#include <timsframe.h>

Inheritance diagram for pappso::TimsFrame:

Classes
struct	XicComputeStructure

Public Member Functions
	TimsFrame (std::size_t timsId, quint32 scanNum, char *p_bytes, std::size_t len)
	TimsFrame (const TimsFrame &other)
virtual	~TimsFrame ()
virtual std::size_t	getScanPeakCount (std::size_t scanIndex) const override
	get the number of peaks in this spectrum need the binary file
virtual Trace	cumulateScansToTrace (std::size_t scanIndexBegin, std::size_t scanIndexEnd) const override
	cumulate scan list into a trace
virtual Trace	combineScansToTraceWithDowngradedMzResolution (std::size_t mzindex_merge_window, std::size_t scanNumBegin, std::size_t scanNumEnd, quint32 &mz_minimum_index, quint32 &mz_maximum_index) const override
	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
virtual Trace	combineScansToTraceWithDowngradedMzResolution2 (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 override
	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
void	combineScansInTofIndexIntensityMap (TimsDataFastMap &rawSpectrum, std::size_t scan_index_begin, std::size_t scan_index_end) const override
	cumulate scan list into a trace into a raw spectrum map
virtual void	combineScansInTofIndexIntensityMap (TimsDataFastMap &tof_index_intensity_map, std::size_t scan_index_begin, std::size_t scan_index_end, quint32 tof_index_begin, quint32 tof_index_end) const override
	cumulate scan list into a trace into a raw spectrum map The intensities are NOT normalized with respect to the frame accumulation time
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 override
	get a single mobility scan m/z + intensities
virtual quint64	cumulateScanIntensities (std::size_t scanNum) const override
virtual quint64	cumulateScanRangeIntensities (std::size_t scanNumBegin, std::size_t scanNumEnd) const override
	...
virtual std::vector< quint32 >	getScanTofIndexList (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::vector< quint32 >	getScanIntensityList (std::size_t scanNum) const override
	get raw intensities without transformation from one scan it needs intensity normalization
virtual pappso::MassSpectrumSPtr	getMassSpectrumSPtr (std::size_t scanNum) const override
	get Mass spectrum with peaks for this scan index need the binary file
virtual std::vector< TofIndexIntensityPair >	getRawValuePairList (std::size_t scanNum, quint32 accepted_tof_index_range_begin, quint32 accepted_tof_index_range_end) const
	get the raw index tof_index and intensities (normalized)
Public Member Functions inherited from pappso::TimsFrameBase
	TimsFrameBase (std::size_t frameId, quint32 scanCount)
	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	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 pappso::MassSpectrumCstSPtr	getMassSpectrumCstSPtr (std::size_t scan_index) const final
	get the mass spectrum corresponding to a scan index
bool	checkScanNum (std::size_t scanNum) const
	check that this scan number exists
void	setAcqDurationInMilliseconds (double acquisition_duration_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	setRtInSeconds (double time)
void	setMsMsType (quint8 type)
unsigned int	getMsLevel () const
double	getRtInSeconds () const
std::size_t	getId () const
double	getDriftTimeInMilliseconds (std::size_t scan_index) const
	get drift time of a scan number in milliseconds
double	getOneOverK0Transformation (std::size_t scan_index) const
	get 1/K0 value of a given scan (mobility value)
std::size_t	getScanIndexFromOneOverK0 (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	getTraceFromTofIndexIntensityMap (TimsDataFastMap &accumulated_scans) const
	transform accumulation of raw scans into a real mass spectrum
virtual const MzCalibrationInterfaceSPtr &	getMzCalibrationInterfaceSPtr () const final
	get the MzCalibration model to compute mz and TOF for this frame
void	setMzCalibrationInterfaceSPtr (MzCalibrationInterfaceSPtr mzCalibration)
virtual Trace	getIonMobilityTraceByTofIndexRange (std::size_t tof_index_begin, std::size_t tof_index_end, Enums::XicExtractMethod method, std::size_t scan_index_begin, std::size_t scan_index_end) const
	get a mobility trace cumulating intensities inside the given mass index range

Protected Member Functions
	TimsFrame (std::size_t timsId, quint32 scanNum)
	constructor for binary independant tims frame
void	extractTimsXicListInRtRange (std::vector< XicCoordTims * >::iterator &itXicListbegin, std::vector< XicCoordTims * >::iterator &itXicListend, Enums::XicExtractMethod method) const
virtual void	cumulateScan (std::size_t scanNum, TimsDataFastMap &accumulate_into) const
	cumulate a scan into a map
virtual void	cumulateScan2 (std::size_t scanNum, TimsDataFastMap &accumulate_into, quint32 accepted_tof_index_range_begin, quint32 accepted_tof_index_range_end) const
virtual pappso::TraceSPtr	getRawTraceSPtr (std::size_t scanNum) const
	get the raw index tof_index and intensities (normalized)
Protected Member Functions inherited from pappso::TimsFrameBase
virtual std::vector< TofIndexIntensityPair > &	downgradeResolutionOfTofIndexIntensityPairList (std::size_t tof_index_merge_window, std::vector< TofIndexIntensityPair > &spectrum) const
	Downgrade the TOF index resolution to lower the number of real m/z computations.

Protected Attributes
QByteArray	m_binaryData
Protected Attributes inherited from pappso::TimsFrameBase
quint32	m_scanCount
	total number of scans contained in this frame
std::size_t	m_frameId
	Tims frame database id (the SQL identifier of this frame).
double	m_acqDurationInMilliseconds = 0
	acquisition duration in milliseconds
quint8	m_msMsType = 0
double	m_rtInSeconds = 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

Private Member Functions
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

Private Attributes
friend	TimsDirectXicExtractor

Detailed Description

Todo: write docs

Definition at line 53 of file timsframe.h.

Constructor & Destructor Documentation

◆ TimsFrame() [1/3]

pappso::TimsFrame::TimsFrame	(	std::size_t	timsId,
		quint32	scanNum,
		char *	p_bytes,
		std::size_t	len )

Parameters

timsId	tims frame id
scanNum	total number of scans in this frame
p_bytes	pointer on the decompressed binary buffer
len	size of the decompressed binary buffer

Definition at line 57 of file timsframe.cpp.

