Kurt's Weblog

On your Mac, try this:

  Highlight some text in your web browser
  Apple-C copy it
  Go to a terminal or xterm window and run



  pbpaste  

pbpaste dumps the contexts of the clipboard to standard out. Use pbcopy to put text into the clipboard (aka pasteboard). I did not know that there are 4 different pasteboards. Crazy. What other little handy programs are laying around the Mac OSX filesystem?

It has been a busy day with sampling two more Santa Barbara core sections, measuring them on the kappa bridge and present my initial results to the Driscoll group.

The Griffin PowerMate looks like a fun little input device. Might may a good complement to the space mouse if I can ever finish the driver for 3D stuff. Would be great for editing video and audio if it works smoothly with everything. On sale for $39.99!

Looks like Thursday sugarbush will be getting a new Mandrake install. That will be nice to get a clean start. There is a new interview with the president of Mandrake here

Exxon Mobil profits exceed $25bn, Revenues hit a record $298bn. Wow. (BBC)

The U.S. Army's field manual guide to Cryptanalysis

white_dune is a graphical VRML97 editor, simple NURBS/Superformula 3D modeler and animation tool. Even has an OSX package. I need to try this.

Why do I need shell sql to use sqlite from the shell? I am already doing that. Oh... it lets me batch commands and then commit them. Might be some serious performance gains over my super slow shell scripts.

The screenshots for MiNews looks more like NewsFire. Seems to take my opml file from NewsFire once I deselected slashdot. Then crashed. This is not useable yet.

Also kind of cool, but does not yet support Nannoblogger: BloGTK

libferris - Interesting virtual filesystem that lets you see inside db and tar files too. Nifty idea.

I was saved by USENET today. I was trying to figure out how to get multiple tall skinny plots next to each other in a row. I posted via Google groups and 2 hours later I had the answer to check out multiplots.

  gnuplot
  set size 0.7,0.7
  set origin 0.1,0.1
  set multiplot
  set size 0.4,0.4
  set origin 0.1,0.1
  plot sin(x)
  set size 0.2,0.2
  set origin 0.5,0.5
  plot cos(x)
  unset multiplot

Another thing that I have been wanting to write for the last 2 years is a low-level segy library. Something that is simple enough that most c++ programmers could open up a segy file and start working with it. Having to know field numbers is truly insane and not productive. I was thinking that it needed to have a system for people to define how each segy type really is. This would, for example, with the SIO xstar data say how fields really are mapped. There really does not seem to be a segy standard in practice. In sioseis, people are always remapping fields between each other. These config files could also have an entry like the Unix magic/file database for detecting data formats by providing finger prints. There would be a truly standard compliant spec file provided with the library plus format files for each vendor device that writes out funky stuff. This would allow extraction of fields from the unstructured text block in the initial header. Basic operation should be simple. I should be able to verify the segy file and find out what type it is. Get a bounding box and shot range. Be able to dumb to ASCII a particular shot, etc. Then whatever applications could be layered on top. Jeff D. could write his Matlab trace viewer easily. We could make a python version of the basic features in sioseis with just a couple of days. The list goes on.

The trigger for writing this entry was thinking about how I could use libsegy to import all the header info into an SQL database. Then we could start making interpretation programs. It would not be too hard to start building tools that helped you define a layer by picking from processed images. I had talked to Jeff Dingler about using g3data to pick time/shot pairs. We could then drop this back into a database. Then build a mesh surface between lines for this picked layer.

The basic idea is that when we have a rock solid and flexible read/write open source library (LGPL?) people could build whatever suited them quickly.

Random slashdot link: Hints to new consultants

I am not really sure what the MetaWeblog API is, but it is supported by Archipelago, Blojsom, Radio Userland, NetNewsWire, Python Desktop Server, and Zoe. Which I put here more as a list of programs that do blogging. Manila and Moveable Type are in the pricy non-open source catagory. What about Blosxom, Conversant, TypePad, and WordPress?

Checking out newnewswire lite which says it is freeware with donations. Looks more like NewsFire or is it the other way around?

Check out these dunes on Mars! (Photojournal PIA07306)

On the RSS News Reader front, all you FireFox RSS news readers are going to shake your heads at me. "If you just used an open source tool..." I have to say that I appreciate the simplicity of NewsFire. I tried NewsMac for about 15 minutes and got totally frustrated by the three level hierarchy. I could not figure out how to nuke Spanish, French, Japanese, Sports. I just want MY feeds. Import from OPML was easy. But the interface was so cluttered. It is easy to tell that the authors of NewsMac have worked very hard on the program. I just do not have the energy to figure it all out.

I am going to try something new with Nanoblogger: an attachments directory with year-month subdirectories. I often have stuff that I do not really know where to put on the web and maybe the best thing is to order them by date. http://schwehr.org/blog/attachments/. My first attachment will be an opml export of my feeds that I am using in NewsFire. Some of these are broken, but this is what I have in there. If you want to see what I have in my feed, look at newsfire-29Jan2005.opml

Now back to my thesis. I have been thinking more about what I would like to do in the next version of X-Core when I get a chance. The main thing I need is to have a better core description, data entry, and export tool. Right now, I am resorting to g3data and emacs to do data entry along with producing a parallel Excel spreadsheet. The Excel spreadsheet really only serves the purpose of making handwriting legible, allowing the addition of a photo without a glue stick, and printing/sharing the data. The xls files are not good for getting data into anything else. Here is what one looks like:



Here are my ideas of what this mythical open source core description program should be able to do:

1. Be able to import and register images. This includes images from multi-spectral core logger CCD/CMOS strips, SIO style overhead multi-section photos, and oblique digital camera images. With the SIO style core photos, this is a matter of picking out the rulers and the corners and edges of each section on the table. For the oblique or otherwise distorted images, it should be able to ortho-rectify the image using say, the edge of the core liner that have been measured.
2. Allow the user to designate points, lines, and polygons on the core and attach either a description, photo, or measurement, or category.
3. Categories might be like the ODP lithology types.
4. Be able to generate color or greyscale graphs from the core photo. The ability to skip strips of the core are critical for getting around things like shell fragments when looking at the characteristics of the mud.
5. The ability to do multilayer imaging would be awesome. If I could also drop in x-rays and other types of imager data and have it be like layers in Photoshop that would be a big help.
6. Be able to import/export simple ASCII csv files, xml, and sql would make integration with a wide range of tools a snap.
7. It has got to be cross platform. I can not force people into one OS. The age of Windows only tools must die.
8. It must be open source so that folks can customize it at all levels. It also can not cost or hardly anyone will use it at the university level. This has to be a part of standard operating procedure. This can not be something that could possibly go away based on corporate whims!
9. No way can it be web based. It needs to be a simple stand alone application that a user can grab and use where ever. This might be in Haughton Crater, on a ship, in the lab, and who knows where else!
10. I would really like to hook this up to a 3D viewer. Click on the core in the 3D world and it brings up the core in this app. In the app, select a core and tell it to have the core be the focus in the 3D world.
11. Import/export from an online repository. Allow sharing of this data. If I have finished and published a paper on a core, let me hit one button and upload this to a server so that anyone can download the core.
12. REVISION CONTROL! Be able to take a photo each time the core is sampled and have this as a layer. Then when someone wants to know the status of the core, the look in the viewer and see that the section they wanted is down to nothing with only core liner showing.
13. USERS! Be able to have each person enter their comments on a core. Then if we can see who described what and when. If you see comments from me on micro fossils and later comments that say something else from someone like Dick Norris or Chris Charles, you will know to trust comments by those guys over me!

Miscellaneous link for this entry: simple-glade-codegen.py. If you use glade, this will help generate code for pygtk. Not that I have tried glade in years. It is going to take fink an hour or two to build glade2 while I do other stuff.

Libya has some pretty cool geology, not that I want to visit. When I heard last year that American companies were back in that this would be HUGE business. Here is a BBC article about US Oil companies getting back in there. We used Libya as our final exam area for Basin Analysis and all I can say is wow!

Newsfire just went shareware asking for $20. Doh. Guess I had better find something else, preferably open source. Newsfire is a nice program. Very clean.

I am going to give NewsMac a try. It says it has ipod syncing support. That would be nice.

Just entered bpsio-5g-sec2 description into Excel. I then dumped a pdf via print. This is the first sheet for this cruise to have the photograph inserted in the left hand column. That is easy to do now that I have processCore working again and the photo xpd files already created. Now, how do I control excel so the pdf is just one page. This 4 page business is painful!

Core Descriptions Directory
PNG of 5g-sec2

I should now have a static index that gets updated when I tell it to. This is from an ugly shell script called nb-build-index.bash. Check out the links on the right hand column of the front page.

I am down to 1800 emacs in my inbox. Whew! Some serious cruft in there.

