29 #include "../../../pappsomspp/pappsoexception.h"
30 #include "../../../pappsomspp/exception/exceptionoutofrange.h"
70 if(p_bytes !=
nullptr)
80 QObject::tr(
"TimsFrame::TimsFrame(%1,%2,nullptr,%3) FAILED")
105 QObject::tr(
"TimsFrame::unshufflePacket error: len%4 != 0"));
108 quint64 nb_uint4 = len / 4;
111 quint64 src_offset = 0;
113 for(quint64 j = 0; j < 4; j++)
115 for(quint64 i = 0; i < nb_uint4; i++)
117 dest[(i * 4) + j] = src[src_offset];
140 std::size_t cumul = 0;
145 return (nb_uint4 - cumul) / 2;
151 return (*(quint32 *)(
m_timsDataFrame.constData() + ((scanNum + 1) * 4))) / 2;
157 std::size_t offset = 0;
158 for(std::size_t i = 0; i < (scanNum + 1); i++)
171 std::vector<quint32> scan_tof;
179 qint32 previous = -1;
180 for(std::size_t i = 0; i < scan_tof.size(); i++)
185 previous = scan_tof[i];
196 std::vector<quint32> scan_intensities;
199 return scan_intensities;
205 for(std::size_t i = 0; i < scan_intensities.size(); i++)
208 (offset * 4) + (i * 8) + 4));
211 return scan_intensities;
217 std::map<quint32, quint32> &accumulate_into)
const
230 qint32 previous = -1;
231 for(std::size_t i = 0; i < size; i++)
234 (*(quint32 *)((
m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
241 auto ret = accumulate_into.insert(std::pair<quint32, quint32>(
x,
y));
243 if(ret.second ==
false)
246 ret.first->second +=
y;
255 std::size_t scanNumEnd)
const
265 std::map<quint32, quint32> raw_spectrum;
268 std::size_t imax = scanNumEnd + 1;
270 for(std::size_t i = scanNumBegin; i < imax; i++)
285 for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
292 new_trace.push_back(data_point_cumul);
298 catch(std::exception &error)
301 "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
302 .arg(scanNumBegin, scanNumEnd)
311 std::size_t scanNumBegin,
312 std::size_t scanNumEnd)
const
321 std::size_t imax = scanNumEnd + 1;
323 for(std::size_t i = scanNumBegin; i < imax; i++)
332 catch(std::exception &error)
334 qDebug() << QString(
"Failure in %1 %2 to %3 :\n %4")
354 qDebug() <<
" scanNum=" << scanNum;
361 std::make_shared<pappso::MassSpectrum>();
365 return mass_spectrum_sptr;
376 qint32 previous = -1;
378 std::vector<quint32> index_list;
380 for(std::size_t i = 0; i < size; i++)
383 (*(quint32 *)((
m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
391 previous = tof_index;
396 mass_spectrum_sptr.get()->push_back(data_point);
399 return mass_spectrum_sptr;
405 std::vector<TimsXicStructure>::iterator &itXicListbegin,
406 std::vector<TimsXicStructure>::iterator &itXicListend,
409 qDebug() << std::distance(itXicListbegin, itXicListend);
410 std::vector<TimsFrame::XicComputeStructure> tmp_xic_list;
412 for(
auto it = itXicListbegin; it != itXicListend; it++)
416 qDebug() <<
" tmp_xic_struct.mobilityIndexBegin="
417 << tmp_xic_list.back().mobilityIndexBegin
418 <<
" tmp_xic_struct.mobilityIndexEnd="
419 << tmp_xic_list.back().mobilityIndexEnd;
421 qDebug() <<
" tmp_xic_struct.mzIndexLowerBound="
422 << tmp_xic_list.back().mzIndexLowerBound
423 <<
" tmp_xic_struct.mzIndexUpperBound="
424 << tmp_xic_list.back().mzIndexUpperBound;
426 if(tmp_xic_list.size() == 0)
434 std::vector<std::size_t> unique_scan_num_list;
435 for(
auto &&struct_xic : tmp_xic_list)
437 for(std::size_t scan = struct_xic.mobilityIndexBegin;
438 scan <= struct_xic.mobilityIndexEnd;
441 unique_scan_num_list.push_back(scan);
