PFCfg.py

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# Copyright (C) 2002-2024 CERN for the benefit of the ATLAS collaboration
from AthenaConfiguration.ComponentFactory import CompFactory
from AthenaConfiguration.ComponentAccumulator import ComponentAccumulator
from AthenaConfiguration.Enums import LHCPeriod
 
def PFTrackSelectorAlgCfg(inputFlags,algName,useCaching=True):
    PFTrackSelectorFactory=CompFactory.PFTrackSelector
    PFTrackSelector=PFTrackSelectorFactory(algName)
 
    result = ComponentAccumulator()
 
    from TrackToCalo.TrackToCaloConfig import ParticleCaloExtensionToolCfg
    pcExtensionTool = result.popToolsAndMerge(ParticleCaloExtensionToolCfg(inputFlags))
 
    eflowTrackCaloExtensionTool=CompFactory.eflowTrackCaloExtensionTool
    TrackCaloExtensionTool=eflowTrackCaloExtensionTool(TrackCaloExtensionTool=pcExtensionTool)
    if (not useCaching):
      TrackCaloExtensionTool.PFParticleCache = ""
 
    PFTrackSelector.trackExtrapolatorTool = TrackCaloExtensionTool
 
    from InDetConfig.InDetTrackSelectionToolConfig import PFTrackSelectionToolCfg
    PFTrackSelector.trackSelectionTool = result.popToolsAndMerge(PFTrackSelectionToolCfg(inputFlags))
 
    # P->T conversion extra dependencies
    if inputFlags.Detector.GeometryITk:
        PFTrackSelector.ExtraInputs = {
            ("InDetDD::SiDetectorElementCollection", "ConditionStore+ITkPixelDetectorElementCollection"),
            ("InDetDD::SiDetectorElementCollection", "ConditionStore+ITkStripDetectorElementCollection"),
        }
    else:
        PFTrackSelector.ExtraInputs = {
            ("InDetDD::SiDetectorElementCollection", "ConditionStore+PixelDetectorElementCollection"),
            ("InDetDD::SiDetectorElementCollection", "ConditionStore+SCT_DetectorElementCollection"),
            ("InDetDD::TRT_DetElementContainer", "ConditionStore+TRT_DetElementContainer"),
        }
 
    result.addEventAlgo (PFTrackSelector, primary=True)
 
    return result
 
def getPFClusterSelectorTool(inputFlags,clustersin,calclustersin,algName):
 
    PFClusterSelectorToolFactory = CompFactory.PFClusterSelectorTool
    PFClusterSelectorTool = PFClusterSelectorToolFactory(algName)
    if clustersin is not None:
        PFClusterSelectorTool.clustersName = clustersin
    if calclustersin is not None:
        PFClusterSelectorTool.calClustersName = calclustersin
 
    if inputFlags.PF.useTruthCheating:
        if inputFlags.PF.useTrackClusterTruthMatching: 
            PFClusterSelectorTool.CaloClusterReadDecorHandleKey_NLeadingTruthParticles = "CaloTopoClusters." + inputFlags.Calo.TopoCluster.CalibrationHitDecorationName
 
    if inputFlags.PF.useTopoTowers:
        PFClusterSelectorTool.clustersName="CaloTopoSignal"
        PFClusterSelectorTool.calClustersName="CaloCalTopoSignal"
 
    return PFClusterSelectorTool
 
def getPFTrackClusterMatchingTool(inputFlags,matchCut,distanceType,clusterPositionType,name):
    PFTrackClusterMatchingTool = CompFactory.PFTrackClusterMatchingTool
    MatchingTool = PFTrackClusterMatchingTool(name)
    MatchingTool.ClusterPositionType = clusterPositionType
    MatchingTool.DistanceType = distanceType
    MatchingTool.MatchCut = matchCut*matchCut
    return MatchingTool
 
 
def getPFCellLevelSubtractionTool(inputFlags,toolName):
    PFCellLevelSubtractionToolFactory = CompFactory.PFSubtractionTool
    PFCellLevelSubtractionTool = PFCellLevelSubtractionToolFactory(toolName,useNNEnergy = inputFlags.PF.useMLEOverP)
 
