Merge branch 'main' into rcdb-sqlite

CODEOWNERS

@@ -9,10 +9,14 @@
 #################################################################################
 
 * @c-dilks
+src/iguana/algorithms/clas12/EventBuilderFilter/* @c-dilks
+src/iguana/algorithms/clas12/FTEnergyCorrection/* @asligonulacar
+src/iguana/algorithms/clas12/FiducialFilter/* @Gregtom3
 src/iguana/algorithms/clas12/MomentumCorrection/* @RichCap @c-dilks
-src/iguana/algorithms/clas12/ZVertexFilter/* @rtysonCLAS12
+src/iguana/algorithms/clas12/PhotonGBTFilter/* @Gregtom3
 src/iguana/algorithms/clas12/SectorFinder/* @rtysonCLAS12
-src/iguana/algorithms/clas12/FTEnergyCorrection/* @asligonulacar
+src/iguana/algorithms/clas12/ZVertexFilter/* @rtysonCLAS12
+src/iguana/algorithms/physics/DihadronKinematics/* @c-dilks
+src/iguana/algorithms/physics/InclusiveKinematics/* @c-dilks
+src/iguana/algorithms/physics/SingleHadronKinematics/* @c-dilks
 src/iguana/services/YAMLReader.* @rtysonCLAS12 @c-dilks
-src/iguana/algorithms/clas12/PhotonGBTFilter/* @Gregtom3
-src/iguana/algorithms/clas12/FiducialFilter/* @Gregtom3

doc/gen/Doxyfile.in

@@ -302,6 +302,8 @@ ALIASES += end_doc_example="@}"
 # ignore things we don't want to document
 ALIASES += doxygen_off="@cond NO_DOC"
 ALIASES += doxygen_on="@endcond"
+# latex
+ALIASES += latex{1}="@f$\1@f$"
 
 # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources
 # only. Doxygen will then generate output that is more tailored for C. For

examples/config/my_combined_config_file.yaml

@@ -21,17 +21,15 @@ example::ExampleAlgorithm:
 
 clas12::ZVertexFilter:
 
-  # default cuts
-  - default:
-    electron_vz: [ -33.0, 11.0 ]
+  log: debug  # NOTE: you may control algorithm log levels here, like so
 
-  #RG-A fall2018 inbending
+  electron:
+  - default:
+    vz: [ -33.0, 11.0 ]
   - runs: [ 4760, 5419 ]
-    electron_vz: [ -13.0, 12.0 ]
-
-   #RG-A fall2018 outbending
+    vz: [ -13.0, 12.0 ]
   - runs: [ 5420, 5674 ]
-    electron_vz: [ -18.0, 10.0 ]
+    vz: [ -18.0, 10.0 ]
 
 another::Algorithm:
   #Cuts below are just examples:

examples/config/my_config_directory/algorithms/clas12/ZVertexFilter/Config.yaml

@@ -1,14 +1,17 @@
 # Cut values for different run periods
 clas12::ZVertexFilter:
 
-  # default cuts
-  - default:
-    electron_vz: [ -15.0, 15.0 ]
+  # scattered electron cuts
+  electron:
 
-  # RG-A fall2018 inbending
-  - runs: [ 4760, 5419 ]
-    electron_vz: [ -5.0, 3.0 ]
+    # default cuts
+    - default:
+      vz: [ -15.0, 15.0 ]
 
-  # RG-A fall2018 outbending
-  - runs: [ 5420, 5674 ]
-    electron_vz: [ -8.0, 7.0 ]
+    # RG-A fall2018 inbending
+    - runs: [ 4760, 5419 ]
+      vz: [ -5.0, 3.0 ]
+
+    # RG-A fall2018 outbending
+    - runs: [ 5420, 5674 ]
+      vz: [ -8.0, 7.0 ]

examples/config/my_z_vertex_cuts.yaml

@@ -1,14 +1,22 @@
 # Cut values for different run periods
 clas12::ZVertexFilter:
 
-  # default cuts
-  - default:
-    electron_vz: [ -1.5, 1.3 ]
+  ###################################################################################
+  # NOTE: for convenience, you can also set the log level from the configuration file
+  log: trace
+  ###################################################################################
 
