BTD

Repositories for observers

2010-11-03T09:03:00.000-07:00

I should have posted these a while ago....
casaradio is a subversion repository for folks at The Center for Astrophysics and Space Astronomy at CU Boulder to post radio astronomy related codes. So far, emphasizes single dish (GBT, Arecibo), but will include EVLA, CARMA, and ALMA eventually.
aposoftware is a similar page, but is a mercurial repository and is meant to include instrument-specific software for the Apache Point Observatory 3.5m telescope. Right now includes a TUI script or two and the TSPEC and DIS IRAF-twodspec pipelines.

I'd be remiss to leave out the BGPS pipeline even though it's mentioned on the previous post.

Also, agpy is my personal code repository.

BGPS data paper published

2010-11-03T08:57:00.000-07:00

Metalinking! The BGPS paper finally made it onto astro-ph today. It will be published in ApJS before the year's end.

Links to all of the published BGPS papers at the Bolocam Data Team website

And just because I want more linking, here they all are again:
The Bolocam Galactic Plane Survey I. Survey Description and Data Reduction arXiv
The Bolocam Galactic Plane Survey II. Catalog of the Image Data arXiv
The Bolocam Galactic Plane Survey III. Characterizing Physical Properties of Massive Star-Forming Regions in the Gemini OB1 Molecular Cloud arXiv
The Bolocam Galactic Plane Survey IV: λ = 1.1 and 0.35 mm Dust Continuum Emission in the Galactic Center Region

The same set of links is reproduced at the pipeline googlecode page.

Neat new things....

2010-08-16T17:37:00.000-07:00

1. sptool is a quick way to compare standards to stellar spectra. Nice, I'd been looking for a tool like that.
2. GNU screen captions are useful especially when working in a screen-within-a-screen environment (who does that, really?)
3. finally got SPLAT to work... turns out I just hadn't reduced my damned data
4. kill -STOP and kill -CONT are really useful ways to pause programs that are sucking up resources if you want to resume them later. Haven't tried this on "real" code yet.

Filled step plots in matplotlib

2010-08-13T12:20:00.000-07:00

It's not possible to do a simple filled step plot in matplotlib using default
commands. Workaround:

def steppify(arr,isX=False,interval=0):
    """
    Converts an array to double-length for step plotting
    """
    if isX and interval==0:
        interval = abs(arr[1]-arr[0]) / 2.0
        newarr = array(zip(arr-interval,arr+interval)).ravel()
        return newarr

plot(xx,yy,linestyle='steps-mid',color='b',linewidth=1.5)
fill_between(steppify(xx[x1:x2],isX=True),
    steppify(yy[x1:x2])*0,
    steppify(yy[x1:x2]),
    facecolor='b',alpha=0.2)

Histogram in Google Spreadsheet

2010-07-28T08:09:00.000-07:00

It's not easy to make a histogram in google spreadsheets without replicating data. The "countif" function would be great, except it only allows very simple criteria. However, there's a workaround:
=count(Filter('Grades'!V2:V30,'Grades'!V2:V30>0.9))
=count(Filter('Grades'!V2:V30,'Grades'!V2:V30<0.9,'Grades'!V2:V30>0.8))

The Filter() function returns an array, which can be operated on like any other set of cells.

It's still not easy to make a nice-looking histogram, but the output of this process is at least usable.

IDL-to-Python

2010-07-09T07:55:00.000-07:00

astrobetter started up an idl-to-python guide on their wiki.

Ghostscript error?

2010-06-13T00:04:00.000-07:00

I've been receiving the following error when attempting to compile (ps2pdf) my w5 outflows paper:

Error: /rangecheck in --get--
Operand stack:
   pdfmark   --dict:20/25(ro)(L)--   --nostringval--   50
Execution stack:
   %interp_exit   .runexec2   --nostringval--   --nostringval--   --nostringval--   2   %stopped_push   --nostringval--   --nostringval--   --nostringval--   false   1   %stopped_push   1878   1   3   %oparray_pop   1877   1   3   %oparray_pop   1861   1   3   %oparray_pop   1755   1   3   %oparray_pop   --nostringval--   %errorexec_pop   .runexec2   --nostringval--   --nostringval--   --nostringval--   2   %stopped_push   --nostringval--   %finish_show   --nostringval--   --nostringval--   8   6   1   --nostringval--   (pdf_text_enum_t)   %op_show_continue   --nostringval--
Dictionary stack:
   --dict:1153/1684(ro)(G)--   --dict:0/20(G)--   --dict:71/200(L)--   --dict:125/300(L)--   --dict:44/200(L)--   --dict:138/224(L)--
Current allocation mode is local
Last OS error: 2
Current file position is 267478928
GPL Ghostscript 8.71: Unrecoverable error, exit code 1

I get the same error with Ghostscript 8.64, but on my laptop, using the fink version, it works. Similarly, there are errors with the postscript, so I'm led to believe it's an error in latex:

$ latex --version
pdfTeX 3.1415926-1.40.10-2.2 (TeX Live 2009)
kpathsea version 5.0.0
Copyright 2009 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
Compiled with libpng 1.2.39; using libpng 1.2.39
Compiled with zlib 1.2.3; using zlib 1.2.3
Compiled with xpdf version 3.02pl3

No idea what the cause is but it's time to start documenting steps and looking for a workaround. Compiling on the lappy isn't a good option.

EVLA information

2010-05-26T14:01:00.001-07:00

It has been really hard to find EVLA information like beam size, largest angular scale, sensitivity, etc. on the VLA pages because all of the google searches point to old VLA information. The most useful and recent EVLA information on beam size and largest angular scale is here

usetex failure in latex documents

2010-05-25T15:35:00.000-07:00

When I use matplotlib's internal tex (rcParams['text.useTex']=False), the postscript files generated cause errors that look like this when you try to ps2pdf them:


ps2pdf h2co_pilot.ps
Error: /rangecheck in --get--
Operand stack:
   --dict:20/25(ro)(L)--   --nostringval--   71
Execution stack:
   %interp_exit   .runexec2   --nostringval--   --nostringval--   --nostringval--   2   %stopped_push   --nostringval--   --nostringval--   --nostringval--   false   1   %stopped_push   1862   1   3   %oparray_pop   1861   1   3   %oparray_pop   1845   1   3   %oparray_pop   1739   1   3   %oparray_pop   --nostringval--   %errorexec_pop   .runexec2   --nostringval--   --nostringval--   --nostringval--   2   %stopped_push   --nostringval--   %finish_show   --nostringval--   --nostringval--   9   6   0   --nostringval--   (pdf_text_enum_t)   %op_show_continue   --nostringval--
Dictionary stack:
   --dict:1147/1684(ro)(G)--   --dict:0/20(G)--   --dict:70/200(L)--   --dict:116/300(L)--   --dict:44/200(L)--   --dict:25/42(L)--
Current allocation mode is local
Last OS error: 2
Current file position is 791626
GPL Ghostscript 8.64: Unrecoverable error, exit code 1
make: *** [h2co_pilot.pdf] Error 1

They will not open in MacOS's Preview.app either.

Solution: Make figures with rcParams['text.useTex'] = True

RATRAN on Mac OS X

2010-05-01T11:31:00.001-07:00

Mac OS X doesn't like the defaults built in to RATRAN. It died unhappily with errors like:

ld_classic: can't locate file for: -lcrt0.o
and
ld: warning: in /usr/local/lib//libcfitsio.a, file is not of required architecture

In order to get it to run, I had to do the following:

Install CFITSIO with CFLAGS="-arch x86_64 -arch i386 -g -O2" to /usr/local/lib
Edit the sky/Makefile OPT variable (line 23) to read:
OPT = -I. -O2 -fno-automatic -arch x86_64

Also, you need to set up system variables:


export RATRAN=/path/to/Ratran 
export RATRANRUN=/path/to/Ratran/run

Gildas CLASS

2010-04-22T08:55:00.000-07:00

It's absurdly difficult to find help on GILDAS Class, probably because you can't google "class" and most people probably don't label every piece of code with "GILDAS class".

Anyway, here are some scripts that I refer back to often:


file in August2009BGPS.dat
file out August2009fits.dat multiple
on error "file out August2009fits.dat"
say "READ IN FILES"
define character sourcelist*10[300]
accept sourcelist /column observed_sources.txt
on error "continue"
get 1001
set window -100 160
set mask -400 -100 160 400
set mode x -400 400
set align velocity
for i 1 to 161
    say "Working on SOURCE "'i'
    find /source 'sourcelist[i]' /telescope "CSO 4GHZ IF1" /offset 0 0 /quality 5
    average
    on error "@avplot2 'sourcelist[i]' 'i'; next"
    base 3
    line 0
    min
    plot
    vis
    write i
!    on error "continue"
next

and


file in araya-2004.cls
find
define character filename*20
for i 1 to 20 
    say "Working on source "'i'
    get next
    let filename "araya-2004_"'i'".fits" 
    say "fits write "'filename'" /mode spectrum"
    fits write 'filename' /mode spectrum
next

!file in araya-2002.cls
!find
!define character filename*20
!for i 1 to 42 
!    say "Working on source "'i'
!    get i
!    let filename "araya-2002_"'i'".fits" 
!    say "fits write "'filename'" /mode spectrum"
!    fits write 'filename' /mode spectrum
!next

IRAF append/prepend/replace

2010-03-28T10:25:00.001-07:00

IRAF has special syntax to append/replace, so you can do something like:
imarith *.fits - dark.fits ds_//*.fits
...though I can't remember right now how to do replacement etc.

command line & escape key

2010-03-18T15:29:00.000-07:00

Problem: in both the bash command line and ipython, if I hit escape twice, I can never again do history-search-backwards (i.e. when you type part of a command and type "up" and reverse-search through your command history). Any idea how to fix this?