    if inputFlags.GeoModel.Run <= LHCPeriod.Run3:
        eflowCellEOverPTool_Run2_mc20_JetETMiss = CompFactory.eflowCellEOverPTool_Run2_mc20_JetETMiss
        PFCellLevelSubtractionTool.eflowCellEOverPTool = eflowCellEOverPTool_Run2_mc20_JetETMiss()
    else:
        if inputFlags.PF.useLegacyEOverPRun4:
            eflowCellEOverPTool_mc12_HLLHC = CompFactory.eflowCellEOverPTool_mc12_HLLHC 
            PFCellLevelSubtractionTool.eflowCellEOverPTool = eflowCellEOverPTool_mc12_HLLHC ()
        else:
            PFCellEOverPTool = CompFactory.PFCellEOverPTool
            PFCellLevelSubtractionTool.eflowCellEOverPTool = PFCellEOverPTool("PFCellEOverPTool", referenceFileLocation = inputFlags.PF.EOverP_CellOrdering_ReferenceLocation)
            #this should always be false for any reference derived, except eflowCellEOverPTool_mc12_HLLHC.h or eflowCellEOverPTool_Run2_mc20_JetETMiss.h
            PFCellLevelSubtractionTool.useLegacyEBinIndex=False
 
    if(inputFlags.PF.EOverPMode):
        PFCellLevelSubtractionTool.CalcEOverP = True
        PFCellLevelSubtractionTool.nClusterMatchesToUse = -1
    else:
        PFCellLevelSubtractionTool.nClusterMatchesToUse = 1
 
    if(inputFlags.PF.EOverPMode):
        PFCellLevelSubtractionTool.PFTrackClusterMatchingTool = getPFTrackClusterMatchingTool(inputFlags,0.2,"EtaPhiSquareDistance","PlainEtaPhi","CalObjBldMatchingTool")
    else:
        PFCellLevelSubtractionTool.PFTrackClusterMatchingTool = getPFTrackClusterMatchingTool(inputFlags,1.64,"EtaPhiSquareSignificance","GeomCenterEtaPhi","CalObjBldMatchingTool")
 
    PFCellLevelSubtractionTool.PFTrackClusterMatchingTool_015 = getPFTrackClusterMatchingTool(inputFlags,0.15,"EtaPhiSquareDistance","PlainEtaPhi","MatchingTool_Pull_015")
    PFCellLevelSubtractionTool.PFTrackClusterMatchingTool_02 = getPFTrackClusterMatchingTool(inputFlags,0.2,"EtaPhiSquareDistance","PlainEtaPhi","MatchingTool_Pull_02")
 
    if inputFlags.PF.useMLEOverP:
        PFEnergyPredictorTool = CompFactory.PFEnergyPredictorTool("PFCellLevelEnergyPredcictorTool",ModelPath = inputFlags.PF.EOverP_NN_Model)
        PFCellLevelSubtractionTool.NNEnergyPredictorTool = PFEnergyPredictorTool
    PFCellLevelSubtractionTool.addCPData = inputFlags.PF.addCPData
 
    if inputFlags.PF.useTruthCheating:
        if inputFlags.PF.useTrackClusterTruthMatching: 
            PFCellLevelSubtractionTool.CaloClusterReadDecorHandleKey_NLeadingTruthParticles = "CaloTopoClusters." + inputFlags.Calo.TopoCluster.CalibrationHitDecorationName
            PFCellLevelSubtractionTool.useTrackClusterTruthMatching=True
 
        if inputFlags.PF.useTruthForChargedShowerSubtraction:
            PFCellLevelSubtractionTool.useTruthForChargedShowerSubtraction = True
            PFCellLevelSubtractionTool.PFSimulateTruthShowerTool = CompFactory.PFSimulateTruthShowerTool("PFSimulateTruthShowerTool")
 
    return PFCellLevelSubtractionTool
 
def getPFRecoverSplitShowersTool(inputFlags,toolName):
    PFRecoverSplitShowersToolFactory = CompFactory.PFSubtractionTool
    PFRecoverSplitShowersTool = PFRecoverSplitShowersToolFactory(toolName,useNNEnergy = inputFlags.PF.useMLEOverP)
 
    if inputFlags.GeoModel.Run <= LHCPeriod.Run3:
        eflowCellEOverPTool_Run2_mc20_JetETMiss = CompFactory.eflowCellEOverPTool_Run2_mc20_JetETMiss
        PFRecoverSplitShowersTool.eflowCellEOverPTool = eflowCellEOverPTool_Run2_mc20_JetETMiss("eflowCellEOverPTool_Run2_mc20_JetETMiss_Recover")
    else:
        if inputFlags.PF.useLegacyEOverPRun4:
            eflowCellEOverPTool_mc12_HLLHC = CompFactory.eflowCellEOverPTool_mc12_HLLHC 
            PFRecoverSplitShowersTool.eflowCellEOverPTool = eflowCellEOverPTool_mc12_HLLHC ()
        else:
            PFCellEOverPTool = CompFactory.PFCellEOverPTool
            PFRecoverSplitShowersTool.eflowCellEOverPTool = PFCellEOverPTool("PFCellEOverPTool_Recover", referenceFileLocation = inputFlags.PF.EOverP_CellOrdering_ReferenceLocation)
            #this should always be false for any reference derived, except eflowCellEOverPTool_mc12_HLLHC.h or eflowCellEOverPTool_Run2_mc20_JetETMiss.h
            PFRecoverSplitShowersTool.useLegacyEBinIndex=False
 
