29#include "../../../pappsomspp/pappsoexception.h"
74 if(p_bytes !=
nullptr)
84 QObject::tr(
"TimsFrame::TimsFrame(%1,%2,nullptr,%3) FAILED")
109 QObject::tr(
"TimsFrame::unshufflePacket error: len%4 != 0"));
112 quint64 nb_uint4 = len / 4;
115 quint64 src_offset = 0;
117 for(quint64 j = 0; j < 4; j++)
119 for(quint64 i = 0; i < nb_uint4; i++)
121 dest[(i * 4) + j] = src[src_offset];
144 std::size_t cumul = 0;
149 return (nb_uint4 - cumul) / 2;
155 return (*(quint32 *)(
m_timsDataFrame.constData() + ((scanNum + 1) * 4))) / 2;
161 std::size_t offset = 0;
162 for(std::size_t i = 0; i < (scanNum + 1); i++)
175 std::vector<quint32> scan_tof;
183 qint32 previous = -1;
184 for(std::size_t i = 0; i < scan_tof.size(); i++)
189 previous = scan_tof[i];
200 std::vector<quint32> scan_intensities;
203 return scan_intensities;
209 for(std::size_t i = 0; i < scan_intensities.size(); i++)
212 (offset * 4) + (i * 8) + 4));
215 return scan_intensities;
224 quint64 summed_intensities = 0;
227 return summed_intensities;
234 qint32 previous = -1;
236 for(std::size_t i = 0; i < size; i++)
239 (*(quint32 *)((
m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
247 summed_intensities +=
y;
255 return summed_intensities;
268 std::size_t scanNumEnd)
const
270 quint64 summed_intensities = 0;
272 qDebug() <<
"begin scanNumBegin =" << scanNumBegin
273 <<
"scanNumEnd =" << scanNumEnd;
276 return summed_intensities;
280 std::size_t imax = scanNumEnd + 1;
282 for(std::size_t i = scanNumBegin; i < imax; i++)
289 catch(std::exception &error)
291 qDebug() << QString(
"Failure in %1 %2 to %3 :\n %4")
300 return summed_intensities;
306 std::map<quint32, quint32> &accumulate_into)
const
318 qint32 previous = -1;
319 for(std::size_t i = 0; i < size; i++)
322 (*(quint32 *)((
m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
329 auto ret = accumulate_into.insert(std::pair<quint32, quint32>(
x,
y));
331 if(ret.second ==
false)
334 ret.first->second +=
y;
343 std::size_t scanNumEnd)
const
353 std::map<quint32, quint32> raw_spectrum;
356 std::size_t imax = scanNumEnd + 1;
358 for(std::size_t i = scanNumBegin; i < imax; i++)
373 for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
380 new_trace.push_back(data_point_cumul);
386 catch(std::exception &error)
389 "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
390 .arg(scanNumBegin, scanNumEnd)
399 std::size_t scanNumBegin,
400 std::size_t scanNumEnd)
const
402 qDebug() <<
"begin scanNumBegin=" << scanNumBegin
403 <<
" scanNumEnd=" << scanNumEnd;
410 std::size_t imax = scanNumEnd + 1;
412 for(std::size_t i = scanNumBegin; i < imax; i++)
421 catch(std::exception &error)
423 qDebug() << QString(
"Failure in %1 %2 to %3 :\n %4")
444 qDebug() <<
" scanNum=" << scanNum;
451 std::make_shared<pappso::MassSpectrum>();
455 return mass_spectrum_sptr;
466 qint32 previous = -1;
470 for(std::size_t i = 0; i < size; i++)
473 (*(quint32 *)((
m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
481 previous = tof_index;
486 mass_spectrum_sptr.get()->push_back(data_point);
489 return mass_spectrum_sptr;
495 std::vector<XicCoordTims *>::iterator &itXicListbegin,
496 std::vector<XicCoordTims *>::iterator &itXicListend,
499 qDebug() << std::distance(itXicListbegin, itXicListend);
500 std::vector<TimsFrame::XicComputeStructure> tmp_xic_list;
502 for(
auto it = itXicListbegin; it != itXicListend; it++)
506 qDebug() <<
" tmp_xic_struct.mobilityIndexBegin="
507 << tmp_xic_list.back().mobilityIndexBegin
508 <<
" tmp_xic_struct.mobilityIndexEnd="
509 << tmp_xic_list.back().mobilityIndexEnd;
511 qDebug() <<
" tmp_xic_struct.mzIndexLowerBound="
512 << tmp_xic_list.back().mzIndexLowerBound
513 <<
" tmp_xic_struct.mzIndexUpperBound="
514 << tmp_xic_list.back().mzIndexUpperBound;
516 if(tmp_xic_list.size() == 0)
524 std::vector<std::size_t> unique_scan_num_list;
525 for(
auto &&struct_xic : tmp_xic_list)
527 for(std::size_t scan = struct_xic.mobilityIndexBegin;
528 (scan <= struct_xic.mobilityIndexEnd) && (scan <
m_scanNumber);
531 unique_scan_num_list.push_back(scan);
534 std::sort(unique_scan_num_list.begin(), unique_scan_num_list.end());
535 auto it_scan_num_end =
536 std::unique(unique_scan_num_list.begin(), unique_scan_num_list.end());
537 auto it_scan_num = unique_scan_num_list.begin();
539 while(it_scan_num != it_scan_num_end)
543 for(
auto &&tmp_xic_struct : tmp_xic_list)
545 if(((*it_scan_num) >= tmp_xic_struct.mobilityIndexBegin) &&
546 ((*it_scan_num) <= tmp_xic_struct.mobilityIndexEnd))
550 tmp_xic_struct.tmpIntensity +=
551 ms_spectrum.get()->maxY(tmp_xic_struct.mzIndexLowerBound,
552 tmp_xic_struct.mzIndexUpperBound);
554 qDebug() <<
"tmp_xic_struct.tmpIntensity="
555 << tmp_xic_struct.tmpIntensity;
560 tmp_xic_struct.tmpIntensity +=
561 ms_spectrum.get()->sumY(tmp_xic_struct.mzIndexLowerBound,
562 tmp_xic_struct.mzIndexUpperBound);
563 qDebug() <<
"tmp_xic_struct.tmpIntensity="
564 << tmp_xic_struct.tmpIntensity;
571 for(
auto &&tmp_xic_struct : tmp_xic_list)
573 if(tmp_xic_struct.tmpIntensity != 0)
575 qDebug() << tmp_xic_struct.xic_ptr;
576 tmp_xic_struct.xic_ptr->push_back(
577 {
m_time, tmp_xic_struct.tmpIntensity});
602 qint32 previous = -1;
603 std::vector<quint32> index_list;
604 for(std::size_t i = 0; i < size; i++)
607 (*(quint32 *)((
m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
615 previous = data_point.
x;
616 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
check that this scan number exists
QByteArray m_timsDataFrame
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 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)
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 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
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
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.
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 XicCoordTims &xic_struct)
std::size_t mobilityIndexBegin
std::size_t mzIndexUpperBound
std::size_t mzIndexLowerBound
std::size_t mobilityIndexEnd
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
MzRange mzRange
the mass to extract
handle a single Bruker's TimsTof frame