This is my last week in Aubert, so this week I tried to get everything in order before I move out of my office. The start of this week I finished up work on the spectral index site, which came out pretty well. There is also room to add data if need be. Earlier this week I also took a look at the MVCO stress data that was sent to me. I matched it up with dive data and plotted it against time,

The results are similar to what I saw before, unfortunately. I haven’t had a chance to add this into the paper yet, because I will need to learn a little more about the topic before I can explain it in the paper. How was it calculated? Is it stress from waves or currents? Anyway, I can always add that at a later date. I took your offer up on borrowing the computer since I was not able to get matlab onto my computer. Student employees cannot download matlab from the IT site. Also I can now access the server with this computer so I will need it in order to run my website program.

I met with Lisa Taylor on Wednesday and discussed the websites I wanted add. It went well and she gave me the templates for the MISC lab websites. I had to do a bit of work to fit things into the template nicely. However, I was only able to get the HTML template to work. Lisa also sent me a .php template, but I cannot get it to work. I assuming she would rather have me use the .php template so we are currently working on getting that up and running. The link to the spectral index site is,

http://misclab.umeoce.maine.edu/SpecIndex/SpecIndexPage2.htm


On Thursday I met with Steve and he set me up with access to the server where I have uploaded my websites. Once I had access to the server I got working on updating my float program. The directories had to be changed to the location of the folders on the server. I worked hard today and yesterday on making the directories as variables in the script. This will give Lisa a bit more freedom in moving and renaming files. It should be rather simple to update the script if the files are renamed or moved. I realize this program may be a bit hard to work with so I have made every effort to make it as user friendly as possible. I do still need to change it to the .php template when I figure out why that template is not working. It is done for the most part, just a couple tweaks here and there and updating the site will take only a couple key strokes!

Today I uploaded all the folders, files, and m files to the server and ran the program a couple times. I believe I have most of the bugs out. I will run myself for the next week or so, to make sure it functioning right. I reorganized the images to fit into the template, thumbnails I figured were the easiest way, but it doesn’t necessarily have to be thumbnails. I am open to suggestions if anyone has a better idea. I threw together I quick float homepage which I will improve if Lisa decides to keep it. The link to the homepage and my other pages can be found here,


http://misclab.umeoce.maine.edu/FloatUpdates/FloatHome.htm


A finer detail about the program is that in order to run the program, you must network with the server. The server must be mounted and be under a directory on the computer you are running the program from. The default directory is ‘Z’, but just to be safe the script prompts you to enter the directory. This is in case for some reason you cannot mount the server under ‘Z’. The program takes a couple minutes, but it will do everything I’ve promised.

Well, it’s been a good summer. I am interested in working with both of you again in the spring or next summer. I am glad I was able to be a part of the MISC lab, even for such a brief period. I will certainly be in touch. I am going to need help getting my presentation ready in the next couple weeks, so I’m sure we will be seeing each other again soon. I will return the computer as soon as I get the websites squared away.

Adiós

On Monday of this week, I got equipment for the DMC trip ready and packed. I also started to set up the website that will contain all the spectral data we have collected. I have already added most of the new data we collected on Tuesday to the site. I have pictures and names corresponding to the each spectrum. The names are specific as possible, some organisms I have tagged with genus and species, others just genus. Then I have just substrates (e.g. sand, shell, mud). All data on the site is referenced to the 99% reflectance standard. I applied the equitation I derived last week to all the Satalantic radiometer data. It’s looking pretty good so far, come check it out next week sometime. Hopefully next week I can work with Lisa Taylor to get both the float site and the reflectance data site up and running.


Ok, now to the data we collected on Tuesday. The Satalantic data matched up excellent with Mike’s notes! No trouble there. The DiveSpec data does not match up quite as well, the headings and Mike’s notes differ a couple times, but I have being using the headings entered by Emmanuel as the final decider in these situations. With the DiveSpec, six Didemnum spectra were taken,

I Hope these look familiar to you by now, it’s quite obvious when you are looking at Didemnum. Only one seems slightly different than the rest. Emmanuel told me that “D2” was not a prime specimen of Didemnum, however the outlier we see here is not “D2”, just so you know. Wayne and I also did some work in the touch tank with the DiveSpec, these were our results.

