Python Day4

Munchen Scientic Computing in Computer Science, Technische Universitat
Part VI Scientic Computing in Python
Tobias Neckel: Scripting with Python... and beyond Compact Course @ GRS, June 03 - 07, 2013 80
More on Maths
Module math
Constants pi and e Functions that operate on int and float All return values float ceil ( x ) floor ( x ) exp ( x ) fabs ( x ) ldexp (x , i ) log ( x [ , base ]) log10 ( x ) modf ( x ) pow (x , y ) sqrt ( x )
# same as globally defined abs () # x * 2** i # == log (x , 10) # ( fractional , integer part ) # x ** y
Module math (2)

Trigonometric functions assume radians cos ( x ); cosh ( x ); acos ( x ) sin ( x ); ... tan ( x ); ... degrees ( x ) radians ( x ) # rad -> deg # deg -> rad
Module math (2)

Trigonometric functions assume radians cos ( x ); cosh ( x ); acos ( x ) sin ( x ); ... tan ( x ); ... degrees ( x ) radians ( x ) inf/nan float ( " inf " ) float ( " - inf " ) float ( " nan " ) # rad -> deg # deg -> rad
Module math (2)

Trigonometric functions assume radians cos ( x ); cosh ( x ); acos ( x ) sin ( x ); ... tan ( x ); ... degrees ( x ) radians ( x ) inf/nan float ( " inf " ) float ( " - inf " ) float ( " nan " ) Use module cmath for complex numbers
# rad -> deg # deg -> rad
Now to Real Maths. . .

Standard sequence types (list, tuple, . . . )
Can be used as arrays Can contain different types of objects

Very exible, but slow Loops are not very efcient either
For efcient scientic computing, other datatypes and methods
required
Now to Real Maths. . .

Standard sequence types (list, tuple, . . . )
Can be used as arrays Can contain different types of objects

Very exible, but slow Loops are not very efcient either
For efcient scientic computing, other datatypes and methods
required
Modules
NumPy Matplotlib SciPy
NumPy
Module numpy
Homogeneous arrays
NumPy provides arbitrary-dimensional homogeneous arrays Example from numpy import * a = array ([[1 ,2 ,3] ,[4 ,5 ,6]]) print a type ( a ) a . shape print a [0 ,2] a [0 ,2] = -1 b = a *2 print b
Array creation
Create from (nested) sequence type Direct access with method [] a = array ([1 ,2 ,3 ,4 ,5 ,6 ,7 ,8]) a [1] a = array ([[1 ,2 ,3 ,4] ,[5 ,6 ,7 ,8]]) a [1 ,1] a = array ([[[1 ,2] ,[3 ,4]] ,[[5 ,6] ,[7 ,8]]]) a [1 ,1 ,1]
Array creation
Create from (nested) sequence type Direct access with method [] a = array ([1 ,2 ,3 ,4 ,5 ,6 ,7 ,8]) a [1] a = array ([[1 ,2 ,3 ,4] ,[5 ,6 ,7 ,8]]) a [1 ,1] a = array ([[[1 ,2] ,[3 ,4]] ,[[5 ,6] ,[7 ,8]]]) a [1 ,1 ,1] Properties of arrays a . ndim a . shape a . size a . dtype a . itemsize # # # # # number of dimensions dimensions number of elements data type number of bytes
Data Types
Exact, C/C++-motivated type of array elements can be specied Otherwise, defaults are used Some types (different storage requirements): int_, int8, int16, int32, int64, float_, float8, float16, float32, float64, complex_, complex64, bool_, character, object_ Standard python type names result in default behaviour array ([[1 ,2 ,3] ,[4 ,5 ,6]] , dtype = int ) array ([[1 ,2 ,3] ,[4 ,5 ,6]] , dtype = complex ) array ([[1 ,2 ,3] ,[4 ,5 ,6]] , dtype = int8 ) array ([[1 ,2 ,3] ,[4 ,5 ,1000]] , dtype = int8 ) # wrong array ([[1 ,2 ,3] ,[4 ,5 , " hi " ]] , dtype = object ) Exception: object_ stores pointers to objects
Create Arrays
(Some) default matrices (optional parameter: dtype) arange ([ a ,] b [ , stride ]) zeros ( (3 ,4) ) ones ( (1 ,3 ,4) ) empty ( (3 ,4) ) linspace (a , b [ , n ]) logspace (a , b [ , n ]) identity ( n ) # as range , 1 D
# # # #
uninitialized ( fast ) n equidistant in [a , b ] 10** a to 10** b 2d
fromfunction ( lambda i , j : i +j , (3 ,4) , dtype = int ) def f (i , j ): return i + j fromfunction (f , (3 ,4) , dtype = int )
Manipulate Arrays
Reshaping arrays a = arange (12) b = a . reshape ((3 ,4)) a . resize ((3 ,4)) a . transpose () a . flatten ()
# in - place !
# Example use - case : a = arange (144) a . resize ((12 ,12))
Create Arrays (2)

