28#include "../../../pappsomspp/pappsoexception.h"
29#include "../../../pappsomspp/exception/exceptionoutofrange.h"
65 double digitizerTimebase,
66 double digitizerDelay,
108 QObject::tr(
"Invalid scan number : scanNum %1 > m_scanNumber %2")
121 "ERROR unable to get number of peaks in TimsFrameBase for scan number %1")
136 "ERROR unable to getMassSpectrumSPtr in TimsFrameBase for scan number %1")
150 std::size_t scanNumEnd)
const
153 QObject::tr(
"ERROR unable to cumulateScanToTrace in TimsFrameBase for scan "
154 "number begin %1 end %2")
161 std::size_t mzindex_merge_window [[maybe_unused]],
162 std::size_t scanNumBegin [[maybe_unused]],
163 std::size_t scanNumEnd [[maybe_unused]],
164 quint32 &minimum_index [[maybe_unused]],
165 quint32 &maximum_index [[maybe_unused]])
const
175 std::size_t mz_index_merge_window [[maybe_unused]],
176 double mz_range_begin [[maybe_unused]],
177 double mz_range_end [[maybe_unused]],
178 std::size_t mobility_scan_begin [[maybe_unused]],
179 std::size_t mobility_scan_end [[maybe_unused]],
180 quint32 &mz_minimum_index_out [[maybe_unused]],
181 quint32 &mz_maximum_index_out [[maybe_unused]])
const
191 std::size_t mz_index_merge_window
193 double mz_range_begin [[maybe_unused]],
194 double mz_range_end [[maybe_unused]],
195 quint32 &mz_minimum_index_out [[maybe_unused]],
196 quint32 &mz_maximum_index_out
197 [[maybe_unused]])
const
208 std::size_t scanNumBegin,
209 std::size_t scanNumEnd)
const
213 "ERROR unable to cumulateScansInRawMap in TimsFrameBase for scan "
214 "number begin %1 end %2")
225 "ERROR unable to cumulateSingleScanIntensities in TimsFrameBase for scan "
235 std::size_t scanNumEnd)
const
239 "ERROR unable to cumulateScansInRawMap in TimsFrameBase for scan "
240 "number begin %1 end %2")
257 qDebug() <<
" m_msMsType=" << type;
287 [[maybe_unused]]
double C5,
293 if(tims_model_type != 2)
296 "ERROR in TimsFrame::setTimsCalibration tims_model_type != 2"));
320 QObject::tr(
"ERROR in TimsFrame::getVoltageTransformation invalid tims "
321 "calibration, v < m_timsVmin"));
328 QObject::tr(
"ERROR in TimsFrame::getVoltageTransformation invalid tims "
329 "calibration, v > m_timsVmax"));
349 double temp = 1 / one_over_k0;
355 return (std::size_t)std::round(temp);
375 std::map<quint32, quint32> &accumulated_scans)
const
387 for(
auto &scan_element : accumulated_scans)
395 local_trace.push_back(element);
406 std::map<quint32, quint32> &accumulated_scans)
const
411 std::vector<quint32> keys;
412 transform(begin(accumulated_scans),
413 end(accumulated_scans),
415 [](std::map<quint32, quint32>::value_type
const &pair) {
418 std::sort(keys.begin(), keys.end());
420 data_point_cumul.
x = 0;
421 data_point_cumul.
y = 0;
429 quint32 last_key = 0;
431 for(quint32 key : keys)
433 if(key == last_key + 1)
436 if(accumulated_scans[key] > accumulated_scans[last_key])
438 if(data_point_cumul.
x == last_key)
441 data_point_cumul.
x = key;
442 data_point_cumul.
y += accumulated_scans[key];
448 if(data_point_cumul.
y > 0)
457 local_trace.push_back(data_point_cumul);
461 data_point_cumul.
x = key;
462 data_point_cumul.
y = accumulated_scans[key];
467 data_point_cumul.
y += accumulated_scans[key];
473 if(data_point_cumul.
y > 0)
484 local_trace.push_back(data_point_cumul);
488 data_point_cumul.
x = key;
489 data_point_cumul.
y = accumulated_scans[key];
495 if(data_point_cumul.
