PXDHotPixelMaskCalibrationAlgorithm Class Reference

Class implementing PXD hot pixel masking calibration algorithm. More...

#include <PXDHotPixelMaskCalibrationAlgorithm.h>

Inheritance diagram for PXDHotPixelMaskCalibrationAlgorithm:

Public Types
enum	EResult {   c_OK ,   c_Iterate ,   c_NotEnoughData ,   c_Failure ,   c_Undefined }
	The result of calibration. More...

Public Member Functions
	PXDHotPixelMaskCalibrationAlgorithm ()
	Constructor set the prefix to PXDHotPixelMaskCalibrationAlgorithm.
void	setDebugHisto (bool debugHisto)
	setter for m_debugHisto
std::string	getPrefix () const
	Get the prefix used for getting calibration data.
bool	checkPyExpRun (PyObject *pyObj)
	Checks that a PyObject can be successfully converted to an ExpRun type.
Calibration::ExpRun	convertPyExpRun (PyObject *pyObj)
	Performs the conversion of PyObject to ExpRun.
std::string	getCollectorName () const
	Alias for prefix.
void	setPrefix (const std::string &prefix)
	Set the prefix used to identify datastore objects.
void	setInputFileNames (PyObject *inputFileNames)
	Set the input file names used for this algorithm from a Python list.
PyObject *	getInputFileNames ()
	Get the input file names used for this algorithm and pass them out as a Python list of unicode strings.
std::vector< Calibration::ExpRun >	getRunListFromAllData () const
	Get the complete list of runs from inspection of collected data.
RunRange	getRunRangeFromAllData () const
	Get the complete RunRange from inspection of collected data.
IntervalOfValidity	getIovFromAllData () const
	Get the complete IoV from inspection of collected data.
void	fillRunToInputFilesMap ()
	Fill the mapping of ExpRun -> Files.
std::string	getGranularity () const
	Get the granularity of collected data.
EResult	execute (std::vector< Calibration::ExpRun > runs={}, int iteration=0, IntervalOfValidity iov=IntervalOfValidity())
	Runs calibration over vector of runs for a given iteration.
EResult	execute (PyObject *runs, int iteration=0, IntervalOfValidity iov=IntervalOfValidity())
	Runs calibration over Python list of runs. Converts to C++ and then calls the other execute() function.
std::list< Database::DBImportQuery > &	getPayloads ()
	Get constants (in TObjects) for database update from last execution.
std::list< Database::DBImportQuery >	getPayloadValues ()
	Get constants (in TObjects) for database update from last execution but passed by VALUE.
bool	commit ()
	Submit constants from last calibration into database.
bool	commit (std::list< Database::DBImportQuery > payloads)
	Submit constants from a (potentially previous) set of payloads.
const std::string &	getDescription () const
	Get the description of the algoithm (set by developers in constructor)
bool	loadInputJson (const std::string &jsonString)
	Load the m_inputJson variable from a string (useful from Python interface). The rturn bool indicates success or failure.
const std::string	dumpOutputJson () const
	Dump the JSON string of the output JSON object.
const std::vector< Calibration::ExpRun >	findPayloadBoundaries (std::vector< Calibration::ExpRun > runs, int iteration=0)
	Used to discover the ExpRun boundaries that you want the Python CAF to execute on. This is optional and only used in some.
template<>
std::shared_ptr< TTree >	getObjectPtr (const std::string &name, const std::vector< Calibration::ExpRun > &requestedRuns)
	Specialization of getObjectPtr<TTree>.

Public Attributes
bool	forceContinueMasking
	Force continue masking in almost empty runs instead of returning c_NotEnoughData.
int	minEvents
	Minimum number of collected events.
int	minHits
	Minimum median number of hits per pixel needed for dead pixel masking.
float	pixelMultiplier
	The occupancy threshold for masking hot single pixels is the median occupancy x pixelMultiplier.
bool	maskDrains
	Mask hot drain lines with too high average occupancy after single pixel masking.
float	drainMultiplier
	The occupancy threshold for masking hot drains is the median occupancy x drainMultiplier.
bool	maskRows
	Mask hot rows with too high average occupancy after single pixel masking.
float	rowMultiplier
	The occupancy threshold for masking hot rows is the median occupancy x rowMultiplier.
std::string	deadPixelPayloadName
	Payload name for PXDDeadPixelPar used for more defective pixels from damaged gates.
float	inefficientPixelMultiplier
	The occupancy threshold for inefficient (or dead) pixels is the median occupancy x inefficientPixelMultiplier.
int	minInefficientPixels
	The minimum number of inefficient (or dead) pixels per row to define an inefficient row.

Protected Member Functions
virtual EResult	calibrate () override
	Run algo on data.
void	setInputFileNames (std::vector< std::string > inputFileNames)
	Set the input file names used for this algorithm.
virtual bool	isBoundaryRequired (const Calibration::ExpRun &)
	Given the current collector data, make a decision about whether or not this run should be the start of a payload boundary.
virtual void	boundaryFindingSetup (std::vector< Calibration::ExpRun >, int)
	If you need to make some changes to your algorithm class before 'findPayloadBoundaries' is run, make them in this function.
virtual void	boundaryFindingTearDown ()
	Put your algorithm back into a state ready for normal execution if you need to.
const std::vector< Calibration::ExpRun > &	getRunList () const
	Get the list of runs for which calibration is called.
int	getIteration () const
	Get current iteration.
std::vector< std::string >	getVecInputFileNames () const
	Get the input file names used for this algorithm as a STL vector.
template<class T >
std::shared_ptr< T >	getObjectPtr (const std::string &name, const std::vector< Calibration::ExpRun > &requestedRuns)
	Get calibration data object by name and list of runs, the Merge function will be called to generate the overall object.
template<class T >
std::shared_ptr< T >	getObjectPtr (std::string name)
	Get calibration data object (for all runs the calibration is requested for) This function will only work during or after execute() has been called once.
template<>
shared_ptr< TTree >	getObjectPtr (const string &name, const vector< ExpRun > &requestedRuns)
	We cheekily cast the TChain to TTree for the returned pointer so that the user never knows Hopefully this doesn't cause issues if people do low level stuff to the tree...
std::string	getGranularityFromData () const
	Get the granularity of collected data.
void	saveCalibration (TClonesArray *data, const std::string &name)
	Store DBArray payload with given name with default IOV.
void	saveCalibration (TClonesArray *data, const std::string &name, const IntervalOfValidity &iov)
	Store DBArray with given name and custom IOV.
void	saveCalibration (TObject *data)
	Store DB payload with default name and default IOV.
void	saveCalibration (TObject *data, const IntervalOfValidity &iov)
	Store DB payload with default name and custom IOV.
void	saveCalibration (TObject *data, const std::string &name)
	Store DB payload with given name with default IOV.
void	saveCalibration (TObject *data, const std::string &name, const IntervalOfValidity &iov)
	Store DB payload with given name and custom IOV.
void	updateDBObjPtrs (const unsigned int event, const int run, const int experiment)
	Updates any DBObjPtrs by calling update(event) for DBStore.
void	setDescription (const std::string &description)
	Set algorithm description (in constructor)
void	clearCalibrationData ()
	Clear calibration data.
Calibration::ExpRun	getAllGranularityExpRun () const
	Returns the Exp,Run pair that means 'Everything'. Currently unused.
void	resetInputJson ()
	Clears the m_inputJson member variable.
void	resetOutputJson ()
	Clears the m_outputJson member variable.
template<class T >
void	setOutputJsonValue (const std::string &key, const T &value)
	Set a key:value pair for the outputJson object, expected to used interally during calibrate()
template<class T >
const T	getOutputJsonValue (const std::string &key) const
	Get a value using a key from the JSON output object, not sure why you would want to do this.
template<class T >
const T	getInputJsonValue (const std::string &key) const
	Get an input JSON value using a key. The normal exceptions are raised when the key doesn't exist.
const nlohmann::json &	getInputJsonObject () const
	Get the entire top level JSON object. We explicitly say this must be of object type so that we might pick.
bool	inputJsonKeyExists (const std::string &key) const
	Test for a key in the input JSON object.

