libpappsomspp
Library for mass spectrometry
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timsframe.cpp
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1/**
2 * \file pappsomspp/vendors/tims/timsframe.cpp
3 * \date 23/08/2019
4 * \author Olivier Langella
5 * \brief handle a single Bruker's TimsTof frame
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 "timsframe.h"
29#include "../../../pappsomspp/pappsoexception.h"
30#include <QDebug>
31#include <QObject>
32#include <QtEndian>
33#include <memory>
34
35
36namespace pappso
37{
38
40 const TimsFrame *fram_p, const XicCoordTims &xic_struct)
41{
42 xic_ptr = xic_struct.xicSptr.get();
43
45 mobilityIndexEnd = xic_struct.scanNumEnd;
47 fram_p->getMzCalibrationInterfaceSPtr().get()->getTofIndexFromMz(
48 xic_struct.mzRange.lower()); // convert mz to raw digitizer value
50 fram_p->getMzCalibrationInterfaceSPtr().get()->getTofIndexFromMz(
51 xic_struct.mzRange.upper());
52 tmpIntensity = 0;
53}
54
55TimsFrame::TimsFrame(std::size_t timsId, quint32 scanNum)
56 : TimsFrameBase(timsId, scanNum)
57{
58 // m_timsDataFrame.resize(10);
59}
60
61TimsFrame::TimsFrame(std::size_t timsId,
62 quint32 scanNum,
63 char *p_bytes,
64 std::size_t len)
65 : TimsFrameBase(timsId, scanNum)
66{
67 // langella@themis:~/developpement/git/bruker/cbuild$
68 // ./src/sample/timsdataSamplePappso
69 // /gorgone/pappso/fichiers_fabricants/Bruker/Demo_TimsTOF_juin2019/Samples/1922001/1922001-1_S-415_Pep_Pur-1ul_Slot1-10_1_2088.d/
70 qDebug() << timsId;
71
72 m_timsDataFrame.resize(len);
73
74 if(p_bytes != nullptr)
75 {
76 unshufflePacket(p_bytes);
77 }
78 else
79 {
80 if(m_scanNumber == 0)
81 {
82
84 QObject::tr("TimsFrame::TimsFrame(%1,%2,nullptr,%3) FAILED")
85 .arg(m_timsId)
86 .arg(m_scanNumber)
87 .arg(len));
88 }
89 }
90}
91
93{
94}
95
99
100
101void
103{
104 qDebug();
105 quint64 len = m_timsDataFrame.size();
106 if(len % 4 != 0)
107 {
109 QObject::tr("TimsFrame::unshufflePacket error: len % 4 != 0"));
110 }
111
112 quint64 nb_uint4 = len / 4;
113
114 char *dest = m_timsDataFrame.data();
115 quint64 src_offset = 0;
116
117 for(quint64 j = 0; j < 4; j++)
118 {
119 for(quint64 i = 0; i < nb_uint4; i++)
120 {
121 dest[(i * 4) + j] = src[src_offset];
122 src_offset++;
123 }
124 }
125 qDebug();
126}
127
128std::size_t
129TimsFrame::getNbrPeaks(std::size_t scanNum) const
130{
131 if(m_timsDataFrame.size() == 0)
132 return 0;
133 /*
134 if(scanNum == 0)
135 {
136 quint32 res = (*(quint32 *)(m_timsDataFrame.constData() + 4)) -
137 (*(quint32 *)(m_timsDataFrame.constData()-4));
138 return res / 2;
139 }*/
140 if(scanNum == (m_scanNumber - 1))
141 {
142 auto nb_uint4 = m_timsDataFrame.size() / 4;
143
144 std::size_t cumul = 0;
145 for(quint32 i = 0; i < m_scanNumber; i++)
146 {
147 cumul += (*(quint32 *)(m_timsDataFrame.constData() + (i * 4)));
148 }
149 return (nb_uint4 - cumul) / 2;
150 }
151 checkScanNum(scanNum);
152
153 // quint32 *res = (quint32 *)(m_timsDataFrame.constData() + (scanNum * 4));
154 // qDebug() << " res=" << *res;
155 return (*(quint32 *)(m_timsDataFrame.constData() + ((scanNum + 1) * 4))) / 2;
156}
157
158std::size_t
159TimsFrame::getScanOffset(std::size_t scanNum) const
160{
161 std::size_t offset = 0;
162 for(std::size_t i = 0; i < (scanNum + 1); i++)
163 {
164 offset += (*(quint32 *)(m_timsDataFrame.constData() + (i * 4)));
165 }
166 return offset;
167}
168
169
170std::vector<quint32>
171TimsFrame::getScanIndexList(std::size_t scanNum) const
172{
173 qDebug();
174 checkScanNum(scanNum);
175 std::vector<quint32> scan_tof;
176
177 if(m_timsDataFrame.size() == 0)
178 return scan_tof;
179 scan_tof.resize(getNbrPeaks(scanNum));
180
