References

Salinity Determination

OVERVIEW: This procedure describes the method for the determination of seawater salinity using a Guildline Portasal™ Salinometer (Model 8410).

1. Principle

During a cruise a 24 bottle rosette is used to collect seawater salinity samples of ~225 mL from all bottles closed from pre-designated depths. A Guildline Instruments Portasal™ Salinometer (8410A) makes the precise conductivity comparisons between the water samples and a reference water standard. From these comparisons salinities are then calculated and logged using PC based software that averages data that meet replicate criteria. Concurrent with the water sampling, a Sea-Bird Electronics CTD (SBE 911 plus) profiles in situ data. Data processing software is used to compare the bottle salts to in situ CTD measurements. This is useful to confirm bottle closure, monitor CTD performance, and to select the best salinity data for future comparison.

2. Sample Bottles

Salinity bottles are collected in ~250 ml borosilicate KIMAX-35 bottles. These square cross sectioned bottles have screw tops and lids with separate plastic thimbles to prevent leakage and evaporation. Numbered stackable divider boxes hold 24 numbered bottles to match the 24 Niskins on the rosette water sampler. Bottles are filled with previously unused sample water to limit salt crystallization and to pre-leech silicate from the glass.

3. Sample Collection

Numbered salt bottles are drawn from corresponding Niskin bottles and filled to the shoulder after three ~40 ml rinses. The last fill is done without interruption until overflowing; then ~10 ml is poured out over the thimble and the bottle is stoppered and capped. Samples are left to equilibrate to room temperate for >8 hours prior to measurement. Before being placed in the salinometer samples are: gently inverted 3 times to remove any possible stratification, wiped around the bottom of the cap to draw out as much water as possible that may be trapped under and around the cap, wiped around the thimble and threaded neck once the cap is removed to eliminate any excess water or salt precipitate, and flushed by dumping out ~10 ml into a collection bucket.

4. Guildline Portasal™ Salinometer (8410A)

Guildline Portasal Salinometer model 8410A is used to make the precise conductivity comparisons between the water samples and reference water standards. Two of these instruments are taken on each cruise. Guildline specifications state an accuracy of ±0.003 PSU (same set point temperature as standization and within -2°C and +4°C of ambient), and a precision of 0.0003 PSU.

3. configuring the PORTASAL™

Bath temperature must be within 2 degrees below and 4 degrees above ambient. To check bath temperature set point press the TSET key. Compare set point to actual by pressing ENTER for actual bath temperature. Set point and actual temperature must be within 0.02°C. Press UP ARROW key to view temperatures of the dual bath thermistors (TH1 and TH2). TH1 and TH2 must agree to within 0.04°C.

The Portasal must be powered up for >3 hours to ensure bath temperature regulation has begun before Reference values can be calibrated. While the the FUNCTION switch is in STDBY pressing REF key will display alternating Reference readings plus (+), minus (-), and Reference readings. After several cycles, when + and - values are within 1 unit of each other, pressing the COND key will initiate salinometer self-calibration.

With the FUNCTION switch set to ZERO, pressing the COND key will initiate the ZERO calibration process. When satisfied that the displayed value is stable, press the ZERO key. When the subsequent displayed number is stable (but not necessarily zero) press the COND key. The display should then read 0.00000. Setting the FUNCTION switch back to STDBY will ready the Portasal for Standardization.

4. SubStandard Preparation

Deep sea water is collected on cruises from bottles tripped at depths greater than 300m in 10 liter polyethtylene jerry jugs. The seawater is then transfered to 50 liter carboys at the lab for filtration. During the transfer 10 ml hypochlorate (bleach) is added to inhibit biological activity. Concentrated high salinity seawater is prepared by evaporating deep sea water (>300m) by heating the seawater at about 90°C in an oven overnight. A volume of 1800 ml will evaporate down to about 1000 ml in 24 hours, final volume can be adjusted with DI water, this will give a salinity of around 60psu. Filter the concentrate through GF/F filter before using it for adjusting the sub-standard. Filter the deep seawater through GF/F to 46 liter mark. Add 10 ml laundry bleach to inhibit biological activity. Measure the salinity of the filtered water. Adjustment of the substandard salinity is usually done in two steps. For the first adjustment, add concentrate to the filtered sea water to adjust to the desired salinity using the relationship:

(vol. sw)(sal. sw) + (vol. conc.)(sal. conc.) = (vol. sw + vol. conc.)( final sal. sub)

