PHYS.py

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# Copyright (C) 2002-2026 CERN for the benefit of the ATLAS collaboration
#====================================================================
# DAOD_PHYS.py
# This defines DAOD_PHYS, an unskimmed DAOD format for Run 3.
# It contains the variables and objects needed for the large majority 
# of physics analyses in ATLAS.
# It requires the flag PHYS in Derivation_tf.py   
#====================================================================
 
from AthenaConfiguration.ComponentAccumulator import ComponentAccumulator
from AthenaConfiguration.ComponentFactory import CompFactory
from AthenaConfiguration.Enums import MetadataCategory
from AthenaCommon.Logging import logging
logPHYS = logging.getLogger('PHYS')
 
# Main algorithm config
def PHYSKernelCfg(flags, name='PHYSKernel', **kwargs):
    """Configure the derivation framework driving algorithm (kernel) for PHYS"""
    acc = ComponentAccumulator()
 
    # Common augmentations
    from DerivationFrameworkPhys.PhysCommonConfig import PhysCommonAugmentationsCfg
    acc.merge(PhysCommonAugmentationsCfg(
        flags, 
        TriggerListsHelper     = kwargs['TriggerListsHelper']
    ))
 
    # Thinning tools
    # These are set up in PhysCommonThinningConfig. Only thing needed here the list of tools to schedule
    nametag = name.replace('Kernel', '') #get the name to label the tools below such that other formats can use this KernelCfg
    thinningToolsArgs = {
        'TrackParticleThinningToolName'       : nametag+"TrackParticleThinningTool",
        'MuonTPThinningToolName'              : nametag+"MuonTPThinningTool",
        'TauJetThinningToolName'              : nametag+"TauJetThinningTool",
        'TauJets_MuonRMThinningToolName'      : nametag+"TauJets_MuonRMThinningTool",
        'DiTauThinningToolName'               : nametag+"DiTauThinningTool",
        'DiTauTPThinningToolName'             : nametag+"DiTauTPThinningTool",
        'DiTauLowPtThinningToolName'          : nametag+"DiTauLowPtThinningTool",
        'DiTauLowPtTPThinningToolName'        : nametag+"DiTauLowPtTPThinningTool",
    } 
    # for AOD produced before 24.0.17, the electron removal tau is not available
    if flags.Tau.TauEleRM_isAvailable:
        thinningToolsArgs['TauJets_EleRMThinningToolName'] = nametag+"TauJets_EleRMThinningTool"
    # Configure the thinning tools
    from DerivationFrameworkPhys.PhysCommonThinningConfig import PhysCommonThinningCfg
    acc.merge(PhysCommonThinningCfg(flags, StreamName = kwargs['StreamName'], **thinningToolsArgs))
    # Get them from the CA so they can be added to the kernel
    thinningTools = []
    for key in thinningToolsArgs:
        thinningTools.append(acc.getPublicTool(thinningToolsArgs[key]))
 
    # The kernel algorithm itself
    DerivationKernel = CompFactory.DerivationFramework.DerivationKernel
    acc.addEventAlgo(DerivationKernel(name, ThinningTools = thinningTools))       
    return acc
 
 
def PHYSCoreCfg(flags, name_tag='PHYS', StreamName='StreamDAOD_PHYS', TriggerListsHelper=None, addExtraVariables=None):
    
    if TriggerListsHelper is None:
        from DerivationFrameworkPhys.TriggerListsHelper import TriggerListsHelper
        TriggerListsHelper = TriggerListsHelper(flags)
    
    acc = ComponentAccumulator()
 
    
    from DerivationFrameworkHiggs.HiggsPhysContent import  HiggsAugmentationAlgsCfg
    acc.merge(HiggsAugmentationAlgsCfg(flags))
 
    
    from IsolationSelection.IsolationSelectionConfig import  IsoCloseByAlgsCfg
    acc.merge(IsoCloseByAlgsCfg(flags, isPhysLite = False, stream_name = StreamName))
 
    
    from LeptonTaggers.LeptonTaggersConfig import DecoratePLITAlgsCfg
    acc.merge(DecoratePLITAlgsCfg(flags))
 
