Spring 2011

Our intern, Ali - an undergraduate student from Middlebury College, details her experiences from her summer with the HOT program.

Monday, July 25, 2011

Out of the Bean Bag, Into the Hard Hat

Walking down the halls of the KM on Day 1 of the cruise felt familiar for the first time. Now I walk with confidence around corners at which I used to stop and ponder before. I know the doors that are sticky and expect the sweeping rolls of the double hull chucking me from starboard to port.  My memory of the watch routine – taking samples, labeling bottles, observing the meteorology – was a little rustier than my memory of the ship’s halls. I followed along behind Reagan, the volunteer, as Cammy oriented her to these tasks and paid more attention to her instruction than a veteran HOT cruiser should.  

I became acquainted with a new part of the routine this cruise, which got me out of my bean bag chair and into my hard hat: tagging. It’s a bit like it sounds. The CTD and I play tag, except I am always it and he is always swaying back and forth trying to wiggle from my grip. Brett standing on one side and I on the other, we tame the swings of the CTD until we’re told to slip our lines and let the CTD take the plunge.  After an intermission of bottle labeling or meteorological observations, Tagging, Act II, begins. In Act II the plot thickens with the introduction of a new character: the claw extension. Known more generically as a hook on the end of a pole, in my hands it feels like an extension of my arm in claw-form. Brett and I reach over the railing to hook our long claw arms claw around the frame of the CTD and guide the CTD back on deck.

Thursday, July 21, 2011

A Lazy Sunday Morning of Lifting

The adventures of my last HOT cruise started on Sunday morning ferrying the much needed but heavily begrudged boxes of salinity samples from the storage room to the truck. Filled with the remaining water from last cruise’s CTD casts, the glass bottles were heavier than I remember. Other oddly shaped or overweight boxes followed into the back of the truck and we headed to Snug Harbor to load them from truck to ship. The most oddly shaped and overweight object of all awaited us there: the CTD. It’s taller than I am and big enough to have a party of three take tea in its round center.  While waiting between cruises, the springs that close the Niskin bottles, in which the water samples are captured, are unstrung. Before loading the CTD on the ship, we had to reattach these springs so that the bottles are ready to capture water. Craig yanked on the spring while I attempted to attach each end of the spring to the bottle caps, 48 caps in all. This involved 50 “Got it”s plus two “Don’t got it”s accounting for my two failed attempts. We carried our boxes over the gangway to the back deck for the rest of the morning. Though lifting heavy objects is not my activity of choice on Sunday mornings, any opportunity to wear my hard hat outweighs the unhappy arms.

Everything was loaded on the ship by noon. Unfortunately this meant I had to take off my hard hat. Quickly, though, my spirits were brightened when Cammy handed me the Walkie-Talkie.  It was time to test the CTD’s bottle firing, Fluorometer, and other instruments.  The CTD closes bottles on command by releasing a hook, which had been holding the top and bottom bottle caps open. Reagan and I climbed onto the CTD in the wet lab to pull on each hook until Cammy fired the bottle from the computer.  By Walkie-Talkie I told Cammy that the “Bottle fired, next.”  We tested the Fluorometer, which measures chlorophyll by light emission and absorption, by sticking our finger in front of the sensor and tested the temperature, conductivity and oxygen sensors by pouring water through. By 1 pm, all the laptops were tied down to the counters and the instruments ready for deployment, so a lazy Sunday could begin. 

Wednesday, June 15, 2011

Three Colors, Two Axes, One Timescale

Now that I am back from the ACO cruise, I am back to the office and back to my neglected friend, Matlab. I am making my brain and fingers work in different ways. There will be less pondering on the hydrodynamics of ADCP hard hats and visualization of physical things and more pondering on the algebra of matrices and visualization of columns of numbers.   I will coax my fingers out of trying to lash computers to desks and books to bookshelves in favor of tapping away Matlab commands until the error responses disappear.  The adjustment has already begun and successes in creating multicolored graphs have given me energy to pick up where I left off – that is, if I can find where I left off.

Looking at my notes from a month earlier, Matlab is again a language foreign to me. It took me the better part of an hour to even decipher what my task had been: plot depth data from the CTD against wire out data from the Caley crane to determine their synchrony.  The CTD will give the more accurate data set, so this is mainly to test the accuracy of the Caley.  Once I determined my task, it seemed simple. Almost immediately it proved much harder when the two data sets had different frequencies – one at 2 Hz, one at 1 Hz.  I needed to assign time to the CTD data set to match that of the Caley crane. Last month, I tried to stuff them into the same graph on different axes and approximately line them up. Lining them up properly proved futile to so I moved on to assigning each CTD data point a year, month, day, hour, minute and second. Year, month and day were easy – it all happened on April 12, 2011. Seconds were less cooperative because the data frequency was 2 Hz. Joseph helped me ask Matlab to take each row and assign it a seconds value equal to the row number multiplied by ½ – since each row is a step of half a second.  With a long wait – Matlab had to calculate this for over 13000 rows – I had a column of cumulative seconds. 