The “unknown tunicate” was just that. We took two pictures of it, but they came out blurry. Besides the unknown tunicate everything is significantly different from Didemnum. There is a lot of DiveSpec data, so I am not going to put all the graphs up. I will work on condensing and adding it all to the website next week. With the Satlantic radiometer we collected two Didemnum spectra.

The dashed lines are the original spectra; the solid line is after it had been referenced to the 99% reflectance standard. These look similar to our light data we collected last time we were at DMC. Here is another comparative plot but using the some of the Satlantic data. The numbers next to the name in legend are the 550/500 ratio.

 After I organized all the Didemnum spectra I calculated the 550/500 ratio again.


Dive                       Mean               Stand Dev.

1(DiveSpec)          2.5822              0.6986

2(HyperOCR)       2.2518              0.2441

3(DiveSpec)         1.7056               0.1788

4(HyperOCR)      1.5939               0.1774

Total                     2.1514              0.5034



Dive 1 also includes the Didemnum spectra Wayne and I took in the lab. The first time we went, both the means are above two and the second time we went, both are below two. It is possible that we see a difference between the two trips to DMC because conditions were different. Also perhaps we sampled old growth the first time and new growth on the second trip. Regardless, dive 1 is definitely an outlier. The mean is very high and so is the standard deviation. We may have to reevaluate that data, because some spectra have very low reflectance, perhaps the DiveSpec was not functioning correctly.

We also have a significant amount of fluorescence data. Emmanuel took four fluorescence readings of Didemnum.

There all seem to have a small bump around 550, it is rather small however. I suppose this is good news. Wayne and I also collected fluorescence data in the touch tanks. Here are four the six fluorescence readings we took.

Note that the scale is different for each plot. Just like Didemnum, the sea star shows a similar rise at 550, which is unfortunate. As you can see both macroalgae show a large spike around 680.

I have most of the data we collected organized and named. As you know, next week is my last week of work. I will compile all the data and some of the m files I wrote and pass them on to Wayne. I will try to organize everything so he will know what is what. Hopefully i can wrap everything up next week, I will try my best to get everything done, websites finished and launch, stress data added to my current MVCO data, and all spec data organized and in Wayne's hands. See you next week.

Ok, quite a bit of stuff to share with you this week. Most if it is the data I collected in the lab this week. First off, the paper on the data we collected at DMC is done, but you already knew that. It is going to be exciting after we collect data next week to see if the new data reinforces our 550/500 ratio. So, that brings me to my first topic which is our new light source.


In the lab this week I measured the output of our new light with the radiometer. I placed both the radiometer and the light source in the sink and filled it with water. I propped the spectralon plate up against the far side of the sink. The setup was similar to when Wayne and I and looked at LED lights in the lab, except this time the light and radiometer were submerged. First I logged data for only a minute or so to see what the spectra looked like. I also pointed the LEDs of the DiveSpec and the radiometer at the spectralon plate. However this was not done underwater. The graph below displays spectra from the AquaSun, the DiveSpec, and from Wayne’s LED flashlight.

Interestingly enough, they all appear to be quite different. Next I let the light run for ten minutes in the sink while logging data. This is what the spectra looked like. The numbers on the color bar are in seconds.

Over the ten minute period the brightness of the light had dropped! I assume the brightness of the light will drop to a certain level then remain constant. I looked over the box after I was done and discovered that this is mentioned on the back of the box. On the back of the box there is a small graph of lumens vs. time. It shows that it starts high and drops slightly for the first 10-15 minutes, then levels out. Hopefully this won’t be too big an issue. I figure as long as the shape of the spectra remains relatively constant, we are going to be OK.
In the lab I also measured the blue LEDs of the DiveSpec used during the fluorescence function with the radiometer. I measured them the same way i measured the white LED lights. Just like with the white LED lights this measurement was not done underwater. Below is the spectrum of the blue LEDs.

It appears that Didemnum may fluoresce! The spike at 550 was not produced by the DiveSpec LEDs. This is what I expected, but I wanted to double check.