-  # RG-A fall2018 inbending
-  - runs: [ 4760, 5419 ]
-    electron_vz: [ -0.5, 0.5 ]
+  # scattered electron cuts
+  electron:
 
-  # RG-A fall2018 outbending
-  - runs: [ 5420, 5674 ]
-    electron_vz: [ -0.8, 0.7 ]
+    # default cuts
+    - default:
+      vz: [ -1.5, 1.3 ]
+
+    # RG-A fall2018 inbending
+    - runs: [ 4760, 5419 ]
+      vz: [ -0.5, 0.5 ]
+
+    # RG-A fall2018 outbending
+    - runs: [ 5420, 5674 ]
+      vz: [ -0.8, 0.7 ]

examples/iguana_ex_fortran_01_action_functions.f

@@ -51,6 +51,7 @@ program iguana_ex_fortran_01_action_functions
       logical(c_bool) accept(N_MAX)  ! filter
       real(c_double) qx, qy, qz, qE  ! q vector
       real(c_double) Q2, x, y, W, nu ! inclusive kinematics
+      real(c_double) beamPz, targetM ! beam and target
       integer(c_int) key_vz_filter   ! key for Z-vertex filter
       integer(c_int) key_inc_kin     ! key for inclusive kinematics
 
@@ -273,7 +274,8 @@ program iguana_ex_fortran_01_action_functions
      &      px(i_ele), py(i_ele), pz(i_ele),
      &      key_inc_kin,
      &      qx, qy, qz, qE,
-     &      Q2, x, y, W, nu)
+     &      Q2, x, y, W, nu,
+     &      beamPz, targetM)
           print *, '===> inclusive kinematics:'
           print *, '  q = (', qx, qy, qz, qE, ')'
           print *, ' Q2 = ', Q2

meson/this_iguana.sh.in

@@ -22,6 +22,8 @@ for arg in "$@"; do
       unset arg_githubCI
       return 2
       ;;
+    source*|.*) # handle callers which cause `$1` to be 'source this_iguana.sh' or '. this_iguana.sh'
+      ;;
     *)
       echo "ERROR: unknown option '$arg'" >&2
       unset arg

meson/ubsan.supp

@@ -3,3 +3,4 @@ alignment:hipo::structure::getFloatAt
 alignment:hipo::structure::getShortAt
 alignment:hipo::structure::getDoubleAt
 alignment:hipo::structure::putDoubleAt
+alignment:hipo::structure::putIntAt

src/iguana/algorithms/Algorithm.cc

@@ -16,17 +16,17 @@ namespace iguana {
   template <typename OPTION_TYPE>
   OPTION_TYPE Algorithm::GetOptionScalar(std::string const& key, YAMLReader::node_path_t node_path) const
   {
-    try {
-      CompleteOptionNodePath(key, node_path);
-      auto opt = GetCachedOption<OPTION_TYPE>(key);
-      auto val = opt ? opt.value() : m_yaml_config->GetScalar<OPTION_TYPE>(node_path);
-      PrintOptionValue(key, val);
-      return val;
+    CompleteOptionNodePath(key, node_path);
+    auto opt = GetCachedOption<OPTION_TYPE>(key);
+    if(!opt.has_value()) {
+      opt = m_yaml_config->GetScalar<OPTION_TYPE>(node_path);
     }
-    catch(std::runtime_error const& ex) {
-      m_log->Error("Failed to `GetOptionScalar` for key '{}'", key);
+    if(!opt.has_value()) {
+      m_log->Error("Failed to `GetOptionScalar` for key {:?}", key);
       throw std::runtime_error("config file parsing issue");
     }
+    PrintOptionValue(key, opt.value());
+    return opt.value();
   }
   template int Algorithm::GetOptionScalar(std::string const& key, YAMLReader::node_path_t node_path) const;
   template double Algorithm::GetOptionScalar(std::string const& key, YAMLReader::node_path_t node_path) const;
@@ -37,17 +37,17 @@ namespace iguana {
   template <typename OPTION_TYPE>
   std::vector<OPTION_TYPE> Algorithm::GetOptionVector(std::string const& key, YAMLReader::node_path_t node_path) const
   {
-    try {
-      CompleteOptionNodePath(key, node_path);
-      auto opt = GetCachedOption<std::vector<OPTION_TYPE>>(key);
-      auto val = opt ? opt.value() : m_yaml_config->GetVector<OPTION_TYPE>(node_path);
-      PrintOptionValue(key, val);
-      return val;
+    CompleteOptionNodePath(key, node_path);
+    auto opt = GetCachedOption<std::vector<OPTION_TYPE>>(key);
+    if(!opt.has_value()) {
+      opt = m_yaml_config->GetVector<OPTION_TYPE>(node_path);
     }
-    catch(std::runtime_error const& ex) {
-      m_log->Error("Failed to `GetOptionVector` for key '{}'", key);
+    if(!opt.has_value()) {
+      m_log->Error("Failed to `GetOptionVector` for key {:?}", key);
       throw std::runtime_error("config file parsing issue");
     }
+    PrintOptionValue(key, opt.value());
+    return opt.value();
   }
   template std::vector<int> Algorithm::GetOptionVector(std::string const& key, YAMLReader::node_path_t node_path) const;
   template std::vector<double> Algorithm::GetOptionVector(std::string const& key, YAMLReader::node_path_t node_path) const;
@@ -108,19 +108,35 @@ namespace iguana {
 
