The prodo module has had some significant updates: first, there is a new scintillation asc import module that saves the counts into a station-bottle indexed csv. It uses the specific activity and blank values from the casts.csv unless over-ridden by user-entered values in the asc import/export module.
The Prodo data processing module uses this csv (or up to 3 variations, if needed) to generate the prodo data report. The update sta+casts.csvs checkbox will add prodo values to both prodo station csvs & prodo station cast entries in the casts.csv. There is also a specific activity & blank feature in the prodo data processing module that will supersede the csv values if that option is checked (checkbox must be checked). This allows individual stations to be processed with different values, if necessary.
The prodo data processing file still uses the prd### files generated by the PIC program at sea. It also expects start & end incubation times to be key-entered. If these values are missing, the user will be prompted to use LAN & Civil Twilight from the prd### file. These values are entered when running the PIC program.
All ties to 22 files have been removed (hopefully).
Files needed: YYMMscin.asc > YYMMscin.csv; prd###, casts.csv, sta.csvs. Prodo.cfg is needed by DECODR for use by the PIC module at-sea. Light levels, default specific activity & blank values from the prodo.cfg will be embedded into the prd### by PIC. It is important to remember to save any changes to the bottle numbering as the final step in PIC before generating the prd###.

The 89 column station csv format was put in service on CalCOFI 1301SH. CESL & DECODR have been updated to allow 82 (pre-1210), 84 (1210), & 89 (1301+) column station csvs. This will allow the addition of oxygen in um/kg to be included. These extra columns were added near the end so only effect the comments columns.

DECODR will not update the nutrient datacodes when processing nutrients with csv updater checked. Nutrient & chlorophyll datacodes will not be updated when CTD data is added to sta.csvs. Ammonia data will be coded '4' on offshore stations at depths below 200m unless already datacoded '9'.

Other updates: terpling bottle data 'broke' when changing the recind '3' to a range - '>2 <6' - so it was recoded back to '3'. This will cause recind 5 depths to not be used to terple. Recind 5 usually denotes a bottle depth without water samples (mistrip or missed), so use CTD data.

Added an 'Additional Comments' cleanup tool - sometimes duplicate oxygen datacodes get appended so they repeat (ie Ox1S;Ox2S;Ox1S;Ox2S). Under the [CSV] tab is a new module that checks the additional comments column for this issue and saves only the last pair. It checks for duplicate pairs (ie Ox1S;Ox2S; or Ox1C;Ox2C; or Ox1U;ox2U) but not differing pairs (ie Ox1S;Ox2C or Ox1C;Ox2U...). Additional permutations could be added if needed but are not in place currently.

 

Database module [db connection] was hardwired to G: drive, this has been fixed. Also Btl_Cnt & Cst_Cnt incremental routines were tweaked - they were adding 2 to the initial entry, not 1.

DECODR respacer module was tweaked to handle 82, 84 or 89 column sta.csvs. Other DECODR modules were modified to handle sta.csvs of 82, 84, or 89 columns properly. 82 column sta.csvs are pre-1210 (no DIC or Total Alkalinity); 84 column sta.csvs are 1210-only (include DIC or Total Alkalinity at cols 80 & 81); 89 column sta.csvs will begin 1301, include DIC, Ttl Alkalinity, oxygen in umoles/kg.

With the sta.csv format evolving with the addition of oxygens in umoles/kg, 4 columns were added at column 82 (82-86; to have less impact on the first 81 cols modules). Only the last 3 comment cols are affected, shifting cols 82-84 to 87-89. Bottle oxygen in umoles/kg are not available yet but CTD data files contain primary & secondary oxygens in umoles/kg.

Other programs involved are: CESL (CESL1301.exe), generating sta.csvs of 89 columns; BtlVsCTD (BtlVsCTD1301.exe), generating ctd.csvs with umoles/kg columns for both bottle, primary, & secondary oxygen. Please refer to the individual entries for these other programs.

After discussing some missing data, it became apparent some documentation of how data are added to casts.csv was needed. This guide outlines all 63 columns: col #,  col width, format, and the original source of the data ie what program/process adds or updates data to the file. Some metadata columns are still under development. All columns are generated & some columns populated by CESL after samples are taken at-sea but updated during the different phases of the data process. DECODR keeps process logs and backup versions of the data files for all processes/updates applied to either casts.csv or sta.csvs.