The salinity of the concentrate will be too high to measure on the salinometer. If you have prepared the concentrate as above you can do your initial adjustment using an estimated salinity of 60 for the concentrate. The final salinity of the sub should be close to your standard value ± 0.015 PSU. For the initial adjustment it works well to add about 90% of the concentrate volume calculated above. Be sure you have thoroughly mixed the solution by stirring gently. A motorized paddle wheel is used to thoroughly stir the mixture. Measure the salinity of the sub after the first adjustment. Using the equation above you can now calculate the apparent salinity of the concentrate, by using the salinity of the concentrate as an unknown, along with the known values for the initial salinity of the seawater, and the adjusted value of the substandard as just measured. Applying the calculated salinity value for the concentrate, use the equation again to calculate a new volume of concentrate to be added to get to the final desired salinity of the substandard. If your initial concentrate addition was to large you may have to dilute with DI water using zero for salinity concentrate in the equation. When you have arrived at the desired salinity for the sub-standard add a layer dimethylpolysiloxane to prevent evaporation resulting in salinity changes.

6. IAPSO Standard Seawater

Cut and Paste from WHP Operations and Methods July 1991

Standard Seawater prepared by Ocean Scientic International Ltd. (OSI) is the recognized standard for the calibration of instruments measuring conductivity (salinity). This water is natural surface water which has been collected in the North Atlantic and carefully ltered and diluted with distilled water to yield seawater with a conductivity ratio near unity and a salinity near 35. The seawater is sealed in glass vials and labeled with the date, batch number, K15 value and chlorinity. Mantyla (1987) has compared batches of this seawater (P-29 to P-102) and found inter-batch dierences as great as about 0.003 in some of the older batches. Since batch P- 93 however, inter-batch dierences have not exceeded about 0.001.

It is recommended that a single batch of SSW be used during each cruise and that it be identied in the cruise report. It is the responsibility of the salinity analyst and chief scientist to ensure that the quality of the salinity observations are the highest attainable. It follows, therefore, that the inter-batch differences described by Mantyla (1987) should be used to correct the nal salinities before they are reported. It has also been noted that the conductivity of some Standard Seawater changes with time. Vials more than 4-5 years old should be compared with fresher Standards to determine possible changes in conductivity due to aging.

7. Wolga Water

In addition to using IAPSO SSW, a batch of aforementioned substandard water has been bottled and sealed in glass vials. This is done to decrease dependence on IAPSO standard while maintaining acceptable standardization accuracies.

8. Standardizing the Portasal with substandard

Before standardization can begin the conductivity cell must be flushed rigorously as it had been filled with detergent or 50% ethanol between uses. To flush, attach the peristaltic pump to the Portasal sampling tube. Turn on both the Portasal and peristaltic pumps, and open the valve on the on the substandard feed line. Flush repeatedly (~10 flushes) until the cell is free of contamination. It is convenient to do this during Portasal configuration. Begin the salt program on the salt computer, and complete requisite data fields.

With the conductivity cell full of substandard and a stable value being displayed turn the FUNCTION switch to READ. When displayed value is stable press STD key. When the Portasal display reads STD STANDARDIZE press ENTER key. The display will show the conductivity of the standard being used. Press ENTER key to proceed (if values of substandard need to be adjusted use ARROW keys.) The BATCH # will be displayed and should match what is being used. If values need to be changed modify with the ARROW keys, pressing the ENTER key will ready Portasal for standardization. The display will read ENTER WHEN READY, press ENTER key. The Portasal will begin measurement and display a substandard value. When stable press the COND key. This will terminate the standardization and the displayed conductivity ratio should match that of your sub-standard within ± 0.00001. Pressing the ENTER key on the salt computer will save it to file.

At the beginning of each sample run the Portasal is standardized with substandard. However, every other day IAPSO and Wolga standards are also sampled. All three standards are run before and after the sample run in order to ascertain instrument drift.

9. Salt Data ACQUISITION Program

The SIO-CalCOFI-authored conductivity recording software, PSal.exe, is a Windows-based data acquisition program that records conductivity values from discreet salinity samples. Averaging five or more conductivity readings from the Guildline Portasal, the operator saves a stable reading. The flow cell is flushed and refilled and additional readings are performed. A pair of conductivity values which agree within 0.0010 standard deviation are recorded and salinity calculated. The software compares this calculated bottle measurement to the matching CTD salinity when available. This comparison is a good indicator of sensor performance and bottle sampling accuracy.
The data are saved as salt run files which may contain more than one station. Keeping the salt runs combined is necessary to calculate the drift-over-time calculated from any change in the end standard or substandard reading. The data are also save in a single, combined, database-friendly csv for database processing (in development).

10. CTD Equipment and Data Processing

A SBE 9ll+ CTD is equipped with dual conductivity and temperature sensors. These are routinely calibrated (~6 months), but because of superior stability the pressure sensor in calibrated much less frequently (~24 months).

The SBE 11plus Deck Unit applies a real time alignment correction to conductivity during data collection, and the accompanying software generates a marker file for each profile containing CTD data at the instant of each Niskin closure.
Seasoft-processed CTD salinities are processed and imported into station csvs for comparison to bottle salinities.

