MK5 CTD OPERATING INSTRUCTIONS 2/2/95

The following notes are geared toward the mk5 set up aboard the
ALBATROSS IV. Changes to these instruction may be necessary for cruises aboard the ENDEAVOR. If necessary, an addendum will be
provided after February 1995.


MK5

The MK5 CTD records conductivity, temperature, depth and fluorescence at a sampling rate of 16 observations per second.
It is equipped with a 12 bottle rossette water sampler. The following text will provide:

1) a physical description of the MK5
2) description of how the MK5 is configured 3) making up a "Y" cable (if necessary)
4) Setting up the niskins on the rossette
5) Powering up the MK5
6) Performing the MK5 cast
7) Post processing instructions
8) Plotting routines available
9) Care and maintenance of the mk5 at sea

Illustrations of the MK5 and its sensors are shown below.


1.























2. The connections:






















1. IBM PC in electronics lab (RS232)
2. 1401 deck unit (RS232 should be
plugged into "data")
3. power supply
4. Rossette go-fire box
red --> center conductor
black --> shield (ground)
5. winch slip ring assembly
6. Sea cable (for terminations,
center conductor is all wires
wrapped together, ground is the
cable shield)
7. terminal end fitting (center conductor
comes out the side so that no strain is
on the "Y" cable-center conductor conn-
ection. Bolt at end of fitting attaches
to top of CTD bridle).
8. 3 pin male at btm of rossette to 3 pin
female of "Y" cable.
9. 2 pin male on ctd to 2 pin female of
"Y" cable.
10. 2 pin female from sea cable termin-
ation to 2 pin male of "Y" cable.
11. Rossette niskin in deployment
position.

3. THE "Y" CABLE

• Connecting the MK5 CTD with Rossette to sea cable using a "Y" cable
  TERMINATION ON THE SEA CABLE:
  
  RMG-2-FS (two fin female connector, or pigtail):
  
• Center Conductor (all wires twisted together on A4 to reduce -resistance) to small pin (black wire) of pigtail
  
• cable shield (couple strands) to large pin (white wire)
  
  MAKING UP THE "Y" CABLE:
  
  1) RMG-2-MP connector (2 pin, male) connects to RMG-2-FS connector on the sea cable
  
  2) RMG-3-FS connector (3 pin, female) connects to the Rossette
  
  3) RMG-2-FS connector (2 pin, female) connects to the MK5 CTD
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  4. HOW TO SET UP THE NISKIN(S) ON THE ROSSETTE:
  
  The best way to get the hang of cocking the niskins on the rossette is to practice a few times. Basically, the niskin fits in a slot on the rossette that is the width of the niskin clamps. When all niskins are on, you must secure them from being able to float away by loosening the screws on "a ring" on the top of the rossette. Turn the ring such that it will prevent the niskins from sliding up and then tighten down the screws again. again, seeing and doing for yourself will be the best instructor.
  
  To cock the niskins for deployment, first make sure that the next bottle that will close is the one that you want it to be. In the top center of the rossette is a little cylindrical like pin that has a slot that a flat-head screwdriver could fit. If you turn this (with a little flat head screwdriver) you will notice that each "click" corresponds to a bottle being fired. To fire bottle #1, you want to turn the pin so that it is past the bottle before #1 (which would be #12 on our rossette) BUT just before #1. If you turn too far, you will trip the bottle. This takes practice so that is why it is recommended that the pin be set in its proper place before you cock the niskins. NOTE: the pin turns only one way so if you go too far, you have to turn it all the way around the rossette again.
  
  When the pin is set, take the smaller lanyard on the top of the niskin and place (more like push) the loop in the appropriate numbered slot of the Rossette. Using an xbt pin (or a similar substitute) push the white little button from behind so that it will hold the loop in place. This sometimes is tricky but eventually you'll get it. Next take the other lanyard that is attached to the top and clip it to the bottom lanyard as shown in figure 4.
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  5. POWERING UP THE MK5 CTD
  