The free math help is not from me! It is from the UCSD math department:

http://math.ucsd.edu/~mathstorm
mathstorm@math.ucsd.edu

Conference poster advice

SIO Tsunami webpage

Making a sphere in parametric mode with gnuplot:

 
  set parametric
  set urange [-pi/2:0]
  set vrange [0:2*pi]
  set isosamples 10,10
  splot  'as2-slump-sample-100.xyz' \
       ,'as2-slump-sample-100.xyz' using 4:5:6\
       ,'as2-slump-sample-100.xyz' using 7:8:9\
       , cos(u)*cos(v)/3,cos(u)*sin(v)/3,sin(u)/3

From Jeff Love at the USGS: Software for paleo-vector analysis (directions and intensities)

  Love, J. J. & Constable, C. G., 2003. Gaussian statistics for
  palaeomagnetic vectors, Geophys. J. Int., 152, 515-565.



  http://geomag.usgs.gov/papers.html

A good example of a research cruise web page:

http://www.soest.hawaii.edu/STOWA/

There are 2600 emails sitting in my inbox going back to July 2003. It is time to clean house a bit. So far I have gotten rid of 300 messages. I will use this log entry to cache some of the more interesting items I find that are of public interest.

Community Model for Coastal Sediment Transport - Chris Sherwood who put up the java applets for basic water parameters like settling velocity. Would be nice to keep adding all we can to a large community body of software for analyzing these types of problems.

ArsDigita University online computer science courses. I should really watch Database Management Systems

Danah Boyd recommended looking at David Laidlaw's work for inspiration on scientific visualization.

NGDC Coastal Data for the SoCal area.

ODP Lat Lon search

ODP "hole trivia" - Where the holes are. However, they are only to the nearest minute. Ouch.

ODP Database front door.

Geometrics sells a lot of the towed magnetometers that we use. They have a new digital streamer of hydrophones at AGU that looks interesting called the GeoEel

Killer Sediment waves in the EuroSTRATAFORM area - Bottom center of the top image.

ipod hacks

Data Structures and Algorithms with Object-Oriented Design Patterns in Python an online book by B. R. Preiss.

SIO Pier Chlorophyll from a CTD sensor sampling fluorescence.

Fiona's recommended Chicken Tikka Masala

GemSys makes magnetometers.

I have always had a strong dislike for Fortran. It only got worse after seeing what the compiler vendors did with F90 and F95. Why would I want to pay $900 for a junky Fortran compiler? I have tried 3 different compilers at about that price each. I only use Fortran for legacy code at this point.

How Not to Write FORTRAN in Any Language

Of course there is a rebuttal from JPL

The f90 homepage

Check out snopes on the crazy deep sea creatures.

Just tried sending my first Fax from OSX. I opened a scanned image in Preview and selected print. I then inserted the fax number from my address book, discovering that a 1- in the number makes life easier. Why does it insist on defaulting to a bluetooth modem when I have bluetooth turned off? I select the internal modem and type in a cover sheet being carful to not press return and use Apple-V to past in carrage returns. Then send it. The "Internal Modem" printer window pops up and starts dialing. The first one went fine until it said sent and then just hang then looking busy and saying finished, but then not going on two document 2. I stopped the jobs, deleted the first one, and restarted to stat doc 2 would go. That dialed, got the fax machine and just sat there saying connecting. Hey Apple, how about some more debugging info. Not much int the window, so I went into /var/log/system.log, where I get this kind of thing:

Jan 28 09:30:46 localhost kernel: AppleModemOnHoldNub::start--registered service
Jan 28 09:30:46 localhost kernel: AppleModemOnHoldService: Initializing
Jan 28 09:30:46 localhost kernel: AppleModemOnHoldService: Probing
Jan 28 09:30:46 localhost kernel: AppleModemOnHoldService: Starting
Jan 28 09:30:46 localhost /System/Library/Extensions/IOSerialFamily.
   kext/Contents/PlugIns/InternalModemSupport.kext/
   Contents/Resources/AppleModem
OnHold.app/Contents/MacOS/AppleModemOnHold: ModemOnHoldOpen >> 
Jan 28 09:30:46 localhost /System/Library/Extensions/IOSerialFamily.
   kext/Contents/PlugIns/InternalModemSupport.kext/Contents/Resources/
   AppleModem
OnHold.app/Contents/MacOS/AppleModemOnHold: MOHServiceAddedProc >> 
Jan 28 09:30:46 localhost /System/Library/Extensions/IOSerialFamily.
   kext/Contents/PlugIns/InternalModemSupport.kext/Contents/Resources/
   AppleModem
OnHold.app/Contents/MacOS/AppleModemOnHold: MOHServiceAddedProc <<< 
Jan 28 09:34:07 localhost kernel: AppleModemOnHoldService: Stopping
Jan 28 09:34:07 localhost kernel: AppleModemOnHoldNub::stop()
Jan 28 09:34:07 localhost kernel: AppleModemOnHoldService: Freeing

That does not tell me much.

I just found out that the iPod Photo can not actually take pictures. Crazy. I thought it had a built in camera. Looking at the iPod accessories, I do not see a camera attachment. Yo Apple, what is the deal? Cameras a so cheap that it is going to be hard to find a cell phone without one soon. That will cause more problems with places not letting you take your cell phone along, but that is another issue.

The Griffin iTalk rocks one you add a microphone to it. How about Griffin making a camera attachment? Stick the image into a wav file or something to shoehorn it in there. Or make a camera that can directly dump frames to the iPod. Or do both.

In this month's Wired magazine one of their "wired" terms is "Blogging your book." One thing that I would like to write about is the history of the rover program at NASA Ames. I certainly do not know all the details since I was only there for a while but I'll start with a time line of events that I know.

• 1991 - Bill Borucki sent me over N-244 to meet Butler Hine
• 1992 - TROV goes to the south shore of Lake Tahoe
• 1992 - TROV goes to Antarctica under the ice in Lake Hoare, Dry Valleys
• 1993 - I take the Stanford Space Systems Engineering class. Marsokhod comes to the US with its Russian engineering team. Visits Stanford.
• 1994 - Virtual Planetary Exploration Lab with McGreevy
• 1995 - MAPS program take TROV to Mono Lake.
• 1996 - I start working in the Intelligent Mechanisms Group
• 1996 - Desert96: Marsokhod goes to Arizona for a field test.
• 1997 - CMU Nomad rover goes to the Atacama Desert
• 1997 - Ames stereo pipeline (STP), VEVI 5, and MarsMap
• 1997 - 4th Planet builds Vermilion viewer with Java/VRML/EAI. Those technologies turn out to seriously suck despite heroic efforts by 4th Planet.
• 1997 - Laurent and I create Viz to follow on to VEVI and MarsMap
• 1998 - CMU/Ames team does to Antarctica to prepare for Robotic Antarctic Meteorite Search
• 1998 - First start participating in Pascal's Haughton Mars Project on the impact crater on Devon Island.
• 1998 - Take the stereo rig and pipeline to Yellowstone hot springs and geysers.
• 1998 - I move to CMU for the Intelligent Robotics Program
• 1999 - Marsokhod field test - first with Lisp on board
• 1999 - Mars Polar Lander, DS-? (the penetrators) and ? crash
• 2000 - I go to grad school and try to not think about robots for a while
• 2004 - MER A & B land on Mars and kick butt!

Things I am missing on dates:

• Marsokhod field test at Mars Hill
• Marsokhod field test in Hawaii
• TROV dives in McMurdo Sound. 1994 or 1995?
• RoCS - Rover Control Station task tries to integrate VEVI and WITS
• Dex/Poindexer by Hans, Dave
• Snake robots
• Santa Monica rover demo
• Chernobyl/CMap project
• And tons of other stuff
• Rocky 7 field test at Silver Lake

Even with this list, I am leaving out things that did not have direct impact on me. There are a ton of Rocky field tests, Dave Miller switching JPL to smaller robots, Ambler, Dante I, Dante II, the NavLabs that all had an impact on robotics at Ames.

I am also missing things about the evolution of the computation hardware and software solutions that we tried to put on these vehicles. Things like when TROV got VxWorks and how. Jay Steele putting Control Shell on the Marsokhod and Mel robots. Dan and I taking Control Shell off of Marsokhod so it was just NDDS. Anne and ? taking NDDS off of Marsokhod and switching to Ace/Dao. When we switched from VME to the ruggedized zillion PCI slot x86 machines. The evil attempt to use CompactPCI (yuck). That little floating ball inside and outside the space station that Hans and Sib made. Working with the upstairs AI guys on many projects. The influence of TCA and RTC on networking and planning.

Think of a giant Amoeba that streaches over NASA Ames, CMU, Stanford, JPL, and more. That would be the best way to describe the progress of these systems and the knowledge of working on them.