Rebuilding python from scratch again

2010-03-05T07:55:00.001-08:00

I got scipy working a week or two ago, but doing so killed matplotib's tkagg. So, I switched to the MacOSX backend, which worked ok until I realized that the interactive (connect) features of macosx failed miserably. This led me to try to get matplotlib working.... which broke with those awful "symbol not found" errors in ft2font.so and _path.so, which I've determined all have to do with linking to the wrong library files.

The most worrisome part of this process was discovering that a full Time Machine recovery of /usr and /Library/Frameworks and /Library/Python did *not* restore python - it stayed dead with IDENTICAL errors. So there are probably additional layers of hidden links.

The process below is based on hyperjeff's blog post but differs substantially based on Sam Skillman's recommendations and the very big issue I ran into that my /usr/local files appeared to be corrupted. After this install, my path no longer includes /usr/local/bin and /sw has been moved to /_sw... hopefully one of these days I'll be ballsy enough to delete it.

Install python 2.6.4
1. Needed a clean terminal with no flags set at all. Don't know why - all I had set were a bunch of -arch x86_64 flags.
  export LD_LIBRARY_PATH="/usr/local/lib:/usr/X11/lib" ./configure --enable-framework=/Library/Frameworks MACOSX_DEPLOYMENT_TARGET=10.6 make -j 17 sudo make install
2. Reset PYTHONPATH to blank
3. alias clearflags='export CFLAGS=""; export CCFLAGS=""; export CXXFLAGS=""; export LDFLAGS=""; export FFLAGS="";' to make sure
Install FFTW
cd ~/tmp curl -O http://www.fftw.org/fftw-3.2.2.tar.gz tar xf fftw-3.2.2.tar.gz cd fftw-3.2.2 clearflags ./configure CC="gcc -arch x86_64" CXX="g++ -arch x86_64" CPP="gcc -E" CXXCPP="g++ -E" make -j 17 sudo make install
Install UMFPACK
cd ~/tmp curl -O http://www.cise.ufl.edu/research/sparse/umfpack/current/UMFPACK.tar.gz curl -O http://www.cise.ufl.edu/research/sparse/UFconfig/current/UFconfig.tar.gz curl -O http://www.cise.ufl.edu/research/sparse/amd/current/AMD.tar.gz tar xf AMD.tar.gz tar xf UFconfig.tar.gz tar xf UMFPACK.tar.gz sed -ibck 's/F77 = f77/F77 = gfortran/' UFconfig/UFconfig.mk sed -ibck '299,303s/# //' UFconfig/UFconfig.mk cp UFconfig/UFconfig.h AMD/Include/ cp UFconfig/UFconfig.h UMFPACK/Include/ cd UMFPACK make -j 17 make hb make clean
Install numpy
1. Set environment variables
  export MACOSX_DEPLOYMENT_TARGET=10.6 export CFLAGS="-arch x86_64" export FFLAGS="-m64" export LDFLAGS="-Wall -undefined dynamic_lookup -bundle -arch x86_64" export PYTHONPATH="/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/" echo "[amd] library_dirs = /Users/adam/tmp/AMD/Lib include_dirs = /Users/adam/tmp/AMD/Include amd_libs = amd [umfpack] library_dirs = /Users/adam/tmp/UMFPACK/Lib include_dirs = /Users/adam/tmp/UMFPACK/Include umfpack_libs = umfpack" > site.cfg
2. Setup & Install
  python setup.py build --fcompiler=gnu95 sudo python setup.py install
3. Test: python -c "import numpy"
Install scipy. The important thing is to use g++-4.2 because g++-4.5 doesn't accept the -arch flag. Also, get rid of /sw if it's on your computer at all.
sudo mv /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpyX cd ~/repos/scipy-0.7.1 python setup.py clean rm -rf build clearflags FFLAGS="-m64" CFLAGS="-arch x86_64 -I/usr/local/include/freetype2 -I/usr/X11/include -L/usr/X11/lib" LDFLAGS="-Wall -undefined dynamic_lookup -bundle -lpng -arch x86_64" CXX="/usr/bin/g++-4.2" CC="/usr/bin/gcc-4.2" python setup.py build python setup.py install
Test the install:
python -c "import scipy, scipy.fftpack, scipy.interpolate"
1. Install matplotlib. MAKE SURE /usr/bin/texbin is in front of /usr/local/bin and /sw/bin so that dvipng comes from MacTEX. I also ended up having to remove /usr/local/bin from my path completely
  sudo mv /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpyX cd ~/repos/matplotlib-svn python setup.py clean rm -rf build clearflags
2. Do hyperjeff's recommended edits except don't use /usr/local because it's f'd:
  make.osx:
  MACOSX_DEPLOYMENT_TARGET=10.6 PREFIX=/usr PYTHON=/Library/Frameworks/Python.framework/Versions/Current/bin/python ## You shouldn't need to configure past this point (and yet…) PKG_CONFIG_PATH="${PREFIX}/lib/pkgconfig" CFLAGS="-arch i386 -arch x86_64 -I${PREFIX}/include -I${PREFIX}/include/freetype2 -isysroot /Developer/SDKs/MacOSX10.6.sdk" LDFLAGS="-arch i386 -arch x86_64 -L${PREFIX}/lib -syslibroot,/Developer/SDKs/MacOSX10.6.sdk" FFLAGS="-arch i386 -arch x86_64"
  setup.cfg:
  wxagg = False
3. Do the install (different from hyperjeff b/c I don't want root)
  sudo make -f make.osx fetch deps make -f mpl_build mpl_install python setup.py install
Install setuptools
easy_install ipython
install everything else pythonically

apache/php/mysql on snow leopard

2010-03-01T12:53:00.000-08:00

This post helped me out

macvim crash

2010-02-25T12:14:00.000-08:00

well, it finally happened.... my reliable, trusty editor crashed. That should be impossible. I am ready to call it quits for the week....


Process:         MacVim [650]
Path:            /Applications/Vim.app/Contents/MacOS/MacVim
Identifier:      org.vim.MacVim
Version:         7.2 (49)
Code Type:       X86 (Native)
Parent Process:  Vim [649]

Date/Time:       2010-02-25 13:12:43.001 -0700
OS Version:      Mac OS X 10.6.2 (10C540)
Report Version:  6

Interval Since Last Report:          871676 sec
Crashes Since Last Report:           26
Per-App Interval Since Last Report:  938504 sec
Per-App Crashes Since Last Report:   1
Anonymous UUID:                      03159B9E-2257-4E38-8C4A-4D4DAF5641A7

Exception Type:  EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: 0x000000000000000d, 0x0000000000000000
Crashed Thread:  0  Dispatch queue: com.apple.main-thread

Thread 0 Crashed:  Dispatch queue: com.apple.main-thread
0   com.apple.CoreFoundation       0x99119480 __CFSetCallback + 0
1   com.apple.CoreFoundation       0x990c78bc ___CFBasicHashFindBucket1 + 444
2   com.apple.CoreFoundation       0x990cfaac CFBasicHashFindBucket + 252
3   com.apple.CoreFoundation       0x990e8293 CFSetGetValue + 131
4   com.apple.AppKit               0x961bae7e -[NSWindow _discardTrackingRect:] + 59
5   com.apple.AppKit               0x961badca -[NSView(NSInternal) _uninstallTrackingArea:] + 123
6   com.apple.AppKit               0x960d2c32 -[NSView(NSInternal) _uninstallRemovedTrackingAreas] + 293
7   com.apple.AppKit               0x960dac40 -[NSView(NSInternal) _updateTrackingAreas] + 646
8   com.apple.CoreFoundation       0x990ea4e0 CFArrayApplyFunction + 224
9   com.apple.AppKit               0x960daefb -[NSView(NSInternal) _updateTrackingAreas] + 1345
10  com.apple.CoreFoundation       0x990ea4e0 CFArrayApplyFunction + 224
11  com.apple.AppKit               0x960daefb -[NSView(NSInternal) _updateTrackingAreas] + 1345
12  com.apple.CoreFoundation       0x990ea4e0 CFArrayApplyFunction + 224
13  com.apple.AppKit               0x960daefb -[NSView(NSInternal) _updateTrackingAreas] + 1345
14  com.apple.AppKit               0x960da8db _handleInvalidCursorRectsNote + 392
15  com.apple.CoreFoundation       0x99135892 __CFRunLoopDoObservers + 1186
16  com.apple.CoreFoundation       0x990f218d __CFRunLoopRun + 557
17  com.apple.CoreFoundation       0x990f1864 CFRunLoopRunSpecific + 452
18  com.apple.CoreFoundation       0x990f1691 CFRunLoopRunInMode + 97
19  com.apple.HIToolbox            0x936f6f0c RunCurrentEventLoopInMode + 392
20  com.apple.HIToolbox            0x936f6bff ReceiveNextEventCommon + 158
21  com.apple.HIToolbox            0x936f6b48 BlockUntilNextEventMatchingListInMode + 81
22  com.apple.AppKit               0x960b0ac5 _DPSNextEvent + 847
23  com.apple.AppKit               0x960b0306 -[NSApplication nextEventMatchingMask:untilDate:inMode:dequeue:] + 156
24  com.apple.AppKit               0x9607249f -[NSApplication run] + 821
25  com.apple.AppKit               0x9606a535 NSApplicationMain + 574
26  org.vim.MacVim                 0x0000238b _start + 209
27  org.vim.MacVim                 0x000022b9 start + 41

