libpappsomspp
Library for mass spectrometry
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pappso::TimsFrameBase Class Reference

#include <timsframebase.h>

Inheritance diagram for pappso::TimsFrameBase:
pappso::TimsFrame pappso::TimsFrameType1

Public Member Functions

 TimsFrameBase (std::size_t timsId, quint32 scanNum)
 constructor for binary independant tims frame
 
 TimsFrameBase (const TimsFrameBase &other)
 
virtual ~TimsFrameBase ()
 
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 between frames
 
virtual std::size_t getNbrPeaks (std::size_t scanNum) const
 get the number of peaks in this spectrum need the binary file
 
virtual std::size_t getTotalNumberOfScans () const
 get the number of scans contained in this frame each scan represents an ion mobility slice
 
virtual quint32 getMaximumRawMassIndex () const
 get the maximum raw mass index contained in this frame
 
virtual MassSpectrumSPtr getMassSpectrumSPtr (std::size_t scanNum) const
 get Mass spectrum with peaks for this scan number need the binary file
 
virtual Trace cumulateScanToTrace (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 respect to the frame accumulation time
 
virtual Trace cumulateScanToTraceMzDownResolution (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 respect to the frame accumulation time to leverage computing performance, this function decreases the mz resolution
 
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
 
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 respect to the frame accumulation time
 
virtual quint64 cumulateSingleScanIntensities (std::size_t scanNum) const
 
virtual quint64 cumulateScansIntensities (std::size_t scanNumBegin, std::size_t scanNumEnd) const
 
bool checkScanNum (std::size_t scanNum) const
 check that this scan number exists
 
void setAccumulationTime (double accumulation_time_ms)
 
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)
 
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)
 
void setTime (double time)
 
void setMsMsType (quint8 type)
 
unsigned int getMsLevel () const
 
double getTime () const
 
std::size_t getId () const
 
double getDriftTime (std::size_t scanNum) const
 get drift time of a scan number in milliseconds
 
double getOneOverK0Transformation (std::size_t scanNum) const
 get 1/K0 value of a given scan (mobility value)
 
std::size_t getScanNumFromOneOverK0 (double one_over_k0) const
 get the scan number from a given 1/Ko mobility value
 
double getVoltageTransformation (std::size_t scanNum) const
 get voltage for a given scan number
 
pappso::Trace getTraceFromCumulatedScans (std::map< quint32, quint32 > &accumulated_scans) const
 transform accumulation of raw scans into a real mass spectrum
 
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
 
virtual const MzCalibrationInterfaceSPtrgetMzCalibrationInterfaceSPtr () const final
 get the MzCalibration model to compute mz and TOF for this frame
 
void setMzCalibrationInterfaceSPtr (MzCalibrationInterfaceSPtr mzCalibration)
 
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
 
virtual std::vector< quint32 > getScanIntensities (std::size_t scanNum) const
 get raw intensities without transformation from one scan it needs intensity normalization
 
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
 

Protected Attributes

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)
 
double m_accumulationTime = 0
 accumulation time in milliseconds
 
quint8 m_msMsType = 0
 
double m_time = 0
 retention time
 
double m_timsDvStart = 0
 
double m_timsSlope
 
double m_timsTtrans = 0
 
double m_timsNdelay = 0
 
double m_timsVmin = 0
 
double m_timsVmax = 0
 
double m_timsC6 = 0
 
double m_timsC7 = 0
 
MzCalibrationInterfaceSPtr msp_mzCalibration = nullptr
 

Detailed Description

Todo:
write docs

Definition at line 47 of file timsframebase.h.

Constructor & Destructor Documentation

◆ TimsFrameBase() [1/2]

pappso::TimsFrameBase::TimsFrameBase ( std::size_t  timsId,
quint32  scanNum 
)

constructor for binary independant tims frame

Parameters
timsIdtims frame identifier in the database
scanNumthe total number of scans contained in this frame

Definition at line 39 of file timsframebase.cpp.

40{
41 qDebug() << timsId;
42 m_timsId = timsId;
43
44 m_scanNumber = scanNum;
45}
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)

References m_scanNumber, and m_timsId.