Protected Attributes
std::vector< Calibration::ExpRun >	m_boundaries
	When using the boundaries functionality from isBoundaryRequired, this is used to store the boundaries. It is cleared when.

Private Member Functions
void	createDebugHistogram ()
	Perform debug histogram file creation.
std::string	getExpRunString (Calibration::ExpRun &expRun) const
	Gets the "exp.run" string repr. of (exp,run)
std::string	getFullObjectPath (const std::string &name, Calibration::ExpRun expRun) const
	constructs the full TDirectory + Key name of an object in a TFile based on its name and exprun

Private Attributes
const unsigned short	c_nVCells = 768
	Number of vCells of Belle II PXD sensors.
const unsigned short	c_nUCells = 250
	Number of uCells of Belle II PXD sensors.
const unsigned short	c_nDrains = 1000
	Number of drain lines of Belle II PXD sensors.
int	m_debugHisto = false
	Set if a debugging histogram should be created in the algorithm output directory.
std::map< VxdID, double >	m_medianOfHitsMap
	map of VxdID to median hits of each sensor
std::shared_ptr< TFile >	m_file
	Pointer for TFile.
std::vector< std::string >	m_inputFileNames
	List of input files to the Algorithm, will initially be user defined but then gets the wildcards expanded during execute()
std::map< Calibration::ExpRun, std::vector< std::string > >	m_runsToInputFiles
	Map of Runs to input files. Gets filled when you call getRunRangeFromAllData, gets cleared when setting input files again.
std::string	m_granularityOfData
	Granularity of input data. This only changes when the input files change so it isn't specific to an execution.
ExecutionData	m_data
	Data specific to a SINGLE execution of the algorithm. Gets reset at the beginning of execution.
std::string	m_description {""}
	Description of the algorithm.
std::string	m_prefix {""}
	The name of the TDirectory the collector objects are contained within.
nlohmann::json	m_jsonExecutionInput = nlohmann::json::object()
	Optional input JSON object used to make decisions about how to execute the algorithm code.
nlohmann::json	m_jsonExecutionOutput = nlohmann::json::object()
	Optional output JSON object that can be set during the execution by the underlying algorithm code.

Static Private Attributes
static const Calibration::ExpRun	m_allExpRun = make_pair(-1, -1)
	allExpRun

Detailed Description

Class implementing PXD hot pixel masking calibration algorithm.

Definition at line 22 of file PXDHotPixelMaskCalibrationAlgorithm.h.

Member Enumeration Documentation

EResult

enum EResult

inherited

The result of calibration.

Enumerator
c_OK	Finished successfuly =0 in Python.
c_Iterate	Needs iteration =1 in Python.
c_NotEnoughData	Needs more data =2 in Python.
c_Failure	Failed =3 in Python.
c_Undefined	Not yet known (before execution) =4 in Python.

Definition at line 40 of file CalibrationAlgorithm.h.

                 {
      c_OK,           
      c_Iterate,      
      c_NotEnoughData,
      c_Failure,      
      c_Undefined     
    };

Constructor & Destructor Documentation

PXDHotPixelMaskCalibrationAlgorithm()

PXDHotPixelMaskCalibrationAlgorithm

(

)

Constructor set the prefix to PXDHotPixelMaskCalibrationAlgorithm.

Definition at line 25 of file PXDHotPixelMaskCalibrationAlgorithm.cc.

                                                                        : CalibrationAlgorithm("PXDHotPixelMaskCollector"),
  forceContinueMasking(false), minEvents(10000), minHits(20), pixelMultiplier(7), maskDrains(true),
  drainMultiplier(7), maskRows(true),  rowMultiplier(7),
  deadPixelPayloadName("PXDDeadPixelPar"),
  inefficientPixelMultiplier(0), minInefficientPixels(250)
{
  setDescription(
    " -------------------------- PXDHotPixelMak Calibration Algorithm ------------------------\n"
    "                                                                                         \n"
    "  Algorithm which masks hot pixels with too large occupancy and dead pixels w/o no hits. \n"
    " ----------------------------------------------------------------------------------------\n"
  );
}

Member Function Documentation

boundaryFindingSetup()

virtual void boundaryFindingSetup ( std::vector< Calibration::ExpRun >  , int    )

inlineprotectedvirtualinherited

If you need to make some changes to your algorithm class before 'findPayloadBoundaries' is run, make them in this function.

Reimplemented in TestBoundarySettingAlgorithm, TestCalibrationAlgorithm, PXDAnalyticGainCalibrationAlgorithm, PXDValidationAlgorithm, SVD3SampleCoGTimeCalibrationAlgorithm, SVD3SampleELSTimeCalibrationAlgorithm, and SVDCoGTimeCalibrationAlgorithm.

Definition at line 252 of file CalibrationAlgorithm.h.

{};

boundaryFindingTearDown()

virtual void boundaryFindingTearDown ( )

inlineprotectedvirtualinherited

Put your algorithm back into a state ready for normal execution if you need to.

Definition at line 257 of file CalibrationAlgorithm.h.

{};

calibrate()

CalibrationAlgorithm::EResult calibrate ( )

overrideprotectedvirtual

Run algo on data.

Implements CalibrationAlgorithm.

Definition at line 93 of file PXDHotPixelMaskCalibrationAlgorithm.cc.

{
 
  auto collector_pxdhits = getObjectPtr<TH1I>("PXDHits");
  auto collector_pxdhitcounts = getObjectPtr<TH1I>("PXDHitCounts");
 
  // Check if there is any PXD hit
  if (!collector_pxdhits) {
    if (forceContinueMasking)
      return c_OK;
    else
      return c_NotEnoughData;
  }
 
  // We should have some minimum number of events
  auto nevents = collector_pxdhits->GetEntries();
  if (nevents < minEvents) {
    if (not forceContinueMasking) {
      B2INFO("Not enough data: Only " << nevents << " events were collected!");
      return c_NotEnoughData;
    } else {
      B2WARNING("Not enough data: Only " << nevents << " events were collected! The masking continous but the mask may be empty.");
    }
  }
 
  B2RESULT("Found total of " << nevents << " events in collected data.");
 
  // Get the total number of PXD hits and sensors
  unsigned long long int nPXDHits = 0;
  int nPXDSensors = 0;
  for (auto sensBin = 1; sensBin <= collector_pxdhitcounts->GetXaxis()->GetNbins(); sensBin++) {
    // The bin label is assumed to be a string representation of VxdID
    string sensorDescr =  collector_pxdhitcounts->GetXaxis()->GetBinLabel(sensBin);
    VxdID id(sensorDescr);
    //Increment number of sensors
    nPXDSensors += 1;
    // Increment number of  of collected hits
    unsigned long long int nSensorHits = collector_pxdhitcounts->GetBinContent(sensBin);
    nPXDHits += nSensorHits;
 
    B2RESULT("Number of hits for sensor sensor=" << id << " is " << nSensorHits);
  }
 
  // We should have enough hits in the PXD before we decide a single sensor is dead
  unsigned long long int minPXDHits =  minHits * nPXDSensors * c_nUCells * c_nVCells;
  if (nPXDHits < minPXDHits) {
    if (not forceContinueMasking) {
      B2INFO("Not enough data: Only " << nPXDHits << " raw hits were collected!");
      return c_NotEnoughData;
    } else {
      B2WARNING("Not enough data: Only " << nPXDHits << " raw hits were collected! The masking continous but the mask may be empty.");
    }
  }
 
  B2RESULT("Found total of " << nPXDHits  << " raw hits in collected data.");
 
  // Check that the median number of hits is large enough
  for (auto sensBin = 1; sensBin <= collector_pxdhitcounts->GetXaxis()->GetNbins(); sensBin++) {
    // The bin label is assumed to be a string representation of VxdID
    string sensorDescr =  collector_pxdhitcounts->GetXaxis()->GetBinLabel(sensBin);
    VxdID id(sensorDescr);
 
    m_medianOfHitsMap[id] = 0.0;
 