  : TimsFrameBase(timsId, scanNum)
{
  // langella@themis:~/developpement/git/bruker/cbuild$
  // ./src/sample/timsdataSamplePappso
  // /gorgone/pappso/fichiers_fabricants/Bruker/Demo_TimsTOF_juin2019/Samples/1922001/1922001-1_S-415_Pep_Pur-1ul_Slot1-10_1_2088.d/
  // qDebug() << timsId;
 
  m_binaryData.resize(len);
 
  if(p_bytes != nullptr)
    {
      unshufflePacket(p_bytes);
    }
  else
    {
      if(m_scanCount == 0)
        {
 
          throw pappso::PappsoException(QObject::tr("TimsFrame::TimsFrame(%1,%2,nullptr,%3) FAILED")
                                          .arg(m_frameId)
                                          .arg(m_scanCount)
                                          .arg(len));
        }
    }
}

References pappso::TimsFrameBase::TimsFrameBase(), m_binaryData, pappso::TimsFrameBase::m_frameId, pappso::TimsFrameBase::m_scanCount, and unshufflePacket().

Referenced by TimsFrame(), pappso::TimsFrameType1::TimsFrameType1(), pappso::TimsFrameType1::TimsFrameType1(), and pappso::TimsFrame::XicComputeStructure::XicComputeStructure().

◆ TimsFrame() [2/3]

pappso::TimsFrame::TimsFrame ( const TimsFrame & other )

Copy constructor

Parameters

other TODO

Definition at line 84 of file timsframe.cpp.

                                           : TimsFrameBase(other)
{
}

References TimsFrame(), and pappso::TimsFrameBase::TimsFrameBase().

◆ ~TimsFrame()

pappso::TimsFrame::~TimsFrame ( )

virtual

Destructor

Definition at line 88 of file timsframe.cpp.

89{

90}

◆ TimsFrame() [3/3]

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

protected

constructor for binary independant tims frame

Parameters

timsId	tims frame identifier in the database
scanNum	the total number of scans contained in this frame

Definition at line 52 of file timsframe.cpp.

                                                      : TimsFrameBase(timsId, scanNum)
{
  // m_timsDataFrame.resize(10);
}

References pappso::TimsFrameBase::TimsFrameBase().

Member Function Documentation

◆ combineScansInTofIndexIntensityMap() [1/2]

void pappso::TimsFrame::combineScansInTofIndexIntensityMap	(	TimsDataFastMap &	rawSpectrum,
		std::size_t	scan_index_begin,
		std::size_t	scan_index_end ) const

overridevirtual

cumulate scan list into a trace into a raw spectrum map

Parameters

rawSpectrum	simple map of integers to cumulate raw counts
scanNumBegin	first scan to cumulate
scanNumEnd	last scan to cumulate

Reimplemented from pappso::TimsFrameBase.

Definition at line 638 of file timsframe.cpp.

{
  // qDebug() << "begin mobility_scan_begin=" << mobility_scan_begin
  //<< " mobility_scan_end=" << mobility_scan_end;
 
  if(m_binaryData.size() == 0)
    return;
  try
    {
 
      std::size_t mobility_scan_max = scan_index_end + 1;
      // if (mobility_scan_max > m_scanCount) mobility_scan_max = m_scanCount;
      // qDebug();
      for(std::size_t i = scan_index_begin; i < mobility_scan_max; i++)
        {
          // qDebug() << i;
          cumulateScan(i, rawSpectrum);
          // qDebug() << i;
 
          // local_accumulationTime += m_accumulationTime;
        }
    }
 
  catch(std::exception &error)
    {
      qDebug() << QString("Failure in %1 %2 to %3 :\n %4")
                    .arg(__FUNCTION__)
                    .arg(scan_index_begin)
                    .arg(scan_index_end)
                    .arg(error.what());
    }
 
  // qDebug() << "end";
}

References cumulateScan(), and m_binaryData.

◆ combineScansInTofIndexIntensityMap() [2/2]

void pappso::TimsFrame::combineScansInTofIndexIntensityMap	(	TimsDataFastMap &	tof_index_intensity_map,
		std::size_t	scan_index_begin,
		std::size_t	scan_index_end,
		quint32	tof_index_begin,
		quint32	tof_index_end ) const

overridevirtual

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

Parameters

tof_index_intensity_map	simple map of integers to cumulate raw counts
scan_index_begin	scan index in the frame in the order it lies in binary file, from 0 to N-1
scan_index_end	scan index in the frame in the order it lies in binary file, from 0 to N-1
tof_index_begin
tof_index_end

Reimplemented from pappso::TimsFrameBase.

Definition at line 677 of file timsframe.cpp.

{
  // qDebug() << "tof_index_begin=" << tof_index_begin
  //          << " tof_index_end=" << tof_index_end;
 
  //<< " mobility_scan_end=" << mobility_scan_end;
 
  if(m_binaryData.size() == 0)
    return;
  try
    {
 
      std::size_t mobility_scan_max = scan_index_end + 1;
      // if (mobility_scan_max > m_scanCount) mobility_scan_max = m_scanCount;
      // qDebug();
      for(std::size_t i = scan_index_begin; i < mobility_scan_max; i++)
        {
          // qDebug() << i;
          cumulateScan2(i, rawSpectrum, tof_index_begin, tof_index_end);
          // qDebug() << i << rawSpectrum.getTofIndexList().size();
          // local_accumulationTime += m_accumulationTime;
        }
    }
 
  catch(std::exception &error)
    {
      qDebug() << QString("Failure in %1 %2 to %3 :\n %4")
                    .arg(__FUNCTION__)
                    .arg(scan_index_begin)
                    .arg(scan_index_end)
                    .arg(error.what());
    }
 
  // qDebug() << "end";
}

References cumulateScan2(), and m_binaryData.

◆ combineScansToTraceWithDowngradedMzResolution()

Trace pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution	(	std::size_t	mzindex_merge_window,
		std::size_t	scanNumBegin,
		std::size_t	scanNumEnd,
		quint32 &	mz_minimum_index,
		quint32 &	mz_maximum_index ) const

overridevirtual

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_window	width of the mzindex window used to merge all intensities into a single point. This results in faster computing.
scanNumBegin	scan number in the frame in the order it lies in binary file, from 0 to N-1
scanNumEnd	scan number in the frame in the order it lies in binary file, from 0 to N-1
mz_minimum_index	report the minimum mz index contained in the resulting trace
mz_maximum_index	report the maximum mz index contained in the resulting trace

Reimplemented from pappso::TimsFrameBase.

