The Moni-Blog

UNH now has a seismometer!

2011-05-17T09:56:00.005-04:00

On Friday, April 29th, Mike Hagerty, from the New England Seismic Network came up to UNH to help us install our very own seismometer. It is installed in the basement of James Hall in a vault that has been dug out beneath the building:

The seismic vault in the basement of James Hall

Our location in New Hampshire means we don't have to dig very deep to hit bedrock, and so the vault is only a couple feet deep. The seismometer sits in the vault, coupled to the bedrock, while the data cables are kept safe and secure in the PVC pipe running from the vault to the cabinet. The seismometer is a Trillium 120 P with a RefTek 130 broadband seismic recorder.

Reftek 130 seismic recorder

Trillium 120P seismometer

We still have to properly align the seismometer so that its north axis is actually pointing north, but in the meantime we can have some fun looking at the data. James Hall is located rather close to the train tracks; fortunate for those wishing to take the train, but unfortunate for seismometers (unless you wish to study seismograms of passing trains). Below is a high-frequency seismogram from our station, the big spike in blue is a passing freight train:

click to see full-size

You can also see when the building's HVAC system kicks in. This means that eventually we'll probably try to find the UNH seismometer a new home, so that we don't have to worry about local small earthquakes getting lost in the noise of trains and building maintenance.

The nice thing is that building noise and passing trains get filtered out when you just look at the long-period signal. This is excellent for looking at teleseisms (a tremor cause by an earthquake more than 1000 km from the station). Below we can see two teleseisms in the seismic recordings from 5/15/2011:

click to see full size

The spike in red is a teleseism from a Mw 6.0 earthquake (event time = 13:08 UTC) located on the St. Paul transform fault system in the mid-Atlantic. The much larger teleseism in green -- if you look you can see that it actually starts in blue around 18:57 and continues on through the black wave until about 20:55 or so -- is from a Mw 6.5 quake off Papua New Guinea. The Papua New Guinea quake occurred at 18:37 UTC, but it took about 20 minutes for the first p-waves to hit our stations. The s-waves appear kick in around 18 minutes after the p-waves, and the surface waves start to hit at 19:37, a full hour after the event time. This may seem like a long time, but remember that seismic waves can take a while to travel through the earth, particularly as they reflect and refract through different layers in the earth's mantle. Surface waves take the longest to arrive, as they alternatively speed up and slow down through different surface materials such as rock, sand, soil, etc. The chart below gives an estimate of travel time for various seismic waves versus angular distance from the earthquake:

source: http://geophysics.eas.gatech.edu/classes/Geophysics/misc/Seismology.html

If you wish to check out the seismograms that are being generated by the UNH seismometer, or any of the New England Seismic Network (NESN) stations, check them out here. You can select DUNH from the station drop-down list and check out the seismograms for any day since the seismometer was successfully installed. If you click on station list, you can see all the stations in the NESN. If you want to hunt for teleseisms, check the period to long-period. If you think you've found one, you can go to the USGS Earthquake page (http://earthquake.usgs.gov/earthquakes/recenteqsww/) and see if you can find a matching event. Large earthquakes greater than Mw 5.5 usually generate teleseisms that most modern seismometers anywhere in the world can see. You can also use the above chart to figure out how long after the event you should see seismic waves arriving at the station.

UPDATE: Kurt Schwehr just blogged about the UNH seismometer as well. He talks about network setup and how we initially configure the seismometer with a Palm Pilot. He also shows the results of a jump test.

How to fix PostBox email client preferences

2011-01-04T15:56:00.001-05:00

I use Postbox 2.1 for my email client on the Mac. It is efficient, has advanced searching, and let's you view photo thumbnails, attachments, and todos from any folder and directly export them to another program. This makes finding that lost attachment somewhere on the server very easy.

I recently encountered a problem, however, where despite having set the account-specific preferences to not quote the original email in a reply, it was doing it anyway. No matter what I did or tweaked, Postbox would automatically included the quoted message. It was pretty annoying, as I had to delete everything manually, and for emails that include a lot of HTML that can be a pain. So if you have issues with your Postbox preferences too, you can do what I did ($ refers to command link prompt in the terminal)

Make sure preferences are set to how you want them to behave (e.g. quote message on reply box in unchecked) and the close Postbox.
Navigate to the Postbox preference file location: $ cd /Users/username/Library/Application\ Support/Postbox/Profiles/random.default/
save a backup: $ mv prefs.js prefs.js.backup
open prefs.js (I just did $ open prefs.js to open it in xcode)
if your problem is quoting on reply, find the: user_pref("mail.identity.id4.reply_quoting_style", 2) and set it to user_pref("mail.identity.id4.reply_quoting_style", 0)
save the file and reopen Postbox and it should be fixed

You can scroll through and pretty easily figure out what the different preferences are from there name, just be sure that you have a backup in case you mess something up. Worst case scenario you just rename your prefs.js.backup back to prefs.js and you're good to go

Jabref export to HTML Table is awesome!

2011-01-04T14:30:00.001-05:00

So I just discovered that Jabref, the free, open-source, cross-platform citation manager that I use has a very kick-ass feature thanks to Mark Schenk. Mark wrote a very nifty export tool for Jabref that exports selected entries to an interactive HTML table that is searchable and lets you view abstracts and the raw bibtex entry. Here is an example provided by Mark.

Here are the features as listed in the exported HTML source code:

optionally searches Abstracts and reviews
allows Regular Expression searches
e.g. to search for entries between 1980 and 1989, type: 198[0-9]
e.g. for any entry ending with 'symmetry', type: symmetry$
e.g. for all reftypes that are books: ^book$, or ^article$
e.g. for entries by either John or Doe, type john|doe

UPDATE: Browsing around Mark's page, I found that he has added even more features to this HTML table export, including the ability to sort columns by clicking on the header, and filtering list entries by entry type, year, author, etc. Here is an example from Mark.

Jabref comes with the first version of the export tool I described as well as a more simplified table (no abstracts or bibtex) already. To get more enhanced versions, visit Mark Schenk's Jabref tools webpage.

My First Earthquake

2010-12-19T12:39:00.000-05:00

I've been studying faults and earthquakes for over a year now, but it was not until just now that I felt my first trembler. I'm currently visiting my fiancé's family in Los Altos, CA. We were all sitting around the breakfast table when all the sudden the plates all started rattling. It was very brief, only a couple seconds long, but it was definitely an earthquake.

The USGS has it initially sized at a magnitude (local magnitude, ML) of 3.1

http://earthquake.usgs.gov/earthquakes/recenteqsus/Quakes/nc71498795.html

Donate to charity simply by browsing the web

2010-12-19T11:41:00.001-05:00

Google Chrome is now offering an extension that tracks the number of tabs you browse in a day. Google will donate an as-yet-unspecified amount of money per tab viewed, up to 250 tabs a day per user, up to 1 million dollars. The effort started Wednesday and stops today, but I just now learned of it now. Grab it while you can and spend the day helping charities as you browse the web.

http://www.google.com/chrome/intl/en/p/cause/#tnc

CCOM/JHC seminars now offered as webinars!

2010-12-02T21:46:00.001-05:00

The CCOM/JHC seminar series, that occurs each fall and spring semester, and pulls in some fantastic speakers, is now offered as a webinar so anyone, anywhere can join in.

Each week, generally by Wednesday (and certainly by Thursday), you will see a headline on CCOM's homepage of their website advertising the coming Friday's seminar, along with a link that allows you to register for the webinar. The webinars will play in almost any browser on a Mac or PC. For a full list of requirements, view here and click on "attending a webinar."

If you attended our very first attempt at this, Friday, Nov. 19th, you know we had some "technical difficulties." Our speaker was using Keynote on her Mac, and we did not realize that by default Keynote is set to not allow screen sharing. As a result, our webinar had audio, but not video. We now have all the kinks worked out and tomorrow's webinar so hopefully go off without a hitch, video, audio, and all. You'll even be able to text in questions!

Tomorrow's seminar: Multi-Source Geospatial Information Integration and Analysis for Coastal Management and Decision Making by Ron Li, Director of the Mapping and GIS Laboratory at Ohio State University. Just click the title to register.

BTW, if you want to know how to make Keynote and GoToWebinar play nicely (in case you're ever giving a webinar), check out the super quick solution here, you just have to change one preference.

Digital Mapping Camp for Kids

2010-07-20T21:35:00.000-04:00

This is very, very cool! I hope when I have kids, I'll be able to bring them to conferences as well, and while the adults sit in talks, the kids can learn how to put together bathymetric images of the seafloor!

For Kids Of Cartographers, Digital Mapping Class Is In : NPR

Free Amazon Prime for Students

2010-07-14T14:07:00.000-04:00

Amazon Prime is normally 79 bucks a year. For that, you get free two-day shipping on any eligible item without having a required minimum purchase. You can also upgrade to 1-day shipping for only 4 bucks an item.

This sounds great, but not enough that I am willing to fork over the 80 bucks to get it. Well, now I don't have to. Amazon is giving away free 1-year memberships to Amazon Prime to all college students currently enrolled in at least one course (this means waiting until fall semester for me...). In the fine print, it also mentions that this offer may be extended beyond the initial 1-year period. In addition to the free shipping, Amazon will also email out exclusive student-related discounts and promotions, though you can opt out of these emails at any time.

The idea of all this, of course, is to get more students buying things like textbooks from Amazon. Given that Amazon pretty much ALWAYS has the cheapest prices for new textbooks - I'm anal and prefer new to used - I generally always order through them anyway.

Check out this free Amazon Prime offer yourself: Amazon Student.

Holy Guacamole: ArcGIS for iPhone/iPad..Free!

2010-07-06T10:46:00.001-04:00

The title pretty much says it all!

You can view maps available from ArcGIS.com, including ones that you upload yourself. This means you can access your own GIS data. They also provide tools to digitize and measure your own routes, right on the iPhone or iPad!

Here a link to a blog post with some more info:
GeoGeek

Here is the iTunes Store link:
iTunes Store

Sea Monster Fossil Unearthed

2010-06-30T15:51:00.000-04:00

A 12-million-year-old, 17-m long whale fossil, with huge teeth, unearthed in Peru:

http://news.bbc.co.uk/2/hi/science_and_environment/10461066.stm

Italian earthquake scientists indicted for failing to predict quake

2010-06-15T18:50:00.001-04:00

Excert from an email I received from the Seismological Society of America (SSA):

Two weeks ago the L’Aquila Prosecutor’s office indicted of manslaughter the members of the National High Risk Committee that met in L'Aquila one week before the Mw6.3 earthquake. The charges are for failing to provide a short term alarm to the population before the earthquake struck, killing more than 300 people.
The president of INGV (National Institute of Geophysics and Vulcanology), Enzo Boschi (member of the High Risk Committee), and the director of the National Earthquake Center, Giulio Selvaggi (just accompanying Boschi to the meeting as technical specialist), are among the scientists in seismology and earthquake engineering now under investigation together with some civil protection officials.

This is insane. Earthquake prediction is notoriously difficult and there is no current accepted method for predicting an event. The best scientists can do now is to develop seismic hazard maps and risk assessment in order to help guide better building codes, train response teams, and help prepare the community as much as possible. The SSA has drafted an open-letter addressed to the President of the Italian Republic, and asks anyone working in seismology or the Earth sciences in general to sign the letter and show your support for these scientists.

The letter can be found here: open-letter in support of Italian scientists

M5.7 Quake shakes up my folks

2010-06-15T14:41:00.001-04:00

Ahh... nothing like waking up in the morning and finding a Facebook post from your dad mentioning they just got rocked by a M5.7 earthquake. At least I know they are alright if they can post a status update about it. That's a pretty decent sized quake, and they said they felt the rolling for about 10 - 15 seconds. Luckily they are far enough away from the epicenter, near Mexicali, CA, that most of the higher frequency energy was already absorbed and they just felt the lower energy stuff.

Here's a link to the USGS webpage for the quake: USGS event map. If you live near the area and felt the quake, be sure to go to the USGS link provided and fill out their shaking intensity form. Scientists use this data to determine the shaking intensity of the event and it helps provide data in areas that may not be covered by instrumentation.

Track Oil Spill Response Vessels in Real-Time

2010-06-14T13:27:00.001-04:00

Want to see what all the response vessels are doing in the Gulf of Mexico?

Go to the government's Environmental Response Management Application (ERMA) website. This site leads you to a Web-based interactive GIS platform where you can turn on various layers such as "Response Vessels Snapshot" and the National Marine Fisheries Service (NMFS) fisheries closures. There is currently a typo in the Response Vessels Snapshot layer, where it says the snapshot is from June 10. Don't let this throw you off, these snapshots are real-time, with the exception of an approx. 10-minute delay while data is uploaded to the server, processed, and loaded into Erma.

Green triangles represent research vessels, including NOAA ships, and blue represent other response vessels. You can click on the information icon (the "i"), and then click on individual vessels for more information.

A Blogger Worth Following

2010-06-09T13:23:00.004-04:00

While Googling how to set a certain preference in Emacs, I came across Sacha Chua's website. Sacha is an Enterprise consultant for IBM and she helps people learn how to use wikis, blogs, etc and be more productive as a result. She blogs about her work, geeky-like things such as Org-mode and Emacs, and life in general. I really dig her site and what she is about in general, and I recommend that folks check her out.

I wonder if Blogger has a way for me to organize my posts in clickable category links... I have the labels widget to the side that uses keywords to organize your posts, but it would be nice to have major categories as their own clickable links like Sacha does, where then each category has its own set of labels.

Time Machine not Working after Logic Board Replacement

2010-06-09T11:16:00.003-04:00

I just got my Macbook back from Apple this morning with a new logic board and new screen. Hooray!

I connected my Time Machine drive and immediately noticed a problem. Time Machine could not see any of my previous backups. When I browse the drive using Finder, I see them, but not with Time Machine. Turns out that Time Machine is closely coupled with your MAC address in 10.5.8 (not so in 10.6 Apple told me, so you 10.6-ers will not face this issue). Anyway, new logic board = new MAC address = unhappy Time Machine.

