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,
348 quint32 accepted_tof_index_range_begin,
349 quint32 accepted_tof_index_range_end) const
350{
351 // qDebug();
352
353 if(m_timsDataFrame.size() == 0)
354 return;
355
356 // checkScanNum(scanNum);
357
358 std::size_t scan_size = getNbrPeaks(scanNum);
359 std::size_t scan_offset = getScanOffset(scanNum);
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 < accepted_tof_index_range_begin)
369 {
370 // qDebug() << "TOF index still not in range, x:" << x;
371 continue;
372 }
373 if(x > accepted_tof_index_range_end)
374 {
375 // qDebug() << "TOF index already out of range, x:" << x;
376 break;
377 }
378
379 // qDebug() << "TOF index in range, x:" << x;
380
381 quint32 y = (*(quint32 *)(m_timsDataFrame.constData() +
382 (scan_offset * 4) + (i * 8) + 4));
383
384 previous = x;
385
386 auto ret = accumulate_into.insert(std::pair<quint32, quint32>(x, y));
387
388 if(ret.second == false)
389 {
390 // already existed : cumulate
391 ret.first->second += y;
392 }
393 }
394
395 // qDebug();
396}
397
398
399Trace
400TimsFrame::cumulateScansToTrace(std::size_t mobility_scan_begin,
401 std::size_t mobility_scan_end) const
402{
403 // qDebug();
404
405 Trace new_trace;
406
407 try
408 {
409 if(m_timsDataFrame.size() == 0)
410 return new_trace;
411 std::map<quint32, quint32> raw_spectrum;
412 // double local_accumulationTime = 0;
413
414 std::size_t mobility_scan_max = mobility_scan_end + 1;
415 qDebug();
416 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
417 {
418 // qDebug() << i;
419 cumulateScan(i, raw_spectrum);
420 // qDebug() << i;
421
422 // local_accumulationTime += m_accumulationTime;
423 }
424
425 // qDebug();
426
427 pappso::DataPoint data_point_cumul;
428
429
430 MzCalibrationInterface *mz_calibration_p =
432
433
434 for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
435 {
436 data_point_cumul.x =
437 mz_calibration_p->getMzFromTofIndex(pair_tof_intensity.first);
438 // normalization
439 data_point_cumul.y =
440 pair_tof_intensity.second * ((double)100.0 / m_accumulationTime);
441 new_trace.push_back(data_point_cumul);
442 }
443 new_trace.sortX();
444
445 // qDebug();
446 }
447
448 catch(std::exception &error)
449 {
450 qDebug() << QString(
451 "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
452 .arg(mobility_scan_begin, mobility_scan_end)
453 .arg(error.what());
454 }
455 return new_trace;
456}
457
458Trace
460 std::size_t mz_index_merge_window,
461 std::size_t mobility_scan_begin,
462 std::size_t mobility_scan_end,
463 quint32 &mz_minimum_index_out,
464 quint32 &mz_maximum_index_out) const
465{
466 // qDebug();
467
468 Trace new_trace;
469
470 try
471 {
472 if(m_timsDataFrame.size() == 0)
473 {
474 qDebug() << "The frame is empty, returning empty trace.";
475 return new_trace;
476 }
477
478 // Allocate a map for (TOF,intensity) pairs to
479 // accumulate ion mobility scans.
480
481 std::map<quint32, quint32> raw_spectrum;
482 // double local_accumulationTime = 0;
483
484 std::size_t mobility_scan_max = mobility_scan_end + 1;
485
486 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
487 {
488 // qDebug() << "Going to cumulate currently iterated mobility scan:"
489 // << i;
490 cumulateScan(i, raw_spectrum);
491 // qDebug() << "Done cumulating currently iterated mobility scan:" <<
492 // i;
493
494 // local_accumulationTime += m_accumulationTime;
495 }
496
497 // qDebug();
498
499 pappso::DataPoint data_point_cumul;
500
501 MzCalibrationInterface *mz_calibration_p =
503
504 // If the caller asks that m/z values be binned larger than they are,
505 // ask that the m/z raw map be reduced in resolution.
506 if(mz_index_merge_window > 0)
507 raw_spectrum = downsizeMzRawMap(mz_index_merge_window, raw_spectrum);
508
509 // Store the first mz index and the last mz index of the current spectrum.
510 // The values are set to the out parameters.
