.clang-format

+---
+Standard: Cpp11
+BasedOnStyle:  Chromium
+AccessModifierOffset: -2
+AlignConsecutiveAssignments: true
+AlignConsecutiveDeclarations: true
+AlignEscapedNewlines: true
+AlignTrailingComments: true
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: false
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: true
+BreakConstructorInitializersBeforeComma: true
+BreakStringLiterals: true
+ColumnLimit: 100
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+Cpp11BracedListStyle: true
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+PointerBindsToType: true
+SpaceAfterControlStatementKeyword: true
+TabWidth:        8
+UseTab:          Never
+...

.gitignore

+# File extensions
 *~
-*.sw?
-ROOTfiles
-ROOTfiles/*
-ROOTfiles.old/*
-bck/*
-#*
-*#*
-hcana
-raw
-cache
-.root_history
-HISTOGRAMS/*
-REPORT_OUTPUT
-REPORT_OUTPUT/*
-log/*
-full_hms.sh
-full_shms.sh
-onlineGUI/Config/kpp_*
+*#*#*
 *.d
 *.so
-*Auto*
-run_*
-CALIBRATION/shms_cal_calib/pcal.param*
-CALIBRATION/hms_cal_calib/hcal.param*
-CALIBRATION/shms_cal_calib/calibrated.deb
-CALIBRATION/hms_cal_calib/calibrated.deb
-CALIBRATION/hms_cal_calib/hcal_calib_cpp_ACLiC_dict_rdict.pcm
-CALIBRATION/shms_cal_calib/pcal_calib_cpp_ACLiC_dict_rdict.pcm
-CALIBRATION/*/data_files/*		
-CALIBRATION/*/root_files/*
-CALIBRATION/shms_dc_calib/data_files/
-onlineGUI/onlineGUI_v1.2.1/onlineDict_rdict.pcm
+*.pcm
+*.png
+*.ps
+*.eps
+*.pdf
 .nfs*
-raw.copiedtotape
+*.root
+*.swp
+*.sw*
+
+# Analysis output
+hel_scalers_*.json
+
+# ROOT history file
+.root_history
+
+# Directories
+RAID
+REPORT_OUTPUT
 HISTOGRAMS
-*.png
-*.ps
\ No newline at end of file
+MON_OUTPUT
+ROOTfiles
+raw
+raw.copiedtotape
+cache
+logs
+scratch
+output
+output.*
+.root_build_dir
+
+# Symbolic links
+hcana

.gitmodules

+[submodule "UTIL_OL"]
+	path = UTIL_OL
+	url = https://github.com/JeffersonLab/UTIL_OL
+	branch = master

.rootlogon.C

+#include <string>
+
+void _rootlogon() {
+  // ensure we have format loaded. Should be able to move to C++20 fmt library
+  // some point in the future
+  R__LOAD_LIBRARY(libfmt);
+
+  // check if we requested a special build directory through the environment,
+  const char*       build_dir_from_env = gSystem->Getenv("ROOT_BUILD_TMPDIR");
+  const std::string build_dir = build_dir_from_env ? build_dir_from_env : "$PWD/.root_build_dir";
+
+  // ensure the build directory exists to avoid crashes due to it missing
+  // note: in principle this allows us to execute arbitrary code, but seeing
+  //       as this can only be manipulated through the shell environment in the
+  //       first place this should not be a safety concern.
+  const std::string mkdir = "mkdir -p " + build_dir;
+  gSystem->Exec(mkdir.c_str());
+
+  // Communicate what build directory we are using 
+  std::cout << "---> Setting ACLiC build directory to: " << build_dir << "\n\n";
+  // Make the ROOT build process use a flat build directory by setting
+  // second arg to kTRUE.  This avoids an apparent race condition in ROOT
+  // associated with child directory creation in the default 'kFALSE' mode.
+  // The default mode will work correctly on the 2nd execution.  OK for
+  // interactive use, but not great for the Farm environment.
+  gSystem->SetBuildDir(build_dir.c_str(), kTRUE);
+
+  // Ensure we have our environment setup
+  gROOT->ProcessLine(".include /usr/local/include/hcana");
+  gROOT->ProcessLine(".include SCRIPTS/include");
+  gROOT->ProcessLine(".include .");
+
+  // Some basic plotting setup
+  gROOT->SetStyle("Plain");
+  gStyle->SetPalette(1);
+
+  // Load extra ROOT libraries, TODO check if this is still
+  // needed in the newer ROOT versions we are using.
+  gSystem->Load("libTree");
+  gSystem->Load("libTreePlayer");
+  gSystem->Load("libHist");
+}

