There have been quite a few tweaks of the DECODR program since last entry. Here is a list of the main addition or changes:

UTC-PST issues - when using RV Sally Ride or any shipboard computer to collect CTD data, the .btl bottle closure times are in the computer's time. If the computer is UTC, the bottle closures imported into the sta.csvs will be UTC. Now BtlVsCTD will replace .btl times with CTD PST when CTD.csv data are imported into the sta.csvs. But on cruises, like 1711, where sta.csvs have been point checked, re-importing the CTD.csvs could negate point-checking corrections. DECODR has a new module in the CSV tab that will update the sta.csvs or staT.csvs with CTD PSTs without changing any other column.

Nutrients - multiple RMNS will be saved: previous versions, only the last RMNS run would be saved to the RMNS tabulation QC file. If additional RMNS runs were done between stations or samples in the same run, only the last one was saved. DECODR will now save and tabulate all RMNS runs.

Nutrients: The zeroing of values below the MDL for nitrite NO2 is working fine except that the ISL values still go in as actual calculated from csv data datacoded "0". Datacodes should follow suit and be "4" when there is an adjacent "4" - fixed. (11/06/2017)

Create New Directories - DECODR can now create all the directories required for a new cruise:

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

CSVs for contour mapping can be generated from different hydrographic data sources: sta.csvs, data reports, IEHs, CTD .asc or .mrk files. A character code is appended to the map csvs distinguishing the various sources: "S" for sta.csvs, "D" for data report, "I" for IEHs, "" for CTD sources. In previous versions of DECODR, the character codes were "turned off" so only map.csvs without the character code were plotted (ie "1607_010m.csv" vs "1607_010mS.csv").

Sta.csvs are the recommended source for contour map data but Data Report are used for derived data plots such as Dynamic Height.

Also changed - when using a Data Report (TXT > csv in DECODR) as a source, the data files previously generated were shallow to deep. But DECODR1703 now inverts the Line.csvs from deep to shallow - horizontal plot csvs are unchanged since they only include one depth such as 10m data

It should be noted that when auto-contouring using DECODR, if the Surfer plot "shrinks" to an illegible thumbnail. It's a range problem with the master file used as a template. I've updated the templates in my C:\CODES\map_masters\ subdir to use local files such as "current_coast_w_islands1.bln" and gridded data from a previous cruise that has been copied to the map_masters subdir.