    PFRecoverSplitShowersTool.RecoverSplitShowers = True
 
    if inputFlags.PF.useMLEOverP:
        PFEnergyPredictorTool = CompFactory.PFEnergyPredictorTool("PFRecoverSplitShowersEnergyPredcictorTool",ModelPath = inputFlags.PF.EOverP_NN_Model)
        PFRecoverSplitShowersTool.NNEnergyPredictorTool = PFEnergyPredictorTool
 
    return PFRecoverSplitShowersTool
 
def getPFMomentCalculatorTool(inputFlags, momentsToCalculateList):
    result=ComponentAccumulator()
    PFMomentCalculatorToolFactory = CompFactory.PFMomentCalculatorTool
    PFMomentCalculatorTool = PFMomentCalculatorToolFactory("PFMomentCalculatorTool")
 
    from CaloRec.CaloTopoClusterConfig import getTopoMoments
    PFClusterMomentsMaker = result.popToolsAndMerge(getTopoMoments(inputFlags))
    if (len(momentsToCalculateList) > 0):
        PFClusterMomentsMaker.MomentsNames = momentsToCalculateList
    PFMomentCalculatorTool.CaloClusterMomentsMaker = PFClusterMomentsMaker
 
    PFClusterCollectionTool = CompFactory.PFClusterCollectionTool
    PFMomentCalculatorTool.PFClusterCollectionTool = PFClusterCollectionTool("PFClusterCollectionTool")
 
    if(inputFlags.PF.useCalibHitTruthClusterMoments):
        PFMomentCalculatorTool.UseCalibHitTruth=True
        from CaloRec.CaloTopoClusterConfig import getTopoCalibMoments
        PFMomentCalculatorTool.CaloCalibClusterMomentsMaker2 = getTopoCalibMoments(inputFlags)
 
    result.setPrivateTools(PFMomentCalculatorTool)
    return result
 
def getPFLCCalibTool(inputFlags):
    PFLCCalibTool = CompFactory.PFLCCalibTool
    PFLCCalibTool = PFLCCalibTool("PFLCCalibTool")
 
    PFClusterCollectionTool = CompFactory.PFClusterCollectionTool
    PFLCCalibTool.eflowRecClusterCollectionTool = PFClusterCollectionTool("PFClusterCollectionTool_LCCalib")
    PFLCCalibTool.UseLocalWeight = False
 
    from CaloRec.CaloTopoClusterConfig import getTopoClusterLocalCalibTools
    lcCalibToolList = getTopoClusterLocalCalibTools(inputFlags)
 
    PFLCCalibTool.CaloClusterLocalCalib=lcCalibToolList[0]
    PFLCCalibTool.CaloClusterLocalCalibOOCC=lcCalibToolList[1]
    PFLCCalibTool.CaloClusterLocalCalibOOCCPi0=lcCalibToolList[2]
    PFLCCalibTool.CaloClusterLocalCalibDM=lcCalibToolList[3]
 
    return PFLCCalibTool
 
def getChargedFlowElementCreatorAlgorithm(inputFlags,chargedFlowElementOutputName,nameSuffix="",eflowCaloObjectContainerName="eflowCaloObjects"):
    FlowElementChargedCreatorAlgorithmFactory = CompFactory.PFChargedFlowElementCreatorAlgorithm
    FlowElementChargedCreatorAlgorithm = FlowElementChargedCreatorAlgorithmFactory("PFChargedFlowElementCreatorAlgorithm"+nameSuffix)
    FlowElementChargedCreatorAlgorithm.eflowCaloObjectContainerName = eflowCaloObjectContainerName
    if chargedFlowElementOutputName:
        FlowElementChargedCreatorAlgorithm.FlowElementOutputName=chargedFlowElementOutputName
    if(inputFlags.PF.EOverPMode):
        FlowElementChargedCreatorAlgorithm.FlowElementOutputName="EOverPChargedParticleFlowObjects"
        FlowElementChargedCreatorAlgorithm.EOverPMode = True
    if inputFlags.PF.addCPData:
        FlowElementChargedCreatorAlgorithm.addCPData = True
 