   void Algorithm::ParseYAMLConfig()
   {
+
+    // start YAMLReader instance, if not yet started
     if(!m_yaml_config) {
+      // set config files and directories specified by `::SetConfigFile`, `::SetConfigDirectory`, etc.
       o_user_config_file = GetCachedOption<std::string>("config_file").value_or("");
       o_user_config_dir  = GetCachedOption<std::string>("config_dir").value_or("");
       m_log->Debug("Instantiating `YAMLReader`");
       m_yaml_config = std::make_unique<YAMLReader>("config|" + m_name);
-      m_yaml_config->SetLogLevel(m_log->GetLevel());
+      m_yaml_config->SetLogLevel(m_log->GetLevel()); // synchronize log levels
       m_yaml_config->AddDirectory(o_user_config_dir);
       m_yaml_config->AddFile(m_default_config_file);
       m_yaml_config->AddFile(o_user_config_file);
     }
     else
       m_log->Debug("`YAMLReader` already instantiated for this algorithm; using that");
+
+    // parse the files
     m_yaml_config->LoadFiles();
+
+    // if "log" was not set by `SetOption` (i.e., not in `m_option_cache`)
+    // - NB: not using `GetCachedOption<T>` here, since `T` can be a few different types for key=='log'
+    if(m_option_cache.find("log") == m_option_cache.end()) {
+      // check if 'log' is set in the YAML node for this algorithm
+      auto log_level_from_yaml = m_yaml_config->GetScalar<std::string>({m_class_name, "log"});
+      if(log_level_from_yaml) {
+        m_log->SetLevel(log_level_from_yaml.value());
+        m_yaml_config->SetLogLevel(log_level_from_yaml.value());
+      }
+    }
   }
 
   ///////////////////////////////////////////////////////////////////////////////

src/iguana/algorithms/Algorithm.h

@@ -88,8 +88,7 @@ namespace iguana {
           else
             m_log->Error("Option '{}' must be a string or a Logger::Level", key);
         }
-        else
-          m_option_cache[key] = val;
+        m_option_cache[key] = val;
         return val;
       }
 
@@ -136,17 +135,17 @@ namespace iguana {
       /// @param name the directory name
       void SetConfigDirectory(std::string const& name);
 
-    protected: // methods
-
-      /// Parse YAML configuration files. Sets `m_yaml_config`.
-      void ParseYAMLConfig();
-
       /// Get the index of a bank in a `hipo::banklist`; throws an exception if the bank is not found
       /// @param banks the list of banks this algorithm will use
       /// @param bank_name the name of the bank
       /// returns the `hipo::banklist` index of the bank
       hipo::banklist::size_type GetBankIndex(hipo::banklist& banks, std::string const& bank_name) const noexcept(false);
 