181 std::size_t offset = getScanOffset(scanNum);
182
183 qint32 previous = -1;
184 for(std::size_t i = 0; i < scan_tof.size(); i++)
185 {
186 scan_tof[i] =
187 (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
188 previous;
189 previous = scan_tof[i];
190 }
191 qDebug();
192 return scan_tof;
193}
194
195std::vector<quint32>
196TimsFrame::getScanIntensities(std::size_t scanNum) const
197{
198 qDebug();
199 checkScanNum(scanNum);
200 std::vector<quint32> scan_intensities;
201
202 if(m_timsDataFrame.size() == 0)
203 return scan_intensities;
204
205 scan_intensities.resize(getNbrPeaks(scanNum));
206
207 std::size_t offset = getScanOffset(scanNum);
208
209 for(std::size_t i = 0; i < scan_intensities.size(); i++)
210 {
211 scan_intensities[i] = (*(quint32 *)(m_timsDataFrame.constData() +
212 (offset * 4) + (i * 8) + 4));
213 }
214 qDebug();
215 return scan_intensities;
216}
217
218
219quint64
221{
222 qDebug();
223
224 quint64 summed_intensities = 0;
225
226 if(m_timsDataFrame.size() == 0)
227 return summed_intensities;
228 // checkScanNum(scanNum);
229
230 std::size_t size = getNbrPeaks(scanNum);
231
232 std::size_t offset = getScanOffset(scanNum);
233
234 qint32 previous = -1;
235
236 for(std::size_t i = 0; i < size; i++)
237 {
238 quint32 x =
239 (*(quint32 *)((m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
240 previous);
241
242 quint32 y = (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) +
243 (i * 8) + 4));
244
245 previous = x;
246
247 summed_intensities += y;
248 }
249
250 // Normalization over the accumulation time for this frame.
251 summed_intensities *= ((double)100.0 / m_accumulationTime);
252
253 qDebug();
254
255 return summed_intensities;
256}
257
258
259/**
260 * @brief ...
261 *
262 * @param mobility_scan_begin p_mobility_scan_begin:...
263 * @param mobility_scan_end p_mobility_scan_end:...
264 * @return quint64
265 */
266quint64
267TimsFrame::cumulateScansIntensities(std::size_t mobility_scan_begin,
268 std::size_t mobility_scan_end) const
269{
270 quint64 summed_intensities = 0;
271
272 // qDebug() << "begin mobility_scan_begin =" << mobility_scan_begin
273 //<< "mobility_scan_end =" << mobility_scan_end;
274
275 if(m_timsDataFrame.size() == 0)
276 return summed_intensities;
277
278 try
279 {
280 std::size_t mobility_scan_max = mobility_scan_end + 1;
281
282 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
283 {
284 qDebug() << i;
285 summed_intensities += cumulateSingleScanIntensities(i);
286 qDebug() << i;
287 }
288 }
289 catch(std::exception &error)
290 {
291 qDebug() << QString("Failure in %1 %2 to %3 :\n %4")
292 .arg(__FUNCTION__)
293 .arg(mobility_scan_begin)
294 .arg(mobility_scan_end)
295 .arg(error.what());
296 }
297
298 // qDebug() << "end";
299
300 return summed_intensities;
301}
302
303
304void
305TimsFrame::cumulateScan(std::size_t scanNum,
306 std::map<quint32, quint32> &accumulate_into) const
307{
308 // qDebug();
309
310 if(m_timsDataFrame.size() == 0)
311 return;
312
313 // checkScanNum(scanNum);
314
315 std::size_t scan_size = getNbrPeaks(scanNum);
316
317 std::size_t scan_offset = getScanOffset(scanNum);
318
319 qint32 previous = -1;
320 for(std::size_t i = 0; i < scan_size; i++)
321 {
322 quint32 x = (*(quint32 *)((m_timsDataFrame.constData() +
323 (scan_offset * 4) + (i * 8))) +
324 previous);
325 quint32 y = (*(quint32 *)(m_timsDataFrame.constData() +
326 (scan_offset * 4) + (i * 8) + 4));
327
328 previous = x;
329
330 auto ret = accumulate_into.insert(std::pair<quint32, quint32>(x, y));
331
332 if(ret.second == false)
333 {
334 // already existed : cumulate
335 ret.first->second += y;
336 }
337 }
338
339 // qDebug();
340}
341
