[mCBM] Generalize macro to use algo TOF clusterizer as task and gen. YAML files + HowTo

HowTo for now placed close to the macro, may be moved to docs later

macro/tools/HowTo_TofYaml.md

+# Generation of TOF parameter YAML files for the algo version of the TOF HitFinder/Clusterizer
+
+**!!! WORKING ONLY FOR mCBM RUNS !!!**
+
+1. Pick a run (`<RUN ID>` in later parts), check in `core/base/utils/CbmMcbmUtils.cxx` to which setup it corresponds and check in `geometry/setup` that this would load the geometries you expect (if not modify te setup file)
+1. Locate where you have your custom TOF calibration file (`.....tofClust.hst.root`)
+1. Locate where you have your custom geometry alignment file (typ. `AlignmentMatrices_<setup_name>.root`) and make sure it fit you (eventually custom) setup
+1. Create the geo root file in `macro/run` by running
+   ```
+   root -l -b -q 'create_mcbm_geo_setup.C(<RUN ID>)'
+   ```
+1. Create an unpacked file with at least 1 TS for this run (with `macro/run/run_unpack_tsa.C`) or locate an existing unpacked file and make a symlink for it called `<RUN ID>.digi.root` in `macro/run/data`
+1. Go to `macro/tools`
+1. Run the following command (replacing the `<....>` parts with the corresponding info)
+   ```
+   root -l -b -q 'tof_hitfinder_run.C(<RUN ID>, 1, "../run/data/", "../run/data/", -1, "", <FULL PATH TO TOF CALIB FILE>, <FULL PATH TO ALIGNMENT FILE>, true)'
+   ```
+1. You should now find in the folder you are two new YAML files called `TofCalibratePar.yaml` and `TofHitfinderPar.yaml`
+   - If you want you can try to compare them with `diff` or `meld` to the ones in `parameters/online`
+1. To test the new YAML param files
+   1. Copy the files to `parameters/online`
+   1. Run (using the dummy/example file made for the yaml generation) 
+      ```
+      root -l -b -q 'tof_hitfinder_run.C(<RUN ID>, 1, "./data/", "./data/", -1)'
+      ```

macro/tools/tof_hitfinder_run.C

@@ -7,13 +7,34 @@
 #include <stdio.h>
 #include <string.h>
 
+template<typename TofTaskType>
+void CreateTask(TofTaskType* tofCluster, FairRunAna* run, TString& myName, TString& cFname, Int_t& calMode,
+                Double_t& dDeadtime)
+{
+  tofCluster->SetCalParFileName(cFname);
+  tofCluster->SetCalMode(calMode);
+  tofCluster->SetTotMax(20.);                 // Tot upper limit for walk corection
+  tofCluster->SetTotMin(0.);                  //(12000.);  // Tot lower limit for walk correction
+  tofCluster->SetTotMean(5.);                 // Tot calibration target value in ns
+  tofCluster->SetMaxTimeDist(1.0);            // default cluster range in ns
+  tofCluster->SetChannelDeadtime(dDeadtime);  // artificial deadtime in ns
+  tofCluster->PosYMaxScal(0.75);              //in % of length
+
+  run->AddTask(tofCluster);
+  std::cout << "-I- " << myName << ": Added task " << tofCluster->GetName() << std::endl;
+}
+
 /// FIXME: Disable clang formatting to keep easy parameters overview
 /* clang-format off */
 Bool_t tof_hitfinder_run(UInt_t uRunId                   = 2391,
-                       Int_t nTimeslices               = 1,
-                       TString sInpDir                 = "/home/dsmith/cbmroot/macro/beamtime/mcbm2022/data/",
-                       TString sOutDir                 = "rec/",
-                       Int_t iUnpFileIndex             = -1)
+                         Int_t nTimeslices               = 1,
+                         TString sInpDir                 = "../beamtime/mcbm2022/data/",
+                         TString sOutDir                 = "rec/",
+                         Int_t iUnpFileIndex             = -1,
+                         TString TofFileFolder           = "", // Your folder with the Tof Calibration files;
+                         TString calibFile               = "",
+                         TString alignmentMatrixFileName = "",
+                         bool bGenerateYamlFiles         = false)
 {
   /// FIXME: Re-enable clang formatting after parameters initial values setting
   /* clang-format on */
@@ -40,9 +61,6 @@ Bool_t tof_hitfinder_run(UInt_t uRunId                   = 2391,
   TString parFileOut = sOutDir + "/reco_event_mcbm_params_" + sRunId;
   TString outFile    = sOutDir + "/reco_event_mcbm_" + sRunId;
 
-  // Your folder with the Tof Calibration files;
-  TString TofFileFolder = "/home/dsmith/cbmroot/macro/run/data/";
-
   /// Add index of splitting at unpacking level if needed
   if (0 <= iUnpFileIndex) {
     inFile += TString::Format("_%02u", iUnpFileIndex);
@@ -82,6 +100,16 @@ Bool_t tof_hitfinder_run(UInt_t uRunId                   = 2391,
   if (uRunId >= 2391) iCalSet = 22002500;
 
   const Int_t iTofCluMode = 1;
+
+  if (TofFileFolder.Length() != 0) {
+    // Use user provided path
+    TofFileFolder = Form("%s/%s", TofFileFolder.Data(), cCalId.Data());
+  }
+  else {
+    // use default path
+    TofFileFolder = srcDir + "parameter/mcbm/";
+    // TofFileFolder = "../run/data/" + cCalId;
+  }
   // ------------------------------------------------------------------------
 
