• Supplies:

• 250ml amber rubberized glass Qorpak bottles with teflon insert lids
• Liqui-Nox (Alconox) detergent (diluted according to bottle directions)
• 10% HCl solution
• tap water
• Q-water

• Wash bottles inside and out (and lids) with Liqui-Nox (Alconox) detergent. Rinse with tap water until all detergent bubbles are gone.
• Fill each bottle about 1/3 full with 10% HCl solution. Cap and shake well. If you have time, let the bottles sit with the HCl solution for a while (or overnight if you so desire or if the bottles are new or had some nasty crud in them [like boat discharge getting into the samples]).
• Empty bottles and rinse bottles and lids 6 times with Q-water.
• Fill bottles to the top with Q-water for storage.
• Prior to sampling, bottles should be refrigerated at 4°C.

• When ready for sampling, dump Q-water out of bottle, rinse bottle 3 times with sample water, then fill the bottle with sample water.

• After the bottle is filled, record the bottle number, depth, station, etc. on the log sheet and refrigerate the sample at 4°C until ready to filter.

• Supplies:

• Samples in Qorpak bottles
• Vacuum pump and all glass (or glass with stainless steel support) filter rig for 47mm membrane filters with glass 1L filter flask
• 47mm Poretics membrane filters - 0.2 micron pore size
• Forceps
• Beaker or squeeze bottle (something to hold Q-water for rinsing down filter funnel)
• Q-water

• Before filtering samples:

• Rinse the filter rig well with Q-water before starting. Fill the filter cup with Q-water, filter it through as if it were a sample (only with no filter), swirl the water in the filter flask and discard the water. Repeat this twice more for a total of 3 Q-water rinses.

• Things to log in notes: Time you started and finished filtering, anything out of the norm that happens while filtering that might affect sample quality, bottle numbers filtered, cruise ID.

• For each sample:

• Place a filter on the filter support. Small wrinkles don’t matter, but make sure you cover the entire frit and make sure you have a good seal between the filter funnel and the filter support.
• Filter about 30-50ml of Q-water through the filter. Swirl in filter flask, and discard this water. This Q-water rinse and the sample rinses in the next step get rid of any leachate that might initially come from the filter.
• Turn sample bottle upside-down 3 times to make sure sample is well mixed (but don’t shake bottle – you may break cells if you shake too harshly). Pour about 10ml of sample into the filter funnel and filter this through. Swirl in filter flask and discard water. Repeat this twice more. The purpose here is to get rid of any leachate that might initially come from the filter and to make sure all Q-water droplets are out of the filter flask to avoid dilution of the filtered sample.
• Filter the remaining sample left in the sample bottle. If you know there is significant crud in the water (i.e. process cruise or any cruise where TSM samples take seemingly forever to filter), you may not want to pour the entire sample into the filter funnel immediately as the filter may clog half-way through. The ideal way to handle filter clogs is to prepare a filter on a second filter setup (Q-water rinse filter rig, then rinse down a filter with about 50ml Q-water and one rinse with 10ml of sample), replace the filter flask on this second setup with the one from the original setup (so all of the filtered sample is in the same filter flask), and continue filtering using this new filter. Make a note in the logbook anytime you need to use more than one filter for a sample bottle. Bottles generally take 5-15 minutes to filter.
• Rinse the Qorpak sample bottle for the sample you just filtered: fill partway with Q-water, cap, shake vigorously, and discard the water. Repeat this twice more. The objective here is to get rid of anything from the unfiltered sample that may have stuck to the sides of the bottle.
• After 3 Q-water rinses, rinse the Qorpak bottle 3 times with 10ml of filtered sample from the filter flask (pour 10ml in bottle, cap and shake, then discard water). The objective here is to remove any remaining Q-water droplets in the bottle to avoid diluting the sample.
• Fill the Qorpak bottle with the remaining filtered sample in the filter flask.
• If you are going to scan the samples immediately after filtering the batch, then set the bottle out on the counter to warm to room temperature. If running at a later time/date, put the bottle back in the refrigerator and store at 4°C until ready to scan.
• Discard the filter – Do NOT use the same filter for more than one sample bottle. They almost always clog partway through the second sample bottle.

