Kurt's Weblog

  sqlite db ".schema weights"



  CREATE TABLE weights (id INTEGER PRIMARY KEY, samplename
  VARCHAR(40), weight REAL, timeMeasured TIMESTAMP, status
  VARCHAR(20), operator VARCHAR(20), sticker VARCHAR(15), step
  INTEGER);



  sqlite db ".schema ams"



  CREATE TABLE ams (id INTEGER PRIMARY KEY, samplename VARCHAR(40),
  user VARCHAR(40), datemeasured TIMESTAMP, cruise VARCHAR(20),
  corenum INTEGER, coretype VARCHAR(1), corehalf VARCHAR(1), section
  INTEGER, sectionoffset REAL, depth REAL,counts INTEGER, sampleholder
  REAL  ... and so forth

  sqlite db "DELETE FROM weights WHERE weights.id IN (SELECT\
  weights.id FROM weights,ams WHERE weights.samplename=ams.samplename\
  AND corenum=3 AND section=2 AND weights.step=1);"

  sqlite db "select weights.id,weights.samplename,weights.step from\
  weights,ams where weights.samplename=ams.samplename AND corenum=3\
  and section=2 AND weights.step=1;" | tail -6



310|bp04-3gw-s2-132|1
311|bp04-3gw-s2-135|1
312|bp04-3gw-s2-138|1
313|bp04-3gw-s2-141|1
314|bp04-3gw-s2-144|1
315|bp04-3gw-s2-147|1

  sqlite db "select weights.* FROM weights,ams WHERE weights.samplename=ams.samplename AND step=1 AND corenum=3 AND section=2"



Nothing



  sqlite db "select weights.* FROM weights,ams WHERE \
  weights.samplename=ams.samplename AND step=1 AND corenum=3" | head -3



316|bp04-3gw-s1-004|9.7838|2005-04-25 10:30:00|wet|schwehr|no-sticker|1
317|bp04-3gw-s1-007|9.8447|2005-04-25 10:30:00|wet|schwehr|no-sticker|1
318|bp04-3gw-s1-010|9.9916|2005-04-25 10:30:00|wet|schwehr|no-sticker|1



  sqlite db "select weights.* FROM weights,ams WHERE \
  weights.samplename=ams.samplename AND step=2 AND corenum=3" | head -3



561|bp04-3gw-s2-123|5.9082|2005-05-16 09:14:00|dry|schwehr|sticker|2
562|bp04-3gw-s2-126|5.8825|2005-05-16 09:14:00|dry|schwehr|sticker|2
563|bp04-3gw-s2-141|5.5927|2005-05-16 09:14:00|dry|schwehr|sticker|2

  WASTE (waste.sf.net) is software for setting up small, secure,
  private filesharing networks. WASTE provides chat, instant
  messaging, and file transfers between connected users, all of which
  is encrypted. The software is entirely peer to peer so no server is
  required. WASTE facilitates connections between NATed users with
  routing through addressable nodes. It works best for transferring
  files between small groups of people, like a group of friends. 

  wallykeyster asks: "I'm an IT Director for a small private
  university in the U.S., and we are largely a Microsoft shop. We pay
  over $15,000 each year for our Campus Agreement so that we can
  upgrade the desktop OS to our version of choice, run Office, and
  have some Client Access Licenses. I would like to move to FOSS
  solutions, but I'm having trouble finding support for Enterprise
  management. For example, OpenOffice and Firefox (both of which I use
  personally) would be easy first steps, but IE is updated
  automatically via our SUS server (and settings pushed to clients via
  group policies) and Office updates will be included soon. How are
  other larger organizations (i.e. more than 200 desktops) dealing
  with software deployment and updates? Is anyone using Zen with
  Novell Desktop Linux?"

  ZEB17 writes "Anybody out there have any experience using Bacula to
  back up a Mac? How about with Tiger? We've been Retrospect users
  forever, but we find their upgrade and support policies a bit tough
  to swallow. Plus we've never been all that impressed with their
  software. So we started thinking about the open source project
  Bacula. It is supposed to work well on heterogenous networks with
  Linux, Windows, and Mac clients. But doing the usual searches
  reveals little about actual Mac usage. Is it so good that nobody
  ever posts anything? Or is it so bad that nobody even tries it?
  Thanks for any info."

#!/usr/bin/env python



def subsetList (list, min, max):
    """
    return a subregion of a list of (x,y) pairs based on the x range



    >>> subsetList([(1,11),(2,22),(12,1212),(15,1515),(21,2121),(30,3030)], 10,20)
    [(12, 1212), (15, 1515)]
    """
    newList=[]
    for item in list:
        if item[0]>=min and item[0]<=max:
            newList.append(item)
    return newList



def _test():
    import doctest, foo
    doctest.testmod(foo)



if __name__ == '__main__':
    _test()

  chmod +x foo.py
  ./foo.py -v



Trying:
    subsetList([(1,11),(2,22),(12,1212),(15,1515),(21,2121),(30,3030)], 10,20)
Expecting:
    [(12, 1212), (15, 1515)]
ok
2 items had no tests:
    foo
    foo._test
1 items passed all tests:
   1 tests in foo.subsetList
1 tests in 3 items.
1 passed and 0 failed.
Test passed.