    #===================================================
    # HEAVY FLAVOR CLASSIFICATION FOR ttbar+jets EVENTS
    #===================================================
    from DerivationFrameworkMCTruth.HFClassificationCommonConfig import HFClassificationCommonCfg
    acc.merge(HFClassificationCommonCfg(flags))
    
    # ============================
    # Define contents of the format
    # =============================
    from OutputStreamAthenaPool.OutputStreamConfig import OutputStreamCfg
    from xAODMetaDataCnv.InfileMetaDataConfig import SetupMetaDataForStreamCfg
    from DerivationFrameworkCore.SlimmingHelper import SlimmingHelper
    
    PHYSSlimmingHelper = SlimmingHelper(name_tag+"SlimmingHelper", NamesAndTypes = flags.Input.TypedCollections, flags = flags)
    PHYSSlimmingHelper.SmartCollections = ["EventInfo",
                                           "Electrons",
                                           "Photons",
                                           "Muons",
                                           "PrimaryVertices",
                                           "InDetTrackParticles",
                                           "AntiKt4EMTopoJets",
                                           "AntiKt4EMPFlowJets",
                                           "MET_Baseline_AntiKt4EMTopo",
                                           "MET_Baseline_AntiKt4EMPFlow",
                                           "TauJets",
                                           "TauJets_MuonRM",
                                           "DiTauJets",
                                           "DiTauJetsLowPt",
                                           "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets",
                                           "AntiKtVR30Rmax4Rmin02PV0TrackJets",
                                          ]
    if flags.Tau.TauEleRM_isAvailable:
        PHYSSlimmingHelper.SmartCollections.append("TauJets_EleRM")
 
    excludedVertexAuxData = "-vxTrackAtVertex.-MvfFitInfo.-isInitialized.-VTAV"
    StaticContent = []
    StaticContent += ["xAOD::VertexContainer#SoftBVrtClusterTool_Tight_Vertices"]
    StaticContent += ["xAOD::VertexAuxContainer#SoftBVrtClusterTool_Tight_VerticesAux." + excludedVertexAuxData]
    StaticContent += ["xAOD::VertexContainer#SoftBVrtClusterTool_Medium_Vertices"]
    StaticContent += ["xAOD::VertexAuxContainer#SoftBVrtClusterTool_Medium_VerticesAux." + excludedVertexAuxData]
    StaticContent += ["xAOD::VertexContainer#SoftBVrtClusterTool_Loose_Vertices"]
    StaticContent += ["xAOD::VertexAuxContainer#SoftBVrtClusterTool_Loose_VerticesAux." + excludedVertexAuxData] 
    StaticContent += ["xAOD::VertexContainer#NVSI_SecVrt_Tight"]
    StaticContent += ["xAOD::VertexAuxContainer#NVSI_SecVrt_TightAux."+excludedVertexAuxData]   
 
