On Clouds, Poems, Python and more...: 2012

Wednesday, November 7, 2012

Issues with GDL Python module

1-) Importing GDL segfaults in IPython

$ ii # this is alias for ipython --pylab

Python 2.7, IPython 0.14.dev

I1 import GDL

I2 Segmentation fault (core dumped)

however, works fine in Python shell

>>> import GDL

>>> GDL.findgen(5)

>>> GDL.function('findgen',5)

array([ 0., 1., 2., 3., 4.], dtype=float32)

possibly readline module issue? Interestingly, works fine in Spyder's IPython console.

2-) Source compiled (with --enable-python_module option) GDL Python module fails to work

>>> import GDL

Traceback (most recent call last):

File "", line 1, in

ImportError: ./GDL.so: invalid ELF header

possibly, due to wrong lib arch use, during compilation?

3-) GDL's dindgen yields wrong result while accessed through its Python module

>>> GDL.function('dindgen',10)

array([ 0.00000000e+000, 1.00000000e+000, 2.00000000e+000,

3.00000000e+000, 4.00000000e+000, 0.00000000e+000,

5.92878775e-323, 3.30571061e-313, 6.94380683e-310,

4.03179200e-313])

Posted this issue on dindgen with GDL python module

Calling IDL, GDL, and FL from Python

Thanks to Anthony Smith's pIDLy module, accessing IDL, and its clones GDL and FL from within Python becomes really easy.

Launch an IPython session, then typing these example lines to see pidly in action:

I1 import pidly

I2 idl = pidly.IDL()

I3 fl = pidly.IDL('fl', idl_prompt='FL> ')

I4 gdl = pidly.IDL('gdl', idl_prompt='GDL> ')

I5 idl.findgen(10)

O5 array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.], dtype=float32)

I6 fl.findgen(10)

O6 array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.], dtype=float32)

I7 gdl.findgen(10)

O7 array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.], dtype=float32)

I8 np.arange(10, dtype='float32')

O8 array([ 0., 1., 2., 3., 4., 5., 6., 7., 8., 9.], dtype=float32)

Testing these with:

I2 pidly.__version__

O2 '0.2.4+'

I3 np.__version__

O3 '1.8.0.dev-82c0bb8'

$ idl

$ gdl # the version that ships with Fedora 16

GDL - GNU Data Language, Version 0.9.2

$ fl # latest development snapshot (10/Oct/2012)

Example access to an IDL procedure:

I5 idl.pro('cgplot', np.sin(np.linspace(0, 6*np.pi, 1000)))

I6 idl.pro('iplot', np.sin(np.linspace(0, 6*np.pi, 1000)))

For more information, just read the quick usage guide on pidly's web-site, or clone the source from https://github.com/anthonyjsmith/pIDLy

Here is a worldcloud created for my code repository on:

http://code.google.com/p/ccnworks/

First get the commit message history into a text file (the last commit is r287):

svn log >> test.txt

Then with a bit of VIM trick and manual step, remove unwanted lines:

sort u

Select of all the text, and import into

http://www.wordle.net/create

Tadaaa, here comes the result :)

Indeed, we are data scientists here in atmospheric science!

Alternative wordcloud implementation comes from Andreas Mueller. I saw his A Wordcloud in Python titled posting via Planet SciPy. In order to run his wordcloud.py I needed to change unsigned int[:,:] integral_image -> unsigned long[:,:] integral_image in query_integral_image.pyx to get past 'ValueError: Buffer dtype mismatch, expected 'unsigned int' but got 'unsigned long''.

Then feeding the same log data I get the following image, which is nicer looking than the wordle's image :)