There is supposedly a fix that involves resetting the attributes of a plist file and renaming a hidden file in Time Machine. This method is detailed on the MAC OS X Hints website. The Apple tech told me that Apple engineers say this fix should work, but he has never had success personally. One little typo and it won't work.

I followed the directions to a "t," and it did not work for me. I was very careful about the spaces in my Time Machine backup disk name, but something still went wrong. Anyway, the old backups are still there, I just still cannot see them with Time Machine. Although now when I follow the Mac OS X Hints tips for finding the mac address associated with Time Machine, it shows the correct one.

Apple's suggestion, assuming you are not missing any major files on your system: Abandon your old backups and start fresh with Time Machine. Either that or update to 10.6 (which for me would involve purchasing a new version of Matlab, so no thank you).

Looks like I'll be starting over with Time Machine tonight, *sigh*.

Another reason to use a version control system

2010-06-07T11:10:00.003-04:00

I have posted about usefulness of Subversion version control system (svn) a couple of times already, but this morning has prompted me to do another one. Subversion allows you to backup all your valuable data, saving each commit as a separate version. You can see the differences between any two versions, checkout earlier versions, have multiple working copies, etc. If you are a coder, a version control system like svn is essential.

Anyway, this morning made me love svn even more. My main computer is being shipped off for repairs, and I am currently using the boyfriend's old Mac PowerBook G4. I needed to get it setup with all my files so I can continue to do my work. Instead of having to transfer files over one-at-a-time from one computer to the other, I simply did an svn "checkout" of what I needed.

A simple "svn co https:\\my repository path\trunk\Code" and "svn co https:\\my repository path\trunk\References" at the terminal prompt (from within the directory I want to download them to) and I am good to go. All my latest scripts, and my complete reference directory (all the pdfs of all the journal articles I use as references) are now on this computer, within seconds. If I make any changes to these files while on the boyfriend's computer I can simply "commit" them to my svn repository and when I get my computer back, do an "update" and I am all set!

JabRef has also proven to me, once again, its awesomeness this morning. I simply open up my main library.bib bibtex file (just checked out from svn) within JabRef, and there are all my journals, instantly organized and searchable. The PDF links work automatically, simply click on the icon, and the journal articles pops open before me in Acrobat Reader. To see why JabRef is such an awesome reference database software, check my initial blogpost on it here, and the follow-up (showing how, in conjunction with Zotero, it can make organizing and collecting references a breeze) here.

The Topsy Turvy Experiment

2010-06-04T15:13:00.003-04:00

One Topsy Turvy, One Tomato Plant, One Summer....

I am not sure what it is about the Topsy Turvy that has me so fascinated, but for some reason I could not resist buying one when I saw them on the shelf in Rite Aide. Perhaps it is the pleasure of being able to grow fresh tomatoes without having to deal with all the slugs our garden attracted last year, or the idea that this plant may escape the blight that claimed the lives of so many of our brave, young tomatoes last year. Whatever it is, I gave in to temptation. I also decided that this would make a fun topic for a photo log. Throughout the summer I'll occasionally post about the progress of this little tomato plant in the Topsy Turvy. If you've thought of buying one yourself, you may want to stay tuned...

(Topsy Turvy and Purple Cherokee Heirloom Tomato plant)

(Topsy Turvey hanging off our side porch)

ERMA tracks the oil spill through web-based GIS

2010-06-03T12:19:00.006-04:00

Some of my fellow CCOM-ers have been helping out with the oil spill mediation attemps, and now that some of it has been made public, I can finally share!

ERMA, which stands for Environmental Response Management Application, is now up and running in a web-based GIS portal that allows users to turn on and off different layers. You can view where the spill is now, predicted trajectories, current weather conditions, etc. While not everything in ERMA is viewable yet by the public, what is available is pretty cool and starts to gives you an idea of all the things that going into an emergency disaster response such as this one.

Free SQLite Manager for Mac OS

2010-05-25T17:40:00.007-04:00

Sqlite-manager is a tool that originated as a Mozilla (Thunderbird, Lightening, FireFox) plug-in for managing SQLite databases. However, over at the Kiveo website blog, I found instructions for making this plug-in a stand-alone application.

I followed the directions exactly as posted (note though, that the current version of the sqlitemanager-xr packageis now 0.5.16) and it works perfectly.

Here's a running list of the current features:

dialogs for creation, deletion of tables, indexes, views and triggers
ability to rename, copy, reindex tables
ability to add and drop columns
create new db, open any existing db, copy an existing db
supports writing your own queries (single or multiple)
supports saving the queries with a name
a tab for database settings (no need to write the pragma statements) where you can view and change the sqlite library settings
export tables/views as csv, sql or xml files
import tables from csv, sql or xml files
a dropdown menu showing all profile db (.sqlite)
an intuitive heirarchical tree showing all tables, indexes, views and triggers
ability to see the master tables
ability to see the temporary tables, indexes, views and triggers
ability to browse data from any table/view
dialogs to allow searching in a table/view
allows editing and deleting selected record while browsing a table's data
allows adding, saving and changing blob data
an extensive menu that helps with writing sql by hand and then executing it
remembers the last used db, table and the tab (structure, browse & search, etc.) across sessions

And here's a screenshot of it running happily on my Mac (OS 10.5.8)

Radar for accurate draft measurements

2010-05-20T10:06:00.010-04:00

Here at CCOM, we have been testing a small radar for use as an accurate tide gauge out in the field. The WaterLog Series radar has an accuracy of +/- 3mm and and typical report time of 800 milliseconds, which is pretty snazzy.

(Radar mounted above CCOM's wave tank)

I was thinking it would be pretty sweet if we could mount one of these radars on the sonar mount of the R/V Coastal Surveyor, CCOM's main survey ship. Right now we have to take draft measurements by holding a yard stick up to a clear tube and measuring the distance between the meniscus of the water in the tube and the top of the Inertial Motion Unit (IMU). This leaves A LOT of room for human error.

(R/V Coastal Surveyor, with the hydraulic ram out of the water)

On the Surveyor, sonars are mounted to the bottom of a hydraulic ram that moves up and down. Every morning prior to surveying, surveyors measure the height of the ram above a specific point on the deck of the ship. This is then used to calculate the depth of the sonar below the IMU since you know the total length of the ram, and you know the height of the IMU in relation to the point on the deck that you measure the ram height to. This means, each day, we would also know the height of the radar in reference to the sonar as well. We could simply take a running average of say, a minute of data, and get a much more accurate draft than we could ever measure with a yard stick. Furthermore, we could get continuous draft measurements throughout the day, which is something you cannot readily do now, barring someone taking several yard sticks measurements in a row and hoping that the average somehow actually represents the real draft. Plus, trying to measure a meniscus in a tube with a yard stick, on a small moving vessel that is rocking in waves is not something I particularly want to do.

Typo perhaps not Google's after all...

2010-05-19T10:33:00.003-04:00

So yesterday I posted about how I had found a typo in the name of a fracture zone in Google Earth's Ocean layer.

The Vernadsky fracture zone (~ 7º10'43" N and 34º35'05"W) is spelled "Vernadskiy" in Google Earth.

The IHO-IOC GEBCO Gazetteer of Undersea Feature Names (2009) lists the spelling as Vernadsky, and I took this as gospel, since this document tends to be to go-to document to check the name of any feature on the seafloor.

The feature is named after the very famous Russian geochemist Vladimir I. Vernadsky, considered one of the founders of geochemistry. I did a search and actually found several references to him using both spellings, including this one:

Vernadksiy Tavricheskiy National University in the Ukraine. Now I would imagine that if they are going to name a university after someone, they make sure to spell the name right.

So perhaps the misspelling is in the actual Gazetteer and not Google. This guy is pretty famous, he is considered one of the founders of geochemistry, so you would think this would be easier to sort out.

I suppose it could be due to the westernized spelling of an eastern name, in which case, the eastern spelling (Vernadskiy) should be the correct one.

Hmmm...

Google Earth Typo

2010-05-18T17:40:00.007-04:00

I was flying through Google Earth earlier looking at some oceanic transform faults when I came across something that gave me pause: a typo. I never really expected to see a typo in Google Earth. I posted it to their user help forum, but I am not sure if the right people will see it.

The misspelled feature is a fracture zone in the Google Earth ocean layer. The Vernadsky Fracture Zone (~ 7º10'43" N and 34º35'05"W, named after the very famous Russian geochemist Vladimir I. Vernadsky) is spelled "Vernadskiy" in Google Earth.

I checked the IHO-IOC GEBCO Gazetteer of Undersea Feature Names (2009) just to be sure, and it lists the correct spelling.

Here's a picture of the offending fracture zone:

Make Your Facebook More Secure

2010-05-18T08:49:00.004-04:00

A friend pointed me tool a great little tool that helps you lock down your Facebook and make your personal information more secure. ReclaimPrivacy.org has developed a scanner tool that will check your privacy settings and show you all your vulnerabilities. Best of all, it works on any browser and on any system. Simply drag their tool to your toolbar to make a bookmark (or bookmark using the menu options in your browser), navigate over to Facebook, and then click on the "Scan for Privacy" bookmark link. Below is an example of the result:

Google Maps of the Oil Spill

2010-05-05T11:17:00.003-04:00

Google is tracking the oil spill in the Gulf of Mexico. Check out this weblink to their map as well as some KML files for Google Earth

Two Must-Have Mac Tools to Manage Hard Disk Space and Time Machine

2010-04-13T16:22:00.007-04:00

So earlier today I had a bit of a freak-out! Inexplicably, the remaining 25 GB or so of free disk space on my Mac disappeared. I got a little pop-up warning telling me my disk was full, and sure enough when I checked I only had about 150 MB left. I immediately assumed the worst, that my drive was corrupted, my computer was going to die, all my work would be lost, I would subsequently fail out of my PhD, and that I would end up working at McDonald's. OK, this might be a stretch, and in any case, I have yesterday's Time Machine backup, but I was still freaked out. How do you suddenly lose 25 GB of free space? I noticed it after plugging in my Time Machine disk and letting a backup start. I checked my drive but saw nothing out of the ordinary. On my boyfriend's advice, I let Time Machine finish the backup. This way I could hopefully do a diff between two backups and find out what was eating up the hard disk space.

During the backup, I deleted some small files to help make space and emptied my trash. Then suddenly, viola! My free space came back. My trash had been emptied before, so that was not the cause. Perhaps my Entourage address book had become corrupted? This was one of the files I deleted to help create space since I do not use Entourage at all. My boyfriend thinks perhaps Time Machine itself created some weird temp file that got out of control and that it disappeared as Time Machine finished doing its thing. I do not know what happened, but in the process my boyfriend and I found two great FREE tools that we have now decided everyone should have.

1) Disk Inventory X

This awesome program will show all attached drives, the space used and available, and gives you a really nifty graphical interface so you can immediately see which files are space-hoggers. It takes a little time to get going if you decide to view your entire computer, but trust me, it is worth it!

2) TimeTracker

This utility will list all your Time Machine backups, the space they are using, and a complete breakdown of what has changed since the previous backup.

New CCOM-er, New Blogger

2010-04-10T11:20:00.004-04:00

Jonathan Beaudoin, from the University of New Brunswick, just recently joined us at CCOM. His work on looking at the uncertainty of 4-dimensional sound speed in the water column is pretty fascinating!

Jonathan is also a blogger and Mac user, so I thought I would give his blog a shout-out. You can find it here: Jonathan's Blog.

I must admit though, I am not sure how I feel about him now that I saw his knock on EMACS. I use Aquamacs on my Mac and I love it!

Can Toads Be Used to Predict Earthquakes?

2010-04-01T17:54:00.001-04:00

There is a long history of animals acting strangely prior to an earthquake. The Japanese believe that the catfish may be used as a predictor of seismic activity. Dogs, cats, chickens, and horses are also believed by some to be able to detect p-wave energy well before humans can. Now it appears that toads may be added to that list:

Can Toads Be Used to Predict Earthquakes?

Want to go to the Arctic? Just donate 25K to the La Jolla Symphony

2010-03-11T22:15:00.002-05:00

Check out this article: http://www.lajollalight.com/life/266876-one-cool-gift-bassoonist-hopes-to-thank-benefactors-with-trip-to-arctic

Dr. James Swift, from the Scripps Institute of Oceanography, is offering up the chance to go on the Coast Guard icebreaker, the Healy, for a research cruise up in the Arctic. All you have to do is donate 25,000 smackaroos or more to the La Jolla Symphony, and you get entered in to the drawing.

Sure glad I study the ocean; I got to go for free :)

R.I.P. ABE

2010-03-09T14:43:00.003-05:00

This past Friday, March 5, 2010, the AUV ABE was lost during a dive off the coast of Chile. Here is the formal WHOI obituary, I mean announcement, and here is an nice exert highlighting some of ABE's many accomplishments during his life:

Built as a prototype, ABE quickly became a workhorse. It was the first autonomous robot to make detailed maps of mid-ocean ridges, the 40,000-mile undersea volcanic mountain chain at the boundaries of Earth’s tectonic plates where new seafloor crust is created. It was also the first AUV to locate hydrothermal vents, where hot chemical-rich fluids spew from the seafloor and sustain lush communities of deep-sea life. ABE explored seamounts, undersea volcanoes, and other areas with harsh, rugged terrain. In addition to researchers and students from the United States, ABE advanced research for scientists and engineers from Canada, the United Kingdom, Germany, Australia, New Zealand, Japan, China, Italy, Ecuador, and most recently Chile.

Chilean Earthquake Shortens Earth Days

2010-03-05T13:38:00.002-05:00

Scientists now estimate that our Earth days are ~ 1.26 millionth of a second shorter. Here is a nifty blog post explaining why.

Look Ma, I Created an Anaglyph!