444 std::sort(unique_scan_num_list.begin(), unique_scan_num_list.end());
445 auto it_scan_num_end =
446 std::unique(unique_scan_num_list.begin(), unique_scan_num_list.end());
447 auto it_scan_num = unique_scan_num_list.begin();
449 while(it_scan_num != it_scan_num_end)
453 for(
auto &&tmp_xic_struct : tmp_xic_list)
455 if(((*it_scan_num) >= tmp_xic_struct.mobilityIndexBegin) &&
456 ((*it_scan_num) <= tmp_xic_struct.mobilityIndexEnd))
460 tmp_xic_struct.tmpIntensity +=
461 ms_spectrum.get()->maxY(tmp_xic_struct.mzIndexLowerBound,
462 tmp_xic_struct.mzIndexUpperBound);
464 qDebug() <<
"tmp_xic_struct.tmpIntensity="
465 << tmp_xic_struct.tmpIntensity;
470 tmp_xic_struct.tmpIntensity +=
471 ms_spectrum.get()->sumY(tmp_xic_struct.mzIndexLowerBound,
472 tmp_xic_struct.mzIndexUpperBound);
473 qDebug() <<
"tmp_xic_struct.tmpIntensity="
474 << tmp_xic_struct.tmpIntensity;
481 for(
auto &&tmp_xic_struct : tmp_xic_list)
483 if(tmp_xic_struct.tmpIntensity != 0)
485 qDebug() << tmp_xic_struct.xic_ptr;
486 tmp_xic_struct.xic_ptr->push_back(
487 {
m_time, tmp_xic_struct.tmpIntensity});
512 qint32 previous = -1;
513 std::vector<quint32> index_list;
514 for(std::size_t i = 0; i < size; i++)
517 (*(quint32 *)((
m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
525 previous = data_point.
x;
526 trace_sptr.get()->push_back(data_point);
virtual double getMzFromTofIndex(quint32 tof_index)=0
get m/z from time of flight raw index
pappso_double lower() const
pappso_double upper() const
double m_accumulationTime
accumulation time in milliseconds
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
QByteArray m_timsDataFrame
virtual std::size_t getNbrPeaks(std::size_t scanNum) const override
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)
virtual pappso::MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const override
void extractTimsXicListInRtRange(std::vector< TimsXicStructure >::iterator &itXicListbegin, std::vector< TimsXicStructure >::iterator &itXicListend, XicExtractMethod method) const
void unshufflePacket(const char *src)
std::size_t getScanOffset(std::size_t scanNum) 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
std::vector< quint32 > getScanIndexList(std::size_t scanNum) const
get raw index list for one given scan index are not TOF nor m/z, just index on digitizer
std::vector< quint32 > getScanIntensities(std::size_t scanNum) const
get raw intensities without transformation from one scan it needs intensity normalization
pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr(std::size_t scanNum) const
get the mass spectrum corresponding to a scan number
pappso::TraceSPtr getRawTraceSPtr(std::size_t scanNum) const
A simple container of DataPoint instances.
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< Trace > TraceSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
@ max
maximum of intensities
XicComputeStructure(const TimsFrame *fram_p, const TimsXicStructure &xic_struct)
std::size_t mobilityIndexBegin
std::size_t mzIndexUpperBound
std::size_t mzIndexLowerBound
std::size_t mobilityIndexEnd
structure needed to extract XIC from Tims data
std::size_t scanNumEnd
mobility index end
MzRange mzRange
mass range to extract
XicSPtr xicSptr
extracted xic
std::size_t scanNumBegin
mobility index begin
handle a single Bruker's TimsTof frame