Merge branch 'AliceO2Group:master' into master

Author: JimunLee

.github/workflows/mega-linter.yml

@@ -38,7 +38,7 @@ jobs:
         id: ml
         # You can override MegaLinter flavor used to have faster performances
         # More info at https://megalinter.io/flavors/
-        uses: oxsecurity/megalinter@v9.4.0
+        uses: oxsecurity/megalinter@v9.5.0
         env:
           # All available variables are described in documentation:
           # https://megalinter.io/configuration/

.mega-linter.yml

@@ -21,11 +21,13 @@ DISABLE_LINTERS:
   - REPOSITORY_DEVSKIM
   - REPOSITORY_GITLEAKS
   - REPOSITORY_KICS
+  - REPOSITORY_OSV_SCANNER
   - REPOSITORY_SECRETLINT
   - REPOSITORY_TRIVY
   - YAML_PRETTIER
   - YAML_V8R
 DISABLE_ERRORS_LINTERS: # If errors are found by these linters, they will be considered as non blocking.
+  - ACTION_ZIZMOR
   - PYTHON_BANDIT # The bandit check is overly broad and complains about subprocess usage.
 SHOW_ELAPSED_TIME: true
 FILEIO_REPORTER: false
@@ -42,3 +44,4 @@ CPP_CLANG_FORMAT_FILE_EXTENSIONS: [".C", ".c", ".c++", ".cc", ".cl", ".cpp", ".c
 CPP_CPPCHECK_FILE_EXTENSIONS: [".C", ".c", ".c++", ".cc", ".cl", ".cpp", ".cu", ".cuh", ".cxx", ".cxx.in", ".h", ".h++", ".hh", ".h.in", ".hpp", ".hxx", ".inc", ".inl", ".macro"]
 CPP_CPPCHECK_ARGUMENTS: --language=c++ --std=c++20 --check-level=exhaustive --suppressions-list=cppcheck_config
 REPOSITORY_GITLEAKS_PR_COMMITS_SCAN: true
+ACTION_ZIZMOR_UNSECURED_ENV_VARIABLES: [GITHUB_TOKEN]

ALICE3/Core/Decayer.h

@@ -126,6 +126,7 @@ class Decayer
       particle.setPDG(pdgCodesDaughters[i]);
       particle.setVxVyVz(mVx, mVy, mVz);
       particle.setPxPyPzE(dau.Px(), dau.Py(), dau.Pz(), dau.E());
+      particle.setBitOn(o2::upgrade::DecayerBits::ProducedByDecayer);
       decayProducts.push_back(particle);
     }
 

ALICE3/Core/OTFParticle.h

@@ -21,13 +21,18 @@
 #include <CommonConstants/MathConstants.h>
 
 #include <array>
+#include <bitset>
 #include <cmath>
 #include <cstdint>
 #include <span>
 
 namespace o2::upgrade
 {
 
+enum class DecayerBits { ProducedByDecayer = 0,
+                         IsPrimary,
+                         IsAlive };
+
 class OTFParticle
 {
  public:
@@ -47,20 +52,32 @@ class OTFParticle
     mVy = particle.vy();
     mVz = particle.vz();
     mVt = particle.vt();
+    mFlag = particle.flags();
+    mStatusCode = particle.statusCode();
     mIsFromMcParticles = true;
     if (particle.has_mothers()) {
       mIndicesMother = {particle.mothersIds().front(), particle.mothersIds().back()};
     }
+    if (particle.has_daughters()) {
+      mIndicesDaughter = {particle.daughtersIds().front(), particle.daughtersIds().back()};
+    }
+    if constexpr (requires { particle.decayerBits(); }) {
+      mBits = particle.decayerBits();
+    } else {
+      // If we are here, we created particle in the standard workflow -- without secondaries
+      // Then we should set all particles as physical primaries accordingly
+      setBitOn(DecayerBits::IsPrimary);
+    }
   }
 
   // Setters
-  void setIsAlive(const bool isAlive) { mIsAlive = isAlive; }
   void setIsPrimary(const bool isPrimary) { mIsPrimary = isPrimary; }
   void setCollisionId(const int collisionId) { mCollisionId = collisionId; }
   void setPDG(const int pdg) { mPdgCode = pdg; }
   void setIndicesMother(const int start, const int stop) { mIndicesMother = {start, stop}; }
   void setIndicesDaughter(const int start, const int stop) { mIndicesDaughter = {start, stop}; }
   void setProductionTime(const float vt) { mVt = vt; }
+  void setFlags(uint8_t flag) { mFlag = flag; }
   void setVxVyVz(const float vx, const float vy, const float vz)
   {
     mVx = vx;
@@ -74,6 +91,14 @@ class OTFParticle
     mPz = pz;
     mE = e;
   }
+  void setIndexOffset(const std::size_t offset)
+  {
+    static constexpr int NotFound = -1;
+    mIndicesMother[0] = (mIndicesMother[0] >= 0) ? mIndicesMother[0] + static_cast<int>(offset) : NotFound;
+    mIndicesMother[1] = (mIndicesMother[1] >= 0) ? mIndicesMother[1] + static_cast<int>(offset) : NotFound;
+    mIndicesDaughter[0] = (mIndicesDaughter[0] >= 0) ? mIndicesDaughter[0] + static_cast<int>(offset) : NotFound;
+    mIndicesDaughter[1] = (mIndicesDaughter[1] >= 0) ? mIndicesDaughter[1] + static_cast<int>(offset) : NotFound;
+  }
 
