CELogGPS user-interface has been redesigned for horizontal touch-screen use - CELog1511H is the latest version. The buttons will cycle through the different station activities and when [Record Event] is pressed, the activity will be recorded.

In this version, I've tuned the button selected to match the activity field until the [Record Event] is pressed. Then the next stage of an activity will be auto-selected, the user just needs to press [Record Event] button again. Once all the stages of the station activity are done, the event log user selects the next activity. Example: if CTD DEPLOYED is selected and [Record Event] pressed, the CTD AT DEPTH next stage will automatically fill the activity field, the user only needs to press [Record Event] when the CTD arrives at depth. Once pressed, the activity will auto-select CTD RECOVERED. Once recorded the event log selection will be neutral until the next activity is selected such as PAIROVET DEPLOYED.

A vertical version of the event log program, CELog1511V.exe, has also been created for tablet-use in the vertical orientation. All routines are identical to the horizontal version. Eventually, I'd like to make the horizontal or vertical form-format a dynamic option like most commercial tablet programs.

It came to my attention that salts can be miscalculated if the sample count in the header is wrong. If the last sample indicated by the sample count is not the end sub, the drift will be miscalculated. This was obvious when the bottle and CTD salts were merge by BtlVsCTD.

So there is a new module under the Salinity Tab that will read the selected H###02 files, count the number of samples which should be n-2. It will also check the header for start station and end station - basically it is a header checker. Nothing is done to the H###02 files but a YYMMHSaltCheck.txt file is created and tabulates the correctness or incorrectness of all the files processed. Additional features may be added to future versions.

Simple change - in the contour-building module, when using the CTD asc files to build the contour csvs. If the primary oxygen is reading negative then the secondary oxygen sensor will be used. This was specific to 1507OC when the primary oxygen sensor failed on casts 4 & 5. It was replaced on cast 6.

New features - umol/Kg for bottle oxygen calculated when using IEH bottle data. IEHs do not include oxygen in umol/kg so it is calculated from bottle oxygen ml/l and CTD sigma-theta. Using IEH sigma-theta would be preferable but some IEHs do not have sigma-theta.

Algorithm used is the same as Seabird references: [µmole/Kg] = [ml/L] * 44660 / (sigma_theta(P=0,PoT,S) + 1000)

Also when bottle umol/Kg is not present but regression coefficients are available, cruise-corrected CTD primary & secondary oxygens in umol/Kg are calculated.

CTD.csvs were re-generated to include these values and pH.

Complete hydrographic data reports are now available on our website for cruises 2014-02 and 2014-04.  Reports include cruise data report, primary productivity data report, spartial pattern figures and the zooplankton volume report.

The list of 2014-2015 CalCOFI CIMEC publications and presentations are now available on our website at http://www.calcofi.com/ccpublications/recent-publications/publications-2014-2015.html

Several updates have been made to the website:

• Imported final data from 201404 and 201407 into bottle and cast tables.
• Imported DIC data from 2014-04 and 2014-07 in the DIC csv
• Imported zooplankton data from 2013-11 through 2014-04 in the zooplankton csv
• Fixed 90.45 Prodo in 2010-08.  Had values from station 93.3 26.7 of that cruise.

CELog has been updated many times since it was created in 2005 to record CalCOFI (& LTER) cruise data-generating events. Here are some key features & modifications to the program:

• CELog (2005) - Uses GPS date-time lat-lon from either MET or ship's GPS serial feed which is saved every 30secs to the data server by METCapture or GPSCapture (another SIO-CalCOFI authored Windows program).
• CELogGPS (2006) - direct ingestion of the GPS string added by adding a GPS serial module to CELog = CELogGPS. Using a directly connected GPS feed, CELogGPS can parse and serve the GPS string to the data network. One workstation or tablet is configured this way and other eventlog workstations can ingest the currentpos.csv string. If a data network is not available, all versions can run independently if configured with their own GPS feed. GPS format is configured in the celoggps.cfg file.
• Checkbox mode: this feature was added so the event log could "nest" observations. From a list of multiple choices defined by the events.txt (e.g. MMammalEvents.txt), an observation string could be appended with multiple selections from the list. This allowed the event string to be built from a variety of choices - such as whale sighted + blue whale or whale sighted + fin whale then include other annotations.
• In 2015, CELogGPS was modified to work on a touchscreen tablet PC (ASUS Transformer T100TAF). Normally fed by txt files to customize the activities listed, some buttons are hard-coded for certain activities or group of activities. An activity is selected then repeated touches of the button will toggle the activity from "deployed" to "at depth" to "recovered" as appropriate. The Record Event button needs to be pressed to actually log the event.