511 mz_minimum_index_out = std::numeric_limits<quint32>::max();
512 mz_maximum_index_out = 0;
513
514 for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
515 {
516 if(pair_tof_intensity.first > mz_maximum_index_out)
517 mz_maximum_index_out = pair_tof_intensity.first;
518 if(pair_tof_intensity.first < mz_minimum_index_out)
519 mz_minimum_index_out = pair_tof_intensity.first;
520
521 // Convert the TOF index to m/z
522 data_point_cumul.x =
523 mz_calibration_p->getMzFromTofIndex(pair_tof_intensity.first);
524
525 // Normalization
526 data_point_cumul.y =
527 pair_tof_intensity.second * ((double)100.0 / m_accumulationTime);
528
529 // Finally make the data point a new Trace point.
530 new_trace.push_back(data_point_cumul);
531 }
532
533 // qDebug() << "At this point we have mz_minimum_index_out:"
534 // << mz_minimum_index_out
535 // << "and mz_maximum_index_out:" << mz_maximum_index_out;
536
537 // FIXME: this does not seem to be necessary since raw_spectrum is a map
538 // with auto-sorting on the keys which are quint32.
539 // new_trace.sortX();
540
541 // qDebug();
542 }
543 catch(std::exception &error)
544 {
545 qDebug() << QString(
546 "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
547 .arg(mobility_scan_begin, mobility_scan_end)
548 .arg(error.what());
549 }
550
551 // qDebug() << "Returning new trace of size:" << new_trace.size();
552
553 return new_trace;
554}
555
556
557Trace
559 std::size_t mz_index_merge_window,
560 double mz_range_begin,
561 double mz_range_end,
562 std::size_t mobility_scan_begin,
563 std::size_t mobility_scan_end,
564 quint32 &mz_minimum_index_out,
565 quint32 &mz_maximum_index_out) const
566{
567 // qDebug();
568
569 Trace new_trace;
570
571 try
572 {
573 if(m_timsDataFrame.size() == 0)
574 {
575 qDebug() << "The frame is empty, returning empty trace.";
576 return new_trace;
577 }
578
579 // Allocate a map for (TOF index,intensity) pairs to
580 // accumulate ion mobility scans.
581
582 std::map<quint32, quint32> raw_spectrum;
583 // double local_accumulationTime = 0;
584
585 std::size_t mobility_scan_max = mobility_scan_end + 1;
586
587 quint32 only_in_mz_begin_tof_index_range =
588 getMzCalibrationInterfaceSPtr().get()->getTofIndexFromMz(
589 mz_range_begin);
590 quint32 only_in_mz_end_tof_index_range =
591 getMzCalibrationInterfaceSPtr().get()->getTofIndexFromMz(mz_range_end);
592
593 // qDebug() << "20231129 TOF index range begin:"
594 // << only_in_mz_begin_tof_index_range;
595 // qDebug() << "20231129 TOF index range end:"
596 // << only_in_mz_end_tof_index_range;
597
598 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
599 {
600 // qDebug() << "Going to cumulate currently iterated mobility scan:"
601 // << i;
603 raw_spectrum,
604 mz_range_begin,
605 mz_range_end,
606 only_in_mz_begin_tof_index_range,
607 only_in_mz_end_tof_index_range);
608 // qDebug() << "Done cumulating currently iterated mobility scan:" <<
609 // i;
610
611 // local_accumulationTime += m_accumulationTime;
612 }
613
614 // qDebug();
615
616 pappso::DataPoint data_point_cumul;
617
618 MzCalibrationInterface *mz_calibration_p =
620
621 // If the caller asks that m/z values be binned larger than they are,
622 // ask that the m/z raw map be reduced in resolution.
623 if(mz_index_merge_window > 0)
624 raw_spectrum = downsizeMzRawMap(mz_index_merge_window, raw_spectrum);
625
626 // Store the first mz index and the last mz index of the current spectrum.
627 // The values are set to the out parameters.
628 mz_minimum_index_out = std::numeric_limits<quint32>::max();
629 mz_maximum_index_out = 0;
630
631 for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
632 {
633 if(pair_tof_intensity.first > mz_maximum_index_out)
634 mz_maximum_index_out = pair_tof_intensity.first;
635 if(pair_tof_intensity.first < mz_minimum_index_out)
636 mz_minimum_index_out = pair_tof_intensity.first;
637
638 // Convert the TOF index to m/z
639 data_point_cumul.x =
640 mz_calibration_p->getMzFromTofIndex(pair_tof_intensity.first);
641
642 // Normalization
643 data_point_cumul.y =
644 pair_tof_intensity.second * ((double)100.0 / m_accumulationTime);
645
646 // Finally make the data point a new Trace point.
647 new_trace.push_back(data_point_cumul);
648 }
649
650 // qDebug() << "At this point we have mz_minimum_index_out:"
651 // << mz_minimum_index_out
652 // << "and mz_maximum_index_out:" << mz_maximum_index_out;
653
654 // FIXME: this does not seem to be necessary since raw_spectrum is a map
655 // with auto-sorting on the keys which are quint32.
