pappso::TimsDataFastMap Class Reference

replacement for std::map More...

#include <timsdatafastmap.h>

Classes
struct	TimsDataFastMapElement

Public Member Functions
std::size_t	accumulateIntensity (quint32 tofIndex, std::size_t intensity)
	accumulates intesity for the given tof index
std::size_t	readIntensity (quint32)
	reads intensity for a tof_index
void	downsizeMzRawMap (std::size_t mzindex_merge_window)
	downsize mz resolution to lower the number of real mz computations
void	builtInCentroid ()
	simple filter to agregate counts on neigbhor mobility slots (+1)
void	removeArtefactualSpike ()
const std::vector< quint32 > &	getTofIndexList () const
void	clear ()

Static Public Member Functions
static TimsDataFastMap &	getTimsDataFastMapInstance ()

Static Public Attributes
static std::map< QThread *, TimsDataFastMap >	m_preAllocatedFastMapPerThread = {}

Private Member Functions
	TimsDataFastMap ()

Private Attributes
std::vector< quint32 >	tofIndexList
std::vector< TimsDataFastMapElement >	mapTofIndexIntensity

Detailed Description

replacement for std::map

Beware to use it carefully : clear the tofIndexList before using it

Definition at line 45 of file timsdatafastmap.h.

Constructor & Destructor Documentation

TimsDataFastMap()

pappso::TimsDataFastMap::TimsDataFastMap ( )

private

Definition at line 53 of file timsdatafastmap.cpp.

{
  // map.resize(500000);
}

Referenced by getTimsDataFastMapInstance().

Member Function Documentation

accumulateIntensity()

std::size_t pappso::TimsDataFastMap::accumulateIntensity	(	quint32	tofIndex,
		std::size_t	intensity )

accumulates intesity for the given tof index

sets the count value on the first access ( first_access is true) and add the tof index to the tofIndexList then increments it if it is called on the same tof index

Definition at line 59 of file timsdatafastmap.cpp.

{
  qDebug();
  try
    {
      TimsDataFastMapElement &map_element = mapTofIndexIntensity.at(key);
 
      if(map_element.first_access)
        {
          map_element.first_access = false;
          map_element.count        = intensity;
          tofIndexList.push_back(key);
        }
      else
        {
          map_element.count += intensity;
        }
      qDebug();
      return map_element.count;
    }
  catch(std::out_of_range &error)
    {
      throw pappso::ExceptionOutOfRange(
        QObject::tr("out of range exception for tof index %1 ").arg(key));
    }
}

References pappso::TimsDataFastMap::TimsDataFastMapElement::count, pappso::TimsDataFastMap::TimsDataFastMapElement::first_access, mapTofIndexIntensity, and tofIndexList.

Referenced by builtInCentroid(), pappso::TimsFrame::cumulateScan(), pappso::TimsFrameType1::cumulateScan(), pappso::TimsFrame::cumulateScan2(), pappso::TimsFrameType1::cumulateScan2(), and downsizeMzRawMap().

builtInCentroid()

void pappso::TimsDataFastMap::builtInCentroid

(

)

simple filter to agregate counts on neigbhor mobility slots (+1)

the map is modified in place

Definition at line 117 of file timsdatafastmap.cpp.

{
  qDebug() << "tofIndexList.size()=" << tofIndexList.size();
  if(tofIndexList.size() > 2)
    {
      std::vector<quint32> tof_index_list_tmp = tofIndexList;
      std::sort(tof_index_list_tmp.begin(), tof_index_list_tmp.end());
 
      tofIndexList.clear();
 
      quint32 previous_tof_index     = tof_index_list_tmp[0];
      std::size_t previous_intensity = readIntensity(previous_tof_index);
      for(std::size_t i = 1; i < tof_index_list_tmp.size(); i++)
        {
          quint32 tof_index = tof_index_list_tmp[i];
          if(previous_tof_index == tof_index - 1)
            {
              std::size_t intensity = readIntensity(tof_index);
              if(previous_intensity > intensity)
                {
                  // flush writing current accumulated intensity
                  accumulateIntensity(previous_tof_index, previous_intensity + intensity);
                  previous_intensity = 0;
                  previous_tof_index = tof_index;
                }
              else
                {
                  // accumulate while intensity increases
                  previous_intensity += intensity;
                  previous_tof_index = tof_index;
                }
            }
          else
            {
              // write accumulated intensity :
              if(previous_intensity > 0)
                {
                  // flush
                  accumulateIntensity(previous_tof_index, previous_intensity);
                }
              previous_tof_index = tof_index;
              previous_intensity = readIntensity(tof_index);
            }
        }
 
      // write remaining intensity :
      if(previous_intensity > 0)
        {
          // flush
          accumulateIntensity(previous_tof_index, previous_intensity);
        }
    }
 
  qDebug() << "tofIndexList.size()=" << tofIndexList.size();
}

References accumulateIntensity(), readIntensity(), and tofIndexList.

Referenced by pappso::TimsDiaSlices::getMs1QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), and pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr().

clear()

void pappso::TimsDataFastMap::clear

(

)

Definition at line 202 of file timsdatafastmap.cpp.

{
  tofIndexList.clear();
}

References tofIndexList.

Referenced by pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution(), pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution2(), pappso::TimsFrame::cumulateScansToTrace(), pappso::TimsDiaSlices::getCombinedMs2ScansByGlobalSliceIndex(), pappso::TimsDdaPrecursors::getCombinedMs2ScansByPrecursorId(), pappso::TimsDiaSlices::getMs1QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), and pappso::TimsData::getScanByGlobalScanIndex().

downsizeMzRawMap()

void pappso::TimsDataFastMap::downsizeMzRawMap

(

std::size_t

mzindex_merge_window

)

downsize mz resolution to lower the number of real mz computations

the map is modified in place

Parameters

mzindex_merge_window

width of the mzindex window used to merge all intensities into a single point. This results in faster computing.