  ./Stumbler
  IOConnectMapMemory (ipc/send) invalid destination port (10000003)
  Abort trap

  Forensic Psychology is the application of the science and profession
  of psychology to questions and issues relating to law and the legal
  system. The word "forensic" comes from the Latin word "forensis,"
  meaning "of the forum," where the law courts of ancient Rome were
  held. Today forensic refers to the application of scientific
  principles and practices to the adversary process where specially
  knowledgeable scientists play a role.

#!/usr/bin/env python
import math
import time
import Numeric



totalMath=0.
totalNumeric=0.



for j in range(1,100):
    start = time.time()
    for i in range(1,100):
        x = math.exp(float(i)+.1)
    end = time.time()
    totalMath += end-start



    start = time.time()
    for i in range(1,100):
        x = Numeric.exp(float(i)+.1)
    end = time.time()
    totalNumeric += end-start



print " totalMath    = ",totalMath
print " totalNumeric = ",totalNumeric

./speed.py 
 totalMath    =  0.064
 totalNumeric =  0.192

  700
  1.01423205474e+304
  1.01423205474e+304
  800
  inf
  Traceback (most recent call last):
    File "./speed.py", line 17, in ?
      print math.exp(max)
  OverflowError: math range error

  As the others have pointed out, you can call any gnuplot command from
  Gnuplot.py.  The other issue with "fit", however, is how do you get the
  results of the fit back into Python?  This is a problem because
  Gnuplot.py doesn't have access to gnuplot's standard output.
  
  Luckily this is easy--you write the parameters to a "parameters file"
  (which fortuitously is valid python code) then read them back into
  python.  This is untested but should approximately work:
  
    >>> g = Gnuplot.Gnuplot()
    >>> open('fit.par', 'w').write('m=0\nb=0\n')
    >>> g('fit m*x+b "data.in" via "fit.par"')
    >>> g('update "fit.par" "fit2.par"') # saves fitted parameters to fit2.par
    >>> parameters = {}
    >>> execfile('fit2.par', globals(), parameters)
    >>> print parameters
  {'b': 1.5015, 'm': 1e-30}
    >>> print parameters['m'], parameters['b']
  1e-30 1.5015
  
  In principle you could also parse "fit.log" to get the gory details
  about the fit (standard errors, correlation matrix, etc).
  
  Hope this helps,
  Michael
  
  -- Michael Haggerty mhagger at alum dott mit.edu

  Sometimes it is useful to get variables from a gnuplot session
  steered from python, e.g. to extract parameters from a
  fit. GnuplotBiDir.py is a test of bidirectional interfacing with
  gnuplot. For this you need a really recent gnuplot (from CVS) . The
  basic usage is 
    from GnuplotBiDir import Gnuplot
    gp=Gnuplot()
    gp("a=10")
    print "var=",gp.getvar("a")
  Remark: for an excellent python interface to gnuplot see gnuplot-py
  and the interactive add-ons to this from IPython. 

MayaVi is a free, easy to use scientific data visualizer. It is
written in Python and uses the amazing Visualization Toolkit (VTK) for
the graphics. It provides a GUI written using Tkinter.

  >>> from Scientific.Functions.LeastSquares import *
  >>> from Numeric import exp
  >>> def f(param, t):
  ...     return param[0]*exp(-param[1]/t)
  ...
  >>> data = [(100, 4.999e-8),(200, 5.307e+2),
    (300, 1.289e+6),(400, 6.559e+7)]
  >>> print leastSquaresFit(f, (1e13,4700), data)
  ([8641551709749.7666, 4715.4677901570467], 1080.2526437958597)

  Sedimentary Protocols [pdf]

• Installing Custom Certificate Authorities for OpenSSL by Chris Adams
• Secure IMAPd for OS X 10.3 by Michael Johnson
• http://www.cse.ucsd.edu/users/lbreyer/rootcert/OSX/
• http://www-no.ucsd.edu/documentation/application/macosx/mail/
• http://www-no.ucsd.edu/documentation/application/macosx/mail/ssl/index.html

• Tom Furness - uman Interface Technology Lab at UW.
• Alex Pang at UCSC. Research interests: tensor visualization, scientific visualization, collaboration software, uncertainty visualization, virtual reality interfaces.
• Terry Winograd

  Bernhard Breinbauer:



  Maybe also not what you are looking for, but kwrite/kate from the
  KDE project have syntax highlighting for vrml files, and also a HTML
  export function.  It's not the direct way, but you get coloured html
  output :-)

  Morton:



  Not exactly what you're looking for, but in case it would be useful:
  Emacs comes with a VRML mode, which also works with Inventor
  files. As they usually do, the Emacs mode comes with syntax
  highlighting and indentation. Very useful.