• Supplies

• Filtered water samples warmed up to room temperature (warm-up time is usually 2-4 hours)
• Q-water
• 2 matched 10-cm quartz cuvettes (if more than 2 cuvettes exist, make sure you have a matched pair)
• Glass beaker or clean, empty glass Qorpak bottle for filling cuvettes with Q-water
• Squeeze bottle of ethanol
• Lots and lots of extra-low lint Kimwipes
• Latex lab gloves (if you so desire for a better grip on the cuvettes)
• Lambda 2 spectrophotometer
• Plate for Lambda 2 spectrophotometer with cuvette holders for the 10-cm quartz cuvettes – along with this you will need a long-handled hex wrench to fit the screws on this plate
• Computer with PECSS software, RS-232 cable and gender changer – computer should be hooked up to the port labeled "1^st RS-232" on the Lambda 2 spectrophotometer

NOTE ON CUVETTE HANDLING: Bare fingers should never touch the outside of the cuvette other than the stoppers. Fingerprints and oils in the skin have optical properties that will show up in the scans if you are not careful about keeping the cuvettes clean. The same goes for glove prints if you use gloves. Ideally, only kimwipes actually touch the cuvettes. The cuvette should be handled by the stoppers as much as possible with minimal contact with the rest of the cuvette. When filling the cuvettes, stoppers should be set down on their tops, not laid down on their side as they can roll around and pick up stuff off the counter (and who knows what’s been on those counters!). If a stopper does roll around or get dropped, rinse well with Q-water before placing back in the cuvette.