Last but not least, I measured our spectralon plate with the DiveSpec. After calibrating the DiveSpec with the 99% reflectance standard, I measured each corner and the center of the plate on each side. Using this data I was able to reshape the radiometer data to how it would look, had it been referenced with the 99% standard. I did this by taking the median of the 10 DiveSpec measurements I took and fitting a linear equation to that measurement.

After that I took the existing data and put it into the equation Reflectance = Lw(sample)*(1.07 – 0.00022713*lambda). This shifted the spectra to what they would have looked like had they been referenced to the 99% reflectance standard. The two graphs show how the spectra changed after applying the above equation. The dashed lines are the original spectra.

These new spectra brought the total standard deviation of our 550/500 ratio down by small amount.

Also this week, I added information on float 6810 to my website. Unfortunately the files sent by 6810 contain more NaNs than actual data, but it did report its location. So I added a map to show its trajectory while it was deployed. The website should be up soon. I will need help from Lisa to add the umaine header and navigation bars, but once that’s done it should be good to go.

Anyway, there is game of disc with my name on it, see you next week!

This week I finished the report on the radiometer data we collected. However I will be revising it with some new calculations soon. I have done a couple wavelength comparisons to look at patterns in the reflected spectra. The following table shows the calculation I have done.




Calculation               Mean         Standard Deviation

(550/500)                2.2789       0.2471

(550-500)               0.0619       0.0172

((550-500)/50)        1.2e-3       3.4e-4



The calculations in the above table only include the 12 light and dark radiometer readings and no data from the DiveSpec. DiveSpec data will be included after I add a couple lines to the script that performs these calculations. I will add all of this data to the paper next week. I was also considering fitting a parabola through some of reflectance spectra. In the DiveSpec data, and to a lesser extent in the dive light illuminated radiometer spectra, there is a nice curve that looks like the top of a parabola. I don’t know if this is common practice but a quadratic equation could be calculated between 500-675 based on the average of all the spectra. Then when looking at spectra of an unknown object, a quadratic best fit line could be run through 500-675. Then it can be identified as Didemnum or not, depending on how far this line deviates from the previous parabola we have calculated based on our field work. Just for reference look at the following graph.

From wavelengths 500 to 675 the spectra looks like a nice parabola. This curve isn’t so obvious in the Satlantic radiometer data, but it may be worth a shot…

I have been putting the finishing touches on my website/program this week. I say ‘website/program’ because what I am really doing is writing a program that produces a website. I am doing all the work in matlab and hardly writing any html. It would be best to have the program run automatically every day or two, but I’m not sure how to do this. I found out how to use colored scatter plots to give a big picture view of the float profiles. I was able to plot all profiles done by float 4738 using a colored scatter plot method. Here is an example of two of the graphs that will be on the site.

I will fix the dates and the positions of the color bar label next week. I like these graphs because they are very visual, these are an alternative to the three dimensional graphs I wanted to add last week. These graph plot three variable, just like the three dimensional graphs I wanted. I have also added links at the bottom of the page that allow visitors to look at plots of individual profiles. I have incorporated this all into my website program. Float 4738 is the only float that requires updating. However, I was initially building a program to update information on three floats. I spent a good amount of time revamping the program to run more efficiently. Originally every time the program updated the website, it started from scratch. It would process information from the first profile to the most recent. I have modified it so it saves past data in .mat an .fig files so when new profiles are available, it appends them onto the existing data. This makes much more sense and allows the program to run faster.

Float 6959 is no longer sending data, however it is sending its location. So I took it upon myself to write up a function to pull the location out of the partial files it sending. I have made 6959’s location part of the site updating program. So, even though we are not getting data we can still keep tabs on its location.

I will most likely include data from float 0005 and 0015 on the site, but have not added them yet. I also don’t have the routines for reading float 6810’s data. All three of these floats should be easy to add to the site after I compile the data. None of these floats will require to be updated by the program, so I don’t have to write any matlab code for these floats.