11. DECODR: Data Entry Compiler & Output Data Reports

CalCOFI-authored Windows program will process the bottle sample conductivity data files generated by the SalReCap.exe data acquisition program. Using beginning and end standards, a linear drift is applied to each conductivity pair before salinity (PSU) is calculated. DECODR combines all stations selected into a single text file for data-quality assessment. When CTD salinities for matching depths are available, DECODR compares the bottle & CTD salinities, calculating & reporting the differences. DECODR, as an option, will save the bottle salinity values into each station's csv. DECODR can generate data products using bottle or CTD data such as IEH or data reports.

New(er) Beckman LS 6000IC (SysID# 231220) scintillation counter donated to SIO-CalCOFI by NOAA in early 2008. Repaired by SIO-CalCOFI and in service Oct 2008, replacing our broken/non-repairable Beckman LS 1801.

First cruise counted on new counter: 0810NH
New productivity import routine (DECODR, in-house data processing suite) written to ingest the new file format. Replicate 14C uptake calculations compared between old and new Beckman counters; agree within 95% CL.

Please note, the processing methods described use SIO-CalCOFI-developed software (DECODR & BtlVsCTD) to merge and correct Seabird 911+ CTD data with bottle samples. The Seasoft portion of our data processing protocol follow their recommended settings for our 911+ v2 CTD & deck unit.
"Sta.csvs" are bottle data collected at each station cast combined with 1m binavg CTD data from matching bottle depths (~20). Preliminary comparisons & plots of CTD sensor data versus bottle data are generated after each cruise. These comparisons are used to point-check the bottle data and QC the CTD sensor data. Once final bottle data are generated, eliminating fliers & mistrips, a final comparison of 1m binavg CTD to bottle data is performed. This generates final CTD data csv files for each cast that contain 1m binavg Seasoft-processed CTD sensor data, bottle-corrected Seasoft-processed CTD sensor data, and final bottle data.
The CTD temperatures are Seasoft-processed with no additional corrections applied. CTD salinities are corrected using bottle samples from depths >350m, where the profile is near vertical - offset are typically very small (<0.001). CTD SBE43 oxygen data are significantly improved using bottle oxygen samples for calibration; a linear regression is applied to bottle-correct SBE43 O2 profiles. Fluorometer and ISUS-NO3 sensor data require bottle data to generate regressions and convert their voltages to quantitative measurements. Transmissometer & PAR data are collected, processed using Seasoft and not QC'd further.
Seabird's CTD data processing software suite, Seasoft, is available for free at seabird.com JRW 06/2019

CTD Data Processing Quick Guide (rev Jun 2019)

see sections below for more information & settings - these instructions reference SIO-CalCOFI inhouse software which merges CTD & bottle data then applies regression corrections to sensor data based on sensor vs calibration sample plots. CTD data compared to bottle data are 4-second averages prior-to-bottle-closure.

1. Data Conversion... (SBE): Match CON or XMLCON files accordingly.
    1a. Calculate transmissometer M & B values from deck tests if not done during the cruise, edit/update tranmissometer .xmlcon coefficients to derive beam attenuation coefficients and % light transmission.
2. Window Filter... (SBE): To smooth profiles & reduce spikes (median filter: 9 for all except cosine 500 for ISUS Voltage, usually setup on V6).
3. Filter... (SBE): Filter B = 0.15 on Pressure only.
4. Align CTD... (SBE): Oxygen sensors only (4 seconds).
5. Cell Thermal Mass... (SBE): Default settings.
6. Derive... (SBE): Match CON or XMLCON files accordingly.
7. ASCII Out... (SBE): Select desired variables (see figure below for selection example), check output HDR for errors. DatCNV overwrites the existing .hdr files with new .hdr from embedded information. If the hdr information was keyed-in incorrectly during the cast and the .hdr file was corrected (cast or line.station number, for example) post-cast. The correction is lost when DatCNV generates a new hdr from the .hex file. Hexediting the .hex file, done carefully with a hex editor, will eliminate this problem.
    7a. Sta.csvs updated with .btl data (for 4sec depth value) then 1m .asc data followed by bottle data (salt, O2, chl, nutrients)
8. Step 1... (BTLvsCTD): Individual station BL files and recent preliminary sta.csvs (ieh option still works), unaveraged CTD asc files are required.
9. CSV to .XLS... (Excel): Open the YYMM_CCTD.CSV generated by BtlVsCTD Step 1 in Excel then save as an XLS file.
10. Salt... (Excel): Calculate BTL-CTD offsets (>350m), remove outliers, derive means & statistics.
11. Oxygen... (Excel): Calculate regressions for both oxygen sensors Sbeox0/1ML/L vs. BTL_O2.
    11a. Oxygen (Excel): Calculate regressions for both oxygen sensors Sbeox0/1uM/KG vs. BTL_O2.
12. Nitrate... (Excel): Calculate regression for ISUS vs. BTL_NO3.
13. Chlorophyll... (Excel): Calculate regression for FLSP vs. BTL_CHL.
14. Split... (SBE): Apply the split to the derived CNV files.
15. Bin Average... (SBE): Bin by Depth in 1 meter increments.
16. ASCII Out... (SBE): Select correct variables.