Definition at line 425 of file timsframe.cpp.

{
  // qDebug();
 
  Trace new_trace;
 
  try
    {
      if(m_binaryData.size() == 0)
        {
          qDebug() << "The frame is empty, returning empty trace.";
          return new_trace;
        }
 
      // Allocate a map for (TOF,intensity) pairs to
      // accumulate ion mobility scans.
 
      TimsDataFastMap &raw_spectrum = TimsDataFastMap::getTimsDataFastMapInstance();
      raw_spectrum.clear();
      // double local_accumulationTime = 0;
 
      std::size_t mobility_scan_max = mobility_scan_end + 1;
 
      for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
        {
          // qDebug() << "Going to cumulate currently iterated mobility scan:"
          // << i;
          cumulateScan(i, raw_spectrum);
          // qDebug() << "Done cumulating currently iterated mobility scan:" <<
          // i;
 
          // local_accumulationTime += m_accumulationTime;
        }
 
      // qDebug();
 
      pappso::DataPoint data_point_cumul;
 
      MzCalibrationInterface *mz_calibration_p = getMzCalibrationInterfaceSPtr().get();
 
      // If the caller asks that m/z values be binned larger than they are,
      // ask that the m/z raw map be reduced in resolution.
      if(mz_index_merge_window > 0)
        {
          raw_spectrum.downsizeMzRawMap(mz_index_merge_window);
        }
 
      // Store the first mz index and the last mz index of the current spectrum.
      // The values are set to the out parameters.
      mz_minimum_index_out = std::numeric_limits<quint32>::max();
      mz_maximum_index_out = 0;
 
      // FIXME: donc je comprends que les index sont contigus
      // puisqu'on utilise at(key) ?
      for(quint32 tof_index : raw_spectrum.getTofIndexList())
        {
          if(tof_index > mz_maximum_index_out)
            mz_maximum_index_out = tof_index;
          if(tof_index < mz_minimum_index_out)
            mz_minimum_index_out = tof_index;
 
          // Convert the TOF index to m/z
          data_point_cumul.x = mz_calibration_p->getMzFromTofIndex(tof_index);
 
          // Normalization
          data_point_cumul.y =
            raw_spectrum.readIntensity(tof_index) * ((double)100.0 / m_acqDurationInMilliseconds);
 
          // Finally make the data point a new Trace point.
          new_trace.push_back(data_point_cumul);
        }
 
      // qDebug() << "At this point we have mz_minimum_index_out:"
      //          << mz_minimum_index_out
      //          << "and mz_maximum_index_out:" << mz_maximum_index_out;
 
      // FIXME: this does not seem to be necessary since raw_spectrum is a map
      // with auto-sorting on the keys which are quint32.
      // new_trace.sortX();
 
      // qDebug();
    }
  catch(std::exception &error)
    {
      qDebug() << QString("Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
                    .arg(mobility_scan_begin, mobility_scan_end)
                    .arg(error.what());
    }
 
  // qDebug() << "Returning new trace of size:" << new_trace.size();
 
  return new_trace;
}

References pappso::TimsDataFastMap::clear(), cumulateScan(), pappso::TimsDataFastMap::downsizeMzRawMap(), pappso::TimsFrameBase::getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), pappso::TimsDataFastMap::getTimsDataFastMapInstance(), pappso::TimsDataFastMap::getTofIndexList(), pappso::TimsFrameBase::m_acqDurationInMilliseconds, m_binaryData, pappso::TimsDataFastMap::readIntensity(), pappso::DataPoint::x, and pappso::DataPoint::y.

Referenced by pappso::TimsFramesMsRunReader::readSpectrumCollection2().

◆ combineScansToTraceWithDowngradedMzResolution2()

Trace pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution2	(	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

overridevirtual

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_window	width of the mzindex window used to merge all intensities into a single point. This results in faster computing.
mz_range_begin
mz_range_end
scanNumBegin	scan number in the frame in the order it lies in binary file, from 0 to N-1
scanNumEnd	scan number in the frame in the order it lies in binary file, from 0 to N-1
mz_minimum_index	report the minimum mz index contained in the resulting trace (constrained by the mz_range_begin)
mz_maximum_index	report the maximum mz index contained in the resulting trace (constrained by the mz_range_end)

Reimplemented from pappso::TimsFrameBase.

Definition at line 525 of file timsframe.cpp.

{
  // qDebug() << "Calling cumulateScansToTraceMzDownResolution2 for both mz and "
  //             "im ranges accounting.";
 
  Trace new_trace;
 
  try
    {
      if(m_binaryData.size() == 0)
        {
          qDebug() << "The frame is empty, returning empty trace.";
          return new_trace;
        }
 
      // Allocate a map for (TOF index,intensity) pairs to
      // accumulate ion mobility scans.
 
      TimsDataFastMap &raw_spectrum = TimsDataFastMap::getTimsDataFastMapInstance();
      raw_spectrum.clear();
      // double local_accumulationTime = 0;
 
      std::size_t mobility_scan_max = mobility_scan_end + 1;
 
      quint32 tof_index_for_mz_range_begin =
        getMzCalibrationInterfaceSPtr().get()->getTofIndexFromMz(mz_range_begin);
      quint32 tof_index_for_mz_range_end =
        getMzCalibrationInterfaceSPtr().get()->getTofIndexFromMz(mz_range_end);
 
      // qDebug() << "TOF index for mz range begin:"
      //          << tof_index_for_mz_range_begin;
      // qDebug() << "TOF index for mz range end:"
      //          << tof_index_for_mz_range_end;
 
      for(std::size_t iter = mobility_scan_begin; iter < mobility_scan_max; iter++)
        {
          // qDebug() << "Going to cumulate currently iterated mobility scan:"
          // << iter;
          cumulateScan2(
            iter, raw_spectrum, tof_index_for_mz_range_begin, tof_index_for_mz_range_end);
          // qDebug() << "Done cumulating currently iterated mobility scan:" <<
          // i;
 
          // local_accumulationTime += m_accumulationTime;
        }
 
      // qDebug();
 
      pappso::DataPoint data_point_cumul;
 
