Introduction to Pythonand Scientific Python

Francois Bianco

Unige

21th Dec 2011

Francois Bianco Introduction to Python

Outlook

1 Python features and syntax

2 Examples, pylab, and iPython

3 Flat files examples

Based on :

Learn Python in 10 minutes :http://www.poromenos.org/tutorials/python

Python documentation : http://docs.python.org/index.html

Matplotlib : http://matplotlib.sourceforge.net/

Scipy : http://www.scipy.org/

Francois Bianco Introduction to Python

Python is

Strongly typed (i.e. types are enforced)

Dynamically, implicitly typed (i.e. you don’t have to declarevariables)

Python is

case sensitive (i.e. var and VAR are two different variables)

object-oriented (i.e. everything is an object)

able to handle memory by itself (i.e has a garbadge collector)

Francois Bianco Introduction to Python

Example

Example

l i s t = [ 1 , 1 . 1 , 1 + 1 j , ’ 1 ’ , True ]f o r e l em en t i n l i s t :

p r i n t e lement , t y p e ( e l em en t ) , e l e me nt ==1.1

No mandatory statement termination character

Blocks are specified by indentation (4 spaces, or 1 tab)

Statements that expect an indentation level end in a colon “:”

Values are assigned (in fact, objects are bound to names) withthe equals sign “=”

Equality testing is done using two equals signs “==”

Francois Bianco Introduction to Python

Data structures

Three main data structures

list = [1,2,3,4,5,6] are mutable

tuples = (1,2,3,4,5,6) are unmutable

dictionary = { ’key’:’value’, ’answer’:42, ’obj’:list } also calledhash tables, access by key

List and tuples are access by index : list[index] (see array slicing).Dictionary by key dictionary[’answer’].

Francois Bianco Introduction to Python

Modules loading

Classes and functions are stored in modules

from math import s i n #on l y one f u n c t i o ns i n ( 0 . 3 )

import math #the whole module keep ing namespacemath . s i n ( 0 . 3 )

from math import * #the whole modulecos ( 0 . 3 )

import m a t p l o t l i b as mptl #rename namespacemptl . c o n v e r t e r ( )

Francois Bianco Introduction to Python

Other features of Python

Modern way of handling errors

t r y :f i l e O b j = open ( ’ f i l e N a m e . t x t ’ )

except I O E r r o r :p r i n t E r r o r M e s s a g e

Lambda functions

f i t f u n c = lambda x , y : s q r t ( x/ y )f i t f u n c ( 4 . 5 , 2 . 3 )

Francois Bianco Introduction to Python

Other features of Python

Classes, functions...

def funct ionName ( param , o p t i o n a l P a r a m=v a l u e ) : . . .c l a s s C h i l d C l a s s ( P a r e n t C l a s s ) : . . .

Automatic documentation generation (with Doxygen)

def t o g g l e I m a g e s ( s e l f , e v e n t ) :””” Toggle the two images a c co r d i n gto the t r i g g e r even t .

\param event Key or mouse even tt r i g g e r i n g the f u n c t i o n”””

Francois Bianco Introduction to Python

Flow control statements

Example: Fibonnaci in a simple while loop

a , b = 0 ,1whi le b<10:

p r i n t ba , b = b , a+b

Easy variables assignation, and permutation, no extra variableneeded.

Francois Bianco Introduction to Python

Array slicing

Example: access to specific elements in an array

x = a ran ge ( 1 0 ) #c r e a t e a v e c t o r from 0 to 9x #the whole v e c t o rx [ 0 ] #on l y the f i r s t e l ementx [ 3 ] #the 3 rd e l ementx [−2] #the second l a t e s t e l ementx [ 1 : 4 ] #element s from 1 to 4x [ : 5 ] #element s up to 5x [ −3 : ] #the t h r e e l a s t e l ement s

Francois Bianco Introduction to Python

Array masking

Example: create a mask on an array

a = a ra nge ( 1 0 )mask = ( ( a % 2) == 0)a [ mask ] = 0

This sets all the even value in a to 0.

Francois Bianco Introduction to Python

Easy plot

Example : plot with label and LATEX title

p l o t ( a ran ge ( 5 ) )x l a b e l ( ’ I n d e x ’ )y l a b e l ( ’Sum ’ )t i t l e ( r ’ $\ sum { i =0}ˆ\ i n f t y i $ ’ )

Francois Bianco Introduction to Python

Display matrix as an image

Example : create an image from a matrix

x = randn ( 2 0 , 2 0 ) #c r e a t e a random 20 x20 mat r i ximshow ( x ) #p i x e l s c a l eimshow ( x , e x t e n t = ( 0 , 1 , 0 , 1 ) ) #add custom s c a l e

Francois Bianco Introduction to Python

Histogramm plot

Example : create an histogramm plot

mu, s igma = 100 , 15x = mu + sigma * randn (10000)h i s t ( x , 1 0 0 )

Francois Bianco Introduction to Python

Many plots

Example : create two plots with legend

t = a ran ge ( 0 , 5 , 0 . 0 5 ) # Vect . 0 , 0 . 0 5 , 0 . 1 , . . . , 5s1=s i n (2* p i * t )s2=s1 * exp(− t )p l o t ( t , s1 , ’ g−−o ’ , t , s2 , ’ r : s ’ ) # custom s t y l e sl e g e n d ( ( ’ S i n wave ’ , ’ Damped exp . ’ ) )

Francois Bianco Introduction to Python

iPython

Usefull magic commands in iPython

h e l p ( o b j ) #Show he l po b j ? #Show doc s t r i n go b j ?? #Show sou r c e code

#r e t u r n l a s t v a l u e\%who #l i s t o b j e c t s\%whos #d e t a i l l e d o b j e c t s l i s t\% h i s t −n #h i s t o r y w i thout l i n e number\%exec I n [ 4 : 7 ] #redo l i n e 4 to 7\% e d i t 4 : 7 #ed i t l i n e 4 to 7 i n s c r i p t\%run #launch a s c r i p t\% p f i l e #show sou r c e f i l e con t en t

You want more of it ? Try %lsmagic

Francois Bianco Introduction to Python

Pro and cons

Cons

No GUI

Documentation spread on different websites

Requires basics programming skills

Pro

Easy to learn

Work on every plateform (WinXP,Vista,MacOS,Linux,...)

Could be bind to Gwyddion

It’s a free software

Francois Bianco Introduction to Python

Other good reasons to learn Python

Used by different universities and research centers : Universityof Montreal, Princeton University, Space Telescope ScienceInstitute, Los Alamos National Laboratory, UC Berkeley, CERN,NASA ...

If you want to look for a job in some “small” companies :Google, HP, IBM, Nokia, Thawte Consulting (SSL certificates), EAGames, Industrial Light & Magic (Hollywood), ...

Francois Bianco Introduction to Python

The end

“There should be one – and preferably only one –obvious way to do it.”

Tim Peters, The Zen of Python

Francois Bianco Introduction to Python