CALIBRATION/README.md

+# Hall C Calibration Codes
+
+1. This is the directory containing subdirectories for Hall C calibration codes.
+2. A few of the directories are obsolete. 
+3. Each subdirectory has a README or HOWTO which explains how to run the calibration code.
+
+## Obsolete directories
+
+1. hms_dc_calib : old HMS DC Tzero and time-to-distance maps calibration code
+2. shms_dc_calib : old SHMS DC Tzero and time-to-distance maps calibration code
+3. hodo_calib: old hodoscope calibration code used during the 6GeV running
+
+## Directories
+
+1. bcm_current_map : Contains scripts to create parameter files of the beam current as a function of event number to be used in the code for cutting data according to a beam current cut.
+
+2. bpm_calib : Contains scripts for fitting HARP vs BPM scans and creating a parameter file.
+
+3. dc_calib/scripts : Contains scripts for calibrating tzero parameters and time-to-dsitance maps for eithe the HMS or SHMS drift chambers. 
+
+4. hms_cal_calib : Contains scripts for calibrating the HMS calorimeter energy/ADC conversion for each block. 
+
+5. shms_cal_calib : Contains scripts for calibrating the SHMS calorimeter energy/ADC conversion for each block. 
+
+6. hms_hodo_calib : Contains scripts for calibrating the time offsets for the HMS hodoscope. Creates the time walk correction parameters, time difference between negative-postive PMTs in a paddle and the relative time offsets of the paddles.
+
+7. shms_hodo_calib : Contains scripts for calibrating the time offsets for the SHMS hodoscope. Creates the time walk correction parameters, time difference between negative-postive PMTs in a paddle and the relative time offsets of the paddles.
+
+8. shms_aero_calib : Contains a script to calibrate the NPE/ADC conversion parameters from SPE peaks for the SHMS aerogel.
+
+9. shms_hgcer_calib : Contains scripts to calibrate hte NPE/ADC conversion parameters for SHMS Gas Cerenkovs.
+
+10. set_peddefault : Contains script to determine the default pedestals for each SHMS and HMS detector.
+
+
+
+

CALIBRATION/bcm_current_calib/ScalerCalib.C → CALIBRATION/bcm_current_map/ScalerCalib.C

@@ -5,6 +5,9 @@
 
 using namespace std;
 
+const double kBig = 1.e38;
+const int NBCM = 5;
+
 ofstream outfile;
 
 //_________________________________
@@ -37,8 +40,18 @@ int ScalerCalib::Run()
       return -1;
     }
 
-  int pos = filename.find("scalers_");
-  runstr = (filename.substr(pos+8)).substr(0,4);
+  int pos;
+  pos = filename.find("scalers_");
+
+  if(pos == -1)
+    {
+      pos = filename.find("production_");
+      runstr = (filename.substr(pos+11)).substr(0,4);
+    }
+  else
+    {
+      runstr = (filename.substr(pos+8)).substr(0,4);  
+    }
 
   ofilename = "bcmcurrent_" + runstr + ".param";
   outfile.open(ofilename.c_str());
@@ -63,15 +76,15 @@ int ScalerCalib::Run()
       PrintContainer(bcm4b);
 
       outfile << "\n" << "\n";
-      outfile << "scal_read_bcm17_current = ";
-      PrintContainer(bcm17);
+      outfile << "scal_read_bcm4c_current = ";
+      PrintContainer(bcm4c);
     }
   
   outfile << "\n" << "\n";
   outfile << "scal_read_event = ";
   PrintContainer(evnum);
 
-  //  outfile.close();
+  outfile.close();
 
   return 0;
   
