pappso::TimsFrame Class Reference

#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)
	~TimsFrame ()
virtual std::size_t	getNbrPeaks (std::size_t scanNum) const override
virtual Trace	cumulateScanToTrace (std::size_t scanNumBegin, std::size_t scanNumEnd) const override
	cumulate scan list into a trace More...
virtual void	cumulateScansInRawMap (std::map< quint32, quint32 > &rawSpectrum, std::size_t scanNumBegin, std::size_t scanNumEnd) const override
	cumulate scan list into a trace into a raw spectrum map More...
void	cumulateScans (std::size_t scanNumBegin, std::size_t scanNumEnd, std::map< quint32, quint32 > &accumulate_into) const
	cumulate a scan list into a map of integers More...
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 More...
std::vector< quint32 >	getScanIntensities (std::size_t scanNum) const
	get raw intensities without transformation from one scan it needs intensity normalization More...
pappso::MassSpectrumCstSPtr	getMassSpectrumCstSPtr (std::size_t scanNum) const
	get the mass spectrum corresponding to a scan number More...
virtual pappso::MassSpectrumSPtr	getMassSpectrumSPtr (std::size_t scanNum) const override
Public Member Functions inherited from pappso::TimsFrameBase
	TimsFrameBase (std::size_t timsId, quint32 scanNum)
	constructor for binary independant tims frame More...
	TimsFrameBase (const TimsFrameBase &other)
	~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 More...
bool	checkScanNum (std::size_t scanNum) const
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 More...
double	getOneOverK0Transformation (std::size_t scanNum) const
	get 1/K0 value of a given scan (mobility value) More...
std::size_t	getScanNumFromOneOverK0 (double one_over_k0) const
	get the scan number from a given 1/Ko mobility value More...
double	getVoltageTransformation (std::size_t scanNum) const
pappso::Trace	getTraceFromCumulatedScans (std::map< quint32, quint32 > &accumulated_scans) const
	transform accumulation of raw scans into a real mass spectrum More...
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 More...
virtual const MzCalibrationInterfaceSPtr &	getMzCalibrationInterfaceSPtr () const final
	get the MzCalibration model to compute mz and TOF for this frame More...
void	setMzCalibrationInterfaceSPtr (MzCalibrationInterfaceSPtr mzCalibration)

Protected Member Functions
void	extractTimsXicListInRtRange (std::vector< TimsXicStructure >::iterator &itXicListbegin, std::vector< TimsXicStructure >::iterator &itXicListend, XicExtractMethod method) const

Private Member Functions
void	unshufflePacket (const char *src)
std::size_t	getScanOffset (std::size_t scanNum) const
void	cumulateScan (std::size_t scanNum, std::map< quint32, quint32 > &accumulate_into) const
	cumulate a scan into a map More...
pappso::TraceSPtr	getRawTraceSPtr (std::size_t scanNum) const

Private Attributes
friend	TimsDirectXicExtractor
QByteArray	m_timsDataFrame

Additional Inherited Members
Protected Attributes inherited from pappso::TimsFrameBase
quint32	m_scanNumber
	total number of scans contained in this frame More...
std::size_t	m_timsId
	Tims frame database id (the SQL identifier of this frame) More...
double	m_accumulationTime = 0
	accumulation time in milliseconds More...
quint8	m_msMsType = 0
double	m_time = 0
	retention time More...
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 52 of file timsframe.h.

Constructor & Destructor Documentation

TimsFrame() [1/2]

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

Default constructor

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_timsDataFrame.resize(len);
 
  if(p_bytes != nullptr)
    {
      unshufflePacket(p_bytes);
    }
  else
    {
      if(m_scanNumber == 0)
        {
 
          throw pappso::PappsoException(
            QObject::tr("TimsFrame::TimsFrame(%1,%2,nullptr,%3) FAILED")
              .arg(m_timsId)
              .arg(m_scanNumber)
              .arg(len));
        }
    }
}

References pappso::TimsFrameBase::m_scanNumber, m_timsDataFrame, pappso::TimsFrameBase::m_timsId, and unshufflePacket().

TimsFrame() [2/2]

pappso::TimsFrame::TimsFrame

(

const TimsFrame &

other

)

Copy constructor

Parameters

other

TODO

Definition at line 88 of file timsframe.cpp.

                                           : TimsFrameBase(other)
{
}

~TimsFrame()

pappso::TimsFrame::~TimsFrame

(

)

Destructor

Definition at line 92 of file timsframe.cpp.

{
}

Member Function Documentation

cumulateScan()

void pappso::TimsFrame::cumulateScan ( std::size_t  scanNum, std::map< quint32, quint32 > &  accumulate_into  ) const

private

cumulate a scan into a map

Definition at line 216 of file timsframe.cpp.