2010-02-17T17:30:00.007-05:00

I just stumbled across a pretty sweet Matlab-framework tool called Mirone that allows you to do all sorts of analyses to various grid/image formats.

If you do not have Matlab, there is a standalone version that runs on Windows. For Mac folks, it will run under Snow Leopard if you have Matlab 2009, but sadly does not seem to work in Matlab 2007 on 10.5.

I am currently running it on my Windows desktop at school using Matlab 2009b and I am pretty impressed. It has a bunch of image processing/geophysical tools at its disposal. In just a few minutes of playing, I was able to open a GMT grid and plot plate boundaries and earthquake epicenters on it.

What mainly got me excited about it was that I was also able to generate a pretty sweet anaglyph. If you have a pair of red-blue glasses, give it a looksie! The area is the Carlsberg Ridge in the Indian Ocean. I recommend double-clicking the image to open it in full-size.

Maybe I should work at Google...

2010-02-12T10:10:00.006-05:00

I love my job. Well, more precisely, I love being a graduate student in oceanography. I get to do amazingly cool research, and get to go to amazingly cool places as well (even the Arctic! - no pun intended). However, every now-and-then I come across something that causes me to daydream about what it would be like to be in a different field. Today's daydream came courtesy of Google and their Google Lat/Long blog.

Recently they rigged up a Google "Street View" snow mobile to give us a true 3d look at the slopes for the upcoming Winter Olympics. People actually got paid to snow mobile around the slopes for a day!!!

Street View Hits the Slopes at Whistler

Evidence confirms mud-volcano was man-made

2010-02-12T09:21:00.006-05:00

Mud Volcano Was Man-Made, New Evidence Confirms

This Wired.com article discusses the findings of Richard Davies, director of the Durham Energy Institute and co-author of a new paper in the journal Marine and Petroleum Geology. The results of his analysis is that the Lusi mud volcano in Sidoarjo, Indonesia was indeed caused by the drilling company when they pulled their drill out from an unstable hole. Since its first eruption May 29, 2006, Lusi has dumped out 100,000 tons of mud a day. It now covers almost 3 square miles to a depth of 65 feet, and displaced thirty thousand people. The drilling company maintains that an earthquake that occurred 175 miles away on May 27, 2006 is the real cause of the mud volcano, although there is plenty evidence to the contrary.

One of the things I find interesting about this story is that both scientists working for the drill company and independent scientists have papers about this very issue in the journal of Marine and Petroleum Geology. The scientists working for the company all find that the real cause of the volcano was the earthquake, which in turn means that their company should not be held financially responsible. The independent scientists all find flaws with that reasoning and claim that the earthquake could not have been the cause. Clearly, the drill company scientists have every reason to be biased. If their results indicate the drill company was at all responsible, not only would they probably be out of a job, but they would be setting the company up for a huge financial burden. So how can we as a reader, or the journal for that matter, look at this article objectively? It is hard to see it as just another scientific exploration and discussion of a dataset. Furthermore, I am curious if this article mentions that the authors work for the company in question. Surely that disclosure should be made somewhere where the reader can easily find it, shouldn't it?

This brings up whole other questions for me about how science deals with conflict-of-interest pieces such as this. Should journals have more strict peer-review requirements for articles they suspect of having a conflict-of-interest, or should the burden of knowing exactly what we are reading and by who be on the reader? How would this type of issue be handled in a medical journal?

Geodesic Distance in ArcMap

2010-01-26T16:40:00.006-05:00

One of the things I like about ESRI ArcMap is the ease with which you can measure features in your data. Recently I wanted a a simple way to measure geodesic distances of some projected data. The measure tool in ArcMap, by default, measures distances in projected units in projected data, and geodesic distances only for data displayed in geographic lat/long. If you hold down the shift key while measuring a distance, Arc will calculate geodesic distances regardless of projection. What I really wanted to be able to do, however, was to be able to draw lines in a shapefile, and then have Arc calculate the geodesic distance of those lines. This is something that Arc cannot do, without you first unprojecting (or more correctly, reprojecting) your data to geographic coordinates.

Luckily, I found this: http://137.227.239.67/pigwad/tutorials/scripts/

Looks like some of the folks at ESRI got together with the USGS a designed a plug-in that will let you, among other things, calculate geodesic distances from projected data. It uses the parameters specified by your projection to unproject the data into geographic coordinates and then calculates the geodesic distance on the fly. Since it uses the semi-major and semi-minor radii that you specify in your projection, the distortion should be minimized. This tool is definitely a time saver, as it does the reprojection for you only on the data you are calculating, and enables you to keep your whole project in projected space.

ArcMap Projection double-check

2010-01-21T14:42:00.014-05:00

I recently posted about how I had written a python script to convert Smith/Sandwell topography data to an ARC ASCII grid. I brought my resulting data in Arc and everything appeared to be correct. It all seemed to be going quite swimmingly; until that is, I noticed that the Prime Meridian appeared to pass just off the eastern coast of Australia. Hmmmm.. Last I checked, the Prime Meridian was still in Greenwich, UK. Clearly something was wrong. In my grid image, Greenwich fell on the very edge of my map. It seems that while I can bring the data into Arc and tell it what the projection is, Arc has a hard time displaying correct Lat/Long coordinates if you range of from 0 ->360 rather than -180 -> 180. There does not seem to be a way to specify that your longitude range is 0 -> 360 versus -180 -> 180 in Arc. I find this strange and am wondering if I am simply just missing it. Anyway, since I could not figure how to make it right in Arc, I went back to my original python code.

I decided to make my grid actually go from -180 -> 180 by amending my code. I basically grabbed the western half of my grid and appended it to the beginning of my file. I then cut off the redundant data. Using Struct.unpack to decode binary data results in a tuple, which cannot be modified, so the first step is to convert to a

#now unpack img data write out the ASCII file data
for j in range(nrow):
if v:
if j% 500 == 0:
print 'row:', j #print row # every 500 rows
raw_data = img.read(2*ncol)
row_tuple = struct.unpack('>'+str(ncol)+'h', raw_data)

#now move western half of data to the east
row = list(row_tuple)
east = row[ncol/2:ncol]
row.reverse()
east.reverse()
row.extend(east)
row.reverse()
corrected_row = row[0:ncol]

I had to reverse the rows before I could append the data, because the extend command places the data to be appended at the end of the row only. Once the data is correctly added, I simply reverse it back and snip off the extra. I could also just as easily grabbed the first half of the row instead (east = row[0:ncol/2]) and avoided the reversals, but this just happened to be how I worked through it first.

UPDATE: I showed Kurt my code last night and pointed out how I went about switching up the columns in my row variable. He said it was good that I figured out the two long ways, and then he showed me the one line method. Sure, you cannot really modify tuples after they have been created (e.g. no tuple.append or tuple.extend) but you can grab sections of them and switch them around like so:

In [1]: t = (1.2,3.4,5.6,7.8,9.1,10.2)

In [2]: t = t[3:] + t[:3]

In [3]: t
Out[3]:
(7.7999999999999998,
9.0999999999999996,
10.199999999999999,
1.2,
3.3999999999999999,
5.5999999999999996)

Applying this method to my code, I can switch up the western and eastern halves of the line I read in from the img file simply by:

#now move western half of data to the east
row = row[ncol/2:] + row[:ncol/2]

Pylint: The Python Code bug/quality checker

2010-01-20T11:38:00.004-05:00

Now that I am off and running in Python, I thought I should install Pylint. Pylint will review your code for bugs and quality (as determined by some formalized Python standards).

You can run it via command line simply by typing:

pylint myscript.py

There are also a lot of options for silencing reports, getting more detail from messages, etc. If you leave the reports on, you get a global evaluation score. I just ran my script the decodes a binary SIO IMG file into an ARC ASCII grid through pylint and got this result:

Global evaluation
-----------------
Your code has been rated at 4.92/10

Not bad, considering this is my first ever script. My code runs fine; the majority of the messages involved formatting issues, such as some of my lines being too long. For code readability, the convention is to keep lines as short as possible. I definitely have some that I could break up into 2 lines. I also get some messages about not following my commas with a space (picky, picky).

After shortening just a couple lines and putting in some spaces after some commas, I ran it again:

Global evaluation
-----------------
Your code has been rated at 6.44/10 (previous run: 4.92/10)

It is still complaining about some line lengths and the fact that I have some variables named with single letters, but in general my code is pretty good. If you want to help make your code better, especially if you are just learning like I am or if you plan to distribute your code, I recommend Pylint.

Leaving the shallows...

2010-01-20T10:02:00.004-05:00

So I recently have experienced a huge change in my research direction, and for those possibly going through the same thing, I thought I would share the hows and whys.

Last year, my original research project began taking a serious nose-dive. I knew what I wanted to do and thought I had a good plan of attack, but I simply could not account for some variables. Amongst other issues, there was some crucial information I was going to need to make it work, and I was not going to be able to get it. Lesson learned: beware projects involving potential proprietary information. However, if someone wants to give me hundreds of thousands of dollars so I can buy my own plane, lidar system, and hire a pilot, I may still be able to do it though...

Anyway, after a couple months of feeling like I was drowning in trying to find another project, I was getting scared. I was nearing the start of my third year and I had no project. Sure, I had like 45 credits worth of class that I had taken, but my research had basically gone up in smoke. I got to the point were I was considering taking a leave from school to give myself time to decide what I wanted to do and if I even wanted to continue in grad school. The best advice I got was to talk to some of the faculty outside my department, particularly young, fresh-faced, faculty that were still full of excitement. I did so, and it saved me.

Now, I have finally came across a project that I think is a perfect fit. It brings me back to my undergrad days of awe when I was first learning about oceanography and geology and everything amazed me. I am leaving the shallows and heading into the deep! My new research focuses (in a nutshell) on using high-resolution multibeam sonar data to determine fault structure and earthquake potential along oceanic transform faults. I am so excited. My committee is also very excited and very supportive. This is key, as last year this was not always the case.

I am sharing this because I think it is important for other grad students (especially the PhD-ers out there) to know that sometimes setbacks happen, and sometimes they are for the best. This new project definitely has me more excited than my old. There is much more room for collaboration, and I am going to get to work with some great folks down at Woods Hole! My committee changed slightly as a result of the new direction, and is more excited and supportive than ever before. Did I lose some time? Probably about 6 months of research time. Does it matter? No. In the long run, who cares? As one of my committee members said to me, "the setback itself matters not, what does matter is whether or not you bounce back." Setbacks in grad school are common. They happen to the best of us. After all, we are still learning how to ask the questions that lead to great projects in the first place.

So 2010 certainly has been a fresh start for me. A new year, a new project, and now, a new blog layout.

Converting SIO img file format to Arc ASCII grid w/ Python

2010-01-17T19:50:00.019-05:00

Recently I have been battling with getting a SIO binary file format of predicted bathymetery (from Smith/Sandwell satellite topography data) into an Arc-friendly ASCII grid format. GMT has a nifty img2grd command which generates a netcdf of the img file; however, it takes some manual tweaking afterwards to get the coordinate bounds of the data to be Arc-happy (even if one follows img2grd grd2xyz with the -E option). I have decided I want a one-stop solution, where I could just feed in the img file and spit out an ARC ASCII grid and this means I need to write my own script. Therefore, I sat myself down this afternoon and began to teach myself Python (with some input from Kurt). Now, after just a couple hours of Googling, tweaking, and testing, I have a working Python script that does just what I need it to. It reads in an img file, and spits out a space-delimited ASCII grid file complete with the ARC header.

In order to test that I was decoding the binary properly, I wrote the first row of data out to its own little text file and used gnuplot to graph it up.

in my script I have the following:


for i in range(1):
row = struct.unpack('>'+str(ncol)+'h',img.read(2*ncol))
for depth in row:
    o.write(str(depth)+"\n")
print "\n"

then in terminal I call gnuplot and at the prompt type:


plot 'filename' with l

Certainly looks like a nice depth profile to me:

Org-mode for note organization

2010-01-03T16:43:00.008-05:00

New Year: new attempt at note organization

I am always trying to find the best way to organize my random work notes and tips that I tend to collect in various notebooks, post-its, etc. I started keeping a text file last year, which was rather plain-Jane, but did the trick. Kurt, however, just introduced me to org-mode in Emacs, and I love it! Org-mode is extremely powerful. You can insert date stamps, create tags and link across multiple entries, create levels and sublevels and fold/unfold sections, highlight code blocks according to the scripting language, etc. Included html links are active from the get-go, and you can even include equations, graphics, and tables. One of the best parts is that you can export to HTML, PDF (via LaTeX), and DocBook.

Here is a sample of what my notes look like in Aquamacs using org-mode. I have organized my notes by program/tool, but you could also organize by date and use org-mode to keep a daily log. On the org-mode website, you'll see tons of examples. You can also use org-mode as a task scheduler and day planner. The possibilities seem endless.

And here is the resulting HTML file (ignore the old dates, I imported my old notes from last year):

Healy gets a new MBES

2009-12-03T23:25:00.003-05:00

Healy is getting a brand-spanking-new multibeam: an EM122!

Check out Dale Chayes' photo album of the replacement here. The pictures of them cutting into the hull are pretty sweet!

Robot Clam to Detonate Underwater Mines!

2009-12-02T08:36:00.003-05:00

I think this is really cool. My master's project involved using multibeam sonar to observe scour and burial of mines on the seafloor. It is a very real danger for ships going into some foreign waters. If this provides a safe means of detonation, then that is awesome!

http://www.livescience.com/technology/091201-robot-clam.html

Accent marks in JabRef

2009-11-25T10:42:00.003-05:00

I have a lot of PDFs with authors that have accent marks in their names, such as Ekström. I had thought that using the LaTeX code for the letter in my JabRef entries might work since the database is just a BibTex file. No such luck. Turns out you can just use the regular keyboard shortcuts for Mac/Win in JabRef to get the right letters. For a guide to the keyboard shortcuts, check out this about.com link.