@@ -91,6 +104,7 @@ int ScalerCalib::PrintContainer(ScalerContainer sc)
 
   for(SCIterator i = sc.begin(); i != sc.end()-1; ++i)
     {
+      if(*i<=1E6)outfile<<std::fixed<<std::setprecision(0);
       outfile << *i << ", ";
     }
   
@@ -129,29 +143,31 @@ int ScalerCalib::FillContainer()
       return -1;      
     }
   
-  if(! file->GetListOfKeys()->Contains("TSH") )
+  string tname = "TS" + fName;
+
+  if(! file->GetListOfKeys()->Contains(tname.c_str()) )
     {
       cout << "ERROR: Couldn't find the Scaler Tree"  << endl;
       return -1;      
     }
 
-  TTree* T = (TTree*)file->Get("TSH");  
+  TTree* T = (TTree*)file->Get(tname.c_str());  
 
   double evnumber;
   double bcm1_current;
   double bcm2_current;
   double bcm4a_current;
   double bcm4b_current;
-  double bcm17_current;
+  double bcm4c_current;
 
-  string bname[5];
-  string sarray[5] = {".BCM1.scalerCurrent",
+  string bname[NBCM];
+  string sarray[NBCM] = {".BCM1.scalerCurrent",
 		      ".BCM2.scalerCurrent", 
 		      ".BCM4A.scalerCurrent",
 		      ".BCM4B.scalerCurrent",
-		      ".BCM17.scalerCurrent"};
+		      ".BCM4C.scalerCurrent"};
 
-  for(int i=0; i<5; i++)
+  for(int i=0; i<NBCM; i++)
     {
       bname[i] = "";
       bname[i] += fName;
@@ -163,21 +179,23 @@ int ScalerCalib::FillContainer()
   T->SetBranchAddress(bname[1].c_str(), &bcm2_current);
   T->SetBranchAddress(bname[2].c_str(), &bcm4a_current);
   T->SetBranchAddress(bname[3].c_str(), &bcm4b_current);
-  T->SetBranchAddress(bname[4].c_str(), &bcm17_current);
+  T->SetBranchAddress(bname[4].c_str(), &bcm4c_current);
 
   Long64_t nentries = T->GetEntries();
   for(Long64_t ientry=0; ientry<nentries; ientry++)
     {
       T->GetEntry(ientry);
 
-      if(evnumber < 0) continue;
+      if(evnumber < 0)
+	evnum.push_back(kBig);
+      else
+	evnum.push_back(evnumber);
 
-      evnum.push_back(evnumber);
       bcm1.push_back(bcm1_current);
       bcm2.push_back(bcm2_current);
       bcm4a.push_back(bcm4a_current);
       bcm4b.push_back(bcm4b_current);
-      bcm17.push_back(bcm17_current);
+      bcm4c.push_back(bcm4c_current);
 
     }
 
@@ -196,7 +214,7 @@ void ScalerCalib::ClearContainers()
   bcm2.clear();
   bcm4a.clear();
   bcm4b.clear();
-  bcm17.clear();
+  bcm4c.clear();
 
 }
 

CALIBRATION/bcm_current_calib/ScalerCalib.h → CALIBRATION/bcm_current_map/ScalerCalib.h

@@ -44,7 +44,7 @@ class ScalerCalib {
   ScalerContainer bcm2;
   ScalerContainer bcm4a;
   ScalerContainer bcm4b;
-  ScalerContainer bcm17;
+  ScalerContainer bcm4c;
 
   ClassDef(ScalerCalib,0)
 

CALIBRATION/bcm_current_calib/run.C → CALIBRATION/bcm_current_map/run.C

 R__LOAD_LIBRARY(ScalerCalib_C)
 
-void run(string fin="fin.root")
+void run(string fin="fin.root", string spec_name="H")
 {
 
   //H: HMS, P: SHMS
-  ScalerCalib scalib("H");
+  ScalerCalib scalib(spec_name);
   scalib.SetInputFile(fin);
   scalib.SetPrintFlag(1); //0: bcm1 and bcm2 only, 1: all
   scalib.Run();

