoMinMax & getFilterMorphoMinMax() const
FilterMorphoMinMax m_filterMorphoMinMax
Definition: filtermorpho.h:232
transform the trace with the maximum of the minimum equivalent of the erode filter for pictures
Definition: filtermorpho.h:138
Trace & filter(Trace &data_points) const override
FilterMorphoMaxMin(std::size_t half_window_size)
FilterMorphoMax m_filterMax
Definition: filtermorpho.h:141
std::size_t getMaxMinHalfEdgeWindows() const
FilterMorphoMaxMin & operator=(const FilterMorphoMaxMin &other)
FilterMorphoMin m_filterMin
Definition: filtermorpho.h:140
transform the trace into its maximum over a window
Definition: filtermorpho.h:81
double getWindowValue(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) const override
std::size_t getMaxHalfEdgeWindows() const
FilterMorphoMax(std::size_t half_window_size)
FilterMorphoMax & operator=(const FilterMorphoMax &other)
mean filter apply mean of y values inside the window : this results in a kind of smoothing
Definition: filtermorpho.h:210
FilterMorphoMean(std::size_t half_window_size)
FilterMorphoMean & operator=(const FilterMorphoMean &other)
double getWindowValue(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) const override
std::size_t getMeanHalfEdgeWindows() const
median filter apply median of y values inside the window
Definition: filtermorpho.h:191
FilterMorphoMedian & operator=(const FilterMorphoMedian &other)
double getWindowValue(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) const override
FilterMorphoMedian(std::size_t half_window_size)
transform the trace with the minimum of the maximum equivalent of the dilate filter for pictures
Definition: filtermorpho.h:118
FilterMorphoMax m_filterMax
Definition: filtermorpho.h:120
FilterMorphoMin m_filterMin
Definition: filtermorpho.h:121
FilterMorphoMinMax(std::size_t half_window_size)
std::size_t getMinMaxHalfEdgeWindows() const
Trace & filter(Trace &data_points) const override
FilterMorphoMinMax & operator=(const FilterMorphoMinMax &other)
transform the trace into its minimum over a window
Definition: filtermorpho.h:99
std::size_t getMinHalfEdgeWindows() const
FilterMorphoMin(std::size_t half_window_size)
double getWindowValue(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) const override
FilterMorphoMin & operator=(const FilterMorphoMin &other)
FilterMorphoSum & operator=(const FilterMorphoSum &other)
FilterMorphoSum(std::size_t half_window_size)
double getWindowValue(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) const override
base class that apply a signal treatment based on a window
Definition: filtermorpho.h:41
virtual Trace & filter(Trace &data_points) const override
virtual double getWindowValue(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end) const =0
FilterMorphoWindowBase(std::size_t half_window_size)
virtual std::size_t getHalfWindowSize() const
FilterMorphoWindowBase & operator=(const FilterMorphoWindowBase &other)
A simple container of DataPoint instances.
Definition: trace.h:148
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition: aa.cpp:39
std::vector< DataPoint >::iterator findDifferentYvalue(std::vector< DataPoint >::iterator begin, std::vector< DataPoint >::iterator end, const double &y_value)
find the first element in which Y is different of value
Definition: trace.cpp:127
std::vector< DataPoint >::const_iterator maxYDataPoint(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
Definition: trace.cpp:180
double medianYTrace(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
calculate the median of y value of a trace
Definition: trace.cpp:291
double meanYTrace(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
calculate the mean of y value of a trace
Definition: trace.cpp:253
double sumYTrace(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end, double init)
calculate the sum of y value of a trace
Definition: trace.cpp:244
std::vector< DataPoint >::const_iterator minYDataPoint(std::vector< DataPoint >::const_iterator begin, std::vector< DataPoint >::const_iterator end)
Definition: trace.cpp:158