• Setup for Scanning

• Filtered samples need to be room temperature before scanning to avoid condensation on the cuvettes, so set samples out at least 2 hours before scanning. Additionally, you do not want samples to be sitting out for extended periods of time and samples can degrade with exposure to light, so do not set sample bottles out too far in advance. If running a large batch of samples, set out bottles in small groups, about 10 at a time. Avoid setting samples directly under a light. Almost all of the detectable CDOM absorption is in the ultraviolet part of the spectrum and UV radiation should be almost all attenuated by the Qorpak bottles, so light exposure in the lab shouldn’t be a big deal as long as you don’t have the bottles directly under a bright light.
• If the cuvette plate isn’t already installed in the sampling compartment of the spec, then install it. Screw in the screws until you just feel pressure, but do not tighten them. The screw heads are getting in bad shape and if you tighten them, you may not be able to get them back out later! If the integrating sphere is in the sampling compartment and you can’t find the cuvette plate, it is most likely in the box labeled "integrating sphere." The box labeled "integrating sphere" is used for storing either the integrating sphere or the cuvette plate, whichever is not currently in use in the spec. Both the cuvette sets and the integrating sphere are expensive to replace, so it is not a good idea to leave either one setting out on the counter unprotected.
• Turn on the spec (green switch on top of spec – back, right corner). The spec needs to warm-up for one hour before taking any data. Make sure the computer is attached to the 1^st RS-232 port on the spec before turning it on, but that the computer is turned OFF. The spec must be turned on and go through its little boot cycle before the computer is turned on. The LCD display on the spec will read "busy" and it will make lots of noises when it’s going through its initial boot cycle.
• Clean the sampling compartment of the spec with ethanol and kimwipes. Remove the cuvette holders from the plate and clean the plate. Make sure to clean all 4 windows of the sampling compartment well – no lint. Clean the cuvette holders with ethanol and reattach to the plate. The cuvette holders are marked on the bottom with either blue or red tape. The blue one is for the reference cuvette and goes in the back of the sampling compartment and the red one is for the sample cuvette and goes in the front of the sampling compartment (they should match the blue and red tape on the top of the spec by the sampling compartment door). The cuvette holders only attach to the plate in one orientation, so if it doesn’t seem to fit, turn it around. The arrows on the blue/red tape on the bottom of the cuvette holders should point to the right.
• The cuvettes should have been stored with Q-water in them. Empty them, rinse them with Q-water (6 rinses to make sure well-rinsed), fill them with Q-water, rinse the stoppers in Q-water, put stoppers in cuvettes, wipe off all water on outside of cuvettes with kimwipes and clean outside of cuvettes with ethanol and kimwipes. When filling cuvettes with Q-water, clean and fill a glass beaker or spare Qorpak bottle with Q-water from the carboy, then fill the cuvette from the beaker or Qorpak bottle. Do not fill the cuvette directly from the carboy. The spigot on the carboy creates a lot of turbulence and puts a lot of teeny tiny bubbles in the water in the cuvette. All these little bubbles can cause problems as bubbles aggregate and move during a scan. It’s difficult to avoid bubbles altogether. If you do end up with some little bubbles, after you have put the stoppers in the cuvette, turn the cuvette so one stopper is higher than the other and tap the end of the cuvette lightly (with a kimwipe covering the end of your finger as you tap – of course). You want to get any bubbles that move up under one of the stoppers. If bubbles are tiny enough that they don’t move when you tap the cuvette, they shouldn’t be a problem during a scan and you can let them be. When you are at the point of cleaning the outside of the cuvette with ethanol, you should not handle the cuvette by anything other than the stoppers before scanning. After cleaning with ethanol, check the outside of the cuvette to make sure it is truly clean (no lint! no fingerprints!) and place it in the cuvette holder. Make sure the blue squares and the lettering on the cuvettes face forward and the cuvettes are as far to the right of the sampling compartment as possible against the sampling compartment windows. One cuvette should have the letter R on the stoppers and used to have a label on it to identify it as the reference cuvette. This one goes in the cuvette holder in the back of the sampling compartment – nothing but Q-water should ever be put in this cuvette! The reference cuvette will keep this same Q-water in it through the entire run and should not be touched or moved during the run. The other one (used to have S’s on the stoppers, but the S’s and sample cuvette label keep washing off, so may be unlabelled), goes in the forward cuvette holder in the sampling compartment of the spec. Close the sampling compartment door on the spec after you’ve finished cleaning everything to keep dust, etc. out while you finish setting up.
• Turn on the computer. The PECSS software runs in DOS, so if the computer is running Windows ’95, you will need to press F8 before Windows ’95 starts loading and choose the option for "command prompt only" to get to the DOS prompt. After Windows ’95 loads, you can get to a DOS prompt either by opening a DOS window or choosing shutdown, restart computer in MS-DOS mode. Neither of these is recommended because they both start DOS without unloading the Windows drivers, caching, etc. and this can cause problems with some data collection communication software programs. So, if Windows ’95 loads, choose "shutdown" and "restart the computer," then press F8 before Windows ’95 loads again.
• Change directories to C:\PECSS\DATA\ (in other words, type cd \pecss\data). In this directory, make sure scanac.mth and scanac.lst exist. If scanac.mth is missing, we will make it later. We will want to edit scanac.lst if it exists and create it if it doesn’t. Type edit scanac.lst. This file is the sample list for the run. Each line should contain a unique filename of up to 8 characters followed by 2 commas followed by a description of the sample of up to 60 characters. The first line should be an autozero. No file is saved for an autozero, but you must input a filename anyway to conform to convention for the rest of the samples, so the first line is autozero,,autozero. The first 4 characters of each filename should be ac##, where ## is the 2-digit cruise number for regular Plumes and Blooms cruises (ma was used for the McArthur cruise). Characters 5-7 of the filename should be the 3-digit Qorpak sample bottle number and character 8 is a letter denoting replicate scans from each sample bottle starting with replicate a. For Q-water blanks, character 5 of the filename is q, characters 6-7 are 2 digits, starting with 01 and incrementing by one each time the sample cuvette is filled with new Q-water, and character 8 is usually a for the first replicate (if there are more than 99 Q-water blanks, like the McArthur cruise, characters 6-8 become 3 digits to identify new Q-water blanks and the replicate letter is dropped). All filenames need to have the same number of characters for the post-processing software to run properly. A typical run consists of an initial autozero, followed by 2 Q-water blanks, 3 replicates of a sample, a Q-water blank, 3 replicates of the next sample, a Q-water blank, ... (continue for remaining sample bottles) ..., 3 replicates of last sample, 2 Q-water blanks.

