Ocean Carbon and Biogeochemistry: Data System

MedFlux cruise: SJII May 2003
CTD profile data processing notes

17 January 2006: Prepared for OCB data system by Terry McKee (PO Dept, WHOI) and Cyndy Chandler, OCB DMO (WHOI).

Data were processed using the standard set of Seabird utilities, to generate final 2-decibar pressure sorted downtrace files for all CTD casts.

Final CTD station header record showing history of processing steps:
SJ002002.hdr

CTD Configuration reports:
SJII_0303001.txt   stations 1 - 10 (no PAR/Irradiance, Biospherical/Licor)
SJII_0303011.txt   stations 11 - 18 (added PAR/Irradiance, Biospherical/Licor)
SJII_0303019.txt   stations 19 - 22 (changed PAR/Irradiance, Biospherical/Licor)
SJII_0303023.txt   station 23 (no PAR/Irradiance, Biospherical/Licor)

Some parameters were calculated using MATLAB Physical Properties of Seawater Toolbox:

Depth   [ sw_dpth.m ]

depth=sw_dpth(data.prs,43);   % latitude fixed at 43 ° N

Density   [ sw_dens.m ]

sigma-t=sw_dens(data.ctdsal1,data.ctdtmp1,data.ctdprs,0)-1000;

Potential Density   [ sw_pden.m ]

sigma_0=sw_pden(data.ctdsal1,data.ctdtmp1,data.ctdprs,0)-1000;

Potential Temperature   [ sw_ptmp.m ]

potemp=sw_ptmp(data.ctdsal1,data.ctdtmp1,data.ctdprs,0);

Details of CTD data processing steps:

Raw Seabird acquisition data files were contributed on the CD-ROM generated during the cruise and we used Seabird processing programs found in /utilities – no psas or processing info pertinent to the ctd stations taken

The cal sheets were reviewed to determine what data had been acquired:

in sub-dir of \CTD\Cal Sheets\seabird
cond has 1740; 1851; 2172; 2190  --
1740 not used in any .CON files
1851 is used in 1-23 (all)  secondary
2172 is used in 1-23 (all)  Primary
2190 not used

oxygen has 0032 and 0056
0032 not used in any .CON files
0056 not used in any .CON files

temp has 2146;2318;2320;2659
2146 used is all             secondary
2320 used in all
2659 used in all             Primary

other sensor ids:

0441       (PRESSURE?)
4542       (?)
CST-487dr

SJII Seabird Processing

built Seasave processing scripts in C:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\
used test.bat to run station 1 and station 2
copyfiles.cmd writes cdn and cup to directory \processed as .cdn and .cup
used an iterative process to get through setting up the .psa files and create a working script.
generated 22 .cdns and .cups
Note: Station 17 - no bottles were fired (see .BL file - no entries)

Note: unable to locate any bottle data to calibrate or compare with CTD profile data

Raw Seabird acquisition files were named 0303xxx, etc and were renamed to SJIIxxx during processing. The raw files were run through the entire Seabird process, which is self-documenting in the header records generated with each final .cdn data file (see example header).

The processing sequence was the same as that used standardly for CTD data processed in the Physical Oceanography Department at WHOI, the first program (datcnv) being the most difficult to set up since I did not know for sure what had been acquired.

datcnv /iC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.dat /cC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.con /oc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD  /pC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\SJII_dat.psa
bottlesum /ic:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.ros /oc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD  /f%1.btl /cc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.con /pc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\SJII_bot.psa
alignctd /iC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.cnv /oc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD /f%1 /pC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\SJII_alig.psa
wildedit /iC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.cnv /oc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD /f%1 /pC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\SJII_wild.psa
celltm /iC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.cnv /oc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD /f%1 /pC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\SJII_cell.psa
filter /iC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.cnv /oc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD /f%1 /pC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\SJII_filt.psa
loopedit /iC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.cnv /oc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD /f%1 /pC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\SJII_loop.psa
derive /iC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.cnv /oc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD /f%1 /cC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.con /pC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\SJII_oxy.psa
binavg /iC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.cnv /oc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD /f%1 /pC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\SJII_bin.psa
derive /iC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.cnv /oc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD /f%1 /cC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.con /pC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\SJII_sal.psa
split /iC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\%1.cnv /oc:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\processed  /pC:\cygwin\home\tmckee\OCB\data\Medflux\working\2003\SJII\CTD\SJII_split.psa

Special Notes Regarding Oxygen

There was only one oxygen sensor on this CTD. This is clear because Seabird Program datcnv uses the instrument configuration to determine which variables can be output or derived. Why were there 2 oxygen fields in the raw files? I computed sbeox0ML/L in the datcnv program and then used derive to compute it (sbeox0ML/L WS=2). At that point, the data had been edited and filtered, so the value is slightly different, but is probably the better one to include in the final data product.

For this data set, O2_sat is Oxygen Saturation [ml/l] as derived from as measured; O2_ml_L (oxygen, dissolved from SBE CTD reported in ml/liter; sbeox0ML/L: Oxygen, SBE 43 [ml/l]) and O2_satP (sbeox0PS: Oxygen, SBE 43 [% saturation]) are both DERIVED parameters (as explained above), calculated after alignctd;wildedit;celltm;filter;loopedit and with WS = 2.

 from initial sensor measurement:
 O2_sat        oxygen, saturation from SBE CTD      ml/liter

 DERIVED during post-processing of CTD data:
 O2_ml_L       oxygen, dissolved from SBE CTD       ml/liter
 O2_satP       oxygen, saturation from SBE CTD      percent
 

DATA CONVERSION was written to accommodate most (if not all) sensors that have been installed on Sea-Bird products. Consult the configuration page at the beginning of your instrument manual for the sensors that were installed in your system.

If you plan to post-process the data, select only the primary variables to be converted.
Use DERIVE to compute derived oceanographic parameters such as salinity, density, sound velocity,
oxygen, and dynamic height anomaly.

If you will use DERIVE:

** To compute oxygen - include in the output file (along with pressure, temperature, and conductivity):
For SBE 13 or 23 - oxygen current and oxygen temperature
For SBE 43 -  oxygen value

Oxygen values computed by SEASAVE and DATA CONVERSION will be somewhat different from values computed by DERIVE, because the oxygen algorithm uses the derivative of the oxygen signal with respect to time. SEASAVE and DATA CONVERSION compute the derivative looking backward in time, since they share common code and SEASAVE cannot use future values of oxygen while acquiring data in real time. DERIVE uses a centered window (equal number of points before and after the scan) to obtain a better estimate of the derivative. Use SEASAVE and DATA CONVERSION to obtain a quick look at oxygen values; use DERIVE to obtain the most accurate values.