- I use a symlink chain rooted off 'output/' to redirect the ROOT
  output to different locations.  Just making git ignore them
  so I don't accidentally commit them.

- Also added Murchhana's calibration scripts and supporting files
  under POLHE3_SCRIPTS/ for now.
  - Normally I wouldn't include the pdfs, but I think they may be
    needed/userful for future sanity checks with the fully merged code.

=======================================================================
Summary of changes from Murchhana
=======================================================================

*****************************************************************
A1n analysis before starting d2n analysis:

1. May 1st, 2020: git clone from
https://eicweb.phy.anl.gov/jlab/hallc/exp/polhe3/hallc_replay.git

2. May 26th, 2020: Created branch murchhana_replays. All A1n analysis
work was done in this branch.

3. May 27th, 2020 : merge request created for the fixed typo in hms
replay script h_fadc_debug_param. Merge branch "murchhana_replays" into
"master".

4. October 6th, 2020: Pulled "master" to branch "murchhana_replays".

****************************************************************
Starting point for d2n analysis:

1. August 18th, 2020: Created new branch murchhana_d2n. All d2n analysis
work is being done in this branch.

2. October 12th, 2020: Pulled "master" to branch "murchhana_d2n".

3. Most recent SHMS/HMS run numbers were not present in the
standard.kinematics files. Added those run numbers manually to replay
required SHMS/HMS runs.

***************** Reference timing cuts ******************
1. Changed all t_shms_TdcTimeWindowMin and t_hms_TdcTimeWindowMin to 0
and t_shms_TdcTimeWindowMax and t_hms_TdcTimeWindowMax to 100000.

2. Did  a 200000 replay for SHMS runs
11395,11396,11398,11358,11369,11210,11217,11498,11538 and HMS runs
4195,4196,4192,4148,4160,3993,3994,4306,4331.

3. The script to check reference time cuts are in
/group/c-polhe3/Users/murchhana/d2n_2020/Ref_time_analysis folder.

4. Checked reference time cuts for all those runs and the cuts were
determined to be same as A1n.

******************** Detector time window cuts *****************

1. Performed the detector time window check for HMS and SHMS Noble gas Cherenkov.

2. Set the determined reference time cuts in param files.
/group/c-polhe3/Users/murchhana/hallc_replay/PARAM/HMS/GEN/h_reftime_cut.param
/group/c-polhe3/Users/murchhana/hallc_replay/PARAM/SHMS/GEN/p_reftime_cut.param
/group/c-polhe3/Users/murchhana/hallc_replay/PARAM/TRIG/thms.param
/group/c-polhe3/Users/murchhana/hallc_replay/PARAM/TRIG/tshms.param

3. Made the software time window cuts wider fot Cherenkov
(pngcer_cuts.param, hCER_cuts.param), Hodoscope (phodo_cuts.param,
hhodo_cuts.param), Calorimeter (pcal_cuts.param, hcal_cuts.param), Drift
Chamber (pdc_cuts.param, hdc_cuts.param).

4. Did a 200000 replay for SHMS runs
11498,11538,11395,11396,11398,11358,11369,11210,11217 and HMS runs
4306,4331,4195,4192,4196,3994,4148.

5. Junhao, Mingyu and Melanie used these root files to check the
Hodoscope, DC and calorimeter time window. I did the Cherenkov time
window check.

6. All Cherenkov time window scripts are in
/group/c-polhe3/Users/murchhana/d2n_2020/Detector_time_window_cuts/cherenkov
folder.

7. The Cherenkov time window cuts were found to be for SHMS/ HMS were
same as A1n.

**************** Cherenkov Calibration ******************

1. Set the obtained detector time window cuts were set in
hcer_cuts.param/p_ngcer_cuts.param filed in hallc_replay/PARAM folder.

2. Did a 200000 replay of HMS runs 4306,4267,4195,3732 and SHMS run
11538.

3. Both HMS and SHMS calibration scripts are in
/group/c-polhe3/Users/murchhana/d2n_2020/cherenkov_calibration folder.

4. HMS Cherenkov calibration was done using both Method 1 and Method 2
and the result differed by significat amount for run 4306. As Method 1
is reliable because we directly fit the single photo electron peak,
chose the calibration constant obtained from cosmic run 03732 (lowest
background gived better peak location). Set the calibration constant in
hcer_calib.param file.

5. SHMS CHerenkov calibration was done using Method 2 only for run
11538.The old calibration constants present in the param file were
obtained from run 9643,9644,9645. The new calibration constants obtained
from run 11538 agrees well with the old oned for PMT2, PMT 3 and PMT 4.
I will update the SHMS calibration constant in the p_ngcer_calib.param
file after discussing with others.