Create/Copy from existing data a = arange (12); a . resize ((3 ,4)) copy ( a ) diag ( a ); tril ( a ); triu ( a ) empty_like ( a ) zeros_like ( a ) ones_like ( a ) # copy shape
a = loadtxt ( " matrix . txt " ) # fromfile () if binary # plenty of options : comments , delim . , usecols , ... Matrix output a . tolist () savetxt ( " matrix . txt " , a )
# tofile ()
if binary
Array Access and Manipulation

Typical slicing operations can be used Separate dimensions by comma a = arange (20); a . resize ((4 ,5)) a [1] a [1:2 ,:] a [: ,::2] a [::2 ,::2] a [::2 ,::2] = [[0 , -2 , -4] ,[ -10 , -12 , -14]] a [1::2 ,1::2] = -1* a [1::2 ,1::2] Selective access a [ a > 3] a [ a > 3] = -1
Array Access
Iterating over entries for row in a : print row b = arange (30); b . resize ((2 ,3 ,4)) for row in b : for col in row : print col for entry in a . flat : print entry
Computing with Arrays

Fast built-in methods working on arrays a = arange (12); a . resize ((3 ,4)) 3* a a **2 a + a ^2 sin ( a ) sqrt ( a ) prod ( a ) sum ( a ) it = transpose ( a ) x = array ([1 ,2 ,3]) y = array ([10 ,20 ,30]) inner (x , y ) dot ( it , x ) cross (x , y )
Computing with Arrays

There is much more. . . var () mean () min () svd () tensordot () ... cov () median () max () std ()
Matrices (with mat) are subclasses of ndarray, but strictly
two-dimensional, with additional attributes

m = mat ( a ) m.T # transpose m.I # inverse m.A # as 2 d array m.H # conjugate transpose
Submodules
Module numpy.random
Draw from plenty of different distributions More powerful than module random Work on and return arrays from numpy . random import * binomial (10 , 0.5) # 10 trials , success 50% binomial (10 , 0.5 , 15) randint (0 , 10 , 15) # [0 ,10) , int rand () rand (3 ,4) # [0 ,1) #
(3 x4 ) array
Submodules (2)
Module numpy.linalg
Core linear algebra tools norm ( a ); norm ( x ) inv ( a ) solve (a , b ) # LAPACK LU decomp . det ( a ) eig ( a ) cholesky ( a )
Submodules (2)
Module numpy.linalg
Module numpy.fft
Fourier transforms
Submodules (2)
Module numpy.linalg
Module numpy.fft
Fourier transforms
There is more. . .
Version Mania
Current Situation
SciPy
Matplotlib IPython pylab NumPy
python
Version Mania
Problems:
Numpy, scipy, pylab, ipython and matplotlib often used
simultaneously arrays, e.g.)
The packages depend on each other (matplotlib uese numpy Depending on OS (version), different packages may have to be
installed (i.e. the module name in import command may be different!).
Vision: All in one (new) module PyLab!

exists as unofcial package Attention Name: again pylab!
Matplotlib
Matplotlib
What is it?
Object-oriented library for plotting 2D Designed to be similar to the matlab plotting functionality Designed to plot scientic data, built on numpy datastructures
Several Ways to do the Same

python/ipython interactive
> ipython import scipy , matplotlib . pylab x = scipy . randn (10000) matplotlib . pylab . hist (x , 100) > ipython import numpy . random , matplotlib . pylab x = numpy . random . randn (10000) matplotlib . pylab . hist (x , 100)
ipython in pylab mode

> ipython - pylab x = randn (10000) hist (x , 100)
Example - First Plot

partially taken from http://matplotlib.sourceforge.net/users/screenshots.html
from pylab import * x = arange (0.0 , 2* pi , 0.01) y = sin ( x ) plot (x , y , linewidth =4) plot (x , y ) xlabel ( Label for x axis ) ylabel ( Label for y axis ) title ( Simple plot of sin ) grid ( True ) show ()
Example Using Subplots

from pylab import * def f ( t ): s1 = cos (2* pi * t ) e1 = exp ( - t ) return multiply ( s1 , e1 ) t1 = arange (0.0 , 5.0 , 0.1) t2 = arange (0.0 , 5.0 , 0.02) t3 = arange (0.0 , 2.0 , 0.01) show () # gives error but helps ; -) subplot (2 ,1 ,1) # rows , columns , which to show plot ( t1 , f ( t1 ) , go , t2 , f ( t2 ) , k - - ) subplot (2 ,1 ,2) plot ( t3 , cos (2* pi * t3 ) , r . )
Example Using Subplots
# previous slide continued subplot (2 ,1 ,1) grid ( True ) title ( A tale of 2 subplots ) ylabel ( Damped oscillation ) subplot (2 ,1 ,2) grid ( True ) xlabel ( time ( s ) ) ylabel ( Undamped )
Example - Histogram
# start ipython - pylab or use imports : # from matplotlib . mlab import * # from matplotlib . pyplot import * from numpy import * mu , sigma = 100 , 15 x = mu + sigma * random . randn (10000) n , bins , patches = hist (x , 50 , normed =1 , \ facecolor = green , alpha =0.75) # add a best fit line y = normpdf ( bins , mu , sigma ) plot ( bins , y , r - - , linewidth =1) axis ([40 , 160 , 0 , 0.03]) plt . show ()
SciPy
More than NumPy?