CELogGPS is a SIO-CalCOFI Windows program that records cruise events and activities timestamped with GPS date-time-lat-lon. Other notable events such as marine mammal-avifauna sightings, CUFES, or any data-generating activity may also be recorded. The GPS position can be ingested basically two ways:

• On UNOLS vessels with MET, the MET (meterological system) string provides GPS data. A workstation is setup to run MetCapture, another SIO-CalCOFI program, that collects the MET data and appends event numbers when updated. METCapture saves the current MET string (with GPS date-time-lat-lon) to a file (currpos.csv) on the shipboard data network that all eventlogging workstations can harvest. Please review the METCapture documentation for more info. (Standard GPS input is acceptable; METCapture can log GPS instead of MET data or the GPS feed may be connected directly to the CELogGPS tablet serial port.)
• On NOAA vessels, a USB GPS (current model: GlobalSat BU-353 USB GPS Receiver with SiRF Star III based Serial GPS receiver with WAAS/EGNOS support for enchance position accuracy) is attached directly to the CELogGPS tablet and provides the GPS data (currpos.csv) to the shipboard data server and other networked eventloggers. See the GPS settings section below for setup information.

gTool modules 'makeMAT.m", "makeNutTab.m", "remakeMAT.m" and "makePlotBut.m" have been modified to accept individual nutrient data codes: P4DC for PO4; SIDC for SIL; N2DC for NO2; N3DC for NO3.

gTool's nutrient data table will display the new columns and allow the point-checker to change the data codes for each bottle nutrient. This will replace the combined data codes "NDC".

First cruise that will be processed with the additional data codes will be CalCOFi 1504NH.

Starting on CalCOFI 1504NH, individual data codes will populate the sta.csvs. Modifications to CESL, DECODR, seaPt, and gTool will use the individual nutrient data codes: P4DC = PO4, SIDC = SIL, N2DC = NO2DC, N3DC = NO3DC. Data codes are : "0" for good bottle data; "4" to zero the data; "9" to omit the data.

DECODR1504 will use the new nutrient datacodes (P#;S#;O#;T#) when interpolating bottle values.
It will preserve the existing datacodes - if the nitrate datacodes are T4, the terpled nitrate datacode will be T4. Please note that, although the T4 datacode means to zero nitrate, the interpolated value will be calculated using observed nitrates so may be non-zero. Its datacode will be inherited from the 1st observed value datacode, so if T4, it would be zero in generated data products.
Nitrate is used for the example but this applies to phosphate silicate nitrite interpolations as well.

Odd problem cropped up when running the 200/500 Dynamic Height Extrapolater. First the array to parse the record was set to default which was 0 and resulted in an "infinite loop" error. In DECODR1503 it is hardwired at '5' when reading in the YYMM_DHt?.csv which is 5 columns wide.

Also - in order to calculate 200/500, the depths in the YYMM_DHt?.csv need to be deep to shallow. If they are inverse, the 200m dynamic height will miscalculate and so will the 200/500 extrapolation. Run the Invert Depth module under the CSV tab until a more streamline solution is implemented.

The NASes occasionally have issues with directory permissions changing particularly after a firmware update. If directories "disappear" or are read-only, check the permissions.

The State of the Current map is now available for CalCOFI cruise 2014-11.  Map includes 0/500m Dynamic Height, 10m Temp, 10m Salinity and 10m Chlorophyll.  http://www.calcofi.com/data/SOC/pdf/1411_soc.pdf

The new version of DECODR1502.exe 'DataCode Checker' module will "9" the LTER duplicate bottle oxygen datacode if it does not already have a "9", "6" or "4" AND there is a "L" in the DPTHNT column.

When starting a PSal run, the initial sub is given a sta number of 999 since no station base file has been loaded yet. This causes the routine to skip subsequent values. I will fix PSal to not give initial subs readings a 999 designation but look for this issue by examining salt files when they do not run.

The new version DECODR1502.exe - changed the label MRK SALT to CTD SALT - the source of the CTD salt value is the sta.csv. The option to use primary or secondary salt (right side of processing screen) does work. I ran it and got primary sta.csv salts in the CTD SALT (formerly MRK SALT) column. I added an extra sig fig so CTD salt is 33.xxxx but reduced the bottle-CTD salt to three sig figs ie 0.004 as per DMW's request.

Fine tuned the nutrient datacodes for MDL handling.

Addressed some problems with the contour-csv-generation from CTD asc files.

Fixed chl ave blank, F, tau zeroing issue - array index glitch fixed, it was using blank for all fields.

Nutrient sta.csv update bug fixed - using new nutrient datacodes was causing an error resulting in "bak dir..." dialog repeatedly appearing.

Note: when a prodo station is not identified or saved as prodo by CESL, "P" footnotes are not added to the DEPTHFN column of the station csv. This results in the scintillation importer not recognizing the cast or depths as prodo bottles. This happened on sta 001 on 1411NH - "P"s were added to the 1411001.csv prodo bottles and the import was correct.

Two problems fixed:

Problem 1:  when updating .csv with CHL values - values placed in the boxen for Blank, F and Tau uses blank values for everything resulting in 0.00 in all fields for Chl in sta.csv files. Solution - F & Tau array elements were not index properly so Blank was used for all three values - fixed.

Problem 2: recurrent "no .bak directory" error message when trying to update sta.csvs for Nuts.  Solution: when there is an error, this is the default response even though the error may be the result of something else. Error descriptor has been updated to describe other problems.

