Wednesday, December 31, 2008

Puppy vacu-sucked out of well!

As I sit here in front of the computer waiting for the ball to drop on MSNBC's live webcast (my poor, sick boyfriend snoozing on the couch), I have come across this video:

I am not sure which is better: that they actually had to vacu-suck the puppy out of the well or that the firefighter actually said "mouth-to-snout resuscitation."

Happy New Year!

MB-System 5.1.1 update in Fink

As Kurt points out in his lastest blog post, Fink now supports the latest beta version of MB-System (ver. 5.1.1). The OpenGL features now work, so not only can you view and manipulate 3D grids, but you can edit 3D swath data as well. Check out Kurt's blog for some sample grids to download and play with. The controls take some getting used, but once you get the hang of it, it is quite easy. If you want to use the 3D editor, you will need a grid as well as the associated swath files. I cannot wait to create some grids of my own and test out the editor after the New Year's. In the meantime, here is what the 3D grid viewer (mbgrdviz) looks like with one of Kurt's grids loaded and a profile taken:

Tuesday, December 30, 2008

Upgrading to X11 2.3.1 w/ some slight issues

Recently I updated my X11 environment to the open source version (2.3.1) provided by the xQuartz project. The x11 that shipped with my Mac with OS 10.5.6 did not seem to be happy and did not play well with Fink (lots of missing libraries, making certain Fink installs fail).

Upon install I noticed a couple of things:

1) Matlab would no longer start

For some reason after the X11 update, some of the links for required lib files during Matlab startup no longer worked. I searched online and found that if you start Matlab using the alias icon (the one with the up arrow on it in your Matlab directory, for me called Matlab Student 7.4 (also can be found at Matlab/bin/maci/StartMatlab)), the problem is somehow avoided. So I simply removed the original app icon from my dock and dropped the alias there instead. I still may submit a help ticket to Matlab though. I did try a reinstall and it did not solve the issue.

2) Fonts appear out of whack

When Matlab did finally start, the font was huge; I had to go into preferences and adjust it. After I reinstalled Matlab and got the registration window, the font was so big that letters were overlapping. I am not sure what is causing this, but adjusting the font under preferences seemed to do the trick.

3) Window resizing does not always seem to work right

In MB-System, sometimes the windows seem to cut off part of the text, making it hard to read. This happens in both mbedit and in the mbgrdviz control window. Resizing the window makes the grey bounding box bigger, but does not nothing to make the inner boxes around the text bigger. This could be an issue in MB-System itself and not X11, but that still remains to be determined. I know Kurt Schwehr, who packages MB-System for Fink (see his maintained Fink packages here), as well as the MB-System guys themselves, are hard at work with updates so if it is an issue on that end I am sure it will be worked out soon.

Monday, December 29, 2008

Asteroid Hitting Earth - set to Pink Floyd

Happy New Year! Here is a YouTube animation of an asteroid hitting the Earth. If you have the bandwidth and screen resolution for it, click the video to go to the YouTube site to view the high def version; it is really extraordinary.

Sunday, December 28, 2008

MB-System: free, open-source sonar data editing software!

Recently I decided that I wanted to learn MB-System so that I would have a familiarity with a free, open-source swath sonar data editing software. I like CARIS -I use it A LOT- but since I cannot afford a personal license, it is not something I can have installed on my personal computer. Furthermore, I am starting to hate being dependent on software that requires separate license keys. I was on a ship when a license file for the processing software became corrupt (or expired, not sure exactly what happened) and it was a rather frustrating situation; with no way to get a new license at sea, the IT guys had to resort to using a Norton Ghost image to reinstall everything on the machine. Anyway, now that I have my new macbook, I figured I would go ahead and give MB-System a try.

First I installed MB-System using Fink. If you have not heard of Fink, check it out here. It packages up open-source unix programs and compiles them to run on a mac. The only incompatibility as of now is that the MB-System grid viewer is not supported by Fink due to an issue with OpenGL and some differences in the naming conventions between the OS X 10.4 and 10.5 environments, but it is currently being worked on. Once I had fink installed and updated, I simply ran:

$ fink install mbsystem (for me, the dollar sign is my command prompt)

I decided to test out MB-System with a single data file from my summer hyd
rographic field course. First I ran mbinfo to get an idea of the scope of the data I was dealing with:

$ mbinfo -I 0162_20080616_161142_RVCS.all

This provides a neatly organized output that includes navigation info, start and end info (times, lat, long, depth, etc.), total number of pings, etc.

remember, you can click an image to see it full-size

Another good thing to check early on in your processing is the navigation, which can be done using mbnavlist:

$ mbnavlist -I 0162_22080616_161142_RVCS.all

This command can be modified to display different data, but by default it displays date and time, unix time (in decimal seconds), longitude, latitude, heading, and speed.