Thread 1:  Dispatch queue: com.apple.libdispatch-manager
0   libSystem.B.dylib              0x98d0c0ea kevent + 10
1   libSystem.B.dylib              0x98d0c804 _dispatch_mgr_invoke + 215
2   libSystem.B.dylib              0x98d0bcc3 _dispatch_queue_invoke + 163
3   libSystem.B.dylib              0x98d0ba68 _dispatch_worker_thread2 + 234
4   libSystem.B.dylib              0x98d0b4f1 _pthread_wqthread + 390
5   libSystem.B.dylib              0x98d0b336 start_wqthread + 30

Thread 2:
0   libSystem.B.dylib              0x98ce58da mach_msg_trap + 10
1   libSystem.B.dylib              0x98ce6047 mach_msg + 68
2   com.apple.CoreFoundation       0x990f277f __CFRunLoopRun + 2079
3   com.apple.CoreFoundation       0x990f1864 CFRunLoopRunSpecific + 452
4   com.apple.CoreFoundation       0x990f1691 CFRunLoopRunInMode + 97
5   com.apple.Foundation           0x91b24430 +[NSURLConnection(NSURLConnectionReallyInternal) _resourceLoadLoop:] + 329
6   com.apple.Foundation           0x91aeb8d8 -[NSThread main] + 45
7   com.apple.Foundation           0x91aeb888 __NSThread__main__ + 1499
8   libSystem.B.dylib              0x98d12fbd _pthread_start + 345
9   libSystem.B.dylib              0x98d12e42 thread_start + 34

Thread 3:
0   libSystem.B.dylib              0x98d04856 select$DARWIN_EXTSN + 10
1   com.apple.CoreFoundation       0x99131ddd __CFSocketManager + 1085
2   libSystem.B.dylib              0x98d12fbd _pthread_start + 345
3   libSystem.B.dylib              0x98d12e42 thread_start + 34

Thread 4:
0   libSystem.B.dylib              0x98d0b182 __workq_kernreturn + 10
1   libSystem.B.dylib              0x98d0b718 _pthread_wqthread + 941
2   libSystem.B.dylib              0x98d0b336 start_wqthread + 30

Thread 0 crashed with X86 Thread State (32-bit):
  eax: 0x00515db0  ebx: 0x990c7711  ecx: 0x00516460  edx: 0xbfffcabc
  edi: 0x00001041  esi: 0x00504270  ebp: 0xbfffca38  esp: 0xbfffc99c
   ss: 0x0000001f  efl: 0x00010246  eip: 0x99119480   cs: 0x00000017
   ds: 0x0000001f   es: 0x0000001f   fs: 0x00000000   gs: 0x00000037
  cr2: 0x97a20000

Command of the Day

2010-02-17T14:20:00.001-08:00

ls | wc

and for when ls * fails

find . -name "*" | xargs -I {} mv {} away/

DS9 gaussian fitting

2010-02-16T20:44:00.001-08:00

One thing DS9 desperately needs is an interactive gaussian fitter. I have NOT implemented one yet, but it is high on my to do list. Has anyone else (googlers?) tried or succeeded in implementing such a thing? Ideally, something with NO dependencies: if I write one, it will require python, numpy, and probably pyds9 - ick. Straight-up TCL would be very much preferable.

Another attempt to get 64 bit python on Snow Leopard

2010-02-16T13:47:00.000-08:00

Sam Skillman posted his attempt to get 64 bit python on snow leopard. It worked, but you need to install python with --enable-framework and NOT --prefix and NOT --enable-universalSDK. It is 64-bit only, not universal: universal causes trouble.

Python 64-bit on Mac OS X 10.6 Snow Leopard

2010-02-15T08:57:00.000-08:00

After yesterday's disastrous attempt to install various python packages, I started from scratch. First, I got rid of all of my python frameworks (backed up but removed from the path). Then, I compiled python 2.7 from scratch:

I got some help from http://blog.mahmoudimus.com/2009/12/python-2-6-4-and-twisted-9-on-os-x-10-6-snow-leopard/

./configure --enable-framework --enable-universalsdk=/Developer/SDKs/MacOSX10.6.sdk MACOSX_DEPLOYMENT_TARGET=10.6 --with-universal-archs=intel -with-readline-dir=/usr/local
make -j 17
make -j 17 test

make results:

Python build finished, but the necessary bits to build these modules were not found:
_bsddb             dl                 gdbm            
imageop            linuxaudiodev      ossaudiodev     
spwd               sunaudiodev                        
To find the necessary bits, look in setup.py in detect_modules() for the module's name.

I'm not concerned about these - I don't use any of them and I assume I need to install some other packages to get them to work.

During make test, I had two failures that resulted in "python crash" pop-up boxes:

test_subprocess
.
    this bit of output is from a test of stdout in a different process ...
.
    this bit of output is from a test of stdout in a different process ...
test_sunaudiodev

Then, I got some malloc errors:

test_io

Testing large file ops skipped on darwin.
It requires 2147483648 bytes and a long time.
Use 'regrtest.py -u largefile test_io' to run it.

Testing large file ops skipped on darwin.
It requires 2147483648 bytes and a long time.
Use 'regrtest.py -u largefile test_io' to run it.
python.exe(22914,0x7fff70d3ebe0) malloc: *** mmap(size=9223372036854775808) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
python.exe(22914,0x7fff70d3ebe0) malloc: *** mmap(size=9223372036854775808) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
python.exe(22914,0x7fff70d3ebe0) malloc: *** mmap(size=9223372036854775808) failed (error code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
test_ioctl

Installing Snow Leopard

2010-02-14T12:23:00.000-08:00

I'm going to attempt to install snow leopard today. This post will serve as a record of the difficulties I run into.

Things to install (and ensure they are 64-bit):

ipython
numpy
scipy
matplotlib
stsci-python
starlink
gfortran
latex
idl (check)

Things that have happened:

Had to restart again (twice) to install additional updates
My bash command line looked funny - something about bash changed, but I don't know what. The fix was easy: commented out some code from http://pseudogreen.org/blog/set_tab_names_in_leopard_terminal.html that I had been using to set the tab title
My locate db broke. Needed repair: sudo /usr/libexec/locate.updatedb
numpy svn failed to build:
python setup.py build Running from numpy source directory.non-existing path in 'numpy/distutils': 'site.cfg' F2PY Version 2_8111 numpy/core/setup_common.py:86: MismatchCAPIWarning: API mismatch detected, the C API version numbers have to be updated. Current C api version is 4, with checksum 59750b518272c8987f02d66445afd3f1, but recorded checksum for C API version 4 in codegen_dir/cversions.txt is 3d8940bf7b0d2a4e25be4338c14c3c85. If functions were added in the C API, you have to update C_API_VERSION in numpy/core/setup_common.pyc. MismatchCAPIWarning) blas_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec', '-I/System/Library/Frameworks/vecLib.framework/Headers'] lapack_opt_info: FOUND: extra_link_args = ['-Wl,-framework', '-Wl,Accelerate'] define_macros = [('NO_ATLAS_INFO', 3)] extra_compile_args = ['-faltivec'] running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building py_modules sources building library "npymath" sources customize NAGFCompiler Found executable /usr/local/bin/f95 customize AbsoftFCompiler Could not locate executable f90 Found executable /usr/bin/f77 absoft: no Fortran 90 compiler found absoft: no Fortran 90 compiler found customize IBMFCompiler Could not locate executable xlf90 Could not locate executable xlf customize IntelFCompiler Could not locate executable ifort Could not locate executable ifc customize GnuFCompiler Found executable /usr/local/bin/g77 gnu: no Fortran 90 compiler found gnu: no Fortran 90 compiler found customize Gnu95FCompiler Found executable /usr/local/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using config C compiler: gcc -arch i386 -arch ppc -arch ppc64 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.5.sdk -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c' gcc: _configtest.c gcc _configtest.o -o _configtest ld: library not found for -lcrt1.10.5.o collect2: ld returned 1 exit status ld: library not found for -lcrt1.10.5.o collect2: ld returned 1 exit status failure. removing: _configtest.c _configtest.o Traceback (most recent call last): File "setup.py", line 210, in setup_package() File "setup.py", line 203, in setup_package configuration=configuration ) File "/Users/adam/repos/numpy-svn/numpy/distutils/core.py", line 186, in setup return old_setup(**new_attr) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/core.py", line 152, in setup dist.run_commands() File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 975, in run_commands self.run_command(cmd) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build.py", line 37, in run old_build.run(self) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/command/build.py", line 134, in run self.run_command(cmd_name) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/cmd.py", line 333, in run_command self.distribution.run_command(command) File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/distutils/dist.py", line 995, in run_command cmd_obj.run() File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 152, in run self.build_sources() File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 163, in build_sources self.build_library_sources(*libname_info) File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 298, in build_library_sources sources = self.generate_sources(sources, (lib_name, build_info)) File "/Users/adam/repos/numpy-svn/numpy/distutils/command/build_src.py", line 385, in generate_sources source = func(extension, build_dir) File "numpy/core/setup.py", line 670, in get_mathlib_info raise RuntimeError("Broken toolchain: cannot link a simple C program") RuntimeError: Broken toolchain: cannot link a simple C program