{
  qDebug();
 
  if(m_timsDataFrame.size() == 0)
    return;
  // checkScanNum(scanNum);
 
 
  std::size_t size = getNbrPeaks(scanNum);
 
  std::size_t offset = getScanOffset(scanNum);
 
  qint32 previous = -1;
  for(std::size_t i = 0; i < size; i++)
    {
      quint32 x =
        (*(quint32 *)((m_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
         previous);
      quint32 y = (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) +
                                (i * 8) + 4));
 
      previous = x;
 
      auto ret = accumulate_into.insert(std::pair<quint32, quint32>(x, y));
 
      if(ret.second == false)
        {
          // already existed : cumulate
          ret.first->second += y;
        }
    }
  qDebug();
}

References getNbrPeaks(), getScanOffset(), m_timsDataFrame, and pappso::y.

Referenced by cumulateScansInRawMap(), and cumulateScanToTrace().

cumulateScans()

void pappso::TimsFrame::cumulateScans	(	std::size_t	scanNumBegin,
		std::size_t	scanNumEnd,
		std::map< quint32, quint32 > &	accumulate_into
	)		const

cumulate a scan list into a map of integers

Parameters

scanNumBegin	first scan to cumulate
scanNumEnd	last scan to cumulate
accumulate_into	map of x and y integer values

cumulateScansInRawMap()

void pappso::TimsFrame::cumulateScansInRawMap ( std::map< quint32, quint32 > &  rawSpectrum, std::size_t  scanNumBegin, std::size_t  scanNumEnd  ) 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 310 of file timsframe.cpp.

{
  qDebug();
 
  if(m_timsDataFrame.size() == 0)
    return;
  try
    {
 
      std::size_t imax = scanNumEnd + 1;
      qDebug();
      for(std::size_t i = scanNumBegin; i < imax; 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(scanNumBegin)
                    .arg(scanNumEnd)
                    .arg(error.what());
    }
}

References cumulateScan(), and m_timsDataFrame.

cumulateScanToTrace()

Trace pappso::TimsFrame::cumulateScanToTrace ( std::size_t  scanNumBegin, std::size_t  scanNumEnd  ) 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 254 of file timsframe.cpp.

{
  qDebug();
 
  Trace new_trace;
 
  try
    {
      if(m_timsDataFrame.size() == 0)
        return new_trace;
      std::map<quint32, quint32> raw_spectrum;
      // double local_accumulationTime = 0;
 
      std::size_t imax = scanNumEnd + 1;
      qDebug();
      for(std::size_t i = scanNumBegin; i < imax; 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(std::pair<quint32, quint32> pair_tof_intensity : raw_spectrum)
        {
          data_point_cumul.x =
            mz_calibration_p->getMzFromTofIndex(pair_tof_intensity.first);
          // normalization
          data_point_cumul.y =
            pair_tof_intensity.second * ((double)100.0 / m_accumulationTime);
          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(scanNumBegin, scanNumEnd)
                    .arg(error.what());
    }
  return new_trace;
}

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

extractTimsXicListInRtRange()

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

protected

Definition at line 404 of file timsframe.cpp.

{
  std::vector<TimsFrame::XicComputeStructure> tmp_xic_list;
 
  for(auto it = itXicListbegin; it != itXicListend; it++)
    {
      tmp_xic_list.push_back(TimsFrame::XicComputeStructure(this, *it));
    }
  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++)
        {
          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);
      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 == XicExtractMethod::max)
                {
                  tmp_xic_struct.tmpIntensity +=
                    ms_spectrum.get()->maxY(tmp_xic_struct.mzIndexLowerBound,
                                            tmp_xic_struct.mzIndexUpperBound);
                }
              else
                {
                  // sum
                  tmp_xic_struct.tmpIntensity +=
                    ms_spectrum.get()->sumY(tmp_xic_struct.mzIndexLowerBound,
                                            tmp_xic_struct.mzIndexUpperBound);
                }
            }
        }
      it_scan_num++;
    }
 
  for(auto &&tmp_xic_struct : tmp_xic_list)
    {
      if(tmp_xic_struct.tmpIntensity != 0)
        {
          tmp_xic_struct.xic_ptr->push_back(
            {m_time, tmp_xic_struct.tmpIntensity});
        }
    }
}

References getRawTraceSPtr(), pappso::TimsFrameBase::m_time, and pappso::sum.

getMassSpectrumCstSPtr()

pappso::MassSpectrumCstSPtr pappso::TimsFrame::getMassSpectrumCstSPtr

(

std::size_t

scanNum

)

const

get the mass spectrum corresponding to a scan number

Parameters

scanNum

the scan number to retrieve

Definition at line 344 of file timsframe.cpp.