    // Get hitmap from collector
    string name = str(format("PXD_%1%_PixelHitmap") % id.getID());
    auto collector_pxdhitmap =  getObjectPtr<TH1I>(name.c_str());
 
    // Check if there was data collected for this sensor
    if (collector_pxdhitmap == nullptr) continue;
 
    // Compute the median number of hits to define a robust baseline for judging a channel fires too often
    int nBins = collector_pxdhitmap->GetXaxis()->GetNbins();
    double prob = 0.5;
    vector<double> hitVec(nBins);
 
    for (auto bin = 1; bin <= nBins; bin++) {
      hitVec[bin - 1] = (double) collector_pxdhitmap->GetBinContent(bin);
    }
    double medianNumberOfHits;
    TMath::Quantiles(nBins, 1, &hitVec[0], &medianNumberOfHits, &prob, kFALSE);
    if (medianNumberOfHits <= 0) {
      B2WARNING("Median number of hits per senor is smaller <1. Raise median to 1 instead.");
      medianNumberOfHits = 1;
    } else {
      B2RESULT("Median of hits is "  << medianNumberOfHits  << " for sensor " << id);
    }
 
    // Keep the median of later use
    m_medianOfHitsMap[id] = medianNumberOfHits;
 
    // Check median number of hits is large enough
    if (medianNumberOfHits < minHits) {
      if (not forceContinueMasking) {
        B2INFO("Not enough data: Median number of his is only  " << medianNumberOfHits << "!");
        return c_NotEnoughData;
      } else {
        B2WARNING("Not enough data: Median number of hits is only  " << medianNumberOfHits <<
                  "! The masking continous but the mask may be empty.");
      }
    }
  }
 
  // This is the occupancy info payload for conditions DB
  PXDOccupancyInfoPar* occupancyInfoPar = new PXDOccupancyInfoPar();
 
  // This is the dead pixels payload for conditions DB
  PXDDeadPixelPar* deadPixelsPar = new PXDDeadPixelPar();
 
  // This is the hot pixel masking payload for conditions DB
  PXDMaskedPixelPar* maskedPixelsPar = new PXDMaskedPixelPar();
 
  // Remember the number of events, helps to judge the reliability of calibrations.
  occupancyInfoPar->setNumberOfEvents(nevents);
 
  // Compute the masks for all sensors
  for (auto sensBin = 1; sensBin <= collector_pxdhitcounts->GetXaxis()->GetNbins(); sensBin++) {
    // The bin label is assumed to be a string representation of VxdID
    string sensorDescr =  collector_pxdhitcounts->GetXaxis()->GetBinLabel(sensBin);
    VxdID id(sensorDescr);
 
    // If we reach here, a sensor with no hits is deemed dead
    int nSensorHits = collector_pxdhitcounts->GetBinContent(sensBin);
    if (nSensorHits == 0)  {
      deadPixelsPar->maskSensor(id.getID());
      continue;
    }
 
    // Get hitmap from collector
    string name = str(format("PXD_%1%_PixelHitmap") % id.getID());
    auto collector_pxdhitmap =  getObjectPtr<TH1I>(name.c_str());
    if (collector_pxdhitmap == nullptr) {
      B2WARNING("Cannot find PixelHitmap although there should be hits. This is strange!");
      continue;
    }
 
    double medianNumberOfHits = m_medianOfHitsMap[id];
    int nBins = collector_pxdhitmap->GetXaxis()->GetNbins();
 
    // Dead pixel masking
    if (medianNumberOfHits >= minHits) {
 
      // Bookkeeping for masking of drains and rows
      vector<int> hitsAlongRow(c_nVCells, 0);
      vector<int> hitsAlongDrain(c_nDrains, 0);
      vector<int> nDeadAlongRow(c_nVCells, 0);
 
      // Mask all single pixels exceeding medianNumberOfHits x multiplier
      double inefficientPixelHitThr = inefficientPixelMultiplier * medianNumberOfHits;
      B2RESULT("Pixel hit threshold for dead rows is "  << inefficientPixelHitThr  << " for sensor " << id);
      // Accumulate hits along drains and rows
      for (auto bin = 1; bin <= nBins; bin++) {
        // Find the current pixel cell
        int pixID = bin - 1;
        int uCell = pixID / c_nVCells;
        int vCell = pixID % c_nVCells;
        int drainID = uCell * 4 + vCell % 4;
        int nhits = collector_pxdhitmap->GetBinContent(bin);
        hitsAlongDrain[drainID] += nhits;
        hitsAlongRow[vCell] += nhits;
        if (inefficientPixelMultiplier > 0 && nhits < inefficientPixelHitThr)
          nDeadAlongRow[vCell] += 1;
      }
 
      // Dead row masking
      B2INFO("Entering masking of dead rows ...");
      for (auto vCell = 0; vCell < c_nVCells; vCell++) {
        // Get number of hits per row
        int nhits = hitsAlongRow[vCell];
        int nDeadPixels = nDeadAlongRow[vCell];
        // Mask dead row
        if (nhits == 0 || nDeadPixels >= minInefficientPixels) {
          deadPixelsPar->maskRow(id.getID(), vCell);
          B2RESULT("Dead row with vCell=" << vCell << " on sensor " << id);
        }
 
      }
 
      // Dead drain masking
      B2INFO("Entering masking of dead drains  ...");
      for (auto drainID = 0; drainID < c_nDrains; drainID++) {
        // Get number of hits per drain
        int nhits = hitsAlongDrain[drainID];
        // Mask dead drain
        if (nhits == 0) {
          deadPixelsPar->maskDrain(id.getID(), drainID);
          B2RESULT("Dead drain line at drainID=" << drainID << " on sensor " << id);
        }
      }
 
      // Dead pixel masking
      B2INFO("Entering masking of single dead pixels  ...");
      for (auto bin = 1; bin <= nBins; bin++) {
        // First, we mask single pixels exceeding hit threshold
        int nhits = collector_pxdhitmap->GetBinContent(bin);
        int pixID = bin - 1;
        int uCell = pixID / c_nVCells;
        int vCell = pixID % c_nVCells;
        int drainID = uCell * 4 + vCell % 4;
        // Mask dead pixel
        if (nhits == 0 && !deadPixelsPar->isDeadRow(id.getID(), vCell) && !deadPixelsPar->isDeadDrain(id.getID(), drainID)) {
          // This pixel is dead, we have to mask it
          deadPixelsPar->maskSinglePixel(id.getID(), pixID);
          B2RESULT("Dead single pixel with ucell=" << uCell << ", vcell=" << vCell << " on sensor " << id);
        }
      }
    }
 
    // Hot pixel masking
 
    // Bookkeeping for masking hot drains
    vector<float> unmaskedHitsAlongDrain(c_nDrains, 0);
    vector<int> unmaskedCellsAlongDrain(c_nDrains, 0);
 
    // Bookkeeping for maskign hot rows
    vector<float> unmaskedHitsAlongRow(c_nVCells, 0);
    vector<int> unmaskedCellsAlongRow(c_nVCells, 0);
 
    // Mask all single pixels exceeding medianNumberOfHits x multiplier
    double pixelHitThr = pixelMultiplier * medianNumberOfHits;
    B2RESULT("Pixel hit threshold is "  << pixelHitThr  << " for sensor " << id);
 
    // Mask all hot pixel for this sensor
    for (auto bin = 1; bin <= nBins; bin++) {
      // Find the current pixel cell
      int pixID = bin - 1;
      int uCell = pixID / c_nVCells;
      int vCell = pixID % c_nVCells;
      int drainID = uCell * 4 + vCell % 4;
 
      // First, we mask single pixels exceeding hit threshold
      float nhits = collector_pxdhitmap->GetBinContent(bin);
      bool masked = false;
 
      if (nhits > pixelHitThr) {
        // This pixel is hot, we have to mask it
        maskedPixelsPar->maskSinglePixel(id.getID(), pixID);
        masked = true;
        B2RESULT("Masking single pixel with ucell=" << uCell << ", vcell=" << vCell << " on sensor " << id);
      }
 