From the SIO list serv:

Two weeks ago I sent out the following advertisement for 3
undergraduate volunteers to join us during a three week cruise to
Samoa this coming April. I sent it out to the entire list of
undergraduates with an interest in Earth Sciences and on the Volcano
listserver. Remarkably I have not received one application or inquiry
from any of our UCSD students, while the response from around the US
has been very good, even when considering the fact that our cruise may
fall together with finals week on most campuses.  Maybe either one of
you knows of a good student that we might want to take on our cruise?
The students should have a good background in Petrology of basalts, if
possible. Note that our deadline is this coming Saturday. Today I sent
out a reminder to the UCSD undergraduates as well.

I am very surprised that students here have not jumped all over this. When I was an undergraduate, I would have jumped all over this kind of thing. I went on trips to Yellowstone, Mono Lake, and Eastern Nevada. I never got asked to go on an ocean going cruise or I would have. For my TTN136B cruise to the Humboldt area, I got three SUPER undergrads from Humboldt State who went along and helped core and run the hydrosweep.

IRM-manual PDF - where IRM == the Institute for Rock Magnetism at the University of Minnesota. It is handy to have a lab manual. I want to convert volume susceptibility to mass normalized susceptibility. This should be assuming a 10cc size. So to convert is should be something like MassΧ = VolΧ * 10 cc / mass in g, where Χ is Chi or bulk susceptibility.

LinkQuest of San Diego sold two TrakLink systems for AUVs to University of Southern Mississippi and the Memorial University of Newfoundland. Both of these will by on ISE Explorer AUVs. ISE products

This morning I was just a block away from the LinkQuest office and did not know it. They are no where near the water.

everyvideogame.com - Things to do after I finish my thesis!

Bazaar del Mundo

To cook a Leek:

Leek recipe
Cut down center but not all the way
Swish in water until all grit/dirt is out
Cover in butter, sprinkle with sweet basil, thyme, and parsley
Wrap in foil
Cook at 380degF for 25 minutes in the toaster oven
Worked pretty well

I started writing my next paper and have gone back to using TeX. I need to figure out how to export EndNote to BibTeX. No more word. I hate writing with word. Need to figure out how I want to do TeX editing. Lisa uses TeXShop. I prefer X based tools where I can use emacs.

BRL-CAD - "constructive solid geometry solid modeling system that includes an interactive geometry editor, ray tracing support for rendering and geometric analysis, network distributed framebuffer support, and image and signal-processing tools." And has Mac OSX support. Need time to try some of these links I keep finding.

samldap - Samba + ldap. Maybe this will help when I setup a lab network someday along with LDAP Account Manager or maybe Apple will put their XServe GUI tools on all Macs. I tried to setup OpenLDAP about 5 years ago and to call it confusing is an understatement.

Apples Mail.app just considered my AGU convener email as spam. Grrr.

Sometimes when I burn CDs on my laptop, Mac OSX leave the temp volume around on /Volumes and it takes a reboot for it to disappear. It will not umount and I am a bit nervous to do an "rm -rf".

DHL seems a bit scetchy. I had a DHL package I wanted to get out today. I found the nearest drop box and it was about a 4 mile drive. When I got there, their drop says "Airborn Express" with ZERO indication that they are DHL. No yellow or anything. Then I opened the drop box and there were DHL yellow mailers and all. Come on guys! How hard is it to slap a sticker on the outside of the drop box that says DHL?

Another link - Python code metrics with PyMetrics Linux Journal article

Condor Earth Technologies came by the USGS sometime during the 94-95 timeframe showing off milspec tablet PC's with the Leica laser range finding binoculars with magnetic compass. At the Dec AGU, I saw that people are starting to pick up this idea again as these things get cheaper. I just wish people would stop using MS Windows on these things.

TeXShop

yaprm - Yet Another POV-Ray Modeller

gas - analyze your cars gas consumption

Log Application Usage - Track what OSX applications you use for that human factors paper you were thinking of writing. Lots more fun and useful apps. TreeSize is exactly what I was wanting yesterday as my laptop fills up yet again.

Installing Debian

burn to external DVD for iDVD. This link is for Becca.

Edit and sync iCal calendars on multiple machines

openModeller is a static spatial distribution modelling library. It provides a uniform method for modelling distribution patterns using a variety of algorithms. It can be used to predict species distribution (fundamental niche) based on a set of georeferenced occurrence points and a set of environmental layers.

Myche pointed out that MySQL has all sorts of cool importing stuff:

http://dev.mysql.com/doc/mysql/en/load-data.html

http://dev.mysql.com/doc/mysql/en/mysqlimport.html

I'm starting to use Hibernate (http://www.hibernate.org/) to do
automated persistence.  I'm also thinking of using HSQLDB
(http://hsqldb.sourceforge.net/) in certain applications.  I have a
need to use an in-memory database and HSQLDB allows such a thing with
SQL92 (well, a subset).  this means I can build my quick app and if it
grows move it to MySQL without changing the Java code.

redet is on my list of things to check out and possibly add to fink. "Regular Expression Development and Execution Tool"

All I can say is that there has to be a better way! I created this script today: build-db.bash that creates the database of cores and k15/s7 data for each paleomag cube. This is just out and out ugly. Probably 80% of the problem is that I am using bash. Python or perl would make this less painful. The rest of the problem comes from that this is not a straight import. Data for each sample takes 4 lines: 1 line of header and 3 lines of 5 measurements each. In that header is a lot of information. My sample names look like this:

   bp04-6gw-s2-141.2
   |    |||  | |   |- Optional cm decimal place
   |    |||  | |- Depth in cm
   |    |||  |- Section number.  1 is the top section (water/bottom interface)
   |    |||- (w)orking or (a)rchive half
   |    ||- (g)ravity, (p)iston, (t)rigger
   |    |- Core number
   |- Cruise abbreviation -> BPSIO 2004 == bp04

And then there is the trouble of making an SQL date out of "1/3/05 4:33 PM." It all adds up to a whacked out script. Suggestions?

Dingler's link: Tsunami Visualization

Dear Paleomagnetist/Geomagnetist



I thought you would be interested in knowing that people at the
Barr Smith Library at the University of Adelaide, Australia, have put
together a remarkable website on R. A. Fisher: Fisher.
The Australian statistician John Henry Bennet has been a prime
mover. Fisher spent his last years at the University of Adelaide where
he was much appreciated.



Those of us privileged to know Fisher, admired his critical and
capacious mind, his elegant and concise writing style. To say that he
was a distinctive presence would be a gross understatement. His
"Dispersion on a Sphere" formulated in 1951 (altho not published until
1953) placed paleomagnetic and studies of the prehistory of the
geomagnetic field on a quantitative basis. I wouldn't be suprised if
his paper is the most widely cited reference in our discipline.



Fisher regarded himself as a biologist: statistics the tool,
biology the objective. But during his lifetime, his reputation as a
statistician probably out-shone his reputation as a biologist or
geneticist. In the last few decades, his work has come to be
increasingly admired by biologist, particulary evolutionary biologists
and Darwinists generally.  As I understand from Henry Bennet, this was
one of the motivations for creating this excellent website about one
of the great luminaries of the last century.
                                                Ted Irving 21 Jan 2005

There are a lot of lessons about ideas and invention. ME 101 at stanford pummeled us with this: Ideas are not rare. They are everywhere. The ability to communicate an idea and get it implemented is rare. The idea may be great, but if people are judging your presentation they will never get to the content.

Some random ideas I had while standing at the Kappabridge for a few hours (the mind will wander):

• I need to make a sample storage container for cubes. It should hold them all in a nice foam padding and in order. Ziplocks suck for this.
• What open source software (or other types of) projects do you try to emulate or look up to? Especially in the documenation department. My best attempt to date (density) is really not that good in terms of docs. Yes, there are man pages and web doxygen, but they are WEAK. Who does the best job? I frequetly learn my emulation. I useually snag a tar ball of some GNU project like grep or one of the SIM projects to look inside for how they did things like command line args, man pages, or doxygen.

Workshop Announcement - Antarctic Geological Drilling (ANDRILL)

For further information, please go to: andrill.org

The ANDRILL - United States Steering Committee invites applications for
participation in the United States ANDRILL Workshop to be held at the
Embassy Suites Hotel, Denver International Airport, 1-2 April 2005.



ANDRILL is an international research program designed to investigate
Antarctica's role in Cenozoic global environmental change through
stratigraphic drilling and numerical modeling. ANDRILL will obtain
stratigraphic records of key intervals and events in Earth's history
from locations proximal to the Antarctic cryosphere, using sea-ice and
glacial-ice as drilling platforms.
...

Jeff Ota says that he teaches his Santa Clara classes with a tablet computer. Jeff, how about some details of how it works. Good and bad?

Played with pysqlite from fink yesterday. Eh? Sounds like it is kind of like connection pooling/batching type ideas. Batch up a bunch of changes and do them all at once. More complicated than I am interested in. Maybe someday soon.

Myche mentioned an alternative to OpenOffice on the Mac since they nixxed the Aqua port: NeoOffice/J. It is Java based.