SOLUTION: Use the Mac OS X 10.6 python (/usr/bin/python). I will do this until I run into another problem. Numpy build successfully
Build/install matplotlib - failed! Completely!
Acquired gcc/gfortran from hpc
Followed instructions from hyperjeff on fortran install...
Get rid of numpy 1.2.1: mv /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/numpy /System/Library/Frameworks/Python.framework/Versions/2.6/Extras/lib/python/.not_numpy.bak
Try to install scipy. Fail on missing umfpack, follow hyperjeff's instructions (but make sure to edit the site.cfg in scipy, not just the one in numpy)

Had to add the following code:
sudo cp AMD/Lib/libamd.a /System/Library/Frameworks/Python.framework/Versions/2.6/lib sudo cp UMFPACK/Lib/libumfpack.a /System/Library/Frameworks/Python.framework/Versions/2.6/lib sudo cp AMD/Include/amd.h /System/Library/Frameworks/Python.framework/Versions/2.6/include sudo cp UFconfig/UFconfig.h /System/Library/Frameworks/Python.framework/Versions/2.6/include sudo cp UMFPACK/Include/*.h /System/Library/Frameworks/Python.framework/Versions/2.6/include
Installed fftw from fftw.org with simple ./configure, make, sudo make install - no compiler opts as they killed the install
Get SoundSource from rogueamoeba
Updated istatmenus

PSDs, cross-correlation...

2010-02-12T08:01:00.000-08:00

scipy is capable of doing fft-base cross-correlation, convolution, etc., but it requires the stsci package, which is not generally easy to install. For that matter, scipy can be a pain some of the time. So agpy now includes a 2D cross-correlation code and a power spectrum / power spectral density code. These are pure-numpy codes that should be easy to use without any other bothersome dependencies.

EDIT: I have them check for scipy (which can cause crashes if you have a bad scipy install, e.g. 32 bit executables on a 64 bit system) because scipy uses FFTW and numpy appears not to. Also, this code & related stuff has been discussed on astrobetyter

agpy
correlate2d
psds

Logarithmic Colormap / Other Colormap in Matplotlib

2010-02-04T18:31:00.000-08:00

This is kind of a pain to find out:


from matplotlib.colors import LogNorm

im = imshow(.... cmap=... , norm=LogNorm(vmin=clevs[0], vmax=clevs[-1]))

It also works for contours, and can be particularly useful if you only want to display contours at a few levels, but you want the colormap to start at a different point. e.g.:


contour(xx,levels=[2,3,4,5,6,7,8,9,10],norm=matplotlib.colors.Normalize(vmin=0,vmax=10))

will start at light blue instead of dark blue in the default colormap

wrapping text around a figure in latex

2010-01-27T17:52:00.001-08:00

An example from Devin:

%\begin{wrapfigure}{l}{0.5\textwidth}
% \vspace{-27pt}
% \begin{center}
% \includegraphics[width=0.48\textwidth]{nsf_fig3.ps}
% \end{center}
% \vspace{-27pt}
% \caption{\it{}}
% \vspace{-12pt}
%\end{wrapfigure}
1:16
\usepackage{wrapfig}

my month of travel

2010-01-03T16:39:00.000-08:00

I figure most people spending a month away from home would bring more than a small duffel full of clothes. I was quite satisfied with what I had. The things I missed (as a reminder for next time):
My desktop, eta
My music collection
Powerbars

...nothin else, really

Detexify!

2009-12-15T00:58:00.001-08:00

for when you can't remember how to draw an angstrom:
detexify

wget

2009-11-19T19:39:00.001-08:00

wget is very useful for acquiring data from, e.g., IRSA, the NASA Infrared Science Archive.

wget -nd -r -l1 -A*g09*_b4_20.fits http://irsa.ipac.caltech.edu/data/IGA/images/

The important elements:
-nd: don't reproduce the host directory structure
-r: recursive. Grab the files referred to by the page, not just the page itself
-l#: number of recursion levels
-A: "accept" wildcard

New python software

2009-10-21T06:52:00.000-07:00

IDLsave was released on my birthday. It does what you'd expect - read IDL save files into Python.
APLpy has a make_RGB_cube function now that takes care of all the internals of making an RGB image.... haven't tried it yet but I need to because it is awesome.

astro-better post

2009-10-21T06:49:00.000-07:00

I contributed to a post on Astro Better asking about mosaicing software.

#6 on Astro-ph today

2009-10-18T18:51:00.000-07:00

IRAS 05358 on astro-ph. Check out my page on the region too.

This week at the Sun

2009-10-18T15:21:00.000-07:00

Wednesday, Thursday, Saturday, Sunday @ The Southern Sun: Delicious. The Holler's Haze Smoked Porter is new on tap, and it's delicious. Very smooth, the smoke is pretty subtle (i.e. not overpowering the way most porters are), and it's 6.4%.

Cleveland Brown is back on tap too. It's not as good as I remember, but it will probably be better on nitro.

Still no word on whether the Carne Asada burrito will return.

First paper accepted

2009-10-16T09:26:00.000-07:00

My Comps II paper on IRAS 05358+3543 was accepted by ApJ on Wednesday. It will show up on arxiv in a few days and I'll post the link then. Unfortunately, there were significant problems rendering the paper, so I recommend downloading my version.

Also, working on the HISA KDA... I have a nice section of cutouts

Galaxy Map

2009-10-14T09:22:00.000-07:00

If you're ever interested in seeing a face-on view of the Milky Way, check out the Spitzer press release. This link is very surprisingly hard to find on google.

cython vs f2py

2009-08-26T10:40:00.000-07:00

I had a go at optimizing some code this past week, and ended up learning to use both cython and f2py.

f2py is much easier to use. If you want to write a function in fortran and use it in python, all you do is write the code and add specifications using comments in the fortran code.

cython is more natural to code. The code style is C/fortran-like: think in terms of loops instead of arrays. The syntax is python-like, which makes coding somewhat clearer and simpler.

For my code, I found that cython was ~10% slower than fortran.

Check out the plfits in:
http://code.google.com/p/agpy/source/browse/#svn/trunk/

How to make a pretty image

2009-08-17T07:45:00.000-07:00

The most difficult requirement to satisfy is WCS matching. Each image has to be in exactly the same pixel space in order to overlay them successfully in an image program. The process is generally to use Montage's mProject to project the images into the same plane, then mAdd with a blank map of a given size so that the dimensions in pixels are identical.

Once that's done, I load the images into GIMP. However, GIMP reads .fits files as 256 bit data - which is essentially useless because most (interesting) images have a dynamical range >~1000. So I usually make images emphasizing the faint emission in log scale with the high and low ends cut off (I use DS9 to determine high/low). I make a second copy showing the details of the very bright regions, again in logscale but it ends up being a different log scale - essentially, my transfer function becomes a broken power law.

The tricks in GIMP are numerous, but primarily two:
1. Rotate the color table ~60 degrees
2. Use images as "Layer Masks" (aka alpha layers) on a solid color background

There's also the nice trick when using radio data of using optical or some other wavelength to provide the high-resolution details, while the radio emission provides the intensity.

FITS manipuation with imagemagick, gimp, etc.

2009-08-15T13:46:00.001-07:00

It is possible to convert .fits files to .png, .jpg, etc:
convert -normalize a.fits a.png

To get things to come out nicely, you have to do the scaling essentially by hand in python/idl/iraf. DS9 is only useful for finding out what scaling you want to use; past that it's pretty much not useable.

To make colors look nice in the GIMP, use solid background layers with your image as the alpha mask. Then put your image in with itself as an alpha mask so you can easily control the whiteness (saturation) of the color you've selected.

I'll be blogging about this more as I prep my next entry for the NRAO photo contest.

Acquiring DSS images

2009-08-14T08:21:00.001-07:00

This is the way to get DSS images:
ESO's batch downloader

login shell

2009-08-13T08:25:00.001-07:00

to change your default login shell, use chsh

Quicksilver sounds

2009-08-12T08:49:00.001-07:00

To switch sound source from the command line:
switchaudio

Use this to make scripts such as:


#!/bin/bash
/Users/adam/humor/SwitchAudioSource -s "Built-in Line Output"
afplay /Users/adam/humor/losinghorn.wav
/Users/adam/humor/SwitchAudioSource -s "Built-in Output"

Then make triggers in Quicksilver by:

Go to trigger pane, make new hotkey trigger
press "." to allow you to type a command
make sure the action is "Run"
hook up a hotkey
if it doesn't work, just try again. Persist through crashes, they happen often.

Follow-up: You can also control the volume!
http://discussions.apple.com/thread.jspa?threadID=585781
osascript -e 'set volume output volume 100'

Movie Review: Public Enemies

2009-07-25T22:51:00.000-07:00

Boring.

Year in review

2009-07-12T16:37:00.000-07:00

It's been just over a year since I started this blog. I posted a LOT more than I thought I would. Also, I apparently dropped the tradition of reviewing beers. So I'll start by reviewing some beers!