◆ TimsFrameBase() [2/2]

pappso::TimsFrameBase::TimsFrameBase ( const TimsFrameBase other)

Copy constructor

Parameters
otherTODO

Definition at line 47 of file timsframebase.cpp.

48{
49}

◆ ~TimsFrameBase()

pappso::TimsFrameBase::~TimsFrameBase ( )
virtual

Destructor

Definition at line 51 of file timsframebase.cpp.

52{
53}

Member Function Documentation

◆ checkScanNum()

bool pappso::TimsFrameBase::checkScanNum ( std::size_t  scanNum) const

check that this scan number exists

Parameters
scanNumscan number in the frame in the order it lies in binary file, from 0 to N-1

Definition at line 103 of file timsframebase.cpp.

104{
105 if(scanNum >= m_scanNumber)
106 {
108 QObject::tr("Invalid scan number : scanNum %1 > m_scanNumber %2")
109 .arg(scanNum)
110 .arg(m_scanNumber));
111 }
112
113 return true;
114}

References m_scanNumber.

Referenced by pappso::TimsFrame::getMassSpectrumSPtr(), pappso::TimsFrameType1::getMassSpectrumSPtr(), pappso::TimsFrame::getNbrPeaks(), pappso::TimsFrame::getScanIndexList(), pappso::TimsFrameType1::getScanIndexList(), pappso::TimsFrame::getScanIntensities(), and pappso::TimsFrameType1::getScanIntensities().

◆ cumulateScansInRawMap()

void pappso::TimsFrameBase::cumulateScansInRawMap ( std::map< quint32, quint32 > &  rawSpectrum,
std::size_t  scanNumBegin,
std::size_t  scanNumEnd 
) const
virtual

cumulate scan list into a trace into a raw spectrum map The intensities are NOT normalized with respect to the frame accumulation time

Parameters
rawSpectrumsimple map of integers to cumulate raw counts
scanNumBeginscan number in the frame in the order it lies in binary file, from 0 to N-1
scanNumEndscan number in the frame in the order it lies in binary file, from 0 to N-1

Reimplemented in pappso::TimsFrame.

Definition at line 165 of file timsframebase.cpp.

169{
170 throw PappsoException(
171 QObject::tr(
172 "ERROR unable to cumulateScansInRawMap in TimsFrameBase for scan "
173 "number begin %1 end %2")
174 .arg(scanNumBegin)
175 .arg(scanNumEnd));
176}

◆ cumulateScansIntensities()

quint64 pappso::TimsFrameBase::cumulateScansIntensities ( std::size_t  scanNumBegin,
std::size_t  scanNumEnd 
) const
virtual

Reimplemented in pappso::TimsFrame.

Definition at line 193 of file timsframebase.cpp.

195{
196 throw PappsoException(
197 QObject::tr(
198 "ERROR unable to cumulateScansInRawMap in TimsFrameBase for scan "
199 "number begin %1 end %2")
200 .arg(scanNumBegin)
201 .arg(scanNumEnd));
202
203 return 0;
204}

◆ cumulateScanToTrace()

Trace pappso::TimsFrameBase::cumulateScanToTrace ( std::size_t  scanNumBegin,
std::size_t  scanNumEnd 
) const
virtual

cumulate spectrum given a scan number range need the binary file The intensities are normalized with respect to the frame accumulation time

Parameters
scanNumBeginscan number in the frame in the order it lies in binary file, from 0 to N-1
scanNumEndscan number in the frame in the order it lies in binary file, from 0 to N-1

Reimplemented in pappso::TimsFrame.

Definition at line 140 of file timsframebase.cpp.