    return FlowElementChargedCreatorAlgorithm
 
def getNeutralFlowElementCreatorAlgorithm(inputFlags,neutralFlowElementOutputName,nameSuffix="",eflowCaloObjectContainerName="eflowCaloObjects"):
    FlowElementNeutralCreatorAlgorithmFactory = CompFactory.PFNeutralFlowElementCreatorAlgorithm
    FlowElementNeutralCreatorAlgorithm = FlowElementNeutralCreatorAlgorithmFactory("PFNeutralFlowElementCreatorAlgorithm"+nameSuffix)
    FlowElementNeutralCreatorAlgorithm.eflowCaloObjectContainerName = eflowCaloObjectContainerName
    if neutralFlowElementOutputName:
        FlowElementNeutralCreatorAlgorithm.FlowElementOutputName=neutralFlowElementOutputName
    if(inputFlags.PF.EOverPMode):
        FlowElementNeutralCreatorAlgorithm.FlowElementOutputName="EOverPNeutralParticleFlowObjects"
    if(inputFlags.PF.useCalibHitTruthClusterMoments and inputFlags.PF.addClusterMoments):
        FlowElementNeutralCreatorAlgorithm.UseCalibHitTruth=True
    if inputFlags.PF.addCPData:
        FlowElementNeutralCreatorAlgorithm.addCPData = True
 
    return FlowElementNeutralCreatorAlgorithm
 
def getLCNeutralFlowElementCreatorAlgorithm(inputFlags,neutralFlowElementOutputName):
    LCFlowElementNeutralCreatorAlgorithmFactory = CompFactory.PFLCNeutralFlowElementCreatorAlgorithm
    LCFlowElementNeutralCreatorAlgorithm = LCFlowElementNeutralCreatorAlgorithmFactory("PFLCNeutralFlowElementCreatorAlgorithm")
    if neutralFlowElementOutputName:
      LCFlowElementNeutralCreatorAlgorithm.FELCOutputName=neutralFlowElementOutputName
    if(inputFlags.PF.EOverPMode):
      LCFlowElementNeutralCreatorAlgorithm.FEInputContainerName="EOverPNeutralParticleFlowObjects"
      LCFlowElementNeutralCreatorAlgorithm.FELCOutputName="EOverPLCNeutralParticleFlowObjects"
    
    return LCFlowElementNeutralCreatorAlgorithm 
 
# Factory function to create the ML-based neutral flow element creator algorithm
def getPFOClusterMLCorrectionAlgorithmCfg(inputFlags, inputNameBase = "JetETMiss", outputNameBase = "JetETMissClusterMLCorrected"):
    alg = CompFactory.PFOClusterMLCorrectionAlgorithm("PFOClusterMLCorrectionAlgorithm")
    suffix = "ParticleFlowObjects"
    alg.NeutralPFlowInputContainer = inputNameBase + "Neutral" + suffix
    alg.ChargedPFlowInputContainer = inputNameBase + "Charged" + suffix
    alg.NeutralPFlowOutputContainer = outputNameBase + "Neutral"  + suffix
    alg.ChargedPFlowOutputContainer = outputNameBase + "Charged" + suffix
    
    return alg
 
def getNeutralPFOClusterMLCorrectionToolCfg(inputFlags, toolName="NeutralPFOClusterMLCorrectionTool", clusterMLCorrectedEnergyDecorationKey="clusterE_ML"):
    if toolName == "NeutralPFOClusterMLCorrectionTool":
        tool = CompFactory.NeutralPFOClusterMLCorrectionTool(toolName)
        tool.ClusterMLCorrectedEnergyDecorationKey = clusterMLCorrectedEnergyDecorationKey
    else:
        raise ValueError(f"Unknown tool name: {toolName}")
    
    ca = ComponentAccumulator()
    ca.setPrivateTools(tool)
    return ca
 
 
 
def getEGamFlowElementAssocAlgorithm(inputFlags, algName="", **kwargs):
 
    kwargs.setdefault("neutral_FE_cont_name", "")
    kwargs.setdefault("charged_FE_cont_name", "")
    kwargs.setdefault("doTCC", False)
    kwargs.setdefault("useGlobal", False)
 
    PFEGamFlowElementLinkerAlgorithmFactory=CompFactory.PFEGamFlowElementAssoc
    if not algName:
        algName = "PFEGamFlowElementAssoc"
    PFEGamFlowElementLinkerAlgorithm=PFEGamFlowElementLinkerAlgorithmFactory(algName)
 
    #set an an alternate name if needed
    #this uses some gaudi core magic, namely that you can change the name of the handle as it is a callable attribute, despite the attribute not being explicitly listed in the header
    #for a key of type SG::WriteDecorHandle<xAOD::SomeCont>someKey{this,"SpecificContainerName","myContainerName","other-labels"}
    #setting algorithm.SpecificContainerName="myNewContainerName" changes parameter "myContainerName"
    #(also applies to ReadHandles)
    if kwargs['neutral_FE_cont_name']:
        PFEGamFlowElementLinkerAlgorithm.JetEtMissNeutralFlowElementContainer = kwargs['neutral_FE_cont_name']
 
    if kwargs['charged_FE_cont_name']:
        PFEGamFlowElementLinkerAlgorithm.JetEtMissChargedFlowElementContainer = kwargs['charged_FE_cont_name']
 
    if kwargs['doTCC']:
        # ReadHandles to change
        PFEGamFlowElementLinkerAlgorithm.JetEtMissNeutralFlowElementContainer="TrackCaloClustersNeutral"
        PFEGamFlowElementLinkerAlgorithm.JetEtMissChargedFlowElementContainer="TrackCaloClustersCharged"
        
