CalCOFI 9901RR CTD Data Processing Notes

THe sensor data look very clean, running the standard Seabird 911+ dual T & C 
pumped. A primary Beckman/YSI oxygen sensor was also plumbed in-line with the
primary T & C sensors, pumped. Additionally, a second Beckman/YSI oxygen sensor 
from the MOCNESS CTD was deployed on nearly half the stations. When deploying 
the second oxygen sensor,the altimeter was removed so the voltage configuration 
is slightly different.
It should be noted that 2 different Beckman/YSI oxygen sensors were used as the 
secondary O2 sensor. Casts with dual O2 were: 008-027, 038-051. Cast using serial
#13205 were 008-017 + 038-039; casts using serial #13204 were 040-051.
Base on the bottle vs sensor data, #13204 performed better than #13205 - #13204 
sensor data vs bottle samples relationship is linear. A 2nd-order polynomial
works better on the primary #13120 & MOCNESS sensor #13205. Cruise-average 
bottle-corrected secondary oxygen data were generated using polynomial coefficients.
Primary Beckman/YSI sensor was serial #13120.

Sensor cfg for casts 001-007, 028-037, 052-072:
V0 - Transmissometer, V1 - Fluorometer, V2 - Remote PAR, V3 - open, V4 - Ox1 Current,
V5 - Ox1 Temperature, V6 - Altimeter, V7 - open

Sensor cfg for casts 008-017, 038-039:
V0 - Transmissometer, V1 - Fluorometer, V2 - Remote PAR, V3 - open, V4 - Ox1 Current,
V5 - Ox1 Temperature, V6 - Ox2 Current, V7 - Ox2 Temperature (#13205)

Sensor cfg for casts 018-027, 040-051:
V0 - Transmissometer, V1 - Fluorometer, V2 - Remote PAR, V3 - open, V4 - Ox1 Current,
V5 - Ox1 Temperature, V6 - Ox2 Current, V7 - Ox2 Temperature (#13204)
 
If you plot all secondary oxygen data on a single plot. You definitely
see two distinct lines. I used these to separate the secondary oxygen data & when
reviewing the secondary O2 sensor serial number in the .con files, they match.
I do not have access to the console ops binder (hardcopy cast log which may have
annotations/notes). SO relied solely on hdr notes and visual data comparisons.

Other sensors look good with no changes during the cruise. T1, C1, T2, C2, transmissometer,
fluorometer, remote PAR had no changes. Altimeter & secondary oxygen sensors were
swapped on V6/V7 channel.
There were some cast numbers aka "order occupied" assigned to MOCNESS casts. That's why a 
66 station cruise has cast numbers over 66. MOCNESS casts were: 25, 26, 30, 34
Cast 072 was a CTD-profiles-only cast, no bottle samples collected. This was for
data-quality assessment of the MOCNESS CTD. Only primary T, S, O2, trans, fl, alt, PAR
were deployed. Secondary T & C were not deployed. Since there were no bottle samples
to dynamically correct the sensor data, cruise-average data were plotted. 

Corrections: cast 054 83.40.6 was changed to 83.3 40.6

Data flagged: 
Cast 009U: secondary O2 data from 96-115 were data coded "9"
Cast 010D: secondary T & C 0-5m data coded "9"
Cast 014D: T2 from 0-9m & S2 from 0-31m data coded "9"
Cast 017D: T2 from 0-3m & S2 from 0-10m data coded "9"
Cast 040D: T2 from 0-16m & S2 from 0-24 coded "9"; S2 25-33m coded "8"

Casts 045-047, end of line 83.3 had unusual profiles but both primary & secondary sensor
agreed so the data were not flagged as questionable. Probably the edge of the California
Current mixing with offshore water.
Also observed on many casts - the Beckman/YSI oxygen sensor under-estimates O2
on the downcast from ~0-50m data; over-estimates the upcast O2 data ~0-50m.

JRW 08/12/2021