MOD_fish_calibrations

Calibration files needed for MOD_fish_acquisition and MOD_fish_processing

• Initial commit with .CAL files has the oldest calibration files for each Seabird 49.
• Later commits replace the calibration files when new ones come in from Seabird.
• There will only ever be one file per instrument. To use previous files, see Using old calibration files to reprocess data - don't just check out an old commit.

Files every processing run needs

Besides the per-instrument calibrations (SBE/, SHEAR_PROBES/), MOD_fish_processing needs:

File	What it's for
SHEAR/cap1nFres200Meg_5KohmInput.mat	Shear charge-amp electronics response - without it epsilon is computed with no electronics correction
FPO7/FPO7_benchnoise.mat	FP07 bench noise floor - used to find where an FP07 spectrum drops into noise for chi

These were added later than many calibration tags, so an old commit or tag may not have them.

Initial commit:

SBE Calibration File	Calibration Date
0057.CAL	2022_04
0060.CAL	2022_04
0131.CAL	2022_04
0133.CAL	2019_02
0237.CAL	2023_03
0387.CAL	2019_02
0536.CAL	2020_03
0537.CAL	2020_03
0664.CAL	2023_01
0674.CAL	2023_04

Example of later commits:

SBE 0387 and 0537 came back from factory calibration in March 2023.

cp NEWCALS/0387.CAL SBE/0387.CAL
cp NEWCALS/0537.CAL SBE/0537.CAL
git add SBE/0387.CAL SBE/0537.CAL
git commit -m "Update 0387.CAL and 0537.CAL - factory calibrations March 2023"
git tag -a cal/2023-03 -m "Calibration update March 2023"

Working with tags

Tag naming convention

sbe/YYYY-MM           # marks when a SBE calibration file was updated
shear/YYYY-MM         # marks when new shear probe calibration files were uploaded or existing files updated
cruise/YYYY-MM-CRUISE # marks which files were on the instruments for a cruise

See all tags

git tag -l "sbe/*"       # see all SBE calibration date tags
git tag -l "cruise/*"    # see all cruise tags

See which files changed between two tags

git diff sbe/2023-03 sbe/2025-03

See the history of a specific instrument:

git log --oneline -- SBE/0387.CAL

Using old calibration files to reprocess data

If you need to reprocess data from an old cruise with the calibrations that were in use then, don't just check out (or archive) the old commit - an old snapshot can be missing files processing now needs (see Files every processing run needs), and processing would quietly run without them. Instead, start from the current files and replace only the calibration files you need from the old tag. Do it in a new folder, so the calibrations repo itself stays untouched and on main.

mkdir ~/Desktop/reprocess_CRUISE_NAME
cd ~/GitHub/MOD_fish_calibrations
git archive main | tar -x -C ~/Desktop/reprocess_CRUISE_NAME     # everything, current
# then each old file you need, on top (here SBE 0387 and 0537 as of March 2023):
git show sbe/2023-03:SBECAL/0387.CAL > ~/Desktop/reprocess_CRUISE_NAME/SBE/0387.CAL
git show sbe/2023-03:SBECAL/0537.CAL > ~/Desktop/reprocess_CRUISE_NAME/SBE/0537.CAL

Note the old path: before the folder was renamed (commit d14f32c), the SBE files were in SBECAL/, so tags up to and including sbe/2025-03 have them there, while the current files are in SBE/. git ls-tree -r --name-only <tag> lists what a tag holds. For an old shear probe calibration, copy from SHEAR_PROBES/<SN>/Calibration_<SN>.txt the same way.

Point your processing scripts at ~/Desktop/reprocess_CRUISE-NAME instead of the calibrations repo for the duration of reprocessing.