29 #include "../../../pappsomspp/pappsoexception.h"
30 #include "../../../pappsomspp/exception/exceptionoutofrange.h"
42 const TimsFrame *fram_p,
const TimsXicStructure &xic_struct)
44 xic_ptr = xic_struct.xicSptr.get();
49 xic_struct.mzRange.lower());
67 if(p_bytes !=
nullptr)
77 QObject::tr(
"TimsFrame::TimsFrame(%1,%2,nullptr,%3) FAILED")
102 QObject::tr(
"TimsFrame::unshufflePacket error: len%4 != 0"));
105 quint64 nb_uint4 = len / 4;
108 quint64 src_offset = 0;
110 for(quint64 j = 0; j < 4; j++)
112 for(quint64 i = 0; i < nb_uint4; i++)
114 dest[(i * 4) + j] = src[src_offset];
137 std::size_t cumul = 0;
142 return (nb_uint4 - cumul) / 2;
148 return (*(quint32 *)(
m_timsDataFrame.constData() + ((scanNum + 1) * 4))) / 2;
154 std::size_t offset = 0;
155 for(std::size_t i = 0; i < (scanNum + 1); i++)
168 std::vector<quint32> scan_tof;
176 qint32 previous = -1;
177 for(std::size_t i = 0; i < scan_tof.size(); i++)
182 previous = scan_tof[i];
193 std::vector<quint32> scan_intensities;
196 return scan_intensities;
202 for(std::size_t i = 0; i < scan_intensities.size(); i++)
205 (offset * 4) + (i * 8) + 4));
208 return scan_intensities;
214 std::map<quint32, quint32> &accumulate_into)
const
227 qint32 previous = -1;
228 for(std::size_t i = 0; i < size; i++)
238 auto ret = accumulate_into.insert(std::pair<quint32, quint32>(x, y));
240 if(ret.second ==
false)
243 ret.first->second +=
y;
252 std::size_t scanNumEnd)
const
262 std::map<quint32, quint32> raw_spectrum;
265 std::size_t imax = scanNumEnd + 1;
267 for(std::size_t i = scanNumBegin; i < imax; i++)
277 for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
284 new_trace.push_back(data_point_cumul);
290 catch(std::exception &error)
293 "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
294 .arg(scanNumBegin, scanNumEnd)
303 std::size_t scanNumBegin,
304 std::size_t scanNumEnd)
const
313 std::size_t imax = scanNumEnd + 1;
315 for(std::size_t i = scanNumBegin; i < imax; i++)
324 catch(std::exception &error)
326 qDebug() << QString(
"Failure in %1 %2 to %3 :\n %4")
346 qDebug() <<
" scanNum=" << scanNum;
353 std::make_shared<pappso::MassSpectrum>();
357 return mass_spectrum_sptr;
364 qint32 previous = -1;
365 std::vector<quint32> index_list;
366 for(std::size_t i = 0; i < size; i++)
369 (*(quint32 *)((
m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
377 previous = data_point.x;
383 mass_spectrum_sptr.get()->push_back(data_point);
386 return mass_spectrum_sptr;
392 std::vector<TimsXicStructure>::iterator &itXicListbegin,
393 std::vector<TimsXicStructure>::iterator &itXicListend,
396 std::vector<TimsFrame::XicComputeStructure> tmp_xic_list;
398 for(
auto it = itXicListbegin; it != itXicListend; it++)
400 tmp_xic_list.push_back(TimsFrame::XicComputeStructure(
this, *it));
402 if(tmp_xic_list.size() == 0)
410 std::vector<std::size_t> unique_scan_num_list;
411 for(
auto &&struct_xic : tmp_xic_list)
413 for(std::size_t scan = struct_xic.mobilityIndexBegin;
414 scan <= struct_xic.mobilityIndexEnd;
417 unique_scan_num_list.push_back(scan);
420 std::sort(unique_scan_num_list.begin(), unique_scan_num_list.end());
421 auto it_scan_num_end =
422 std::unique(unique_scan_num_list.begin(), unique_scan_num_list.end());
423 auto it_scan_num = unique_scan_num_list.begin();
425 while(it_scan_num != it_scan_num_end)
428 for(
auto &&tmp_xic_struct : tmp_xic_list)
430 if(((*it_scan_num) >= tmp_xic_struct.mobilityIndexBegin) &&
431 ((*it_scan_num) <= tmp_xic_struct.mobilityIndexEnd))
435 tmp_xic_struct.tmpIntensity +=
436 ms_spectrum.get()->maxY(tmp_xic_struct.mzIndexLowerBound,
437 tmp_xic_struct.mzIndexUpperBound);
442 tmp_xic_struct.tmpIntensity +=
443 ms_spectrum.get()->sumY(tmp_xic_struct.mzIndexLowerBound,
444 tmp_xic_struct.mzIndexUpperBound);
451 for(
auto &&tmp_xic_struct : tmp_xic_list)
453 if(tmp_xic_struct.tmpIntensity != 0)
455 tmp_xic_struct.xic_ptr->push_back(
456 {
m_time, tmp_xic_struct.tmpIntensity});
479 qint32 previous = -1;
480 std::vector<quint32> index_list;
481 for(std::size_t i = 0; i < size; i++)
484 (*(quint32 *)((
m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
492 previous = data_point.
x;