This repository contains the code to analyze data from the ARCONS array.
Environment variables that need to be set:
MKID_RAW_PATH - path to the root of the raw data directory structure MKID_PROC_PATH - path to the root of the processed data directory structure MKID_BEAMMAP_PATH - path to the default beammap file to be used by h5quicklook.py (only used for quicklook)
Enthought Python Distribution (EPD) 7.3 (http://www.enthought.com/products/epd.php)
PyEphem (http://rhodesmill.org/pyephem/)
PyGuide (http://www.astro.washington.edu/users/rowen/PyGuide/Manual.html)
(you can check if you have them with help('modules') within the (i)python interpreter)
gittle -- represents the state of the git repository in python (easy_install gittle)
ds9 -- need to download pyds9 and install. Download the package from the download/pyds9 section of the ds9 web page: http://ds9.si.edu See instructions at: http://hea-www.harvard.edu/RD/pyds9/
If you are having troubles with PyTables (which you shouldn't since it is built into EPD), see http://www.tumblr.com/tagged/pytables and instructions therein for Mac.
We also use astropy. The version on Turk is 0.3.1 Anaconda installs a newer version which is pretty much the same, but in some code this import needs to work:
from astropy.stats.funcs import sigma_clip
Newer versions of astropy have something called astropy.stats.sigma_clipping which may or not may not be the same algorithm.
To make nicer looking plots, you need the packages configobj and mpltools
$ easy_install configobj $ git clone git@github.com:tonysyu/mpltools.git $ cd mpltools $ python setup.py install
Another package you will need is pyinterval. It depends on crlibm
NOTE: the python package interval is not the same thing. If this got installed by mistake, things might not work so well. A tell-tale sign that you have the correct thing installed is that this line works in ipython:
from interval import interval, inf, imath
On Turk, these packages installed in the usual way without fuss.
On bender, there was a problem with the how libcrlibm.a was build: relocation R_X86_64_32S against `.rodata' can not be used when making a shared object; recompile with -fPIC
To fix this, in the crlibm source tree,in scs_lib/Makefile add the -fPIC option in this line: CPPFLAGS = -fPIC
On a Mac, you need to do this:
I downloaded crlibm-1.0beta4.tar.gz from http://lipforge.ens-lyon.fr/www/crlibm/
$ untar $ configure $ make $ sudo make install.
Then I downloaded pyinterval-1.0b21.tar.gz from http://pypi.python.org/pypi/pyinterval and untarred it.
Here is the tricky part.
in setup.py pyinterval, change the lines near the end from this
include_dirs = ['/opt/crlibm/include'],
library_dirs = ['/opt/crlibm/lib'],to this
include_dirs = ['/usr/local/include'],
library_dirs = ['/usr/local/lib'],and then
python setup.py build sudo python setup.py install
The tests in cosmic/TestTimeMask.py uses the class Cosmic which uses this, and it will also be used to locate times to mask hot pixels.
Note that in the photonlist package/directory you will need to compile the fortran routine 'boxer.f'. This should do the trick:
f2py -c -m boxer boxer.f
... After running that, you can check it works in python by trying to import with 'import boxer' at the python command line. See the readme.txt file in photonlist/ for (possibly) more info.
Aptana Studio 3 (http://www.aptana.com/products/studio3/download)
/headers contains standard definitions
/params contains files that provide inputs to the pipeline
/utils contains commonly used functions
/examples contains simple examples to show how to use the software
/cosmic contains a module for cosmic ray cleaning
/wavelengthcal contains a module to do wavelength calibration
/flatcal contains a module for normalizing the QE as a function of wavelength between pixels
/fluxcal contains a module to calibrating the system compared to a standard star
/astrometry contains a module to determine the RA and DEC of each photon
/skysub contains a module to subtract the sky background
[/imagecube contains a module to generate a FITS image cube based on an observations (no timing info) ]
/legacy contains ARCONS analysis code that predates this repository
/quicklook contains tools for quickly looking at ARCONS h5 files
/beammap contains tools for creating, viewing, and modifying beam maps
/hotpix contains tools for finding location and time of hot (and possibly 'cold') pixels
/photonlist contains tools for creating calibrated photon lists and creating stacked, RA/dec-mapped images from them.
Each directory contains a /test subdirectory, where code to test the module will be stored.
A beginner's guide and the observing log for the Palomar 2012 run are in examples/demos
This document uses the markdown syntax, see http://daringfireball.net/projects/markdown/
Getting it working on bender during the Palomar 2013 run.
Bender has the canopy version of python installed. To get pyqt working:
yum install qt4
I then tried yum install PyQt4 but the canopy version of python did not pick it up.
sudo scp -r stoughto@turk.physics.ucsb.edu:/usr/local/epd/lib/python2.7/site-packages/PyQt4 . This needs the same version of sip. On turk, sip -V says it is version 4.13.2 so I downloaded sip-4.13.3.zip, unzip, python configure.py; make; sudo make install.