{
  qDebug();
  return getMassSpectrumSPtr(scanNum);
}

References getMassSpectrumSPtr().

getMassSpectrumSPtr()

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

overridevirtual

Reimplemented from pappso::TimsFrameBase.

Definition at line 351 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_timsDataFrame.size() == 0)
    return mass_spectrum_sptr;
  qDebug();
 
  std::size_t size = getNbrPeaks(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_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
         previous);
      data_point.y = (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) +
                                   (i * 8) + 4));
 
      // intensity normalization
      data_point.y *= 100.0 / m_accumulationTime;
 
      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(), getNbrPeaks(), getScanOffset(), pappso::TimsFrameBase::m_accumulationTime, m_timsDataFrame, pappso::DataPoint::x, and pappso::DataPoint::y.

Referenced by getMassSpectrumCstSPtr().

getNbrPeaks()

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

overridevirtual

Reimplemented from pappso::TimsFrameBase.

Definition at line 125 of file timsframe.cpp.

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

References pappso::TimsFrameBase::checkScanNum(), pappso::TimsFrameBase::m_scanNumber, and m_timsDataFrame.

Referenced by cumulateScan(), getMassSpectrumSPtr(), getRawTraceSPtr(), getScanIndexList(), and getScanIntensities().

getRawTraceSPtr()

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

private

Definition at line 476 of file timsframe.cpp.

{
 
  qDebug();
 
  pappso::TraceSPtr trace_sptr = std::make_shared<pappso::Trace>();
  // std::vector<DataPoint>
 
  if(m_timsDataFrame.size() == 0)
    return trace_sptr;
  qDebug();
 
  std::size_t size = getNbrPeaks(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_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
         previous),
        (*(quint32 *)(m_timsDataFrame.constData() + (offset * 4) + (i * 8) +
                      4)));
 
      // intensity normalization
      data_point.y *= 100.0 / m_accumulationTime;
 
      previous = data_point.x;
    }
  qDebug();
  return trace_sptr;
}

References getNbrPeaks(), getScanOffset(), pappso::TimsFrameBase::m_accumulationTime, m_timsDataFrame, pappso::DataPoint::x, and pappso::DataPoint::y.

Referenced by extractTimsXicListInRtRange().

getScanIndexList()

std::vector< quint32 > pappso::TimsFrame::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

Definition at line 167 of file timsframe.cpp.

{
  qDebug();
  checkScanNum(scanNum);
  std::vector<quint32> scan_tof;
 
  if(m_timsDataFrame.size() == 0)
    return scan_tof;
  scan_tof.resize(getNbrPeaks(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_timsDataFrame.constData() + (offset * 4) + (i * 8))) +
        previous;
      previous = scan_tof[i];
    }
  qDebug();
  return scan_tof;
}

References pappso::TimsFrameBase::checkScanNum(), getNbrPeaks(), getScanOffset(), and m_timsDataFrame.

getScanIntensities()

std::vector< quint32 > pappso::TimsFrame::getScanIntensities

(

std::size_t

scanNum

)

const

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

Definition at line 192 of file timsframe.cpp.

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

References pappso::TimsFrameBase::checkScanNum(), getNbrPeaks(), getScanOffset(), and m_timsDataFrame.

getScanOffset()

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

private

Definition at line 155 of file timsframe.cpp.

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

References m_timsDataFrame.

Referenced by cumulateScan(), getMassSpectrumSPtr(), getRawTraceSPtr(), getScanIndexList(), and getScanIntensities().

unshufflePacket()

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

private

Definition at line 98 of file timsframe.cpp.

{
  qDebug();
  quint64 len = m_timsDataFrame.size();
  if(len % 4 != 0)
    {
      throw pappso::PappsoException(
        QObject::tr("TimsFrame::unshufflePacket error: len%4 != 0"));
    }
 
  quint64 nb_uint4 = len / 4;
 
  char *dest         = m_timsDataFrame.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_timsDataFrame.

Referenced by TimsFrame().

Member Data Documentation

m_timsDataFrame

QByteArray pappso::TimsFrame::m_timsDataFrame

private

Definition at line 158 of file timsframe.h.

Referenced by TimsFrame(), cumulateScan(), cumulateScansInRawMap(), cumulateScanToTrace(), getMassSpectrumSPtr(), getNbrPeaks(), getRawTraceSPtr(), getScanIndexList(), getScanIntensities(), getScanOffset(), and unshufflePacket().

TimsDirectXicExtractor

friend pappso::TimsFrame::TimsDirectXicExtractor

private

Definition at line 54 of file timsframe.h.

---

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

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