Kurt's Weblog

Today is the first time that I have played with the gnuplot index feature. This helps to reduce the number of loose data files in a directory. Here is a quick sample from the section boundary markers in my Santa Barbara data. The key thing is to have TWO blank lines after each group.

cat << EOF > dec-sec-bound.dat
# There is no core 0
0 0






# Core num: 1
37.5 0
37.5 360






# Core num: 2 - no values
0 0






# Core num: 3
39.5 0
39.5 360






# Core num: 4 - no values
0 0






# Core num: 5
44.0 0
44.0 360






# Core num: 6 - no values
0 0
EOF

Then here are the gnuplot commands to print this. Core 0 is there so core 1 is refered to as the 1 index.

gnuplot
  set xrange [-10:370]
  set yrange [0:200] reverse # to plot with zero on top
  plot 'dec-sec-boundary.dat' index 1 using 2:1 with lines \
       , 'dec-sec-boundary.dat' index 3 using 2:1 with lines

I hope Apple adds this kind of thing to iCal and Address Book. GroupDAV. I haven't looked closely, but this is the right direction. It is time that the world catch up to what Solaris could do in the mid 90's.

I got a really nice response from David Flacker at IODP. When I get back to the odp data in a day or two, I will try this out. I am currently trying to rotate my cores bases on the nrm direction in a way that is easy to tweak. I am aiming for a zero centered -180 to 180 graph.

USING WGET



Yes, you can use tools like wget:



	wget
http://iodp.tamu.edu/janusweb/physprops/msldat.cgi?leg=146&site=893&hole=a&outputtype=5&depthmin=5&depthmax=10



There is no formal publication of the input parameters accepted, but
the variable names and the variable range and form can generally be
gleaned from the "name" parameters found when viewing the source of our
.shtml pages.



	outputtype=5	is equivalent to the Excel Integration delimiter
preference on the Report Options popup and should result in fairly
clean, non-html comma-separated vector files



	depthmax=10	when only upper limit is specified depths <=
limit are returned, vice versa for depthmin parameter; when both a
depthmin and depthmax are specified, values between and including the
range end-points are returned ( depthmin <= x <= depthmax)



All of the reports you can run are browseable in the janusweb URL tree:
 http://iodp.tamu.edu/janusweb 
or are otherwise summarized in the links here:
http://iodp.tamu.edu/janusweb/links/links_all.shtml 






QUERY CAVEATS and RECOMMENDATIONS



Apologies for the aggravations. While it serves the bulk of data
request needs without additional human intervention, it is very possible
to generate queries that will not run to completion within the timeouts
of the typical web-browser. The query system in place generates reports
directly from the underlying database. We do not provide any kind of
pre-query analysis to offer automated estimates on how long a query will
take. The amount of time is highly variable with data type, data model
structure, the exact specifics of the query inputs, and the amount of
data being searched/sorted.



Best practice suggestions:



	Look at the Database Overview page
(http://iodp.tamu.edu/janusweb/general/dbtable.cgi) to see what data is
available on-line.



	Be as specific as possible about what you want: e.g. if you know
the site, specify the expedition with it--often the database can bring a
data index into play that result in orders of magnitude improvements on
turn-around time. The problem from the server perspective is not how
much data is returned, but how much data has to be sifted through to
figure out what should be returned.



	Avoid doing queries by depth ranges where possible. Depth is a
calculated value, not an absolute stored value. A lot of overhead is
incurred by the database server in the way these depth filters are
currently implemented. If you need it, though, it will work, just set
your timeout limits for wget high (quarters of hours rather than
minutes).



Experience notes:



The CGI-based query system does use cookies to remember expedition,
site, hole, and report options settings throughout a browser session.
The values remembered are prefilled in forms. Enable cookies for the
iodp.tamu.edu site if that fits your usage patterns at all.



The query system uses popups for the Report Options dialog and for
query result errors and warnings. E.g. default query behaviour when no
data is found is to generate a popup window and a page-back event. When
popups are disabled by the browser, all you see is the page-back
event--no time to look at the empty result page.



Regards,
Fackler

From ScienceDaily: Scripps Researchers Find Clear Evidence Of Human-Produced Warming In World's Oceans

I never noticed this before, but XCore is in the FSF software directory!

http://directory.fsf.org/science/visual/XCore.html

And hey, this is a picture of me working on Devon Island in the Haughton Crater. This is the first I have seen this one. The picture is by Peter Essick who shot pictures for a National Geographic article.

  MarsOnEarth img 931

You are now a Ninja!

And Escape!

I managed to get the 893a MSL (mag susc) data a week or two ago, but had trouble getting any other data.

http://iodp.tamu.edu/janusweb/physprops/msldat.cgi with site 893 hole a gives:

Error - 504
Gateway Timeout:
165.91.53.158 (80)
Reason: Timed out while waiting for data from the remote host.

Things like http://iodp.tamu.edu/janusweb/paleomag/tensdat.cgi with site 893 hole A just flash up something and jump back to the page. When I hit forward, there is no data on the page. Is there no data available or am I doing something wrong? Is there a way to tell what is actually available for 893A and B?

Also, is there a way to put a query in a URL? I'd like to be able to do something like:

  wget http://iodp.tamu.edu/janusweb/paleomag/tensdat.cgi?site=893&hole=A

You get the idea. Then it would be easy to snag the data from any shell or python script.

Today, we had what turned into a mini lab meeting for part of the sed group. Really, it was just who we ran into in the hallway. But with all the rain, landslides are all over San Diego County. So we had to go out and see what is happening with the NOAA Fisheries building at the other end of the SIO campus. We walked down the beach and found what looked like an extremely fresh slide. We grabbed a life guard and found out that it happened last night. The hill came down on dike rock! Some bits and pieces of metal came down too. The fresh debris exposed some really great sedimentary geology. I got 70 pictures of it before the ocean erodes away all this great stuff. Check it out!

  Galerie photo show of Slides at SIO

Woo hoo! Much progress in the land of working computers. Here are the fixes:

Roi's flailing gcc... Go into /Library/Receipts and remove each receipt for the developer tools one by one and install the package again from the developer dmg.

Lisa's stubborn X11SDK... Do NOT enable Virex. Virus software should not run all the time on Mac OSX. It just causes problems. Scanning programs are fine. One 10.2, Norton AntiVirus destroyed several machines to the point of having to reinstall everything. Once Virex was disabled from active scanning, X11SDK installed right away on Lisa's G5.

Doh! Got a bug report that weka failed to build on 10.3.8 with fink. I confirmed it:

init_all:



init_tests:
    [mkdir] Created dir: /sw/src/weka-3.4.3-1/weka-3.4.3/build/testcases
    [mkdir] Created dir: /sw/src/weka-3.4.3-1/weka-3.4.3/reports



init_compile:
    [mkdir] Created dir: /sw/src/weka-3.4.3-1/weka-3.4.3/build/classes



compile:
    [javac] Compiling 635 source files to /sw/src/weka-3.4.3-1/weka-3.4.3/build/
classes
    [javac] Note: Some input files use or override a deprecated API.
    [javac] Note: Recompile with -deprecation for details.
     [copy] Copying 167 files to /sw/src/weka-3.4.3-1/weka-3.4.3/build/classes
     [rmic] RMI Compiling 1 class to /sw/src/weka-3.4.3-1/weka-3.4.3/build/class
es



compile_tests:



run_tests:
    [junit] Class not found "weka.AllTests"



BUILD FAILED
/sw/src/weka-3.4.3-1/weka-3.4.3/weka/build.xml:139: Java returned: 1

Microsoft is trying to patent a pointer comparison operator. You have to be kidding.