• After editing and saving scanac.lst, make a backup directory for this run in the \pecss\data\ directory (for this example for cruise PB34, in the \pecss\data\ directory, you would type mkdir pb34). Copy scanac.lst to this backup directory with a filename appropriate for the cruise (i.e. copy scanac.lst pb34\pb34ac.lst). If the spec freaks out during a run, you will have to edit scanac.lst so you restart the run where you left off. Part of the post-scan data processing relies on knowing the scan order of samples for an entire run. If you’ve had to stop a run and restart it in the middle, scanac.lst will only contain the last part of the run when you’re done. Making a backup of the lst file before starting a run will ensure you have a full run list for post-processing (assuming you don’t add any replicates).
• Type cd \ to get back to the C:\ directory and type pecss to start the PECSS software. The PECSS software will only load properly from the C:\ directory. If PECSS does not load properly (it gives you lots of errors), check to make sure you aren’t still in the C:\PECSS\DATA\ directory or some directory other than C:\.
• If the scanac.mth file existed in the C:\PECSS\DATA\ directory, then type restore scanac. This should bring up a parameter screen. Check to make sure the parameters are set as indicated below, make changes if necessary and hit <Enter> when satisfied that all parameters are correct. You are now ready to start the run if the spec has warmed up for an hour, water samples are warmed to room temperature, the cuvettes are filled with Q-water, cleaned and in their proper orientation in their respective holder, and the sampling compartment has been cleaned with ethanol. If the scanac.mth file was missing, then you will need to make it. From the PECSS main screen, type scan. This will bring up the parameter screen. Set the parameters as listed below and hit <Enter>. At the prompt on the next screen, enter n to indicate you are not ready to start a scan. At the following prompt, enter store scanac. This will create the scanac.mth file. Now you can type restore scanac, recheck the parameters on the parameter screen, and hit <Enter> when you are satisfied the parameters are correct. Anytime you change something on the parameter screen that you want to save from now on (usually ymin and ymax values as they change seasonally), you can use the store scanac command to overwrite the scanac.mth file. Scanac is just the PECSS scan command with the parameters pre-set for Plumes and Blooms a_cdom scans. When you restore scanac, PECSS will look for the scanac.lst file for filenames and comments for the run. You will know that it found this file if the filename on the parameter screen matches the first filename in the scanac.lst file that you made or edited earlier (this will be autozero at the beginning of a run). If the filename is user0001, then PECSS did not find scanac.lst in the C:\PECSS\DATA\ directory and will just increment the last 4 digits of the user0001 filename for each scan. This can turn into a mess quickly, so make sure you are running from the proper lst file.

• Things to log in notes:

• Log the time you set out the bottles to warm-up, the time you turned on the spec to warm up, the time you started scanning a run, the time you finished scanning a run and the time you turned off the spec. Also note anything that happens to the samples, Qorpak sample bottles, cuvettes or spec that may affect data quality (i.e. scratches on the cuvette, cleaning or moving the reference cuvette during a run, Q-water with a resistance other than 18.2 megohm-cm, "features" that appear in spectra that are suspected to originate from the spec and not the sample). Finally, make sure to note when the spec "freaks" (usually because the optical filter wheel gets out of sync) and what you do when the spec "freaks" (rescan until the spec fixes the problem or turn spec off for 10 minutes and turn back on for 10-20 minutes before continuing – note time you turned spec off and back on and time you resumed scanning).

• Here’s what the current status of everything should be:

• Qorpak sample bottles have been warmed to room temperature
• Cuvettes are filled with fresh Q-water, cleaned and placed in proper position in cleaned spec sampling compartment. The door to the sampling compartment is closed.
• The spec has been turned on and warmed up for at least one hour.
• The files scanac.mth and scanac.lst exist in C:\PECSS\DATA\ and scanac.lst has been updated and backed up. The PECSS software is running, the scanac method has been restored and parameters checked. Hit <Enter> from the parameter screen and you should be at the data collection screen which has the options of yes, no, autozero/background correction, and change parameters at the bottom of the screen.