CALIBRATION/bcm_current_map/run4shms.sh

+#!/bin/bash
+
+list=$1
+
+while read line
+do
+
+fname=/home/cdaq/hallc-online/hallc_replay/ROOTfiles/shms_replay_production_${line}_-1.root
+
+root -b<<EOF
+.x run.C("${fname}", "P")
+EOF
+
+[ ! -d "shms" ] && `mkdir shms`
+
+mv bcmcurrent* ./shms/
+
+done < ${list}

CALIBRATION/bpm_calib/Harp_files/harp_info.txt

+1771 0.194 -0.605 -1.548 0.328 345.528 154.612 -0.56 -0.62 0.67 -0.47 1.0 0.0 0.1 
+1770 0.838 -0.620 0.155 0.2969 345.528 154.612 -0.98 -0.61 -0.35 -0.43 -1.0 0.0 0.1 
+1769 0.683 -1.079 -0.677 -0.512 345.528 154.612 -0.99 -0.99 0.05 -1.00 0.0 -1.0 0.1
+1768 0.956 -1.194 1.033 -1.220 345.528 154.612 -1.00 -0.98 -0.80 -1.32 -2.0 -2.0 0.1
+1767  -0.620 -1.153 -2.499 -1.261 345.528 154.612 0.26 -1.0 1.46 -1.42 2.0 2.0 0.1
+1766 -0.557 2.319 -2.482 2.077 345.528 154.612 0.15 1.10 1.47 0.97 2.0 2.0 0.1
+1765  0.927 1.035 0.992 1.998 345.528 154.612 -1.01 1.17 -0.76 1.05 -2.0 2.0 0.1
+1763 0.691 -0.645 -0.630 0.201 345.528 154.612 -1.00 -0.61 0.02 -0.47 0.0 0.0 0.1
+1762 0.825 -1.063 0.221 -0.517 345.528 154.612 -1.00 -0.99 -0.40 -0.96 -1.0 -1.0 0.1 

CALIBRATION/bpm_calib/Harp_files/harp_info.txt.extra

+1771 0.194 -0.605 -1.548 0.328 345.528 154.612 -0.56 -0.62 0.67 -0.47 1.0 0.0 0.1 
+1770 0.838 -0.620 0.155 0.2969 345.528 154.612 -0.98 -0.61 -0.35 -0.43 -1.0 0.0 0.1 
+1769 0.683 -1.079 -0.677 -0.512 345.528 154.612 -0.99 -0.99 0.05 -1.00 0.0 -1.0 0.1
+1768 0.956 -1.194 1.033 -1.220 345.528 154.612 -1.00 -0.98 -0.80 -1.32 -2.0 -2.0 0.1
+1767  -0.620 -1.153 -2.499 -1.261 345.528 154.612 0.26 -1.0 1.46 -1.42 2.0 2.0 0.1
+1766 -0.557 2.319 -2.482 2.077 345.528 154.612 0.15 1.10 1.47 0.97 2.0 2.0 0.1
+1765  0.927 1.035 0.992 1.998 345.528 154.612 -1.01 1.17 -0.76 1.05 -2.0 2.0 0.1
+1763 0.691 -0.645 -0.630 0.201 345.528 154.612 -1.00 -0.61 0.02 -0.47 0.0 0.0 0.1
+1762 0.825 -1.063 0.221 -0.517 345.528 154.612 -1.00 -0.99 -0.40 -0.96 -1.0 -1.0 0.1 
+1764 0.659 1.08 -0.660 2.034 345.528 154.612 -0.99 1.17 -0.76 1.05 0.0 2.0 0.1 