If you get bored with reading my blog, perhaps you should gizoogle it. WARNING: strong language - Blame the language on gizoogle and Snoop Dog, not me.

Rey et al have a very interesting paper in the 25 March 2005 Marine Geology:

Early diagenesis of magnetic minerals in marine transitional
environments: geochemical signatures of hydrodynamic forcing.

I will be reading this one right after Roi's Tarduno02 paper.

Just finished up the full database creation python scripts. The bash script was getting to be 5-10 minutes long and I have a long ways to go before I am done. Right now I am at 7-8 seconds with the python script. There were just so many calls to awk, cut, and sqlite. Now with the python code, the script is much simpler and tons faster. It uses the string split method extensively and I have some classes that handle converting k15 data into hext and s formats. Check out the two scripts:

ams.py
build_db.py

ams.py is my module of helper functions that includes the classes Hext, S_Matrix, DepthLookup and SampleName. I really like SampleName. I give it a string from one of my sample names and it pulls apart all the fields. It also has a __str__ method so that if I turn it into a string, it goes back to the original.

build_db.py is a little more complicated. It reads each of the text data files off of disk, creates the table, and inserts all the values. Having really string processing in python makes the core location and core section tables so much simpler and easy to read.

With help from Martin Costabel I started replacing missing files on Lisa's G5 that the X11SDK did not install. I am starting to thing that Apple's package manager is a piece of junk beyond just basic usage. There is (easy) way to query, uninstall, reinstall, verify, packages especially when logged in remotely. On Lisa's machine with 11SDK, it missed all but a couple headers, all the .a's, and /etc/font... and that is what I have found so far. I finally just copied these from another machine. That got a lot back on track, but not all.

Last night mbsytem-5.0.6 was released to the wild. I just finished putting it in the fink unstable tree. This now forces you to upgrade to gmt 4.0. You should see a speedup of the mb edit commands since Dave and Dale enabled optimization with the compiler. Please email me about any troubles from the fink install.

Just found an email in my inbox from Dave Caress talking about the new features in the just released MB-System 5.0.6. I am about to set forth on the task of getting it into fink. In the meantime here is the email from Dave:

  One new feature that is not strongly highlighted in the release
  notice is the inclusion of MBgrdviz, an OpenGL based tool that
  provides some simple visualization capabilities for GMT grid
  files. Since MBgrdviz is not yet well documented, this note is
  to provide some extra hints on building and using this new
  program. MBgrdviz is essentially a demo and test program for a
  visualization library called MBview that will be central to
  several new MB-System tools now under development. These new
  tools will include interactive project management, improved
  bathymetry editing, and patch test tools in the relatively near
  term.
  
  Since the visualization API depends on OpenGL as well as X11
  and Motif, the install_makefiles script now includes an
  OPENGLLIBS parameter. If you do not define (or comment out)
  OPENGLLIBS, then install_makefiles will construct the Makefiles
  structure so that MBview and MBgrdviz are not built. In this
  case, the rest of the MB-System tools will build and install as
  before. Thus, to build MBgrdviz, you must define the OPENGLLIBS
  parameter properly for your system. The comments in the
  install_makefiles script include appropriate settings for
  MacOSX and IRIX.
  
  Since there is no real documentation yet, early users of
  MBgrdviz will be determining if the interface is sufficiently
  obvious to be used without documentation. Feedback on
  ease-of-use will be appreciated.
  
  Here are some hints for using MBgrdviz:
  
  1. MBgrdviz can display up to ten instances, each potentially
  displaying different grids. The program will work with grids
  that are in geographic (longitude latitude) coordinates or in
  projected coordinates systems (e.g. UTM eastings and
  northings). However, the program will only recognize projected
  coordinate system grids that have been made by mbgrid, as
  mbgrid embeds the projection used in the grid file comments.
  
  2. Each grid is displayed in an MBview window with its own view
  control widgets.
  
  3. The basic controls for display type are in the View
  menu. Options include 2D or 3D display, setting the primary
  data displayed in color (e.g. the topography in the primary
  grid, the topographic slope, or an overly grid), shading style
  (none, shading by illumination, shading by slope, shading using
  an overlay grid such as backscatter), and turning topography
  contours on or off.
  
  4. Interaction with the data is controlled by a number of mouse
  modes; the mouse mode is set through the options in the Mouse
  menu. Options include Pan & Zoom, Rotate Model, Rotate View,
  Shading, Pick Area, Edit Sites, Edit Routes, and Pick Nav. If
  the MBview window is resized large enough, a set of buttons
  appears on the lower left that duplicates the Mouse menu
  options, making it easier to switch modes. The top status
  display box on the left always displays the mouse button
  behaviour for the current mouse mode. So, in Pan & Zoom mode,
  this box shows that the left button does pick operations, the
  middle button does pan operations, and the right button does
  zoom operations.
  
  5. The Rotate Model and Rotate View mouse modes are only
  available when the data is displayed in 3D.
  
  6. The basic pick operation will pick a single point on the
  topography, display a red X at that location, and show
  information about the pick in the middle status box on the
  left. If the user drags the cursor while the right button is
  down, two points will be picked (the point where the button was
  pressed and the point where the button was released), and the
  two points will be displayed as red X's connected by a line
  segment between the points. In 3D views this line will be
  draped along the topography. The status window will show the
  positions of both picks and the distance between them.
  
  7. The Pick Area mode allows regions and areas to be picked
  interactively. In MBview, a region is rectangular with sides
  that are oriented N-S and E-W in the grid coordinates, is
  picked with the left button in Pick Area mode, and is displayed
  as a yellow box. An area is an arbitrarily oriented rectangle
  defined by dragging the middle button in Pick Area mode, and is
  also displayed in yellow. The aspect ratio, and therefore the
  width, of an active area can be altered by dragging the right
  button up or down in Pick Area mode. In 3D views both region
  and area bounds are draped on the topography.
  
  8. MBgrdviz also supports display of Sites, Routes, and
  Navigation.  Sites and Routes may be created and altered
  interactively in MBgrdviz, and can also be exported to files
  and imported from files. Site and Route files created by
  MBgrdviz include comments documenting the format. The
  file-naming convention for Site files uses an *.ste suffix, and
  an *.rte suffix for route files. Navigation is imported by
  reading datalists of swath files supported by MB-System.
  
  9. The Edit Site mouse mode allows the user to select and move
  sites with the left button, create new sites using the middle
  button, and delete already selected sites using the right
  button.
  
  10. The Edit Route mouse mode allows the user to select and
  move route waypoints using the left button, create new route
  waypoints using the middle button, and delete selected route
  waypoints using the right button.
  