Next week I will polish up the website and update the paper with new information. Hopefully I will be able to collect some data in the lab next week as well. Our light source should be here next week; we can look at the reflected spectra of the light in the lab. Also, I am curious about the fluorescence function on the DiveSpec. I said in the paper that the spike at 550 could have been caused the LEDs of the DiveSpec. I am not sure how the blue light in the DiveSpec is produced. Is there a filter over white LEDs that only allows blue light through? If so, it’s possible that this does not stop ALL of the white light and there is still enough to see a small peak at 550. That is why I am hesitant to say that the peak at 550 is caused by fluorescence. Next week in the lab I will take a fluorescence spectrum of something that we know does not fluoresce and see if the peak still appears. Farther down the road, I look forward to going back to DMC to collect data!

See you next week

It’s finally Friday! This week I continued work on the float website. I organized most of my matlab scripts and nested them all into one script so I can run it and update all the pages. I am a bit stuck right now because I’m not sure how to present the data. Currently I have plotted all the profiles, so you get an idea of the general trend as depth increases. Some of the plots that Emmanuel’s scripts produce are logarithmic and others are not. I’ll need an explanation of why some are and some are not on a log scale. I would really like to use three dimensional graphs to plot variables such as temperature, salinity, and depth. What I want to do is make a three dimensional graph that visitors can move and spin with their mouse. This would be much better than having a couple jpeg pictures of a three dimensional graph. I worked hard on trying to do this, however have not found a way yet. I tried using vrml first. Matlab has a function that will export a .wrl file, which was very convenient. I was able to embed this file into html code after exporting it. However, vrml files require special downloads that allow you to see them, and it just did not look very good once on the webpage. It would not plot tick marks on the axis and would not rotate the graph correctly, so I bagged that idea.


Next I found a function someone wrote to put a three dimensional graph into java format and embed that in html. So I fooled around with this, but I ended up needing the symbolic math toolbox for matlab. If you know where I could get this toolbox it would be a great help. If I were to get this toolbox I could put graphs such as these on the site

http://wwwpub.zih.tu-dresden.de/~s9034647/peaksurface.html

This would allow me to use some pretty cool graphing techniques to show float profiles. Using java was the only way I found to put a decent looking 3D object on the site. I felt like learning java would not be the best use of my time, so I am holding out hope I can get my hands on the symbolic math toolbox. If not, less exciting 2D plots are always an option. Other than that, I have changed the way matlab finds the pixels needed for clickable areas on the stereographical map. I have made each float (4738,6959,6810) on the map appear as red, green, or blue. Then I read the image into matlab in RGB format and used that to locate the red, green, and blue pixels that correspond to a specific float. Finally I exported a second map that is presented on the website, with the floats appearing as uniform colors. On a side note, I am afraid 4738 is the only float that is sending usable data.

The float data and website building has kept me occupied most of the week, but I have also worked on the paper discussing the radiometer data we collected. This is done for the most part, however I didn’t know if was supposed to include DiveSpec data in this paper as well….? If so I could do that quite easily. I divided the samples by the closes spectralon plaque readings, which gave me a percent reflectance. What I wasn’t thinking about was that the spectralon plaque is only 95% not 100% reflectance. Dividing the sample by the spectralon plaque implies that plaque reflectance is 100%. This will cause the percent reflectance to be slightly higher than it truly is, but it will not change the shape of the graph. Correct me if I am wrong, but I don’t believe this to be a problem as long as it is mentioned in the paper. It is also unfortunate that the only way I can identify the algae and sponge readings is by “a species of sponge” or “a species of algae” and not a species name. It’s rather unscientific to say that a comparison was done between Didemnum sp. and a sponge. I am disappointed I couldn’t have been there to get a look at these sponges and get somewhat of identification. I just found out this week that my surgeon apparently never returned the doctor in Bangor’s call. So I need to get a hold of him and have him call this guy in Bangor. I am rather sour about this whole situation. I’ve been diving almost every weekend since the beginning of June. It’s unfortunate I can’t help with the in water radiometer work. In any case I want to have this cleared up before I head to DMC this fall.