Warren's link to Mac OSX software by Marc Liyanage in Switzerland entropy

UCSD's ask a librarian live. Anyone tried this yet?

Arg. I have not followed up with the Harvard CFA about ADSABS RSS feeds.

That was a quick dump of interesting things sitting in my inbox.

The patent system is so broken it hurts. I just saw that McAffee was granted this patent for a firewall that tracks the incoming packets and geographically shows where they are coming from. There have been algorithms that attempt to show the physical location of IP addresses for MANY years. One example is NeoGeo/CAIDE This is just combining that with the age old etherman that only ran on SGI's that used coff libraries (IRIX up to 5.3).

There was also interman or something like that. These programs made a graphical representation of the location of all traffic seen by a host. During the Marsokhod Desert 1996 field deployment to Arizona, I had an old Indigo R3K machine sitting down in front of the projection screen running etherman. I could then see traffic to all the science team computers, our file server, and traffic out from the desert dropping in from our private satellite link to the field. I could then see Marsokhod sending traffic back in along with Dan and Eric on the SGI Indy logging back into the Intelligent Mechanisms Group.

Ethereal claims to be an etherman clone, but I did not see any of the standard nodes with links graphics that were the mainstain of etherman.

I found through google the name of the family of programs (they were binary only): etherman, interman, packetman, loadman. These were all a part of the Austrialian netman package.

         (C) Copyright 1993
    Curtin University of Technology
       Perth Western Australia

Found solaris binaries here: netman

Code Complete Rev 2 by McConnell might be worth a look the next time I am in borders.

plans is another web calendaring system, this time in perl. I still think phpcalendar would be better for the Driscoll group.

MPCA - Principle component analysis on 100 MB data sets. GPL'ed.

Ugh. Just heard President George W. tell a reporter that the reporter was acting like a senior citizen. That is not a stateman like act.

How to Record a Podcast. This covers how to snag audio from phone calls to do interviews using skype for your phone calls.

Bjork's new video with a cat.

Maybe elog is what I want over a blog. It is an electronic log book with a web publishing side.

SciAm article on Seeking Better Web Searches.

flatgallery produces photo galleries by just dropping images into the directory on the web server. Uses php and no database. Might be nice.

VCG Metro computes distance between meshes. Might be good for mesh registration/alignment projects.

So now that I am working up a script to inject my data into a little sqlite database, things are getting exciting.

   open `sqlite bpsio04.db 'select sheetURL from \
   CoreLoc where corenum=1;'`

The database finds the URL for time image and Mac OSX pops up Safari with the right URL:

  bpsio-log-35.jpg

I believe this is where Alex gets to say "Why did you not listen to me about how useful/easy/cool SQL is back in 2000?"

My first try with sqlite is showing success. I am using sqlite 2.8.5 from fink. The goal is to create tables for the BPSIO / Gaviota / Goleta / Santa Barbara cruise from August 2004. If I can get used to this whole sql thing (better than with MER), I think this may be a better way to work with core data. Here are the first few commands that I ran from the shell to get started:

1. sqlite gaviota.db " create table CoreLoc (id INTEGER PRIMARY KEY, cruise VARCHAR(20), corenum INTEGER, coretype varchar(1), datecollected TIMESTAMP, lat REAL, lon REAL, depth REAL, sheetURL TEXT);"
2. sqlite gaviota.db " insert into CoreLoc (cruise, corenum, coretype, datecollected, lat, lon, depth, sheetURL) values (' BPSIO04' ,1,' g' ,' 2004-08-04 21:09:15' , 34.36116666, 120.108, 480, ' http://schwehr.org/Gaviota/bpsio-Aug04/bpsio-log/images/bpsio-log-35.jpg' );"
3. sqlite gaviota.db " select * from CoreLoc"

Random links:

bib2html for BibTeX

1-159268954-6 - Magnetic dust on mars

I bet the whole net has slowed down today due to the 1984 mac video. I snagged a copy from this mirror. The original release site.

One feature that fink commander really needs is a "Pause Build Function." I have been trying to build kdebase3-ssl for about 4 days now, and everytime I have had to kill the build after a couple hours because I'm mobile somewhere and need to save battery power. Today, while I work, I am going to give it another try starting at 7:46 AM.

Saw an announcement about ANT and was confused thinking that it was a java build tool with RSS. This is something different: antnottv - video blogging. Hmmm... I already watch too much TV. More ways to clog my DSL link.

Update: kdsbase-ssl 3.3.2-21 finished building at 10:10 AM. 2 hours and 20 minutes.

Freshmeat just changed their RSS feed. Yikes! Now it comes with the screen shot and more description. Great improvement.

UCSD Ship rates

	Ship Rates		Technician Rates
	(Provisional)		Fixed	Projected
	2004	2005	2004	2005
R/V Roger Revelle	$19,368	$20,336	$3,000	$3,150
R/V Melville	17,976	18,874	2,814	2,955
R/V New Horizon	11,757	12,345	1,239	1,301
R/V Robert G. Sproul	7,438	7,810	929	975

Do not forget to add 13% overhead.

Here is a program I would like to see. I call it "ScienceBlog." This would be a weblog with some different features. MER for example, each entry would be a raw, color, or mosaic image. Then for comments, people could define a region of discussion in the image. They could draw a box around an image and say, "Check the layering in this rock" or "This rock is weird" or "Is this a dust storm in the distance". Then you could have scientific discussions right on the image. You could do the same for graphs like the APXS and Mossbauer graphs. There it would be, "This peak indicates Jarosite, but we did not see it pre-RAT". The site could have groups such there are people who can see certain posts and others who are not able to see them. You could then have a time release too. For example, there could be a mode where a comment is automatically released in 6 months and another mode where the author gets bugged in 6 months about release and then if they do not answer in 1 month, it goes public. Would this help capture the scientific process? Scientists could blank out the public or groups to stay focused.

There is a title. X-Core has been re-animated. This is a great lesson to myself. I wrote this code as fast as I could to win the first SIO Visualization Competition (which I did win), so I cut as many corners as possible. When I code fast, I do what I am used to, so I added some asserts to arguments passed in and made as many things const as possible. Where I was lacking what in return code checks and DOCUMENTATION. I did not know doxygen at that point so I had not really knocked the need for documentation completely into my brain. After density, I know what is required for minimal documentation. Return code checking is easy to let slip, especially when no easy to get at documentation is available. I still have never written great documentation to date. So the lesson today is:

• Use doxygen and document all functions, methods, parameters and especially return codes.
• Take that doxygen output and make sure that you check all return codes!

But the upside is that I ran processCore using an input file generated with g3data and some hand tweaking. It worked! I got some surprises. I forgot that it generates a meter stick image file along side. Very handy, but the mind slips. processCore makes each section an image and then a total core image. Woo hoo! Now I need to use g3data on the rest of the sections. And this time, i will be checking the description files into cvs. Right now, I am using the "XCore-v1.0" format. Why did I put a "v" in there? Here is the extension I want to use:

  xpd - Xcore Photo Description

Now that I think about it, making a color image will be easy. All I have to is make separate grayscale images for each channel of red, green, and blue.

Ever wanted a keyboard shortcut to zoom in and out of your powerpoint like in photoshop and ill? Check out this hint.

After using Mac OSX for almost 4 years, I would not want a linux box as my desktop anymore, BUT they make fantastic servers of all kinds (including graphics rendering, file serving, compute farms, and embedded). Looking at the nForce Professional makes me drool. My ultimate work setup would be a 15 inch Mac laptop, highest end Mac desktop, and a dual opteron running 64bit only linux (it is time to trash 32 bit with linux). Anandtech review

Interesting links:

cfg - OSSP cfg for C/C++ style config files. Maybe good to have in addition to gengetopt?

tsep is yet another website search engine. May require mySQL?

cw is a text colorizer for command line programs. An alternative to the that I maintain the info file for.

Medical Geology is a new one to me. 4.4K hits in google.

Been working on my old xcore stuff. I have processCore building on the Mac, which was pretty easy, but it will take a bit to make the input files with g3data. The C++ code inside processCore is not good. Hardly and documentation and some not so valid code. Whoops. I was trying lots of new things back in 2002.

I just added a robots.txt file to my website. The msnbot is the highest traffic load and I have no interest in supporting Microsoft. Here is my robots.txt file:

  User-agent: msnbot
  Disallow: /

I did a search on www.msn.com for msnbot to get info about the bots name and robot.txt preferences.

Here are the links that I used to get some info on the robots.txt:

• How to Set Up a robots.txt to Control Search Engine Spiders
• robotcop - which looks like it might be useful if this robot stuff gets too annoying.

Last but not least, some info on the msnbot:

Non-authoritative answer:
61.98.46.207.in-addr.arpa       name = msnbot.msn.com.