142{
143 throw PappsoException(
144 QObject::tr("ERROR unable to cumulateScanToTrace in TimsFrameBase for scan "
145 "number begin %1 end %2")
146 .arg(scanNumBegin)
147 .arg(scanNumEnd));
148}

◆ cumulateScanToTraceMzDownResolution()

Trace pappso::TimsFrameBase::cumulateScanToTraceMzDownResolution ( std::size_t  mzindex_merge_window,
std::size_t  scanNumBegin,
std::size_t  scanNumEnd,
quint32 &  minimum_index,
quint32 &  maximum_index 
) const
virtual

cumulate spectrum given a scan number range need the binary file The intensities are normalized with respect to the frame accumulation time to leverage computing performance, this function decreases the mz resolution

Parameters
mzindex_merge_windowwidth of the mzindex window used to merge all intensities into a single point. This results in faster computing.
scanNumBeginscan number in the frame in the order it lies in binary file, from 0 to N-1
scanNumEndscan number in the frame in the order it lies in binary file, from 0 to N-1

Reimplemented in pappso::TimsFrame.

Definition at line 151 of file timsframebase.cpp.

157{
158 throw PappsoException(QObject::tr("Non implemented function %1 %2 %3")
159 .arg(__FILE__)
160 .arg(__FUNCTION__)
161 .arg(__LINE__));
162}

◆ cumulateSingleScanIntensities()

quint64 pappso::TimsFrameBase::cumulateSingleScanIntensities ( std::size_t  scanNum) const
virtual

Reimplemented in pappso::TimsFrame.

Definition at line 180 of file timsframebase.cpp.

181{
182 throw PappsoException(
183 QObject::tr(
184 "ERROR unable to cumulateSingleScanIntensities in TimsFrameBase for scan "
185 "number %1.")
186 .arg(scanNum));
187
188 return 0;
189}

◆ downsizeMzRawMap()

std::map< quint32, quint32 > & pappso::TimsFrameBase::downsizeMzRawMap ( std::size_t  mzindex_merge_window,
std::map< quint32, quint32 > &  rawSpectrum 
) const

downsize mz resolution to lower the number of real mz computations

Parameters
mzindex_merge_windowwidth of the mzindex window used to merge all intensities into a single point. This results in faster computing.
rawSpectrumthe spectrum to shrink

Definition at line 606 of file timsframebase.cpp.

608{
609 std::map<quint32, quint32> new_spectrum;
610
611 for(auto &pair_mz_intensity : rawSpectrum)
612 {
613 quint32 mzkey = (pair_mz_intensity.first / mzindex_merge_window);
614 mzkey *= mzindex_merge_window + (mzindex_merge_window / 2);
615 auto it = new_spectrum.insert({mzkey, pair_mz_intensity.second});
616 if(it.second == false)
617 {
618 it.first->second += pair_mz_intensity.second;
619 }
620 }
621 rawSpectrum = new_spectrum;
622 return rawSpectrum;
623}

Referenced by pappso::TimsFrame::cumulateScanToTraceMzDownResolution(), and pappso::TimsFrame::cumulateScanToTraceMzDownResolution2().

◆ getDriftTime()

double pappso::TimsFrameBase::getDriftTime ( std::size_t  scanNum) const

get drift time of a scan number in milliseconds

Parameters
scanNumscan number in the frame in the order it lies in binary file, from 0 to N-1
Returns
time in milliseconds of mobility delay (drift time)

Definition at line 293 of file timsframebase.cpp.

294{
295 return (m_accumulationTime / (double)m_scanNumber) * ((double)scanNum);
296}
double m_accumulationTime
accumulation time in milliseconds

References m_accumulationTime, and m_scanNumber.

◆ getId()

std::size_t pappso::TimsFrameBase::getId ( ) const

◆ getIonMobilityTraceByMzIndexRange()

Trace pappso::TimsFrameBase::getIonMobilityTraceByMzIndexRange ( std::size_t  mz_index_lower_bound,
std::size_t  mz_index_upper_bound,
XicExtractMethod  method 
) const
virtual

get a mobility trace cumulating intensities inside the given mass index range

Parameters
mz_index_lower_boundraw mass index lower bound
mz_index_upper_boundraw mass index upper bound
methodmax or sum intensities

Definition at line 542 of file timsframebase.cpp.