   // --- Load the geometry setup ----
@@ -96,7 +124,7 @@ Bool_t tof_hitfinder_run(UInt_t uRunId                   = 2391,
     return kFALSE;
   }
 
-  TString geoFile    = srcDir + "/macro/mcbm/data/" + geoSetupTag + ".geo.root";
+  TString geoFile    = sInpDir + "/" + geoSetupTag + ".geo.root";
   CbmSetup* geoSetup = CbmSetup::Instance();
   geoSetup->LoadSetup(geoSetupTag);
 
@@ -105,7 +133,6 @@ Bool_t tof_hitfinder_run(UInt_t uRunId                   = 2391,
 
   //-----  Load Parameters --------------------------------------------------
   TList* parFileList = new TList();
-  TofFileFolder      = Form("%s/%s", TofFileFolder.Data(), cCalId.Data());
 
   // ----- TOF digitisation parameters -------------------------------------
   TString geoTag;
@@ -138,6 +165,39 @@ Bool_t tof_hitfinder_run(UInt_t uRunId                   = 2391,
   FairMonitor::GetMonitor()->EnableMonitor(kTRUE, monitorFile);
   // ------------------------------------------------------------------------
 
+  // =========================================================================
+  // ===                        GEO Alignment                              ===
+  // =========================================================================
+  if (alignmentMatrixFileName.Length() != 0) {
+    std::cout << "-I- " << myName << ": Applying alignment for file " << alignmentMatrixFileName << std::endl;
+
+    // Define the basic structure which needs to be filled with information
+    // This structure is stored in the output file and later passed to the
+    // FairRoot framework to do the (miss)alignment
+    std::map<std::string, TGeoHMatrix>* matrices{nullptr};
+
+    // read matrices from disk
+    LOG(info) << "Filename: " << alignmentMatrixFileName;
+    TFile* misalignmentMatrixRootfile = new TFile(alignmentMatrixFileName, "READ");
+    if (misalignmentMatrixRootfile->IsOpen()) {
+      gDirectory->GetObject("MisalignMatrices", matrices);
+      misalignmentMatrixRootfile->Close();
+    }
+    else {
+      LOG(error) << "Could not open file " << alignmentMatrixFileName << "\n Exiting";
+      return kFALSE;
+    }
+
+    if (matrices) {
+      run->AddAlignmentMatrices(*matrices);
+    }
+    else {
+      LOG(error) << "Alignment required but no matrices found."
+                 << "\n Exiting";
+      return kFALSE;
+    }
+  }
+  // -------------------------------------------------------------------------
 
   // -----   Logger settings   ----------------------------------------------
   FairLogger::GetLogger()->SetLogScreenLevel(logLevel.Data());
@@ -151,15 +211,25 @@ Bool_t tof_hitfinder_run(UInt_t uRunId                   = 2391,
     TString cFname;
     switch (iTofCluMode) {
       case 1: {
-
-        // For production of YAML files
-        //CbmTaskTofClusterizerParWrite* tofCluster = new CbmTaskTofClusterizerParWrite("Task TOF Clusterizer", 0, 1);
-
-        // For actual processing
-        CbmTaskTofClusterizer* tofCluster = new CbmTaskTofClusterizer("Task TOF Clusterizer", 0, 1);
-
-        cFname = Form("/%s_set%09d_%02d_%01dtofClust.hst.root", cCalId.Data(), iCalSet, calMode, calSel);
-        tofCluster->SetCalParFileName(TofFileFolder + cFname);
+        cFname = Form("%s/%s_set%09d_%02d_%01dtofClust.hst.root", TofFileFolder.Data(), cCalId.Data(), iCalSet, calMode,
+                      calSel);
+        if (calibFile.Length() != 0) {
+          // Use user provided calib file, overriding the automatic determination based on run ID
+          cFname = calibFile;
+        }
+
+        if (bGenerateYamlFiles) {
+          // For production of YAML files
+          CbmTaskTofClusterizerParWrite* tofCluster = new CbmTaskTofClusterizerParWrite("Task TOF Clusterizer", 0, 1);
+          CreateTask<CbmTaskTofClusterizerParWrite>(tofCluster, run, myName, cFname, calMode, dDeadtime);
+        }
+        else {
+          // For actual processing
+          CbmTaskTofClusterizer* tofCluster = new CbmTaskTofClusterizer("Task TOF Clusterizer", 0, 1);
+          CreateTask<CbmTaskTofClusterizer>(tofCluster, run, myName, cFname, calMode, dDeadtime);
+        }
+        /*
+        tofCluster->SetCalParFileName(cFname);
         tofCluster->SetCalMode(calMode);
         tofCluster->SetTotMax(20.);                 // Tot upper limit for walk corection
         tofCluster->SetTotMin(0.);                  //(12000.);  // Tot lower limit for walk correction
@@ -170,6 +240,7 @@ Bool_t tof_hitfinder_run(UInt_t uRunId                   = 2391,
 
         run->AddTask(tofCluster);
         std::cout << "-I- " << myName << ": Added task " << tofCluster->GetName() << std::endl;
+        */
       } break;
 
       default: {