Mountain Sun Hummingbird - a strong honey-ale (meade-beer?) brewed with orange blossom honey. Slightly darker than a typical Belgian Golden but similar in style. The beer is mildly sweet but very drinkable. Hmm... there are flavors I should mention but they escape me.

Mountain Sun/Avery Van Diemens - brewed with Tasmanian Pepper Berry, this is a very curious, semi-dark beer. When I first sampled it, I tasted a little bit of pepper kick at the end, but couldn't really identify any other flavors. Yesterday I sampled it next to a burrito with some somewhat spicy salsa. Somehow, since my mouth was already sensitized to spiciness, the flavor I got was root beer (sassafras?). It was... odd. Pretty good, but I didn't end up purchasing a glass.

Moving on to code. I don't know why I haven't mentioned this, but with my discovery of svn, I started uploading my code to the webternets: agpy is my Google Code page and includes a number of useful python codes, especially readcol and gaussfitter, which I have tested and used extensively since writing them. Python is still a long way from a cohesive astrolib code base, but with individual contributions, the STSCI development group, and APLpy underway, we're getting closer.

SUCCESS! 64 bit python with 64 bit tcl/tk!!!

2009-07-08T08:11:00.001-07:00

After a long, tedious process (see previous posts), I got 64 bit python, 64 bit tcl/tk, and 64 bit tkinter all to work! I can now use the TkAgg backend in matplotlib!

Python 64 bit on Mac OS X: Sam Skillman's post

Tcl/Tk 64 bit: a post on the tcl/tk forums

tkinter 64 bit: python bug report 4017 (last two posts give the solution) and my posted solution

Failure to compile 64 bit gtk on mac os

2009-07-05T16:52:00.000-07:00

Attempted to install gtk+-2.17.2 on my mac. Had to install:
glib-2.21.2
which would not let me compile with multiple architectures, and
pkgconfig-0.9.0,
which won't configure because:


configure: configuring in glib-1.2.8
configure: running /bin/sh './configure' --prefix=/usr/local  CC= CFLAGS= LDFLAGS= --cache-file=/dev/null --srcdir=.
configure: warning: CC=: invalid host type
configure: warning: CFLAGS=: invalid host type
configure: error: can only configure for one host and one target at a time
configure: error: /bin/sh './configure' failed for glib-1.2.8

which is bs because I don't have any compiler flags set.

So, gtk+ seems hopeless.

UPDATE: 0.9.0 is not the latest version, 0.23.0 is. Dumb version numbering.

GTK is absurd to install. You need:
pkg-config
glib
cairo
pixman
pango (MUST be installed AFTER cairo)
atk
libtiff
libjpg
jpeg2000 - but I just passed a flag to not do this because it didn't install right. --without-libjasper
fontconfig I mean, really? at this point it's just ridiculous....

and finally, it died with this:
checking Pango flags... configure: error:
*** Pango not found. Pango built with Cairo support is required
*** to build GTK+. See http://www.pango.org for Pango information.

which meant that I had to reinstall Pango because I had installed it before Cairo.

I believe this is where the term dependency hell comes from.

Also, I don't think any of these are x86-64 compatible.

Then I'm STILL not done.

PyGTK dies with an import error on dsextras, which a painful google search traces to pygobject. pygobject makes and installs fine.... but then I find out it installed to /usr/local/lib/python2.6/site-packages/gtk-2.0/, which is obviously not on my python path since I installed a framework.

So:
./configure --prefix=/Library/Frameworks/Python.framework/Versions/2.6/
in both pygobject and pygtk.

Oh, guess what? Need pycairo too. What happens there? What you'd guess:
ld warning: in /Developer/SDKs/MacOSX10.5.sdk/usr/local/lib/libcairo.dylib, file is not of required architecture

so when I configure pygtk:

The following modules will be built:

atk
pango

The following modules will NOT be built:

pangocairo
gtk
gtk.glade
gtk.unixprint

Damn. That blows.

python-64 -c "import gtk"
ImportError: dlopen(/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/gtk-2.0/glib/_glib.so, 2): no suitable image found. Did find:
/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/gtk-2.0/glib/_glib.so: mach-o, but wrong architecture

FAIL.

Installing 64 bit tcl/tk on Mac OS X

2009-07-02T17:43:00.000-07:00

Everything is described in this post:
http://www.nabble.com/Error-compiling-tk-8.5.7-on-Mac-OS-X-10.5-td23790967.html

But here's a script too:


curl -O 'http://osdn.dl.sourceforge.net/sourceforge/tcl/t{cl,k}8.5.7-src.tar.gz'
for f in t*8.5.7*.gz; do tar zxf $f; done 
cd tcl8.5.7/unix/
./configure --enable-framework --enable-64-bit
cd tk8.5.7/unix/
./configure --enable-framework --enable-64-bit
make -j 4 -C tcl8.5.7/unix 
make -j 4 -C tk8.5.7/unix
sudo make install -C tcl8.5.7/unix 
sudo make install -C tk8.5.7/unix

Concerns:
-might be necessary to do this in the macosx directory for some reason, though Aqua doesn't support 64 bits
-have to recompile python to get _tkinter to work (see a later post)

Make PDFs open with the thumbnails window open

2009-06-29T08:47:00.000-07:00

Neat trick I picked up from here:
http://www.ghostscript.com/~ghostgum/pdftips.htm

Add this code:


  \special{! /pdfmark 
              [/View [/XYZ null null 1]  % unspecified x and y offset, 100% zoom
               /Page 1
               /PageMode /UseThumbs % /UseNone /UserOutlines /UseThumbs /FullScreen
              /DOCVIEW pdfmark 
              }

to a LaTeX document (probably near the top) and when you ps2pdf it, it will open the PDF with the thumbnail bar open. This is very useful for proofreading after you latex a file. Of course, xdvi also works well for this, but xdvi is VERY unstable on the Mac. At least adobe, being a native Mac program, doesn't crash as often.

BGPS public release

2009-06-22T16:31:00.001-07:00

http://irsa.ipac.caltech.edu/

Art mimicing reality

2009-06-15T16:49:00.001-07:00

An artist who likes painting astronomical objects:
Marianne Beacham Gallery

Comps 2 reflections

2009-06-14T18:48:00.000-07:00

Comps 2 included some successes and some failures.

The most successful part of my Comps preparation was the Monday talk. The previous talk on Tuesday was somewhat helpful in terms of realizing that I needed larger figure axes, but otherwise provided no useful feedback. The Monday talk allowed me to realize what needed to be done to make my talk accessible to a larger audience.

At the defense, I ended up going only ~40 minutes despite having gone far over time in the Monday version and spending ~5 minutes answering questions from Don and Mike. I think that was a good thing; I didn't need to say anything more even though there was an enormous amount of additional material I could have covered.

The main change I made from Monday to Friday was reorganizing such that I discussed the largest scales first and zoomed in, and I spent much more time discussing the larger context of my work. Unfortunately, I also spent most of the week before the presentation determining the larger context and reading papers. Ideally, I would have done that before handing in the paper.

The closed door Q&A section went OK but not great. There were a few important bits of information related to the IMF that I didn't know off the top of my head - e.g. the ratio of total # of stars to the # of B stars. I got the lowest mass star (.07) confused with the most common star mass (.3). I wasn't particularly able to integrated the IMF on the board either. I didn't remember the Jeans mass-temperature and mass-density relationships but was able to derive them quickly enough.

Probably the biggest problem was dealing with a question about the partition function - specifically how did the partition function come into play in the column density equation. I didn't come up with the right answer at all, and in particular quoted the wrong distribution. However, I think a big part of what they expected to hear was a dependence on temperature AND degeneracy, and I never explicitly mentioned degeneracy. It turned out that the equation I had quoted in both the paper and the talk was correct, but I couldn't come anywhere close to proving that on the spot.

My expected result is therefore a low pass, though it was not made explicit. That's rather unfortunate as it's possible that another month of preparation could have gotten me the high pass, but at the same time, it's well worth having the project done.

Most important astronomical publications

2009-06-02T09:52:00.000-07:00

I'm interested to hear input on this. Some I know of:
Cardelli, Clayton, Mathis 1989 - determined interstellar extinction law
Kurucz 1993 - possibly a book? Stellar atmosphere calculations

public perception of astronomers

2009-05-26T06:49:00.000-07:00

Public Perception of Astronomers

While the article has some.... almost-interesting points, I don't agree with the thesis or the suggested methods. I don't really have a problem with the stereotype of astronomers being the old, white, socially inept guy - because for the most part that's a fair assessment. We're scientists, and at least for me and my peers, that's directly correlated with not fitting in to some social circles.

I agree that we should become better communicators in general, but it's silly to think that embracing new technologies (i.e. social networking tools) is going to change the public image of astronomers at all. Personally I hope to see a backlash against social networking and blogs sometime in the next 5 years, but who knows.... after all, I'm writing a blog post.

some comics

2009-05-25T20:22:00.000-07:00

http://ableandbaker.net/index.php?comic=198
http://ableandbaker.net/index.php?comic=222
http://ableandbaker.net/index.php?comic=357
http://ableandbaker.net/index.php?comic=396
http://ableandbaker.net/index.php?comic=471
545 "Put on your snuggle trunks and jump in the cuddle pool."
http://ableandbaker.net/index.php?comic=905
http://ableandbaker.net/index.php?comic=922

2009-05-07T10:07:00.001-07:00

Comedic timing has been fixed using quicksilver's command line execution abilities.