The next tool I ran was mbm_plot, so I could look at the line an see what it looked like:

$ mbm_plot -I 0162_20080616_161142_RVCS.all

this command generates a .cmd file that contains all the necessary com
mands to generate a postscript file and display it using ghostview. To run the command:

$ ./0162_20080616_161142_RVCS.all.cmd

Since I do not have ghostview, I get a small error message which I ignore and just run the open command to view it in Preview. The last command simply plotted the navigation trackline, but now say I want to see what the actual bathymetry looks like. I can run mbm_plot again and indicate that I want to use a color-fill of the bathymetry by using the graphics mode (-G). I can also specify to overlay the trackline by
adding -N:

$ mbm_plot -I 0162_20080616_161142_RVCS.all -G1 -N

Again, a .cmd file is generated that I can run to plot the data and view it. The mbm_plot function utilizes GMT to create the plot and handle the axes. You can customize mbm_plot quite a bit, but aside from specifying color-fill and navigation, I left mine at the default settings. Here is the result:

In order to edit the actual pings, you use a command called mbedit. Right now you can only edit using a 2D viewer, but there is a 3D MB-System editor in the works (it is currently in a beta version now). To open up mbedit for the line, I simply ran:

$ mbedit -I 0162_20080616_161142_RVCS.all

I could also have just opened mbedit by itself and then opened the line file from within the program. In mbedit you can apply filters to blank out the outer beams, flag bad data poin
ts, edit individual beams and pings, etc. There are many different view options in mbedit that makes examining the data fairly easy. In the example below I am using the waterfall display with the option to color by bottom detection algorithm turned on. The data was collected with a Simrad EM3002 dual-head system, and the waterfall displays enables you to see the individual pings of each transducer. Red beams are phase-detected and black are amplitude-detected.

These tools represent only a few of the things that MB-System can do. To really get a sense of it all, you need to check it out for yourself. I highly recommend Val Schmidt's MB-System Cookbook as a must-have manual.

So far, the only quirk I have noticed with editing my data in MB-System is
that when I plot it, it appears that the actual ping data and the navigation data start and stop at different times. It is hard to see in the plot figure above, but you can clearly see it in the plot of a turn line below. This could be due to how MB-System handles the extrapolation of the navigation data for Simrad systems, or it could just be something weird on the Simrad side. Simrad does not store navigation for each individual ping, so it is possible to have pings without nav and vice-versa. Kurt looked at some Hydrosweep data in MB-System (Hydrosweep does store nav data for each ping) and his data did not have this problem. I am definitely going to have to play around with it and see if I can figure out exactly what is going on. Regardless, I think MB-System is a great tool and fills a very real-world need. Not everyone can afford the multi-thousand dollar price tag that comes with many of the more mainstream sonar processing software suites, and it is nice to know that there are other options available.

Saturday, December 27, 2008

Stars Wars on Apple Terminal

Happy Holidays!
I am currently sitting in the San Jose airport waiting to board my plane and as taking advantage of the free wifi to putz around on my mac. Here a couple fun terminal commands that I just ran across:

1) say hello
just type say and then whatever else you want and your mac will speak to you.

2) telnet
allows you to play Star Wars IV (all in ascii) on your mac. Someone had way too much time on their hands.

for these and more, check out:

Monday, December 22, 2008

Sync iCal and Google! (and other cool Mac tools)

So now that I have my new macbook (oh yeah, btw, I have a new macbook and I love it!) I am spending part of my time trying to find some cool little tips and tricks to make my mac as cool and as efficient as possible. Some of the things I have come across are just plan fun, like when my brother showed me command+option+control+8, which inverts your display colors to have a negative-like effect. Hit the key combo again to turn it off. However, some of the tools are quite handy indeed.

Here's a little list of tools I have found really beneficial to have:

1) CalDav: a little tool that will sync your iCal and Google calendars. The refresh rate is very fast. Once I add an event in iCal, by the time I load my Google calendar page, it is there.

2) MenuMeter: this little tool Kurt pointed me to. You can display graphs and meters for your CPUs and network traffic (as well as memory and disk usage) in your menu bar.

3) KeyCue: displays a floating window of keyboard shortscuts whenever you press and hold the command key. It will tailor the shortcuts to whatever application you are working in. The professional version costs money, but the unregistered version works very well and just displays the registration screen every once in a wh
ile when you hit command instead of the shortcut menu (it will go away after a second). As a mac newbie, this tools has been great for me!

4) Caffeine: this tool prevents your mac from dimming the display or going into sleep mode. This is essential if you watch Netflix on your mac. It simply puts a little icon in your menu bar, and you click it once to turn it on and once more to turn it off.

5) Zoom: zoom can be found under Universal Access in your System Preferences. Turning this on allows you to zoom into and out of your screen using command+option and the + or - keys. This is great for zooming in programs and on web pages that do not normally support the zoom feature.

6) Flip4Mac: this plug-in feature allows Quicktime to playback Windows Media files (wma, wmv).

7) DivX: this tool includes a trial version of their media player (it expires after 180 days), but more importantly adds DivX functionality to Quicktime (which does not expire).

8) VLC: this is a separate media player from Quicktime, but can play a lot of videos that Quicktime cannot (such as ogg files).

Here is one more that is not necessarily beneficial per se (at least not to the average user), but sure is cool as heck:

9) Seismac: this tool will turn your Sudden Motion Sensor (SMS) equipped mac (any newer mac model, and some of the older powerbooks and ibooks) into a real-time three-axis accelerometer!

Wednesday, December 10, 2008

Interactive 3D models in PDFs!

I just saw this on Kurt's blog and had to post about it. Imagine turning in a cruise report with an interactive 3D model of your bathymetric data! Better yet, imagine a Ph.D. or Master's thesis with interactive models!