  Chris Scharver



  GNU enscript is another option. It can pretty-print the file and
  output to RTF, HTML, or PostScript as needed. It defaults to vrml
  syntax for .wrl files, but you can force it to use that mode for .iv
  files too. Very handy! I use it quite a bit on Linux, Mac OS X, and
  Windows via cygwin.



  http://mega.ist.utl.pt/~ic-cg/laboratorio/vrmlTutorials/tutorial/source/tut7.html

  http://schwehr.org/xcore/xcore-py-0.1.tar.bz2

  With the new Safari in Tiger, it is easy to import self-signed SSL
  certificates you may come across. Just click Show More in the alert
  box, and then drag the certificate icon to a folder or your
  desktop. Then double-click the certificate, and Keychain Access will
  prompt to import it. Select the "X509Anchors" keychain from the
  Select box and click OK. Finally, enter your admin password to allow
  that keychain to be modified.



  For example, my university has a self-signed SSL certificate for
  their IMAP server, and Mail.app constantly complains about this. So
  I pointed Safari at the IMAP SSL port eg: https://imap.ufl.edu:993/
  to grab and import the certificate into the system keychain. Now
  when I start up Mail.app, it doesn't complain when connecting
  securely to my school's IMAP server

#Inventor V2.1 ascii



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#Inventor V2.1 ascii



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    PointSet { }
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  .schema mag
  CREATE TABLE mag ( samplename VARCHAR(40), treatment REAL, csd REAL,
  intensity REAL, dec REAL, inc REAL, timeMeasured TIMESTAMP,  type
  VARCHAR(10), operator VARCHAR(20),  depth REAL,  cruise VARCHAR(20),
  corenum INTEGER, coretype VARCHAR(1), corehalf VARCHAR(1) ,  section
  INTEGER, sectionoffset REAL);

  SELECT arm.samplename,arm.intensity,irm.intensity
   FROM mag arm 
   INNER JOIN mag irm 
   ON arm.samplename=irm.samplename 
   WHERE arm.type='arm'
    AND irm.type='irm' 
    AND arm.treatment=100
    AND arm.corenum=5 
   ORDER BY arm.depth;

  ...
  bp04-5gw-s2-126|0.0000317600|0.0014030000
  bp04-5gw-s2-129|0.0000277200|0.0011360000
  bp04-5gw-s2-132|0.0000372000|0.0014940000
  bp04-5gw-s2-135|0.0000351100|0.0013400000
  bp04-5gw-s2-138|0.0000301600|0.0011740000
  bp04-5gw-s2-141|0.0000346500|0.0014260000
  bp04-5gw-s2-144|0.0000361300|0.0014160000

  Just read your blog and we got some software from the xray guy on
  the cruise - Barry. He uses some free software called ImageJ



  http://rsb.info.nih.gov/ij/download.html



  it is medical software but is very useful for viewing xrays in tif format
  and Barry wrote a macro using the pixel intensity (~density) to calculate
  out the cracks and voids in the core to get the true length. I have not
  really used it yet but he swears by it so definetly worth a look!

  Barry brought a ct and a really really high res xray machine that he
  built on the boat - it can xray cores that are stil under pressure
  in an autoclave! and then if that is not enough he can also do "time
  lapse" measurements of the core degassing as the pressure is
  released slowly.  All sorts of techno gradgetry is going on!

• Make nice mosaics for publications
• Make mosaics that best show off all of the features in the core
• Be able to make quantative statements about xray density

#Inventor V2.1 ascii
# Small IV file to give a depth reference line so that I stop
# spending so much time guessing depths.

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  Geologists believe that Earth experienced at least three global ice
  ages from 800 to 580 million years ago (mya) during the
  Neoproterozoic Era, at the end of the Precambrian Age. In most
  places, evidence of the glaciations has disappeared, but traces
  remain in several areas with "cap carbonates," thin layers of
  limestone containing distinctive ratios of carbon isotopes. "When
  the ice melts, the oceans rapidly precipitate carbonate, which
  appears in the sedimentary rock," explains one of the geologists,
  Daniel Condon, a postdoctoral fellow in geology/geochemistry. "Cap
  carbonates are very unusual and restricted to glacial periods in the
  Neoproterozoic."

>>>> When I run updatedb from findutils in fink, I get this error:
>
>>> Does /usr/bin/find have the same problem?
>
>> It doesn't say it does.
>
> Sorry to bother everyone, but found a fix. I added fsdec to the list 
> of fstypes to prune, and it worked fine (/dev/fd/3 couldn't be 
stat'd)
> Maybe we can still track down why it says the hard link count is 
> incorrect though; if it doesn't have that error there is a very nice 
> speed boost because it doesn't stat each file then.
>
Hey folks,



I'd like to add that this is a *critical* bug, and it occurs on 10.3, 
too -- maybe the new findutils version introduce the problem?



Today and yesterday my HD run full. The problem is that apparently, for 
updatedb /dev/fd/3 is an alias for /. So when updatedb scans my FS, it 
gets into an infinite recursion loop. In my case it created about 15 GB 
of temp files (indexing the "infinitely many files" on my HD), before 
it run out of HD space.



Running out of HD space is rather dangerous, if you notice it too late 
it can cause data loss (10.3 really tries to warn you about this, but 
if your machine is running while you are absent, as in my case, you can 
be too late)...