1. The Joy of SciPy
Part I, Dinu Gherman
Part II, Dave Kammeyer (not included here)
Python Users Berlin
Meet-up, 2013-02-14

2. About…
Science…
Visualisation
Analytics
Numbers
Data
Math
Big Data Algorithms
Machine Learning
… and Python

3. Science, a Reminder
Domains
Math Education
Visualisation
Data
Models Publication
Theory
Experiments

4. From Scientific
Python “Components”…
Nat. Language Toolkit Matplotlib
Mol. Modelling Toolkit SymPy Chaco PIL
BioPython.org NumPy Veusz OpenCV
PsychoPy.org Blaze … Scikit-image
AstroPython.org
Scikit-learn
Stackless Pandas …
PyPy PyTables
Cython Disco Sphinx
Numba ReST (sample)
Theano ………

5. … to Integrated
Scientific Environments
Legacy: Py-Distributions: Py-Environments:
Mathematica ScientificPython IPython.org
Matlab Enthought, EPD SciPy.org
Maple Anaconda Sagemath.org
Magma Python(x, y) Wakari.io
Mathics.org
Orange

6. IPython Shell
• Extended Inter-
active Python shell
• Extensions
• Help
• Tab completion
• History
• Multi-line editing
• Debugger
• Shell access
• Bookmarks
• Magic functions
• DEMO…

7. IPython Notebook
• IPython shell in the browser
• Markdown text + executable Python code
• JSON container, including output
• Literate Programming – finally
• Great tutorial experience
• Easy to share running code – w/o hassle

8. IPython Notebook
Demo
• Tour of the IPython notebook (built-in)
• Installing a custom extension
• Combined later with Matplotlib demo

9. IPython Extension Demo
• Show object graphs
• Reuse a previously written package
• Run interactively in the notebook
• Notebook:
http://nbviewer.ipython.org/4770302/
• Code:
https://gist.github.com/deeplook/4731035

10. Matplotlib
• Scientific plots
• 2D, 3D, interactive
• Smart axes, grids
• Beautiful math (TeX)
• Widgets, annotations, …
• http://matplotlib.org/gallery.html

11. Matplotlib Demo
• Simple plots
• Bézier path editor
• Magic cube

12. Conferences
• http://conference.scipy.org
• https://www.euroscipy.org
• http://pydata.org
†
Videos (e.g. by John Hunter , Fernando Pérez et al.):
http://pyvideo.org/category/17/pycon-us-2012

13. Selected Books

14. What to take away
• Use available Python tools for your
scientific domain (trivia)!
• Use IPython shell & notebook, Matplotlib
– far too powerful to leave to scientists! ;-)
• Have fun with science
– seriously!
http://io9.com/5973726/15+year-old-whiz-kid-has-
research-on-dwarf-galaxies-published-in-nature

15. Questions?
Exercise?

16. Exercise
Run the algorithm below using CPython, Cython, PyPy and Numba and
compare their performance. This is implementing a spigot algorithm
by A. Sale, D. Saada, S. Rabinowitz, as mentioned on
http://mail.python.org/pipermail/edu-sig/2012-December/010721.html.
Code: https://gist.github.com/deeplook/4947835.
def pi_digits(n):
"Generate n digits of Pi."
k, a, b, a1, b1 = 2, 4, 1, 12, 4
while n > 0:
p, q, k = k * k, 2 * k + 1, k + 1
a, b, a1, b1 = a1, b1, p * a + q * a1, p * b + q * b1
d, d1 = a / b, a1 / b1
while d == d1 and n > 0:
yield int(d)
n -= 1
a, a1 = 10 * (a % b), 10 * (a1 % b1)
d, d1 = a / b, a1 / b1
>>> list(pi_digits(20))
[3, 1, 4, 1, 5, 9, 2, 6, 5, 3, 5, 8, 9, 7, 9, 3, 2, 3, 8, 4]