      MzCalibrationInterface *mz_calibration_p = getMzCalibrationInterfaceSPtr().get();
 
      // If the caller asks that m/z values be binned larger than they are,
      // ask that the m/z raw map be reduced in resolution.
      if(mz_index_merge_window > 0)
        {
          raw_spectrum.downsizeMzRawMap(mz_index_merge_window);
        }
 
      // Store the first mz index and the last mz index of the current spectrum.
      // The values are set to the out parameters.
      mz_minimum_index_out = std::numeric_limits<quint32>::max();
      mz_maximum_index_out = 0;
 
      // for(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
      for(quint32 tof_index : raw_spectrum.getTofIndexList())
        {
          std::size_t intensity = raw_spectrum.readIntensity(tof_index);
          if(tof_index > mz_maximum_index_out)
            mz_maximum_index_out = tof_index;
          if(tof_index < mz_minimum_index_out)
            mz_minimum_index_out = tof_index;
 
          // Convert the TOF index to m/z
          data_point_cumul.x = mz_calibration_p->getMzFromTofIndex(tof_index);
 
          // Normalization
          data_point_cumul.y = intensity * ((double)100.0 / m_acqDurationInMilliseconds);
 
          // Finally make the data point a new Trace point.
          new_trace.push_back(data_point_cumul);
        }
 
      // qDebug() << "At this point we have mz_minimum_index_out:"
      //          << mz_minimum_index_out
      //          << "and mz_maximum_index_out:" << mz_maximum_index_out;
 
      // FIXME: this does not seem to be necessary since raw_spectrum is a map
      // with auto-sorting on the keys which are quint32.
      // new_trace.sortX();
 
      // qDebug();
    }
  catch(std::exception &error)
    {
      qDebug() << QString("Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
                    .arg(mobility_scan_begin, mobility_scan_end)
                    .arg(error.what());
    }
 
  // qDebug() << "Returning new trace of size:" << new_trace.size();
 
  return new_trace;
}

References pappso::TimsDataFastMap::clear(), cumulateScan2(), pappso::TimsDataFastMap::downsizeMzRawMap(), pappso::TimsFrameBase::getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), pappso::TimsDataFastMap::getTimsDataFastMapInstance(), pappso::TimsDataFastMap::getTofIndexList(), pappso::TimsFrameBase::m_acqDurationInMilliseconds, m_binaryData, pappso::TimsDataFastMap::readIntensity(), pappso::DataPoint::x, and pappso::DataPoint::y.

Referenced by pappso::TimsFramesMsRunReader::readSpectrumCollection2().

◆ cumulateScan()

void pappso::TimsFrame::cumulateScan	(	std::size_t	scanNum,
		TimsDataFastMap &	accumulate_into ) const

protectedvirtual

cumulate a scan into a map

Parameters

scanNum scan number 0 to (m_scanNumber-1)

Reimplemented in pappso::TimsFrameType1.

Definition at line 290 of file timsframe.cpp.

{
  // qDebug();
 
  if(m_binaryData.size() == 0)
    return;
  // qDebug();
 
  // checkScanNum(scanNum);
 
  std::size_t scan_size = getScanPeakCount(scanNum);
 
  std::size_t scan_offset = getScanOffset(scanNum);
 
  qint32 previous = -1;
  for(std::size_t i = 0; i < scan_size; i++)
    {
      quint32 x =
        (*(quint32 *)((m_binaryData.constData() + (scan_offset * 4) + (i * 8))) + previous);
      quint32 y = (*(quint32 *)(m_binaryData.constData() + (scan_offset * 4) + (i * 8) + 4));
 
      previous = x;
      // qDebug() << "x=" << x << " y=" << y;
      accumulate_into.accumulateIntensity(x, y);
    }
 
  qDebug();
}

References pappso::TimsDataFastMap::accumulateIntensity(), getScanOffset(), getScanPeakCount(), m_binaryData, pappso::x, and pappso::y.

Referenced by combineScansInTofIndexIntensityMap(), combineScansToTraceWithDowngradedMzResolution(), and cumulateScansToTrace().

◆ cumulateScan2()

void pappso::TimsFrame::cumulateScan2	(	std::size_t	scanNum,
		TimsDataFastMap &	accumulate_into,
		quint32	accepted_tof_index_range_begin,
		quint32	accepted_tof_index_range_end ) const

protectedvirtual

Reimplemented in pappso::TimsFrameType1.

Definition at line 321 of file timsframe.cpp.

{
  // qDebug();
 
  if(m_binaryData.size() == 0)
    return;
 
  // checkScanNum(scanNum);
 
  std::size_t scan_size   = getScanPeakCount(scanNum);
  std::size_t scan_offset = getScanOffset(scanNum);
  qint32 previous         = -1;
 
  for(std::size_t i = 0; i < scan_size; i++)
    {
      quint32 x =
        (*(quint32 *)((m_binaryData.constData() + (scan_offset * 4) + (i * 8))) + previous);
 
      previous = x;
 
      if(x < accepted_tof_index_range_begin)
        {
 
          // qDebug() << "TOF index still not in range, x:" << x;
          continue;
        }
      if(x > accepted_tof_index_range_end)
        {
          // qDebug() << "TOF index already out of range, x:" << x;
          break;
        }
 
      // qDebug() << "TOF index in range, x:" << x;
 
      quint32 y = (*(quint32 *)(m_binaryData.constData() + (scan_offset * 4) + (i * 8) + 4));
 
      accumulate_into.accumulateIntensity(x, y);
    }
 
  // qDebug();
}

References pappso::TimsDataFastMap::accumulateIntensity(), getScanOffset(), getScanPeakCount(), m_binaryData, pappso::x, and pappso::y.

Referenced by combineScansInTofIndexIntensityMap(), and combineScansToTraceWithDowngradedMzResolution2().

◆ cumulateScanIntensities()

quint64 pappso::TimsFrame::cumulateScanIntensities ( std::size_t scanNum ) const

overridevirtual

Reimplemented from pappso::TimsFrameBase.

Definition at line 208 of file timsframe.cpp.