CALIBRATION/bpm_calib/Harp_files/harp_info.txt.extra.no1766

+1771  0.194 -0.605 -1.548  0.328 345.528 154.612 -0.56 -0.62  0.67 -0.47  1.0  0.0 0.1 
+1770  0.838 -0.620  0.155  0.297 345.528 154.612 -0.98 -0.61 -0.35 -0.43 -1.0  0.0 0.1 
+1769  0.683 -1.079 -0.677 -0.512 345.528 154.612 -0.99 -0.99  0.05 -1.00  0.0 -1.0 0.1
+1768  0.956 -1.194  1.033 -1.220 345.528 154.612 -1.00 -0.98 -0.80 -1.32 -2.0 -2.0 0.1
+1767 -0.620 -1.153 -2.499 -1.261 345.528 154.612  0.26 -1.00  1.46 -1.42  2.0  2.0 0.1
+1765  0.927  1.035  0.992  1.998 345.528 154.612 -1.01  1.17 -0.76  1.05 -2.0  2.0 0.1
+1764  0.659  1.080 -0.660  2.034 345.528 154.612 -0.99  1.17 -0.76  1.05  0.0  2.0 0.1 
+1763  0.691 -0.645 -0.630  0.201 345.528 154.612 -1.00 -0.61  0.02 -0.47  0.0  0.0 0.1
+1762  0.825 -1.063  0.221 -0.517 345.528 154.612 -1.00 -0.99 -0.40 -0.96 -1.0 -1.0 0.1 

CALIBRATION/bpm_calib/Harp_files/harp_info.txt.extra.no1766.small

+1771 0.194 -0.605 -1.548 0.328 345.528 154.612 -0.56 -0.62 0.67 -0.47 1.0 0.0 0.05 
+1770 0.838 -0.620 0.155 0.2969 345.528 154.612 -0.98 -0.61 -0.35 -0.43 -1.0 0.0 0.05 
+1769 0.683 -1.079 -0.677 -0.512 345.528 154.612 -0.99 -0.99 0.05 -1.00 0.0 -1.0 0.05
+1768 0.956 -1.194 1.033 -1.220 345.528 154.612 -1.00 -0.98 -0.80 -1.32 -2.0 -2.0 0.05
+1767  -0.620 -1.153 -2.499 -1.261 345.528 154.612 0.26 -1.0 1.46 -1.42 2.0 2.0 0.05
+1765  0.927 1.035 0.992 1.998 345.528 154.612 -1.01 1.17 -0.76 1.05 -2.0 2.0 0.05
+1764 0.659 1.08 -0.660 2.034 345.528 154.612 -0.99 1.17 -0.76 1.05 0.0 2.0 0.05 
+1763 0.691 -0.645 -0.630 0.201 345.528 154.612 -1.00 -0.61 0.02 -0.47 0.0 0.0 0.05
+1762 0.825 -1.063 0.221 -0.517 345.528 154.612 -1.00 -0.99 -0.40 -0.96 -1.0 -1.0 0.05 

CALIBRATION/bpm_calib/Harp_files/harp_info.txt.extra.no1766.with3129

+1771  0.194 -0.605 -1.548  0.328 345.528 154.612 -0.56 -0.62  0.67 -0.47  1.0  0.0 0.1 
+1770  0.838 -0.620  0.155  0.297 345.528 154.612 -0.98 -0.61 -0.35 -0.43 -1.0  0.0 0.1 
+1769  0.683 -1.079 -0.677 -0.512 345.528 154.612 -0.99 -0.99  0.05 -1.00  0.0 -1.0 0.1
+1768  0.956 -1.194  1.033 -1.220 345.528 154.612 -1.00 -0.98 -0.80 -1.32 -2.0 -2.0 0.1
+1767 -0.620 -1.153 -2.499 -1.261 345.528 154.612  0.26 -1.00  1.46 -1.42  2.0  2.0 0.1
+1765  0.927  1.035  0.992  1.998 345.528 154.612 -1.01  1.17 -0.76  1.05 -2.0  2.0 0.1
+1764  0.659  1.080 -0.660  2.034 345.528 154.612 -0.99  1.17 -0.76  1.05  0.0  2.0 0.1 
+1763  0.691 -0.645 -0.630  0.201 345.528 154.612 -1.00 -0.61  0.02 -0.47  0.0  0.0 0.1
+1762  0.825 -1.063  0.221 -0.517 345.528 154.612 -1.00 -0.99 -0.40 -0.96 -1.0 -1.0 0.1 
+3129  1.010 -0.420  0.400 -0.160 345.528 154.612 -1.00 -0.99 -0.40 -0.96 -1.0 -1.0 0.1