Authoritative answers can be found from:
46.207.in-addr.arpa     nameserver = ns3.msft.net.
46.207.in-addr.arpa     nameserver = ns4.msft.net.
46.207.in-addr.arpa     nameserver = ns5.msft.net.
46.207.in-addr.arpa     nameserver = ns1.msft.net.
46.207.in-addr.arpa     nameserver = ns2.msft.net.
ns1.msft.net    internet address = 207.46.245.230
ns2.msft.net    internet address = 64.4.25.30
ns3.msft.net    internet address = 213.199.144.151
ns4.msft.net    internet address = 207.46.66.75
ns5.msft.net    internet address = 207.46.138.20

msnbot has been 17% of the hits this month, 17% of the files, and 327MB! Thanks microsoft. Would you rather I just sent you a DVD of the whole site?

Entries for NSF Visualization contest for this year are due May 31st.

How do I tell Safari to hang onto the Yahoo https cert? I sign onto yahoo mail using ssl and am starting to get annoyed by the popup to accept the cert as ok. The same goes for ssl pop to ucsd in Mail.app. I should be able to save the cert and have neon lights come on if it changes! That would be security 101.

A Yellowstone Adventure - Deep in the Norris Geyser Basin

You may want this map of Norris Geyser Basin up while reading on. Unfortunately, most of what is below is off the map to the North.

Driving in the car this morning, I went by some place with this smell that triggered a very vivid memory that I have from working in Yellowstone National Park. That strong sulfur smell. I think it was May of 1995, and I went with Deena and Don L. to help out working on hot spring research. Deena was focusing on silica sinter growth. We met up with one of the parks research rangers and headed up to the Norris geyser basin for an in depth tour. At the top of the stairs before you go down, we went right along the side and straight down past the railings to the bottom of the basin. We entered into another planet from my perspective. To kneel down at the edge and see all the crazy structures of the very first pool was like landing on another planet. I believe this was the Porcelain Basin. We then followed the ranger around to the right side of the basin to the north eastern edge. If memory serves me, this is close to where the original hotel was. We then walked west onto this dome area and mist and snow started to come in. We sat down on this dome which was a nice 80°F and listened and felt the thumping of the geyser basin enveloped us. The air was freezing and we could not see more than 50 feet, but we were warm and safe sitting on this spot. This is where one of the key reasons for this guided tour became apparent. The ranger was instilling all of his knowledge about safe travel through geyser fields. The basic rules are that you should never enter a geyser field if you are not a professional, and even then you must be extremely cautious. There are hidden traps and what was safe yesterday is not necessarily safe today.

After sitting on this other planet for about 20 minutes, the snow flurry subsided turning into a light drizzle and we headed into the geyser field. I can only imaging what the tourists thought of us all in our official outfits out there in this geyser basin. This place is so huge that we surely looked like ants. We traversed through many places I do not remember out to the boiling sulfur pool. This pool is covered by black spheres of sulfur so completely that the surface looked to be solid ground. Yet, slide the beads aside and there was sub-critical water, just waiting to burn you. We heard the story of when they put a sample bucket down into the brown water quite a ways and returned with near molten sulfur. Think back, I wonder what the temperature is that sulfur becomes like the taffy that was described.

We then crossed some braided streams out to Realgar Spring where arsenic minerals are sitting right there on the surface with that distinctive realgar color.

This got us to not even noon that day. The number of adventures in just one day was phenomenal. That whole trip was, for me, just like be an astronaut landing on the surface of another planet.

And now, back to working on mud of the Santa Barbara Basin and my thesis.

Just got a book called JAPANESE cooking by Emi Kazuko and the movie THX 1138. The cook book looks nice with some interesting ideas like using spinach instead of seaweed for wrapping sushi. It has excellent color photos and was on sale at Borders for $6. I can't wait to sit down and watch THX 1138 again, plus it has his original student film that I have never seen before.

I looked in the Google Hacks and Google Pocket Guide. I still have not found the conversions trick that I used before and now can not remember. I did write down a list of things.

  filetype:pdf
  filetype:txt
  info:schwehr.org
  phonebook:
  rphonebook:
  bphonebook:
  stock:yahoo
  -"foo"   (exclude a term)
  "foo * bar"
  site:schwehr.org inventor
  features

But then I looked up the conversions and found this conversion of convert 10 inches to centimeters.

Search google for geology news

I have been thinking of quick writing up all my ideas on what are the ways you can do model construction for images. I may site down one morning and pound that out. This topic needs to leave my head as I don't have time to think about this stuff!

The Free Software Magazine. Will this be any good?

RMS has a blog. This should be interesting. And I quote: "About two months ago I heard about a project at the MIT Media Lab to develop a web browser for parrots. The smarter kinds of parrots can get very bored if they are home for hours with nobody to play with, so the idea makes sense." Need I say more? I really should become a FSF member.

I need to summarize the traffic about installing fink across large number of machines. Definitely some interesting stuff, but nothing yet that I would want to hang my hat on. I got one comment about deploying MS Windows instead. Err... no thanks. We already had multiple major failures outside of flight operations from viruses romping through the JPL professionally managed Windows boxes. That was not fun.

datamaster is another Dia UML sketch to code tool.

Delcom has a little USB development kit for $50. Now I need an excuse to get and play with one of these. They specifically mention Mac OSX, which is great. But why not Linux? Anyone have any good sites describing little projects with these? How about a wheel encoder for the winches on the ship? That would be a big help for those that don't have one! I never did use that little HC11 that I bought like 10 years ago. Maybe the Linux support just comes with the kernel?

I just saw this book while browsing last weekend: Mars: The NASA Mission Reports Vol 2. Funny thing is that I saw a very large number of pictures that I created. Lots of MER pictures. There were stills of Viz and RSVP that I made. In addition, there were tons of stuff created by Aurelio, Shigeru, Steve, and Zareh. It looks like they went through the photojournal for most of their images.

Someday, I would like to setup cvsweb for density and xcore packages. But that will not be until after I finish my thesis.

The Open 3D Visualization Toolkit is here: ltc.smm.org/visualize/toolkit. The site has been slashdotted so I haven't been able to look at it yet.

itk - NLM Insight; Segmentation and Registration Toolkit to support the Visual Human project.

openqvis - Open source volume rendering. Has some interesting datasets that would be easy to import and it is based on Coin! But not Voleon?

gcx - CCD photometry tools.

As for everyone who is upset about the Hubble, I understand, but my opinion is that we should spend that money for another space telescope and launch it with something other than the shuttle. I know there there is another space telescope set for 2011, but why not make it two? These projects are so valuable. Why waste time, energy, and possibly lives when we could build something for probably around the price of repair? Ok, so politics makes it easier to repair than get something new which has a high likelihood of being canceled by congress.

mathomatic - This one is already in fink. Symbolic math program. Wow. That built and installed in under a minute. Funky green screen. Now what can I do with this?

On my todo list is the type exactly this CVS tutorial for Jeromy B.

New fink version in cvs: 0.23.5 - "Fink: The Mojito of computing."

Tim Burton's Corpse Bride trailer. Can't wait!

From all-at-sio. This evening:

Jerry Bode is retiring from the Deep Sea Drilling Project and has
graciously donated the beer for tonight's TG.  So, come on down and
enjoy the yummy muchies, good beer, as well as the beautiful weather.

2P159388343EFFA2HPP2514R1M1 - Check out the textures in this pancam image from Spirit. It is hard to tell what I am looing at, but that might be some layering. Spacecraft 2 is spirit, right?

  MER A  ==  2  ==  Spirit
  MER B  ==  1  ==  Opportunity

I have been reading copies of the magazine Vision Systems Design while on the bus. (www.vision-systems.com) There is interesting stuff in here, but it mostly reads like a big sales brochure. I had never heard of Camera Link before. In their May 2004 issue, they tried to compare camera link with GigEther (why?), FireWire (only 400, not 800. Why?), and some other things. They got a lots of their bits versus bytes all messed up. Now I am reading about calibrating noise in CMOS imagers using a highly controllable sphere of light that you put over the camera. I always think that calling a light by a "Color Tempurature" is so strange.

I really get annoyed by the AOL messages about being connected in multiple locations. It usually happens with wireless hickups. Plus the messages do not tell me from WHERE?!?!

Welcome to Friday morning.

Yesterday a few interesting things came up. First, Catherine showed me a teaching tool that seems to have huge promise for larger classes. Each student gets a remote that is keyed to their student ID. Then in class there are receivers. You can ask questions in class and get immediate responses in terms of a bar graph. This is like the Pittsburgh Science Center for Nomad, but you get to know who answers what. At the PSC, each chair could vote on of three ways to control the Nomad rover as it went through the Atacama desert. You could use this kind of tool to get students to collaborate. Answer first on your own, then discuss, and see if as a group you can improve your answer. This is a device with a lot of potential. What exactly was this thing called? Google would not tell me.