      // Then we accumulate hits along u and v direction for unmasked
      // pixels
      if (not masked) {
        ++unmaskedCellsAlongDrain[drainID];
        unmaskedHitsAlongDrain[drainID] += nhits;
        ++unmaskedCellsAlongRow[vCell];
        unmaskedHitsAlongRow[vCell] += nhits;
      }
    }
 
    if (maskDrains) {
      double drainHitThr = drainMultiplier * medianNumberOfHits;
      B2RESULT("Drain hit threshold is "  << drainHitThr << " for sensor " << id);
 
      for (auto drainID = 0; drainID < c_nDrains; drainID++) {
        if (unmaskedCellsAlongDrain[drainID] > 0) {
          // Compute average number of hits per drain
          float nhits = unmaskedHitsAlongDrain[drainID] / unmaskedCellsAlongDrain[drainID];
          // Mask residual hot drain
          if (nhits > drainHitThr) {
            for (auto iGate = 0; iGate < 192; iGate++) {
              int uCell = drainID / 4;
              int vCell = drainID % 4 + iGate * 4;
              maskedPixelsPar->maskSinglePixel(id.getID(),  uCell * c_nVCells + vCell);
            }
            B2RESULT("Masking drain line with drainID=" << drainID << " on sensor " << id);
          }
        }
      }
    }
 
    if (maskRows) {
      double rowHitThr = rowMultiplier * medianNumberOfHits;
      B2RESULT("Row hit threshold is "  << rowHitThr << " for sensor " << id);
 
      for (auto vCell = 0; vCell < c_nVCells; vCell++) {
        if (unmaskedCellsAlongRow[vCell] > 0) {
          // Compute average number of hits per row
          float nhits = unmaskedHitsAlongRow[vCell] / unmaskedCellsAlongRow[vCell];
          // Mask residual hot row
          if (nhits > rowHitThr) {
            for (auto uCell = 0; uCell < c_nUCells; uCell++)
              maskedPixelsPar->maskSinglePixel(id.getID(),  uCell * c_nVCells + vCell);
 
            B2RESULT("Masking complete row with vCell=" << vCell << " on sensor " << id);
          }
        }
      }
    }
 
    // After the masking is done, we compute the average sensor occupancy after
    // hot pixel masking.
 
    // Count all unmasked hits
    int numberOfUnmaskedHits = 0;
 
    for (auto bin = 1; bin <= nBins; bin++) {
      // Find the current pixel cell
      int pixID = bin - 1;
 
      if (maskedPixelsPar->pixelOK(id.getID(), pixID)) {
        numberOfUnmaskedHits += collector_pxdhitmap->GetBinContent(bin);
      }
    }
 
    // Compute mean occupancy before masking
    float meanOccupancyAfterMasking = (float)numberOfUnmaskedHits / nevents / c_nVCells / c_nUCells;
    B2RESULT("Hotpixel filtered occupancy sensor=" << id << " is " << meanOccupancyAfterMasking);
 
    occupancyInfoPar->setOccupancy(id.getID(), meanOccupancyAfterMasking);
  }
 
  for (auto elem : maskedPixelsPar->getMaskedPixelMap()) {
    auto id = elem.first;
    auto singles = elem.second;
    B2RESULT("SensorID " << VxdID(id) << " has filtered occupancy of " << occupancyInfoPar->getOccupancy(id));
    B2RESULT("SensorID " << VxdID(id) << " has fraction of masked pixels of " << (float)singles.size() / (c_nVCells * c_nUCells));
  }
 
  // Save the hot pixel mask to database. Note that this will set the database object name to the same as the collector but you
  // are free to change it.
  saveCalibration(maskedPixelsPar, "PXDMaskedPixelPar");
  saveCalibration(deadPixelsPar, deadPixelPayloadName);
  saveCalibration(occupancyInfoPar, "PXDOccupancyInfoPar");
 
  // Create debugging histo if we asked for it
  if (m_debugHisto) createDebugHistogram();
 
  B2INFO("PXDHotPixelMask Calibration Successful");
  return c_OK;
}

checkPyExpRun()

bool checkPyExpRun ( PyObject *  pyObj )

inherited

Checks that a PyObject can be successfully converted to an ExpRun type.

Checks if the PyObject can be converted to ExpRun.

Definition at line 28 of file CalibrationAlgorithm.cc.

{
  // Is it a sequence?
  if (PySequence_Check(pyObj)) {
    Py_ssize_t nObj = PySequence_Length(pyObj);
    // Does it have 2 objects in it?
    if (nObj != 2) {
      B2DEBUG(29, "ExpRun was a Python sequence which didn't have exactly 2 entries!");
      return false;
    }
    PyObject* item1, *item2;
    item1 = PySequence_GetItem(pyObj, 0);
    item2 = PySequence_GetItem(pyObj, 1);
    // Did the GetItem work?
    if ((item1 == NULL) || (item2 == NULL)) {
      B2DEBUG(29, "A PyObject pointer was NULL in the sequence");
      return false;
    }
    // Are they longs?
    if (PyLong_Check(item1) && PyLong_Check(item2)) {
      long value1, value2;
      value1 = PyLong_AsLong(item1);
      value2 = PyLong_AsLong(item2);
      if (((value1 == -1) || (value2 == -1)) && PyErr_Occurred()) {
        B2DEBUG(29, "An error occurred while converting the PyLong to long");
        return false;
      }
    } else {
      B2DEBUG(29, "One or more of the PyObjects in the ExpRun wasn't a long");
      return false;
    }
    // Make sure to kill off the reference GetItem gave us responsibility for
    Py_DECREF(item1);
    Py_DECREF(item2);
  } else {
    B2DEBUG(29, "ExpRun was not a Python sequence.");
    return false;
  }
  return true;
}

clearCalibrationData()

void clearCalibrationData ( )

inlineprotectedinherited

Clear calibration data.

Definition at line 324 of file CalibrationAlgorithm.h.

{m_data.clearCalibrationData();}

commit() [1/2]

bool commit ( )

inherited

Submit constants from last calibration into database.

Definition at line 302 of file CalibrationAlgorithm.cc.

{
  if (getPayloads().empty())
    return false;
  list<Database::DBImportQuery> payloads = getPayloads();
  B2INFO("Committing " << payloads.size()  << " payloads to database.");
  return Database::Instance().storeData(payloads);
}

commit() [2/2]

bool commit ( std::list< Database::DBImportQuery >  payloads )

inherited

Submit constants from a (potentially previous) set of payloads.

Definition at line 311 of file CalibrationAlgorithm.cc.

{
  if (payloads.empty())
    return false;
  return Database::Instance().storeData(payloads);
}

convertPyExpRun()

ExpRun convertPyExpRun ( PyObject *  pyObj )

inherited

Performs the conversion of PyObject to ExpRun.

Converts the PyObject to an ExpRun. We've preoviously checked the object so this assumes a lot about the PyObject.

Definition at line 70 of file CalibrationAlgorithm.cc.

{
  ExpRun expRun;
  PyObject* itemExp, *itemRun;
  itemExp = PySequence_GetItem(pyObj, 0);
  itemRun = PySequence_GetItem(pyObj, 1);
  expRun.first = PyLong_AsLong(itemExp);
  Py_DECREF(itemExp);
  expRun.second = PyLong_AsLong(itemRun);
  Py_DECREF(itemRun);
  return expRun;
}

createDebugHistogram()

void createDebugHistogram ( )

private

Perform debug histogram file creation.

Definition at line 39 of file PXDHotPixelMaskCalibrationAlgorithm.cc.