JabRef might complain about not being able to encode certain characters when you go to save your database. If so, just chose UTF-8 for the character encoding option. UTF-8 will preserve any letters with accents, as well as foreign characters you might have (e.g. Greek letters in the abstracts).

Zotero AND JabRef: how to make both work for you

2009-11-25T09:36:00.004-05:00

So yesterday I posted about how I switched over to JabRef reference software, mainly because it allows relative links, but also because it easily lets you see and edit the BibTex entry, which as a LaTeX user, is very helpful. There are two things JabRef does not really do that Zotero does that I find really useful:

1) Zotero can easily capture reference information from a variety of website formats, even if no Bibtex or RIS entry is provided

2) You can drop a pdf directly into Zotero, index it, and then retrieve the reference information automatically, assuming the article is online somewhere

If the article's webpage has a BibTex or RIS entry available for download, you can simply download this and import it into your JabRef database, but I have noticed some journals still do not offer this service (shame on them!)

So this morning I have been happily using Zotero to collect reference information I find online and to auto-generate some entries based off some PDFs I already had. Once I am done, I can export to a RIS file and then import that RIS file to my current JabRef database. My BibTex keys are automatically generated on import, so I simply select the new entries, go to Tools -> Scan Database -> Sync Files and any new PDFs I obtained during the day will be linked to their entry in JabRef.

I keep my Main.bib file that is my current JabRef database inside my folder with all my reference PDFs. At the end of the day, I can simply commit the whole folder to subversion. Everything is not only backed up, but when I checked out the folder on my Windows machine, all my PDF links will work perfectly and I won't have to tweak my database one bit!

I used to hesitate putting all my PDFs in svn, but our school server is pretty huge and the 1 GB or so of PDFs that I have now does not even make a dent. Plus, after hearing from a friend how he lost his whole PDF database and had to go download or even scan (yikes!) all his references again, I decided backing up all my articles in svn was not only OK, but necessary!

Zotero to JabRef: switching reference software

2009-11-24T14:04:00.007-05:00

If you know the academic me, you know I love, and regularly tout, using Zotero to manage my ever-growing bibliography. There is one problem with Zotero, however, that I just cannot move past: its inability to use relative links for linking to files.

update: I edited the following paragraph to clear up some confusion pointed out in a posted comment. I should also point out that on Zotero's website, there are numerous posts from users requesting relative links, but with absolutely no reply from Zotero. This again makes me think that the way Zotero is written, relative links are not possible. Otherwise, they would have it, wouldn't they?

I love being able to sync my Zotero database between my personal Mac and school PC, but the syncing breaks the file links. If you sync your database to a second computer, it shows the links as still being there, but if you try to click on a file to open it within Zotero you get an error message saying Zotero cannot find it. You can tell Zotero where the file is, but you would have to do this for every file in the database. I am guessing this has something to do with Zotero running as a FireFox plug-in. When you add a PDF from another directory, Zotero copies it into its own internal structure, which is confusing and involves folders with random letter names. This is just not working for me. I want to be able to sync my database between my computers, and have functional links to the associated files.

I just switched today to JabRef and love it. It is free, works on Windows, Linux, and Mac, and let's you use relative links. It is simply a frontend for your BibTex file, but it has some really cool tricks:

1. It can autogenerate bibtex keys based on a format you specify
2. It can automatically link entries to files in any directory you specify based on the bibtex keys.
3. It is all stored in a small, easily transferable, BibTex file
4. It supports online searches so you can find and easily capture references online
5. It supports field-based views, but let's you view and directly edit the BibTex code as well as
4. I am sure there are a ton more, but I just started using it today

There are a couple tricks to switching over, so here is what I did:

1. Export the Zotero library in RIS format (my BibTex format export from Zotero caused issues with JabRef)

2. Import the RIS file into a new database in JabRef and save it

3. The internal PDF links from Zotero were written out to the URL field, meaning there are now a bunch of broken URL links in JabRef. To fix this, I navigated to the location of my new database file via terminal (or Cygwin in Windows) and did the following:

egrep -v "internal-pdf" original.bib > new.bib

This will delete all those pesky broken URLs that think they are internal PDF links, but still keep any legit URL links

4. Open the new.bib with JabRef (you can close out the old database now).

5. Under Options -> Preferences -> External Programs: Set the file and PDF directories to whatever directories you are already using (ex: /Users/mwolfson/Documents/School/Articles). Also check the "Autolink files with names starting with BibTex Key" option

6. Under the BibTex Key generator options, setup your BibTex key to match how you name your PDFs. My PDFs are named: author_year.pdf. So my BibTex Keys were set to [auth]_[year].

7. Select all your entries in your database, then go to Tools -> autogenerate BibTex Keys (let it overwrite old keys if necessary). Now all your entries should have the proper BibTex Key appended to them

8. While still selecting all records, Tools -> Scan Database -> Synchronize File Links (they have a specific PDF link, which works, but does not add the PDF icon to the entries for some reason -- perhaps because it uses a special pdf = {} in the bibtex code instead of file = {} -- so there is no way to know which entries have PDFs and which don't). Allow overwriting and hit OK. Now, if your PDF/file names in the specified directory match any of the BibTex keys, they will be auto-linked to the JabRef entry. Entries with linked PDFs should now show a PDF icon next to it.

update: There is an option under preferences to "show PDF/PS column" which would then, in fact, display the PDF icon if you choose to PDF sync rather than File sync. I have heard PDF/PS sync is being phased out since File sync handles these file types and more though, so I still recommend using File sync instead.

Viola! You should now have a working BibTex database in JabRef with all your articles linked. If you work across multiple computers like me, simply open up this database in JabRef on the new machine, set up your file directories to point to the appropriate files, and you are done. All your PDF links will work because the links themselves are relative! This is especially awesome when working cross-platform between Windows, Linux, and Mac.

Here is a screen grab showing what JabRef looks like running on my Mac:

If you get stuck feel free to drop me a comment and I'll try to help.

Installing GMT under Cygwin

2009-11-02T15:40:00.007-05:00

I just struggled through installing GMT under Cygwin, and since I not only had to rely on piecing together information from out-of-date online tutorials, but also on direct help from Kurt, I figured I would write everything down here for future reference and to also hopefully make someone else's life easier.

First things first, check your home directory:

Always check your home directory in cygwin to see if it is actually what it should be. When you install Fledermaus on your machine, it sets a 'HOME' variable that is Program File/IVS/Fledermaus. Now Cygwin thinks this is its home as well. The CCOM wiki offers this solution:

To resolve this, you can create a system-wide HOME area that may be more suitable for any/all programs. To do this, create (or decide) the folder you'd like to be your Cygwin home area. Once you have the folder, edit the HOME variable in the Advanced System properties in Windows and specify that folder. Finally, copy the contents of the previously specified home area into your new home area folder. This will prevent IVS or GMT from breaking. This situation may not be limited to these two products, so it's important to check your 'HOME' environment variable before installing Cygwin software.

Once you are happy with your home directory, here are the steps I followed to successfully install GMT:

1) Make sure you have bzip2 installed. You will also need the 'make' utility and a good C++ compiler (I have a couple different ones, including the gcc one. netcdf will fail to compile without the right one, so if it fails, try grabbing another C compiler. I think gcc is the one to have).

2) Go to the GMT webpage and create an install parameter file. Save this as GMTparams.txt in your usr/local/ directory under your cygwin directory. (If you do not have netcdf already, make sure to let GMT get it and install it for you)

3) Get the GMT install file here, and save it as install_gmt to usr/local/

4) Under cygwin, navigate to usr/local/ and type the following command (this may fail, but this is okay):

./install_gmt GMTparams.txt > install.log

5) If it failed, you probably got a message about a missing -lnetcdf file. This is because netcdf is bad, and uses a .lib extension rather than .a. To fix this, you can just create a symbolic link:

navigate to usr/local/netcdf-xxx/lib
type ln -s libnetcdf.lib libnetcdf.a

Now modify your GMTparams.txt so that netcdf is not downloaded or installed again. You can also modify not to download the GMT files again.

6) navigate back to usr/local/ and rerun ./install_gmt GMTparams.txt >install.log. This should complete without failing, though you may see warnings scroll by.

7) Once it is installed, you must edit your .bashrc or .bash_profile. Cygwin, by default, does not create a .bashrc or .bash_profile in your home directory, so you may need to create one from scratch. GMT looks for a .bash_profile, so if you use .bashrc, make sure you create a .bash_profile that points to it. I'll share mine below:

my .bashrc file (all are needed for GMT to work):

export PATH=/usr/local/gmt/bin:$PATH
export NETCDFHOME=/usr/local/netcdf
export GMTHOME=/usr/local/gmt
export MANPATH=/usr/local/gmt/man:$MANPATH
export DISPLAY=:0

my .bash_profile file:

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi

export BASH_ENV=$HOME/.bashrc

8) Now you may notice that my paths in .bashrc do not seem to be correct. I use "gmt" and "netcdf" instead of "GMT4.5.1" and "netcdf-3.6.3." This is because I want to be able to update both of these in the future without having to edit any scripts or my .bashrc every time. Therefore I set up the following symbolic links:

navigate to usr/local/ and then type the following commands:

ln -s GMT4.5.1 gmt
ln -s netcdf-3.6.3 netcdf

9) You should be good to go!

To test one of the examples GMT runs upon successful install, you can navigate to any one of the examples found in /GMT4.5.1/share/doc/gmt/examples/. Each ex directory will contain the example scripts, necessary files, and the resulting postscript. I found that to view these files, I need to make sure the X-windows environment is up and running (from cygwin command prompt, type startx). Then I use ghostview (gs) to view the ps:

gs example_27.ps

here is the result:

Fun with Apple Terminal

2009-11-02T10:17:00.004-05:00

I am starting to do more and more stuff on my Mac via the Apple Terminal, so I decided to spruce mine up a bit.

Using Fink I first installed "fortune-mod" (the program that actually displays the fortunes) and then installed "fortunes" (the fortunes themselves).

Next I simply added "/sw/bin/fortune" to my .bashrc file.

Now, whenever I open a new terminal window, I am greeted with a fun fortune. Most of the time, these seem to be just silly sayings, such as this:

Old programmers never die, they just become managers.

but every now and then you get something unexpected, such as a recipe for Glogg (a traditional Scandinavian holiday drink).

2009-10-20T14:25:00.002-04:00

AGU recently announced a special late-breaking session for the fall meeting this year. Abstract deadline is Oct. 30th. This session is sure to be full of some exciting talks!

The 2009 Samoan and Sumatran Earthquakes: Origins, Impacts and Consequences
Category: Seismology

Co-Sponsors: G, NG, NH, OS, DI, T

On 29 September 2009 the Pacific plate ruptured in a normal faulting earthquake of magnitude 8.3 close to its subduction beneath the Australian plate. The resulting sea-floor displacement generated a tsunami that resulted in loss of life and great destruction in Samoa and American Samoa. Less than 20 hours later and some 10000 great circle kilometres distant a magnitude 7.6 event shook the city of Padang in Sumatra. At the time of writing over 1100 are confirmed dead, many more are still missing and great areas of the city are devastated. One day later another earthquake M6.6 ruptured the great Sumatran fault more than 250 km to the southeast.
Many important questions arise from these events: What was their mechanism and tectonic context?
What were the features of the Samoan event which generated the tsunami and how could its effect have been mitigated? Why was the Padang earthquake so devastating and what was its relationship to the recent great megathrust earthquakes on the Sunda subduction zone? What are the implications of this event for the high seismic and tsunami risk from near-future megathrust earthquakes west of Sumatra? How can we best prepare vulnerable populations for them? Finally, is the temporal clustering of these large events purely coincidence or if not, what physical mechanisms might explain it? We encourage submissions on all aspects of these earthquakes.

From GeoMapApp to Google Earth: Visualize your data in a jiffy!

2009-10-06T23:00:00.009-04:00

Seriously!

I am not sure if the old version of GeoMapApp supported such an easy import/export of data, but the new version, released October 1, sure does!

Here is how to bring in your data, view it, color and scale by value, and export it to Google Earth in a jiffy. A jiffy, of course, being relative to the amount of data you actually have.

1) Under the File menu, import your data into GeoMapApp. This can be a shapefile, a 2D grid, or a table/spreadsheet in ASCII or Excel. I selected an Excel file of oceanic transform fault data and it worked flawlessly.

2) Once loaded, your data should display on the map and the data table will appear below. On the right you will notice several options related to the data table, including Color by Value and Scale by Value. Selecting these brings up a drop down box of all your data parameters. Select one and a color bar will pop up that you can edit. Once done, be careful not to close out the colorbar box or you will lose your settings (perhaps a bug? I simply minimize it to get it out of the way).

Here is what the transform fault data look like, colored by slip rate and sized by length:

3) To export to Google Earth simply click on the save drop-down box on the right and select Export to Google Earth (KMZ). You can either export selected data points or your entire table. Once you make your selection, a box pops that enables you to select which parameters to export. The next step lets you choose what parameter the placemark name will take, as well as rename parameters and set units. Once you click okay, GeoMapApp will export the kmz file.

Here is my exported kmz file inside Google Earth:

It does not color the placemarks by the value you selected in GeoMapApp, nor does it allow you to select your icon, but these things can be edited in the kmz file itself. What it does do is provide an easy way to get the data into Google Earth to begin with. Simply click on a placemark, and all your parameters for that point pop up!

So there you have it! Quick and easy data visualization in two great (and free!) geospatial data applications!

Glossaries package in Texnic Center on Windows

2009-10-06T10:58:00.007-04:00

Okay, yesterday I posted about how to set up and use the glossaries package with TexShop on a Mac. Here is the Windows version using TexnicCenter. This is basically a condensed version of Nicole Talbot's (creator of the glossaries package) post on the same matter:

If your TexnicCenter frontend is using the MikTex tex distribution, you can use the MikTix package browser to install packages (very easy to do, and the recommended method.) Otherwise you can install them manually from CTAN.

