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.