{
  // Run list of current IoV and all runs to be calibrated
  auto expRuns = getRunList();
  auto expRunsAll = getRunListFromAllData();
 
  // Save the current directory to change back later
  TDirectory* currentDir = gDirectory;
 
  // Create TFile if not exist
  if (!m_file) {
    std::string fileName = (this->getPrefix()) + "debug.root";
    B2INFO("Creating file " << fileName);
    m_file = std::make_shared<TFile>(fileName.c_str(), "RECREATE");
  }
 
  //m_file->cd();
  string iov_str = str(format("E%1%_R%2%_E%3%_R%4%") % expRuns.front().first
                       % expRuns.front().second % expRuns.back().first % expRuns.back().second);
  m_file->mkdir(iov_str.c_str());
  m_file->cd(iov_str.c_str());
 
  // Collector info
  auto collector_pxdhits = getObjectPtr<TH1I>("PXDHits");
  auto collector_pxdhitcounts = getObjectPtr<TH1I>("PXDHitCounts");
 
  auto nevents = collector_pxdhits->GetEntries();
 
  for (auto sensBin = 1; sensBin <= collector_pxdhitcounts->GetXaxis()->GetNbins(); sensBin++) {
    string sensorDescr =  collector_pxdhitcounts->GetXaxis()->GetBinLabel(sensBin);
    VxdID id(sensorDescr);
 
    // Get hitmap from collector
    string name = str(format("PXD_%1%_PixelHitmap") % id.getID());
    auto collector_pxdhitmap =  getObjectPtr<TH1I>(name.c_str());
    if (collector_pxdhitmap == nullptr) {
      continue;
    }
    TH1I* debugHisto = new TH1I(*collector_pxdhitmap);
    // Set overflow to total number of events
    debugHisto->SetBinContent(debugHisto->GetNbinsX() + 1, nevents);
    debugHisto->Write();
    delete debugHisto;
  }
 
  // Close TFile
  if (expRuns.back() == expRunsAll.back()) {
    B2INFO("Reached Final ExpRun: (" << expRuns.back().first << ", " << expRuns.back().second << ")");
    m_file->Close();
 
  }
  currentDir->cd();
}

dumpOutputJson()

const std::string dumpOutputJson ( ) const

inlineinherited

Dump the JSON string of the output JSON object.

Definition at line 223 of file CalibrationAlgorithm.h.

{return m_jsonExecutionOutput.dump();}

execute() [1/2]

CalibrationAlgorithm::EResult execute ( PyObject *  runs, int  iteration = 0, IntervalOfValidity  iov = IntervalOfValidity()  )

inherited

Runs calibration over Python list of runs. Converts to C++ and then calls the other execute() function.

Definition at line 83 of file CalibrationAlgorithm.cc.

{
  B2DEBUG(29, "Running execute() using Python Object as input argument");
  // Reset the execution specific data in case the algorithm was previously called
  m_data.reset();
  m_data.setIteration(iteration);
  vector<ExpRun> vecRuns;
  // Is it a list?
  if (PySequence_Check(runs)) {
    boost::python::handle<> handle(boost::python::borrowed(runs));
    boost::python::list listRuns(handle);
 
    int nList = boost::python::len(listRuns);
    for (int iList = 0; iList < nList; ++iList) {
      boost::python::object pyExpRun(listRuns[iList]);
      if (!checkPyExpRun(pyExpRun.ptr())) {
        B2ERROR("Received Python ExpRuns couldn't be converted to C++");
        m_data.setResult(c_Failure);
        return c_Failure;
      } else {
        vecRuns.push_back(convertPyExpRun(pyExpRun.ptr()));
      }
    }
  } else {
    B2ERROR("Tried to set the input runs but we didn't receive a Python sequence object (list,tuple).");
    m_data.setResult(c_Failure);
    return c_Failure;
  }
  return execute(vecRuns, iteration, iov);
}

execute() [2/2]

CalibrationAlgorithm::EResult execute ( std::vector< Calibration::ExpRun >  runs = {}, int  iteration = 0, IntervalOfValidity  iov = IntervalOfValidity()  )

inherited

Runs calibration over vector of runs for a given iteration.

You can also specify the IoV to save the database payload as. By default the Algorithm will create an IoV from your requested ExpRuns, or from the overall ExpRuns of the input data if you haven't specified ExpRuns in this function.

No checks are performed to make sure that a IoV you specify matches the data you ran over, it simply labels the IoV to commit to the database later.

Definition at line 114 of file CalibrationAlgorithm.cc.

{
  // Check if we are calling this function directly and need to reset, or through Python where it was already done.
  if (m_data.getResult() != c_Undefined) {
    m_data.reset();
    m_data.setIteration(iteration);
  }
 
  if (m_inputFileNames.empty()) {
    B2ERROR("There aren't any input files set. Please use CalibrationAlgorithm::setInputFiles()");
    m_data.setResult(c_Failure);
    return c_Failure;
  }
 
  // Did we receive runs to execute over explicitly?
  if (!(runs.empty())) {
    for (auto expRun : runs) {
      B2DEBUG(29, "ExpRun requested = (" << expRun.first << ", " << expRun.second << ")");
    }
    // We've asked explicitly for certain runs, but we should check if the data granularity is 'run'
    if (strcmp(getGranularity().c_str(), "all") == 0) {
      B2ERROR(("The data is collected with granularity=all (exp=-1,run=-1), but you seem to request calibration for specific runs."
               " We'll continue but using ALL the input data given instead of the specific runs requested."));
    }
  } else {
    // If no runs are provided, infer the runs from all collected data
    runs = getRunListFromAllData();
    // Let's check that we have some now
    if (runs.empty()) {
      B2ERROR("No collected data in input files.");
      m_data.setResult(c_Failure);
      return c_Failure;
    }
    for (auto expRun : runs) {
      B2DEBUG(29, "ExpRun requested = (" << expRun.first << ", " << expRun.second << ")");
    }
  }
 
  m_data.setRequestedRuns(runs);
  if (iov.empty()) {
    // If no user specified IoV we use the IoV from the executed run list
    iov = IntervalOfValidity(runs[0].first, runs[0].second, runs[runs.size() - 1].first, runs[runs.size() - 1].second);
  }
  m_data.setRequestedIov(iov);
  // After here, the getObject<...>(...) helpers start to work
 
  CalibrationAlgorithm::EResult result = calibrate();
  m_data.setResult(result);
  return result;
}

fillRunToInputFilesMap()

void fillRunToInputFilesMap ( )

inherited

Fill the mapping of ExpRun -> Files.

Definition at line 330 of file CalibrationAlgorithm.cc.

{
  m_runsToInputFiles.clear();
  // Save TDirectory to change back at the end
  TDirectory* dir = gDirectory;
  RunRange* runRange;
  // Construct the TDirectory name where we expect our objects to be
  string runRangeObjName(getPrefix() + "/" + RUN_RANGE_OBJ_NAME);
  for (const auto& fileName : m_inputFileNames) {
    //Open TFile to get the objects
    unique_ptr<TFile> f;
    f.reset(TFile::Open(fileName.c_str(), "READ"));
    runRange = dynamic_cast<RunRange*>(f->Get(runRangeObjName.c_str()));
    if (runRange) {
      // Insert or extend the run -> file mapping for this ExpRun
      auto expRuns = runRange->getExpRunSet();
      for (const auto& expRun : expRuns) {
        auto runFiles = m_runsToInputFiles.find(expRun);
        if (runFiles != m_runsToInputFiles.end()) {
          (runFiles->second).push_back(fileName);
        } else {
          m_runsToInputFiles.insert(std::make_pair(expRun, std::vector<std::string> {fileName}));
        }
      }
    } else {
      B2WARNING("Missing a RunRange object for file: " << fileName);
    }
  }
  dir->cd();
}

findPayloadBoundaries()

const std::vector< ExpRun > findPayloadBoundaries ( std::vector< Calibration::ExpRun >  runs, int  iteration = 0  )

inherited

Used to discover the ExpRun boundaries that you want the Python CAF to execute on. This is optional and only used in some.

Definition at line 520 of file CalibrationAlgorithm.cc.