Using your preferred method, install the following packages:

* ifthen
* xkeyval at least version 2.5f (2006/11/18)
* xfor
* amsgen (part of amstex)

Make sure you have the following in your preamble:

\usepackage[acronym]{glossaries}%makes a separate acronym list

\makeglossaries

If you want your terms in your text to be hyperlinked to their definition (way cool), add the following BEFORE \usepackage{glossaries}:

\usepackage[colorlinks]{hyperref}

Now, as mentioned in the yesterday's post, you can either define terms and acronyms in your preamble, or have them as separate tex files and use the \include{} command.

When you get to the location in your main document (after the \begin{document}) where you want your glossary to be, simply add the command:

\printglossaries

Now, here is where it can get a bit tricky. You need to build the glossary file first, and there really isn't an easy way to simply add an engine to TexnicCenter (at least not that I found). Glossaries uses a Perl script to build, so I found the easiest way to do this is to make sure I have Perl installed on my machine (recommend Active Perl, they have windows installers). There are other ways to build the file using makeindex or xindy commands (see Nicola's post, but you have to run them 3 times for every type of glossary file, and the Perl way is just easier and faster.

Once you are good to go with Perl installed, open a command prompt (start->run->cmd) and navigate to the directory with your Tex files.

Type the following at the command prompt (you do not need to include a filename extension):

makeglossaries filename

You should see a bunch of stuff fly by on the screen indicating your glossary file was created. Now simply go back to TexnicCenter and build the file as you normally would, and Viola!, you should have a document with a glossary file.

Creating Glossaries in TexShop on Mac

2009-10-05T14:24:00.015-04:00

I was searching for a way to create a word list or dictionary in Latex, and came across the Glossaries package. This package is already installed if you use TexShop for Mac, but I still had problems getting it to work.

The problem is that you first have to be able to build the glossary file before you build your main latex document (similar to when you create a bibliography using Bibtex).

I found a very helpful blog post about all this here: http://www.ict-cloud.ch/2009/07/glossaries-acronyms-and-texshop.html.

I followed his steps and created a text file called "glossary_run.engine" that contained the following code:


#!/bin/sh

bfname=$(dirname "$1")/"`basename "$1" .tex`"

makeindex -s "$bfname".ist -t "$bfname".alg -o "$bfname".acr "$bfname".acn
makeindex -s "$bfname".ist -t "$bfname".glg -o "$bfname".gls "$bfname".glo

Save this file (you must use the .engine extension) to Users/.../Library/TexShop/Engines directory.

(Note: I first tried this with TextEdit. Even if you remove the .rtf extension, this will not work. It will work if you copy and paste the code into Emacs and then save it)

Next, make the file executable. In terminal, navigate to the above directory and type

$ chmod a+x glossary_run.engine

There you have it. The next time you open TexShop, the glossary_run engine (or whatever you named it) will be in the dropdown list next to typeset. Before you build your latex document, select this engine from the drop down and click typeset to build your glossary file first.

To use the glossaries package you will need the following in your preamble:

\usepackage[acronym]{glossaries} %makes a separate acronym list
%there are lots of different options for this package. acronym enables me to define acronyms as well as words

\makeglossaries

%Glossary-File - can include a separate glossary file here
\include{glossary file name.tex}

%Acronyms - can include a separate acronym file
\include{acronym file name.tex}

\begin{document}

Here is the test code I played around with. Instead of including separate files, I defined some terms and acronyms in the preamble. If I do it this way, I do not need the include terms, and instead just use the makeglossaries command:

\documentclass{article}
\usepackage[colorlinks]{hyperref}
\usepackage[acronym]{glossaries} % make a separate list of acronyms

\makeglossaries

%new glossary term
\newglossaryentry{sample}{name={sample}, description={a sample entry}}

%new acronym
\newacronym[\glsshortpluralkey=cas,\glslongpluralkey=contrived acronyms]{aca}{aca}{a contrived acronym}

\begin{document}
A \gls{sample} entry and %\gls{aca}.

Second use: \gls{aca}.

Plurals: \glspl{sample}.

%Reset acronym to first count

\glsreset{aca}

%note this now uses the plural form
First use: \glspl{aca}. Second use: \glspl{aca}.

\printglossaries

\end{document}

Yum! A nice, hot cup of putresince!

2009-10-05T10:07:00.003-04:00

I suggest reading this with a nice hot mug of coffee by your side, as I did:

What's inside a cup of coffee?

Leaf Peepers Report 2009!

2009-09-22T10:14:00.003-04:00

New Hampshire maintains a foliage report website. It's pretty cool actually. Now I know that the leaves should still be turning when my folks are here in October. Check out the website for yourself here: http://foliage.visitnh.gov.ns1www.silvertech.net/index-flash.html

Northeast Passage Navigible Once Again!

2009-09-20T07:37:00.002-04:00

Two German tankers just became the first two Western ships to ever transit through the Northeast Passage!

http://news.bbc.co.uk/2/hi/europe/8264345.stm

A Call for Generic Sensor Format (GSF) files

2009-08-31T10:46:00.004-04:00

I am putting out a call for GSF files to help test out the GSF-reader I am writing.

I have tested my GSF-reader with files I have found around CCOM; however, they all seem to be generated by CARIS, which only outputs certain records within the GSF file.

I am particularly interested in GSF files containing one or all of the following records:

1) BRB Intensity subrecord with time-series intensity records for each beam

2) Simrad, or non-Reson, sonar-specific subrecords

3) Sector Number, and Detection Info subrecord arrays

4) Reson-specific Quality Flags array

5) HV Navigation Error record

If you have such a GSF file that you can send me, please email me.

Cheers!

Installing a Zagg Invisishield on iPhone 3G

2009-08-27T23:27:00.004-04:00

I am posting this because a lot of people have posted about how hard it is to install a Zagg InvisibleShield on the iPhone 3G. I just put mine on and found it to be relatively easy, so I thought I would share a few tips in case it benefits anyone else.

1) Some folks complain that for best results you have to leave the phone off so it can "set up" for 12 to 24 hours to let the product cure. I simply installed mine at night so it can do most of its setting up while I am asleep.

2) Use the shield spray liberally! I ended up using the entire bottle just putting on the back piece because I had to realign it once and I wanted to keep my fingers moist. You can refill the bottle up to three times, so do not worry if you use a lot.

3) The corner pieces, were indeed, somewhat hard to do. They sort of stuck where they fell when I first placed the piece on the phone, so I had to peel them up, respray, and then press down again. Letting them set up a bit definitely helps as does the "palming method".

4) THE BEST ADVICE I found online was to stretch a piece of saran wrap over the top and bottom of the phone to help keep the corner pieces down while it cures. I did this for about 10 - 15 minutes only as I did not want to trap any moisture from the spray, but it did make a difference. My corners are all now nice and smooth.

The squeegee really did get most of the bubbles out, but some very small ones will remain. Zagg says these will work themselves out as the products settles down over the next day or two. I have been checking periodically as I let the phone sit, and indeed some of the small guys are already gone.

So far so good. I really like the shield and the phone looks great. I will still use my case for drop protection, but now I can rest assured about scratches.

I originally had an iFrogz Luxe case that I LOVED, until I realized it trapped stuff between the case and the phone, so the chrome and the back of the phone got scratched up a bit. I was always careful with the phone too, keeping it in a sunglasses pouch when in my purse, or keeping it in a separate pocket when in my book bag, so the scratches really annoyed me. Also, one of the tabs broke off after only a couple weeks, so I was worried about the case staying together if I were to drop the phone.

I now have a SwitchEasy Rebel. The case is not as nice looking or feeling as the iFrogz (in my opinion), but the protection seems to be way better and I am not worried about pieces snapping off.

Here are some pics of the phone about an hour and a half after putting on the Zagg:

UPDATE: Just FYI, by the next day, all micro-bubbles were gone, all the corners were smooth, and it looked awesome!

Follow Healy in Google Earth!

2009-08-27T15:43:00.002-04:00

Thanks to Google and Kurt Schwehr, we can now follow Healy in Google Earth. Kurt's GeoRSS feed of the Healy's Aloftcon images is what is feeding the Google Earth visualization.

Check out Kurt's blog to see how to view it: Kurt's blog.

Healy Photostream on Flickr

2009-08-26T11:40:00.002-04:00

The USCGC Healy has a photostream up on Flickr! Now we can all follow along as they traverse the Arctic! Check out the recently updated stream to see pics of a polar bear spotted just a couple days ago!

http://www.flickr.com/photos/cutterhealy/

CARIS GSF: Update

2009-08-26T11:27:00.003-04:00

So CARIS sure is speedy with their replies. I normally always hear back within a few hours, and sure enough, I had a response waiting for me this morning!

As with most programs that can write to GSF, CARIS simply implements the C-code available for download from SAIC's website. The extra-padding issue could be a bug in the original C-code then. Perhaps the 0 - 3 byte padding allowance listed in the specification document is not actually enforced.

However, I also wonder if this issue is related to the fact that CARIS only writes out sonar-specific sub-records for RESON systems. The GSFs I generate from RESON systems do not have the extra padding, but the SIMRAD ones do. I wonder if something about how the C-code writes out the records causes there to be extra bytes when the sonar sub-record it missing.

Maybe it is supposed to signify an unknown sonar type with an empty subrecord?

If someone happens to stumble along this post that has had a similar issue, feel free to drop me a line.

CARIS GSF and the Mysterious 2 Extra Bytes

2009-08-25T12:11:00.002-04:00

I have been plowing along trying to get my GSF-reader I am coding up in Matlab to work with a variety of different GSF files (diff. versions as well as files from different GSF-generators). This morning I got my code to work with some CARIS-generated GSF files that were giving me a bit of a problem.

GSF records are often packed so that the total record size is an integral multiple of 4, so I wrote a little clean-up statement in all my sub-routines that will automatically read any extra characters needed to pad the particular record.

This one group of CARIS GSF files, however, keep crashing the reader. Within the Bathymetry Ping Record, I kept getting sub-record types of 0, which do not exist. I was at the end of the ping subrecords for the first ping in the file, and I had padded the record to be divisible by 4. The problem was that the total size of the ping record (including all sub-records) was 868 bytes, and even with the padding, I was only reading 864. Where were the extra two bytes coming from?

I ended up opening the GSF file itself and looking at it in Hex mode. This can be done using UltraEdit on Windows (automatically opens binary in Hex format) or by using AquaMacs on the Mac. I used ftell(fid) in Matlab to tell me where in the file I was when the error occurred and then went to that spot in the Hex mode file (in UltraEdit: Search -> GoTo line/Page and type in the number of bytes to move forward. in AquaMacs: C-u #bytes and then hit the right arrow key).

What I saw when I did this was that, sure enough, the record had extra padding. The total number of bytes in the ping sub-records for each ping is 862. To make this divisible by 4, you only have to add 2 bytes (thus my initial reading of 864 bytes). Looking at the binary in Hex mode, however, I was able to see that the record was actually padded with 6 bytes, bring the total up 868. Once I made this correction, the code ran happily and I was able to read the whole GSF file successfully.

I am still not sure what is up with the extra two bytes though, and I am curious to see if this may be the cause of GeoCoder and Fledermaus crashing when trying to read these files. I am going to submit this to CARIS and suggest they take a peak at it themselves. This bug only seems to occur in GSF files exported from CARIS 6.1 (I have tested it with different files). GSF files exported using CARIS 5.4 do not have the extra padding.

GSF-reader now working!!

2009-08-24T17:31:00.004-04:00

Okay, so I am really excited because my GSF-reader that I coded up in Matlab is now working!! It is not fully-functional yet (I still have to add some sonar-specific readers, and some other optional record types) but it works for one of the sample CARIS-generated GSF files I have.

One of the things holding me up was the fact that I did not realize records were padded with extra bytes to ensure the record size in bytes was divisible by 4. I am not sure why it matters if it is divisible by 4, but apparently it does to GSF.

My next issue to tackle is a Reson sonar-specific quality flag indicator that is written in bits, not bytes, and uses all kinds of bit shifts and masks (joy!). This record is no longer used, but some older GSF versions will include them. Once that is tackled, some of the other GSF files should start working as well.

Also, if I want others to be able to benefit from this work, I should probably eventually convert it over to Python. Having a Python-based GSF reader would be pretty sweet.

There already exists C-code of course that does all this, but I want to have something that generates separate records for the data so that I can play with the ping depths for example, or the backscatter intensities, in a familiar environment. The C-code is really written so that it can be incorporated into other programs. By writing a reader myself, I not only gain a better understanding of the data and how GSF stores them, but I read them into a program where I can readily perform mathematical analysis on them.

Methane Seeps from Arctic Seabed

2009-08-22T18:29:00.003-04:00

Check out this discovery of deep-water methane seeps off Norway by a joint British-German research team:

http://news.bbc.co.uk/2/hi/science/nature/8205864.stm

below is a sonar image of some of the seeps

Writing a GSF-reader in Matlab

2009-08-18T14:00:00.020-04:00

I recently ran across a couple issues with some GSF (Generic Sensor Format) files I have, so I decided to attempt to write a GSF reader in order to see what, exactly, I was dealing with. I have never written any kind of binary format reader before (though I did tinker around and add features to one written in Python), so I sort of jumped in the deep-end with this. I decided to use Matlab, since I am most comfortable with it's scripting language at this point in time.

Here is a valuable lesson I just learned: Never take the binary specification file at face-value. Typos happen, and they certainly happened here. I have the GSF v. 3.01 specification file available from the SAIC website, and have been following it to write my reader. Everything has been going fine for the most part until I reached the attitude record.

