Integrated the Fisheries' zooplankton and sta activities database table formatting modules from CIFT into DECODR. Under the Database tab - a new module that will ingest the exported zooplankton displacement volume table from the Fisheries database, formatting it for importing into our hydrographic database. A second module ingests the exported station activities table to use online for tabulating station activities. Used in conjunction with the event log.

Revamped CalCOFI's Facebook page since integration into the operating system (iOS, OSX) is proliferating. We will use it for additional event & cruise-related photos and information

During key-entry, whenever <Enter> is used to record O2 draw temperatures (not mouse-click), CESL saves that sample log depth records to a local (C:\CESL) 'insurance' file. If the form is not properly saved because of a hardware or operator error, previous key-entries can be recalled by pressing F3. Procedure - after restarting the tablet & CESL, reload the current station log, if not done automatically; configure the O2 case, Salt case, Nut rack color then press F3. Previously entered O2 draw temperatures, Prodo bottles, DIC bottle #s, and comments will be re-entered from the insurance file. Note: only depths with O2 draw temperatures will be re-entered. Any comments or DIC bottle #s pre-entered on deeper depths are not in the insurance file. Re-flagging specific bottle types, such as mistrips, extra bottles, or test cases, will also be necessary. This feature is designed to re-enter the O2 draw temperatures since they would have to be redone.

New menu entry & hotkey enabled - pressing Ctrl-F5 will prompt you to automatically reload all the sample logs (001-100; YYMM###sLog.csv) & regenerate the sta.csvs & casts.csv entries. This is useful for upgrading 82-col sta.csvs to 84-col sta.csvs or any other batch reprocessing of sta.csvs.
Update - moved this feature to the menu under Utils and made it Ctrl-F5 instead of F5, which may be too easy to press. Also added a confirmation step so you have to say "yes" to overwriting the old sta.csvs & casts.csv.

To regenerate a specific sta.csv or casts.csv entry, load the specific sta by typing in the Ord_Occ in the upper left field. The saved station log will load and once complete, press Ctrl-C to save the single sta.csv & update the casts.csv. Note: you will have to manually delete the original cast entry for that sta in the casts.csv or cut & paste the new entry over the old.

Configuring ERDDAP to access our MySql hydrographic database requires installation of the java JDBC plugin. This was installed on sio-calcofi.ucsd.edu. Editing the web.xml file to connect to the hydrographic database (ccdb) is still needed.

This weeks DECODR updates:

• added two cols to the sta.csv format for DIC & TA, changing the format from 82 to 84 cols. DECODR can handle both versions of the sta.csv, using TO_DO in either col 82 or 84 to distinguish the two formats. Fixed a glitch that added two commas to the end of the 82 col sta.csv - 82 or 84 test failed initially in the respacer reformat routine.


• fine-tuned some glitches with interpolated standard level bottle data calculations ie missing data on OSLs


• fine-tuned NH4 datacoded "4"


• fine-tuned 14C assimilation prodo precision & column alignment for values < 1 in ieh data product


• fixed the data report txt to html header - it was cutting off the sta decimal value (49. instead of 49.0)


• wrote a new module that combines sta.csvs with DIC bottles for importing into Access and generating DIC Data Reports


• fixed the 200/500 dynamic height extrapolation module so values on shallow station would calculate properly. Solution was inverting the format from deep to shallow to shallow to deep (sta.csv vs ieh format difference).

This blog will keep track of changes in SIO-CalCOFI Technical Group methodology.

In order to use the datacodes to control which values are used in an interpolation, the 'terple' routine was switched from row-oriented to col-oriented. Instead of starting at surface and going to terminal depth, the routine starts with a particular datatype, say salts, then interpolates standard depth values for that column. Using the data codes as criteria on which salt values to use. This is a significant change from the legacy terple routine which was changed from quadratic interpolation to linear interpolation and now col-oriented vs row-oriented.

Generating CalCOFI hydrographic database cast & bottle csvs required generating an IEH then CIFTing into two csvs. With the migration to casts.csv & sta.csvs, the ability to generate database-friendly cast & bottle csvs directly eliminates the need for the IEH intermediate step. This module is online and working - generating cast & bottle csvs with proper labeling for direct import into the hydrographic database. It is possible to make DECODR update the database directly, saving a few steps, but this seems 'dangerous' since you cannot undo a bad import.

The sta.csvs, generated by CESL during sample drawing on the cruise, were 82-cols wide. DIC & TA values are now added to the sta.csvs in cols 80 & 81 with DIC bottle # in col 79, generating a new 84-col sta.csv format. This will integrate the DIC data with other bottle data and allow inclusion of those values into data products such as the hydrographic database or data reports.

Under the CSV tab, there is a module to generate a merged DIC stations csv with all cast depths and DIC bottle #'s for the point-checking database. The csv can be sent directly to Dickson's DIC analytical lab for data import/key-entry. Or imported into the point-checking database where the DIC Report query will generate forms for Dickson's analysts with the bottle data formatted.

ERDDAP recommended upgrade (1.38 Apr 2012) was installed on sio-calcofi.ucsd.edu.

CTD-derived data, such as sigma-theta, oxsat, dyn height, are available using Seabird's data processing suite. But to get comparable-compatible data to replace bad bottle-derived data, it is necessary to use the bottle algorithms on CTD values. DECODR now uses the same routines for both bottle & CTD data when populating the sta.csvs with derived data. This allows us to use CTD-derived data to QC the bottle-derived data & replace bad values with CTD values. This change is only is the sta.csvs and has not been implemented in the BltVsCTD CTD+bottle csvs yet. The CTD 1m binavg derived-data are calculated using the Seabird algorithms so will differ from the bottle-derived data.