{
  m_boundaries.clear();
  if (m_inputFileNames.empty()) {
    B2ERROR("There aren't any input files set. Please use CalibrationAlgorithm::setInputFiles()");
    return m_boundaries;
  }
  // Reset the internal execution data just in case something is hanging around
  m_data.reset();
  if (runs.empty()) {
    // Want to loop over all runs we could possibly know about
    runs = getRunListFromAllData();
  }
  // Let's check that we have some now
  if (runs.empty()) {
    B2ERROR("No collected data in input files.");
    return m_boundaries;
  }
  // In order to find run boundaries we must have collected with data granularity == 'run'
  if (strcmp(getGranularity().c_str(), "all") == 0) {
    B2ERROR("The data is collected with granularity='all' (exp=-1,run=-1), and we can't use that to find run boundaries.");
    return m_boundaries;
  }
  m_data.setIteration(iteration);
  // User defined setup function
  boundaryFindingSetup(runs, iteration);
  std::vector<ExpRun> runList;
  // Loop over run list and call derived class "isBoundaryRequired" member function
  for (auto currentRun : runs) {
    runList.push_back(currentRun);
    m_data.setRequestedRuns(runList);
    // After here, the getObject<...>(...) helpers start to work
    if (isBoundaryRequired(currentRun)) {
      m_boundaries.push_back(currentRun);
    }
    // Only want run-by-run
    runList.clear();
    // Don't want memory hanging around
    m_data.clearCalibrationData();
  }
  m_data.reset();
  boundaryFindingTearDown();
  return m_boundaries;
}

getAllGranularityExpRun()

Calibration::ExpRun getAllGranularityExpRun ( ) const

inlineprotectedinherited

Returns the Exp,Run pair that means 'Everything'. Currently unused.

Definition at line 327 of file CalibrationAlgorithm.h.

{return m_allExpRun;}

getCollectorName()

std::string getCollectorName ( ) const

inlineinherited

Alias for prefix.

For convenience and less writing, we say developers to set this to default collector module name in constructor of base class. One can however use the dublets of collector+algorithm multiple times with different settings. To bind these together correctly, the prefix has to be set the same for algo and collector. So we call the setter setPrefix rather than setModuleName or whatever. This getter will work out of the box for default cases -> return the name of module you have to add to your path to collect data for this algorihtm.

Definition at line 164 of file CalibrationAlgorithm.h.

{return getPrefix();}

getDescription()

const std::string & getDescription ( ) const

inlineinherited

Get the description of the algoithm (set by developers in constructor)

Definition at line 216 of file CalibrationAlgorithm.h.

{return m_description;}

getExpRunString()

string getExpRunString ( Calibration::ExpRun &  expRun ) const

privateinherited

Gets the "exp.run" string repr. of (exp,run)

Definition at line 254 of file CalibrationAlgorithm.cc.

{
  string expRunString;
  expRunString += to_string(expRun.first);
  expRunString += ".";
  expRunString += to_string(expRun.second);
  return expRunString;
}

getFullObjectPath()

string getFullObjectPath ( const std::string &  name, Calibration::ExpRun  expRun  ) const

privateinherited

constructs the full TDirectory + Key name of an object in a TFile based on its name and exprun

Definition at line 263 of file CalibrationAlgorithm.cc.

{
  string dirName = getPrefix() + "/" + name;
  string objName = name + "_" + getExpRunString(expRun);
  return dirName + "/" + objName;
}

getGranularity()

std::string getGranularity ( ) const

inlineinherited

Get the granularity of collected data.

Definition at line 188 of file CalibrationAlgorithm.h.

{return m_granularityOfData;};

getGranularityFromData()

string getGranularityFromData ( ) const

protectedinherited

Get the granularity of collected data.

Definition at line 383 of file CalibrationAlgorithm.cc.

{
  // Save TDirectory to change back at the end
  TDirectory* dir = gDirectory;
  RunRange* runRange;
  string runRangeObjName(getPrefix() + "/" + RUN_RANGE_OBJ_NAME);
  // We only check the first file
  string fileName = m_inputFileNames[0];
  unique_ptr<TFile> f;
  f.reset(TFile::Open(fileName.c_str(), "READ"));
  runRange = dynamic_cast<RunRange*>(f->Get(runRangeObjName.c_str()));
  if (!runRange) {
    B2FATAL("The input file " << fileName << " does not contain a RunRange object at "
            << runRangeObjName << ". Please set your input files to exclude it.");
    return "";
  }
  string granularity = runRange->getGranularity();
  dir->cd();
  return granularity;
}

getInputFileNames()

PyObject * getInputFileNames ( )

inherited

Get the input file names used for this algorithm and pass them out as a Python list of unicode strings.

Definition at line 245 of file CalibrationAlgorithm.cc.

{
  PyObject* objInputFileNames = PyList_New(m_inputFileNames.size());
  for (size_t i = 0; i < m_inputFileNames.size(); ++i) {
    PyList_SetItem(objInputFileNames, i, Py_BuildValue("s", m_inputFileNames[i].c_str()));
  }
  return objInputFileNames;
}

getInputJsonObject()

const nlohmann::json & getInputJsonObject ( ) const

inlineprotectedinherited

Get the entire top level JSON object. We explicitly say this must be of object type so that we might pick.

Definition at line 357 of file CalibrationAlgorithm.h.

{return m_jsonExecutionInput;}

getInputJsonValue()

const T getInputJsonValue ( const std::string &  key ) const

inlineprotectedinherited

Get an input JSON value using a key. The normal exceptions are raised when the key doesn't exist.

Definition at line 350 of file CalibrationAlgorithm.h.

    {
      return m_jsonExecutionInput.at(key);
    }

getIovFromAllData()

IntervalOfValidity getIovFromAllData ( ) const

inherited

Get the complete IoV from inspection of collected data.

Definition at line 325 of file CalibrationAlgorithm.cc.

{
  return getRunRangeFromAllData().getIntervalOfValidity();
}

getIteration()

int getIteration ( ) const

inlineprotectedinherited

Get current iteration.

Definition at line 269 of file CalibrationAlgorithm.h.

{ return m_data.getIteration(); }

getObjectPtr()

std::shared_ptr< T > getObjectPtr ( std::string  name )

inlineprotectedinherited

Get calibration data object (for all runs the calibration is requested for) This function will only work during or after execute() has been called once.

Definition at line 285 of file CalibrationAlgorithm.h.

    {
      if (m_runsToInputFiles.size() == 0)
        fillRunToInputFilesMap();
      return getObjectPtr<T>(name, m_data.getRequestedRuns());
    }

getOutputJsonValue()

const T getOutputJsonValue ( const std::string &  key ) const

inlineprotectedinherited

Get a value using a key from the JSON output object, not sure why you would want to do this.

Definition at line 342 of file CalibrationAlgorithm.h.

    {
      return m_jsonExecutionOutput.at(key);
    }

getPayloads()

std::list< Database::DBImportQuery > & getPayloads ( )

inlineinherited

Get constants (in TObjects) for database update from last execution.

Definition at line 204 of file CalibrationAlgorithm.h.

{return m_data.getPayloads();}

getPayloadValues()

std::list< Database::DBImportQuery > getPayloadValues ( )

inlineinherited

Get constants (in TObjects) for database update from last execution but passed by VALUE.

Definition at line 207 of file CalibrationAlgorithm.h.

{return m_data.getPayloadValues();}

getPrefix()

std::string getPrefix ( ) const

inlineinherited

Get the prefix used for getting calibration data.

Definition at line 146 of file CalibrationAlgorithm.h.

{return m_prefix;}

getRunList()

const std::vector< Calibration::ExpRun > & getRunList ( ) const

inlineprotectedinherited

Get the list of runs for which calibration is called.

Definition at line 266 of file CalibrationAlgorithm.h.

{return m_data.getRequestedRuns();}

getRunListFromAllData()

vector< ExpRun > getRunListFromAllData ( ) const

inherited

Get the complete list of runs from inspection of collected data.

Definition at line 318 of file CalibrationAlgorithm.cc.

{
  RunRange runRange = getRunRangeFromAllData();
  set<ExpRun> expRunSet = runRange.getExpRunSet();
  return vector<ExpRun>(expRunSet.begin(), expRunSet.end());
}

getRunRangeFromAllData()

RunRange getRunRangeFromAllData ( ) const

inherited

Get the complete RunRange from inspection of collected data.

Definition at line 361 of file CalibrationAlgorithm.cc.