According to the specification, the attitude record should look like this:

*Field Name*	*Description*	*Field Type*	*Count*
NUM_MEASUREMENTS	Number of attitude measurements in this record.	I	2
ATTITUDE_TIME	Array of attitude measurement times	I	N24
PITCH	Array of pitch measurements	I	N*4
ROLL	Array of roll measurements	I	N*4
HEAVE	Array of heave measurements	T	N*4
HEADING	Array of heading measurements	T	N*4
*Attitude Record Size:*			*Variable*

Should be pretty straightforward, so in my Matlab code I wrote the following function:


function [Num_meas, ATT_Time, ATT_Pitch, ATT_Roll, ATT_Heave, ATT_Heading] = readATTrecord(fid)
%% This function reads the Attitude record in a GSF file.

%% Element          Bytes   Type         Description
% Num_Measurements    2      int      number of attitude measurements (N)
% Attitude_Time       N*2*4  int      array of attitude meas. times
% Pitch               N*4    int      array of pitch measurements (hundreths of deg)
% Roll                N*4    int      array of roll measurements (hundreths of deg)
% Heave               N*4    char      array of heave measurements (hundreths of deg)
% Heading             N*4    char      array of heading measurements (hundreths of deg)

Num_meas = fread(fid,1,'int16');

for i = 1:Num_meas
ATT_Time(i,:) = fread(fid,2,'int32');
end
for i = 1:Num_meas
ATT_Pitch(i,:) = fread(fid,1,'int32');
end
for i = 1:Num_meas
ATT_Roll(i,:) = fread(fid,1,'int32');
end
for i = 1:Num_meas
ATT_Heave(i,:) = fread(fid,4,'char');
end
for i = 1:Num_meas
ATT_Heading(i,:) = fread(fid,4,'char');
end

This returned all sorts of funky data that made no sense, most notably the negative times and pitch angles of 120 degrees (that would be worse than the perfect storm!). I decided to look at the GSF library also available on the SAIC website in order to check out the source code. In the library directory, there is a file called GSF_dec.c, a C-code source file for decoding the GSF binary format. I looked up how the Attitude record was decoded in C, and saw this:


gsfDecodeAttitude(gsfAttitude *attitude, GSF_FILE_TABLE *ft, unsigned char *sptr)
{
unsigned char  *p = sptr;
gsfuLong        ltemp;
gsfuShort       stemp;
gsfsShort       signed_short;
int             i;
struct timespec basetime;
double          time_offset;

/* First four byte integer contains the observation time seconds */
memcpy(&ltemp, p, 4);
p += 4;
basetime.tv_sec = ntohl(ltemp);

/* Next four byte integer contains the observation time nanoseconds */
memcpy(&ltemp, p, 4);
p += 4;
basetime.tv_nsec = ntohl(ltemp);

/* Next two byte integer contains the number of measurements in the record */
memcpy(&stemp, p, 2);
p += 2;
attitude->num_measurements = ntohs(stemp);

>and a little farther down I saw:


/* Now loop to decode the attitude measurements */
for (i = 0; i <>num_measurements; i++)
{
/* Next two byte integer contains the time offset */
memcpy(&stemp, p, 2);
time_offset = ((double) ntohs (stemp)) / 1000.0;
p += 2;

LocalAddTimes (&basetime, time_offset, &attitude->attitude_time[i]);

/* Next two byte integer contains the pitch */
memcpy(&stemp, p, 2);
signed_short = (signed) ntohs(stemp);
attitude->pitch[i] = ((double) signed_short) / 100.0;
p += 2;

/* Next two byte integer contains the roll */
memcpy(&stemp, p, 2);
signed_short = (signed) ntohs(stemp);
attitude->roll[i] = ((double) signed_short) / 100.0;
p += 2;

/* Next two byte integer contains the heave */
memcpy(&stemp, p, 2);
signed_short = (signed) ntohs(stemp);
attitude->heave[i] = ((double) signed_short) / 100.0;
p += 2;

/* Next two byte integer contains the heading */
memcpy(&stemp, p, 2);
attitude->heading[i] = ((double) ntohs(stemp)) / 100.0;
p += 2;

The C-code shows that the specification table was completely wrong! There is only one reference time for the attitude reading, and the rest of the times are simply how many seconds past that reference time the rest of the measurements take place. Furthermore, the specifications stated that the Heave and Heading fields were text (something I thought was weird anyway) and in the C-code we clearly see they are integers. The specification also stated everything was 4-bytes, but it is actually only 2 (16 bits). This is very frustrating that the specification and the C-code do not match, especially since they both come from the same source.

At any rate, I am now able to write a working function that can be called in my main code:

function [ATT_Time, Num_meas, ATT_Offset, ATT_Pitch, ATT_Roll, ATT_Heave, ATT_Heading] = readATTrecord(fid)
%% This function reads the Attitude record in a GSF file.

%% Element          Bytes   Type         Description
% ATT_Time            2*4    int      time of attitude meas.
% Num_Measurements    2      int      number of attitude measurements (N)
% Time_Offset         N*2    int      time offset in seconds
% Pitch               N*2    int      array of pitch measurements (hundreths of deg)
% Roll                N*2    int      array of roll measurements (hundreths of deg)
% Heave               N*2    int      array of heave measurements (hundreths of deg)
% Heading             N*2    unit     array of heading measurements (hundreths of deg)

ATT_Time = fread(fid,2,'int32');
Num_meas = fread(fid,1,'int16');

for i = 1:Num_meas
ATT_Offset(i,:) = fread(fid,1,'int16');
end
for i = 1:Num_meas
ATT_Pitch(i,:) = fread(fid,1,'int16');
end
for i = 1:Num_meas
ATT_Roll(i,:) = fread(fid,1,'int16');
end
for i = 1:Num_meas
ATT_Heave(i,:) = fread(fid,1,'int16');
end
for i = 1:Num_meas
ATT_Heading(i,:) = fread(fid,1,'uint16');
end

Mobile Blog Photo Test

2009-08-02T20:57:00.002-04:00

I wanted to test Google's mobile blogging with a photo, so here is a
pic I snapped with my phone of a weird bug on my porch.

Mobile Blogging

2009-08-02T20:51:00.003-04:00

So google blogger lets users blog on the go in a couple different ways. You can use SMS messaging (standard text messages), MMS messaging (multimedia messaging), or your email. Since I do not have a text plan, I opted for the latter. You set up an email address for your blog (under your existing blog's settings) and then just email your posts. You can select to have mobile posts immediately published or saved as drafts.

So here is my first post sent from my phone. I can also see this as a great way to blog from sea, when you often have email access but not full web capabilities.

Importing Music into GarageBand and Making Ringtones

2009-08-02T15:36:00.004-04:00

Okay, so I do not know about you, but I was somewhat annoyed to find out that not only will iTunes only let you create a ringtone from music you purchase from the iTunes Store, but that they still charge you an additional 99 cents to convert the song sample into ringtone format.
Total rip-off! Especially considering you already own the song!

Here's a free workaround: Kurt suggested that I try GarageBand, a music creation software that comes free with the Mac. It took a little futzing around, but I have now successfully (and freely) created a ringtone from Michael Jackson's The Way You Make Me Feel.

Here are the steps:

1) Open GarageBand and then drag-n-drop your music file (.mp3 works for sure, not sure about AAC) in it. The file should open right up as long as it is not DRM, so no purchases music from iTunes (though supposedly if you burn them to disc and then re-import, it loses the DRM)

2) Click on the scissors icon on the bottom left to bring up the track editor, and from there, click on the loop arrow icon to enable the loop feature. GarageBand ringtones are limited to loops of 40 seconds or less.

3) You should now see a second time bar appear just below the first at the top of the window (click the screen grab below to see what I am talking about). Just click and drag within the bar to select a portion of the song. The time bar will turn yellow where you select.

4) Just hit play to preview your selection. GarageBand will continuously loop through the selection, so you can get a pretty good idea of how your ringtone will sound.

5) Once you are happy with your selection, click on Share in the Menu Bar and select Send Ringtone to iTunes. It will convert the song for you and automatically open iTunes, where your song is stored in a new Ringtones folder. Now all you have to do is transfer it to your device.

A Bookstore and Free WiFi: Like Peanut Butter and Chocolate!

2009-07-31T06:31:00.002-04:00

It's finally happened. Barnes and Nobles is now offering free WiFi in all their stores.

http://www.barnesandnoble.com/help/cds2.asp?r=1&PID=27206

One of my favorite combinations (outside peanut butter and chocolate) is a good bookstore (avec cafe) and free wifi.

USGS Woods Hole: An Excellent Metadata Example!

2009-07-21T13:48:00.008-04:00

Over the last couple years or so, I have become more and more concerned about metadata. Metadata is basically a file (txt, html, or xml) that accompanies a dataset and describes how, why, and when the data were collected, how they were processed, and who the primary contacts are. It can get more complicated, and there is also the matter of formats and whether or not it is compliant with the FGDC (Federal Geographic Data Committee) standards, but suffice to say the role of metadata is to give anyone reading it sufficient knowledge to be able to confidently use the data.

Good metadata is hard to find, and people routinely seem to underestimate its importance. Even if people do fill out metadata, they often skip a lot of important fields or simply do not include all the pertinent information (e.g. the tide station used to correct their data). What good is a multibeam dataset, for example, if I do not know how it was collected, if/how they corrected for tides and vessel motion, how they processed it, etc.? Oh sure, maybe you know what organization collected it, but what if they cannot remember? What if the main person responsible for that data no longer works there? A proper metadata file that accompanies the data will solve these issues.

Today I came across what I consider to be perhaps one of the best examples of metadata that I have seen. The metadata is for a multibeam dataset collected by the USGS in Woods Hole. All the pertinent fields are filled out, and for each section there is a point of contact listed. The reasons for the survey are given, as are the vessel used, the sonar used, how the sonar was mounted, etc. Not only did they specifically mention how they measured their vertical/horizontal accuracy and include an estimated uncertainty, but they include their tidal station information complete with NOAA tide station number so I can easily go and obtain the same tide record myself. What is most impressive, however, is that they list all their processing steps. They processed their data using SwathEd, a program developed at UNB that I am not familiar with. No problem though, because in the metadata, they actually give a numbered list of their processing steps complete with the command lines needed to do it myself! It is even broken up into editing that was done at sea, and the final editing steps undertaken to create the grids once they were back in the office.

Of course, no matter how good the metadata are, there is always room for some improvement. For example, it would be nice to see a separate ancillary data section perhaps, that lists the specific type and brand of IMU used, the type of CTD or sound velocimeter used, etc., along with manufacturer-stated (or observed) uncertainties.

Check out the USGS metadata, and of course the accompanying data, here: USGS Stellwagen Bank data. The data and metadata are all located under the GIS data links. The specific file I was looking at is here.

Here are some snippets of the metadata file to give you an idea (Note there are chunks of metadata skipped between snippets):

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report: No attributes are associated with these data.

Completeness_Report:

These data were corrected for tidal elevation using the NOAA Boston tide gage. This assumes that the tidal elevation and phase are the same as Boston across the survey area. Further processing to correct for the spatial and temporal changes in tidal elevation across the survey area may be undertaken at a later time.

Positional_Accuracy:

Horizontal_Positional_Accuracy:

Horizontal_Positional_Accuracy_Report:: These data were navigated with a Differential Global Positioning System (DGPS); they are accurate to +/- 3 meters, horizontally.

Vertical_Positional_Accuracy:

Vertical_Positional_Accuracy_Report:: These data have been corrected for vessel motion (roll, pitch, heave, yaw) and tidal offsets, and referenced to mean lower low water. The theoretical vertical resolution of the Simrad EM-1000 multibeam echosounder is 1 % of water depth, approximately 0.3 - 1.0 m within the study area.

____________________________________________________

Process_Step:

Process_Description:: Data acquisition at sea
These multibeam data were collected with a Simrad EM1000 multibeam echo sounder mounted on the starboard pontoon of the Canadian Hydrographic Service Vessel Frederick G. Creed. The data were collected over four cruises carried out between the fall of 1994 and fall of 1998. Operation of the Simrad EM1000 was carried out by hydrographers of the Canadian Hydrographic Service. Data were collected along tracklines spaced 5-7 times the water depth apart at a speed of 10-14 knots. The frequency of the sonar was 95kHz. Sound velocity profiles were obtained and input into the Simrad processing system to correct for refraction. Navigation was by means of differential GPS.

____________________________________________________

Process_Step:

Process_Description:: Final data processing and editing
Processing was carried out to further edit and correct the data and to produce final grids and images of the data. Processing and editing steps included:
1. Correct errors in soundings due to sound refraction, caused by variations in sound velocity profile, using the SwathEd refraction tool. These artifacts can be recognized in a cross-swath profile of a relatively flat patch of sea floor. When viewing the swath data across a profile, the sea floor will appear to have a "frown" or "smile" when in fact the data should be flat across the profile. Insufficient and/or erroneous sound velocity information, which is usually due to widely spaced or non-existent velocity profiles within an area, results in an under or over-estimate of water depth which increases with distance from the center of the swath. For a discussion of how this effect can be recognized in a swath bathymetric data file, see < >.
2. Remove erroneous soundings that were not edited in the field using the SwathEd program.
3. Correct the bathymetric data to mean lower low water by subtracting the observed tide at Boston, Massachusetts from the edited bathymetric soundings. This correction assumes that the tidal phase and amplitude are the same as Boston across the survey area.
Mean Lower Low Water (MLLW) tidal information was obtained from the NOAA tide server using tide station 8443970 located at Boston, MA (42 degrees 21.3 minutes N, 71 degrees 3.1 minutes W) (). The binary tide file used in the command line below was generated by reformatting the 6 minute tidal information from the NOAA site into a text file that contains Julian Day (DDD) , time (HH MM), and water level height(H.HH) in this format: DDD HH MM SS H.HH. This file was then converted to a binary tide file with:
Command line: binTide -year YYYY asciiTideFile BinaryTideFile
The program mergeTide brings the swath soundings to the MLLW vertical tidal datum:
Command line (tides): mergeTide -tide BinaryTideFile filename.merged Command line (navigation): mergeNav -ahead 5.379 -right 3.851 -below 4.244 filename (prefix only)
4. Create a 6-m grid of the bathymetric soundings for western Massachusetts Bay Quadrangles using the SwathEd routine weigh_grid.
Command line: weigh_grid -fresh_start -omg -tide -coeffs -mindep -2 -maxdep -800 -beam_mask -beam_weight -custom_weight EM1000_Weights -butter -power 2 -cutoff 12 -lambda 3 gridFile filename.merged
5. Convert binary bathymetric grid to ESRI ASCII raster format:
Command line: r4toASCII gridFile.r4
This creates a file called gridFile.asc.