{
  // qDebug();
 
  quint64 summed_intensities = 0;
 
  if(m_binaryData.size() == 0)
    return summed_intensities;
  // checkScanNum(scanNum);
 
  std::size_t size = getScanPeakCount(scanNum);
 
  std::size_t offset = getScanOffset(scanNum);
 
  qint32 previous = -1;
 
  for(std::size_t i = 0; i < size; i++)
    {
      quint32 x = (*(quint32 *)((m_binaryData.constData() + (offset * 4) + (i * 8))) + previous);
 
      quint32 y = (*(quint32 *)(m_binaryData.constData() + (offset * 4) + (i * 8) + 4));
 
      previous = x;
 
      summed_intensities += y;
    }
 
  // Normalization over the accumulation time for this frame.
  summed_intensities *= ((double)100.0 / m_acqDurationInMilliseconds);
 
  // qDebug();
 
  return summed_intensities;
}

References getScanOffset(), getScanPeakCount(), pappso::TimsFrameBase::m_acqDurationInMilliseconds, m_binaryData, pappso::x, and pappso::y.

Referenced by cumulateScanRangeIntensities().

◆ cumulateScanRangeIntensities()

quint64 pappso::TimsFrame::cumulateScanRangeIntensities	(	std::size_t	mobility_scan_begin,
		std::size_t	mobility_scan_end ) const

overridevirtual

...

Parameters

mobility_scan_begin	p_mobility_scan_begin:...
mobility_scan_end	p_mobility_scan_end:...

Returns: quint64

Reimplemented from pappso::TimsFrameBase.

Definition at line 252 of file timsframe.cpp.

{
  quint64 summed_intensities = 0;
 
  // qDebug() << "begin mobility_scan_begin =" << mobility_scan_begin
  //<< "mobility_scan_end =" << mobility_scan_end;
 
  if(m_binaryData.size() == 0)
    return summed_intensities;
 
  try
    {
      std::size_t mobility_scan_max = mobility_scan_end + 1;
 
      for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
        {
          // qDebug() << i;
          summed_intensities += cumulateScanIntensities(i);
          // qDebug() << i;
        }
    }
  catch(std::exception &error)
    {
      qDebug() << QString("Failure in %1 %2 to %3 :\n %4")
                    .arg(__FUNCTION__)
                    .arg(mobility_scan_begin)
                    .arg(mobility_scan_end)
                    .arg(error.what());
    }
 
  // qDebug() << "end";
 
  return summed_intensities;
}

References cumulateScanIntensities(), and m_binaryData.

Referenced by pappso::TimsFramesMsRunReader::computeTicChromatogram().

◆ cumulateScansToTrace()

Trace pappso::TimsFrame::cumulateScansToTrace	(	std::size_t	scanIndexBegin,
		std::size_t	scanIndexEnd ) const

overridevirtual

cumulate scan list into a trace

Parameters

scanNumBegin	first scan to cumulate
scanNumEnd	last scan to cumulate

Returns: Trace mz and intensity values

Reimplemented from pappso::TimsFrameBase.

Definition at line 368 of file timsframe.cpp.

{
  // qDebug();
 
  Trace new_trace;
 
  try
    {
      if(m_binaryData.size() == 0)
        return new_trace;
      TimsDataFastMap &raw_spectrum = TimsDataFastMap::getTimsDataFastMapInstance();
      raw_spectrum.clear();
      // double local_accumulationTime = 0;
 
      std::size_t mobility_scan_max = mobility_scan_end + 1;
      qDebug();
      for(std::size_t i = mobility_scan_begin; i < mobility_scan_max; i++)
        {
          // qDebug() << i;
          cumulateScan(i, raw_spectrum);
          // qDebug() << i;
 
          // local_accumulationTime += m_accumulationTime;
        }
 
      // qDebug();
 
      pappso::DataPoint data_point_cumul;
 
 
      MzCalibrationInterface *mz_calibration_p = getMzCalibrationInterfaceSPtr().get();
 
 
      for(quint32 tof_index : raw_spectrum.getTofIndexList())
        {
          data_point_cumul.x = mz_calibration_p->getMzFromTofIndex(tof_index);
          // normalization
          data_point_cumul.y =
            raw_spectrum.readIntensity(tof_index) * ((double)100.0 / m_acqDurationInMilliseconds);
          new_trace.push_back(data_point_cumul);
        }
      new_trace.sortX();
 
      // qDebug();
    }
 
  catch(std::exception &error)
    {
      qDebug() << QString("Failure in TimsFrame::cumulateScanToTrace %1 to %2 :\n %3")
                    .arg(mobility_scan_begin, mobility_scan_end)
                    .arg(error.what());
    }
  return new_trace;
}

References pappso::TimsDataFastMap::clear(), cumulateScan(), pappso::TimsFrameBase::getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), pappso::TimsDataFastMap::getTimsDataFastMapInstance(), pappso::TimsDataFastMap::getTofIndexList(), pappso::TimsFrameBase::m_acqDurationInMilliseconds, m_binaryData, pappso::TimsDataFastMap::readIntensity(), pappso::Trace::sortX(), pappso::DataPoint::x, and pappso::DataPoint::y.

◆ extractTimsXicListInRtRange()

void pappso::TimsFrame::extractTimsXicListInRtRange	(	std::vector< XicCoordTims * >::iterator &	itXicListbegin,
		std::vector< XicCoordTims * >::iterator &	itXicListend,
		Enums::XicExtractMethod	method ) const

protected

Definition at line 828 of file timsframe.cpp.

{
  // qDebug() << std::distance(itXicListbegin, itXicListend);
 
  std::vector<TimsFrame::XicComputeStructure> tmp_xic_list;
 
  for(auto it = itXicListbegin; it != itXicListend; it++)
    {
      tmp_xic_list.push_back(TimsFrame::XicComputeStructure(this, **it));
 
      // qDebug() << " tmp_xic_struct.mobilityIndexBegin="
      //          << tmp_xic_list.back().mobilityIndexBegin
      //          << " tmp_xic_struct.mobilityIndexEnd="
      //          << tmp_xic_list.back().mobilityIndexEnd;
 