  11. Navigation may imported in two fashions from the Action
  menu. The Open Navigation menu item allows a datalist to be
  selected and opened; the program then reads the navigation in
  each swath file referenced by the datalist and displays it as a
  simple black navigation line. The Open Swath menu item also
  reads navigation data from a datalist, but it causes the
  program to also read and store the acrosstrack bounds of the
  swath bathymetry associated with each navigation point, with
  implications covered in point (12). In 3D views, the navigation
  can be displayed using it's real vertical position (the
  navigation tracks will usually display somewhere above the
  topography), or it can displayed draped along the topography,
  or both.
  
  12. The Pick Nav mouse mode allows the user to pick individual
  nav points and to select and deselect arbitrary sections of the
  navigation.  If the navigation has been imported using the Open
  Navigation menu item, then the selected navigation will simply
  be displayed in red, and information about the selected
  navigation will appear in the middle status window on the
  left. If the navigation has been imported using the Open Swath
  menu item, then the selected navigation will also have the
  bounds of the associated swath bathymetry displayed in
  yellow. In 3D views, the swath bathymetry bounds will be draped
  on the topography.
  
  13. MBgrdviz displays the topography in three
  resolutions. Whenever an operation modifies the display, the
  data will first be redrawn in low resolution, and then in a
  high resolution. During operations involving mouse dragging
  (e.g. panning, rotating, zooming, or two-point picking), the
  display will be refreshed rapidly in low resolution, with the
  high resolution display appearing once the operation is ended
  by releasing the mouse. For large grids, the high resolution
  display may not be at the full resolution of the grid. A full
  resolution display can be obtained by clicking the Full button
  below the middle status box on the left. The lower status
  window on the left shows the current status of drawing the
  display - typically users only see a "Done" status except
  during full resolution drawing.
  
  14. The Reset button below the middle status box on the left
  resets the display to the original scale and orientation.
  
  15. The Clear button below the middle status box on the left
  clears any picks and selections.
  
  There are some known bugs in this first release version of
  MBgrdviz:
  
  1. The Rotate View function simply doesn't work right. I don't
  have the order of the OpenGL rotations set properly so that
  Rotate View operations actually rotate the 3D display around
  the user's viewpoint.
  
  2. There is a memory leak that produces error messages when
  MBview instances are dismissed.
  
  3. In 3D displays the program tries to figure out what part of
  the grid is actually in the display window so that it can skip
  drawing areas that cannot be seen. MBgrdviz also then adjusts
  the resolution used during low and high resolution drawing
  accordingly. This allows the effective resolution to increase
  as one zooms in on a particular area.  However, the current
  algorithm frequently underestimates the viewable area, with the
  result that visible parts of the grid are left undrawn.

So Mac OSX makes level 3, so Suse Linux goes and makes CC EAL 4+. For some reason, I have never tried Suse.

Test-Driven Development in Python

PythonPocketReference

I created the original twisted fink packages, but guess what?!?! I don't know how to use twisted. I know NOTHING! Here is a twisted intro so maybe I will now know something.

RealClimate.org was mentioned in this months Scientific American. Here is what the site is in their own words:

  RealClimate is a commentary site on climate science by working
  climate scientists for the interested public and journalists. We aim
  to provide a quick response to developing stories and provide the
  context sometimes missing in mainstream commentary. The discussion
  here is restricted to scientific topics and will not get involved in
  any political or economic implications of the science.

pybliographer and bibtex2html are both in fink, but pybliographer does not currently build. Maybe I can use bibtex2html to do a better job of my papers web page. num-utils also looks cool. Maybe after I install gnome-python-py23 I can get pybliographer to build. I finally created a temporary gnome-python-py24 and that got me to a pybliographer that built and installed. I have not tested it.

If I had more time, it sounds like what I need is Pexpect. Bummer that it is not in fink.

I have not been able to get k15_hext to hang out and let me talk to it. I figured that it would be easy to pass it 4 lines at a time, but no. There is no time to really figure out how to do this, so I am on to the next thing. Here is the code that works for cat, but not k15_hext:

#!/usr/bin/env python
import os,string
fin,fout=os.popen4("cat")
fin.write("bp04-6gw-s1-141.2	schwehr	1/3/05	4:33 PM	 1716	 -4.75\n")
fin.write("9.3800E+1	9.2950E+1	9.3550E+1	9.3550E+1	9.2950E+1\n")
fin.write("8.9150E+1	8.9100E+1	9.2900E+1	8.9150E+1	8.8900E+1\n")
fin.write("8.9950E+1	8.8750E+1	8.5100E+1	8.9950E+1	8.8800E+1\n")
#fout.close()
fin.flush()  # <---- this works for cat, but not k15_hext!!!????
print fout.readline(),
print fout.readline(),
print fout.readline(),
print fout.readline(),
fout.close()

Here is what I have so far which starts and kills a k15_hext instance each time. Not efficient, but it works.

#!/usr/bin/env python
import popen2,string



class K15HextEngine:
    """
    Doc for K15.  Uses the k15_hext from Lisa's pmag to convert k15
    Kappabridge measurements to hext statistics.
    """
    
    def __init__(self):
        self.totCount=0
        print "finished init"



    def getHext (self, line1, line2, line3, line4):
        """Unable to keep a k15_hext open and write to it over time.  Why not?"""
        # FIX: check if new line at end, if not, add one
        blah=2
        fin,fout=popen2.popen2("k15_hext")
        fout.write(line1)
        fout.write(line2)
        fout.write(line3)
        fout.write(line4)
        fout.close()
        hline1 = fin.readline()
        hline2 = fin.readline()
        hline3 = fin.readline()
        hline4 = fin.readline()
        hline5 = fin.readline()
        self.totCount += 1
        print "total = ",self.totCount
        return hline1,hline2,hline3,hline4,hline5



# Test code
if __name__ == '__main__':
    print K15HextEngine.__doc__
    k15_hext = K15HextEngine()



    l1 = "bp04-6gw-s1-141.2	schwehr	1/3/05	4:33 PM	 1716	 -4.75\n"
    l2 = "9.3800E+1	9.2950E+1	9.3550E+1	9.3550E+1	9.2950E+1\n"
    l3 = "8.9150E+1	8.9100E+1	9.2900E+1	8.9150E+1	8.8900E+1\n"
    l4 = "8.9950E+1	8.8750E+1	8.5100E+1	8.9950E+1	8.8800E+1\n"
    
    h1,h2,h3,h4,h5 = k15_hext.getHext(l1,l2,l3,l4)
    h1,h2,h3,h4,h5 = k15_hext.getHext(l1,l2,l3,l4)
    h1,h2,h3,h4,h5 = k15_hext.getHext(l1,l2,l3,l4)
    print "  RESULTS: "
    print h1,h2,h3,h4
    del k15_hext

Now I just need to make this a nice module that lets me get some sort of hext object.

My beta of NewsFire expired this week. That was enough motivation to really go start using NetNewsWire Lite. I am starting to really like this new world. Not quite as clean and simple as NewsFire, but it does have things like letting you know when it is checking each news feed. I still have not played with the Firefox RSS capabilities which might be pretty cool.