• Press y or <Enter> to start a scan. The first scan of the list should be an autozero and the spectrum will not be displayed on the screen. When the autozero is complete, the computer will beep (if the sound is turned on) and the word "Ready" will return at the bottom of the screen. Without opening the sampling compartment, press y or <Enter> to rescan the same Q-water in the cuvettes to make sure the absorption values are zero. If some part of the spectrum is outside ±0.002, restart the run as follows: When the scan is finished and "Ready" reappears at the bottom of the screen, press n, then type restore scanac, and hit <Enter> from the parameters screen after checking to make sure all parameters are set properly. Now you are back to the point at which you started for this step.
• When the previous scan is finished (you need only wait until the wavelength on the spec LCD display reads 249.8, not until "Ready" reappears at the bottom of the computer screen), remove the sample cuvette from its holder, empty it, rinse it 6 times with Q-water, refill it with Q-water, clean the outside of the cuvette with ethanol and kimwipes and replace it in the holder. Close the sampling compartment and press y or <Enter> to scan.
• The next scan is the first sample. When the previous scan is finished, remove the sample cuvette from its holder, empty it, tilt the Qorpak sample bottle upside-down 3 times to make sure it’s well mixed (mainly for uniform temperature at this point), rinse the cuvette 3 times with about 5-10ml sample, fill the cuvette with sample, clean the outside of the cuvette with ethanol and kimwipes and replace it in the holder. Close the sampling compartment and press y or <Enter> to scan.
• Repeat step (4) twice more for three replicate scans, rinsing the cuvette 3 times with sample and refilling it each time.
• Repeat step (3), rinsing the cuvette 6 times with Q-water and refilling it, making sure to rinse the stoppers in Q-water as well.
• Continue in the same manner for the remainder of the run list. If you forget where you are in the list, when the previous screen is finished and the word "Ready" reappears at the bottom of the screen, the name of the next file will appear at the bottom of the screen as well. The filename and description at the top of the screen remains the sample just scanned until you press y or <Enter> to start the next scan.
• There are two Q-water blanks at the end of the scan. Rinse and refill the cuvette with additional Q-water for the second Q-water blank scan.
• When the last scan is finished, press n, then type stop to exit the PECSS software and turn off the spec. Leave the cuvettes filled with Q-water in the sampling compartment of the spec for storage.
• At the C:\ prompt, type cd \pecss\data. In the C:\PECSS\DATA\ directory, backup all spectra to the backup directory by typing copy .sp budir\*.* where budir is the name of the backup directory. Backup the .lst file and all spectra (.sp files) to floppy disk and upload them to the network to /home/data65/pb/IOP/acdom/cruise/binary/ (where cruise is the cruise ID) as soon as possible.
• Acid rinse the Qorpak sample bottles and prepare them for the next cruise (see Pre-cruise preparation of bottles). Do not let the bottles sit with sample in them for extended periods of time. Crud may stick to the sides of the bottles and accumulate over time, which will make cleaning more difficult later. If they do happen to sit for more than a week with sample in them, give them a more vigorous detergent rinse with Liqui-Nox and let the bottles sit at least overnight with HCl solution in them.