Image Processing in Matlab: Update 1: Filters

2009-07-16T15:21:00.010-04:00

Okay, so I have been continuing to play around, trying to get my feet wet with image processing. I sort of jumped ahead here and begin fiddling with filters. Since I have the nadir artifact in my mosaic, I need to see if I can easily remove it.
I decided to use an adaptive filter since the noise I am most concerned is repetitive through the image (though not truly periodic as survey line spacing varies), so I do not need the same level of filtering over the whole image. I have been reading through the Matlab Image Processing documentation(pdf), and followed their directions for using "wiener2" which adaptively applies a Wiener linear filter to the image.

from the description under "help wiener2":

WIENER2 lowpass filters an intensity image that has been degraded by
constant power additive noise. WIENER2 uses a pixel-wise adaptive Wiener
method based on statistics estimated from a local neighborhood of each
pixel.

I used a 10x10 pixel neighborhood for filtering. Then, I ran the Sobel edge detect algorithm as described in my previous post. The results are below:

on the left: orginal image on the right: wiener2 filtered image. Click to see full-size image so you can see the differences.

The nadir artifacts are clearly less noticeable in the filtered image, and indeed the edge detect algorithm is now starting to pick up on the actual different patches of seafloor. The outline of the bright patch in the middle can now be seen.

I then increased the size of my filter to 20x20 pixels. Check out how well the edge detect performs now.

Beginning Image Processing in Matlab

2009-07-16T13:58:00.009-04:00

I am starting to explore image processing in Matlab, and so far I am impressed with how easy it seems. I began with a 2000 x 2000 pixel gray scale image of a backscatter mosaic from EM3002 multibeam sonar data. I saved this image as a .tif and loaded it into Matlab using the 'imread' function. Once loaded, using "imshow" will display the image.

One of the first things I tried was the histogram function "imhist", to see how spread out my pixel values were between 0 - 255. Clearly my image does not make use of the full range of colors. I then used "histeq" to stretch the intensity values between the full range of colors. Below are the resulting histogram and new higher contrast image.You can clearly see the artifacts from the nadir beam of the sonar where you get a brighter return. I figured this would be a good test of one of the edge detect algorithms to see if it picks them all out. I used the "edge" command and specified the Sobel method, leaving the threshold value blank. You can also specify a direction, however, I left it as the default, which looks for both horizontal and vertical edges. Here are the results:
Pretty cool. It almost looks like a trackline map of the survey!

Daylilies in full bloom

2009-07-04T11:13:00.004-04:00

After an exhausting roadtrip from KY back to NH, it was nice to come home and see the Daylilies in full bloom.

Blogger likes to resample the color scheme when it resizes the image to fit inside the blog post, so if you want to see the lilies in all their glory, be sure to click on the pic to see it full size:

iPhone as a tool for hydrographers

2009-06-25T00:08:00.005-04:00

So from Kurt's post on the iPhone as a tool for field geologists, and the subsequent posts he linked to, I began thinking about applications that I would like to see on an iPhone (not that I own one or anything) to help make it a handy little field tool for hydrographers. There are some pretty sweet hydro-licious applications for the iPhone that already exist (check out TideApp and iNavX), and I am sure this is only the beginning. Here are a couple of proposed apps of my own:

1) Equipment/Serial Number App:
Something like this may exist. It would be handy to have a little app that could organize lists of equipment and their serial numbers. Each entry could link to a picture of the object stored within the iPhone. Clicking on each entry would then bring up the picture, manufacturer, contact info for service/repair, a link to the website, and perhaps even a link to the online manual (or a PDF stored on the phone).

2) Ship Light App:
I am not sure if the flashlight app has this feature already or not, but having the screen emit a red light for night-safe vision on the ship instead of a bright white light would be excellent.

3) Vessel Offset App:
An app that could be used to generate a little diagram of the ship complete with vessel offsets between the transducers, IMU, etc. Perhaps it could sort of be a fill-in-the-blank type of program, so you know right away if you are missing a crucial value. This happened during my field course, and while I am sure seasoned hydrographers have much less of a chance of making this mistake, and if you always survey on the same ship it is probably not as necessary, I still think this would be pretty helpful. With this app, you could always have a copy with you that could be used for reference or could be emailed to someone else.

M&M Mars: Free Chocolate Relief Act!

2009-06-11T16:22:00.002-04:00

Tired of everyone getting stimulus packages but you? Well, M&M Mars is helping out by giving away free full-size chocolate bars every Friday through September. All you have to do is sign up every Friday morning, and within a couple weeks you will get a coupon for a free candy bar in the mail.

Check it out: https://secure.realchocolate.com/

Fugro to buy Tenix LADS

2009-06-08T08:46:00.003-04:00

Fugro, one of the world's leading survey companies both on- and offshore, looks like they are about to acquire the Australian-based Tenix LADS Cooporation. Tenix LADS is one of the global providers of airborbe lidar bathymetry, and has completed many contracts under NOAA and the US Navy. Another one of Fugro's subsidies, Fugro Pelagos Inc., also conducts surveys for NOAA utilizing an Optech SHOALS-1000T lidar system.

Here is the full blurb at Hydro International: http://www.hydro-international.com/news/id3216-Fugro_Acquires_Tenix_LADS.html

Seafloor Images of Air France Crash Site Available

2009-06-04T13:25:00.003-04:00

CCOM/JHC has been putting together seafloor images to help aid in the search for Air France Flight 447

http://www.unh.edu/news/cj_nr/2009/june/bp4seafloor.cfm

The Exploration of Challenger Deep

2009-06-04T10:04:00.004-04:00

Man, I cannot even imagine the excitement and anticipation the scientists on this project must feel!!

Point Loma scientists on team taking vehicle to the deepest place on Earth

Posted using ShareThis

Easy Tables in TexShop on a Mac

2009-05-29T19:11:00.004-04:00

Okay, so while Excel2Latex works great on my PC at school, it does not work so hot on my Mac running Excel 2004. TexShop was not happy with the output code at all. I tried some tips I found online, but no luck. Then I came across:

Cal2LaTex for OpenOffice and NeoOffice. This tool works like a charm and its menu options are superior to that of Excel2Latex. It did take me a few minutes to figure out how to assign the Macro its own listing under my Tools menubar, but other than that getting it working was a breeze.

And let's face it, on a Mac at least, NeoOffice seems to run better than MS Office anyway. Of course, since I discovered LaTex I generally only ever open Word when I have to open someone else's document. :)

Tables in LaTex Made Easy!

2009-05-29T11:49:00.006-04:00

Tables in Latex can be rather tricky, and I wanted to find some way of creating a table quickly that would look good. In Googling around, I stumbled across Excel2Latex. This little macros tool will add a toolbar button that will allow you to export directly from a table you have formatted in Excel (Mac or PC versions) into a piece of Latex code that can be pasted into you Tex document. Once in Tex, you can add some snazzy formatting (like lines, etc.) and you are all set. Excel2Latex will even convert all font formatting (bold, italic, etc.) for you.

Check out the results (I used /hline to add some lines to the original exported code):

Note: I did have some troubles running the macros at first. I kept getting: "Error: Can't find project or library."

The Solution: Open your VBA editor in Excel (from Excel hit alt+F11) and then go to Tools -> References. Scroll down until you see the reference labeled MISSING and simply uncheck it.
The tool should now work.

Seamless land/sea mapping with Lidar

2009-05-25T22:05:00.006-04:00

I am currently working up some Tenix LADS MKII lidar data over the Isles of Shoals off the coast of New Hampshire. I must say, the data set is quite impressive. Not only does the lidar bathymetry match very well with EM3002 multibeam bathymetry we have in the same area (initial comparison shows a mean difference of 0.6 m w/ a std: 0.3 m), but the seamless transition of the lidar data from water to land follows very closely the transition between the foreshore and the water (soundings are reduced to MLLW).

Here you can see the transition from depth soundings (blue) to terrain heights (brown) from the LADS lidar system. The flightlines are oriented north-northeast by south-southwest. NOAA chart 13283 is peeking out from behind the soundings. You can just see how the transition in sounding type roughly follows the foreshore line (MLLW) on the chart.

What does the bathymetry from the LADS MKII lidar look like? Here's a peak of some of the lidar bathy data (blue soundings only) gridded at a 4-meter resolution and displayed in Fledermaus. Sun illumination is from the northwest and the vertical exaggeration is 3. NOAA chart 13283 is in the background.

LIDAR view of the Golden Gate Bridge

2009-05-08T10:58:00.004-04:00

The Seafloor Mapping Lab at the California State University in Monterey Bay has recently obtained a new vessel-mounted Lidar system for shoreline surveys. From their website:

The high-resolution data set seen above was collected using SFML's new vessel-mounted mobile marine LIDAR system. Working with our industry partners, Riegl and Applanix, we have implemented an easily and rapidly deployable laser scanner capable of achieving decimeter accuracy with sub-meter resolution at a 1 kilometer range. This system gives SFML the ability to map the intertidal shoreline, offshore rocks and pinnacles and coastal features in unprecedented detail without the need for more costly airborne LIDAR surveys. The high spatial precision and accuracy of the system enable SFML to reliably monitor and quantify coastal erosion and landslide rates, bridge deformation, railway subsidence and coastal highway slippage through repetitive shoreline mapping surveys; information critical to coastal communities as they plan for climate change and sea level rise.

Integration of this technology with their existing mapping systems allows for some pretty impressive data displays:

Combined bathy/topo DEM of the Golden Gate built by merging SFML's laser scanner (gray) and multibeam sonar (colored by depth) data (source: http://seafloor.csumb.edu/laserscanner.html)

They also have some pretty sweet 3D fly-throughs of the Golden Gate Bridge and the Los Padres Reservoir. I have included their Golden Gate Bridge fly-through below:

How to Brew Beer Onboard an Oceanographic Vessel

2009-04-28T15:25:00.003-04:00

My friend Maria just sent this my way and I thought I would pass it on. I have definitely seen a lot "mystery cups" while I have been at sea, and even some pretty efficient smuggling techniques, but I have never seen this:

Southern Fried Science: How to brew beer in a coffee maker, using only materials commonly found on a modestly sized oceanographic research vessel.

Fire Safety Training

2009-04-28T13:45:00.004-04:00

Today in my Seamanship class, we had something I believe everyone should have at some point in their lives: fire safety training. No, I don't mean like when you were a kid and the fire department came to your elementary school and you got to climb on the truck. I mean actual here-is-a-fire-and-a-fire-extinguisher-now-go-to-town type of fire training. The video we watched beforehand was, admittedly, rather cheesy and may have dated back to the early 90s; however, the information was still good. Then we had some hands-on experience. One of the fire inspectors from the Durham Fire Station and the main inspector for UNH came by and actually set some fires. They set the fire in a water tank using a propane hose and showed us all how to use different types of extinguishers. You can't simply call the fire department on a ship, so in most cases, if you are on a ship, you are a fireman. A lot of bigger vessels have their own specially trained crew that run through drills and exercises, but that does not mean that us scientists are off the hook, especially if we are the first to notice the problem. That is why training like this, along with proper first aid/first responder training is so important.

Below are some pictures from today:

setting the fire

me, extinguishing the blaze

take that, fire!

Right Whales and Healy Now in Google Earth

2009-04-27T17:14:00.004-04:00

Kurt Schwehr, a research professor here at CCOM, has been doing a lot of Google Earth visualizations lately and his work is definitely getting noticed. Last year, Kurt was invited to Google to give a Google Tech Talk, and even more recently the folks over at Google asked Kurt to pick one of his visualizations to be highlighted in Google Earth's own blog and added to the extensive list of downloadable visualizations that anyone with the free Google Earth browser can view. Kurt picked his right whale one, which shows North Atlantic right whale sightings for 2009. The Google Earth blog also mentions Kurt's Healy visualization, which tracks the USCG's icebreaker Healy as she makes her way around the Arctic. The positions are updated every hour, along with a new photo captured from Healy's aloftconn camera.
It is really cool to see the kind of data that can be viewed in Google Earth. Not only does GE provide a free way to view geo-referenced data, it does so relatively easily. That is key. Even if you have a GIS software, getting some nice chart images, or world maps or images, properly referenced behind your data is not always a straightforward task. In Google Earth, the spatial context is already there, in the form of an interactive, easy-to-manipulate globe.

Here is a screen shot of Kurt's right whale visualization in Google Earth:

Zotero 1.5b: Sync multiple computers and more!

2009-04-22T10:43:00.005-04:00

New version of Zotero is now available (though still in Beta form). Version 1.5b2 allows you to back up your library for free on Zotero's server, and thus sync your libraries across multiple computers. Another neat feature is that you can add a PDF to your library and ask Zotero to go and find all the reference information for you! It will capture part of the text and search Google Scholar (other databases to be added soon); if it finds a matching entry, it fills out all the metadata for you (author, journal, etc.) So far I have only actually gotten this to work a couple times (even when I pulled the articles directly from Google Scholar), but this is still a beta version after all. I am sure the main dependency for it working is where the data is found; journal webpage versus someone' s CV publication listing, for example. At any rate, when the journal can be found, it is quite a time saver!

Be sure to check out the new version. Below is a screen grab showing my local library and my library stored on Zotero.org.

CCOM Cover Girl!