Just when I was about to bang my head against my computer to figure out how to assign hours and minutes to the CTD data, Craig and his magic fingers arrived. He informed me of a clever Matlab function called “datenum” that assigns a serial number to a date in decimals of a day.  Given the datenum of the start of the cast, in this case 01:16:29 April 12, 2011 is 734,605.05, I could add the seconds to it as a fraction of a day – 1 second equals 1/86400 of a day. Matlab made converting the Caley data to this form easy as well, so shortly I had two synchronized data sets. Plotting this showed an expected and somewhat boring result: the depth profile lines matched up.

Plotting wire speed – the variable that is most concerning for the safety of the equipment during a cast – would be more exciting.  The Caley crane supplies a column of wire speed pre-calculated so only the CTD data needed attention.  With a simple rate = distance/time calculation, the two data sets were ready to be plotted. To be able to reference at what depth the wire speeds occurred, I added a depth profile to the chart in the same timescale. Though this meant battling with the double axes that had been so troublesome a month before, I ended triumphantly with a graph in three colors, two axes, and one timescale.  The battles ahead will be the fancy stuff: labeling axes and giving titles.

Thursday, May 19, 2011

A Change of Plans, and of Link

As I found out on Monday, I somehow wiggled my way into a berth the ACO cruise to depart this friday about which I couldn't be more excited.  The length of time floating on the big blue, the hands on nature of much of the work to be done for the observatory, the sheer quantity of new instruments and equipment to be deployed all have me antsy to haul away the anchor and head for Station Aloha. For the next 18 days I will be channeling my enthusiasm and my blogging to that project so you can find details of the cables I get tangled in and quantities of M&M's I consume at the link below:


Wednesday, May 18, 2011

Donning a Hard Hat Always Means Good Things

A flurry is how the office felt upon returning to it after two weeks away.  I received a message from Craig a few days before saying “things have changed” and that I should plan to work outside on Monday.  This easily could have meant that the Marine Sciences Building had come crashing down and now my desk was located under a tree in the courtyard. In reality, the only thing that came crashing down was the A/C, causing problems accessing overheated and grumpy computers. What most significantly had changed was the schedule and personnel for the HOT and Aloha Cabled Observatory (ACO) cruises. The HOT cruise that had been originally scheduled to embark on Monday had already happened while I was away.  Though I missed that cruise, a vacancy had appeared on the ACO cruise for which I was trying to contain my excitement at filling.  Nothing was certain at 0900 so they told me not to get my hopes up. Trying to reel in my helium balloon of hopes was my challenge for the day.

As my desk was still located in it’s normal corner, working outside meant going to Snug Harbor with Jeffrey to help prepare equipment for the upcoming cruise.  Everyone chuckled a bit when I said that I was excited to go down to the harbor because the glass balls are very heavy, as I soon found out, and things are much dirtier than when tapping away at my computer.  New things are always exciting, however, and no one could convince me otherwise.

I started by wheeling around bicycles with flat tires trying to find a way to inflate them. Then I graduated to helping move around glass balls contained in two firm yellow plastic bowls that strikingly resemble yellow hard hats. With moving these you must be as careful as if decorating the Christmas tree with glass ornaments because no one wants chards of glass everywhere but as firm as if hoisting the weight of the whole tree onto the top of the car.

In the afternoon the spool of 200 m of cable, which will be lower to the bottom of the ocean with eleven temperature sensors attached to it, and I had a fine time rolling around the pier. In order to measure out the positions at which the instruments will be attached to the cable, I was supposed to get the cable as straight as possible. A bit like herding an oversized, uncooperative farm animal back to the barn, the spool needs constant nudging and alteration of course in order to unravel in a straight line. As dirty as a farm animal too, the spool somehow covered my legs in black and brown smudges. Had I only perfected my log rolling skills, this process would have been much easier.

