Tag Archive | iPython

The IPython Notebook


The IPython notebook is amazing. It is so amazing that I could not resist writing yet another blog entry about it, when there are probably hundreds of sources of information about the notebook.

Imagine you have run some calculations with a certain code. Then you have a short script that copies output files and/or extracts important data into a text file, which you then import into a spreadsheet. You work with the data, and produce some plots which you copy&paste into a word-processor file where you have explained your aims, your set-up and the data manipulation.

Are you familiar with this? Don’t you think that the lab notebooks your colleagues have are more efficient? and more trustful? Aren’t you tired of repeating this cycle again and again every time you re-run some of the calculations?
If you answered ‘yes’ to some if these questions, the IPython notebook is for you. Even if you have never used python!

The Ipython notebook is the lab notebook of the computational scientists. You can insert complex mathematical formulas as with .\LaTeX. The recent extension to use a spell-check render the notebook even more useful. You can also insert videos and images from the web. For example to compare your results with that of a published paper a couple of lines suffice:

from IPython.display import Image
Image(url='http://www.ploscompbiol.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pcbi.1000497\
.g001&representation=PNG_L')

Of course, you can also have python code in the notebook, But also bash, Ruby or Fortran code!

%%fortran
real function sincos(x)
    implicit none
    real*8 :: x
    sincos = sin(x)*cos(x)
end function

And then use the Fortran function directly in your python cells (you’ll need to install the
%fortranmagic extension)

sincos(1.5) - math.sin(1.5)*math.cos(1.5) < 1e-7
True

You can share the code as static notebooks with the http://nbviewer.ipython.org or convert them into LaTeX, PDFs or HTML.

I’ve only sketched a few capabilities of the notebook. Take a look at these examples to decide where you want to focus. And after all the praise, some criticism:

  • The notebook is evolving so fast that you never know if your installed version is able to do some of the awesome tricks you read somewhere. And the versions packed in the repositories usually lag behind. That means you are forced to do a manual installation.

  • For some reason the image linked in my notebooks disappeared from the exported PDF version.

I finish this post with a confession. I should have used IPython to blog directly. This is possible but I am new to wordpress.com and I still have to check how to do it. Shame on me!

Python for Fortran programmers II: why Python?


Python is a general-purpose language, used in extremely different fields. Take a look at http://wiki.python.org/moin/PythonProjects Many of the projects are available at the Python repository PyPI. That means the language is active and adequate for many applications. But of course, we want it to be also good at number crunching and data visualization.

For that you need some packages. Packages are extensions of the core language, a kind of library in Fortran. They need to be imported before they are used. Some packages are a must for scientists: numpy, matplotlib and possible, scipy. Installing python packages is easy. I will explain that in the future, but these three packages are on most Linux repositories (certainly in Ubuntu) and that is the simplest way to install them.

Because python is an interpreted language (It’s gonna be very slow!! Wait, wait…) you can use different ‘shells’. I recommend iPython. That, together with the previous packages, turns python into a powerful scientific development tool. If you have time (I promise to keep this post short) watch this amazing talk by Fernando Perez, the author of ipython:

http://www.youtube.com/watch?feature=player_embedded&v=F4rFuIb1Ie4#!

If you are still not convinced, take a look at this survey which compares Python to Fortran:

http://hammerprinciple.com/therighttool/items/python/fortran

Convinced? Then start by typing import this and start absorbing the Zen of python. Then impress your colleagues by defying gravity with import antigravity (only in Python 3). Aha! You look more pythonic now…

If you are new to Python and want to install it you will have to decide whether to use Python 2 or Python 3. In the next post we will see how to make this decision. The short answer is ‘use Python 3’.