First you open your 3D mesh with MeshLab and convert it to Universal 3D (U3D) format. Meshlab then generates a snippet of code using the Latex document markup language. You include this code in your Latex document, compile, and voila: a PDF is created with the interactive 3D model built right in!

Check out the example PDF here: Laurana.pdf.

I wonder if it would be possible to export directly to U3D format from say Fledermaus or CARIS. This would necessitate some patches or hotfixes, but boy! what a powerful addition it would be.

Friday, December 5, 2008

File version control with Subversion

CCOM uses Subversion (svn) on their server to enable folks to have version control on their important documents. What this means is that I can commit a file to my subversion account on the server, and each time I modify the file, a new version will be saved. If I realize I made a mistake or need to go back to a previous copy of the file, I simply "checkout" an earlier version. This is great for constantly changing documents such as source code, html, my thesis proposal, etc. One neat thing is that everytime you "commit" a new version of the document to svn, it only saves the actual changes. Therefore, your memory usage increases only the minimal required amount each time.

To access svn on my Windows machine, I use a program called
Tortoise. Tortoise allows me to upload, checkout, update, and commit files easily to svn. For example, initially I uploaded some source code of mine to the repository. It is now safely stored on the server. When I checkout the file from svn, the most recent version (unless I specify otherwise) is dropped onto my local machine. Once I am happy with any edits I make to this local copy, I simply commit the file back to svn. This new copy autmatically gets a new version number (called revision in SVN) and will be stored as the most recent version. The update command is used to update any checked out copies on your local machine to most recent version in the svn repository. This is handy when multiple people are working on the same file.

The only potentially confusing thing thus far is that revision numbering in svn is global. This means that everytime I commit a file, the global revision number for the whole repository increments by one. For example, say I upload a file and svn assigns it a revision number of 25. Then I checkout a file with a revision number 2. Once I edit the file and commit it back to svn, its revision number will update to 26, instead of 3.

A typical svn reposity is set up with three main directories (note this is only a recommended structure):

  • trunk - this is the main directory for your files and where you commit regular changes
  • tags - a collection of snapshots of the trunk (or a branch) at a user-defined point in time. This basically contains pointer files to specific versions. This is good for a version you want to be able to access quickly. For example, if I used a specific version of my source code to process some data for a publication, I will want to quickly be able to access this exact version.
  • branches - active variations of the project compared to the trunk (or even another branch). Branches are good for when you are editing a file already in the trunk, but you do not have a working version yet. Perhaps you are trying out some new addition to your code, and you are still in the testing phase. This is also a good place to store any revisions you have to make to older versions of files in your trunk directory. For example, say I use version X of my code to process data for a paper. Now, a year later, I am on version Z of that code. Someone using version X from my paper finds a bug in it I need to fix but I do not wish to give them version Z yet. I can fix the bug in version X, and commit the new version of that code to the branch directory. That version Z of the code is still my most recent version in the trunk directory.
I found a good guide on svn here. This guide is for a specific svn client called Subclipse, but I find it a better tutorial than the one for Tortoise. Now I can stop pestering my poor boyfriend with svn questions over IM.

Oh, I should also note that Windows users who use Cygwin can also use svn via command line .

Saturday, November 29, 2008

Everybody do the wave! (Lightwave, that is!)

One of the faculty members on my committee pointed this out to me yesterday:

I took this as a hint and have begun practicing my moves. 

The guy who came up with this idea (who calls himself the Gonzo Scientist) also has apparently created a science guild within the online game World of Warcraft. The guild even had a science conference in WoW this past May! I personally never bought World of Warcraft after trying the demo, when I realized I would never accomplish anything in the real world ever again if I did (it seems pretty addictive). Now however, I realize it is a valuable platform where I can present my research to undead elves, trolls, and giants! I wonder if I can get my committee chair to cover the costs... 

Tuesday, November 25, 2008

CCOM Seminar Series Calendar

Since I have been in charge of organzing this year's CCOM/JHC seminar series, I starting keeping a Google calendar to help me keep track of who is coming when, when we do not have seminar, and when we have open dates.  Lately some issues have been affecting the computer that enables me to push this information out to the CCOM website, and so my only way to get the information out to folks is via email and flyers. Since it seems my blog gets a lot of UNH traffic - I am still shocked I really get any traffic to be honest, especially since I do not update regularly - I figured I would embed the calendar here. So if you scroll down to the bottom of this webpage, you should see the unofficial CCOM/JHC Seminar calendar. I am just now starting to schedule the Spring semester dates, so hopefully you will see this start to fill up soon. 

For local folk, remember, all CCOM seminars are held on Fridays, 3 - 4 pm, in the Chase Ocean Engineering Bldg. rm. 130 (the video classrom).

Friday, November 7, 2008

Code search and Blogger Backup

I found two cool tools during my morning procrastination today:

1) Google code search:
This lets you search for public source code. I am sure this will become a great resource for me as I try to learn Python. 

This freeware utility (source code is also availavle) lets you backup your Blogger posts as atom/XML files stored locally on your machine.  It took less than a minute to back up all of my posts into individual XML files that can easily be restored to Blogger if need be. There is no image support yet, but that is in the works. 