The next day I got to participate in the dirty work again, starting with loading the flatbed truck with several instruments and boxes of supplies.  A forklift loaded the heavier items such as the ‘parking station,’ which is used for ‘parking’ wires as they are waiting to be connected to the observatory but which looks more like Snoopy’s doghouse. The forklift also swung the node, a large orange cylinder that Jeffrey described as a bird perch, Woodstock’s perhaps, onto the flatbed. This seems like a perfectly acceptable answer and the only thing that makes me skeptical is the logo stamped on the side of it is that of the Applied Physics Laboratory, not Petsmart. 

When we arrived in the flatbed at the harbor, I was handed a hard hat, which always means good things. It means I get to load with the rest of them and watch the happenings on the quarterdeck, which is hosting a flurry of activity currently.  Jason, the remotely operated vehicle (ROV), who will descend with the cable to install the instruments, has his innards exposed to have his wires tickled by engineers.  Swinging overhead at the end of the crane are platforms, weights, and other equipment being loaded.  I am slowly meeting all the scientists, engineers and crew involved in this project by bumping into them with boxes I’m carrying or asking them to hold the door for me.

When not loading boxes, I spent a lot of time with Nicholas in the stuffy beige tent trying to figure out how to attach two glass balls together and string a chain across them. After an hour of wrestling the hard hats together with no success, Jeffrey arrived to tell us that we needed to use the retrofitted hard hat covers shaped to fit together. Easy as pie from there. At least we got plenty of exercise lifting various glass balls.

To make this day even better, we filled the flat tires on the bicycles we were wheeling around yesterday with air enabling us to zoom around the parking lot in with alacrity and style.  Need me to grab something from the warehouse, bring it to the tent, skip over from the tent to the blue van, wait no, the PO van, then meet you over to the KM and head back to the tent? No problem.

At the end of the day, I was handed my second power tool for the day to unscrew the boxes in which some of the instruments are stored.  I helped Jeffrey set up these instruments on the observatory and in a tub of water in order to test them tomorrow.  

Thursday, May 5, 2011

A Brief, Codeless Intermission

After a busy day on Friday of scampering back and forth between Branden's room and my own trying to find the links that hadn't been updated to the new ADCP plots website and pouring over Matlab Help in an attempt to understand time conversions it feels odd now to be computer codeless. I am on vacation in Kauai this week and next with minimal electronic contact. Perhaps a detox treatment away from typing will bring me back to Matlab with a sudden comprehension of the construction of double axes -- or at least a newfound enthusiasm with which to greet my old friend. In either case, the accounts of my adventures in code will recommence on Monday May 16th, so check back then to learn more Matlab vocab.

Friday, April 29, 2011

World Wide Weblearner

I am an official weblearner. I don’t want to risk calling myself webmaster again for fear that it may induce some sort of error in the html sending me back to the drawing board. For now, I am a weblearner – but I am official. The Shipboard ADCP Plots website is linked to the HOT website now and out for the world to explore.  Please enjoy the Bulging Spry Menu Bar and engaging color scheme for yourself at:

Of course, two days ago when I claimed that the html was complete, it was not.  Many vector fields appeared, which wanted entry into the Spry Menu Bar. There were margins to adjust. There was text to be edited. Then there were margins to readjust.  All small things are worth it, though, for the satisfaction of having that html pop up on the World Wide Web in more or less the same format in which I designed it. Naturally, it does not end here. I am sure I will have the opportunity to readjust the margins at some point in the future. For now, I will focus on artistically rendering plots of wire out versus time, and crafting haikus into m-files.

The more I calculate, the more I must recalculate. I spent yesterday and today averaging and re-averaging the wire speed from the Caley crane because each time I made a new calculation, I found a problem with the last calculation.  To start, I calculated the wire speed from the total depth of the cast over the time from start to finish. However, I had neglected to take into account the starting and ending wire out values, which were invariably non-zero. After I recomputed these averages, I realized that the boundaries I set for each cast were inconsistent. All the better though, because each set of equations I concoct make me think more closely about the 68947 rows of numbers.  I have also become increasingly crafty with my use of Matlab, making up functions until one works. Craig ‘Magic Fingers’ came by and remarked at how slow calculations by hand are, which spurred me to ask Matlab to do these calculations for me. Matlab, charmingly, obliged – however, only one column at a time.  For tomorrow, the goal will be to plot CTD data and Caley data in the same figure with dueling scales on the x-axis.

Unix language lesson for today:

‘!!’                   means ‘do what I just asked you to do again, this time with enthusiasm’

Matlab language lesson for today:

‘hold on’          contrary to intuition, does not mean ‘be patient with me, I’m learning,’ rather it means ‘keep this line on the plot while I add another’

‘r’                    means ‘make this line a vibrant color red’