        #Now to change the writeHandles
        # first the Electron -> FE links
        EL_NFE_Link=str(PFEGamFlowElementLinkerAlgorithm.ElectronNeutralFEDecorKey)
        PFEGamFlowElementLinkerAlgorithm.ElectronNeutralFEDecorKey=EL_NFE_Link.replace("FELinks","TCCLinks")
        EL_CFE_Link=str(PFEGamFlowElementLinkerAlgorithm.ElectronChargedFEDecorKey)
        PFEGamFlowElementLinkerAlgorithm.ElectronChargedFEDecorKey=EL_CFE_Link.replace("FELinks","TCCLinks")
        #then the converse case (FE -> Electron)
        
        PFEGamFlowElementLinkerAlgorithm.ChargedFEElectronDecorKey="TrackCaloClustersCharged.TCC_ElectronLinks"
        PFEGamFlowElementLinkerAlgorithm.NeutralFEElectronDecorKey="TrackCaloClustersNeutral.TCC_ElectronLinks"
        
 
        # first the Photon -> FE links
        PH_NFE_Link=str(PFEGamFlowElementLinkerAlgorithm.PhotonNeutralFEDecorKey)
        PFEGamFlowElementLinkerAlgorithm.PhotonNeutralFEDecorKey=PH_NFE_Link.replace("FELinks","TCCLinks")
        PH_CFE_Link=str(PFEGamFlowElementLinkerAlgorithm.PhotonChargedFEDecorKey)
        PFEGamFlowElementLinkerAlgorithm.PhotonChargedFEDecorKey=PH_CFE_Link.replace("FELinks","TCCLinks")
        #then the converse case (FE -> Photons)
        
        PFEGamFlowElementLinkerAlgorithm.ChargedFEPhotonDecorKey="TrackCaloClustersCharged.TCC_PhotonLinks"
        PFEGamFlowElementLinkerAlgorithm.NeutralFEPhotonDecorKey="TrackCaloClustersNeutral.TCC_PhotonLinks"
        
    if kwargs['useGlobal']:
        # ReadHandles to change
        PFEGamFlowElementLinkerAlgorithm.JetEtMissNeutralFlowElementContainer="GlobalNeutralParticleFlowObjects"
        PFEGamFlowElementLinkerAlgorithm.JetEtMissChargedFlowElementContainer="GlobalChargedParticleFlowObjects"
        
        #Now to change the writeHandles
        # first the Electron -> FE links
        EL_NFE_Link=str(PFEGamFlowElementLinkerAlgorithm.ElectronNeutralFEDecorKey)
        PFEGamFlowElementLinkerAlgorithm.ElectronNeutralFEDecorKey=EL_NFE_Link.replace("FELinks","GlobalFELinks")
        EL_CFE_Link=str(PFEGamFlowElementLinkerAlgorithm.ElectronChargedFEDecorKey)
        PFEGamFlowElementLinkerAlgorithm.ElectronChargedFEDecorKey=EL_CFE_Link.replace("FELinks","GlobalFELinks")
        #then the converse case (FE -> Electron)
        
        PFEGamFlowElementLinkerAlgorithm.ChargedFEElectronDecorKey="GlobalChargedParticleFlowObjects.GlobalFE_ElectronLinks"
        PFEGamFlowElementLinkerAlgorithm.NeutralFEElectronDecorKey="GlobalNeutralParticleFlowObjects.GlobalFE_ElectronLinks"
        
 
        # first the Photon -> FE links
        PH_NFE_Link=str(PFEGamFlowElementLinkerAlgorithm.PhotonNeutralFEDecorKey)
        PFEGamFlowElementLinkerAlgorithm.PhotonNeutralFEDecorKey=PH_NFE_Link.replace("FELinks","GlobalFELinks")
        PH_CFE_Link=str(PFEGamFlowElementLinkerAlgorithm.PhotonChargedFEDecorKey)
        PFEGamFlowElementLinkerAlgorithm.PhotonChargedFEDecorKey=PH_CFE_Link.replace("FELinks","GlobalFELinks")
        #then the converse case (FE -> Photons)
        