Onward with the python k15 program. Here is my first working example. After this, I need to turn it into a class, so I can have an object that takes k15 strings and spits back the k15_hext stats. The other thing it has to handle is that after 100 samples, it has to close the k15_hext process and start a new one since that is the maximum number of samples setup in that fortran program. Here is my working example:

#!/usr/bin/env python
import popen2,string
fin,fout=popen2.popen2("k15_hext")
fout.write("bp04-6gw-s1-141.2	schwehr	1/3/05	4:33 PM	 1716	 -4.75\n")
fout.write("9.3800E+1	9.2950E+1	9.3550E+1	9.3550E+1	9.2950E+1\n")
fout.write("8.9150E+1	8.9100E+1	9.2900E+1	8.9150E+1	8.8900E+1\n")
fout.write("8.9950E+1	8.8750E+1	8.5100E+1	8.9950E+1	8.8800E+1\n")
fout.close()
print fin.readline(),
print fin.readline(),
print fin.readline(),
print fin.readline(),
fin.close()

Running ./k15.py returns:

  ./k15.py 
   bp04-6gw-s1-141.2    bulk susceptibility =   90.5700073
  F =      2486.69  F12 =        63.74  F23 =      4088.38
  0.34519  156.2    3.4    0.8   10.3   86.0    7.4  246.3    2.3
  0.34164  246.3    2.3    0.9   10.3   86.0    7.4  156.2    3.4

This is take two on setting up webalizer and I did it this time where it is not a problem to give all the details of what I did. So here is what I did! This is using the Apple supplied Apache web server (not the fink Apache - that would use different paths to all the files).

  fink install webalizer
  cd /Library/WebServer/Documents
  mkdir webalizer
  export EDITOR=emacs
  crontab -e

Now when crontab pops up emacs to edit your crontab file, enter this, but put everything starting with "30" and ending with /dev/null all on one line:

MAILTO=''
30 2 * * * /sw/bin/webalizer -p -N 2 -D \
/Library/WebServer/Documents/webalizer/dnscache -n sorcerer.ucsd.edu \
-o /Library/WebServer/Documents/webalizer \
/private/var/log/httpd/access_log > /dev/null

You can change -n sorcerer.ucsd.edu to your websever. You can kick things off right away by running webalizer with those options. Otherwise you will have to wait until after 2:30 AM for this cron job to get run. To see the results, take a look at:

http://sorcerer.ucsd.edu/webalizer/

I also added a robots.txt to the webserver to tell microsoft to bugger off.

User-agent: msnbot
Disallow: /

Check out Alan Boyle's Cosmic Log for more info on the mars life craziness. Thanks to Kiley for the link!

From the NASA HQ press release:

Dolores Beasley/Gretchen Cook-Anderson 
Headquarters, Washington 



Feb. 18, 2005



RELEASE: 05-052 



NASA Statement on False Claim of Evidence of Life on Mars 



News reports on February 16, 2005, that NASA scientists from Ames
Research Center, Moffett Field, Calif., have found strong evidence
that life may exist on Mars are incorrect.



NASA does not have any observational data from any current Mars
missions that supports this claim. The work by the scientists
mentioned in the reports cannot be used to directly infer anything
about life on Mars, but may help formulate the strategy for how to
search for martian life. Their research concerns extreme environments
on Earth as analogs of possible environments on Mars. No research
paper has been submitted by them to any scientific journal asserting
martian life.

It was nice to know that I was right in warning that this was not a good thing to cover. Now I can stop worrying about ideas of how methane variations could be explained by non-biological means. I was starting to think about methane hydrates either in the near surface in the non-polar regions or on the ice in the polar regions. I do not know that the stability fields look like at the low pressures of Mars, but it might be possible to have methane hydrates in the cold parts of the planets, no? Anyone else want to do the stability calculations? I am too lazy.

On another note, I tried to fix Roi's laptop today without success. We removed the /Library/Receipt file for DeveloperTools.pkg and were able to install the package again, but got the same ncurses bomb. Then we tried gcc3.3.pkg, but the installer said that we could not install gcc3.3 on that machine. Strange! GUI's that don't tell you what they really are doing or thinking drive me nuts.

Today I measured AMS for core 2GW, so the main AMS data has all been collected. I need to fixup my database creation code and start crunching and evaluating this stuff!

CrappyApps - Documents what is wrong with lots of software

Lisa showed me an AMAZING program today that one of her sons discovered: Processing 68 The demos are amazing and the code is C-like yet fantastically simple.

Processing is a programming language and environment built for the
electronic arts and visual design communities. It is created to teach
fundamentals of computer programming within a visual context and to
serve as a software sketchbook. It is used by students, artists,
designers, architects, and researchers for learning, prototyping, and
production.

Need to try this:

Q9.13: I'm still having problems with X11 and Fink.



A: If the hints in the Fink tries to install XFree86 or X.org or X11
and upgrade from 10.2 entries don't help, or aren't applicable to your
situation, you may need to flush out your X11 installation and remove
any old placeholders and partially/fully installed X11-related
packages:



sudo dpkg -r --force-all system-xfree86 system-xfree86-42 system-xfree86-43 \
xorg xorg-shlibs xfree86 xfree86-shlibs \
xfree86-base xfree86-base-shlibs xfree86-rootless xfree86-rootless-shlibs \
xfree86-base-threaded xfree86-base-threaded-shlibs \
xfree86-rootless-threaded xfree86-rootless-threaded-shlibs
rm -rf /Library/Receipts/X11SDK.pkg /Library/Receipts/X11User.pkg
fink selfupdate; fink index



(the first line may give you warnings about trying to remove
nonexistent packages). Then, reinstall Apple's X11 and the X11SDK.

OSX 10.3.6 makes EAL 3. Not too exciting for my day-to-day use of OSX, but this has implications for working on things like spacecraft operations.

I have been looking at how to pass text via stdin to programs called from python. os.system can not do this. Looks like os.popen, os.popen2, or os.popen3. I have yet to find a nice working example on the web. Maybe one of these modules would do the trick: pipes or commands. Hey wait, I found something that works!