    PHYSSlimmingHelper.StaticContent = StaticContent
   
    # Extra content
    PHYSSlimmingHelper.ExtraVariables += ["AntiKt4EMTopoJets.ConeExclBHadronsFinal.ConeExclCHadronsFinal.GhostBHadronsFinal.GhostCHadronsFinal.GhostBHadronsFinalCount.GhostBHadronsFinalPt.GhostCHadronsFinalCount.GhostCHadronsFinalPt.IsoFixedCone5PtPUsub",
                                          "AntiKt4EMPFlowJets.ConeExclBHadronsFinal.ConeExclCHadronsFinal.GhostBHadronsFinal.GhostCHadronsFinal.GhostBHadronsFinalCount.GhostBHadronsFinalPt.GhostCHadronsFinalCount.GhostCHadronsFinalPt.isJvtHS.isJvtPU.IsoFixedCone5PtPUsub",
                                          "TruthPrimaryVertices.t.x.y.z",
                                          "InDetTrackParticles.eProbabilityHT.numberOfTRTHits.numberOfTRTOutliers",
                                          "EventInfo.GenFiltHT.GenFiltMET.GenFiltHTinclNu.GenFiltPTZ.GenFiltFatJ.HF_Classification.HF_SimpleClassification.HF_ClassificationC5J20.HF_ClassificationC5J25.HF_ClassificationC15J20.HF_ClassificationC15J25",
                                          "TauJets.dRmax.etOverPtLeadTrk",
                                          "TauJets_MuonRM.dRmax.etOverPtLeadTrk",
                                          "HLT_xAOD__TrigMissingETContainer_TrigEFMissingET.ex.ey",
                                          "HLT_xAOD__TrigMissingETContainer_TrigEFMissingET_mht.ex.ey",
                                          "HLT_AnomDet_ComboHypo.adScore"]
 
    if addExtraVariables:
        PHYSSlimmingHelper.ExtraVariables += addExtraVariables
 
    # HSGNN Score
    from TrkConfig.VertexFindingFlags import VertexSortingSetup
    if flags.Tracking.PriVertex.sortingSetup is VertexSortingSetup.GNNSorting:
        PHYSSlimmingHelper.ExtraVariables += ["PrimaryVertices.gnnScore"]
 
    if flags.Tau.TauEleRM_isAvailable:
        PHYSSlimmingHelper.ExtraVariables += ["TauJets_EleRM.dRmax.etOverPtLeadTrk"]
 
    # IFF extra content
    from LeptonTaggers.LeptonTaggersConfig import GetExtraPLITVariablesForDxAOD
    PHYSSlimmingHelper.ExtraVariables += GetExtraPLITVariablesForDxAOD()
                                  
    # Truth extra content
    if flags.Input.isMC:
 
        from DerivationFrameworkMCTruth.MCTruthCommonConfig import addTruth3ContentToSlimmerTool
        addTruth3ContentToSlimmerTool(PHYSSlimmingHelper)
        PHYSSlimmingHelper.AllVariables += ['TruthLHEParticles','InTimeAntiKt4TruthJets','OutOfTimeAntiKt4TruthJets']
        PHYSSlimmingHelper.ExtraVariables += ["Electrons.TruthLink",
                                              "Muons.TruthLink",
                                              "Photons.TruthLink",
                                              "AntiKt4TruthDressedWZJets.IsoFixedCone5Pt.HFHadronOriginID",
                                              "TruthHFWithDecayParticles.prodVtxLink.prodVtxLink.prodVtxLink.decayVtxLink.decayVtxLink.decayVtxLink.parentLinks.childLinks.m.px.py.pz.e.pdgId.Classification.uid.classifierParticleOrigin.classifierParticleType.classifierParticleOutCome.status",
                                              "TruthHFWithDecayVertices.incomingParticleLinks.outgoingParticleLinks.uid.status.x.y.z.t",
                                              "TruthCharm.prodVtxLink.prodVtxLink.prodVtxLink.decayVtxLink.decayVtxLink.decayVtxLink.parentLinks.childLinks.m.px.py.pz.e.pdgId.Classification.uid.classifierParticleOrigin.classifierParticleType.classifierParticleOutCome.status.barcode.polarizationPhi.polarizationTheta",
                                              "TruthPileupParticles.prodVtxLink.prodVtxLink.prodVtxLink.decayVtxLink.decayVtxLink.decayVtxLink.m.px.py.pz.e.pdgId.Classification.uid.classifierParticleOrigin.classifierParticleType.classifierParticleOutCome.status.barcode.PVz.pileupEventNumber.parentHadronID"]
 
        from DerivationFrameworkMCTruth.MCTruthCommonConfig import AddTauAndDownstreamParticlesCfg
        acc.merge(AddTauAndDownstreamParticlesCfg(flags))
        PHYSSlimmingHelper.ExtraVariables += ["TruthTausWithDecayParticles.prodVtxLink.prodVtxLink.prodVtxLink.decayVtxLink.decayVtxLink.decayVtxLink.m.px.py.pz.e.pdgId.Classification.uid.classifierParticleOrigin.classifierParticleType.classifierParticleOutCome.status",
                                              "TruthTausWithDecayVertices.incomingParticleLinks.outgoingParticleLinks.uid.status.x.y.z.t"]
        
