Fixed default arguments for SHMS def files

See merge request !5

Crude PARAM file checker + fixed PARAM files

See merge request !7

Brad Sawatzky authored 4 years ago and Sylvester Joosten committed 4 years ago

- Side effect of running PARAM/* files through 'param-check.pl' script
  which flagged a number of formatting and consistency issues.

- None of these lead to fatal parsing errors.  Hopefully the hcana/podd
  parsers ignored the errors instead of silently misinterpretting bad data
  into arrays/params..

- Corrections:
  - Improved some whitespace consistency (replaced mix of tabs/space
    with spaces only)
  - Removing invalid trailing commas on arrays
  - Identified and fixed a few broken comments (an accidental <cr> put
    the comment in a 'non-comment' line like this:
      . . .
      val01 = 100
      ; this is a comment
      val02 = 1.23
      . . .
    was left like this instead:
      val01 = 100
      ;
        this is a comment
      val02 = 1.23

* best shms optics

* reads new matrix elements

Calibration merge, part 1

See merge request jlab/hallc/exp/polhe3/hallc_replay!3

- Clean merge with no conflicts with other calibrations.
  - Note: retime and trig timing cuts are different than what Junhao and
          Murchhana used

- FIXME: SHMS and HMS calorimeter files are dropped in 'PARAM/{SHMS,HMS}/CAL/'
         with suffixes that represent the kinematic setting.
         - They must linked to in the replay/steering scripts before
           they will be used!!

- NOTE: I am not very comfortable with the significant variation in
    calibration coeffs I see between the param files for different
    kinematics...  It makes me nervous that we are cutting on 'E/p' when
    E is being explicitly tuned to match p for each kinematic.
    - This is a bit circular...

========================================================
Starting point was a clone of the master branch of
  https://eicweb.phy.anl.gov/jlab/hallc/exp/polhe3/hallc_replay.git
to: /group/c-polhe3/Users/mrehfuss/hallc_replay/ in March

UPDATED PARAM FILES:

Done first in April/May:
Reference Time Cuts
    • located in
    /group/c-polhe3/Users/mrehfuss/hallc_replay/PARAM/(S)HMS/GEN/(p)(h)_reftime_cut.param
    • SHMS runs used for studies: 10614, 10602, 10744, 10698, 10337,
      10433, 9779, 9780, 10793, 10794
    • HMS runs used for studies: 2608, 2636, 3408, 3419, 2673, 2716,
      3199, 3615, 3616

* HMS/SHMS Calorimeter Detector Time Window studies done next, and all params were unchanged**

Done third in June/July:
CALORIMETERS
    • “(S)HMS_final_cal_param”
        ◦ contains new gain constants for each spectrometer for A1n:
            ▪️ 2.129, 2.6, & 3.4 GeV for SHMS
            ▪️ 2.9 & 3.5 GeV for HMS
        ◦ HMS: calibration script
          CALIBRATION/hms_cal_calib/hcal_calib.cpp+ was used for runs
          chained together for each momentum setting
            ▪️ 2.9 GeV: 3196 - 3205
            ▪️ 3.5 GeV: 3408, 3411, 3418-3425
        ◦ SHMS: calibration script
          CALIBRATION/shms_cal_calib/pcal_calib.cpp+ was used for runs
          chained together for each momentum setting:
            ▪️ 2.129 GeV: 9833, 9839, 9840-9842
            ▪️ 2.6 GeV: 10337-10341, 10433 - 10437
            ▪️ 3.4 GeV: 10602, 10614, 10698, 10678, 10641-10646
        ◦ located in
          /group/c-polhe3/Users/mrehfuss/hallc_replay/PARAM/HMS/CAL/hcal_calib.param

**git pull done periodically throughout**

Done fourth in September/October
BCMs
    • “gscalers.param”
        ◦ located in /group/c-polhe3/Users/mrehfuss/hallc_replay/PARAM/GEN/gscalers.param
        ◦ Used Deb Biswas’ BCM calibration script for the procedure: https://github.com/JeffersonLab/hallc_bcm_calib

- also renamed Murchhana's directory in an attempt to be consistent

- Looks like good merge with Murchhana's work.