#!/usr/bin/env python
import popen2,string
fin,fout=popen2.popen2("sort")
fout.write("foo\n")
fout.write("bar\n")
fout.close()
print fin.readline()
print fin.readline()
fin.close()

Oceans on Mars: LPI 1741

More random notes for fink problems. Lisa has the forever disappearing Apple X11. Perhaps this command will help debug the problem.

  fink list system-xfree86
  fink-virtual-pkgs --debug

Here is what "fink-virtual-pkgs --debug 2&>1 foo" gives on a happy machine:

Package: broken-gcc
Status: purge ok not-installed
Version: 3.3-1
builddependsonly: true
description: [virtual package representing a broken gcc compiler]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: cctools
Status: install ok installed
Version: 498-1
builddependsonly: true
description: [virtual package representing the developer tools]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: cctools-single-module
Status: install ok installed
Version: 1.0-1
builddependsonly: true
description: [virtual package, your dev tools support -single_module]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: darwin
Status: install ok installed
Version: 7.8.0-1
description: [virtual package representing the kernel]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: gcc3.1
Status: install ok installed
Version: 3.1-1
builddependsonly: true
description: [virtual package representing the gcc 3.1 compiler]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: gcc3.3
Status: install ok installed
Version: 3.3-1
builddependsonly: true
description: [virtual package representing the gcc 3.3 compiler]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: gimp-print-shlibs
Status: install ok installed
Version: 4.2.5-1
description: [virtual package representing Apple's install of Gimp Print]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: macosx
Status: install ok installed
Version: 10.3.8-1
description: [virtual package representing the system]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-java
Status: install ok installed
Version: 1.4.2-1
description: [virtual package representing Java 1.4.2]



Package: system-java-dev
Status: install ok installed
Version: 1.4.2-1
description: [virtual package representing Java SDK 1.4.2]



Package: system-java12
Status: purge ok not-installed
Version: 1.2-1
provides: system-java
description: [virtual package representing Java 1.2]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-java13
Status: install ok installed
Version: 1.3.1-1
provides: system-java
description: [virtual package representing Java 1.3.1]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-java13-dev
Status: install ok installed
Version: 1.3.1-1
description: [virtual package representing Java 1.3.1 development headers]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-java14
Status: install ok installed
Version: 1.4.2-1
provides: system-java, jdbc, jdbc2, jdbc3, jdbc-optional
description: [virtual package representing Java 1.4.2]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-java14-dev
Status: install ok installed
Version: 1.4.2-1
description: [virtual package representing Java 1.4.2 development headers]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-java15
Status: purge ok not-installed
Version: 1.5-1
provides: system-java, jdbc, jdbc2, jdbc3, jdbc-optional
description: [virtual package representing Java 1.5]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-java3d
Status: purge ok not-installed
Version: 0-0
description: [virtual package representing Java3D]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-javaai
Status: purge ok not-installed
Version: 0-0
description: [virtual package representing Java Advanced Imaging]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-perl
Status: install ok installed
Version: 5.8.1-1
provides: perl581-core, system-perl581, attribute-handlers-pm581,
  cgi-pm581, digest-md5-pm581, file-spec-pm581, file-temp-pm581,
  filter-simple-pm581, filter-util-pm581, getopt-long-pm581,
  i18n-langtags-pm581, libnet-pm581, locale-maketext-pm581,
  memoize-pm581, mime-base64-pm581, scalar-list-utils-pm581,
  test-harness-pm581, test-simple-pm581, time-hires-pm581
description: [virtual package representing perl]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-xfree86
Status: install ok installed
Version: 2:4.3-2
provides: xserver, x11, libgl, xft2, fontconfig1, rman, xfree86-base-threaded
description: [placeholder for user installed x11]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-xfree86-dev
Status: install ok installed
Version: 2:4.3-2
builddependsonly: true
provides: x11-dev, libgl-dev, xft2-dev, fontconfig1-dev
description: [placeholder for user installed x11 development tools]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-xfree86-shlibs
Status: install ok installed
Version: 2:4.3-2
provides: x11-shlibs, libgl-shlibs, xft1-shlibs, xft2-shlibs,
  fontconfig1-shlibs, xfree86-base-threaded-shlibs
description: [placeholder for user installed x11 shared libraries]
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage

Here is the cranky machine:

fink list system-xfree86



 i   system-xfree86   2:4.3-2      [placeholder for user installed x11]
 i   system-xfree...  2:4.3-2      [placeholder for user installed x11 devel...
 i   system-xfree...  2:4.3-2      [placeholder for user installed x11 share...



fink-virtual-pkgs --debug



...



- found gimp-print-shlibs 4.2.5-1
- checking for library libX11.6.dylib... found in /usr/X11R6/lib
- checking for X servers... Xquartz
  - system-xfree86-shlibs provides x11-shlibs
  - found an X server, system-xfree86 provides xserver and x11
- checking for header X11/Xlib.h... missing
- checking for library libGL.1.dylib... found in /usr/X11R6/lib
  - system-xfree86-shlibs provides libgl-shlibs
  - system-xfree86 provides libgl
- checking for header GL/gl.h... missing
- checking for library libXft.1.dylib... found in /usr/X11R6/lib
  - system-xfree86-shlibs provides xft1-shlibs
- checking for library libXft.2.dylib... found in /usr/X11R6/lib
  - system-xfree86-shlibs provides xft2-shlibs
- checking for library libXft.dylib... found in /usr/X11R6/lib
  - libXft points to Xft2
    - system-xfree86-dev provides xft2-dev
    - system-xfree86 provides xft2
- checking for library libfontconfig.1.dylib... found in /usr/X11R6/lib
  - system-xfree86-shlibs provides fontconfig1-shlibs
- checking for library libfontconfig.dylib... found in /usr/X11R6/lib
- checking for header fontconfig/fontconfig.h... missing
- checking for rman... found, system-xfree86 provides rman
- checking for threaded libXt... threaded
  - system-xfree86-shlibs provides xfree86-base-threaded-shlibs
  - system-xfree86 provides xfree86-base-threaded



...



Package: system-xfree86
Status: install ok installed
Version: 2:4.3-2
description: [placeholder for user installed x11]
provides: xserver, x11, libgl, xft2, rman, xfree86-base-threaded
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage



Package: system-xfree86-dev
Status: install ok installed
Version: 2:4.3-2
description: [placeholder for user installed x11 development tools]
provides: xft2-dev
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage
builddependsonly: true



Package: system-xfree86-shlibs
Status: install ok installed
Version: 2:4.3-2
description: [placeholder for user installed x11 shared libraries]
provides: x11-shlibs, libgl-shlibs, xft1-shlibs, xft2-shlibs,
  fontconfig1-shlibs , xfree86-base-threaded-shlibs
homepage: http://fink.sourceforge.net/faq/usage-general.php#virtpackage

So what the heck is wrong??? This looks okay to me. Now I try installing something from X11 and get:

fink install g3data



fink needs help picking an alternative to satisfy a virtual
dependency. The candidates:



(1)      xfree86: Free X11 implementation for Darwin and Mac OS X
(2)      xorg: Free X11 implementation for Darwin and Mac OS X

Trying a fink selfupdate (which is rsync). Got a new version of fink. Damn! The 2.5GHz G5 with 4GB of ram is errr.... FAST!!! Then did a scanpackages. Still no go! Grr. fink index. Here is the build depend list for g3data...