=======================================================================

commit 47b01089a701c46b30d089ac06a925cce08b27f6
Author: Brad Sawatzky <brad@swatter.net>
Date:   Mon Nov 9 23:25:34 2020 -0500

    Add Murchhana's calibration scripts and supporting files

    - I'll be putting htese under POLHE3_SCRIPTS/ for now.

    - Normally I wouldn't include the pdfs, but I think they may be
      needed/userful for future sanity checks with the fully merged code.

commit 73adbd7125160aa24acb3d83c7524966a145451a
Author: Brad Sawatzky <brad@swatter.net>
Date:   Mon Nov 9 23:09:31 2020 -0500

    Remove hel_scalers*.json trash; add pattern to .gitignore

commit 93e091bbd4c3a2c7ee575e5bc5aca0f5ff1b8108
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Mon Nov 2 14:33:20 2020 -0500

    Changes in hel_scalers_#.json files which were marked as untracked files

commit 75ae57eaac97a17c7cad1aaf1c2ec024817e5290
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Mon Nov 2 13:27:53 2020 -0500

    Updated HMS cherenkov calibration constants obtained from Cosmic run 03732 using Method-1.

commit 379beb44433e8439ad495a0239699b3bcfdfcbb1
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Mon Nov 2 13:26:34 2020 -0500

    Updated SHMS cherenkov timing window cuts from d2n runs, cuts are the same as that obtained from A1n runs.

commit eb6eaf7ccdea32c8dee45fe13a1cfe45525a3132
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Mon Nov 2 13:26:05 2020 -0500

    Updated HMS cherenkov timing window cuts from d2n runs, cuts are the same as that obtained from A1n runs.

commit 1893f23f14299ad32293a3167060b5be33142ffd
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Mon Nov 2 13:24:29 2020 -0500

    Updated HMS refernece time cuts from analyzing d2n runs, cuts are same as obtained from the A1n runs

commit 1e69e98b5ba90ad8dce24eb531ed346f15cd2430
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Mon Nov 2 13:24:15 2020 -0500

    Updated SHMS refernece time cuts from analyzing d2n runs, cuts are same as obtained from the A1n runs

commit d074248818c19233e5e1c1971b662962c5426349
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Mon Nov 2 13:23:40 2020 -0500

    Updated SHMS refernece time cuts from analyzing d2n runs, cuts are same as obtained from the A1n runs

commit c8162e2e3c58bb877a3777b48b2c1927dc69b8bf
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Mon Nov 2 13:23:09 2020 -0500

    Updated HMS refernece time cuts from analyzing d2n runs, cuts are same as obtained from the A1n runs

commit 1896a48b5bec5b3b02fae810c5ad9b84c03111c3
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Mon Nov 2 13:21:05 2020 -0500

    Added a few branches to be displayed in root files, required for reference time, detector time window and detector calibration.

commit 712163b5eea9bb76ee44f98c5a0d97d3400e1e66
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Mon Nov 2 13:20:48 2020 -0500

    Added a few branches to be displayed in root files, required for reference time, detector time window and detector calibration.

commit 83c2a03a6190ebd2fb984f11842cdcee231a7ffe
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Mon Nov 2 13:18:23 2020 -0500

    Most recent SHMS run numbers were not present in the file. Added those run numbers manually to replay them.

commit f41e25dd85027057cc460672275aa1105169c1b6
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Mon Nov 2 13:17:34 2020 -0500

    Most recent HMS run numbers were not present in the file. Added those run numbers manually to replay them.

commit ee7a3da38af76b007fcfd36166afa1f0641c08fe
Merge: e924ebf dadac70e
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Tue Oct 6 16:25:44 2020 -0400

    Merge branch 'master' into murchhana_d2n

commit e924ebfe4d2ddb9006e7322f66e4437748239503
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Tue Aug 18 12:40:15 2020 -0400

    test

commit 3bbe9cfcf236cd6484ab0fcd48adf06aba1a63ae
Author: Murchhana Roy <mroy@ifarm1802.jlab.org>
Date:   Tue Aug 18 12:23:10 2020 -0400

    test

* re-calibrated the HMS calorimeter and put the SHMS calorimeter calibration constanst for the new setting

* remove hms xptar offset and add delta cuts to target histos

* remove calorimeter layer histos and shift SHMS delta range

* modified standard.database to use the calorimeter calibration files per run based