Also been playing with dashboard... Safari's new dashboard feature is pretty cool, but also incompetent. It refreshes every time you reload the dashboard, which is inefficient and makes saving settings impossible. Also, the gmail compose feature fails miserably. So, dashboard must die again.

Quicksilver and Awesome

2009-05-06T08:38:00.000-07:00

Set up f17-19 today to play amusing sounds. Also, recalled that I use ScreenSaverEngine to lock my screen with a shortcut key.

Quicksilver triggers are the way to do it. Mac is stupid w/o quicksilver.

Python 64 bit!

2009-04-21T10:41:00.000-07:00

I got python 64 bit to compile, but it required a number of tricky steps.

First, this guy has the instructions I followed:
captnswing

However, it didn't work entirely as advertised. I ran the configure as advertised:


./configure --enable-framework=/Library/Frameworks \
--enable-universalsdk=/ \
MACOSX_DEPLOYMENT_TARGET=10.5 \
--with-universal-archs=all \
--with-readline-dir=/usr/local

then the make install, but /usr/local/bin/python pointed to the wrong place, so I replaced the symbolic link in my python path with the correct one:


sudo rm /Library/Frameworks/Python.framework/Versions/2.6/bin/python 
sudo ln -s /Library/Frameworks/Python.framework/Versions/2.6/bin/python-64 /Library/Frameworks/Python.framework/Versions/2.6/bin/python

Now python is 64 bit:


eta ~$ python -c "import sys; print sys.maxint"
9223372036854775807

I haven't checked whether it works yet though...

Update: Had to reinstall with gnu readline installed. Also have to install PyQt4 and might have to recompile numpy...

numpy won't compile with python 2.6.2:

C compiler: gcc -arch i386 -arch ppc -arch ppc64 -arch x86_64 -isysroot / -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes

compile options: '-Inumpy/core/include -Ibuild/src.macosx-10.5-universal-2.6/numpy/core/include/numpy -Inumpy/core/src -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c'
gcc: build/src.macosx-10.5-universal-2.6/numpy/core/src/_sortmodule.c
In file included from numpy/core/include/numpy/ndarrayobject.h:26,
                 from numpy/core/include/numpy/noprefix.h:7,
                 from numpy/core/src/_sortmodule.c.src:29:
numpy/core/include/numpy/npy_endian.h:33:10: error: #error Unknown CPU: can not set endianness
lipo: can't figure out the architecture type of: /var/folders/ni/ni+DtdqFGMeSMH13AvkNkU+++TI/-Tmp-//cceaWIvZ.out
In file included from numpy/core/include/numpy/ndarrayobject.h:26,
                 from numpy/core/include/numpy/noprefix.h:7,
                 from numpy/core/src/_sortmodule.c.src:29:
numpy/core/include/numpy/npy_endian.h:33:10: error: #error Unknown CPU: can not set endianness
lipo: can't figure out the architecture type of: /var/folders/ni/ni+DtdqFGMeSMH13AvkNkU+++TI/-Tmp-//cceaWIvZ.out
error: Command "gcc -arch i386 -arch ppc -arch ppc64 -arch x86_64 -isysroot / -fno-strict-aliasing -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -Inumpy/core/include -Ibuild/src.macosx-10.5-universal-2.6/numpy/core/include/numpy -Inumpy/core/src -Inumpy/core/include -I/Library/Frameworks/Python.framework/Versions/2.6/include/python2.6 -c build/src.macosx-10.5-universal-2.6/numpy/core/src/_sortmodule.c -o build/temp.macosx-10.5-universal-2.6/build/src.macosx-10.5-universal-2.6/numpy/core/src/_sortmodule.o" failed with exit status 1

That sucks.

Hosting on my mac

2009-04-20T07:52:00.000-07:00

I'm hosting my website off my mac; it should be accessible to the outside world now: eta.colorado.edu.

A few things went into this....

Don't install the fink version. The two versions clash and depending on how you access your computer you could end up looking at entirely different directories (e.g. localhost and eta.colorado.edu referred to different sites for a while)
The configuration file is /private/etc/apache2/httpd.conf
I needed to change DirectoryIndex to index.htm (from index.html)
uncommmented "LoadModule php5_module libexec/apache2/libphp5.so"
had to allow override so that .htaccess files would work.

Mac stuff cont'd

2009-04-15T07:57:00.000-07:00

Trying to get Apache server to run, and it's just a pain.

I frequently forget how to update the locate database because it's different on macs. Marcos' Mac Singularity has the instructions .

In short:
sudo /usr/libexec/locate.updatedb

Google has failed me

2009-04-14T09:43:00.001-07:00

So, either no one on the internet has successfully installed 64-bit python on a mac (which I find nothing short of impossible) or google has totally failed. None of the hits for any combination of 64 bit, python, mac, etc. has shown a useful result. Wow.

Caffeine

2009-04-06T21:46:00.000-07:00

Caffeine consumption stopped around mid-October. I think it was when I got back from observing so October 20 give or take. Re-started consumption mid-March. Date is hard to say... I think it was Sunday before Spring Break, but hard to say because I still took it easy until ~last week.

Conclusions? I'm probably more tired in the mornings with caffeine than without. Also, probably perform better @ ulty when I'm not addicted. However.... not really conclusive. Just addictive.

weekend

2009-04-04T17:39:00.001-07:00

What did I do this weekend?
-upgraded PyRAF from 1.6.1 to 1.7
-switched matplotlib backends from TkAgg to Qt4
-put up a new article on molecularclouds

So... totally unproductive, but only in an awesome way?

I tried to switch PyRAF from X11 to Aqua a la Ticket 86 on the PyRAF trac site, but it failed with a can't-load error.

Also, updated readcol documentation so that it makes sense. Sam has used it, Robbie might.

April 1st, 2009

2009-04-01T08:31:00.000-07:00

No April fools' day would be complete without scientists' contributions:

http://arxiv.org/abs/0903.5308
http://arxiv.org/abs/0903.5321
http://arxiv.org/abs/0903.5377

although it's not obvious whether .5308 is actually intended to be humorous

Astronomy gets some recognition

2009-02-25T13:41:00.001-08:00

First off, this guy does some amazing work, like measuring the galactic rotation curve. He got recognized by the Colbert Report. Sweet.

My works featured...

2009-02-18T17:38:00.001-08:00

Curiously, one of my wikimedia commons images has been included in this article: http://www.scienceinschool.org/2008/issue10/tamaradavis, though the image has little to do with the subject in question. Noodle (can't remember her real name... that's sad on my part) is in the picture. Neat!

This might not be something to be proud of:
http://www.denverptc.org/denver.html

GC was featured in:
http://www.strudel.org.uk/blog/astro/000855.shtml

ps2pdf keep resolution, crop to bounding box

2009-01-22T18:20:00.000-08:00

  ps2pdf -dEPSCrop -dAutoRotatePages=/None -dAutoFilterColorImages=false -dColorImageFilter=/FlateEncode -dUseFlateCompression=true l007_displaycrop.ps

ref: this post

Making a postscript plot of a gigantic fits image

2009-01-22T09:26:00.001-08:00


    map = readfits('MOSAIC.fits',hdr)

    crpix1 = sxpar(hdr,'CRPIX1')
    crpix2 = sxpar(hdr,'CRPIX2')
    crval1 = sxpar(hdr,'CRVAL1')
    crval2 = sxpar(hdr,'CRVAL2')
    cd1_1 = sxpar(hdr,'CD1_1')
    cd2_2 = sxpar(hdr,'CD2_2')
   
    x = lindgen(n_e(map[*,0]))
    y = lindgen(n_e(map[0,*]))
    l = (x-crpix1)*cd1_1+crval1-360
    b = (y-crpix2)*cd2_2+crval2

    imdisp,map,/axis,xrange=[max(l),min(l)],yrange=[min(b),max(b)],range=[-1,8]

This code makes use of imdisp.pro.

MOSAIC data reduction

2009-01-14T13:05:00.000-08:00

MOSAIC reduction is very difficult.
http://www.noao.edu/noao/noaodeep/ReductionOpt/frames.html has the official instructions.

Important things:
Have the latest version of MSCRED and MSCDB installed. Both will give cryptic errors or "cannot open file" errors (because the files don't exist) otherwise.


mscred
setinstrument kpno CCDMosaThin1
msccmatch obj09*.fits coords="!mscgetcat $I $C" search=60 rsearch=1 nfit=30 accept=yes interactive=no fit=no

Site visits, comps

2009-01-13T21:06:00.000-08:00

Amusing - visits to my site increased steadily leading up to Jan 9, then crashed precipitously.

LaTeX: replace double quotes with tex quotes

2008-12-27T16:17:00.000-08:00

People often make the mistake of putting " in place of `` in LaTeX documents. To repair this, the only easy solution is something like:
s/$\s$"/\1``/g
in VIM or sed.

I've seen alternate solutions posted but they're all too complicated. One recommendation was to switch to XeTeX, which sounds like overkill, and others all stated that a complicated perl script is required. The latter is technically true, but why isn't such a thing readily available?

Any other ideas?