BuildDepends: pkgconfig, gtk+2 (>= 2.2-1), gtk+2-dev (>= 2.2-1), imlib, atk1, pango1-dev, glib2, glib2-dev, x11-dev

fink list xfree86 xorg x11-
Information about 4669 packages read in 1 seconds.
 i   system-xfree86             2:4.3-2   placeholder for user installed x11]
 i   system-xfree86-dev         2:4.3-2   [placeholder for user installed x11 development tools]
 i   system-xfree86-shlibs      2:4.3-2   [placeholder for user installed x11 shared libraries]
     x11-app                    1.0-2     Apple's X11.app X server
     x11-dev                              [virtual package]
     x11-shlibs                           [virtual package]
     x11-ssh-askpass            1.2.4.1-1 X11-based SSH passphrase dialog
     xfree86                    4.4.0-14  Free X11 implementation for Darwin and Mac OS X
     xfree86-base-threaded                [virtual package]
     xfree86-base-threaded-...            [virtual package]
     xfree86-shlibs             4.4.0-14  Free X11 implementation for Darwin and Mac OS X
     xorg                       6.8.1-12  Free X11 implementation for Darwin and Mac OS X
     xorg-shlibs                6.8.1-12  Free X11 implementation for Darwin and Mac OS X

Finally, here is where fink is at on this machine:

  fink --version
  Package manager version: 0.23.6
  Distribution version: 0.7.1.rsync

Roi's problem with the developer tool kit I have no idea on.

Jason has a G3 laptop in the lab that has gcc crashing in ncurses...

Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
make[1]: *** [../objects/read_entry.o] Error 1
make: *** [all] Error 2
### execution of /var/tmp/tmp.2.jS01rl failed, exit code 2
Failed: compiling ncurses-5.4-20041023-4 failed

Today I measured AMS on 3GW-s2 and took pmag cubes from 2GW-s1. This core comes from the evacuated zone of the Gaviota slide. That was the last major working half to sample.

This morning I sampled pmag cubes out of core BPSIO-2004-4GW-Sec1. The photos are here

Sample, measure, sample, measure ....

Today is the paper that I picked for the weekly paleomag meetings. Here is what I chose:

  Kawamura, Ogawa, 2004. "Progressive change of pelagic clay microstructure
  during burial process: examples from piston cores and ODP cores,"
  Marine Geology, 207, 131-144.

First some definitions to help out:

  ped - A "large" aggregate separated by voids or sufaces of weakness.
        By large they mean like 10 μm

From macosxhints:

  Luckily, MySQL 4.1 has a feature to preserve backward compatibility by
  using the "old" encryption for your passwords -- users with such
  password are able to connect via CocoaMySQL without any problem at
  all. Creating an "old" password is simple in the Terminal, using the
  MySQL command line interface:



  SET PASSWORD FOR 'mysql_username'  = OLD_PASSWORD('password');  

quicksilver - Extends the concept of Apple-Tab. The official site: quicksilver

Use Yahoo! maps with Address Book. I haven't had a chance to try it yet, but this would be really nice since the Google one did not work with Safari.

The annodex plugin looks cool for Firefox. If only I used firefox.

Ocean wave energey off of Scottland. What is the environmental impacts of this kind of thing? A pdf report about wave power in the US. Why is the US not going for more of these alternative energy resources?

voodoopadlite sounds interesting. Too bad the lite version does not export to html.

I took a l look Roi's fink installation today. Fink seems to be fine but what happened to his developer tools? First I tried helloworld.c. No crt2.o. What? So I copied that from my machine to his. helloworld works fine. Then I tried building something in fink and ncurses still will not build. I also got rid of the UseBinaryDist flag in his /sw/etc/fink. Yikes. That is not a good thing to have. Here is where I am now with fink failing build anything. autoconf dies with the c pre processor...

checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking version of gcc... 3.3
checking how to run the C preprocessor... /lib/cpp
configure: error: C preprocessor "/lib/cpp" fails sanity check
### execution of /var/tmp/tmp.2.UHpHJC failed, exit code 1
Failed: compiling ncurses-5.4-20041023-4 failed

I tried to reinstall the developer tools but they say there is a newer version on the machine and refuse to install. Doh.

I sampled core 3 today. I am really liking the Galerie created web pages.

  3GW-Sec2-pmag

Some interesting web sites:

postsecret - Very interesting.  And a bit scary.
broken

Sumatra Earthquake Three Times Larger Than Originally Thought

I took Figure 1 from Baumgartner et al 1992 and used g3data to extract the locations of the cores in the figures. I then made a text file that looks like this:

  -120.05847761  34.2642265575   "241"
  -120.042416247  34.2650120181  "224"
  -120.035680911  34.2654127726  "230"
  -120.020617309  34.2290362724  "239"
  -120.02320158  34.2228575909   "214"
  -119.983294404  34.2124333872  "P-2"
  -120.042857811  34.1911209481  "265"

I then ran the fledermaus command line program to generate an sd file:

  /Applications/IVS\ Fledermaus/tools/cmdop mkpoint3d -type ascii\
  -format "x y" -in baumgartner92-cores.dat -out\
  baumgartner92-cores.sd

And that was all there was to it. I can now see these cores in the scene file

I am now trying out using Galerie to generate the web pages for core sampling photos. The generally look pretty good accept 2 of the photos have their aspect ratios munched on the first batch. Here are the parameters that I used:

Main page title: Sampling 1GW Sec 1
Link:  BPSIO04 
Link addr: http://schwehr.org/Gaviota/bpsio-Aug04/core-sampling/
Thumbs:
  Max size: 160
  Cols 4
  Rows 2
  Add title
  Add date
Template: Black
Pictures:
  Max: 600
  Add titel, Add date, Add EXIF, Add IPTC
  Add full-size orig
Quality 80
Create separate folders

Check out the results here:

1GW-Sec1-pmag
5GW-Sec1-pmag

The tops of the cores are pretty ratty since the cores are so soupy up at the top.

SQLite 3 is now in fink. Woohoo! Not that I will notice any difference since I hardly use any of SQL's features.

The is the first time that I have hit a lock with a fink cvs update. People, you need to stop using Mac OSX 10.2. 10.3 is so much better in many ways plus having fink maintainers worrying about 10.2 is wasted effort. I picked a busy time to do a cvs update...

  cvs update: [17:43:30] waiting for planetmirror's lock 
      in /cvsroot/fink/dists/10.3/stable/main/finkinfo/libs

Here is multibeam data from the Brits. No links to the actual data.

  ... British Royal Navy, Wednesday Feb. 9, 2005, shows a slide from a
  presentation that took place Wednesday at the United Kingdom
  Hydrographic Office in Taunton, Somerset, England. The picture shows
  the coastline off Sumatra in south east Asia at the epicentre of the
  earthquake that caused the tsunami in south east Asia on December 26,
  2004. The deep blue shows the deepest parts of seabed. (AP Photo/PA,
  Royal Navy)

Larry Smarr of CalIt2 visited JPL last week. You will find Schwehr et al referenced at slide 16 with MER data visualization. The panoramas were created by JPL/MIPL with MICA.

2.04.05 Invited Talk to the NASA Jet Propulsion Laboratory
"LambdaGrids--Earth and Planetary Sciences Driving High Performance Networks and High Resolution Visualizations" Pasadena, CA

Versions: [html] [ppt]

This is great! You have got to check this out if you are a fink user.

fink install dict

  dict ferrimagnetism



  1 definition found



  From WordNet (r) 2.0 [wn]:



    ferrimagnetism
       n : a phenomenon in ferrites where there can be incomplete
           cancellation of antiferromagnetic arranged spins giving a
           net magnetic moment

or

  dict yacc



  2 definitions found



  From The Free On-line Dictionary of Computing (27 SEP 03) [foldoc]:
  yacc
          {Yet Another Compiler Compiler}
       
  From Virtual Entity of Relevant Acronyms (Version 1.9, June 2002) [vera]:
  YACC
       Yet Another Compiler Compiler (Unix)

Now I need to pass this through acoc to colorize the responses!