Generating CTD.csvs for point-checking and plots

17. Step 2... (BTLvsCTD): ASC- HDR with current sta.csvs (or IEH) and corrected Events file in folder.
18. Plot Profiles... (Matlab): Plot up cast CSV data with bottles from BTLvsCTD Step 2.
18a. Zip & post preliminary CTD+Bottle csvs with metadata files online.
18b. Copy preliminary CTD+Bottle csvs to dataserver for GTool point-checking.

For Final CTD data, repeat steps 8 - 18 using final data sta.csvs
19. Step 1... (BTLvsCTD): Regenerate comparisons using final sta.csvs (or IEH).
20. Coefficients... (Excel): Recalculate final regressions and coefficients.
21. Step 2... (BTLvsCTD): Regenerate final CTD.CSV files.
22. Plot Profiles... (Matlab): Create final up and down cast profiles with bottles.
23. Misc... (BTLvsCTD): Rename ASC/HDR files, column voltages (optional), and create ZIP files.
24. Database... (Access): Import files into annual database (usually done by JLW).
25. Data Upload... (WinScp): Upload files to sio-calcofi.ucsd.edu in correct folders.

Recent Changes

2013 - large data files warehoused on sio-calcofi.ucsd.edu, includes CTD data & underway data
201108 - new sta.csv format replaces 00/20/ieh
5-5-11 Removed Check on Tau Correction during Step One CNV creation.
5-6-11 No longer plotting downcast without bottles

Underway Data Processing Methods

1. Navigate to Underway Data folder and join into a single file, do so using Advanced File Joiner or similar: http://download.cnet.com/Advanced-File-Joiner/3000-2094_4-169639.html

a. CalCOFI collects its own data while aboard SIO ships (New Horizon). These are saved in the Events folder of the appropriate cruise. A single file name is similar to: 0901NHMETEV_06012009.csv. Although each filename is labeled by date, date data my not correlate. This is of no particular consequence, just be aware of it.

b. When a cruise is aboard a NOAA ship, it is normal to receive a CD-ROM at the cruise with a variety of SCS data. These data formats are highly variable by ship and by year. It will usually take a combination of files to find all that you will require (i.e., one file type for TSG, one for fluorescence, one for lat long). Just merge each file type, then cut and paste columns into the correct order. Make all SCS data available on the web.

c. The resultant file becomes the RAW UNDERWAY DATA for that cruise. This file contains all unedited data from the Shipboard Computer System (SCS). This file may include navigational, meteorological, oceanographic, and other mechanical data. In your local working directory (e.g., ../UnderwayData/2009/0911NH) save raw data in tab delimited ASCII format and name as YYMMSS_UnderwayRaw.txt (e.g., 0901NH_RawUnderway.txt)

d. *Links to SCS information

i. http://oceanexplorer.noaa.gov/technology/tools/scs/scs.html

ii. http://www.unols.org/meetings/2006/200610inm/SessionIIIa/SessionIIIa_Shields.pdf

iii. http://sdsioa.ucsd.edu/

2. Open merged file and crop data columns to include the following, in order and with the following column headers:

a. DATE_UTC, TIME_UTC, LA, LO, ST, SA, FL, FI (Date(UTC), Time(UTC), Lat, Lon, Temp, Salinity, Fluor, Pump)

i. *Note - There is the possibility that power gets toggled on/off to underway sensors during the cruise. This results in changes in the total number of data columns (i.e., the first days may have 100 columns of data and the next few only 98). Attention is needed to make sure that when cropping data that the correct data is sub sampled.

ii. **Note - Different ships have different underway column headers/variable designations/configurations. Consult Underway Data Formats (link) for more information.

3. Delete rows with:

a. pump speed not within than manufacturer's specifications

i. Doubling the flow rate from what we recommend will have at least one main problem. This flow rate will probably be too high for the conductivity cell and overtime you can see a degradation of the conductivity readings due to this flow rate. What can happen is that the high flow rate may slowly remove the platinum on the electrode within the conductivity cell, especially in areas with a lots of debris and particulate in the water. This will change the area of the conductivity cell which can cause the readings to be high of correct. I am unsure how long this process would take but it is something we have seen before. I really suggest using the recommended flow rate for this instrument. ~SBE Technical Support

b. no spatial coordinates

c. erroneous values

i. *Note - There is the possibility that one or more columns may be missing some or all of the data. There are several workarounds depending on the missing variable. Consult WTF Moments (link) for more information.

ii. **Note - With upwards of 100,000 rows of data it is inevitable that most bad values will go unnoticed at this point. Subsequent data processing steps (i.e., plotting) will make it easier to find errors and to remove them. Just try to find the large and obvious discrepancies.