• There isn’t enough water in the sample bottle to do 5-10ml rinses in triplicate for each scan. The cuvette needs to be rinsed at least once before filling it for the first replicate to remove any remaining Q-water from the cuvette; 2-3 rinses is better. Rinses can be eliminated if absolutely necessary before the second and third replicate. Rinses before the second and third replicate are done to loosen and remove anything that might be sticky and accumulate on the inside of the cuvette when refilling with additional sample.
• There is oil (or something else extremely sticky) in the sample. Rinse the inside of the cuvette with ethanol until it runs clear (the ethanol will be cloudy if there is a lot of oil in the cuvette). Rinse the cuvette 3 times with Q-water to make sure the ethanol is removed from the cuvette, then continue rinsing and filling the cuvette with sample (3 rinses and fill) or Q-water (6 rinses and fill) as normal. Do the ethanol rinse between each scan/replicate. For most samples, one or two ethanol rinses are all that is needed.
• The baseline (Q-water blanks) become non-zero as the run progresses. This is normal. Generally, the baseline drifts more at the shorter wavelengths than the longer wavelengths. There may also be drift at wavelengths greater than 700nm that are temperature dependent. These are normal as well. Generally, wavelengths greater than 700nm are eliminated in post-processing.
• A dip appears in the spectrum around 715nm and a peak around 740-750nm. These are temperature/salinity dependent and cannot be avoided. Wavelengths greater than 700nm are eliminated in post-processing due to this problem. Since you can’t do anything to remove this feature from the spectrum, just ignore it.
• The spectrum is highly erratic or has unexpected "features." Smooth bumps covering a range greater than 10nm can be real features of sample absorption, but jagged or highly variable spectra are usually a "feature" originating from the spec or a dirty cuvette. The spec adjusts itself every now and then (usually about every 5-6 scans). It makes a kind of grinding sound when it does this adjustment. Occasionally, the filter wheel will get out of sync and there will be a jump in the spectrum around 380nm or 420nm. When this happens, you can usually just rescan the sample until the spec does its next adjustment and gets back to normal (see below for instructions on rescanning). Whenever you have doubt as to whether a spectrum is correct, first check the cuvettes to make sure they are clean. If a piece of lint/dust/dirt gets on the reference cuvette, absorption values will go erratically negative. Lint/dust/dirt on the sample cuvette will cause absorption values to increase. The middle of the ends of the cuvettes are the most critical areas that must remain free of all lint, dust, dirt, fingerprints, gloveprints, scratches, condensation, and residues of any sorts. Rescan the sample (see below). If rescanning does not resolve the problem and the spectrum is still jagged and erratic (smooth spectra are probably real features if they remain after rescanning), and you’ve rescanned through the next spec adjustment, then turn off the spec. Whenever you turn off the spec, the spec must remain off for at least 10 minutes to keep from damaging the lamps. After the spec has been off for at least 10 minutes, turn the spec back on and let it warm-up for 10-20 minutes before resuming rescanning. Also remember that the spec must be turned on before the computer, so you will have to shutdown and restart the computer after you turn the spec back on and restart PECSS.

• When the current scan is finished and "Ready" reappears at the bottom of the data collection screen, press n, then type stop at the "Ready for next command" prompt. This will exit PECSS.
• At the C:\ prompt, type cd \pecss\data. At the C:\PECSS\DATA\ prompt, type edit scanac.lst. Delete all the lines in this file before the sample you wish to rescan. An easy way to do this is to hold down the <Shift> key while pressing the down arrow key to highlight all the rows you wish to delete, then press the <Delete> key. Save this file and exit back to the DOS prompt.
• Delete the .sp file for the sample you wish to rescan (double and triple check to make sure you have the correct filename before you delete the file because once you delete this file, the scan is gone!) by typing del filename where filename is the name of the .sp file. Backup all remaining .sp files to the backup directory by typing copy .sp budir\*.* where budir is the name of the backup directory. This will keep these spectra from being overwritten in case you edited scanac.lst incorrectly. PECSS does not alert you when overwriting a file, it just overwrites it.
• Type cd \ to get back to the C:\ directory, then type pecss to restart the PECSS software.
• When the PECSS software has reloaded, type restore scanac. Check the parameters on the parameter screen and make sure the filename and comment are the filename and comment for the sample you wish to rescan. When satisfied that the parameters are correct, press <Enter> and you are back to the data collection screen and you can continue scanning like before.

NOTE: all directories names are subdirectories of /home/data65/pb/IOP/ unless

otherwise noted

• Make directories for the new cruise. There is an executable file named setup in /home/data65/pb/IOP/. Type "setup cruiseID" while in the /home/data65/pb/IOP/ directory, where cruiseID is the directory name you want for the current cruise (i.e. pb20). NOTE: from here on, cruiseID will be used to inidcate the directory name for the current cruise. setup will create all the necessary directories and set permissions so other people can access them.