342// Proof of concept m/z range-conditions for accumulations
343void
344TimsFrame::cumulateScan2(std::size_t scanNum,
345 std::map<quint32, quint32> &accumulate_into,
346 double mz_range_begin,
347 double mz_range_end) const
348{
349 // qDebug();
350
351 if(m_timsDataFrame.size() == 0)
352 return;
353
354 // checkScanNum(scanNum);
355
356 std::size_t scan_size = getNbrPeaks(scanNum);
357
358 std::size_t scan_offset = getScanOffset(scanNum);
359
360 qint32 previous = -1;
361
362 for(std::size_t i = 0; i < scan_size; i++)
363 {
364 quint32 x = (*(quint32 *)((m_timsDataFrame.constData() +
365 (scan_offset * 4) + (i * 8))) +
366 previous);
367
368 if(x < mz_range_begin)
369 continue;
370 if(x > mz_range_end)
371 break;
372
373 quint32 y = (*(quint32 *)(m_timsDataFrame.constData() +
374 (scan_offset * 4) + (i * 8) + 4));
375
376 previous = x;
377
378 auto ret = accumulate_into.insert(std::pair<quint32, quint32>(x, y));
379
380 if(ret.second == false)
381 {
382 // already existed : cumulate
383 ret.first->second += y;
384 }
385 }
386
387 // qDebug();
388}
389
390
391Trace
392TimsFrame::cumulateScanToTrace(std::size_t mobility_scan_begin,
393 std::size_t mobility_scan_end) const
394{
395 // qDebug();
396
397 Trace new_trace;
398
399 try
400 {
401 if(m_timsDataFrame.size() == 0)
402 return new_trace;
403 std::map<quint32, quint32> raw_spectrum;
404 // double local_accumulationTime = 0;
405
406 std::size_t mobility_scan_max = mobility_scan_end + 1;
407 qDebug();
408 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
409 {
410 // qDebug() << i;
411 cumulateScan(i, raw_spectrum);
412 // qDebug() << i;
413
414 // local_accumulationTime += m_accumulationTime;
415 }
416
417 // qDebug();
418
419 pappso::DataPoint data_point_cumul;
420
421
422 MzCalibrationInterface *mz_calibration_p =
424
425
426 for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
427 {
428 data_point_cumul.x =
429 mz_calibration_p->getMzFromTofIndex(pair_tof_intensity.first);
430 // normalization
431 data_point_cumul.y =
432 pair_tof_intensity.second * ((double)100.0 / m_accumulationTime);
433 new_trace.push_back(data_point_cumul);
434 }
435 new_trace.sortX();
436
437 // qDebug();
438 }
439
440 catch(std::exception &error)
441 {
442 qDebug() << QString(
443 "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
444 .arg(mobility_scan_begin, mobility_scan_end)
445 .arg(error.what());
446 }
447 return new_trace;
448}
449
450Trace
452 std::size_t mz_index_merge_window,
453 std::size_t mobility_scan_begin,
454 std::size_t mobility_scan_end,
455 quint32 &mz_minimum_index_out,
456 quint32 &mz_maximum_index_out) const
457{
458 // qDebug();
459
460 Trace new_trace;
461
462 try
463 {
464 if(m_timsDataFrame.size() == 0)
465 {
466 qDebug() << "The frame is empty, returning empty trace.";
467 return new_trace;
468 }
469
470 // Allocate a map for (TOF,intensity) pairs to
471 // accumulate ion mobility scans.
472
473 std::map<quint32, quint32> raw_spectrum;
474 // double local_accumulationTime = 0;
475
476 std::size_t mobility_scan_max = mobility_scan_end + 1;
477
478 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
479 {
480 // qDebug() << "Going to cumulate currently iterated mobility scan:"
481 // << i;
482 cumulateScan(i, raw_spectrum);
483 // qDebug() << "Done cumulating currently iterated mobility scan:" <<
484 // i;
485
486 // local_accumulationTime += m_accumulationTime;
487 }
488
489 // qDebug();
490
491 pappso::DataPoint data_point_cumul;
492
493 MzCalibrationInterface *mz_calibration_p =
495
496 // If the caller asks that m/z values be binned larger than they are,
497 // ask that the m/z raw map be reduced in resolution.