Yesterday, I took a look at sugarbush, our Linux seismic server, that runs Mandrake 8.1. Now I can not remember for sure when 8.1 was the current version, but it must have been 2001. So this machine needs an update no matter what, but at the moment it would boot under its own power. It comes up into the boot process and makes it two past the interactive selection and hangs as it says it is starting DevFS. I tried to do fsck.xfs, since it uses SGI's XFS for the root partitions. However, I later discovered from the man page that fsck.xfs does nothing and returns success (EXIT_SUCCESS in C). Thanks. Then I looked up the xfs_repair man page and here is what I had to do while booted in knoppix:

  sudo -s
  umount /mnt/sdb1
  mount -w /mnt/sdb1
  umount /mnt/sdb1
  xfs_repair -v /mnt/sdb1

Guess what... Still did not work. I tried removing devfs from the lilo boot line, but got nervous about this since knoppix does all sorts of renaming of what is sda and sdb, so maybe I would push the system over the edge. It was really strange looking at the logs. syslog stops in November and the messages log ends on Jan 10th. Time for a total wipe of the / and /usr partitions and an install of the latest Mandrake version.

I am currently debating putting my AMS K15 and s[7] matrix data into sqlite for working on the rest of my thesis. There is a nice python module for working with sqlite. This might make it much easier to select portions of the data for doing things like a windowed bootstrap that I want to try out. The idea is that I would set a window of N samples, where N > 6. I would move this window along the core and bootstrap a group. Then slide the window my one sample and bootstrap again. The idea is to bootstrap the smallest region of the core so that samples are as genetically related as possible. For the samples in BPSIO Core 1 Sec 2, there is a sample every 3 cm. That would give me a minimum window of 18cm. This method would suffer the same problems as U-channeling does, but I might be able to find coherent deformation.

For the todo list: look up and explain what exactly a statistical null hypothesis is.

Here are some interesting links on industrial control and instrument data acquisition from Linux Weekly News. ProcessViewBrowser looks like it has had much more development. Exciting projects! Qt is still on my list of things to learn more about, but which will not happen until some time way in the future. By the way, SCADA stands for Supervisory Control And Data Acquisition.

• Qt4Lab
• ProcessViewBrowser
• qwt Qt Widgets for Technical Applications

A geologic article on yahoo: Volcanic Warming Eyed in 'Great Dying'. They talk about massive volcanic flows in Siberia. The technical term would be Large Igneous Province (LIP), right? Like the Ontong Java plateau or the Decan Traps in India.

I have a little story from doing my research yesterday. I was working away measuring paleomag cubes on the Kappabridge when I realized that a contract lens was bugging me. After about an hour of this, I was getting kind of annoyed. It is about time to go for a new pair, so I figured I would just throw out that one and work some more. It would only be a couple hours before I would get home. I was mostly okay, but it was a not the most fun looking at the computer screen. I finally had to just go home. That was when the trouble started. I decided to read a computer vision magazine I had with me while I was on the bus. I wanted to bury myself away from the wet cough lady behind me who was insisting on clinging to the back of my seat for dear life. Bus drivers on the 34 route are not all alike. Some are good drivers, but other treat the breaks like a binary switch so everyone is banging back and forth for the whole ride. Yesterday was a binary switch kind of guy. Between the driver, the reading with one contact, and the nasty bus area, I was pretty nauseous by the time I got off that bus.

I added MulleSite and gcam to my MacOSX 10.3 install notes doc yesterday. I still have not got around to working on turning my two talks into a movie.

Methane rain on Titan [bbc.com]

From the "Tao of Mac" is a list of essential osx software

cvstraq uses sqlite.

SimplybibTeX - PHP BibTeX web program with RSS and more. Any good?

Last but not least, Sarah and I got to hang out with Mike M. last night down in LJ last night.

I finished measuring the AMS for the Santa Barbara Core number one for the working half, section two. My first impression is wow. The samples almost all have distinct maximum and intermediate eigen vectors.

pywrat - Tools for using ssh and scp from in python scripts.

This evening I went to a secret showing at AMC La Jolla. Ridley Scott was there along with the head of Fox studios. That was cool.

Wow. I am actually getting feed back on my blog. This comes from Myche:

I thought I'd relay that I've been using blojsom
(http://blojsom.sf.net/).  Though this app has a rather odd name, it
is implemented in a way that I can both understand and appreciate.
Namely, it uses servlets and page templates to render your blog
entries (which are still kept as flat files).  It doesn't have to
"precompile" the pages like nanoblogger.  Dunno yet what implications
this has versus using a database to store the entries, but I like it
quite a bit.



Blojsom also has the obligatory plugin interface.  I use a few of
these (like weather) and had an interesting time learning how to
install and configure them.  Also, I'm using the "kubrick" theme,
which is not the default.

An article about the CDC guide to land and mud slides.

VisIt - Scientific Visualization software caught my eye in freshmeat today.

This morning I went over to the Intelligent Robotics Group (IRG) at NASA Ames and talked to bunch of folks about a new type of autonomous vehicle. It was cool to see how similar our thoughts are even though we both started separately without knowing the others intentions.

Before that I got a demo of Anne and Randy of their GameBoy based bot-ball device. Holly-smokes! This thing is awesome!

I now have to cleanup my disk from SPIE, Electronic Imaging, Visualization and Data Analysis, or what ever it was called. My disk is a mess at 97% full after two days of rendering frames. I will try to get a movie file with overlaid with audio. I was able to up the gain in Audacity and write out audio that does not force me to crank the volume.

I started writing my first article for my blog call "About." Talk about surprising. It is an attempt to explain why I am blogging, what I intend to use it for and what will and will not be included. For example, I do not have a lot of the actual analysis from my thesis in here. That is for my thesis.

Talking to Anne and Randy crystallized my feeling that at some point I need to move past Nannoblogger to a more powerful tool. The biggest gripe right now is the time it takes to update the html from a change to the data files. This makes the write, update, test cycle a major pain when you have an html tag that is wonked.

I just gave iMovie a try with exported frames from PowerPoint. Ugh. It chopped the side edges off the frame. Then when I resized the frame it seems the video freaks out about 1/3 of the way through that frame. What is the official NTSC frame size? I always forget. Is it 640x480?

One little time about the new terminal in San Jose Airport is that if you go down to the higher numbered gates, it is quieter and there outlets on the columns. Not the most comfortable place to sit, but better to have power, which is not available anywhere at gates A1-8.

What is the best way to edit php code with emacs? Dropping into html mode does not seem all the helpful.

I hear that Navtech is the engine for all the mapping web applications. Who are these guys?

Couple random links and notes:

Read an article in the newspaper talking about how OYO Geospace (Houston, TX) is trying to get their technology used in tsunami warning systems. What really makes up a tsunami warning system?

Marie - a LGPL'ed robotic design tool.

VIPS - IPS is an image processing suite designed for extremely large images and colorimetry.

What is VTK CISG Registration toolkit

That is it for my talks. I got one question: Are you using this kind of thing to manage AUVs in real time. Yes, but I have not had a chance yet. I think the audio recorded okay, but I have not tried to listen to it yet.

How copyright could be killing culture

A quote from this BBC news article:

Ms Rice retorted: "I have to say that I have never, ever, lost respect
for the truth in the service of anything."

BBC on the Shackleton hut to be resurrected.

Got a chance to talk to Justin Maki at lunch time. He is the only person I have talked to here that I knew from before.

Titan RAW frames from Huygens released by the ESA.

MER Cad images - I am not sure where this came from and if is an okay release, but it is neat to take a look at.

All of my twisted python work accept cvstoys and build bot is now in the fink cvs tree and I am not the maintainer. Woohoo!

Justin Maki's "20 Cameras on Mars" talk was excellent. This was definitely the best overview of the imagers that I have seen to date. I recorded Justin's talk for myself, so I will try to write some highlights at a later date. Also, he presented 30 polarized stereo pairs. I was worried that since the projectors were way at the pack of the room onto two 15foot tall screens that getting the horizontal and vertical match might be a problem, but just the opposite. These were the best static stereo images I have seen to day. Now keep in mind that I have not been back to JPL in 9 months. The synthetic stereo pairs from the microscopic imager were rockin!

SPIE could do with some better support. It is almost as bad as the Chicago airport. Power outlets are few and full of people using them. Wireless works and is free, but it takes about 2 minutes for an ssh connection to be established. Once I got a connection, I was getting 359KB/s, but yesterday, I thought they were blocking ssh for the first couple hours I was here. I can not seem to get pop-ssl to get out to my mail, so it is back to pine.

I think I am the only person here with a Mac laptop. Crazy! I have seen two or three with linux desktops, but this place is Windows XP crazy. I am a fish out of water.

Looking at Webalizer, I had a huge usage spike! I was averaging about 2800 hits a day, then yesterday it hit 5200. What happened? this can not be from my SPIE talk. There were only 30 people there, and I do not think that it was my, since my laptop was barely on the net. Maybe it was the msnbot which is now up to 8499 hits (15.35%).

