physicsnlinux

some python resources

physicsnlinux — Tue, 01 Nov 2011 22:02:26 +0000

python tutorial:
http://docs.python.org/tutorial/
numpy tutorial [arrays]:
http://www.scipy.org/Tentative_NumPy_Tutorial
plotting tutorial:
http://matplotlib.sourceforge.net/users/pyplot_tutorial.html

free online books:
http://diveintopython.org/toc/index.html
http://www.ibiblio.org/swaroopch/byteofpython/read/

install enthought python:
http://www.enthought.com/products/edudownload.php

video tut:

cfitsio wrapper in python

physicsnlinux — Tue, 21 Jun 2011 03:43:06 +0000

After several issues with pyfits, and tired of it being so overengineered, I’ve wrote my own fits I/O package in python, wrapping the C library cfitsio with ctypes.

Pretty easy, first version completely developed in 1 day.

https://github.com/zonca/pycfitsio

unit testing happiness

physicsnlinux — Tue, 21 Jun 2011 03:39:57 +0000

nosetests -v
test_all_cols (pycfitsio.test.TestPyCfitsIoRead) ... ok
test_colnames (pycfitsio.test.TestPyCfitsIoRead) ... ok
test_move (pycfitsio.test.TestPyCfitsIoRead) ... ok
test_open_file (pycfitsio.test.TestPyCfitsIoRead) ... ok
test_read_col (pycfitsio.test.TestPyCfitsIoRead) ... ok
test_read_hdus (pycfitsio.test.TestPyCfitsIoRead) ... ok
test_create (pycfitsio.test.TestPyCfitsIoWrite) ... ok
test_write (pycfitsio.test.TestPyCfitsIoWrite) ... ok

----------------------------------------------------------------------
Ran 8 tests in 0.016s

OK

Pink noise (1/f noise) simulations in numpy

physicsnlinux — Wed, 18 May 2011 22:49:21 +0000

https://gist.github.com/979729

Vim regular expressions

physicsnlinux — Fri, 29 Apr 2011 01:14:41 +0000

very good reference of the usage of regular expressions in VIM:

http://www.softpanorama.org/Editors/Vimorama/vim_regular_expressions.shtml

set python logging level

physicsnlinux — Wed, 13 Apr 2011 00:02:46 +0000

often using logging.basicConfig is useless because if the logging module is already configured upfront by one of the imported libraries this is ignored.

The solution is to set the level directly in the root logger:
logging.root.level = logging.DEBUG

pyfits memory leak in new_table

physicsnlinux — Mon, 28 Mar 2011 16:22:10 +0000

I found a memory leakage issue in pyfits.new_table, data were NOT deleted when the table was deleted, I prepared a test on github, using objgraph, which shows that data are still in memory:
https://gist.github.com/884298

the issue was solved by Erik Bray of STSCI on March 28th, 2011 , see bug report:
http://trac6.assembla.com/pyfits/ticket/49
and changeset:
http://trac6.assembla.com/pyfits/changeset/844

git make local branch tracking origin

physicsnlinux — Wed, 02 Feb 2011 01:58:35 +0000

git branch --set-upstream master origin/master

you obtain the same result as initial cloning

memory map npy files

physicsnlinux — Fri, 07 Jan 2011 20:04:11 +0000

Mem-map the stored array, and then access the second row directly from disk:

X = np.load('/tmp/123.npy', mmap_mode='r')

force local install of python module

physicsnlinux — Fri, 03 Dec 2010 21:18:45 +0000

python setup.py install --prefix FOLDER

creates lib/python2.6/site-packages, to force a local install you should use:

python setup.py install --install-lib FOLDER