4. Save cropped file as 0901NH_UnderwayCrop.txt in same folder as the raw file.

5. It is necessary to compare and calculate correction regressions based on the comparison of CTD to Underway Data. Navigate to the final CTD Downcast .csv file folder and join all csvs into a single file (as in Step 1). These csv files are the ones with IEH bottle data added to them. In your local working directory (e.g., ../UnderwayData/2009/0901NH) save raw data in tab delimited ASCII format and name as YYMMSS_CTDd.txt (e.g., 0901NH_CTDd.txt). If the YYMM_CTDd.csv file is available open in Excel and crop columns accordingly (#7).

6. Open file with MS Excel and select the first column 'A' and Text-to-Column the Data with comma delimiter.

a. *Note - DO NOT save this file as YYMMSS_CTDd.txt while in Excel. A host of things can go wrong. Data will be Cut and Pasted into a new file shortly. If you must you can save it as some tempfile.xlsx.

7. Crop data columns to include the following, in order and with the following column headers:

a. Date_Time_UTC, Lat_Dec, Lon_Dec, Temp0, Temp1, BTL_Depth, BTL_Salt, BTL_Chl

i. *Note - If Underway Data was only available with Date and Time in PST select Date_Time_PST instead.

8. Sort Ascending (Smallest to Largest) based on BTL_Depth and Delete all depths greater than 2m, all rows with no BTL_Depth values, and all Header rows except for one which needs to be cut and pasted back at the top after we are finished sorting.

9. Sort Ascending based on Date_Time.

10. Delete any rows that are missing any information.

11. Delete any duplicate stations. You can tell if two subsequent rows are from the same station by the time, delete the deeper.

12. Make sure Header row is at the top.

13. After the Temp 1 column, insert 2 additional blank columns.

a. Average the two Temp columns into the first blank column, then copy and paste 'values only' into the second. Delete the Temp0, Temp1, and first column. Header the remaining column as TempAvg.

14. Add three extra headers/columns at the end of the existing

a. ..., ST, SA, FL, FI (..., T, S, Fluro, Pump)

15. Open a previously completed copy of YYMMSS_CTDvsUnderway.xlsx. Select, Copy, and Paste all rows and columns from the sorted and corrected ...CTDd.txt file into the recently opened xlsx file. Save and RENAME the xlsx file accordingly (i.e., NEW YYMMSS ). Make sure no old data lingers in the spreadsheet as this would cause errors in the fit of the regression.

a. *Note - We reuse the xlsx file because it already has multiple graphs set up. You will of course need to resize the data sets for each graph as necessary, and rename the graph titles. But if you followed the above steps the columns will be in the right places and everything should fall into place.

16. Open the ...UnderwayCrop.txt in MS Excel, Tab delimited. Arrange both files in Tile View.

17. Using this new ...CTDvsUnderway.xlsx file's Date_Time as a guide, scroll down the ...UnderwayCrop.txt and find a corresponding date and time. There will be more than one row of data for the time you are trying to match. Try not to bias the selection of the Underway data and just pick the first one you see. Select the four columns, Temp, Salinity, Fluor, Pump, from UnderwayCrop and Copy them, and Paste them to the xlsx file in the last four columns ST, SA, etc. Do this for all the rows in the CTDvsUnderway file.

a. Because the number of rows will change from cruise to cruise, the graph data source will need to be adjusted accordingly. This is important as the linear regression equations shown on the graphs are used to correct the Underway Data in subsequent steps. Save file.

18. For export to MATLAB it is necessary to Cut the xlsx data (numbers no graph info) and paste it into a new UltraEdit .txt file. Name it accordingly (YYMMSS_CTDvsUnderway.txt). This is done to remove any .xlsx formatting that may cause MATLAB to choke on import.

19. Start Matlab and load a previously completed .m file as a template (e.g., 0901NH.m). The .m file will have incorrect variable names and notes pertaining to that specific cruise. Change and update accordingly. Also make sure you are working in your current underway folder.

a. Import UnderwayCrop.txt and follow along the notes in the script for error checking and saving data as a .mat file.

b. Import ...CTDvsUnderway.txt. There will be an error with this as the Date_Time will not ingest properly. Ignore it, the date is not important for plotting unless GPS has failed and you need the data and time to correlate with the Event Log GPS to get some coordinates to make these maps.

c. An important step to be aware of is toward the end of the script it asks you to use dlmwrite function to export the final underway data product.