Fire has plugins? Where do I get them and what do they do? Does Fire allow logging of sessions? I'd like to log some and not others. How?

Morning links:

cms made simple? Seems to use static files too?

Durability of Usability Guidelines

8 AM Tuesday morning - I am sitting in the big ball room before Justin Maki's talk. Should be a great one. They have polarized stereo images on the screens. Last night, my talk went well. The room the VDA section is in has about 65 chairs and it was half full. I hit record on my iPod with iTalk as the speaker before me was doing his conclusions. The one drawback of the iTalk is that it obscures the lock button. I was worried that the pause button would get hit during my talk. But checking when I got hope last night, it sounds like I have a good audio file. I need to boost the level, but the sound quality is good. Is there a way to change the record gains a little on the iTalk?

I now have used the dlo Jam Jacket 20 (that thing that wraps my ipod 20GB) for a week now. Overall I like it. The iTalk fits and I never feel like the iPod is going to slip out of my hands anymore. There are a few drawbacks. First off, this this is the great lint attractor. I think that my dress pant pockets must be devoid of all pocket link because it is plastered to my ipod case. My other worry is that it does no cover the back top edge of the ipod, so if I drop the ipod just so, it will hit metal on the ground instead of the rubber case.

While I am waiting for 15 minutes, I will see how much of yesterday I can capture. The most exciting talk in my view was the invited paper by C. Chen. It was a little frightening when we all saw his powerpoint had 76 slides. Yikes. He ended up blasting through may of his slides. But more to the point he talked about looking at citation relationships between research articles. The basic unit that he works with is that if two journal articles site an older paper, those two new articles and the older article are strongly linked. The main drawback of this is that technique is that the new cutting edge papers that are the hot topic get left out until the citations get farther on in time. There is an advancing front that this system tracks. He then talked about pruning algorithms to prune all but the most important links. He then looked for seminal papers: those that link clouds or flurries of research. He showed the prion research and the mad cow disease research as two clouds that linked through an early key paper that introduces the link between the two. This could be an excellent tool for those new to a field to discover some older key research on a topic that they need to review first. This method tends to highlight the summary or survey papers since they tend to be strong linkers.

I quickly jumped on the idea of McGreevy's word relationship work in the 90's where he looked at what words relate to other key words in a paper. McGreevy's work could be used to test links. If the word associations between two linked papers are totally dissimilar, then maybe they are not related papers. Check out McGreevy's work here:

McGreevy's work

10:15 AM I'm not in the San Carlos room for the Visualization and Data Analysis section. This section is right by the stairs in the Marriot. This is a very small room about the size of Vaughn Hall 300.

Things of interest for Monday:

2:50 Recovery of a missing color component in stereo images (or helping NASA find little green Martians)

Tuesday:

8:30 20 Cameras on Mars: The Mars Exploration Rover Imaging System
11:00 Low-cost photogrammetry for real-time 3D measurements
11:20 Photogrammetry for geological applications: automatic retrieval of discontinuity orientation in rock slopes
2:50 Three-dimensional scene reconstruction using multiview images and depth camera
3:10 Smoothing region boundaries in variable depth mapping for real time stereoscopic images
5:30 Videometrics Posters
5:30 Color Imaging X: Processing, Hardcopy, & Apps - Posters


WARNING: unstructured dump follows...

---

Making python programs into apps: py2app

The Marriot hotel's wifi settings sent my laptop into spasams.

• Self organizing maps - projecting higher dimensions to 2D:
  
  With neural networks, what is "Extremal Energies?"
  
  Unwrapping a tessellated sphere. Efficient representation, but some nodes are duplicated. This saves neighborhood pointers. Uses O(n) space, rather than O(n^2)
  
  By mapping geo-political data onto a sphere this gets rid of the political issue of everyone wanting to be in the center of the map.
• Haptics of Fluid Dynamics - Anders Ynnerman - Sweden
  
  CFD data from SAAB of Unmanned Aerial Vehicles - Case study on how to deploy volume haptics.
  
  Visual Rending - surface rendering, volume rendering (pressure field, curl for opacity, stream ribbons)
  
  Used the ReachIn Desktop Display
  
  Proxies for haptics - passive representations - keep pen stable. Apply spring equation as you go through the surface. Extending this to volumes. Dragging the proxy with you as you force the pen along. Jumping the proxies within the streamlines. Feels like you are trapped in a cylinder.
  
  For volume rendering, how can you know that you have fully explored the volume data set? How do you know that you have the right transfer function and have not missed a tumor in the body?



• Illustrative City Models
  
  Photorealistic obscures data changes and thematic information. Also leads to high expectations from the user. Hard to keep up changes.
  
  This guy would get in trouble with the dept of homeland security if he was using US cities.
  
  This is the kind of data that Peter Selkin got out of UCSD with special permission for his GIS/surveying class.
  
  Shading by face with small number of different hues using N-tone shading along with depth cueing by decreasing color saturation with depth. Then add shadow casting. Add facade texturing by say using light and dark windows on buildings. Then add variable edges to buildings and window LOD.

Lunch Break

Invited talk by C. Chen - Measuring the movement of a research paradigm.

Unit of Analysis = a knowledge domain

Pioneers: kuhn (1962), Englebart, science mapping: h small

I am heading in to SPIE. My talk first talk will be this afternoon at what looks like 5:00PM. This will be the SIO Mars talk. Tomorrow afternoon at 2:20 will be the visualization architecture talk.

9:45AM I am in the conference hall. This place is very quiet. Off to the San Carlos room. If you are lost, the conference is hidden upstairs.

OpendTect Student Competition and free licenses for this OpenInventor based seismic tool. This is OpenSource, but what license?

The comments are starting to flow in about fink deployment and Mac OSX for Mars operations. Keep them coming and I will summarize later this week.

There was an assertion that pro graphics cards are basically the same as the high end gaming cards. I have intentionally ignored the details of graphics cards for the last 4 or 5 years since that knowledge goes out of date year. But, with statements like that, what really is the difference between the $500 cards and the $2-5K cards? Is the texture ram different? Is the quality of graphics different? Quality of rendering used to be massively different. There was less effort spent making sure the graphics are 100% correct in the consumer cards when I looked a few years back. Can the cheaper cards do LCD shutter glasses in a window? Can they blend two neighboring screens for Panorams?

What is this SIFT algorithm for making control point panoramas? Is this a valid patent with JPL's Vicar software being around for a while? autopano-sift which needs hugin

sMArTH - My hope for MathML never ends.

In addition to version tracker:

• MacUpdate.com
• HyperJeff Mac OSX Apps - With RSS feed!
• sofotex - looks very yahoo like.

xwinmanimp is like xtermcontrol but even more low level. Control anything. Note that I have not tried this one yet.

Great news! Looks like Daniel Henninger is going to take over and submit all of my twisted related fink info files. Thanks Daniel!

Check out the Phoenix - Mars Lander 2007 web site. The PI is Peter Smith at the University of Arizona, Tucson. There are a lot of familiar faces on the web page from previous Mars missions.

Dia is an open source diagram package. Maybe with uml2php5 I might actually use the UML training from 1998. Not likely, but it is still a possibility. The Dia homepage. There is also umbrello in fink.

How does wikindx stack up to Endnote? Arg. Another application that uses mysql. Would be nice if it were self contained.

While waiting to board the plain to SJO, I opened the SPIE Electronic Imaging list of talks and the first thing I see is Justin Maki's picture. Excellent. That will go well with my two talks. The first one on Monday is an overview type talk where I will cover general concepts that are important to the scientific end users visualization tools. There will be movies made from both Fledermaus and OpenInventor/density. The imagery will focus on the Spirit rover and Gusev crater.

My second talk is more a systems overview. This will be a look at the flexibility require for working on visualization system for a wide variety of crafter from Mars surface rovers (what if Hugyens had been a rover with and RTG?) back to peopled ships on Earth and underwater vehicles. The key is being able to throw out or tweak any part that is necessary. I will start with the Viz architecture and show how it lets you layer on top of plain old ivview. People watching Viz 1.0 did not always realize that they were seeing more than ivview until a 3D model appears out of nowhere
I probably have to cut the second talk down substantially. Well see how the rehearsals go! 20 slides in 15 minutes is not going to happen! So the disclamer is as aways, all talks subject to change until I actually give them!

Myche just let me know that the Titan images are up on the Titan PhotoJournal Page It looks like the folks at the ESA did not project the images MIPL style, so their images so the mosaics are a bit strange. These are amazing images!

Sounds from Titan. Worth a listen. The radar is very amuzing.

