Adam Ginsburg's blog

Quicksilver sounds

2012/09/20
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:
1. Go to trigger pane, make new hotkey trigger
2. press "." to allow you to type a command
3. make sure the action is "Run"
4. hook up a hotkey
5. 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'``

RATRAN on Mac OS X

2012/09/20
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:
1. Install CFITSIO with CFLAGS="-arch x86_64 -arch i386 -g -O2" to /usr/local/lib
2. 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
```

Rebuilding python from scratch again

2012/09/20
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.
1. 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 17sudo make install
  2. Reset PYTHONPATH to blank
  3. `` alias clearflags='export CFLAGS=""; export CCFLAGS=""; export CXXFLAGS=""; export LDFLAGS=""; export FFLAGS="";'`` to make sure
2. Install FFTW cd ~/tmpcurl -O http://www.fftw.org/fftw-3.2.2.tar.gztar xf fftw-3.2.2.tar.gzcd fftw-3.2.2clearflags./configure CC="gcc -arch x86_64" CXX="g++ -arch x86_64" CPP="gcc -E" CXXCPP="g++ -E"make -j 17sudo make install
3. Install UMFPACK cd ~/tmpcurl -O http://www.cise.ufl.edu/research/sparse/umfpack/current/UMFPACK.tar.gzcurl -O http://www.cise.ufl.edu/research/sparse/UFconfig/current/UFconfig.tar.gzcurl -O http://www.cise.ufl.edu/research/sparse/amd/current/AMD.tar.gztar xf AMD.tar.gztar xf UFconfig.tar.gztar xf UMFPACK.tar.gzsed -ibck 's/F77 = f77/F77 = gfortran/' UFconfig/UFconfig.mk sed -ibck '299,303s/# //' UFconfig/UFconfig.mkcp UFconfig/UFconfig.h AMD/Include/cp UFconfig/UFconfig.h UMFPACK/Include/cd UMFPACKmake -j 17make hbmake clean
4. Install numpy
  1. Set environment variables export MACOSX_DEPLOYMENT_TARGET=10.6export 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/Libinclude_dirs = /Users/adam/tmp/AMD/Includeamd_libs = amd[umfpack]library_dirs = /Users/adam/tmp/UMFPACK/Libinclude_dirs = /Users/adam/tmp/UMFPACK/Includeumfpack_libs = umfpack" > site.cfg
  2. Setup & Install python setup.py build --fcompiler=gnu95sudo python setup.py install
  3. Test: python -c "import numpy"
5. 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/numpyXcd ~/repos/scipy-0.7.1python setup.py cleanrm -rf buildclearflagsFFLAGS="-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 buildpython setup.py install Test the install: python -c "import scipy, scipy.fftpack, scipy.interpolate"
6. 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/numpyXcd ~/repos/matplotlib-svnpython setup.py cleanrm -rf buildclearflags
  2. Do hyperjeff's recommended edits except don't use /usr/local because it's f'd: make.osx: MACOSX_DEPLOYMENT_TARGET=10.6PREFIX=/usrPYTHON=/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_installpython setup.py install``
7. Install setuptools
8. easy_install ipython
9. install everything else pythonically

Reinstalling a system

2012/09/20

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

Repositories for observers

2012/09/20

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.

Review: Fruition restaurant

2012/09/20

I ate at Fruition restaurant last night with the family. They serve haute cuisine. I had the beef coulotte. It was pretty tasty, but overall a bit too creamy for my taste. The wine had a hint of cherry flavor to it. The dinner was pretty good, but overall a little disappointing for the price. The French press coffee was a bit much as I would have preferred a small cup of cappuccino. I wouldn't object to going back when they switch to a new seasonal menu, but I'm not going out of my way.

running at altitude

2012/09/20

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

Russell Owen, DS9

2012/09/20

As I might have expected, Russell Owen from the University of Washington - the man responsible for the Telescope User Interface, TUI, on the Apache Point Observatory telescope - has written up a help page for XPA access points on ds9. He knows his stuff... I think I need to aspire to that.

sage casjobs

2012/09/20

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

SAVE / RESTORE in Python

2012/09/20

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

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