Aliased Circles

Inspired by this I wrote a little script to create antialiased circles in python
The Gist:
Example output:

difflib

Found another standard library gem: difflib, which allows you to do intelligent string comparisons.

For example:

will find the longest palindrome in a string, e.g.

>>> from palindrome import *
>>> longest_palindrome('asdfracecarasdf')
'racecar'
>>> longest_palindrome('asdffasdfaipreferpiasdfasdfa')
'aipreferpia'

SWIG and numpy

I've been looking into C/C++ interface creator known as SWIG for use with a molecular dynamics program that is in the works. It is nice in that from an interface file, that you can create entirely by hand or just use a standard header file, you can create a python module that looks and feels like python, but is really some nifty C that you've written. There are some drawbacks of course in that if a function returns a pointer, it is actually a wrapped object that can be passed to other wrapped functions, but will have little use in python without some other work. Of course for the purposes of this post I would like these pointers to be an array of floating point numbers, or a numpy array. Wouldn't it be great if you could easily pass numpy arrays back and forth to C/C++ without having to deal with writing your own wrapper using Python.h?

Well you can with a little gem called numpy.i which is a SWIG interface wrapper for the numpy array. With it, you specify certain arguments you want to be treated as numpy arrays and it does so automatically.

So on with the example. I have two C functions which fill an array sequentially and can take the dot product of two arrays. They are found below in two files

Let's now provide a python interface to these using SWIG. Here, we specify the python module name and the functions that make up the module's functions. Then we include the numpy.i interface. Next, we have to say how we want our C arguments treated. The details of what's written in the file can be found here but I have used most of the common ones: modifying an array in place, taking an input array, and returning an array as output. NOTE: the far right section of the line matches verbatim to the arguments in the C code. The interface file is as follows:

Then, we need to build the module and test. To make this module we used a setup.py script (which will not be the case for future SWIG posts). I'm not sure of the details here, but it is listed for your information.

After that, let's build with `python setup.py build` and run some speed tests. For example,

Returns

Numpy says: 3.33332833333e+17

SWIG says: 3.33332833333e+17

Time of numpy: 0.0032000541687

Time of SWIG: 0.00278091430664

Wahoo, we are actually slightly faster than the built-in numpy dot product with just a little bit of work. Next time, moving on to SWIGing classes and incorporating numpy with them as well.

A Dictionary of Links

I wanted a dictionary of links for an MD type simulation, and I wanted the links to be unique, and I didn't want to have to check for the order the guys appeared in the dictionary keys every time, so I wrote my own dictionary by extending the native one.



Where I put that code on gist. To pull it off, you see that I subclass dict, and define a decorator that pulls out and sorts the first argument. After that it is just decorating the '__setitem__','__getitem__',and '__delitem__' methods. This lets us do nice things now:

>>> z = Links()
>>> z[1,2] = 5
>>> z[4,3] = 10
>>> z
{(1, 2): 5, (3, 4): 10}
>>> z[2,1]
5
>>> z[1,2]
5
>>> z[2,1] = 11
>>> z
{(1, 2): 11, (3, 4): 10}
>>> del z[2,1]
>>> (3,4) in z
True
>>> (4,3) in z
True
>>> z
{(3, 4): 10}
>>> z[5] = 1
Traceback (most recent call last):
  File "", line 1, in 
  File "links.py", line 10, in orderedversion
    assert hasattr(first,"__len__"), "Key must be iterable"
AssertionError: Key must be iterable
>>> z[4,4,3] = 1
Traceback (most recent call last):
  File "", line 1, in 
  File "links.py", line 11, in orderedversion
    assert len(first)==2, "Key must be 2-tuple"
AssertionError: Key must be 2-tuple
>>> z
{(3, 4): 10}

Setting up ROOT and pyROOT on a new Mac

I just got a Mac and need to re-do the setup of my software stack. I'm keeping a log of anything tricky here, both for my own future reference and so others can use it as a reference. These instructions work for Lion and may work for other versions of OS X, but I haven't tested them.

Getting ROOT and pyROOT up and running:

Note: you can't use the pre-compiled ROOT because it's linked against the wrong version of python.

1. Install Xcode from the Mac App Store. I got a few errors the first few times I tried to install it, but eventually it worked.
2. Download and install the newest version of the enthought python distribution from http://www.enthought.com. If you hunt around, you can find a link to download it for free for academic use.
3. Set up some environment variables. You can set ROOTSYS to the directory you want to install ROOT to.

   export PYTHONDIR=/Library/Frameworks/EPD64.framework/Versions/Current
   export ROOTSYS=/usr/local/root
   export LD_LIBRARY_PATH=$ROOTSYS/lib:$PYTHONDIR/lib/:$LD_LIBRARY_PATH
   export PATH=$ROOTSYS/bin:$PYTHONDIR/bin:$PATH
   export PYTHONPATH=$ROOTSYS/lib:$PYTHONPATH

4. Download the source for the newest production version of ROOT from http://root.cern.ch/drupal/content/downloading-root
5. Unpack the tarball:

   tar -xf root_blah_blah.tar

6. cd root

7. Configure ROOT installation and compile

   ./configure macosx64 --enable-python --with-python-incdir=$PYTHONDIR/include --with-python-libdir=$PYTHONDIR/lib
   make
   sudo su
   export ROOTSYS=/usr/local/root
   make install
   exit

Now you should have working installs of both ROOT and pyROOT.

Planet Walk 2.0

We can make our own real-time planet walk.

Planetary positions are obtained according to this NASA brief

Code available as a gist here

Results: here

Making animated gifs

I always lose this command, so I'm putting here so I can find it again

convert pics/*.png [-delay 100 -layers Optimize] anim.gif

And for sticking around, here is an animated gif for you: