Added a new "Step 3" button to add Quality Codes to CTD.csv output (see CTD.csv data format web page) -

• PrQ = pressure quality code;
• T1Q & T2Q = primary & secondary temperature quality codes;
• S1Q & S2Q = primary & secondary salinity quality codes;
• Ox1Q & Ox2Q = primary & secondary oxygen sensor quality codes (these carry over to the umol/Kg oxygen values since they are derived from ml/L);
• FlQ = fluorometer quality code;
• ISUSQ = ISUS nitrate sensor quality code;
• SigTheta1Q & SigTheta2 = T1S1 & T2S2 calculated sigma-theta densities
• TransQ = Transmissometer quality code
• pHQ = pH sensor quality code
• SPARQ = Surface PAR quality code
• PARQ = Remote PAR quality code

Codes - the data quality codes will follow the CalCOFI legacy codes

• no code = good data
• 8 = questionable data; bad calibration or bio-fouling
• 9 = bad or no data; sensor or pump failure

These quality codes have been added to flag bad or questionable data collected by our Seabird 911+ CTD sensors. Sensor failure, bio-fouling, or bad calibrations can generate poor or bad data but may still be included in the data file.

New features - umol/Kg for bottle oxygen calculated when using IEH bottle data. IEHs do not include oxygen in umol/kg so it is calculated from bottle oxygen ml/l and CTD sigma-theta. Using IEH sigma-theta would be preferable but some IEHs do not have sigma-theta.

Algorithm used is the same as Seabird references: [µmole/Kg] = [ml/L] * 44660 / (sigma_theta(P=0,PoT,S) + 1000)

Also when bottle umol/Kg is not present but regression coefficients are available, cruise-corrected CTD primary & secondary oxygens in umol/Kg are calculated.

CTD.csvs were re-generated to include these values and pH.

Reporting CTD oxygen(s) in umole/Kg from the Seabird sensor(s) is standard practice. Reporting bottle oxygens in um/Kg in the CalCOFI Data Reports will formally begin in 2013 (1301).
Using draw temperatures saved by CESL (CalCOFI Electronic Sample Log) into the sta.csvs, we can calculate sigma-theta for each O2 sample at draw time. Using this value, pressure=0, & CTD salinity, the ml/L values are converted to umoles/Kg using Seabird's conversion algorithm (Seabird Application Note 64):
[µmole/Kg] = [ml/L] * 44660 / (sigma_theta(P,T,S) + 1000); P = 0

CESL1304 will generate the latest casts & sta.csv formats which allow oxygen values in um/Kg to be archived.
BtlVsCTD1304 will compile the CTD sensor values plus the bottle values, include O2 in um/Kg. This allows bottle oxygen in um/Kg to be regressed against sensor values. The combined CTD+bottle data csv includes: CTD primary & secondary oxygen sensor values in ml/L & um/Kg. Plus bottle corrected CTD oxygen values - cruise-average corrected oxygen in ml/L & um/Kg; station-corrected oxygen in ml/L & um/Kg. Cruise-average corrected = CTD sensor data vs all cruise bottle oxygen regression coefficients are applied (n = ~1300 samples) . Station-corrected = primary & secondary CTD oxygen sensor data are corrected using the corresponding station bottle oxygen samples only (n = ~20 samples). Station-corrected CTD oxygen values are considered the best since station-to-station variability in sensor performance is addressed. Stations that do not have adequate calibration samples are cruise-corrected only and those CTD oxygen values are the best available.

From Seabird Application Note No. 64: SBE 43 Dissolved Oxygen Sensor
"[µmole/Kg] = [ml/L] * 44660 / (sigma_theta(P,T,S) + 1000)

For the µmole/Kg conversion, there is disagreement in the scientific community about the conversion constant 44660:
The value 44660 is exact for oxygen gas.
The value 44615 is the average value for atmospheric gas (N2,O2,Ar,H2O,CO2,...). It is not exact for any individual gas, but has been used historically by oceanographers.
The argument distills to exact versus historic, with oceanographers split; Sea-Bird uses 44660 in all calculations."

CTD asc files contain CTD primary & secondary (when installed) oxygen measurements in umoles/kg. These data were not included in the CTD-bottle data merged csvs. With the mandate to include oxygen in umoles/kg as part of our dataset, these columns are now included in the ctd.csvs. Eight additional columns have been added: Ox1uM, Ox1uM_CruiseCorr, Ox1uM_StaCorr, Ox2uM, Ox2uM_CruiseCorr, Ox2uM_StaCorr, OxuMAve_StaCorr, plus the OxBuM column for the bottle value.

Reporting of bottle oxygens in umoles/kg should begin on CalCOFI 1301SH (Jan 2013). With the addition of bottle oxygens in umoles/kg, bottle-corrected CTD oxygens in umoles/kg will populate the ctd.csvs. These data will be archive with final data.

CalCOFI started running oxygens with the ODF auto-titrator in Oct 2003 so it may be possible to generate umoles/kg values from archived runs as time permits (which it rarely does). Further investigation of this possibility is necessary ie whether older cruise bottle oxygens can be reprocessed to umoles/kg easily.