* modified the standard.database

* add delta cuts to kinematic histos

* add various macros

* updated standard.database for continued phase2 running

* updated db2

* updated kinematics database

* updates corresponding to the conclusion of jpsi-007 running

* merge useful changes from hallc_replay_kaonlt

* add back in ngc histos and comment out comment line in aero calib

clean up online GUI

fix bug so that all cherenkovs are handeled

add expert config files which contain more online histos than what the shift crew is exposed too

update to latest util-ol

update util-kaonlt

* new Cher calib. coeffs. for HMS and SHMS

* fix def-file bugs

* comment out shms histograms not used in online monitoring

* comment out hms histograms not used in online monitoring

* Added back the DC efficiency plots

* Fix T3 in hms_stack.map

Modified hms_stack.map to put T3 in the right channel.

* Modify hdc_cuts.param and hdc_tzero_per_wire.param

1) Changed the per wire tzero offsets for the formerly bad  TDC
  since now that TDC module has it own reference time and tzero
  offsets for these channels match the other TDC modules.

2) Change the per plane tzero offsets by 50ns.

* add hT3 to htrig map

* add per wire dc eff to singles replay

* minor aesthetic changes

* remove line which was producing error

* remove creation of root file for monitoring histos

* clean up .gitignore

* update coin cuts and report file templates

* Kinematics files update

* Update parameter files for new time cuts and calibrations

* Correct replay_production_hms_coin_all.C

* Update pcal_calib.param

put back a old pcal_calib.param to replace a bad recent calibration.

* Commiting some of the calibrations and changes that have occured over our physics runs

* Modified onlineGUi ped_tracking.C and ped_tracking_trigger.C

Set the Y-axis of the pedestal difference plot to the minimum of 15
or 1.2 times the largest difference.

In ped_tracking
---------------
If both golden and current run do not have a pedestal for that channel,
then ped diff is zero.

If only the golden run does not have a pedestal for that channel , then
sets the ped difference to  negative pedestal value for the current run.

If only the current run does not have a pedestal for that channel , then
sets the ped difference to pedestal value for the golden run.

* Add onlineGUI/UTIL/GEN/flyeye_occupancy.C

Takes the 1D histogram of the shower block occupancy and makes
a 2D plot of occupancy for each row and column.

* Add histograms of the DC wiremaps for all DC hits.

Modified HMS/PRODUCTION/DC/hdc_histos.def and SHMS/PRODUCTION/DCpdc_histos.def to
have histograms of wiremaps for all hits in the DC.

Modified CONFIG/HMS/PRODUCTION/hms_coin_production.cfg and
CONFIG/SHMS/PRODUCTION/shms_coin_production.cfg to plt the histograms.

* Updated COIN/standard.kinematics

* Updated the aerogel calibrations and made some changes to the calibration script to make it easier to use

* Aerogel calibration was updated by Vladimir and I for new kinematics

* intermediate backup after hallc_replay file system restore

* Updated standard.kinematics with most recent runs at 6.495

* Updated version of standard.kinematics for first setting of Q2=5.5, W=3.02

* Update to standard.kinematics for luminosity and physics

* Updated versions of current calibrations for each luminosity run (5150-5168)

* Updated standard.kinematics for 9.53 SHMS angle

* BCM calibration updates for rest of luminosity runs

* Update to standard.kinematics for 9.555 angle change

* Updates to standard.kinematics for 6.5 deg setting change

* add bcm current files

* update hms cal calib and shms hgc timing cuts

* update kinematics file at end of kaon-lt running

* update submodules

* update kaonlt sub module after recen updates

* update kaon-lt submodule, yet again...

* remove bcm param files

* revert experiment specific changes

* Simplification of hallc-replay to specifically support hallc-online hallc_replay operations.

* Re-add bcm_current_calib files

* Updates to CT kinematics file and macro

* Add utilities directory

* Move shell scripts into utilities directory and symbolicaly link them in the top level directory

* Modify protoroot file to point to symbollically linked latest file

* Correct pdc online GUI proto-root file name

* Minor changes to SHMS maps

* Minor changes to HMS maps

* Update merge list

* Update crate 3 map for coin

* Update coin maps

* Initial attempt at coincidence replay

* Update coin maps and replay script

* Update SHMS maps with FADC reference times

* Same for HMS

* Add FADC reference times to coin maps

* ignor nfs temp files

* Add SHMS FADC reference time signal

* Modify report files and templates to better quantify the deadtimes

* Push initial changes for Steve

* Include failed state of HMS scalers replay script

* Include proper(?) method for obtaining event 129 scaler reads

* Ensure that trigger apparatus cut file has similar flow to stack and production to avoid confusion

* Remove reference time which serves as a reference time for the trigger apparatus

* Update maps corresponding to previous commit

* Ignore # files

* Update test stand cuts file to match production and stack

* Update test stand cuts file to match production and stack on HMS side

* Add vim lint to .gitignore

* Update replay scripts to search in a list of paths

- NOTE: This requires the podd submodule be updated to include
  modifcations to the THaRun constructor that can search a pathList.