I have been using the subplot tool in matlab frequently this week, both for the radiometer data and the float data. For example:

Also this week, Alina and I finally got some more pictures taken. We ended up putting the laser pointer as close to the camera as possible, but out of the frame. The solutions were made in five liters of water, and the pictures were taken in the same five liter bucket they were made in. The pictures came out relatively well; unfortunately I don’t have them on my computer to show you. They will require a fare amount of cropping to remove bits of reflected light off the bucket and surrounding objects. I’m glad we were able to get something usable though.

Looking toward the future, when Emmanuel gets back, I had some ideas about the next time we collect data for the Didemnum project. I have been thinking about it this week, and I think we should invest in a light source for the next time we take data. We should be collecting data in conditions similar to what will be present when the radiometer is on the AUV. So this means using the same light source that will be on the AUV. I have mentioned this light to Wayne and still think it would be a good choice to use as our illumination,

http://www.intova.net/products/intova-super-nova/

This is a power full LED light, that is very durable. It rated to 400 feet, although I’m not sure what kind of depth rating we are looking for. The beam angle is quite wide which I don’t see as a problem. Even if the acceptance angle of the radiometer is much smaller than the beam angle I still believe it would work fine. This would help insure that there would be even light coverage in uneven terrain. It would also make the mounting of the light on the AUV more flexible because it covers a wide area. Regardless I think we should purchase this light or another LED light that we can use next time we take samples. This way we have a consistent procedure for collecting the data, instead of using various dive lights. If it was the same light we plan to mount on the AUV that would be even better. Unfortunately we don’t have a waterproof xenon strobe, or a way to sync the strobe to the radiometer (that I know of). If we do want to take that route we will have to make a new plan where we can get some data using a strobe. Pretty much what I’m trying to say is we should keep the light source constant. The DiveSpec uses LEDs, our light on the AUV will be LEDs (I vote LEDs instead of the strobe), so we should use LEDs when we are collecting our data.

Last but not least I have contacted Chris down at DMC to get some information on the Didemnum growth down at DMC. He hasn’t been in around the dock lately but he saw quite a bit at Damariscove Island. He has referred me to Robert Russell at the Dept. of Marine Resources. Apparently he has added Didemnum to a survey of marine life along the coast of Maine. I’m sure he can clue us in on some good spots. That being said, it’s hard to beat the convenience of the dock at DMC and the nearby labs. The DiveSpec is self contained but the radiometer is not. I assume the radiometer can run off a battery, but the question is do we have such a battery? If we want to consider changing locations I will contact Mr. Russell.

That’s all that’s fit to print. Sorry if this was a bit lengthy.

Mapping!

This week has been a refreshing change of pace. I have enjoyed organizing the float data and thinking of creative ways to display it. I started this week by downloading some mapping software for matlab. It took me a couple hours to learn the ins and outs of the program. I am able to make some nice graphs using this software. These graphs can display the trajectory and current location of the floats. The software has a number of different style maps and a built in coastline generator. Here are a few Lambert maps I made displaying information on float trajectory.

I think information like this for each float would look nice on the website. This would be included along with graphs, tables, and raw data for people to download. I also mapped all the floats on a stereographic map.

 

The way I am envisioning it, this will be on the float homepage and each float (red dot) will be click-able, bringing the user to information about that float. I made the dots red on purpose, I will explain this later. I have started learning html in order to make the websites. I downloaded Microsoft Frontpage express, but have not used it much at all. I’m finding html not that difficult and it’s probably more beneficial to learn code rather than use Frontpage. So far it is going well. The commands are pretty strait forward, and as long I have a list of commands I can do pretty much whatever I need to.

After reviewing the University of Washington float page I got some ideas. It would be best is to have the website auto update. The University of Washington page updates itself with no human intervention. I believe I can make it so our float page requires no manual updating as well.

The first problem I ran into is much of html code is repetitive. Putting large amounts of data into a table using html requires you to type LOTS of code. So I used matlab to write code for me. This is the easiest way to make auto updating code. I can insert variables into a repetitive string, and then export it into a .htm file. This is good, because a matlab script can be used to write text to the .htm file that the site reads from, thus updating the information.