Standalone nutrient data codes (NDC) '4' or '9' still work for all PO4, Sil, NO2, & NO3. '4' will zero, '9' will blank all values at that depth. But in order to resolve individual nutrients data columns, additional data codes were added. These additional annotations also reside in NDC column 32 of the sta.csvs.

• Phosphate
  • P4 - Phosphate-specific nutrient data code 'P4' will zero the phosphate value in data products. The phosphate measurement is retained in the sta.csv. A 'P4' NDC is automatically added if, during nutrient processing, the phosphate is below the MDL and the zero checkbox is checked.
  • P9 - Phosphate-specific nutrient data code 'P9' will blank the value in data products, value is preserved in sta.csv.
• Silicate
  • S4 - Silicate specific data code 'S4' will zero the silicate value in data products; this is automatically done if, during nutrient processing, the silicate is below the MDL and the zero checkbox is checked.
  • S9 - Silicate-specific nutrient data code 'S9' will blank the value in data products. Original measurement will be retained in the sta.csv.
• Nitrite
  • O4 - Nitrite specific data code 'O4' will zero the nitrite value in data products; this is automatically done if, during nutrient processing, the nitrite is below the MDL and the zero checkbox is checked.
  • O9 - Nitrite-specific nutrient data code 'O9' will blank the value in data products. Original measurement will be retained in the sta.csv.
• Nitrate
  • T4 - Nitrate specific data code 'T4' will zero the nitrate value in data products; this is automatically done if, during nutrient processing, the nitrate is below the MDL and the zero checkbox is checked.
  • T9 - Nitrate-specific nutrient data code 'T9' will blank the value in data products. Original measurement will be retained in the sta.csv.

The Complete Final Data Report PDF for the summer CalCOFI cruise is now available on the new data website.

The database and all associated database generated files are now available through the Winter 2014 CalCOFI cruise:

ACCESS Database

csv's

SQL

XML

From CalCOFI 1411NH on, pH samples will be logged separately from DIC samples although the same flask type, same draw technique and storage containers are used. The DECODR Dickson csv sample log csv generator will now output two additional columns - pH_Btl1 & pH_Btl2. This csv sample log is used by the Dickson lab to index the DIC & pH samples during analysis. Bottle numbers for DIC and pH samples will populate the appropriate columns - ph_Btl1, pH_Btl2, DIC_Btl1, DIC_Btl2.

8 CalCOFI stations have 0 & 30m pH samples. On previous samples logs, these samples were labeled 'DIC' although they were drawn for pH analysis. CESL1411 resolves these pH stations, commenting the samples "PH". Although the sample bottles numbers are logged in the same column as DIC bottles (col 12), the comments field will contain "PH" or "PHx2". PH samples are drawn in the same way as DIC samples - same flask type, same draw technique. PH & DIC samples are collected and stored in the same seagoing bins so only the bottle number distinguishes the samples.

pH 0 & 30m Stations: 93.3 28.0, 90.0 120.0, 90.0 45.0, 90.0 37.0 , 90.0 28.0, 86.7 33.0, 83.3 42.0, 83.3 40.6

DECODR will build a database-friendly csv using a cruise's Dickson-Cervantes pH-DIC-TA csv (spreadsheet export) and sta.csvs. This version adds two pH columns (pH1, pH2) left of the DIC & TA columns (DIC1, DIC2, TA1, TA2).

A slight modification to the DIC record parser - no "COFI" is needed in front of the DIC bottle number in column 1. But, there should be no description lines above the data table - the first line should be the data column headers; lines 2+ are data.

The line.sta calculator uses station position GPS latitude & longitude to calculate the actual CalCOFI station Line.Sta. There was a problem when a negative (W) longitude was used from the YYMMcasts.csv, saved by CESL. A negative longitude causes the decimal longitude parsing back to degrees to be negative, so the longitude minutes were miscalculated. This resulted in an incorrect 'actual line' (Ac_Line) & 'actual sta' Ac_Sta calculations during the csv>database conversion. 

DECODR1410 now checks for a longitude < 0 and multiplies it by -1 to insure a positive longitude is parsed. The decimal longitude (Lon_Dec) and longitude degrees are still reported as a negative. So this change does not affect the outputted data signs, only the internal calculations.

Added Report Order Line.Sta filter for Lines 78.0 55.0, 79.0 55.0, 81.0 55.0, 82.0 55.0 to handle CalCOFI 1311NH's extra DIC stations. Also included additional DIC stations 80.0 53.0 & 80.0 57.5.

Also added a second cast option for sta 90.0 90.0 3500m cast in case there is an extra prodo cast (CalCOFI 1311NH cast 021 & 521). This feature may need to be expanded for other duplicate stations but for now it only works for 90.90.

The Hydrographic and Primary Productivity reports for the Winter 2014 cruise are now available on our new data website.

LD recommended I update our ERDDAP server from 1.46 to 1.52. It took a couple tries but it is online. Hydrographic database is still not visible - continuing work in progress.