+    protected: // methods
+
+      /// Parse YAML configuration files. Sets `m_yaml_config`.
+      void ParseYAMLConfig();
+
       /// Get the reference to a bank from a `hipo::banklist`; optionally checks if the bank name matches the expectation
       /// @param banks the `hipo::banklist` from which to get the specified bank
       /// @param idx the index of `banks` of the specified bank

src/iguana/algorithms/AlgorithmSequence.cc

@@ -67,4 +67,22 @@ namespace iguana {
       m_log->Print(level, " - {}", algo->GetName());
   }
 
+  void AlgorithmSequence::SetConfigFileForEachAlgorithm(std::string const& name)
+  {
+    for(auto const& algo : m_sequence)
+      algo->SetConfigFile(name);
+  }
+
+  void AlgorithmSequence::SetConfigDirectoryForEachAlgorithm(std::string const& name)
+  {
+    for(auto const& algo : m_sequence)
+      algo->SetConfigDirectory(name);
+  }
+
+  void AlgorithmSequence::ForEachAlgorithm(std::function<void(algo_t&)> func)
+  {
+    for(auto& algo : m_sequence)
+      func(algo);
+  }
+
 }

src/iguana/algorithms/AlgorithmSequence.h

@@ -93,6 +93,29 @@ namespace iguana {
       /// @param level the log level of the printout
       void PrintSequence(Logger::Level level = Logger::info) const;
 
+      /// @brief Set a custom configuration file for each algorithm in the sequence
+      ///
+      /// Use this function if you have a single configuration file for all the
+      /// algorithms in your sequence
+      /// @param name the configuration file name
+      void SetConfigFileForEachAlgorithm(std::string const& name);
+
+      /// @brief Set a custom configuration file directory for each algorithm in the sequence
+      ///
+      /// Use this function if you have a single configuration file directory for all the
+      /// algorithms in your sequence
+      /// @param name the directory name
+      void SetConfigDirectoryForEachAlgorithm(std::string const& name);
+
+      /// @brief Call a function for each algorithm in the sequence
+      ///
+      /// Use as:
+      /// ```cpp
+      /// ForEachAlgorithm([](auto& algo){ algo->...; });
+      /// ```
+      /// @param func the function to call for each algorithm `algo`
+      void ForEachAlgorithm(std::function<void(algo_t&)> func);
+
     private:
 
       /// The sequence of algorithms

src/iguana/algorithms/clas12/ZVertexFilter/Algorithm.cc

@@ -64,7 +64,7 @@ namespace iguana::clas12 {
     std::lock_guard<std::mutex> const lock(m_mutex); // NOTE: be sure to lock successive `ConcurrentParam::Save` calls !!!
     m_log->Trace("-> calling Reload({}, {})", runnum, key);
     o_runnum->Save(runnum, key);
-    o_electron_vz_cuts->Save(GetOptionVector<double>("electron_vz", {GetConfig()->InRange("runs", runnum), "electron_vz"}), key);
+    o_electron_vz_cuts->Save(GetOptionVector<double>("electron_vz", {"electron", GetConfig()->InRange("runs", runnum), "vz"}), key);
   }
 
   bool ZVertexFilter::Filter(double const zvertex, int const pid, int const status, concurrent_key_t key) const

src/iguana/algorithms/clas12/ZVertexFilter/Config.yaml

@@ -1,14 +1,16 @@
-# Cut values for different run periods
 clas12::ZVertexFilter:
 
-  # default cuts
-  - default:
-    electron_vz: [ -20.0, 20.0 ]
+  # scattered electron cuts
+  electron:
 
-  # RG-A fall2018 inbending
-  - runs: [ 4760, 5419 ]
-    electron_vz: [ -13.0, 12.0 ]
+    # default cuts
+    - default:
+      vz: [ -20.0, 20.0 ]
 
-  # RG-A fall2018 outbending
-  - runs: [ 5420, 5674 ]
-    electron_vz: [ -18.0, 10.0 ]
+    # RG-A fall2018 inbending
+    - runs: [ 4760, 5419 ]
+      vz: [ -13.0, 12.0 ]
+
+    # RG-A fall2018 outbending
+    - runs: [ 5420, 5674 ]
+      vz: [ -18.0, 10.0 ]