Thursday, November 6, 2008

Recovering files off my very old and very dead Macbook G4

My beloved old Macbook G4 (circa 2001) finally died. Nothing, and I mean nothing, happened when I pressed the power button, meaning it was probably a power board issue. I removed the back cover and took out the hard drive. Apparently you are supposed to have some fancy smancy screwdriver to remove two Torx screws holding the drive to the mount plate, but luckily I was able to carefully pry the drive out with a non-smancy screwdriver (the screws are fitted into rubber rings in the plastic mount plate, which has some give).

The drive itself could not fit into my external casing due to the Torx screws, but I was able to connect the USB connector to the IDE interface anyway and connect it to my ACER.

(here the drive is sitting on a protective sheet that came in my Mac. I would not recommend just plunking it down on just any old surface)

Windows XP could not recognize the MAC formatted drive (Quel surprise!) so I booted up in Ubuntu, which recognized the drive right away.

The next challenge was to unlock all the directories so I could access the files. All my personal files were denoted with:
meaning that only the owner can access them. Since I cannot login to my MAC, this is a problem.

I was not actually sure if this would work, but I ran a chmod command as root to add the needed permissions. I opened a terminal window and navigated to the mounted hard drive where I ran the following command:

monica@Tzedakah:/media/Scooby$ sudo chmod -R +xrw Documents/

the -R causes the permissions to be changed for the Documents directory as well as all subdirectories and files. Now all the permissions on all the files denoted by:
meaning I can read/write/execute all files, group permissions are read/execute, and others can only execute.

This is great, as I can now look into to the subdirectories and see what is there. I found a bunch of papers I had written in college, including my undergrad thesis.

Saturday, November 1, 2008

Netflix "Watch Instantly" on Ubuntu

I just spent some time trying to see if I could get my beloved Netflix "Watch Instantly" to somehow run on Ubuntu. I first tried using wine, but that was a no go. You have to have Windows XP sp2 and Windows Media Player 11. I probably do not have the right version of WMP installed under wine, but an internet search implies this still will not work. I then tried using it in CrossOver, which I was able to score a free copy of last week during a giveaway they were having on their website (thanks, Kurt!). I set up my WinXP bottle, but the install of WMP11 would not complete. An internet search showed others have had this problem before...blast. I was just about to give up on the idea of being able to enjoy entire seasons of AbFab without the hassle of rebooting in Windows, when another internet search lead me to VirtualBox. Apparently, "Watch Instantly" will work (albeit not the most efficiently) with a VirtualBox XP emulation.

Getting this working might just be my Ubuntu project for tomorrow...


CrossOver is a commercialized version of wine that seems to have slightly better implementation of some windows programs and games. Although I used both for the first time tonight, I noticed the difference right off. For example, once IE is running in CrossOver, I can view and use the IE toolbar as if it were running on a true Windows platform. In wine, however, I must run a terminal command each time I want to open a new website, as the toolbar is not displayed.

Hibernate happy in Ubuntu 8.10: Itrepid Ibex

This morning I updated my Ubuntu distribution to 8.10: Intrepid Ibex. It took a fair amount of time on the hotel's wireless connection to download all the necessary packages, but after that the actual install was pretty quick. Upon restart, my tablet pen no longer worked. A quick peek at the xorg.conf file showed me why. Ubuntu 8.10 uses HAL (Hardware Abstraction Layer) to control a lot of the input devices (such as my trackpad) and it therefore commented out a lot of the device specifications in the config file. I removed the comment symbol (#) only from the sections dealing with my tablet pen (detailed in a previous blog) and restarted. Now everything seems to be happy and I once again have a working tablet pen. The hibernate function also seems to be working now, which is something I never did get figured out in 8.04. It takes a few seconds to go into and come out of hibernate (long enough to make you wonder), but it does indeed work.

The only weird thing I have discovered so far is again related to the function keys. After installing the acerhk module in 8.04, the mail client would open whenever I hit the web browser button and nothing would happen when I hit the mail button. Under 8.10, the web browser button still opens my mail client,
but now mail button opens my web browser. At some point I should figure out what file controls how these keys are mapped and reconfigure it.

Wednesday, October 29, 2008

Lidar data in Caris pt. 2: waveform view

I have been looking at more lidar data in CARIS today with one of my committee members and am now starting to really figure out how CARIS displays the data. In my previous post I mentioned that the peak with the green line represents the determined depth and the peak with the red line represents an "alternate depth." This "alternate depth" designation in CARIS is somewhat misleading, as this peak actually represents the small amount of energy from the green (532 nm) pulse that is reflected by the water surface. The reason that the peak appears larger, in some instances, than the bottom return is presumably due to the gain settings being amped up so a detection could be made.

Looking at the image below, this does seem to make sense. In this dataset, 3 peaks can clearly be seen. In CARIS, the 1064 nm and 532 nm returns are shown on the same graph, with the first x number of bins coming from the IR return, and the remaining bins coming from the green return. The first unmarked peak represents the IR return from the water surface. The red marked peak is the 532 nm surface return ("alternate depth") and the green marked peak is the 532 nm bottom return. If you look under the lidar tab, the depth for the "alternate depth" is 0.16 m, which becomes negative (out of the water) once a tide value is applied. I am assuming that this depth reading is due to the fact that the green surface return, though nominal, would still have a slight penetration through the water surface. It could also be related to the difference between the IR detected distance to the water surface and the green detected distance to the water surface.

