California Cooperative Oceanic Fisheries Investigations

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CalCOFI Shipboard Software And Data Network 2014
 
CalCOFI’s data network has become a key component to data collection & analysis at-sea. Using several CalCOFI-develop software and third-party programs, all computer systems interact with the CalCOFI data network server (currently SeaServ2) so network connectivity on all data collection & analysis workstations is highly desirable. Standalone operation is possible, but not optimal – see the individual program documentation for more details.
 
1.      MetCapture (used primarily on SIO vessels with MET) - GPS/MET/SCS serial capture program with CalCOFI additions
a.       Location: C:\CELogGPS; on backup CTD blade
b.      Configuration file: C:\CELogGPS\metcapture.cfg (see MetCapture documentation)
c.       Input: MET, SCS, or GPS serial feed.
d.      Outputs: two filetypes –
1). currpos.csv, the GPS/positional data used by CELogGPS;
2). MET/SCS data files when MET/SCS is available, YYMMSSMETEV_DDMMYYYY.csv
(eg 1311NHMETEV_23112013.csv; one file per day). This file compiles MET/SCS data with event numbers (from CELogGPS) appended to the end of the data record when it has changed.
Note: METCapture is not typically run on NOAA vessels unless a SCS serial feed is available to the CTD data acquisition area. A GPS is attached to the CELogGPS tablet directly, providing lat-lon-date-time to the event log & network.
2.      CELogGPS - Cruise/CalCOFI Event Log w/ GPS option
a.   Location: C:\CELogGPS; on event tablet & multiple PCs (running in background on CTD PC).
b.  Configuration file: C:\CELogGPS\celoggps.cfg (see CELogGPS documentation)
c.   Input: positional feed – uses either a MET/GPS/SCS string via METCapture's currpos.csv or a direct GPS feed (serial, usb, or tablet’s internal GPS; may require external antenna).
Several text (.txt) files are used to label this program's event activities & other parameters. The specific .txt filenames are defined in the CELogGPS.cfg file – refer to CELogGPS documentation for details.
d.  Outputs: YYMMevents.csv master event file plus individual (local) event csvs on each workstations running the program; a html version is available for network viewing. CAUTION: avoid opening the master event.csv from anywhere on the network during data logging since it may lock the file from updates & crash the program; browse the html version.
3.      CTDBackup (<Ctrl><Alt>B) - zips the Seabird CTD cast files and backs the zip file to flash & individual files to the data server.
a.       Location: C:\Ctdbackup; on the primary CTD data acquisition pc
b.      Configuration file: C:\ctdbackup\ctdbackup.cfg (see CTDBackup documentation)
c.       Input: CTD data & cast files whose path are mapped in the cfg file; CTD-At-Depth event file (YYMMCTDatDepth.csv); it is important that the primary CTD operator or Bridge/Aft-control generates a CTD-AT-DEPTH event once the CTD reaches terminal depth and the first bottle is tripped.
d.      Outputs: YYMM###.log for CESL; a zip archive of all Seabird CTD files which is then copied to the drives mapped in the cfg (usually a flash drive and SeaServ2); CTD .hex, .bl, .mrk, .nav, .hdr files are copied to the data server CTD subdir (Q:\CODES\YYYY\YYMM\CTD)
Important note: CTDBackup uses 7-zip so a copy of 7za.exe is required in the CTDBackup dir. Also a "readme.txt" file (which can contain anything) is needed in the zip destination dirs otherwise the zip file will not be transferred - a weird but necessary requirement.
a.       Location: C:\CESL; on wet-lab tablet pc
b.      Configuration file: C:\CESL\cesl.cfg (see CESL documentation)
c.       Input: sample log base file (YYMM###.log) generated by the CTDBackup program & prd### for prodo bottle designation. Note: CTD header cast type must be set to "PRODO" for CESL to load prd###. It can be selected from the CastType box on CESL if necessary.
d.      Outputs: base files for most analyses -
1). salt program base files (Q:\CODES\YYYY\YYMM\SALT\salt###);