  1) double check all your connections (figure 2)
  2) if you are just checking to make sure the ctd is operating properly and are not doing a cast, it is not necessary to start
  the acquisition software.
  ) Turn on the 1401 deck unit....4 red lights should be on.
  4) make sure the voltage control button on the power supply is all the way down before turning on the power supply.
  5) turn the power supply on
  6) Turn up the voltage and watch the current consumption.
  7) You will notice a sharp spike in the current ( to about .6 - .7 milliamps) indicating that the "dummy load" is on and that the
  voltage is adequate to power the CTD. Basically the dummy load
  is a mechanism whereby no power is sent to the ctd until a certain theshold is met ..i.e. the voltage/current is adequate to power the CTD.
  8) Turn up the voltage a little bit more to ensure that the CTD has enough "juice." We have found that in the past when we didn't do this, we were draining the instrument's internal capacitors and that made powering up the instrument more difficult.
  9) The SIG light on the deck unit should now be seen flashing, and a steady, high pitched alternating tone will be heard from the speaker. The instrument is ready for the cast. NOTE: when doing an actual cast, you will not be powering up the CTD until it is put in the water (held at the surface) and no one is touching the cable or CTD for safety.
  10) To "test" fire Rossette btls, press the button on the rossette go-fire box (figure 5). If successful, you will see a green light shine on either the even or odd fired lights (depending if the btl you fired was even or odd numbered). Wait until you see the status light blink green again before firing another bottle. The red "misfire" light shines if it didn't work. This sometimes happens if the button wasn't pushed hard or long enough, or if the bottles were not set properly.
  11) Turn off the power supply using the on/off switch.
  12) Turn down the voltage knob on the power supply.
  13) Turn off the deck unit
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  6. PERFORMING THE CAST
  
  THE ACQUISITION SOFTWARE:
  
  1) When the ship arrives on station, you should first fill out
  the MK5 CTD log...sta #, date, time, lat, lon, depth. The computer should be in the directory c:\mk5
  2) Start the acquisition software by typing MKVACQ
  You will see the screen shown below in figure 6.
  3) Check the cast set up by arrowing over to "Settings" and hitting [enter] on "cast set up" (figure 7)
  
• make sure the cruise, date, time, cast # and direction
  are correct ...ex. al10d001 is Albatross cruise #10,
  downcast of cast #1. The correct Cal file to use for
  our instrument is IU221028.C03. If you didn't need to make any changes, [esc] out of this menu. If you did make changes, F2 will save them.
  4) The "Graph set up" usually is set up for the entire cruise and doesn't routinely need changing. But if you want to check it, a screen similar to figure 8 will appear. We usually view temperature, salinity and fluorescence during the cast. Depth will be shown at the top left hand corner of the screen.
  5) On Albatross the deck crew will guide the Mk5 over the side of
  the ship. It is important that when it gets deployed that there
  be no strain on the "Y" cable - Sea cable connections. Also make sure that the yellow caps are off the conductivity cell.
  6) When the MK5 is in the water, at the surface, the winch operator
  will let you know.
  7) Arrow over to "Acquisition" and hit [enter] on "deploy inst- rument." Your graph window will appear (figure 9) and a message
  will appear saying "Make sure instrument is ready to transmit data, press any key when ready"
  8) Follow the instructions for powering up the CTD
  9) When you have signal, press any key on the computer and you will
  now see the depth #'s on the screen coming from the CTD.
  10) Go ahead with the cast, use the intercomm to tell the winch operator to let the ctd down. Bring the CTD to approximately 5 meters off the bottom by watching the depth on the screen. Tell the winch operator when to stop.
  11) When the CTD is stopped at the bottom, hit [CTRL] F10 on the computer. This will end the downcast, and you will be prompted whether or not you want to acquire data on the upcast...enter Y. Your filename is now al10U001.
  12) Fire any bottles that you need to at the btm. When you fire a bottle, hit a [CTRL] F3 which will put a "mark" in the file (as well as a red line across the computer screen). This lets us know where and at what stations we fired btls. Also record on the log the depth you fired any btls...this is necessary in case we forget to hit the [CTRL] F3 .....it happens.
  13) when the signal light is again flashing on the rossette go-fire box, tell the winch operator to bring it up. On the way up, tell the operator to stop the winch wherever it is necessary to fire bottles.
  14) When the CTD is back at the sfc (the winch operator will tell you its there but you will also know from your depth read out) and all necessary btls have been fired, end the upcast on the computer by hitting a [CTRL] F10.
  
• You often get the message saying that "this was a short cast, do you want to increment cast number ?" enter Y.
  5) turn off the power supply and turn down the voltage knob.
  16) power off the deck unit.
  17) "Post Process" and back up of the cast data.
  
• run ctdpost, first differencing, and the smart editor
  (if necessary)
  
• run "endcast xxx" where xxx = mk5 cast #
  
• run "mk5bot.exe" if bottles were fired
  
  
• description of the above routines will follow.
  
  18) Rinse off the ctd with fresh water (ideally distilled but tap water is O.K. there will be a jug provided).
  
• The conductivity cell should be filled with fresh water using the provided yellow caps
  
• The temperature probe should be somehow protected...in the past we have used a paper cup with an elastic band
  around it to secure it in place.
  19) Draw the samples (whatever they may be) out of the niskins...remember that when taking a sample, rinse three times before filling the sample btl.
  20) When all the necessary sampling (filterring) and processing is finished, empty the niskins and cock the niskins for the next
  cast.
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  
  7.
  POST PROCESSING - ENDCAST.BAT
  
  ENDCAST.BAT is a dos batch routine that will: 1) back up the cast data files, 2) run MK5proc.exe which will pressure average the '.edt' files, and 3) will update a header file (NODC format) which will be used by other programs. To run endcast succesfully, you should type endcast xxx where xxx is the mk5 cast # (3 digits pls.) from the c:\mk5 directory. If you choose not to run endcast, you may do all of the above tasks individually. A copy of endcast.bat is attached. NOTE: endcast does NOT run the bottle extraction routine. If bottles were fired during the cast, you will also have to run MK5BOT.EXE to update the cruise bottle file.
  