Tuesday, October 28, 2008

Hibernate fails in Ubuntu 8.04

Upon, first installing Ubuntu, I am pretty sure that both the sleep and hibernate functions worked on my computer. They have not been working recently though. When the computer attempts to hibernate, I see this issue:

[ some varying # (time stamp I assume) ]: i8042 kbd 00:07: activation failed

The screen then goes blank after a few minutes and the computer shuts down. When I hit the power button, I must completely reboot. 

I reverted back to the old kernel (2.6.24-19) to see if this solved the issue, but to no avail. Interestengly though, the function keys still worked, so that means another update besides the kernel was responsible for them suddenly working.

The Ubuntu mystery continues....

If anyone has any ideas on the hibernate issue, I am all ears. 

Monday, October 27, 2008

Shallow Survey 2008

You may have noticed a lack of blog posts the past week or so. This is because I have been volunteering at the Shallow Survey 2008 conference hosted by CCOM and held at the Wentworth by the Sea hotel in Portsmouth, NH. Shallow Survey is a conference dedicated to the techniques and issues related to mapping in shallow water environments. A common dataset, made up of a specific patch of seafloor that is repeatedly surveyed using many different methods (multibeam, lidar, interferometric, etc.), is provided for analysis by anyone wishing to do so. Although papers do not have to specifically use that dataset, many do, in order to show comparisons between different systems or methods.

In exchange for volunteering, I got to attend all the events and talks, which was really nice. I met a lot of interesting people doing really cool research, made some very valuable contacts, and even got to catch up with some of my old NAVO coworkers.

The program can be found here: Shallow Survey 2008 program

There were many excellent talks, but one of the most exciting as far as my research is concerned was the one by Valérie Robitaille, entitled "Identification of Sedimentary Facies and Biological Habitats through Reflectance Measurements Using a Multi-Beam Autonomous Portable Laser Equipment (MAPLE) to Standardize Airborne Laser Bathy Systems." Her abstract can be downloaded from the program link above. This research was done for her Master's, and she is about to move into her Ph.D. Hopefully I will get to see more of Valérie at future conferences.

At the very end of the conference they announced that Shallow Survey 2011 will be held in Wellington, New Zealand. I am definitely going to try to go that!

Acer Hotkeys in Ubuntu

Recently, I decided I would try and see if I could get my ACER hotkeys working under Ubuntu. These control the special function buttons (wireless, bluetooth,e mail, web, P1, P2) as well as the function keys such as the volume and screen brightness control.

First I downloaded and installed:

I did an lsmod > txt file before and after installation and performed a difference on the two to see if the linux module was indeed changed. The module had certainly been modified. An lsmod | grep Acer returned the following:

monica@Tzedakah:~$ lsmod | grep acer
acerhk 26036 0
wmi_acer 9644 0

I then edited the /etc/modules and added "acerhk" to the top of the list, so the module will boot at startup.

I restarted my system and voila: nothing. I decided not to mess with it for a while and went about other business.

A few days later I tried controlling volume using the function keys out of habit, forgetting they would not work. But it did work! Complete with a little image that popped up showing the volume bar. I could not believe it! The only thing I could figure is that a day or so before I had updated my system to the latest Linux kernel: 2.6.24-21.

So all of my "Fn" keys seem to work and some of my special softkeys work too, albeit not exactly in the correct way. For example, my mail button does nothing, but press the web button and Eudora (the mail client) opens. Another interesting one is that if I press the bluetooth button, my screen locks and asks for my passowrd. The screen rotations buttons also do not work. Once I have time, I will have to tackle this issue. In the meantime, I am happy to be able to control volume using the keyboard again.

Friday, October 10, 2008

Ubuntu on an Acer TM C300

I recently replaced the hard drive in my Acer Travelmate C300 Tablet PC and decided I wanted to be able to dual-boot Windows XP Tablet and Ubuntu 8.04 Hardy Heron. In order to do this, the Acer recovery disks were used to install XP on the entire drive (recovery disks do not allow for partitioning and you cannot buy a clean install of XP tablet....*sigh*). Once Windows was happy (and before installing any other software), one of the IT guys at school used Partition Magic to create a 30 GB partition, which left Windows with about 80. I installed Ubuntu from the hot boot cd and followed the directions for a dual boot system, creating a main partition for Ubuntu and a swap partition. The swap should be created as a logical partition at a size that is ~ 2 times your RAM (e.g. I used 1 GB, having 512 ram). The main partition is also set as logical and the mount location should be set to "/". After the partitions are set, I let the rest of the install run accordingly. Now when I boot up my system, I have an option of which operating system I would like to use. My goal is to only put open-source software on my Ubuntu partition.