It looks like my previous entry about setting up fink for a large number of machines got snagged by the spam filters. Before I write to the fink lists again, I want to briefly add to those questions with a list of the things that I believe it will take to make Mac OSX the dominate OS for the next Mars lander mission. For MER, Linux (RedHat 7.2) was the OS for about 80% of the machines inside the flight firewall. There rest were almost all SunOS 5.9 (Solaris 9) boxes. The primary file server was a two refrigerator sized Sun (I'll save the performance comments for another day - summary: "Not Good"). I also saw two full sized rack SGIs. No one I talked to knew what they were for. I believe they were Origins running IRIX. They lived not in the server room, but in the FAX room. There were a number of G5 OSX 10.3 machines, but they were all outside the firewall, not as banded as Windows and the foreign nationals, but not in for the main party. What will Mac OSX need to be able to do to dominate next time?

• Stabilize 10.4 quickly. The OS tends to be locked down a year or two before landing to avoid surprises both in security and stability.
• Better graphics card support. We need to be able to use the top of the line pro graphics cards for 3D models. If Linux has better support, then that is what will be used.
• Be able to drive 3D stereo shutter in a window. Every other OS does. And be able to do this in both X windows and Aqua.
• Get SGI to port Performer to OSX. RSVP uses Performer on Linux right now.
• Make sure Java 3D is fully supported and fast. The science interface (formerly WITS) uses Java 3D
• Push fink even farther in terms of packages supported and improved testing. There needs to be guidelines and documentation of how fink has been deployed across 200+ machines at one site.
• Being able to make sure that all relevant fink packages are able to be build optimized if possible. Having fink on a G5 with code not taking full advantage of the compiler optimizations will frustrate the team.
• Improved support for clustering, especially for render farms. It should not require Xserves.
• Get OpenAFS shipping with OSX (and not just osx server). Many flight people count on AFS up to the transition to the flight line activities. Then they have to drop back to NFS for flight ops.
• Go for more CPUs in one box... how about 4?
• Really push 64bit support into more of the os and get way beyond 8GB of RAM per machine. We want 32GB and more soon.
• Support the big Panoram displays.
• Start shipping OSX with fugu preinstalled and do everything to make secure systems easy on the admins and users.
• Make sure that there is good support for the VxWorks tools on OSX. I have not touched VxWorks since 2000, but since this is what is on the flight vehicles, all the cross compilers and tools need to work well on OSX. That will make testing easier. The Windows boxes that many people use for VxWorks are not allowed inside the flight systems.

Those are the main things I can think of right now. I really would like to see OSX and fink taking a bit part in the next missions.

Additional notes:

Forgot to mention that these are my personal opinions and ideas. These posts in no way represent the ideas of any institution! Nor do I have any say about the makeup of the flight computers.

Some more things OSX could do:

• Stop the distinction between OSX Server and standard OSX.
• Make sharing home directories between disparate Macs super easy. I have seen too many weird hacks to make this work right.
• Provide something like SGI's FAM. This would make programs like the Collaborative Information Portal (CIP) easier to implement and easier of the servers. The idea is a filesystem change notification system. Some programs need to watch for changes in large/deep filesystems. Stat'ing large parts of a tree is totally unacceptable.
• Make deploying servers with raid arrays in the 100's of terrabytes easy. 5.6 TB is not really that much storage for a mission these days. That's scratch space for just a couple of people processing stereo 3D data. Plus make backup easy.

Just stopped by the ODP West Coast Repository building to wish Jerry Bode well for his retirement. He was serving up some insane cheese cake, strong coffee, and cookies. There was some serious story swapping going on including the Glomar Challenger being taken over by the Argentinian Navy way back. I had not heard about that one before. Right up there with the Ewing (sp?) being attacked by pirates over on the East side of Africa in Aug/Sep 2001. At least in Argentina there were no bullets fired.

ODP West Coast Repository

Quicksilver - What exactly is this Mac OSX app? Something about global hot keys?

A little applescript to set the osx desktop background from this article:

tell application "Finder"
  set currentPicture to the desktop picture as string
  set the desktop picture to ¬
   ":Library:Desktop Pictures:Solid Colors:Solid Aqua Blue.png"
  set the desktop picture to currentPicture
end tell

BTW, Sarah and I donated $40 to tsunami relief last weekend.

The painters are still working on our building. Some guy is sanding away next door to the north. Will they ever do a 2nd coat on our railings? They never did sand the old paint before the 1st coat.

I have been working on movies now for SPIE, but I am desperate to get back to the AMS data. The Santa Barbara data looks so exciting at this point. I have got to measure the rest ASAP.

3:30 PM PST - Just saw my first picture from Huygens on CNN. Give me more! Nothing on the Saturn Photojournal. Give me more! I can not wait! The first picture I saw had a dendritic pattern. Rivers of methane with erosion? That would be amazing! Aha. Here is the Huygens Descent page. Landing on another planet or moon for the first time is a HUGE deal.

MathWorld article on simulating the tsunami wave. Scroll down for a graphic of the simulation.

How the heck do I listen to NPR sound smil files on Mac OSX. Do I have to install Windows Media player? I do not really feel like doing that!

OSX hidden doc preferences

Forgot to mention that today I got a dlo Jam Jacket 20 (crazy name, eh?) for my new 20GB iPod. It got the clearish one. Some of the colors were a little crazy. Seems to fit with my iTalk. My iPod feels less like it is going to slip out of my hands or pocket now. I'll try to remember to write what I think of it after a week or two.

I just tried to search my blog using google. It is not getting indexed very often. I need to fixup swish-e and the keyword/phrase index. I was hoping to find the ITConversations blog, but no luck. I have now listened to all 6 talks that I downloaded. Today I went through 2 on the bus: Phil Zimmermann and Rasmus Lerdorf. Both were pretty good. Now here is what I would like. I would got for 2 general catagories. The first and most important would be in geology and geophysics. How about interviewing people who are really good at a technique. Have them explain what it is and what it is good for. Go grab someone who does ground penetrating radar and grill them. What kinds of things can be studied with it? How do I go about getting a unit? How do I process the data? What is coming in the future? What about people recording their own conference talks. Most would really suck, but if we could get a stream of good ones going, I think there would be a huge impact on the community. It is easy to learn about computers... go to any bookstore or news stand and you will find tons. But the easy access to geology and geophysics just is not there. geology.it is better than nothing, but it is not /. Hmmm... I think I wrote about this before, but since it is hard to search my blog, I can't tell you in which entry and just how much of a broken record/scratched CD I am.
I was thinking of going for iPodderX to get pod casts from ITConversations, but I did not realized that it costs. No thanks. Into the trashcan it goes. I think I'll go for free software. What about iPodder? I installed that back in November, but have not touched it since. I'll give the big lemon on my dock a try for a bit. I see Adam Curry's name in the credits for the idea. I can say that he is a visionary, but I listened to two of his podcasts and that was enough.

So now that iPodder downloaded some audio files, did it do anything with them?

PHP iCalendar looks like it might be what we need for a calendar program. Have to give this one a try. And I did. Took about 15 minutes to setup everything since I am already running apache2 on my laptop. Here is what I did:

• Download phpicalendar from http://sourceforge.net/projects/phpicalendar - I got 2.0beta from Oct 2004.
• Edit your /sw/etc/apache2/httpd.conf and add this for php4:

    AddHandler php-script php
    AddType text/html       php
    # PHP Syntax Coloring
    # (optional but useful for reading PHP source for debugging):
    AddType application/x-httpd-php-source phps
  

• Uncomment the php module in httpd.conf

  LoadModule php4_module        /sw/lib/apache2/modules/libphp4.so
  

• Change the httpd.conf index list:

    DirectoryIndex index.html index.php
  

• cd ~/Sites
• tar xfz ~/Desktop/phpicalendar-2.0b.tgz
• cd phpicalendar-2.0b/calendars
• cp ~/Library/Calendars/Work.ics Kurt.ics
• sudo /sw/sbin/apachectl restart
• open http://localhost/~$USER/phpicalendar-2.0b/index.php
• That's it! Now you can go figure out how to configure other stuff

I used this blog entry to get the apache2 configuration tips.

Apple's iCalendar parsing page

Galarie looks handy for generating galleries of images. Ok! This is really nice. I made a test web page call GalTest from some pictures in iPhoto. It noticed my selected pictures.

Maybe Lisa would want to try PyBlosxom? Are comments build into it? Seems poorly maintained. Very messy and broken web pages.

Actually WordPress is GPL and sounds pretty good. wordpress.org If I was not already using NanoBlogger, I might try it out myself.

Just out: A new 0.18 release fixes up density for SPIE Electronic Imaging. First, I added the headlight option to render. The more important change in density-0.18 is that the render and simpleview command scripts actually should be able to find the associated _bin binaries.

I should check out bashlib for writing CGI scripts easier with bash.

MIT has another tutorial on OpenInventor ASCII scene graphs. The InventorMentor is online here. I need to buy a new copy of this book!

Just sent out a request for ideas on deploying fink across some place like IGPP. Here is the text of the message:

This is something that I am not directly involved, but I would be int