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);
390 element.
y = ((double)accumulated_scans.
readIntensity(tof_index)) * 100.0 /
396 local_trace.push_back(element);
412 QObject::tr(
"ERROR in %1, %2, %3 msp_mzCalibration is null")
425 if(mzCalibration ==
nullptr)
429 QObject::tr(
"ERROR in %1, %2, %3 msp_mzCalibration is null")
441 quint32 max_value = 0;
444 qDebug() <<
"m_scanNumber=" <<
m_scanNumber <<
" i=" << i;
446 auto it = std::max_element(index_list.begin(), index_list.end());
447 if(it != index_list.end())
449 max_value = std::max(max_value, *it);
460 "ERROR unable to getScanIndexList in TimsFrameBase for scan number %1")
470 "ERROR unable to getScanIntensities in TimsFrameBase for scan number %1")
476 std::size_t mz_index_lower_bound,
477 std::size_t mz_index_upper_bound,
486 qDebug() <<
"m_scanNumber=" <<
m_scanNumber <<
" i=" << i;
488 auto it_lower = std::find_if(index_list.begin(),
490 [mz_index_lower_bound](quint32 to_compare) {
491 if(to_compare < mz_index_lower_bound)
499 if(it_lower == index_list.end())
507 std::find_if(index_list.begin(),
509 [mz_index_upper_bound](quint32 to_compare) {
510 if(mz_index_upper_bound >= to_compare)
517 for(
int j = std::distance(index_list.begin(), it_lower);
518 j < std::distance(index_list.begin(), it_upper);
523 data_point.
y += intensity_list[j];
528 std::max((
double)intensity_list[j], data_point.
y);
532 im_trace.push_back(data_point);
539std::vector<TimsFrameBase::RawValuePair> &
540TimsFrameBase::downsizeMzRawValuePairList(
541 std::size_t mzindex_merge_window,
542 std::vector<TimsFrameBase::RawValuePair> &rawSpectrum)
const
545 qDebug() << rawSpectrum.size();
546 std::vector<TimsFrameBase::RawValuePair> new_spectrum;
551 for(
auto &pair_mz_intensity : rawSpectrum)
553 quint32 mzkey = (pair_mz_intensity.mz_tof_index / mzindex_merge_window);
554 mzkey = (mzkey * mzindex_merge_window) + (mzindex_merge_window / 2);
560 new_spectrum.push_back(current_point);
574 new_spectrum.push_back(current_point);
576 rawSpectrum = new_spectrum;
577 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
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
void setTime(double time)
std::size_t m_timsId
Tims frame database id (the SQL identifier of this frame)
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)
pappso::Trace getTraceFromCumulatedScans(TimsDataFastMap &accumulated_scans) const
transform accumulation of raw scans into a real mass spectrum
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 ...
virtual void cumulateScansInRawMap(TimsDataFastMap &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 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
std::size_t readIntensity(quint32)
reads intensity for a tof_index
std::vector< quint32 > tofIndexList
handle a single Bruker's TimsTof frame without binary data