2). O2 box files (###01.box; copied to the auto-titrator pc's O2 box subdir, mapped in CESL.cfg as O:\);
3). chl base files (Q:\CODES\YYYY\YYMM\chl\chl###) & filtration form; uses Excel 2010 & form template (CHLformMaster.xls, located in the local CESL dir).
4). printout of sample log
5). sta.csv & casts.csv entry
5.      PSAL – Portasal Data Acquisition Program
a.       Location: C:\PSal; on the Portasal pc
b.      Configuration file: C:\PSAL\psal.cfg (see SaliReCap PSal documentation)
c.       Input: salt### base files (Q:\CODES\YYYY\YYMM\SALT\salt###); analyst.txt; YYMM###.csv sta.csv for CTD salinity comparisons. Note: initial CTD salts come from the .mrk file; to improve the CTD data, update the sta.csv with .btl or processed .asc files BEFORE running the station.
d.      Outputs: H###02 legacy salt files; salt###.csv .prn .htm files; YYMM_salt###.con (tabulating all average conductivity reads for the run); YYMM_saltdb.csv (combined station salt data csv for data processing database). PSal writes each record to the printer one sample at-a-time so it is important the Portasal has its own dedicated printer. If a dedicated printer is not available turn off the "Print Harcopy" (under PSal's Run Info tab) then print the 'salt###.prn' file after your salt session is finished.
6). sta.csv & casts.csv entry
6.      FLOG – Fluorometer Logger: Chlorophyll Data Acquisition Program
a.       Location: C:\FLog; on the fluorometer pc
b.      Configuration file: C:\FLog\flog.cfg (see FLog documentation)
c.       Input: chl### base files (Q:\CODES\YYYY\YYMM\CHL\chl###)
d.      Outputs: chl### legacy chl files; chl###Base (original file), chl###.csv (run file) .prn .htm output files; YYMM###Chldb1.csv (individual database-friendly csv format) plus YYMMChlDB.csv combined database-friendly csv (combined station chl data csv for data processing database). Flog writes a .prn file & prints the 'chl###.prn' file immediately after each station - be sure the default printer (local or network) is available or uncheck 'Print Hardcopy'.
7). sta.csv & casts.csv entry
7.      Auto-titrator, Oxygen Sample Analysis – uses ODF-developed Auto-titration software with National Instruments drivers
a.       Location: C:\LVO2; on the autotitrator micro-pc
b.      Configuration files: C:\LVO2/LVO2T.cfg, C:\LVO2/wbin/LVO2T.ini (see Autotitration documentation); O2Flasks.vol.
c.       Input: CESL generates O2Box files (O:\###O2) that contain oxygen draw temperatures & flask numbers. Once the station run is setup, these values will auto-enter when running samples in the autotitration program.
d.      Outputs: YYMM### data files (one per station); YYMM###-##.STD, YYMM###.LST files in the O2LST dir; & YYMM###.raw files in the O2Raw dir (standard & blanks file, print file, & run files). These are manually copied to the data server & printed (YYMM###.LST & YYMM###.STD) using Filesync or Ztree. All directories are copied to the server during the cruise & especially at the end of the cruise.
7). sta.csv & casts.csv entry
8.      Nutrient Auto-analyzer, Nutrient Sample Analysis – uses SEAL-developed nutrient analysis software with SEAL QuAAtro drivers
a.       Location: C:\Program Files (x86)/SEAL Analytical; on the autotitrator micro-pc
b.      Configuration files: AACE.ini, SignalSettings.ini, Aim3000.ini (see SEAL Autoanalyzer documentation); YYMMSS.anl analysis file in the cruise data dir
c.       Input: All station & run parameters are entered by the nutrient analyst or stored in cruise setting files.
d.      Outputs: YYMM### data files; several files per run (YYMM###.CHD .COR .par .raw .RES .rlg .rs# .run .TMP .TXT .VTC). Short runs (stations with fewer than 15 samples) may be combined into one run data file. All nutrient files are manually copied to the data server using Filesync or Ztree. All directories are copied to the server during the cruise & especially at the end of the cruise.
Note: a data file with multiple stations must be edited before data processing, a blank 'cup' line with sta### is entered between stations.
 
Last Updated on Monday, 06 January 2014 16:50