Also... Map Address Book addresses via Google Maps - Uses Firefox since Safari is not supported by google maps.

A good bit of rain today in San Diego today. It is nice to have a rainy day to offset all the sun.

Icebreakers Clear Channel Into McMurdo Station - There is the RVIB Palmer in the background. Glad they made it after there was all that trouble with the B15 iceberg.

Ultra-low Cost Well Monitoring Could Save Thousands Of Marginal Oil Wells - Cheap wireless devices let the operators shut down a system temporarily when the system is not producing enough flow to be profitable. These things are already out there, so better to keep them going that shut them down.

3-D Seismic Technology Locates Natural Gas In Fractured Reservoirs - The diffractions in fractured systems must make it really hard to see what is really going on down there.

ssh-tweaks - ssh tunneling. I should check out SSH Tunnel Manager (stm). I should really tunnel my email in to ucsd so that I stop getting these annoying ssl cert popups all the time.

Why does the iTunes Party Shuffle insist on playing lectures and speeches? I don't really want to hear myself talk while working.

H.R. 418 is supposed to stop terrorists. It is only going to punish regular citizens. It would force all state DMV's to share driving record information. Sorry, but I'm all for sharing felony convictions, but not this kind of stuff!

A friend and I got one ticket each in the span of 1/2 an hour outside of Dallas. I'm sorry, but they were just making money, not helping the public good. Or how about the cop hiding in the orange grove in the central valley of Calif. Thank goodness I was driving a federal vehicle so I could prove to the insurance company that I was driving for work. The cop was sure that I had stolen it. Now why would I steal a US Government minivan? How stupid do I look?

Yet every day here in SD, I see people really dangerous maneuvers (right turn from the left hand land, and visa-versa) right in front of cop cars and NOTHING?

That's enough of a rant for now. This law would seriously suck.

Here is the contact info for the senators from CA.

Here is a couple minutes of playing with emacs lisp evaluation. Emacs lisp must be the most widely installed version of lisp/scheme. I tried starting with the emacs list intro, but was not able to do anything so here is what I did:

  emacs test.el
  M-x lisp-interaction-mode
  (+ 2 2) C-j
  ; 4 gets printed to the screen when you hit the C-j
  ; Wow, a caculator
  '(yada yada "blah blah") C-j
  fill-column C-j
  ; Emacs says that the fill-column is 70
  C-u 6 6 C-x f
  fill-column C-j
  ; Emacs says that the fill-column is 66
  (set 'fill-column 10) C-j
  fill-column C-j
  ; Emacs says the fill column is 10... fun fun
  (concat "abc" "def") C-j
  ; Emacs says "abcdef"
  (substring "The one true editor is emacs uber alles" 23 28) C-J
  ; "emacs"
  (+ fill-column 60) C-j
  ; add 60 and fill-column.  Very important math
  (concat "The " (number-to-string 2) " two" ) C-j
  ; emacs says "The 2 two"
  (+ 1 2 3 4) C-j
  ; 10

I am now having flash backs to Nick Parante's CS107 class in 1993. That was the only time I really wrote any lisp other than when I tried to create an emacs mode for ESRI's Arc Macro Language (AML). The AML mode actually kinda worked, but I forgot to copy the code from sierra.wr.usgs.gov before I lost my account. Back to work!

psvn.el is an emacs subversion(svn) interface. The Red-Bean SVN book

If you are at UCSD and looking for system support for you computer, consider contacting the Chemistry and Biochemistry Computer Facility

Joe Keefe setup recording one of my talks at the VizCenter 09-July-2003. Check it out here

Or jump straight to the RealPlayer stream: http://chemcomp1.ucsd.edu:8080/ramgen/ks-vislect2.rm. I had to open RealPlayer and then File->OpenLocation and paste in the URL.

Attached to Wolf Berger et al (2004) is a data file of varve thickness, TOC, and fish scales that I wanted to take a look at. Here how I did it. First get the data and make it text

  wget ftp://rock.geosociety.org/pub/reposit/2004/2004055.pdf
  pdf2text 2004055.pdf
  emacs 2004055.txt

Use your text editor to save the varve years to one file and the varve thicknesses to another. It must be one value per line. e.g. M-x replace-string space C-q C-j. Then use the unix paste command (thanks Julie!) to bring the two columns together:

  paste mm.dat year.dat > varves-mm-year.dat

Now use this python script to convert the mm for each year into a depth of each year:

#!/usr/bin/env python



import os	# os.remove()
import sys	# sys.exit()
import string



inFile=open("varves-mm-year.dat")
depth=0. # cm
print "# depth in cm, calendar year"
for line in inFile.xreadlines():
    mm,year=line.split()
    depth+=float(mm)/10.
    print depth,year

Then fire up gnuplot:

  set yrange [] reverse
  set xrange [] reverse
  set xlabel "year"
  set ylabel "depth(cm)"
  plot 'varve-depthcm-year.dat' using 2:1

And now you have a nice graph showing the varve thickness decreases with depth and that compaction happens. Woowee.

Here is the crontab for root that updates man pages and the locate commands database. Do "sudo crontab -e"

MAILTO=''
5 0 * * * /sw/bin/updatedb
30 0 * * * /usr/libexec/locate.updatedb
15 0 * * * /usr/libexec/makewhatis /sw/share/man

To view your crontabs you can do:

  crontab -l
  sudo crontab -l

Here is my abstract for AGU New Orleans. I am only part way through the lab work and data processing so there will be more results in the meeting than what is discussed here:

                Slumps and sediment deformation:
              AMS of the Gaviota and Goleta Slides

During the last year, we have collected six gravity cores from the
northern side of the Santa Barbara Basin for paleomagnetic
deformation tests. The first two cores were collected on the
smaller Gaviota Slide on the western side of the basin.  These
cores provide the slump end member, since one core comes from the
evacuated zone while the other comes from the toe or accumulation
zone.  Two additional cores were collected on the toes of the much
older Goleta Slides and were designed to provide an undeformed
reference fabric; it was our hope that they would be mostly
pelagic drape but also penetrate into the top of the deformed
material.  One core appears to be an excellent reference core with
clear laminations, while the other has distorted laminations that
show the sediment has undergone some type of deformation.  In
between the two slides, we collected two cores on either side of
the crack that runs between the two slides to investigate creep
and slope stability.  All cores have been sampled at a 3 cm
interval with 8cc cubes to measure anisotropy of magnetic
susceptibility (AMS) and AF demagnetiziation.  The Gaviota slide
sediments show a dominantly triaxial fabric with some alignment of
the maximum eigen values, while the drape materials from the
Goleta Slide show a typical oblate undeformed fabric.  There are
hints of deformation at major clay layers, which we continue to
investigate.  Several of these cores appear to show a biogentic
component to the AMS signal that fades with depth.  This component
has a tendency to mask the deformation signal in the top sections
of the cores.  The NRM inclinations of the deformed core regions
tend to be shallow and erratic showing what look at first glance
to be excursional features.



http://schwehr.org/Gaviota/bpsio-Aug04/

Experimental Radar Provides 3-D Forest View - Using SAR to measure the biomass between the forest canopy and the ground.