546{
547 Trace im_trace;
548 DataPoint data_point;
549 for(quint32 i = 0; i < m_scanNumber; i++)
550 {
551 data_point.x = i;
552 data_point.y = 0;
553 qDebug() << "m_scanNumber=" << m_scanNumber << " i=" << i;
554 std::vector<quint32> index_list = getScanIndexList(i);
555 auto it_lower = std::find_if(index_list.begin(),
556 index_list.end(),
557 [mz_index_lower_bound](quint32 to_compare) {
558 if(to_compare < mz_index_lower_bound)
559 {
560 return false;
561 }
562 return true;
563 });
564
565
566 if(it_lower == index_list.end())
567 {
568 }
569 else
570 {
571
572
573 auto it_upper =
574 std::find_if(index_list.begin(),
575 index_list.end(),
576 [mz_index_upper_bound](quint32 to_compare) {
577 if(mz_index_upper_bound >= to_compare)
578 {
579 return false;
580 }
581 return true;
582 });
583 std::vector<quint32> intensity_list = getScanIntensities(i);
584 for(int j = std::distance(index_list.begin(), it_lower);
585 j < std::distance(index_list.begin(), it_upper);
586 j++)
587 {
588 if(method == XicExtractMethod::sum)
589 {
590 data_point.y += intensity_list[j];
591 }
592 else
593 {
594 data_point.y =
595 std::max((double)intensity_list[j], data_point.y);
596 }
597 }
598 }
599 im_trace.push_back(data_point);
600 }
601 qDebug();
602 return im_trace;
603}
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
virtual std::vector< quint32 > getScanIntensities(std::size_t scanNum) const
get raw intensities without transformation from one scan it needs intensity normalization
@ sum
sum of intensities

References getScanIndexList(), getScanIntensities(), m_scanNumber, pappso::sum, pappso::DataPoint::x, and pappso::DataPoint::y.

◆ getMassSpectrumSPtr()

MassSpectrumSPtr pappso::TimsFrameBase::getMassSpectrumSPtr ( std::size_t  scanNum) const
virtual

get Mass spectrum with peaks for this scan number need the binary file

Parameters
scanNumscan number in the frame in the order it lies in binary file, from 0 to N-1

Reimplemented in pappso::TimsFrame, and pappso::TimsFrameType1.

Definition at line 132 of file timsframebase.cpp.

133{
134 throw PappsoException(
135 QObject::tr(
136 "ERROR unable to getMassSpectrumSPtr in TimsFrameBase for scan number %1")
137 .arg(scanNum));
138}

◆ getMaximumRawMassIndex()

quint32 pappso::TimsFrameBase::getMaximumRawMassIndex ( ) const
virtual

get the maximum raw mass index contained in this frame

Definition at line 506 of file timsframebase.cpp.

507{
508 quint32 max_value = 0;
509 for(quint32 i = 0; i < m_scanNumber; i++)
510 {
511 qDebug() << "m_scanNumber=" << m_scanNumber << " i=" << i;
512 std::vector<quint32> index_list = getScanIndexList(i);
513 auto it = std::max_element(index_list.begin(), index_list.end());
514 if(it != index_list.end())
515 {
516 max_value = std::max(max_value, *it);
517 }
518 }
519 return max_value;
520}

References getScanIndexList(), and m_scanNumber.

◆ getMsLevel()

unsigned int pappso::TimsFrameBase::getMsLevel ( ) const

Definition at line 221 of file timsframebase.cpp.

222{
223 if(m_msMsType == 0)
224 return 1;
225 return 2;
226}

References m_msMsType.

◆ getMzCalibrationInterfaceSPtr()

const MzCalibrationInterfaceSPtr & pappso::TimsFrameBase::getMzCalibrationInterfaceSPtr ( ) const
finalvirtual

get the MzCalibration model to compute mz and TOF for this frame

Definition at line 473 of file timsframebase.cpp.

474{
475 if(msp_mzCalibration == nullptr)
476 {
477
479 QObject::tr("ERROR in %1, %2, %3 msp_mzCalibration is null")
480 .arg(__FILE__)
481 .arg(__FUNCTION__)
482 .arg(__LINE__));
483 }
484 return msp_mzCalibration;
485}
MzCalibrationInterfaceSPtr msp_mzCalibration

References msp_mzCalibration.

