Update (U)CTD Processing

[jrenfree]

Working in new branch called 'update-ctd-uctd-processing' on estimATM.

Will implement the following:

• CTD and UCTD data are processed using two different scripts, despite them having many similarities. They should be combined into a single script that handles whether the data comes from a CTD (.hex files) or UCTD (.csv files).
• The 'processCTD.R' script does not properly compensate calibration values by changes in sound speed, so the new script should implement that part from 'processUCTD.R'.
• One-off scripts have been created to process (U)CTD casts from one vessel and applying the results to a template ECS file from another vessel (e.g., creating Saildrone ECS files using Shimada CTD casts in 2023). There would not be a need for these one-off scripts if the code was updated to automate the creating of the 'T_vars' variable, which is manually specified to indicate which frequency the 'Tx' variables pertain to in the ECS file.
• The ECS file creation section should be updated to put a sound speed profile in the ECS file, which we hope to use in the EV templates going forward.

[jrenfree]

Have updated the code to at least work with processing UCTD data, however am waiting to hear back from Echoview on how the non-depth profile environmental variables are utilized. For example, when the ECS file only species the depth and sound speed profiles, Echoview is still indicating that it's using static values of sound speed, temperature, salinity, and absorption depth. This is likely so that they can compute a static absorption coefficient. So I emailed Echoview to inquire if depth profiles can or should also be specified for these variables in order to have a depth profile of absorption coefficients.

[jrenfree]

It looks like the CTD processing does not use AlignCTD, while UCTD processing does. Will update so that the CTD processing also conducts AlignCTD.

[jrenfree]

I believe the CTD rosette on Lasker (an SBE 9) automatically aligns the conductivity sensor relative to temperature (by 0.073 seconds), which is why the AlignCTD program was not previously used for the CTD processing. However it might be useful to still include that processing step, although the CTD .psa file might just use a time offset that's essentially 0.

[kstierhoff]

This seems like a good approach to me, not that you were asking. 🤓

[jrenfree]

I wasn't asking

[jrenfree]

Finished updating CTD processing script, however will wait until after survey processing is done to merge the branch 'update-ctd-uctd-processing' into master. Will also need to update EstimATM to use the updated PSA directories/files that exist on my local Desktop in the 'TEMP' folder.