498 if(mz_index_merge_window > 0)
499 raw_spectrum = downsizeMzRawMap(mz_index_merge_window, raw_spectrum);
500
501 // Store the first mz index and the last mz index of the current spectrum.
502 // The values are set to the out parameters.
503 mz_minimum_index_out = std::numeric_limits<quint32>::max();
504 mz_maximum_index_out = 0;
505
506 for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
507 {
508 if(pair_tof_intensity.first > mz_maximum_index_out)
509 mz_maximum_index_out = pair_tof_intensity.first;
510 if(pair_tof_intensity.first < mz_minimum_index_out)
511 mz_minimum_index_out = pair_tof_intensity.first;
512
513 // Convert the TOF index to m/z
514 data_point_cumul.x =
515 mz_calibration_p->getMzFromTofIndex(pair_tof_intensity.first);
516
517 // Normalization
518 data_point_cumul.y =
519 pair_tof_intensity.second * ((double)100.0 / m_accumulationTime);
520
521 // Finally make the data point a new Trace point.
522 new_trace.push_back(data_point_cumul);
523 }
524
525 // qDebug() << "At this point we have mz_minimum_index_out:"
526 // << mz_minimum_index_out
527 // << "and mz_maximum_index_out:" << mz_maximum_index_out;
528
529 // FIXME: this does not seem to be necessary since raw_spectrum is a map
530 // with auto-sorting on the keys which are quint32.
531 // new_trace.sortX();
532
533 // qDebug();
534 }
535 catch(std::exception &error)
536 {
537 qDebug() << QString(
538 "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
539 .arg(mobility_scan_begin, mobility_scan_end)
540 .arg(error.what());
541 }
542
543 // qDebug() << "Returning new trace of size:" << new_trace.size();
544
545 return new_trace;
546}
547
548
549Trace
551 std::size_t mz_index_merge_window,
552 double mz_range_begin,
553 double mz_range_end,
554 std::size_t mobility_scan_begin,
555 std::size_t mobility_scan_end,
556 quint32 &mz_minimum_index_out,
557 quint32 &mz_maximum_index_out) const
558{
559 // qDebug();
560
561 Trace new_trace;
562
563 try
564 {
565 if(m_timsDataFrame.size() == 0)
566 {
567 qDebug() << "The frame is empty, returning empty trace.";
568 return new_trace;
569 }
570
571 // Allocate a map for (TOF,intensity) pairs to
572 // accumulate ion mobility scans.
573
574 std::map<quint32, quint32> raw_spectrum;
575 // double local_accumulationTime = 0;
576
577 std::size_t mobility_scan_max = mobility_scan_end + 1;
578
579 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
580 {
581 // qDebug() << "Going to cumulate currently iterated mobility scan:"
582 // << i;
583 cumulateScan2(i, raw_spectrum, mz_range_begin, mz_range_end);
584 // qDebug() << "Done cumulating currently iterated mobility scan:" <<
585 // i;
586
587 // local_accumulationTime += m_accumulationTime;
588 }
589
590 // qDebug();
591
592 pappso::DataPoint data_point_cumul;
593
594 MzCalibrationInterface *mz_calibration_p =
596
597 // If the caller asks that m/z values be binned larger than they are,
598 // ask that the m/z raw map be reduced in resolution.
599 if(mz_index_merge_window > 0)
600 raw_spectrum = downsizeMzRawMap(mz_index_merge_window, raw_spectrum);
601
602 // Store the first mz index and the last mz index of the current spectrum.
603 // The values are set to the out parameters.
604 mz_minimum_index_out = std::numeric_limits<quint32>::max();
605 mz_maximum_index_out = 0;
606
607 for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
608 {
609 if(pair_tof_intensity.first > mz_maximum_index_out)
610 mz_maximum_index_out = pair_tof_intensity.first;
611 if(pair_tof_intensity.first < mz_minimum_index_out)
612 mz_minimum_index_out = pair_tof_intensity.first;
613
614 // Convert the TOF index to m/z
615 data_point_cumul.x =
616 mz_calibration_p->getMzFromTofIndex(pair_tof_intensity.first);
617
618 // Normalization
619 data_point_cumul.y =
620 pair_tof_intensity.second * ((double)100.0 / m_accumulationTime);
621
622 // Finally make the data point a new Trace point.