        PFEGamFlowElementLinkerAlgorithm.ChargedFEPhotonDecorKey="GlobalChargedParticleFlowObjects.TCC_PhotonLinks"
        PFEGamFlowElementLinkerAlgorithm.NeutralFEPhotonDecorKey="GlobalNeutralParticleFlowObjects.TCC_PhotonLinks"
        
        
        
    return PFEGamFlowElementLinkerAlgorithm
 
def getMuonFlowElementAssocAlgorithm(inputFlags, algName="", **kwargs):
    
    kwargs.setdefault("neutral_FE_cont_name", "")
    kwargs.setdefault("charged_FE_cont_name", "")
    kwargs.setdefault("LinkNeutralFEClusters", True)       
    kwargs.setdefault("doTCC", False)
    kwargs.setdefault("useGlobal", False)
 
    useMuonTopoClusters = False
    from AthenaConfiguration.Enums import ProductionStep
    # set 'useMuonTopoClusters=True' if running on AOD, as do not have calorimeter cells for CaloCalTopoCluster
    # Assumes that in production workflows this only happens in "Derivation" or if DQ environment is AOD
    if inputFlags.Common.ProductionStep in [ProductionStep.Derivation] or inputFlags.DQ.Environment == "AOD":
        useMuonTopoClusters = True
 
 
    PFMuonFlowElementLinkerAlgorithmFactory=CompFactory.PFMuonFlowElementAssoc
    if not algName:
        algName="PFMuonFlowElementAssoc"
    PFMuonFlowElementLinkerAlgorithm=PFMuonFlowElementLinkerAlgorithmFactory(algName)
 
    #set an an alternate name if needed
    #this uses some gaudi core magic, namely that you can change the name of the handle as it is a callable attribute, despite the attribute not being explicitly listed in the header as such
    #for a key of type SG::WriteDecorHandle<xAOD::SomeCont>someKey{this,"SpecificContainerName","myContainerName","other-labels"}
    #setting algorithm.SpecificContainerName="myNewContainerName" changes parameter "myContainerName" to "myNewContainerName"
    if kwargs['neutral_FE_cont_name']:
        #update the readhandle
        PFMuonFlowElementLinkerAlgorithm.JetEtMissNeutralFlowElementContainer = kwargs['neutral_FE_cont_name']
        #update the write handle for the link
        
    if kwargs['charged_FE_cont_name']:
        PFMuonFlowElementLinkerAlgorithm.JetEtMissChargedFlowElementContainer = kwargs['charged_FE_cont_name']
    
    PFMuonFlowElementLinkerAlgorithm.LinkNeutralFEClusters = kwargs['LinkNeutralFEClusters']
    PFMuonFlowElementLinkerAlgorithm.useMuonTopoClusters = useMuonTopoClusters
 
    #prototype on AOD with the linkers already defined - so need to rename the output links to something besides their default name.
 
    #Track Calo cluster (TCC) specific configuration. Input is differently named FE container, and in the AOD step specifically
    if kwargs['doTCC']:
        #input containers are TrackCaloClustersCharged and TrackCaloClustersNeutral, so rename them
        #service_key="StoreGateSvc+"
        service_key=""
        PFMuonFlowElementLinkerAlgorithm.JetEtMissChargedFlowElementContainer=service_key+"TrackCaloClustersCharged"
        PFMuonFlowElementLinkerAlgorithm.JetEtMissNeutralFlowElementContainer=service_key+"TrackCaloClustersNeutral"
        
        #Output
        #rename the FE_MuonLinks as TCC_MuonLinks
        #rename output containers
        PFMuonFlowElementLinkerAlgorithm.MuonContainer_chargedFELinks=service_key+"Muons.chargedTCCLinks"
        PFMuonFlowElementLinkerAlgorithm.MuonContainer_neutralFELinks=service_key+"Muons.neutralTCCLinks"
        PFMuonFlowElementLinkerAlgorithm.JetETMissNeutralFlowElementContainer_FE_MuonLinks=service_key+"TrackCaloClustersNeutral.TCC_MuonLinks"
        PFMuonFlowElementLinkerAlgorithm.JetETMissChargedFlowElements_FE_MuonLinks=service_key+"TrackCaloClustersCharged.TCC_MuonLinks"
        PFMuonFlowElementLinkerAlgorithm.FlowElementContainer_ChargedFE_ennergy_matched_muon="TrackCaloClustersCharged.TCC_efrac_matched_muon"
        # several variables relating to Neutral Flow Elements/TCCs to Muons for debug. perhaps at some point these should be removed by default 
        PFMuonFlowElementLinkerAlgorithm.FlowElementContainer_nMatchedMuons="TrackCaloClustersNeutral.TCC_nMatchedMuons"
        PFMuonFlowElementLinkerAlgorithm.FlowElementContainer_FE_efrac_matched_muon="TrackCaloClustersNeutral.TCC_efrac_matched_muon"
        