I spent a lot of time this week setting up the stereographic map above to update automatically. The way I have the map set up now, each red dot is a click-able region that opens a web page containing float information. However, when the float changes location, the map must update. Having the map itself update was quite simple, but in the html text the click-able region must be identified using pixels. So when the float moves location, the click-able regain must move as well. This meant correlating pixels with latitude and longitude. The way I solved this was to generate the map in matlab using the mapping software I downloaded, then exporting it out of matlab. Then I read it back into matlab as a grayscale image, and then used the intensity values to find the red dots. Red dots made this easy, because they are the only red pixels on the map. Finally, I wrote a string in matlab containing the html text and inserted the pixel locations into the string. Then I exported the string into an .htm file.

I don’t know how I am going to work everything out yet, but I got a pretty good start this week. I really like the idea of the website self updating. This may not be totally necessary, but I want to set it up this way. I believe the float information is sent to the ftp site that Emmanuel sent to me. I am banking on this, because my plan is to pull the data off that site (or any ftp site), then run some scripts and spit out html. However, I haven’t seen any updated information on the site since it was sent to me. Looking at past data, it appears that data sent almost daily. Also the more recent files from the float in the Atlantic contain no data.

Last but not least, I started writing up a report on the Didemnum spectra we took down at DMC in June. I didn’t spend too much time on this, but I got a start on it. One thing that would be good to include is what kind of dive light was used for the illuminated spectra. I’m guesses it was a halogen light but, I will have to double check. That about sums it up…

This week was spent mostly in the lab. I worked on finding the Cp* of bentonite clay and then taking pictures of back scatted light from solutions with different Cp values. To find the Cp* of the bentonite clay I used data collected by Wayne and Alina last week along with data I collected this week. I used the LISST to find the Cp of four different concentrations. The graph below shows the results.

I found the slope of the linear regression line formed by the points above. I forced the regression line through the origin of the graph because if there are zero particles, the Cp should be zero. The regression line is not on the graph above because I could not figure out how to force it through the origin in matlab. So I graphed it in excel to find the slope. I came up with a slope (Cp*) of 238936 mL/m*g or 0.24 m^2/g. Wayne's measurements after salt had been added to form aggregates was 0.4-0.5 m^2/g. So i believe my value to be reasonable and accurate enough for my purposes.

Next I attempted taking pictures using the mirror set up, having the laser shine through a hole in a mirror positioned at a 45 degree angle. Back scatted light should hit the mirror and be reflected to the camera lens. It seemed like i good idea, but i could not get it to work properly. The hole in the mirror was purposely smaller then the laser beam, this forced the laser beam to be a round beam. However this illuminated the inside of the hole in the mirror, the camera was picking up this light and ruining the picture. So i tried using a pinhole in a piece of paper to shrink the laser beam before it went through the mirror. This reduced the light to almost nothing. Next i tried drilling the hole in the mirror larger and making the pinhole larger. This worked to some extent, but the reflected light off the surface was still illuminating the hole in the mirror. After trying to get everything positioned just right for hours, I abandon the mirror idea.

Next up was our other idea of putting the laser pointer in the center of the camera frame. This way the camera looked down on the solution with the laser pointing directly in the center of the picture. The light reflected off the waters surface should be reflected directly back at the laser pointer and never make it to the camera lens. I tried using the polarized lens with this setup and found that it was eliminating the back scattered light. I went into a completely dark room to take the pictures and coated the inside of a beaker with black rubber to reduce reflection off the sides. I tried using a pinhole again but it made the pictures much darker and placed more unwanted objects in the picture. The pictures looked much better without it. Next I made the solutions and took some pictures. On the camera I used an iso of 1600 and an exposure time of 13 seconds. For the 0.5 1/m solutions I used pure water and could not see any back scattered light. For the rest i got reasonable pictures. Here are the pictures, from top to bottom the C total values are: 2 1/m, 8 1/m, and 32 1/m.

I am still kicking myself for the first picture. It looked great on the camera screen, but once i got it on the computer, i realized i must have moved it during the 13 second picture. I don't have a picture for pure water because the camera picked up very little light and the pictures looked terrible. The only thing i don't like about the above pictures is the ring formed at the edge of the beaker. I need a larger beaker that the edges will be out of the camera frame, or a lens that can focus over smaller distances. Given more time I don't see why I won't be able to get excellent pictures now that I have experimented.

