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 mobility_scan_end)
const
270 quint64 summed_intensities = 0;
276 return summed_intensities;
280 std::size_t mobility_scan_max = mobility_scan_end + 1;
282 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
289 catch(std::exception &error)
291 qDebug() << QString(
"Failure in %1 %2 to %3 :\n %4")
293 .arg(mobility_scan_begin)
294 .arg(mobility_scan_end)
300 return summed_intensities;
306 std::map<quint32, quint32> &accumulate_into)
const
319 qint32 previous = -1;
320 for(std::size_t i = 0; i < scan_size; i++)
323 (scan_offset * 4) + (i * 8))) +
326 (scan_offset * 4) + (i * 8) + 4));
330 auto ret = accumulate_into.insert(std::pair<quint32, quint32>(
x,
y));
332 if(ret.second ==
false)
335 ret.first->second +=
y;
345 std::map<quint32, quint32> &accumulate_into,
346 double mz_range_begin,
348 quint32 accepted_tof_index_range_begin,
349 quint32 accepted_tof_index_range_end)
const
360 qint32 previous = -1;
362 for(std::size_t i = 0; i < scan_size; i++)
365 (scan_offset * 4) + (i * 8))) +
368 if(
x < accepted_tof_index_range_begin)
373 if(
x > accepted_tof_index_range_end)
382 (scan_offset * 4) + (i * 8) + 4));
386 auto ret = accumulate_into.insert(std::pair<quint32, quint32>(
x,
y));
388 if(ret.second ==
false)
391 ret.first->second +=
y;
401 std::size_t mobility_scan_end)
const
411 std::map<quint32, quint32> raw_spectrum;
414 std::size_t mobility_scan_max = mobility_scan_end + 1;
416 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
434 for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
441 new_trace.push_back(data_point_cumul);
448 catch(std::exception &error)
451 "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
452 .arg(mobility_scan_begin, mobility_scan_end)
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
474 qDebug() <<
"The frame is empty, returning empty trace.";
481 std::map<quint32, quint32> raw_spectrum;
484 std::size_t mobility_scan_max = mobility_scan_end + 1;
486 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
506 if(mz_index_merge_window > 0)
511 mz_minimum_index_out = std::numeric_limits<quint32>::max();
512 mz_maximum_index_out = 0;
514 for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
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;
530 new_trace.push_back(data_point_cumul);
543 catch(std::exception &error)
546 "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
547 .arg(mobility_scan_begin, mobility_scan_end)
559 std::size_t mz_index_merge_window,
560 double mz_range_begin,
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
575 qDebug() <<
"The frame is empty, returning empty trace.";
582 std::map<quint32, quint32> raw_spectrum;
585 std::size_t mobility_scan_max = mobility_scan_end + 1;
587 quint32 only_in_mz_begin_tof_index_range =
590 quint32 only_in_mz_end_tof_index_range =
598 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
606 only_in_mz_begin_tof_index_range,
607 only_in_mz_end_tof_index_range);
623 if(mz_index_merge_window > 0)
628 mz_minimum_index_out = std::numeric_limits<quint32>::max();
629 mz_maximum_index_out = 0;
631 for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
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;
647 new_trace.push_back(data_point_cumul);
660 catch(std::exception &error)
663 "Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
664 .arg(mobility_scan_begin, mobility_scan_end)
676 std::size_t mobility_scan_begin,
677 std::size_t mobility_scan_end)
const
687 std::size_t mobility_scan_max = mobility_scan_end + 1;
689 for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
698 catch(std::exception &error)
700 qDebug() << QString(
"Failure in %1 %2 to %3 :\n %4")
702 .arg(mobility_scan_begin)
703 .arg(mobility_scan_end)
730 std::make_shared<pappso::MassSpectrum>();
734 return mass_spectrum_sptr;
746 qint32 previous = -1;
750 for(std::size_t i = 0; i < size; i++)
753 (*(quint32 *)((
m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
761 previous = tof_index;
766 mass_spectrum_sptr.get()->push_back(data_point);
771 return mass_spectrum_sptr;
777 std::vector<XicCoordTims *>::iterator &itXicListbegin,
778 std::vector<XicCoordTims *>::iterator &itXicListend,
781 qDebug() << std::distance(itXicListbegin, itXicListend);
783 std::vector<TimsFrame::XicComputeStructure> tmp_xic_list;
785 for(
auto it = itXicListbegin; it != itXicListend; it++)
789 qDebug() <<
" tmp_xic_struct.mobilityIndexBegin="
790 << tmp_xic_list.back().mobilityIndexBegin
791 <<
" tmp_xic_struct.mobilityIndexEnd="
792 << tmp_xic_list.back().mobilityIndexEnd;
794 qDebug() <<
" tmp_xic_struct.mzIndexLowerBound="
795 << tmp_xic_list.back().mzIndexLowerBound
796 <<
" tmp_xic_struct.mzIndexUpperBound="
797 << tmp_xic_list.back().mzIndexUpperBound;
799 if(tmp_xic_list.size() == 0)
807 std::vector<std::size_t> unique_scan_num_list;
808 for(
auto &&struct_xic : tmp_xic_list)
810 for(std::size_t scan = struct_xic.mobilityIndexBegin;
811 (scan <= struct_xic.mobilityIndexEnd) && (scan <
m_scanNumber);
814 unique_scan_num_list.push_back(scan);
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();
822 while(it_scan_num != it_scan_num_end)
826 for(
auto &&tmp_xic_struct : tmp_xic_list)
828 if(((*it_scan_num) >= tmp_xic_struct.mobilityIndexBegin) &&
829 ((*it_scan_num) <= tmp_xic_struct.mobilityIndexEnd))
833 tmp_xic_struct.tmpIntensity +=
834 ms_spectrum.get()->maxY(tmp_xic_struct.mzIndexLowerBound,
835 tmp_xic_struct.mzIndexUpperBound);
837 qDebug() <<
"tmp_xic_struct.tmpIntensity="
838 << tmp_xic_struct.tmpIntensity;
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;
854 for(
auto &&tmp_xic_struct : tmp_xic_list)
856 if(tmp_xic_struct.tmpIntensity != 0)
858 qDebug() << tmp_xic_struct.xic_ptr;
859 tmp_xic_struct.xic_ptr->push_back(
860 {
m_time, tmp_xic_struct.tmpIntensity});
885 qint32 previous = -1;
886 std::vector<quint32> index_list;
887 for(std::size_t i = 0; i < size; i++)
890 (*(quint32 *)((
m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
898 previous = data_point.
x;
899 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
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
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 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)
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.
void sortX(SortOrder sort_order=SortOrder::ascending)
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