Referenced by pappso::TimsFrame::XicComputeStructure::XicComputeStructure(), pappso::TimsFrame::cumulateScanToTrace(), pappso::TimsFrame::cumulateScanToTraceMzDownResolution(), pappso::TimsFrame::cumulateScanToTraceMzDownResolution2(), pappso::TimsFrame::getMassSpectrumSPtr(), pappso::TimsFrameType1::getMassSpectrumSPtr(), getTraceFromCumulatedScans(), and getTraceFromCumulatedScansBuiltinCentroid().

◆ getNbrPeaks()

std::size_t pappso::TimsFrameBase::getNbrPeaks ( std::size_t  scanNum) const
virtual

get the number of peaks in this spectrum need the binary file

Parameters
scanNumscan number in the frame in the order it lies in binary file, from 0 to N-1

Reimplemented in pappso::TimsFrame, and pappso::TimsFrameType1.

Definition at line 117 of file timsframebase.cpp.

118{
119 throw PappsoException(
120 QObject::tr(
121 "ERROR unable to get number of peaks in TimsFrameBase for scan number %1")
122 .arg(scanNum));
123}

◆ getOneOverK0Transformation()

double pappso::TimsFrameBase::getOneOverK0Transformation ( std::size_t  scanNum) const

get 1/K0 value of a given scan (mobility value)

Parameters
scanNumscan number in the frame in the order it lies in binary file, from 0 to N-1

Definition at line 299 of file timsframebase.cpp.

300{
301 return 1 / (m_timsC6 + (m_timsC7 / getVoltageTransformation(scanNum)));
302}
double getVoltageTransformation(std::size_t scanNum) const
get voltage for a given scan number

References getVoltageTransformation(), m_timsC6, and m_timsC7.

◆ getScanIndexList()

std::vector< quint32 > pappso::TimsFrameBase::getScanIndexList ( std::size_t  scanNum) const
virtual

get raw index list for one given scan index are not TOF nor m/z, just index on digitizer

Reimplemented in pappso::TimsFrame, and pappso::TimsFrameType1.

Definition at line 523 of file timsframebase.cpp.

524{
525 throw PappsoException(
526 QObject::tr(
527 "ERROR unable to getScanIndexList in TimsFrameBase for scan number %1")
528 .arg(scanNum));
529}

Referenced by getIonMobilityTraceByMzIndexRange(), and getMaximumRawMassIndex().

◆ getScanIntensities()

std::vector< quint32 > pappso::TimsFrameBase::getScanIntensities ( std::size_t  scanNum) const
virtual

get raw intensities without transformation from one scan it needs intensity normalization

Reimplemented in pappso::TimsFrame, and pappso::TimsFrameType1.

Definition at line 533 of file timsframebase.cpp.

534{
535 throw PappsoException(
536 QObject::tr(
537 "ERROR unable to getScanIntensities in TimsFrameBase for scan number %1")
538 .arg(scanNum));
539}

Referenced by getIonMobilityTraceByMzIndexRange().

◆ getScanNumFromOneOverK0()

std::size_t pappso::TimsFrameBase::getScanNumFromOneOverK0 ( double  one_over_k0) const

get the scan number from a given 1/Ko mobility value

Parameters
one_over_k0the mobility value to tranform
Returns
integer the scan number in the frame in the order it lies in binary file, from 0 to N-1

Definition at line 306 of file timsframebase.cpp.

307{
308 double temp = 1 / one_over_k0;
309 temp = temp - m_timsC6;
310 temp = temp / m_timsC7;
311 temp = 1 / temp;
312 temp = temp - m_timsDvStart;
313 temp = temp / m_timsSlope + m_timsTtrans + m_timsNdelay;
314 return (std::size_t)std::round(temp);
315}

References m_timsC6, m_timsC7, m_timsDvStart, m_timsNdelay, m_timsSlope, and m_timsTtrans.

◆ getTime()

double pappso::TimsFrameBase::getTime ( ) const

Definition at line 229 of file timsframebase.cpp.

230{
231 return m_time;
232}
double m_time
retention time

References m_time.