        #Truth jet matching variables - largeR
        PHYSSlimmingHelper.ExtraVariables += ["AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10TruthLabel_R22v1_TruthMatch_Jet",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10TruthLabel_R22v1_TruthMatch_m",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10TruthLabel_R22v1_TruthMatch_pt",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10TruthLabel_R22v1_TruthMatch_rapidity",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10TruthLabel_R22v1_TruthMatch_phi",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10TruthLabel_R22v1_TruthMatch_dR",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10TruthLabel_R22v1_TruthMatch_GroomedJetMass",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10TruthLabel_R22v1_TruthMatch_GroomedJetPt",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10WZTruthLabel_R22v1_TruthMatch_Jet",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10WZTruthLabel_R22v1_TruthMatch_m",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10WZTruthLabel_R22v1_TruthMatch_pt",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10WZTruthLabel_R22v1_TruthMatch_rapidity",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10WZTruthLabel_R22v1_TruthMatch_phi",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10WZTruthLabel_R22v1_TruthMatch_dR",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10WZTruthLabel_R22v1_TruthMatch_GroomedJetMass",
                                              "AntiKt10UFOCSSKSoftDropBeta100Zcut10Jets.R10WZTruthLabel_R22v1_TruthMatch_GroomedJetPt"]
 
    
    from DerivationFrameworkHiggs.HiggsPhysContent import  setupHiggsSlimmingVariables
    setupHiggsSlimmingVariables(flags, PHYSSlimmingHelper)
 
    
    PHYSSlimmingHelper.AllVariables += [ 'AFPSiHitContainer', 'AFPToFHitContainer' ]
 
    
    PHYSSlimmingHelper.AppendToDictionary.update({'MET_Core_AntiKt4EMPFlowHR':'xAOD::MissingETContainer', 'MET_Core_AntiKt4EMPFlowHRAux':'xAOD::MissingETAuxContainer',
                                                   'METAssoc_AntiKt4EMPFlowHR':'xAOD::MissingETAssociationMap', 'METAssoc_AntiKt4EMPFlowHRAux':'xAOD::MissingETAuxAssociationMap'})
 
    PHYSSlimmingHelper.AllVariables += ['METAssoc_AntiKt4EMPFlowHR']
 
    PHYSSlimmingHelper.ExtraVariables += ['Muons.UEcorr_Pt','Electrons.UEcorr_Pt','MET_Core_AntiKt4EMPFlowHR.name.mpx.mpy.sumet.source']
 
    # Trigger content
    PHYSSlimmingHelper.IncludeTriggerNavigation = False
    PHYSSlimmingHelper.IncludeJetTriggerContent = False
    PHYSSlimmingHelper.IncludeMuonTriggerContent = False
    PHYSSlimmingHelper.IncludeEGammaTriggerContent = False
    PHYSSlimmingHelper.IncludeTauTriggerContent = False
    PHYSSlimmingHelper.IncludeEtMissTriggerContent = False
    PHYSSlimmingHelper.IncludeBJetTriggerContent = False
    PHYSSlimmingHelper.IncludeBPhysTriggerContent = False
    PHYSSlimmingHelper.IncludeMinBiasTriggerContent = False
    # Compact b-jet trigger matching info
    PHYSSlimmingHelper.IncludeBJetTriggerByYearContent = True
 
