Doc_5--Appendix_II _SEAS-ACCESS_Volunteer_Instructions.pdf

The following are complete protocols for launch, recovery, maintenance, and down loading data from the CTD. Volunteers will be supervised by staff and typically will be involved in launch, recovery and maintenance of CTD.

CTD Data Collection Protocol – SEAS-ACCESS

Written by Lisa Etherington and Michael Carver

CTD data are collected with a Sea-Bird Electronics, Inc., SEACAT-SBE-19 profiler

(serial number 1912884-2192), rated to a depth of 600m and containing 256K of memory. (NOTE: This CTD is a 19, not a 19plus. Some commands within software differ between these two versions). In addition to conductivity, temperature, and pressure, the CTD is equipped with sensors to measure light levels (Photosynthetically

Active Radiation (PAR); Biospherical QSP-200PD; serial number 4447) and fluorescence of chlorophyll-a (WetLabs WETStar fluorometer instrument; serial number

WS3S-0140). The instrument is calibrated annually by Seabird Electronics. The auxiliary sensors are calibrated semi annually. A new configuration file is generated after each calibration.

1. Prior to CTD deployment (in office)

a. Hook CTD up to a computer and run Sea-Bird SeaTerm software. (There is a rubber bump on the wet water connector that you use to align the pins from the computer interface cable).

b. Within SeaTerm software, click “Connect” button on toolbar. If everything connects properly, you will see a “S>” prompt. If having trouble getting a connection, be sure that the pigtail is properly connected with the cable (with pins lining up and a proper seal).

c. Click “status” button to check the status of CTD, including date, time, voltage (vmain), number of casts (should be zero if cleared), sample rate

(should be 1 scan every 0.5 sec.), pump delay (should be 45 sec.) and mode (should be set to profiling).

d. To change date and/or time, type ST in the command line (note that the code for the SBE19 is different from the SBE19 plus). Date and time should be set to local time.

e. If voltage is low (below 10 volts), the batteries need to be changed (see

CTD manual for detailed description for changing batteries). Note that it is sometimes difficult to get the CTD top to reseat after changing the batteries.

2. Deployment of the CTD

a. If the conductivity cell was stored dry, it should be soaked with Triton X prior to deployment. Connect tygon tubing and syringe to water intake

(See Appendix 1). Pour enough Triton X into tygon tubing to fill conductivity cell. Soak for 30 minutes and then drain out Triton X. If the conductivity cell was stored wet (distilled water), it should be ready for deployment.

b. Add lead weights to CTD. Shackle CTD to winch wire and use a wire tie or wire to secure shackle.

c. Right before deployment, remove PAR sensor cap and turn CTD on. Note the time the CTD is turned on and the bottom depth on the data sheet.

d. The CTD is lowered to 1 m below the surface for 1 min for equilibration

(it takes the pump ~45 seconds to prime thoroughly).

e. Record position on data sheet. Be sure to note units for latitude and longitude (degrees (°) minutes (’) seconds (”)).

f. The profiler is then lowered at a rate of 50-60 m/minute to a depth of 5 m above the bottom or to a maximum depth of 200 m.

g. At the completion of the cast, turn the CTD off, replace the PAR sensor cap, rinse the conductivity cell with distilled water, and place the tygon tubing over the conductivity cell opening.

3. Routine maintenance

a. At the end of the day, the weights should be removed from the CTD.

b. At the end of the day, CTD should be thoroughly rinsed with fresh water.

Pour enough Triton X into tygon tubing to fill conductivity cell. Soak for

30 minutes and then drain out Triton X. The conductivity cell should then be flushed with distilled water. The CTD should then be stored with the tygon tubing filled with distilled water.

c. Check the anode and replace as needed.

d. Check the bolts and lock washers that secure the CTD to the frame.