◆ getTotalNumberOfScans()

std::size_t pappso::TimsFrameBase::getTotalNumberOfScans ( ) const
virtual

get the number of scans contained in this frame each scan represents an ion mobility slice

Definition at line 126 of file timsframebase.cpp.

127{
128 return m_scanNumber;
129}

References m_scanNumber.

Referenced by pappso::BaseColorMapPlotWidget::addColorMap().

◆ getTraceFromCumulatedScans()

pappso::Trace pappso::TimsFrameBase::getTraceFromCumulatedScans ( std::map< quint32, quint32 > &  accumulated_scans) const

transform accumulation of raw scans into a real mass spectrum

Definition at line 333 of file timsframebase.cpp.

335{
336 qDebug();
337 // qDebug();
338 // add flanking peaks
339 pappso::Trace local_trace;
340
341 MzCalibrationInterface *mz_calibration_p =
343
344
345 DataPoint element;
346 for(auto &scan_element : accumulated_scans)
347 {
348 // intensity normalization
349 element.y = ((double)scan_element.second) * 100.0 / m_accumulationTime;
350
351 // mz calibration
352 element.x = mz_calibration_p->getMzFromTofIndex(scan_element.first);
353
354 local_trace.push_back(element);
355 }
356 local_trace.sortX();
357
358 qDebug();
359 // qDebug();
360 return local_trace;
361}
virtual const MzCalibrationInterfaceSPtr & getMzCalibrationInterfaceSPtr() const final
get the MzCalibration model to compute mz and TOF for this frame
A simple container of DataPoint instances.
Definition trace.h:148
void sortX(SortOrder sort_order=SortOrder::ascending)
Definition trace.cpp:1086

References getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), m_accumulationTime, pappso::Trace::sortX(), pappso::DataPoint::x, and pappso::DataPoint::y.

◆ getTraceFromCumulatedScansBuiltinCentroid()

pappso::Trace pappso::TimsFrameBase::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

Definition at line 364 of file timsframebase.cpp.

366{
367 qDebug();
368 // qDebug();
369 // add flanking peaks
370 std::vector<quint32> keys;
371 transform(begin(accumulated_scans),
372 end(accumulated_scans),
373 back_inserter(keys),
374 [](std::map<quint32, quint32>::value_type const &pair) {
375 return pair.first;
376 });
377 std::sort(keys.begin(), keys.end());
378 pappso::DataPoint data_point_cumul;
379 data_point_cumul.x = 0;
380 data_point_cumul.y = 0;
381
382 pappso::Trace local_trace;
383
384 MzCalibrationInterface *mz_calibration_p =
386
387
388 quint32 last_key = 0;
389
390 for(quint32 key : keys)
391 {
392 if(key == last_key + 1)
393 {
394 // cumulate
395 if(accumulated_scans[key] > accumulated_scans[last_key])
396 {
397 if(data_point_cumul.x == last_key)
398 {
399 // growing peak
400 data_point_cumul.x = key;
401 data_point_cumul.y += accumulated_scans[key];
402 }
403 else
404 {
405 // new peak
406 // flush
407 if(data_point_cumul.y > 0)
408 {
409 // intensity normalization
410 data_point_cumul.y *= 100.0 / m_accumulationTime;
411
412
413 // mz calibration
414 data_point_cumul.x =
415 mz_calibration_p->getMzFromTofIndex(data_point_cumul.x);
416 local_trace.push_back(data_point_cumul);
417 }
418
419 // new point
420 data_point_cumul.x = key;
421 data_point_cumul.y = accumulated_scans[key];
422 }
423 }
424 else
425 {
426 data_point_cumul.y += accumulated_scans[key];
427 }
428 }
429 else
430 {
431 // flush
432 if(data_point_cumul.y > 0)
433 {
434 // intensity normalization
435 data_point_cumul.y *= 100.0 / m_accumulationTime;
436
437
438 // qDebug() << "raw data x=" << data_point_cumul.x;
439 // mz calibration
440 data_point_cumul.x =
441 mz_calibration_p->getMzFromTofIndex(data_point_cumul.x);
442 // qDebug() << "mz=" << data_point_cumul.x;
443 local_trace.push_back(data_point_cumul);
444 }
445
446 // new point
447 data_point_cumul.x = key;
448 data_point_cumul.y = accumulated_scans[key];
449 }
450
451 last_key = key;
452 }
453 // flush
454 if(data_point_cumul.y > 0)
455 {
456 // intensity normalization
457 data_point_cumul.y *= 100.0 / m_accumulationTime;
458
459
460 // mz calibration
461 data_point_cumul.x =
462 mz_calibration_p->getMzFromTofIndex(data_point_cumul.x);
463 local_trace.push_back(data_point_cumul);
464 }
465
466 local_trace.sortX();
467 qDebug();
468 // qDebug();
469 return local_trace;
470}
pappso_double x
Definition datapoint.h:23
pappso_double y
Definition datapoint.h:24

References getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), m_accumulationTime, pappso::Trace::sortX(), pappso::DataPoint::x, and pappso::DataPoint::y.

◆ getVoltageTransformation()

double pappso::TimsFrameBase::getVoltageTransformation ( std::size_t  scanNum) const

get voltage for a given scan number

Parameters
scanNumscan number in the frame in the order it lies in binary file, from 0 to N-1
Returns
double volt measure

Definition at line 271 of file timsframebase.cpp.

272{
273 double v = m_timsDvStart +
274 m_timsSlope * ((double)scanNum - m_timsTtrans - m_timsNdelay);
275
276 if(v < m_timsVmin)
277 {
279 QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "
280 "calibration, v < m_timsVmin"));
281 }
282
283
284 if(v > m_timsVmax)
285 {
287 QObject::tr("ERROR in TimsFrame::getVoltageTransformation invalid tims "
288 "calibration, v > m_timsVmax"));
289 }
290 return v;
291}

References m_timsDvStart, m_timsNdelay, m_timsSlope, m_timsTtrans, m_timsVmax, and m_timsVmin.

Referenced by getOneOverK0Transformation().

◆ hasSameCalibrationData()

bool pappso::TimsFrameBase::hasSameCalibrationData ( const TimsFrameBase other) const
virtual

tells if 2 tims frame has the same calibration data Usefull to know if raw data can be handled between frames

Definition at line 318 of file timsframebase.cpp.

319{
320 if((m_timsDvStart == other.m_timsDvStart) &&
321 (m_timsTtrans == other.m_timsTtrans) &&
322 (m_timsNdelay == other.m_timsNdelay) && (m_timsVmin == other.m_timsVmin) &&
323 (m_timsVmax == other.m_timsVmax) && (m_timsC6 == other.m_timsC6) &&
324 (m_timsC7 == other.m_timsC7) && (m_timsSlope == other.m_timsSlope))
325 {
326 return true;
327 }
328 return false;
329}

References m_timsC6, m_timsC7, m_timsDvStart, m_timsNdelay, m_timsSlope, m_timsTtrans, m_timsVmax, and m_timsVmin.

◆ setAccumulationTime()

void pappso::TimsFrameBase::setAccumulationTime ( double  accumulation_time_ms)

Definition at line 56 of file timsframebase.cpp.

57{
58 m_accumulationTime = accumulation_time_ms;
59}

References m_accumulationTime.

◆ setMsMsType()

void pappso::TimsFrameBase::setMsMsType ( quint8  type)

Definition at line 213 of file timsframebase.cpp.

214{
215
216 qDebug() << " m_msMsType=" << type;
217 m_msMsType = type;
218}

References m_msMsType.

◆ setMzCalibration()

void pappso::TimsFrameBase::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 
)

Definition at line 63 of file timsframebase.cpp.

76{
77
78 /* MzCalibrationModel1 mzCalibration(temperature_correction,
79 digitizerTimebase,
80 digitizerDelay,
81 C0,
82 C1,
83 C2,
84 C3,
85 C4);
86 */
87 msp_mzCalibration = std::make_shared<MzCalibrationModel1>(T1_frame,
88 T2_frame,
89 digitizerTimebase,
90 digitizerDelay,
91 C0,
92 C1,
93 C2,
94 C3,
95 C4,
96 T1_ref,
97 T2_ref,
98 dC1,
99 dC2);
100}

References msp_mzCalibration.