Skim: a PDF reader that allows annotations

2008-12-21T12:33:00.001-08:00

from Sam: http://skim-app.sourceforge.net/

neat

skill set

2008-12-11T13:10:00.001-08:00

is it a marketable skill that I can bring down almost any computer system I'm given access too entirely unintentionally?

post rate

2008-12-05T15:53:00.001-08:00

my post rate is too low I need to up it so that my front page doesn't show the same posts any more

scary

2008-12-03T12:20:00.000-08:00

I think this is my worst nightmare:
http://antwrp.gsfc.nasa.gov/apod/ap081203.html

LA. Not the smiley.

.inputrc

2008-11-24T10:50:00.000-08:00

New unix stuff!

This is, again, stuff I'd searched for forever but never found the right collection of terms. This is what bash readline is REALLY all about.

if you make an inputrc file, you can get awesome readline capabilities (similar to ipython). This post at lifehacker showed me how to do it. This site has a more complete description of how to use readline/inputrc.

Even better: VI command line editing .

There's also something called magic space but I don't know what purpose it serves all the time... it will replace 'magic' characters like !* and !& and !! with whatever command they represent if you hit space immediately after typing them (explained better here).

Wow. Awesome.

MOVIES!

2008-11-20T17:42:00.000-08:00

Making movies is surprisingly difficult. No matter what language you use, apparently true movie files can only be made by stringing together images, i.e. there is no native movie-producing feature. Gnuplot can do some simple animations but to do anything sophisticated you need to start delving into variables, and for that I switch to a real language.

So, I returned to python. As usual, it took no more than a few hours of coding and learning to come up with something. But it bothers me that it took that long: I still think python is most deficient in its failure to create a default column-text reader like 'readcol' in IDL. I can't complain that much, though: I wrote my own in about 5 minutes.

Anyway, the key is to use the .set_xdata and .set_ydata functions of a plot to update a canvas. I still don't have nearly as high a plotting speed as I'd like, but it works alright if I don't display to screen. Probably a different backend would be more effective but I don't like to mess with backends.

I use savefig(filename,dpi=50) to reduce the image quality so that it's easier for the animator to handle.

ImageMagick's convert can be used to stitch any kind of image into a movie given that you've installed an mpeg2 encoder (fink gave me mpeg2vidcodec ). The command is very simple:


convert -size 300x300 *.png movie.mpg

I had to use a smaller image size because a series of 1000x12kb files somehow chomped ~6-8 GB of RAM and swap space.

Screen cont'd

2008-11-17T10:54:00.000-08:00

Guide to screen

Particularly useful features:

Scrollback:


ctrl-a [
[scroll keys]

Switch to a numbered screen (doesn't work for me so far):


ctrl-a [number]

Ultimate today

2008-11-16T20:12:00.001-08:00

We went 2-1 in the tournament, losing the final in a windy game on universe point, 15-14. We won the first game 13-5 or 13-6, and the second by a similarly wide margin. I think I scored 15-20 points on the day and threw an additional few. 2-3 drops and 3-4 throwaways to balance that out. Pretty good on the whole for what was probably my last ultimate of the season.

Of course, that made me very exhausted for the review session this evening. Oh well, I think it worked out. I need to remember to come up with (and post!) a clear explanation of why you can use that silly little triangle to come up with the translation between angle on the sky and image size.

BASH discoveries, readline questions

2008-11-13T20:53:00.000-08:00

1. shopt -p
Maybe my hostname completion worked and then stopped working because the bash option hostcomplete was not set. Duh! Why? I don't know. Anyway, shopt -s hostcomplete solves the problem.

nocaseglob is also pretty cool (case insensitive tab completion)

2. it's really hard to search for readline stuff on google. Can anyone explain to me how BASH readline works? I would REALLY like to make bash readline work like ipython, in which you can start typing a command and hit the 'up' key to search through the history for anything beginning with the stuff you've typed up to that point. But I can't even find documentation for the ipython readline! Any hints, anyone?

3. my desktop at work blocks ssh connections. I can ssh into some computers and then into it, but not directly into it.

...as usual, I made a list where not-a-list would have sufficed, and I had to add the last thing because a 2-item list is dumb.

Why do astronomers have such a strong presence on the web?

2008-11-12T21:28:00.000-08:00

I'm not making this a complete post, just a few examples of blogs and websites I'm aware of. But we do have a strong presence on the web - astronomers have an unusually high google ranking etc. Is it just because 'we' were here first ('we' excludes me, I'm just jumping on the bandwagon and getting a free ride)?

Examples:
Pamela Gay
Dr Lisa

Science writers who write on astronomy:
Dave Mosher

Photo Contest

2008-11-05T23:28:00.000-08:00

http://www.nrao.edu/index.php/learn/gallery/imagecontest

Python magic / advanced numpy indexing

2008-10-28T22:19:00.000-07:00

Yeah, indexing python arrays should really be easy.

Stefan van der Walt's page


In [85]: bi = (f.bolo_indices[np.newaxis,:] + zeros([7751,1])).astype('int')

In [86]: whc = (whscan[:,np.newaxis] + zeros([1,107])).astype('int')

In [87]: array2d[whc,bi] = temp2d

Python: one-line arrays

2008-10-28T13:34:00.000-07:00

Ahhh, refreshing:


      whscan = asarray([arange(scanlen)+i for i in scans_info[:,0]]).ravel()

Not like IDL, which takes at least 4 lines b/c of the variable declaration. There's probably a better way to do that too.

Port vs Fink

2008-10-28T06:49:00.000-07:00

Port failed to install:


adam-macbook ~$ sudo port install py25-matplotlib
--->  Building py25-hashlib with target build
--->  Staging py25-hashlib into destroot
--->  Installing py25-hashlib 2.5.2_0
--->  Activating py25-hashlib 2.5.2_0
--->  Cleaning py25-hashlib
--->  Fetching py25-zlib
--->  Verifying checksum(s) for py25-zlib
--->  Extracting py25-zlib
--->  Configuring py25-zlib
--->  Building py25-zlib with target build
--->  Staging py25-zlib into destroot
--->  Installing py25-zlib 2.5.2_0
--->  Activating py25-zlib 2.5.2_0
--->  Cleaning py25-zlib
--->  Fetching py25-setuptools
--->  Attempting to fetch setuptools-0.6c8.tar.gz from http://cheeseshop.python.org/packages/source/s/setuptools/
--->  Verifying checksum(s) for py25-setuptools
--->  Extracting py25-setuptools
--->  Applying patches to py25-setuptools
--->  Configuring py25-setuptools
--->  Building py25-setuptools with target build
--->  Staging py25-setuptools into destroot
--->  Installing py25-setuptools 0.6c8_2
--->  Activating py25-setuptools 0.6c8_2
--->  Cleaning py25-setuptools
--->  Fetching py25-tz
--->  Attempting to fetch pytz-2007k.tar.bz2 from http://cheeseshop.python.org/packages/source/p/pytz/
--->  Verifying checksum(s) for py25-tz
--->  Extracting py25-tz
--->  Configuring py25-tz
--->  Building py25-tz with target build
--->  Staging py25-tz into destroot
--->  Installing py25-tz 2007k_0
--->  Activating py25-tz 2007k_0
--->  Cleaning py25-tz
--->  Fetching py25-dateutil
--->  Attempting to fetch python-dateutil-1.4.1.tar.gz from http://labix.org/download/python-dateutil
--->  Verifying checksum(s) for py25-dateutil
--->  Extracting py25-dateutil
--->  Configuring py25-dateutil
--->  Building py25-dateutil with target build
--->  Staging py25-dateutil into destroot
--->  Installing py25-dateutil 1.4.1_0
--->  Activating py25-dateutil 1.4.1_0
--->  Cleaning py25-dateutil
--->  Fetching fftw-3
--->  Attempting to fetch fftw-3.1.3.tar.gz from http://www.fftw.org/
--->  Verifying checksum(s) for fftw-3
--->  Extracting fftw-3
--->  Configuring fftw-3
--->  Building fftw-3 with target all
--->  Staging fftw-3 into destroot
--->  Installing fftw-3 3.1.3_0
--->  Activating fftw-3 3.1.3_0
--->  Cleaning fftw-3
--->  Fetching py25-nose
--->  Attempting to fetch nose-0.10.4.tar.gz from http://somethingaboutorange.com/mrl/projects/nose/
--->  Verifying checksum(s) for py25-nose
--->  Extracting py25-nose
--->  Configuring py25-nose
--->  Building py25-nose with target build
--->  Staging py25-nose into destroot
--->  Installing py25-nose 0.10.4_0
--->  Activating py25-nose 0.10.4_0
--->  Cleaning py25-nose
--->  Fetching py25-numpy
--->  Attempting to fetch numpy-1.2.0.tar.gz from http://downloads.sourceforge.net/numpy
--->  Verifying checksum(s) for py25-numpy
--->  Extracting py25-numpy
--->  Applying patches to py25-numpy
--->  Configuring py25-numpy
--->  Building py25-numpy with target build
Error: Target org.macports.build returned: shell command " cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0" && /opt/local/bin/python2.5 setup.py build " returned error 1
Command output:     setup_package()
  File "setup.py", line 89, in setup_package
    configuration=configuration )
  File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0/numpy/distutils/core.py", line 184, in setup
    return old_setup(**new_attr)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/distutils/dist.py", line 974, in run_commands
    self.run_command(cmd)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/distutils/dist.py", line 994, in run_command
    cmd_obj.run()
  File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0/numpy/distutils/command/build.py", line 37, in run
    old_build.run(self)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/distutils/command/build.py", line 112, in run
    self.run_command(cmd_name)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/distutils/dist.py", line 994, in run_command
    cmd_obj.run()
  File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0/numpy/distutils/command/build_src.py", line 130, in run
    self.build_sources()
  File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0/numpy/distutils/command/build_src.py", line 147, in build_sources
    self.build_extension_sources(ext)
  File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0/numpy/distutils/command/build_src.py", line 250, in build_extension_sources
    sources = self.generate_sources(sources, ext)
  File "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_python_py25-numpy/work/numpy-1.2.0/numpy/distutils/command/build_src.py", line 307, in generate_sources
    source = func(extension, build_dir)
  File "numpy/core/setup.py", line 87, in generate_config_h
    raise SystemError,"Failed to test configuration. "\
SystemError: Failed to test configuration. See previous error messages for more information.