20. The template m-file will guide you through the entire process. When you get to the regression corrections take the values from the xlsx file graphs that you generated earlier. When you make the Matlab plots they should print into your working folder.

21. Open a previous yymmplot.ai file in Adobe Illustrator and the first plot from Matlab (i.e., t0901NHpath.eps). Save the .ai file with the current cruise YYMM.

a. In dealing with the .eps file from Matlab you will find that all we really need is the color path and the gradient bar frame and numbers. Ungroup and delete all you don't need (coastline, grid, tick marks, gradient color, etc.)

b. Since the path is thousands of small circles, select them all, group them, then copy them to the clipboard. Delete the preexisting path in the .ai file and make sure you paste the new one in the correct .ai layer and resize to fit the station layout / cruise path. This isn't an exacting process, just make it fit best you can. Make sure to lock/unlock layers as you go to prevent the pasting / editing in the wrong place.

c. Go back to the eps and copy the gradient bar box, tickmarks, and numbers. Since each cruise's graph has a different range of values these gradient bars change. The colors stay the same (if you followed the Matlab m-file correctly) but we need to make the new numbers fit the template. Delete the old box and numbers and paste in the new and resize accordingly. Resizing will skew the font so once everything is in the right place check the font setting and set to 18pt Myriad Pro with 100% font stretching in both directions. You will also have to change the decimals and numbers a bit as Matlab tend to separate the numbers after the decimal in eps format. Just delete the end and retype the number using the left half.

d. Unlock and Edit the Title layer to the correct cruise designation and dates and title.

e. In Illustrator to save as pdf "save a copy", to save as png Use Export (white background, medium resolution, anti aliased) . Open each png in Photoshop and shrink to 75 pixels keep proportionality and rename with a " _t" at the end for the web thumb.

31. Upload all data and images to calcofi.com FTP Underway_Data directory.

32. Edit calcofi.com Joomla site with new underway data accordingly.

CalCOFI's primary hydrographic instrument is a Seabird 911+ CTD equipped with dual temperature, conductivity and oxygen sensors mounted on a 24-10L bottle rosette. Additional CTD sensors mounted on the rosette frame include a fluorometer, transmissometer, nitrate sensor, PAR, pH and altimeter.
The CTD-Rosette is lowered into the ocean measuring a suite of seawater properties throughout the water column. Occupying the same stations (specific GPS locations) four times a year - Winter, Spring, Summer, Fall - we measure physical & biological properties: temperature, salinity, oxygen, fluorescence (chlorophyll), nutrients, and productivity from surface to 500m. Additional measurements from seawater samples collected using the rosette are combined with CTD sensor data, filling out the dataset. These seasonal measurements are published in Cruise Data Reports & added to our time-series database, both available online.
The CTD-Rosette is electronically tethered to the ship using a winch with conductive wire. This allows a computer on the ship to control the CTD and monitor the temperature, conductivity, oxygen sensor arrays plus single fluorometer, transmissometer, altimeter & nitrate sensors. As the CTD-Rosette is lowered to 500m, the temperature, salinity, oxygen, chlorophyll, nitrate, and other measurements are displayed real-time & stored on the ship's computer. Depending on the downcast profiles, mainly the depth of highest chlorophyll & mixed layer, bottles are closed at standard depths as the CTD-Rosette is brought back to surface. The seawater samples collected will be analysed & used to calibrate the various sensors or provide measurements that cannot be measured electronically.

