DECODR - new O2 Module - Data Processing & Integration of RINKO O2 Data with CalCOFI CTD Data

Seasave & SBE Data Processing suite which we use to process our Seabird 911+ CTD data does not include RINKO data processing capabilities (as of Sept 2017). At-sea, the RINKO III deployed on CalCOFIs 1210NH & 1611SR were attached to two channels. Removing the secondary SBE43 oxygen sensor and altimeter were necessary to free up two channels (since CTD temperature is used for RINKO oxygen calculations, it's possible that only the RINKO current - single channel - may need to be interfaced).
Using a Matlab script from the Australian Ocean Data Network (AODN) and Integrated Marine Observing System (IMOS) & white paper ("Update of CTD oxygen data for the cruises MR07-04 and MR07-06" September 24, 2009 by Hiroshi Uchida (JAMSTEC)). I adapted the formula for calculating RINKO O2 saturation, mg/l, & umol into the units we typically report - ml/l, %sat, umol/Kg:

'depthR! is actually pressure, A!-F! are coefficients from RINKO manufacturer calibration
DissO2! = DissO2! * (1 + E! * depthR! / 100)
DissO2! = A! / (1 + D! * (T! - 25)) + B! / ((RINKOV! - F!) * (1 + D! * (T! - 25)) + C! + F!)

'aging foil correction - G & H are 0% & 100% coefficients derived by SIO-CalCOFI at-sea using saturated seawater & sodium sulfite solutions
DissO2! = G! + H! * DissO2!

'pressure correction
DissO2! = DissO2! * (1 + E! * depthR! / 100)
HoldCTDCSV$(rowcnt%, CalcCol%(5)) = Format(DissO2!, "0.000")  '%Sat

T1! = T! + 273.15
logO2star! = -173.4292 + (249.6339 * 100) / T1! + 143.3483 * log(T1! / 100) - 21.8492 * (T1! / 100) + S! * (-0.033096 + 0.014259 * (T1! / 100) - 0.0017 * (T1! / 100) ^ 2)
O2star! = Exp(logO2star!)

'ml/L
O2uM! = (O2star! * (DissO2! * 1.42857) / 100) * 0.7  '/ 1.33  '10ml/l = 13.3mg/l  1 mg/l = 22.391 ml/31.998 = 0.700 ml/l
HoldCTDCSV$(rowcnt%, CalcCol%(4)) = Format(O2uM!, "0.000")  'ml/L

'uMol/Kg
oxyum! = (O2uM! * 44660) / (HoldCTDCSV$(rowcnt%, CalcCol%(7)) + 1000)
HoldCTDCSV$(rowcnt%, CalcCol%(6)) = Format(oxyum!, "0.000")  'uMol/Kg

DECODR1705.exe addresses a problem seen on CalCOFI 1704SH where the nutrient data file was missing the NH4 column. The original routine expect there to be the expected number (and order) of nutrient columns: N+N NO2 PO4 Sil NH4 NO3(virtual). Runs of sta 32 - 38 were missing the NH4 channel so the 6th column was NO3, shifting the NO3 column into the NH4 column. DECODR1705 reads in the "METH" column headers, indexing the nutrients accordingly. Although the nutrient output file format is printed in a particular column order. The nutrient input file can have the nutrient columns in any order and DECODR1705 should parse them properly. This could use more testing but it appears to work when NH4 is missing or the data are "999".

DECODR has always expected the base cruise data-path to be Q:\CODES\YYYY\YYMM\ where Q: is the data drive, YYYY is the year, and YYMM is the year-month associated with the cruise ie 1701. The base cruise data-path and other settings are set in C:\DECODR\decodr.cfg (this path is hard-wired and has to be named exactly as shown).
This is our data acquistion directory structure used at-sea so all systems can contribute to the proper directories over the network. Since data-processing is done throughout the cruise for data-quality control, DECODR has been programmed to find data in these folders.

But since the data-path of completed cruises may be different once ashore, DECODR will now accept any data-path as long as "YYMM\" is the last part of the string ie "Q:\CODES\2010S\2013\1311\". As always, users should double-check the Current Data Path: displayed in DECODR is correct before running any module. Each modules add to the base data-path so the directory structure under the base data-path is fixed, for example using base data directory Q:\CODES\2017\1704\:

• Salinities module adds "SALT\" ie Q:\CODES\2017\1704\SALT\
• Oxygens module adds "O2\" ie Q:\CODES\2017\1704\O2\
• Chlorophyll module adds "CHL\" ie Q:\CODES\2017\1704\CHL\
• Nutrients module adds "NUT\ ie Q:\CODES\2017\1704\NUT\
• Prodos module adds "PRODO\" ie Q:\CODES\2017\1704\PRODO\

Other module file paths are:

• CTD data under "CTD\" ie Q:\CODES\2017\1704\CTD\
• station and casts csvs under "CSV\" ie Q:\CODES\2017\1704\CSV\
• cruise eventlog under "EVENTS\" ie Q:\CODES\2017\1704\EVENTS\
• bottle sample logs (CESL) under "LOGS\" ie Q:\CODES\2017\1704\LOGS\
• contour maps files under "MAPS\"; ie Q:\CODES\2017\1704\MAPS\
• CTD .mrk & .hdr files under "MRK\"  ie Q:\CODES\2017\1704\MRK\
• Processing logs (modules run on all data files) under "PROCESS\" ie Q:\CODES\2017\1704\PROCESS\
• Legacy station cast description file under "STACST\" ie Q:\CODES\2017\1704\STACST\
• Legacy weather file under "WEATHER\" ie Q:\CODES\2017\1704\WEATHER\

Other support directories under the base data folder but not used directly by DECODR:

• "0020" - obsolete IEH-data-processing subdir, remove on cruises after 2011; used for IEH data-processing on cruises earlier than Jan 2012
• "Matlab" - current data-processing subdir for GTool, our Matlab data-quality control visualization tool
• "NCOG" - support dir for NCOG samples
• "Planning" - cruise planning and information files
• "UWay" - underway data directory

Ship codes for RV Sally Ride - SR - and RV Reuben Lasker - RL - are now properly outputted to data products of DECODR.

DECODR 0m ISL salt datacode SDC is hard-wired to "0" if the bottle salt column is not empty. Currently, there is no way to make it equal to the SDC of the surface bottle, which it mirrors.