Don't expect a post next week, because I will be relaxing and BBQing in the mountains of Vermont!

At the start of this week I organized the radiometer data and paired the readings with the appropriate subject. At first glance the majority of the spectra looked like one green spike. However, after taken the median of a reading and dividing it by the median of the the closest plate reading, the spectra look a bit more familiar. Under ambient light the Didemnum spectra look somewhat similar to what we got with the DiveSpec. Below is a graph of the seven different ambient Didemnum spectra taken on the second dive. All the spectra have been divided by the closest ambient plate reading.

The radiometer was also used with a dive light. This produced more variability in the reflected light. This is most likely due to the distance and angle the light was from the subject. Below are the five different spectra of Didemnum using the dive light. Again, all these spectra have been divided by the closest dive light illuminated plate reading.

I was surprised that the ambient light readings looked similar to the DiveSpec readings. When looking at the raw data and seeing a single spike around 550, I figured there was to much organic material between the radiometer and the subject. However, to my surprise I discovered by using the plate readings, this unwanted light can be removed. I expect that if the radiometer were to be deployed on an AUV, it would be in less turbid waters then these.

In other news I should be finishing the visibility report soon. I will be happy to be done with it. Having never used matlab before I second guessed myself on a lot of the operations I did. However, this has helped me build confidence in my matlab skills. That being said, I find it quite frustrating that I can not find any strong correlations. I compared diver reports of currents and MVCO reports and they do not match at all. I assume the currents are variable and can change within a short time span. I have looked at a comparison between what the diver reports the current as and what the diver reports the visibility as and there is a relationship. However, the diver reports of current do not match the MVCO reports so I do not see the same relationship between MVCO current and diver visibility. So this gets me no where. I have been experimenting with three dimensional graphs in matlab. Even with the three dimensional graphs, swell height is still the only condition I can find any correlations with. Here are two three dimensional graphs,

Again, I don't see the correlation with period I have been expecting. I have looked at wave and swell period, and its just not there. I have no doubt that swell period does affect particle suspension, but it is not apparent in this data. I have recently learned that someone else at WHOI is doing the same comparison as I am. I look forward to comparing results.

This week I also got a quick introduction to the LISST. Next week I will be using it to determine the attenuation coefficient of Bentonite clay.

Early this week, I started compiling graphs and data from the MVCO visibility study. I am organizing this information so I can write a paper on what i found, or more realistically what i did not find. On Monday I ran a test to see if my data was matched correctly by comparing temperature recorded by the divers and by the 12 meter node. If the data is matched correctly they should be close to the same. The graph below shows the relationship.

As you can see they match up well. This gives me confidence that the matlab scripts i wrote were operating correctly. I will include this information in the paper.

The rest of the week has been spent either collecting or sorting radiometer data. All the data taken on Tuesday has been saved to my computer and organized using matlab.

Lets start with the Satlantic data taken on the second dive. With the Satlantic radiometer we logged data for 36 minutes, during this time the radiometer took 1294 light frames and 259 dark frames. 383 of the light frames had the lens cover on. That leaves us with 912 frames of usable data. I am still in the process of finding the best way to separate the spectralon plaque readings from readings of Didemnum and other objects. The plaque readings seem to fall into two categories, high reflectance and low reflectance. I'm assuming the high reflectance was when the dive light was in use. I can separate the brighter plaque readings easily but separating the rest of them is still in the works. Next week I will have some spectra from the second dive. Below is a picture of Didemnum taken on one of the dives.

The DiveSpec gave us surprisingly good results. On the first dive two usable spectra were taken with the DiveSpec. Afterwords spectra were taken of various organisms in the flowing seawater lab. The graph below shows some of the results.

When using the LED illumination of the DiveSpec, Didemnum produced a rather consistent reflectance spectra. The black lines are spectra taken while diving and the red lines are spectra taken in the flowing seawater lab.

Another characteristic of Didemnum we will have to look into is its ability to fluoresce. In the flowing seawater lab we used the DiveSpec to take one fluorescence reading of Didemnum. here are the results,

The spike at the beginning is blue light emitted by the blue LED's of the DiveSpec, however the small spike at 675 is not being emitted by the LED's. Its possible that Didemnum could fluoresce under certain conditions. In the future we will have to repeat this and see if we get similar results.