2009-04-22T08:07:00.004-04:00

The 2008 CCOM Annual Report recently came out, detailing all the activities and research that have been going on at the center during the last year. Yours truly even made the cover! The picture was taken while I was on Healy and I am pointing something out to the other scientists on the screen displaying the real-time multibeam data.

CCOM and Healy make National Geographic!

2009-04-20T15:07:00.004-04:00

The Center for Coastal and Ocean Mapping, and all the mapping it has been doing aboard the USCGC Healy, has made this month's National Geographic Magazine!

here is the link:
http://ngm.nationalgeographic.com/2009/05/healy/funk-text

I like that they go into detail about the Russians planting the flag, rather than just go off the handle and imply that there was a rushed American response and not check their sources for any of it (ahem! *cough* Discover Magazine *cough*). They actually interviewed Larry Mayer and got the story straight.

Here is the accompanying map, provided by Larry Mayer. It even includes that data I helped collect on the cruise this past autumn!

Modeling Grating Lobes in Matlab

2009-04-08T11:30:00.006-04:00

For a project for my underwater acoustics class, I am modeling acoustic pressure amplitudes and beam patterns in Matlab. The project involves a continuous line array that we are discretizing in order to calculate the contributing pressure of each point on the array to some arbitrary field point at range r. Basically we are breaking up the line source into n number of elements. When you do this, the spacing of your elements becomes an important factor. If your spacing is equal to, or greater than, one wavelength, you end up with grating lobes. Grating lobes have the same pressure amplitude as your main lobe, but they occur off-nadir and get progressively wider. Each grating lobe has its own associated side lobes.

Below are two examples of what I am talking about. In the first figure, I spaced my elements at a distance equal to 1 wavelength of the transducer. In the second figure, the spacing is 2 wavelengths. In both figures, the main lobe is centered on zero degrees, and you can see that the first side lobe occurs at -13.3 dB. In the first figure the grating lobes start at 90 degrees, and in the second they start at 30. In both cases, the side lobes of the grating lobes also start at -13.3 dB.

Lidar is going mainstream (MTV baby!)

2009-03-24T13:36:00.004-04:00

My friend Christiana pointed me to the new Radiohead video that used lidar technology to create various 3D models of people and terrain . The whole video is simply a composite of these data. It all appears to be terrestrial lidar, but it is still pretty sweet!

How to create an outline of your data in ArcMap

2009-03-23T14:13:00.007-04:00

Recently I had some XYZ data gridded up in ArcMap, and I wanted to create a simple outline of it. I could not, for the life of me, figure out how to do it, save digitizing the entire thing myself. Luckily, someone showed me a very valuable trick, and I now know there is a quick way to do it, though this method is by no means straight forward:

create a raster of your data. Whether you chose natural neighbors, an IDW grid, whatever, does not matter. Any resolution that will not exaggerate you data coverage will work.
use raster calculator to convert this grid to an integer grid. You can use Raster Calculator under the Spatial Analyst tool and simply multiply your grid by 0. You need to put your expression between parentheses, with an "int" in front. For example: [mb_int_grid] = int([mb_grid] * 0)
Also under Spatial Analyst, use the Convert Raster to Features to convert your integer grid to a polygon.
You can now alter your polygon symbology to give you a nice outline.

Below you can see my original gridded data and the resulting outline.

Udel AUV in Second Life

2009-03-14T23:01:00.006-04:00

Art Trembanis gave a great seminar yesterday about some of the AUV development and research going on at the University of Delaware. He mentioned that UDel had actually set up some property in Second Life, and that users could come and check out the new Gavia-class AUV that will soon be undergoing sea trials. I decided to join Second Life myself (membership is free) and check out what UDel had to offer. Below are two screen grabs where you can see me checking out the AUV as well as UDel's research vessel.

Modeling a Lidar System: Part 1

2009-03-08T16:54:00.008-04:00

Now that I am really starting to get into my research with lidar systems, I feel that it is important to understand as many of the intricacies and nuances of the system as possible, and how they interact with each other. Although I am certainly learning a lot from reading countless articles and texts, and having great directed study sessions with my chairs, I feel one of the best ways to learn is through a more experiential approach. Since I do not have full-fledged lidar system at my disposal to fly around with and image things (anyone offering?), I figure the next best thing I can do is theoretically model the system.

To get myself started, I found a paper by H. Michael Tulldahl and K. Ove Steinvall entitled: "Analytical waveform generation from small objects in lidar bathymetry," (App. Optics, v.38 n.6, 1999). The authors present a model to simulate received lidar waveforms in order to observe the influence of variously-shaped objects on the seabed. I am tweaking the modeled system parameters to match those of the systems I am working with, as well as the water-dependent parameters to match different water types. I am also not dealing with any objects on the seabed, and for now am assuming a flat bottom. I have only just started, so my model is nowhere near complete. Although this model is not the primary focus of my research, I see it as a way to help me understand not only what I am seeing in the data, but also predict features in the data that I might look for. Eventually I would like to have a user interface where I could simply select the lidar system and approximate water type (most likely based off Jerlov), and perhaps bed type and approximate roughness, and just hit "go!"

The model is currently in Matlab, though as it develops I may switch to a more object-oriented scripting language such as Python (I can hear Kurt applauding from here). The point is, models (and the more specifically, the development of models) can be a powerful learning tool. I wish that modeling itself (or at least an introduction to modeling) was taught as more of a core research tool, opposed to a special one.

Below is a snippet of some of the model output as it now stands. The top graph shows the volume backscattered power reaching the receiver. The middle graph shows the amount of power incident on the seabed (one-way travel), and the bottom graph shows the percentage of transmitted power returned to the receiver, all as a function of depth. In this case, the off-nadir angle of the laser is 0 degrees and I am looking only at the nadir beam. I am assuming pure seawater (just to make my initial attempts a little easier) and treating the water surface return of the green wavelength and the atmospheric loss as negligible.

Sun Illumination in 3D Imagery: why 2 views are better than 1

2009-03-05T10:03:00.006-05:00

Sun illumination is one of the key concepts in 3D imagery. Depending what illumination angle you chose, certain features will either be highlighted or muted. Bad data can often be made to look good, and good data can certainly be made to look bad. One popular convention (or at least one I heard a lot back when I first started doing all this) is to simply illuminate everything from the northeast (45°). Another is to illuminate perpendicular to the features you wish to highlight. Recently, it has become common to provide two different images or scenes with two opposing sun illumination angles, so that the end-users can get a better sense of the data quality. I was thinking about all this this morning as I was working with some lidar data. Below are two 3D images of some lidar data I am working with rendered in Fledermaus. All the input parameters for the sun illumination were kept exactly the same, and only the illumination angle was changed. In the first image, the data is illuminated from the northeast (45°), while in the second, the data is illuminated from the southwest (225°). Note the dramatic differences.

At 45°, the imagery looks quite nice and the rocky areas are clearly delineated.

At 225°, the imagery still looks nice, but now you can also see linear NE-SW trending features in the data. These features could be real, or they could be artifacts in the data. Either way, if I had only rendered the data at 45°, I never would have seen them.

Here is a side-by-side comparison of the two illuminations:

Now that I have seen the linear features in the second view (225°), I can just start to make them out in the first one (45°), but they are still hard to see. By looking at different illumination angles, I can really start to get an idea of features and trends in the data, as well as any artifacts.

ClamAV: Easy Antivirus on the Mac

2009-03-04T10:26:00.003-05:00

We all know Macs are less susceptible to malware and viruses, but that does not mean it isn't good to check your system from time to time. I go back-and-forth between my Mac and my Windows machine at school all the time. Even if my Mac is safe, I do not want to potentially carry something over to my Windows machine and vice-versa. Also, given that I have recently discovered the Vuze BitTorrent client, I like to know that the files I have grabbed are safe.

ClamAV is a UNIX-based open-source anti-virus client, particularly designed (but not limited to) email scanning. I installed it via fink and run it via command line. It is really easy to scan individual files, directories, or your whole machine this way. I recently did a scan of my whole home directory, and true to its speciality, it detected two potential problems, both email phishing attempts (for some reason, our school servers get tons of email from people asking for help with 10 million dollar deposits):

Happy Square Root Day!

2009-03-03T19:36:00.002-05:00

Just came across this and found it humorous:

http://en.wikipedia.org/wiki/Square_Root_Day

Of course, now I have missed my chance to take a Square Root Day holiday until 9/9/2081.

LaTeXiT: LaTeX equations without the fuss

2009-02-25T21:24:00.007-05:00

It did not take much for me to be sold on the idea that LaTeX typesets equations better than OpenOffice or MS Office. In a recent project I typed up in MS Word for my acoustics class, every time I made phi lowercase in one of my equations, it messed up the entire equation format. Why? It makes no sense. I tried NeoOffice, but finding the necessary symbols in its equation editor is a headache all on its own. Then I saw my friend Brian show how well LaTeX can generate equations. But what if you do not want to bother creating a whole LaTeX document? What if you just want a little equation or two?

Enter LaTexIt. This little tool lets you create LaTeX quality equations that can be saved in various formats (PDF, TIFF, etc.) and dropped into any number of programs, such as Word, Powerpoint, etc. It is great if you just want to make a quick equation without having to do a complete LaTex file creation.

Sorry Windows users, this one is Mac only, though I am sure there is a Windows equivalent.

Here is the program up and running, with an example of an equation I just typed:

Excellent FREE book on subversion

2009-02-24T22:44:00.002-05:00

The O'Reilly book on Subversion Control by Ben Collins-Sussman, Brian W. Fitzpatrick, and C. Michael Pilato is available for free online. This is probably old news, but for a new user like me, this is great!

Find the book here (note there are different versions): http://svnbook.red-bean.com/

MacGyvering a sonar with a car battery

2009-02-16T18:26:00.003-05:00

Did the power supply for your Simrad 710 sonar die? No problem, simply hook it up to a car battery. Apparently this is what happened during leg 1 of the cruise I am on. I boarded the R/V Pelican yesterday for a week long research cruise off the Florida panhandle, and the Simrad EM710 sonar's power supply was a simple car battery. We surveyed with this all day today, but are now back in port waiting for a FedEx delivery containing the new, proper, power supply. I must say, that was some impressive MacGyvering!

Once again, Sprint Customer Service proves they suck

2009-02-14T12:46:00.004-05:00

I just received my Sprint bill and noticed an erroneous charge. There was a 90 cent fee for trying to check my voicemail on January 27. Their bill code claims that not only was I over my minutes, but that I was also out of network. I looked at the bill and realized I was actually 50 minutes under my limit still at the time of the call and I also had free roaming included in my plan. Of course, I should also mention that I have not traveled in the last month, so that is a moot point anyway. I decided to call them, because even though the charge was only about a buck, I was curious about how they got it wrong. I spent nearly 20 minutes on the phone and the guy helping me kept saying I was over my minutes. I asked him that if that were the case, why my other calls that day and the next were not charged. I also pointed out that the according the bill, I did not actually reach my maximum minutes until a couple days later. He just kept saying nights and weekends are free. Nights start at 7 pm, and Tuesday is not a weekend day. I tried explaining this to him, but he kept repeating that the reason my other calls were fine was due to nights and weekends. Nevermind the fact the other calls were before 7 pm and were mid-week (Tuesday through Thursday). I ended up completely frustrated, and just told him that I did not waste any more time with him explaining the order of the days of the week, not to mention simple math.

Honestly, Sprint is the worst phone company I have ever dealt with. When I first got the phone it came with a 50 dollar service credit (even said so on my receipt). It took three months and three phone calls for them to honor it, and one guy actually accused me of making it up because he could not find the promotional code in his computer. When I told him I still had the receipt and that my next call would be to the better business bureau if he did not fix the issue immediately, he finally transferred me to someone who issued the credit.

I was warned Sprint had the worst customer service and I believe it to be true. Unfortunately, where I live, only Sprint gets service. Everywhere else in NH seems fine, but Newmarket seems to be a black hole. I cannot wait to get rid of my Sprint phone for good!

The Arctic, Healy, and Larry Mayer featured on NYT blog

2009-01-28T10:50:00.002-05:00

Today's New York Times Dot Earth blog features a post about the current battle over the Arctic. The video not only shows the Healy, but also interview snippets with Larry Mayer, co-director of the Center for Coastal and Ocean Mapping at UNH and one of the chairs of my PhD committee.

Read the post and see the video here.

Converting Arc/Info 5 and 6 to e00 for use with ArcMap

2009-01-18T22:57:00.002-05:00

Tonight I was helping Kurt convert some of his old Arc/Info version 5 and 6 files into .e00 files so that he could actually read them. It took some hunting around, but I finally found a handy little open-source tool that did it for me. AVCE00 is written in C, and the website has a pre-compiled version that will run on a Windows command line. I think Kurt may have plans to add it to fink so it can easily be used on a Mac as well. Remember, if you want to be able to view the data in ArcMAP 9.x, you can use the import71 tool located in C:Program Files/ArcGIS/Bin to convert the .e00 files into compatible coverages.

Website, anyone?

2009-01-18T14:13:00.006-05:00

UNH provides free website hosting for UNH students, faculty, and staff. There are no formatting constraints and you have 256 MB of space. I followed the directions provided by CIS for setting up my public_html directory (if they mention telnet or ftp however, use shh and sftp instead so your password stays encrypted). From my home directory, I then ran the command:

$ umask 022

which will automatically apply world readable permissions to all files that I add to my public_html directory. If you chose to use umask as well, be careful and double-check the results. You do not want to inadvertently open up secure documents to the world.

I decided to cheat on making my webpage (at least until I have more time), so I used the free iWeb program that came with my Mac. It is pretty simply to use, and while not truly WYSIWYG, it seems to work well enough. This webpage effort has also led me to finally start playing around with Photoshop, and as a result I was able to do some pretty nifty things with the images behind the text on my C.V. page. *Sigh* I think my dork factor just went up another notch.

Anyway, the webpage is still a work in progress, but you can check it out here.