Not all of my Tabet PC functions worked with Ubuntu out of the box. A fe
w things needed some tweaking. The first challenge was getting my wacom stylus to work under Ubuntu. Here is what eventually worked for me (pulled from various online sources, including this site from Ubuntu forums):

1. Run any Ubuntu updates that are ready for the system

2. Go to System -> Administration -> Synaptic Package Manager -> (or use apt-get install from a terminal window) and install the following:


3. Edit your xorg.conf file to add information for your stylus. Add the following:

Section "InputDevice"
Driver "wacom"
Identifier "cursor"
Option "Device" "/dev/ttyS0"
Option "Type" "cursor"
Option "ForceDevice" "ISDV4"
Option "BottomX" "28800"
Option "BottomY" "21760"
Option "Mode" "absolute"
Option "TPCButton" "on"

Section "InputDevice"
Driver "wacom"
Identifier "stylus"
Option "Device" "/dev/ttyS0"
Option "Type" "stylus"
Option "ForceDevice" "ISDV4"
Option "BottomX" "28800"
Option "BottomY" "21760"
Option "Mode" "absolute"
Option "TPCButton" "on"

Section "InputDevice"
Driver "wacom"
Identifier "eraser"
Option "Device" "/dev/ttyS0"
Option "Type" "eraser"
Option "ForceDevice" "ISDV4"
Option "BottomX" "28800"
Option "BottomY" "21760"
Option "Mode" "absolute"
Option "TPCButton" "on"

Then under the "Server Layout" section, add the following:
InputDevice     "cursor" "SendCoreEvents"
InputDevice "stylus" "SendCoreEvents"
InputDevice "eraser" "SendCoreEvents"

4. Edit/create a /etc/serial.conf file:

#Stylus pen
/dev/ttyS0 port 0x06f8 irq 6 uart 16550A

5. Go to System -> Preferences -> Sessions -> Start up Programs
Add the following command:

/usr/X11R6/bin/./xinput set-button-map stylus 1 3 2 4

6. Reboot the system and Voila! Your stylus should now be working and you can create lovely works of art such as the example below, created in GIMP:

Thursday, October 9, 2008

AIS helps save the whales

This weekend I helped Kurt replace an AIS transponder out at the Cape Cod National Seashore's Province Lands Visitors Center.  The transponder is an integral part of the current effort to help save the North Atlantic right whales.  

The setup was located down in the basement, in a room that the ranger refered to as the "zombie room." The small grey box on the left rack next to the white keypad is the transponder unit (photo credit: Kurt). 

The AIS antenna and a weather station are located on the roof of the visitors center (photo credit: Kurt). 

So what is AIS and how can it help the whales? 

Big tanker ships are all equipped with their own AIS transponders. These transponders not only broadcasts the ship's identifying information and location, but also receives AIS messages from other ships as well as port/harbor authorities. Just like the port/habor AIS systems transmit information about vessel traffic, the transponder at the Cape is transmitting information about right whale sightings. The next step is to create a patch for current AIS software run on the ships so that it can correctly decode the whale message and display the proper information on the navigation display. 

So where does  the right whale sighting information come from? 

The right whale listening network is comprised of 13 smart buoys that listen for whales 24 hours a day. The buoys have a listening radius of five nautical miles. The line of 10 buoys within the TSS provides full coverage for a 55-mile stretch of the commercial shipping lanes into and out ofBoston Harbor. When a whale call is detected, the buoys upload the data via cell or satellite phone to a server at Cornell.  Analysts at Cornell listen to the uploaded sound clips to verify the authenticity of the whale call. They continuously issue updates via websites and alerts to the ships. Time from detection at the buoy to posting on the site can be as short as 20 minutes.

In addition, whales spotted by vessels can also be called in to NOAA and the Coast Guard. 

Thursday, October 2, 2008

Lidar Data in CARIS HIPS and SIPS

The new version of CARIS HIPS and SIPS (v. 6.1) can now bring in SHOALS and LADS lidar data and waveforms for quality control and to merge it with multibeam data. The import procedure is pretty painless, though there still seem to be a few bugs to work out.

I tested it out with some LADS data I have from Portsmouth Harbor. You can see the selected data points highlighted in yellow in the plan view. The point highlighted in blue is the current "super-selected" point, and it is for this data point that CARIS will display the waveform. If you click either "next" or "previous" in the lefthand lidar menu, the "super-selected" point will move to the next yellow highlighted point and you can view the waveforms for each of the selected soundings.

The waveform box shows the surface and bottom returns for the green waveform. The green line represents the detected bottom depth for the waveform, while the red line represents a possible alternate depth. Unfortunately, there is no way to display axes (neither time nor intensity) or any type of scale on the waveform in order to get a better sense of what is being displayed. This is something CARIS will hopefully correct in later versions or hotfixes.

Tuesday, September 30, 2008

Lidar on Mars: The Movie

Kurt sent me a great movie clip showing an animation of the Optech lidar system on the Phoenix Mars Polar Lander and a series of false-color composite still frames.

You can really see the laser as it reflects off particles in the atmosphere. Note the rather large flash that shows up to the left of the laser. I am not sure what is going on there. Perhaps an accumulation of dust particles?

(if this plays really fast the first time, try playing it again. For some reason, the second time plays slow enough that you can see the flash)

Friday, September 26, 2008

Mac Tablets

Though not distributed by Apple, it appears that Mac tablets are here:

Axiotron Modbook

I have to admit, they do seem pretty sweet. I think I am too tied to manually typing to be able to work sans keyboard though (this guy is a slate, not a convertible), and the price is pretty steep (entry price $2,290). I currently have an Acer Tablet PC (the Travelmate C300, which is a convertible) that is about 4 years old. I cannot remember how much it cost when I first got it, but I know it was nowhere near this much. Of course, the Modbook is a lot more powerful (2.1 gHz processor, available w/ 2.4) and it even comes with a built-in GPS!

How long can I survive?

Apparently not very long....

I could survive for 47 seconds chained to a bunk bed with a velociraptor

Sunday, September 21, 2008

The Fighting Cartographers!