- Notes from Junhao:
  The new parameter files are from the new method of extracting the tzero per
  wire by fitting the integrated drift time per wire with step function. By
  merging the branch dc_calib_distonly the new tzero per wire fitting method,

  A new drift distance only calibration method and a fix to an error that will
  cause wrong tzero param for wires with no events during calibration will be
  added. The affected files are CALIBRATION/dc_calib/scripts/DC_calib.h(C) and
  added a new file CALIBRATION/dc_calib/scripts/main_calib_distonly.C
  in addition the new .params files for SHMS.

=======================================================================
Squashed commits from Junhao's 'dc_calib_distonly' branch
=======================================================================
commit f455316aff10acf5799fb35f26d4fb200c65f3e2
Author: jhchen28 <jhchen0577@gmail.com>
Date:   Mon Nov 2 23:16:12 2020 -0500

    Update README.md

commit 307c37fe9d4cb4fde0612f2a3e6e7a2da3c4d4bc
Author: jhchen <jhchen@jlab.org, jchen11@email.wm.edu>
Date:   Mon Nov 2 22:16:58 2020 -0500

    update the SHMS DC calibration parameters with the new method of tzero fitting which fit the integrated tzero per wire with setp function, the params are calibed from run 9644

commit 6a6d4561757dfc5d55586407edceb61e109b6030
Author: Junhao Chen <jhchen@jlab.org, jchen11@email.wm.edu>
Date:   Tue Oct 20 14:18:51 2020 -0400

    fix the error for DC calibration code that for empty wires during calibration the tzero in the resulting param file will be incorrect

commit d6c33e685bdffe29b89e6188ca196cbf675105e9
Author: Junhao Chen <jhchen@jlab.org, jchen11@email.wm.edu>
Date:   Mon Oct 12 23:33:26 2020 -0400

    add option to use step function fit integrated wire tzero

commit a6f1ce9a01f4c8a48cb00a30f77ebbb90807b419
Author: Junhao Chen <jhchen@jlab.org, jchen11@email.wm.edu>
Date:   Sun Oct 11 12:47:54 2020 -0400

    add functions to DC_Calib.C to linear fit the integrated drift time per wire, anda also merger adjacent time/wire histograms to get histogram with entries above certain threshold for fitting

commit 33da2f5c6edf58a0d81d2a2ffb7ae214dc622359
Author: Junhao Chen <jhchen@jlab.org, jchen11@email.wm.edu>
Date:   Sun Oct 4 00:50:01 2020 -0400

    Minor changes to CALIBRATION/dc_calib/scripts/DC_calib.h and CALIBRATION/dc_calib/scripts/DC_calib.C, also added new CALIBRATION/dc_calib/scripts/main_calib_distonly.C script to calibrate the drift chamber dift distance without redo t0 calibration first.

- 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

use new SHMS ME

- Updated the following to use ngcer cuts instead of hgcer
   pcut_cer_pi_both
   pcut_cer_elec_both
   shmsScinShoulde

updated matrix elements

- Includes copies of:
  - 'simple' (non EDTM) computer live time calculations
  - 'E SING FID TRACK EFFIC tracking efficiency

- This addresses a few nanosec timing shift introduced by
  the FADC ref time reshaper fix last week.  The old cuts
  were unnecessarily tight.  Argh.
    https://logbooks.jlab.org/entry/3819103

- HMS script was pulling in p_fadc_debug.param and screwing up
  the 'all' replays...

Updated calorimeter calibration code.

See merge request !2

Updated calorimeter calibration code.  See https://hallcweb.jlab.org/DocDB/0010/001039/001/calorimeterCommis.pdf for examples of new plots.  The calibration algorithm is unchanged, I only added a bunch of diagnostic plots.

Fixed typo in hms replay script: h_fadc_debug_param

See merge request !1