        PFMuonFlowElementLinkerAlgorithm.MuonContainer_muon_efrac_matched_FE="Muons.muon_efrac_matched_TCC"
        # this is because the algorithm adds this debug container which we don't need 
        PFMuonFlowElementLinkerAlgorithm.MuonContainer_ClusterInfo_deltaR="Muons.deltaR_muon_clus_TCCalg"
 
    if kwargs['useGlobal']:
        PFMuonFlowElementLinkerAlgorithm.JetEtMissChargedFlowElementContainer="GlobalChargedParticleFlowObjects"
        PFMuonFlowElementLinkerAlgorithm.JetEtMissNeutralFlowElementContainer="GlobalNeutralParticleFlowObjects"
 
        PFMuonFlowElementLinkerAlgorithm.MuonContainer_chargedFELinks="Muons.chargedGlobalFELinks"
        PFMuonFlowElementLinkerAlgorithm.MuonContainer_neutralFELinks="Muons.neutralGlobalFELinks"
 
        PFMuonFlowElementLinkerAlgorithm.JetETMissNeutralFlowElementContainer_FE_MuonLinks="GlobalNeutralParticleFlowObjects.GlobalFE_MuonLinks"
        PFMuonFlowElementLinkerAlgorithm.JetETMissChargedFlowElements_FE_MuonLinks="GlobalChargedParticleFlowObjects.GlobalFE_MuonLinks"
        PFMuonFlowElementLinkerAlgorithm.FlowElementContainer_ChargedFE_ennergy_matched_muon="GlobalChargedParticleFlowObjects.GlobalFE_efrac_matched_muon"
 
        PFMuonFlowElementLinkerAlgorithm.FlowElementContainer_nMatchedMuons="GlobalNeutralParticleFlowObjects.GlobalFE_nMatchedMuons"
        PFMuonFlowElementLinkerAlgorithm.FlowElementContainer_FE_efrac_matched_muon="GlobalNeutralParticleFlowObjects.GlobalFE_efrac_matched_muon"
 
        PFMuonFlowElementLinkerAlgorithm.MuonContainer_muon_efrac_matched_FE="Muons.muon_efrac_matched_GlobalFE"
        # this is because the algorithm adds this debug container which we don't need 
        PFMuonFlowElementLinkerAlgorithm.MuonContainer_ClusterInfo_deltaR="Muons.deltaR_muon_clus_GlobalFEalg"
 
    if kwargs['LinkNeutralFEClusters'] and not useMuonTopoClusters:
       # We dereference links to cells, so make sure we have the
       # dependency.
       PFMuonFlowElementLinkerAlgorithm.ExtraInputs.add(('CaloCellContainer', inputFlags.Egamma.Keys.Input.CaloCells))
 
    if kwargs['LinkNeutralFEClusters']:
        if kwargs['doTCC']:
            # since the cells are deleted on AOD, if you try to run the link between NFE and Muon on AOD, it will crash. Terminate to catch this.
            # This is a known bug to rectify soon
            from AthenaCommon.Logging import logging
            msg=logging.getLogger("PFCfg.py::getMuonFlowElementAssocAlgorithm")
            msg.error("Neutral FE from AOD configured to be linked with Muon. This link will fail due to missing CaloCells in the AOD")
            msg.info("Terminating job")
            exit(0)
        
 
    return PFMuonFlowElementLinkerAlgorithm
 
def getTauFlowElementAssocAlgorithm(inputFlags, algName="", **kwargs):
 
    kwargs.setdefault("neutral_FE_cont_name", "")
    kwargs.setdefault("charged_FE_cont_name", "")
    kwargs.setdefault("doTCC", False)
    kwargs.setdefault("useGlobal", False)
 
    PFTauFlowElementLinkerAlgorithmFactory=CompFactory.PFTauFlowElementAssoc
    if not algName:
        algName = "PFTauFlowElementAssoc"
 
    PFTauFlowElementLinkerAlgorithm=PFTauFlowElementLinkerAlgorithmFactory(algName)
 