- The default './raw' and './cache' pathnames that are searched here
  should generally be symlinks to the relevant local path on the Hall C
  cluster, and the /cache/mss/hallc/.../raw/ path, respectively. For
  example:
    cd hallc_replay
    ln -s /net/cdaq/cdaql3data/coda/data/raw raw
    ln -s /cache/mss/hallc/spring17/raw      cache

- FWIW: The batch filtering of the replay scripts was done with
  this perl script:
    cd SCRIPTS/
    find . -name '*.C' -exec ./filter.pl {} \;
  --- filter.pl ---
  #!/usr/bin/perl

  use File::Slurp;

  my $file = read_file($ARGV[0]);

  $file =~ s/\Qchar RunFileName[100];\E\W*\Qsprintf(RunFileName, RunFileNamePattern, RunNumber);\E\W*\QTHaRun* run = new THaRun(RunFileName);\E/THaRun* run = new THaRun( pathList, Form(RunFileNamePattern, RunNumber) );/s;

  $file =~ s/\Qconst char* RunFileNamePattern = "\E.*?\/(.*?\.dat)";/const char* RunFileNamePattern = "$1";\n  vector<TString> pathList;\n    pathList.push_back(".");\n    pathList.push_back(".\/raw");\n    pathList.push_back(".\/cache");\n/s;

  write_file("$ARGV[0]", $file);
  ---

* Add ignore stuff

* Include TI trigger inputs into scalers

* Add TI trigger inputs to param files

* Add TI trigger inputs to trigger maps

* Add HMS trigger apparatus variables to trigger test stand

* Remove raster from trigger apparatus map

Update HMS maps to include new TI trigger inputs

* Remove fast raster from trigger apparatus map

* Add TI trigger inputs to SHMS maps

* Create separate DBASE directory for SHMS

* Create separate DBASE for SHMS

Fix plethora of issues in HMS replay scripts

* Do not delete onlineDict.h

* Ignor header file

* Fix typo in map file and get rid of debug statement

* Adapt shms scaler online GUI for new naming scheme

* Remove deprecated config files

Move scaler config files to own directory

* Fix scalers replay script so it does not seg fault

* Modify online GUI for HMS scalers to function with new naming scheme

* Auto-indent

* Move staggaling files to examples

* Add directory structure to online GUI

* Add summer 2017 software analysis workshop example

* Add summer 2017 software analysis workshop example for real this time

* May 26, 2017 -- Long overdue push, some old Calibration Scripts but also the presently working analysis and Calibration scripts in Final Scripts directory.

* Updated Calibration with pulseAmp script.

* root file

* added Rootfiles

* Rewrote pulseAmp analysis, works much better now.
Included Degtiarenko's code to evaluate as a better alternative.
Started the write up for the actual calibration process

* Updated Analysis scripts, started deciphering Fortran code.

* test

* TEST

* test

* bla

* blah

* boring git stuff

* git stuff

* Made the master branch much more organized/presentable

* Finializing directory. Modified how calibration appears/output the calibration constants

* Updated the analysis and visualization scripts for NGC.

* Version of Calibration suitable for the Summer presentation.

* Removed debugging line

hcal.param
   1) gains for run 303,
   2) hcal_AdcNegThreshold=0.
   3) hcal_AdcPosThreshold=0.

pcal.param
   1) gains for run 464
   2)pcal_AdcNegThreshold=0.
   3)pcal_AdcPosThreshold=0.
   4)pcal_arr_AdcThreshold=0.0

Modified DEF-files for new names for the Cherenkov and Aerogel

The heavy gas and noble gas signals were mislabled at the FADC.
Decided to change map and leave cables in place.

Made replay_hms_report.C which expands on replay_hms.C
Need to create REPORT_OUTPUT directory

new HMS Hodo timing offsets for 3/4 trigger
save old HMS Hodo timing for 4/4 trigger
new SHMS Hodo timing offsets for 3/4 trigger
Updated HMS and SHMS onlineGUI config and macros

+#*
+hcana
+raw