• Upload data from PC and make text files from binary data files. Which order you do depends on how the PC accesses the network and personal preference. Conversion from binary *.sp files to ascii data files, you need to use a program Norm Nelson wrote, called pconvert, in DOS on the PC. A copy of pconvert is in /home/data65/pb/IOP/pconvert/. Copy pconvert.exe over to the PC you are working on. To convert the binary files, at the DOS prompt, type "pconvert *.sp" and pconvert will create *.txt files. A few words of caution for pconvert:

• After 10-15 files, pconvert crashes, so you will probably need to run it several times to convert all of the files. You can put characters before the * in *.sp to limit the number of files pconvert looks. Since the last character of the filename before the .sp extension is the replicate letter, you can usually at least convert all replicates of one sample at a time.
• pconvert uses the header information in the binary *.sp file to create the output filename. Normally, the filename without the extension is the same; however, if you have renamed files for some reason, the output filename will not be the same as the input filename (excluding extension).

• The list file (*.lst file for the run(s)), *.sp files and *.txt files should be uploaded to the following directories: acdom's should be uploaded to cruiseID/acdom/raw/ ap's (first run) should be uploaded to cruiseID/ap/rawap/ ap's (extracted) should be uploaded to cruiseID/ap/rawad/

• Get rid of all the ^M's from the *.txt and *.lst files. The ^M's are there because PC's use 2 characters to indicate the end of a line and Unix only uses one. In /home/data65/pb/IOP/, type "dem_all cruiseID" and this little script will use the script deM written by Kirk Waters to strip off all the ^M's from the *.txt and *.lst files in the cruiseID/acdom/raw/, cruiseID/ap/rawap/, and cruiseID/ap/rawad/ directories. DON'T EVER DE-M BINARY FILES! This is mainly a cleaning step, but some Unix applications have problems with the ^M's too, so it's not just for neatness. The unix2dos command can put ^M's back in if for some reason you need to port stuff back to the PC at a later date.

• Process acdom's.

a) Make an info file with the following format in cruiseID/acdom/raw/:

• no header information

• 2 columns separated by a comma

• first column is a list of *.txt files in the order in which they were scanned (make sure to include the .txt extension and remember that in Unix, case matters, so if the filenames are all uppercase letters, make sure the filenames are all uppercase in this file)

• second column is the bottle number (use -999 for Q water blanks). See /home/data65/pb/IOP/pb41/acdom/raw/pb41_od.csv for an example. I have been calling the file cruiseID_od.csv for all cruises.

b) Change to the /home/data65/pb/IOP/idlprogs/ directory.

• first column is the name of the *.od files in this directory

• second column is the name of the output files for each input file. Filenames should be cruiseID_ac#.Z where: cruiseID is the same as the cruiseID from step (1), _ac denotes an acdom file, # is the station number (one digit for core cruises, but may be some other character and/or number code for process cruises), . is just a separator, Z is the depth (for core cruises, this is 0 for all stations, but station 4 also has depths of 75, 50, 30, 20, 10 and 5 meters)

• third column is the cruise ID

• fourth column is the station ID (for Plumes and Blooms core cruise stations 1-7, use the syntax PB-# where # is the station number)

• fifth column is date the samples were collected in the format DD-MMM-YY where DD is the day of the month, MMM is the first 3 letters of the month and YY is the last 2 digits of the year.

• sixth column is the time the niskin bottle was closed on the CTD (after the CTD data are processed, these times generally are spit out into a .btl file for each cast)

• seventh and eighth columns are latitude and longitude in degrees and decimal minutes with positive values being North and East and negative values being South and West (i.e. 34 9.50,-119 57.21 is 34 degrees 9.50 minutes North and 119 degrees 57.21 minutes West).

• ninth column is depth with an m after the depth to indicate meters (i.e. 0m)

• tenth column is bottle number (just for keeping track of things)

• See /home/data65/pb/IOP/pb41/acdom/od/list.od for an example.

g) Start IDL.

j) Change directories back to /home/data65/pb/IOP/idlprogs/.