    #set an an alternate name if needed
    #this uses some gaudi core magic, namely that you can change the name of the handle as it is a callable attribute, despite the attribute not being explicitly listed in the header
    #for a key of type SG::WriteDecorHandle<xAOD::SomeCont>someKey{this,"SpecificContainerName","myContainerName","other-labels"}
    #setting algorithm.SpecificContainerName="myNewContainerName" changes parameter "myContainerName"
    #(also applies to ReadHandles)
    if kwargs['neutral_FE_cont_name']:
        PFTauFlowElementLinkerAlgorithm.JetETMissNeutralFlowElementContainer = kwargs['neutral_FE_cont_name']
 
    if kwargs['charged_FE_cont_name']:
        PFTauFlowElementLinkerAlgorithm.JetETMissChargedFlowElementContainer = kwargs['charged_FE_cont_name']
 
    if kwargs['doTCC']:
         PFTauFlowElementLinkerAlgorithm.JetETMissNeutralFlowElementContainer="TrackCaloClustersNeutral"
         PFTauFlowElementLinkerAlgorithm.JetETMissChargedFlowElementContainer="TrackCaloClustersCharged"
 
         PFTauFlowElementLinkerAlgorithm.TauNeutralFEDecorKey="TauJets.neutralTCCLinks"
         PFTauFlowElementLinkerAlgorithm.TauChargedFEDecorKey="TauJets.chargedTCCLinks"
         
         PFTauFlowElementLinkerAlgorithm.NeutralFETauDecorKey="TrackCaloClustersNeutral.TCC_TauLinks"
         PFTauFlowElementLinkerAlgorithm.ChargedFETauDecorKey="TrackCaloClustersCharged.TCC_TauLinks"
 
    #This allows to set the links on the global particle flow containers created by JetPFlowSelectionAlg in JetRecTools
    if kwargs['useGlobal']:
        PFTauFlowElementLinkerAlgorithm.JetETMissNeutralFlowElementContainer="GlobalNeutralParticleFlowObjects"
        PFTauFlowElementLinkerAlgorithm.JetETMissChargedFlowElementContainer="GlobalChargedParticleFlowObjects"
 
        PFTauFlowElementLinkerAlgorithm.TauNeutralFEDecorKey="TauJets.neutralGlobalFELinks"
        PFTauFlowElementLinkerAlgorithm.TauChargedFEDecorKey="TauJets.chargedGlobalFELinks"
 
        PFTauFlowElementLinkerAlgorithm.NeutralFETauDecorKey="GlobalNeutralParticleFlowObjects.GlobalFE_TauLinks"
        PFTauFlowElementLinkerAlgorithm.ChargedFETauDecorKey="GlobalChargedParticleFlowObjects.GlobalFE_TauLinks"
 
    return PFTauFlowElementLinkerAlgorithm
 
def getOfflinePFAlgorithm(inputFlags):
    result=ComponentAccumulator()
 
    PFAlgorithm=CompFactory.PFAlgorithm
    PFAlgorithm = PFAlgorithm("PFAlgorithm")
    
    
    if inputFlags.HeavyIon.Egamma.doSubtractedClusters: 
        PFAlgorithm.PFClusterSelectorTool = getPFClusterSelectorTool(inputFlags,inputFlags.HeavyIon.Egamma.UncalibCaloTopoCluster,inputFlags.HeavyIon.Egamma.CaloTopoCluster,"PFClusterSelectorTool")
    else:
        topoClustersName="CaloTopoClusters"
        PFAlgorithm.PFClusterSelectorTool = getPFClusterSelectorTool(inputFlags,topoClustersName,"CaloCalTopoClusters","PFClusterSelectorTool")
    
    PFAlgorithm.SubtractionToolList = [getPFCellLevelSubtractionTool(inputFlags,"PFCellLevelSubtractionTool")]
 
    if(False is inputFlags.PF.EOverPMode and False is inputFlags.PF.useTruthCheating):
        PFAlgorithm.SubtractionToolList += [getPFRecoverSplitShowersTool(inputFlags,"PFRecoverSplitShowersTool")]
 
    PFMomentCalculatorTools=result.popToolsAndMerge(getPFMomentCalculatorTool(inputFlags,[]))
    PFAlgorithm.BaseToolList = [PFMomentCalculatorTools]
    PFAlgorithm.BaseToolList += [getPFLCCalibTool(inputFlags)]
    if inputFlags.PF.EOverPMode:
        PFAlgorithm.BaseToolList += [CompFactory.PFRadialEnergyCalculatorTool()]
 
    result.addEventAlgo(PFAlgorithm)
    return result
 
def PFGlobalFlowElementLinkingCfg(inputFlags, **kwargs):
    result=ComponentAccumulator()
 
    kwargs.setdefault("useGlobal", True)
 
    result.addEventAlgo(getTauFlowElementAssocAlgorithm(inputFlags, algName="PFTauGlobalFlowElementAssoc", **kwargs))
    result.addEventAlgo(getMuonFlowElementAssocAlgorithm(inputFlags, algName="PFMuonGlobalFlowElementAssoc", **kwargs))
    result.addEventAlgo(getEGamFlowElementAssocAlgorithm(inputFlags, algName="PFEGamGlobalFlowElementAssoc", **kwargs))
    return result