      // qDebug() << " tmp_xic_struct.mzIndexLowerBound="
      //          << tmp_xic_list.back().mzIndexLowerBound
      //          << " tmp_xic_struct.mzIndexUpperBound="
      //          << tmp_xic_list.back().mzIndexUpperBound;
    }
  if(tmp_xic_list.size() == 0)
    return;
  /*
  std::sort(tmp_xic_list.begin(), tmp_xic_list.end(), [](const
  TimsXicStructure &a, const TimsXicStructure &b) { return
  a.mobilityIndexBegin < b.mobilityIndexBegin;
            });
            */
  std::vector<std::size_t> unique_scan_num_list;
  for(auto &&struct_xic : tmp_xic_list)
    {
      for(std::size_t scan = struct_xic.mobilityIndexBegin;
          (scan <= struct_xic.mobilityIndexEnd) && (scan < m_scanCount);
          scan++)
        {
          unique_scan_num_list.push_back(scan);
        }
    }
  std::sort(unique_scan_num_list.begin(), unique_scan_num_list.end());
  auto it_scan_num_end = std::unique(unique_scan_num_list.begin(), unique_scan_num_list.end());
  auto it_scan_num     = unique_scan_num_list.begin();
 
  while(it_scan_num != it_scan_num_end)
    {
      TraceSPtr ms_spectrum = getRawTraceSPtr(*it_scan_num);
      // qDebug() << ms_spectrum.get()->toString();
      for(auto &&tmp_xic_struct : tmp_xic_list)
        {
          if(((*it_scan_num) >= tmp_xic_struct.mobilityIndexBegin) &&
             ((*it_scan_num) <= tmp_xic_struct.mobilityIndexEnd))
            {
              if(method == Enums::XicExtractMethod::max)
                {
                  tmp_xic_struct.tmpIntensity += ms_spectrum.get()->maxY(
                    tmp_xic_struct.mzIndexLowerBound, tmp_xic_struct.mzIndexUpperBound);
 
                  // qDebug() << "tmp_xic_struct.tmpIntensity="
                  //          << tmp_xic_struct.tmpIntensity;
                }
              else
                {
                  // sum
                  tmp_xic_struct.tmpIntensity += ms_spectrum.get()->sumY(
                    tmp_xic_struct.mzIndexLowerBound, tmp_xic_struct.mzIndexUpperBound);
 
                  // qDebug() << "tmp_xic_struct.tmpIntensity="
                  //          << tmp_xic_struct.tmpIntensity;
                }
            }
        }
      it_scan_num++;
    }
 
  for(auto &&tmp_xic_struct : tmp_xic_list)
    {
      if(tmp_xic_struct.tmpIntensity != 0)
        {
          // qDebug() << tmp_xic_struct.xic_ptr;
 
          tmp_xic_struct.xic_ptr->push_back({m_rtInSeconds, tmp_xic_struct.tmpIntensity});
        }
    }
 
  // qDebug();
}

References getRawTraceSPtr(), pappso::TimsFrameBase::m_rtInSeconds, pappso::TimsFrameBase::m_scanCount, and pappso::Enums::max.

Referenced by pappso::TimsDirectXicExtractor::protectedExtractXicCoordSPtrList().

◆ getMassSpectrumSPtr()

pappso::MassSpectrumSPtr pappso::TimsFrame::getMassSpectrumSPtr ( std::size_t scan_index ) const

overridevirtual

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

Parameters

scan_index scan index in the frame in the order it lies in binary file, from 0 to N-1 (this is the mobility index)

Reimplemented from pappso::TimsFrameBase.

Reimplemented in pappso::TimsFrameType1.

Definition at line 718 of file timsframe.cpp.

{
 
  // qDebug() << " scanNum=" << scanNum;
 
  checkScanNum(scanNum);
 
  // qDebug();
 
  pappso::MassSpectrumSPtr mass_spectrum_sptr = std::make_shared<pappso::MassSpectrum>();
  // std::vector<DataPoint>
 
  if(m_binaryData.size() == 0)
    return mass_spectrum_sptr;
 
  // qDebug();
 
  std::size_t size = getScanPeakCount(scanNum);
 
  std::size_t offset = getScanOffset(scanNum);
 
  MzCalibrationInterface *mz_calibration_p = getMzCalibrationInterfaceSPtr().get();
 
 
  qint32 previous = -1;
  qint32 tof_index;
  // std::vector<quint32> index_list;
  DataPoint data_point;
  for(std::size_t i = 0; i < size; i++)
    {
      tof_index    = (*(quint32 *)((m_binaryData.constData() + (offset * 4) + (i * 8))) + previous);
      data_point.y = (*(quint32 *)(m_binaryData.constData() + (offset * 4) + (i * 8) + 4));
 
      // intensity normalization
      data_point.y *= 100.0 / m_acqDurationInMilliseconds;
 
      previous = tof_index;
 
 
      // mz calibration
      data_point.x = mz_calibration_p->getMzFromTofIndex(tof_index);
      mass_spectrum_sptr.get()->push_back(data_point);
    }
 
  // qDebug();
 
  return mass_spectrum_sptr;
}

References pappso::TimsFrameBase::checkScanNum(), pappso::TimsFrameBase::getMzCalibrationInterfaceSPtr(), pappso::MzCalibrationInterface::getMzFromTofIndex(), getScanOffset(), getScanPeakCount(), pappso::TimsFrameBase::m_acqDurationInMilliseconds, m_binaryData, pappso::DataPoint::x, and pappso::DataPoint::y.

◆ getMobilityScan()

Trace pappso::TimsFrame::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

overridevirtual

get a single mobility scan m/z + intensities

Parameters

scanNum	scan number in the frame in the order it lies in binary file, from 0 to N-1
mzindex_merge_window	width of the mzindex window used to merge all intensities into a single point. This results in faster computing.
mz_range_begin
mz_range_end
mz_minimum_index	report the minimum mz index contained in the resulting trace (constrained by the mz_range_begin)
mz_maximum_index	report the maximum mz index contained in the resulting trace (constrained by the mz_range_end)

Reimplemented from pappso::TimsFrameBase.

Definition at line 769 of file timsframe.cpp.