Updating my Macs to 10.3.8. Seems that things are ok so far.

More todo item:

• Add gplate.org to fink
• Add CoinDesigner to fink
• Add the SGI Inventor programs to the fink/Coin/SoXt system (needs a new release of Coin past 2.3.0)

Sounds like the meeting between CalIt2 and JPL went well last week with posibilities for future collaboration.

Today I resurrected some paleomag data from last weekend. It had been quite a while since I had used flow with cubes, so I had put the cubes in with the arrow point down into flo rather ran out of the side of flow/up at the ceiling. Lisa's pmag library has a nice little program call di_geo to help that I wrapped into a little script:

#!/bin/bash
rm -f better.mag
cat bad.mag | while read line; do
    decinc_bad=`echo $line | awk '{print $5,$6,0,-90}'`
    decinc_good=`echo $decinc_bad | di_geo`
    first=`echo $line | awk '{print $1,$2,$3,$4}'`
    last=`echo $line | awk '{print $7,$8}'`
    echo "$first    $decinc_good $last" >> better.mag
done

By the way, I used code2html to make html out of the script.

Check this out when then slashdot traffic has died down:

Panoramas.dk - This site even beat us to the MER quicktime VR's since we were so overloaded early in the mission.

Is AMQ real? It is supposed to be a Wall street version of network. Supposedly like ActiveMQ? What a terrible press release. I was pretty confused by the end. Why would Sun put this in their kernel? Is this a replacement for Tibco's software? How does this compair to the standard the RTI helped make with NDDS? Or Ensemble?

Then there is Spread which has its own open source license. Arg. Another license.

Or corba. Or yada yada yada...

Handheld Transmitters Connect Students And Teachers In Class

print from the command line using the Print Center's default printer like this:

open -a Print\ Center /path/to/file_to_print.pdf

This morning, I got fooled by the UCSD network folks. It looked like a virus bombarding my webserver with IIS attacks. Turns out they were just doing a sweep for vulnerable machines.

I was reading an article the other day that was pro-nuclear power. I have been very against nuclear power for a long time, but I came up with a twisted reason for why I should be pro-nuke.

As practitioner of marine geology and geophysics, I am always on the lookout for environmental markers in my study areas. These markers can be ash layers, certain fossils, storm events, 14C datable material, Pb210, Cs, major climate shifts, etc. Note that Cesium is in that list. Most of these we, as humans, do not create. But sometimes, scientists are able to do "labeled releases." For example, you could coat a pile of sand gains with something unusual like a special paint and then release a couple kilograms of marked sand in the mouth of a river. Then down the coast at a beach by a submarine canyon head, you could continually sample the sediments looking for these marked grains to appear. You have a really nice experiment for the residence time and transport rate of sand in your local beach cell.

Back to Cs. There is often things we would like to do to label things on the Earth that are not environmentally sound, so we don't do them. I would not go dumping a giant amount of radioactive tracer into the ocean. Here is where the nuclear industry comes into action. It seems that we been having a nuclear disaster about once every decade or two. Chernobyl, England, Washington State / Hanford, etc. These are perfect marker events. The release very unusually compounds and elements into an environment. We then come along and look for the, say, early 90's Cs spike. How handy. Now if we were to really ramp up the nuclear industry, especially in the developing world, the number of accidents would go way up and give us all kinds of great radionuclide markers. Wonderful! Go nukes! But you might want to pass on the three eyed fish for your sushi.

Nisus Thesaurus - This appears to be free. 0.4 will add a system-wide dictionary and thesaurus, but until then...

I think I live in the middle of a crow convention. Quite the ruckus.

MacOSX hint:

I dragged an AAC file to ~/Library/Sounds and launched iCal. To
my horror, the sound that I put in there didn't appear in the
pop-up list of alarm sounds. "Okay," I thought, "maybe it's
expecting an AIFF file."



Not having an AIFF lying around on my new machine, I decided to
rename the AAC file to have a AIFF extension. Magically, the
sound appeared in the alarm settings dialog, but I didn't expect
it to play. Guess what? It did!

Here is my todo list for stuff outside my thesis that probably will not get done for a while. This is the "I have not forgotten" list. Unless a quick solution lands in my email inbox, I will not be doing these until after I get my thesis done!

• Get fink cwp-su to release 38. At 37 now.
• Get OpenDTect into fink... or even just try it
• Upgrade acoc from 0.6.0 to 0.7.0 in fink. 0.7.0 bombed on me for some reason.
• Get gmtplus into fink cvs assuming that it worked for Steve Cande on the Palmer
• Add --enable-darwin-x11 to the Coin fink configure and test
• Get fink mbsystem working with GMT 4. Waiting for mbsystem 5.0.6
• Talk to Bill Danforth and get xsonar info fink
• Update fink proj to 4.4.9
• Add thuban to fink
• Help get fink sqlite to version 3.
• Add hsv2rgb and rgb2hsv to density
• Release a new version of xcore that works on Mac OSX 10.3
• Setup a real backup program like I described. Maybe hdup will do it.
• Have nanoblogger add the DESC field to the index
• Fix my phrase index for nb to use the article number
• Fix my phrase index to list phrases by article
• Robustify my phrase index. Maybe use python sets or regex?
• add mactounix and unixtomac in density
• Setup phpicalender
• Why does my phrase index not include fink?
• Get more of the tools at www.remotesensing.org/ into fink
• Check out all the projects that use gdal: gdal projects
• Get OpenEV on the Mac

Uh oh. I have some shared lib packages.

From - TheSin Subject - Proposed Policy Change for all Maintainers IMPORTANT

With the upcoming shlibs change, the packaging engine needs to be changed a little and this will break many packages.

first let me explain the shlibs change. Basically fink will beable to automatically insert all share library deps to the Depends line by using Depends: {SHLIB_DEPS}, curl | curl-ssl. This is an example and I added curl | curl-ssl to show that we will still need to add runtime depends by hand, but now dylib pkgs.

Now currently fink treats Depends and builddepends in the pretty much the same manor. In the new layout Depends will be Install/Run tim depends, so not needed to build a package. And since in the new policy all -dev pkgs will be required to depend on there own -shlibs, we can rest assured that the -shlibs will be present at build time so no need to list them in the BuildDepends, except if a -dev isn't currently following that policy. But there are only a few that aren't at this point so that won't be a big change.

Anyhow, any maintainer wishing to help us out and help speed this new great tool up for us, please follow this next set of instructions to fix your pkgs:

all pkgs such be able fink build foo with out the depends line so comment it out and add what is needed to builddep line. This is to test build only, so use fink build to test this and not install. Also please don't commit it like this. Again this is only to test that the pkg will build sans the Depends line. Install and Run time deps are still required at this point and that includes the -shlibs pkgs so don't start removing those yet.

Also we NEE