Scientific python + IPython intro Alexey Buzmakov

Shubnikov Institute of Crystallography RAS, Moscow 28/11/2013, XFEL, Hamburg

Scientific python + Ipython intro

Outline Headline  Why python?  What is python?  How to use python and IPython?

Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

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Scientific python + Ipython intro

Why Python? The scientist’s needs  Get data (simulation, experiment control, data files)  Manipulate and process data.  Visualize results... to understand what we are doing!  Communicate results: produce figures for reports or publications, write presentations.

Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

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Scientific python + Ipython intro

Existing solutions   

Compiled languages: C, C++, Fortran, etc. Scripting languages: Matlab Other scripting languages: Scilab, Octave, Igor, R, IDL, etc.

Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

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Scientific python + Ipython intro

Python 

General characteristics of Python:

 clean and simple language: Easy-to-read and intuitive code, easy-to-learn minimalistic syntax, maintainability scales well with size of projects.  expressive language: Fewer lines of code, fewer bugs, easier to maintain. 

Technical details:

 dynamically typed: No need to define the type of variables, function arguments or return types.  automatic memory management: No need to explicitly allocate and deallocate memory for variables and data arrays. No memory leak bugs.  interpreted: No need to compile the code. The Python interpreter reads and executes the python code directly. Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

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Scientific python + Ipython intro

What about Python?  Advantages: 







Very rich scientific computing libraries (a bit less than Matlab, though) Well thought out language, allowing to write very readable and well structured code: we “code what we think”. Many libraries for other tasks than scientific computing (web server management, serial port access, etc.) Free and open-source software, widely spread, with a vibrant community.

 Drawbacks: 



– less pleasant development environment than, for example, Matlab. (More geek-oriented). – Not all the algorithms that can be found in more specialized software or toolboxes.

Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

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Scientific python + Ipython intro

Scientific Python building blocks

Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

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Scientific python + Ipython intro

Versions of python 





There are currently two versions of python:  Python 2 and Python 3.  Python 3 will eventually supercede Python 2, but it is not backward-compatible with Python 2.  A lot of existing python code and packages has been written for Python 2, and it is still the most widespread version. To see which version of Python you have, run  $ python --version Several versions of Python can be installed in parallel

Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

8

Scientific python + Ipython intro

Python interpreter 

For example, to run a file my-program.py that contains python code from the command prompt, use:  $ python my-program.py  or run interpretator $python

Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

9

Scientific python + Ipython intro

Why IPython?  



In scientific computing, we typically don’t know what we’re doing IPython is an Interactive shell that addresses the limitation of the standard python interpreter, and it is a work-horse for scientific use of python. It provides an interactive prompt to the python interpreter with a greatly improved user-friendliness.

Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

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Scientific python + Ipython intro

IPython notebook

Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

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Scientific python + Ipython intro

Ipython, numpy and scipy demonstration   

http://bit.ly/WPG-wiki -> Tutorial files -> Ipython presentation Download it Run in this folder  ipython notebook

Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

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Scientific python + Ipython intro

Publishing Ipython notebooks  

Generate html and pdf reports Free online publishing service http://nbviewer.ipython.org/

Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

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Scientific python + Ipython intro

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Python http://www.python.org/



Numpy + Scipy + matplotlib http://www.scipy.org/



H5py http://www.h5py.org/



Numpy for Matlab users http://wiki.scipy.org/NumPy_for_Matlab_Users



Free tutorials (some materials was taken in this tutorials)  http://scipy-lectures.github.io/

 http://jrjohansson.github.io/ 

Free binary distribution with a lots of scientific stuff (especially for windows users)  https://store.continuum.io/cshop/anaconda/



Free scientific python IDE (Matlab like)  https://code.google.com/p/spyderlib/

Tutorial course on wavefront propagation simulations, 28/11/2013, XFEL, Hamburg. Alexey Buzmakov, Shubnikov Institute of Crystallography RAS, Moscow, Russia

Scientific python + IPython intro - GitHub

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