{
  // qDebug() << "mz_range_begin:" << mz_range_begin
  //          << "mz_range_end:" << mz_range_end
  //          << "mz_index_merge_window:" << mz_index_merge_window;
 
  Trace spectrum;
 
  quint32 mz_index_begin = 0;
  quint32 mz_index_end   = std::numeric_limits<quint32>::max();
 
  if(mz_range_end > 0)
    {
      // qDebug() << "m/z range is requested.";
 
      mz_index_begin = msp_mzCalibration.get()->getTofIndexFromMz(mz_range_begin);
      mz_index_end   = msp_mzCalibration.get()->getTofIndexFromMz(mz_range_end);
    }
 
  // qDebug() << "After conversion of mz indices, mz_index_begin:"
  //          << mz_index_begin << "mz_index_end;" << mz_index_end;
 
  auto raw_spectrum = getRawValuePairList(scanNum, mz_index_begin, mz_index_end);
 
  // qDebug() << " raw_spectrum.size();" << raw_spectrum.size();
 
  if(mz_index_merge_window > 0)
    {
      // qDebug() << "mz_index_merge_window;=" << mz_index_merge_window
      //          << " raw_spectrum.size()=" << raw_spectrum.size();
      raw_spectrum =
        downgradeResolutionOfTofIndexIntensityPairList(mz_index_merge_window, raw_spectrum);
    }
 
  if(raw_spectrum.size() > 0)
    {
      mz_minimum_index_out = raw_spectrum.front().tof_index;
      mz_maximum_index_out = raw_spectrum.back().tof_index;
 
      for(auto &&element : raw_spectrum)
        {
          spectrum.push_back(
            DataPoint(msp_mzCalibration.get()->getMzFromTofIndex(element.tof_index),
                      static_cast<double>(element.intensity_index)));
 
          // intensity normalization
          spectrum.back().y *= 100.0 / m_acqDurationInMilliseconds;
        }
    }
 
  return spectrum;
}

References pappso::TimsFrameBase::downgradeResolutionOfTofIndexIntensityPairList(), getRawValuePairList(), pappso::TimsFrameBase::m_acqDurationInMilliseconds, and pappso::TimsFrameBase::msp_mzCalibration.

Referenced by pappso::TimsMsRunReader::readSpectrumCollection2().

◆ getRawTraceSPtr()

pappso::TraceSPtr pappso::TimsFrame::getRawTraceSPtr ( std::size_t scanNum ) const

protectedvirtual

get the raw index tof_index and intensities (normalized)

Parameters

scanNum the scan number to extract

Returns: trace vector

Reimplemented in pappso::TimsFrameType1.

Definition at line 918 of file timsframe.cpp.

{
 
  // qDebug();
 
  pappso::TraceSPtr trace_sptr = std::make_shared<pappso::Trace>();
  // std::vector<DataPoint>
 
  if(m_binaryData.size() == 0)
    return trace_sptr;
  // qDebug();
 
  std::size_t size = getScanPeakCount(scanNum);
 
  std::size_t offset = getScanOffset(scanNum);
 
  qint32 previous = -1;
  std::vector<quint32> index_list;
  for(std::size_t i = 0; i < size; i++)
    {
      DataPoint data_point(
        (*(quint32 *)((m_binaryData.constData() + (offset * 4) + (i * 8))) + previous),
        (*(quint32 *)(m_binaryData.constData() + (offset * 4) + (i * 8) + 4)));
 
      // intensity normalization
      data_point.y *= 100.0 / m_acqDurationInMilliseconds;
 
      previous = data_point.x;
      trace_sptr.get()->push_back(data_point);
    }
  // qDebug();
  return trace_sptr;
}

References getScanOffset(), getScanPeakCount(), pappso::TimsFrameBase::m_acqDurationInMilliseconds, m_binaryData, pappso::DataPoint::x, and pappso::DataPoint::y.

Referenced by extractTimsXicListInRtRange().

◆ getRawValuePairList()

std::vector< TimsFrame::TofIndexIntensityPair > pappso::TimsFrame::getRawValuePairList	(	std::size_t	scanNum,
		quint32	accepted_tof_index_range_begin,
		quint32	accepted_tof_index_range_end ) const

virtual

get the raw index tof_index and intensities (normalized)

Parameters

scanNum	the scan number to extract
accepted_tof_index_range_begin	mz index begin
accepted_tof_index_range_end	mz index end

Returns: vector of RawValuePair

Reimplemented in pappso::TimsFrameType1.

Definition at line 954 of file timsframe.cpp.

{
  // qDebug() << accepted_tof_index_range_begin;
 
  std::vector<TimsFrame::TofIndexIntensityPair> raw_value_pairs;
  // std::vector<DataPoint>
 
  if(m_binaryData.size() == 0)
    return raw_value_pairs;
  // qDebug();
 
  std::size_t size = getScanPeakCount(scanNum);
 
  std::size_t offset = getScanOffset(scanNum);
 
  // qDebug() << size;
  qint32 previous = -1;
  std::vector<quint32> index_list;
  for(std::size_t i = 0; i < size; i++)
    {
 
      // qDebug() << i;
      TimsFrame::TofIndexIntensityPair raw_value_pair(
        {(*(quint32 *)((m_binaryData.constData() + (offset * 4) + (i * 8))) + previous),
         (*(quint32 *)(m_binaryData.constData() + (offset * 4) + (i * 8) + 4))});
 
      previous = raw_value_pair.tof_index;
      if(raw_value_pair.tof_index < accepted_tof_index_range_begin)
        {
          // qDebug() << "TOF index still not in range, x:" << x;
          continue;
        }
      if(raw_value_pair.tof_index > accepted_tof_index_range_end)
        {
          // qDebug() << "TOF index already out of range, x:" << x;
          break;
        }
 
      raw_value_pairs.push_back(raw_value_pair);
    }
  // qDebug() << raw_value_pairs.size();
  return raw_value_pairs;
}

References getScanOffset(), getScanPeakCount(), m_binaryData, and pappso::TimsFrameBase::TofIndexIntensityPair::tof_index.

Referenced by getMobilityScan().

◆ getScanIntensityList()

std::vector< quint32 > pappso::TimsFrame::getScanIntensityList ( std::size_t scanNum ) const

overridevirtual

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

Reimplemented from pappso::TimsFrameBase.

Reimplemented in pappso::TimsFrameType1.

Definition at line 185 of file timsframe.cpp.

{
  // qDebug();
  checkScanNum(scanNum);
  std::vector<quint32> scan_intensities;
 
  if(m_binaryData.size() == 0)
    return scan_intensities;
 
  scan_intensities.resize(getScanPeakCount(scanNum));
 
  std::size_t offset = getScanOffset(scanNum);
 
  for(std::size_t i = 0; i < scan_intensities.size(); i++)
    {
      scan_intensities[i] = (*(quint32 *)(m_binaryData.constData() + (offset * 4) + (i * 8) + 4));
    }
  // qDebug();
  return scan_intensities;
}

References pappso::TimsFrameBase::checkScanNum(), getScanOffset(), getScanPeakCount(), and m_binaryData.

