toor.GateLink.RootToTor package

Submodules

toor.GateLink.RootToTor.addanglestorootfile module

class toor.GateLink.RootToTor.addanglestorootfile.AddMotorInfoToRoot(filename=None, doubleScannerFormat=True, path_to_macs=None)

Bases: ReadRootFile

createMotorArrays()

readMotorFiles()

saveMotorArraysIntoRoot(array_keys)

toor.GateLink.RootToTor.findcoincidencesRoot2Numpy module

class toor.GateLink.RootToTor.findcoincidencesRoot2Numpy.GenerateCoincidencesAndAnhnilationsPositions(filename=None, method='time_diff', coincidenceWindow=0.1)

Bases: ReadRootFile

This class is used to generate the coincidences and anhnilations positions from the root file data. The coincidences algorithm is based on the time of the events. It assumed that GATE digitizer is used to join multiple events that occur the same detector. For more information about the GATE digitizer, please refer to the GATE documentation. :type filename: :param filename: the path to the root file :type method: :param method: the method used to generate the coincidences. The options are:

SameID: the coincidence is generated when the events have the same ID SameTime: the coincidence is generated when the events have the same time

Parameters:

• coincidenceWindow – the coincidence window in nano seconds

• doubleScannerFormat – if the root file returns two arrays for the singles, one for each scanner

• _filename – the path to the root file

• _method – the method used to generate the coincidences. The options are: SameID: the coincidence is generated when the events have the same ID SameTime: the coincidence is generated when the events have the same time

• _coincidenceWindow – the coincidence window in nano seconds

• doubleScannerFormat – if the root file returns two arrays for the singles, one for each scanner

• _fileBodyData – the list mode data

• _coincidences – the coincidences data

• _anhnilations – the anhnilations data

• _singlesScanner1 – the singles data for the first module

• _singlesScanner2 – the singles data for the second module

findCoincidences(coincidenceWindow=0.1, array_keys=None)

Slower version: This method is used to find the coincidences in the singles data. :type coincidenceWindow: :param coincidenceWindow: the coincidence window in nano seconds

findCoincidencesBigArrays(coincidenceWindow=1, array_keys=None)

This method is used to find the coincidences in the singles data.

findCoincidencesTrueEventID(array_keys=None)

printCoincidenceStats()

readCoincidencesNumpyRecordsArray()

saveCoincidencesAsNumpyRecordsArray(array_keys=None)

saveCoincidencesAsRootFile(array_keys=None, filename=None)

toor.GateLink.RootToTor.readroot module

class toor.GateLink.RootToTor.readroot.ReadRootFile(filename=None)

Bases: object

Class to read root files :type filename: :param filename: str

Path to the root file

Parameters:

• _filename – str Path to the root file

• _partNumber – int Part number of the root file

• _singlesScanner1 – ExtractSingles ExtractSingles object for the singles of the first scanner

• _singlesScanner2 – ExtractSingles ExtractSingles object for the singles of the second scanner

• _singles – ExtractSingles ExtractSingles object for the singles of the single scanner

• _keysUsed – list List of the keys used to create the singles

• _doubleScannerFormat – bool True if the root file is in double scanner format

property doubleScannerFormat

property partNumber

readRoot()

setArraysToConvert(obj=None, keys=None, arr=None)

setDoubleScannerFormat(value)

setPartNumber(partNumber)

property singles

property singlesScanner1

property singlesScanner2

toor.GateLink.RootToTor.recreatedata module

toor.GateLink.RootToTor.rootToTor module

toor.GateLink.RootToTor.rootjoiner module

class toor.GateLink.RootToTor.rootjoiner.RootJoiner(file_path, path_to_save=None, tree_name='Singles', double_scanner_format=False)

Bases: object

chooseJustFilteredData()

property globalArray

property globalArray_scanner1

property globalArray_scanner2

join()

toor.GateLink.RootToTor.singlesstruct module

class toor.GateLink.RootToTor.singlesstruct.ExtractSingles(parent=None)

Bases: object

This class is used to extract the singles data from the root file and to convert into numpy array. :type parent: :param parent: the uproot object containing the singles data

Parameters:

• _parent – the uproot object containing the singles data

• _runID – the run ID

• _eventID – the event ID

• _sourceID – the source ID

• _sourcePosX – the source position in x

• _sourcePosY – the source position in y

• _sourcePosZ – the source position in z

• _globalPosX – the global position in x

• _globalPosY – the global position in y

• _globalPosZ – the global position in z

• _time – the time

• _energy – the energy

• _baseID – the base ID

• _level1ID – the level 1 ID (moduleID)

• _level2ID – the level 2 ID (submoduleID)

• _level3ID – the level 3 ID (crystalID

• _level4ID – the level 4 ID (pixelID)

• _level5ID – the level 5 ID (?)

• _comptonPhantom – the compton phantom

• _comptonCrystal – the compton crystal

• _comptonDetector – the compton detector

• _comptonWorld – the compton world

_createAllTreeArrays()

create all the tree arrays from the root file to numpy arrays

runID()

get the run ID

setRunID()

set the run ID

eventID()

get the event ID

setEventID()

set the event ID

sourceID()

get the source ID

setSourceID()

set the source ID

sourcePosX()

get the source position in x

setSourcePosX()

set the source position in x

sourcePosY()

get the source position in y

setSourcePosY()

set the source position in y

sourcePosZ()

get the source position in z

setSourcePosZ()

set the source position in z

globalPosX()

get the global position in x

setGlobalPosX()

set the global position in x

globalPosY()

get the global position in y

setGlobalPosY()

set the global position in y

globalPosZ()

get the global position in z

setGlobalPosZ()

set the global position in z

time()

get the time

setTime()

set the time

energy()

get the energy

setEnergy()

set the energy

baseID()

get the base ID

setBaseID()

set the base ID

level1ID()

get the level 1 ID (moduleID)

setLevel1ID()

set the level 1 ID (moduleID)

level2ID()

get the level 2 ID (submoduleID)

setLevel2ID()

set the level 2 ID (submoduleID)

level3ID()

get the level 3 ID (crystalID)

setLevel3ID()

set the level 3 ID (crystalID)

level4ID()

get the level 4 ID (pixelID)

setLevel4ID()

set the level 4 ID (pixelID)

level5ID()

get the level 5 ID (?)

setLevel5ID()

set the level 5 ID (?)

comptonPhantom()

get the compton phantom

setComptonPhantom()

set the compton phantom

comptonCrystal()

get the compton crystal

setComptonCrystal()

set the compton crystal

comptonDetector()

get the compton detector

setComptonDetector()

set the compton detector

comptonWorld()

get the compton world

property baseID

property comptonCrystal

property comptonPhantom

property energy

property eventID

property globalPosX

property globalPosY

property globalPosZ

property level1ID

property level2ID

property level3ID

property level4ID

property level5ID

property parent

property runID

property setBaseID

property setComptonCrystal

property setComptonPhantom

property setEnergy

property setEventID

property setGlobalPosX

property setGlobalPosY

property setGlobalPosZ

property setLevel1ID

property setLevel2ID

property setLevel3ID

property setLevel4ID

property setLevel5ID

property setRunID

property setSourceID

property setSourcePosX

property setSourcePosY

property setSourcePosZ

property setTime

property sourceID

property sourcePosX

property sourcePosY

property sourcePosZ

property time

toor.GateLink.RootToTor.validation_plots module

class toor.GateLink.RootToTor.validation_plots.CoincidenceValidationPlots(listmode_file, array_keys, directory)

Bases: object

generateCharts()

Module contents