CalCOFI 0204JD CTD Data Processing Notes

The sensor data were pretty clean this cruise, very few spikes so not much data coding required.
But there were some issues outlined below. First, there was a change of fluorometers after 
cast 028 and some initial sensor misconfiguration in casts 001-006. 

Casts 001-006: sensor configuration (.con) files do not list a fluorometer at all but 
a SCUFA fluorometer sensor is listed in cast 007 .con file on V6. Since cast 001-006 V6 
voltages are non-zero, it is most likely SCUFA data. So cast 007 .con file was used to 
process casts 001-006.

Cast 013 - 013B: cast 031 was restarted at depth after the first bottle was tripped. The 
.mrk & .asc files were merged during processing to compare to bottles in BtlVsCTD.
But these files remain separated in the asc-hdr directory. 

Cast 015: the Remote PAR was removed from the .con for the remainder of the cruise.

Cast 020: no downcast data; CTD operator did not start logging data until reaching terminal
depth. Typically, when this happens, the CTD is brought back to surface and the data
acquistion started. But due to a shortage in time, only upcast data & bottle samples were collected.

Cast 029: the SCUFA fluorometer on V6 was replaced with a Seapoint fluorometer on V6.
Two fluorometer regressions were calculated. The SCUFA "estimated chlorophyll-a" data 
does not appear as good as the Seapoint "estimated chl-a" data. See the regressions in
the Metadata/Plots folder.

Cast 059 - 059B: cast 059 was aborted, 059B is the entire cast and after Datcnv'd,
relabeled to 059 to match bottle samples.

Cast 535: was a 200m prodo cast, only primary productivity incubation seawater samples were
taken. Refer to cast 035 sensor & bottle sample data for hydrographic measurements.

Data were processed in two groups: Casts 001-028 was run first in BtlVsCTD then casts 
029-535 run second, resulting in metadata files for each group.

There were three casts, 005, 035, & 535, with GPS issues in the .hdr files which 
affected the lat, lon, & UTC time. The errors were manually corrected, editing the hdr 
files for all three casts. If CTD data are reprocessed, the files will have to be
corrected again.

Other corrections:
Casts 001 & 050 CalCOFI Line value in the hdr file required edits: 93.26.7 on cast
001 was changed to 93.3 26.7; 8340.6 on cast 050 was changed to 83.3 40.6.

Cast 022 downcast: secondary salinity spikes at 38-39m required data flag 9. 

Notations on the console operations logs were not available as I am processing these
cruises from home during the COVID-19 pandemic quarantine. It may be useful to refer
to these (hard copy) logs later when they are available.

JRW 06/22/2020