To reprocess CTD data with bottle oxygen in um/Kg, a DECODR utility for inserting additional columns into existing point-checked, annotated sta.csvs & casts.csv was created. The new DECODR module under the CSV tab - [Add um/kg cols to csvs] updates older cruises whose csvs are missing columns for DIC, Ttl_Alk, and um/kg columns (5: OxBumKg=bottle O2, Ox1umKg=CTD Ox1, Ox2umKg=CTD Ox2, OumDC=DataCode based on bottle OxB (ml/L) datacode, OumPI=Point-check code for future use.
Rerunning the O2 module with sta.csv update checked will populate the new columns. Since only observed data is used to correct CTD sensor data, the module uses & updates the non-standard level sta.csvs. Updating the station t.csvs standard levels with um/Kg may be added to [Derive Bottle Data] module later.
Other fixes - lots of reformatting done to sta & casts csvs so visual parsing of columns with a text editor is easier. Changed some column widths to match headers in both sta & casts csvs.
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.
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."
Fixed some glitches introduced yesterday when modifying the update csv routines, mainly the update casts.csv. It was updating the casts.csv after every station instead of once at the end of the run, so a casts.csv bak file was attempted every sta. Moving the casts.csv updater outside the station loop was the simple fix.
Oxygen module: adjusted the data quality criteria for flagging disagreement with CTD oxygens.
0.00 - 0.04 = no stars
0.05 - 0.14 = *
0.15 - 0.24 = **
0.25+ = ***
Plus the total *'s/bottle are printed at the end of the .out data processing report. Hopefully, the comparisons to CTD oxygens plus flagging disagreements will help troubleshooting at sea and improve data quality.
Stopped using the Name function to rename bak files and implemented a simple read/write bak file routine in WriteNuCastCsv & WriteStaCsv, used to update the casts.csv & sta.csv, when checked.
The Oxygen data processing output has additional columns: added CTD Ox0 ml/l, OxBtl-CTDOx0 ml/l, CTD Ox1 ml/l, OxBtl-CTDOx1 ml/l, OxBtl in um/kg - converted ml/l using Seabird's routine. If the bottle-ctd oxygen is greater than 0.45 it gets one star; if it is greater than 0.9 it gets two stars.
[µmole/Kg] = [ml/L] * 44660 / (sigma_theta(P,T,S) + 1000) (P = 0; T = draw T, S = Btl or CTD S1 or 2)
Chl - fixed a col error, now it puts the tau & F values in the right column. Still needs more work on pre & post-cruise + ave value entries.
Prodo - fixed the column update misalignment problem created by Ox um/kg additional columns; added scin data (counts & eff%) to sta.csv depths; improved the data processing coefficient-saving and use, when ave spec act &/or blank are entered on the form. It will remember your last run values and whether you checked the box to use ave values. The values are saved in ...\YYMM\YYMMprodcoef.txt file. If you want to use values added during the scintillation asc file import then uncheck the box.