Temperature (T) - Seabird Electronic SBE 3plus temperature sensors: are dependable, requiring no additional calibration other than annual service and calibration performed by Seabird. Dual T sensors are plumbed horizontally, separately to SBE 5T submersible pumps. Measurements are reported in degC.
Conductivity (C) - Seabird SBE 4C: paired/plumbed with SBE 3plus temperature sensor, measure seawater pumped by the SBE 5T pump. Standard SBE Data Processing offsets are applied to this measurement prior to deriving salinities as PSU. When using the SBE11 v2 Deck Unit, a SBE Data Processing Alignctd offset is not applied to secondary conductivity sensor since it is applied by the deck unit.
- Salinities (in PSU) - are derived from T & C after standard SBE Data Processing modules are applied. Although salinities directly from the CTD are considered excellent, when bottle salts from greather than 350m are available, bottle-correction offsets are applied. These data are reported alongside the uncorrected salinities in our CTD data products.
Oxygen - Seabird SBE 43 Dissolved Oxygen Sensor: dual SBE 43 O2 sensors are plumbed inline with the paired T & C sensors, between the T-C pair and pump. Since the response time of the SBE 43 oxygen sensor is slower that T & C, SBE Data Processing's AlignCTD module is used to apply a 4-second to sensor data before oxygen measurements are derived.
In addition to standard Seabird SBE Data Processing recommended data processing, when seawater oxygen samples are analysed during the cruise. They are used to calibrate sensor oxygen values: cruise-corrected CTD oxygen & station-corrected CTD oxygen data are derived and included in the CTD data products.
Wetlabs ECO AFL/FL FLuorometer: measures fluorescence-chlorophyll-a; used during the downcast to identify the depth of the chlorophyll-a maximum, which determines the bottle sample depths. Although an estimated chlorophyll-a can be derived using the fluorometer factory calibration. CalCOFI uses cold-extracted chlorophyll-a sample data versus fluorometer voltages to derive estimated chlorophyll-a measurements.
WetLabs C-Star 25cm 440nm Transmissometer measures % light transmission & beam attenuation coefficients. Before the first cast, CalCOFI measures the dark & light voltages on deck, calculates the M & B coefficients and enters these values under the transmissometer calibration in the CTD .xmlcon file. This is the only calibration done on the transmissometer during a cruise. A Triton or RBS (mild soap, squirt bottle) rinse of the transmissometer optics is done routinely before a cast to clean the optical surfaces.
Satlantic MBARI-ISUS v3 Nitrate Sensor: recently upgraded to firmware version 3, the ISUS can now be recalibrated by CalCOFI. MBARI-ISUS Version 2 deployed on cruises prior to 1708SR required calibration by Satlantic (prior to Seabird Electronics merger). Estimated nitrate may be displayed real-time using user-polynomial coefficients (from the previous cruise) entered into Seasave .xmlcon. Estimated nitrate data are derived post-cruise from the ISUS voltages using seawater nitrate samples plotted versus average ISUS voltages. Cruise-corrected and station-corrected values are calculated and reported in the CTD data products. The ISUS has been deployed on most cruises since 2004, on casts 1000m or less.
Seabird SBE 18 pH Sensor: has been deployed on all cast (1000m or less) since 2009. This sensor is serviced annually and is checked before each cruise using 3 buffer solutions (pHs 4, 8, 10). The sensor electrode is stored in buffer solution between casts to prevent drying out.
Biospherical Single-Channel Photoradiometers (QSP-2300 PAR & QSR 2200 Surface PAR): a remote PAR is deployed on casts up to 1000m; surface PAR is interfaced with the SBE 11 Deck Unit on most cruises. Factory calibration and coefficients are entered into Seasoft .xmlcon file for both sensor. No additional calibration is performed; standard SBE Data Processing is performed but nothing specific to either PAR other than WFilter.
Benthos Altimeter (PSA-916): used on all cruises and all casts unless a oxygen optode is deployed (CC1210NH, CC1611SR) then only on stations less than 500m deep. Factory calibration coefficients are entered into Seasave .xmlcon but no calibration is performed. Height off the bottom typically is displayed ~50m from bottom but depends on sea state, bottom composition or wire angle.

How to update the CCDB Hydrographic Database in MySQL

In addition to ERDDAP, SIO-CalCOFI has a smaller, queryable, online, hydrographic database. This query form includes bottle-related data only and resides at cappuccino.ucsd.edu. These instructions were composed after multiple attempts to update the large mySQL database table with new data.

Create a new CCDB data table containing only newer final data (last update included 201710). The CCDB queriable online database is a distillation of the cast & bottle tables of the CalCOFI Hydrographic Database (webpage). Refer to the query form or CCDB table in the complete database for data columns. In the MSAccess hydrographic database there is a make-table query, !MT-CCDB. In Design View, edit the Cruise criteria to extract the latest data only. The query will create a new table called CCDB so rename this table CCDB???? where ???? are the start & end years eg 4956 for 1949-1956 (or any unique label). Add the month if necessary ie CCDB1304, for a single cruise or yearmonth(YYMM), CCDB 13041311, for multiple cruises. This is the table you will be using next.
Create a .sql dump MySQL file of this CCDB new table. Using MSAccess to MySQL (free Windows utility by Bullzip.com), connect to the MSAccess hydrographic database. Select the new CCDB???? table then 'sql dump' it to CCDB????.sql. The sql dump file cannot be larger than 100mb. If it is larger then split it up using the make-table (!MT-CCDB) query multiple times with multiple Cruise criteria. For the entire database, I used: 194901-195612, 195701-196912, 197001-198912, & 199001-present. Each file was ~200,000 records & 60mb.
Login into cappucino.ucsd.edu using Synology Assistant. In Package Manager, run PHPMyAdmin to manage the online databases. Select the CCDB database then Import. Using Choose File, select the CCDB????.sql file generated in step 2 then click GO. This should import the new data into a new table - it is important it be a new table (something other than CCDB) otherwise the original data table will be replaced.
Copy the new table into CCDB (main data table). Select the new table in ccdb then select Operations from the phpMyAdmin tabs. Using Copy table to (database.table); change the CCDB??? in the right box to CCDB (both boxes read ccdb & CCDB). Select Data only then click GO - I've also clicked Add AUTO_INCREMENT value but that does not seem to do anything since the primary index of CCDB is Btl_Cnt.
If all went well, that's it. The new row count will appear when you select CCDB. Currently, with 201301 data added, the row count is 835,407.