In a segment called "Smokin' Pole - American Arctic Expert" Stephen Colbert gives his spin on the Arctic mapping effort:

The Great Arctic Conflict - Media spin of Law of the Sea

In Betsy Baker's lastest blog post, #19 Conflict in the Arctic? The Tenacity of Media Spinshe highlights an important issue in current Law of the Sea operations: the media spin. I guess the idea that the US can peacefully map in the Arctic alongside Canadaian vessels and without causing a Russian military response is just too humdrum for the media. They need hype, they need drama, they need the threat of an international incident. 

Earlier in the year I was dismayed by an arcticle in Discover Magazine (January 2008 issue, page 22) that played up last year's Law of the Sea mapping expedition as a hurried response to the Russian's dropping their flag at the North Pole. They actually implied that the Healy was diverted off her current course to run up to the Arctic in a show of American force:

"Within days of the twin Mir descent, the U.S. Coast Guard had dispatched the icebreaker Healy north of Alaska to spend nearly a month mapping the Arctic Ocean's floor..."

Nevermind the fact that a quick Google search would have taken them to CCOM's Law of the Sea  webpage where not only can you see that we have been mapping up there since 2003, but also that the data is publicly available for download. Yes, even the Ruskies can download it (gasp!). I should also point out that in June of 1990, the US and Russia signed the U.S.-USSR Maritime Boundary Agreement, which will still hold even during EEZ extensions under Law of the Sea.

Sadly, Discover was only one in any number of magazines and newspapers to twist this story. This year, it seems, will be no different. The New York Times is another culprit, as evidenced by a recent article, "Arctic in Retreat" (September 8, 2008), the subject of Betsy's blog. The "disputes" and "conflicts" mentioned in these articles are simply nonexistent. Sure, countries are mapping the Arctic so they can submit their claims to the Law of the Sea Commission, but that is about as heated as gets right now. 

I am sure this is just the start. It will be interesting to see how the media continues to spin international mapping expeditions in the Arctic, especially as the ice continues to retreat and the Arctic itself becomes more accessible. 

Friday, September 19, 2008

Healy makes Ship of the Week!

Thanks to Kurt for pointing this out to me:

"In keeping with the arctic theme, this weeks Interesting Ship is the United States Coast Guard Cutter Healy  (WAGB-20).  The ship is a research icebreaker that was first put into commission on November 10, 1999.  Healy  provides more than 4,200 square feet of laboratory space, numerous electronic sensor systems, oceanographic  winches, and accommodations for up to 50 scientists.  It is capable of breaking 4 1/2 feet of ice continuously at  three knots and can operate in temperatures as low as -50 degrees F."

Wednesday, September 17, 2008

USCGC Healy and the CCGS Louis St-Laurent

After we disembarked the Healy on Sept. 5  and helo ops were completed the next day, Healy met up with the Canadian Coast Guard icebreaker the Louis St. Laurent. During this mission, Healy will be breaking ice for the Louis St-Laurent allowing her to tow seismic gear in order to map the sub-bottom. Healy will be collecting multibeam data during the course of the operations. 

According to the USCG's Healy update webpage,  the Louis St-Laurent has been helping out Healy as well, breaking ice for her as they transit to the seismic sites in order to improve the multibeam data quality. 

Back on Sept. 3, as we were headed back to Barrow,  the Louis St-Laurent sent her helicopter over to say hello:

On Sept. 5 the Healy commenced her own helo ops, bringing new people aboard, taking old people off, and of course, delivering the mail (no mail buoys for this Coast Guard vessel!):

USCGC Healy Blogs and Twitter

The USCGC Healy, the ice breaker I just spent 3 and a half weeks on in the Arctic, is now twittering! 

Follow along here:

You can also read about our Healy cruise and other Law of Sea news in the blog of Betsy Baker, a lawyer and professor who specializes in Law of the Sea was onboard with us.

Read Betsy Baker's blog here:

Betsy did what I should have done, send the blog updates and photos to someone with web access and have them update it for you.

For more polar science goodies check out the Exploratorium's weblog entitled "Ice Stories: Dispatches from Polar Scientists", which also includes tales from the Healy.

As for me, over the next couple days I intend to get some of pictures posted on here from the trip. It was an amazing 3 weeks and I am hopeful that I will have the chance to go back one day.

Sunday, September 14, 2008

The Foot

If you got my Healy emails, then you probably saw an example of what the foot of the continental slope looks like in the sub-bottom profiler image. I thought I would post the image here as well, because I just think it is so cool. I am still amazed sometimes at how far technology has come. I mean think about it. We are using sound to map what is beneath the seafloor. How cool is that??

Below is an image of the foot of the slope captured as we first passed over it on August 18 (click on it to get the full size image). You can see the layers of sediment pile up on the slope as it drops off. This is a raw image, so the numbers running vertically along the image are time in seconds, not depth. In a nutshell, depth is measured by recording the two-way travel time of the sound wave and multiplying it by the speed of sound through the water and sediment. This image also has a roughly 20x vertical exaggeration, so the slope looks a lot steeper than it really is. 

Wednesday, September 10, 2008

Back to Reality

As the jet lag wears off and I readjust to normal day/night cycles, I am slowly coming back to reality.