623 new_trace.push_back(data_point_cumul);
624 }
625
626 // qDebug() << "At this point we have mz_minimum_index_out:"
627 // << mz_minimum_index_out
628 // << "and mz_maximum_index_out:" << mz_maximum_index_out;
629
630 // FIXME: this does not seem to be necessary since raw_spectrum is a map
631 // with auto-sorting on the keys which are quint32.
632 // new_trace.sortX();
633
634 // qDebug();
635 }
636 catch(std::exception &error)
637 {
638 qDebug() << QString(
639 "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
640 .arg(mobility_scan_begin, mobility_scan_end)
641 .arg(error.what());
642 }
643
644 // qDebug() << "Returning new trace of size:" << new_trace.size();
645
646 return new_trace;
647}
648
649
650void
651TimsFrame::cumulateScansInRawMap(std::map<quint32, quint32> &rawSpectrum,
652 std::size_t mobility_scan_begin,
653 std::size_t mobility_scan_end) const
654{
655 // qDebug() << "begin mobility_scan_begin=" << mobility_scan_begin
656 //<< " mobility_scan_end=" << mobility_scan_end;
657
658 if(m_timsDataFrame.size() == 0)
659 return;
660 try
661 {
662
663 std::size_t mobility_scan_max = mobility_scan_end + 1;
664 qDebug();
665 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
666 {
667 qDebug() << i;
668 cumulateScan(i, rawSpectrum);
669 qDebug() << i;
670 // local_accumulationTime += m_accumulationTime;
671 }
672 }
673
674 catch(std::exception &error)
675 {
676 qDebug() << QString("Failure in %1 %2 to %3 :\n %4")
677 .arg(__FUNCTION__)
678 .arg(mobility_scan_begin)
679 .arg(mobility_scan_end)
680 .arg(error.what());
681 }
682
683 // qDebug() << "end";
684}
685
686
688TimsFrame::getMassSpectrumCstSPtr(std::size_t scanNum) const
689{
690 // qDebug();
691
692 return getMassSpectrumSPtr(scanNum);
693}
694
696TimsFrame::getMassSpectrumSPtr(std::size_t scanNum) const
697{
698
699 // qDebug() << " scanNum=" << scanNum;
700
701 checkScanNum(scanNum);
702
703 // qDebug();
704
705 pappso::MassSpectrumSPtr mass_spectrum_sptr =
706 std::make_shared<pappso::MassSpectrum>();
707 // std::vector<DataPoint>
708
709 if(m_timsDataFrame.size() == 0)
710 return mass_spectrum_sptr;
711
712 // qDebug();
713
714 std::size_t size = getNbrPeaks(scanNum);
715
716 std::size_t offset = getScanOffset(scanNum);
717
718 MzCalibrationInterface *mz_calibration_p =
720
721
722 qint32 previous = -1;
723 qint32 tof_index;
724 // std::vector<quint32> index_list;
725 DataPoint data_point;
726 for(std::size_t i = 0; i < size; i++)
727 {
728 tof_index =
729 (*(quint32 *)((m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
730 previous);
731 data_point.y = (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) +
732 (i * 8) + 4));
733
734 // intensity normalization
735 data_point.y *= 100.0 / m_accumulationTime;
736
737 previous = tof_index;
738
739
740 // mz calibration
741 data_point.x = mz_calibration_p->getMzFromTofIndex(tof_index);
742 mass_spectrum_sptr.get()->push_back(data_point);
743 }
744
745 // qDebug();
746
747 return mass_spectrum_sptr;
748}
749
750
751void
753 std::vector<XicCoordTims *>::iterator &itXicListbegin,
754 std::vector<XicCoordTims *>::iterator &itXicListend,
755 XicExtractMethod method) const
756{
757 qDebug() << std::distance(itXicListbegin, itXicListend);
758
759 std::vector<TimsFrame::XicComputeStructure> tmp_xic_list;
760
761 for(auto it = itXicListbegin; it != itXicListend; it++)
762 {
763 tmp_xic_list.push_back(TimsFrame::XicComputeStructure(this, **it));
764
765 qDebug() << " tmp_xic_struct.mobilityIndexBegin="
766 << tmp_xic_list.back().mobilityIndexBegin
767 << " tmp_xic_struct.mobilityIndexEnd="
768 << tmp_xic_list.back().mobilityIndexEnd;
769
770 qDebug() << " tmp_xic_struct.mzIndexLowerBound="
771 << tmp_xic_list.back().mzIndexLowerBound
772 << " tmp_xic_struct.mzIndexUpperBound="
773 << tmp_xic_list.back().mzIndexUpperBound;
774 }
775 if(tmp_xic_list.size() == 0)
776 return;
777 /*
778 std::sort(tmp_xic_list.begin(), tmp_xic_list.end(), [](const
779 TimsXicStructure &a, const TimsXicStructure &b) { return
780 a.mobilityIndexBegin < b.mobilityIndexBegin;