y > 0)
504 local_trace.push_back(data_point_cumul);
520 QObject::tr(
"ERROR in %1, %2, %3 msp_mzCalibration is null")
533 if(mzCalibration ==
nullptr)
537 QObject::tr(
"ERROR in %1, %2, %3 msp_mzCalibration is null")
549 quint32 max_value = 0;
552 qDebug() <<
"m_scanNumber=" <<
m_scanNumber <<
" i=" << i;
554 auto it = std::max_element(index_list.begin(), index_list.end());
555 if(it != index_list.end())
557 max_value = std::max(max_value, *it);
568 "ERROR unable to getScanIndexList in TimsFrameBase for scan number %1")
578 "ERROR unable to getScanIntensities in TimsFrameBase for scan number %1")
584 std::size_t mz_index_lower_bound,
585 std::size_t mz_index_upper_bound,
594 qDebug() <<
"m_scanNumber=" <<
m_scanNumber <<
" i=" << i;
596 auto it_lower = std::find_if(index_list.begin(),
598 [mz_index_lower_bound](quint32 to_compare) {
599 if(to_compare < mz_index_lower_bound)
607 if(it_lower == index_list.end())
615 std::find_if(index_list.begin(),
617 [mz_index_upper_bound](quint32 to_compare) {
618 if(mz_index_upper_bound >= to_compare)
625 for(
int j = std::distance(index_list.begin(), it_lower);
626 j < std::distance(index_list.begin(), it_upper);
631 data_point.
y += intensity_list[j];
636 std::max((
double)intensity_list[j], data_point.
y);
640 im_trace.push_back(data_point);
646std::map<quint32, quint32> &
647TimsFrameBase::downsizeMzRawMap(std::size_t mzindex_merge_window,
648 std::map<quint32, quint32> &rawSpectrum)
const
650 std::map<quint32, quint32> new_spectrum;
652 for(
auto &pair_mz_intensity : rawSpectrum)
654 quint32 mzkey = (pair_mz_intensity.first / mzindex_merge_window);
655 mzkey = (mzkey * mzindex_merge_window) + (mzindex_merge_window / 2);
656 auto it = new_spectrum.insert({mzkey, pair_mz_intensity.second});
657 if(it.second ==
false)
659 it.first->second += pair_mz_intensity.second;
662 rawSpectrum = new_spectrum;
666std::vector<TimsFrameBase::RawValuePair> &
667TimsFrameBase::downsizeMzRawValuePairList(
668 std::size_t mzindex_merge_window,
669 std::vector<TimsFrameBase::RawValuePair> &rawSpectrum)
const
672 qDebug() << rawSpectrum.size();
673 std::vector<TimsFrameBase::RawValuePair> new_spectrum;
678 for(
auto &pair_mz_intensity : rawSpectrum)
680 quint32 mzkey = (pair_mz_intensity.mz_tof_index / mzindex_merge_window);
681 mzkey = (mzkey * mzindex_merge_window) + (mzindex_merge_window / 2);
687 new_spectrum.push_back(current_point);
701 new_spectrum.push_back(current_point);
703 rawSpectrum = new_spectrum;
704 qDebug() << rawSpectrum.size();
virtual double getMzFromTofIndex(quint32 tof_index)=0
get m/z from time of flight raw index
double m_accumulationTime
accumulation time in milliseconds
virtual quint64 cumulateSingleScanIntensities(std::size_t scanNum) const
double getVoltageTransformation(std::size_t scanNum) const
get voltage for a given scan number
virtual std::size_t getTotalNumberOfScans() const
get the number of scans contained in this frame each scan represents an ion mobility slice
virtual Trace getIonMobilityTraceByMzIndexRange(std::size_t mz_index_lower_bound, std::size_t mz_index_upper_bound, XicExtractMethod method) const
get a mobility trace cumulating intensities inside the given mass index range
virtual std::size_t getNbrPeaks(std::size_t scanNum) const
get the number of peaks in this spectrum need the binary file
MzCalibrationInterfaceSPtr msp_mzCalibration
virtual MassSpectrumSPtr getMassSpectrumSPtr(std::size_t scanNum) const
get Mass spectrum with peaks for this scan number need the binary file
TimsFrameBase(std::size_t timsId, quint32 scanNum)
constructor for binary independant tims frame
virtual 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
double getDriftTime(std::size_t scanNum) const
get drift time of a scan number in milliseconds
pappso::Trace getTraceFromCumulatedScansBuiltinCentroid(std::map< quint32, quint32 > &accumulated_scans) const
transform accumulation of raw scans into a real mass spectrum with a simple centroid on raw integers
double m_time
retention time
virtual quint64 cumulateScansIntensities(std::size_t scanNumBegin, std::size_t scanNumEnd) const
void setAccumulationTime(double accumulation_time_ms)
quint32 m_scanNumber
total number of scans contained in this frame
virtual void cumulateScansInRawMap(std::map< quint32, quint32 > &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const
cumulate scan list into a trace into a raw spectrum map The intensities are NOT normalized with respe...