    #Trigger content for DarkJetPEB 
    if flags.Input.TriggerStream=='physics_DarkJetPEBTLA' and not flags.Input.isMC:
        PHYSSlimmingHelper.AllVariables += ['HLT_AntiKt4EMPFlowJets_subresjesgscIS_ftf_TLA',
                                            'HLT_MET_pfopufit']
 
    # Trigger matching
    # Run 2
    if flags.Trigger.EDMVersion == 2:
        from DerivationFrameworkPhys.TriggerMatchingCommonConfig import AddRun2TriggerMatchingToSlimmingHelper
        AddRun2TriggerMatchingToSlimmingHelper(SlimmingHelper = PHYSSlimmingHelper, 
                                               OutputContainerPrefix = "TrigMatch_", 
                                               TriggerList = TriggerListsHelper.Run2TriggerNamesTau)
        AddRun2TriggerMatchingToSlimmingHelper(SlimmingHelper = PHYSSlimmingHelper, 
                                               OutputContainerPrefix = "TrigMatch_",
                                               TriggerList = TriggerListsHelper.Run2TriggerNamesNoTau)
    # Run 3, or Run 2 with navigation conversion
    if flags.Trigger.EDMVersion == 3 or (flags.Trigger.EDMVersion == 2 and flags.Trigger.doEDMVersionConversion):
        from TrigNavSlimmingMT.TrigNavSlimmingMTConfig import AddRun3TrigNavSlimmingCollectionsToSlimmingHelper
        AddRun3TrigNavSlimmingCollectionsToSlimmingHelper(PHYSSlimmingHelper)
 
    # L1 trigger objects
    from Campaigns.Utils import getDataYear
    if getDataYear(flags) >= 2024:
        # Run 3 with Phase I jet RoIs.
        from DerivationFrameworkPhys.TriggerMatchingCommonConfig import AddjFexRoIsToSlimmingHelper
        AddjFexRoIsToSlimmingHelper(SlimmingHelper = PHYSSlimmingHelper)
    elif getDataYear(flags) >= 2015:
        # Run 2 and early Run 3, legacy L1 RoIs
        from DerivationFrameworkPhys.TriggerMatchingCommonConfig import AddLegacyL1JetRoIsToSlimmingHelper
        AddLegacyL1JetRoIsToSlimmingHelper(SlimmingHelper = PHYSSlimmingHelper)
 
    # Output stream    
    PHYSItemList = PHYSSlimmingHelper.GetItemList()
    acc.merge(OutputStreamCfg(flags, "DAOD_"+name_tag, ItemList=PHYSItemList, AcceptAlgs=[name_tag+"Kernel"]))
    acc.merge(SetupMetaDataForStreamCfg(flags, "DAOD_"+name_tag, AcceptAlgs=[name_tag+"Kernel"], createMetadata=[MetadataCategory.CutFlowMetaData, MetadataCategory.TruthMetaData]))
 
    return acc
 
def PHYSCfg(flags):
 
    logPHYS.info('****************** STARTING PHYS *****************')
 
    stream_name = 'StreamDAOD_PHYS'
    acc = ComponentAccumulator()
 
    # Get the lists of triggers needed for trigger matching.
    # This is needed at this scope (for the slimming) and further down in the config chain
    # for actually configuring the matching, so we create it here and pass it down
    # TODO: this should ideally be called higher up to avoid it being run multiple times in a train
    from DerivationFrameworkPhys.TriggerListsHelper import TriggerListsHelper
    PHYSTriggerListsHelper = TriggerListsHelper(flags)
 
    # Common augmentations
    acc.merge(PHYSKernelCfg(
        flags,
        name="PHYSKernel",
        StreamName = stream_name,
        TriggerListsHelper = PHYSTriggerListsHelper
    ))
    # PHYS content
    acc.merge(PHYSCoreCfg(
        flags,
        "PHYS",
        StreamName = stream_name,
        TriggerListsHelper = PHYSTriggerListsHelper
        ))
    
    return acc