  MK5PROC.EXE
  
  The data from each cast are stored in files with the extension '.edt'. To process the '.edt' files to pressure averaged files the program MK5PROC.EXE is used.
  

Before running MK5PROC the first time on a cruise, a file MK5CRU.TXT should be edited to include the proper information. An example of this file is listed below, with an explanation of each line:

AL03 : the cruise ID on the '.edt' files
d:\for\bin\ : the directory with the '.edt' files
C00 : the extension for the calibration files
1 : the starting pressure
30 : the initial value of conductivity to use
1 : the pressure interval for averaging
1 : the starting record # in the '.edt' file
Y : indicating to use fast temperature

The first two lines need to be changed for each cruise.

Running MK5PROC, you are asked to enter the first and last station numbers for processing - e.g., 1,30. Then you are asked to choose processing only down casts, up casts or both types of casts. If one cast in the requested series is missing, the program will note it, but will not bomb. The resulting pressure averaged files have the extension '.pre' and are located in the same directory with the '.edt' files.

Extracting Bottle Data - MK5BOT.EXE

To get the CTD data at the time that rosette bottles were fired can be done by the program MK5BOT.EXE. It uses the same MK5CRU.TXT file as MK5PROC.EXE (above), and has the same prompts for first and last station number and cast direction as MK5PROC.EXE. A single output file is created for each cruise, e.g. AL03.BT2. Each time MK5BOT is run for stations in the same cruise, the output is appended to the same '.BT2' output file.

8.

Plotting '.pre' files -

Any time after the first cast, you may run a windows-based program called CTDPLOT in the "BROADSCALE" icon. This program will look for the .hdr file (updated each time you run endcast.bat) and the .pre files which are found in c:\mk5\data. This program will give you station positions, station header information, vertical profiles of temperature, salinity, density (sigma - t) and fluorescence, and a listing of the above data. If you are familiar with the windows environment, the menus will be easy to follow.

The program TEMPCK will create 10 contour files of the cast data:

• sfc and btm temperature and salinity
  
• sfc and btm temperature and salinity anomalies
  
• stratification index (density difference 0 - 30 meters)
  
• stratification anomaly based on MARMAP data
  
  The program TSVOL will compute average volumetric (0 - 30 meters) temperature and salinity values for 4 chosen quadrants of Georges bank including the bank as a whole. It will also create a file containing volumetric t/s values that can later be contoured using Matlab or Surfer.
  
  The above plotting routines were written by David Mountain and
  further documentation and instructions will be provided by him.
  
  Contouring the data files from tempck
  
  Surfer for windows has a nice utility that allows you to write scripts that automate the steps of creating plots. If you would like to use this, there are three "script" files available for you.
  1) BRSCALE.BAS will produce station, sfc and btm
  temperature and salinity plots
  2) TSPLOT.BAS will produce contour plots of sfc and
  btm temperature and salinity anomaly,
  stratification (0-30m) and stratific- ation anomaly.
  3) FISH.BAS will produce larval cod and haddock
  distribution figures using input files
  called "cod.dat", "had.dat", fscale.txt and station .txt. Symbols are posted linearly proportional to the estab- lished symbol size range.
  
  
• there will be a notebook on board that will hopefully clearly
  document these script routines. The plotting and posting parameters may be changes as desired. The intent of the script programming is to get the "rough" plot on the screen and then you
  can customize it to meet your needs.
  
  9.
  

GENERAL CARE OF THE MK5 AT SEA

• After each cast, the MK5 should be rinsed down with fresh water - Make sure that the Rossette is thoroughly rinsed, if the pins that hold the lanyards in place are sticking, you may want to
  squirt some wd-40 in there.
  
• The conductivity cell should be filled with distilled (if available) or fresh water by using the yellow caps
  
• The platinum temperature probe should be protected from damage by placing a paper cup (or a similar substitute) around it and securing it with a rubber band.
  
• After all sampling requirments have been met, the niskins should
  be emptied and set for the next cast.
  
• Keep a watchful eye on the CTD...make sure none of the nuts/bolts
  have somehow come loose...make sure that the "Y" cable and sea cable termination are free and that there is no stress on them.
  
• Make sure that there are no "kinks" in any of the cables that could cause wires to break and subsequent loss of connection.
  
• Make sure the MK5 itself is secured and won't topple over with the rolling of the ship.