Also this week, Alina and I have been discussing the best way to get a picture of back scattered light off of suspended particles in water. We have come up with a few good ideas, and should be able to image only the back scattered light without the surface reflected light. In the lab I was able to eliminate all visible surface reflected light with Wayne's polarized lens. However, its my understanding that light reflecting off the particles will be polarized as well. So by using the polarized lens we may be eliminating a far amount of back scattered light. We will work this out and hopefully take the pictures next week.

I apologize, some of the graphs have very thick lines, i will correct that in future posts. Just as a side note i wanted to add this last graph of swell period plotted against swell height. This data was taken by the 12 meter node.

This graph shows some correlation between swell height and visibility. However it does not show a relationship between swell period and visibility. All three visibility categories cover a wide range of swell periods. The three categories begin to separate from one another when we look at swell height. This is the strongest relationship I've seen yet.

Hello and welcome to my new blog. As Emmanuel has requested I will post an entry every Friday about the weeks events/findings.

Early this week I finished, for the most part, comparing data from the WHOI dive logs to the data taken from the MVCO nodes. This was a good exercise in learning matlab, the amount of data taken by the MVCO nodes is enormous. Matlab was terribly confusing at first, but after working throught this data I have a good understanding of matlab.

That being said, my results are not what I expected. I expected taht the correlation between oceanic conditions and diver visbility would be obvious. When graphing teh data i see only weak trends. this leads me to believe that i may have made a mistake in matching the data up, or chaning the time in the dive logs from EST to GMT (I also took into account daylight savings time). However, I don't Believe this to be the case. One sign that my calculations are correct is that when divers were in the water at the MVCO site, the node was not logging data. this makes sense because the divers were making adjustments to the node. When matching the data I accepted the closest node reading within two hours of the dive start time. In some cases over 200 dives had no node reading whthin two hours, this leads me to believe my calculations are correct. Below is a graph of how the 12 meter nod readins deviate from the dive times.

In the dive logs visibility was rated A-E: A is 0-2, B is 3-10', C is 11-20', D is 21-40', and E is >50'. At the MVCO sight visibility was very rarely above C, and for the dives that visibility was higher then C there was no node data within two hours. Below is a graph of the distribution of visibility for all 929 dives done at the MVCO site in the last ten years.

The following two graphs are wave period and wave height over time, the color and shape of the data points describe the visibility.

I expected that visibility would be layered, with the best visibility occurring at low wave height and low wave period, and vise versa for the worst visibility. However, this is not the case. There is a large amount of data including numerous more graphs that show similar findings, that I am not going to post here. I will continue to see if I can make any conclusions based on the data I have.

In other news, we gathered spectra using both the DiveSpec and the Satlantic radiometer. The DiveSpec is functional, and I compared the Spectralon 99 and 95 plaques above and below water. I used the 99% as a reference for the DiveSpec, the spectra above and below water looked like this,

I then read the 95% plaque,

The reflectance of the 95% plaque was between 80-95% for both above and below water readings. These readings were at a 90 degree angle to the plaque. I also used the signature mode the DiveSpec to examine so other reflectance patterns. This graph shows reflectance of fluorescent light looking down into water and a second reflectance pattern from below the water surface, the difference between these two spectra give you a rough estimate of reflectance off only the waters surface.

The next set of graphs show reflectance spectra taken by the Satlantic radiometer. The spectra were taken by pointing both the light and the radiometer at the Spectralon 95 plaque. The first is of a white LED light and its very smooth and consistent. The graph shows 35 different readings from the radiometer. The second graph shows the reflectance of a xenon strobe. This shows 35 different readings as well. This gives you an idea of what the reflectance spectra looks like, however the radiometer and strobe were not synchronized, thus producing the variation you see.

Hopefully next week we will have reflectance spectra from various objects in the water including Didemnum. I have written a matlab program for importing and graphing data from both the Dive Spec and the Satlantic radiometer. I look forward to seeing what Didemnum spectra look like next week.