void setTime(double time)
std::size_t m_timsId
Tims frame database id (the SQL identifier of this frame)
pappso::Trace getTraceFromCumulatedScans(std::map< quint32, quint32 > &accumulated_scans) const
transform accumulation of raw scans into a real mass spectrum
virtual bool hasSameCalibrationData(const TimsFrameBase &other) const
tells if 2 tims frame has the same calibration data Usefull to know if raw data can be handled betwee...
virtual quint32 getMaximumRawMassIndex() const
get the maximum raw mass index contained in this frame
unsigned int getMsLevel() const
void setTimsCalibration(int tims_model_type, double C0, double C1, double C2, double C3, double C4, double C5, double C6, double C7, double C8, double C9)
virtual const MzCalibrationInterfaceSPtr & getMzCalibrationInterfaceSPtr() const final
get the MzCalibration model to compute mz and TOF for this frame
virtual Trace cumulateScansToTraceMzDownResolution(std::size_t mzindex_merge_window, std::size_t scanNumBegin, std::size_t scanNumEnd, quint32 &minimum_index, quint32 &maximum_index) const
cumulate spectrum given a scan number range need the binary file The intensities are normalized with ...
std::size_t getScanNumFromOneOverK0(double one_over_k0) const
get the scan number from a given 1/Ko mobility value
virtual Trace cumulateScansToTrace(std::size_t scanNumBegin, std::size_t scanNumEnd) const
cumulate spectrum given a scan number range need the binary file The intensities are normalized with ...
void setMsMsType(quint8 type)
void setMzCalibration(double T1_frame, double T2_frame, double digitizerTimebase, double digitizerDelay, double C0, double C1, double C2, double C3, double C4, double T1_ref, double T2_ref, double dC1, double dC2)
double getOneOverK0Transformation(std::size_t scanNum) const
get 1/K0 value of a given scan (mobility value)
bool checkScanNum(std::size_t scanNum) const
check that this scan number exists
virtual Trace getMobilityScan(std::size_t scanNum, std::size_t mz_index_merge_window, double mz_range_begin, double mz_range_end, quint32 &mz_minimum_index_out, quint32 &mz_maximum_index_out) const
get a single mobility scan m/z + intensities
virtual 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
cumulate spectrum given a scan number range need the binary file The intensities are normalized with ...
void setMzCalibrationInterfaceSPtr(MzCalibrationInterfaceSPtr mzCalibration)
std::size_t getId() const
virtual std::vector< quint32 > getScanIntensities(std::size_t scanNum) const
get raw intensities without transformation from one scan it needs intensity normalization
virtual pappso::MassSpectrumCstSPtr getMassSpectrumCstSPtr(std::size_t scanNum) const final
get the mass spectrum corresponding to a scan number
A simple container of DataPoint instances.
void sortX(SortOrder sort_order=SortOrder::ascending)
implement Bruker's model type 1 formula to compute m/z
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
std::shared_ptr< MzCalibrationInterface > MzCalibrationInterfaceSPtr
std::shared_ptr< const MassSpectrum > MassSpectrumCstSPtr
std::shared_ptr< MassSpectrum > MassSpectrumSPtr
handle a single Bruker's TimsTof frame without binary data