4. Data upload steps

a. Check CTD data sheets for any data gaps and change all position entries to decimal degrees.

b. Enter data sheet records into the available data table. On the masterCTD_Log sheet, include: Date, Cast #, Station, Lat (decimal degrees), Lon (decimal degrees), Bottom depth (m), Cast Depth (m), local time, notes, processed status, and con file used. On the CTD_casts sheet, include: number of casts completed and date, date casts uploaded, processed date, person who processed casts, and battery voltage,

c. Create a new folder for the month’s cruise: Example:

\\Cbserver\cbpublic\CBOMP\Data\2007\200711\CTD_Data\CTD_Raw

d. Connect CTD to computer and open SeaTerm software.

e. Check settings:

1. Go to Configure menu → choose SBE 19

Com Settings tab:

v. 3.0 or greater

Comm port: 1

Baud rate: 9600

Bits: 7

Parity: even

Mode: RS-232 (full duplex)

Upload Settings tab:

Upload baud rate: 38400

Upload data: All separated by cast

Header Information tab:

Header info: Prompt for header information

2. Go to Configure menu → choose Header Form

Check to make sure that header prompts are correct for each month. This information is saved as “C:\Windows\SeaTerm.ini” on Lisa’s computer, in case this file needs to be copied to a different machine. Currently, header prompts include:

f. Within SeaTerm software, click “Connect” button on toolbar. If everything connects properly, you will see a “S>” prompt. If having trouble getting a connection, be sure that the pigtail is properly connected with the cable (with pins lining up and a proper seal).

g. Click “Status” to confirm number of casts stored on CTD.

h. Click “Upload” button on toolbar. You will be prompted to save the first file. Choose the new CTD_Raw folder that was created for the cruise.

Name the file “yyyymmdd_cast”. SeaTerm will append a number for each cast, beginning with 000 (saves as .hex files).

i. There will then be a prompt to enter information for each of the headers for this first cast. If too much time elapses between typing the connection will be lost and the uploading process will have to be started over. After clicking ‘ok’ the upload process will begin.

j. The rest of the casts will be uploaded in the same manner, one at a time prompting for header information.

k. Open up the CTD_Raw data folder and check each of the casts to make sure the data are present and appear to be ok (e.g., rows have uniform number of columns).

l. Rename each .hex file by removing the three extra zeros that are appended to the name.

5. Data Processing and Plotting

a. Use SeaBird (SBE) Data Processing-Win32 to process the .hex files to

.cnv files and create plots. The process can be done with each cast individually within the Win32 program or a batch files can be used to process all of the files together. Program set-up files (PSA) are used by the SBE Data Processing to remember the way the program was set up.

You can save the .psa file to a desired filename and location, and then use it when you run the software the next time to ensure that the software will be set up the same way. The PSA configuration files can be found in

Appendix 2.

b. Move a copy of the original .hex files from the server to the computer that will be used for processing. Save them in the root folder C:/Data along with all psa files, con file, and batch .txt file. Create an empty folder named “Processed” for the processed files to be placed into

(C:\Data\Processed).

c. For the first time that data processing is conducted on a computer, you need to go through each of the routines in the SBE data processing program. For example, within the program, go to run and choose 1. Data conversion. In the main tab, you will need to select the proper psa (the program defaults to a program file folder with default psa’s). Select the first hex file as the input file and select the proper .con file. There is no need to go to the other tabs in this window. During this first time of setting up the data processing, you will want to save the psa’s (it will ask you if you want to save when you click exit). After doing the datcnv step, follow with filter, alignCTD, loopedit, derive, binaverage, and seaplot. Note that we are skipping the cell thermal mass step. During these steps, it will ask if you want to overwrite the .cnv file. You should select Yes.

d. Modules and parameters used for data processing (For specific settings of all psa files please reference the psa set up files in appendix 2)

1. Data convert (DatCnv.psa )- converts .hex file to engineering units:

pressure (db), temperature (ITS-90, deg C), Conductivity (S/m), Fluorescence (mg/m ), PAR, decent rate (m/s), scan count

2. Filter (Filter.psa)- filters data for all sensors with low pass filter B of

2.0 sec. for pressure (SBE 19) and low pass filter A of 0.5 sec. for all other sensors. These are the factory default settings for the SBE 19.