   // Getters
   int pdgCode() const { return mPdgCode; }
@@ -87,16 +112,8 @@ class OTFParticle
     static constexpr float Weight = 1.f;
     return Weight;
   }
-  uint8_t flags() const
-  {
-    static constexpr uint8_t Flags = 1;
-    return Flags; // todo
-  }
-  int statusCode() const
-  {
-    static constexpr int StatusCode = 1;
-    return StatusCode; // todo
-  }
+  uint8_t flags() const { return mFlag; }
+  int statusCode() const { return mStatusCode; }
   float vx() const { return mVx; }
   float vy() const { return mVy; }
   float vz() const { return mVz; }
@@ -112,7 +129,8 @@ class OTFParticle
   float phi() const { return o2::constants::math::PI + std::atan2(-1.0f * py(), -1.0f * px()); }
   float eta() const
   {
-    // As https://github.com/AliceO2Group/AliceO2/blob/dev/Framework/Core/include/Framework/AnalysisDataModel.h#L1943
+    // Conditionally defined to avoid FPEs
+    // As https://github.com/AliceO2Group/AliceO2/blob/dev/Framework/Core/include/Framework/AnalysisDataModel.h#L1959
     static constexpr float Tolerance = 1e-7f;
     if ((p() - mPz) < Tolerance) {
       return (mPz < 0.0f) ? -100.0f : 100.0f;
@@ -122,7 +140,8 @@ class OTFParticle
   }
   float y() const
   {
-    // As https://github.com/AliceO2Group/AliceO2/blob/dev/Framework/Core/include/Framework/AnalysisDataModel.h#L1922
+    // Conditionally defined to avoid FPEs
+    // As https://github.com/AliceO2Group/AliceO2/blob/dev/Framework/Core/include/Framework/AnalysisDataModel.h#L1980
     static constexpr float Tolerance = 1e-7f;
     if ((e() - mPz) < Tolerance) {
       return (mPz < 0.0f) ? -100.0f : 100.0f;
@@ -139,8 +158,8 @@ class OTFParticle
   std::span<const int> getMotherSpan() const { return hasMothers() ? std::span<const int>(mIndicesMother.data(), 2) : std::span<const int>(); }
 
   // Checks
-  bool hasDaughters() const { return (mIndicesDaughter[0] > 0); }
-  bool hasMothers() const { return (mIndicesMother[0] > 0); }
+  bool hasDaughters() const { return (mIndicesDaughter[0] >= 0); }
+  bool hasMothers() const { return (mIndicesMother[0] >= 0); }
   bool hasNaN() const
   {
     return std::isnan(mPx) || std::isnan(mPy) || std::isnan(mPz) || std::isnan(mE) ||
@@ -151,13 +170,27 @@ class OTFParticle
     return (mGlobalIndex != -1);
   }
 
+  // Bits
+  bool checkBit(DecayerBits bit) const { return mBits.test(static_cast<size_t>(bit)); }
+  void setBit(DecayerBits bit, bool value = true) { mBits.set(static_cast<size_t>(bit), value); }
+  void setBitOn(DecayerBits bit) { mBits.set(static_cast<size_t>(bit), true); }
+  void setBitOff(DecayerBits bit) { mBits.set(static_cast<size_t>(bit), false); }
+
+  std::bitset<8> getBits() const { return mBits; }
+  uint8_t getBitsValue() const { return static_cast<uint8_t>(mBits.to_ulong()); }
+  void setBits(std::bitset<8> bits) { mBits = bits; }
+
  private:
   int mPdgCode{}, mGlobalIndex{-1};
-  int mCollisionId{};
+  int mCollisionId{-1};
   float mVx{}, mVy{}, mVz{}, mVt{};
   float mPx{}, mPy{}, mPz{}, mE{};
   bool mIsAlive{}, mIsFromMcParticles{false};
   bool mIsPrimary{};
+
+  int mStatusCode{};
+  uint8_t mFlag{};
+  std::bitset<8> mBits{};
   std::array<int, 2> mIndicesMother{-1, -1}, mIndicesDaughter{-1, -1};
 };
 

ALICE3/Core/TrackUtilities.cxx

@@ -17,6 +17,8 @@
 
 #include "TrackUtilities.h"
 