My days on the ship were spent watching data being collected at a rate that is slightly less than the rate of grass growing, processing said data, snapping more pictures of ice than one would think possible, and keeping my fingers crossed for polar bear sightings.

Now my days are spent in a cubicle with no ice (though that will surely change in a couple months) and no chance of polar bears. Today I spent a portion of my day Googling where to buy sediment.


Thursday, September 4, 2008

Update from the Arctic!

Hello again from the Arctic! Now that we are headed back to Barrow and are subsequently south of 80 degrees, we have web access again (albeit, intermittently). A lot of you have been getting semi-regular updates via email of my adventures while at sea, but I thought I would summarize some of the highlights for the blog:

Tuesday, Aug 19:

I saw my first set of polar bear tracks today! Actually, I saw two. At least one of them was fairly fresh because you could still see detail (e.g. the individual pad marks) in each print. I think I heard a ring seal today as well. I did not see it, but I heard it bark. There are also bearded seals up here, but apparently they are of the non-barking seal variety.

I also saw an icebow, which is essentially a rainbow that forms over ice. The colors are very faint and for the most part the icebow is all white. Now some folks out here have said the icebows are really fogbows, since although they start and end over the ice, the main body is in the fog. Fogbows can form wherever there is fog though, and are not constrained to the ice. Whatever it is, they are pretty cool!

Thursday, Aug 21:

Today was simply amazing. Just after I got off shift we entered an area of pressure ridging, where two ice flows are pushed together. For you geo buffs, this is analogous to convergent margins. Sometimes both edges of the ice ride up and form ridges of ice and snow. Polar bears like to use these to perch on and look out over the land (probably for their next meal). Depending on the thickness and age of the two ice flows, one can override the other, just like in subduction zones. Pretty cool, eh?

The pressure ridges today were pretty vast and were surrounded by pools of aquamarine. As the ice gets old, it becomes compacted and less saline, turning more and more blue as it does so. We got stuck several times and had to back up and ram repeatedly. We finally broke through when they brought on a second engine. The Healy has four engines, 3 that can be used together if necessary and one that is always kept for emergencies only. Standing on the bow as Healy broke through the ice was an amazing experience. You could really hear the ice break and watch the crack propagate out in front of us. As ice is pushed down underneath the ship, the sound of it scrapping along the hull is tremendous. Luckily, the multibeam sonar and sub-bottom profiler are protected by ice windows!

Right now we are still in "drive-by-cursor" mode. Essentially we are just following the foot of the continental slope to see where it goes. Most continental margins are comprised of a continental shelf, slope, and rise. The foot of the slope is defined as the maximum change in slope where the slope and the rise meet. Up here in the Arctic the continental margin has no rise, and oceanic sediments pile directly up onto the slope. We can see this clearly using the sub-bottom profiler, which produces a low frequency sound wave that sweeps between 3.6 and 6 kHz. The low freq. sound is able to penetrate the seafloor and reflect off layers of sediment and underlying rock, giving us an image.

Still no polar sightings. Well, not by me anyway… The bridge has spotted a couple, and did a couple of the night watchstanders. I am keeping my fingers crossed.

Thurday, Aug. 28:

Last night I managed to stay up and watch the sunset. Actually, it is more of a sun-"lowering" I suppose and really all it does is make a slight arc in the sky. We are at ~ 83 degrees North, so it never gets dark at all now. At the most, we get some shades of pink.

Dredging operations are slated to start on Friday and we hope to have our first ice buoy deployment sometime in the next couple of days. This will involve actually putting people on the ice (not me, unfortunately). There will be two watchstanders armed with rifles, one with the guys on the ice, and one on the boat, to look out for polar bears.

Still have not seen a polar bear. L Word has it that a number of bears have been seen just off the north Alaskan coast, so we are hopefully to spot more bears on our return to Barrow.

Wednesday, Sept. 3:


At approximately 10 pm local time, a bear was spotted off our fantail. When I first ran outside I could not see him and I was crushed. The boat slowly started coming around to starboard and inching up to the ice. The encounter was amazing! We must have spent 15 or 20 minutes or so just watching as the bear walked around, sniffing the air and searching for food. At one point he stuck his nose in a hole in the ice and starting digging around. Eventually he crossed in front of our bow and walked off into the distance.

Here are some pics from my adventures. Once I have a better internet connection, I will post some more.

me on the bow of the Healy:

The sun and the bear (he's small, but he's there):

A picture of the bear taken with a camera much better than mine:

Friday, August 15, 2008

The Ice Shelf!

A Special Sensor Microwave Imager (SSM/I) ( a microwave satellite radiometer) image of sea ice concentrations in the Arctic gridded (resolution is 12 km). Healy is represented by the ship icon in the center of the image. Looks like we are going to be doing a lot of breaking starting tonight!

(this image appears cut off when I view the blog, but if you click on it you can see the full image)

We Have Breakage! (of ice that is...)

Just about 30 minutes ago we felt the first real shudders as the Healy broke through some pretty impressive chunks of ice. I must admit that sitting through the last 5 minutes of the science lecture was pretty hard as all I could think about was grabbing my camera and running outside! I eventually made it out, and here are some of the shots I snapped:

Some pictures from the Arctic

Here are some pictures to give you an idea of what it's like up here in Arctic!

all ready for my helo ride!

a view from the helicopter as we make our approach

recovering the HARP buoys

sea ice!