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

◆ getScanOffset()

std::size_t pappso::TimsFrame::getScanOffset ( std::size_t scanNum ) const

private

get offset for this spectrum in the binary file

Parameters

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

Definition at line 150 of file timsframe.cpp.

{
  std::size_t offset = 0;
  for(std::size_t i = 0; i < (scanNum + 1); i++)
    {
      offset += (*(quint32 *)(m_binaryData.constData() + (i * 4)));
    }
  return offset;
}

References m_binaryData.

Referenced by cumulateScan(), cumulateScan2(), cumulateScanIntensities(), getMassSpectrumSPtr(), getRawTraceSPtr(), getRawValuePairList(), getScanIntensityList(), and getScanTofIndexList().

◆ getScanPeakCount()

std::size_t pappso::TimsFrame::getScanPeakCount ( std::size_t scanIndex ) const

overridevirtual

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

Parameters

scanIndex scan index in the frame in the order it lies in frame's binary data, from 0 to N-1

Reimplemented from pappso::TimsFrameBase.

Reimplemented in pappso::TimsFrameType1.

Definition at line 120 of file timsframe.cpp.

{
  if(m_binaryData.size() == 0)
    return 0;
  /*
    if(scanNum == 0)
      {
        quint32 res = (*(quint32 *)(m_timsDataFrame.constData() + 4)) -
                      (*(quint32 *)(m_timsDataFrame.constData()-4));
        return res / 2;
      }*/
  if(scanNum == (m_scanCount - 1))
    {
      auto nb_uint4 = m_binaryData.size() / 4;
 
      std::size_t cumul = 0;
      for(quint32 i = 0; i < m_scanCount; i++)
        {
          cumul += (*(quint32 *)(m_binaryData.constData() + (i * 4)));
        }
      return (nb_uint4 - cumul) / 2;
    }
  checkScanNum(scanNum);
 
  // quint32 *res = (quint32 *)(m_timsDataFrame.constData() + (scanNum * 4));
  // qDebug() << " res=" << *res;
  return (*(quint32 *)(m_binaryData.constData() + ((scanNum + 1) * 4))) / 2;
}

References pappso::TimsFrameBase::checkScanNum(), m_binaryData, and pappso::TimsFrameBase::m_scanCount.

Referenced by cumulateScan(), cumulateScan2(), cumulateScanIntensities(), getMassSpectrumSPtr(), getRawTraceSPtr(), getRawValuePairList(), getScanIntensityList(), and getScanTofIndexList().

◆ getScanTofIndexList()

std::vector< quint32 > pappso::TimsFrame::getScanTofIndexList ( std::size_t scanNum ) const

overridevirtual

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

Reimplemented from pappso::TimsFrameBase.

Reimplemented in pappso::TimsFrameType1.

Definition at line 162 of file timsframe.cpp.

{
  // qDebug();
  checkScanNum(scanNum);
  std::vector<quint32> scan_tof;
 
  if(m_binaryData.size() == 0)
    return scan_tof;
  scan_tof.resize(getScanPeakCount(scanNum));
 
  std::size_t offset = getScanOffset(scanNum);
 
  qint32 previous = -1;
  for(std::size_t i = 0; i < scan_tof.size(); i++)
    {
      scan_tof[i] = (*(quint32 *)(m_binaryData.constData() + (offset * 4) + (i * 8))) + previous;
      previous    = scan_tof[i];
    }
  // qDebug();
  return scan_tof;
}

References pappso::TimsFrameBase::checkScanNum(), getScanOffset(), getScanPeakCount(), and m_binaryData.

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

◆ unshufflePacket()

void pappso::TimsFrame::unshufflePacket ( const char * src )

private

unshuffle data packet of tims compression type 2

Parameters

src	is a zstd decompressed buffer pointer

Definition at line 94 of file timsframe.cpp.

{
  // qDebug();
  quint64 len = m_binaryData.size();
  if(len % 4 != 0)
    {
      throw pappso::PappsoException(QObject::tr("TimsFrame::unshufflePacket error: len % 4 != 0"));
    }
 
  quint64 nb_uint4 = len / 4;
 
  char *dest         = m_binaryData.data();
  quint64 src_offset = 0;
 
  for(quint64 j = 0; j < 4; j++)
    {
      for(quint64 i = 0; i < nb_uint4; i++)
        {
          dest[(i * 4) + j] = src[src_offset];
          src_offset++;
        }
    }
  // qDebug();
}

References m_binaryData.

Referenced by TimsFrame().

Member Data Documentation

◆ m_binaryData

QByteArray pappso::TimsFrame::m_binaryData

protected

Definition at line 288 of file timsframe.h.

◆ TimsDirectXicExtractor

friend pappso::TimsFrame::TimsDirectXicExtractor

private

Definition at line 55 of file timsframe.h.

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

pappsomspp/core/vendors/tims/timsframe.h
pappsomspp/core/vendors/tims/timsframe.cpp

Classes

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TimsFrame() [1/3]

◆ TimsFrame() [2/3]

◆ ~TimsFrame()

◆ TimsFrame() [3/3]

Member Function Documentation

◆ combineScansInTofIndexIntensityMap() [1/2]

◆ combineScansInTofIndexIntensityMap() [2/2]

◆ combineScansToTraceWithDowngradedMzResolution()

◆ combineScansToTraceWithDowngradedMzResolution2()

◆ cumulateScan()

◆ cumulateScan2()

◆ cumulateScanIntensities()

◆ cumulateScanRangeIntensities()

◆ cumulateScansToTrace()

◆ extractTimsXicListInRtRange()

◆ getMassSpectrumSPtr()

◆ getMobilityScan()

◆ getRawTraceSPtr()

◆ getRawValuePairList()

◆ getScanIntensityList()

◆ getScanOffset()

◆ getScanPeakCount()

◆ getScanTofIndexList()

◆ unshufflePacket()

Member Data Documentation

◆ m_binaryData

◆ TimsDirectXicExtractor