SIO-CalCOFI's Cappucino.ucsd.edu Bottle Data Query Form

A Sea-Bird Electronics 911plus V2 CTD collects vertical profile data at every CalCOFI station. In addition to being a dual TCO (temperature, conductivity, and oxygen) system, the CTD also interfaces with a transmissometer, fluorometer, PAR/SPAR meters, altimeter, nitrate, and pH sensor. Connected to a shipboard data-acquisition computer through an electronically-conductive winch wire, sensor data are collected and displayed real-time using Seasave V7 on a Windows PC. The CTD is normally lowered to terminal depth of 515 m, bottom-depth permitting, but is routinely deployed within meters from the seafloor at nearshore SCCOOS and basin stations. To ensure high resolution sampling in areas with significant hydrological and biological gradients a speed of ~30 m/min is used for the first 100 m then ~60 m/min to depth without stopping. During retrieval, the CTD is paused for at least 20 seconds at target bottle depths to adequately flush each 10 liter sample bottle prior to closure. Seawater samples are analyzed onboard (e.g., salinity, oxygen, nutrients, chl) and are used to correct measured CTD values.

Information from Seasoft v7.23.1 (May 2014)

Algorithms used for calculation of derived parameters in Data Conversion, Derive, Sea Plot, SeaCalc III [EOS-80 (Practical Salinity) tab], and Seasave are identical, except as noted in Derived Parameter Formulas (EOS-80; Practical Salinity), and are based on EOS-80 equations.

Derived Parameter Formulas (EOS-80)

For formulas for the calculation of conductivity, temperature, and pressure, see the calibration sheets for your instrument.

Formulas for the computation of salinity, density, potential temperature, specific volume anomaly, and sound velocity were obtained from "Algorithms for computation of fundamental properties of seawater", by N.P. Fofonoff and R.C Millard Jr.; Unesco technical papers in marine science #44, 1983.

Temperature used for calculating derived variables is IPTS-68, except as noted. Following the recommendation of JPOTS, T68 is assumed to be 1.00024 * T90 (-2 to 35 °C).
Salinity is PSS-78 (Practical Salinity) (see Application Note 14: 1978 Practical Salinity Scale on Sea-Bird's website). By definition, PSS-78 is valid only in the range of 2 to 42 psu. Sea-Bird uses the PSS-78 algorithm in SBE software, without regard to those limitations on the valid range. Unesco technical papers in marine science 62 "Salinity and density of seawater: Tables for high salinities (42 to 50)" provides a method for calculating salinity in the higher range (http://unesdoc.unesco.org/images/0009/000964/096451mb.pdf). Salinity measurements in the CalCOFI sampling area never been outside the 2 to 42 psu range - typically between 32 - 36 psu.

Subcategories

CalCOFI Handbook

The CalCOFI Handbook is a compilation of information for cruise participants. It explains many aspects of the science performed at sea, particularly the sample drawing methods for each sample type.

Data Formats

CalCOFI Data File Formats

Methods

CalCOFI standard practices for sample analysis, data processing, metadata & general methodology.

Software

SIO-CalCOFI software used at-sea and ashore, developed by the SIO CalCOFI Technical Group. Plus other software: auto-titrator oxygen analysis software developed by SIO's Ocean Data Facility; Seabird Seasoft & Data Processing software; Microsoft Office, Ultraedit, Ztree, hxD hex editor, Matlab, Surfer, Ocean Data View.

Salinity

Salinity Determination

1. Principle

2. Sample Bottles

3. Sample Collection

4. Guildline Portasal™ Salinometer (8410A)

3. configuring the PORTASAL™

4. SubStandard Preparation

6. IAPSO Standard Seawater

7. Wolga Water

8. Standardizing the Portasal with substandard

9. Salt Data ACQUISITION Program

10. CTD Equipment and Data Processing

11. DECODR: Data Entry Compiler & Output Data Reports

Scintillation Counter 2008

CTD Data Processing Protocol

Underway Data Processing

CTD Standard Sensors

Updating CalCOFI Hydrographic Database

How to update the CCDB Hydrographic Database in MySQL

CTD System

CalCOFI CTD FAQ

Satlantic ISUS Operation

CTD Data Algorithms