656 // new_trace.sortX();
657
658 // qDebug();
659 }
660 catch(std::exception &error)
661 {
662 qDebug() << QString(
663 "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
664 .arg(mobility_scan_begin, mobility_scan_end)
665 .arg(error.what());
666 }
667
668 // qDebug() << "Returning new trace of size:" << new_trace.size();
669
670 return new_trace;
671}
672
673
674void
675TimsFrame::cumulateScansInRawMap(std::map<quint32, quint32> &rawSpectrum,
676 std::size_t mobility_scan_begin,
677 std::size_t mobility_scan_end) const
678{
679 // qDebug() << "begin mobility_scan_begin=" << mobility_scan_begin
680 //<< " mobility_scan_end=" << mobility_scan_end;
681
682 if(m_timsDataFrame.size() == 0)
683 return;
684 try
685 {
686
687 std::size_t mobility_scan_max = mobility_scan_end + 1;
688 qDebug();
689 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
690 {
691 qDebug() << i;
692 cumulateScan(i, rawSpectrum);
693 qDebug() << i;
694 // local_accumulationTime += m_accumulationTime;
695 }
696 }
697
698 catch(std::exception &error)
699 {
700 qDebug() << QString("Failure in %1 %2 to %3 :\n %4")
701 .arg(__FUNCTION__)
702 .arg(mobility_scan_begin)
703 .arg(mobility_scan_end)
704 .arg(error.what());
705 }
706
707 // qDebug() << "end";
708}
709
710
712TimsFrame::getMassSpectrumCstSPtr(std::size_t scanNum) const
713{
714 // qDebug();
715
716 return getMassSpectrumSPtr(scanNum);
717}
718
720TimsFrame::getMassSpectrumSPtr(std::size_t scanNum) const
721{
722
723 // qDebug() << " scanNum=" << scanNum;
724
725 checkScanNum(scanNum);
726
727 // qDebug();
728
729 pappso::MassSpectrumSPtr mass_spectrum_sptr =
730 std::make_shared<pappso::MassSpectrum>();
731 // std::vector<DataPoint>
732
733 if(m_timsDataFrame.size() == 0)
734 return mass_spectrum_sptr;
735
736 // qDebug();
737
738 std::size_t size = getNbrPeaks(scanNum);
739
740 std::size_t offset = getScanOffset(scanNum);
741
742 MzCalibrationInterface *mz_calibration_p =
744
745
746 qint32 previous = -1;
747 qint32 tof_index;
748 // std::vector<quint32> index_list;
749 DataPoint data_point;
750 for(std::size_t i = 0; i < size; i++)
751 {
752 tof_index =
753 (*(quint32 *)((m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
754 previous);
755 data_point.y = (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) +
756 (i * 8) + 4));
757
758 // intensity normalization
759 data_point.y *= 100.0 / m_accumulationTime;
760
761 previous = tof_index;
762
763
764 // mz calibration
765 data_point.x = mz_calibration_p->getMzFromTofIndex(tof_index);
766 mass_spectrum_sptr.get()->push_back(data_point);
767 }
768
769 // qDebug();
770
771 return mass_spectrum_sptr;
772}
773
774
775void
777 std::vector<XicCoordTims *>::iterator &itXicListbegin,
778 std::vector<XicCoordTims *>::iterator &itXicListend,
779 XicExtractMethod method) const
780{
781 qDebug() << std::distance(itXicListbegin, itXicListend);
782
783 std::vector<TimsFrame::XicComputeStructure> tmp_xic_list;
784
785 for(auto it = itXicListbegin; it != itXicListend; it++)
786 {
787 tmp_xic_list.push_back(TimsFrame::XicComputeStructure(this, **it));
788
789 qDebug() << " tmp_xic_struct.mobilityIndexBegin="
790 << tmp_xic_list.back().mobilityIndexBegin
791 << " tmp_xic_struct.mobilityIndexEnd="
792 << tmp_xic_list.back().mobilityIndexEnd;
793
794 qDebug() << " tmp_xic_struct.mzIndexLowerBound="
795 << tmp_xic_list.back().mzIndexLowerBound
796 << " tmp_xic_struct.mzIndexUpperBound="
797 << tmp_xic_list.back().mzIndexUpperBound;
798 }
799 if(tmp_xic_list.size() == 0)
800 return;
801 /*
802 std::sort(tmp_xic_list.begin(), tmp_xic_list.end(), [](const
803 TimsXicStructure &a, const TimsXicStructure &b) { return
804 a.mobilityIndexBegin < b.mobilityIndexBegin;
805 });
806 */
807 std::vector<std::size_t> unique_scan_num_list;
808 for(auto &&struct_xic : tmp_xic_list)
809 {