Error: The following dependencies failed to build: py25-numpy py25-tkinter tcl tk
Error: Status 1 encountered during processing.

I don't want to deal with it so I'm just using Fink.

Reinstalling a system

2008-10-26T23:45:00.000-07:00

Python died tonight when I foolishly tried to update numpy or matplotlib. One was not compatible with the other in upgraded form, and the update for matplotlib wouldn't install because of GTK issues that were totally opaque.

So, I reinstalled EVERYTHING - fink AND macports - from scratch. If I don't get things running by morning I'm going to have to do a restore, which is ugly as death.

Things I need to do post-install:


        sudo port install python_select  
        sudo python_select python25

test ipython
test matplotlib
test numpy

Python: setting matplotlib defaults

2008-10-26T19:20:00.000-07:00

Setting matplotlib defaults is a lot more difficult than it should be.


matplotlib.defaultParams['image.origin']='lower'
matplotlib.defaultParams['image.interpolation']='nearest'

Observing 10/20

2008-10-20T04:51:00.000-07:00

I don't have a better place to post this one, so here it is:
http://sites.google.com/site/iras05358/figure-discussion/figures/iras05358_triple_17.29.png?attredirects=0

My automated fitter (Gaussfitting Cube Collapser) has come a long way. I now adaptively choose to fit 1, 2, or 3 Gaussian components to output to a data cube.

The purpose of that code is primarily to find a two-dimensional way to display information about the 3D structure, specifically about the presence/absence of outflows. Outflows will inevitably be confused with multiple velocity components, but they are also likely to be convolved with them.

Screen, nohup, ssh, scp

2008-10-19T20:42:00.000-07:00

I learned a lot about the above in the past day, but I didn't keep track of the links.

First, screen is very useful: it allows you to run any task, detach the screen, and let it run in the background. You can resume it later.

Example:


screen
ipython run_fitter.py
<ctrl-a> d
screen -r

Second, it's a huge pain to type a password every time I use scp and ssh. The solution is to make a key on your computer and put it in the authorized_keys file.


ssh-keygen -t rsa
scp ~/.ssh/id_rsa ginsbura@milkyway.colorado.edu:.
ssh ginsbura@milkyway.colorado.edu
cat id_rsa >> ~/.ssh/authorized_keys
ssh -v ginsbura@milkyway.colorado.edu

Use ssh -v to figure out why it fails if it still asks you for a password. In one case, this happened because the computer I was using expected the id to be in ~/.ssh/identity instead of ~/.ssh/id_rsa. There may also be permissions issues (i.e. you want restrictive permissions on your ssh keys).

With the latter, you can still use nohup, which is helpful if you want to pipe your output to a log file.

Listing variables (e.g IDL help) in Python

2008-10-17T23:02:00.000-07:00

Again, IDL has the simple 'help' command to tell you all variables in your namespace. Python has the same thing, but the namespace tends to be cluttered with imported functions. The commands who, who_ls, and whos are meant for interactive use. They are a hell of a lot more useful than var, locals, globals, and dir.

examples:


whos float
whos ndarray
who module
float_vars = %who_ls float
grep('x',float_vars)

I'm afraid I don't know how to make the last two lines into a one-liner, as would be desirable.

SAVE / RESTORE in Python

2008-10-17T21:46:00.000-07:00

Save/Restore is probably the single best feature of IDL that, sadly, is very poorly replicated in Python. For 1 or 2 dimensional variables, you can use Pylab's save/load, but I never use such piddling tiny arrays. For higher dimensional objects, either using FITS files (a pain because of header definitions) or pickling ought to work.

e.g.:


import numpy
import pickle
x=ones([10,10,10,10],dtype='float64')
pickle.dump(x,open('x.pysav','w'))
X = pickle.load(open('x.pysav','r'))

Last month's observations in L111

2008-10-15T00:58:00.000-07:00

Mapped sources:
SH 2-156 [no high resolution observations; covered by 1.2m CO 1-0 survey]
SH 2-157 Yancy CS 5-4 , CO, 13CO 1-0, CS 2-1 , HCN & SCUBA too....
IRAS 23151 (two pointings)

Unmapped:
BFS 18 = IRAS 23042+6000 = IRCO 859
Wu et al mapped this in CO 2-1 and detected no outflows. They used the NRAO 12m with a heterodyne array with very high T_sys ~700-1100K.

How do I print a multi-page postscript?

2008-10-12T20:34:00.000-07:00

I want to print a multi-page postscript duplexed and, if possible, two per page. pstopng, pstopdf, and the variants failed me horribly by making postscripts that don't fit the bounding box at all. Any ideas?

So far the best I've come up with is switching gnuplot's output to pdf, which is a workaround rather than a solution, but is useful nonetheless:
set terminal pdf enhanced dashed

Mathematica & Series expansions

2008-10-12T11:23:00.000-07:00

Mathematica does something stupid and incomprehensible (to me) with their series expansions. For no clear reason, it makes the O[x]ⁿ uneditable, and adds a bunch of formatting things that prevent you from copying & pasting the expression and then solving for a variable. Argh. While this is repairable using the "show expression" tool (Shift-Apple-E), it's a pain and "show expression" is not meant to be human readable.

teaching

2008-10-11T22:10:00.001-07:00

this is the only right way to teach

gardening

2008-10-07T21:00:00.000-07:00

I realized I don't have a gardening category and I should.

I have eaten 2 garden tomatoes. There have been a total of 3 that ripened. There is a fourth on the vine. There are ~40-50 big green ones being big and green.

I ate basil in my pasta sauce yesterday. I need to buy some pine nuts. But I'm not pining for nuts.

Next year, start growing in March!

sage casjobs

2008-10-07T20:55:00.001-07:00

annoying feature of sage casjobs: no spaces are allowed, no matter what, even if quoted. so when importing must remove all spaces. gurrh.

mathematica

2008-10-07T06:14:00.000-07:00

//. and /. use 'rules' of the form {x->y} for substitutions

how do you make the layout of a page look nice? How do you change line spacing?

Observing run summary

2008-09-27T06:46:00.001-07:00

3 nights of worse than grade 4 weather (tau ~.4, i.e. the atmosphere is nearly opaque) have given me a few interesting results.

1. Non-detections of CS 5-4 in a few bright BGPS cores. My best guess is that the pointing was off, though, because I definitely got down to a noise level around 50mK.
2. Lots of CO 2-1 mapping, 13CO/C18O too. That means I can now use this plot: http://dustem.astro.umd.edu/pdrt/co3221web.html to try to measure the incident flux.
3. I can't do homework at the summit. Maybe it's just that I can't do stellar structures homework, but I really am not processing this stuff well. Damn.
4. Running at altitude uphill is really, really hard. All the running I've been doing the past N months has not even come close to preparing me. Need to correct that...
5. "I am inappropriate." I probably violate a bunch of those rules... the important ones...
6. gotta get back to the mountains. Really. Seriously. OMFG.
7. ARGH those papers need writing! Lots of it!

For the next observing run, need the following:
1. Pre-prepared A3 rasters
2. Larger selection of summit music
3. Better sleep schedule preparation
4. More caffeinated drinks per night
5. Cloud cannons.

running at altitude

2008-09-25T21:00:00.000-07:00

wow dude. I suck at that.

I swear there were some other things I had to write down but I can't remember them now.

precipitable water vapor precipitates and that can be good

pwv

2008-09-25T01:33:00.001-07:00

precipitable water vapor, precipitable water vapor, go away, come again some other observer's day
little HARPy wants to receive
so clear up before I leave

stupid bumping-head old man.

Marc Pound's toolbox

2008-09-24T09:36:00.001-07:00

This is neat:

Line Ratio as a function of density, incident flux from Marc Pound. Sadly, straight CO 3-2 intensity isn't included.

python stuff

2008-09-24T05:59:00.001-07:00

to get imshow defaults to be nearest neighbor, need to edit ~/.matplotlib/matplotlibrc. Still don't know how to change default command-line output format.

Do not install 10.5.5

2008-09-24T00:45:00.000-07:00

Well, I didn't obey that excellent advice from Charles. I installed the 10.5.5 update. Now DS9 - in my opinion, one of the heartiest and most reliable programs I've dealt with in the astronomy world - won't work because TCL is broken. I doubt TUI or most of the other things I use will work either. That's a tragedy of significant proportions - I NEED ds9 to make my observing files! I can only pray that an update of TCL using port will work... if not I'm basically screwed.