+#include <CommonConstants/PhysicsConstants.h>
+#include <MathUtils/Primitive2D.h>
 #include <MathUtils/Utils.h>
 #include <ReconstructionDataFormats/Track.h>
 

ALICE3/Core/TrackUtilities.h

@@ -24,9 +24,7 @@
 
 #include <TLorentzVector.h>
 
-#include <array>
 #include <cmath>
-#include <span>
 #include <vector>
 
 namespace o2::upgrade

ALICE3/DataModel/OTFMCParticle.h

@@ -37,6 +37,8 @@ DECLARE_SOA_INDEX_COLUMN_FULL(PosTrack, posTrack, int, Tracks, "_Pos");
 DECLARE_SOA_INDEX_COLUMN_FULL(NegTrack, negTrack, int, Tracks, "_Neg");             //!
 DECLARE_SOA_INDEX_COLUMN_FULL(BachTrack, bachTrack, int, Tracks, "_Bach");          //!
 
+DECLARE_SOA_INDEX_COLUMN(McParticle, mcParticle);
+
 // topo vars
 DECLARE_SOA_COLUMN(DcaV0Daughters, dcaV0Daughters, float);
 DECLARE_SOA_COLUMN(DcaCascadeDaughters, dcaCascadeDaughters, float);
@@ -70,6 +72,9 @@ DECLARE_SOA_TABLE(UpgradeCascades, "AOD", "UPGRADECASCADES",
 
 using UpgradeCascade = UpgradeCascades::iterator;
 
+DECLARE_SOA_TABLE(A3CascadeMcLabels, "AOD", "A3CASCADEMCLABELS",
+                  o2::soa::Index<>, otfcascade::McParticleId);
+
 namespace otfv0
 {
 DECLARE_SOA_INDEX_COLUMN(Collision, collision);                         //!

ALICE3/DataModel/OTFStrangeness.h

@@ -0,0 +1,41 @@
+// Copyright 2019-2020 CERN and copyright holders of ALICE O2.
+// See https://alice-o2.web.cern.ch/copyright for details of the copyright holders.
+// All rights not expressly granted are reserved.
+//
+// This software is distributed under the terms of the GNU General Public
+// License v3 (GPL Version 3), copied verbatim in the file "COPYING".
+//
+// In applying this license CERN does not waive the privileges and immunities
+// granted to it by virtue of its status as an Intergovernmental Organization
+// or submit itself to any jurisdiction.
+
+///
+/// \file   collisionExtra.h
+/// \author David Dobrigkeit Chinellato
+/// \since  11/05/2023
+/// \brief  Table for ALICE 3 collision-related info
+///
+
+#ifndef ALICE3_DATAMODEL_PREFILTERDILEPTON_H_
+#define ALICE3_DATAMODEL_PREFILTERDILEPTON_H_
+
+// O2 includes
+#include <Framework/AnalysisDataModel.h>
+
+namespace o2::aod
+{
+
+namespace dileptonanalysisflags
+{
+// DECLARE_SOA_COLUMN(IsMCEventSelected, isMCEventSelected, int);
+DECLARE_SOA_COLUMN(IsEventCentSelected, isEventCentSelected, int);
+DECLARE_SOA_COLUMN(IsTrackPrefilter, isTrackPrefilter, int);
+} // namespace dileptonanalysisflags
+
+// DECLARE_SOA_TABLE(EventMCCuts, "AOD", "EVENTMCCUTS", emanalysisflags::IsMCEventSelected);
+DECLARE_SOA_TABLE(DiEventCentCuts, "AOD", "DIEVENTCENTCUTS", dileptonanalysisflags::IsEventCentSelected);
+DECLARE_SOA_TABLE(DiTrackPrefilter, "AOD", "DITRACKPREFILTER", dileptonanalysisflags::IsTrackPrefilter);
+
+} // namespace o2::aod
+
+#endif // ALICE3_DATAMODEL_PREFILTERDILEPTON_H_

ALICE3/DataModel/prefilterDilepton.h

@@ -50,11 +50,15 @@ namespace mcparticle_alice3
 {
 DECLARE_SOA_COLUMN(NHits, nHits, int);     //! number of silicon hits
 DECLARE_SOA_COLUMN(Charge, charge, float); //! particle charge
+DECLARE_SOA_BITMAP_COLUMN(DecayerBits, decayerBits, 8); //! Bit mask for particle produced by the OTF decayer
 } // namespace mcparticle_alice3
 DECLARE_SOA_TABLE(MCParticlesExtraA3, "AOD", "MCParticlesExtraA3",
                   mcparticle_alice3::NHits,
                   mcparticle_alice3::Charge);
 using MCParticleExtraA3 = MCParticlesExtraA3::iterator;
+
+DECLARE_SOA_TABLE(OTFDecayerBits, "AOD", "OTFDecayerBits", mcparticle_alice3::DecayerBits);
+
 } // namespace o2::aod
 
 #endif // ALICE3_DATAMODEL_TRACKSALICE3_H_