See the SeaBird Training Module 9, p7 for filter details.

3. Align (AlignCTD.psa)- aligns temperature and conductivity measurements in time relative to pressure, ensuring that calculations are made from the same parcel of water and minimizing salinity spiking errors. Used whole scan value of 0.5 for temperature and salinity (0.5 is the factory default). (To further assess the alignment of parameters, conductivity and temperature where plotted together to determine lag times).

Note: in the processing software, there will be an option of running a “cell thermal mass” routine. We are not using this and this step can be bypassed.

4. Loop edit (LoopEdit.psa)- removes ship roll and soak time. Data that fell below a fixed speed of 0.25 m/s were removed and the surface soak bin was removed (default from Seabird).

5. Derive (Derive.psa)- Compute density (kg/m ), Sigma-t, salinity (psu), and depth (m) (Lat=38.0 deg.)

6. BinAverage (BinAvg.psa)- averages the data every 1 meter.

7. Seaplot (SeaPlot.psa)- plots the data with fixed scales. The following minimum and maximum values were chosen for plotting:

Parameter Minimum Maximum

Fluorescence 0 28

Temperature 7 16

Salinity 31 35

Depth 0 Auto

PAR 0 1200

Density 1022 1029

e. After setting up a computer for the first time, you should then be able to run the processing through the batch file.

f. To run the SBE batch files

1. Place all the .hex files in the C:\Data folder.

2. Place the correct .con file in the same folder.

3. Place the batch file (SBE_19_batch.txt) in the same folder.

4. Under the Start menu in Windows, select RUN and type:

a. sbebatch

b. the path and file name of the batch file

c. the path and file name of the con file e.g., “sbebatch C:\data\SBE_19_batch.txt C:\data 4_2006.con”

Remember to use the correct con file for the data you are processing and edit the run command accordingly.

5. The batch file will then open and close all SBE data processing modules such that the final .cnv file is placed in the processed folder along with its appropriate plot (.wmf).

g. After the processing is complete, move all of the processed cast data and plots to the CTD processed folder

(e.g.,\\Cbserver\cbpublic\CBOMP\Data\2006\200605\CTD_Data\CTD_Pr ocessed)

h. Examine each individual .cnv file to ensure that the data are good. If satisfied, erase cast data from the CTD by going into SeaTerm software again and selecting the “Init Log” button. Verify the CTD is in fact cleared by checking the status (click status button). Check the battery level of the

CTD before disconnecting.

i. Enter the upload information into Available_data.xls, under the tab “CTD casts,” including number of casts taken, number of casts uploaded, status of processing, and battery status.

6. Calibration

a. For detailed calibration records please reference the calibration binder in the CBNMS office. Note: Calibration can normally take six weeks if all sensors are removed by Seabird and sent to various 3 rd party vendors for calibration. It is important that Seabird remove and send in for calibration all 3 rd party sensors so that a complete con file is on record for the CTD.

Furthermore, Seabird tests the CTD following all 3 rd party calibrations.

Con files are produced every year a calibration was completed. Con files are located on the server in the CBNMS office. Some variables are constant and unique to our instrument such as the log amplifier which boosts the signal from the Biospherical PAR sensor. The log amps are

M= -.763433 and log amp B= -3.417117.

b. (Serial numbers for sensors and calibration history for Seabird CTD purchased May 08, 1996: Sebird SBE 19 Seacat CTD: S/N 1912884-2191, calibrated in 1997, 1999, 2001, 2003, 2005, 2006, 2007, 2008;

Biospherical QSP-200PD PAR light sensor S/N:4447, calibrated in 2001, 2003, Wet Labs Wet Star Fluorometer S/N: WS#S-140, calibrated in

1996, 2001, 2003, 2005, 2007)

Appendix 1. CTD schematic

SEAS-ACCESS, Phytoplankton Sampling Protocols, 2004