781 });
782 */
783 std::vector<std::size_t> unique_scan_num_list;
784 for(auto &&struct_xic : tmp_xic_list)
785 {
786 for(std::size_t scan = struct_xic.mobilityIndexBegin;
787 (scan <= struct_xic.mobilityIndexEnd) && (scan < m_scanNumber);
788 scan++)
789 {
790 unique_scan_num_list.push_back(scan);
791 }
792 }
793 std::sort(unique_scan_num_list.begin(), unique_scan_num_list.end());
794 auto it_scan_num_end =
795 std::unique(unique_scan_num_list.begin(), unique_scan_num_list.end());
796 auto it_scan_num = unique_scan_num_list.begin();
797
798 while(it_scan_num != it_scan_num_end)
799 {
800 TraceSPtr ms_spectrum = getRawTraceSPtr(*it_scan_num);
801 // qDebug() << ms_spectrum.get()->toString();
802 for(auto &&tmp_xic_struct : tmp_xic_list)
803 {
804 if(((*it_scan_num) >= tmp_xic_struct.mobilityIndexBegin) &&
805 ((*it_scan_num) <= tmp_xic_struct.mobilityIndexEnd))
806 {
807 if(method == XicExtractMethod::max)
808 {
809 tmp_xic_struct.tmpIntensity +=
810 ms_spectrum.get()->maxY(tmp_xic_struct.mzIndexLowerBound,
811 tmp_xic_struct.mzIndexUpperBound);
812
813 qDebug() << "tmp_xic_struct.tmpIntensity="
814 << tmp_xic_struct.tmpIntensity;
815 }
816 else
817 {
818 // sum
819 tmp_xic_struct.tmpIntensity +=
820 ms_spectrum.get()->sumY(tmp_xic_struct.mzIndexLowerBound,
821 tmp_xic_struct.mzIndexUpperBound);
822 qDebug() << "tmp_xic_struct.tmpIntensity="
823 << tmp_xic_struct.tmpIntensity;
824 }
825 }
826 }
827 it_scan_num++;
828 }
829
830 for(auto &&tmp_xic_struct : tmp_xic_list)
831 {
832 if(tmp_xic_struct.tmpIntensity != 0)
833 {
834 qDebug() << tmp_xic_struct.xic_ptr;
835 tmp_xic_struct.xic_ptr->push_back(
836 {m_time, tmp_xic_struct.tmpIntensity});
837 }
838 }
839
840 qDebug();
841}
842
843
845TimsFrame::getRawTraceSPtr(std::size_t scanNum) const
846{
847
848 // qDebug();
849
850 pappso::TraceSPtr trace_sptr = std::make_shared<pappso::Trace>();
851 // std::vector<DataPoint>
852
853 if(m_timsDataFrame.size() == 0)
854 return trace_sptr;
855 // qDebug();
856
857 std::size_t size = getNbrPeaks(scanNum);
858
859 std::size_t offset = getScanOffset(scanNum);
860
861 qint32 previous = -1;
862 std::vector<quint32> index_list;
863 for(std::size_t i = 0; i < size; i++)
864 {
865 DataPoint data_point(
866 (*(quint32 *)((m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
867 previous),
868 (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) + (i * 8) +
869 4)));
870
871 // intensity normalization
872 data_point.y *= 100.0 / m_accumulationTime;
873
874 previous = data_point.x;
875 trace_sptr.get()->push_back(data_point);
876 }
877 // qDebug();
878 return trace_sptr;
879}
880
881} // namespace pappso
virtual double getMzFromTofIndex(quint32 tof_index)=0
get m/z from time of flight raw index
pappso_double lower() const
Definition mzrange.h:71
pappso_double upper() const
Definition mzrange.h:77
double m_accumulationTime
accumulation time in milliseconds
std::map< quint32, quint32 > & downsizeMzRawMap(std::size_t mzindex_merge_window, std::map< quint32, quint32 > &rawSpectrum) const
downsize mz resolution to lower the number of real mz computations
double m_time
retention time
quint32 m_scanNumber
total number of scans contained in this frame
std::size_t m_timsId
Tims frame database id (the SQL identifier of this frame)
virtual const MzCalibrationInterfaceSPtr & getMzCalibrationInterfaceSPtr() const final
get the MzCalibration model to compute mz and TOF for this frame
bool checkScanNum(std::size_t scanNum) const
check that this scan number exists
QByteArray m_timsDataFrame
Definition timsframe.h:223
virtual std::vector< quint32 > getScanIndexList(std::size_t scanNum) const override
get raw index list for one given scan index are not TOF nor m/z, just index on digitizer
virtual std::size_t getNbrPeaks(std::size_t scanNum) const override
get the number of peaks in this spectrum need the binary file
virtual ~TimsFrame()
Definition timsframe.cpp:96
virtual quint64 cumulateScansIntensities(std::size_t scanNumBegin, std::size_t scanNumEnd) const override
...