{
  // Save TDirectory to change back at the end
  TDirectory* dir = gDirectory;
  RunRange runRange;
  // Construct the TDirectory name where we expect our objects to be
  string runRangeObjName(getPrefix() + "/" + RUN_RANGE_OBJ_NAME);
  for (const auto& fileName : m_inputFileNames) {
    //Open TFile to get the objects
    unique_ptr<TFile> f;
    f.reset(TFile::Open(fileName.c_str(), "READ"));
    RunRange* runRangeOther = dynamic_cast<RunRange*>(f->Get(runRangeObjName.c_str()));
    if (runRangeOther) {
      runRange.merge(runRangeOther);
    } else {
      B2WARNING("Missing a RunRange object for file: " << fileName);
    }
  }
  dir->cd();
  return runRange;
}

getVecInputFileNames()

std::vector< std::string > getVecInputFileNames ( ) const

inlineprotectedinherited

Get the input file names used for this algorithm as a STL vector.

Definition at line 275 of file CalibrationAlgorithm.h.

{return m_inputFileNames;}

inputJsonKeyExists()

bool inputJsonKeyExists ( const std::string &  key ) const

inlineprotectedinherited

Test for a key in the input JSON object.

Definition at line 360 of file CalibrationAlgorithm.h.

{return m_jsonExecutionInput.count(key);}

isBoundaryRequired()

virtual bool isBoundaryRequired ( const Calibration::ExpRun &  )

inlineprotectedvirtualinherited

Given the current collector data, make a decision about whether or not this run should be the start of a payload boundary.

Reimplemented in TestBoundarySettingAlgorithm, PXDAnalyticGainCalibrationAlgorithm, PXDValidationAlgorithm, TestCalibrationAlgorithm, SVD3SampleCoGTimeCalibrationAlgorithm, SVD3SampleELSTimeCalibrationAlgorithm, and SVDCoGTimeCalibrationAlgorithm.

Definition at line 243 of file CalibrationAlgorithm.h.

    {
      B2ERROR("You didn't implement a isBoundaryRequired() member function in your CalibrationAlgorithm but you are calling it!");
      return false;
    }

loadInputJson()

bool loadInputJson ( const std::string &  jsonString )

inherited

Load the m_inputJson variable from a string (useful from Python interface). The rturn bool indicates success or failure.

Definition at line 502 of file CalibrationAlgorithm.cc.

{
  try {
    auto jsonInput = nlohmann::json::parse(jsonString);
    // Input string has an object (dict) as the top level object?
    if (jsonInput.is_object()) {
      m_jsonExecutionInput = jsonInput;
      return true;
    } else {
      B2ERROR("JSON input string isn't an object type i.e. not a '{}' at the top level.");
      return false;
    }
  } catch (nlohmann::json::parse_error&) {
    B2ERROR("Parsing of JSON input string failed");
    return false;
  }
}

resetInputJson()

void resetInputJson ( )

inlineprotectedinherited

Clears the m_inputJson member variable.

Definition at line 330 of file CalibrationAlgorithm.h.

{m_jsonExecutionInput.clear();}

resetOutputJson()

void resetOutputJson ( )

inlineprotectedinherited

Clears the m_outputJson member variable.

Definition at line 333 of file CalibrationAlgorithm.h.

{m_jsonExecutionOutput.clear();}

saveCalibration() [1/6]

void saveCalibration ( TClonesArray *  data, const std::string &  name  )

protectedinherited

Store DBArray payload with given name with default IOV.

Definition at line 297 of file CalibrationAlgorithm.cc.

{
  saveCalibration(data, name, m_data.getRequestedIov());
}

saveCalibration() [2/6]

void saveCalibration ( TClonesArray *  data, const std::string &  name, const IntervalOfValidity &  iov  )

protectedinherited

Store DBArray with given name and custom IOV.

Definition at line 276 of file CalibrationAlgorithm.cc.

{
  B2DEBUG(29, "Saving calibration TClonesArray '" <<  name << "' to payloads list.");
  getPayloads().emplace_back(name, data, iov);
}

saveCalibration() [3/6]

void saveCalibration ( TObject *  data )

protectedinherited

Store DB payload with default name and default IOV.

Definition at line 287 of file CalibrationAlgorithm.cc.

{
  saveCalibration(data, DataStore::objectName(data->IsA(), ""));
}

saveCalibration() [4/6]

void saveCalibration ( TObject *  data, const IntervalOfValidity &  iov  )

protectedinherited

Store DB payload with default name and custom IOV.

Definition at line 282 of file CalibrationAlgorithm.cc.

{
  saveCalibration(data, DataStore::objectName(data->IsA(), ""), iov);
}

saveCalibration() [5/6]

void saveCalibration ( TObject *  data, const std::string &  name  )

protectedinherited

Store DB payload with given name with default IOV.

Definition at line 292 of file CalibrationAlgorithm.cc.

{
  saveCalibration(data, name, m_data.getRequestedIov());
}

saveCalibration() [6/6]

void saveCalibration ( TObject *  data, const std::string &  name, const IntervalOfValidity &  iov  )

protectedinherited

Store DB payload with given name and custom IOV.

Definition at line 270 of file CalibrationAlgorithm.cc.

{
  B2DEBUG(29, "Saving calibration TObject = '" <<  name << "' to payloads list.");
  getPayloads().emplace_back(name, data, iov);
}

setDebugHisto()

void setDebugHisto ( bool  debugHisto )

inline

setter for m_debugHisto

Definition at line 62 of file PXDHotPixelMaskCalibrationAlgorithm.h.

{m_debugHisto = debugHisto;}

setDescription()

void setDescription ( const std::string &  description )

inlineprotectedinherited

Set algorithm description (in constructor)

Definition at line 321 of file CalibrationAlgorithm.h.

{m_description = description;}

setInputFileNames() [1/2]

void setInputFileNames ( PyObject *  inputFileNames )

inherited

Set the input file names used for this algorithm from a Python list.

Set the input file names used for this algorithm and resolve the wildcards.

Definition at line 166 of file CalibrationAlgorithm.cc.

{
  // The reasoning for this very 'manual' approach to extending the Python interface
  // (instead of using boost::python) is down to my fear of putting off final users with
  // complexity on their side.
  //
  // I didn't want users that inherit from this class to be forced to use boost and
  // to have to define a new python module just to use the CAF. A derived class from
  // from a boost exposed class would need to have its own boost python module definition
  // to allow access from a steering file and to the base class functions (I think).
  // I also couldn't be bothered to write a full framework to get around the issue in a similar
  // way to Module()...maybe there's an easy way.
  //
  // But this way we can allow people to continue using their ROOT implemented classes and inherit
  // easily from this one. But add in a few helper functions that work with Python objects
  // created in their steering file i.e. instead of being forced to use STL objects as input
  // to the algorithm.
  if (PyList_Check(inputFileNames)) {
    boost::python::handle<> handle(boost::python::borrowed(inputFileNames));
    boost::python::list listInputFileNames(handle);
    auto vecInputFileNames = PyObjConvUtils::convertPythonObject(listInputFileNames, vector<string>());
    setInputFileNames(vecInputFileNames);
  } else {
    B2ERROR("Tried to set the input files but we didn't receive a Python list.");
  }
}

setInputFileNames() [2/2]

void setInputFileNames ( std::vector< std::string >  inputFileNames )

protectedinherited

Set the input file names used for this algorithm.

Set the input file names used for this algorithm and resolve the wildcards.

Definition at line 194 of file CalibrationAlgorithm.cc.