Definition at line 96 of file timsdatafastmap.cpp.

{
  std::vector<std::pair<quint32, std::size_t>> temp_vector;
  for(quint32 tof_index : tofIndexList)
    {
      temp_vector.push_back({tof_index, readIntensity(tof_index)});
    }
 
  tofIndexList.clear();
 
  for(auto &pair_tof_intensity : temp_vector)
    {
 
      quint32 mzkey = (pair_tof_intensity.first / mzindex_merge_window);
      mzkey         = (mzkey * mzindex_merge_window) + (mzindex_merge_window / 2);
 
      accumulateIntensity(mzkey, pair_tof_intensity.second);
    }
}

References accumulateIntensity(), readIntensity(), and tofIndexList.

Referenced by pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution(), and pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution2().

getTimsDataFastMapInstance()

pappso::TimsDataFastMap & pappso::TimsDataFastMap::getTimsDataFastMapInstance ( )

static

Definition at line 40 of file timsdatafastmap.cpp.

{
 
  auto it = TimsDataFastMap::m_preAllocatedFastMapPerThread.insert(
    {QThread::currentThread(), TimsDataFastMap()});
 
  if(it.second)
    {
      it.first->second.mapTofIndexIntensity.resize(500000);
    }
  return it.first->second;
}

References TimsDataFastMap(), and m_preAllocatedFastMapPerThread.

Referenced by pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution(), pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution2(), pappso::TimsFrame::cumulateScansToTrace(), pappso::TimsFrameMobilityTraces::extractMobilityTraces(), pappso::TimsDiaSlices::getCombinedMs2ScansByGlobalSliceIndex(), pappso::TimsDdaPrecursors::getCombinedMs2ScansByPrecursorId(), pappso::TimsDiaSlices::getMs1QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDiaSlices::getMs2QualifiedSpectrumByGlobalSliceIndex(), pappso::TimsDdaPrecursors::getQualifiedMs2MassSpectrumBySpectrumDescr(), and pappso::TimsData::getScanByGlobalScanIndex().

getTofIndexList()

const std::vector< quint32 > & pappso::TimsDataFastMap::getTofIndexList

(

)

const

Definition at line 196 of file timsdatafastmap.cpp.

{
  return tofIndexList;
}

References tofIndexList.

Referenced by pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution(), pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution2(), pappso::TimsFrame::cumulateScansToTrace(), pappso::TimsFrameMobilityTraces::extractMobilityTraces(), and pappso::TimsFrameBase::getTraceFromTofIndexIntensityMap().

readIntensity()

std::size_t pappso::TimsDataFastMap::readIntensity

(

quint32

key

)

reads intensity for a tof_index

reads the cumulated intensity for this tof index and replaces the first access boolean to true. => this is important to reuse the map in an other computation No need to erase the content or initialize it

Definition at line 87 of file timsdatafastmap.cpp.

{
  TimsDataFastMapElement &map_element = mapTofIndexIntensity.at(key);
  // FIXME: why set first_access to true below?
  map_element.first_access = true;
  return map_element.count;
}

References pappso::TimsDataFastMap::TimsDataFastMapElement::count, pappso::TimsDataFastMap::TimsDataFastMapElement::first_access, and mapTofIndexIntensity.

Referenced by builtInCentroid(), pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution(), pappso::TimsFrame::combineScansToTraceWithDowngradedMzResolution2(), pappso::TimsFrame::cumulateScansToTrace(), downsizeMzRawMap(), pappso::TimsFrameMobilityTraces::extractMobilityTraces(), and pappso::TimsFrameBase::getTraceFromTofIndexIntensityMap().

removeArtefactualSpike()

void pappso::TimsDataFastMap::removeArtefactualSpike

(

)

Definition at line 174 of file timsdatafastmap.cpp.

{
 
  std::vector<quint32> tof_index_list_tmp = tofIndexList;
  tofIndexList.clear();
  for(quint32 tof_index : tof_index_list_tmp)
    {
      if((tof_index > 0) && mapTofIndexIntensity[tof_index - 1].first_access &&
         mapTofIndexIntensity[tof_index + 1].first_access &&
         (mapTofIndexIntensity[tof_index].count == 10))
        {
          // this measure is too small and alone : remove it
          mapTofIndexIntensity[tof_index].first_access = true;
        }
      else
        {
          tofIndexList.push_back(tof_index);
        }
    }
}

References mapTofIndexIntensity, and tofIndexList.

Member Data Documentation

m_preAllocatedFastMapPerThread

std::map< QThread *, TimsDataFastMap > pappso::TimsDataFastMap::m_preAllocatedFastMapPerThread = {}

static

Definition at line 48 of file timsdatafastmap.h.

Referenced by getTimsDataFastMapInstance().

mapTofIndexIntensity

std::vector<TimsDataFastMapElement> pappso::TimsDataFastMap::mapTofIndexIntensity

private

Definition at line 106 of file timsdatafastmap.h.

Referenced by accumulateIntensity(), readIntensity(), and removeArtefactualSpike().

tofIndexList

std::vector<quint32> pappso::TimsDataFastMap::tofIndexList

private

Definition at line 104 of file timsdatafastmap.h.

Referenced by accumulateIntensity(), builtInCentroid(), clear(), downsizeMzRawMap(), getTofIndexList(), and removeArtefactualSpike().

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

• pappsomspp/core/vendors/tims/timsdatafastmap.h
• pappsomspp/core/vendors/tims/timsdatafastmap.cpp