SciPy depends on NumPy Built to work on NumPy arrays Providing functionality for mathematics, science and engineering Still under development NumPy is mostly about (N-dimensional) arrays SciPy comprises a large number of tools using these arrays SciPy includes the NumPy functionality (only one import
necessary)
A lot more libraries for scientic computing are available, some of
them using NumPy and SciPy
Here, just a short overview will be given www.scipy.org for more material (incl. the content of the
following slides)
SciPy Organisation - Subpackages

cluster constants fftpack integrate interpolate io linalg maxentropy ndimage odr optimize signal sparse spatial special stats weave Clustering algorithms Physical and mathematical constants Fast Fourier Transform routines Integration and ordinary differential equation solvers Interpolation and smoothing splines Input and Output Linear algebra Maximum entropy methods N-dimensional image processing Orthogonal distance regression Optimization and root-nding routines Signal processing Sparse matrices and associated routines Spatial data structures and algorithms Special functions Statistical distributions and functions C/C++ integration
108
Tobias Neckel: Scripting with Python... and beyond Compact Course @ GRS, June 03 - 07, 2013
Special Functions
Airy functions Elliptic functions Bessel functions (+ Zeros, Integrals, Derivatives, Spherical,
Ricatti-) Struve functions A large number of statistical functions Gamma functions Legendre functions Orthogonal polynomials (Legendre, Chebyshev, Jacobi,...) Hypergeometric functios parabolic cylinder functions Mathieu functions Spheroidal wave functions Kelvin functions ...
Example: Interpolation - Linear
import numpy as np import matplotlib . pyplot as plt from scipy import interpolate x = np . arange (0 ,10) y = np . exp ( - x /3.0) f = interpolate . interp1d (x , y ) xnew = np . arange (0 ,9 ,0.1) plt . plot (x ,y , o , xnew , f ( xnew ) , - ) plt . title ( Linear interpolation ) plt . show ()
Example: Interpolation - Cubic Spline

import numpy as np import matplotlib . pyplot as plt from scipy import interpolate x = np . arange (0 , 2.25* np . pi , np . pi /4) y = np . sin ( x ) spline = interpolate . splrep (x ,y , s =0) xnew = np . arange (0 ,2.02* np . pi , np . pi /50) ynew = interpolate . splev ( xnew , spline ) plt . plot (x ,y , o , xnew , ynew ) plt . legend ([ Linear , Cubic Spline ]) plt . axis ([ -0.05 ,6.33 , -1.05 ,1.05]) plt . title ( Cubic - spline interpolation ) plt . show ()

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Munchen Scientic Computing in Computer Science, Technische Universitat

Part VI Scientic Computing in Python

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Module math (2)

Munchen Scientic Computing in Computer Science, Technische Universitat

Module math (2)

Munchen Scientic Computing in Computer Science, Technische Universitat

Module math (2)

# rad -> deg # deg -> rad

Munchen Scientic Computing in Computer Science, Technische Universitat

Now to Real Maths. . .

For efcient scientic computing, other datatypes and methods

Munchen Scientic Computing in Computer Science, Technische Universitat

Now to Real Maths. . .

For efcient scientic computing, other datatypes and methods

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

uninitialized ( fast ) n equidistant in [a , b ] 10** a to 10** b 2d

Munchen Scientic Computing in Computer Science, Technische Universitat

# Example use - case : a = arange (144) a . resize ((12 ,12))

Munchen Scientic Computing in Computer Science, Technische Universitat

Create Arrays (2)

Munchen Scientic Computing in Computer Science, Technische Universitat

Array Access and Manipulation

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Computing with Arrays

Munchen Scientic Computing in Computer Science, Technische Universitat

Computing with Arrays

Matrices (with mat) are subclasses of ndarray, but strictly

two-dimensional, with additional attributes

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Matplotlib IPython pylab NumPy

Munchen Scientic Computing in Computer Science, Technische Universitat

simultaneously arrays, e.g.)

installed (i.e. the module name in import command may be different!).

Vision: All in one (new) module PyLab!

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Several Ways to do the Same

ipython in pylab mode

Munchen Scientic Computing in Computer Science, Technische Universitat

Example - First Plot

Munchen Scientic Computing in Computer Science, Technische Universitat

Example Using Subplots

Munchen Scientic Computing in Computer Science, Technische Universitat

Example Using Subplots

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

Munchen Scientic Computing in Computer Science, Technische Universitat

More than NumPy?

A lot more libraries for scientic computing are available, some of

them using NumPy and SciPy

Munchen Scientic Computing in Computer Science, Technische Universitat

uninitialized ( fast ) n equidistant in [a , b ] 10 a to 10 b 2d