810 for(std::size_t scan = struct_xic.mobilityIndexBegin;
811 (scan <= struct_xic.mobilityIndexEnd) && (scan < m_scanNumber);
812 scan++)
813 {
814 unique_scan_num_list.push_back(scan);
815 }
816 }
817 std::sort(unique_scan_num_list.begin(), unique_scan_num_list.end());
818 auto it_scan_num_end =
819 std::unique(unique_scan_num_list.begin(), unique_scan_num_list.end());
820 auto it_scan_num = unique_scan_num_list.begin();
821
822 while(it_scan_num != it_scan_num_end)
823 {
824 TraceSPtr ms_spectrum = getRawTraceSPtr(*it_scan_num);
825 // qDebug() << ms_spectrum.get()->toString();
826 for(auto &&tmp_xic_struct : tmp_xic_list)
827 {
828 if(((*it_scan_num) >= tmp_xic_struct.mobilityIndexBegin) &&
829 ((*it_scan_num) <= tmp_xic_struct.mobilityIndexEnd))
830 {
831 if(method == XicExtractMethod::max)
832 {
833 tmp_xic_struct.tmpIntensity +=
834 ms_spectrum.get()->maxY(tmp_xic_struct.mzIndexLowerBound,
835 tmp_xic_struct.mzIndexUpperBound);
836
837 qDebug() << "tmp_xic_struct.tmpIntensity="
838 << tmp_xic_struct.tmpIntensity;
839 }
840 else
841 {
842 // sum
843 tmp_xic_struct.tmpIntensity +=
844 ms_spectrum.get()->sumY(tmp_xic_struct.mzIndexLowerBound,
845 tmp_xic_struct.mzIndexUpperBound);
846 qDebug() << "tmp_xic_struct.tmpIntensity="
847 << tmp_xic_struct.tmpIntensity;
848 }
849 }
850 }
851 it_scan_num++;
852 }
853
854 for(auto &&tmp_xic_struct : tmp_xic_list)
855 {
856 if(tmp_xic_struct.tmpIntensity != 0)
857 {
858 qDebug() << tmp_xic_struct.xic_ptr;
859 tmp_xic_struct.xic_ptr->push_back(
860 {m_time, tmp_xic_struct.tmpIntensity});
861 }
862 }
863
864 qDebug();
865}
866
867
869TimsFrame::getRawTraceSPtr(std::size_t scanNum) const
870{
871
872 // qDebug();
873
874 pappso::TraceSPtr trace_sptr = std::make_shared<pappso::Trace>();
875 // std::vector<DataPoint>
876
877 if(m_timsDataFrame.size() == 0)
878 return trace_sptr;
879 // qDebug();
880
881 std::size_t size = getNbrPeaks(scanNum);
882
883 std::size_t offset = getScanOffset(scanNum);
884
885 qint32 previous = -1;
886 std::vector<quint32> index_list;
887 for(std::size_t i = 0; i < size; i++)
888 {
889 DataPoint data_point(
890 (*(quint32 *)((m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
891 previous),
892 (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) + (i * 8) +
893 4)));
894
895 // intensity normalization
896 data_point.y *= 100.0 / m_accumulationTime;
897
898 previous = data_point.x;
899 trace_sptr.get()->push_back(data_point);
900 }
901 // qDebug();
902 return trace_sptr;
903}
904
905} // 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:225
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 Trace cumulateScansToTraceMzDownResolution(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 ~TimsFrame()
Definition timsframe.cpp:96
virtual quint64 cumulateScansIntensities(std::size_t scanNumBegin, std::size_t scanNumEnd) const override
...
virtual Trace cumulateScansToTrace(std::size_t scanNumBegin, std::size_t scanNumEnd) const override
cumulate scan list into a trace
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 void cumulateScan2(std::size_t scanNum, std::map< quint32, quint32 > &accumulate_into, double mz_range_begin, double mz_range_end, quint32 accepted_tof_index_range_begin, quint32 accepted_tof_index_range_end) const
virtual std::vector< quint32 > getScanIntensities(std::size_t scanNum) const override
get raw intensities without transformation from one scan it needs intensity normalization
void unshufflePacket(const char *src)
unshuffle data packet of tims compression type 2
Trace cumulateScansToTraceMzDownResolution2(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
std::size_t getScanOffset(std::size_t scanNum) const
get offset for this spectrum in the binary file
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
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