virtual void cumulateScan(std::size_t scanNum, std::map< quint32, quint32 > &accumulate_into) const
cumulate a scan into a map
TimsFrame(std::size_t timsId, quint32 scanNum, char *p_bytes, std::size_t len)
Definition timsframe.cpp:61
virtual pappso::MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const override
get Mass spectrum with peaks for this scan number need the binary file
virtual quint64 cumulateSingleScanIntensities(std::size_t scanNum) const override
virtual Trace cumulateScanToTraceMzDownResolution(std::size_t mzindex_merge_window, std::size_t scanNumBegin, std::size_t scanNumEnd, quint32 &minimum_index, quint32 &maximum_index) const override
cumulate spectrum given a scan number range need the binary file The intensities are normalized with ...
virtual std::vector< quint32 > getScanIntensities(std::size_t scanNum) const override
get raw intensities without transformation from one scan it needs intensity normalization
Trace cumulateScanToTraceMzDownResolution2(std::size_t mz_index_merge_window, double mz_range_begin, double mz_range_end, std::size_t mobility_scan_begin, std::size_t mobility_scan_end, quint32 &mz_minimum_index_out, quint32 &mz_maximum_index_out) const
void unshufflePacket(const char *src)
unshuffle data packet of tims compression type 2
std::size_t getScanOffset(std::size_t scanNum) const
get offset for this spectrum in the binary file
virtual void cumulateScan2(std::size_t scanNum, std::map< quint32, quint32 > &accumulate_into, double mz_range_begin, double mz_range_end) const
virtual void cumulateScansInRawMap(std::map< quint32, quint32 > &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const override
cumulate scan list into a trace into a raw spectrum map
virtual Trace cumulateScanToTrace(std::size_t scanNumBegin, std::size_t scanNumEnd) const override
cumulate scan list into a trace
void extractTimsXicListInRtRange(std::vector< XicCoordTims * >::iterator &itXicListbegin, std::vector< XicCoordTims * >::iterator &itXicListend, XicExtractMethod method) const
virtual pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr(std::size_t scanNum) const
get the mass spectrum corresponding to a scan number
virtual pappso::TraceSPtr getRawTraceSPtr(std::size_t scanNum) const
get the raw index tof_index and intensities (normalized)
A simple container of DataPoint instances.
Definition trace.h:148
void sortX(SortOrder sort_order=SortOrder::ascending)
Definition trace.cpp:1086
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
Definition aa.cpp:39
std::shared_ptr< Trace > TraceSPtr
Definition trace.h:135
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
XicExtractMethod
Definition types.h:240
@ max
maximum of intensities
pappso_double x
Definition datapoint.h:23
pappso_double y
Definition datapoint.h:24
XicComputeStructure(const TimsFrame *fram_p, const XicCoordTims &xic_struct)
Definition timsframe.cpp:39
coordinates of the XIC to extract and the resulting XIC after extraction
std::size_t scanNumEnd
mobility index end
std::size_t scanNumBegin
mobility index begin
XicSPtr xicSptr
extracted xic
Definition xiccoord.h:130
MzRange mzRange
the mass to extract
Definition xiccoord.h:120
handle a single Bruker's TimsTof frame