{
  // A lot of code below is tweaked from RootInputModule::initialize,
  // since we're basically copying the functionality anyway.
  if (inputFileNames.empty()) {
    B2WARNING("You have called setInputFileNames() with an empty list. Did you mean to do that?");
    return;
  }
  auto tmpInputFileNames = RootIOUtilities::expandWordExpansions(inputFileNames);
 
  // We'll use a set to enforce sorted unique file paths as we check them
  set<string> setInputFileNames;
  // Check that files exist and convert to absolute paths
  for (auto path : tmpInputFileNames) {
    string fullPath = fs::absolute(path).string();
    if (fs::exists(fullPath)) {
      setInputFileNames.insert(fs::canonical(fullPath).string());
    } else {
      B2WARNING("Couldn't find the file " << path);
    }
  }
 
  if (setInputFileNames.empty()) {
    B2WARNING("No valid files specified!");
    return;
  } else {
    // Reset the run -> files map as our files are likely different
    m_runsToInputFiles.clear();
  }
 
  // Open TFile to check they can be accessed by ROOT
  TDirectory* dir = gDirectory;
  for (const string& fileName : setInputFileNames) {
    unique_ptr<TFile> f;
    try {
      f.reset(TFile::Open(fileName.c_str(), "READ"));
    } catch (logic_error&) {
      //this might happen for ~invaliduser/foo.root
      //actually undefined behaviour per standard, reported as ROOT-8490 in JIRA
    }
    if (!f || !f->IsOpen()) {
      B2FATAL("Couldn't open input file " + fileName);
    }
  }
  dir->cd();
 
  // Copy the entries of the set to a vector
  m_inputFileNames = vector<string>(setInputFileNames.begin(), setInputFileNames.end());
  m_granularityOfData = getGranularityFromData();
}

setOutputJsonValue()

void setOutputJsonValue ( const std::string &  key, const T &  value  )

inlineprotectedinherited

Set a key:value pair for the outputJson object, expected to used interally during calibrate()

Definition at line 337 of file CalibrationAlgorithm.h.

{m_jsonExecutionOutput[key] = value;}

setPrefix()

void setPrefix ( const std::string &  prefix )

inlineinherited

Set the prefix used to identify datastore objects.

Definition at line 167 of file CalibrationAlgorithm.h.

{m_prefix = prefix;}

updateDBObjPtrs()

void updateDBObjPtrs ( const unsigned int  event = 1, const int  run = 0, const int  experiment = 0  )

protectedinherited

Updates any DBObjPtrs by calling update(event) for DBStore.

Definition at line 404 of file CalibrationAlgorithm.cc.

{
  // Construct an EventMetaData object but NOT in the Datastore
  EventMetaData emd(event, run, experiment);
  // Explicitly update while avoiding registering a Datastore object
  DBStore::Instance().update(emd);
  // Also update the intra-run objects to the event at the same time (maybe unnessary...)
  DBStore::Instance().updateEvent(event);
}

Member Data Documentation

c_nDrains

const unsigned short c_nDrains = 1000

private

Number of drain lines of Belle II PXD sensors.

Definition at line 75 of file PXDHotPixelMaskCalibrationAlgorithm.h.

c_nUCells

const unsigned short c_nUCells = 250

private

Number of uCells of Belle II PXD sensors.

Definition at line 73 of file PXDHotPixelMaskCalibrationAlgorithm.h.

c_nVCells

const unsigned short c_nVCells = 768

private

Number of vCells of Belle II PXD sensors.

Definition at line 71 of file PXDHotPixelMaskCalibrationAlgorithm.h.

deadPixelPayloadName

std::string deadPixelPayloadName

Payload name for PXDDeadPixelPar used for more defective pixels from damaged gates.

Definition at line 53 of file PXDHotPixelMaskCalibrationAlgorithm.h.

drainMultiplier

float drainMultiplier

The occupancy threshold for masking hot drains is the median occupancy x drainMultiplier.

Definition at line 44 of file PXDHotPixelMaskCalibrationAlgorithm.h.

forceContinueMasking

bool forceContinueMasking

Force continue masking in almost empty runs instead of returning c_NotEnoughData.

Definition at line 29 of file PXDHotPixelMaskCalibrationAlgorithm.h.

inefficientPixelMultiplier

float inefficientPixelMultiplier

The occupancy threshold for inefficient (or dead) pixels is the median occupancy x inefficientPixelMultiplier.

Definition at line 56 of file PXDHotPixelMaskCalibrationAlgorithm.h.

m_allExpRun

const ExpRun m_allExpRun = make_pair(-1, -1)

staticprivateinherited

allExpRun

Definition at line 364 of file CalibrationAlgorithm.h.

m_boundaries

std::vector<Calibration::ExpRun> m_boundaries

protectedinherited

When using the boundaries functionality from isBoundaryRequired, this is used to store the boundaries. It is cleared when.

Definition at line 261 of file CalibrationAlgorithm.h.

m_data

ExecutionData m_data

privateinherited

Data specific to a SINGLE execution of the algorithm. Gets reset at the beginning of execution.

Definition at line 382 of file CalibrationAlgorithm.h.

m_debugHisto

int m_debugHisto = false

private

Set if a debugging histogram should be created in the algorithm output directory.

Definition at line 78 of file PXDHotPixelMaskCalibrationAlgorithm.h.

m_description

std::string m_description {""}

privateinherited

Description of the algorithm.

Definition at line 385 of file CalibrationAlgorithm.h.

m_file

std::shared_ptr<TFile> m_file

private

Pointer for TFile.

Definition at line 84 of file PXDHotPixelMaskCalibrationAlgorithm.h.

m_granularityOfData

std::string m_granularityOfData

privateinherited

Granularity of input data. This only changes when the input files change so it isn't specific to an execution.

Definition at line 379 of file CalibrationAlgorithm.h.

m_inputFileNames

std::vector<std::string> m_inputFileNames

privateinherited

List of input files to the Algorithm, will initially be user defined but then gets the wildcards expanded during execute()

Definition at line 373 of file CalibrationAlgorithm.h.

m_jsonExecutionInput

nlohmann::json m_jsonExecutionInput = nlohmann::json::object()

privateinherited

Optional input JSON object used to make decisions about how to execute the algorithm code.

Definition at line 397 of file CalibrationAlgorithm.h.

m_jsonExecutionOutput

nlohmann::json m_jsonExecutionOutput = nlohmann::json::object()

privateinherited

Optional output JSON object that can be set during the execution by the underlying algorithm code.

Definition at line 403 of file CalibrationAlgorithm.h.

m_medianOfHitsMap

std::map<VxdID, double> m_medianOfHitsMap

private

map of VxdID to median hits of each sensor

Definition at line 81 of file PXDHotPixelMaskCalibrationAlgorithm.h.

m_prefix

std::string m_prefix {""}

privateinherited

The name of the TDirectory the collector objects are contained within.

Definition at line 388 of file CalibrationAlgorithm.h.

m_runsToInputFiles

std::map<Calibration::ExpRun, std::vector<std::string> > m_runsToInputFiles

privateinherited

Map of Runs to input files. Gets filled when you call getRunRangeFromAllData, gets cleared when setting input files again.

Definition at line 376 of file CalibrationAlgorithm.h.

maskDrains

bool maskDrains

Mask hot drain lines with too high average occupancy after single pixel masking.

Definition at line 41 of file PXDHotPixelMaskCalibrationAlgorithm.h.

maskRows

bool maskRows

Mask hot rows with too high average occupancy after single pixel masking.

Definition at line 47 of file PXDHotPixelMaskCalibrationAlgorithm.h.

minEvents

int minEvents

Minimum number of collected events.

Definition at line 32 of file PXDHotPixelMaskCalibrationAlgorithm.h.

minHits

int minHits

Minimum median number of hits per pixel needed for dead pixel masking.

Definition at line 35 of file PXDHotPixelMaskCalibrationAlgorithm.h.

minInefficientPixels

int minInefficientPixels

The minimum number of inefficient (or dead) pixels per row to define an inefficient row.

Definition at line 59 of file PXDHotPixelMaskCalibrationAlgorithm.h.

pixelMultiplier

float pixelMultiplier

The occupancy threshold for masking hot single pixels is the median occupancy x pixelMultiplier.

Definition at line 38 of file PXDHotPixelMaskCalibrationAlgorithm.h.

rowMultiplier

float rowMultiplier

The occupancy threshold for masking hot rows is the median occupancy x rowMultiplier.

Definition at line 50 of file PXDHotPixelMaskCalibrationAlgorithm.h.

---

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

• pxd/calibration/include/PXDHotPixelMaskCalibrationAlgorithm.h
• pxd/calibration/src/PXDHotPixelMaskCalibrationAlgorithm.cc