◆ setMzCalibrationInterfaceSPtr()

void pappso::TimsFrameBase::setMzCalibrationInterfaceSPtr ( MzCalibrationInterfaceSPtr  mzCalibration)

Definition at line 488 of file timsframebase.cpp.

490{
491
492 if(mzCalibration == nullptr)
493 {
494
496 QObject::tr("ERROR in %1, %2, %3 msp_mzCalibration is null")
497 .arg(__FILE__)
498 .arg(__FUNCTION__)
499 .arg(__LINE__));
500 }
501 msp_mzCalibration = mzCalibration;
502}

References msp_mzCalibration.

◆ setTime()

void pappso::TimsFrameBase::setTime ( double  time)

Definition at line 207 of file timsframebase.cpp.

208{
209 m_time = time;
210}

References m_time.

◆ setTimsCalibration()

void pappso::TimsFrameBase::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 
)

Definition at line 240 of file timsframebase.cpp.

251{
252 if(tims_model_type != 2)
253 {
254 throw pappso::PappsoException(QObject::tr(
255 "ERROR in TimsFrame::setTimsCalibration tims_model_type != 2"));
256 }
257 m_timsDvStart = C2; // C2 from TimsCalibration
258 m_timsTtrans = C4; // C4 from TimsCalibration
259 m_timsNdelay = C0; // C0 from TimsCalibration
260 m_timsVmin = C8; // C8 from TimsCalibration
261 m_timsVmax = C9; // C9 from TimsCalibration
262 m_timsC6 = C6;
263 m_timsC7 = C7;
264
265
267 (C3 - m_timsDvStart) / C1; // //C3 from TimsCalibration // C2 from
268 // TimsCalibration // C1 from TimsCalibration
269}

References m_timsC6, m_timsC7, m_timsDvStart, m_timsNdelay, m_timsSlope, m_timsTtrans, m_timsVmax, and m_timsVmin.

Member Data Documentation

◆ m_accumulationTime

◆ m_msMsType

quint8 pappso::TimsFrameBase::m_msMsType = 0
protected

Definition at line 284 of file timsframebase.h.

Referenced by getMsLevel(), and setMsMsType().

◆ m_scanNumber

◆ m_time

double pappso::TimsFrameBase::m_time = 0
protected

retention time

Definition at line 288 of file timsframebase.h.

Referenced by pappso::TimsFrame::extractTimsXicListInRtRange(), getTime(), and setTime().

◆ m_timsC6

double pappso::TimsFrameBase::m_timsC6 = 0
protected

◆ m_timsC7

double pappso::TimsFrameBase::m_timsC7 = 0
protected

◆ m_timsDvStart

double pappso::TimsFrameBase::m_timsDvStart = 0
protected

◆ m_timsId

std::size_t pappso::TimsFrameBase::m_timsId
protected

Tims frame database id (the SQL identifier of this frame)

Warning
in sqlite, there is another field called TimsId : this is not that, because it is in fact an offset in bytes in the binary file.

Definition at line 278 of file timsframebase.h.

Referenced by pappso::TimsFrame::TimsFrame(), TimsFrameBase(), pappso::TimsFrameType1::TimsFrameType1(), getId(), and pappso::TimsFrameType1::lzfDecompressScan().

◆ m_timsNdelay

double pappso::TimsFrameBase::m_timsNdelay = 0
protected

◆ m_timsSlope

double pappso::TimsFrameBase::m_timsSlope
protected

◆ m_timsTtrans

double pappso::TimsFrameBase::m_timsTtrans = 0
protected

◆ m_timsVmax

double pappso::TimsFrameBase::m_timsVmax = 0
protected

◆ m_timsVmin

double pappso::TimsFrameBase::m_timsVmin = 0
protected

◆ msp_mzCalibration

MzCalibrationInterfaceSPtr pappso::TimsFrameBase::msp_mzCalibration = nullptr
protected

The documentation for this class was generated from the following files: